# 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/Crenarchaeota/Desulfurococcus_mucosus_DSM_2162_uid62227/NC_014961.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/Crenarchaeota/Desulfurococcus_mucosus_DSM_2162_uid62227/NC_014961.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Desulfurococcus_mucosus_DSM_2162_uid62227/NC_014961.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|320100210|ref|YP_004175802.1|  [L=60]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       153  (0.00853366); expected 358.6 (0.02)
Passed bias filter:                      124  (0.00691617); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.43
# Mc/sec: 423.90
//
Query:       gi|320100211|ref|YP_004175803.1|  [L=394]
Description: ORC complex protein Cdc6/Orc1 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   55.8   2.1    1.7e-14   53.6   0.2    2.8  2  Cdc6_C           CDC6, C terminal winged helix domain
    6.2e-10   39.5   0.0    2.7e-09   37.4   0.0    1.9  2  AAA_22           AAA domain
    4.1e-09   37.0   0.0    1.1e-08   35.6   0.0    1.8  1  AAA              ATPase family associated with various cellul
    3.1e-08   33.2   0.0    5.3e-08   32.5   0.0    1.3  1  TniB             Bacterial TniB protein
    1.3e-07   32.2   0.0    8.9e-07   29.4   0.0    2.1  1  AAA_16           AAA ATPase domain
      6e-07   29.6   0.4    1.2e-06   28.6   0.4    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
    0.00028   20.2   0.0    0.00036   19.9   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00037   19.7   0.0    0.00055   19.2   0.0    1.3  1  NB-ARC           NB-ARC domain
     0.0031   17.3   0.0     0.0056   16.4   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
     0.0037   16.5   0.0     0.0067   15.6   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
     0.0052   16.3   0.1      0.011   15.2   0.1    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0097   15.6   0.0      0.029   14.1   0.0    1.8  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.014   14.2   0.4       0.95    8.2   0.0    2.2  2  AAA_32           AAA domain
      0.019   15.3   0.1      0.061   13.7   0.1    1.8  1  AAA_assoc_2      AAA C-terminal domain
      0.032   13.3   0.1      0.085   11.9   0.0    1.7  2  T2SSE            Type II/IV secretion system protein
      0.048   13.4   1.0        9.6    5.9   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
      0.058   13.3   0.0      0.099   12.5   0.0    1.4  1  NACHT            NACHT domain
       0.07   13.8   1.9       0.11   13.2   0.3    2.0  2  Mg_chelatase_C   Magnesium chelatase, subunit ChlI C-terminal
      0.079   12.7   0.0       0.13   12.0   0.0    1.4  1  AAA_24           AAA domain
      0.083   13.0   0.0        0.3   11.2   0.0    2.0  1  TIP49_C          TIP49 AAA-lid domain
      0.092   12.9   0.0       0.19   11.8   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
        0.1   13.1   0.0       0.22   12.1   0.0    1.7  1  AAA_18           AAA domain
       0.11   11.7   0.0       0.34   10.0   0.0    1.8  2  PIF1             PIF1-like helicase
       0.14   12.1   0.0       0.27   11.3   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


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 ?    0.4   0.1      0.85   6.3e+02      11      32 ..      92     113 ..      85     146 .. 0.66
   2 !   53.6   0.2   2.2e-17   1.7e-14       4      82 ..     310     385 ..     307     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.85
                                       CSSS-EEHHHHHHHHHHHHHHT CS
                            Cdc6_C  11 sgkeevttgevyevYkslCese 32 
                                        +  +v t+++  +Y+ +++  
  gi|320100211|ref|YP_004175803.1|  92 LDYAYVNTRKLDTTYRVIASIA 113
                                       5666777777777777776644 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 2.2e-17
                                       HHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHH CS
                            Cdc6_C   4 lvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpdd 80 
                                       +v+l +   k ++ttge+y  Y +  +s+ ++pl+ r++s++l +L+m+g++++e+ s+Gr +g t+ ++++ d  +
  gi|320100211|ref|YP_004175803.1| 310 IVELVE--AKGSATTGEIYAAYAESMKSLKYEPLSPRRISEILMQLDMMGLITSETISRGR-YGVTKVVRVKKDVLQ 383
                                       666666..6789************************************************9.*********999877 PP

                                       HH CS
                            Cdc6_C  81 vl 82 
                                       v 
  gi|320100211|ref|YP_004175803.1| 384 VV 385
                                       75 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   3.6e-12   2.7e-09       7     131 ..      59     185 ..      56     191 .. 0.83
   2 ?   -1.1   0.0       2.7     2e+03      41      74 ..     310     342 ..     281     355 .. 0.67

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 3.6e-12
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                        ++++G +GtGKT++++ ++ +l+e a+    r ++++v+  ++ +   +   +++ +gl+  + +l  +e++++  
  gi|320100211|ref|YP_004175803.1|  59 NVLIYGLTGTGKTVVAKYVVGKLKEKASMLSTRLDYAYVNTRKLDTTYRVIASIAQSIGLRIPHTGLAVSEVYRRYI 135
                                       579********************87777766******************************9998899999998888 PP

                            AAA_22  84 qalraravielliiDEaqh.lrs...eealeeLrsllnl..srkgvqliLvGtp 131
                                       +al++ +  +++++DE+++ + +   ++++ +L   +    + +  +++LvG +
  gi|320100211|ref|YP_004175803.1| 136 NALESWGGLHIVVLDEVDYyV-KregDDLIYKL---VRAneELTRAKIVLVGIT 185
                                       888888778**********77.52335555555...444448999******977 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                            AAA_22  41 evvfvtlpsstsskdllrellralglelkaerls 74 
                                        v +v++++s +  +++ + ++ +++ + + +ls
  gi|320100211|ref|YP_004175803.1| 310 IVELVEAKGSATTGEIYAAYAESMKSLKYE-PLS 342
                                       333777777888888888888887765555.444 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 !   35.6   0.0   1.5e-11   1.1e-08       1     122 [.      60     200 ..      60     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.5e-11
                                       EEEESSTTSSHHHHHHHHHHHHT..HE.......EEEEETTTCSSS..........................STTHH CS
                               AAA   1 vllyGppGtGKTllakavakelg..ve.......fleisgsellsk..........................yvges 42 
                                       vl+yG  GtGKT +ak v+ +l+  ++       +  ++                                  v+e 
  gi|320100211|ref|YP_004175803.1|  60 VLIYGLTGTGKTVVAKYVVGKLKekASmlstrldYAYVN------TrkldttyrviasiaqsiglriphtglAVSEV 130
                                       79*******************963322333333333333......12333345678888888888666433333333 PP

                                       HHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GG CS
                               AAA  43 ekkirelfkeakeka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pd 113
                                        ++  + +      +   + +i+++DE+d  +k++       +++++ +L+++ +++++  +k++++g+tn+   ++
  gi|320100211|ref|YP_004175803.1| 131 YRRYINAL------EswgGLHIVVLDEVDYYVKRE-------GDDLIYKLVRANEELTR--AKIVLVGITNDinfVE 192
                                       33333333......1334679**********9999.......99***************..69*********88888 PP

                                       GSTHHHHST CS
                               AAA 114 kldpallrg 122
                                       +ldp ++ +
  gi|320100211|ref|YP_004175803.1| 193 NLDPRVR-S 200
                                       8888887.3 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   7.1e-11   5.3e-08      17     170 ..      39     192 ..      28     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.1e-11
                              TniB  17 keilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLea 93 
                                       +ei +  e+Ll  ++  r++n+l++G + +GKt++++    + +++ +  +++++  +v++++  ++ r  a+i ++
  gi|320100211|ref|YP_004175803.1|  39 NEIKKLAEHLLVSAQGIRPSNVLIYGLTGTGKTVVAKYVVGKLKEKASMLSTRLDYAYVNTRKLDTTYRVIASIAQS 115
                                       555555599************************988877777777888889999*********************** PP

                              TniB  94 lgaplkara.rvskleqqvlrllrel.kvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealra 168
                                       +g ++  +   vs+ +++ ++ l++  +++++++DE++  +  +++    +  +++   +  +  ivlvG+++ +++
  gi|320100211|ref|YP_004175803.1| 116 IGLRIPHTGlAVSEVYRRYINALESWgGLHIVVLDEVDYYV--KREGDDLIYKLVRANEELTRAKIVLVGITNDINF 190
                                       **99988765889***********98359*********999..6667778888999988889999*****9998888 PP

                              TniB 169 lr 170
                                       ++
  gi|320100211|ref|YP_004175803.1| 191 VE 192
                                       75 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.2e-09   8.9e-07       2      75 ..      34     112 ..      33     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.2e-09
                            AAA_16   2 lvGReeeleqL.lsalervrsgrpelvllsGesGvGKsslvrellralekd.........ggiflrgkcdqlesaip 68 
                                       l+ Re+e+++L +++l ++   rp++vl++G  G+GK+ +++ +   l+++         ++++ + k d       
  gi|320100211|ref|YP_004175803.1|  34 LPHRENEIKKLaEHLLVSAQGIRPSNVLIYGLTGTGKTVVAKYVVGKLKEKasmlstrldYAYVNTRKLDTT----- 105
                                       789********6666668887888*********************999999555554443344444444444..... PP

                            AAA_16  69 ysalaqa 75 
                                       y ++a++
  gi|320100211|ref|YP_004175803.1| 106 YRVIASI 112
                                       4333333 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 !   28.6   0.4   1.7e-09   1.2e-06       4     156 ..      37     178 ..      35     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.7e-09
                          ATPase_2   4 Rekelkeleeilerepnei....yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekk 76 
                                       Re+e+k+l e l  + + i    ++iYG  g GKt + k ++ +l++k        +   +++ kld++    ++  
  gi|320100211|ref|YP_004175803.1|  37 RENEIKKLAEHLLVSAQGIrpsnVLIYGLTGTGKTVVAKYVVGKLKEKASMLSTRLDYAYVNTRKLDTT---YRVIA 110
                                       999***9988765444433223389********************999987777777777888888877...67788 PP

                          ATPase_2  77 klekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnlieslt 153
                                       ++++ +g ++p + l          v +   +++++++  g   i+++De+ + +  + ++  +l+++L+++ e+lt
  gi|320100211|ref|YP_004175803.1| 111 SIAQSIGLRIPHTGL---------AVSEVYRRYINALESWGGLHIVVLDEVDYYV--K-REGDDLIYKLVRANEELT 175
                                       99**********999.........78999999*********************99..5.6699**********9999 PP

                          ATPase_2 154 kek 156
                                       + k
  gi|320100211|ref|YP_004175803.1| 176 RAK 178
                                       866 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.9e-07   0.00036       3      96 ..      59     151 ..      57     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.9e-07
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakke..ekkkkkeafeklssfinnls 75 
                                        vl+ G +GtGKtvv+  ++ +l  + + +  +  y++vN + +++ ++ +a+ +   + ++ ++   +s++  ++ 
  gi|320100211|ref|YP_004175803.1|  59 NVLIYGLTGTGKTVVAKYVVGKLkeKASMLSTRLDYAYVNTRKLDTTYRVIASIAqsIGLRIPHTGLAVSEVYRRYI 135
                                       689********************655556788889**************9998773322222222222222222222 PP

                           DUF2075  76 efkkaeekkeepkedvvivDE 96 
                                            ++ ++   +++v+ DE
  gi|320100211|ref|YP_004175803.1| 136 -----NALESWGGLHIVVLDE 151
                                       .....3344666666666666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.3e-07   0.00055       2     112 ..      38     152 ..      37     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.3e-07
                                       HHHHHHHHHHHHC.TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHH CS
                            NB-ARC   2 eksvekviekLle.kdelqslvvalvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilk 74 
                                       e++++k++e+Ll   +++    v ++G  G GKt++ak ++ k++e  +       +a+v   k d+ ++++ +i++
  gi|320100211|ref|YP_004175803.1|  38 ENEIKKLAEHLLVsAQGIRPSNVLIYGLTGTGKTVVAKYVVGKLKEKASMLStrlDYAYVNTRKLDTTYRVIASIAQ 114
                                       7889999999886578888899*******************9999888766533457999999************** PP

                                       HHHCCCTTSSSS-STTSHHHHHHHHCCCT..TEEEEEEEE CS
                            NB-ARC  75 eLslseddleekeeveslkrklvrlLltk..rfllvlDDV 112
                                        ++l+   +   + +e   r+  ++L++     ++vlD V
  gi|320100211|ref|YP_004175803.1| 115 SIGLRIPHTGL-AVSE-VYRRYINALESWggLHIVVLDEV 152
                                       99988333322.2222.45666777776555677777766 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.5e-06    0.0056      20      50 ..      55      85 ..      35     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.5e-06
                                      TSSS-EEEECSTTSSHHHHHHHHHHHSTTTT CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskrke 50
                                        +++vli G +GtGK+++a+ +  + k+k+
  gi|320100211|ref|YP_004175803.1| 55 IRPSNVLIYGLTGTGKTVVAKYVVGKLKEKA 85
                                      3459*****************9987666554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     9e-06    0.0067      29     101 ..      33     111 ..      18     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9e-06
                            DUF815  29 dLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg......Lrlievekedlkelpklv 99 
                                       +L   +++ ++l e     ++g + +nvL++G  GtGK  + k ++ +++e+       L    v+ ++l++  +++
  gi|320100211|ref|YP_004175803.1|  33 TLPHRENEIKKLAEHLLVSAQGIRPSNVLIYGLTGTGKTVVAKYVVGKLKEKAsmlstrLDYAYVNTRKLDTTYRVI 109
                                       5666788999999999999***************************9999887665555555566666666655555 PP

                            DUF815 100 el 101
                                       + 
  gi|320100211|ref|YP_004175803.1| 110 AS 111
                                       55 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 !   15.2   0.1   1.5e-05     0.011      34      66 ..      58      89 ..      43     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylslt 66
                                       +vl++G tGtGKtv++k ++ kl+ ek ++l+
  gi|320100211|ref|YP_004175803.1| 58 SNVLIYGLTGTGKTVVAKYVVGKLK-EKASMLS 89
                                      68******************99999.5555544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.8e-05     0.029      21     187 ..      60     266 ..      42     271 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk................ 81 
                                       +++ G  GtGKt + k ++  ++++     +l+     A v +++l+++ + ia++ ++ +                
  gi|320100211|ref|YP_004175803.1|  60 VLIYGLTGTGKTVVAKYVVGKLKEKA---SMLSTRLDYAYVNTRKLDTTYRVIASIAQSIGlriphtglavsevyrr 133
                                       6899*************988888775...466666666666666666666666666665556666666666666677 PP

                            AAA_30  82 ...grarlepgtllivDEagmv....dtkqlaallkaaek.agakvilvGDerQlasVea..Ggvlrdlveaagi.. 146
                                          + +++   ++++ DE+       + + + +l++a e+ + ak++lvG ++  + Ve+   +v +++ e + +  
  gi|320100211|ref|YP_004175803.1| 134 yinALESWGGLHIVVLDEVDYYvkreGDDLIYKLVRANEElTRAKIVLVGITNDINFVENldPRVRSSMGEVE-Mvf 209
                                       77533345555*********99555555556666666666458*******88877777764344444443322.123 PP

                            AAA_30 147 ...gtaeLtevvRqkes.............eeraaalalregdaeealealadrgri 187
                                          ++ +L ++ Rq+ +             ++ aa  a ++gda++al+ l+  g i
  gi|320100211|ref|YP_004175803.1| 210 ppyNAEQLYTILRQRAElafnpgviddgviSYCAALAAREHGDARRALDLLRVSGEI 266
                                       333666777777776434444455555555555555666666666666666665555 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0013      0.95      32      71 ..      59     101 ..      40     110 .. 0.81
   2 ?    4.0   0.1     0.023        17     478     509 ..     254     285 ..     233     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                            AAA_32  32 NifvlGesgtGrttlvkrlleeiakkeptpd...DwcYvnnfd 71 
                                       N+ + G +gtG+t ++k ++ + ++k++  +   D++Yvn  +
  gi|320100211|ref|YP_004175803.1|  59 NVLIYGLTGTGKTVVAKYVVGKLKEKASMLStrlDYAYVNTRK 101
                                       99***********999998877766666554444*****9755 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.023
                            AAA_32 478 seiadllrEAdywakkegaevveaehVekAle 509
                                       ++  dllr +  +a++ega+ v+ ehV+kA  
  gi|320100211|ref|YP_004175803.1| 254 RRALDLLRVSGEIADREGADRVTIEHVKKATL 285
                                       67789*************************75 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 ?   13.7   0.1   8.2e-05     0.061      13      55 ..     243     284 ..     232     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeakegkieitledleeal 55 
                                       +ala+  +GDaR+aL lL +  e a++ eg  ++t e++++a+
  gi|320100211|ref|YP_004175803.1| 243 AALAAREHGDARRALDLLRVSGEIADR-EGADRVTIEHVKKAT 284
                                       45667778************9999986.99999****999875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011     0.085     128     162 ..      56      90 ..      31     113 .. 0.78
   2 ?   -4.1   0.0       8.6   6.4e+03      76      98 ..     201     224 ..     192     229 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                             T2SSE 128 erglilvsGgTgsGKttllyallkeinksderivt 162
                                       +  ++l+ G Tg+GKt+++  ++ +++++   + t
  gi|320100211|ref|YP_004175803.1|  56 RPSNVLIYGLTGTGKTVVAKYVVGKLKEKASMLST 90 
                                       4579********************99998766665 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 8.6
                             T2SSE  76 kgvrlrvvllPvvagealv.iRkk 98 
                                       +  ++++v++P  a++ ++ +R++
  gi|320100211|ref|YP_004175803.1| 201 SMGEVEMVFPPYNAEQLYTiLRQR 224
                                       556788888998888554404544 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.014        10      14      34 ..      57      77 ..      43     109 .. 0.81
   2 ?    5.9   0.0     0.013       9.6     119     152 ..     141     174 ..      80     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                                      TCEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 14 ggdvlvaaeTGsGKTlaflip 34
                                        +vl+ + TG+GKT ++   
  gi|320100211|ref|YP_004175803.1| 57 PSNVLIYGLTGTGKTVVAKYV 77
                                      4799***********997655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                                       CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                          + ++VlDE+d + + +  d i +++++ ++ 
  gi|320100211|ref|YP_004175803.1| 141 WGGLHIVVLDEVDYYVKREGDDLIYKLVRANEEL 174
                                       567899************9999999988877544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013     0.099       3     116 ..      60     171 ..      58     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-CCHHHHCC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvsevwavlle 78 
                                       v++ G  G GKT+ ++ ++ +++e+     +     +++ r+l +  ++  s+a+ +    p+ + +vse    + +
  gi|320100211|ref|YP_004175803.1|  60 VLIYGLTGTGKTVVAKYVVGKLKEKASMLSTRLDYAYVNTRKLDTTYRViASIAQSIGLRIPHTGLAVSE----VYR 132
                                       899*********************9998887444456777777777766799999999999999999999....444 PP

                                       SCCCEE........EEEE-STT-SS-TCH.........HHHHHCTT CS
                             NACHT  79 lperlL........lilDglDelvtdlgqkekqpvrtlLselirkk 116
                                       +   +L         +lD +D+ v+  g        +l+ +l+r++
  gi|320100211|ref|YP_004175803.1| 133 RYINALeswgglhiVVLDEVDYYVKREGD-------DLIYKLVRAN 171
                                       4444444445556699*****99997777.......8888888875 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       7.1   5.3e+03      43      73 ..      83     113 ..      74     116 .. 0.81
   2 ?   13.2   0.3   0.00014      0.11      51      89 ..     245     283 ..     232     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.1
                    Mg_chelatase_C  43 eaeelleeaierlglsaRaydrilkvArTiA 73 
                                       e++++l++ ++   +++R++d + +v  +iA
  gi|320100211|ref|YP_004175803.1|  83 EKASMLSTRLDYAYVNTRKLDTTYRVIASIA 113
                                       5667888888888899999999999977776 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00014
                    Mg_chelatase_C  51 aierlglsaRaydrilkvArTiADLegseeieeehlaeA 89 
                                       +++r +  aR +  +l+v+  iAD eg+++++ eh+++A
  gi|320100211|ref|YP_004175803.1| 245 LAAREHGDARRALDLLRVSGEIADREGADRVTIEHVKKA 283
                                       56666777899999***********************99 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.13       4      85 ..      59     163 ..      56     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                            AAA_24   4 kiliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdie...................swedfldevv 57 
                                       ++liyG  g+GKT +ak      ++k+ ++ t   ++ ++ +k+++                     ++ +++  + 
  gi|320100211|ref|YP_004175803.1|  59 NVLIYGLTGTGKTVVAKYVvgklKEKASMLSTRLDYAYVNTRKLDTTYrviasiaqsiglriphtglAVSEVYRRYI 135
                                       79****************99999899999988877788888888755544444444444555555554444444444 PP

                            AAA_24  58 elaaeladyktlviDtideleelclaev 85 
                                          + + +++++v+D +d  ++   +++
  gi|320100211|ref|YP_004175803.1| 136 NALESWGGLHIVVLDEVDYYVKREGDDL 163
                                       4477888888888888887776665555 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   0.0   0.00041       0.3      31      60 ..     254     283 ..     252     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                           TIP49_C  31 RYaiqLltpasilakkrkkkevevedveev 60 
                                       R a+ Ll ++  +a ++++++v++e+v+++
  gi|320100211|ref|YP_004175803.1| 254 RRALDLLRVSGEIADREGADRVTIEHVKKA 283
                                       56899***********************98 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 ?   11.8   0.0   0.00026      0.19       6      42 ..      40      78 ..      37     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                                      HHHHHHHHHHHHH..T-SS-EEEEEETT--HHHHHHCC- CS
                   Sigma54_activ_2  6 aiqelkerLeqaa..qsklpvfltGekGsgkelvArlLh 42
                                       i++l+e+L + a   + ++v++ G  G+gk++vA++  
  gi|320100211|ref|YP_004175803.1| 40 EIKKLAEHLLVSAqgIRPSNVLIYGLTGTGKTVVAKYVV 78
                                      58899999988773447899****************975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0003      0.22       1      25 [.      60      96 ..      60     183 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                            AAA_18  1 IlltGtpGvGKttlakeL....skrlgf...........g 25
                                      +l+ G  G+GKt +ak++    ++                
  gi|320100211|ref|YP_004175803.1| 60 VLIYGLTGTGKTVVAKYVvgklKE---KasmlstrldyaY 96
                                      79***************9544422...1222444444452 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00045      0.34       5      52 ..      40      87 ..      37     170 .. 0.73
   2 ?   -1.5   0.0       1.4   1.1e+03      62      83 ..     283     304 ..     272     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00045
                                      HHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCC CS
                              PIF1  5 eQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegki 52
                                      e kk +++ + +++  ++ ++ ++G  GtgKt + k ++ kl+++ ++
  gi|320100211|ref|YP_004175803.1| 40 EIKKLAEHLLVSAQGIRPSNVLIYGLTGTGKTVVAKYVVGKLKEKASM 87
                                      5677888888889999999***********************997554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                       HHHCC.TSEECHHHHT-TTSSS CS
                              PIF1  62 AalllegGrtahsrfkiplekd 83 
                                       A+l +e+Gr+  s + +pl+++
  gi|320100211|ref|YP_004175803.1| 283 ATLEIEEGRIYQSVVTLPLHQK 304
                                       7788999999999999998765 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   0.00036      0.27       3      46 ..      37      84 ..      35     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                                      SHHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  3 seeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve 46
                                      +e+e+++l+++l  ++     + +l++G  G+GKT+ ++ ++ +l+ +
  gi|320100211|ref|YP_004175803.1| 37 RENEIKKLAEHLLVSAqgirPSNVLIYGLTGTGKTVVAKYVVGKLKEK 84
                                      67899999999977665444455*****************99988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2634.43
//
Query:       gi|320100212|ref|YP_004175804.1|  [L=196]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-44  151.0   0.0    2.6e-44  150.8   0.0    1.0  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.8   0.0   1.4e-48   2.6e-44       5     182 ..       9     185 ..       6     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.8 bits;  conditional E-value: 1.4e-48
                                       EEEEEEEE.......-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETTT CS
                             DUF99   5 vlGiddsffe..rkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiagF 79 
                                       v + dd+ff+   k  +g++ +vGv +++++++ ++a +r+ vdG     a+ e+ + l      v++ldG+t+agF
  gi|320100212|ref|YP_004175804.1|   9 VEAYDDGFFPveYKGGRGDTYVVGVKTCGSSRIINIAASRIIVDGGWTHVAVREMSRLL---GGGVIMLDGVTYAGF 82 
                                       5689*****9875568****************************************999...999************ PP

                                       EE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHHH CS
                             DUF99  80 NvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGieleeaa 156
                                       +vvD+ +l++etg Pviav+ ++ +l+++++aL khf d+eeR+++i+ ++++  +ve++++++ v ++Gi+l ea 
  gi|320100212|ref|YP_004175804.1|  83 DVVDPFSLSSETGKPVIAVQLHPLNLERVKAALLKHFADWEERFRVIRDYYNSLVPVETPWRPIQVAYTGISLGEAV 159
                                       ***************************************************************************** PP

                                       HHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 157 klvrkltlegriPEPlRvAhliAsal 182
                                       +++r++++++  PEPlR+A++iAs+l
  gi|320100212|ref|YP_004175804.1| 160 SILRQTCIYSPEPEPLRIADMIASSL 185
                                       ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.40
# Mc/sec: 1484.29
//
Query:       gi|320100213|ref|YP_004175805.1|  [L=629]
Description: phosphoenolpyruvate carboxykinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.2e-100  336.8   0.0   1.7e-100  336.4   0.0    1.2  1  PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loo
      1e-61  208.3   0.0    1.4e-61  207.9   0.0    1.1  1  PEPCK_N    Phosphoenolpyruvate carboxykinase N-terminal domai


Domain annotation for each model (and alignments):
>> PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.4   0.0  1.9e-104  1.7e-100       1     358 []     250     610 ..     250     610 .. 0.92

  Alignments for each domain:
  == domain 1  score: 336.4 bits;  conditional E-value: 1.9e-104
                                       -EEES-EEEEEE-TTS-EEEEEEE-TTTSSHHHHHT---SSTT-EEEEEESS-EEEEE-TTSBEEEE---SEEEEE- CS
                         PEPCK_GTP   1 wLaEhmlilgvtspegkkkyvaaafpsacGKtnlamleptlegwkvetvgdDiawlkfgedgrlraiNpeaGfFgva 77 
                                       wL+Ehm+i+gv+   +  +y+++afp++cGKt++a++++t       +vgdD+a+++   +g+ ra+Npe G+Fg++
  gi|320100213|ref|YP_004175805.1| 250 WLCEHMFIVGVKGTGDTISYFTGAFPAGCGKTSTALIADT-------VVGDDLAMIRNV-NGEARAVNPEIGMFGII 318
                                       9*************************************95.......9**********9.***************** PP

                                       TT-STTT-HHHHHHT.TBS..-EEES-EEETTS-EE-TT--------EE-TTSSEE-T...T-S.....SS-TT-EE CS
                         PEPCK_GTP  78 pgtnektnpnalktl.kkn..tiftNvaltedgdvwWegleeeapaelidwkgkkwtke..kek.....aahpnsrf 144
                                       +g+n  ++p+++ +l +++  +if+Nv+ltedg+vwW+g+ +e p+++++++g +w+++  +ek      +hpn+rf
  gi|320100213|ref|YP_004175805.1| 319 DGVNPVDDPEIYGILsSREteVIFSNVLLTEDGEVWWNGKPSE-PRRGVNYAG-EWWPGklDEKgrpipPSHPNARF 393
                                       ***********99996333569******************755.669******.777764533377899******** PP

                                       EEEGGGSTTB-TTTT-TT-EEEEEEEEEEB-SSSS-SEEE-SSHHHHHHH.HHT-EEE--TTSSS-TT-EEE-GGG- CS
                         PEPCK_GTP 145 tvpakqlpiiapewedpeGvpisaiifggrrsetvplvleafdwehGvfl.gatlesetTaaaegkvgvvrrdPfam 220
                                       t+++  l++++p+++dp+Gvp+s +ifggr+s+t+++v eaf+w hG+++ ga+lese+T+a+ gk+g+ + +Pfa+
  gi|320100213|ref|YP_004175805.1| 394 TTSIFYLSKVDPRINDPNGVPVSGMIFGGRDSDTWVPVEEAFNWVHGIVTkGASLESERTTAVLGKAGEREFNPFAI 470
                                       ************************************************999************************** PP

                                       GGG-SS-HHHHHHHHHHHTTSTT-B--EEEEEES--B-TTSSBSS--GGGHHHHHHHHHHHHTT..S-EEETTEEEE CS
                         PEPCK_GTP 221 lpFlgynlgdYlehwlelgkklekklPkifsvNwfrkdeegkflWPGfgenlrvlkWilkrvegeakavetpiGlvP 297
                                       l+Fl+++ g+++e ++++g+   +k+P+i+ vN+f++de g++l     +    lkW+  rv++e++a etp+Gl+P
  gi|320100213|ref|YP_004175805.1| 471 LDFLSVSPGEFIELHFRFGDG-LEKQPRIYGVNYFLRDEAGRYLT-EKVDKRVWLKWMALRVNNEVDALETPTGLIP 545
                                       *******************99.9*********************6.33333334*********************** PP

                                       -BTTC--TT-.........TT--HHHHS---HHHHHHHHHHHHHHHHHTGGGS-HHHHHHHHHHHHHH CS
                         PEPCK_GTP 298 kkedldlkgl.......dlskedleellsvdkeewkeeveeieelfeklgeklPkelleeleelekrl 358
                                        +edl +  l       ++s e +e+l++v++ +++e++e+i +++e++   +P+ ++++l e+++rl
  gi|320100213|ref|YP_004175805.1| 546 VYEDLAV--LfkrelgkEFSIELYEKLFTVRVGKHLEKAERILRIYENI-PGTPRLFFDTLIEQKRRL 610
                                       ****775..333566999******************************5.699**9999999999886 PP

>> PEPCK_N  Phosphoenolpyruvate carboxykinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   0.0   1.5e-65   1.4e-61       1     217 [.      34     245 ..      34     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 1.5e-65
                                       HHHHHHHHHH--SEEEE----HHHHHHHHHHHHHTTSEEE-TTSBS-EEE---TTSSS--GGGEEEE-SSHHHH-SS CS
                           PEPCK_N   1 efveevaelcqPdkvvvcdgseeeneellkelvekgeliklekypnsylarsdpkDvARvesrTfictekeedagpl 77 
                                       e+++ev+el++P++v+v++gs+e+ e+++ ++vek+e+i+ +  p+++++++   D AR++++T i+t+  + + p+
  gi|320100213|ref|YP_004175805.1|  34 EWITEVVELLEPASVFVNTGSREDLEYIRMRAVEKREEIPSRYNPRHTVHFDGIYDLARDRENTRILTPGGSPI-PM 109
                                       6****************************************99*****************************99.** PP

                                       --EE-HHHHHHHHHHHSTTTTTTSEEEEEEEEES-TTSTT-EEEEEEES-HHHHHHHHHHSEESHHHHTT-SS..TS CS
                           PEPCK_N  78 nnwmdpeemkeelkelfkgcmkGrtmyVipfsmGpvgsplskigveiTdsaYVvlsmrimtrvgkkvleklgeeeef 154
                                        n+ +++e  +el+e+++g+m+G++my+ ++++Gp gsp++ +gv++TdsaYV++s++i++rv+++v+ + g + ++
  gi|320100213|ref|YP_004175805.1| 110 VNTGNRDEGLRELREIYRGIMRGKEMYIGFYCFGPRGSPFTLYGVQVTDSAYVMHSENILYRVCYDVFVEKGGSMRY 186
                                       ***********************************************************************9999** PP

                                       EEEEEE-S--SS-SS-BTB---G.G-EEEEEGGGTEEEEES--SHHHH-TCCHHHHCHHHHHHH CS
                           PEPCK_N 155 vkclHsvgaplegqkdvkWpcne.kkyivhfpeereilsvgsgYgGNaLlgKkcfalRiasvia 217
                                       +++lHs+g+ +    +  W  n  k++i++++ ++ ++sv+++Y+GN++++Kk ++lR++++++
  gi|320100213|ref|YP_004175805.1| 187 MRFLHSAGELN----EYGWSRNIsKRRIYIDTVDNITYSVNTQYAGNTVGLKK-LSLRLCVNQG 245
                                       ********833....446999977*****************************.******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 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:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 4162.56
//
Query:       gi|320100214|ref|YP_004175806.1|  [L=454]
Description: 4-aminobutyrate aminotransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-103  346.4   0.0   2.1e-103  346.1   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
       0.13   11.4   0.0        5.8    6.0   0.0    2.2  2  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.1   0.0  2.4e-107  2.1e-103       9     404 ..      31     432 ..      23     434 .. 0.93

  Alignments for each domain:
  == domain 1  score: 346.1 bits;  conditional E-value: 2.4e-107
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                       +++++ ka +++++d dg++y+D++ss a  n+Gh++ +v++avk+q++k+ h +   l +ep+++lae l+ ++p+
  gi|320100214|ref|YP_004175806.1|  31 FPMIVGKALNARIWDTDGREYIDFLSSAATYNVGHSNREVLEAVKTQLDKFIHYC-LYLYHEPVVELAELLAGITPG 106
                                       458999*************************************************.8999***************** PP

                                       ..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE- CS
                       Aminotran_3  86 gld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlk 161
                                       +++ kv +  sG +A+ +AlK+a        +t++  i++f+ ++HG t + ++v+gs ++  +++ pf  +v++++
  gi|320100214|ref|YP_004175806.1| 107 SFEkKVAFGLSGGDANDAALKAALV------YTRRRVIVSFDYSYHGTTALDIAVSGSFSPELRGLMPF-RDVYFAE 176
                                       **98999******************......99*************************66666666665.79***** PP

                                       TTBGGGTB-HH.HHHHHHHHHHHHHH....CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE- CS
                       Aminotran_3 162 ypdeevlkene.eeeaalleeleale....kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDE 233
                                       ypd++++     + e++ + +l++ e    k    +vaA+i+Ep+qg+gGv +++++f++++r+++ +h+++li DE
  gi|320100214|ref|YP_004175806.1| 177 YPDTYRCIGGVeDPEECGELYLSRFEellkKIGGSNVAAIILEPVQGDGGVLIPPANFIKGVRKMASEHGIVLIDDE 253
                                       ****9986543255666555555555444677889****************************************** PP

                                       TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHH CS
                       Aminotran_3 234 vqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiiee 310
                                       vqtG+GrTG lfA+eh+ v+pDlm+l+Kal+gG+p+sav+++ ++m+   p+s   T ++     a+a+av++ + +
  gi|320100214|ref|YP_004175806.1| 254 VQTGMGRTGRLFAIEHYSVEPDLMVLGKALGGGMPVSAVVGRSDIMDSAPPQSFFATSAAHAASVAAAIAVVKYVTR 330
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETT.. CS
                       Aminotran_3 311 ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGd.. 379
                                       ++l e+a+e+g++  ++L+el++kyev+++vRg+Glmi+++++ +++ k+       +i+ +a ekG+++++ G+  
  gi|320100214|ref|YP_004175806.1| 331 NNLHERAREMGEYALKRLNELKEKYEVVGDVRGLGLMIGVDIVVDKKSKRpdrakaLKIIWRAWEKGLVMMTYGKyg 407
                                       *******************************************999988899*99999******************* PP

                                       TEEEE---TT--HHHHHHHHHHHHH CS
                       Aminotran_3 380 nvirllppliitdeeidelleilkk 404
                                       nv+r++ppl+i  e++d++++i+++
  gi|320100214|ref|YP_004175806.1| 408 NVLRIAPPLTIPREDLDKGIDIIEE 432
                                       **********************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 ?    3.5   0.0    0.0038        34      72     104 ..     114     146 ..      61     151 .. 0.86
   2 ?    6.0   0.0   0.00064       5.8     129     302 ..     195     360 ..     170     430 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0038
                                       EEESHHHHHHHHHHHHHHHTTT-EEEEEESS-T CS
                     Aminotran_1_2  72 vvgsGagaliealifllklnpgdeilvpdptya 104
                                         +sG +a+++al+++l + + ++i+++d +y 
  gi|320100214|ref|YP_004175806.1| 114 FGLSGGDANDAALKAALVYTRRRVIVSFDYSYH 146
                                       5579*************99999*******9996 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.00064
                                       EE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HH.HHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH. CS
                     Aminotran_1_2 129 hldlealeealkeapegnkktkvilvesphNPtGtvatle.eleklldlakkynlllfvDeaYagfvfgsldavat. 203
                                       +l l  +ee+lk+    n+    i++e ++   G++++++  ++ + ++a +++++l+ De+  g+  +   + a+ 
  gi|320100214|ref|YP_004175806.1| 195 ELYLSRFEELLKKIGGSNV--AAIILEPVQGDGGVLIPPAnFIKGVRKMASEHGIVLIDDEVQTGMGRTGRLF-AIe 268
                                       6667778888888777777..89999999999998766651678899999999********999998885433.322 PP

                                       HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 204 ranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqr 280
                                       +  ve+  +l++   l+Ka+G  G  v +++g +++ + +   s + +s ++++ ++aa++  +  ++++l+e++++
  gi|320100214|ref|YP_004175806.1| 269 HYSVEP--DLMV---LGKALG-GGMPVSAVVGRSDIMDSAPPQSFFATSAAHAASVAAAIAVVKYVTRNNLHERARE 339
                                       444444..3333...689997.3556699999998888888777666666666666666555544444466655555 PP

                                       HHHHHHHHHHHHHHSTEEEECC CS
                     Aminotran_1_2 281 lqkrrkelrdeLaelglkvlas 302
                                       + + + +  +eL+e   +v++ 
  gi|320100214|ref|YP_004175806.1| 340 MGEYALKRLNELKE-KYEVVGD 360
                                       55544444444433.4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3113.99
//
Query:       gi|320100215|ref|YP_004175807.1|  [L=73]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy 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:                       648  (0.0361426); 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:                         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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 528.93
//
Query:       gi|320100216|ref|YP_004175808.1|  [L=462]
Description: amino acid carrier protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-108  361.7  24.4   7.6e-108  361.3  24.4    1.1  1  Na_Ala_symp  Sodium:alanine symporter family


Domain annotation for each model (and alignments):
>> Na_Ala_symp  Sodium:alanine symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.3  24.4  4.2e-112  7.6e-108       8     383 ..      55     459 ..      49     462 .] 0.92

  Alignments for each domain:
  == domain 1  score: 361.3 bits;  conditional E-value: 4.2e-112
                       Na_Ala_symp   8 ksegeissfqAlatalaarvGtGniaGvatAialGGpGAvfWmwvvallGmatkfvEstLaqlYkekdekgevrGGp 84 
                                        ++ge+ +f  +a  + a+vG+GniaGv+tA+ lGG+GA+fWmwv+a+lGm tk vE+tLa   ++ + +g+v+GG+
  gi|320100216|ref|YP_004175808.1|  55 GGKGEVKPFALFAAVMGATVGVGNIAGVSTAVHLGGAGALFWMWVCAILGMGTKAVEATLAAWSRRITPDGRVEGGT 131
                                       4799************************************************************************* PP

                       Na_Ala_symp  85 ayyiekg..lkkkwlavlfavlliialglgi.navqansiasaleea.......feveklvvgivlavllalvilgg 151
                                        yyi+    ++  +lav+f+v+++ia+ +gi n+vqan++a  +e          ++++lv g+++ v++alv+lgg
  gi|320100216|ref|YP_004175808.1| 132 PYYIRLVpvIG-PALAVVFSVFTFIAA-YGIgNTVQANNVALGVEYIakgygwdPGLARLVAGVLMFVFTALVVLGG 206
                                       ****9752144.6***********999.5666*************97456554437788****************** PP

                       Na_Ala_symp 152 ikriakvaevvvPvmailYillalvvillniekvpevlalifksAFgleavagGilg....aaialGvkRglfSneA 224
                                       i+ria v++++vP+ma+ Yi+++l++ +  + + p ++++if+ AF+++a+agG++g    +ai++G++RglfSneA
  gi|320100216|ref|YP_004175808.1| 207 IRRIADVSNYLVPFMAFWYIAASLIIWVKYAGNFPLAIKEIFTYAFTPQAAAGGLAGwmvySAIRYGFARGLFSNEA 283
                                       ***************************************************************************** PP

                       Na_Ala_symp 225 GlGsapiaaAaaevshpvkqGlvqalgvfidtlvvCtatalvill.........segvaltqaalesvlgsvgalfv 292
                                       GlGsap+a A  +v+hp + Gl  +++vf+dt+v+Ct+t++v ++          +g+al  +a+ +++g +++ ++
  gi|320100216|ref|YP_004175808.1| 284 GLGSAPNAYAYMTVDHPGRVGLYGVFEVFMDTIVICTMTGIVDVVtrvyierpdLDGAALAMEAFYRAYGGWAPPIL 360
                                       ******************************************9995666666655********************** PP

                       Na_Ala_symp 293 aialllFafstilgnyyygeknleyll...gkkkk......lliyrvlvlllvfvgavas..lelvwnlaDialglm 358
                                        ial+lFa++t+l+++ yge n+ y+               ++i rv++++ ++ +av+   +++ w++aD+++glm
  gi|320100216|ref|YP_004175808.1| 361 GIALALFAYTTLLTWEWYGEVNWLYFWsktL---GlpekplMWIWRVMWVIPIIPAAVSAglFKAFWDFADTMNGLM 434
                                       **************************94440...24555779********999988887544899************ PP

                       Na_Ala_symp 359 alvnliaillLskvvvkalkdYekq 383
                                       a++nlia++  ++v +  +kd+ k+
  gi|320100216|ref|YP_004175808.1| 435 AIPNLIAVAYFAPVGIGLIKDFLKS 459
                                       *********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3233.13
//
Query:       gi|320100217|ref|YP_004175809.1|  [L=563]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-23   84.1   0.0    1.4e-23   84.1   0.0    2.3  3  Radical_SAM  Radical SAM superfamily
    2.4e-09   37.3   1.0    4.6e-09   36.4   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain
      5e-08   33.3   0.4    9.7e-08   32.4   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.026   14.6   0.1      0.054   13.5   0.1    1.4  1  ROS_MUCR     ROS/MUCR transcriptional regulator protein
       0.12   12.2   1.1          3    7.7   0.5    2.5  2  zf-CHC2      CHC2 zinc finger


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.4   8.5e+03      11      17 ..      34      40 ..      33      57 .. 0.71
   2 ?   -3.3   0.7       2.9     1e+04       7      18 ..      99     110 ..      95     113 .. 0.84
   3 !   84.1   0.0   3.9e-27   1.4e-23       1     166 [.     118     283 ..     118     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.4
                                      -TTTSCC CS
                                      xxxxxxx RF
                       Radical_SAM 11 CsfCarp 17
                                      C++C+r 
  gi|320100217|ref|YP_004175809.1| 34 CPYCYRV 40
                                      ****986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                                       ESS--TTTSCCT CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM   7 CnlrCsfCarpe 18 
                                       C+++C  C+ ++
  gi|320100217|ref|YP_004175809.1|  99 CPFNCGLCPMHK 110
                                       ********9875 PP

  == domain 3  score: 84.1 bits;  conditional E-value: 3.9e-27
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavp 76 
                                       +vvt+ Cnl C++C +++  +  g++++ s+e+i   v+++ +++g +  + l+ggepll+ d+v++++ l+++   
  gi|320100217|ref|YP_004175809.1| 118 MVVTNRCNLSCWYCFFYS--EAAGYVYEPSLEQIRGMVRSI-KKQGvTVAIQLTGGEPLLREDLVDIVKLLREE--G 189
                                       689**************9..5********************.79999***************************..9 PP

                                       TEEEEEEECSSCHG..........HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd..........eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                        ++i + tng++             e+++ l+  gv++v+l+ + +++      +n  ++  e+   +e++r+ag+ 
  gi|320100217|ref|YP_004175809.1| 190 VRHIQLNTNGIKFAelyledpgkaVEYARQLRVNGVNTVYLSFDGVSPV-----TNW-KNHWEIPYIFETFRKAGMT 260
                                       ************************************************5.....543.3344555889999****** PP

                                       TEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 144 rvvdrivglpGendeeleellel 166
                                       +vv + ++++G+n +el +++++
  gi|320100217|ref|YP_004175809.1| 261 SVVLVPTVIKGVNTHELGAIVRF 283
                                       *****************999988 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 ?   -2.9   0.7         2   7.3e+03       8      17 ..      99     108 ..      96     114 .. 0.78
   2 !   36.4   0.0   1.3e-12   4.6e-09       3      91 ..     119     201 ..     118     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2
                           Fer4_14   8 CnlsCkgCdn 17 
                                       C+++C  C  
  gi|320100217|ref|YP_004175809.1|  99 CPFNCGLCPM 108
                                       ******9974 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 1.3e-12
                           Fer4_14   3 vrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79 
                                       v +++CnlsC  C+  ++ +  + +p + e++  ++++ kk+ +  + + ltGGePL+    ++l+++vk l+ee+ 
  gi|320100217|ref|YP_004175809.1| 119 VVTNRCNLSCWYCFFYSEAAGYVYEP-SLEQIRGMVRSIKKQGVTVA-IQLTGGEPLLR---EDLVDIVKLLREEG- 189
                                       449***********988655555555.556666888899*****888.*********55...99************. PP

                           Fer4_14  80 ekkiwletngtl 91 
                                         +i+l+tng  
  gi|320100217|ref|YP_004175809.1| 190 VRHIQLNTNGIK 201
                                       789******975 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   2.7e-11   9.7e-08       7     102 ..     116     208 ..     109     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.7e-11
                           Fer4_12   7 rlslfvsgCnlsCkgCfnketwsfksgkeft..kelleeiiedlkkesi.egltllGGEPllpenaeallelvkevk 80 
                                       + ++ +++CnlsC +Cf     s  +g  ++   e ++ +++++kk+ +   + l+GGEPll   +e+l+++vk ++
  gi|320100217|ref|YP_004175809.1| 116 VNMVVTNRCNLSCWYCF---FYSEAAGYVYEpsLEQIRGMVRSIKKQGVtVAIQLTGGEPLL---REDLVDIVKLLR 186
                                       55778899*********...45555555553338888899999998877689**********...************ PP

                           Fer4_12  81 eekpekdiwlytgytleelskk 102
                                       ee++    + ++g ++ el  +
  gi|320100217|ref|YP_004175809.1| 187 EEGVRHIQLNTNGIKFAELYLE 208
                                       ****9999********999765 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 ?   13.5   0.1   1.5e-05     0.054      83     118 ..     512     545 ..     503     550 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                          ROS_MUCR  83 LasahgltpeeYrakwglpkdyPlvApnyaeeRrkl 118
                                       ++++hg+  eeY +k+g+pk   +v ++y ++Rr+l
  gi|320100217|ref|YP_004175809.1| 512 IQREHGIPLEEYSRKYGMPKG--MVTRKYVRDRRRL 545
                                       6789***************96..9**********96 PP

>> zf-CHC2  CHC2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.044   1.6e+02      34      66 ..      32      64 ..      25      84 .. 0.82
   2 ?    7.7   0.5   0.00084         3      33      70 ..     103     141 ..      91     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.044
                           zf-CHC2 34 alCPFHeektpsftvspekqfyyCfgCgagGda 66
                                      ++CP+     p++ v+ e ++y    C ++G+ 
  gi|320100217|ref|YP_004175809.1| 32 SVCPYCYRVLPAVIVEREGKVYIRRVCPEHGEI 64
                                      579999999999999999999999999999975 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00084
                           zf-CHC2  33 valCPFHeektpsft.vspekqfyyCfgCgagGdaikFl 70 
                                        +lCP H+++t+ ++ v++++    C+ C    +a  ++
  gi|320100217|ref|YP_004175809.1| 103 CGLCPMHKQHTALVNmVVTNRCNLSCWYCFFYSEAAGYV 141
                                       69*********9875256667677888886666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 4214.12
//
Query:       gi|320100218|ref|YP_004175810.1|  [L=193]
Description: adenylate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   80.7   0.0    1.6e-22   80.4   0.0    1.1  1  AAA_18           AAA domain
      6e-05   23.5   0.1    0.00014   22.3   0.1    1.7  1  AAA              ATPase family associated with various cellul
    0.00032   21.1   0.1     0.0012   19.2   0.1    1.9  1  AAA_17           AAA domain
    0.00089   19.4   0.1     0.0021   18.2   0.1    1.9  1  AAA_33           AAA domain
     0.0024   17.8   0.0      0.005   16.8   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0041   17.5   0.3     0.0053   17.1   0.3    1.4  1  AAA_16           AAA ATPase domain
     0.0095   16.2   0.1      0.016   15.5   0.1    1.5  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.025   14.3   0.0    1.3  1  AAA_24           AAA domain
      0.018   14.9   0.1          1    9.2   0.1    2.3  1  CPT              Chloramphenicol phosphotransferase-like prot
       0.02   14.7   0.1      0.029   14.1   0.1    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.033   14.5   0.1      0.051   13.9   0.1    1.3  1  AAA_22           AAA domain
      0.045   13.9   0.0       0.44   10.7   0.0    2.0  2  SKI              Shikimate kinase
      0.059   13.0   0.1        4.6    6.9   0.0    2.2  2  CoaE             Dephospho-CoA kinase
      0.061   12.8   0.0      0.074   12.5   0.0    1.2  1  KTI12            Chromatin associated protein KTI12
      0.083   12.1   0.1       0.11   11.7   0.1    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
        0.2   11.0   0.0       0.27   10.6   0.0    1.2  1  IPT              Isopentenyl transferase
       0.22   11.2   0.1       0.38   10.4   0.1    1.3  1  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   1.5e-25   1.6e-22       2     129 ..       6     126 ..       5     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.5e-25
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknl 77 
                                       +++G+pG+GKt++a+eL++++gf  v+l+++a e+gl+ ++d+e    s ++ded l + ++al e+ +     + l
  gi|320100218|ref|YP_004175810.1|   6 VVAGVPGTGKTSVARELASLTGFpLVELGSYAVEKGLVAGFDAE--TGSYVIDEDALSREVSALAESVE-----GRL 75 
                                       69******************9***********************..********************986.....999 PP

                            AAA_18  78 vidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeil 129
                                       +++ h  e ++++ ++++ +vL+a+p +l+eRle Rg+  +ki en  aeil
  gi|320100218|ref|YP_004175810.1|  76 IVSTHYPEILEPDVVEKV-FVLRAHPLVLAERLESRGWGRRKINENVMAEIL 126
                                       ******************.*******************************98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   1.3e-07   0.00014       2      35 ..       6      39 ..       5      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.3e-07
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsell 35
                                      ++ G pGtGKT++a+ +a+ +g++++e+    + 
  gi|320100218|ref|YP_004175810.1|  6 VVAGVPGTGKTSVARELASLTGFPLVELGSYAVE 39
                                      689**********************999766555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.2e-06    0.0012       2     113 ..       9     101 ..       8     123 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                       G+PG GK+ ++++l+   gf+ ++ G++  e     gl+  +d  ++++ +++++ + +   ++ae + ++ ++v +
  gi|320100218|ref|YP_004175810.1|   9 GVPGTGKTSVARELASLTGFPLVELGSYAVEK----GLVAGFD-AETGSYVIDEDALSREVSALAE-SVEGRLIVST 79 
                                       9***********************99987554....5543333.3344444444444433344554.4666777777 PP

                                       -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HH CS
                            AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpe 113
                                       h+         + l+ +v     ++++++l a p 
  gi|320100218|ref|YP_004175810.1|  80 HYP--------EILEPDV-----VEKVFVLRAHPL 101
                                       762........1222222.....334456666664 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     2e-06    0.0021       1      49 [.       4      55 ..       4     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg.tdqqsktdyt 49
                                      l+++ G+pG+GK+ +a++l+  +g   v l s ++ + l++  d ++ ++ +
  gi|320100218|ref|YP_004175810.1|  4 LLVVAGVPGTGKTSVARELASLTGfpLVELGSYAVEKGLVAgFDAETGSYVI 55
                                      68999**************977776666667776666444435555555544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.7e-06     0.005       3      29 ..       6      32 ..       4      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.7e-06
                                      EEE--SSSSHHHHHHHGGGGBS--EEE CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnrevey 29
                                      ++ G pGtgK+++a++la++++ ++++
  gi|320100218|ref|YP_004175810.1|  6 VVAGVPGTGKTSVARELASLTGFPLVE 32
                                      678******************998764 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   0.3   5.1e-06    0.0053      26      49 ..       4      26 ..       1     103 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-06
                            AAA_16 26 lvllsGesGvGKsslvrellrale 49
                                      l+++ G +G+GK+s++rel+ +l+
  gi|320100218|ref|YP_004175810.1|  4 LLVVAGVPGTGKTSVARELA-SLT 26
                                      789****************9.554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.5e-05     0.016       3      28 ..       6      32 ..       4      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                            AAA_28  3 vitGgestGKTtlleaLaar.gypvvp 28
                                      v+ G ++tGKT+++++La+  g+p v+
  gi|320100218|ref|YP_004175810.1|  6 VVAGVPGTGKTSVARELASLtGFPLVE 32
                                      899***************966999884 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05     0.025       5      42 ..       5      59 ..       1      77 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                            AAA_24  5 iliyGpsgiGKTtlakel........gpkplfi..............dtekGlksldadk 42
                                      +++ G +g+GKT++a+el                             d e G+  +d d 
  gi|320100218|ref|YP_004175810.1|  5 LVVAGVPGTGKTSVARELasltgfplV-----ElgsyavekglvagfDAETGSYVIDEDA 59
                                      799***************776433330.....2344444444444447777777777665 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00099         1       4      43 ..       5      44 ..       2     164 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00099
                                      EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-G CS
                               CPT  4 ilLnGgsssGKsslaralqevldepwlhlgvDafvealpp 43
                                      ++  G++ +GK+s+ar l +++  p ++lg+ a  + l +
  gi|320100218|ref|YP_004175810.1|  5 LVVAGVPGTGKTSVARELASLTGFPLVELGSYAVEKGLVA 44
                                      5667888888888888888888877777776554443333 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.7e-05     0.029       1      21 [.       5      25 ..       5      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrt 21
                                      +vv+GvpG GK+++ r+l++ 
  gi|320100218|ref|YP_004175810.1|  5 LVVAGVPGTGKTSVARELASL 25
                                      59***************9976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.8e-05     0.051       7      28 ..       4      25 ..       2      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleq 28
                                      +lvv G +GtGKT ++r+l++ 
  gi|320100218|ref|YP_004175810.1|  4 LLVVAGVPGTGKTSVARELASL 25
                                      689***************9875 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00041      0.44       1      24 [.      11      34 ..      11      43 .. 0.88
   2 ?    1.4   0.0       0.3   3.2e+02      87     154 ..      92     160 ..      52     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                                      TTSSHHHHHHHHHHHHTSEEEEHH CS
                               SKI  1 mGaGKstvGkllAkklglefiDlD 24
                                      +G+GK++v+++lA   g+++++l 
  gi|320100218|ref|YP_004175810.1| 11 PGTGKTSVARELASLTGFPLVELG 34
                                      69*****************99875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.3
                                       EEEEEE--HHHHHHHHHHTTS.SGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHH CS
                               SKI  87 iviyLdvsleellerlkadke.RPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeeil 154
                                        v+ L++++ +l+erl+++   R  ++e+  +e l    ++  + + e + + vd+s++s+ eva+ i+
  gi|320100218|ref|YP_004175810.1|  92 KVFVLRAHPLVLAERLESRGWgRRKINENVMAEILGVVSYNAVEAFGEGKVYEVDTSNASPGEVARLIV 160
                                       466788888899999988887766666666633333333355556666667777777777777766665 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.017        18       5      34 ..       7      37 ..       3      40 .. 0.83
   2 ?    6.9   0.0    0.0044       4.6      10      57 ..      37      85 ..      33      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                                      EEESTTSSHHHHHHHHHH.TT-EEEEHHHHH CS
                              CoaE  5 ltGgiasGKstvanlfad.lgvpivDaDlvA 34
                                      ++G  ++GK+ va+ +a+ +g+p+v    +A
  gi|320100218|ref|YP_004175810.1|  7 VAGVPGTGKTSVARELASlTGFPLVELGSYA 37
                                      567779************8999999877666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0044
                                      TSSHHHHHHHHHHTT-EEEEHHHHHHHTTCCTHHHH.HHHHHHHGGGCB CS
                              CoaE 10 asGKstvanlfadlgvpivDaDlvArqvvepgseal.kkiveeFgeeil 57
                                      a  K +va   a++g +++D D++ r+v +  +++  + iv+++ +eil
  gi|320100218|ref|YP_004175810.1| 37 AVEKGLVAGFDAETGSYVIDEDALSREVSALAESVEgRLIVSTHYPEIL 85
                                      6668888888889***************987665440445555556665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05     0.074       3      24 ..       4      25 ..       1      73 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                                      EEEEE--TTSSHHHHHHHHHHH CS
                             KTI12  3 LvvltGlPssGKstrakeLaka 24
                                      L+v+ G+P +GK+++a+eLa+ 
  gi|320100218|ref|YP_004175810.1|  4 LLVVAGVPGTGKTSVARELASL 25
                                      7899***************975 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011      0.11       3      22 ..       4      23 ..       3      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                           DUF2075  3 vvlVtGvaGtGKtvvllnll 22
                                      +++V Gv+GtGKt v+ +l+
  gi|320100218|ref|YP_004175810.1|  4 LLVVAGVPGTGKTSVARELA 23
                                      579***********998876 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00026      0.27       5      32 ..       6      33 ..       1      43 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                               IPT  5 lifGatttGKtaeaiklaketgapvivl 32
                                      ++ G  +tGKt++a +la  tg+p++ l
  gi|320100218|ref|YP_004175810.1|  6 VVAGVPGTGKTSVARELASLTGFPLVEL 33
                                      567999******************9976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00036      0.38      20      40 ..       4      24 ..       2      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                            AAA_30 20 vavltGpAGtGKttalkalre 40
                                      + v+ G++GtGKt + ++l+ 
  gi|320100218|ref|YP_004175810.1|  4 LLVVAGVPGTGKTSVARELAS 24
                                      67999**********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1252.53
//
Query:       gi|320100219|ref|YP_004175811.1|  [L=286]
Description: Ras superfamily GTP-binding protein YlqF [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   56.1   0.0    5.9e-11   42.5   0.0    2.2  2  MMR_HSR1     50S ribosome-binding GTPase
      6e-14   52.3   0.0    9.3e-14   51.7   0.0    1.2  1  RsgA_GTPase  RsgA GTPase
    5.3e-07   29.3   0.0    4.6e-05   23.0   0.0    2.1  2  FeoB_N       Ferrous iron transport protein B
    5.6e-06   26.5   1.4       0.54   10.3   0.0    3.1  3  Dynamin_N    Dynamin family
     0.0016   18.0   0.0      0.006   16.1   0.0    1.7  2  GTP_EFTU     Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.081   13.3   0.0    2.0  2  AAA_16       AAA ATPase domain
      0.044   13.5   0.0      0.085   12.6   0.0    1.4  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati


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 !   11.6   0.0   8.6e-05      0.22      73     114 .]      19      59 ..       8      59 .. 0.85
   2 !   42.5   0.0   2.3e-14   5.9e-11       2      58 ..     111     168 ..     110     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-05
                                       HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  73 leeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       + ++d++l+v+d++ + l+   ++le++ e+++++lilvlnk
  gi|320100219|ref|YP_004175811.1|  19 VSRVDVVLMVLDSR-DPLSTFSRRLESMVERNGRKLILVLNK 59 
                                       4569********66.8899999*******99**********8 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 2.3e-14
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSST...TSSSSEEEEEEEETTEEEEEEECGGCSS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkp...gtTrdinegrvklkgkeielvDtpGlie 58 
                                       va++G+p vGKS++in l g+  a +s +p   g Tr+ + +rv+   k+i +vD pG+i 
  gi|320100219|ref|YP_004175811.1| 111 VAVAGYPKVGKSSIINGLKGRhSASTSPYPgspGYTRHFQVYRVD---KDIMVVDSPGVIP 168
                                       89******************9778999998666899999999997...69********875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   3.6e-17   9.3e-14      12     161 ..      18     166 ..      10     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 3.6e-17
                                       TEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHT CS
                       RsgA_GTPase  12 kvaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktke 88 
                                        v+ vd +l+v+     +  + +  r+  ++e++g ++++vlnK+Dl+ ++  +ee+ke +++ gy+++++ a ++ 
  gi|320100219|ref|YP_004175811.1|  18 MVSRVDVVLMVLDSR--DPLSTFSRRLESMVERNGRKLILVLNKADLVPRSV-AEEWKEYFTEKGYTTVYMAAARHM 91 
                                       578888877777666..3334444566677899999****************.************************ PP

                                       THHHHHHHCTT......SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS- CS
                       RsgA_GTPase  89 gleelkellkd......ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtP 159
                                       g+ +l++ ++        +++++G   vGKS++in l+++++++t+    + g     T++ ++++++++ +++D+P
  gi|320100219|ref|YP_004175811.1|  92 GTLRLRRTIRRvapslpTLVAVAGYPKVGKSSIINGLKGRHSASTSPYPGSPG----YTRHFQVYRVDKDIMVVDSP 164
                                       999999988753221224678899999*************9999999988755....4999**************** PP

                                       SS CS
                       RsgA_GTPase 160 Gf 161
                                       G+
  gi|320100219|ref|YP_004175811.1| 165 GV 166
                                       *8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0095        24      77     149 ..      20      93 ..       9     100 .. 0.65
   2 !   23.0   0.0   1.8e-08   4.6e-05       3      58 ..     111     167 ..     109     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0095
                                       TSSSEEEEEEEGGGHHHHHHHHHH..HHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTH CS
                            FeoB_N  77 eepdvvvnvvdatnlernLyLtlq..llelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegi 149
                                       +++dvv+ v+d+     ++   l+  +   g +++l+ln+ d + ++  e   k+  ++ g   v ++a+++ g+
  gi|320100219|ref|YP_004175811.1|  20 SRVDVVLMVLDSRDPLSTFSRRLEsmVERNGRKLILVLNKADLVPRSVAEE-WKEYFTEKGYTTVYMAAARHMGT 93 
                                       578999999999887666654433104456799*********998765553.33333334555555555555555 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.8e-08
                                       EEEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE----S CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPGiY 58 
                                       va++G p vGk++++n l g +  + + +pG     ++ ++   +k++ +vD PG+ 
  gi|320100219|ref|YP_004175811.1| 111 VAVAGYPKVGKSSIINGLKGRHsASTSPYPGSPGYTRHFQVYRVDKDIMVVDSPGVI 167
                                       89******************98357999****9999999999999**********86 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00021      0.54     123     168 .]      16      60 ..       9      60 .. 0.91
   2 !    9.0   0.1   0.00052       1.3       1      30 [.     111     140 ..     111     147 .. 0.87
   3 ?    4.8   0.0      0.01        26     100     122 ..     155     177 ..     149     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                                       HHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE-C CS
                         Dynamin_N 123 keyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltkl 168
                                       ++++ + d++l+v+++   ls + +++l+++v+ +g++ i vl+k+
  gi|320100219|ref|YP_004175811.1|  16 EKMVSRVDVVLMVLDSRDPLS-TFSRRLESMVERNGRKLILVLNKA 60 
                                       6677999**************.88999*****************95 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00052
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnp 30 
                                       +av G  + GKSS++n L g++   ++p p
  gi|320100219|ref|YP_004175811.1| 111 VAVAGYPKVGKSSIINGLKGRHSASTSPYP 140
                                       78999999*************987777765 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.01
                                       S-SEEEEE---B-SSSGTTSHHH CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdqelv 122
                                       +k++ +vD+PG++ v+ ++ e+v
  gi|320100219|ref|YP_004175811.1| 155 DKDIMVVDSPGVIPVEGGELEMV 177
                                       68999********9999988876 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 !   16.1   0.0   2.3e-06     0.006      89     145 ..      17      73 ..      12     106 .. 0.84
   2 ?   -1.3   0.0       0.5   1.3e+03      61      79 ..     149     165 ..     144     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                                       HHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHH CS
                          GTP_EFTU  89 rglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeivee 145
                                       + ++ +D++++v+d+++   + ++++  ++ ++g ++i+++NK+D +  ++ e  +e
  gi|320100219|ref|YP_004175811.1|  17 KMVSRVDVVLMVLDSRDPLSTFSRRLESMVERNGRKLILVLNKADLVPRSVAEEWKE 73 
                                       567889*****************************************5555544444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.5
                                       EEEETTCSSEEEEEEEESS CS
                          GTP_EFTU  61 isleketkkylinliDtPG 79 
                                        +++    ++ i ++D+PG
  gi|320100219|ref|YP_004175811.1| 149 FQVY--RVDKDIMVVDSPG 165
                                       5555..6688999*****9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.62   1.6e+03     121     147 ..      36      63 ..      11      76 .. 0.72
   2 ?   13.3   0.0   3.2e-05     0.081      11      47 ..      95     131 ..      93     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.62
                            AAA_16 121 ellkrll.allsrderplvlvlDdlqwa 147
                                        +++r l +  +r++r+l+lvl  ++ +
  gi|320100219|ref|YP_004175811.1|  36 STFSRRLeSMVERNGRKLILVLNKADLV 63 
                                       4455555555566677899999888755 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.2e-05
                            AAA_16  11 qLlsalervrsgrpelvllsGesGvGKsslvrellra 47 
                                       +L+++++rv+ + p lv + G++ vGKss+++ l+ +
  gi|320100219|ref|YP_004175811.1|  95 RLRRTIRRVAPSLPTLVAVAGYPKVGKSSIINGLKGR 131
                                       7999***************************988754 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.3e-05     0.085      56     128 ..      14      88 ..       8     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.3e-05
                         PduV-EutP  56 alivtsaeadvialvqdateeesvfppgfasvfnk...eviGiitkidlaedeenieaveelLksaGaekifevsa 128
                                        l  +   +dv+ +v+d+ ++ s+f+  + s++++   ++i ++ k+dl+  ++  e  +e++++ G ++++   a
  gi|320100219|ref|YP_004175811.1|  14 QLEKMVSRVDVVLMVLDSRDPLSTFSRRLESMVERngrKLILVLNKADLV-PRSVAEEWKEYFTEKGYTTVYMAAA 88 
                                       67788899************************98622269**********.6667788899999999999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2079.25
//
Query:       gi|320100220|ref|YP_004175812.1|  [L=66]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00014   22.4   0.1    0.00015   22.3   0.1    1.1  1  ThiS            ThiS family
       0.01   15.9   0.0      0.011   15.8   0.0    1.2  1  ThiS-like       ThiS-like ubiquitin
  ------ inclusion threshold ------
        0.1   12.6   0.0        0.1   12.6   0.0    1.0  1  Thioredoxin_14  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   2.5e-08   0.00015      13      72 ..      11      61 ..       3      66 .] 0.85

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.5e-08
                                      CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEE CS
                              ThiS 13 eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailp 72
                                      +  +++a g  v+elle Lg            +v++Ng  +++   d++l dgDev +  
  gi|320100220|ref|YP_004175812.1| 11 SPRIVEAAGIRVSELLERLGLSR------SEHIVLRNGVPLTE---DEVLGDGDEVLVYL 61
                                      45678999*************99......**************...**********8755 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.8e-06     0.011      27      52 ..      33      58 ..      19      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                         ThiS-like 27 pdaDvvIlNGFpikeDteLkegDevf 52
                                      +++++v  NG p++eD  L +gDev 
  gi|320100220|ref|YP_004175812.1| 33 RSEHIVLRNGVPLTEDEVLGDGDEVL 58
                                      55679*******************96 PP

>> Thioredoxin_14  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05       0.1     176     204 ..      22      49 ..       5      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHTT--SSS-EEEE.TTEEEESSS CS
                    Thioredoxin_14 176 srefikrlglkeaqepvfllNGvvlpfde 204
                                        +e+++rlgl+ + e+++l NGv+l +de
  gi|320100220|ref|YP_004175812.1|  22 VSELLERLGLSRS-EHIVLRNGVPLTEDE 49 
                                       57899*****766.9**********9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 505.74
//
Query:       gi|320100221|ref|YP_004175813.1|  [L=260]
Description: UBA/THIF-type NAD/FAD-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-55  187.4   0.0    3.4e-55  187.1   0.0    1.0  1  ThiF             ThiF family
    5.1e-05   23.5   0.0    0.00011   22.4   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.045   13.4   0.3      0.074   12.7   0.3    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.12   13.0   0.1       0.26   12.0   0.1    1.6  1  PglD_N           PglD N-terminal domain
        0.2   11.7   0.7        1.3    9.0   0.1    2.3  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase


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 !  187.1   0.0   9.5e-59   3.4e-55       1     239 [.      11     237 ..      11     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 187.1 bits;  conditional E-value: 9.5e-59
                                       THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaeva 77 
                                       ysrql ++g +gq+kL+++++l+ GaGglGs +l +L ++Gvg++ ++D + +elsNl+Rq+l++ +diG++K+++a
  gi|320100221|ref|YP_004175813.1|  11 YSRQLPIIGVEGQAKLKNTSILVAGAGGLGSAVLYYLTAAGVGRIIFIDEGLVELSNLQRQILYTVDDIGRSKVTAA 87 
                                       89*************************************************************************** PP

                                       HHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip 154
                                        e+l+++np+v +e+v+++it e  l+e++++vD+VvdalDn+e+r+ +++a+ ++g+pl++ag+ +++gq++v+ip
  gi|320100221|ref|YP_004175813.1|  88 YERLRRLNPNVLLEPVQASITREL-LDEVMQRVDIVVDALDNWETRFTLDEAAWRHGKPLVHAGVGEHYGQLTVVIP 163
                                       **********************96.99************************************************** PP

                                       CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 155 gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfen 231
                                       gkt+c++ l+      + ++k  ++        ++  +++++++l ++e+ kl+ g  + ++ +   +++++++ e 
  gi|320100221|ref|YP_004175813.1| 164 GKTPCLRYLFH---GVRAREKGRVI--------VMPHIPGLLGLLEVNEVFKLILGYGDVMAGRILLFNAKAPSIEV 229
                                       *********95...55556666666........799******************8888899999999*****99999 PP

                                       ECCEEEEE CS
                                       xxxxxxxx RF
                              ThiF 232 velerakk 239
                                       +e++++ +
  gi|320100221|ref|YP_004175813.1| 230 IEVKCGDF 237
                                       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 !   22.4   0.0   3.1e-08   0.00011       1      98 [.      31     148 ..      31     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.1e-08
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.....................TTTCEEEEE--T CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.....................lgvrfeaialda 56 
                                       +l+ GaG+ G+av+ +l + +    +i+ +d  + +l +l  ++                     l++++  + ++a
  gi|320100221|ref|YP_004175813.1|  31 ILVAGAGGLGSAVLYYLTAAGVG--RIIFIDEGLVELSNLQRQIlytvddigrskvtaayerlrrLNPNVLLEPVQA 105
                                       7999***************9976..***************9999********************************* PP

                                       TTHHHHHHHHHTTSSEEEE-SSGG.GHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  57 enyeavLaallkegdlvvnlsppi.ssldvlkaCietgvhyvd 98 
                                       +  +++L+++++  d+vv+++ ++    ++ +a++++g   v 
  gi|320100221|ref|YP_004175813.1| 106 SITRELLDEVMQRVDIVVDALDNWeTRFTLDEAAWRHGKPLVH 148
                                       ************************5555999999999987775 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   2.1e-05     0.074       1      38 [.      31      70 ..      31      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                      EEEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHHHHH CS
                              ApbA  1 iailGaGaiGsllaakLakagad.vtlilrsr.rlealkk 38
                                      i+++GaG++Gs + ++L++ag   +++i+ +  +l +l++
  gi|320100221|ref|YP_004175813.1| 31 ILVAGAGGLGSAVLYYLTAAGVGrIIFIDEGLvELSNLQR 70
                                      89*****************887668888887766666555 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.2e-05      0.26       2      33 ..      31      61 ..      30      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                            PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflDdn 33
                                      i++ GaGG g  v+  + a g    i+f+D+ 
  gi|320100221|ref|YP_004175813.1| 31 ILVAGAGGLGSAVLYYLTAAG-VGRIIFIDEG 61
                                      899******************.99999**986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00037       1.3       9      41 ..      25      57 ..      20      72 .. 0.88
   2 ?   -0.6   0.0      0.36   1.3e+03     121     135 ..      65      79 ..      62      82 .. 0.84
   3 ?   -1.2   0.0      0.54   1.9e+03      68      84 ..     111     127 ..      88     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00037
                                      ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                      Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvv 41
                                      +lk+  +l+ GaG +++ v+ +L a+gv +++ 
  gi|320100221|ref|YP_004175813.1| 25 KLKNTSILVAGAGGLGSAVLYYLTAAGVGRIIF 57
                                      68999***********************99875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.36
                                       GGGSTTCCCEEHHHH CS
                      Shikimate_DH 121 vaeledvrlytvDdL 135
                                       +++l+   lytvDd+
  gi|320100221|ref|YP_004175813.1|  65 LSNLQRQILYTVDDI 79 
                                       67899999******8 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.54
                                       GHHHHHHT-SEEEE-SS CS
                      Shikimate_DH  68 elkellaeadvvisata 84 
                                        l+e+++++d+v+ a  
  gi|320100221|ref|YP_004175813.1| 111 LLDEVMQRVDIVVDALD 127
                                       46778889999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1822.28
//
Query:       gi|320100222|ref|YP_004175814.1|  [L=94]
Description: sulfur carrier protein ThiS [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   36.6   0.0    7.8e-09   36.1   0.0    1.3  1  ThiS          ThiS family
  ------ inclusion threshold ------
      0.011   15.6   0.1       0.26   11.1   0.1    2.2  1  TrkA_C        TrkA-C domain
      0.017   14.8   0.0      0.029   14.1   0.0    1.4  1  S4            S4 domain
      0.024   14.7   0.0       0.33   11.0   0.0    2.1  2  TGS           TGS domain
      0.026   14.9   0.0      0.049   14.0   0.0    1.5  1  FHA           FHA domain
      0.058   13.6   0.0      0.076   13.2   0.0    1.2  1  Glutaredoxin  Glutaredoxin
      0.079   12.8   0.0        1.8    8.5   0.0    2.1  2  Ub-Mut7C      Mut7-C ubiquitin
       0.08   13.3   0.0       0.34   11.3   0.0    1.9  1  Ub-RnfH       RnfH family 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 !   36.1   0.0   3.5e-12   7.8e-09       3      77 .]      14      94 .]      12      94 .] 0.91

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.5e-12
                                      ETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG......TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEES CS
                              ThiS  3 lfaelrelag..eeelelaegstvaelleaLgerypela......lerrvavavNgeivprlwldtelkdgDevailpp 73
                                      + +++ + ag    elel+e+st++++++aL+er +          +  ++ +vNg+ v +   +t+lkdgD++ +++p
  gi|320100222|ref|YP_004175814.1| 14 VLGRASDYAGvnMAELELPENSTLKDAIRALSERTNPVLyeryinGHYIFVTLVNGKPVLS--PETPLKDGDRITLVTP 90
                                      567778888888899*****************999888799**998899999******999..9*************** PP

                                      TTC- CS
                              ThiS 74 VaGG 77
                                        GG
  gi|320100222|ref|YP_004175814.1| 91 EMGG 94
                                      9988 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00012      0.26      38      58 ..      70      90 ..      10      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                      EES--TT-B--TT-EEEEEEE CS
                            TrkA_C 38 liipsgdtvLeeGDvllvvgs 58
                                       ++ s++t L+ GD++++v++
  gi|320100222|ref|YP_004175814.1| 70 KPVLSPETPLKDGDRITLVTP 90
                                      567899************986 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.029      29      48 .]      66      85 ..      66      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                      EETTEEE--TT-EE-TTCEE CS
                                S4 29 lVNGkvvkdpsyrVkpgDvi 48
                                      lVNGk+v +p +++k gD+i
  gi|320100222|ref|YP_004175814.1| 66 LVNGKPVLSPETPLKDGDRI 85
                                      6*****************98 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   2.4e+02      11      27 ..      29      45 ..       8      48 .. 0.75
   2 ?   11.0   0.0   0.00015      0.33      38      60 .]      66      89 ..      59      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                                      EEEETTB-HHHHHHHHS CS
                               TGS 11 pdlprgatveDfAykIh 27
                                       +lp+++t +D+ ++++
  gi|320100222|ref|YP_004175814.1| 29 LELPENSTLKDAIRALS 45
                                      45999999999877665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                                      EECSE.EEETTSBB-SSEEEEEEE CS
                               TGS 38 lVnGq.rvgldhvLedgdvveIvt 60
                                      lVnG+     +++L+dgd +++vt
  gi|320100222|ref|YP_004175814.1| 66 LVNGKpVLSPETPLKDGDRITLVT 89
                                      7999735589************98 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.2e-05     0.049      45      68 ..      65      87 ..      56      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                                      EEETTEEESTTSEEEE-TTEEEEE CS
                               FHA 45 tfvNgqrigkgepveLksgdviel 68
                                      t vNg+++ + ++++Lk+gd+i+l
  gi|320100222|ref|YP_004175814.1| 65 TLVNGKPVLS-PETPLKDGDRITL 87
                                      899******8.***********98 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.4e-05     0.076      20      60 .]      20      62 ..      13      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                                      HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEE...ETTEEE CS
                      Glutaredoxin 20 kelgvkfeeidvdkdeeireelkelsgvrtvPqvf...idgkhv 60
                                      ++ gv+ +e ++ +++ +++++++ls+ rt P+++   i+g+++
  gi|320100222|ref|YP_004175814.1| 20 DYAGVNMAELELPENSTLKDAIRALSE-RTNPVLYeryINGHYI 62
                                      6789*********************99.******9999999987 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.072   1.6e+02      27      42 ..      29      44 ..      23      45 .. 0.83
   2 ?    8.5   0.0    0.0008       1.8      52      73 ..      65      87 ..      62      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.072
                          Ub-Mut7C 27 vafdeaatvkhviEal 42
                                       +  e +t+k++i al
  gi|320100222|ref|YP_004175814.1| 29 LELPENSTLKDAIRAL 44
                                      567899*******997 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0008
                          Ub-Mut7C 52 ilvnGesv.gfshiledGdrvav 73
                                       lvnG++v +++  l+dGdr+  
  gi|320100222|ref|YP_004175814.1| 65 TLVNGKPVlSPETPLKDGDRITL 87
                                      58*****9568999******975 PP

>> Ub-RnfH  RnfH family Ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.34      14      70 ..      25      87 ..       8      90 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                           Ub-RnfH 14 vllelevpegttveeAieaSgilekfpei.dlekakvGifgkavk......ldavLqegDRvEi 70
                                       + ele+pe++t+++Ai+a    +  p + +   +   if  +v+       +++L++gDR+ +
  gi|320100222|ref|YP_004175814.1| 25 NMAELELPENSTLKDAIRALS-ERTNPVLyERYINGHYIFVTLVNgkpvlsPETPLKDGDRITL 87
                                      56789************9854.222233322222444455444322222259999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 723.36
//
Query:       gi|320100223|ref|YP_004175815.1|  [L=69]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-05   25.1   1.7    2.2e-05   25.0   1.7    1.1  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.049   14.1   0.2       0.06   13.8   0.2    1.2  1  DUF4350   Domain of unknown function (DUF4350)


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 !   25.0   1.7   2.5e-09   2.2e-05      14      77 .]      12      69 .]       4      69 .] 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.5e-09
                                      EEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS 14 eelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      e++++ae++ v+ +le+L  +     ++++v v+vNg++v++     ++++gD+v+++  + GG
  gi|320100223|ref|YP_004175815.1| 12 EVEVDAEEAEVQVILEKLRNEL----SSDGVLVLVNGRLVED--MRRVVRKGDTVVVVEEFLGG 69
                                      457899************9999....78**************..99***********9877776 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   6.7e-06      0.06      33      68 ..      31      63 ..       6      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-06
                           DUF4350 33 g...edgtllvvapdlrlteeelaallewvarGntlvla 68
                                          +dg+l++v+ +  l     +++++ v++G+t+v++
  gi|320100223|ref|YP_004175815.1| 31 NelsSDGVLVLVNGR--LV----EDMRRVVRKGDTVVVV 63
                                      144489999999999..44....578888*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 509.15
//
Query:       gi|320100224|ref|YP_004175816.1|  [L=172]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   98.9   0.4    1.2e-28   98.9   0.4    2.1  2  DUF2148   Uncharacterized protein containing a ferredoxin dom


Domain annotation for each model (and alignments):
>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.7     0.087   1.6e+03      28      28 ..      21      21 ..       2      44 .. 0.51
   2 !   98.9   0.4   6.6e-33   1.2e-28       7      68 .]     104     164 ..      99     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.087
                           DUF2148 28 v 28
                                      v
  gi|320100224|ref|YP_004175816.1| 21 V 21
                                      2 PP

  == domain 2  score: 98.9 bits;  conditional E-value: 6.6e-33
                           DUF2148   7 fkaiDlGiAlgsavkvaadlrvDnRvmysvGaaAkslgllkeasvvlgiplsvsgKsifFDR 68 
                                        ++++lGiAlgsavk+a++l++DnR+m+svG+aA++lgll+ a++v+g+pls+ gK+++FDR
  gi|320100224|ref|YP_004175816.1| 104 NSVVNLGIALGSAVKTASMLNIDNRIMFSVGVAAQELGLLD-ADIVYGVPLSIRGKNMYFDR 164
                                       5789*************************************.*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1339.75
//
Query:       gi|320100225|ref|YP_004175817.1|  [L=240]
Description: purine phosphorylase family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  128.4   0.4      3e-37  128.1   0.4    1.0  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
      0.088   12.8   0.0       0.19   11.8   0.0    1.5  1  FliMN_C    Type III flagellar switch regulator (C-ring) FliN 


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 !  128.1   0.4   3.3e-41     3e-37       3     229 ..      18     236 ..      16     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 3.3e-41
                                       EEEESSHHHHHHHHHHEEEEEEEEEE..TTEEEEEEEETTEEEEEEE--SSHHHHH.HHHHHHHHHHC--SEEEEEE CS
                         PNP_UDP_1   3 aiivgspgevellaespleetpfgre.grgfkfvtGtlkgkpvvivstGiGkpnaa.vvaeirllkefgvkaiiriG 77 
                                       a+ivg+p++vell+     e p+ ++  rg+ +++G++ g++++iv++GiG+p+a+ vv e+   +++gv +++r G
  gi|320100225|ref|YP_004175817.1|  18 ALIVGDPHRVELLSTL--LEEPVVKTgVRGYVYAIGKYRGERISIVTHGIGAPSASiVVEEL---HRLGVNVVVRLG 89 
                                       89**************..56666666689***************************444444...4456******** PP

                                       EEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESES CS
                         PNP_UDP_1  78 taGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgf 154
                                       taG+++++++vGDv++++ a+   g+++          +   ++a ++p l a++  a++ +g+k+ + +v t+d  
  gi|320100225|ref|YP_004175817.1|  90 TAGSIQHEIRVGDVILASTALCRIGGCATSM-----YMRDLTPPASPHPVLAARIIDALKGSGVKTWVAPVFTSDAL 161
                                       *******************999999998665.....4555666667999999999999999**************** PP

                                       S-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHH CS
                         PNP_UDP_1 155 yaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaall 229
                                       +aete  ++ lr +g++av+MEta +++l+ ++++ +a++ +vs+++++g+      ee +e++++ ak + ++l
  gi|320100225|ref|YP_004175817.1| 162 HAETEGLIEELRGYGVAAVDMETAILYTLSWLRKLHAASVLIVSNNLVQGDQSILGTEELGEAFKKVAKVILEVL 236
                                       *********************************************999966666666777777777777666655 PP

>> FliMN_C  Type III flagellar switch regulator (C-ring) FliN C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.1e-05      0.19      17      62 ..      70     115 ..      67     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                                       EEEEHHHHHHHHTTSEEE--TTGGGCEEEEETTEEEEEEEEEEETT CS
                           FliMN_C  17 trltlrellnLkvGdvipLdkpadepvevyvngkpiarGelgvvgg 62 
                                       +++ ++el +L+v+ v++L +  + + e++v+++ +a   l ++gg
  gi|320100225|ref|YP_004175817.1|  70 ASIVVEELHRLGVNVVVRLGTAGSIQHEIRVGDVILASTALCRIGG 115
                                       68889********************************999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1750.30
//
Query:       gi|320100226|ref|YP_004175818.1|  [L=306]
Description: nucleoside ABC transporter membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-35  120.8  32.2    6.9e-35  120.5  32.2    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 !  120.5  32.2   3.8e-39   6.9e-35       2     266 ..       9     284 ..       8     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 3.8e-39
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       ++n+l +a+++++ AlG  +   ++Gv+n+g++g+++++a+++ +   + +s ll++ ++all+++++gll gll +
  gi|320100226|ref|YP_004175818.1|   9 VENTLFSATVILFGALGAIVNE-KSGVVNIGVEGVFIVSAFSTVYFTLATGS-LLAGAVAALLISGLIGLLHGLLAA 83 
                                       5799******************.*****************************.************************ PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltgitsgvkgqs..svkellgfagallsflsavivllalllvlavllllrrtr 153
                                       +l+ d++i++++l+ v++glt +l+   ++++ +++  ++   l+f+ a  +f+  v+++la+++ +a +++l +tr
  gi|320100226|ref|YP_004175818.1|  84 YLRSDQVIAGVGLNMVAYGLTIVLMAITWGDYSQTPqiGKIQSLQFNIAGKPFIIPVFSILAFIIGVAEWFILEKTR 160
                                       **********************6666555555555533333445556666677778888****************** PP

                      BPD_transp_2 154 fGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsll 229
                                       +G++l+a+g+ ++aa+a+G+nv+rv++l+ vi+++l gl G+ l++   + ++  +  g gf a+a      + +++
  gi|320100226|ref|YP_004175818.1| 161 YGLILKACGDEPRAAEAMGVNVFRVRVLATVIGSILMGLGGVYLSAEWFGNYTrATTAGRGFIALANEAFSNW-NPA 236
                                       ***********************************************99999999******************.*** PP

                      BPD_transp_2 230 gtviGaliigvvksllltllgi............ptelarvllgallil 266
                                        +v+Gal++g+ ++l++++ +i             t l++++ ++  il
  gi|320100226|ref|YP_004175818.1| 237 MAVAGALLFGFFEALSISV-PIelqsllgrqftaETYLFKMMPYLATIL 284
                                       **************76665.44355555555544466666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); 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:                         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: 00:00:00.40
# Mc/sec: 2317.74
//
Query:       gi|320100227|ref|YP_004175819.1|  [L=344]
Description: nucleoside ABC transporter membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-34  118.2  35.8    3.5e-34  118.2  35.8    1.8  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.64    9.0   9.1        1.3    8.0   9.1    1.4  1  FUSC-like     FUSC-like inner membrane protein yccS
       0.77   10.2   5.3        0.4   11.1   2.3    2.1  2  YGGT          YGGT family


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4     0.079   4.7e+02      56      75 ..      18      37 ..       8      43 .. 0.80
   2 !  118.2  35.8   5.9e-38   3.5e-34       6     266 ..      58     325 ..      55     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.079
                      BPD_transp_2 56 llallvallvgaavglllgl 75
                                      +l+ll++++++aav l+ g+
  gi|320100227|ref|YP_004175819.1| 18 ALSLLIGFAAAAAVLLVSGY 37
                                      57899999999999888776 PP

  == domain 2  score: 118.2 bits;  conditional E-value: 5.9e-38
                      BPD_transp_2   6 ltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl.......lllallvallvgaavglllgl 75 
                                       + ++++++ ++l++++ + +aG++n+g ++++ +Ga++ +++ + + +         ++++l++ l+g+++gl++g+
  gi|320100227|ref|YP_004175819.1|  58 MEQSTPVIATGLAFSIPM-LAGLFNIGGESQLYIGAFTGLVATYTVYNAvgqpllaSFAGILLGALAGGLWGLIVGY 133
                                       67888889999*******.*******************9999999998899999999******************** PP

                      BPD_transp_2  76 lvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrt 152
                                       l ++  v+e++++++++++ ++l+l+l    + ++      + ++ f ++ +   + + + ++ +++++v+l l+++
  gi|320100227|ref|YP_004175819.1| 134 LRTYRSVNEVVVAIMMNWATYYLVLYLIVSRFTDPV----YSHMSVFVPQPARLPGVAGFTIISIVAVLVYLALKYS 206
                                       *************************66555544444....44444443333333333444445556678999***** PP

                      BPD_transp_2 153 rfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp...nigvglgfnaiaavvlGgag 226
                                        +G+ +ravg n++a+ ++G+n++r+ l t++++g++Agl Gal+++++  +     +   glgf +i + +lG + 
  gi|320100227|ref|YP_004175819.1| 207 GLGYSIRAVGLNPKASLYAGFNIGRTLLSTMALAGGIAGLGGALFVVSTIYSIDttmSSIHGLGFLGIGIGLLGRN- 282
                                       **********************************************9976554346777778**************. PP

                      BPD_transp_2 227 sllgtviGaliigvvksllltllgi....ptelarvllgallil 266
                                       +++g+v+++l i+ ++  +++++      p+ l++v++g+++++
  gi|320100227|ref|YP_004175819.1| 283 NPIGIVLAGLFISGLQF-GGQWVELrtgaPPYLTDVVIGVVVMA 325
                                       ****************9.999988889999***********997 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.1   0.00022       1.3      28     116 ..      64     155 ..      55     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00022
                         FUSC-like  28 lglllstflftmlgal....GqryatiafatLlvaiytmlgasqepeiwqqplllllGalwYgllsllwsllfpnrp 100
                                       ++ ++++f++ ml+ l    G+    i+  t lva+yt+ +a  +p ++   + +llGal  gl+ l++  l  +r 
  gi|320100227|ref|YP_004175819.1|  64 VIATGLAFSIPMLAGLfnigGESQLYIGAFTGLVATYTVYNAVGQP-LLASFAGILLGALAGGLWGLIVGYLRTYRS 139
                                       555555555555554444449999999999*************666.****************************** PP

                         FUSC-like 101 vqqsLaelfealAdYl 116
                                       v + +  ++   A+Y 
  gi|320100227|ref|YP_004175819.1| 140 VNEVVVAIMMNWATYY 155
                                       ********99999995 PP

>> YGGT  YGGT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.6   9.6e+03      37      60 ..       5      32 ..       4      35 .. 0.51
   2 ?   11.1   2.3   6.7e-05       0.4      12      65 ..     144     203 ..     143     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
                              YGGT 37 PllapfRrlip..ggg..iDlSplvall 60
                                       lla + r+i    ++  i +++  a+l
  gi|320100227|ref|YP_004175819.1|  5 ILLAKITRVIAeeALSllIGFAAAAAVL 32
                                      5677777776544222335555555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.7e-05
                              YGGT  12 ilrillswpnpfynpiaqflyklTePllapfRrlip.......gggiDlSplvallvlqll 65 
                                       ++ i++ w + +y +++ ++ ++T+P+++ +  ++p         g+ + ++va+lv+  l
  gi|320100227|ref|YP_004175819.1| 144 VVAIMMNW-ATYYLVLYLIVSRFTDPVYSHMSVFVPqparlpgVAGFTIISIVAVLVYLAL 203
                                       67889999.778**********************887776654345999999999988666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2319.53
//
Query:       gi|320100228|ref|YP_004175820.1|  [L=500]
Description: nucleoside ABC transporter ATP-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-51  173.0   0.0    4.1e-29  101.8   0.0    2.3  2  ABC_tran     ABC transporter
    2.1e-09   37.6   0.7    0.00057   19.8   0.2    2.6  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0051   17.1   2.0       0.03   14.6   0.5    2.7  2  AAA_22       AAA domain
     0.0066   15.7   0.0        4.5    6.5   0.0    2.9  3  Zeta_toxin   Zeta toxin
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.024   15.2   0.0    1.5  1  AAA_23       AAA domain
      0.019   14.7   0.0       0.15   11.8   0.0    2.3  2  AAA_29       P-loop containing region of AAA domain
      0.031   14.0   0.1       0.18   11.5   0.1    2.1  1  AAA_30       AAA domain
      0.034   14.0   0.0       0.25   11.2   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
      0.054   13.9   0.1       0.94    9.8   0.0    2.5  2  AAA_16       AAA ATPase domain
       0.14   12.6   1.2        1.5    9.2   0.3    2.8  2  AAA          ATPase family associated with various cellular a
       0.17   11.8   0.7          9    6.2   0.0    3.3  3  MobB         Molybdopterin guanine dinucleotide synthesis pro
       0.23    8.9   0.0       0.32    8.4   0.0    1.1  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 !  101.8   0.0   2.7e-32   4.1e-29       1     137 []      20     168 ..      20     168 .. 0.97
   2 !   69.1   0.0   3.6e-22   5.4e-19       1     137 []     273     428 ..     273     428 .. 0.93

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 2.7e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+ v+++++ege+++++GenGaGK+tL+++l+g+ + t Gei++ g+ ++   ++   r+ i+++ q+ +l p+++v
  gi|320100228|ref|YP_004175820.1|  20 LRGVDFEVEEGEIHGLLGENGAGKTTLMRILYGEIHATDGEIKVFGRRVRFrSPRDAIRHGIAMIYQHFSLVPTMSV 96 
                                       6789*********************************************99899*********************** PP

                                       HHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        +n               + +e++ek++++ gl     ++v    ++L  G +qrv++ +al++++++l+lDEpt+
  gi|320100228|ref|YP_004175820.1|  97 LDNlylsmsavnpgvsrdDTEERAEKLIAETGLRIPLGKTV----EELPVGVQQRVEILKALIRDARILILDEPTS 168
                                       **************999888888***********9999999....*****************************96 PP

  == domain 2  score: 69.1 bits;  conditional E-value: 3.6e-22
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS..--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx..xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe..pqlfpel 74 
                                       l+ vsl ++ege+++i G  G G + L++++agl kp +G+illd++d++  +++e++r  i+++p+     l  ++
  gi|320100228|ref|YP_004175820.1| 273 LRGVSLVVREGEILGIAGVQGNGQTELCETIAGLRKPYKGRILLDSRDVTWlDTKERYRLGIAYIPESrkIGLIHDM 349
                                       6789**********************************************999**************98899***** PP

                                       BHHHH...................HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEE CS
                                       xxxxx...................xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren...................esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpklll 131
                                       +v en                   +++e++ ++++++g +   +dt+v    + LSgG +q++++ r +++kp++l+
  gi|320100228|ref|YP_004175820.1| 350 SVLENsiltsideytgrlgivnwkKAKEKAVEVIKEYGVQPpNPDTPV----KFLSGGNQQKLMVGREIARKPRILV 422
                                       *************99999999988777778888888887773556666....************************* PP

                                       EESTTT CS
                                       xxxxxx RF
                          ABC_tran 132 lDEpta 137
                                       + Ept+
  gi|320100228|ref|YP_004175820.1| 423 VAEPTQ 428
                                       ****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 !   15.5   0.0   7.7e-06     0.011       2      21 ..      33      52 ..      32      85 .. 0.78
   2 !   19.8   0.2   3.8e-07   0.00057     238     297 ..     141     197 ..     106     200 .. 0.91
   3 ?   -2.6   0.0       2.5   3.7e+03     256     295 ..     416     455 ..     413     457 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.7e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                       +l G Ng+GK++L+++l++
  gi|320100228|ref|YP_004175820.1| 33 HGLLGENGAGKTTLMRILYG 52
                                      689***************76 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3.8e-07
                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       + G+++   +l al+r++   ++l++DEp + L P  +++l++ l++l+++g+ +il TH
  gi|320100228|ref|YP_004175820.1| 141 PVGVQQRVEILKALIRDA---RILILDEPTSVLTPLEVEELFTSLRRLRDKGITIILITH 197
                                       566666668999999999...*************************************** PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.5
                            AAA_21 256 kkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                        k+++l++ Ep  g + + ++ + + l el++ g+ ++l+
  gi|320100228|ref|YP_004175820.1| 416 RKPRILVVAEPTQGVDVASTEFIRKRLLELRNQGIGILLV 455
                                       455999999*******999999998888888878888544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.5     2e-05      0.03      10     128 ..      35     195 ..      28     202 .. 0.73
   2 ?   -3.1   0.0       5.7   8.5e+03       7      26 ..     285     304 ..     281     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee......................................erpevvfvtlp 48 
                                       + Ge G+GKTtl+r l  + ++     +                                       +  ++++ + 
  gi|320100228|ref|YP_004175820.1|  35 LLGENGAGKTTLMRILYGEIHAT----DgeikvfgrrvrfrsprdairhgiamiyqhfslvptmsvLDNLYLSMSAV 107
                                       579************99998543....33456899999999888888888888887776665554433333344444 PP

                            AAA_22  49 sst....sskdllrellralglelkaerlsseellealeqalrarav....ielliiDEaqh.lrs....eealeeL 112
                                       +++    + ++ +++l  ++gl+    +++ eel   ++q ++  ++     ++li+DE    l +    ee+++ L
  gi|320100228|ref|YP_004175820.1| 108 NPGvsrdDTEERAEKLIAETGLRIPL-GKTVEELPVGVQQRVEILKAlirdARILILDEPTSvL-TplevEELFTSL 182
                                       44432255555566666666655555.9999999999*999999999999************77.334568888888 PP

                            AAA_22 113 rsllnlsrkgvqliLv 128
                                       r+l +   kg+++iL+
  gi|320100228|ref|YP_004175820.1| 183 RRLRD---KGITIILI 195
                                       88888...99999998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                            AAA_22   7 ilvvtGesGtGKTtllrrll 26 
                                       il + G  G G T l+++++
  gi|320100228|ref|YP_004175820.1| 285 ILGIAGVQGNGQTELCETIA 304
                                       66688999999999999875 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     0.003       4.5      23      59 ..      37      73 ..      31      82 .. 0.82
   2 !    5.6   0.0    0.0057       8.5     130     187 ..     106     165 ..     100     173 .. 0.85
   3 ?   -2.0   0.0       1.3   1.9e+03     131     144 ..     317     330 ..     286     345 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.003
                        Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDdlRelhP 59
                                      G  GAGK++l++ l  e++++++ +++ + ++R + P
  gi|320100228|ref|YP_004175820.1| 37 GENGAGKTTLMRILYGEIHATDGEIKVFGRRVRFRSP 73
                                      899*************999888888877766666555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0057
                        Zeta_toxin 130 avkkelSrlgvldRyeeevae.g.Rlvpkeehdeafeglresvealeeekqldrvkikdr 187
                                       av++ +Sr ++++R e+ +ae g R+   ++ +e   g+++ ve+l+   +  r+ i d+
  gi|320100228|ref|YP_004175820.1| 106 AVNPGVSRDDTEERAEKLIAEtGlRIPLGKTVEELPVGVQQRVEILKALIRDARILILDE 165
                                       89****************777778********************9998776666766665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.3
                        Zeta_toxin 131 vkkelSrlgvldRy 144
                                        ++ +++l++++Ry
  gi|320100228|ref|YP_004175820.1| 317 DSRDVTWLDTKERY 330
                                       33445555555555 PP

>> AAA_23  AAA 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     0.024      13      43 ..      23      50 ..       4      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            AAA_23 13 qeidF.skgltlItGpNGaGKTTildAiklaL 43
                                      ++++  +  +  + G+NGaGKTT+++     L
  gi|320100228|ref|YP_004175820.1| 23 VDFEVeEGEIHGLLGENGAGKTTLMRI----L 50
                                      44444555788999**********974....4 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.15      15      39 ..      23      47 ..      18      54 .. 0.82
   2 ?   -0.8   0.0      0.86   1.3e+03       3      19 ..     366     382 ..     365     386 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       ++e+++ +++ l G++G+GK+Tl+
  gi|320100228|ref|YP_004175820.1| 23 VDFEVEEGEIHGLLGENGAGKTTLM 47
                                      567777555999***********98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.86
                            AAA_29   3 rlqlvNWgtfdghtiei 19 
                                       rl +vNW   +++ +e+
  gi|320100228|ref|YP_004175820.1| 366 RLGIVNWKKAKEKAVEV 382
                                       6789****999877765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00012      0.18      19      55 ..      31      74 ..      25     199 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                            AAA_30 19 rvavltGpAGtGKttalkal.reaweaag......grviglApt 55
                                       ++ l G  G+GKtt+++ l  e+++++g      +rv   +p 
  gi|320100228|ref|YP_004175820.1| 31 EIHGLLGENGAGKTTLMRILyGEIHATDGeikvfgRRVRFRSPR 74
                                      477899*************9666666667666666555544444 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   0.00017      0.25      99     131 ..      30      62 ..      15      68 .. 0.85
   2 ?   -1.2   0.0       1.1   1.7e+03      30      60 ..     433     463 ..     406     475 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                       TSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +++  l+G+ G+GK+tL+  l +e ++  ge++
  gi|320100228|ref|YP_004175820.1|  30 GEIHGLLGENGAGKTTLMRILYGEIHATDGEIK 62 
                                       488899******************999888886 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                       --HHHHHHHHHHHHHTT-EEEEEEE-GGG-- CS
                       RsgA_GTPase  30 lslnlldrfLvlaeekgiepvivlnKiDlle 60 
                                        s++++ + L+++ ++gi +++v + +D + 
  gi|320100228|ref|YP_004175820.1| 433 ASTEFIRKRLLELRNQGIGILLVSTDLDEIF 463
                                       5778889999999999999988888777655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00063      0.94      29      63 ..      35      70 ..      25     195 .. 0.63
   2 ?    1.4   0.0      0.24   3.6e+02      25     168 ..     284     453 ..     268     455 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00063
                            AAA_16 29 lsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      l Ge G GK++l+r l+ ++ +++g   + g+ +++
  gi|320100228|ref|YP_004175820.1| 35 LLGENGAGKTTLMRILYGEIHATDGEIkVFGRRVRF 70
                                      79***************9999884433355555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.24
                            AAA_16  25 elvllsGesGvGKsslvrellralekd..........ggiflrgkcdqlesaipy.........salaqalareell 82 
                                       e++ + G +G G + l ++++  l+k           ++ +l +k +    +i+y         ++  ++l ++++l
  gi|320100228|ref|YP_004175820.1| 284 EILGIAGVQGNGQTELCETIA-GLRKPykgrilldsrDVTWLDTKERYR-LGIAYipesrkiglIHDMSVL-ENSIL 357
                                       667777777777777777777.455553322333332222222222222.222222222222212233333.22334 PP

                            AAA_16  83 rqlldeaesaeleawrekleeala........avpelagaea.srllellkrll.allsrderp.lvlvlDdlqwad 148
                                       + +++ +       w+++ e+a++        + +++++ +  s  +++ k ++ + ++r  +p +++v +  q +d
  gi|320100228|ref|YP_004175820.1| 358 TSIDEYTGRLGIVNWKKAKEKAVEvikeygvqPPNPDTPVKFlSGGNQQ-KLMVgREIAR--KPrILVVAEPTQGVD 431
                                       4443334444444444444444444445533322222222111222222.2222233333..222777777777777 PP

                            AAA_16 149 easlql.laaLlrllesk.pll 168
                                        as ++  + Ll+l++++  +l
  gi|320100228|ref|YP_004175820.1| 432 VASTEFiRKRLLELRNQGiGIL 453
                                       7777774456666666665655 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 ?    9.2   0.3     0.001       1.5       3      26 ..      35      82 ..      34     215 .. 0.50
   2 ?   -1.6   0.0       2.2   3.3e+03       4      20 ..     289     305 ..     287     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                                      EESSTTSSHHHHHHHHHHHHTHE........................E CS
                               AAA  3 lyGppGtGKTllakavakelgve........................f 26
                                      l G  G GKT+l++ +  e++++                         
  gi|320100228|ref|YP_004175820.1| 35 LLGENGAGKTTLMRILYGEIHATdgeikvfgrrvrfrsprdairhgiA 82
                                      789****************87553333333333333333333333330 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                                       ESSTTSSHHHHHHHHHH CS
                               AAA   4 yGppGtGKTllakavak 20 
                                        G  G G T l++ +a 
  gi|320100228|ref|YP_004175820.1| 289 AGVQGNGQTELCETIAG 305
                                       6999********99986 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0061         9       3      29 ..      34      60 ..      32      67 .. 0.82
   2 ?   -0.3   0.0      0.63   9.4e+02      24      37 ..     212     225 ..     181     243 .. 0.75
   3 ?    1.2   0.0      0.21   3.1e+02       1      19 [.     285     303 ..     285     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0061
                              MobB  3 givgksgsGKTtLleklipelkarglr 29
                                      g+ g +g+GKTtL+  l  e++a + +
  gi|320100228|ref|YP_004175820.1| 34 GLLGENGAGKTTLMRILYGEIHATDGE 60
                                      68899*********9999888877655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.63
                              MobB  24 karglrvgtiKhah 37 
                                        +rg +vgt+K ++
  gi|320100228|ref|YP_004175820.1| 212 LRRGSKVGTVKTSE 225
                                       35777777777654 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.21
                              MobB   1 vlgivgksgsGKTtLlekl 19 
                                       +lgi+g +g G T L e +
  gi|320100228|ref|YP_004175820.1| 285 ILGIAGVQGNGQTELCETI 303
                                       799************9875 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00022      0.32      22      37 ..      35      50 ..      20      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00022
                           DUF3584 22 ieGtNaaGKTtLlrLi 37
                                      + G N+aGKTtL+r++
  gi|320100228|ref|YP_004175820.1| 35 LLGENGAGKTTLMRIL 50
                                      6799**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3576.65
//
Query:       gi|320100229|ref|YP_004175821.1|  [L=412]
Description: nucleoside-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-43  148.2   0.0    3.4e-43  147.8   0.0    1.1  1  Bmp       ABC transporter substrate-binding protein PnrA-like
     0.0032   17.7   1.7      0.013   15.7   1.0    2.1  2  DUF4330   Domain of unknown function (DUF4330)


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 !  147.8   0.0   3.8e-47   3.4e-43       3     283 ..      46     334 ..      44     345 .. 0.91

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 3.8e-47
                                       EEEEECSS-TTTSCHHHHHHHHHHHHHHHCTTEEEEEEEEC.GGGHHHHHHHHHH.CTT-SEEEEESCCHHHHHHHH CS
                               Bmp   3 kvavlvegtidDksfnessyeGirrlkkeqnieliskesslltdedyiadlknlk.eegsdlivatgfalqdalqev 78 
                                       ++ ++++g + D sfn +++ G +++k ++++ + + + ++  + ++ ++l+ l  + ++dliv++gf  +  l+e+
  gi|320100229|ref|YP_004175821.1|  46 VAILFDVGGRGDLSFNDMAWLGAEKAKHDFGVTVEYTTPQS--QGKMKELLETLSsSGEYDLIVLVGFLWTSPLNET 120
                                       67899*************************99999999988..5667777777661567****************** PP

                                       HHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHC...TTTTEECSS-SCCCHHCHHHHHHHHHH CS
                               Bmp  79 ssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmskt...nkigfvgGveipvvksfingFeaGiky 152
                                       ++++p++k++ iDa    +  n + + F+++e++ L+Gv+aA m+ +   nk g+v+G++ip + +f +g+  G+ky
  gi|320100229|ref|YP_004175821.1| 121 ADKYPNQKYALIDASTFINRPNEVDILFSEQEAGALVGVLAADMASKigcNKVGAVAGMSIPPLWRFHVGYLFGVKY 197
                                       **************8877778**********************98866669*************************9 PP

                                       ....H-TT-EEEEEE-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCT....EEEEEES--CG CS
                               Bmp 153 ....vnpdievvvkvagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsn....yvIgvdkdqsy 221
                                           +n+ i     ++gtf D +kg + A+s+ ++g+ v ++ ag++  g ++a+++ +++     ++Ig d +q  
  gi|320100229|ref|YP_004175821.1| 198 yemkTNKTIGFLWDYTGTFGDTQKGYQYATSMLQSGACVLYGLAGLTHVGMFDAVRDWNKQGkgtaLAIGQDASQEW 274
                                       4444688899999**********************************************999999************ PP

                                       CSTTCCEEEEEEEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-S--TCCHHHHCHH CS
                               Bmp 222 lapenvitsiiknvedlvvsiiekvakgevlaggevitlglkegvvgldeesdvledekvke 283
                                         p ++  s  k v+ +v+++ie v+k++  ++g+++ l lk+g+vg+ ++  v +++ + +
  gi|320100229|ref|YP_004175821.1| 275 YMPRYMPFSGAKRVDVAVYKAIEMVVKNQ--WSGGIHVLSLKDGGVGIWDLDGVKYFAEIAY 334
                                       *****************************..*****************97766666666655 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.0   1.5e-06     0.013      20      59 ..      12      50 ..       8      59 .. 0.74
   2 ?   -0.3   0.0      0.12   1.1e+03     100     126 ..      80     109 ..      76     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-06
                           DUF4330 20 lailvilavivgiflkpgtsgsvaqaeaaatkpvevdvvv 59
                                      ++++vil+++vg++++++ts + a++++++ kpv+v +++
  gi|320100229|ref|YP_004175821.1| 12 ILVVVILVAAVGVYYYVSTS-QPAKTTTTTSKPVKVAILF 50
                                      56678888888888888888.4455556689999998765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
                           DUF4330 100 kvvvpqpdGkvkaled..e.pylkdllvtl 126
                                       ++++pq++Gk+k+l    +  + +dl+v +
  gi|320100229|ref|YP_004175821.1|  80 EYTTPQSQGKMKELLEtlSsSGEYDLIVLV 109
                                       6789*******9998889669999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2878.02
//
Query:       gi|320100230|ref|YP_004175822.1|  [L=333]
Description: alcohol dehydrogenase GroES domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-31  107.5   0.8    4.4e-31  107.0   0.8    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    1.1e-14   54.5   0.0    1.8e-14   53.8   0.0    1.3  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.5e-13   50.7   0.0    3.9e-13   49.4   0.0    1.7  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    0.00031   21.8   0.0    0.00067   20.7   0.0    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.017   15.2   0.0       0.41   10.7   0.0    2.3  2  Shikimate_DH  Shikimate / quinate 5-dehydrogenase
      0.031   15.1   0.0      0.061   14.2   0.0    1.5  1  GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fol
      0.086   12.9   0.2       0.86    9.7   0.2    2.3  2  NADH_4Fe-4S   NADH-ubiquinone oxidoreductase-F iron-sulfur bi


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.8   1.7e-34   4.4e-31       1     106 [.      24     128 ..      24     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.7e-34
                                       TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT- CS
                             ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkege 77 
                                       pg++li+v+ agiCg+D  +++g +    k pli+GHE++G+v++vg +v++  vG+rV+ e+++ cg+C +C++g 
  gi|320100230|ref|YP_004175822.1|  24 PGWLLIRVERAGICGTDKAMYTG-TYRLLKKPLIPGHEVSGIVVDVGAGVSRDLVGRRVTTEINVYCGKCWYCRNGM 99 
                                       5799*******************.8999************************************************* PP

                                       GGG-TTBEETTTSS-SSSBSEEEECGGGE CS
                             ADH_N  78 enlCeeakllgvsldGgfaeyvvvpekkl 106
                                       +++C++++++g+++dGg+aey+v++++ +
  gi|320100230|ref|YP_004175822.1| 100 HTHCPYRETIGITRDGGMAEYMVTRADLI 128
                                       ***********************998766 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0     7e-18   1.8e-14       1     116 [.     170     286 ..     170     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 7e-18
                                       HHHHHHHHHHHHTT-EEEEEESSHH..HHHHHHHTTESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSCSHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdssee..klelakklGadevinykeadlverikeltg.gegvdvvfecvGsgatlea 74 
                                       ++Gl+avq+++ ++ e i+++s +   k++la +lGad v++y   +l e +++ t  g+g+d+v+e++Gs + le 
  gi|320100230|ref|YP_004175822.1| 170 AIGLLAVQVLRLFNPELIVAVSRPGspKARLAGELGADLVVDYP--ELTEILRRETPeGQGFDYVVEATGSSKGLEI 244
                                       69*************8888777776679***************5..5*********66******************* PP

                                       HHHCEEEEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSC CS
                        ADH_zinc_N  75 alkllkpgGrlvvvGggkgeeefdlrnlllkeksilGsllgs 116
                                       a+++++p+G +++  + + + +fd  + + ke++++ s +g 
  gi|320100230|ref|YP_004175822.1| 245 AVDIARPRGVVALKSTHGSPVSFDQTKAVIKELRLTTSRCGP 286
                                       ***************9888888*************9998876 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 !   49.4   0.0   1.5e-16   3.9e-13      32     209 ..     161     330 ..     137     333 .] 0.75

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.5e-16
                       Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvds..retpv.deipeaseemdlvv 105
                                       +++ v+G G++GLLa+ +l++    ++   +++     +p+++l  elGa  v    + t++  + + + + +d+vv
  gi|320100230|ref|YP_004175822.1| 161 SRVAVIGVGAIGLLAVQVLRL----FNPELIVAVSRPGSPKARLAGELGADLVVDypELTEIlRRETPEGQGFDYVV 233
                                       4688***************98....44445666666789***********9775411223331333446789***** PP

                       Glu_dehyd_C 106 EaTGsakhafeaiealapnGvaaLlGvpedsevevdgg.elhrelvleNkalvGsvNanrrhfeaavdtLaalpesl 181
                                       EaTGs+k +  a++  +p Gv+aL     +  v++d+  ++ +el l        + ++   f++a++ L +     
  gi|320100230|ref|YP_004175822.1| 234 EATGSSKGLEIAVDIARPRGVVALKSTHGSP-VSFDQTkAVIKELRL--------TTSRCGPFDKAISLLRKR-LVN 300
                                       ************************9877655.666643034455444........46899*******998764.455 PP

                       Glu_dehyd_C 182 ldelvtkvvdldeleeAfedd..detiKtv 209
                                       +d+lvt++++l++ +eAfe++   +++K+ 
  gi|320100230|ref|YP_004175822.1| 301 VDKLVTSEYGLEKGAEAFEKSleRDQVKVH 330
                                       8*****************975215778875 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.6e-07   0.00067       1     122 [.     204     321 ..     204     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.6e-07
                                       TT-SEEEETT.STTHH..HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEE CS
                      ADH_zinc_N_2   1 lGAdevidyr.tedfe..aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvk 74 
                                       lGAd v+dy   +++   +  +g+g+D+v++++g+ + le ++++ +++G +   +     +  +++++++ ++ +k
  gi|320100230|ref|YP_004175822.1| 204 LGADLVVDYPeLTEILrrETPEGQGFDYVVEATGSSKGLEIAVDIARPRGVVALKS-----THGSPVSFDQTKAVIK 275
                                       8*********8777779877789***********888889999***8878875433.....3577888888778888 PP

                                       E--GGG...-.-HHHHHHHHHHHHHHH---..-EEEEEEGGGHHHHHHHH CS
                      ADH_zinc_N_2  75 yeflfsmkasaqadileelaalieeGklrp..vvdrvfpleeaaeAhryl 122
                                          l++   s +   +++   l+ +  +++   v+++++le+ aeA+++ 
  gi|320100230|ref|YP_004175822.1| 276 ELRLTT---S-RCGPFDKAISLLRKRLVNVdkLVTSEYGLEKGAEAFEKS 321
                                       888875...4.444588999999999876533688899999999999975 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.41      13      75 ..     161     221 ..     157     242 .. 0.82
   2 ?    2.5   0.0     0.054   1.4e+02     104     118 ..     241     255 ..     230     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                       -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT CS
                      Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellae 75 
                                       ++v +iG G ++ l+++ L   + + +v + R  +  ++la el+++   ++++ el+e+l++
  gi|320100230|ref|YP_004175822.1| 161 SRVAVIGVGAIGLLAVQVLRLFNPELIVAVSRPGSPKARLAGELGAD--LVVDYPELTEILRR 221
                                       589*****************************************888..78888888888864 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.054
                                       ..EEEEE--SS-SB- CS
                      Shikimate_DH 104 kplllvDiavPRdve 118
                                          + vDia PR v 
  gi|320100230|ref|YP_004175822.1| 241 GLEIAVDIARPRGVV 255
                                       44589*******986 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.4e-05     0.061       2      80 ..     162     246 ..     161     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCT.....TESEEEE-S CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve...aysdleelladp.....eidavivat 70 
                                       rva+iG+G ig   + ++ + ++ e +va+  p++++a+ +a ++g++    y +l e+l+ +       d+v+ at
  gi|320100230|ref|YP_004175822.1| 162 RVAVIGVGAIGLLAV-QVLRLFNPELIVAVSRPGSPKAR-LAGELGADlvvDYPELTEILRREtpegqGFDYVVEAT 236
                                       89*************.666666999************99.6899999966667777777777744333477777777 PP

                                       -GGGHHHHHH CS
                      GFO_IDH_MocA  71 pngtheelak 80 
                                        ++++ e+a 
  gi|320100230|ref|YP_004175822.1| 237 GSSKGLEIAV 246
                                       6666666665 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00034      0.86      15      27 ..      89     101 ..      82     134 .. 0.85
   2 ?    0.2   0.0      0.32   8.1e+02      36      73 ..     258     296 ..     236     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                                       -S--HHHHIIIIH CS
                       NADH_4Fe-4S  15 CGkCtpCreGtkr 27 
                                       CGkC  Cr G++ 
  gi|320100230|ref|YP_004175822.1|  89 CGKCWYCRNGMHT 101
                                       **********876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.32
                                       TBT---HHHHHHHHHHHHHHS.S--SSTHHHHHHHHHHH CS
                       NADH_4Fe-4S  36 aagegteedldlleelaetik.gtslCalgdsaanpvls 73 
                                       ++++g++ ++d+ + + + ++ +ts C+  d+a  ++++
  gi|320100230|ref|YP_004175822.1| 258 KSTHGSPVSFDQTKAVIKELRlTTSRCGPFDKAISLLRK 296
                                       455556667777777777777779999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2272.96
//
Query:       gi|320100231|ref|YP_004175823.1|  [L=150]
Description: ribose-5-phosphate isomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  125.4   0.0    1.8e-36  125.2   0.0    1.0  1  LacAB_rpiB      Ribose/Galactose Isomerase
     0.0084   16.1   0.1      0.011   15.7   0.1    1.3  1  BD_b_sandwich   Bdellovibrio Beta-sandwich
  ------ inclusion threshold ------
      0.042   13.9   0.1        1.6    8.8   0.0    2.3  2  B12-binding     B12 binding domain
      0.048   13.7   0.1      0.063   13.3   0.1    1.2  1  Gly_rich_SFCGS  Glycine-rich SFCGS


Domain annotation for each model (and alignments):
>> LacAB_rpiB  Ribose/Galactose Isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.0   3.9e-40   1.8e-36       1     130 [.       3     133 ..       3     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 3.9e-40
                                       EEEEE-GCGHHHHHHHHHHHHHTTTEEEEECESS.SS---HHHHHHHHHHHHHTTSSSEEEEEESSSHHHHHHHHTS CS
                        LacAB_rpiB   1 iaigsDhagfelkekikeyLkekghevidvgtes.eesvdYpdfakkvaeavasgeadlgiliCgtGiGmsiaaNkv 76 
                                       +a+gsD++ +++   i+eyL++kg+ev+ vg+ +  + + +pd++ +v+  va+ge+d+g++iC tG G+siaaNkv
  gi|320100231|ref|YP_004175823.1|   3 VAVGSDDT-YSVAGFIAEYLRRKGFEVKLVGALAtGKPYPWPDVGFEVGSMVARGEVDYGVVICYTGTGVSIAANKV 78 
                                       68899987.99999******999********7776679*************************************** PP

                                       TT--EEE-SSHHHHHHHHHTT--SEEEEETTTS-HHHHHHHHHHHHHS--.-.HT CS
                        LacAB_rpiB  77 kgiraalchdeesAklarehnnanvlalGarvigeelakeivkaFletef.eegg 130
                                       kg+raal++d+  A+ ar+ n+anvlal+ar+++eelakei++aF++ +  ++++
  gi|320100231|ref|YP_004175823.1|  79 KGVRAALVTDARNAEGARKWNDANVLALSARLTSEELAKEIIDAFFAVREvDPSE 133
                                       **********************************************954424333 PP

>> BD_b_sandwich  Bdellovibrio Beta-sandwich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.4e-06     0.011      41      88 ..      70     117 ..      51     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                     BD_b_sandwich  41 evkasaarvkivevtLvtakGdridvreysnaavletnavvasenlnl 88 
                                        v   a++vk v ++Lvt+  +    r++++a vl   a ++se l  
  gi|320100231|ref|YP_004175823.1|  70 GVSIAANKVKGVRAALVTDARNAEGARKWNDANVLALSARLTSEELAK 117
                                       677899**************************************9974 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00036       1.6      20      38 ..      17      35 ..       9      45 .. 0.90
   2 ?    3.1   0.0      0.02        90      38      75 ..      86     126 ..      39     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00036
                       B12-binding 20 laaalrdagfeVqllganv 38
                                      +a++lr++gfeV+l+ga +
  gi|320100231|ref|YP_004175823.1| 17 IAEYLRRKGFEVKLVGALA 35
                                      9***************987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.02
                       B12-binding  38 venedivaairae.kpdvvglSalltsqleavkelvel...l 75 
                                       v++++ ++ +r++ ++ v++lSa+lts+ e +ke++++   +
  gi|320100231|ref|YP_004175823.1|  86 VTDARNAEGARKWnDANVLALSARLTSE-ELAKEIIDAffaV 126
                                       4446777778888899999999966654.6777777765554 PP

>> Gly_rich_SFCGS  Glycine-rich SFCGS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.4e-05     0.063      36     112 ..      47     124 ..      24     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                    Gly_rich_SFCGS  36 lklgdvmkkeeadlgisfcgsggagaltaqtkygykakyglrsve.egvtaikegkkvlgf.gfldkeelgkrlvea 110
                                         +g ++ + e d g+ +c +g   ++ a++  g +a     + + eg    ++  +vl +   l +eel k +++a
  gi|320100231|ref|YP_004175823.1|  47 FEVGSMVARGEVDYGVVICYTGTGVSIAANKVKGVRAALVTDARNaEGARKWNDA-NVLALsARLTSEELAKEIIDA 122
                                       5789999**************999999999999*999987766551566666665.5555516799*********99 PP

                    Gly_rich_SFCGS 111 yv 112
                                       + 
  gi|320100231|ref|YP_004175823.1| 123 FF 124
                                       85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1156.58
//
Query:       gi|320100232|ref|YP_004175824.1|  [L=612]
Description: glutamine--fructose-6-phosphate transaminase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  150.2   0.1    1.1e-28   99.6   0.3    2.5  2  SIS         SIS domain
    7.2e-21   74.8   0.0    2.8e-20   72.9   0.0    2.1  2  GATase_6    Glutamine amidotransferase domain
    3.9e-15   55.9   0.0      1e-14   54.5   0.0    1.8  1  GATase_7    Glutamine amidotransferase domain
    8.5e-06   25.8   0.3    0.00017   21.6   0.0    2.9  3  SIS_2       SIS domain
     0.0072   16.4   0.0      0.049   13.7   0.0    2.4  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
  ------ inclusion threshold ------
      0.033   13.1   0.0      0.085   11.7   0.0    1.7  1  GATase_4    Glutamine amidotransferases class-II


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 !   99.6   0.3   3.8e-32   1.1e-28       1     130 [.     291     419 ..     291     420 .. 0.97
   2 !   47.9   0.0   3.6e-16   1.1e-12       2     128 ..     465     592 ..     464     595 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 3.8e-32
                                       HHCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHH CS
                               SIS   1 lLakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelak 77 
                                       +La+a++++v+GaGtsy++ +++al  +++++++v +  ase   ++++ + ++d+++++s+sget d+++a++  k
  gi|320100232|ref|YP_004175824.1| 291 MLADADTVFVTGAGTSYHASEYFALISMRLAERPVIAFIASE-YGSYVNAAGPRDVLVAVSQSGETMDTLKALRAFK 366
                                       699***************************************.7777****************************** PP

                                       HTTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  78 ergakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                       +rg ++i++T+  +s++are+d+a+y++a+pe++va+tk++++q++al  lav
  gi|320100232|ref|YP_004175824.1| 367 KRGSRVISLTNAVDSAIARESDVAVYTRAGPEIGVAATKTFLTQTLALTWLAV 419
                                       ********************************************999987765 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 3.6e-16
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEE.SSSHHHHHHHHHH.HH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilis.fsgetkdlvaaae.la 76 
                                       +a +k++y+l +G   ++a+e+alk++ei+++++e+++a+e khg++al+++  +v++      e  ++++ +  ++
  gi|320100232|ref|YP_004175824.1| 465 IAGSKSMYYLSRGVGLPVAREGALKIKEIAYVHAEAYPAGESKHGPIALVEPSFPVVFTIpNDAELQRMLLGNIeEM 541
                                       67899************************************************9999888455667777777777** PP

                                       HHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                               SIS  77 kergakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                       ++rg+ i+++    gs l ++ dla++++ +  +  a+t + ++ql+a++++
  gi|320100232|ref|YP_004175824.1| 542 RARGGVIVGVL-PRGSELRERVDLAIEVPRAHWIATALTHTPPLQLLAYHVA 592
                                       ********998.8999999999988888888888***************986 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   9.3e-24   2.8e-20      12     133 ..      69     197 ..      34     198 .. 0.86
   2 ?   -2.3   0.0       1.6   4.8e+03     113     134 .]     464     485 ..     443     485 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 9.3e-24
                          GATase_6  12 devalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall....eel 84 
                                       + ++++H+R+a++g + +  a+P +     +++vhNG  +ny el+++l+a +g+ frs++Dtev+++l+    +e+
  gi|320100232|ref|YP_004175824.1|  69 GVTGIGHTRWATHGAPSDVNAHPHTDCGNVFAVVHNGVLENYLELKKALSA-RGHVFRSETDTEVVAHLIeeyyRET 144
                                       3489************77777***55555599*******************.******************8888888 PP

                          GATase_6  85 G......eevlerlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafas 133
                                       G       +++++l+G++a  +++  +++++++ar +   +pl+++v  ++ ++as
  gi|320100232|ref|YP_004175824.1| 145 GdvyqafRRAVAALKGAYALLMVTPlEPDKIFFARKD---SPLVIGVGPGYNLVAS 197
                                       899999999999**********************655...8999998888888887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                          GATase_6 113 drlgvkplyyavdesglafase 134
                                          g+k +yy + + gl +a+e
  gi|320100232|ref|YP_004175824.1| 464 RIAGSKSMYYLSRGVGLPVARE 485
                                       3347999999999999999987 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   3.4e-18     1e-14      13     122 ..      89     203 ..      75     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 3.4e-18
                          GATase_7  13 aQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfAf 80 
                                       a P + + ++ +++v+nG + Ny el++ L+a+gh fr+++Dtev+++l+e+         +  ++a+  l+G +A+
  gi|320100232|ref|YP_004175824.1|  89 AHPHT-DCGNVFAVVHNGVLENYLELKKALSARGHVFRSETDTEVVAHLIEEyyretgdvyQAFRRAVAALKGAYAL 164
                                       55666.4566799************************************************99************** PP

                          GATase_7  81 aiwdeeek.rlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       ++++  e  +++ aR      PL +g  +g   l+aS + all
  gi|320100232|ref|YP_004175824.1| 165 LMVTPLEPdKIFFARK---DSPLVIGVGPG-YNLVASDIPALL 203
                                       ***9655448888887...49*******96.88999*999997 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       0.2   6.1e+02      29      57 ..     289     317 ..     282     330 .. 0.77
   2 !   21.6   0.0   5.7e-08   0.00017     101     137 ..     340     376 ..     315     377 .. 0.91
   3 ?   -2.0   0.0       1.1   3.3e+03      50      95 ..     418     465 ..     416     470 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.2
                                       HHHHHTT--EEEEESGGGHHHHHHTSSST CS
                             SIS_2  29 adslenggkvlvfGsGhSaalaeelaara 57 
                                       a+ l++   v+v G+G S  ++e++a   
  gi|320100232|ref|YP_004175824.1| 289 AEMLADADTVFVTGAGTSYHASEYFALIS 317
                                       566777789*********99999887655 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5.7e-08
                                       --TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2 101 lkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                       + p+DvL+ +S+sG+    ++a++a+k+rg +vi lt
  gi|320100232|ref|YP_004175824.1| 340 AGPRDVLVAVSQSGETMDTLKALRAFKKRGSRVISLT 376
                                       5799*******************************99 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.1
                                       HHHTSSSTT-BTTEEEE--GGGSSSSST....THHHHHTT-TTHHHHH CS
                             SIS_2  50 aeelaaragglaeferialpalalhtda..eatkssalerdegyakqi 95 
                                       a e+a+r+g+l + e + l + + +t +  e ++s+  e ++ +a++i
  gi|320100232|ref|YP_004175824.1| 418 AVETATRIGSLRGGEEMELLKELESTPKhvEESISTTSELVKKLAERI 465
                                       678888888888888887777776666546666677766666666665 PP

>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.6e-05     0.049       5     141 ..     458     601 ..     454     607 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTT........SS-GGGGTTEEE CS
                        bact-PGI_C   5 akqlAlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgl........eaeeelkkrlrl 73 
                                        k+lA+++ag+  + y s ++  ++Ar  + +++e+A ++a a    e++h  i+++            ++  +l+ 
  gi|320100232|ref|YP_004175824.1| 458 VKKLAERIAGSKSMYYLSRGVGLPVAREGALKIKEIAYVHAEAYPAGESKHGPIALVepsfpvvfT--IPNDAELQR 532
                                       699*******99999999***************************************888888542..466667777 PP

                                       EEESSHH.........HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S- CS
                        bact-PGI_C  74 vllrdee.ehprvkkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPtp 141
                                       +ll++ e  + r   ++ ++ +  e r      ++   ++ ++  + ++  + + ++++A l+g+DP +
  gi|320100232|ref|YP_004175824.1| 533 MLLGNIEeMRARGGVIVGVLPRGSELRERVDLAIEVPRAHWIATALTHTPPLQLLAYHVASLKGLDPDK 601
                                       777744413344445555554444444444445677788889999999999999999999999999975 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.8e-05     0.085      71     141 ..      69     140 ..      60     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                          GATase_4  71 sknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleel 141
                                           + H R at+G+ ++ n+hp +    g+ +   HnG l++y +      +  +    +TD+E++  +l+ee 
  gi|320100232|ref|YP_004175824.1|  69 GVTGIGHTRWATHGAPSDVNAHPHTD--CGNVFAVVHNGVLENYLELKkalsARGHVFRSETDTEVV-AHLIEEY 140
                                       556699*****************975..69999999*****99644332234222233357888864.4555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4587.94
//
Query:       gi|320100233|ref|YP_004175825.1|  [L=224]
Description: uridylate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-20   72.3   0.0    9.6e-20   71.2   0.0    1.5  1  AA_kinase       Amino acid kinase family
  ------ inclusion threshold ------
        0.1   12.4   0.1        1.1    9.1   0.0    2.2  2  NAD_binding_10  NAD(P)H-binding
       0.17   10.9   0.0       0.26   10.3   0.0    1.3  1  ANF_receptor    Receptor family ligand binding region


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 !   71.2   0.0   1.6e-23   9.6e-20       2     239 ..       3     199 ..       2     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.6e-23
                                       EEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHH CS
                         AA_kinase   2 rvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeage 75 
                                       ++V+K+ G++++  ++   + r++e ++ l  +++++vvV Ggg++++++++   + g+ss++              
  gi|320100233|ref|YP_004175825.1|   3 TLVLKITGKVFDeGASL--VARYIELLRML-LDEYRVVVVAGGGNMARKYISDarALGVSSNYWL------------ 64 
                                       78**********55555..***********.999*******************************............ PP

                                       HHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETT CS
                         AA_kinase  76 vatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldee 152
                                           d ++++++rl++ lla+ l+ + ++  a                     e++ + l++  v+ ++g+i    +
  gi|320100233|ref|YP_004175825.1|  65 ----DTIGIWASRLNSLLLASSLQPYAYPKPAAS------------------LEEVLDALSSHRVVAMGGLI----P 115
                                       ....************************999888..................567778888889******99....9 PP

                                       TEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTHHHHCHHHHHH CS
                         AA_kinase 153 gelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgGmkvkhpaala 228
                                       g+    s+  +a+ +Aea+g+ kl +++ V  Vyd+dp  +pda++l+e+++  +++  +++   g    ++++al+
  gi|320100233|ref|YP_004175825.1| 116 GQ----STASTAVEVAEAVGVGKLYYFSAVGFVYDKDPLRHPDAKPLREVDATRLKAmLEQKQLPGEYALIDEKALD 188
                                       99....9***************************************************9999999************ PP

                                       HHHCTT-EEEE CS
                         AA_kinase 229 aarrggipvvI 239
                                       +a r++i + +
  gi|320100233|ref|YP_004175825.1| 189 LAVRSNIVIQL 199
                                       ****9987765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.063   3.7e+02      56     102 ..      29      70 ..      20      93 .. 0.71
   2 ?    9.1   0.0   0.00018       1.1      51     110 ..      95     153 ..      91     191 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.063
                                       HHHTT-SEEEES---TCCHHHHHHHHHHHHHHCT--EEEEEEETTTT CS
                    NAD_binding_10  56 ealkgadaVvsalggggkdeegaknivdaakeagvkRfvlvsaigvg 102
                                         l+ + +Vv+a+gg+     +a++ +  a++ gv+   ++ +ig+ 
  gi|320100233|ref|YP_004175825.1|  29 MLLDEYRVVVVAGGGN-----MARKYISDARALGVSSNYWLDTIGIW 70 
                                       5566777888888764.....57888888888888877777777765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00018
                                       CCHHHHHHTT-SEEEES---TCCHHHHHHHHHHHHHHCT--EEEEEEETT.TTSGCGCHHH CS
                    NAD_binding_10  51 vedlaealkgadaVvsalggggkdeegaknivdaakeagvkRfvlvsaig.vgdevpgefg 110
                                        e++ +al+ + +V + +   g+   +a ++v++a++ gv ++ + sa+g v+d+ p +++
  gi|320100233|ref|YP_004175825.1|  95 LEEVLDALSSHRVVAMGGLIPGQ--STASTAVEVAEAVGVGKLYYFSAVGfVYDKDPLRHP 153
                                       57888888888888887766664..689********************9944654433322 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 ?   10.3   0.0   4.4e-05      0.26     166     209 ..      20      64 ..       6     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHTT...T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEE CS
                      ANF_receptor 166 vrkllkeiks...karvivlfcssedarellkaarrlgltgeeyvwi 209
                                       v+++ + +++   + rv+v+   + +ar+++  ar lg++++   w+
  gi|320100233|ref|YP_004175825.1|  20 VARYIELLRMlldEYRVVVVAGGGNMARKYISDARALGVSSN--YWL 64 
                                       555555555555466*************************95..566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1748.05
//
Query:       gi|320100234|ref|YP_004175826.1|  [L=237]
Description: short-chain dehydrogenase/reductase SDR [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-40  139.6   0.0    1.5e-40  139.3   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    3.5e-27   95.2   0.0    4.1e-27   94.9   0.0    1.1  1  adh_short     short chain dehydrogenase
    0.00065   19.7   0.0     0.0013   18.7   0.0    1.5  2  KR            KR domain
     0.0022   17.4   0.0     0.0028   17.1   0.0    1.1  1  DUF1776       Fungal family of unknown function (DUF1776)


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 !  139.3   0.0   3.2e-44   1.5e-40      15     233 ..       2     232 ..       1     233 [. 0.93

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 3.2e-44
                                       HHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GG CS
                      adh_short_C2  15 aeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfl 88 
                                        eeGa+vvl  + +e+ +k++ el  +++ +v  +++D t++e+v++lvee ++ +++lD +v   g  ++  g+fl
  gi|320100234|ref|YP_004175826.1|   2 LEEGARVVLNGRTRESvEKALSELRGKYEGRVygVAADLTRREDVHRLVEESARYLDGLDSVVYITGPPRP--GRFL 76 
                                       68***************************99779*************************************..**** PP

                                       GH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGT CS
                      adh_short_C2  89 etsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkg 163
                                       e+ ++e+++     +  ++ l++a +p+++++   siv  +s++ +  + n +  ++ + ++++l+r+lA+elg++g
  gi|320100234|ref|YP_004175826.1|  77 EIREDEWEENTRLLILNAIWLVNASIPYLRRSrnPSIVFSTSIAVKEPLGNLALSNVLRLGIHGLVRTLARELGREG 153
                                       ***************************7776667******************************************* PP

                                       EEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEEST CS
                      adh_short_C2 164 iRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDg 231
                                       iRvNav pg+i+T+ ++++ +          +e ++   +++plgrlg+p+e +++++fL+s+ asy +G+ + vDg
  gi|320100234|ref|YP_004175826.1| 154 IRVNAVMPGYIETDRVRRLIEekagregkpYSEAYRDYVSEIPLGRLGSPKEYGRVVAFLVSEYASYLNGASIPVDG 230
                                       *************99777644244444444556888899************************************** PP

                                       TG CS
                      adh_short_C2 232 Gl 233
                                       Gl
  gi|320100234|ref|YP_004175826.1| 231 GL 232
                                       *7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0   9.1e-31   4.1e-27      20     192 ..       1     174 [.       1     177 [. 0.97

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 9.1e-31
                                       HHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGG CS
                         adh_short  20 lakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfse 95 
                                       +++eGa+vv+ +r+ e +e++++el+ + + +++ +++D+t re+v +lve+ +  l++ld +v  +G  ++g f e
  gi|320100234|ref|YP_004175826.1|   1 MLEEGARVVLNGRTRESVEKALSELRGKyEGRVYGVAADLTRREDVHRLVEESARYLDGLDSVVYITGPPRPGRFLE 77 
                                       579************************************************************************** PP

                                       CSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTE CS
                         adh_short  96 lseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgi 172
                                       + e+ewe+   + +  +++l+ a +p++ ++++ +Iv+ +S+a k+p+ ++a       +++gl+r+la+el ++gi
  gi|320100234|ref|YP_004175826.1|  78 IREDEWEENTRLLILNAIWLVNASIPYLRRSRNPSIVFSTSIAVKEPLGNLALSNVLRLGIHGLVRTLARELGREGI 154
                                       ***************************************************************************** PP

                                       EEEEEEESSBSSHHHHHHCT CS
                         adh_short 173 rvnavaPGlvdTdmakelre 192
                                       rvnav+PG+++Td +++l e
  gi|320100234|ref|YP_004175826.1| 155 RVNAVMPGYIETDRVRRLIE 174
                                       *************9887765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.9e-07    0.0013      20     109 ..       1      87 [.       1     120 [. 0.89
   2 ?   -2.5   0.0      0.88     4e+03      15      72 ..     144     173 ..     137     180 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.9e-07
                                       HHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE-------- CS
                                KR  20 laekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdk 95 
                                       ++e+ga ++vl +R+   +e+ ++ ++el+ + + +v  vaaD++ +++v++l+ee  +  + +  v+   g  r +
  gi|320100234|ref|YP_004175826.1|   1 MLEEGA-RVVLNGRT---RESVEKALSELRGKyEGRVYGVAADLTRREDVHRLVEESARYLDGLDSVVYITGPPRPG 73 
                                       566676.58999**9...67777899999987699***********************999**************** PP

                                       -TTT--HHHHHHHH CS
                                KR  96 lleemtaedleqvl 109
                                        + e  ++++e+ +
  gi|320100234|ref|YP_004175826.1|  74 RFLEIREDEWEENT 87 
                                       *********99865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.88
                                       HHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHH CS
                                KR  15 elarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdaveall 72 
                                       +                            l +el + g++v++v     + d v++l+
  gi|320100234|ref|YP_004175826.1| 144 T----------------------------LARELGREGIRVNAVMPGYIETDRVRRLI 173
                                       3............................44555555555555555555555555555 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 !   17.1   0.0   6.2e-07    0.0028     108     201 ..      75     165 ..      47     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-07
                           DUF1776 108 ietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkre 184
                                       + +i +++w++     +l+ i +++a +p l+     +   iv+++si  +  l + a+  ++   ++ l+++L+re
  gi|320100234|ref|YP_004175826.1|  75 FLEIREDEWEENTRLLILNAIWLVNASIPYLRR---SRNPSIVFSTSIAVKEPLGNLALSNVLRLGIHGLVRTLARE 148
                                       668999*****6666678999***********7...6778899********************************** PP

                           DUF1776 185 lrphnidvtqikLGnld 201
                                       l++ +i v  +  G ++
  gi|320100234|ref|YP_004175826.1| 149 LGREGIRVNAVMPGYIE 165
                                       ********998877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1782.29
//
Query:       gi|320100235|ref|YP_004175827.1|  [L=414]
Description: transposase, IS605 OrfB family [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   74.3   0.2    1.1e-20   73.2   0.2    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0057   16.9   1.0      0.012   15.8   1.0    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.038   14.6   3.7       0.17   12.5   1.5    2.6  2  DUF2285         Uncharacterized conserved protein (DUF2285)
      0.045   13.9   1.3       0.11   12.7   1.3    1.7  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.065   13.3   4.9          3    8.0   0.3    3.2  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.12   12.5   5.4       0.07   13.2   3.2    1.7  2  DZR             Double zinc ribbon
       0.13   11.8   3.1       0.42   10.2   0.5    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.21   11.4   3.2         10    6.0   0.1    2.8  3  zinc_ribbon_2   zinc-ribbon domain
       0.24   11.5   1.6       0.33   11.1   0.8    1.6  1  DUF678          Protein of unknown function (DUF678)
        1.1    9.4   4.1         16    5.8   0.8    2.6  2  Zn-ribbon_8     Zinc ribbon domain
        1.2    9.4   4.7        1.1    9.6   0.9    2.4  2  zinc_ribbon_9   zinc-ribbon
        1.6    8.2   7.3        3.3    7.2   4.4    2.6  3  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.2   7.7e-24   1.1e-20       1      69 []     300     367 ..     300     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 7.7e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +r+l  +l ++++++G++ + vnp  TS+tC+ Cgs++ e    r++kCp+CgfeadrD++A++Ni ++
  gi|320100235|ref|YP_004175827.1| 300 YRRLGYWLDWQCEKHGVPCIAVNPKDTSSTCPLCGSRLVE-SGYRRLKCPSCGFEADRDTVAVLNIRRK 367
                                       789999**********************************.9************************985 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   8.2e-06     0.012      47     104 ..     204     266 ..     164     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.2e-06
                        OrfB_IS605  47 ksdykylakeiaelqsklkkskn.....ykkasrklarlhrkrsrrrkhllhklathliktlk 104
                                        ++  ++++   +lq+k++         ++  + +++r h+k + ++ + ++k++++++    
  gi|320100235|ref|YP_004175827.1| 204 VEKAVRYRELAERLQRKYSNGSYrawlrRRGIRDRVRRFHEKARSIIEDWARKTSHEIVVVAR 266
                                       3445556666666666665554478887899***************************96555 PP

>> DUF2285  Uncharacterized conserved protein (DUF2285)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.5   0.00012      0.17      56      99 ..     206     251 ..     200     252 .. 0.80
   2 ?    1.0   0.0      0.43   6.4e+02      94     105 ..     334     345 ..     333     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                           DUF2285  56 agaslreiAevl...fgaervaaedW.kdsalrsrvrrlvrrgralmr 99 
                                       +   +re Ae l   + +  +  + W ++ ++r+rvrr  +++r+ ++
  gi|320100235|ref|YP_004175827.1| 206 KAVRYRELAERLqrkYSNGSY--RAWlRRRGIRDRVRRFHEKARSIIE 251
                                       56789*******744444443..47******************99875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.43
                           DUF2285  94 gralmrGGYrkL 105
                                       g +l++ GYr+L
  gi|320100235|ref|YP_004175827.1| 334 GSRLVESGYRRL 345
                                       789********8 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 ?   12.7   1.3     7e-05      0.11      15      40 .]     327     351 ..     326     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                     Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCvaCd 40 
                                       ++tCp Cg+ L+++ +  ++ C++C+
  gi|320100235|ref|YP_004175827.1| 327 SSTCPLCGSRLVES-GYRRLKCPSCG 351
                                       789**********9.56899*****6 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3     0.002         3       1      10 [.     329     338 ..     329     341 .. 0.89
   2 ?    5.5   0.1     0.012        17       1      11 [.     346     356 ..     346     361 .. 0.82
   3 ?   -0.8   0.0       1.1   1.6e+03       5      13 ..     392     400 ..     391     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.002
                    DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                       +CP CGs +v
  gi|320100235|ref|YP_004175827.1| 329 TCPLCGSRLV 338
                                       7*******99 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP+CG ++ R
  gi|320100235|ref|YP_004175827.1| 346 KCPSCGFEADR 356
                                       6*****87755 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                    DNA_ligase_ZBD   5 CGsavvRee 13 
                                       CG +v R+ 
  gi|320100235|ref|YP_004175827.1| 392 CGEPVNRPK 400
                                       *****9976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.2   4.7e-05      0.07       4      41 ..     318     357 ..     310     359 .. 0.75
   2 ?   -2.9   0.0       4.8   7.2e+03      17      23 ..     391     397 ..     390     400 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                               DZR   4 Cgeelppdar.fCseCgtklkavaa.edrCpsCgekvdpe 41 
                                       C + +p+d   +C+ Cg++l +      +CpsCg ++d +
  gi|320100235|ref|YP_004175827.1| 318 CIAVNPKDTSsTCPLCGSRLVESGYrRLKCPSCGFEADRD 357
                                       55556655444********975444899******988765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.8
                               DZR  17 eCgtklk 23 
                                       +Cg++++
  gi|320100235|ref|YP_004175827.1| 391 RCGEPVN 397
                                       5776665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00028      0.42       2      27 ..     310     335 ..     309     340 .. 0.92
   2 ?    1.5   0.1      0.14   2.1e+02       2       7 ..     346     351 ..     345     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                                       EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                       +C ++g + + ++p+ +  +C+ CG+
  gi|320100235|ref|YP_004175827.1| 310 QCEKHGVPCIAVNPKDTSSTCPLCGS 335
                                       69999*99*****************7 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                                       EETTTT CS
                      TF_Zn_Ribbon   2 kCPnCg 7  
                                       kCP Cg
  gi|320100235|ref|YP_004175827.1| 346 KCPSCG 351
                                       788888 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.016        25      10      23 .]     324     337 ..     320     337 .. 0.80
   2 ?    6.0   0.1    0.0069        10       1       8 [.     346     353 ..     346     359 .. 0.79
   3 ?   -1.3   0.1       1.4     2e+03      18      22 ..     391     395 ..     390     397 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
                     zinc_ribbon_2  10 qdnakFCpyCGtpl 23 
                                       +d++  Cp CG+ l
  gi|320100235|ref|YP_004175827.1| 324 KDTSSTCPLCGSRL 337
                                       488999****9865 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0069
                     zinc_ribbon_2   1 fCpnCGae 8  
                                       +Cp+CG e
  gi|320100235|ref|YP_004175827.1| 346 KCPSCGFE 353
                                       79999976 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.4
                     zinc_ribbon_2  18 yCGtp 22 
                                       +CG+p
  gi|320100235|ref|YP_004175827.1| 391 RCGEP 395
                                       46655 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.8   0.00022      0.33      15      37 ..     317     339 ..     310     347 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                            DUF678  15 pkttvededdctTCSlCqSkLvk 37 
                                       p ++v+++d + TC lC S+Lv 
  gi|320100235|ref|YP_004175827.1| 317 PCIAVNPKDTSSTCPLCGSRLVE 339
                                       567899***************96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.8      0.01        16       8      36 ..     311     337 ..     308     340 .. 0.60
   2 ?    3.8   0.1     0.042        63      28      38 ..     346     356 ..     341     358 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsev 36 
                                       Ce++g    ++ +  ++   +CP Cgs++
  gi|320100235|ref|YP_004175827.1| 311 CEKHGVPCIAVNP--KDTSSTCPLCGSRL 337
                                       5555544443433..445678******65 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.042
                       Zn-ribbon_8  28 aCPeCgsevrr 38 
                                       +CP+Cg e+ r
  gi|320100235|ref|YP_004175827.1| 346 KCPSCGFEADR 356
                                       48888766555 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.9   0.00072       1.1      14      33 ..     321     339 ..     310     340 .. 0.75
   2 ?    0.4   0.2      0.55   8.2e+02      22      28 ..     346     351 ..     343     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00072
                     zinc_ribbon_9  14 vspdedsdvlCPhCgggFVE 33 
                                       v p+++s  +CP Cg+  VE
  gi|320100235|ref|YP_004175827.1| 321 VNPKDTSS-TCPLCGSRLVE 339
                                       55554444.6******9999 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.55
                     zinc_ribbon_9  22 vlCPhCg 28 
                                       + CP+Cg
  gi|320100235|ref|YP_004175827.1| 346 K-CPSCG 351
                                       4.****7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0036       5.4      11      26 .]     322     337 ..     318     337 .. 0.83
   2 ?    7.2   4.4    0.0022       3.3       4      24 ..     329     352 ..     328     354 .. 0.85
   3 ?   -2.5   0.0       2.6   3.9e+03       7      11 ..     391     395 ..     390     396 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0036
                       zf-ribbon_3  11 plssddnvCpyCGtkl 26 
                                       ++++  ++Cp CG++l
  gi|320100235|ref|YP_004175827.1| 322 NPKDTSSTCPLCGSRL 337
                                       4589999******987 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0022
                       zf-ribbon_3   4 rCPnCGa.plssddn..vCpyCGt 24 
                                       +CP CG+ +++s+ +  +Cp+CG 
  gi|320100235|ref|YP_004175827.1| 329 TCPLCGSrLVESGYRrlKCPSCGF 352
                                       6***********86544******6 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.6
                       zf-ribbon_3   7 nCGap 11 
                                       +CG+p
  gi|320100235|ref|YP_004175827.1| 391 RCGEP 395
                                       69986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3003.26
//
Query:       gi|320100236|ref|YP_004175828.1|  [L=924]
Description: glycoside hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   33.7   0.1    3.7e-08   32.9   0.1    1.2  1  Glyco_hydro_57  Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   2.1e-12   3.7e-08      96     314 ..     291     514 ..     272     523 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.1e-12
                                       HHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHHHHHHHSS-- CS
                    Glyco_hydro_57  96 avlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkarelyeeyfgqeP 172
                                        + +++++sg+l+ ++  w ++  ++  + l  +g v +l+   ++ +++++ d    +   +  + ++++ fg++P
  gi|320100236|ref|YP_004175828.1| 291 RIPVSIHMSGTLIASFLWW-DPGFISYVKGLTARGLVAILGGVWAEHITAYFYD-NFNDPSANFTKWYVRQVFGYNP 365
                                       45699**************.********************************99.56666677788899******** PP

                                       SBEE-GGG-B--S...HHHHHHHTT--EEEE-C------------TTS-EE-TTS......-EEEE--CHH-TTTSG CS
                    Glyco_hydro_57 173 rgfwlpElavspe...ileilaelGfeylftdelaeiledkskespyrpyllkngg.....iavffRdreLsddigF 241
                                       ++ w pE+++++e   i+ +l  + ++ ++ d   +  e++   +py p + ++++     ++v+f+d ++ +++  
  gi|320100236|ref|YP_004175828.1| 366 VTAWVPERTWDDErtgIAYTLS-KYYSAVILDANTHHDEWSPSTNPYKPHKYDTSRtagrtLYVLFIDWDTQQKLLS 441
                                       *************554444444.4599******55555555555*****9999999999************777766 PP

                                       GG-............TTSB..........-TT---TT.T-.-BB-TT-S---H.HHHHHHHHHHHHHHHHHHHHHH CS
                    Glyco_hydro_57 242 ryseqypleavddfinwlkkvkkaksevvtialdgEn.wg.hypetgkkeFle.klyeeleenglielvtpsefik 314
                                       + ++       ++   w  + ++ ++ v+ +a d E+  g    +tg + +l  +  + +  +++i++vt  ++++
  gi|320100236|ref|YP_004175828.1| 442 NTDGGLHM-DLRRKYIWAAT-NSDQQMVFIYADDWEKaAGiAGWYTGNP-YLYnNSLTWIAMHPWIQVVTTDDVVN 514
                                       66644444.56666567774.455999999999****777977789986.99988899999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (924 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 6109.78
//
Query:       gi|320100237|ref|YP_004175829.1|  [L=236]
Description: tRNA/rRNA methyltransferase SpoU [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-30  106.3   0.0      2e-30  105.9   0.0    1.2  1  SpoU_methylase   SpoU rRNA Methylase family
    4.3e-08   33.2   0.0    1.9e-06   27.9   0.0    2.4  2  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
  ------ inclusion threshold ------
      0.086   13.3   0.0        0.2   12.1   0.0    1.6  1  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase 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 !  105.9   0.0   3.3e-34     2e-30       2     142 .]       2     151 ..       1     151 [. 0.87

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 3.3e-34
                                       EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEE CS
                    SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfal 78 
                                       ++vvlv+ie + NlG iaRt+ +fg++el++vkp +   l++ +  aa g  ++ +++v dsl+ea+k ++      
  gi|320100237|ref|YP_004175829.1|   2 IRVVLVGIEGAVNLGVIARTCVNFGVDELYIVKPVAS--LDEALNYAAKGRGFLENAVVTDSLDEAIKGVDMI---- 72 
                                       89*******************************8776..88888888888888888*************8865.... PP

                                       EEESTT-SEGCCS........HHH.......TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHH CS
                    SpoU_methylase  79 vatslkgkslsei........dlk.......ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvail 140
                                       vats +g s s++        d++       ++va++fG+E++Gl++e++ +ad lv+Ip ++ ++ LNv++Ava++
  gi|320100237|ref|YP_004175829.1|  73 VATSDEGYSESDMlrqavdlsDFAerifprtRSVAILFGRESTGLTREEIGRADILVTIPANPAYPVLNVSQAVAVV 149
                                       9998877777755444455553336777888*********************************************9 PP

                                       HH CS
                    SpoU_methylase 141 ly 142
                                       l+
  gi|320100237|ref|YP_004175829.1| 150 LW 151
                                       85 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 !   27.9   0.0   3.1e-10   1.9e-06      28     177 ..      15     150 ..       9     155 .. 0.85
   2 ?   -3.3   0.0       1.1   6.8e+03      57      69 ..     215     227 ..     207     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.1e-10
                                       HHHHHHHHHHTT-SEEEEE---HHHHHHHHHHHHHHHTSGGGGT-SSSHHHHTTEEEESSHHHHHHHHHHHHSS--E CS
                   Methyltrn_RNA_4  28 lhDiaRsartygvkkyyvvtpleaqrelverilehWtegagaeynpdRkealslvkvvesleealeeiekeegkkpl 104
                                       l  iaR++  +gv+++y+v+p+++    +++ l++  +g g          l++  v++sl+ea++ +     ++  
  gi|320100237|ref|YP_004175829.1|  15 LGVIARTCVNFGVDELYIVKPVAS----LDEALNYAAKGRGF---------LENAVVTDSLDEAIKGVDMIVATSDE 78 
                                       5569******************87....56778999999887.........66777889999999988777654444 PP

                                       EEE--SS--SS-B-HHHHHHHHHH--S-EEEEE--.TT---HHHHTT-SEEB--TTTTSS-----HHHHHHHHH CS
                   Methyltrn_RNA_4 105 vvatsArkkentvsyeelrelleeeekpvlllfGt.gwGlaeevlekadyiLepirgaseynHLsvrsAvaiil 177
                                          ++    +++v+++++ e++  ++++v +lfG  + Gl++e + +ad iL  i ++  y  L v  Ava++l
  gi|320100237|ref|YP_004175829.1|  79 -GYSESDMLRQAVDLSDFAERIFPRTRSVAILFGReSTGLTREEIGRAD-ILVTIPANPAYPVLNVSQAVAVVL 150
                                       .44555678999**********************6489*********99.5778******************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHTSGGG CS
                   Methyltrn_RNA_4  57 erilehWtegaga 69 
                                        r+l++W +   +
  gi|320100237|ref|YP_004175829.1| 215 ARVLKYWLQRVRR 227
                                       5889999887655 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   0.0   3.3e-05       0.2      23      81 ..      19      82 ..      16     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                                      HHHHHHCTSE.EEEE-SSTHHCCCCHHGG.....BTCCEEES-CHHHHTT-SEEEE-S--GGGGG CS
                    UDPG_MGDP_dh_C 23 ieeLleegae.vkiyDPkvkeeaveaele.....ekgvevvdsleealkgadaiviltehdefke 81
                                      ++++ + g++ + i+ P+++ +++ ++++     +++++v+dsl+ea+kg+d+iv +   + + e
  gi|320100237|ref|YP_004175829.1| 19 ARTCVNFGVDeLYIVKPVASLDEALNYAAkgrgfLENAVVTDSLDEAIKGVDMIVATS-DEGYSE 82
                                      556666666448888898888888877778999988****************998654.445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1689.60
//
Query:       gi|320100238|ref|YP_004175830.1|  [L=217]
Description: methyltransferase small [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   56.0   0.0    1.5e-14   53.9   0.0    1.8  1  MTS              Methyltransferase small domain
    1.3e-11   44.4   0.2    3.8e-11   42.9   0.1    1.6  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.2e-05   24.2   0.0    9.1e-05   22.2   0.0    1.8  2  Cons_hypoth95    Conserved hypothetical protein 95
    0.00013   22.6   0.1     0.0011   19.6   0.1    2.1  1  Methyltransf_25  Methyltransferase domain
    0.00025   21.0   0.0    0.00067   19.6   0.0    1.6  2  Methyltransf_18  Methyltransferase domain
    0.00044   20.9   0.1     0.0013   19.4   0.1    1.8  1  Methyltransf_12  Methyltransferase domain
     0.0017   19.0   0.1     0.0075   16.9   0.1    1.9  1  Methyltransf_11  Methyltransferase domain
     0.0021   17.9   0.0     0.0043   16.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
     0.0075   16.1   0.2       0.12   12.2   0.2    2.4  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.04   14.9   0.0      0.069   14.2   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
      0.043   13.5   0.0       0.14   11.8   0.0    1.8  1  UPF0020          Putative RNA methylase family UPF0020
      0.069   13.0   0.1        2.3    8.0   0.0    2.0  2  Methyltransf_8   Hypothetical methyltransferase
       0.17   11.3   0.0       0.33   10.3   0.0    1.4  1  TehB             Tellurite resistance protein TehB


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 !   53.9   0.0   1.1e-17   1.5e-14      23     151 ..      22     164 ..      16     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.1e-17
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EE CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfd 99 
                                       Ll+ l+  ++g  +DlGcG G+lg+  + +    + ++vd+d  Al+ + +n+  n+++++ +  +  ++v ++  d
  gi|320100238|ref|YP_004175830.1|  22 LLDSLKP-KAGLCVDLGCGSGILGLYGLIKGYCERTVFVDIDEDALATTLRNIPLNNAQARSIVVSSDNAVLHGAAD 97 
                                       6677777.77889*************999998889************************99999999999999**** PP

                                       EEEE---S............TTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEE...TTSCHHHHHHH CS
                               MTS 100 livsNPPf............hagkatelavaeeliaeAkeaLkegGeLliVan...rklgyesllee 151
                                       l++ NPP+             +g    ++++ ++i+ A+e+L++gG L++V++   ++l +e++l++
  gi|320100238|ref|YP_004175830.1|  98 LVLANPPYlpaaegkvldaaTEGGVHGYEAVLHFINVAHEVLRPGGLLILVYSslsNQLVVEEHLSR 164
                                       *******8444332222222234445678999*******************8611135555555554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.1   2.8e-14   3.8e-11     148     233 ..      16     102 ..      14     103 .. 0.88
   2 ?   -1.5   0.0      0.94   1.3e+03     239     282 ..     128     172 ..     126     178 .. 0.65

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.8e-14
                              PrmA 148 TklclealeklvkegeevlDvGtGSGiLaiaaakLg.akkvvavDiDevAvkvakeNaelNkveaklevalseellk 223
                                       T l+l++l++l  +    +D+G+GSGiL +  +  g  ++ v vDiDe A+  + +N+ lN+ +a+  v  s++++ 
  gi|320100238|ref|YP_004175830.1|  16 TWLALKLLDSLKPKAGLCVDLGCGSGILGLYGLIKGyCERTVFVDIDEDALATTLRNIPLNNAQARSIVVSSDNAVL 92 
                                       7899********9999**************877666268999***********************665666666666 PP

                              PrmA 224 eekadvivaN 233
                                       ++ ad+++aN
  gi|320100238|ref|YP_004175830.1|  93 HGAADLVLAN 102
                                       69*******9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.94
                              PrmA 239 lielaedikklvkeggllilSGilkekaeevaealeq.gfeleev 282
                                       ++++++ + +++++ggllil     + +  v+e+l++ gf+++  
  gi|320100238|ref|YP_004175830.1| 128 VLHFINVAHEVLRPGGLLILVYSSLSNQLVVEEHLSRkGFTMVAF 172
                                       678888899999999998874433334445666665447777665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.6e-08   9.1e-05      43     136 ..      31     117 ..       7     142 .. 0.79
   2 ?   -0.5   0.0      0.58     8e+02     132     175 ..     152     195 ..     145     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.6e-08
                                       -EEEETT-TTSHHHHHHHHTT.-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  43 arvLDlfaGsGalglEAlSRg.akkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                         ++Dl +GsG lgl  l  g +++ v+v+ d+ a+++  +n+   ++++  + ++ ++ +a+l+        d+v 
  gi|320100238|ref|YP_004175830.1|  31 GLCVDLGCGSGILGLYGLIKGyCERTVFVDIDEDALATTLRNIPLNNAQA--RSIVVSSDNAVLHG-----AADLVL 100
                                       4589************99987589*******************9999775..55555555555444.....46**** PP

                                       E--SSSTTCH.HHHHHHH CS
                     Cons_hypoth95 119 lDPPyakellieevlell 136
                                        +PPy   +   +vl++ 
  gi|320100238|ref|YP_004175830.1| 101 ANPPYLPAAE-GKVLDAA 117
                                       *****77654.5666555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.58
                                       HHHHHHHTT-EEEEEEEEEEEECCSSS--.-TTEEEEEEEEETT CS
                     Cons_hypoth95 132 vlelleekkllkenalvvvetekekelpespenlelvkekkyge 175
                                       + ++l  +++l+++++ +v   ++++ +e +    +vk++++g+
  gi|320100238|ref|YP_004175830.1| 152 LSNQLVVEEHLSRKGFTMVAFTSKNMFYETLYVAGVVKARDTGS 195
                                       56677778999999999999999999999999999999999886 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   8.1e-07    0.0011       2      71 ..      34     102 ..      33     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.1e-07
                                       EEET-TTSHHHHH.HHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   2 LdlGcGtGrltla.lakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71 
                                       +dlGcG+G l l+ l k +  ++ + vDi+e++l+++ +++  ++++++ ++ + ++    +g  Dlv+++
  gi|320100238|ref|YP_004175830.1|  34 VDLGCGSGILGLYgLIKGY-CERTVFVDIDEDALATTLRNIPLNNAQARSIVVSSDNAV-LHGAADLVLAN 102
                                       69******99887355554.8****************9999887776666665554443.34566666663 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   4.9e-07   0.00067       7      73 ..      22      88 ..      19     100 .. 0.86
   2 ?   -1.8   0.0       1.9   2.6e+03      94     136 ..     126     170 ..     112     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.9e-07
                   Methyltransf_18  7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73
                                       + sl +k   ++D G+  g+l +y + +g +++ +++Di e +l++  +ni  ++ + +  v+ sd
  gi|320100238|ref|YP_004175830.1| 22 LLDSLKPKAGLCVDLGCGSGILGLYGLIKGYCERTVFVDIDEDALATTLRNIPLNNAQARSIVVSSD 88
                                      555666777799****************************************999998887777665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                   Methyltransf_18  94 elileILeeakeklkkikk..lilqpnseaeelRkylvengfkie 136
                                       e +l+ ++ a+e+l+      l+ ++ s++  + + l ++gf+++
  gi|320100238|ref|YP_004175830.1| 126 EAVLHFINVAHEVLRPGGLliLVYSSLSNQLVVEEHLSRKGFTMV 170
                                       556666666666666555522445677788888888888888765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   9.4e-07    0.0013       1      99 []      34     145 ..      34     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.4e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg............. 64 
                                       +++GcG+G l  + l k    + ++vDi+++a+ ++  +    +n ++  + +  +++     g             
  gi|320100238|ref|YP_004175830.1|  34 VDLGCGSGILGLYGLIKGYCERTVFVDIDEDAL-ATTLRNIPLNNAQARSIVVSSDNA--VLHGaadlvlanppylp 107
                                       59***********99998888999*********.333333333333333333333332..22223567888888888 PP

                   Methyltransf_12  65 ....ssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99 
                                           +  D+ +  +v  + + +  +++ ++++L+pgG l
  gi|320100238|ref|YP_004175830.1| 108 aaegKVLDAATEGGVHGY-EAVLHFINVAHEVLRPGGLL 145
                                       888777888888888777.89999999999999999976 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   5.4e-06    0.0075       1      96 []      34     147 ..      34     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.4e-06
                                       EEET-TTSHHHHHHH.HTT.SEEEEEES-HHHHHHHHHHCCHHT-................EEEETTEECCCTSS-T CS
                   Methyltransf_11   1 LdvGcGtGrlaeala.krg.arvvgvDlskemlklakekaseegl................kvefvvadaeklpfed 59 
                                       +d+GcG+G+l  +   k + +r+v vD+++ +l++  ++++ ++                   ++v a+   lp ++
  gi|320100238|ref|YP_004175830.1|  34 VDLGCGSGILGLYGLiKGYcERTVFVDIDEDALATTLRNIPLNNAqarsivvssdnavlhgAADLVLANPPYLPAAE 110
                                       59******998876643336*************99988877777655444444444444443344666666677666 PP

                                       T.-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  60 n.sfDlvvssevlhhvedpekalkeiaRvLkpgGllvi 96 
                                       +   D+ +    +h  e + ++++ ++ vL+pgGll++
  gi|320100238|ref|YP_004175830.1| 111 GkVLDAATE-GGVHGYEAVLHFINVAHEVLRPGGLLIL 147
                                       414455544.35677789*****************985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.1e-06    0.0043       8     123 ..      34     163 ..      29     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                   Methyltransf_31   8 lDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsn.. 81 
                                       +DlGCG+G l++      g   + v +Di+e+a+     n   ++ +  +  +++ +    + l+    Dl+l+n  
  gi|320100238|ref|YP_004175830.1|  34 VDLGCGSGILGLYGL-IKGYCERTVFVDIDEDALATTLRNIPLNNAQARSIVVSSDN----AvLH-GAADLVLANpp 104
                                       7******99876444.2233345899********99999877555554444444433....3344.89*******88 PP

                   Methyltransf_31  82 .......evl........naladpdkileeiervlkpggilliedprllaelp..akve 123
                                               vl        +   +   +++ +++vl+pgg l++ + +l  +l   ++++
  gi|320100238|ref|YP_004175830.1| 105 ylpaaegKVLdaateggvHGYEAVLHFINVAHEVLRPGGLLILVYSSLSNQLVveEHLS 163
                                       88777774446556777788888888888******************555554664443 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.2   8.5e-05      0.12      20      70 ..      27      77 ..      16     175 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-05
                   Methyltransf_23 20 lraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.......kakkaqkdq 70
                                      +++ g ++d+GcG+Gil  +   +g+    ++vD+++ a +          +       +
  gi|320100238|ref|YP_004175830.1| 27 KPKAGLCVDLGCGSGILGLYGLIKGYceRTVFVDIDEDALA--TtlrniplN-------N 77
                                      45667899********988887777777999****976444..322333331.......2 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     5e-05     0.069       2     103 ..      35     147 ..      34     147 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5e-05
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare...aglddrvrlikads.............eeal 62 
                                        +G  +G   l l  +++ + + r v vd d++  + a  +r+   ++ ++r  ++++d              + +l
  gi|320100238|ref|YP_004175830.1|  35 DLG--CGSGILGLYGLIKGYCE-RTVFVDIDED--ALATTLRNiplNNAQARSIVVSSDNavlhgaadlvlanPPYL 106
                                       567..67777777777777776.7888888884..233333333332222222222111122222223455545566 PP

                   Methyltransf_24  63 aslaagsiDllfiDgghaaeavledleallprlapggvvlf 103
                                       +  + +  D +   g h +eavl+++++++++l+pgg++++
  gi|320100238|ref|YP_004175830.1| 107 PAAEGKVLDAATEGGVHGYEAVLHFINVAHEVLRPGGLLIL 147
                                       66667778999999************************985 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.14      82     179 ..      59     165 ..      51     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                       EES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----.....------HHHH.HHHHHH...HH CS
                           UPF0020  82 sDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPY.....Gerlgskkal.ekLYse...fl 149
                                       +D+d+ +++++ +N    + + +  +++ d+a L+   g  d++++npPY     G+ l+++ +   + Y++   f 
  gi|320100238|ref|YP_004175830.1|  59 VDIDEDALATTLRNIPLNNAQARSIVVSSDNAVLH---GAADLVLANPPYlpaaeGKVLDAATEGgVHGYEAvlhFI 132
                                       79999999999999877777777777777899999...668*********444444445444444344455422266 PP

                                       HHHHHH-TT..-EEEEEES...SHHHHHCC--- CS
                           UPF0020 150 relkrvlrgggrlvlltse...nkalekaleer 179
                                       + +++vlr gg l+l+ s+   +  +e+ l+++
  gi|320100238|ref|YP_004175830.1| 133 NVAHEVLRPGGLLILVYSSlsnQLVVEEHLSRK 165
                                       778888888777777765411133455555555 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.059        82      70     123 ..      27      80 ..      12      88 .. 0.73
   2 ?    8.0   0.0    0.0016       2.3     137     190 ..     128     179 ..     122     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.059
                                       S-TTS-EEEES-TT-HHHHH--S-..EEEEESS-SSTTEEES-TTS-S--TT-E CS
                    Methyltransf_8  70 kkdnlvvadlGcGeakiaeavrekekvrsfdlvavnervvacdlakvPledesv 123
                                       k++    +dlGcG   +      k   +   +v ++e+  a  l+++Pl++  +
  gi|320100238|ref|YP_004175830.1|  27 KPKAGLCVDLGCGSGILGLYGLIKGYCERTVFVDIDEDALATTLRNIPLNNAQA 80 
                                       66777889*****99888544444445556667788899999999999887654 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHEEEEEEEEEEEEGGG-S-HHHHHHHHHCTTEEEEEEE--STTE CS
                    Methyltransf_8 137 ladflkeanrvlkvGGllkvaevksrfesvklfaraltklGfevkskdlsnkqf 190
                                       + +f++ a+ vl++GGll +  v s +++  +++++l++ Gf ++    +n  +
  gi|320100238|ref|YP_004175830.1| 128 VLHFINVAHEVLRPGGLLIL--VYSSLSNQLVVEEHLSRKGFTMVAFTSKNMFY 179
                                       5679999**********987..8999****************999888777655 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00024      0.33      31      94 ..      30      94 ..      18     105 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                                      S-EEEEES-TTSHHHHHHHHTT-EEEE..EES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S CS
                              TehB 31 pgkvldlgcgqgrnslylsllgydvta..wdknensiafleeikekenlknistalydineaklde 94
                                       g ++dlgcg+g   ly  ++gy   +  +d +e+++a   + +  +n +  ++ ++  ++a l+ 
  gi|320100238|ref|YP_004175830.1| 30 AGLCVDLGCGSGILGLYGLIKGYCERTvfVDIDEDALATTLRNIPLNNAQ-ARSIVVSSDNAVLHG 94
                                      45678******************644312677888777655555555544.344444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1610.89
//
Query:       gi|320100239|ref|YP_004175831.1|  [L=278]
Description: ribosomal RNA adenine methylase transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-30  103.8   0.0    9.4e-30  103.6   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    5.2e-05   22.9   0.0    9.3e-05   22.0   0.0    1.4  1  MTS              Methyltransferase small domain
    0.00019   22.0   0.0    0.00043   20.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0029   16.7   0.0     0.0044   16.1   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0076   16.9   0.0      0.027   15.1   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.019   14.4   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      0.023   14.3   0.0      0.041   13.5   0.0    1.4  1  NodS             Nodulation protein S (NodS)
      0.059   14.0   1.4       0.35   11.6   0.1    2.5  2  TPR_16           Tetratricopeptide repeat


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 !  103.6   0.0   4.2e-33   9.4e-30       3     233 ..      29     240 ..      27     270 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 4.2e-33
                                       CCXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEE CS
                            RrnaAD   3 klrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklk 79 
                                       k r++++qnf++++ ++++  ++++    l   eig G G lT +L   +  +  +E+d rL++   +++  + ++ 
  gi|320100239|ref|YP_004175831.1|  29 KPRRRLSQNFIVDPALLKGFTRNVEY---LDTFEIGCGIGTLTMSLSRFVPRLICVEIDWRLLEAAVENID-AANVV 101
                                       6799***************9998865...5669***********************************666.***** PP

                                       EE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SH CS
                            RrnaAD  80 vvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsr 156
                                       +v++D+  +  p+             vv+n+Py+i++++   +  +++    ++++ +q+ +a+r++a+pg+++++r
  gi|320100239|ref|YP_004175831.1| 102 LVNADATVYTPPS-----------KQVVGNIPYHITSEILTGVARLNTV--TRAVFTVQRDVAERITAAPGDRRYGR 165
                                       *******999999...........369*****************99998..9************************* PP

                                       HHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHH CS
                            RrnaAD 157 lsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpgge 233
                                       +++l++a++++k+  + ++s+f P+p v+ +++ + r+++ + + d++ +e+++r++++++r+    +l+++l  +e
  gi|320100239|ref|YP_004175831.1| 166 ITILLNALFEIKVAGTYGSSSFYPEPGVEHSIIVMVRRAP-F-NRDVEALEALTRAVFTQRRRIALRVLERVLGVRE 240
                                       ****************************************.6.9******************988888887776655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.2e-08   9.3e-05      35     112 ..      57     128 ..      42     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.2e-08
                                       EEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTC CS
                               MTS  35 vlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagk 111
                                          +GcG+G l+++l ++ p+  + +v++d+r le+a en+ a ++   +v+ d++  ++      +v N P+h  +
  gi|320100239|ref|YP_004175831.1|  57 TFEIGCGIGTLTMSLSRFVPR--LICVEIDWRLLEAAVENIDAANV--VLVNADATVYTP--PSKQVVGNIPYHITS 127
                                       5679*****************..99****************99986..444444444444..456788898988776 PP

                                       H CS
                               MTS 112 a 112
                                       +
  gi|320100239|ref|YP_004175831.1| 128 E 128
                                       6 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   1.9e-07   0.00043       3      62 ..      59     114 ..      58     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                                       EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSST CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfed 62 
                                       ++GcG G+lt+ l++ +   ++++v+i+ ++leaa e++++  +nv +v++da+ +  ++
  gi|320100239|ref|YP_004175831.1|  59 EIGCGIGTLTMSLSRFV--PRLICVEIDWRLLEAAVENIDA--ANVVLVNADATVYTPPS 114
                                       89************998..7*******************54..59999999998766555 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 !   16.1   0.0     2e-06    0.0044     204     249 ..      56     101 ..      45     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-06
                   tRNA_U5-meth_tr 204 dllelycGnGnfslalarnfekvlateiakssveaaqyniaankid 249
                                       d +e+ cG G ++++l+r++ +++  ei    +eaa  ni+a ++ 
  gi|320100239|ref|YP_004175831.1|  56 DTFEIGCGIGTLTMSLSRFVPRLICVEIDWRLLEAAVENIDAANVV 101
                                       889*************************************998764 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.027       2      53 ..      59     108 ..      58     118 .. 0.90
   2 ?   -2.8   0.0       4.5     1e+04      81      94 ..     265     278 .]     262     278 .] 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadae 53 
                                       ++GcG G l+  l + + r+++v+++ ++l++a e++  ++  v +v ada+
  gi|320100239|ref|YP_004175831.1|  59 EIGCGIGTLTMSLSRFVPRLICVEIDWRLLEAAVENIDAAN--VVLVNADAT 108
                                       79************999********************9998..788999887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                                       HHHHHHHEEEEEEE CS
                   Methyltransf_11  81 lkeiaRvLkpgGll 94 
                                         e+aR L+  Gll
  gi|320100239|ref|YP_004175831.1| 265 YLELARALREAGLL 278
                                       56889999998875 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.4e-06     0.019       5      60 ..      57     107 ..      54     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.4e-06
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                       + eiGcG G++++ l+   P   ++ +Ei  +++++++++i+a    N+ +++ da
  gi|320100239|ref|YP_004175831.1|  57 TFEIGCGIGTLTMSLSRFVPR--LICVEIDWRLLEAAVENIDA---ANVVLVNADA 107
                                       57******************7..68899999999999998876...6788888887 PP

>> NodS  Nodulation protein S (NodS)
   #    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      43      98 ..      53     107 ..      42     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                              NodS  43 siadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdv 98 
                                       +  d++e+Gc  G+lt  l+ +  rl  v++  + ++ a e ++  +++  + +d 
  gi|320100239|ref|YP_004175831.1|  53 EYLDTFEIGCGIGTLTMSLSRFVPRLICVEIDWRLLEAAVENIDA-ANVVLVNADA 107
                                       556899************************998888888888776.6666666665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00016      0.35       7      41 ..     219     253 ..     213     254 .. 0.88
   2 ?    0.7   0.2      0.37   8.4e+02      34      49 ..     262     277 ..     256     278 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllg 41 
                                       a+  ++ + A+++le++l  + +sP++  A+ llg
  gi|320100239|ref|YP_004175831.1| 219 AVFTQRRRIALRVLERVLGVREDSPVHSYASRLLG 253
                                       666788999***********************998 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.37
                            TPR_16  34 aeAllllgdaalrqgr 49 
                                       +e +l+l++a+ ++g 
  gi|320100239|ref|YP_004175831.1| 262 WEVYLELARALREAGL 277
                                       7889999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2272.00
//
Query:       gi|320100240|ref|YP_004175832.1|  [L=211]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-61  205.5   0.2      7e-61  205.3   0.2    1.0  1  DUF655    Protein of unknown function (DUF655)
    0.00047   20.3   0.1     0.0011   19.2   0.1    1.5  1  HHH_6     Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.089   13.1   0.0       0.18   12.1   0.0    1.5  1  HHH_3     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.3   0.2   1.2e-64     7e-61       2     181 .]      18     191 ..      17     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 205.3 bits;  conditional E-value: 1.2e-64
                                       --EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS CS
                            DUF655   2 eeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedL 78 
                                       e   +vLDyl  G+p+d+h ehr++p  q++g+r++ Lle +pl+ + i++l++v++g  +  k+++i  ++sy +L
  gi|320100240|ref|YP_004175832.1|  18 EPALYVLDYLELGNPSDPHYEHRSQPFLQGVGTRYFSLLEATPLPAMKIEILEKVELGYPS--KVKRI-MHVSYGEL 91 
                                       56679***************************************************98765..55553.48****** PP

                                       -HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT-- CS
                            DUF655  79 tdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglk 155
                                       t+va+++Lp++v+ iv e+E +fveffn  ep++iRlHaLelLp++gkk++++il+eR ++rFesFed+++r +   
  gi|320100240|ref|YP_004175832.1|  92 TSVAKTNLPEAVKLIVLENEGVFVEFFNIVEPVNIRLHALELLPDIGKKTMNQILDERSKKRFESFEDIRNRTR--V 166
                                       *************************************************************************9..9 PP

                                       -HHHHHHHHHHHHHH-TTSS--SS-- CS
                            DUF655 156 dpaeilverileEiedktekYylFve 181
                                       dp++++v+r+++E+ +  ekYylFv+
  gi|320100240|ref|YP_004175832.1| 167 DPVKAIVNRVVKELAGG-EKYYLFVR 191
                                       ****************9.******95 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.8e-07    0.0011      28      66 ..     130     172 ..     115     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-07
                             HHH_6  28 GLaaikglgeaaaerivaeRekegpfksledlarrvds.....l 66 
                                       +L+ +  +g++++++i++eR+ ++ f+s+ed+ +r++      +
  gi|320100240|ref|YP_004175832.1| 130 ALELLPDIGKKTMNQILDERS-KKRFESFEDIRNRTRVdpvkaI 172
                                       7888899*************9.8************995444443 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.1e-05      0.18      13      54 ..     128     168 ..     119     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                             HHH_3  13 aeeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgp 54 
                                       +  L+ lp +g+k+ ++I++ R ++++f+s+e+  +  +++p
  gi|320100240|ref|YP_004175832.1| 128 LHALELLPDIGKKTMNQILDER-SKKRFESFEDIRNRTRVDP 168
                                       567999****************.666*******998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1797.26
//
Query:       gi|320100241|ref|YP_004175833.1|  [L=124]
Description: RNA polymerase Rpb4 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   51.9   1.3    1.7e-13   51.0   1.3    1.4  1  RNA_pol_Rpb4    RNA polymerase Rpb4
     0.0011   19.5   0.1     0.0017   18.8   0.1    1.3  1  ADSL_C          Adenylosuccinate lyase C-terminus
  ------ inclusion threshold ------
      0.013   15.4   0.5       0.41   10.6   0.0    2.5  3  Type2_restr_D3  Type-2 restriction enzyme D3 domain
      0.047   14.2   0.0       0.09   13.3   0.0    1.5  1  PRESAN          Plasmodium RESA N-terminal
      0.079   13.2   0.0       0.39   10.9   0.0    2.2  1  PMBR            Pseudomurein-binding repeat
        0.1   13.2   0.6       0.28   11.8   0.1    1.8  2  Pex14_N         Peroxisomal membrane anchor protein (Pex14p) 


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 !   51.0   1.3   5.8e-17   1.7e-13       2     123 .]      15     118 ..       7     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5.8e-17
                                       E-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTST CS
                      RNA_pol_Rpb4   2 LsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeLt 78 
                                       LsnsE++ +l++ +e++++                 +g ++  l ++leyl++ ++r   +ek+ el+ +l+s +L+
  gi|320100241|ref|YP_004175833.1|  15 LSNSEAYAILRSVVEKTRE----------------ETGTVSLLLSRVLEYLEK-NHRIP-PEKAGELRAFLESKGLK 73 
                                       899********77777733................47999************9.89998.***************** PP

                                       HHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHHHT CS
                      RNA_pol_Rpb4  79 kaEklqlvnlkPesavelktlieeleerfedeqleeiLdelkeve 123
                                       +  ++ l+n++P++++el+ l+e +e+  e+  leeiL++l++++
  gi|320100241|ref|YP_004175833.1|  74 EETIVILMNICPSTLDELRYLMELEEKLPEQGVLEEILSTLSKYC 118
                                       ***********************999999**************95 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   5.7e-07    0.0017       3      58 ..       1      68 [.       1      73 [. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.7e-07
                                      GGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC..........HHHHHHT-HHHH.CHHCHHHHHT- CS
                            ADSL_C  3 ifservllaLv.kglgReeAyelVqeaamkawee..........llelLaadpevk.kseeeldalfd 58
                                      + s +vl aL  k l+  eAy++ +    k++ee           le L+++ ++  +++ el+a ++
  gi|320100241|ref|YP_004175833.1|  1 MSSTTVLKALEeKQLSNSEAYAILRSVVEKTREEtgtvslllsrVLEYLEKNHRIPpEKAGELRAFLE 68
                                      5688999999988***************************9988789999*****9558889999876 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.042   1.3e+02      16      41 ..       4      27 ..       1      38 [. 0.73
   2 ?   10.6   0.0   0.00014      0.41      17      52 ..      44      81 ..      42      89 .. 0.77
   3 ?   -1.8   0.0         1   3.1e+03      31      45 ..      94     108 ..      78     116 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.042
                    Type2_restr_D3 16 tiilkylleskkrrsleeikayLkla 41
                                      t +lk+l+e++  +s  e  a L+++
  gi|320100241|ref|YP_004175833.1|  4 TTVLKALEEKQ--LSNSEAYAILRSV 27
                                      899****7777..8888877777665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                    Type2_restr_D3 17 iilkylleskkrrsle...eikayLklagleEdveTIkD 52
                                       +l+yl++++ r+ +e   e++a L+++gl+E+   I  
  gi|320100241|ref|YP_004175833.1| 44 RVLEYLEKNH-RIPPEkagELRAFLESKGLKEETIVILM 81
                                      699***8888.5444433389***********9877765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1
                    Type2_restr_D3  31 leeikayLklagleE 45 
                                       l e+ ++L  +g+ E
  gi|320100241|ref|YP_004175833.1|  94 LMELEEKLPEQGVLE 108
                                       445555555555444 PP

>> PRESAN  Plasmodium RESA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05      0.09      11      66 ..       7      63 ..       3     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                                      HT-S.-SEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHH CS
                            PRESAN 11 insl.neviskkdmyiiwnyvmknekkkyknmikkLsnyleelakkynipeeykkkl 66
                                      ++ l ++ +s+ ++y i+  v++  +++   +   Ls++le+l k+++ip e + +l
  gi|320100241|ref|YP_004175833.1|  7 LKALeEKQLSNSEAYAILRSVVEKTREETGTVSLLLSRVLEYLEKNHRIPPEKAGEL 63
                                      5666348899*****************************************998877 PP

>> PMBR  Pseudomurein-binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.39      14      28 ..      42      56 ..      41      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                              PMBR 14 asrvlafiesngrlP 28
                                      +srvl + e+n+r P
  gi|320100241|ref|YP_004175833.1| 42 LSRVLEYLEKNHRIP 56
                                      89************7 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 ?   -0.4   0.1      0.54   1.6e+03      29      53 ..      10      34 ..       7      58 .. 0.77
   2 ?   11.8   0.1   9.2e-05      0.28      26      44 ..      64      82 ..      50      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.54
                           Pex14_N 29 LesKGLtqeEIeeaLkraereeeas 53
                                      Le K L++ E  + L+ + ++++++
  gi|320100241|ref|YP_004175833.1| 10 LEEKQLSNSEAYAILRSVVEKTREE 34
                                      8889999999888888866555444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.2e-05
                           Pex14_N 26 vaFLesKGLtqeEIeeaLk 44
                                      +aFLesKGL++e I  +++
  gi|320100241|ref|YP_004175833.1| 64 RAFLESKGLKEETIVILMN 82
                                      59**********9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1049.63
//
Query:       gi|320100242|ref|YP_004175834.1|  [L=105]
Description: 50S ribosomal protein L21 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  129.1   4.3    5.5e-38  128.9   4.3    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 !  128.9   4.3   3.1e-42   5.5e-38       2      98 ..       3      96 ..       2      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 3.1e-42
                                      --S-STTTT-TTTTS--GGG-S.S--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEE CS
                    Ribosomal_L21e  2 knskglrrgtrklfskkfrkkg.vpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkk 79
                                      k++kg+r++trkl++k++r+kg vp+ls ++reyk+G+kV+i+i+psv++gmph+ryhG+tg v  v+kr+++++v++ 
  gi|320100242|ref|YP_004175834.1|  3 KAPKGYRHRTRKLLKKNIREKGsVPSLSLIMREYKEGEKVHIVINPSVHSGMPHRRYHGRTGIV--VGKRGKAYVVKVM 79
                                      789*******************9999**************************************..************* PP

                                      ETTE..EEEEEE-GGGEEE CS
                    Ribosomal_L21e 80 vggkileKriivriehlkk 98
                                      +g+k  eK+++vr+eh+++
  gi|320100242|ref|YP_004175834.1| 80 MGSK--EKTLFVRPEHIRP 96
                                      ****..***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 799.85
//
Query:       gi|320100243|ref|YP_004175835.1|  [L=444]
Description: THUMP domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-10   39.0   0.4    9.4e-08   32.3   0.1    2.3  2  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   5.2e-12   9.4e-08      13     136 ..      45     198 ..      33     205 .. 0.74
   2 !    4.8   0.0    0.0015        28      24      72 ..     305     352 ..     290     380 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 5.2e-12
                                       H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST..............TECEEEEE.EEEEESSH.HHHHHHHHH CS
                             THUMP  13 nverveagkgrivvelkgekpeedeellkealekar..............giqrvipv.cevceadl.edileaake 73 
                                       n+er++a+k  + ++l+    ++d ++  e +++++              + ++v p  c++c  +l ++ l+++  
  gi|320100243|ref|YP_004175835.1|  45 NEERGRAVKTLLAMKLHAD--FTDGKTSIEHIQRIAvnsgepvarlyrrlTGESVEPRvCHICLGRLsDEYLDKVAR 119
                                       5555555555555555533..44444444444444455555555555555556677778888877773567777777 PP

                                       HHHHHHHHCT-.EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEE CS
                             THUMP  74 ivkkkfeeeke.tFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdlenPdivvrveii 134
                                            + + ++ +F ++vk+  + +               e  ++e++revGk + + tgl  d+++Pd+vv++ ++
  gi|320100243|ref|YP_004175835.1| 120 EAASLLAGLQAsSFLIGVKLDAEVArrelevslitklassESVKNELKREVGKKVSQITGLQPDFDKPDVVVIINVD 196
                                       777788787779********8888899*************************************************9 PP

                                       TT CS
                             THUMP 135 kd 136
                                       +d
  gi|320100243|ref|YP_004175835.1| 197 RD 198
                                       98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0015
                                       EEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHH CS
                             THUMP  24 ivvelkgekpeedeellkealekargiqrvipvcevceadledileaak 72 
                                       i v+++g+    d e++ke   + + i rv++   +++ +++d++e+  
  gi|320100243|ref|YP_004175835.1| 305 IKVSVTGPASRRDIEAIKEGSRRRKKIYRVSVL-TGKPVTMKDLEELSG 352
                                       6678888999999********************.***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3245.28
//
Query:       gi|320100244|ref|YP_004175836.1|  [L=450]
Description: signal recognition particle subunit FFH/SRP54 (srp54) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-76  256.8   0.0    1.5e-76  256.4   0.0    1.2  1  SRP54       SRP54-type protein, GTPase domain
    3.7e-29  101.2   0.9    9.1e-29  100.0   0.3    1.9  1  SRP_SPB     Signal peptide binding domain
    6.2e-14   52.0   4.1    4.1e-13   49.4   0.0    3.4  3  SRP54_N     SRP54-type protein, helical bundle domain
      9e-06   25.8   0.0      3e-05   24.1   0.0    2.0  2  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00016   21.4   0.2    0.00046   20.0   0.0    1.8  2  AAA_30      AAA domain
    0.00019   21.7   0.0    0.00066   20.0   0.0    1.9  1  AAA_22      AAA domain
    0.00029   20.5   1.9     0.0094   15.6   1.9    2.3  1  cobW        CobW/HypB/UreG, nucleotide-binding domain
    0.00064   19.1   0.0     0.0012   18.2   0.0    1.5  1  Zeta_toxin  Zeta toxin
    0.00069   19.7   0.0     0.0023   18.0   0.0    1.9  1  MMR_HSR1    50S ribosome-binding GTPase
     0.0022   18.2   0.0     0.0051   17.0   0.0    1.7  1  AAA_33      AAA domain
      0.004   16.2   0.1      0.017   14.1   0.1    2.0  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.024   14.1   0.0    1.4  1  ParA        NUBPL iron-transfer P-loop NTPase
      0.014   15.3   0.1       0.03   14.2   0.1    1.6  1  MobB        Molybdopterin guanine dinucleotide synthesis prot
      0.014   15.8   3.0      0.023   15.1   0.6    2.6  2  AAA_17      AAA domain
      0.017   14.4   0.0      0.032   13.5   0.0    1.6  1  6PF2K       6-phosphofructo-2-kinase
      0.027   14.2   0.0      0.089   12.5   0.0    1.9  2  AAA_24      AAA domain
      0.027   14.2   0.3        3.9    7.2   0.1    2.4  2  PduV-EutP   Ethanolamine utilisation - propanediol utilisatio
      0.033   13.8   1.6       0.89    9.1   1.6    2.9  3  AAA_25      AAA domain
      0.054   13.4   0.1       0.16   11.9   0.0    1.8  1  AAA_31      AAA domain
       0.06   13.9   0.6       0.37   11.3   0.6    2.4  1  AAA_18      AAA domain
      0.076   12.4   0.2         11    5.4   0.0    2.4  2  SRPRB       Signal recognition particle receptor beta subunit
      0.097   12.6   0.0       0.23   11.3   0.0    1.7  1  APS_kinase  Adenylylsulphate kinase
        0.1   11.8   0.3        4.6    6.4   0.0    2.6  3  MipZ        ATPase MipZ
       0.17   11.7   0.0       0.47   10.2   0.0    1.7  1  ATP_bind_1  Conserved hypothetical ATP binding protein


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 !  256.4   0.0   2.1e-79   1.5e-76       2     196 .]      97     291 ..      96     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.4 bits;  conditional E-value: 2.1e-79
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                        vi+lvGlqG+GKTtt+aKLa  +k eg +v lvaaDtfR+aA+ QLk+l+e++gvpv+++  ++d++a+a ++ve 
  gi|320100244|ref|YP_004175836.1|  97 WVIMLVGLQGSGKTTTTAKLAYFYKLEGLRVGLVAADTFRPAAYMQLKQLGEQVGVPVYGEPGNSDAVAIAVKGVEF 173
                                       59*************************************************************************** PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                       ++e+k+dv+++DTaGr++ +++l+ee+kk+++ vkpdev+lv+da++gq+a++ a++F+ea+ i+++i+tklDg+ak
  gi|320100244|ref|YP_004175836.1| 174 FRERKMDVIIIDTAGRHHREEDLLEEMKKMSEHVKPDEVMLVIDAAIGQQAFNIARRFHEATPIGSIIVTKLDGTAK 250
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       gG+als++a+++  ikfig+Geki++le+f+p r+vsr+lg
  gi|320100244|ref|YP_004175836.1| 251 GGGALSAVAATGASIKFIGTGEKIDELEVFNPPRFVSRILG 291
                                       ***************************************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 !  100.0   0.3   1.2e-31   9.1e-29       3      97 ..     323     419 ..     321     420 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.2e-31
                                       CTHHHHHHHHHHHCCCCCCHHHHCCC........H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHH CS
                           SRP_SPB   3 tlrdlleqlqqikkmGplskllsmiPgmsae...akaeeeaekklkrieaiidSMTkeErdspekllkesRkrRiAr 76 
                                       ++r +++ql +++kmGpl k+++miPg++ +   + ++++ e+k++++ aii+SMT eE+d+p+ ++++sR++RiAr
  gi|320100244|ref|YP_004175836.1| 323 NMRLVYKQLVSLRKMGPLGKIMQMIPGLGVKipfEVDSKQLEEKMSKWLAIINSMTYEELDNPD-IIDRSRMKRIAR 398
                                       78999**********************998899844557789**********************.9999******** PP

                                       HTTS-HHHHHHHHHHHHHHHH CS
                           SRP_SPB  77 GsGtsvqevnellkqfeqmkk 97 
                                       G+G++v++v+ellkq+e +kk
  gi|320100244|ref|YP_004175836.1| 399 GAGVEVEDVKELLKQYELVKK 419
                                       *****************9887 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 !   49.4   0.0   5.4e-16   4.1e-13       3      75 .]       4      78 ..       2      78 .. 0.92
   2 ?   -1.3   0.1       3.5   2.6e+03      30      46 ..     313     329 ..     293     338 .. 0.59
   3 ?    2.0   0.3      0.33   2.5e+02      41      59 ..     414     431 ..     393     441 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 5.4e-16
                                      HHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  3 kklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      ++++sal+++ +++   e++++e+++el++ L+ aDV++k++++l++++k++a++ +    +++k+ ++ +v++eL
  gi|320100244|ref|YP_004175836.1|  4 DNIRSALARFLKGG-DYEKAVDEFIRELQKELVRADVNLKLAMELTSRIKERALKAEPppgISRKEWFITVVYEEL 78
                                      67999999888777.589*********************************9999555*****************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.5
                                       HHHHHHHTT--HHHHHH CS
                           SRP54_N  30 leeaLleaDVgvkvvkk 46 
                                         + L+e  V++++v k
  gi|320100244|ref|YP_004175836.1| 313 DARRLIEGKVNMRLVYK 329
                                       45667777788877754 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHHHHCTT CS
                           SRP54_N  41 vkvvkklienvkkkavgek 59 
                                       +++vkkl +++++k v  k
  gi|320100244|ref|YP_004175836.1| 414 YELVKKLSKQLRRKDVL-K 431
                                       78999999999998887.3 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 ?   -2.0   0.0       4.8   3.6e+03      81     105 ..      11      37 ..       4      60 .. 0.63
   2 !   24.1   0.0     4e-08     3e-05       9      55 ..     106     294 ..      99     435 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.8
                                       EEEESS...-TTCHHHHHHHHHHC..T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..x RF
                              CbiA  81 lnrvdgeneetllkealeelkqry..g 105
                                       +   +g ++e++  e+++el++++  +
  gi|320100244|ref|YP_004175836.1|  11 ARFLKGGDYEKAVDEFIRELQKELvrA 37 
                                       556677788888888888887766541 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 4e-08
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt++a+La   + +glrV lv aD+ ++++ +  +l++  e+                               
  gi|320100244|ref|YP_004175836.1| 106 GSGKTTTTAKLAYFYKLEGLRVGLVAADTFRPAAYM--QLKQLGEQvgvpvygepgnsdavaiavkgveffrerkmd 180
                                       99*******************************985..333333334578899999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|320100244|ref|YP_004175836.1| 181 viiidtagrhhreedlleemkkmsehvkpdevmlvidaaigqqafniarrfheatpigsiivtkldgtakgggalsa 257
                                       99999999999999999988888888888888888877777777777777777777777777777777777777777 PP

                                       ....................................C CS
                                       ....................................x RF
                              CbiA  55 ....................................d 55 
                                                                           d
  gi|320100244|ref|YP_004175836.1| 258 vaatgasikfigtgekidelevfnpprfvsrilglgD 294
                                       7777766666666666666666666666666665552 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.1e-07   0.00046      19     100 ..      97     190 ..      91     219 .. 0.70
   2 ?   -2.7   0.0       5.4     4e+03      61      87 ..     395     425 ..     391     433 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.1e-07
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkvLa.....eelgi.......eastiakllkrlkg 82 
                                       +v +l+G  G+GKtt+ ++l+  ++ +g rv  ++A t + A+ ++     e++g+       +++ +a  +k  + 
  gi|320100244|ref|YP_004175836.1|  97 WVIMLVGLQGSGKTTTTAKLAYFYKLEGLRVGlVAADTFRPAAYMQlkqlgEQVGVpvygepgNSDAVAIAVKGVE- 172
                                       6899************************999736667778777666555558888777777556666666664444. PP

                            AAA_30  83 rarlepgtllivDEagmv 100
                                         r ++ +++i+D ag  
  gi|320100244|ref|YP_004175836.1| 173 FFRERKMDVIIIDTAGRH 190
                                       233345599999999876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.4
                            AAA_30  61 vLaeelgieastiakllkrlk.....grarle 87 
                                       ++a+++g+e + +++llk+++     + ++l+
  gi|320100244|ref|YP_004175836.1| 395 RIARGAGVEVEDVKELLKQYElvkklS-KQLR 425
                                       566777777888888877776655531.3344 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   8.8e-07   0.00066       7     117 ..      98     205 ..      93     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.8e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseell..ea 81 
                                       +++++G  G+GKTt+ ++l++ ++     e  r+++v  +   +    + l++l +++g++  +e+++s+++    +
  gi|320100244|ref|YP_004175836.1|  98 VIMLVGLQGSGKTTTTAKLAYFYK----LEGLRVGLVAADTFRPAAYMQ-LKQLGEQVGVPVYGEPGNSDAVAiaVK 169
                                       689*******************94....445677777666666665555.599999999999996666655553467 PP

                            AAA_22  82 leqalraravielliiDEaqhlr.seealeeLrslln 117
                                         + +r+r++  ++iiD a +   +e++lee +++++
  gi|320100244|ref|YP_004175836.1| 170 GVEFFRERKM-DVIIIDTAGRHHrEEDLLEEMKKMSE 205
                                       7788999999.99999999886435999999988876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.9   1.3e-05    0.0094       2     155 ..      98     250 ..      97     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCH.CTT-HHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCct.lredllkelea 75 
                                       v++l+G  GsGKTt   +l    + +gl++ ++  +          l++ g+++     G    +     ++k +e 
  gi|320100244|ref|YP_004175836.1|  98 VIMLVGLQGSGKTTTTAKLAyfYKLEGLRVGLVAADTF-RPAAYMQLKQLGEQVGVPVYGEPGNSdAVAIAVKGVEF 173
                                       68899999999999999999998999999999999999.33334444444554333333333333244555566665 PP

                                       HHHHHTT-SEEEEEECTTTTHHHH.HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                              cobW  76 leereerldviliEttGlaePapv.afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                       + er+  +dvi+i t G  +  +  + + ++++++++ d v+ v+Da ++ ++  +i++ +++     + ++++K D
  gi|320100244|ref|YP_004175836.1| 174 FRERK--MDVIIIDTAGRHHREEDlLEEMKKMSEHVKPDEVMLVIDA-AIGQQAFNIARRFHEATPIGS-IIVTKLD 246
                                       55555..9*********6666655256699*****************.666788888888888777665.6678888 PP

                                       HHCH CS
                              cobW 152 llde 155
                                          +
  gi|320100244|ref|YP_004175836.1| 247 GTAK 250
                                       7655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-06    0.0012       6     100 ..      85     183 ..      82     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                        Zeta_toxin   6 kdkk.ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilk...a.dpkkaselt 76 
                                       ++k+ +++ ++P +i+l+G +G+GK+++ ++l+   + ++ +v  + +D++R+    y ++ +   +  +  + e  
  gi|320100244|ref|YP_004175836.1|  85 ERKPsVKPAKKPWVIMLVGLQGSGKTTTTAKLAYFYKlEGLRVGLVAADTFRPAA--YMQLKQlgeQvGVPVYGEPG 159
                                       566666778*********************9998888677888888999999865..44433322234566666666 PP

                        Zeta_toxin  77 qkdaselvekllqeaiengyniiv 100
                                       ++da  ++ k ++   e+++++i+
  gi|320100244|ref|YP_004175836.1| 160 NSDAVAIAVKGVEFFRERKMDVII 183
                                       666666666666666666666554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     3e-06    0.0023       2      93 ..      99     223 ..      98     244 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                                       EEEEESTTSSHHHHHHHHHT....STEEESSSTTSSSSE.EEEEEEETTEE.......................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg....ekaivsdkpgtTrdi.negrvklkgke.......................... 47 
                                       +++vG   +GK+t   +l      e  +v+  +  T  +  + ++k  g++                          
  gi|320100244|ref|YP_004175836.1|  99 IMLVGLQGSGKTTTTAKLAYfyklEGLRVGLVAADTFRPaAYMQLKQLGEQvgvpvygepgnsdavaiavkgveffr 175
                                       78999999999999999986443335688888888888844444553333356666666666677777777777777 PP

                                       .....EEEEECGGCSSHHHHHH.HHHHHHHHHHCTSEEEEEEETT..TTCSHHH CS
                          MMR_HSR1  48 .....ielvDtpGliegaseek.glgkaflaleeadlillvvdas..eeklkpl 93 
                                            ++++Dt+G  +  +e+  ++ k++ ++ + d ++lv+da+  +     +
  gi|320100244|ref|YP_004175836.1| 176 erkmdVIIIDTAG-RHHREEDLlEEMKKMSEHVKPDEVMLVIDAAigQ-----Q 223
                                       77777********.542333336788888889999********77432.....2 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.8e-06    0.0051       1      42 [.      98     144 ..      98     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.8e-06
                            AAA_33   1 lvllvGlpGsGKstlaerl.....lkklgavllssdtlrrrlfgtdq 42 
                                       +++lvGl+GsGK+t   +l     l+ l + l++ dt+r + + + +
  gi|320100244|ref|YP_004175836.1|  98 VIMLVGLQGSGKTTTTAKLayfykLEGLRVGLVAADTFRPAAYMQLK 144
                                       89****************96654433444888888888777766444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   2.3e-05     0.017      30      67 ..      97     134 ..      89     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                       EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                              MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                                        v+ l G+ G+Gk t++ +l+  ++ +G rv+++a D 
  gi|320100244|ref|YP_004175836.1|  97 WVIMLVGLQGSGKTTTTAKLAYFYKLEGLRVGLVAADT 134
                                       578899*****************************995 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 ?   14.1   0.0   3.2e-05     0.024       9      56 ..     101     148 ..      95     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                              ParA   9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveee 56 
                                       l g  G GK+t++++lA+  + +gl+vgl+ aD + p     l+  +e
  gi|320100244|ref|YP_004175836.1| 101 LVGLQGSGKTTTTAKLAYFYKLEGLRVGLVAADTFRPAAYMQLKQLGE 148
                                       5566799**************************998876655555554 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.1e-05      0.03       1      33 [.      98     130 ..      98     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgti 33 
                                       v+ +vg +gsGKTt   kl    k +glrvg++
  gi|320100244|ref|YP_004175836.1|  98 VIMLVGLQGSGKTTTTAKLAYFYKLEGLRVGLV 130
                                       6899***************************98 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.6   3.1e-05     0.023       1     108 [.     102     215 ..     102     230 .. 0.69
   2 ?   -1.9   0.1       5.7   4.2e+03      92     127 ..     363     400 ..     357     412 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC.......TSHHHH.HHHHHHHHHHHH..HH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr.......klplee.kkelqkeaaeki..ae 67 
                                       +G+ GsGK+t  +kl+  y+++ l  G +  ++ ++    ++ +++            e+ + +  ++a + +   +
  gi|320100244|ref|YP_004175836.1| 102 VGLQGSGKTTTTAKLAYFYKLEGLRVGLVAADTFRPAAY-MQLKQLGeqvgvpvY--GEPgNSDAVAIAVKGVefFR 175
                                       79*****************99999999888888777754.233333312223321..22212233333333333334 PP

                                       HHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                            AAA_17  68 eakkkgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                       e+k + +++d+  r  +++++l++++k + e +kpd + l+
  gi|320100244|ref|YP_004175836.1| 176 ERKMDVIIIDTAGRHHREEDLLEEMKK-MSEHVKPDEVMLV 215
                                       4577889*****************996.99*****887764 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.7
                                       SHHHHHHHH...SEEEEEE--HHHHHHH.HHHHTTST- CS
                            AAA_17  92 lpkevleelkp.daiilleadpeeiler.rlkdrtrgr 127
                                       l++++ + l + + +++ e d+ +i++r r+k+  rg 
  gi|320100244|ref|YP_004175836.1| 363 LEEKMSKWLAIiNSMTYEELDNPDIIDRsRMKRIARGA 400
                                       55556565655577788787777777776777755554 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.3e-05     0.032      10      44 ..      93     127 ..      85     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                                       ..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                             6PF2K  10 knsklvivlvGLpargKtyiskkltrylkwlgvrt 44 
                                        +++ vi+lvGL   gKt+++ kl  + k  g+r 
  gi|320100244|ref|YP_004175836.1|  93 AKKPWVIMLVGLQGSGKTTTTAKLAYFYKLEGLRV 127
                                       56789********************9999888876 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   0.00012     0.089       2      90 ..      96     205 ..      95     213 .. 0.68
   2 ?   -3.3   0.0       8.3   6.2e+03      20      61 ..     380     419 ..     376     425 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                            AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtek.Glksldadkfpdieswedfldevvel.................. 59 
                                       ++ i+++G +g+GKTt+ ++l   + f  +e+  +  + ad f  + ++ ++++  +++                  
  gi|320100244|ref|YP_004175836.1|  96 PWVIMLVGLQGSGKTTTTAKL---AYFYKLEGlRVGLVAADTFR-PAAYMQLKQLGEQVgvpvygepgnsdavaiav 168
                                       689******************...88888888444444444443.33454444444444777777777777777777 PP

                            AAA_24  60 ....aaeladyktlviDtid..eleelclaevirqne 90 
                                              +++ ++++iDt++  + ee  l+e+++++e
  gi|320100244|ref|YP_004175836.1| 169 kgveFFRERKMDVIIIDTAGrhHREEDLLEEMKKMSE 205
                                       7777556677899999999722446667777777666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.3
                            AAA_24  20 kelgpkplfidtekGlksldadkfpdieswedfldevvelaa 61 
                                        el ++p +id  + +k++    ++++e ++++l++++ +++
  gi|320100244|ref|YP_004175836.1| 380 EEL-DNPDIIDRSR-MKRIARGAGVEVEDVKELLKQYELVKK 419
                                       556.7777777777.888888888888888888888877654 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0052       3.9       4      21 ..      99     116 ..      97     124 .. 0.91
   2 ?    4.5   0.0     0.036        27      40     102 ..     183     248 ..     175     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0052
                         PduV-EutP   4 illiGkvgsGKttLtqal 21 
                                       i+l+G  gsGKtt t +l
  gi|320100244|ref|YP_004175836.1|  99 IMLVGLQGSGKTTTTAKL 116
                                       9************99887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.036
                         PduV-EutP  40 viDtPGeylenrklysalivts..aeadvialvqdateeesvfppgfasvfnkeviG..iitkidla 102
                                       +iDt G +  ++ l + ++ +s  ++ d ++lv da   ++ f  + +   +   iG  i+tk+d +
  gi|320100244|ref|YP_004175836.1| 183 IIDTAGRHHREEDLLEEMKKMSehVKPDEVMLVIDAAIGQQAFNIARRF-HEATPIGsiIVTKLDGT 248
                                       79****************99993345699******99999998644332.23333555577888865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.6    0.0012      0.89      34      58 ..      97     121 ..      85     219 .. 0.77
   2 ?    0.9   0.0      0.38   2.8e+02      58      87 ..     167     194 ..     159     237 .. 0.55
   3 ?   -0.6   0.0       1.1   8.4e+02      68     111 ..     345     393 ..     333     419 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                            AAA_25  34 elallaGapgtGKttlaldlalava 58 
                                       ++++l+G +g+GKtt +  la+ + 
  gi|320100244|ref|YP_004175836.1|  97 WVIMLVGLQGSGKTTTTAKLAYFYK 121
                                       689******************9876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.38
                            AAA_25  58 a.tGkpwlgpvapeqgkVlyvsaEdsedelr 87 
                                       a +G +++     +++ V+++++ ++ ++ +
  gi|320100244|ref|YP_004175836.1| 167 AvKGVEFFR---ERKMDVIIIDTAGRHHREE 194
                                       455555544...3555666665555533222 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.1
                            AAA_25  68 apeqgkVlyvsaEdsedelrrRlravgeal.....rddarllvldlagv 111
                                       ++ +g  + + +E + ++l+++++++++ +     ++ ++ +++d+ ++
  gi|320100244|ref|YP_004175836.1| 345 QMIPGLGVKIPFEVDSKQLEEKMSKWLAIInsmtyEELDNPDIIDRSRM 393
                                       556666777889999999******9997666666666777777776554 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.16      12      40 ..     106     134 ..      98     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                       G GKTTt+ +la++   +g +v lv +D+
  gi|320100244|ref|YP_004175836.1| 106 GSGKTTTTAKLAYFYKLEGLRVGLVAADT 134
                                       89***********************9997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6    0.0005      0.37       1      19 [.      99     117 ..      99     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0005
                            AAA_18   1 IlltGtpGvGKttlakeLs 19 
                                       I+l G +G+GKtt +  L+
  gi|320100244|ref|YP_004175836.1|  99 IMLVGLQGSGKTTTTAKLA 117
                                       89*************9994 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 ?    5.4   0.0     0.015        11       5      23 ..      98     116 ..      94     123 .. 0.84
   2 ?    4.5   0.0     0.028        21      45      91 ..     175     224 ..     161     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                                       EEEEE-STTSSHHHHHHHH CS
                             SRPRB   5 avllvGlsdsGKTslftrL 23 
                                        ++lvGl+ sGKT+   +L
  gi|320100244|ref|YP_004175836.1|  98 VIMLVGLQGSGKTTTTAKL 116
                                       5789*********988777 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.028
                                       ..GGTT-SEEEETT-GCCSHHHHHHHHHHGG.EE..EEEEEEETTS-HHH CS
                             SRPRB  45 sekgskltliDfPGheklrqklleklkakss.lk..glvfvvDStidpke 91 
                                        e++  + +iD  G ++   +lle++k+ s+ +k   ++ v+D++i ++ 
  gi|320100244|ref|YP_004175836.1| 175 RERKMDVIIIDTAGRHHREEDLLEEMKKMSEhVKpdEVMLVIDAAIGQQA 224
                                       57888999****************99887776875579*******98875 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.23       2      45 ..      96     139 ..      95     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTT CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgL 45 
                                       + v++l Gl gsGK+t + +l+   + +g +v l+  d+ R   
  gi|320100244|ref|YP_004175836.1|  96 PWVIMLVGLQGSGKTTTTAKLAYFYKLEGLRVGLVAADTFRPAA 139
                                       789*******************9999999999999999988655 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.095        71      11      39 ..     106     134 ..      98     145 .. 0.88
   2 ?    6.4   0.0    0.0062       4.6      97     115 ..     176     194 ..     155     209 .. 0.82
   3 ?   -2.8   0.0         4     3e+03     169     206 ..     363     401 ..     359     406 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.095
                                       TSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ  11 GsGksttavhvavaLlkkGarvaaidldl 39 
                                       GsGk+tt+  +a     +G+rv+ +  d+
  gi|320100244|ref|YP_004175836.1| 106 GSGKTTTTAKLAYFYKLEGLRVGLVAADT 134
                                       9**********************998886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0062
                                       HHH-SEEEEE--SS--HHH CS
                              MipZ  97 eaeldfividtPGsdsals 115
                                       e+++d+i+idt G++++  
  gi|320100244|ref|YP_004175836.1| 176 ERKMDVIIIDTAGRHHREE 194
                                       789************9865 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4
                                       T-SS--EEEEEEESB-S--HHHHHHHHH.HHHHHHHHHT CS
                              MipZ 169 aerkevdWvvlrnrlsalearnkkkvee.aleeLskrvG 206
                                        e+k+  W+ + n +++ e  n   +++ +++ +++  G
  gi|320100244|ref|YP_004175836.1| 363 LEEKMSKWLAIINSMTYEELDNPDIIDRsRMKRIARGAG 401
                                       477888999999999999999988887524666666555 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 ?   10.2   0.0   0.00062      0.47       2      33 ..     102     133 ..     101     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00062
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                       vG  GsGKtt + +l+ +++l+g +v +v  D
  gi|320100244|ref|YP_004175836.1| 102 VGLQGSGKTTTTAKLAYFYKLEGLRVGLVAAD 133
                                       899********************999999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 2801.25
//
Query:       gi|320100245|ref|YP_004175837.1|  [L=174]
Description: 50S ribosomal protein L10 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  128.9   0.1    1.3e-37  128.7   0.1    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.1   7.3e-42   1.3e-37       3     132 .]      14     163 ..      12     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 7.3e-42
                                       SSXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSX CS
                     Ribosomal_L16   3 rkkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirv 67 
                                        ++y++++  yi gv+ +k+tk+e+gd        ++Lv++e+gq++++aleaar+++ ++l+ + g+    l+++v
  gi|320100245|ref|YP_004175837.1|  14 GPPYTRKE--YIPGVPqPKITKFEMGDpkldydyeVALVVEEAGQIRHNALEAARVMALKKLSVEAGEnnfYLKVKV 88 
                                       579****9..***********************9999**************************888888999***** PP

                                       XXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE..TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                     Ribosomal_L16  68 fphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei..kagvneeiakealrraasKlpiktkiv 132
                                       +phh+++++     ag+dR+++G+    Gkp g++arv++gq i+ i  ka  + ++akealr aasKlp++ +iv
  gi|320100245|ref|YP_004175837.1|  89 YPHHVIRENkmmafAGADRLQDGMrlsfGKPIGTAARVYPGQEIIVIrvKA-QHGKTAKEALRIAASKLPLPSRIV 163
                                       ***********************************************7533.4999*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1277.18
//
Query:       gi|320100246|ref|YP_004175838.1|  [L=333]
Description: diphthamide biosynthesis protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-60  203.2   0.0    7.1e-60  203.0   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.0   0.0     4e-64   7.1e-60       2     294 ..      31     324 ..      30     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 203.0 bits;  conditional E-value: 4e-64
                   Diphthamide_syn   2 PegllpdsaeiadileefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd...rlpvlYvfve.iel 74 
                                       P+gl+p  + ia  le+ g+e   ++ + YGaC++   +ae++gadllvH+Gh ++ +      ++vlY++v  +++
  gi|320100246|ref|YP_004175838.1|  31 PDGLKPLYNCIAPVLEQAGVEAAFSASPGYGACDIPFEEAEAIGADLLVHIGHLEYFQYGfkpAVKVLYIPVYrRPY 107
                                       *********************************************************977889*******7662455 PP

                   Diphthamide_syn  75 dvehlvetlkknf..kekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeev 149
                                         + l+++l +++      k+++ st+  ++  + v+++l ++g++ ++v+          vlgc ++++++ +++v
  gi|320100246|ref|YP_004175838.1| 108 IEQGLLRELVETLreAGVVKVSVSSTLVEEKIRRVVANHLASNGFKPIEVG--------FPVLGCLYTHVTSLDTSV 176
                                       56777888888885333677********9999999******9999888333........46**************** PP

                   Diphthamide_syn 150 dailyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakd.akkvGiivgtlgvqgrle 225
                                       da+l +++g fh+l+l+l  +k pv+ +dpy++++ +   +a+++l++R  ++ +a++  ++vG+ivg+  +q+r++
  gi|320100246|ref|YP_004175838.1| 177 DAHLMVAGGVFHPLGLALVSKK-PVVVLDPYRGRVWRAGDEASRVLKQRLMRVFEARNsGNRVGVIVGSRPGQYRPW 252
                                       ********************77.**********************************95677*************** PP

                   Diphthamide_syn 226 lverlkkllkeagkksylvlvgelnpakLanfae...idafVlvaCprlsiddgkeFekPvltpyElevalg 294
                                       lve+++++++ +g+++y ++ g l+ ++L  +++   +d++V+++Cprl+idd +eF+kPvltp E++++l+
  gi|320100246|ref|YP_004175838.1| 253 LVEKIEEEAAGRGYRVYRIISGYLTLERLIAVDNalgLDVYVVTSCPRLPIDDLSEFYKPVLTPGEFMMLLK 324
                                       ******************************9965778**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2519.25
//
Query:       gi|320100247|ref|YP_004175839.1|  [L=214]
Description: methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-06   25.3   0.5    1.3e-05   24.7   0.5    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00012   21.7   0.1    0.00025   20.6   0.1    1.5  1  MTS              Methyltransferase small domain
     0.0015   19.2   0.0     0.0028   18.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.017   14.9   0.7      0.029   14.2   0.7    1.3  1  Methyltransf_31  Methyltransferase domain
      0.025   13.8   0.0       0.04   13.2   0.0    1.3  1  DUF43            Branched-chain polyamine synthase A C-termin
      0.036   13.7   0.0        0.2   11.3   0.0    2.0  2  DUF5440          Family of unknown function (DUF5440)
       0.12   12.0   0.0       0.24   11.0   0.0    1.6  1  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.5   5.1e-09   1.3e-05     161     194 ..      50      83 ..      35      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.1e-09
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDe 194
                                       eg ++ D+G+G G ++iaa++Lga+++v +D+De
  gi|320100247|ref|YP_004175839.1|  50 EGLTIADLGCGDGRISIAALLLGASRAVCIDVDE 83 
                                       456899***************************8 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   9.7e-08   0.00025      34     108 ..      53     129 ..      35     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.7e-08
                                       EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STT.TTSTTS-EEEEEE---S CS
                               MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvl.eeveekkfdlivsNPPf 107
                                       +++DlGcG G +++a++    + + +++dvd   l      +     e  +++++ ++  + +   ++d++++NPPf
  gi|320100247|ref|YP_004175839.1|  53 TIADLGCGDGRISIAALLLGAS-RAVCIDVDEDILLHGAWKIYPLFPEaaGRLIHVNADvARLGLVRVDTVLMNPPF 128
                                       69************99988777.6889999998887665555444333345555555541334458*********** PP

                                       T CS
                               MTS 108 h 108
                                        
  gi|320100247|ref|YP_004175839.1| 129 G 129
                                       5 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.1e-06    0.0028       1      40 [.      54      92 ..      54     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHH CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarer 40
                                      + dlGcG Gr+++a++   g+++ +++D++e+ l + + +
  gi|320100247|ref|YP_004175839.1| 54 IADLGCGDGRISIAALLL-GASRAVCIDVDEDILLHGAWK 92
                                      78************9977.79**********998766544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   1.1e-05     0.029       3      40 ..      50      85 ..      48      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                   Methyltransf_31  3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseea 40
                                      +gl++ DlGCG G++++++  +lg  ++ v iD +e+ 
  gi|320100247|ref|YP_004175839.1| 50 EGLTIADLGCGDGRISIAAL-LLG-ASRAVCIDVDEDI 85
                                      5789**************99.665.5888999999875 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 ?   13.2   0.0   1.5e-05      0.04      24      80 ..      29      86 ..      10      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                      -B-HHHHHHHHHH.HHHTT-STT-EEEEES.-TT-HHHHHHHHT--SEEEEE-S-HHHH CS
                             DUF43 24 fvtpettvaRval.lyerGDLegkeilvlG.dDDLtslalaLtglpkkvvvvDiDeRli 80
                                      + tp + va +a  +y rGD+eg  i  lG  D  +s+a+ L g   + v +D+De ++
  gi|320100247|ref|YP_004175839.1| 29 YQTPVSLVAHMAWtAYMRGDVEGLTIADLGcGDGRISIAALLLGA-SRAVCIDVDEDIL 86
                                      66777777777652699*************88999****999986.567789***9875 PP

>> DUF5440  Family of unknown function (DUF5440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.29   7.5e+02      33      56 ..       3      26 ..       1      45 [. 0.76
   2 ?   11.3   0.0   7.8e-05       0.2      29      72 ..     165     208 ..     162     214 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.29
                           DUF5440 33 vktdkayelapatiegWdiPekre 56
                                      vk++k+ ela + ie +   +kr+
  gi|320100247|ref|YP_004175839.1|  3 VKSKKELELALSRIEPYRGSKKRL 26
                                      899999999999999877666655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.8e-05
                           DUF5440  29 vlrdvktdkayelapatiegWdiPekredsrsiivtlkpdvval 72 
                                        lr+v   k +ela+  i +++iP   e+ r  i  +k   v+l
  gi|320100247|ref|YP_004175839.1| 165 LLREVSESKGFELASYEIRDFEIPMMFETHRRRIYRFKTVFVVL 208
                                       59***********************9999998888888776666 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.3e-05      0.24      38     132 ..      47     136 ..      32     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.3e-05
                                       CCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EE CS
                     Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeef 114
                                        ++eg ++ Dl +G G +++ Al  ga++av+++ d+  +     ++  l  e+ +  l++ +  ++ +l     ++
  gi|320100247|ref|YP_004175839.1|  47 GDVEGLTIADLGCGDGRISIAALLLGASRAVCIDVDEDILLHGAWKIYPLFPEA-AGRLIHVN-ADVARL--GLVRV 119
                                       458888999***************************999877666666665443.33333333.333344..23458 PP

                                       EEEEE--SSSTTCH.HHH CS
                     Cons_hypoth95 115 divflDPPyakellieev 132
                                       d v ++PP+  ++  ++ 
  gi|320100247|ref|YP_004175839.1| 120 DTVLMNPPFGVVEG-NRG 136
                                       99999999987765.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1738.04
//
Query:       gi|320100248|ref|YP_004175840.1|  [L=183]
Description: RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   21.2   0.0    0.00099   18.9   0.0    2.3  2  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
     0.0008   19.7   0.5      0.003   17.9   0.2    2.1  1  S1              S1 RNA binding domain
     0.0033   17.3   0.3      0.006   16.5   0.3    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.004   17.7   0.1      0.059   14.0   0.1    2.2  1  EXOSC1          Exosome component EXOSC1/CSL4
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.041   14.0   0.1    1.5  1  DUF2318         Predicted membrane protein (DUF2318)
       0.06   13.2   0.8        0.1   12.5   0.8    1.3  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.16   11.9   0.7       0.29   11.1   0.7    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding 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 !   18.9   0.0   3.9e-07   0.00099       1      33 [.       6      39 ..       6      42 .. 0.91
   2 ?   -2.4   0.0       1.7   4.4e+03      28      36 ..     162     170 ..     155     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.9e-07
                                      EE-TT-EEEETTTSEE-TTEEE.ETTEEEESSSE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYv.rggtiyAsvaG 33
                                      +V+PGe+l+ +ee ++ +G Y   +g i++ v G
  gi|320100248|ref|YP_004175840.1|  6 VVVPGEPLAVEEEAIPVQGAYLdSRGFIRSLVFG 39
                                      69*******************7688999**9999 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                       EESSSEEEE CS
                            ECR1_N  28 yAsvaGtve 36 
                                       + s++G +e
  gi|320100248|ref|YP_004175840.1| 162 VCSLCGNRE 170
                                       668999876 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.2e-06     0.003       3      62 ..      62     126 ..      60     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                                       TTTCEEEEEEEEEETTEEEEEET......TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEE CS
                                S1   3 ekgevveGeVtsvtkgGafVelg......ngvegfvpaselsrdarvedpdevlkvGdevkvkvlk 62 
                                       + g vve+ V  v+++ af ++         ++g +++s+ s+   v++  +v+++Gd vk+kvl+
  gi|320100248|ref|YP_004175840.1|  62 KPGSVVEAYVEAVSDDIAFLRIYsvegqgMSASGVLHVSQASNG-FVQSLLDVVRPGDYVKAKVLN 126
                                       6799*****************97642222346899********9.*******************85 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   2.3e-06     0.006       4      28 ..     144     168 ..     142     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-06
                       Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgt 28 
                                       +  C+vCg  l    D+ vC  Cg 
  gi|320100248|ref|YP_004175840.1| 144 EAYCSVCGGLLYRSGDVLVCSLCGN 168
                                       568********************96 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   2.3e-05     0.059       4      53 ..      63     114 ..      58     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                                       TT-EEEEEEEEEESSEEEEEEEEECTB.SBCCCEEECCCTTSS--STS.TTS CS
                            EXOSC1   4 egdvVLarvtrlrkkqalveilsvege.nnvlsdsgvgangegavkei.eag 53 
                                        g+vV a v  ++  +a++ i sveg+     + ++v++ ++g v+++ +++
  gi|320100248|ref|YP_004175840.1|  63 PGSVVEAYVEAVSDDIAFLRIYSVEGQgMSASGVLHVSQASNGFVQSLlDVV 114
                                       589************************55667899********999986665 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.6e-05     0.041      29      61 ..     139     170 ..     119     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                           DUF2318  29 klrvaldaCevCekkgYvqegeelvCknCgvrf 61 
                                        l v+   C+vC++  Y  +g+ lvC  Cg+r 
  gi|320100248|ref|YP_004175840.1| 139 DLGVVEAYCSVCGGLLYR-SGDVLVCSLCGNRE 170
                                       45677889*****99985.799********985 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   3.9e-05       0.1       3      28 ..     146     167 ..     145     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                       BESTTTSBEEEEECSCCCEEEESSSS CS
                    RNA_POL_M_15KD   3 FCpkCgNlLlpkedkegknfeCrqCg 28 
                                        C+ Cg lL+  +d+++    C+ Cg
  gi|320100248|ref|YP_004175840.1| 146 YCSVCGGLLYRSGDVLV----CSLCG 167
                                       5****************....****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 ?   11.1   0.7   0.00011      0.29      30      58 ..     146     172 ..     145     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadr 58 
                                        Cs+Cg  +++  sg++++C+ Cg +  r
  gi|320100248|ref|YP_004175840.1| 146 YCSVCGGLLYR--SGDVLVCSLCGNREKR 172
                                       5**********..***********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1414.64
//
Query:       gi|320100249|ref|YP_004175841.1|  [L=202]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-45  153.7   0.0    4.4e-45  153.5   0.0    1.0  1  DUF2067   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.5   0.0   2.5e-49   4.4e-45       6     185 ..      14     193 ..       8     194 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 2.5e-49
                           DUF2067   6 eeeleeflekisekiksaeevkievegnrllievyGtekeikdiirrikellreklkkekrglfkyslsdllreaga 82 
                                       +ee+++++e ++ +i+s e+v+++v+g+ l++e+yG+e+++k++++++++++r     ++rgl ++ ++ +++ +g+
  gi|320100249|ref|YP_004175841.1|  14 GEECLKLYEYVKDRIPSLEHVEFKVSGSGLVVEAYGYETDVKRLWSELRSYVRALRHVSTRGLNSFRIDYIVKLTGK 90 
                                       69****************************************************99999****************** PP

                           DUF2067  83 pvppdvLvdaLkllGykaelreenvlktnapleevvelaerlseiykelrfknlskaakrvvavvsvltgldpdevi 159
                                       ++ppdvLv++L+++G+++e   e+v+ t+a ++ev+ l+er+se+ + ++  ++++aa+++++ +s+ltgl+p+e++
  gi|320100249|ref|YP_004175841.1|  91 TFPPDVLVEVLSRQGHRVEAG-EGVIYTSAGVDEVLGLVERISELNSVAKNIAKGTAARYFIVSASLLTGLPPQEIV 166
                                       *********************.******************************************************* PP

                           DUF2067 160 eellekGlLe.eeegkivlrkewkkal 185
                                       e+++   l+e +e+g ++l++ew++al
  gi|320100249|ref|YP_004175841.1| 167 ERAVGLQLMEpDESGAYLLKHEWRRAL 193
                                       ************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1505.27
//
Query:       gi|320100250|ref|YP_004175842.1|  [L=93]
Description: RNA polymerase dimerization [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   66.5   0.0    1.6e-18   66.2   0.0    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.031   13.7   0.0    1.4  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   1.8e-22   1.6e-18       2      73 ..      13      84 ..      12      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.8e-22
                                      EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdele 73
                                      l +e++gEDhTLgnlL ++++++p+Ve+  Y++pHPl++ ++++i  k +++   +Lk+ ++ l+++++e++
  gi|320100250|ref|YP_004175842.1| 13 LVVEVHGEDHTLGNLLAKEAIRHPGVEYSMYRVPHPLKNMFEFTIIVKPGYSVDSVLKEIVEGLKKTLSEFR 84
                                      6789**************************************************************999985 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 ?   13.7   0.0   3.4e-06     0.031       3      67 ..      16      78 ..      14      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-06
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  3 llrgvdhtlgNaLRrillsevpgvaiea.....pvvkvntdkdklilevetdgslkPeealkeAlkiLke 67
                                      ++ g+dhtlgN L +  +   pgv+        p       k+++ +++  +  ++++++lke ++ Lk+
  gi|320100250|ref|YP_004175842.1| 16 EVHGEDHTLGNLLAKEAI-RHPGVEYSMyrvphPL------KNMFEFTIIVKPGYSVDSVLKEIVEGLKK 78
                                      578***************.99***99999886655......89999999988888999999887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 691.91
//
Query:       gi|320100251|ref|YP_004175843.1|  [L=109]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 848.81
//
Query:       gi|320100252|ref|YP_004175844.1|  [L=114]
Description: DNA-directed RNA polymerase subunit M [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-21   74.7  13.8    1.3e-20   72.9   4.7    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
    4.9e-07   29.6   8.8     0.0015   18.5   1.5    2.5  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    2.2e-06   27.5   6.3      0.017   15.0   0.1    2.8  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    2.8e-06   27.1   3.7    8.8e-05   22.3   0.2    3.0  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    9.4e-05   22.3  10.0      0.085   12.8   0.8    4.1  4  zinc_ribbon_4    zinc-ribbon domain
     0.0001   21.9  13.1          2    8.2   0.1    4.2  4  zinc_ribbon_2    zinc-ribbon domain
    0.00046   20.1   6.7     0.0027   17.7   1.7    2.9  2  DZR              Double zinc ribbon
     0.0005   20.2   4.3       0.15   12.2   0.1    2.4  2  DUF2387          Probable metal-binding protein (DUF2387)
    0.00058   19.2  12.4       0.12   11.8   0.2    4.1  4  zf-ribbon_3      zinc-ribbon domain
    0.00062   19.6  10.8      0.012   15.6   2.1    3.4  3  Nudix_N_2        Nudix N-terminal
    0.00072   19.5   1.8         32    4.6   0.0    4.2  4  YhfH             YhfH-like protein
     0.0025   18.0   7.3       0.11   12.8   0.2    3.0  3  IBR              IBR domain, a half RING-finger domain
     0.0033   17.3   1.2        1.6    8.5   0.1    2.7  3  zf-ZPR1          ZPR1 zinc-finger domain
     0.0085   15.4   9.8      0.039   13.3   1.8    3.1  3  zf-TFIIB         Transcription factor zinc-finger
  ------ inclusion threshold ------
      0.012   15.7  14.7        7.5    6.8   0.3    4.3  3  Zn-ribbon_8      Zinc ribbon domain
      0.018   14.8  10.8      0.023   14.5   0.8    2.8  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.02   14.4  14.7       0.61    9.7   2.4    4.1  3  TF_Zn_Ribbon     TFIIB zinc-binding
      0.024   14.3   6.2      0.033   13.9   0.5    3.0  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.055   13.8   8.3       0.52   10.7   0.5    2.8  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.057   13.8   9.9       0.62   10.5   0.2    4.1  4  zf-IS66          zinc-finger binding domain of transposase IS
      0.058   13.0  10.3         16    5.2   0.2    4.6  5  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.11   13.3   8.0       0.21   12.4   2.4    3.1  2  zinc_ribbon_15   zinc-ribbon family
       0.13   12.5   3.8        3.2    8.0   0.1    2.9  3  Rdx              Rdx family
       0.13   12.3   7.1        1.3    9.1   2.3    2.9  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.15   11.9   6.5       0.14   12.0   0.6    2.1  2  FdhE             Protein involved in formate dehydrogenase fo
       0.22   11.2  11.0         15    5.4   3.6    3.6  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.24   11.9   1.6         39    4.8   0.1    3.2  3  zf-C2HE          C2HE / C2H2 / C2HC zinc-binding finger
       0.27   11.1   2.1          3    7.8   0.1    2.3  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
       0.57   10.7   8.8        3.2    8.3   2.3    3.4  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.68    9.9   6.4         23    5.1   0.9    3.6  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
        0.8    9.8   9.6        5.2    7.2   0.2    3.6  4  Zn_Tnp_IS91      Transposase zinc-binding domain
        0.9    9.8  13.4        3.6    7.8   0.1    4.0  4  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.95    9.8   7.3         16    5.8   1.9    3.7  3  Ribosomal_L32p   Ribosomal L32p protein family
        1.6    8.9  16.1        4.3    7.5   0.2    4.4  5  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        2.4    7.9   0.0        2.4    7.9   0.0    3.5  4  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
        2.4    8.0  12.2         23    4.9   0.1    4.1  4  zf-HYPF          HypF finger
        2.6    8.0  10.6          2    8.4   0.5    3.4  4  HalOD2           Halobacterial output domain 2
          4    7.9  10.6        1.6    9.2   0.8    3.6  4  DUF4379          Probable Zinc-ribbon domain
        4.2    7.2  11.2         21    5.0   0.1    4.0  4  A2L_zn_ribbon    A2L zinc ribbon domain
        5.3    6.7  13.5         18    5.1   0.5    4.0  4  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
        5.7    6.6  11.3        6.3    6.4   0.2    3.6  4  zf_C2H2_10       C2H2 type zinc-finger
          7    6.1  13.0       0.13   11.6   3.2    2.6  2  zf_Rg            Reverse gyrase zinc finger
        8.5    6.4  12.0         45    4.1   0.1    3.8  3  Ogr_Delta        Ogr/Delta-like zinc finger
        8.7    6.4  11.6         26    4.9   0.1    3.7  3  ADK_lid          Adenylate kinase, active site lid
        9.5    5.8  11.7         38    3.8   0.1    4.0  4  Mu-like_Com      Mu-like prophage protein Com


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.26     1e+02       3       8 ..       5      10 ..       3      11 .. 0.85
   2 ?    4.3   0.1     0.093        37      29      37 ..      23      31 ..      21      33 .. 0.83
   3 !   72.9   4.7   3.4e-23   1.3e-20       2      39 .]      74     111 ..      73     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.26
                           TFIIS_C  3 CpkCgs 8 
                                      CpkCg+
  gi|320100252|ref|YP_004175844.1|  5 CPKCGG 10
                                      ****95 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.093
                           TFIIS_C 29 ykCtkCghr 37
                                       +Ct Cg+r
  gi|320100252|ref|YP_004175844.1| 23 LVCTRCGYR 31
                                      689999997 PP

  == domain 3  score: 72.9 bits;  conditional E-value: 3.4e-23
                           TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                       +CpkCg +eay+++lQtR+aDEp+t+f+kCt Cgh+Wr
  gi|320100252|ref|YP_004175844.1|  74 TCPKCGWHEAYYWMLQTRAADEPPTRFFKCTRCGHTWR 111
                                       8************************************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 !   15.1   0.9   4.2e-05     0.017      20      45 ..       4      30 ..       2      36 .. 0.94
   2 !   18.5   1.5   3.8e-06    0.0015      19      46 .]      73     109 ..      65     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-05
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayriktrglfqCkeCrk 45
                                       CP+Cg+  ++ ri +  ++ C +C++
  gi|320100252|ref|YP_004175844.1|  4 LCPKCGGLmRPQRIDGKPYLVCTRCGY 30
                                      5************************98 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.8e-06
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayrikt.......rglfqCkeCrkq 46 
                                       ++CP+Cg     ++ ++t        + f+C +C+++
  gi|320100252|ref|YP_004175844.1|  73 VTCPKCGWHeaYYWMLQTraadeppTRFFKCTRCGHT 109
                                       78*****9974455566699*****9********996 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   4.3e-05     0.017      28      62 ..       2      38 ..       1      43 [. 0.84
   2 ?    6.5   0.2      0.02         8      42      55 ..      68      81 ..      60      84 .. 0.76
   3 !   12.6   2.6   0.00024     0.096      30      56 ..      74     110 ..      72     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-05
                    OrfB_Zn_ribbon 28 SktCseCgsknke..alsgrtfkCpnCgfeadrDvnA 62
                                      S  C++Cg  +++   + +  ++C++Cg+++ +   +
  gi|320100252|ref|YP_004175844.1|  2 SRLCPKCGGLMRPqrIDGKPYLVCTRCGYRLEAEASG 38
                                      889*********9855666779********9998766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.02
                    OrfB_Zn_ribbon 42 lsgrtfkCpnCgfe 55
                                      + +r+++Cp+Cg +
  gi|320100252|ref|YP_004175844.1| 68 PVTREVTCPKCGWH 81
                                      56899999999976 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00024
                    OrfB_Zn_ribbon  30 tCseCgsknke..........alsgrtfkCpnCgfea 56 
                                       tC++Cg    +          ++ +r fkC++Cg+++
  gi|320100252|ref|YP_004175844.1|  74 TCPKCGWHEAYywmlqtraadEPPTRFFKCTRCGHTW 110
                                       8*****999999****99999999**********997 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   2.2e-07   8.8e-05       4      35 ..       5      36 ..       3      37 .. 0.94
   2 ?    3.0   0.1      0.24        95       4       8 ..      75      79 ..      68      83 .. 0.75
   3 ?    1.4   0.0      0.73   2.9e+02      20      28 ..      98     107 ..      87     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.2e-07
                                      ESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                      CpkCg l+ p++ + + ++ C  CgY  +a++
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMRPQRIDGKPYLVCTRCGYRLEAEA 36
                                      ****************99*********99986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.24
                                      ESTTT CS
                    RNA_POL_M_15KD  4 CpkCg 8 
                                      CpkCg
  gi|320100252|ref|YP_004175844.1| 75 CPKCG 79
                                      77776 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.73
                                       CE.EEESSSS CS
                    RNA_POL_M_15KD  20 kn.feCrqCg 28 
                                       ++ f C  Cg
  gi|320100252|ref|YP_004175844.1|  98 TRfFKCTRCG 107
                                       4579999997 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.32   1.3e+02      28      32 ..       5       9 ..       2      13 .. 0.76
   2 ?    2.1   0.0      0.48   1.9e+02      28      33 ..      25      30 ..      22      35 .. 0.77
   3 !    8.5   0.1    0.0047       1.9      23      32 ..      70      79 ..      63      80 .. 0.82
   4 !   12.8   0.8   0.00021     0.085      26      36 .]     101     111 ..      95     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.32
                     zinc_ribbon_4 28 CskCg 32
                                      C+kCg
  gi|320100252|ref|YP_004175844.1|  5 CPKCG 9 
                                      77777 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.48
                     zinc_ribbon_4 28 CskCgh 33
                                      C++Cg 
  gi|320100252|ref|YP_004175844.1| 25 CTRCGY 30
                                      888875 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0047
                     zinc_ribbon_4 23 gvkvrCskCg 32
                                      +++v+C+kCg
  gi|320100252|ref|YP_004175844.1| 70 TREVTCPKCG 79
                                      5789999997 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00021
                     zinc_ribbon_4  26 vrCskCghvFr 36 
                                        +C++Cgh++r
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGHTWR 111
                                       69********7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6     0.016       6.6      15      20 ..       4       9 ..       2      10 .. 0.72
   2 !    7.6   0.0    0.0079       3.2       2      12 ..      25      35 ..      24      37 .. 0.75
   3 !    8.2   0.1    0.0051         2      13      20 ..      72      79 ..      66      80 .. 0.78
   4 ?    5.5   1.0     0.036        14       1       7 [.     102     108 ..     100     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.016
                     zinc_ribbon_2 15 FCpyCG 20
                                       Cp+CG
  gi|320100252|ref|YP_004175844.1|  4 LCPKCG 9 
                                      688887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0079
                     zinc_ribbon_2  2 CpnCGaelqdn 12
                                      C++CG+ l+ +
  gi|320100252|ref|YP_004175844.1| 25 CTRCGYRLEAE 35
                                      99999888765 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0051
                     zinc_ribbon_2 13 akFCpyCG 20
                                      ++ Cp+CG
  gi|320100252|ref|YP_004175844.1| 72 EVTCPKCG 79
                                      67788887 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.036
                     zinc_ribbon_2   1 fCpnCGa 7  
                                       +C++CG+
  gi|320100252|ref|YP_004175844.1| 102 KCTRCGH 108
                                       6888886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.7   6.7e-06    0.0027       1      35 [.       5      79 ..       1      86 [. 0.91
   2 ?    3.0   0.2      0.26     1e+02      14      22 ..     102     110 ..      92     114 .] 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.7e-06
                               DZR  1 CpqCgeelppdar......fCseCgtklkavaa..................................edrCpsCg 35
                                      Cp+Cg  ++p+ +      +C +Cg +l+a+a+                                  e +Cp+Cg
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMRPQRIdgkpylVCTRCGYRLEAEASgvrefkvstriehrpdektlvlkseneanlpvtrEVTCPKCG 79
                                      99999998877777777789********98887*****************************************8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.26
                               DZR  14 fCseCgtkl 22 
                                        C +Cg++ 
  gi|320100252|ref|YP_004175844.1| 102 KCTRCGHTW 110
                                       577777665 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00037      0.15      11      60 ..       5      51 ..       3      65 .. 0.76
   2 !    8.5   1.3    0.0054       2.1       9      39 ..      73     109 ..      72     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00037
                           DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsekgqsvakelktrvnkd 60
                                      CP+C     +r  + d+++y  C+ Cg+  e +++g     +++tr+ ++
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGL--MRPQRIDGKPYLVCTRCGYRLEAEASGV-REFKVSTRIEHR 51
                                      9999875..677789*************877777743.345566776655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0054
                           DUF2387   9 avCPrCsemD......kirmweedeveyrECvsCgft 39 
                                       + CP+C          ++r+ +e ++++  C+ Cg+t
  gi|320100252|ref|YP_004175844.1|  73 VTCPKCGWHEayywmlQTRAADEPPTRFFKCTRCGHT 109
                                       57****9888778877788888888999********8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.2    0.0068       2.7      18      24 ..       4      10 ..       2      12 .. 0.76
   2 ?    4.7   0.1     0.054        22      18      26 .]      24      32 ..      23      32 .. 0.90
   3 !   11.8   0.2   0.00031      0.12       2      11 ..      72      81 ..      71      83 .. 0.85
   4 ?    1.7   0.2      0.48   1.9e+02      19      24 ..     103     108 ..     100     109 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0068
                       zf-ribbon_3 18 vCpyCGt 24
                                       Cp+CG+
  gi|320100252|ref|YP_004175844.1|  4 LCPKCGG 10
                                      7999996 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.054
                       zf-ribbon_3 18 vCpyCGtkl 26
                                      vC+ CG++l
  gi|320100252|ref|YP_004175844.1| 24 VCTRCGYRL 32
                                      7******97 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00031
                       zf-ribbon_3  2 tvrCPnCGap 11
                                      +v+CP+CG++
  gi|320100252|ref|YP_004175844.1| 72 EVTCPKCGWH 81
                                      799*****96 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.48
                       zf-ribbon_3  19 CpyCGt 24 
                                       C+ CG+
  gi|320100252|ref|YP_004175844.1| 103 CTRCGH 108
                                       555654 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.1   2.9e-05     0.012       3      30 ..       5      30 ..       3      30 .. 0.87
   2 ?    4.1   0.3      0.11        43      24      30 ..      74      80 ..      70      82 .. 0.81
   3 ?    4.4   0.1      0.09        36      25      30 ..     103     108 ..      88     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-05
                                      -TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgt 30
                                      C++CG+ ++ +    D ++ lvC++Cg+
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMRPQR--IDGKPYLVCTRCGY 30
                                      *******99665..499*********97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                                      EETTTTE CS
                         Nudix_N_2 24 vCpaCgt 30
                                      +Cp+Cg+
  gi|320100252|ref|YP_004175844.1| 74 TCPKCGW 80
                                      5888887 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.09
                                       ETTTTE CS
                         Nudix_N_2  25 CpaCgt 30 
                                       C++Cg+
  gi|320100252|ref|YP_004175844.1| 103 CTRCGH 108
                                       666665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.17        66      16      24 ..       5      13 ..       2      16 .. 0.79
   2 ?    4.3   0.0       0.1        40      15      24 ..      24      33 ..      21      37 .. 0.79
   3 ?    3.4   0.1      0.19        74      15      20 ..      74      79 ..      66      84 .. 0.87
   4 ?    4.6   0.0      0.08        32      15      25 ..     102     112 ..      99     114 .] 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                              YhfH 16 CteCGkeie 24
                                      C++CG  + 
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMR 13
                                      *****8775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                              YhfH 15 kCteCGkeie 24
                                      +Ct CG  +e
  gi|320100252|ref|YP_004175844.1| 24 VCTRCGYRLE 33
                                      7*****8876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.19
                              YhfH 15 kCteCG 20
                                      +C++CG
  gi|320100252|ref|YP_004175844.1| 74 TCPKCG 79
                                      7****9 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.08
                              YhfH  15 kCteCGkeieE 25 
                                       kCt CG    E
  gi|320100252|ref|YP_004175844.1| 102 KCTRCGHTWRE 112
                                       7*****87665 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   0.00027      0.11      19      47 ..       3      31 ..       1      32 [. 0.85
   2 ?    5.6   0.1     0.046        19      38      45 ..      66      79 ..      45      85 .. 0.66
   3 ?    3.9   3.0      0.15        61      19      46 ..      73     108 ..      60     113 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00027
                               IBR 19 kwCprpdCeaiiekseg..cksvtCskCgfe 47
                                      + Cp  +C+++++++    + ++ C++Cg++
  gi|320100252|ref|YP_004175844.1|  3 RLCP--KCGGLMRPQRIdgKPYLVCTRCGYR 31
                                      67*9..******999996667799****996 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.046
                               IBR 38 s......vtCskCg 45
                                      +      vtC+kCg
  gi|320100252|ref|YP_004175844.1| 66 NlpvtreVTCPKCG 79
                                      24444559999998 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.15
                               IBR  19 kwCprpdCe.....aii...eksegcks......vtCskCgf 46 
                                       + Cp  +C+     +++   +      +       +C++Cg+
  gi|320100252|ref|YP_004175844.1|  73 VTCP--KCGwheayYWMlqtRAA----DepptrfFKCTRCGH 108
                                       5566..66643221222322111....123334466777776 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       4.2   1.7e+03       2      37 ..       4       9 ..       1      17 [. 0.63
   2 ?    6.9   0.0     0.013       5.1      32      75 ..      24      63 ..      21      70 .. 0.81
   3 !    8.5   0.1    0.0041       1.6       2      42 ..      74     112 ..      73     114 .] 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.2
                           zf-ZPR1  2 lCpsCgkengetrllltkiPyfkeviimsfeCehCg 37
                                      lCp+C                              g
  gi|320100252|ref|YP_004175844.1|  4 LCPKC------------------------------G 9 
                                      35555..............................4 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                           zf-ZPR1 32 eCehCgyknnevksageieekGkritlkveseedlnrqvlkSet 75
                                      +C +Cgy+ +    a+ ++e   +++ ++e++ d ++ vlkSe 
  gi|320100252|ref|YP_004175844.1| 24 VCTRCGYRLEAE--ASGVRE--FKVSTRIEHRPDEKTLVLKSEN 63
                                      7******97644..444555..78999**************985 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0041
                           zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknne 42 
                                       +Cp+Cg++++   +l+t+     e     f+C +Cg++ +e
  gi|320100252|ref|YP_004175844.1|  74 TCPKCGWHEAYYWMLQTR--AADEPPTRFFKCTRCGHTWRE 112
                                       7*****996666666665..578889999*******98766 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.8   9.7e-05     0.039       2      26 ..       5      29 ..       4      29 .. 0.97
   2 ?    3.4   0.2      0.12        50       2       6 ..      75      79 ..      74      84 .. 0.79
   3 ?    3.0   0.1      0.16        66       1       8 [.     102     109 ..      88     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.7e-05
                          zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                      CPkC+  +++++ +g +  +C++C+
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMRPQRIDGKPYLVCTRCG 29
                                      ************************7 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                          zf-TFIIB  2 CPkCq 6 
                                      CPkC+
  gi|320100252|ref|YP_004175844.1| 75 CPKCG 79
                                      88886 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.16
                          zf-TFIIB   1 kCPkCqde 8  
                                       kC +C+++
  gi|320100252|ref|YP_004175844.1| 102 KCTRCGHT 109
                                       56666654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.024       9.7      29      35 ..       5      11 ..       1      17 [. 0.74
   2 ?    3.7   4.7      0.17        69      25      33 ..      66      79 ..      20      83 .. 0.59
   3 ?    6.8   0.3     0.019       7.5       6      14 ..     101     109 ..      97     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.024
                       Zn-ribbon_8 29 CPeCgse 35
                                      CP+Cg+ 
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGL 11
                                      *****94 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.17
                       Zn-ribbon_8 25 p.....ltaCPeCg 33
                                      +     +++CP+Cg
  gi|320100252|ref|YP_004175844.1| 66 NlpvtrEVTCPKCG 79
                                      14444366699998 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.019
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       ++C++Cgh+
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGHT 109
                                       89*****97 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   5.7e-05     0.023       2      33 ..       3      31 ..       2      37 .. 0.85
   2 ?    6.8   0.5     0.015       5.8       2       8 ..      73      79 ..      72      82 .. 0.83
   3 ?   -1.8   0.1       7.1   2.8e+03       3       8 ..     102     107 ..     101     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-05
                                      EE-SSS--EEEEEE-SSSEEEEESST.T---- CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlkrgkkGkFvGCsnYPeCkft 33
                                      + CPkCgg +  +r   + ++ C++   C + 
  gi|320100252|ref|YP_004175844.1|  3 RLCPKCGGLMRPQRIDGKPYLVCTR---CGYR 31
                                      68************99999999998...7665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.015
                                      EE-SSS- CS
                    zf-C4_Topoisom  2 ekCPkCg 8 
                                      ++CPkCg
  gi|320100252|ref|YP_004175844.1| 73 VTCPKCG 79
                                      79****9 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 7.1
                                       E-SSS- CS
                    zf-C4_Topoisom   3 kCPkCg 8  
                                       kC  Cg
  gi|320100252|ref|YP_004175844.1| 102 KCTRCG 107
                                       799998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.4    0.0015      0.61       3      30 ..       5      33 ..       3      36 .. 0.73
   2 ?    4.9   0.8     0.047        19      19      26 ..      72      79 ..      68      81 .. 0.78
   3 ?    4.0   4.6     0.086        34       2      27 ..      74     108 ..      73     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                                      ETTTTC.EE.CHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  3 CPnCgs.tn.lveDpergelvCtdCGlVle 30
                                      CP+Cg+  + +  D     lvCt+CG+ le
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGlMRpQRID-GKPYLVCTRCGYRLE 33
                                      99999952225555.66778******9887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.047
                                      CEEESSSS CS
                      TF_Zn_Ribbon 19 elvCtdCG 26
                                      e++C++CG
  gi|320100252|ref|YP_004175844.1| 72 EVTCPKCG 79
                                      77888887 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.086
                                       EETTTTCEE.C........HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstn.l........veDpergelvCtdCGl 27 
                                       +CP+Cg  + +          +p +  + Ct+CG 
  gi|320100252|ref|YP_004175844.1|  74 TCPKCGWHEaYywmlqtraADEPPTRFFKCTRCGH 108
                                       79999998866899998855558888899999996 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2       1.1   4.2e+02      47      52 ..       5      10 ..       3      12 .. 0.78
   2 ?    0.9   0.0      0.94   3.8e+02      23      29 ..      23      29 ..      13      32 .. 0.77
   3 ?   13.9   0.5   8.3e-05     0.033       9      53 ..      59     109 ..      56     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.1
                    zinc_ribbon_10 47 CpkCga 52
                                      CpkCg 
  gi|320100252|ref|YP_004175844.1|  5 CPKCGG 10
                                      999985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.94
                    zinc_ribbon_10 23 lICskCh 29
                                      l+C+ C 
  gi|320100252|ref|YP_004175844.1| 23 LVCTRCG 29
                                      6777774 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 8.3e-05
                    zinc_ribbon_10   9 LvGddetsaknryalICskChshnGlap......keeleevkyrCpkCgal 53 
                                       L +++e+       + C+kC +h  ++        +e+ +  ++C  Cg++
  gi|320100252|ref|YP_004175844.1|  59 LKSENEANLPVTREVTCPKCGWHEAYYWmlqtraADEPPTRFFKCTRCGHT 109
                                       5566676677777899*********998887764445555589******85 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 ?   10.7   0.5    0.0013      0.52       6      37 ..       5      37 ..       2      60 .. 0.71
   2 ?    6.6   1.8     0.025        10       5      36 ..      74     108 ..      58     114 .] 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCga......s 37
                                      CP Cgg    +r  +++     +  C+ Cg+      s
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMRPQRIDGKP-----YLVCTRCGYrleaeaS 37
                                      ******66666655555.....9*******96555440 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.025
                   Lar_restr_allev   5 pCPfCggravlersqrvvaeigq...cvyCadCga 36 
                                        CP Cg  + +  + +++a  ++   ++ C+ Cg 
  gi|320100252|ref|YP_004175844.1|  74 TCPKCGWHEAYYWMLQTRAADEPptrFFKCTRCGH 108
                                       59999966665555555544455679999999997 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 ?   10.5   0.2    0.0015      0.62       2      14 ..       3      15 ..       2      18 .. 0.82
   2 ?    2.3   0.1      0.58   2.3e+02       3      15 ..      24      35 ..      23      52 .. 0.65
   3 ?    3.5   0.2      0.24        96       3       8 ..      74      79 ..      72      83 .. 0.78
   4 ?    1.3   0.1       1.1   4.6e+02       4       9 ..     103     108 ..     101     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0015
                           zf-IS66  2 rtCpcCGgllkpi 14
                                      r Cp+CGgl++p 
  gi|320100252|ref|YP_004175844.1|  3 RLCPKCGGLMRPQ 15
                                      67*******9875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.58
                           zf-IS66  3 tCpcCGg.llkpig 15
                                      +C  CG  l  +++
  gi|320100252|ref|YP_004175844.1| 24 VCTRCGYrL--EAE 35
                                      699999844..333 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.24
                           zf-IS66  3 tCpcCG 8 
                                      tCp+CG
  gi|320100252|ref|YP_004175844.1| 74 TCPKCG 79
                                      688887 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1.1
                           zf-IS66   4 CpcCGg 9  
                                       C  CG+
  gi|320100252|ref|YP_004175844.1| 103 CTRCGH 108
                                       888887 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.15        61       4       9 ..       4       9 ..       2      15 .. 0.84
   2 ?    4.1   0.0     0.088        35       4      13 ..      24      33 ..      22      37 .. 0.78
   3 ?   -2.4   0.0       9.8   3.9e+03      11      20 ..      41      50 ..      40      51 .. 0.78
   4 ?    4.5   0.1     0.068        27       3       9 ..      73      79 ..      71      83 .. 0.88
   5 ?    5.2   0.2      0.04        16       3      11 ..     101     109 ..      99     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.15
                            zf_UBZ 4 lCerCg 9
                                     lC++Cg
  gi|320100252|ref|YP_004175844.1| 4 LCPKCG 9
                                     7****9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.088
                            zf_UBZ  4 lCerCgkeip 13
                                      +C rCg +++
  gi|320100252|ref|YP_004175844.1| 24 VCTRCGYRLE 33
                                      8****97765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.8
                            zf_UBZ 11 eipeselqEH 20
                                      e+ +s + EH
  gi|320100252|ref|YP_004175844.1| 41 EFKVSTRIEH 50
                                      5778889999 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.068
                            zf_UBZ  3 ylCerCg 9 
                                      ++C++Cg
  gi|320100252|ref|YP_004175844.1| 73 VTCPKCG 79
                                      79****8 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.04
                            zf_UBZ   3 ylCerCgke 11 
                                       + C rCg++
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGHT 109
                                       89*****85 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4       3.4   1.4e+03      81      86 .]       4       9 ..       2       9 .. 0.72
   2 ?   12.4   2.4   0.00052      0.21      33      72 ..      19      79 ..      12     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.4
                    zinc_ribbon_15 81 yCpkCg 86
                                       CpkCg
  gi|320100252|ref|YP_004175844.1|  4 LCPKCG 9 
                                      688887 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00052
                    zinc_ribbon_15 33 kkkpylacskCkslleaskelgkeiekkesse......................kkeCknCg 72
                                        kpyl+c++C+++lea+ +  +e++ ++++e                      + +C++Cg
  gi|320100252|ref|YP_004175844.1| 19 G-KPYLVCTRCGYRLEAEASGVREFKVSTRIEhrpdektlvlkseneanlpvtrEVTCPKCG 79
                                      4.9****************9999999888888999999**9999999999999877888886 PP

>> Rdx  Rdx family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.069        28       7      17 ..      25      35 ..      23      60 .. 0.92
   2 ?    8.0   0.1    0.0081       3.2       7      21 ..      75      89 ..      72      98 .. 0.91
   3 ?   -1.9   0.4       9.6   3.8e+03       7      12 ..     103     108 ..      99     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.069
                                      ETTTTTHHHHH CS
                               Rdx  7 CtqCkwmlraa 17
                                      Ct+C+++l a+
  gi|320100252|ref|YP_004175844.1| 25 CTRCGYRLEAE 35
                                      ********986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0081
                                      ETTTTTHHHHHHHHH CS
                               Rdx  7 CtqCkwmlraaelaq 21
                                      C +C+w++ + ++ q
  gi|320100252|ref|YP_004175844.1| 75 CPKCGWHEAYYWMLQ 89
                                      9***********998 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 9.6
                                       ETTTTT CS
                               Rdx   7 CtqCkw 12 
                                       Ct+C+ 
  gi|320100252|ref|YP_004175844.1| 103 CTRCGH 108
                                       ****96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.3    0.0031       1.3      70      96 ..      22      82 ..       1      90 [. 0.80
   2 ?    3.1   0.2      0.24        96      71      81 ..     101     111 ..      92     114 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0031
                                      EEEETTTS-EEECHHHHH..................................S-TTTSSS- CS
                              HypA 70 kvrCreCgkefeleekal..................................rCpkCgsad 96
                                       + C++Cg++ e e++ +                                  +CpkCg ++
  gi|320100252|ref|YP_004175844.1| 22 YLVCTRCGYRLEAEASGVrefkvstriehrpdektlvlkseneanlpvtrevTCPKCGWHE 82
                                      5679999999996653113458889999999999999999999999999999999998765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.24
                                       EEETTTS-EEE CS
                              HypA  71 vrCreCgkefe 81 
                                       ++C++Cg++++
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGHTWR 111
                                       68999999987 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 ?    3.2   0.8      0.17        67     169     202 ..       3      30 ..       1      36 [. 0.75
   2 ?   12.0   0.6   0.00034      0.14     165     205 ..      69     111 ..      55     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.17
                                       SS-TTT---EEEEEEE-------EEEEEETTT-- CS
                              FdhE 169 glCPvCgsaPvasvvriggeaeglRylhCslCet 202
                                       +lCP Cg+      +r +   +g  yl C+ C  
  gi|320100252|ref|YP_004175844.1|   3 RLCPKCGGL-----MRPQR-IDGKPYLVCTRCGY 30 
                                       689999975.....44444.67888*****9976 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00034
                                       -TT-SS-TTT---EE.EEEEE----.---EEEEEETTT--EEE CS
                              FdhE 165 aeekglCPvCgsaPv.asvvrigge.aeglRylhCslCeteWh 205
                                        +++ +CP Cg +     +++++++ +  +R+ +C+ C + W+
  gi|320100252|ref|YP_004175844.1|  69 VTREVTCPKCGWHEAyYWMLQTRAAdEPPTRFFKCTRCGHTWR 111
                                       345789*****8765155666655415579************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 ?    5.4   3.6     0.037        15       3      27 ..       8      32 ..       4      32 .. 0.72
   2 ?    3.9   0.0       0.1        42      12      25 ..      67      80 ..      62      84 .. 0.76
   3 ?    4.6   0.2     0.064        26      19      25 ..     102     108 ..      97     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.037
                                      -SSS--B----SSS----SSS---- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGhRi 27
                                      Cg+   + +++ +  + C+ CG+R+
  gi|320100252|ref|YP_004175844.1|  8 CGGLMRPQRIDGKPYLVCTRCGYRL 32
                                      44444566788888899******95 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                                      --SSS----SSS-- CS
                    DNA_RNApol_7kD 12 lkkgdpiRCkeCGh 25
                                      l  +  + C +CG 
  gi|320100252|ref|YP_004175844.1| 67 LPVTREVTCPKCGW 80
                                      55566799****95 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.064
                                       --SSS-- CS
                    DNA_RNApol_7kD  19 RCkeCGh 25 
                                       +C+ CGh
  gi|320100252|ref|YP_004175844.1| 102 KCTRCGH 108
                                       7999998 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.27   1.1e+02      38      44 ..      23      29 ..      18      34 .. 0.85
   2 ?    1.3   0.0       1.2     5e+02      24      44 ..      59      79 ..      38      83 .. 0.71
   3 ?    4.8   0.1     0.099        39      38      45 ..     101     108 ..      87     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.27
                           zf-C2HE 38 LkCtrCg 44
                                      L CtrCg
  gi|320100252|ref|YP_004175844.1| 23 LVCTRCG 29
                                      89****9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.2
                           zf-C2HE 24 lseeqskelilktpLkCtrCg 44
                                      l++e++ +l   ++ +C +Cg
  gi|320100252|ref|YP_004175844.1| 59 LKSENEANLPVTREVTCPKCG 79
                                      455666667778888999998 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.099
                           zf-C2HE  38 LkCtrCga 45 
                                       +kCtrCg+
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGH 108
                                       8*****95 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 ?    2.8   0.2      0.26     1e+02      89     116 ..       4      30 ..       4      31 .. 0.78
   2 ?    7.8   0.1    0.0074         3      88     116 ..      73     108 ..      68     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.26
                                       STSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  89 lCkeCkspetelekeerllvlkCkaCga 116
                                       lC++C+       ++++ + l C+ Cg 
  gi|320100252|ref|YP_004175844.1|   4 LCPKCGGLMRPQRIDGKPY-LVCTRCGY 30 
                                       5888888877777788888.89999996 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0074
                                       TSTSSSTSTCEEECC.......SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCkspetelek.......eerllvlkCkaCga 116
                                       V+C++C+ +e            e  + ++kC+ Cg+
  gi|320100252|ref|YP_004175844.1|  73 VTCPKCGWHEAYYWMlqtraadEPPTRFFKCTRCGH 108
                                       99****99987655444566656788899*****97 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 ?    8.3   2.3    0.0081       3.2       8      32 ..       5      28 ..       4      51 .. 0.85
   2 ?    0.3   0.0       2.7   1.1e+03       7      12 ..      74      79 ..      70      94 .. 0.81
   3 ?    3.8   0.1      0.21        84       6      15 ..     101     110 ..      98     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0081
                   Zn_ribbon_recom  8 CgeCGspmtrrkrkgkrhyYrCsty 32
                                      C +CG+ m+ ++   +++y +C ++
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMRPQRI-DGKPYLVCTRC 28
                                      **********987.67899999875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.7
                   Zn_ribbon_recom  7 rCgeCG 12
                                       C +CG
  gi|320100252|ref|YP_004175844.1| 74 TCPKCG 79
                                      688888 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.21
                   Zn_ribbon_recom   6 lrCgeCGspm 15 
                                        +C +CG++ 
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGHTW 110
                                       69*****986 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2       0.2        78      22      26 ..       5       9 ..       3      10 .. 0.69
   2 ?    2.0   0.0       0.5     2e+02      18      27 ..      21      30 ..      18      31 .. 0.82
   3 ?    5.1   0.9     0.057        23       5      29 ..      75     110 ..      67     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.2
                    PhnA_Zn_Ribbon 22 CpeCa 26
                                      Cp+C+
  gi|320100252|ref|YP_004175844.1|  5 CPKCG 9 
                                      77776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.5
                    PhnA_Zn_Ribbon 18 allvCpeCah 27
                                        lvC  C++
  gi|320100252|ref|YP_004175844.1| 21 PYLVCTRCGY 30
                                      569*****96 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.057
                    PhnA_Zn_Ribbon   5 CplCaSeytY...........edgallvCpeCahEw 29 
                                       Cp+C+  ++Y             +  + C  C+h w
  gi|320100252|ref|YP_004175844.1|  75 CPKCGWHEAYywmlqtraadePPTRFFKCTRCGHTW 110
                                       999988888888888888776667778888888877 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 ?    4.9   0.5     0.068        27      57      73 ..       2      18 ..       1      32 [. 0.76
   2 ?    0.2   0.0       1.9   7.6e+02      60      70 ..      25      35 ..      19      51 .. 0.65
   3 ?    7.2   0.2     0.013       5.2      57      75 ..      72      90 ..      66     100 .. 0.82
   4 ?    1.4   0.2      0.84   3.4e+02      40      48 ..     101     109 ..      94     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.068
                       Zn_Tnp_IS91 57 srhCpsCqkkateewle 73
                                      sr Cp+C+   + + ++
  gi|320100252|ref|YP_004175844.1|  2 SRLCPKCGGLMRPQRID 18
                                      799****9988777665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.9
                       Zn_Tnp_IS91 60 CpsCqkkatee 70
                                      C++C+ + ++e
  gi|320100252|ref|YP_004175844.1| 25 CTRCGYRLEAE 35
                                      77777665555 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.013
                       Zn_Tnp_IS91 57 srhCpsCqkkateewlekq 75
                                      +  Cp+C+ +++  w+ ++
  gi|320100252|ref|YP_004175844.1| 72 EVTCPKCGWHEAYYWMLQT 90
                                      557*********9999554 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.84
                       Zn_Tnp_IS91  40 yeCeeCghe 48 
                                       ++C+ Cgh+
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGHT 109
                                       578888876 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 ?    1.2   0.3       1.1   4.2e+02       2       7 ..       5      10 ..       4      17 .. 0.87
   2 ?    4.0   0.7      0.14        55      36      43 ..      23      30 ..      17      33 .. 0.85
   3 ?    7.8   0.1    0.0089       3.6      36      47 ..      73      84 ..      71      93 .. 0.78
   4 ?    3.5   0.1       0.2        78      37      44 ..     102     109 ..      99     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.1
                    zinc_ribbon_13  2 CpKCgn 7 
                                      CpKCg 
  gi|320100252|ref|YP_004175844.1|  5 CPKCGG 10
                                      ****95 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.14
                    zinc_ribbon_13 36 vsCknCgY 43
                                        C++CgY
  gi|320100252|ref|YP_004175844.1| 23 LVCTRCGY 30
                                      47*****9 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0089
                    zinc_ribbon_13 36 vsCknCgYtelY 47
                                      v+C +Cg+ e Y
  gi|320100252|ref|YP_004175844.1| 73 VTCPKCGWHEAY 84
                                      788888888887 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.2
                    zinc_ribbon_13  37 sCknCgYt 44 
                                        C++Cg+t
  gi|320100252|ref|YP_004175844.1| 102 KCTRCGHT 109
                                       57777776 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.9      0.04        16      29      47 ..       5      30 ..       2      37 .. 0.73
   2 ?    3.0   0.1       0.3   1.2e+02      27      33 ..      73      79 ..      60      85 .. 0.70
   3 ?    0.6   0.0       1.7   6.8e+02      27      35 ..     101     109 ..      89     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.04
                                      ETTTCCEECTTC.......-BTTTTB CS
                    Ribosomal_L32p 29 cpncgelklpHr.......vcpscGy 47
                                      cp+cg l +p r       vc+ cGy
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMRPQRidgkpylVCTRCGY 30
                                      9********99944444444666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.3
                                      EEETTTC CS
                    Ribosomal_L32p 27 vecpncg 33
                                      v+cp+cg
  gi|320100252|ref|YP_004175844.1| 73 VTCPKCG 79
                                      6777777 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.7
                                       EEETTTCCE CS
                    Ribosomal_L32p  27 vecpncgel 35 
                                        +c+ cg++
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGHT 109
                                       578888875 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 ?    4.2   0.3      0.11        46       4       9 ..       5      10 ..       4      12 .. 0.76
   2 ?    0.9   0.2       1.3     5e+02      22      26 .]      24      28 ..      22      29 .. 0.65
   3 ?   -1.8   0.0       8.7   3.5e+03       9      20 ..      56      67 ..      55      69 .. 0.78
   4 ?    5.0   0.4     0.064        26       3       8 ..      74      79 ..      73      80 .. 0.70
   5 ?    7.5   0.2     0.011       4.3       1       9 [.     100     108 ..     100     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                            zf-ACC  4 CpsCge 9 
                                      Cp+Cg 
  gi|320100252|ref|YP_004175844.1|  5 CPKCGG 10
                                      888886 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.3
                            zf-ACC 22 VCPkC 26
                                      VC+ C
  gi|320100252|ref|YP_004175844.1| 24 VCTRC 28
                                      56665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 8.7
                            zf-ACC  9 emlykkeLernl 20
                                      ++++k e e+nl
  gi|320100252|ref|YP_004175844.1| 56 TLVLKSENEANL 67
                                      678999999998 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.064
                            zf-ACC  3 KCpsCg 8 
                                       Cp+Cg
  gi|320100252|ref|YP_004175844.1| 74 TCPKCG 79
                                      588887 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.011
                            zf-ACC   1 WtKCpsCge 9  
                                       ++KC++Cg+
  gi|320100252|ref|YP_004175844.1| 100 FFKCTRCGH 108
                                       79******7 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 ?    1.5   0.2      0.61   2.4e+02      35      41 ..       3       9 ..       1      10 [. 0.87
   2 ?   -1.0   0.6       3.7   1.5e+03      36      41 ..      24      29 ..      22      30 .. 0.81
   3 ?   -0.5   0.3       2.6     1e+03      36      41 ..      74      79 ..      73      80 .. 0.86
   4 ?    7.9   0.0    0.0061       2.4      23      41 ..      89     107 ..      80     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.61
                     Baculo_LEF5_C 35 ryCskCg 41
                                      r C kCg
  gi|320100252|ref|YP_004175844.1|  3 RLCPKCG 9 
                                      89****9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.7
                     Baculo_LEF5_C 36 yCskCg 41
                                      +C +Cg
  gi|320100252|ref|YP_004175844.1| 24 VCTRCG 29
                                      7****9 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.6
                     Baculo_LEF5_C 36 yCskCg 41
                                      +C kCg
  gi|320100252|ref|YP_004175844.1| 74 TCPKCG 79
                                      6****9 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0061
                     Baculo_LEF5_C  23 QnRagDEivsfvryCskCg 41 
                                       Q+Ra DE       C +Cg
  gi|320100252|ref|YP_004175844.1|  89 QTRAADEPPTRFFKCTRCG 107
                                       *******9999999****9 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7      0.82   3.3e+02      24      28 ..       5       9 ..       4      11 .. 0.79
   2 ?    4.9   0.1     0.058        23      23      31 ..      24      32 ..      20      34 .. 0.81
   3 ?    3.8   0.1      0.12        49      22      28 ..      73      79 ..      71      81 .. 0.86
   4 ?    3.8   0.1      0.12        49      21      28 ..     100     107 ..      98     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.82
                                      -TTTS CS
                           zf-HYPF 24 CtnCG 28
                                      C++CG
  gi|320100252|ref|YP_004175844.1|  5 CPKCG 9 
                                      88887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.058
                                      --TTTS--E CS
                           zf-HYPF 23 sCtnCGPrl 31
                                       Ct+CG rl
  gi|320100252|ref|YP_004175844.1| 24 VCTRCGYRL 32
                                      6*****887 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.12
                                      ---TTTS CS
                           zf-HYPF 22 isCtnCG 28
                                      ++C++CG
  gi|320100252|ref|YP_004175844.1| 73 VTCPKCG 79
                                      78****9 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.12
                                       T---TTTS CS
                           zf-HYPF  21 fisCtnCG 28 
                                       f  Ct+CG
  gi|320100252|ref|YP_004175844.1| 100 FFKCTRCG 107
                                       678****9 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       5.3   2.1e+03      34      38 ..       5       9 ..       3      14 .. 0.64
   2 ?    4.7   0.0     0.069        28      34      48 ..      25      38 ..      19      41 .. 0.75
   3 ?   -0.7   0.2       3.5   1.4e+03       5       9 ..      75      79 ..      72      86 .. 0.71
   4 ?    8.4   0.5    0.0051         2      32      40 ..     101     109 ..      98     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.3
                            HalOD2 34 CtrCG 38
                                      C +CG
  gi|320100252|ref|YP_004175844.1|  5 CPKCG 9 
                                      55555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.069
                            HalOD2 34 CtrCGevqaaAdpSh 48
                                      CtrCG  +  A++S+
  gi|320100252|ref|YP_004175844.1| 25 CTRCGYRLE-AEASG 38
                                      9****8664.55555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.5
                            HalOD2  5 CseCs 9 
                                      C++C+
  gi|320100252|ref|YP_004175844.1| 75 CPKCG 79
                                      66665 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0051
                            HalOD2  32 WkCtrCGev 40 
                                       +kCtrCG++
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCGHT 109
                                       69*****98 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3       3.5   1.4e+03      53      56 .]       5       8 ..       1       9 [. 0.69
   2 ?   -0.6   0.0       4.6   1.8e+03      32      41 ..      25      34 ..      17      52 .. 0.77
   3 ?    3.0   0.1      0.34   1.3e+02      31      37 ..      74      81 ..      61      96 .. 0.71
   4 ?    9.2   0.8     0.004       1.6      31      41 ..     102     112 ..      98     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.5
                           DUF4379 53 CpkC 56
                                      CpkC
  gi|320100252|ref|YP_004175844.1|  5 CPKC 8 
                                      8888 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.6
                           DUF4379 32 CakCgheWea 41
                                      C +Cg+  ea
  gi|320100252|ref|YP_004175844.1| 25 CTRCGYRLEA 34
                                      8888875554 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.34
                           DUF4379 31 kCakCg.h 37
                                      +C+kCg h
  gi|320100252|ref|YP_004175844.1| 74 TCPKCGwH 81
                                      47777653 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.004
                           DUF4379  31 kCakCgheWea 41 
                                       kC +Cgh+W++
  gi|320100252|ref|YP_004175844.1| 102 KCTRCGHTWRE 112
                                       9********85 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 ?    2.5   0.1      0.31   1.2e+02      23      28 ..       4       9 ..       2      12 .. 0.77
   2 ?    5.0   0.1     0.053        21      21      29 ..      22      30 ..      19      31 .. 0.89
   3 ?    3.1   0.1       0.2        81      24      29 ..      75      80 ..      72      84 .. 0.75
   4 ?    1.5   0.8      0.64   2.6e+02       5      11 ..     102     108 ..     101     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.31
                     A2L_zn_ribbon 23 vCieCg 28
                                       C++Cg
  gi|320100252|ref|YP_004175844.1|  4 LCPKCG 9 
                                      588887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.053
                     A2L_zn_ribbon 21 ylvCieCga 29
                                      ylvC  Cg+
  gi|320100252|ref|YP_004175844.1| 22 YLVCTRCGY 30
                                      89*****97 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.2
                     A2L_zn_ribbon 24 CieCga 29
                                      C++Cg 
  gi|320100252|ref|YP_004175844.1| 75 CPKCGW 80
                                      999996 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.64
                     A2L_zn_ribbon   5 vCsvCgg 11 
                                       +C+ Cg+
  gi|320100252|ref|YP_004175844.1| 102 KCTRCGH 108
                                       7****98 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5     0.045        18      11      17 ..       3       9 ..       3      12 .. 0.87
   2 ?    0.4   0.2       1.3   5.1e+02      13      17 ..      25      29 ..      24      31 .. 0.87
   3 ?    5.0   0.1     0.048        19      13      17 ..      75      79 ..      67      81 .. 0.89
   4 ?    3.1   0.1      0.18        71      12      17 ..     102     107 ..      99     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.045
                           zf-tcix 11 rkCpkCG 17
                                      r CpkCG
  gi|320100252|ref|YP_004175844.1|  3 RLCPKCG 9 
                                      67****9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                           zf-tcix 13 CpkCG 17
                                      C++CG
  gi|320100252|ref|YP_004175844.1| 25 CTRCG 29
                                      9***9 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.048
                           zf-tcix 13 CpkCG 17
                                      CpkCG
  gi|320100252|ref|YP_004175844.1| 75 CPKCG 79
                                      ***** PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.18
                           zf-tcix  12 kCpkCG 17 
                                       kC++CG
  gi|320100252|ref|YP_004175844.1| 102 KCTRCG 107
                                       9***** 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 ?    5.2   0.2      0.04        16       5       9 ..       5       9 ..       3      12 .. 0.88
   2 ?    0.8   0.0      0.88   3.5e+02       3      12 ..      23      32 ..      21      32 .. 0.78
   3 ?    6.4   0.2     0.016       6.3       4       9 ..      74      79 ..      72      82 .. 0.83
   4 ?   -2.3   0.3       8.7   3.5e+03       3       9 ..     101     107 ..     101     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.04
                        zf_C2H2_10 5 CPKCq 9
                                     CPKC+
  gi|320100252|ref|YP_004175844.1| 5 CPKCG 9
                                     ****7 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.88
                        zf_C2H2_10  3 fsCPKCqekl 12
                                        C +C++ l
  gi|320100252|ref|YP_004175844.1| 23 LVCTRCGYRL 32
                                      5799***976 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.016
                        zf_C2H2_10  4 sCPKCq 9 
                                       CPKC+
  gi|320100252|ref|YP_004175844.1| 74 TCPKCG 79
                                      7****7 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 8.7
                        zf_C2H2_10   3 fsCPKCq 9  
                                       f C +C+
  gi|320100252|ref|YP_004175844.1| 101 FKCTRCG 107
                                       5688886 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.2   0.00033      0.13       7      31 ..       2      28 ..       1      31 [. 0.85
   2 ?    0.8   0.1       0.8   3.2e+02       9      14 ..      74      79 ..      70      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                             zf_Rg  7 eklCPNCgGdisdeRlekG..LpCkrC 31
                                      ++lCP CgG +  +R++    L C+rC
  gi|320100252|ref|YP_004175844.1|  2 SRLCPKCGGLMRPQRIDGKpyLVCTRC 28
                                      68*************97323499*999 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.8
                             zf_Rg  9 lCPNCg 14
                                       CP Cg
  gi|320100252|ref|YP_004175844.1| 74 TCPKCG 79
                                      7****8 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.11        45       2      10 ..       5      13 ..       4      18 .. 0.88
   2 ?    1.4   0.0       0.8   3.2e+02      25      37 ..      22      32 ..      19      40 .. 0.76
   3 ?    2.7   4.9      0.31   1.2e+02       1      36 [.      74     109 ..      74     112 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                         Ogr_Delta  2 CPhCgapaa 10
                                      CP+Cg  ++
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGLMR 13
                                      *****8776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.8
                         Ogr_Delta 25 yyqCsnfeCgatf 37
                                      y +C+   Cg++ 
  gi|320100252|ref|YP_004175844.1| 22 YLVCTR--CGYRL 32
                                      888888..88875 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.31
                         Ogr_Delta   1 rCPhCg.apaaartsrnlskdvre...ryyqCsnfeCgat 36 
                                       +CP+Cg ++a+ +  +   +d  e   r++ C+   Cg+t
  gi|320100252|ref|YP_004175844.1|  74 TCPKCGwHEAYYWMLQTRAAD--EpptRFFKCTR--CGHT 109
                                       699999556666666555554..34489999999..9998 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.066        26       2       8 ..       3       9 ..       3      18 .. 0.80
   2 ?    0.8   0.1       1.3   5.2e+02       3       8 ..      24      29 ..      20      32 .. 0.72
   3 ?    2.6   4.2      0.34   1.3e+02       3      29 ..      74     108 ..      73     111 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.066
                                     EE-TTT- CS
                           ADK_lid 2 rvCpkCG 8
                                     r CpkCG
  gi|320100252|ref|YP_004175844.1| 3 RLCPKCG 9
                                     6788887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.3
                                      E-TTT- CS
                           ADK_lid  3 vCpkCG 8 
                                      vC  CG
  gi|320100252|ref|YP_004175844.1| 24 VCTRCG 29
                                      666666 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.34
                                       E-TTT--EEETT..........T.B--SSTTB-TTT-- CS
                           ADK_lid   3 vCpkCGrsYhvv..........f.npPkveglCDkCGe 29 
                                       +CpkCG  +h +             pP    +C  CG 
  gi|320100252|ref|YP_004175844.1|  74 TCPKCG--WH-EayywmlqtraAdEPPTRFFKCTRCGH 108
                                       899999..33.223444455443478888888888885 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 ?    3.3   0.5      0.14        58      27      33 ..       5      11 ..       2      15 .. 0.89
   2 ?    0.5   0.0         1     4e+02      27      31 ..      25      29 ..      22      41 .. 0.81
   3 ?    3.3   0.2      0.14        57      25      31 ..      73      79 ..      68      82 .. 0.85
   4 ?    3.8   0.1     0.096        38      26      31 ..     102     107 ..      90     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                       Mu-like_Com 27 CPRCGtL 33
                                      CP+CG L
  gi|320100252|ref|YP_004175844.1|  5 CPKCGGL 11
                                      *****88 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1
                       Mu-like_Com 27 CPRCG 31
                                      C RCG
  gi|320100252|ref|YP_004175844.1| 25 CTRCG 29
                                      88888 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.14
                       Mu-like_Com 25 iKCPRCG 31
                                      + CP+CG
  gi|320100252|ref|YP_004175844.1| 73 VTCPKCG 79
                                      679***9 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.096
                       Mu-like_Com  26 KCPRCG 31 
                                       KC RCG
  gi|320100252|ref|YP_004175844.1| 102 KCTRCG 107
                                       899998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        64  (0.00356964); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 790.99
//
Query:       gi|320100253|ref|YP_004175845.1|  [L=249]
Description: proliferating cell nuclear antigen PcnA [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-14   53.1   0.0    4.2e-14   52.3   0.0    1.4  1  PCNA_N      Proliferating cell nuclear antigen, N-terminal do
    4.9e-06   26.7   0.0    8.1e-06   26.0   0.0    1.4  1  PCNA_C      Proliferating cell nuclear antigen, C-terminal do
     0.0023   17.1   0.0      0.005   16.0   0.0    1.4  1  Rad1        Repair protein Rad1/Rec1/Rad17
  ------ inclusion threshold ------
      0.081   12.7   0.0       0.12   12.1   0.0    1.2  1  Chalcone_2  Chalcone isomerase like
       0.45   10.4   4.0         16    5.4   0.0    3.8  4  DUF3117     Protein of unknown function (DUF3117)


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 !   52.3   0.0   1.2e-17   4.2e-14       4     117 ..       3     116 ..       1     124 [. 0.89

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.2e-17
                                       EEESSHHHHHHHHHHHTTTCSEEEEEEE.TTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHH CS
                            PCNA_N   4 arleqasllkklleaikdlvneanfdcd.dsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskil 79 
                                       +r+++a + +  + +i  +++ea f++d ++G+ l+a+D s v Lv++++  ++f+ y  + ++ +gvn++ l+k+l
  gi|320100253|ref|YP_004175845.1|   3 LRFRDAVVWRYAIASISKIIEEAGFKVDpEKGLVLRAMDPSTVVLVEFTMPRDAFSIYEVEGERFIGVNMEELAKVL 79 
                                       6999***********************9689********************************************** PP

                                       TTSTTTSEEEEEEETTSSEEEEEEEECTSSEEEEEEEE CS
                            PCNA_N  80 kcannedsvtlkaedeadtlalvfesekkdkiaeydlk 117
                                       k a + d ++l+   +   l++vfe   + + +  +++
  gi|320100253|ref|YP_004175845.1|  80 KRARKGDELLLEVSGDG-RLSVVFEGRGSRRFTLPSIE 116
                                       **********9987654.67788887777766655555 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 !   26.0   0.0   2.3e-09   8.1e-06      18     127 ..     140     246 ..     123     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.3e-09
                                       HHHHHHHHTTT-SEEEEEEETTEEEEEEE..ETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHHHHHHGGG CS
                            PCNA_C  18 faricrdlsqlsdsvvisvtkegvkfsas..GdiGsasivlkqvkdvdkeeeavklelkepvtltfalkYlaeftka 92 
                                       f  ++ ++  +sd+v  s+ k   k + +   ++ +a     + + ++ e   ++ e++e     ++++Yl+++  a
  gi|320100253|ref|YP_004175845.1| 140 FRDVISEVEPVSDAVEFSAVKGEGKLVVAsrSEVAEA-----EIELSASEGALIEHEITEDSRAKYTVDYLTDISSA 211
                                       5556666666666666666665444443201344444.....3344455667789999******************* PP

                                       GGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  93 tsLservtlslssevPlvveykikdvgllayllak 127
                                       +  +e +++++ +++Pl++ y++  +g l +++a+
  gi|320100253|ref|YP_004175845.1| 212 SQAAELMSVEFGNDTPLKLTYELSGGGRLVFYVAP 246
                                       *********************************98 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06     0.005     167     259 ..     131     218 ..     114     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                              Rad1 167 lkvilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksvlekfevsslsessessYkf 243
                                       +k  +  ++++++++e + +s+ ++++a +   +  +   +++e+ ++e+e+++++  l + e++  ++s+ + Y +
  gi|320100253|ref|YP_004175845.1| 131 FKGRMLPKVFRDVISEVEPVSDAVEFSAVK--GEGKLVVASRSEVAEAEIELSASEGALIEHEIT--EDSRAK-YTV 202
                                       45555567889999999***********99..6899*****************************..666666.*** PP

                              Rad1 244 allkkaakalalssKv 259
                                        +l  +++a ++++ +
  gi|320100253|ref|YP_004175845.1| 203 DYLTDISSASQAAELM 218
                                       *********9999755 PP

>> Chalcone_2  Chalcone isomerase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.4e-05      0.12     124     167 ..      68     108 ..      50     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                        Chalcone_2 124 fgeslkefkslFnrkgsvpkgkeLlLerdangeLsvlyedkkkk 167
                                       +g  ++e+ ++++r   + kg+eLlLe   +g+Lsv++e++ ++
  gi|320100253|ref|YP_004175845.1|  68 IGVNMEELAKVLKR---ARKGDELLLEVSGDGRLSVVFEGRGSR 108
                                       57789999999988...99********************99877 PP

>> DUF3117  Protein of unknown function (DUF3117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.018        66       6      18 ..      94     106 ..      92     107 .. 0.91
   2 ?   -2.2   0.1         1   3.7e+03      33      42 ..     115     124 ..     114     128 .. 0.82
   3 ?   -0.3   0.1      0.28   9.9e+02      26      42 ..     160     175 ..     158     190 .. 0.70
   4 ?    5.4   0.0    0.0046        16      25      39 ..     234     248 ..     230     249 .] 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.018
                           DUF3117   6 gdGplEvvkegrg 18 
                                       gdG l vv egrg
  gi|320100253|ref|YP_004175845.1|  94 GDGRLSVVFEGRG 106
                                       9**********97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                           DUF3117  33 velnkeEaae 42 
                                       +el++eE+ e
  gi|320100253|ref|YP_004175845.1| 115 IELTHEELPE 124
                                       899**99876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.28
                           DUF3117  26 eGGGRLVvelnkeEaae 42 
                                        G G+LVv  +++E+ae
  gi|320100253|ref|YP_004175845.1| 160 KGEGKLVVA-SRSEVAE 175
                                       688999995.4444443 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0046
                           DUF3117  25 leGGGRLVvelnkeE 39 
                                       l GGGRLV  +++ E
  gi|320100253|ref|YP_004175845.1| 234 LSGGGRLVFYVAPRE 248
                                       57******8877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1837.62
//
Query:       gi|320100254|ref|YP_004175846.1|  [L=375]
Description: DNA primase small subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-13   51.3   0.3    2.6e-11   43.9   0.0    2.5  2  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.1    0.0014        25       1      18 [.      98     113 ..      98     117 .. 0.79
   2 !   43.9   0.0   1.5e-15   2.6e-11      30     176 ..     154     301 ..     142     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0014
                                       EEEEEETTT-.TT--HHH CS
                     DNA_primase_S   1 FDiDmddyddcseatvce 18 
                                       FDiD+d+y++cs  +v +
  gi|320100254|ref|YP_004175846.1|  98 FDIDADKYPGCS--QVFK 113
                                       9*********87..4444 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 1.5e-15
                                       HHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH............................. CS
                     DNA_primase_S  30 vldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnly....rplhpflsrs.mlkivkpvve 101
                                       + d ll  d+gf  i+++fsg+rGfH+ v d+ a plt+e+r+++++y+ +       ++p+  ++  +  +++   
  gi|320100254|ref|YP_004175846.1| 154 LRDILL-RDLGFSRIKIYFSGNRGFHVRVLDESALPLTREQRRLLADYVACSnldtARMFPSYRGKvVFHRFEHG-- 227
                                       444445.9****************************************999877664477777776444444444.. PP

                                       ..........HCHHHHCT--------...........................-----------------....--- CS
                     DNA_primase_S 102 eiileeqdpfeikkllrllpdkslre......kkkw...eakedivlvllyprldeqvtkgikhllkapfcihgktg 169
                                                   +++l++++ + l +       k +   e+     l+   + +d+ vt+++++l +   +++ k+g
  gi|320100254|ref|YP_004175846.1| 228 ----------LRRRVLESARARGLVRegeiagLKGLvldEEHLPMLLEENCIGIDKVVTIDTSRLSRFGNSLNMKSG 294
                                       ..........7777777777777777555555444466644444566666788************************ PP

                                       ------. CS
                     DNA_primase_S 170 nvcvpld 176
                                        +++++d
  gi|320100254|ref|YP_004175846.1| 295 LRVTEMD 301
                                       9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2671.74
//
Query:       gi|320100255|ref|YP_004175847.1|  [L=166]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1213.56
//
Query:       gi|320100256|ref|YP_004175848.1|  [L=132]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.022   14.5   0.1      0.033   14.0   0.1    1.3  1  Nucleo_LEF-12  Nucleopolyhedrovirus LEF-12 protein
      0.067   11.6   0.5       0.09   11.2   0.5    1.2  1  DUF515         Protein of unknown function (DUF515)
       0.35    9.7   8.1       0.46    9.3   8.1    1.0  1  MscS_TM        Mechanosensitive ion channel inner membrane do


Domain annotation for each model (and alignments):
>> Nucleo_LEF-12  Nucleopolyhedrovirus LEF-12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.5e-06     0.033      90     156 ..      44     109 ..      38     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-06
                     Nucleo_LEF-12  90 vgprytymnytlfknvvalklvvytrtlqanm.yadglpyfvqnfsetnykhvrvyvrkramqvvatl 156
                                       v   y+ym  + f+   a+ + +yt  +   +  a  lpyf+q +    +kh+r   r r +  v +l
  gi|320100256|ref|YP_004175848.1|  44 VWFNYSYMSPSQFNRFTAFSI-LYTLLIALSIgVAFTLPYFIQSVRPRSFKHIRE-ARLRDIVFVGSL 109
                                       556799*******99999975.688776665537899****************95.466666555555 PP

>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   1.5e-05      0.09      14      56 ..      86     129 ..      80     132 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                            DUF515  14 srrssrisslrekerrkrliiGasvlvvivillvfai.Ysyien 56 
                                       s r+++   +re  +r ++ +G+ +l +ivi   +++ Y y+en
  gi|320100256|ref|YP_004175848.1|  86 SVRPRSFKHIREARLRDIVFVGSLILLLIVISAYIILgYYYMEN 129
                                       67999999*************99999888875443335888877 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 ?    9.3   8.1   7.7e-05      0.46     118     220 ..      24     126 ..      22     127 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7.7e-05
                           MscS_TM 118 svrrlrralkrlilvllplllvlilaealsdalardvlG....rlaflllllllavflarllrpalglyankkeeek 190
                                       +++ + + + ++i++   l+++++ ++ ++++ ++  ++     +++++l +++a++l  ++++ ++   ++++e  
  gi|320100256|ref|YP_004175848.1|  24 RLALYVSTISWIIICGNWLYVWFNYSYMSPSQ-FNRFTAfsilYTLLIALSIGVAFTLPYFIQSVRPRSFKHIRE-- 97 
                                       56778899999999999999999988886544.444444111145555566666666666666666666666544.. PP

                           MscS_TM 191 nslrlrrllyl.llvlaPlalavlaalGYyy 220
                                          rlr ++++  l+l+ +++   ++lGYyy
  gi|320100256|ref|YP_004175848.1|  98 --ARLRDIVFVgSLILLLIVISAYIILGYYY 126
                                       ..478877776167777777778899****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); 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:                         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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 924.64
//
Query:       gi|320100257|ref|YP_004175849.1|  [L=66]
Description: RNA-binding protein Nop10p [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-21   75.9   1.0    2.2e-21   75.6   1.0    1.1  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
    0.00056   19.7   4.5       0.12   12.2   0.9    2.3  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.003   16.9   2.8     0.0053   16.1   2.8    1.4  1  zf-ribbon_3     zinc-ribbon domain
     0.0047   17.0   1.8     0.0062   16.6   1.8    1.2  1  DUF1272         Protein of unknown function (DUF1272)
  ------ inclusion threshold ------
      0.022   14.6   2.0        2.8    7.9   0.2    2.2  2  Fer4            4Fe-4S binding domain
      0.057   11.3   0.7      0.068   11.1   0.7    1.2  1  Med16           Mediator complex subunit 16
      0.063   13.5   1.0        0.1   12.7   1.0    1.3  1  Ribosomal_L37e  Ribosomal protein L37e
       0.12   12.0   0.6       0.12   12.0   0.6    1.5  2  RecR            RecR protein
       0.13   12.2   3.3       0.23   11.4   3.3    1.5  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.16   11.5   4.4        2.1    8.0   0.4    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.17   12.0   3.7        5.3    7.2   0.3    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.18   11.9   0.6       0.23   11.5   0.6    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.42   10.8   4.3        4.6    7.5   4.3    2.1  1  Zn-ribbon_8     Zinc ribbon domain
       0.46   10.1   5.9        4.2    7.1   0.2    2.2  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
       0.67   10.2   5.5    1.2e+02    3.1   5.5    2.3  1  Fer4_2          4Fe-4S binding domain
       0.68    9.4   8.0         26    4.3   8.1    2.2  1  Mu-like_Com     Mu-like prophage protein Com


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   1.0     2e-24   2.2e-21       1      49 [.       1      50 [.       1      52 [. 0.96

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 2e-24
                                      .----EE-TTT--EESS.SB-TTT-SB-B-SS--S--TT-TTCHHHHHCH CS
                            Nop10p  1 mksylrkcgkcrvYTLk.kvcpecggptksahPaRFSPdDkyskyRralK 49
                                      m++ +rkc +c+ YTL  ++cp+cgg+++++hPaRFSP Dky  yR + K
  gi|320100257|ref|YP_004175849.1|  1 MNWLMRKCVRCGSYTLDkEKCPRCGGELTVPHPARFSPVDKYATYRLREK 50
                                      99**************989***************************9877 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 !    8.6   0.1    0.0015       1.7       3      11 ..       7      15 ..       7      17 .. 0.88
   2 !   12.2   0.9   0.00011      0.12       2       9 ..      19      26 ..      18      29 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                                      B-TTT--BB CS
                      zf-FPG_IleRS  3 pCpRCwryi 11
                                      +C RC+ y+
  gi|320100257|ref|YP_004175849.1|  7 KCVRCGSYT 15
                                      8*****996 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00011
                                      SB-TTT-- CS
                      zf-FPG_IleRS  2 epCpRCwr 9 
                                      e+CpRC++
  gi|320100257|ref|YP_004175849.1| 19 EKCPRCGG 26
                                      9******8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.8   4.7e-06    0.0053       2      26 .]       5      28 ..       4      28 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.7e-06
                       zf-ribbon_3  2 tvrCPnCGaplssddnvCpyCGtkl 26
                                      +++C +CG+  + d  +Cp CG++l
  gi|320100257|ref|YP_004175849.1|  5 MRKCVRCGSY-TLDKEKCPRCGGEL 28
                                      899******9.999********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 !   16.6   1.8   5.5e-06    0.0062      32      55 ..       8      33 ..       5      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-06
                           DUF1272 32 CaeCaeevl.envCPncgGel.vkRP 55
                                      C++C   +l ++ CP cgGel v+ P
  gi|320100257|ref|YP_004175849.1|  8 CVRCGSYTLdKEKCPRCGGELtVPHP 33
                                      99***99997899*******934556 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0064       7.2       6      12 ..       6      12 ..       1      13 [. 0.82
   2 ?    7.9   0.2    0.0025       2.8       2      12 ..      15      25 ..      14      26 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0064
                                      TTSSS-T CS
                              Fer4  6 ekCigCG 12
                                       kC++CG
  gi|320100257|ref|YP_004175849.1|  6 RKCVRCG 12
                                      69****9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                                      EEETTTSSS-T CS
                              Fer4  2 videekCigCG 12
                                      + d+ekC +CG
  gi|320100257|ref|YP_004175849.1| 15 TLDKEKCPRCG 25
                                      689*******9 PP

>> Med16  Mediator complex subunit 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   6.1e-05     0.068     715     732 ..       5      22 ..       2      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.1e-05
                             Med16 715 lRrCtRCgavslvgdplv 732
                                       +R+C+RCg+++l++   +
  gi|320100257|ref|YP_004175849.1|   5 MRKCVRCGSYTLDKEKCP 22 
                                       6***********998655 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   9.3e-05       0.1      18      38 ..       7      25 ..       3      28 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.3e-05
                    Ribosomal_L37e 18 lCrrCgkrsyhvqkktCascG 38
                                      +C rCg  sy + k++C  cG
  gi|320100257|ref|YP_004175849.1|  7 KCVRCG--SYTLDKEKCPRCG 25
                                      6****9..8***********9 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6    0.0001      0.12      17      34 ..       6      24 ..       4      27 .. 0.84
   2 ?   -3.0   0.0         5   5.6e+03       4      14 ..      50      60 ..      49      61 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                      EE-TTT--EE.SSSS-CCC CS
                              RecR 17 rhCsrCgnlt.eedlCaIC 34
                                      r C rCg +t +++ C+ C
  gi|320100257|ref|YP_004175849.1|  6 RKCVRCGSYTlDKEKCPRC 24
                                      89*******736699**99 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5
                                      HHHHHHHHHHH CS
                              RecR  4 eLaeaLqeake 14
                                      +L+  L ++ e
  gi|320100257|ref|YP_004175849.1| 50 KLSSNLLKLDE 60
                                      68888887755 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.3   0.00021      0.23      10      33 ..       4      26 ..       2      30 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                           DUF35_N 10 vgqrCpdCGtvqfPPravCphCgs 33
                                      + ++C  CG++       Cp+Cg+
  gi|320100257|ref|YP_004175849.1|  4 LMRKCVRCGSYTL-DKEKCPRCGG 26
                                      5789********7.6677****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 ?    5.7   0.3    0.0096        11       2      10 ..       7      15 ..       6      20 .. 0.77
   2 ?    8.0   0.4    0.0018       2.1       2      10 ..      20      28 ..      19      35 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0096
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      kC  Cgs++
  gi|320100257|ref|YP_004175849.1|  7 KCVRCGSYT 15
                                      9*****975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0018
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      kCP Cg++ 
  gi|320100257|ref|YP_004175849.1| 20 KCPRCGGEL 28
                                      8*****974 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2     0.011        12       3      15 ..       7      19 ..       6      19 .. 0.81
   2 ?    7.2   0.3    0.0047       5.3       3       9 ..      20      26 ..      20      29 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                            zf-ACC  3 KCpsCgemlykke 15
                                      KC +Cg+ ++ ke
  gi|320100257|ref|YP_004175849.1|  7 KCVRCGSYTLDKE 19
                                      9*****9877665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0047
                            zf-ACC  3 KCpsCge 9 
                                      KCp+Cg 
  gi|320100257|ref|YP_004175849.1| 20 KCPRCGG 26
                                      9****96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   0.00021      0.23      72      95 ..       7      27 ..       3      35 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                      EETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 72 rCreCgkefeleekalrCpkCgsa 95
                                      +C +Cg +++l++  ++Cp+Cg++
  gi|320100257|ref|YP_004175849.1|  7 KCVRCG-SYTLDK--EKCPRCGGE 27
                                      8*****.666664..48*****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 ?    7.5   4.3    0.0041       4.6       8      36 ..       8      28 ..       4      30 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0041
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgsev 36
                                      C +Cg  ++ l      ++++CP+Cg+e+
  gi|320100257|ref|YP_004175849.1|  8 CVRCG-SYT-L------DKEKCPRCGGEL 28
                                      55666.333.2......2567*****976 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0037       4.2      11      19 ..       6      14 ..       4      15 .. 0.89
   2 ?    5.3   1.5     0.014        15      12      17 ..      20      25 ..      19      27 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0037
                           zf-tcix 11 rkCpkCGty 19
                                      rkC +CG y
  gi|320100257|ref|YP_004175849.1|  6 RKCVRCGSY 14
                                      9******88 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                           zf-tcix 12 kCpkCG 17
                                      kCp+CG
  gi|320100257|ref|YP_004175849.1| 20 KCPRCG 25
                                      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 ?    3.1   5.5      0.11   1.2e+02       3      14 ..      14      25 ..       4      27 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                            Fer4_2  3 vvvdtdrCigCg 14
                                      +  d ++C +Cg
  gi|320100257|ref|YP_004175849.1| 14 YTLDKEKCPRCG 25
                                      456777777776 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 ?    4.3   8.1     0.024        26      16      31 ..      12      25 ..       5      39 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.024
                       Mu-like_Com 16 KaeAlDeltiKCPRCG 31
                                       +  lD  + KCPRCG
  gi|320100257|ref|YP_004175849.1| 12 GSYTLD--KEKCPRCG 25
                                      345688..88*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 466.65
//
Query:       gi|320100258|ref|YP_004175850.1|  [L=264]
Description: translation initiation factor 2 subunit alpha (aeIF-2a) [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   77.9   0.6    4.4e-21   75.2   0.0    2.2  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    7.6e-13   48.6   0.5    1.4e-12   47.8   0.5    1.4  1  S1           S1 RNA binding domain


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4     0.079   7.1e+02      72     102 ..      50      84 ..      43      86 .. 0.73
   2 !   75.2   0.0   4.9e-25   4.4e-21       1     116 []     120     232 ..     120     232 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.079
                                       HHHHHHHHHHHST.S......TTSSSEEEEEEEES CS
                       EIF_2_alpha  72 veaIkeaLkageeasne....eeveeeeevkikli 102
                                       v++I++++++ge+   +    +++++e++v++k +
  gi|320100258|ref|YP_004175850.1|  50 VKNIRDVIREGEKIVVKvirvDRAKKEVDVSLKKV 84 
                                       89999999988886555666666667777777655 PP

  == domain 2  score: 75.2 bits;  conditional E-value: 4.9e-25
                                       HHHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHH CS
                       EIF_2_alpha   1 lyeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIk 76 
                                       +y+ev w l++ yg+   a+ +++ t+ e+l k+++pee+++ L++++k+++k+++v +ra +++++ ++dGve+++
  gi|320100258|ref|YP_004175850.1| 120 AYREVIWRLEDAYGDPLYALeEAVSTGGEALAKAGVPEEWINPLLTEVKRHIKIKEVSVRARLTVQSRHPDGVERVR 196
                                       599************999998999999************************************************** PP

                                       HHHHHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  77 eaLkageeasneeeveeeeevkikliapPeYvltvetldk 116
                                       ++L+a ++    + +++  ++k+++ ++P+Y l++ ++d+
  gi|320100258|ref|YP_004175850.1| 197 RVLEAVAN----TLKAKGARFKLYTAGAPRYILEIYSQDY 232
                                       ****5554....346789*****************99996 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.5   1.5e-16   1.4e-12       2      75 .]       8      82 ..       7      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.5e-16
                                      STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      p +ge v ++V ++ ++Ga+V l+  ++ ++f+p se++ +  v+++ +v+++G+++ vkv++vd++++++++s+k
  gi|320100258|ref|YP_004175850.1|  8 PDIGEYVVATVREIYDYGAYVTLDeyGDRKAFLPWSEIATK-WVKNIRDVIREGEKIVVKVIRVDRAKKEVDVSLK 82
                                      568999*******************99**************.******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1946.84
//
Query:       gi|320100259|ref|YP_004175851.1|  [L=663]
Description: putative oligosaccharyl transferase STT3 subunit (B5) (integral membrane protein 1) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.7  23.8      0.031   14.5  10.0    3.3  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 ?   14.5  10.0   1.7e-06     0.031      30     146 ..      86     210 ..      70     222 .. 0.73
   2 ?    1.3   5.8      0.02   3.6e+02      34      89 ..     301     359 ..     294     406 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-06
                             PMT_2  30 lagvltil.llyllarrlfgkraallaalllavvplfvalsa..lftpdaplvllwalalylllraleknklkywll 103
                                        a++lt+l ++y ++r l ++  a +++l++a +p +v++s+  ++ + ++   l +l+l++l+   + + ++  ll
  gi|320100259|ref|YP_004175851.1|  86 AASALTVLlVFYTTLRVLGNPALAGVTSLIYASSPAVVFWSTpsNMGHQVLSGILATLILLALYVNEKAGGIRGALL 162
                                       34455555055666666666**********************88888899998999999999999999999****** PP

                             PMT_2 104 agvlfGlgflsKytaallliaall..yllis...arr.ilkekkpyl.al 146
                                       +g++  l+    +   ll+ +al+  +  ++   + r +l+   ++l al
  gi|320100259|ref|YP_004175851.1| 163 LGLSGLLAQVLNPAGWLLVEGALIglA--AEfavGVRgRLNRVAALLlAL 210
                                       **9999999999999999988888642..222353332555555555344 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.02
                             PMT_2  34 ltilllyllarrlfgkraallaalllavvplfvalsa...lftpdaplvllwalalyll 89 
                                         i l+ l   rl++++ ++ +a++ ++v+l++a ++   l+  +a+l++l++ +++++
  gi|320100259|ref|YP_004175851.1| 301 GLIGLIVLSRSRLLSEMPGVKTAIISSTVLLLIAAMLdptLVVAEAFLLALLTSLALYV 359
                                       44555666667889999999999999999999999995544444555554443333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4647.92
//
Query:       gi|320100260|ref|YP_004175852.1|  [L=280]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  32.4    8.4e-19   68.1   9.5    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.29   11.2   8.3        6.9    6.7   0.4    3.2  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 !   68.1   9.5   9.4e-23   8.4e-19       3     136 ..       3     135 ..       1     136 [. 0.98
   2 !   53.6  14.9   2.8e-18   2.5e-14       2     134 ..     145     276 ..     144     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 9.4e-23
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                       +++la  a ++w+++++++k++   ++p+++++ r + a ++l +++l+k+  + + ++++++l+ l +llg vl+ 
  gi|320100260|ref|YP_004175852.1|   3 AVFLAAMAGVLWSLNPPVIKRFAGGMDPVAFNGARGIYAVLVLTLYMLVKGVAP-SVRPEGLALIYLSALLGPVLGD 78 
                                       6899**************************************************.********************** PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +++++a+ +++ +na  i +l   ++ ++++++lgek+    l+g ++++ G++li+
  gi|320100260|ref|YP_004175852.1|  79 IFYIKAIVSIGGGNAITIGYLYIFVAQLIGIYVLGEKPDAHLLIGSLVAFTGIYLIY 135
                                       *******************************************************96 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 2.8e-18
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvl 77 
                                       +g+ +al+aa++w++++v+sk + ++ + l+l f r ++  ++l+i+++    +    ls++++++ +++g l++ +
  gi|320100260|ref|YP_004175852.1| 145 RGVAYALAAAVLWGMSAVCSKLATQYGDALSLGFTRNVF--LVLSIVLVRGLLPArYALSRNGFIAGFITGGLSFGV 219
                                       6999******************************99763..333333333322223356****************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                       +++lf+ al ++++s a+l t ++P+++ + s ++ ge +++++++g+++ ++G++l
  gi|320100260|ref|YP_004175852.1| 220 GMVLFIEALATGGVSLAVLPTIIAPALARFTSRIIAGEVVGWRSIAGTLVTVAGIAL 276
                                       *******************************************************98 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4   0.00077       6.9       3     114 ..       9     133 ..       7     135 .. 0.64
   2 ?    6.4   2.2   0.00096       8.6      56     114 ..     219     276 ..     150     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00077
                           TMEM234   3 lvgilWGitnPllkrgskgleevkekskl..sq.lllelkf.............lllrlkyliplllNqsgSvlffl 63 
                                       ++g+lW +  P +kr + g++ v+ +++      l+l                   l l yl +ll  ++g +++  
  gi|320100260|ref|YP_004175852.1|   9 MAGVLWSLNPPVIKRFAGGMDPVAFNGARgiYAvLVLT--LymlvkgvapsvrpEGLALIYLSALLGPVLGDIFYIK 83 
                                       789*****************999866554211112222..1345566666555545555677777777777777777 PP

                           TMEM234  64 llgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgial 114
                                       ++ ++    a  i     fv+ ++  ++lgek   ++ ++g l+ ++gi+l
  gi|320100260|ref|YP_004175852.1|  84 AIVSIGGGNAITIGYLYIFVAQLIGIYVLGEKP-DAHLLIGSLVAFTGIYL 133
                                       777766666666666666666666667777765.44566676666677666 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00096
                           TMEM234  56 sgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgial 114
                                       +g vlf  +l+   +slav  +  +a ++   t++++  +v+++++++g+l++v+gial
  gi|320100260|ref|YP_004175852.1| 219 VGMVLFIEALATGGVSLAVLPT-IIAPALARFTSRIIAGEVVGWRSIAGTLVTVAGIAL 276
                                       588999999*999999998644.5777778889999999******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2062.43
//
Query:       gi|320100261|ref|YP_004175853.1|  [L=73]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 583.77
//
Query:       gi|320100262|ref|YP_004175854.1|  [L=152]
Description: NADH ubiquinone oxidoreductase 20 kDa subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-21   75.6   0.0    3.7e-21   75.3   0.0    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0     2e-25   3.7e-21       1     129 [.      15     134 ..      15     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2e-25
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C++c+i++l++ +++ d+     +r++ +l+ +++         +adv++ +G+vt ++ +++ ++ e+a++++++i
  gi|320100262|ref|YP_004175854.1|  15 CNACDIEILDALTPFHDA-----ERFGVKLVGSPR---------HADVILMTGPVTLETLPKVLNAIEAAPRPRIII 77 
                                       ******************.....************.........********************************* PP

                                       EESHHHHH-TGGGSTT-TEE-...HHHHHHHC...S-E...EEE-SSS--HHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsvg...eevgellev..vpvd..inipGCPphpeailetll 129
                                       a+G+C + GGi+  ++ +s++   +  +++l++  ++vd  +++pGCP++pea+l++++
  gi|320100262|ref|YP_004175854.1|  78 ALGSCGVGGGIW--HDTYSTIggiKGLEKMLKErgIRVDaiYYVPGCPIRPEALLYAIA 134
                                       ************..6666664233333344444786666669*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1155.36
//
Query:       gi|320100263|ref|YP_004175855.1|  [L=172]
Description: NADH dehydrogenase subunit I [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   52.8  24.0    1.6e-09   37.2   4.6    3.7  4  Fer4           4Fe-4S binding domain
    2.1e-12   47.4  11.5    1.1e-06   29.1   0.1    2.8  2  Fer4_7         4Fe-4S dicluster domain
    8.8e-12   45.0   7.2    8.8e-12   45.0   7.2    2.2  2  Fer4_21        4Fe-4S dicluster domain
    4.2e-10   39.6   8.6    4.2e-10   39.6   8.6    2.8  2  Fer4_10        4Fe-4S dicluster domain
    8.4e-10   38.3  23.6    2.3e-08   33.8   4.2    4.1  4  Fer4_6         4Fe-4S binding domain
    1.7e-09   37.7   7.7    1.7e-09   37.7   7.7    2.8  2  Fer4_9         4Fe-4S dicluster domain
      1e-08   35.9  14.9    0.00076   20.4   6.5    2.7  2  Fer4_16        4Fe-4S double cluster binding domain
    1.9e-06   27.6   3.3    1.9e-06   27.6   3.3    4.2  4  Fer4_2         4Fe-4S binding domain
    3.3e-06   27.5  15.5     0.0022   18.4   9.7    2.7  2  Fer4_8         4Fe-4S dicluster domain
    4.1e-05   23.7   1.5    4.1e-05   23.7   1.5    3.8  4  Fer4_4         4Fe-4S binding domain
     0.0003   21.6   8.2      0.016   16.0   0.2    3.0  3  Fer4_22        4Fe-4S dicluster domain
    0.00074   20.2   0.5    0.00074   20.2   0.5    2.9  2  Fer4_15        4Fe-4S single cluster domain
     0.0015   19.3   7.9     0.0015   19.3   7.9    3.1  2  Fer4_3         4Fe-4S binding domain
     0.0032   18.0  17.5      0.021   15.4   2.4    3.2  3  Fer4_17        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.3   4.1      0.011   16.3   4.1    3.3  4  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
      0.048   13.3   0.2      0.048   13.3   0.2    3.2  2  zf-tcix        Putative treble-clef, zinc-finger, Zn-binding
      0.087   13.1   1.7       0.19   12.0   0.3    2.2  2  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
       0.15   12.2  14.3       0.82    9.9   1.1    2.7  2  Fer4_18        4Fe-4S dicluster domain
       0.66   10.0   7.0        1.6    8.8   7.0    1.8  1  HypA           Hydrogenase/urease nickel incorporation, metal


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 !   37.2   4.6   1.7e-12   1.6e-09       1      23 [.      39      61 ..      39      62 .. 0.94
   2 !   26.3   2.8   4.7e-09   4.5e-06       7      24 .]      78      95 ..      74      95 .. 0.94
   3 ?    0.9   0.1       0.5   4.7e+02       5      12 ..     118     125 ..     114     126 .. 0.75
   4 ?   -0.9   0.2       1.8   1.7e+03       6      11 ..     149     154 ..     147     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.7e-12
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      v+id +kCigCGaCv++CP +A+
  gi|320100263|ref|YP_004175855.1| 39 VEIDASKCIGCGACVNACPPNAL 61
                                      68*******************98 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 4.7e-09
                                      TSSS-THHHHHSTTTEEE CS
                              Fer4  7 kCigCGaCvevCPvgAIt 24
                                      +Ci+C +C++vCPv AI+
  gi|320100263|ref|YP_004175855.1| 78 RCIFCWRCIDVCPVKAIK 95
                                      8****************6 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.5
                                       TTTSSS-T CS
                              Fer4   5 eekCigCG 12 
                                         kC  CG
  gi|320100263|ref|YP_004175855.1| 118 RRKCPSCG 125
                                       669999*9 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.8
                                       TTSSS- CS
                              Fer4   6 ekCigC 11 
                                       +kC  C
  gi|320100263|ref|YP_004175855.1| 149 DKCPEC 154
                                       788888 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   1.1e-09   1.1e-06       1      21 [.      45      65 ..      19      75 .. 0.78
   2 !   19.6   7.1   1.1e-06     0.001       1      42 [.      78     125 ..      78     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.1e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaielde 21
                                      +CigCgaCv+aCp +a++l e
  gi|320100263|ref|YP_004175855.1| 45 KCIGCGACVNACPPNALQLIE 65
                                      577777777777777777655 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.1e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt......ekveidpekClgCg 42 
                                       rCi C +C ++Cpvkai+ + e + +++       +v+++ +kC +Cg
  gi|320100263|ref|YP_004175855.1|  78 RCIFCWRCIDVCPVKAIKGTREFELATNdvadlyVHVVHSRRKCPSCG 125
                                       8*****************997655554434444466677788999997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   7.2   9.3e-15   8.8e-12       2      57 ..      40      94 ..      39      96 .. 0.95
   2 ?   -0.4   1.0       1.4   1.3e+03      23      44 ..     131     154 ..     115     157 .. 0.47

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 9.3e-15
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                       id +kCigCg C+ aC+ ++ q ie ++k vl++   +C+ C  C++vCPv ++i
  gi|320100263|ref|YP_004175855.1| 40 EIDASKCIGCGACVNACPPNALQLIEDSEKLVLRYFIGRCIFCWRCIDVCPV-KAI 94
                                      59*************************************************9.666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                           Fer4_21  23 hqaieid..aktvlkvvedeCvGC 44 
                                          i++   ++++ +   d+C  C
  gi|320100263|ref|YP_004175855.1| 131 ERIIRYVseKAQHSEEYLDKCPEC 154
                                       334443300333444445677666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   8.6   4.4e-13   4.2e-10       1      56 []      38      90 ..      38      90 .. 0.93
   2 !   10.7  10.4   0.00048      0.45       8      24 ..      78     130 ..      76     158 .. 0.63

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 4.4e-13
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      kv+id+++Ci+Cg+Cv+aCP    +  +  e+se+ + r  +++C++c  C+++CP
  gi|320100263|ref|YP_004175855.1| 38 KVEIDASKCIGCGACVNACPP---NALQLIEDSEKLVLRYFIGRCIFCWRCIDVCP 90
                                      589******************...7777888889999999***************9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00048
                           Fer4_10   8 tCirCgkCvkaCPadl....................................t 24 
                                       +Ci C +C ++CP+++                                    t
  gi|320100263|ref|YP_004175855.1|  78 RCIFCWRCIDVCPVKAikgtrefelatndvadlyvhvvhsrrkcpscgtaygT 130
                                       7*************999999998775555554444444444444444444433 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   4.2   2.4e-11   2.3e-08       1      24 []      38      61 ..      38      61 .. 0.94
   2 !   11.1   1.7   0.00035      0.33       8      24 .]      78      94 ..      72      94 .. 0.90
   3 ?    4.6   0.1     0.041        38       2      13 ..     114     125 ..     113     126 .. 0.88
   4 ?    1.0   0.5      0.53     5e+02       7      14 ..     149     156 ..     148     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.4e-11
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +veid++kCigCg+Cv++CP +a+
  gi|320100263|ref|YP_004175855.1| 38 KVEIDASKCIGCGACVNACPPNAL 61
                                      79******************9986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00035
                            Fer4_6  8 kCigCgdCvrvCPegai 24
                                      +Ci C +C++vCP +ai
  gi|320100263|ref|YP_004175855.1| 78 RCIFCWRCIDVCPVKAI 94
                                      799999********998 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.041
                            Fer4_6   2 veidpdkCigCg 13 
                                       v++ + kC +Cg
  gi|320100263|ref|YP_004175855.1| 114 VVHSRRKCPSCG 125
                                       789999*****9 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.53
                            Fer4_6   7 dkCigCgd 14 
                                       dkC  C++
  gi|320100263|ref|YP_004175855.1| 149 DKCPECRK 156
                                       89****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 !   37.7   7.7   1.8e-12   1.7e-09       1      51 []      45      94 ..      45      94 .. 0.93
   2 !   11.0  10.2    0.0004      0.38       1      41 [.      78     126 ..      78     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.8e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC+gCgaCv+aCp ++ +  +  +k  lr +   +Ci+C +C+++Cp +ai
  gi|320100263|ref|YP_004175855.1| 45 KCIGCGACVNACPPNALQLIEDSEKLVLRYFIG-RCIFCWRCIDVCPVKAI 94
                                      7*****************999999999988766.9************9987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0004
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCga 41 
                                       +C+ C +C+++Cp +++++ +  + a ++ a+          +C +Cg+
  gi|320100263|ref|YP_004175855.1|  78 RCIFCWRCIDVCPVKAIKGTREFELATNDVADLyvhvvhsrRKCPSCGT 126
                                       5*************99999998888888777779999999988999985 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 !   20.1   1.2     1e-06   0.00095       1      19 [.      45      63 ..      45      72 .. 0.85
   2 !   20.4   6.5   8.1e-07   0.00076       1      30 [.      78     113 ..      78     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                      +C++Cg+C+++CP na++ 
  gi|320100263|ref|YP_004175855.1| 45 KCIGCGACVNACPPNALQL 63
                                      5***************985 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 8.1e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeieare......c 30 
                                       rC+ C +C++vCP++aik+++e+e+++++       
  gi|320100263|ref|YP_004175855.1|  78 RCIFCWRCIDVCPVKAIKGTREFELATNDvadlyvH 113
                                       6*******************8888887774444440 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   3.3   2.1e-09   1.9e-06       2      21 ..      38      57 ..      37      58 .. 0.93
   2 ?    5.1   1.6     0.028        27       9      21 ..      78      90 ..      73      91 .. 0.82
   3 ?    3.4   0.1     0.099        93       3      15 ..     114     126 ..     112     126 .. 0.81
   4 ?    1.8   0.1      0.33   3.1e+02       8      14 ..     149     155 ..     145     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.1e-09
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      +v++d+ +CigCgaCv+aCP
  gi|320100263|ref|YP_004175855.1| 38 KVEIDASKCIGCGACVNACP 57
                                      689****************9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.028
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      rCi C  C+++CP
  gi|320100263|ref|YP_004175855.1| 78 RCIFCWRCIDVCP 90
                                      6777867****** PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.099
                            Fer4_2   3 vvvdtdrCigCga 15 
                                       vv  +++C +Cg+
  gi|320100263|ref|YP_004175855.1| 114 VVHSRRKCPSCGT 126
                                       677789*****95 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.33
                            Fer4_2   8 drCigCg 14 
                                       d+C +C+
  gi|320100263|ref|YP_004175855.1| 149 DKCPECR 155
                                       89****8 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   9.7   2.3e-06    0.0022       2      64 ..      43      92 ..      42      93 .. 0.72
   2 !   14.5   4.6   3.9e-05     0.037       4      55 ..      78     155 ..      75     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      ++kCi+CgaC +aCp      + l+  ++  +   + +        +++C  c +C +vCpv+
  gi|320100263|ref|YP_004175855.1| 43 ASKCIGCGACVNACPP-----NALQLIEDSEKL--VLRYF------IGRCIFCWRCIDVCPVK 92
                                      79************93.....223333333233..33344......8**************97 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.9e-05
                            Fer4_8   4 kCieCgaCqsaCpvlrrtk.khlldargeaae.........................dvqeeqvleeeealwsCttc 54 
                                       +Ci C +C + Cpv   ++ ++   a +++a+                         + ++e+++++ee+l++C +c
  gi|320100263|ref|YP_004175855.1|  78 RCIFCWRCIDVCPVKAIKGtREFELATNDVADlyvhvvhsrrkcpscgtaygteriiRYVSEKAQHSEEYLDKCPEC 154
                                       8************666666555566666666656666665555555555555555553333344444999****999 PP

                            Fer4_8  55 g 55 
                                       +
  gi|320100263|ref|YP_004175855.1| 155 R 155
                                       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 !   23.7   1.5   4.4e-08   4.1e-05       2      15 ..      44      57 ..      43      66 .. 0.91
   2 !    8.0   1.9    0.0049       4.6       3      16 ..      78      91 ..      76      98 .. 0.91
   3 ?   -0.9   0.8       3.5   3.3e+03       7      10 ..     121     124 ..     119     125 .. 0.81
   4 ?   -0.0   0.4       1.8   1.7e+03       7      11 ..     151     155 ..     148     156 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.4e-08
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++CigCg+Cv+aCP
  gi|320100263|ref|YP_004175855.1| 44 SKCIGCGACVNACP 57
                                      68************ PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0049
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      rCi C +C+++CP+
  gi|320100263|ref|YP_004175855.1| 78 RCIFCWRCIDVCPV 91
                                      8999*********7 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.5
                            Fer4_4   7 CgsC 10 
                                       C+sC
  gi|320100263|ref|YP_004175855.1| 121 CPSC 124
                                       9998 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.8
                            Fer4_4   7 CgsCv 11 
                                       C+ C+
  gi|320100263|ref|YP_004175855.1| 151 CPECR 155
                                       66664 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.7e-05     0.016      76      94 ..      40      58 ..      14      60 .. 0.85
   2 !    9.0   0.3    0.0026       2.5      79      95 ..      76      92 ..      62      94 .. 0.79
   3 ?    0.3   0.2       1.3   1.3e+03      12      25 ..     121     138 ..     110     167 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                      ++++s+C+GCg C++acp 
  gi|320100263|ref|YP_004175855.1| 40 EIDASKCIGCGACVNACPP 58
                                      56899************95 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0026
                           Fer4_22 79 esgCvGCgRCieacpvk 95
                                         C+ C RCi++cpvk
  gi|320100263|ref|YP_004175855.1| 76 IGRCIFCWRCIDVCPVK 92
                                      55799999999999986 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.3
                           Fer4_22  12 CptCsCfdvedet....k 25 
                                       Cp+C     ++++    +
  gi|320100263|ref|YP_004175855.1| 121 CPSCGTAYGTERIiryvS 138
                                       666654444444434321 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.5   7.8e-07   0.00074       1      19 [.      39      57 ..      39      71 .. 0.86
   2 ?    2.8   4.6      0.21     2e+02       7      19 ..      78      97 ..      77     123 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.8e-07
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      V++D ++Cigcg+Cv ++p
  gi|320100263|ref|YP_004175855.1| 39 VEIDASKCIGCGACVNACP 57
                                      89****************6 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.21
                           Fer4_15  7 aCigcglCvaea.......p 19
                                      +Ci c +C++++       +
  gi|320100263|ref|YP_004175855.1| 78 RCIFCWRCIDVCpvkaikgT 97
                                      68888888888844444443 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   7.9   1.6e-06    0.0015       1      15 []      46      60 ..      46      60 .. 0.98
   2 !   12.5   2.6   0.00023      0.22       1      15 []      79      93 ..      79      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCgaCv++CP++A
  gi|320100263|ref|YP_004175855.1| 46 CIGCGACVNACPPNA 60
                                      *************98 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00023
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C +C +vCPv+A
  gi|320100263|ref|YP_004175855.1| 79 CIFCWRCIDVCPVKA 93
                                      9***66*******98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.4   2.2e-05     0.021      42      58 ..      42      58 ..      19      61 .. 0.84
   2 !    8.6   0.8    0.0029       2.7      43      57 ..      76      90 ..      60      94 .. 0.70
   3 ?    4.1   8.5     0.073        69       1      50 [.      78     155 ..      78     157 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                           Fer4_17 42 kaslCieCgeCerkCPq 58
                                       as+Ci+Cg C+ +CP 
  gi|320100263|ref|YP_004175855.1| 42 DASKCIGCGACVNACPP 58
                                      68999999999999995 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0029
                           Fer4_17 43 aslCieCgeCerkCP 57
                                      +++Ci C +C  +CP
  gi|320100263|ref|YP_004175855.1| 76 IGRCIFCWRCIDVCP 90
                                      667777777777777 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.073
                           Fer4_17   1 rCiqCgyClpeCpsyea.............ydnepkkllraakl...................glleeaekeekasl 45 
                                       rCi C  C+++Cp  ++              d + + +     +                    + ++++ ee+ ++
  gi|320100263|ref|YP_004175855.1|  78 RCIFCWRCIDVCPVKAIkgtrefelatndvADLYVHVVH----SrrkcpscgtaygteriiryVSEKAQHSEEYLDK 150
                                       7************86663322222221111111222222....1222244554444443333211122333468888 PP

                           Fer4_17  46 CieCg 50 
                                       C eC+
  gi|320100263|ref|YP_004175855.1| 151 CPECR 155
                                       88886 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 ?   16.3   4.1   1.1e-05     0.011       1      17 [.      41      57 ..      41      59 .. 0.95
   2 ?    4.3   1.8     0.062        59       6      17 ..      79      90 ..      77      95 .. 0.71
   3 ?   -2.4   0.1       7.7   7.2e+03       4      11 ..     119     126 ..     115     130 .. 0.73
   4 ?   -1.0   0.1       2.8   2.6e+03      41      52 ..     141     152 ..     126     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      +D ++Ci+cgaCv+++P
  gi|320100263|ref|YP_004175855.1| 41 IDASKCIGCGACVNACP 57
                                      799*************9 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.062
                           Fer4_13  6 CiacgaCvelaP 17
                                      Ci c  C +++P
  gi|320100263|ref|YP_004175855.1| 79 CIFCWRCIDVCP 90
                                      777777777777 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.7
                           Fer4_13   4 dtCiacga 11 
                                        +C +cg+
  gi|320100263|ref|YP_004175855.1| 119 RKCPSCGT 126
                                       56777765 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.8
                           Fer4_13  41 kadaeeAadaCP 52 
                                        ++ ee +d CP
  gi|320100263|ref|YP_004175855.1| 141 AQHSEEYLDKCP 152
                                       455667778888 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   5.1e-05     0.048      11      22 ..     119     130 ..     115     133 .. 0.91
   2 ?    2.0   0.1      0.16   1.6e+02      12      16 ..     150     154 ..     148     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                           zf-tcix  11 rkCpkCGtyNGt 22 
                                       rkCp+CGt  Gt
  gi|320100263|ref|YP_004175855.1| 119 RKCPSCGTAYGT 130
                                       9*******9887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                           zf-tcix  12 kCpkC 16 
                                       kCp+C
  gi|320100263|ref|YP_004175855.1| 150 KCPEC 154
                                       9**** 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 ?   -0.9   0.0       2.2     2e+03      33      40 ..      88      95 ..      86     119 .. 0.54
   2 ?   12.0   0.3    0.0002      0.19       4      40 ..     120     157 ..     117     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.2
                           zf-Di19 33 vCPvCaek 40
                                      vCPv a k
  gi|320100263|ref|YP_004175855.1| 88 VCPVKAIK 95
                                      78886633 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                           zf-Di19   4 tCPyCgkeltvkeLveHvedeHrvesk.evvCPvCaek 40 
                                       +CP Cg ++ ++++++ v+++ +++++    CP C ++
  gi|320100263|ref|YP_004175855.1| 120 KCPSCGTAYGTERIIRYVSEKAQHSEEyLDKCPECRKR 157
                                       7*****************9987777762469****864 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.1   0.00087      0.82      58      74 ..      76      92 ..      59      98 .. 0.81
   2 ?   -0.9   0.1       1.9   1.8e+03      37      65 ..     127     155 ..     100     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
                           Fer4_18 58 agdcidcescvkvcPtg 74
                                       g ci c  c++vcP++
  gi|320100263|ref|YP_004175855.1| 76 IGRCIFCWRCIDVCPVK 92
                                      57899999999999985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                           Fer4_18  37 iagrkkekkalkekeerkekgagdcidce 65 
                                        +g+++  + ++ek +++e+   +c +c+
  gi|320100263|ref|YP_004175855.1| 127 AYGTERIIRYVSEKAQHSEEYLDKCPECR 155
                                       45555666666667777777777777775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.0    0.0017       1.6      59      96 ..     107     158 ..      38     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                                       T-EEEEEEE--EEEETTTS-EEECHH..HHH.............S-TTTSSS- CS
                              HypA  59 gaeLeieevpvkvrCreCgkefelee..kal.............rCpkCgsad 96 
                                        a+L ++ v+ + +C +Cg+ + +e+  + +             +Cp+C +++
  gi|320100263|ref|YP_004175855.1| 107 VADLYVHVVHSRRKCPSCGTAYGTERiiR-YvsekaqhseeyldKCPECRKRN 158
                                       47899*****************9886432.3677899************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1187.81
//
Query:       gi|320100264|ref|YP_004175856.1|  [L=545]
Description: NADH-ubiquinone oxidoreductase subunit 49kDa [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-63  213.3   0.2    3.1e-47  160.9   0.2    2.1  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    1.2e-21   77.5   0.0    7.3e-21   75.0   0.0    2.1  2  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    2.1e-16   59.9   3.3    6.8e-13   48.3   0.1    3.3  3  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.9   0.2   5.2e-51   3.1e-47       2     170 ..     286     454 ..     285     458 .. 0.98
   2 !   53.3   0.0   3.5e-18   2.1e-14     194     271 .]     450     527 ..     448     527 .. 0.93

  Alignments for each domain:
  == domain 1  score: 160.9 bits;  conditional E-value: 5.2e-51
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkk 78 
                                       lG  + f+ ++r Re+i++l e++tG+R t+ + ++GGv+rD++e+  +k+ e+l+elek+  ++ ++ ++ + +kk
  gi|320100264|ref|YP_004175856.1| 286 LGYDAGFMHMWRIRERIMELAEMLTGSRKTYGINMVGGVRRDINEEKRRKVIEVLSELEKEYWKIIDVAVNVPQVKK 362
                                       678899*********************************************************************** PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       R+ g gvl ke a++lg+ Gpv+RasGv+ D R++ pY+aY++++f+vpv +egD ++R+lvr+eE ++S+++i q+
  gi|320100264|ref|YP_004175856.1| 363 RLSGTGVLPKEWAVKLGVEGPVARASGVDKDARRDLPYAAYKHVSFKVPVYTEGDNMARTLVRIEETKESMSMIIQL 439
                                       ***************************************************************************** PP

                                       HHT--.S-SB---TT CS
                    Complex1_49kDa 156 leklpegpvlaedkk 170
                                       l+ lp+gp++ e+ +
  gi|320100264|ref|YP_004175856.1| 440 LDMLPKGPIMLEEYE 454
                                       **********98866 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 3.5e-18
                                       HS-----SEEE.EEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHH CS
                    Complex1_49kDa 194 tegfkvpkgev.yaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgev 269
                                        e++++p+g + ++ vEap+G  ++y+ + g+ +pyr+++rap+++n+ al+ +l+++ laD++ +++s+d++++++
  gi|320100264|ref|YP_004175856.1| 450 LEEYEIPEGRIgVQVVEAPRGGDVHYVLT-GRGRPYRWRVRAPTYNNIPALRIMLRDQPLADAPLTIASIDPCFSCT 525
                                       688999**98746789******9999886.9********************************************** PP

                                       H- CS
                    Complex1_49kDa 270 DR 271
                                       DR
  gi|320100264|ref|YP_004175856.1| 526 DR 527
                                       *9 PP

>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   1.2e-24   7.3e-21       1     120 [.      32     151 ..      32     153 .. 0.86
   2 ?   -0.7   0.0      0.36   2.1e+03       6      63 ..     300     360 ..     297     372 .. 0.58

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.2e-24
                                       EE--HHHHHHHHHHHHH...TT--EEEEEEEEETT..SSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-S CS
                    Complex1_30kDa   1 lvvepedllevakflkdeeelgfdvlsdltavDek..eerfevvyhllsleknerirvkvevdeeepevpSvtdlfp 75 
                                       +vv++e+l+++a++l +e   g+++ +++ ++De+  ++ f++  +++  ++   + +k+++++ +p+vpS+++ +p
  gi|320100264|ref|YP_004175856.1|  32 IVVPRESLVKAASTLFNE--HGLTHRTCV-GIDERpvNGFFSLTHVFTDDSSGLYVLLKTYMESGDPVVPSIVNEVP 105
                                       5899************95..788888765.7998776666666666665566799*******889************ PP

                                       THHHHHHHHHHHSHHBCTTSSTSS-SSSSTTS..SS-TTSTTS---- CS
                    Complex1_30kDa  76 gadwyEREayDmfGivfeghpdlrrillpedf..eghPLRkdfplsg 120
                                       +adw E Ea+D++Gi+feg+   +r++lp ++    +PLRkdf+ ++
  gi|320100264|ref|YP_004175856.1| 106 AADWCEQEAMDLLGIRFEGRRR-ERLVLPPGWpeDAYPLRKDFQYDQ 151
                                       ********************98.69*******87778******9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHH....TT--EEEEEEEEETT...SSSEEEEEEEE--S-...-EEEEEE....- CS
                    Complex1_30kDa   6 edllevakflkdeee.lgfdvlsdltavDek...eerfevvyhllslekn..erirvkvevdee 63 
                                       e++ e+a++l  +++ +g++++    +v ++   e+r +v+ +l++lek+  + i v v+v++ 
  gi|320100264|ref|YP_004175856.1| 300 ERIMELAEMLTGSRKtYGINMVG---GVRRDineEKRRKVIEVLSELEKEywKIIDVAVNVPQV 360
                                       56667777777743323333332...44433444788888888888865554555677766653 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   1.1e-16   6.8e-13       1      70 [.     209     279 ..     209     289 .. 0.93
   2 ?   -2.3   0.0      0.25   1.5e+03     153     205 ..     292     341 ..     282     352 .. 0.70
   3 !    9.5   0.4   6.7e-05       0.4     371     502 ..     418     524 ..     382     526 .. 0.68

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.1e-16
                                       --HHHHTTTS.-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgr.dprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhF 70 
                                       RG+E++ + r + +++ +l++RiCG+C   H+++ + ave+A ++++p+ a++ir+++  ++ +h+h++++
  gi|320100264|ref|YP_004175856.1| 209 RGIEKLGESRmTYQQVNFLAERICGICGFEHSTCYALAVEKAAKLDVPERAQFIRSIVLEVERIHSHLLWL 279
                                       9999999998356889999*************************************************985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHH CS
                      NiFeSe_Hases 153 YLeaLelqrkaakivaifggknPhpqslvvGGvtcaidllnaerlaevkslik 205
                                       ++++ +++++++++  +++g        +vGGv   i+  + +++    ++++
  gi|320100264|ref|YP_004175856.1| 292 FMHMWRIRERIMELAEMLTGSRKTYGINMVGGVRRDINEEKRRKV---IEVLS 341
                                       66777888888888888888777777789****999665433333...33333 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEEEEEETTEEE CS
                      NiFeSe_Hases 371 tlGRtaaRaleakliaellkewldelvenikkgdtetaneekldkkevpkeakGvglveapRGaLsHwikikdgkie 447
                                        ++Rt+ R  e+k  ++++ + ld+l     kg         l++ e+p+   Gv +veapRG   H++    g+  
  gi|320100264|ref|YP_004175856.1| 418 NMARTLVRIEETKESMSMIIQLLDML----PKG------PIMLEEYEIPEGRIGVQVVEAPRGGDVHYVLTGRGRPY 484
                                       45666666666665555555544444....444......23346679999999****************99999888 PP

                                       EEEEE-HHHHHH--S-TT----HHHHHHTT-B-SSTTS-HHHHHHHHHT--BHHH CS
                      NiFeSe_Hases 448 nYqavvPsTWnasPrdakgqkgayEaaLigtpvadpekPleilrtihSfDPClAC 502
                                       ++ +  P+ +n        +  a+  +L ++p+ad   Pl    ti S DPC +C
  gi|320100264|ref|YP_004175856.1| 485 RWRVRAPT-YN--------NIPALRIMLRDQPLAD--APL----TIASIDPCFSC 524
                                       77777775.33........3345666777777765..355....56677777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3685.81
//
Query:       gi|320100265|ref|YP_004175857.1|  [L=290]
Description: respiratory-chain NADH dehydrogenase subunit 1 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-30  104.0  23.3    1.2e-29  103.6  23.3    1.1  1  NADHdh    NADH dehydrogenase
  ------ inclusion threshold ------
        1.7    8.8   5.0        8.3    6.6   0.7    2.9  3  DUF1003   Protein of unknown function (DUF1003)


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 !  103.6  23.3   1.4e-33   1.2e-29       7     295 ..      10     283 ..       3     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.4e-33
                                       HHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTT CS
                            NADHdh   7 lvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallaf 83 
                                       +++++l+ +++ ++eRkv A +q+R+GP      ++ q++ D+ Kl+ Ke++   +   +++++  vl++il  +++
  gi|320100265|ref|YP_004175857.1|  10 TLLAMLLPVIYDGVERKVKALMQSRIGP------PVYQTILDLRKLMSKETVEFPSYPLVFYTI--VLSIILEAALI 78 
                                       334555556999****************......9****************9887774444444..44444444444 PP

                                       TTS-SSS...SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS CS
                            NADHdh  84 aviPfge...vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagsl 157
                                       av+   +   ++a+l   + +++al++++    +   +   ++Y+ +G++R+a+  +  E +l+  l    ++a+  
  gi|320100265|ref|YP_004175857.1|  79 AVLNTVSlgvYTAQL---VPVAIALIAVAQTTSIAIPLLVPNPYSQVGGMREAMLALVNEFSLIAGLTLYYYAAHPA 152
                                       444433211244444...7888899999999999999999**********************999888777766654 PP

                                       .-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHH CS
                            NADHdh 158 .slseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsa 233
                                        s+ ++         + ++++++++++++++++t+r+PFD++eae EL++G+ +E sg  +al+ ++ y++ ++ s+
  gi|320100265|ref|YP_004175857.1| 153 tSIPRL---------LTVTVPLIVLLVMTTYVSTGRTPFDIAEAEVELASGVLVELSGGALALYLYSVYLKRYIASM 220
                                       144444.........445589999999************************************************** PP

                                       HHHHHCT.SS-HCCS...HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHH CS
                            NADHdh 234 lavllFlgGwllpfs...gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanl 295
                                       l +l+ l    lp++    l+++ + +++  +l+ +   +l R R+d +  + +k+ + l l+++
  gi|320100265|ref|YP_004175857.1| 221 LPALMVL--LPLPLNgvvRLMIVHVAAFATWVLYSLPAVMLGRSRVDLAPATLFKIYIALILISI 283
                                       ******9..45677766667777777888888889999*********************999987 PP

>> DUF1003  Protein of unknown function (DUF1003)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.012   1.1e+02      26      52 ..      52      80 ..       5      84 .. 0.81
   2 ?   -1.3   0.0      0.26   2.4e+03       7      33 ..     158     184 ..     154     186 .. 0.78
   3 ?    6.6   0.7   0.00092       8.3       2      45 ..     234     278 ..     233     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.012
                           DUF1003 26 pglkpfDpypFillnlvlsl..qaalaap 52
                                      +++ +f  yp +++++vls+  +aal+a 
  gi|320100265|ref|YP_004175857.1| 52 KETVEFPSYPLVFYTIVLSIilEAALIAV 80
                                      46788999**********97224666654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.26
                           DUF1003   7 lvlftaivilWialnllvlpglkpfDp 33 
                                       l+++t+ +i+ +++ ++v +g++pfD 
  gi|320100265|ref|YP_004175857.1| 158 LLTVTVPLIVLLVMTTYVSTGRTPFDI 184
                                       667788888888888888889999995 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00092
                           DUF1003   2 GsakFlvlftaivilWialnllvlp.glkpfDpypFillnlvlsl 45 
                                       G ++ +++++a +++W+++ l ++  g++++D  p +l ++ + l
  gi|320100265|ref|YP_004175857.1| 234 GVVRLMIVHVAAFATWVLYSLPAVMlGRSRVDLAPATLFKIYIAL 278
                                       5567889*************9887779999999997777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2034.47
//
Query:       gi|320100266|ref|YP_004175858.1|  [L=93]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 693.76
//
Query:       gi|320100267|ref|YP_004175859.1|  [L=506]
Description: NADH-ubiquinone/plastoquinone (complex I) oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-37  129.2  26.4    1.8e-37  129.2  26.4    2.0  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 !  129.2  26.4     1e-41   1.8e-37      17     278 ..     120     384 ..     111     408 .. 0.88
   2 ?   -0.8   0.2      0.04   7.2e+02      80     119 ..     444     486 ..     429     492 .. 0.75

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 1e-41
                   Proton_antipo_M  17 plylLiglwkkkpksleAslklflltll.gsliLLlgilllynltg.tlefeelskalelglnslelllllllllvg 91 
                                       +l++L+ ++ k +++++ ++++++l+++ ++++ L   +l+ +++g + ++++      ++++ +   l +ll+lvg
  gi|320100267|ref|YP_004175859.1| 120 VLLMLVIMMDKGAENYKVAIYYIVLSAVpADVAVLSLWALIAQYMGlDASLTASPAE-LAAVKIPLSPLPALLILVG 195
                                       57788888889999***********99956777777777999999953333332222.667888999999******* PP

                   Proton_antipo_M  92 llvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllilaiismllgslvalaq 168
                                       +++K++++p+h+Wlp ++ eaP  +sa+l++++ k+g+++l+ +++l+  +s e++++ l+ ++i++l+g+++a  q
  gi|320100267|ref|YP_004175859.1| 196 FATKLGLFPIHMWLPIVHPEAPKHGSAILSGLVIKIGLFGLLLTSSLFT-YSSELHYVTLAQGAITALYGGFAATIQ 271
                                       *************************************************.*************************** PP

                   Proton_antipo_M 169 tdiKrllAySsishlGymlialavatqyg....veaaiihllthalfkallFllagsviyerektrdirayggLakk 241
                                       +d++rllAySs+sh G+m +  +++ +yg    +++++++++ h+l ka  F+ a  +  +  +t d+ ++g+L + 
  gi|320100267|ref|YP_004175859.1| 272 RDVRRLLAYSSLSHAGVMAVTYSLSEIYGsgllLQLLYFYVIYHGLAKAHAFMNAALM-DQLANTFDVYKLGYLGQL 347
                                       ************************88888555569999*****************666.7788************** PP

                   Proton_antipo_M 242 mPilalvllvlllslaGlPptagFlskfliLeaavav 278
                                        P l +  + +++  aG+Pp  gF  k+ +L+++v  
  gi|320100267|ref|YP_004175859.1| 348 HPALIVPAFNIFMNFAGIPPSYGFTMKLVLLASLVML 384
                                       *******************************987643 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.04
                   Proton_antipo_M  80 elllllllllvgllvKsaqvplhlWlpdayvea...Ptpvsal 119
                                        ++l++ l+ +++ + s+ +pl+l +p a vea   P+ +++l
  gi|320100267|ref|YP_004175859.1| 444 SVTLVFPLIYIAISLSSGYMPLQLLVPLAVVEAitlPVFITVL 486
                                       5678889999999999999999999999977763224444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3756.81
//
Query:       gi|320100268|ref|YP_004175860.1|  [L=504]
Description: NADH-ubiquinone/plastoquinone (complex I) oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for 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-29  101.2  22.0      9e-29  100.6  20.7    2.1  1  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 !  100.6  20.7     5e-33     9e-29       3     279 ..     108     397 ..     106     413 .. 0.75

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 5e-33
                   Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsli.LLlgilllynltgtlefeelskal...... 72 
                                       ++l++ +++ +  ++   Li++ +++  s+e sl ++  +l+ s + + ++++ +  ++  + + ++++a       
  gi|320100268|ref|YP_004175860.1| 108 NILAMAVAWTVAEVVGWYLITMGEAH--SVEGSLRSARGFLVTSTLtFEISVFTVVMVSVLTTVAAMASANigllme 182
                                       66666677776666666666655333..4444444444333333210222222222222222233333322333445 PP

                   Proton_antipo_M  73 ..elgln.slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla..vssn 144
                                         ++ +  s   l l  +l++g+++K+a +plh+Wlp a+ +aP+p sa l++++  +g ++l r+l ++    ++ 
  gi|320100268|ref|YP_004175860.1| 183 pfTALKPfSGVGLYLVPFLIIGFITKAANIPLHFWLPGAHSAAPAPASAVLSGLMTLLGFYGLYRVLHIVDltRYYT 259
                                       44444430334455667999**********************************************9999888999* PP

                   Proton_antipo_M 145 eisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav....atqygveaaiihllthalfkallFl 217
                                        i+ ++++l++ s+++g +   +q+d K+llAy +i+  Gy+ + +a+     + ++ +++ + +l+ha  k +lF+
  gi|320100268|ref|YP_004175860.1| 260 VIAAVIATLGASSVIYGWTQIAVQRDGKKLLAYATIATNGYISLVFALyllnPSGMAEDLLKLSILMHATYKTTLFA 336
                                       *****************************************866655544445667778888999************ PP

                   Proton_antipo_M 218 lagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavs 279
                                        +g +  +   tr+i  ++gL+   P+ ++  l+++l+l G+P+t gF  k+l  + +v+  
  gi|320100268|ref|YP_004175860.1| 337 EVGLI-EAVYGTRYIHGVRGLSRILPLSSIGGLLAVLTLIGVPGTIGFTVKALSVYYIVSGT 397
                                       **666.7788*****************************************99988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3619.81
//
Query:       gi|320100269|ref|YP_004175861.1|  [L=163]
Description: 4Fe-4S ferredoxin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-21   76.0   9.8    1.9e-21   76.0   9.8    1.7  2  Fer4_11   4Fe-4S dicluster domain
    2.4e-13   50.0  45.2      3e-06   27.3  11.1    3.0  4  Fer4_9    4Fe-4S dicluster domain
    1.1e-12   47.2  37.2    1.1e-05   25.1   3.5    5.7  6  Fer4      4Fe-4S binding domain
    1.1e-11   44.3  38.9    2.9e-05   23.9   2.8    4.9  4  Fer4_6    4Fe-4S binding domain
    2.2e-11   44.2  51.5    7.2e-06   26.5  13.1    3.9  4  Fer4_7    4Fe-4S dicluster domain
    7.3e-10   38.8  29.0    4.9e-06   26.6  12.2    3.6  4  Fer4_10   4Fe-4S dicluster domain
    1.3e-08   35.2  37.3     0.0039   18.0   3.6    4.4  4  Fer4_3    4Fe-4S binding domain
    4.7e-08   32.7  33.7    0.00037   20.4   1.9    4.6  4  Fer4_2    4Fe-4S binding domain
    3.2e-07   30.3  36.2    0.00078   19.8   2.3    4.7  4  Fer4_4    4Fe-4S binding domain
    3.8e-07   31.0  28.3      0.013   16.5   1.7    4.8  5  Fer4_16   4Fe-4S double cluster binding domain
    1.8e-05   25.2  23.9      0.011   16.2   1.2    4.4  4  Fer4_17   4Fe-4S dicluster domain
    2.1e-05   24.6  29.7     0.0029   17.7  11.8    3.8  4  Fer4_21   4Fe-4S dicluster domain
    3.9e-05   24.0  27.7      0.038   14.5  10.1    4.1  2  Fer4_8    4Fe-4S dicluster domain
     0.0018   18.9  16.4      0.073   13.8   4.8    3.2  3  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.07   13.7   0.8       0.07   13.7   0.8    4.3  4  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.41   10.9  24.0       0.11   12.7   2.5    3.7  4  Fer4_18   4Fe-4S dicluster domain
        1.8    9.4  22.0       0.81   10.6   1.1    4.0  4  Fer4_22   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 ?   -1.1   0.0       1.9     2e+03      43      62 ..      23      42 ..      17      48 .. 0.73
   2 !   76.0   9.8   1.8e-24   1.9e-21       6      99 ..      48     139 ..      44     140 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                           Fer4_11 43 kkeevrevveacPykivrkn 62
                                      +++ ++ ++++ Py +v+++
  gi|320100269|ref|YP_004175861.1| 23 CEAACDFIHDGHPYIKVYRT 42
                                      56667778888888777765 PP

  == domain 2  score: 76.0 bits;  conditional E-value: 1.8e-24
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       +p  C+hC ++pC++++p++a+++d  +GaV +  +++  ++ ++  acP+ i+  +++  +++kCd+c+d+ ++Gl
  gi|320100269|ref|YP_004175861.1|  48 IPVSCMHCAKAPCIDVCPTGAMTRDS-DGAVYVAASKCI-GCMACLYACPFGIPELDRSLRVSTKCDLCMDQRRKGL 122
                                       5889*******************999.***********7.************************************* PP

                           Fer4_11  83 lpacvescptgalnfgd 99 
                                       +p c++ cp+ga+ +g+
  gi|320100269|ref|YP_004175861.1| 123 EPGCSSICPAGAILYGE 139
                                       ***********998886 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   3.2   0.00011      0.12      35      46 ..      16      27 ..       5      31 .. 0.67
   2 !   21.3  11.4   2.1e-07   0.00022       2      51 .]      17      69 ..      16      69 .. 0.71
   3 !   27.3  11.1   2.8e-09     3e-06       2      49 ..      52      97 ..      51      98 .. 0.88
   4 !   26.4   6.8   5.5e-09   5.8e-06       1      51 []      83     135 ..      83     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            Fer4_9 35 aCigCgaCveaC 46
                                       CigCgaC++aC
  gi|320100269|ref|YP_004175861.1| 16 TCIGCGACEAAC 27
                                      466666666665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.1e-07
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase...eaCigCga..CveaCpkgai 51
                                      C+gCgaC++aC + +      + ++           +C++C +  C+++Cp+ga+
  gi|320100269|ref|YP_004175861.1| 17 CIGCGACEAACDFIHDGHPYIKVYRTEIG--LeipVSCMHCAKapCIDVCPTGAM 69
                                      ***********766654444443333211..124568***************985 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 2.8e-09
                            Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      C+ C +  C+++Cp+g++++d+ +           +CigC+aC+ aCp g
  gi|320100269|ref|YP_004175861.1| 52 CMHCAKapCIDVCPTGAMTRDSDGAVYVAAS----KCIGCMACLYACPFG 97
                                      ****8667************99999988754....6************77 PP

  == domain 4  score: 26.4 bits;  conditional E-value: 5.5e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaCpkgai 51 
                                       kC+gC aC +aCp+g+ + d++ r          +C  C++         C  +Cp gai
  gi|320100269|ref|YP_004175861.1|  83 KCIGCMACLYACPFGIPELDRSLRVST-------KCDLCMDqrrkglepgCSSICPAGAI 135
                                       7*****************999999877.......5**********************987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   3.8   1.5e-07   0.00015       2      18 ..      11      27 ..      10      29 .. 0.92
   2 ?   -0.5   0.3       1.2   1.3e+03      10      16 ..      51      57 ..      50      58 .. 0.65
   3 !   11.9   0.8   0.00015      0.16      14      23 ..      60      69 ..      59      70 .. 0.92
   4 !   25.1   3.5     1e-08   1.1e-05       2      22 ..      78      98 ..      77     100 .. 0.87
   5 ?    1.0   0.1       0.4   4.2e+02      10      15 ..     110     115 ..     108     117 .. 0.65
   6 !    8.5   0.2    0.0017       1.8      14      23 ..     126     135 ..     125     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.5e-07
                                      EEETTTSSS-THHHHHS CS
                              Fer4  2 videekCigCGaCvevC 18
                                      +id   CigCGaC+ +C
  gi|320100269|ref|YP_004175861.1| 11 IIDLGTCIGCGACEAAC 27
                                      6999************* PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                                      S-THHHH CS
                              Fer4 10 gCGaCve 16
                                       C+ C++
  gi|320100269|ref|YP_004175861.1| 51 SCMHCAK 57
                                      5777776 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00015
                                      HHHHSTTTEE CS
                              Fer4 14 CvevCPvgAI 23
                                      C++vCP+gA 
  gi|320100269|ref|YP_004175861.1| 60 CIDVCPTGAM 69
                                      *********7 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 1e-08
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                      ++  +kCigC+aC  +CP+g 
  gi|320100269|ref|YP_004175861.1| 78 YVAASKCIGCMACLYACPFGI 98
                                      67789**************97 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.4
                                       S-THHH CS
                              Fer4  10 gCGaCv 15 
                                       +C +C+
  gi|320100269|ref|YP_004175861.1| 110 KCDLCM 115
                                       577776 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0017
                                       HHHHSTTTEE CS
                              Fer4  14 CvevCPvgAI 23 
                                       C ++CP gAI
  gi|320100269|ref|YP_004175861.1| 126 CSSICPAGAI 135
                                       9********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 !   18.0   2.6     2e-06    0.0022       4      19 ..      12      27 ..      11      31 .. 0.87
   2 !   10.3   5.8   0.00057       0.6       8      23 ..      51      68 ..      48      69 .. 0.88
   3 !   23.9   2.8   2.8e-08   2.9e-05       3      23 ..      78      98 ..      76      99 .. 0.87
   4 !    9.2   4.2    0.0013       1.4       8      24 .]     110     135 ..     107     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                            Fer4_6  4 idpdkCigCgdCvrvC 19
                                      id   CigCg+C+++C
  gi|320100269|ref|YP_004175861.1| 12 IDLGTCIGCGACEAAC 27
                                      67778*********** PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00057
                            Fer4_6  8 kCigCgd..CvrvCPega 23
                                      +C +C +  C++vCP+ga
  gi|320100269|ref|YP_004175861.1| 51 SCMHCAKapCIDVCPTGA 68
                                      799**8889*******98 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 2.8e-08
                            Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                       + ++kCigC++C  +CP+g+
  gi|320100269|ref|YP_004175861.1| 78 YVAASKCIGCMACLYACPFGI 98
                                      56689*************996 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0013
                            Fer4_6   8 kCigCgd.........CvrvCPegai 24 
                                       kC+ C+d         C ++CP+gai
  gi|320100269|ref|YP_004175861.1| 110 KCDLCMDqrrkglepgCSSICPAGAI 135
                                       8*****99*****************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9  12.9   2.2e-08   2.3e-05       1      52 []      16      68 ..      16      68 .. 0.77
   2 !   26.5  13.1   6.8e-09   7.2e-06       1      52 []      51      98 ..      51      98 .. 0.91
   3 !   17.8   9.4   3.6e-06    0.0038       1      52 []      83     134 ..      83     134 .. 0.75
   4 ?    6.2   1.2     0.015        16       7      22 ..     125     140 ..     109     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.2e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52
                                      +CigCgaC+aaC     + +++ +  +te     p +C++C +  C++vCPtga
  gi|320100269|ref|YP_004175861.1| 16 TCIGCGACEAACD-FIHDGHPYIKVYRTEIGLEIPVSCMHCAKapCIDVCPTGA 68
                                      6***********9.3344444444445555666799******999*******98 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 6.8e-09
                            Fer4_7  1 rCigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C++C    C ++Cp++a++ d +        v++ ++kC+gC aC  +CP+g+
  gi|320100269|ref|YP_004175861.1| 51 SCMHCAkaPCIDVCPTGAMTRDSD------GAVYVAASKCIGCMACLYACPFGI 98
                                      5****6569************997......47999*****************96 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.6e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga......CvavCPtga 52 
                                       +CigC aC  aCp +  eld + +      v  + + C++ ++      C + CP+ga
  gi|320100269|ref|YP_004175861.1|  83 KCIGCMACLYACPFGIPELDRSLR------VSTKCDLCMDQRRkglepgCSSICPAGA 134
                                       7******************99854......4455555655443333446******997 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.015
                            Fer4_7   7 aCvaaCpvkaieldee 22 
                                        C + Cp++ai + ee
  gi|320100269|ref|YP_004175861.1| 125 GCSSICPAGAILYGEE 140
                                       5999999998887754 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  12.7   7.6e-07    0.0008       3      56 .]      11      65 ..       9      65 .. 0.84
   2 !   26.6  12.2   4.6e-09   4.9e-06       7      56 .]      50      95 ..      44      95 .. 0.94
   3 !   17.1  10.6   4.3e-06    0.0045       3      56 .]      78     131 ..      76     131 .. 0.79
   4 ?    4.8   1.1     0.029        31      14      23 ..     125     134 ..     105     159 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.6e-07
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcg..aCveaCP 56
                                      +id  tCi+Cg+C +aC  d+ ++g  +++ +  ++    + +C++c    C+++CP
  gi|320100269|ref|YP_004175861.1| 11 IIDLGTCIGCGACEAAC--DFIHDGHPYIKVYRTEIGLeIPVSCMHCAkaPCIDVCP 65
                                      79999************..888888888777665555449*******7679*****9 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.6e-09
                           Fer4_10  7 dtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       +C++C+   C ++CP+      +   ++ ++av ++ +kC+gc aC  aCP
  gi|320100269|ref|YP_004175861.1| 50 VSCMHCAkaPCIDVCPT------GAMTRDSDGAVYVAASKCIGCMACLYACP 95
                                      68****9889*******......9999************************9 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 4.3e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg......aCveaCP 56 
                                       ++ +++Ci+C +C  aCP+      +++e +++ +v++k++ C++         C ++CP
  gi|320100269|ref|YP_004175861.1|  78 YVAASKCIGCMACLYACPF------GIPELDRSLRVSTKCDLCMDQRrkglepGCSSICP 131
                                       66789**************......88888888888887777777534446679*****9 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.029
                           Fer4_10  14 kCvkaCPadl 23 
                                        C + CPa +
  gi|320100269|ref|YP_004175861.1| 125 GCSSICPAGA 134
                                       4777888855 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   4.2    0.0003      0.32       1      11 [.      17      27 ..      17      29 .. 0.97
   2 !   13.8   6.2   8.1e-05     0.086       1      15 []      52      68 ..      52      68 .. 0.91
   3 !   18.0   3.6   3.7e-06    0.0039       1      14 [.      84      97 ..      84      98 .. 0.95
   4 !    8.6   0.8    0.0037       3.9       1      15 []     111     134 ..     110     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gCgaC+ +C
  gi|320100269|ref|YP_004175861.1| 17 CIGCGACEAAC 27
                                      *********** PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.1e-05
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C++C   +C +vCP+gA
  gi|320100269|ref|YP_004175861.1| 52 CMHCAkaPCIDVCPTGA 68
                                      ****7668********9 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 3.7e-06
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+gC+aC+ +CP g
  gi|320100269|ref|YP_004175861.1| 84 CIGCMACLYACPFG 97
                                      ************98 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0037
                            Fer4_3   1 CtgCg.........aCvevCPvgA 15 
                                       C+ C+          C   CP gA
  gi|320100269|ref|YP_004175861.1| 111 CDLCMdqrrkglepGCSSICPAGA 134
                                       999*88887776555******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 !   15.9   2.8   9.8e-06      0.01       5      20 ..      12      27 ..       9      27 .. 0.91
   2 !   12.8   2.5     9e-05     0.094       9      22 .]      51      66 ..      43      66 .. 0.87
   3 !   20.4   1.9   3.5e-07   0.00037       3      21 ..      77      95 ..      75      96 .. 0.84
   4 ?    0.6   3.5       0.7   7.3e+02      15      22 .]     125     132 ..     105     132 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.8e-06
                            Fer4_2  5 vdtdrCigCgaCvsaC 20
                                      +d  +CigCgaC  aC
  gi|320100269|ref|YP_004175861.1| 12 IDLGTCIGCGACEAAC 27
                                      78889*********9* PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9e-05
                            Fer4_2  9 rCigCg..aCvsaCPa 22
                                      +C++C   +C+++CP+
  gi|320100269|ref|YP_004175861.1| 51 SCMHCAkaPCIDVCPT 66
                                      5****667*******7 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 3.5e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      v+v + +CigC aC+ aCP
  gi|320100269|ref|YP_004175861.1| 77 VYVAASKCIGCMACLYACP 95
                                      5566789************ PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.7
                            Fer4_2  15 aCvsaCPa 22 
                                        C s CPa
  gi|320100269|ref|YP_004175861.1| 125 GCSSICPA 132
                                       59999*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 !   16.3   3.3   9.4e-06    0.0099       3      14 ..      16      27 ..      14      29 .. 0.93
   2 !    9.7   3.6    0.0012       1.3       3      17 .]      51      67 ..      50      67 .. 0.93
   3 !   19.8   2.3   7.4e-07   0.00078       2      17 .]      82      97 ..      81      97 .. 0.91
   4 ?    1.4   3.6      0.58   6.1e+02       4      16 ..     111     132 ..     108     138 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.4e-06
                            Fer4_4  3 rCigCgsCvaaC 14
                                      +CigCg+C+aaC
  gi|320100269|ref|YP_004175861.1| 16 TCIGCGACEAAC 27
                                      7*********** PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                            Fer4_4  3 rCigCgs..CvaaCPqg 17
                                      +C +C +  C+++CP+g
  gi|320100269|ref|YP_004175861.1| 51 SCMHCAKapCIDVCPTG 67
                                      6**************86 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 7.4e-07
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++CigC++C +aCP+g
  gi|320100269|ref|YP_004175861.1| 82 SKCIGCMACLYACPFG 97
                                      68************86 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.58
                            Fer4_4   4 CigCg.s........CvaaCPq 16 
                                       C  C+ +        C ++CP 
  gi|320100269|ref|YP_004175861.1| 111 CDLCMdQrrkglepgCSSICPA 132
                                       5555531344455559999996 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   1.1     0.002       2.1      53      64 ..      16      27 ..       6      29 .. 0.68
   2 !   16.5   1.7   1.2e-05     0.013       2      23 ..      52      75 ..      51      83 .. 0.85
   3 !   11.3   2.0    0.0005      0.53       1      15 [.      83      97 ..      83     110 .. 0.81
   4 ?    0.1   0.2       1.5   1.6e+03      55      62 ..     109     116 ..      99     117 .. 0.75
   5 !   10.3   0.1     0.001       1.1       8      35 ..     126     153 ..     124     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                           Fer4_16 53 aitgCdiCqdvC 64
                                       ++gC++C+++C
  gi|320100269|ref|YP_004175861.1| 16 TCIGCGACEAAC 27
                                      456666666666 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                           Fer4_16  2 CgtCgk..CaevCPtnaikekkek 23
                                      C  C k  C++vCPt+a++ +++ 
  gi|320100269|ref|YP_004175861.1| 52 CMHCAKapCIDVCPTGAMTRDSDG 75
                                      99**9999***********98654 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0005
                           Fer4_16  1 rCgtCgkCaevCPtn 15
                                      +C++C +C+ +CP +
  gi|320100269|ref|YP_004175861.1| 83 KCIGCMACLYACPFG 97
                                      599999999999976 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.5
                           Fer4_16  55 tgCdiCqd 62 
                                       t Cd C+d
  gi|320100269|ref|YP_004175861.1| 109 TKCDLCMD 116
                                       77888876 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.001
                           Fer4_16   8 CaevCPtnaikekkekeiearecisynt 35 
                                       C ++CP++ai   +e+ +  r+++ +++
  gi|320100269|ref|YP_004175861.1| 126 CSSICPAGAILYGEEAAVFERAKKRTAE 153
                                       9**********88655554444443333 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   0.3   0.00011      0.11      45      56 ..      16      27 ..       7      42 .. 0.77
   2 !    8.2   1.6    0.0035       3.7       2      20 ..      52      72 ..      51      81 .. 0.81
   3 !   16.2   1.2   1.1e-05     0.011      42      60 ..      80      98 ..      69      99 .. 0.85
   4 ?    3.0   0.8      0.14   1.5e+02       4      31 ..     110     149 ..     109     162 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                           Fer4_17 45 lCieCgeCerkC 56
                                      +Ci+Cg Ce++C
  gi|320100269|ref|YP_004175861.1| 16 TCIGCGACEAAC 27
                                      566666666666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0035
                           Fer4_17  2 CiqCgy..ClpeCpsyeaydn 20
                                      C++C+   C+++Cp+++ +++
  gi|320100269|ref|YP_004175861.1| 52 CMHCAKapCIDVCPTGAMTRD 72
                                      *****888******9887665 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.1e-05
                           Fer4_17 42 kaslCieCgeCerkCPqgl 60
                                      +as+Ci+C  C ++CP g+
  gi|320100269|ref|YP_004175861.1| 80 AASKCIGCMACLYACPFGI 98
                                      689*************987 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.14
                           Fer4_17   4 qCgyClp............eCpsyeaydnepkkllraakl 31 
                                       +C  C++             Cp +++   e++ + ++ak 
  gi|320100269|ref|YP_004175861.1| 110 KCDLCMDqrrkglepgcssICPAGAILYGEEAAVFERAKK 149
                                       5777777666666666666888877744445555555443 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5  10.9   3.2e-06    0.0034       3      57 ..      12      69 ..      10      71 .. 0.85
   2 !   17.7  11.8   2.7e-06    0.0029       7      53 ..      51      96 ..      48     100 .. 0.91
   3 ?   -0.8   0.1       1.7   1.8e+03      43      48 ..     110     115 ..     106     117 .. 0.73
   4 ?    2.6   0.2      0.15   1.6e+02      47      57 ..     126     135 ..     124     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.2e-06
                           Fer4_21  3 idedkCigCgkCliaCe..dtshqaieidaktvlkvvedeCvGCnl..CssvCPvedci 57
                                      id  +CigCg C  aC+    +h  i++   ++   +  +C+ C+   C++vCP+ +++
  gi|320100269|ref|YP_004175861.1| 12 IDLGTCIGCGACEAACDfiHDGHPYIKVYRTEIGLEIPVSCMHCAKapCIDVCPT-GAM 69
                                      8889************85567999999999998888999*****8666******6.665 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.7e-06
                           Fer4_21  7 kCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53
                                      +C++C k  C+ +C+   + a++ d++  + v +++C+GC  C+  CP 
  gi|320100269|ref|YP_004175861.1| 51 SCMHCAKapCIDVCP---TGAMTRDSDGAVYVAASKCIGCMACLYACPF 96
                                      6****9888******...588999999999******************5 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.7
                           Fer4_21  43 GCnlCs 48 
                                        C+lC+
  gi|320100269|ref|YP_004175861.1| 110 KCDLCM 115
                                       588886 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.15
                           Fer4_21  47 CssvCPvedci 57 
                                       Css+CP  ++i
  gi|320100269|ref|YP_004175861.1| 126 CSSICPA-GAI 135
                                       ******5.776 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  10.1   3.6e-05     0.038       3      64 ..      15      67 ..      13      68 .. 0.76
   2 !    9.3   9.6    0.0014       1.5       2      20 ..      81      99 ..      80     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                        Ci+CgaC++aC ++++    ++  r e      e           sC++c +  C +vCp+g
  gi|320100269|ref|YP_004175861.1| 15 GTCIGCGACEAACDFIHDGHPYIKVYRTEIGL---EI--------PVSCMHCAKapCIDVCPTG 67
                                      68************999985554444444322...33........569****9999******87 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                            Fer4_8  2 lekCieCgaCqsaCpvlrr 20
                                      ++kCi+C+aC  aCp+   
  gi|320100269|ref|YP_004175861.1| 81 ASKCIGCMACLYACPFGIP 99
                                      689***********95443 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   4.8   6.9e-05     0.073       3      64 ..      12      69 ..      11      71 .. 0.84
   2 !   11.3   1.4   0.00043      0.45       1      27 [.      77     103 ..      77     120 .. 0.80
   3 ?   -0.6   0.0       2.2   2.3e+03      59      64 ..     130     135 ..     127     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.9e-05
                           Fer4_15  3 vDrdaCigcglCvaeapevfeldedglasvllddgeiaeg.evpddeeeaaqe.AaraCPvdAI 64
                                      +D  +Cigcg+C a+++    +  dg++++++ + e   g e+p   + +a+    ++CP++A+
  gi|320100269|ref|YP_004175861.1| 12 IDLGTCIGCGACEAACD----FIHDGHPYIKVYRTE--IGlEIPVSCMHCAKApCIDVCPTGAM 69
                                      8999************7....445799999998766..6679****99999973689***9997 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00043
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfelded 27 
                                       V+v  ++Cigc +C+ ++p  + + ++
  gi|320100269|ref|YP_004175861.1|  77 VYVAASKCIGCMACLYACPFGIPELDR 103
                                       6677899***********966665555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.2
                           Fer4_15  59 CPvdAI 64 
                                       CP++AI
  gi|320100269|ref|YP_004175861.1| 130 CPAGAI 135
                                       *****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 ?   13.7   0.8   6.6e-05      0.07       1      19 [.      12      30 ..      12      44 .. 0.81
   2 ?    1.7   2.5      0.36   3.8e+02       6      32 ..      52      80 ..      49      83 .. 0.75
   3 ?    9.3   4.2    0.0016       1.7       4      17 ..      82      95 ..      79      96 .. 0.91
   4 ?   -0.9   0.3       2.3   2.4e+03      14      53 ..     128     132 ..     125     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPdv 19
                                      +D  tCi+cgaC +++  +
  gi|320100269|ref|YP_004175861.1| 12 IDLGTCIGCGACEAACDFI 30
                                      7999**********99655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.36
                           Fer4_13  6 Ciacga..CvelaPdvFeeddeggasvva 32
                                      C+ c++  C +++P      d +ga++va
  gi|320100269|ref|YP_004175861.1| 52 CMHCAKapCIDVCPTGAMTRDSDGAVYVA 80
                                      77776555999999988888888888886 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0016
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      ++Ci+c+aC  ++P
  gi|320100269|ref|YP_004175861.1| 82 SKCIGCMACLYACP 95
                                      79***********9 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.3
                           Fer4_13  14 elaPdvFeeddeggasvvaeqptseeekadaeeAadaCPv 53 
                                       +++P                                    
  gi|320100269|ref|YP_004175861.1| 128 SICP-----------------------------------A 132
                                       5555...................................3 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.9     0.022        23      84     100 ..      16      32 ..      11      40 .. 0.85
   2 ?    8.0  10.4     0.003       3.2      60      95 ..      51      94 ..      41      94 .. 0.78
   3 ?   12.7   2.5    0.0001      0.11      54      94 ..      77     117 ..      68     124 .. 0.76
   4 ?   -0.7   0.0       1.5   1.6e+03       6      24 ..     126     141 ..     119     161 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
                           Fer4_18  84 eciscllcidacdkvme 100
                                        ci c+ c  acd + +
  gi|320100269|ref|YP_004175861.1|  16 TCIGCGACEAACDFIHD 32 
                                       59999999999998865 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                           Fer4_18 60 dcidces..cvkvcPtgidirk..G....lqleciscllcidac 95
                                       c++c +  c++vcPtg   r+  G       +ci c+ c+ ac
  gi|320100269|ref|YP_004175861.1| 51 SCMHCAKapCIDVCPTGAMTRDsdGavyvAASKCIGCMACLYAC 94
                                      699997555*********999733432223459*********99 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.0001
                           Fer4_18  54 kekgagdcidcescvkvcPtgidirkGlqleciscllcida 94 
                                          +a++ci c +c+  cP gi   +       +c lc+d 
  gi|320100269|ref|YP_004175861.1|  77 VYVAASKCIGCMACLYACPFGIPELDRSLRVSTKCDLCMDQ 117
                                       5567899***************6555444445799999996 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.5
                           Fer4_18   6 cvyvcPyarvqsvlydeet 24 
                                       c  +cP +   ++ly ee+
  gi|320100269|ref|YP_004175861.1| 126 CSSICPAG---AILYGEEA 141
                                       66666654...34555554 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.1   0.00077      0.81      78      93 ..      13      28 ..       5      30 .. 0.81
   2 ?    2.9   2.0      0.19     2e+02       2      17 ..      52      69 ..      51      83 .. 0.78
   3 ?    7.5   2.2     0.007       7.4      79      95 ..      81      97 ..      69      98 .. 0.75
   4 ?   -0.2   0.0       1.8   1.9e+03       8      24 ..     126     142 ..     123     161 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00077
                           Fer4_22 78 gesgCvGCgRCieacp 93
                                      +  +C+GCg C++ac 
  gi|320100269|ref|YP_004175861.1| 13 DLGTCIGCGACEAACD 28
                                      5568999999999995 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                           Fer4_22  2 ClsCga..CtlvCptCsC 17
                                      C++C++  C  vCpt   
  gi|320100269|ref|YP_004175861.1| 52 CMHCAKapCIDVCPTGAM 69
                                      99998656999***9765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.007
                           Fer4_22 79 esgCvGCgRCieacpvk 95
                                      +s+C+GC  C  acp +
  gi|320100269|ref|YP_004175861.1| 81 ASKCIGCMACLYACPFG 97
                                      56788888888888765 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.8
                           Fer4_22   8 CtlvCptCsCfdvedet 24 
                                       C+ +Cp+      e+ +
  gi|320100269|ref|YP_004175861.1| 126 CSSICPAGAILYGEEAA 142
                                       88888887666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1185.83
//
Query:       gi|320100270|ref|YP_004175862.1|  [L=359]
Description: sulfide dehydrogenase (flavoprotein) subunit SudA [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-34  118.5   0.0    4.1e-34  118.1   0.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    9.5e-12   45.3   1.1    2.8e-06   27.8   0.1    3.4  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    4.2e-11   42.6   1.0    2.3e-07   30.4   0.0    3.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.4e-09   37.1   2.0     0.0006   19.3   0.0    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
    2.9e-09   37.0   2.9    3.6e-08   33.5   0.2    2.4  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.8e-08   32.8   0.5     0.0015   17.7   0.0    3.2  3  FAD_binding_2  FAD binding domain
    2.1e-06   26.7   2.1    9.3e-05   21.3   0.2    2.6  3  HI0933_like    HI0933-like protein
    4.8e-06   26.0   0.4      0.026   13.8   0.0    2.3  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    9.1e-06   25.0   2.5      0.017   14.3   0.3    2.4  2  GIDA           Glucose inhibited division protein A
    3.9e-05   23.4   6.5      0.014   15.0   0.3    3.2  3  DAO            FAD dependent oxidoreductase
    0.00013   21.4   0.5    0.00053   19.3   0.1    2.1  3  FAD_binding_3  FAD binding domain
     0.0021   17.3   0.5      0.014   14.7   0.1    2.1  2  Thi4           Thi4 family
     0.0029   18.0   0.1       0.12   12.9   0.0    2.3  2  NAD_binding_7  Putative NAD(P)-binding
     0.0031   17.6   0.1       0.87    9.7   0.0    2.8  3  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
     0.0048   16.2   0.0       0.66    9.2   0.0    2.2  2  Amino_oxidase  Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
      0.011   15.7   0.5      0.071   13.0   0.0    2.1  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.011   15.8   1.1       0.79    9.7   0.1    3.1  3  NAD_binding_9  FAD-NAD(P)-binding
      0.024   13.8   0.3       0.26   10.4   0.0    2.5  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
      0.033   12.6   0.0       0.37    9.2   0.0    2.1  2  FMO-like       Flavin-binding monooxygenase-like


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 !  118.1   0.0   4.4e-37   4.1e-34       2     294 .]      17     338 ..      16     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 4.4e-37
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllg 72 
                                       +v+viG+GpAGlaaa +la +g+ v ++ ++  +++ g l+  a+  ++ +++ ++      e  k  + g++++++
  gi|320100270|ref|YP_004175862.1|  17 KVAVIGAGPAGLAAAGYLACQGYSVDVY-DK--LPHPGGLMVFAIPPWRIPRSRVLegvrdlE--K--RLGVRFITR 86 
                                       79**************************.44..444444554566666655555553454332..2..234677777 PP

                                       CTCEEEE...ESCEEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T... CS
                                       xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Pyr_redox_2  73 eevvkid...pgkkkvklekkkegdeekiaydklvlAtGs.sprdlgipGvaenvgklvrtldsaealklkllp... 142
                                       ++v +     +++++  +ek+ + +e    yd ++l tG  +++++ ipG   ++++  ++l+ + +++l +l    
  gi|320100270|ref|YP_004175862.1|  87 TKVYASPepaHEEGDGFVEKTLSLEEIVGSYDLVLLSTGTwRSKIPRIPGSDAKGVE--SALEYVHGFRLYELGlaa 161
                                       4433332333444555555555566667789********7488888****9333332..366666666666666666 PP

                                       ......SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETT CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ......krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgng 213
                                             kr+vvvGgGy +++ A ++ + g+e++lv++r+      +  ++ +  e++++ Gve++   s++ei++++
  gi|320100270|ref|YP_004175862.1| 162 skpfpgKRVVVVGGGYSAIDAAEQAVREGAEAYLVYRRTVK----EAPAGLFEVERVKRLGVEFMELVSPVEIISEN 234
                                       777888*******************************5544....356677777999999***************99 PP

                                       E.....EEE.EEETTSCE...............EEESEEEE-S-EEES-HHCS.....HCCT-EEEETTEEE--TTS CS
                                       x.....xxx.xxxxxxxx...............xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 214 e.....kle.vvledgee...............idadlvvvavGvrpstelle.....eklglelderggivvdefl 264
                                             kl+ ++l+  +e               ++ad vv+a+G +p ++l +      +lg++l+++g ivv++ +
  gi|320100270|ref|YP_004175862.1| 235 GavkavKLQrMQLGPPDEtgrpqpipvpgseivVEADRVVFATGETPTPPLPQseeymGRLGIKLKKDGSIVVNQIM 311
                                       9555443335555555559999***************************997787778899**************** PP

                                       BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       +t  p+++a+GDv+   +gp  +  A+++G
  gi|320100270|ref|YP_004175862.1| 312 QTGNPKVFAAGDVV---HGPSKVGPAIRSG 338
                                       **************...8998888888776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00014      0.14       1      34 [.      17      50 ..      17      55 .. 0.90
   2 ?    1.3   0.0      0.54   5.1e+02      49      64 ..      74      90 ..      67     107 .. 0.80
   3 !   27.8   0.1     3e-09   2.8e-06       1      79 [.     169     243 ..     169     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                      kv+v+G+G  gl +Ag+la  g +V v +  +++
  gi|320100270|ref|YP_004175862.1| 17 KVAVIGAGPAGLAAAGYLACQGYSVDVYDKLPHP 50
                                      79***********************998887776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.54
                                      HHHHT.TEEEECSEEEE CS
                         Pyr_redox 49 klekn.gievllntkve 64
                                       lek+ g+++++ tkv 
  gi|320100270|ref|YP_004175862.1| 74 DLEKRlGVRFITRTKVY 90
                                      456666********985 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 3e-09
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +vvvvGgGy+++++A+ + + g++ ++v r+       ++ a+    e+++++g+e++   +++ei  ++  v++vk
  gi|320100270|ref|YP_004175862.1| 169 RVVVVGGGYSAIDAAEQAVREGAEAYLVYRRTV-K---EAPAGLFEVERVKRLGVEFMELVSPVEIISENGAVKAVK 241
                                       79****************************954.4...477888889********************66655****9 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       l+
  gi|320100270|ref|YP_004175862.1| 242 LQ 243
                                       96 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2   0.00066      0.62       2      20 ..      20      38 ..      19      49 .. 0.80
   2 !   30.4   0.0   2.5e-10   2.3e-07     159     305 .]     162     322 ..     120     322 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00066
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkag 20
                                      +iGaGPaGlaaa  l   g
  gi|320100270|ref|YP_004175862.1| 20 VIGAGPAGLAAAGYLACQG 38
                                      8**********97776555 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 2.5e-10
                       Pyr_redox_3 159 fhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsy.slkpdienrleelvke.ekikvlfna 233
                                        +++ g++vvV+Gg+ Sa+DaA + vr+gae  +v+r++  e+    +++ ++k    + + elv+  e   + +n 
  gi|320100270|ref|YP_004175862.1| 162 SKPFPGKRVVVVGGGYSAIDAAEQAVREGAEAYLVYRRTVKEAPAGLFEVeRVKRLGVEFM-ELVSPvE--IISENG 235
                                       56899*********************************98777654444424444433333.4443322..112223 PP

                       Pyr_redox_3 234 evkeikekeeey..........kvktedgkkvevkddvvlatGykpdlsflkk......slfeldedgrpvlteete 294
                                        vk++k +  +            +  +  + v + d+vv+atG +p+  + ++       +++l++dg +v++ + +
  gi|320100270|ref|YP_004175862.1| 236 AVKAVKLQRMQLgppdetgrpqPIPVPGSEIVVEADRVVFATGETPTPPLPQSeeymgrLGIKLKKDGSIVVN-QIM 311
                                       3333333222220000000000233333344444777777888777643222222333366777777776666.456 PP

                       Pyr_redox_3 295 etnvpglflaG 305
                                       +t  p +f aG
  gi|320100270|ref|YP_004175862.1| 312 QTGNPKVFAAG 322
                                       66677777666 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.4e-07    0.0006       2      48 ..      18      64 ..      17     110 .. 0.80
   2 !   16.7   1.3   3.9e-06    0.0037       2      32 ..     170     200 ..     169     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.4e-07
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdig 48
                                      v V+G+gpaG+aAA   a +G +v + ++ ++ GGl+  ++ ++ i 
  gi|320100270|ref|YP_004175862.1| 18 VAVIGAGPAGLAAAGYLACQGYSVDVYDKLPHPGGLMVFAIPPWRIP 64
                                      89***********************************9888666555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.9e-06
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                       vvVvGGg + + AA +A r+Ga+  Lv +r 
  gi|320100270|ref|YP_004175862.1| 170 VVVVGGGYSAIDAAEQAVREGAEAYLVYRRT 200
                                       9**************************8875 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 !   33.5   0.2   3.8e-11   3.6e-08       1      35 [.      20      54 ..      20      58 .. 0.96
   2 ?    3.4   0.2     0.094        89       1      21 [.     172     192 ..     172     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.8e-11
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      ++GaG +Gl+aA +La +g++v++++k +++GG +
  gi|320100270|ref|YP_004175862.1| 20 VIGAGPAGLAAAGYLACQGYSVDVYDKLPHPGGLM 54
                                      8********************************65 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.094
                                       EE--SHHHHHHHHHHHCCTEE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfd 21 
                                       +vG+G s+  aA  + ++g++
  gi|320100270|ref|YP_004175862.1| 172 VVGGGYSAIDAAEQAVREGAE 192
                                       8*************9999886 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.6e-06    0.0015       2      41 ..      18      57 ..      17      77 .. 0.90
   2 ?    4.0   0.2     0.023        21       2      28 ..     170     196 ..     169     205 .. 0.87
   3 !    7.8   0.0    0.0016       1.5     148     204 ..     211     282 ..     208     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.6e-06
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG- CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggataws 41
                                      v ViG+G AGLaAA  +a +G +v v +k +  gg  +++
  gi|320100270|ref|YP_004175862.1| 18 VAVIGAGPAGLAAAGYLACQGYSVDVYDKLPHPGGLMVFA 57
                                      89***************************99888866665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.023
                                       EEEE--SHHHHHHHHHHHHTTT-EEEE CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavv 28 
                                       v+V+G+G +   AA +a ++G++  +v
  gi|320100270|ref|YP_004175862.1| 170 VVVVGGGYSAIDAAEQAVREGAEAYLV 196
                                       9*****************999977766 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0016
                                       HHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET...............TTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 148 vesarkagvdfqerteadeLivedgrvtGavvenp...............esgrevrirakavvlatgGfgr 204
                                       ve+++++gv+f+e  + +e+i e+g v  + ++ +                 g+e  ++a++vv atg  + 
  gi|320100270|ref|YP_004175862.1| 211 VERVKRLGVEFMELVSPVEIISENGAVKAVKLQRMqlgppdetgrpqpipVPGSEIVVEADRVVFATGETPT 282
                                       5889999**************************99******99999999988888899**********9886 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   9.8e-08   9.3e-05       2      36 ..      17      51 ..      16      56 .. 0.94
   2 ?    4.3   0.1     0.014        14       2      29 ..     169     196 ..     168     201 .. 0.90
   3 ?   -3.7   0.0       3.8   3.6e+03     153     168 ..     268     283 ..     264     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.8e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +v+viG+G+AGl aA  +a +g +V +++k +++g
  gi|320100270|ref|YP_004175862.1| 17 KVAVIGAGPAGLAAAGYLACQGYSVDVYDKLPHPG 51
                                      79****************************98877 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.014
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlll 29 
                                       +v+v+GgG + + aA++a ++g++  l+
  gi|320100270|ref|YP_004175862.1| 169 RVVVVGGGYSAIDAAEQAVREGAEAYLV 196
                                       79*****************999998775 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.8
                                       EEESEEEE----SS-G CS
                       HI0933_like 153 leadklvlAtGGlSiP 168
                                       +ead++v+AtG +  P
  gi|320100270|ref|YP_004175862.1| 268 VEADRVVFATGETPTP 283
                                       799********87776 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   2.7e-05     0.026      25      59 ..      12      46 ..       5      50 .. 0.89
   2 !   10.2   0.1   0.00036      0.34      29      60 ..     168     199 ..     153     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                                      CB---EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C 25 gvepakvlviGgGvaGlqAiatakglgakVtvlDv 59
                                      g ++ kv viG+G aGl+A+   +  g +V v+D+
  gi|320100270|ref|YP_004175862.1| 12 GSTNIKVAVIGAGPAGLAAAGYLACQGYSVDVYDK 46
                                      556789**************************997 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00036
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvr 60 
                                        +v+v+GgG   + A++ a++ ga+ +++  r
  gi|320100270|ref|YP_004175862.1| 168 KRVVVVGGGYSAIDAAEQAVREGAEAYLVYRR 199
                                       58**********************98876555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   1.7e-05     0.017       1      28 [.      17      44 ..      17      56 .. 0.89
   2 !   10.3   0.1   0.00027      0.26       2      30 ..     170     198 ..     169     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      +v ViG+G AG++AA  +a  G++v  +
  gi|320100270|ref|YP_004175862.1| 17 KVAVIGAGPAGLAAAGYLACQGYSVDVY 44
                                      699********************99877 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00027
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                       v+V+GgG + + AA +a r Ga+  L+  
  gi|320100270|ref|YP_004175862.1| 170 VVVVGGGYSAIDAAEQAVREGAEAYLVYR 198
                                       9**********************999943 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   1.5e-05     0.014       1      33 [.      17      51 ..      17      53 .. 0.91
   2 !    9.0   0.0     0.001      0.95     147     222 ..      67     141 ..      59     156 .. 0.67
   3 ?   -0.2   1.3      0.62   5.8e+02       1      22 [.     169     190 ..     169     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      +v++iG+G +Gl++A +La +g  V +++k + +g
  gi|320100270|ref|YP_004175862.1| 17 KVAVIGAGPAGLAAAGYLACQGysVDVYDKLPHPG 51
                                      59*****************9999******987776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEE..TCEEEEEEECT.EEE.EEEEEEEE--GGGHHHHHTTCTTTSEEEE CS
                               DAO 147 kltaalaraaealGveilegtevtgleeed..gkvwgverttp.gen.daadavVnaaGawsdllgllkeldlpisp 219
                                       +++ ++++  ++lGv+++++t+v +  e+   ++ + ve+t + +e+  ++d v +++G w +++   +++  p s 
  gi|320100270|ref|YP_004175862.1|  67 RVLEGVRDLEKRLGVRFITRTKVYASPEPAheEGDGFVEKTLSlEEIvGSYDLVLLSTGTWRSKI---PRI--PGSD 138
                                       5666666777899************9554443333444433344444347899********5455...444..5455 PP

                                       EEE CS
                               DAO 220 vrg 222
                                       ++g
  gi|320100270|ref|YP_004175862.1| 139 AKG 141
                                       555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.62
                                       EEEEECTSHHHHHHHHHHHHTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg 22 
                                       +vv++GGG+  + +A ++ r+g
  gi|320100270|ref|YP_004175862.1| 169 RVVVVGGGYSAIDAAEQAVREG 190
                                       59******98877777776666 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   5.6e-07   0.00053       2      33 ..      16      47 ..      15      51 .. 0.90
   2 ?   -1.6   0.0       1.3   1.2e+03       4      34 ..     170     200 ..     168     206 .. 0.85
   3 ?   -2.2   0.0         2   1.9e+03     281     294 ..     311     326 ..     306     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.6e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      ++V+++GaGpaGl +a  L+ +G +v + +k 
  gi|320100270|ref|YP_004175862.1| 16 IKVAVIGAGPAGLAAAGYLACQGYSVDVYDKL 47
                                      58*********************999888875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                       V++VG+G + + +a    + G +  lv +r+
  gi|320100270|ref|YP_004175862.1| 170 VVVVGGGYSAIDAAEQAVREGAEAYLVYRRT 200
                                       99*****999999999999999999988876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                                       SEET..TEEE-GGGTE CS
                     FAD_binding_3 281 yrkg..rvflaGDAaH 294
                                       ++ g  +vf aGD +H
  gi|320100270|ref|YP_004175862.1| 311 MQTGnpKVFAAGDVVH 326
                                       5666569*******99 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.4e-05     0.014      18      55 ..      16      52 ..       6      56 .. 0.84
   2 ?    0.2   0.0      0.38   3.6e+02      19      38 ..     169     188 ..     163     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                        v+++GaG++GL+aa yla + +  v + ++   pGG
  gi|320100270|ref|YP_004175862.1| 16 IKVAVIGAGPAGLAAAGYLACQ-GYSVDVYDKLPHPGG 52
                                      5799****************99.888888877666666 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.38
                                       EEEEE--SHHHHHHHHHHHH CS
                              Thi4  19 DvvivGaGssGLtaayylak 38 
                                        vv+vG+G s + aa    +
  gi|320100270|ref|YP_004175862.1| 169 RVVVVGGGYSAIDAAEQAVR 188
                                       59**********99987655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.13   1.2e+02       7      38 ..      15      46 ..      12     125 .. 0.87
   2 !   12.9   0.0   0.00012      0.12       7      48 ..     167     209 ..     164     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvap 38
                                      + kv v+G+G+ ++  +  l+ +g  v v+++
  gi|320100270|ref|YP_004175862.1| 15 NIKVAVIGAGPAGLAAAGYLACQGYSVDVYDK 46
                                      6789**********999999999999998876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeele.elv 48 
                                       gk+v+vvGgG  A   +++ +++ga+  +v  ++ +e++ +l+
  gi|320100270|ref|YP_004175862.1| 167 GKRVVVVGGGYSAIDAAEQAVREGAEAYLVYRRTVKEAPaGLF 209
                                       89************************99988775444334333 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.029        27      10      36 ..      13      39 ..       6      45 .. 0.81
   2 ?   -2.1   0.0         4   3.8e+03      68      85 ..     109     126 ..     102     133 .. 0.84
   3 !    9.7   0.0   0.00092      0.87      10      51 ..     165     206 ..     156     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.029
                                      .TT-EEEEES-SHHHHHHHHHHHCCT- CS
                      Shikimate_DH 10 lkekkvlliGaGemaelvakhLlakgv 36
                                       ++ kv +iGaG  +  +a +L+ +g+
  gi|320100270|ref|YP_004175862.1| 13 STNIKVAVIGAGPAGLAAAGYLACQGY 39
                                      45789*************999998876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                                       GHHHHHHT-SEEEE-SSS CS
                      Shikimate_DH  68 elkellaeadvvisatas 85 
                                       +l+e++ ++d+v+ +t++
  gi|320100270|ref|YP_004175862.1| 109 SLEEIVGSYDLVLLSTGT 126
                                       68899999******9986 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00092
                                       .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHH CS
                      Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerake 51 
                                       + +k+v+++G G  a  +a++ +++g+++ +v  Rt++ a +
  gi|320100270|ref|YP_004175862.1| 165 FPGKRVVVVGGGYSAIDAAEQAVREGAEAYLVYRRTVKEAPA 206
                                       5689*********************************98865 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0007      0.66       2      30 ..      26      54 ..      25      55 .. 0.95
   2 ?    4.8   0.0     0.015        14     414     451 ..     311     345 ..     303     346 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0007
                                      HHHHHHHHHHHTTEEEEEEESSSSSBTTS CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGGRi 30
                                      aGLaaA +L+ +G++V v+   +++GG +
  gi|320100270|ref|YP_004175862.1| 26 AGLAAAGYLACQGYSVDVYDKLPHPGGLM 54
                                      9**************************76 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                                       HCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 414 akpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                       +++ g p +f AG+ ++   p+ v  Ai+SG  aA+ +
  gi|320100270|ref|YP_004175862.1| 311 MQT-GNPKVFAAGDVVH--GPSKVGPAIRSGFYAARYM 345
                                       566.899**********..**99************976 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-05     0.071       1      30 [.      17      46 ..      17      50 .. 0.95
   2 ?    0.6   0.1      0.48   4.5e+02       2      31 ..     170     199 ..     167     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdi 30
                                      kvaviGaG  G   a  +a +g++V ++d 
  gi|320100270|ref|YP_004175862.1| 17 KVAVIGAGPAGLAAAGYLACQGYSVDVYDK 46
                                      79**************************96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.48
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdis 31 
                                       v v+G G      a++++++g e  lv ++
  gi|320100270|ref|YP_004175862.1| 170 VVVVGGGYSAIDAAEQAVREGAEAYLVYRR 199
                                       789999999999999999999888887664 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00084      0.79       1      39 [.      19      53 ..      19      59 .. 0.80
   2 ?    1.9   0.1      0.21     2e+02       1      19 [.     171     189 ..     171     197 .. 0.87
   3 ?    0.7   0.0      0.48   4.5e+02     143     155 ..     267     279 ..     257     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00084
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgag 39
                                      a++GaGp+Gla++  L+ +       +++++d+  +pg  
  gi|320100270|ref|YP_004175862.1| 19 AVIGAGPAGLAAAGYLACQ-----GYSVDVYDKlPHPGGL 53
                                      89**************999.....4888899985455634 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.21
                     NAD_binding_9   1 aivGaGprGlavlerLlar 19 
                                       ++vG+G +++ ++e+ +++
  gi|320100270|ref|YP_004175862.1| 171 VVVGGGYSAIDAAEQAVRE 189
                                       69************99987 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.48
                     NAD_binding_9 143 slaadaVvLAlGh 155
                                        ++ad+Vv A+G+
  gi|320100270|ref|YP_004175862.1| 267 VVEADRVVFATGE 279
                                       579*********7 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.7   6.6e+02     193     203 ..      17      27 ..       5      43 .. 0.62
   2 ?   10.4   0.0   0.00028      0.26     188     221 ..     164     195 ..     111     206 .. 0.76
   3 ?   -0.7   0.0      0.63   5.9e+02     328     339 ..     267     278 ..     261     290 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.7
                       K_oxygenase 193 riaVvGsGqSa 203
                                       ++aV+G+G  +
  gi|320100270|ref|YP_004175862.1|  17 KVAVIGAGPAG 27 
                                       55555555433 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00028
                       K_oxygenase 188 llakkriaVvGsGqSaaeifedllrrqkkvelkl 221
                                          +kr++VvG+G Sa + +e+++r+ +  e  l
  gi|320100270|ref|YP_004175862.1| 164 PFPGKRVVVVGGGYSAIDAAEQAVREGA--EAYL 195
                                       55689*****************999976..3444 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.63
                       K_oxygenase 328 tlevdavvlATG 339
                                       ++e+d+vv+ATG
  gi|320100270|ref|YP_004175862.1| 267 VVEADRVVFATG 278
                                       345555555555 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.12   1.1e+02       3      17 ..      17      31 ..      15      57 .. 0.74
   2 ?    9.2   0.0   0.00039      0.37     140     212 ..     118     196 ..     103     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.12
                          FMO-like  3 kvaviGaGvsGlasi 17
                                      kvaviGaG +Gla+ 
  gi|320100270|ref|YP_004175862.1| 17 KVAVIGAGPAGLAAA 31
                                      8***********975 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00039
                          FMO-like 140 davmvctGhh..vnphlplesfpGiek....fkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvl 210
                                       d v++ tG +    p +p     G+e       G  ++       + f gkrv+v+G G s+ d a ++ r  ++ +
  gi|320100270|ref|YP_004175862.1| 118 DLVLLSTGTWrsKIPRIPGSDAKGVESaleyVHGFRLYELGLAASKPFPGKRVVVVGGGYSAIDAAEQAVREGAEAY 194
                                       66666666541134666666666665411112333333344456778*******************99988877666 PP

                          FMO-like 211 ls 212
                                       l 
  gi|320100270|ref|YP_004175862.1| 195 LV 196
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2684.90
//
Query:       gi|320100271|ref|YP_004175863.1|  [L=240]
Description: phosphoglycolate phosphatase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-20   72.0   0.0    5.6e-11   42.7   0.0    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00035   20.2   0.0      0.003   17.1   0.0    2.0  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
     0.0015   18.9   0.8       0.92    9.7   0.2    2.4  2  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.061   13.4   0.0       0.11   12.6   0.0    1.4  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
      0.078   12.1   0.0        3.8    6.6   0.0    2.1  2  Trehalose_PPase  Trehalose-phosphatase
       0.09   13.1   0.2        2.1    8.7   0.0    2.3  2  PHA_gran_rgn     Putative polyhydroxyalkanoic acid system pro
       0.26   11.7   9.0        4.7    7.6   0.0    3.8  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 !   27.6   0.0   8.6e-10   2.2e-06       1      71 [.       6      77 ..       6     103 .. 0.86
   2 !   42.7   0.0   2.2e-14   5.6e-11     151     254 ..     129     230 ..      99     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 8.6e-10
                                      EEEEIIIIIS-TTS-..--HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTT CS
                       Hydrolase_3  1 ialDlDGTLlnsdkk..isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekg 71
                                      +++D+DGTL  + ++  +  +++ea++ l +kg+ v + + + l  v  + + +gl+ pv++  Gal+ ++++
  gi|320100271|ref|YP_004175863.1|  6 VFTDIDGTLTVNRESyrLAVEAVEALRMLVDKGVIVSLVSSNALPVVVALSRYIGLNGPVVGESGALV-YHDE 77
                                      79*******66555525779************************************************.4333 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 2.2e-14
                                       HHHHHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEE CS
                       Hydrolase_3 151 kekldelekelksklnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvA 227
                                       +e +del+ +++sk++    ++++s++ + + +kgv Kg a+ +++ +l++s  e + +GD+  D+  + + g+  A
  gi|320100271|ref|YP_004175863.1| 129 REVVDELRRYVESKYKG--FTVDYSGYAIHVHAKGVGKGVAVDYILRRLGLSGGEALGIGDSYMDVDFIARLGYRAA 203
                                       45667777777777766..99******************************************************** PP

                                       ETTS-HHHHHHSSEEE--GGGTHHHHH CS
                       Hydrolase_3 228 mgnaseevkkaAdyvtksnnedGVaka 254
                                       +g a+ee+  +++ v +  +  GVa++
  gi|320100271|ref|YP_004175863.1| 204 VGGADEELVRVCNIVAEAPSGLGVAEV 230
                                       ****************99999999986 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.091   2.3e+02       3      25 ..       4      29 ..       2      64 .. 0.73
   2 !   17.1   0.0   1.2e-06     0.003     128     216 ..     127     214 ..      92     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.091
                                      EEEEE-TBTTTB....S-HHHHHHHH CS
                              S6PP  3 lllvsdLDntlv...dgdnealarln 25
                                      +++ +d+D+tl+   ++ + a+++ +
  gi|320100271|ref|YP_004175863.1|  4 KIVFTDIDGTLTvnrESYRLAVEAVE 29
                                      5789*******965433344444444 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.2e-06
                                       S-THHHHHHHHHHHTTTS-EEEEEETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEE CS
                              S6PP 128 kaaevlkeleqlLekreldvkviyssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgV 204
                                       +a+ev++el+++ e++     v ys g ++ v +k+ +kg A+ y++++l+l   + l  Gds  D + +    +  
  gi|320100271|ref|YP_004175863.1| 127 RAREVVDELRRYVESKYKGFTVDYS-GYAIHVHAKGVGKGVAVDYILRRLGLSGGEALGIGDSYMDVDFIARLGYRA 202
                                       6789999999999999999999997.7899****************************************8777778 PP

                                       E-TT--HHHHHH CS
                              S6PP 205 vVgnaqeellqw 216
                                        Vg a+eel++ 
  gi|320100271|ref|YP_004175863.1| 203 AVGGADEELVRV 214
                                       999999998865 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2   0.00036      0.92       1      26 [.       3      28 ..       3     139 .. 0.77
   2 !    8.2   0.0    0.0011       2.8     175     210 .]     164     199 ..     123     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                                      SSEEEEESBTTTBCHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgepsvedvivsa 26
                                      +k v+ D+dGTLt  + s + +++ +
  gi|320100271|ref|YP_004175863.1|  3 VKIVFTDIDGTLTVNRESYRLAVEAV 28
                                      689**********7775555555554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                                       SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 175 spegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +  ++ +++r+L+ ++ e + +GD+  D+ ++a+ g
  gi|320100271|ref|YP_004175863.1| 164 KGVAVDYILRRLGLSGGEALGIGDSYMDVDFIARLG 199
                                       6677889**********************9999765 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.3e-05      0.11       1      39 [.       6      47 ..       6      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                                      EEEESTTTSE...ETTEE-TTHHHHHHHHHHTT-EEEEEE-- CS
                       Hydrolase_6  1 flfDidGvLw...rgdkaipgaaealnalraagkpvvllTNn 39
                                      +++DidG+L    + +++  +a+eal++l ++g+ v l++ n
  gi|320100271|ref|YP_004175863.1|  6 VFTDIDGTLTvnrESYRLAVEAVEALRMLVDKGVIVSLVSSN 47
                                      589*******44335666778888888888999988888877 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.012        31       1      44 [.       7      46 ..       7      73 .. 0.80
   2 ?    6.6   0.0    0.0015       3.8     133     190 ..     132     187 ..     116     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.012
                                      EEETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-S CS
                   Trehalose_PPase  1 flDydGTlspivedpdaavpssellslLkkLasdpknvvaivSG 44
                                      f+D+dGTl+   e   + ++  e++++L++L ++   +v +vS 
  gi|320100271|ref|YP_004175863.1|  7 FTDIDGTLTVNRE---SYRLAVEAVEALRMLVDKGV-IVSLVSS 46
                                      79******97666...9999999999**99999966.6667765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0015
                                       HHHHHH.HHHHH.--EEEE-SSEEEEE-S---HHHHHHHHHHTS--------EEEEEE- CS
                   Trehalose_PPase 133 aehles.vltdkpdlevtqgkkvvevrpqgvsKGkaverlleslgsadseddfvlciGD 190
                                        + l++ v  ++ +  v+     + v+++gv KG av+ +l++lg +      +l iGD
  gi|320100271|ref|YP_004175863.1| 132 VDELRRyVESKYKGFTVDYSGYAIHVHAKGVGKGVAVDYILRRLGLS---GGEALGIGD 187
                                       444444033445567888888899********************998...444444555 PP

>> PHA_gran_rgn  Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.098   2.5e+02      44      64 ..       7      27 ..       2      47 .. 0.79
   2 ?    8.7   0.0   0.00082       2.1      11      47 ..     125     162 ..     118     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.098
                      PHA_gran_rgn 44 rsgvdGqlevepdkvrleakL 64
                                       + +dG+l+v+ ++ rl+++ 
  gi|320100271|ref|YP_004175863.1|  7 FTDIDGTLTVNRESYRLAVEA 27
                                      5689**********9999985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00082
                      PHA_gran_rgn  11 leeAreraeelaekleeef.glelewegdtlkfkrsgv 47 
                                       + +Are+++el + +e+++ g+++ ++g  ++++++gv
  gi|320100271|ref|YP_004175863.1| 125 RGRAREVVDELRRYVESKYkGFTVDYSGYAIHVHAKGV 162
                                       468********************************998 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.019        49       1      15 [.       6      21 ..       6      28 .. 0.72
   2 ?    7.6   0.0    0.0018       4.7      89     130 ..      26      63 ..      17      80 .. 0.80
   3 ?    2.7   1.5     0.057   1.5e+02      58      84 ..     120     146 ..      78     195 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.019
                               HAD  1 alfDfDgTLldg.dsl 15
                                      ++ D+DgTL+ + +s+
  gi|320100271|ref|YP_004175863.1|  6 VFTDIDGTLTVNrESY 21
                                      799******8773544 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                               HAD  89 galellaahraaGdrvvvvSgglrplvepllaelgadevlat 130
                                       +a+e+l+   ++G+ v +vS++  p+v +l +  g    l+ 
  gi|320100271|ref|YP_004175863.1|  26 EAVEALRMLVDKGVIVSLVSSNALPVVVALSRYIG----LNG 63 
                                       8899999666*********************9999....555 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.057
                               HAD  58 leallaglseelaaelerfvaevirpk 84 
                                       l++ ++g + e+ +el+r+v+++++  
  gi|320100271|ref|YP_004175863.1| 120 LRREHRGRAREVVDELRRYVESKYKGF 146
                                       445555555555555555554444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 1999.60
//
Query:       gi|320100272|ref|YP_004175864.1|  [L=230]
Description: HAD-superfamily hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-37  128.1   0.0    4.5e-37  127.9   0.0    1.0  1  HAD_2            Haloacid dehalogenase-like hydrolase
    2.1e-14   54.4   0.0    2.6e-12   47.5   0.0    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.8e-11   43.9   0.0    4.9e-11   42.5   0.0    1.7  2  Hydrolase_like   HAD-hyrolase-like
    5.1e-11   43.3   0.0    9.2e-11   42.5   0.0    1.4  1  HAD              haloacid dehalogenase-like hydrolase
    0.00043   20.2   0.0       0.04   13.8   0.0    2.6  2  Acid_PPase       Acid Phosphatase
  ------ inclusion threshold ------
      0.076   12.4   0.6        2.3    7.5   0.2    2.7  2  Put_Phosphatase  Putative Phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   0.0   1.5e-40   4.5e-37       1     178 []      11     190 ..      11     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 1.5e-40
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee....kieellrkyneek 73 
                                       i+FDlDgT++d+e++i+ +f e+ +  g+  +++ ++r+lig++l+ +l+ +  +    e     ie  ++ ++e+ 
  gi|320100272|ref|YP_004175864.1|  11 ILFDLDGTIVDSEDFIVWSFVEAGRLTGI-RVDPLKVRELIGFPLESILEAVVGTGLSREdaarFIEVRRKLVQENW 86 
                                       89**********************98888.9********************99987766677888999988888898 PP

                             HAD_2  74 kkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklkl 150
                                        k +v+++++v+ +L +L++ gy lg+++s+ re ve +l++lg+  yF+v+ + e   k KP+p+vi +al+  ++
  gi|320100272|ref|YP_004175864.1|  87 FK-HVRLFPDVIPVLRQLSSTGYMLGVASSSIRERVELFLSHLGVSGYFKVVSGLEPGVKGKPEPDVIVNALKAAGV 162
                                       98.************************************************************************** PP

                             HAD_2 151 kkeeviyvGDsptDieaakkagikviav 178
                                        ++e++yvGD   D +aa++ag+kv+ v
  gi|320100272|ref|YP_004175864.1| 163 PRSEALYVGDRMVDCIAARRAGVKVVIV 190
                                       *************************976 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   8.5e-16   2.6e-12       1     210 []       8     184 ..       8     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 8.5e-16
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       i++++fD+dGT++++e  ++  +v+a                         +++ +  ++++      +    +  l
  gi|320100272|ref|YP_004175864.1|   8 IRLILFDLDGTIVDSEDFIVWSFVEA---------------------GRLTGIRVDPLKVRE-----LIGFPLESIL 58 
                                       789*************7777777777.....................555555555555555.....3333344455 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                       +a      +g   + + ++  +++    +++++ +++   +++p++  ++++L + g+ +++++++ +e +e  +++
  gi|320100272|ref|YP_004175864.1|  59 EAV-----VGTGLSREDAARFIEVRR--KLVQENWFK-HVRLFPDVIPVLRQLSSTGYMLGVASSSIRERVELFLSH 127
                                       555.....444444445555555555..666666666.559************************************ PP

                                       TT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       lG   yf++v + +  + +kp+p+  v a++  +++ +e + VGD++ D  a+++Ag
  gi|320100272|ref|YP_004175864.1| 128 LGvSGYFKVVSGLEPGVKGKPEPDVIVNALKAAGVPRSEALYVGDRMVDCIAARRAG 184
                                       *******************************************************98 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.3     4e+03      47      62 ..      61      76 ..      59      85 .. 0.71
   2 !   42.5   0.0   1.6e-14   4.9e-11       3      75 .]     146     215 ..     144     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                                      EESSSSS-TTTHHHHH CS
                    Hydrolase_like 47 LVltGvtrpedleepe 62
                                       V tG +r+++++  e
  gi|320100272|ref|YP_004175864.1| 61 VVGTGLSREDAARFIE 76
                                      6899999998876544 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 1.6e-14
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES- CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlaea 75 
                                       gKPep ++  al++ g++++e l++GDr   D ++A++aG+k v V +G  ++ +  ++e+ p++++ +l e+
  gi|320100272|ref|YP_004175864.1| 146 GKPEPDVIVNALKAAGVPRSEALYVGDR-MVDCIAARRAGVKVVIVDRGSVNRWK--QEECVPDAWISSLLEL 215
                                       9***************************.9********************99855..4689****99999885 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   3.1e-14   9.2e-11       1     185 [.      11     178 ..      11     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3.1e-14
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv 77 
                                       +lfD+DgT++d++ ++++ ++ ++r     ++ +r+ +l+ +  el  +  +++ e++     gls e+aa++ + +
  gi|320100272|ref|YP_004175864.1|  11 ILFDLDGTIVDSEDFIVWSFVEAGR-----LTGIRVDPLKVR--ELIGFPLESILEAVV--GTGLSREDAARFIEVR 78 
                                       79**********8888887766666.....777777777777..333333334444433..4677766666666666 PP

                               HAD  78 aevirpk......lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkp 148
                                       ++ +++       l+ p++  +l++  + G+ + v S+++r+ ve +l +lg    ++        +++ + + ++ 
  gi|320100272|ref|YP_004175864.1|  79 RKLVQENwfkhvrLF-PDVIPVLRQLSSTGYMLGVASSSIRERVELFLSHLG----VSG-------YFKVVSGLEPG 143
                                       444444444444477.********999*************************....999.......77788999*** PP

                               HAD 149 vrgegkvaalrewlaaegegidleevvayGDspsDlp 185
                                       v+g+  ++++    a + +g +++e  ++GD + D  
  gi|320100272|ref|YP_004175864.1| 144 VKGKPEPDVIVN--ALKAAGVPRSEALYVGDRMVDCI 178
                                       ***9***99999..6666777777899*****99965 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.032        95       4      14 ..       9      19 ..       7      31 .. 0.89
   2 !   13.8   0.0   1.3e-05      0.04      35     156 ..      81     196 ..      68     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.032
                                      SEEEE-STTTS CS
                        Acid_PPase  4 klivFDLDyTL 14
                                      +li FDLD T+
  gi|320100272|ref|YP_004175864.1|  9 RLILFDLDGTI 19
                                      69********8 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.3e-05
                                       -EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT-G..........GGESEEEESSS..-H CS
                        Acid_PPase  35 evvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLklleindakekekklldvfddveiykg..sk 109
                                        v+ ++ ++++l+pdv  +l++l+s +  l vaS++ + ++ +  L++l +           +v++++e + +    
  gi|320100272|ref|YP_004175864.1|  81 LVQENWFKHVRLFPDVIPVLRQLSSTGYMLGVASSSIRERV-ELFLSHLGVS-------GYFKVVSGLEPGVKgkPE 149
                                       67888999**************************9988665.6789999988.......677777777665541133 PP

                                       HHHHHHHHHHH---GGGEEEEES-HHHHHHHHTTT-EEEE-SSS--H CS
                        Acid_PPase 110 tkhfeklkkktgieyedmlfFDdesrnievesrlgvtfvlvpdGltr 156
                                          + ++ k+ g++ ++ l+  d   ++   +r gv++v v++G  +
  gi|320100272|ref|YP_004175864.1| 150 PDVIVNALKAAGVPRSEALYVGDRMVDCIAARRAGVKVVIVDRGSVN 196
                                       45677888888999999999999888888888899999888888655 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2   0.00078       2.3       2     119 ..      10     137 ..       9     144 .. 0.55
   2 ?    0.1   0.0      0.14   4.2e+02     166     197 ..     161     192 ..     151     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00078
                   Put_Phosphatase   2 lvvfDFDktiidedsdnwvv......delpatelfeelretlrkglwnelmdrvlke.lheqg.vseadik...... 64 
                                       l++fD D ti+d++    v       ++ + +  + ++re +     ++ ++ v+ + l  ++  +  +++      
  gi|320100272|ref|YP_004175864.1|  10 LILFDLDGTIVDSEDFI-VWsfveagRLTGIRVDPLKVRELIG-FPLESILEAVVGTgLSREDaARFIEVRrklvqe 84 
                                       78889999998765322.1111111133444555555555554.333444444443213332222333333100011 PP

                   Put_Phosphatase  65 kvlrsiplspglvelikslakkkleldliiiSDaNsffieeileaagledlFsei 119
                                       + ++++ l p +++++++l  +++++ l + S + +  +e  l+++g++ +F+ +
  gi|320100272|ref|YP_004175864.1|  85 NWFKHVRLFPDVIPVLRQL--SSTGYMLGVASSSIRERVELFLSHLGVSGYFKVV 137
                                       3457788888888888888..5677888888888888888888888888888755 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                   Put_Phosphatase 166 gveyerliYvGDganDlCpvlklrekDvampR 197
                                       gv  +  +YvGD + D  +  +   k v++ R
  gi|320100272|ref|YP_004175864.1| 161 GVPRSEALYVGDRMVDCIAARRAGVKVVIVDR 192
                                       55667789******998777776666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 1902.46
//
Query:       gi|320100273|ref|YP_004175865.1|  [L=283]
Description: geranylgeranylglycerol-phosphate geranylgeranyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-33  114.1   7.5    8.4e-33  113.7   7.5    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.16   11.7   4.7       0.14   11.9   0.5    2.6  3  PAP2      PAP2 superfamily
        1.6    8.2   6.3       0.14   11.6   0.4    2.0  3  DUF1129   Protein of unknown function (DUF1129)


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 !  113.7   7.5   1.4e-36   8.4e-33      21     240 ..      41     257 ..      20     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.4e-36
                              UbiA  21 lllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgl 97 
                                        l++ +++++ ++aa++++Nd++D   D+   ++p+ Pl+sGr sp+ al+++i+l +++l++  l +   +al+++
  gi|320100273|ref|YP_004175865.1|  41 RLAAGFATGFTVTAASMLVNDVVDLGVDRV--NKPWKPLPSGRASPRVALALSILLPLIALAVN-LPVDKGLALVTV 114
                                       4577788899********************..*******************************9.************ PP

                              UbiA  98 lalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl..sllalllalavflltwaialandlrdregDr 172
                                       ++ +l++ Y+  +l ++++  +++++++ + p+  g++a++        al l++ +f++t++  + ++++d+egDr
  gi|320100273|ref|YP_004175865.1| 115 VYSALGLGYS--FLRKHWW-SQLIVAASTTGPIAYGYVAAGSPSssIHVALGLSITIFVVTLGREVLKAMQDVEGDR 188
                                       **********..9988888.*******************98877543344555666788888888888********* PP

                              UbiA 173 kagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraarlvrrrdak 240
                                         g+ t+p++lG + ++ ll+++ ++  +a +++ ++a+ + +y ++ +++++l l+  ++ +r+ ++k
  gi|320100273|ref|YP_004175865.1| 189 LHGYSTIPLKLGVEESAKLLVFAGIAGPAAgITTGVVAGSGIVYKAVISVAGGLYLYSMVKAYRKPREK 257
                                       *****************97554444444457899999999999999999999**999999999988766 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.18   1.1e+03      62     103 ..      16      58 ..      14      62 .. 0.61
   2 ?   11.9   0.5   2.4e-05      0.14      50     121 ..      71     142 ..      50     156 .. 0.74
   3 ?    0.3   0.1     0.093   5.5e+02      58      98 ..     157     220 ..     144     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                              PAP2  62 afafalalllalllrrkrkkig.lvllalillllavlvalsRl 103
                                       ++++++a++++l++ +        v+la+ +++  +++a+s l
  gi|320100273|ref|YP_004175865.1|  16 LMSGVGAVFMSLMFSNYCVDCLgVVRLAAGFATGFTVTAASML 58 
                                       5677777777777777777655556666666666556555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.4e-05
                              PAP2  50 keakesfPSgHs....afafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGi 121
                                       +++++ +PSg +    a a++++l l++l  ++         +++++++    +l+  +l+ H++s++++++   +
  gi|320100273|ref|YP_004175865.1|  71 NKPWKPLPSGRAsprvALALSILLPLIALAVNLPVD----KGLALVTVVYSALGLGYSFLRKHWWSQLIVAASTTG 142
                                       6778889***99777788888888888888888888....455555555556789999***********9986555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.093
                              PAP2  58 SgHsafafalalllalllrrkrkkig.......................lvllalillllavlv 98 
                                       S H a ++++ ++++ l r+  k ++                       ++l+++ ++  a+++
  gi|320100273|ref|YP_004175865.1| 157 SIHVALGLSITIFVVTLGREVLKAMQdvegdrlhgystiplklgveesaKLLVFAGIAGPAAGI 220
                                       7788888888888888877777777777777777777777777777774444444444444443 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.6      0.19   1.2e+03     171     171 ..      98      98 ..       7     134 .. 0.54
   2 ?   -1.7   0.2      0.28   1.7e+03     112     128 ..     110     126 ..      86     150 .. 0.63
   3 ?   11.6   0.4   2.3e-05      0.14      91     162 ..     209     281 ..     205     283 .] 0.67

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.19
                           DUF1129 171 p 171
                                        
  gi|320100273|ref|YP_004175865.1|  98 A 98 
                                       2 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                           DUF1129 112 GlitlllvalvgGlamv 128
                                        l+t++ +al  G+ ++
  gi|320100273|ref|YP_004175865.1| 110 ALVTVVYSALGLGYSFL 126
                                       45555555555555443 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 2.3e-05
                           DUF1129  91 lfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrll..illlllvvwlv 162
                                       +fa + g  a +++      +G+++ +++++ gGl+++ +++   +  +k+  +++ k +l  ++l+l+++w++
  gi|320100273|ref|YP_004175865.1| 209 VFAGIAGPAAGITTGVVAG-SGIVYKAVISVAGGLYLYSMVKAYRKPREKNVLEEARKETLleMMLGLVAFWMF 281
                                       5666666666677654445.5*****************999988776444444444443331256667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2330.87
//
Query:       gi|320100274|ref|YP_004175866.1|  [L=287]
Description: phosphoesterase PA-phosphatase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for 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   57.7   4.3      1e-15   57.7   4.3    3.5  3  PAP2        PAP2 superfamily
    7.5e-08   32.3   8.0    2.4e-07   30.7   8.1    1.7  1  PAP2_3      PAP2 superfamily
  ------ inclusion threshold ------
       0.04   14.5   1.9      0.044   14.3   0.2    1.9  2  PAP2_C      PAP2 superfamily C-terminal
       0.17   12.2   2.5       0.37   11.1   2.3    1.7  1  P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation


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 ?   -1.4   0.3       0.4   1.8e+03       2      19 ..      13      30 ..      12      52 .. 0.73
   2 !   57.7   4.3   2.3e-19     1e-15       5     127 ..      63     162 ..      60     170 .. 0.88
   3 ?   -1.4   0.4      0.42   1.9e+03      64      74 ..     236     246 ..     204     278 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.4
                              PAP2  2 llalllalalaalltsvl 19
                                      +l++++alal++ll++ +
  gi|320100274|ref|YP_004175866.1| 13 ALYMGVALALSMLLNNTA 30
                                      566777777777776654 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 2.3e-19
                              PAP2   5 lllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkk 81 
                                        +la +++++l+ +lK+l++ pRP    +     +             +++fPSgH++++++++ +l+ll r++   
  gi|320100274|ref|YP_004175866.1|  63 TVLATTASGALNLALKHLFNTPRPPNPLV-----KVE-----------GPGFPSGHAQVSASFWSMLTLLRREACLA 123
                                       6788999*****************87654.....331...........259************************99 PP

                              PAP2  82 iglvllalillllavlvalsRlylgvHflsDvlaGlliGialaala 127
                                              ++ l+++++v+lsRlyl++H++ Dv +G+++G+++ +++
  gi|320100274|ref|YP_004175866.1| 124 -------ALSLVMVTGVSLSRLYLRAHYPIDVAGGVVVGLTVSVAL 162
                                       .......899999***************************998866 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.42
                              PAP2  64 afalalllall 74 
                                       a++++l+++l+
  gi|320100274|ref|YP_004175866.1| 236 AASGVLIAVLY 246
                                       22333333333 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   8.1   5.3e-11   2.4e-07      72     187 ..      44     158 ..      12     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.3e-11
                            PAP2_3  72 lgllvyalfPaagPrlleeagfvdtvaaaslagalrdgasravllrgtienglaa.....fPSlHvawallvalalw 143
                                         +++ +lf+ + P++   +++  t a+++l+ al+  ++     +    n+l+      fPS H+ ++  +  +l 
  gi|320100274|ref|YP_004175866.1|  44 YLFTGIILFYLVDPYIG-VYTVLATTASGALNLALKHLFN-----TPRPPNPLVKvegpgFPSGHAQVSASFWSMLT 114
                                       35555666666666444.4444555555555553333333.....333355666666666***************** PP

                            PAP2_3 144 rlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalva 187
                                        lrr   l +l l+++  + ++ +++  HY +Dv++Gv+++l +
  gi|320100274|ref|YP_004175866.1| 115 LLRREACLAALSLVMVTGVSLSRLYLRAHYPIDVAGGVVVGLTV 158
                                       ****************************************9976 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1         2   8.9e+03      54      54 ..      53      53 ..      19      67 .. 0.59
   2 ?   14.3   0.2   9.9e-06     0.044       8      68 ..     100     158 ..      98     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                            PAP2_C 54 Y 54
                                      Y
  gi|320100274|ref|YP_004175866.1| 53 Y 53
                                      2 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.9e-06
                            PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlv 68 
                                       SGH+ v  ++  +++   ++ +  l  ++l+++   +++ ++ r HY +DV  g+++  +v
  gi|320100274|ref|YP_004175866.1| 100 SGHAQVSASFWSMLTLLRREAC--LAALSLVMVTGVSLSRLYLRAHYPIDVAGGVVVGLTV 158
                                       9999988887777777777777..9999999999999999************999998876 PP

>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.3   8.4e-05      0.37      27      91 ..     149     217 ..     130     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.4e-05
                                       HHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS...HHHHHHHH--TTSHHHHHHHHHHH.TTHHHHHHH CS
                        P5CR_dimer  27 dagvklGlsreeArelaaqtvaGaaklllese...paelrdkvtspgGtTiaglkelee.gglraavie 91 
                                        +gv  Gl+ ++A++ a + +    ++l+++    +  l++ v  pgGtT++gl    + ++++a++ie
  gi|320100274|ref|YP_004175866.1| 149 AGGVVVGLTVSVALNQAGTRLSLGKTMLATGTavsALSLIALVLNPGGTTAQGLLGVGAaTAISAVFIE 217
                                       57888899999998887766655555665554566778***************9877652445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2331.53
//
Query:       gi|320100275|ref|YP_004175867.1|  [L=214]
Description: type 11 methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-15   55.0   0.0    1.5e-14   54.4   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
      1e-09   38.5   0.0    1.7e-09   37.7   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    8.3e-08   32.8   0.0    1.4e-07   32.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
      0.001   18.5   0.0     0.0038   16.6   0.0    1.7  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.016   15.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      0.027   15.2   0.0      0.081   13.7   0.0    1.8  1  Methyltransf_12  Methyltransferase domain
      0.034   13.7   0.0      0.044   13.4   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
       0.29    9.6   0.0       0.37    9.3   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   6.9e-18   1.5e-14       1      96 []      42     127 ..      42     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 6.9e-18
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       L++G+G+Gr++ +l       vg+D+s++ + la e+++e+      vv+  e+lpf+d+ f  v++  +l++v++p
  gi|320100275|ref|YP_004175867.1|  42 LEIGVGSGRFSSPLR----IDVGIDPSERIISLAYERGVES------VVGVGEELPFRDSCFGGVFIIVTLCFVDNP 108
                                       89*************....668*********9998888877......9***************************** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                        ++lke +RvL+ +G++++
  gi|320100275|ref|YP_004175867.1| 109 LRVLKESWRVLRDDGYVIV 127
                                       ****************986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   7.5e-13   1.7e-09      12     164 ..      29     175 ..      12     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 7.5e-13
                   Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvl 88 
                                       ++e+++   r +  +L+iG G+G++++ lr      +g+D+s++ +++a   +  +++    +e ++ +  f  +  
  gi|320100275|ref|YP_004175867.1|  29 AVEKAS--TRVPRPWLEIGVGSGRFSSPLRID----VGIDPSERIISLAY-ERGVESVVGVGEELPFRDSCFGGVFI 98 
                                       344444..688999*************99888....8*******999984.3333333333568888999******* PP

                   Methyltransf_23  89 revlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpag.rhisffsarslkelleeaGlevve 164
                                       + +l+ v++p ++l+  ++ l+++Gy+++  + +++++ rl+ + ++  ++  r+ +f+s +++ e+le++G++ v+
  gi|320100275|ref|YP_004175867.1|  99 IVTLCFVDNPLRVLKESWRVLRDDGYVIVGFVPRESPWGRLYVEKKAKGHRFyRLARFYSVSEVYEMLEASGFKTVS 175
                                       *******************************99999*****888877777766888******************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   6.3e-11   1.4e-07       2      97 .]      42     123 ..      42     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.3e-11
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                       L++G G+Gr++  l         +g+D+se+ +  a er       ve v+g  e+lpf d+ f  v+++ +l++++
  gi|320100275|ref|YP_004175867.1|  42 LEIGVGSGRFSSPLRID------VGIDPSERIISLAYERG------VESVVGVGEELPFRDSCFGGVFIIVTLCFVD 106
                                       89************966......69**************9......9**********************87799998 PP

                                       HHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                       ++   ++lke +rvL+++G
  gi|320100275|ref|YP_004175867.1| 107 NP--LRVLKESWRVLRDDG 123
                                       55..59***********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 !   16.6   0.0   1.7e-06    0.0038      99     151 ..      75     127 ..      62     133 .. 0.89
   2 ?   -1.0   0.0      0.42   9.3e+02     197     217 ..     155     175 ..     139     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                                       TEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran  99 nieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                        +e +++ +eeLpf d  f  v +   l  v + l++Lke +rvl+  G ++v
  gi|320100275|ref|YP_004175867.1|  75 GVESVVGVGEELPFRDSCFGGVFIIVTLCFVDNPLRVLKESWRVLRDDGYVIV 127
                                       6999******************************************9998875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.42
                                       HS--HHHHHHHHHHTTEEEEE CS
                   Ubie_methyltran 197 afPdqetlkeliedaGfksve 217
                                       +f    ++ e++e +Gfk+v+
  gi|320100275|ref|YP_004175867.1| 155 RFYSVSEVYEMLEASGFKTVS 175
                                       566677888999999999986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     7e-06     0.016       8     110 ..      42     128 ..      38     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7e-06
                   Methyltransf_31   8 lDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl 84 
                                       l++G G+G+++  l       ++ vGiD se+ i+lA e+        ve  +g  eel+  + d++f  ++   +l
  gi|320100275|ref|YP_004175867.1|  42 LEIGVGSGRFSSPLR------ID-VGIDPSERIISLAYER-------GVESVVGVGEELP--FRDSCFGGVFIIVTL 102
                                       788999999999999......33.9**************8.......88899999999**..*************** PP

                   Methyltransf_31  85 naladpdkileeiervlkpggillie 110
                                       + + +p  +l+e  rvl+++g++++ 
  gi|320100275|ref|YP_004175867.1| 103 CFVDNPLRVLKESWRVLRDDGYVIVG 128
                                       ***********************985 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.081       1      98 [.      42     124 ..      42     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       LeiG G+G+++++l+ +      +g+D+s++ i        ++e+     v    ++l  +d+   f  v+++ +l+
  gi|320100275|ref|YP_004175867.1|  42 LEIGVGSGRFSSPLRID------VGIDPSERII------SLAYERGVE-SVVGVGEELPFRDS--CFGGVFIIVTLC 103
                                       8****************......**********......333333333.33344444444444..8999******** PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                        ++++ +vl++  ++L+++G+
  gi|320100275|ref|YP_004175867.1| 104 FVDNPLRVLKESWRVLRDDGY 124
                                       ******************997 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05     0.044      18     109 ..      42     129 ..      25     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                              MetW  18 ldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnpkev 94 
                                       l++G G G + + l+        G++ +e+ +  + ++G++ + g + ++l  f+d+ f  v +  tl  + np +v
  gi|320100275|ref|YP_004175867.1|  42 LEIGVGSGRFSSPLRI-----DVGIDPSERIISLAYERGVESVVG-VGEEL-PFRDSCFGGVFIIVTLCFVDNPLRV 111
                                       6778888887777744.....3699***************99987.55666.59*********************** PP

                              MetW  95 ldellrigrr...aivsf 109
                                       l+e+ r+ r    +iv f
  gi|320100275|ref|YP_004175867.1| 112 LKESWRVLRDdgyVIVGF 129
                                       ****99976433366666 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00017      0.37     149     218 ..      62     128 ..      53     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00017
                   Methyltransf_29 149 DeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihC..srCridwteedgilllevdRvlRpgGyfvls 218
                                       D  e  + +a eRgv ++++v   + lp+  + f  +    + C   + ++   +l e  RvlR +Gy ++ 
  gi|320100275|ref|YP_004175867.1|  62 DPSERIISLAYERGVESVVGV--GEELPFRDSCFGGVFIivTLC---FVDNPLRVLKESWRVLRDDGYVIVG 128
                                       55678899************8..689********9765411555...55677889*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1612.40
//
Query:       gi|320100276|ref|YP_004175868.1|  [L=263]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-17   64.2   0.0    3.3e-17   63.4   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    5.1e-05   23.6   0.0    7.7e-05   23.0   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.021   15.0   0.0    1.2  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   5.5e-21   3.3e-17       6     146 ..      54     195 ..      52     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 5.5e-21
                                       EESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                       gCnlrC+fC+ +        +g++ s++e+   + +++ ++g ++v ++g ep+l +    +l++l + +   +++ 
  gi|320100276|ref|YP_004175868.1|  54 GCNLRCRFCWGWIPrDNYSSYGEFYSPREVYGRLVAIASRRGYRYVRVSGNEPTLAWQHLLELLELFEQD-GRYTFI 129
                                       9**********9889788889999999999988888866777***************9999999999996.****** PP

                                       EEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEE CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  82 vetngtlpd..eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvv 146
                                       +etng+ +   + k++ l+     +v ++l+ ++++++++l++ r++ f+ +l+ale+l + g+   +
  gi|320100276|ref|YP_004175868.1| 130 LETNGIIIGadKAKARDLAGFKHLHVRVSLKGVNEDEFHRLTGaRREFFSLQLKALENLLNEGVS--T 195
                                       ********99999999999999**************************************99987..4 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.3e-08   7.7e-05      14     122 ..      54     162 ..      45     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.3e-08
                           Fer4_12  14 gCnlsCkgCfnketwsfk.....sgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp 84 
                                       gCnl+C++C     w ++     +g+ ++ +e+  ++++ ++ +  + + ++G EP l    + llel++ +++ + 
  gi|320100276|ref|YP_004175868.1|  54 GCNLRCRFCW---GWIPRdnyssYGEFYSpREVYGRLVAIASRRGYRYVRVSGNEPTL--AWQHLLELLELFEQDGR 125
                                       9*******99...44333233447777755***********99***************..99*************99 PP

                           Fer4_12  85 ekdiwlytgytleelskkekeellkeidvlvdGkfees 122
                                          i++++g ++ + ++k  ++l    +  v + ++  
  gi|320100276|ref|YP_004175868.1| 126 YTFILETNGIIIGADKAK-ARDLAGFKHLHVRVSLKGV 162
                                       889**********99976.5555444444444444433 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.5e-06     0.021       7      92 ..      54     137 ..      51     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-06
                           Fer4_14   7 gCnlsCkgCd......nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                       gCnl C++C       n +++ + + + +++  l++i    + + +  + + ++G eP      ++ll+l++   + 
  gi|320100276|ref|YP_004175868.1|  54 GCNLRCRFCWgwiprdNYSSYGEFYSPREVYGRLVAIA---SRRGY--RYVRVSGNEPT--LAWQHLLELLELFEQD 123
                                       9*********9985444444444444444444444444...33333..56889*****9..55789********999 PP

                           Fer4_14  78 ypekkiwletngtle 92 
                                       +  +   letng + 
  gi|320100276|ref|YP_004175868.1| 124 G-RYTFILETNGIII 137
                                       9.8999999*99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2064.54
//
Query:       gi|320100277|ref|YP_004175869.1|  [L=327]
Description: bifunctional phosphoglucose/phosphomannose isomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-36  124.7   0.0    4.4e-36  124.2   0.0    1.2  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    2.6e-05   24.1   0.0    0.00026   20.8   0.1    2.1  2  SIS         SIS domain


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.2   0.0   4.9e-40   4.4e-36       2     151 ..     174     320 ..     173     321 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 4.9e-40
                                       G-HHHHHHHHHTT..SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEE CS
                        bact-PGI_C   2 knpakqlAlelag..klpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvll 76 
                                       +++a++lA++++    l vi++ +++le++A+R kn++nen+Kip+ + v pe++hn+ivg+e   + + +lr+v +
  gi|320100277|ref|YP_004175869.1| 174 EEEARRLAEWINSvqGLLVIAT-HTPLEPLAVRGKNEFNENSKIPVKVDVAPEWMHNDIVGYE---QPGIPLRVVEV 246
                                       6899*******99966777766.***************************************5...889******** PP

                                       SSHH........HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH. CS
                        bact-PGI_C  77 rdeeehprvkkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKee 151
                                        d++ + + + ++e++  ++ e g++++++ ++g+++le+++++ l+++++S++lA lrg+DP ++++I+++Ke 
  gi|320100277|ref|YP_004175869.1| 247 VDPS-DRVGRGLVEFMHGVYVETGASTYRLALRGGTLLEKMMYGSLVLGLASCRLARLRGIDPLETKSIKRYKES 320
                                       *998.478888**************************************************************96 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.9e-08   0.00026       6      76 ..      29      95 ..      28     108 .. 0.81
   2 ?    0.5   0.0     0.056     5e+02      18      46 ..     201     229 ..     188     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-08
                                      SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHH CS
                               SIS  6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaela 76
                                      ++i+vlG+G s+ ++++l++  + +gg +v+  +++    g    id+++l i +s+sg+t+++++a   +
  gi|320100277|ref|YP_004175869.1| 29 NKIVVLGMGGSGIVGDFLSALSMIHGGLPVFTLKSHV-SPG---FIDSGTLAISVSYSGNTRETILATMGV 95
                                      69****************9877777777766655555.666...*********************998744 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHTSEEEEEEHHHHHHT CS
                               SIS  18 aiakelalkleeiggivvevedaselkhg 46 
                                       ++a  ++  ++e ++i+v v+ a+e +h+
  gi|320100277|ref|YP_004175869.1| 201 PLAVRGKNEFNENSKIPVKVDVAPEWMHN 229
                                       57889999*****************7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2684.35
//
Query:       gi|320100278|ref|YP_004175870.1|  [L=210]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   0.5      0.012   15.5   0.5    1.4  1  MarR_2       MarR family
  ------ inclusion threshold ------
      0.016   15.0   0.1      0.037   13.8   0.1    1.6  1  HTH_IclR     IclR helix-turn-helix domain
       0.02   14.5   0.8      0.045   13.4   0.8    1.5  1  GntR         Bacterial regulatory proteins, gntR family
      0.025   14.4   0.0      0.044   13.6   0.0    1.3  1  TFIIE_alpha  TFIIE alpha subunit
      0.036   14.4   0.1      0.072   13.5   0.1    1.5  1  Rrf2         Transcriptional regulator
        0.1   12.6   1.1        0.3   11.1   0.3    2.1  3  HTH_Crp_2    Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   3.9e-06     0.012      21      56 ..     171     205 ..     151     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                                       EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  21 dltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                       d +v+++  +lg+s+ a+ ril rLv+  +++ ++g
  gi|320100278|ref|YP_004175870.1| 171 D-AVRAISLELGVSREAARRILYRLVEERYLRIVRG 205
                                       3.7888888*********************998765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.3e-05     0.037      21      49 ..     173     201 ..     153     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  21 lselArrtglpkStvhRlLqtLvelGyve 49 
                                       ++ ++ ++g+++ +++R+L  Lve++y++
  gi|320100278|ref|YP_004175870.1| 173 VRAISLELGVSREAARRILYRLVEERYLR 201
                                       678999*********************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 ?   13.4   0.8   1.5e-05     0.045      27      60 ..     173     206 ..     163     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR  27 ereLaaefgVsrttvReALrrLeaeglverrqgr 60 
                                       +r+++ e+gVsr   R+ L rL++e ++ + +gr
  gi|320100278|ref|YP_004175870.1| 173 VRAISLELGVSREAARRILYRLVEERYLRIVRGR 206
                                       799**************************99986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.044      10      62 ..     149     205 ..     147     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                                       CS-HHHHHHHHHHHCTTSEBHHH....HHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                       TFIIE_alpha  10 fygeeavlvldvLlekgevteed....lakelkidlnelrklLnrLyearlvkykrr 62 
                                       +yg    lv   ++e+gevt  d    ++ el++ ++  r++L+rL e+r   ++r 
  gi|320100278|ref|YP_004175870.1| 149 AYGRAYDLVTGLMAEHGEVTVKDavraISLELGVSREAARRILYRLVEERYLRIVRG 205
                                       677777888888999999987765566899********************9999886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.4e-05     0.072      27      61 ..     172     206 ..     153     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2  27 sseeiaerqnispsylekilakLrkaglvksvrGk 61 
                                       ++++i+ + ++s++ +++il +L ++ +++ vrG+
  gi|320100278|ref|YP_004175870.1| 172 AVRAISLELGVSREAARRILYRLVEERYLRIVRGR 206
                                       5789******************************7 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.1   3.3e+03      50      63 ..      29      43 ..      24      46 .. 0.67
   2 ?   -3.3   0.0       3.2   9.7e+03      55      66 ..     129     141 ..     121     141 .. 0.58
   3 ?   11.1   0.3    0.0001       0.3      27      57 ..     176     207 ..     157     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                                      SEE.ETEEEEES-HH CS
                         HTH_Crp_2 50 lis.rgrririldle 63
                                      +i   g r+++ld+ 
  gi|320100278|ref|YP_004175870.1| 29 IIAeAGSRVTLLDPG 43
                                      566346349999985 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                                       EE.EEES-HHHHH CS
                         HTH_Crp_2  55 rr.irildleaLr 66 
                                       r+  ++ ++e+Lr
  gi|320100278|ref|YP_004175870.1| 129 RTlRILVNPEGLR 141
                                       3333466777776 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0001
                                       HHHHTTSSHHHHHHHHHHHHHTTSEE..ETEEE CS
                         HTH_Crp_2  27 lAsmlGltretvsrilseLkreglis..rgrri 57 
                                       ++  lG++re   ril +L +e +++  rgr i
  gi|320100278|ref|YP_004175870.1| 176 ISLELGVSREAARRILYRLVEERYLRivRGR-I 207
                                       66779*********************84455.7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1546.64
//
Query:       gi|320100279|ref|YP_004175871.1|  [L=155]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1145.75
//
Query:       gi|320100280|ref|YP_004175872.1|  [L=78]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 548.37
//
Query:       gi|320100281|ref|YP_004175873.1|  [L=263]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-28   96.6   1.3    1.1e-27   95.9   0.3    1.9  3  DUF2258   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2258  Uncharacterized protein conserved in archaea (DUF2258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.3   6.2e-32   1.1e-27       1      73 [.       9      81 ..       9      84 .. 0.97
   2 ?   -3.5   0.0      0.68   1.2e+04      12      14 ..     116     118 ..     102     124 .. 0.55
   3 ?   -2.9   0.0      0.44   7.8e+03      40      47 ..     242     249 ..     215     259 .. 0.58

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 6.2e-32
                                      EEEECEEGGGHHHHHHHHHHHHTCCCCHTTSS.HHHHHHHHHHHHHHHHHHHHCCTT--TTSEEEEEEEEEEE CS
                           DUF2258  1 lsTGlviaaaYAdKlRrvlfaalsklvkkkkeekkeiaraiaeLNkklYevlveklkidKldvvrirveyeve 73
                                      l+TG++ia+aYA K+Rr+l+a+ls+ vk++ke+++e+ara++eLN  lY++lv +lk++K+d vr+rv+y ve
  gi|320100281|ref|YP_004175873.1|  9 LNTGIIIAGAYAGKVRRTLYAQLSSRVKTDKEFAREVARASGELNMLLYHILVGELKVNKGDAVRVRVKYVVE 81
                                      79********************************************************************987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.68
                                       HHH CS
                           DUF2258  12 AdK 14 
                                       A+K
  gi|320100281|ref|YP_004175873.1| 116 AEK 118
                                       333 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.44
                                       HHHHHHHH CS
                           DUF2258  40 aiaeLNkk 47 
                                       + ++LN++
  gi|320100281|ref|YP_004175873.1| 242 KPSQLNRE 249
                                       33566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1911.46
//
Query:       gi|320100282|ref|YP_004175874.1|  [L=325]
Description: phosphoesterase DHHA1 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   53.1   0.0    7.1e-14   52.4   0.0    1.5  1  DHHA1     DHHA1 domain
    0.00041   20.5   0.0    0.00078   19.6   0.0    1.4  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   7.9e-18   7.1e-14      38     137 ..     213     318 ..     172     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 7.9e-18
                                       C.......TCEEEEEECHCCHHH.HHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSHSS-HHHHHHHHHHH CS
                             DHHA1  38 k.......gvkvlvaevgeewda.galgiaadklksklkkpvivfvakeegdkvkvsarskkdgvdagelakeaaak 106
                                       +         +v++ +vg  +++ g +g aa++ +  ++++ i ++++e+g+++  s+rs +  vd++++++ ++++
  gi|320100282|ref|YP_004175874.1| 213 EelrlwvkANTVVYGAVGYVVNPpGSVGKAANYARV-YGRARIGVAVEERGETYVMSLRSDG-SVDLNKVLRLMSRE 287
                                       244455668889999999999999************.788**********************.************** PP

                                       TTCCEEEETCEEEEEEEHCHHHHHHHHHHHH CS
                             DHHA1 107 lgggGGGHdlAaGagipaekleealealeea 137
                                       +   GGGH++AaGa++++  ++++l +l+ea
  gi|320100282|ref|YP_004175874.1| 288 IPVMGGGHPFAAGARLEKRLFKDFLTKLNEA 318
                                       ****************9999********997 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.7e-08   0.00078       8      88 ..       8     127 ..       4     139 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.7e-08
                                       CSSSHHHHHH.HHHHHH................CECS--TCGGCGCCH....................HCCCSEEEE CS
                                       xxxxxxxxxx.xxxxxx................xxxxxxxxxxxxxxx....................xxxxxxxxx RF
                               DHH   8 knpDtDsigS.aialan................llvDhneksqavege....................akeeaedvi 47 
                                        + D D+++S a+a+a                 ll D +e ++  ++                      + +  +v+
  gi|320100282|ref|YP_004175874.1|   8 VHGDSDGVASgALAYAFfsartdtqvffthpvgLLGDLKEFTRNGDDLliadialnettavdvlrlleERGRYGNVV 84 
                                       578**************7777777766666666344444444444433444444444444444555333344568** PP

                                       EEE-S---S..S---SS--EEEE-SSS-HHHHHHHHHHHTT-- CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  48 iiDHHrlge..efetlapilflnepvgstaeivaelleekkee 88 
                                        iDHH  +   +++  + i +++ ++ s++e+ +++l e++ +
  gi|320100282|ref|YP_004175874.1|  85 YIDHHPEPLgvSLSSVESINIVHDTCCSASELTFRYLVENGLD 127
                                       *****998788888999999***************99987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2342.97
//
Query:       gi|320100283|ref|YP_004175875.1|  [L=334]
Description: integrase family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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      1e-33  116.6   0.0    1.3  1  Phage_integrase  Phage integrase family
    1.9e-10   41.0   0.0    7.5e-07   29.5   0.0    2.6  3  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    1.8e-07   30.7   1.4    3.1e-07   29.9   1.4    1.3  1  zinc_ribbon_2    zinc-ribbon domain
    4.8e-07   30.0   0.1    3.9e-05   23.9   0.0    2.8  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    6.2e-05   22.9   0.4     0.0001   22.3   0.4    1.2  1  DZR              Double zinc ribbon
    0.00035   19.9   1.1    0.00061   19.1   1.1    1.3  1  zf-ribbon_3      zinc-ribbon domain
     0.0006   20.5   0.1      0.001   19.8   0.1    1.3  1  zinc_ribbon_15   zinc-ribbon family
     0.0011   19.0   1.6     0.0018   18.3   1.6    1.3  1  UPF0547          Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
      0.014   15.2   2.5      0.032   14.1   2.5    1.6  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.16   12.0   0.5       0.32   11.0   0.5    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met


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 !  116.6   0.0   5.6e-37     1e-33       3     170 ..     127     282 ..     125     284 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 5.6e-37
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealel 79 
                                       l  +e+e+l++a+++     dkl+l+ll++tGlR  Ell+Lrv+d+d+  +vi+v  +  K +ker+v+ + e  e+
  gi|320100283|ref|YP_004175875.1| 127 LSDEEIEKLMNAART---PLDKLILRLLVDTGLRSRELLGLRVEDVDFHSRVIRV--SSAKYGKERYVTATGETFEM 198
                                       7889***********...88***********************************..******************** PP

                                       HHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S.SC--TTHHHHHHHHHHHHHCTSHHHHHHHH CS
                   Phage_integrase  80 lkellskaleeaeksellfaskrgkplsrqtvrkafkraveeagie.kpltpHtlRhsfataLleagvdlrvvqkll 155
                                       l+ +++ +         l +  r   l+ + ++k +kr++ +agi  ++++pH lRh+fat+ l++g++l  +q+ll
  gi|320100283|ref|YP_004175875.1| 199 LRSWIALN--------GLKPGDRLFNLTYSGLYKKLKRLAARAGIPpEKIRPHVLRHTFATRALRRGLSLPSLQRLL 267
                                       ********........555555555678************************************************* PP

                                       T-SSCCHHHHHHCCC CS
                   Phage_integrase 156 GHssisttqiYthva 170
                                       GH++i+ttq+Y h++
  gi|320100283|ref|YP_004175875.1| 268 GHADIKTTQVYLHLS 282
                                       *************75 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   4.2e-10   7.5e-07       1      53 [.      22      74 ..      22      81 .. 0.92
   2 !    8.8   0.0    0.0012       2.2       7      48 ..      82     134 ..      76     141 .. 0.76
   3 ?   -3.6   0.0       9.2   1.6e+04      17      30 ..     273     287 ..     269     293 .. 0.58

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.2e-10
                   Phage_int_SAM_4  1 LlerfrealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyL 53
                                      +le+f   l+++g s +T+k+Ylsa+k+fl f+ +k+ +e+t +d+ a  n  
  gi|320100283|ref|YP_004175875.1| 22 ILEEFKVSLEASGASSETVKAYLSAVKDFLSFIGGKPLREVTLKDVVAWRNER 74
                                      6899******************************************9887765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                   Phage_int_SAM_4   7 ealrlaglserTiksYlsaikrflrflkkk...........apeeltkediea 48 
                                       ++++ +++ + T ++Y+  +krf ++l              +++ l++e+ie 
  gi|320100283|ref|YP_004175875.1|  82 RKMEGREKWQVTLHYYTMFLKRFFEWLGLNigvssvkkppaRINALSDEEIEK 134
                                       68999999999****************62234444555555666777777765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 9.2
                   Phage_int_SAM_4  17 rTiksYls.aikrfl 30 
                                       +T ++Yl+  i+++ 
  gi|320100283|ref|YP_004175875.1| 273 KTTQVYLHlSIEDLK 287
                                       677777752455554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   1.4   1.7e-10   3.1e-07       1      21 [.     303     323 ..     303     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.7e-10
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                       +C +CG+e++ +a +CpyCG+
  gi|320100283|ref|YP_004175875.1| 303 RCVKCGREIPADALYCPYCGS 323
                                       6*******************7 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 !   23.9   0.0   2.2e-08   3.9e-05       2      80 ..      24     108 ..      23     110 .. 0.86
   2 ?    2.9   0.0     0.077   1.4e+02      30      70 ..     226     267 ..     218     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS-----..........-----HHH CS
                   Phage_int_SAM_1   2 eqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeg..........lsatslar 68 
                                       e+f+  L+ + g+s  T+ aY+ ++++fl f      + l+++t +dv+a+ +e++++g          + + +l+ 
  gi|320100283|ref|YP_004175875.1|  24 EEFKVSLE-ASGASSETVKAYLSAVKDFLSFIGG---KPLREVTLKDVVAWRNERLRNGfpnrkmegreKWQVTLHY 96 
                                       66666666.6677*********************...*********************9988888777777788888 PP

                                       HHHHHHHHHHHH CS
                   Phage_int_SAM_1  69 rlsalrsFfqfl 80 
                                       ++  l++Ff +l
  gi|320100283|ref|YP_004175875.1|  97 YTMFLKRFFEWL 108
                                       888888888876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.077
                                       HHHHHH.TS--TTT--HHHHH.HHHHS----------HHHHH CS
                   Phage_int_SAM_1  30 lkflaergkesleqlttedvr.aflaeleeeglsatslarrl 70 
                                       lk la r +   e+++++ +r +f  + +++gls  sl r l
  gi|320100283|ref|YP_004175875.1| 226 LKRLAARAGIPPEKIRPHVLRhTFATRALRRGLSLPSLQRLL 267
                                       566777789999********868999999999**99999977 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.4   5.6e-08    0.0001       1      23 [.     304     326 ..     286     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.6e-08
                               DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                       C +Cg+e+p+da +C++Cg++ +
  gi|320100283|ref|YP_004175875.1| 304 CVKCGREIPADALYCPYCGSSQQ 326
                                       77888888888888888887765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.1   3.4e-07   0.00061       3      24 ..     302     323 ..     301     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.4e-07
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGt 24 
                                       +rC +CG  +  +d+  CpyCG+
  gi|320100283|ref|YP_004175875.1| 302 RRCVKCGReI-PADALYCPYCGS 323
                                       69******77.***********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 !   19.8   0.1   5.6e-07     0.001      64      86 .]     293     322 ..     270     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.6e-07
                    zinc_ribbon_15  64 e.......kkeCknCgkeveeefkyCpkCg 86 
                                       +        ++C +Cg+e+ ++  yCp+Cg
  gi|320100283|ref|YP_004175875.1| 293 KigggtggLRRCVKCGREIPADALYCPYCG 322
                                       2445566689*******************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.6   9.9e-07    0.0018       2      21 ..     303     322 ..     302     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.9e-07
                           UPF0547   2 vCPeCeakvPvaaqfCphCG 21 
                                       +C  C +++P++a  Cp+CG
  gi|320100283|ref|YP_004175875.1| 303 RCVKCGREIPADALYCPYCG 322
                                       6778***************9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.5   1.8e-05     0.032      12      35 ..     302     325 ..     301     327 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                           DUF35_N  12 qrCpdCGtvqfPPr.avCphCgsdd 35 
                                       +rC +CG+ + P+   +Cp+Cgs++
  gi|320100283|ref|YP_004175875.1| 302 RRCVKCGREI-PADaLYCPYCGSSQ 325
                                       7********8.***********986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   0.00018      0.32      72      96 ..     303     325 ..     298     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                       EETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  72 rCreCgkefeleekalrCpkCgsad 96 
                                       rC +Cg+e+  +  al Cp Cgs++
  gi|320100283|ref|YP_004175875.1| 303 RCVKCGREIPAD--ALYCPYCGSSQ 325
                                       8********987..578*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      742  (0.0413855); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2248.10
//
Query:       gi|320100284|ref|YP_004175876.1|  [L=155]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1128.73
//
Query:       gi|320100285|ref|YP_004175877.1|  [L=516]
Description: aminopeptidase Iap family-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.071   13.1   0.0    2.1  2  PA        PA domain


Domain annotation for each model (and alignments):
>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     4e-06     0.071      20      88 ..      71     157 ..      34     158 .. 0.62
   2 ?   -0.5   0.0     0.074   1.3e+03      36      57 ..     217     238 ..     177     255 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-06
                                PA  20 e.........gvdvkGkivLvqrtf.......aeKarnAqaaGAagviiv.......ndgelgaatgasgnegepdg 73 
                                       +         +  ++G+++L +  +       +  +  A +aGA++v+++       +d    +++ + +n   +++
  gi|320100285|ref|YP_004175877.1|  71 AlqastlrvvAGGLNGRVLLYK--YpesilelRFMVGEALKAGAEAVVLIggkgrrmSDA-VLSSSIPVMN--PDTP 142
                                       4555555666566777777773..333344557788899***********8777654222.2233333444..4455 PP

                                PA  74 itiPavgvsredgea 88 
                                        +iP+v +  +++ +
  gi|320100285|ref|YP_004175877.1| 143 PGIPVVVLEADAARN 157
                                       ******998887765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.074
                                PA  36 aeKarnAqaaGAagviivndge 57 
                                       ++ ++ A++ G+  vi+++ ++
  gi|320100285|ref|YP_004175877.1| 217 RDIVASAATVGGSSVILISFTA 238
                                       7889999999999999996555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3825.17
//
Query:       gi|320100286|ref|YP_004175878.1|  [L=480]
Description: prolyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-29  103.4   0.1    2.8e-29  102.3   0.0    1.5  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.1e-21   76.8   0.2    2.2e-21   75.8   0.2    1.6  1  HGTP_anticodon  Anticodon binding domain
    2.2e-05   24.6   0.1    6.9e-05   23.0   0.0    1.8  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.0   4.7e-33   2.8e-29       8     176 ..     105     273 ..      96     276 .. 0.92
   2 ?   -3.8   0.0       1.8   1.1e+04      65      92 ..     370     396 ..     364     404 .. 0.61

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 4.7e-33
                                       SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEE.EEEEEEEES.GGGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFh.qkdgyvfha.easlddslr 81 
                                       ++++ ++Pt+e+ ++ + + + ++  k+LPlk+yq+  ++R+E++ ++++lRvre+    +++  ha  ++++ +++
  gi|320100286|ref|YP_004175878.1| 105 NERLFVRPTSETVMYYMWNMW-IKGrKDLPLKMYQVVNVFRYETKMTHPILRVREIMgFIEAHTAHAtMEEAEKQIS 180
                                       6899**************988.888799*****************999*******97369*******8899****** PP

                                       HHHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  82 dlikaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennrek 157
                                       + i  ++++f+rl l+++ ++   ++++ a +++ ++f  v++  +kg+e+g++ +lg++++++++++++d ++ ek
  gi|320100286|ref|YP_004175878.1| 181 EAIAIYKEFFNRLQLPYFIVKTPpWDTF-AGAEYNYDFITVMP-DGKGLELGSVINLGQKFAKAFEIKYMDTDGVEK 255
                                       ****************886666687755.99************.9******************************** PP

                                       EEEEEEEEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 158 svimicaaigveRllsail 176
                                       +v+ +c++++ eR+l+a++
  gi|320100286|ref|YP_004175878.1| 256 HVYQTCYGVS-ERVLGAVI 273
                                       **********.*****997 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.8
                                       EEEEEEESGGGHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  65 kdgyvfhaeaslddslrdlikaisrife 92 
                                        + +v+ +e+ + d lr+++ +i++ ++
  gi|320100286|ref|YP_004175878.1| 370 REKHVVKLEE-AVDLLRKIWSEINEYLR 396
                                       4556666554.56666666666666655 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.2   3.7e-25   2.2e-21       1      93 [.     292     386 ..     292     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 3.7e-25
                                       SEEEEESSSS.HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETT CS
                    HGTP_anticodon   1 qvvviplnek.aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrd 75 
                                       qvv++p+ +  +++++eya k+ + L+a+g+rv +d  ++ ++g+k+ +++++g+p +++vG kel+  tvt+ +rd
  gi|320100286|ref|YP_004175878.1| 292 QVVIVPVMKPgENQVLEYAFKVSNILKAHGVRVFVDTdQEHTPGWKYYYWEMKGVPTRIEVGRKELDASTVTIARRD 368
                                       89*****998877799*********************9*************************************** PP

                                       TCEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  76 treqervsldelveklke 93 
                                       +re+  v+l+e+v+ l++
  gi|320100286|ref|YP_004175878.1| 369 KREKHVVKLEEAVDLLRK 386
                                       **************9987 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 ?   -2.2   0.1      0.84     5e+03      20      32 ..     171     183 ..     161     187 .. 0.78
   2 !   23.0   0.0   1.1e-08   6.9e-05      12      69 .]     421     480 .]     412     480 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.84
                                       SGHHHHHHHHHHH CS
                         ProRS-C_1  20 geeecEekIkeet 32 
                                         ee+E++I e +
  gi|320100286|ref|YP_004175878.1| 171 TMEEAEKQISEAI 183
                                       5689999999876 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.1e-08
                                       -EEEEEESSGHHHHHHHHHHHS-EEEEEESSB..-SSCCCSB-TTT.-SB-SEEEEEE-B- CS
                         ProRS-C_1  12 gfvlapWcgeeecEekIkeetgakslcipfdq..epseegtkCivc.gkpakkwvlfgrsY 69 
                                       g+v+apW+g+ ec e++++etg ++l+  +++  + ++  ++  +c + +a++++l g +Y
  gi|320100286|ref|YP_004175878.1| 421 GLVIAPWDGSRECAEELEKETGKNVLGEITESplN-LPPPSQYTACgKAKADRYALLGVTY 480
                                       59*************************98887642.3444444555157899***999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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 0.24s 00:00:00.76 Elapsed: 00:00:00.61
# Mc/sec: 2380.05
//
Query:       gi|320100287|ref|YP_004175879.1|  [L=82]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.5   0.1       0.21   12.0   0.1    1.2  1  PilA4     Pilin A4


Domain annotation for each model (and alignments):
>> PilA4  Pilin A4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.1e-05      0.21      56      75 ..      43      61 ..      31      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.1e-05
                                      TSS.EEEEE.EESSSSSSEE CS
                             PilA4 56 tnkdytvtatsvtGktftyd 75
                                      ++kdy +t+t+++Gk+f+yd
  gi|320100287|ref|YP_004175879.1| 43 DEKDY-ITLTTADGKSFKYD 61
                                      56779.*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 620.73
//
Query:       gi|320100288|ref|YP_004175880.1|  [L=244]
Description: ATP-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-51  172.7   0.0    8.9e-51  172.5   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5   0.0     5e-55   8.9e-51       1     213 [.       1     217 [.       1     223 [. 0.97

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 5e-55
                   Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekeved 76 
                                       m + vl+ GGkDs++aL+ka++  + +  L s+i+  + s  +h +  +++++++ s+Gipl    ++ e e e++ 
  gi|320100288|ref|YP_004175880.1|   1 MNATVLFTGGKDSVYALHKAAEAgYRIVVLSSIIPLYRYSMLYHQPYFNILQAQSQSLGIPLETIGVS-EGEMEIDA 76 
                                       6789******************989*************************************999999.999***** PP

                   Diphthami_syn_2  77 Lkgtlkkld....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaeglde 149
                                       L+  l +++    v  vv+Gai+s+yq++r+e+v  elGl +  PLW+++p ++l e +e++ + i+++++ +g   
  gi|320100288|ref|YP_004175880.1|  77 LRMLLTRVRdrygVKVVVSGAIASNYQRKRFEQVVGELGLELYTPLWGRNPYKYLGELLENGIRFIIMSITSMGIPL 153
                                       *******999999**************************************************************** PP

                   Diphthami_syn_2 150 slLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyld 213
                                       ++LGr i+ + ++ l kl+ kyg d+++egG+aet+v+D+Plfk rl +   +k  +e  gy++
  gi|320100288|ref|YP_004175880.1| 154 EILGREIEAEDVERLIKLARKYGFDPSFEGGDAETIVVDSPLFKYRLLIAGEKKILSEYEGYYE 217
                                       **************************************************99999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1840.26
//
Query:       gi|320100289|ref|YP_004175881.1|  [L=470]
Description: H+transporting two-sector ATPase subunit alpha/beta [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-64  215.8   0.0    7.5e-64  215.3   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
     0.0058   17.1   0.5      0.012   16.1   0.5    1.5  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
       0.02   15.0   0.3      0.048   13.8   0.3    1.6  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 !  215.3   0.0   1.3e-67   7.5e-64       1     213 []     136     354 ..     136     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 1.3e-67
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D lf+iv+Gq++ i++++g++++ i++++++q++      + a+++++iG   +++  ++e+f+++++++rt
  gi|320100289|ref|YP_004175881.1| 136 GISAIDGLFSIVRGQKLPIFSGSGLPHNRIAAQIVRQARVLgkeeKfAMVFAAIGVPYDDAMFFIENFRRTGALERT 212
                                       89***********************************8655888768****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       v ++nt+++pv++r+a++++++t+AE+++  ++++vl+++++++ ++eAlre+s++ +e+p+++gyp+y++++la++
  gi|320100289|ref|YP_004175881.1| 213 VALINTASSPVIERIATPRVALTIAEHLAWtHDMHVLVVLTDMTFYCEALRELSAAREEVPGRRGYPGYMYTDLATI 289
                                       *****************************989********************************************* PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag+++ ++Gsvt++++++++++D+++p+++ t +it+g++vL+++l  ++++P+ ++l+S+S
  gi|320100289|ref|YP_004175881.1| 290 YERAGRVRGKKGSVTQLPILTMPDDDITHPIPDLTGYITEGQLVLSRQLWMKGIYPPFDPLMSLS 354
                                       ***************************************************************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 !   16.1   0.5     2e-06     0.012       6      66 ..      18      76 ..      14      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-06
                                      TTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEE CS
                     ATP-synt_ab_N  6 GpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVk 66
                                      G ++ +e  +g+ +g+++ +  +    g+  lg+++ ++ d  +++v+g++  ++   ++Vk
  gi|320100289|ref|YP_004175881.1| 18 GGLLFAETIPGVTYGEIVEVLLP--T-GEAKLGQVIDVSRDATVIQVFGGVADVDLlKSRVK 76
                                      77888989999999999999999..6.99*********************999987777776 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3     8e-06     0.048      22      83 ..      28      74 ..      15      96 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8e-06
                        HAS-barrel 22 dvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedt........g 83
                                      +v +Ge Ve+ lp+ge  lG+v d++r                       d  v+++++++        +
  gi|320100289|ref|YP_004175881.1| 28 GVTYGEIVEVLLPTGEAKLGQVIDVSR-----------------------DATVIQVFGGVadvdllksR 74
                                      79*************************.......................55555555544444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 3151.43
//
Query:       gi|320100290|ref|YP_004175882.1|  [L=585]
Description: H+transporting two-sector ATPase subunit alpha/beta [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-84  280.6   0.0    1.2e-83  280.0   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      1e-40  138.4   0.0    1.8e-40  137.6   0.0    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    7.9e-17   61.5   2.9      2e-16   60.3   2.9    1.7  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 


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 !  280.0   0.0     2e-87   1.2e-83       1     213 []     210     433 ..     210     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 280.0 bits;  conditional E-value: 2e-87
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+rv+D lfp+++G++ ++pg+fg+Gktv+++s++k+s++d ++iy+g+Gergne+a+ l++f +      g+ +m+
  gi|320100290|ref|YP_004175882.1| 210 GVRVIDFLFPLAKGGKAAVPGGFGTGKTVLLHSITKWSEAD-ITIYIGCGERGNEMADALNSFIKlvdprtGKpMME 285
                                       89***********************************9888.***********************999986337*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       r++ +antsn+pvaareas+++g+t++Eyfrd+g+nvll+ads+srwaeA+reis+rl+e p+++g+payl+++la+
  gi|320100290|ref|YP_004175882.1| 286 RSIFIANTSNMPVAAREASVFLGVTIGEYFRDMGYNVLLVADSTSRWAEAMREISGRLEELPGEEGFPAYLASRLAQ 362
                                       ***************************************************************************** PP

                                       HHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yER+g +      +r Gs+ti+ avsp+g Dfs+pvt+atl+++ +   Ld +la r+h+P+in+l+S+S
  gi|320100290|ref|YP_004175882.1| 363 FYERSGYVktigsAERLGSLTIMGAVSPPGADFSEPVTQATLRLIRALYALDVNLAYRRHYPSINWLTSFS 433
                                       ********99999889*****************************************************98 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 !  137.6   0.0     3e-44   1.8e-40       1     121 []      86     201 ..      86     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 3e-44
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvke 77 
                                       +DGiqrpL  +++ sg f+++G+k+p+l r+kkw f+p vk g+kvs+gd++G v+et++++h imvpp+v+g+v++
  gi|320100290|ref|YP_004175882.1|  86 FDGIQRPLPVLEALSGIFVRKGIKAPPLPRDKKWYFTPLVKPGEKVSEGDFIGYVNETDVVRHYIMVPPGVKGSVEW 162
                                       9**************************************************************************** PP

                                       E--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                   ATP-synt_ab_Xtn  78 iaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                       +a eg+yt+ + +a+++      +++t+lq+wPvr+prp++ekl
  gi|320100290|ref|YP_004175882.1| 163 VAGEGDYTMVEPVARING-----RDVTMLQEWPVRRPRPFREKL 201
                                       ****************94.....469****************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 !   60.3   2.9   3.3e-20     2e-16       1      69 []       8      70 ..       8      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.3e-20
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i++v+Gp+v +e+++g     y+++e++  e  ++l+g+a+++++dk++++v+++t+Gl++G++V++TG
  gi|320100290|ref|YP_004175882.1|  8 IYRVSGPLVVAEGMRG--VSVYEVIEIG--E--EKLIGEAIGVEGDKAIIQVYEDTSGLKVGDPVYPTG 70
                                      789*************..**********..8..***********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4089.75
//
Query:       gi|320100291|ref|YP_004175883.1|  [L=105]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 819.14
//
Query:       gi|320100292|ref|YP_004175884.1|  [L=315]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2265.51
//
Query:       gi|320100293|ref|YP_004175885.1|  [L=191]
Description: H+transporting two-sector ATPase subunit E [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   59.2  16.0    8.9e-16   57.9  16.0    1.6  1  vATP-synt_E    ATP synthase (E/31 kDa) subunit
    0.00058   20.2  28.4     0.0077   16.6  25.6    2.7  3  V-ATPase_G_2   Vacuolar (H+)-ATPase G subunit
      0.003   17.6  17.8       0.47   10.5   9.6    2.7  2  DivIVA         DivIVA protein
  ------ inclusion threshold ------
      0.062   13.6   0.7       0.94    9.8   0.0    2.4  2  SMC_hinge      SMC proteins Flexible Hinge Domain
      0.071   13.2  25.1        1.2    9.3  15.9    2.3  2  ATP-synt_B     ATP synthase B/B' CF(0)
      0.071   12.5  21.9       0.41   10.0  12.8    2.2  2  DUF3552        Domain of unknown function (DUF3552)
      0.086   13.1   8.0        8.5    6.7   0.0    3.2  3  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
       0.39   11.1   3.5       0.58   10.5   2.2    1.8  2  UvsY           Recombination, repair and ssDNA binding protei
       0.42   10.5  10.8       0.82    9.5  10.8    1.6  1  HrpE           HrpE/YscL/FliH and V-type ATPase subunit E
        0.6   10.3   0.1        0.6   10.3   0.1    3.8  4  DUF2007        Putative prokaryotic signal transducing protei


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 !   57.9  16.0   4.9e-19   8.9e-16       3     198 ..      13     189 ..      11     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 4.9e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   3 rqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfe 79 
                                         eAe++Ae+I ++ae+e+e ++++++++ +e+ e +++    +ae++ + +iS+al +arl v k  e+ +e+v+ 
  gi|320100293|ref|YP_004175885.1|  13 LREAEARAEQIVRDAEAEAERIVKEAEAKWRERAEAERKRITSEAEREANTIISEALREARLLVSKEYEKAVEDVLR 89 
                                       57*************************************************************************99 PP

                                       HHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSE CS
                       vATP-synt_E  80 eaekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeedf 156
                                       ea   +++ + d    ++ +++Li + l  +++p+ iv + k D e  +     +++e+          v+++    
  gi|320100293|ref|YP_004175885.1|  90 EAYDSVRKRSFDI---ENSIRNLIRESLRLVNAPKKIVVS-KGDLEAARR----IVAELGL------PGVVVEA--- 149
                                       9999999988888...999*****************9987.568877666....8999999......4667777... PP

                                       BTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCH CS
                       vATP-synt_E 157 ledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaL 198
                                         d+ GGv++e+++g i v+nT e+rL  +  + + e+r+ L
  gi|320100293|ref|YP_004175885.1| 150 -GDIDGGVIVESESG-IVVDNTYESRLREFQSKHMDEVRRIL 189
                                       .8999*****99887.99*********************988 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  25.6   4.3e-06    0.0077      13     101 ..       5      90 ..       3      90 .. 0.89
   2 !   12.7   6.9   7.3e-05      0.13      22      78 ..      44     101 ..      43     125 .. 0.79
   3 ?   -2.5   0.0         4   7.1e+03      47      61 ..     171     185 ..     165     188 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      V-ATPase_G_2  13 rEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraea 89 
                                       +E + ++ l +A   ae+ v  AeaeA+ri++eAeak ++ +++ +++++ e +r+++ + ++a  ea+ +  +  +
  gi|320100293|ref|YP_004175885.1|   5 QEDAKAKLLREAEARAEQIVRDAEAEAERIVKEAEAKWRERAEAERKRITSEAEREANTIISEALREARLLVSKEYE 81 
                                       57777888999******************************************************999988776655 PP

                                       SHHHHHHHHHHH CS
                      V-ATPase_G_2  90 rlqqAvelilka 101
                                          +Ave +l++
  gi|320100293|ref|YP_004175885.1|  82 ---KAVEDVLRE 90 
                                       ...588888875 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  22 EaArkeaereveaAeaeAarilreAeakakal.qaeyeqelaeevarireeararaea 78 
                                       E A  e +r  ++Ae eA+ i++eA  +a+ l  +eye+++++  ++  + +r+r+  
  gi|320100293|ref|YP_004175885.1|  44 ERAEAERKRITSEAEREANTIISEALREARLLvSKEYEKAVEDVLREAYDSVRKRSFD 101
                                       778888899999*************999998835789999999999999999988755 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4
                                       HHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  47 eakakalqaeyeqel 61 
                                       e +++++q+++ +e+
  gi|320100293|ref|YP_004175885.1| 171 ESRLREFQSKHMDEV 185
                                       445555555555544 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   9.6   0.00026      0.47      73     111 ..       6      44 ..       1      52 [. 0.72
   2 !    9.6   5.5   0.00051      0.91      78     113 ..      41      76 ..      38     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  73 qetaeevkanakkeaeliikeAekkaekiveeaeeeakk 111
                                       +++  ++ ++a++ ae+i+++Ae++ae+iv+eae + ++
  gi|320100293|ref|YP_004175885.1|   6 EDAKAKLLREAEARAEQIVRDAEAEAERIVKEAEAKWRE 44 
                                       455566667888888889999999999998888887665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00051
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  78 evkanakkeaeliikeAekkaekiveeaeeeakkia 113
                                       + ++ a++e + i++eAe +a++i++ea +ea+ + 
  gi|320100293|ref|YP_004175885.1|  41 KWRERAEAERKRITSEAEREANTIISEALREARLLV 76 
                                       668889999999999999999999998888876543 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.19   3.3e+02      27      54 ..      17      44 ..      13      62 .. 0.82
   2 ?    9.8   0.0   0.00053      0.94      14      51 ..      76     113 ..      72     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                         SMC_hinge 27 gnrlqalvvedeetakkiieflkkknag 54
                                      ++r++ +v + e++a++i++  ++k   
  gi|320100293|ref|YP_004175885.1| 17 EARAEQIVRDAEAEAERIVKEAEAKWRE 44
                                      6789999************887777444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00053
                         SMC_hinge  14 vdegyekAveaalgnrlqalvvedeetakkiieflkkk 51 
                                       v ++yekAve +l ++++++  ++ ++  +i + +++ 
  gi|320100293|ref|YP_004175885.1|  76 VSKEYEKAVEDVLREAYDSVRKRSFDIENSIRNLIRES 113
                                       789*****************999999988888888876 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 ?    9.3  15.9   0.00066       1.2      50      95 ..       2      48 ..       1      52 [. 0.84
   2 ?    5.5   9.4    0.0092        17      50     106 ..      44      89 ..      37     108 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00066
                        ATP-synt_B 50 aallaeaeqq.lkeAraeAaeiiknAkkeaeklkeeieaeaeaeaer 95
                                      ++++++a+++ l+eA+a+A++i+++A++eae++ +e+ea+ ++ ae 
  gi|320100293|ref|YP_004175885.1|  2 QKMQEDAKAKlLREAEARAEQIVRDAEAEAERIVKEAEAKWRERAEA 48
                                      6777777655279**************************99998876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0092
                        ATP-synt_B  50 aallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeq 106
                                       + ++ae+++   eA++eA++ii +A +ea+ l             +  e+A +++ +
  gi|320100293|ref|YP_004175885.1|  44 ERAEAERKRITSEAEREANTIISEALREARLLV-----------SKEYEKAVEDVLR 89 
                                       455555555566666666666666666655544...........4444444444433 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  12.8   0.00023      0.41      22      71 ..       6      55 ..       2      56 .. 0.87
   2 ?    6.4   6.5    0.0029       5.2      32      75 ..      46      90 ..      43     119 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                           DUF3552 22 kkiaekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelek 71
                                      +  ++k ++eAe++A++i+ +A+ eAe + kea  + +e +   r+ + +
  gi|320100293|ref|YP_004175885.1|  6 EDAKAKLLREAEARAEQIVRDAEAEAERIVKEAEAKWRERAEAERKRITS 55
                                      556677899******************************99999987765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0029
                           DUF3552 32 AeeeAkkiieeAkkeAeakkkealleakeeihk.lreelekelke 75
                                      Ae+e k+i +eA++eA+++  eal ea+  + k + + +e+ l+e
  gi|320100293|ref|YP_004175885.1| 46 AEAERKRITSEAEREANTIISEALREARLLVSKeYEKAVEDVLRE 90
                                      666666666666666666666666666654433133344444444 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.3    0.0084        15       6      49 ..      18      62 ..      16      69 .. 0.92
   2 ?    6.7   0.0    0.0048       8.5      23      51 ..      70      98 ..      63      99 .. 0.91
   3 ?   -0.6   0.0       0.9   1.6e+03      36      64 ..     105     133 ..     102     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0084
                                      HHHHHHHHCC.TTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                     CBFD_NFYB_HMF  6 arvkkImksd.pdarkiakdAkeliaecveefieelaseAaeick 49
                                      ar ++I++++  +a++i+k+A     e +e   ++++seA ++++
  gi|320100293|ref|YP_004175885.1| 18 ARAEQIVRDAeAEAERIVKEAEAKWRERAEAERKRITSEAEREAN 62
                                      7889******999**************************998776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0048
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                     CBFD_NFYB_HMF 23 kdAkeliaecveefieelaseAaeickke 51
                                      ++A+ l+++  e  +e++++eA++ + k+
  gi|320100293|ref|YP_004175885.1| 70 REARLLVSKEYEKAVEDVLREAYDSVRKR 98
                                      699*********************99876 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.9
                                       HHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                     CBFD_NFYB_HMF  36 fieelaseAaeickkekrKtikaehiklA 64 
                                        i+ l +e+ +++++ k+  +++ +++ A
  gi|320100293|ref|YP_004175885.1| 105 SIRNLIRESLRLVNAPKKIVVSKGDLEAA 133
                                       58888999999999999999999998876 PP

>> UvsY  Recombination, repair and ssDNA binding protein UvsY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.2   0.00032      0.58      32     120 ..      18     106 ..      10     111 .. 0.87
   2 ?   -1.0   0.0       1.2   2.1e+03     112     125 ..     175     188 ..     171     191 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTSSSSB--SS---HH.HHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              UvsY  32 sdlkkekikleakkkkllkerleyYtgraddevykeeveksdelkvvlaaDeevikidakiqyidqvldFleealka 108
                                       + ++++   +ea++++ +ke    +  ra++e  + + e + e +++++      ++  + +y ++v d l+ea + 
  gi|320100293|ref|YP_004175885.1|  18 ARAEQIVRDAEAEAERIVKEAEAKWRERAEAERKRITSEAEREANTIISEALREARLLVSKEYEKAVEDVLREAYDS 94 
                                       678899999*********************99999999988899999986655566666779*************** PP

                                       HHHHHHHHHHHH CS
                              UvsY 109 ikqrgfsiknai 120
                                       +++r f i n i
  gi|320100293|ref|YP_004175885.1|  95 VRKRSFDIENSI 106
                                       ********9976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHH CS
                              UvsY 112 rgfsiknaielrkl 125
                                       r f+ k++ e+r++
  gi|320100293|ref|YP_004175885.1| 175 REFQSKHMDEVRRI 188
                                       88999999999987 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 ?    9.5  10.8   0.00046      0.82      28     121 ..      16     111 ..       1     123 [. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00046
                              HrpE  28 eslrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLr.glqqeRealeeqlltaveqLLsdal 103
                                       ++ ra++++ +A   Ae ++++a+ k +e  e   +    +  ++An ++  +l++ R  + ++   ave++L++a 
  gi|320100293|ref|YP_004175885.1|  16 AEARAEQIVRDAEAEAERIVKEAEAKWRERAEAERKRITSEAEREANTIISeALREARLLVSKEYEKAVEDVLREAY 92 
                                       35677888888888888888888777777777666666666777888877524777788888888888888888887 PP

                              HrpE 104 arlLdet.plaeRasALlR 121
                                         + +   +  + ++ L+R
  gi|320100293|ref|YP_004175885.1|  93 DSVRKRSfDIENSIRNLIR 111
                                       7776654133334455555 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   3.2      0.88   1.6e+03      54      66 ..      26      38 ..      11      39 .. 0.71
   2 ?   -1.6   0.0       1.7     3e+03      55      66 ..      57      68 ..      53      69 .. 0.80
   3 ?   -0.7   0.4      0.91   1.6e+03      47      65 ..      72      90 ..      57      91 .. 0.55
   4 ?   10.3   0.1   0.00033       0.6      44      66 ..     118     140 ..     100     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.88
                           DUF2007 54 edleeAreileea 66
                                      + ++eA++i++ea
  gi|320100293|ref|YP_004175885.1| 26 DAEAEAERIVKEA 38
                                      5567777777776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                           DUF2007 55 dleeAreileea 66
                                       + eA++i+ ea
  gi|320100293|ref|YP_004175885.1| 57 AEREANTIISEA 68
                                      5789****9986 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.91
                           DUF2007 47 vrilVaeedleeAre.ilee 65
                                       r+lV  + +e+A e +l+e
  gi|320100293|ref|YP_004175885.1| 72 ARLLVS-KEYEKAVEdVLRE 90
                                      444554.3456665556665 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00033
                           DUF2007  44 elpvrilVaeedleeAreileea 66 
                                         p  i V + dle+Ar+i++e+
  gi|320100293|ref|YP_004175885.1| 118 NAPKKIVVSKGDLEAARRIVAEL 140
                                       45789***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1891  (0.105472); expected 358.6 (0.02)
Passed bias filter:                      795  (0.0443416); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 1304.19
//
Query:       gi|320100294|ref|YP_004175886.1|  [L=178]
Description: V-type ATPase subunit K [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-15   57.4  13.3    3.6e-09   36.8   1.0    2.2  2  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   1.0     2e-13   3.6e-09       1      60 []      32      91 ..      32      91 .. 0.97
   2 !   25.4   5.4   7.2e-10   1.3e-05       1      59 [.     113     172 ..     113     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2e-13
                                      HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                      l+a+l ++ + +gs  g+  a+s+g++ ++++p  f ++li++a++ ++  ygLi ++ +
  gi|320100294|ref|YP_004175886.1| 32 LAAALPLAGGIIGSTTGMRHAASVGASVLSEDPTQFRNVLILAALPMTQTFYGLIQMIYM 91
                                      79*****************************************************98875 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 7.2e-10
                                       HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSG.HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnp.klftksliilafaeaialygLivali 59 
                                       lg+gla  l+   s++++G+++++gi  + r   k  + s++++a +e  +++g+++ ++
  gi|320100294|ref|YP_004175886.1| 113 LGIGLAGFLAEWLSAWAQGIICASGIAELPRTKgKNLMSSIVLAAYVELWGILGIVFTIL 172
                                       79************************999998889*********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1305.76
//
Query:       gi|320100295|ref|YP_004175887.1|  [L=656]
Description: V-type ATPase 116 kDa subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-22   78.8   4.8    4.8e-11   41.4   3.5    2.8  3  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.28   11.1   0.0    1.6  2  SCO1-SenC   SCO1/SenC
       0.32   11.7   1.0       0.84   10.3   0.1    2.1  2  ABATE       Putative stress-induced transcription regulator
        1.6    9.2   6.1        7.7    6.9   0.1    3.1  3  CLZ         C-terminal leucine zipper domain of cyclic nucleo


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 !   35.3   0.0   7.2e-13   3.2e-09     307     415 ..     278     382 ..     214     391 .. 0.74
   2 ?   -1.7   0.3      0.12   5.2e+02     513     573 ..     445     503 ..     444     521 .. 0.78
   3 !   41.4   3.5   1.1e-14   4.8e-11     719     812 ..     550     646 ..     542     647 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 7.2e-13
                        V_ATPase_I 307 kvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpal 383
                                       ++    gW+p+++++ +++ +k+       +++     ++  ++pP+ f+   + + fQ i   YG++ Y E  p++
  gi|320100295|ref|YP_004175887.1| 278 HLSAVTGWIPRDSIRLLEDLVKSSGIPVFIEYKDP---LRGVDNPPSRFNNKGVLRYFQVITRLYGVPGYWEPDPTP 351
                                       55567899999999888888877543222222222...333478********************************* PP

                        V_ATPase_I 384 ftiitFPFlFavMFGDiGHGll.lllfalllvl 415
                                       +   +F F F++M  D+G +l  ll++al  v+
  gi|320100295|ref|YP_004175887.1| 352 LIAYSFAFFFGLMNSDAGYALAgLLAIAL--VM 382
                                       *******************9862334444..43 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.12
                        V_ATPase_I 513 mKlsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsifgY.lvlliiyKWlvd 573
                                       +Kl+ ++G+i+  ++  l  v +  +++k d++ e     lf+  +fg   vl +++K+ v 
  gi|320100295|ref|YP_004175887.1| 445 IKLALLIGLIHINIAHALATVKFAREERKGDLLNEA---GLFISQLFGIpYVLQVFFKYQVP 503
                                       599********************9999999998884...56777777642355667777665 PP

  == domain 3  score: 41.4 bits;  conditional E-value: 1.1e-14
                        V_ATPase_I 719 nTASYLRLWALSLAHaqLseVlwemvlkkallksk....svlgvillvilfavfavltvavLllmeglsafLHaLRL 791
                                       +  SY RL  +SLA   + +V ++m++k a+++      ++ gv+l +++ a  +++   v++++  l af H+LRL
  gi|320100295|ref|YP_004175887.1| 550 DVMSYVRLAGVSLASFYM-AVSFNMMVKLAINSVAgfipGAAGVALAYVVSAPLLFMIHLVIMILSELGAFVHSLRL 625
                                       567***********8776.5999999999885544111156678888999998888999999999************ PP

                        V_ATPase_I 792 hWVEfqsKFykgdGykFepfs 812
                                          Ef  KFy g+G +++pfs
  gi|320100295|ref|YP_004175887.1| 626 CMLEFLMKFYDGSGREYSPFS 646
                                       ********************8 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.2   9.7e+03      88     112 ..      18      43 ..      12      47 .. 0.74
   2 ?   11.1   0.0   6.3e-05      0.28      48     110 ..     107     169 ..     100     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.2
                         SCO1-SenC  88 gltGskeeiakaakefrvy.vekved 112
                                        l+G++e++ ++ +e +v+ ve ve 
  gi|320100295|ref|YP_004175887.1|  18 FLSGDREKVLRVLQEAGVVeVEPVEA 43 
                                       58999999999999977765666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.3e-05
                         SCO1-SenC  48 ldalgeeaekvqplfiTvDPerDtpevlkeyleafdpriigltGskeeiakaakefrvyvekv 110
                                        ++l e+ e++++l  ++ P  D++++ + y e  + + i l+G++e++ ++ ++ rv  + +
  gi|320100295|ref|YP_004175887.1| 107 ARHLRESIESLRMLLSSLAPLPDSMDAAEIYYEGRHVSSILLSGKQEAVMELLEKSRVLKASK 169
                                       5678888899*********************************************99984443 PP

>> ABATE  Putative stress-induced transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00019      0.84      24      85 ..      22      92 ..      19     127 .. 0.70
   2 ?   -2.6   0.1       1.9   8.4e+03      54      74 ..     217     231 ..     186     248 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                                      T-HHHHHH--TTHHHHHH...........HHHHHHHHHHHHHHTHHHH..................HHHHHH CS
                             ABATE 24 tpadLaaWleaagllpagtaaagada.elararaLRealrallaaaaag.........dpppaaalaalnal 85
                                      + + +++ l++ag++  ++ +a+    e +r+ +LRe++  ll+ a+ g          +++  +++ + + 
  gi|320100295|ref|YP_004175887.1| 22 DREKVLRVLQEAGVVEVEPVEAEKVIgEYERLQSLRERINNLLQKAK-GlvidasitgVELASLDVDKVEKH 92
                                      78999*********999988888766999**************9554.324444443344444455555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHTHHHH.... CS
                             ABATE  54 araLRealrallaaaaagdpp 74 
                                         +LRe+l + + +      +
  gi|320100295|ref|YP_004175887.1| 217 IGSLREHLARRISE------L 231
                                       33445555444332......2 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 ?    0.5   0.1      0.18   8.2e+02      37      52 ..      50      65 ..      29      82 .. 0.64
   2 ?    3.0   0.2     0.029   1.3e+02      23      48 ..      97     122 ..      82     126 .. 0.70
   3 ?    6.9   0.1    0.0017       7.7      35      68 ..     212     245 ..     204     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.18
                               CLZ 37 essLeaLqtrlarLla 52
                                      +++L++L  r++ Ll+
  gi|320100295|ref|YP_004175887.1| 50 YERLQSLRERINNLLQ 65
                                      3345555555555544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.029
                               CLZ  23 gaeqkeleekverLessLeaLqtrla 48 
                                         e+  leek+++L +s+e+L + l 
  gi|320100295|ref|YP_004175887.1|  97 YGEATLLEEKARHLRESIESLRMLLS 122
                                       36777789999999999999877655 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0017
                               CLZ  35 rLessLeaLqtrlarLlaeyessqrkLkqRitkL 68 
                                       +L +s+ +L  +lar ++e+++ +++ ++Ri+++
  gi|320100295|ref|YP_004175887.1| 212 QLHGSIGSLREHLARRISELDAEASRVEARIAEI 245
                                       6899***************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); 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):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4273.31
//
Query:       gi|320100296|ref|YP_004175888.1|  [L=97]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0012   18.9   9.1      0.037   14.1   2.2    2.1  2  DivIVA         DivIVA protein
  ------ inclusion threshold ------
      0.052   13.4   2.9      0.093   12.6   2.7    1.5  1  HrpE           HrpE/YscL/FliH and V-type ATPase subunit E
       0.11   13.5   3.2        2.8    8.9   0.4    2.0  2  ERp29          Endoplasmic reticulum protein ERp29, C-termina
       0.12   12.8  13.9        0.3   11.5  13.9    1.9  1  V-ATPase_G_2   Vacuolar (H+)-ATPase G subunit
        2.7    7.8   4.4        1.5    8.6   2.0    1.7  2  PRKCSH-like    Glucosidase II beta subunit-like
        2.8    7.7   7.6        6.3    6.6   1.1    2.1  2  Peptidase_M41  Peptidase family M41


Domain annotation for each model (and alignments):
>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.7   0.00037       1.1      75     102 ..      10      37 ..       2      39 .. 0.68
   2 !   14.1   2.2   1.2e-05     0.037      84     121 ..      47      84 ..      43      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00037
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  75 taeevkanakkeaeliikeAekkaekiv 102
                                       + +++ ++a+++  +i+keAekka +i+
  gi|320100296|ref|YP_004175888.1|  10 AIDNILKEAERKKLVILKEAEKKAAEIL 37 
                                       5556666777777777777777777665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  84 kkeaeliikeAekkaekiveeaeeeakkiaeeieelkr 121
                                       ++eae i++eA k+ ++i+e+a++ea++ia+   e kr
  gi|320100296|ref|YP_004175888.1|  47 RREAEAILAEAVKRRNEILEKARREAEEIAKIPPEKKR 84 
                                       79**************************9986666555 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.7   3.1e-05     0.093       5      66 ..      21      73 ..      13      92 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                              HrpE  5 rslalvagaavleeeilrreqlaeslrarel.laeArlqAeqllaqarekaeellevaveqAe 66
                                      ++l+++  a+ + +eil          +r + ++e r  Ae++la+a ++++e+le+a  +Ae
  gi|320100296|ref|YP_004175888.1| 21 KKLVILKEAEKKAAEIL----------GRPIpVEEYRREAEAILAEAVKRRNEILEKARREAE 73
                                      44444445555555555..........444433444555555555555555555555544444 PP

>> ERp29  Endoplasmic reticulum protein ERp29, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.011        32       3      34 ..       4      35 ..       3      40 .. 0.85
   2 ?    8.9   0.4   0.00093       2.8       5      48 ..      45      91 ..      42      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                             ERp29  3 ieeldelaaefvaaakaereelleeakkaaek 34
                                      i+ +de + +++++a+ ++  +l+ea+k+a++
  gi|320100296|ref|YP_004175888.1|  4 IKDIDEAIDNILKEAERKKLVILKEAEKKAAE 35
                                      67899999999999989999999999998876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00093
                             ERp29  5 eldelaaefvaaakaereelleeakkaaeklk...sekekkaaeyYv 48
                                      e+ + a++++a+a ++r+e+le+a+++ae+++    ek++ka+ey v
  gi|320100296|ref|YP_004175888.1| 45 EYRREAEAILAEAVKRRNEILEKARREAEEIAkipPEKKRKAVEYIV 91
                                      55566777888888999999999999999998776688888888765 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  13.9    0.0001       0.3      29     103 ..      12      95 ..       1      96 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHH CS
                      V-ATPase_G_2  29 ereveaAeaeAarilreAeakakal......qaeyeqela...eevarireeararaeaeaqavrkraearlqqAve 96 
                                        + +++Ae     il+eAe+ka ++       +ey++e +   +e  + r+e+ ++a+ ea+++ k   ++  +Ave
  gi|320100296|ref|YP_004175888.1|  12 DNILKEAERKKLVILKEAEKKAAEIlgrpipVEEYRREAEailAEAVKRRNEILEKARREAEEIAKIPPEKKRKAVE 88 
                                       455677777777777777777776633333336777766611146667899************************** PP

                                       HHHHHH- CS
                      V-ATPase_G_2  97 lilkaVl 103
                                        i++ V+
  gi|320100296|ref|YP_004175888.1|  89 YIVRKVV 95 
                                       ****996 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 ?   -0.1   0.1      0.24   7.1e+02     131     158 ..       9      36 ..       2      41 .. 0.60
   2 ?    8.6   2.0   0.00052       1.5     126     167 ..      43      84 ..      26      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                       PRKCSH-like 131 eeankkvkkglkikeelllaakkkldel 158
                                       e  ++ +k++ + k  +l++a+kk  e+
  gi|320100296|ref|YP_004175888.1|   9 EAIDNILKEAERKKLVILKEAEKKAAEI 36 
                                       4445555555555556666777777666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00052
                       PRKCSH-like 126 feelleeankkvkkglkikeelllaakkkldelkkklkeled 167
                                       +ee+++ea++ + +++k+++e+l +a++  +e+ k   e + 
  gi|320100296|ref|YP_004175888.1|  43 VEEYRREAEAILAEAVKRRNEILEKARREAEEIAKIPPEKKR 84 
                                       578999***************************998766655 PP

>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.1    0.0021       6.3     142     173 ..       5      36 ..       1      45 [. 0.87
   2 ?    5.2   0.8    0.0056        17     146     175 ..      48      77 ..      42      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHH CS
                     Peptidase_M41 142 eeideevkelveeayerakeileekreeleal 173
                                       ++ide + ++++ea ++   il+e +++  ++
  gi|320100296|ref|YP_004175888.1|   5 KDIDEAIDNILKEAERKKLVILKEAEKKAAEI 36 
                                       78**********************99988766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0056
                                       HHHHHHHHHHHHHHHHHHHHTHHHHHHHHH CS
                     Peptidase_M41 146 eevkelveeayerakeileekreelealae 175
                                       +e +++++ea +r +eile+ r e e++a+
  gi|320100296|ref|YP_004175888.1|  48 REAEAILAEAVKRRNEILEKARREAEEIAK 77 
                                       68899*********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1599  (0.0891851); expected 358.6 (0.02)
Passed bias filter:                      783  (0.0436723); 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):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 650.39
//
Query:       gi|320100297|ref|YP_004175889.1|  [L=137]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  118.6   0.0    1.8e-34  118.5   0.0    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 !  118.5   0.0     1e-38   1.8e-34       1     126 [.       7     130 ..       7     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 1e-38
                                       -S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE CS
                             DUF61   1 drilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelge 77 
                                       dr+l +e++ +nkh P+erk+L++lL++e p+iv++dgs h+f+ +el +l eil +++ ++l+LPI++e++p+ ge
  gi|320100297|ref|YP_004175889.1|   7 DRFLIEELRLVNKHAPYERKNLCDLLKMEVPYIVLRDGSSHLFNPRELAMLTEILGDDA-CRLELPIIVEYTPSNGE 82 
                                       699*******************************************************6.***************** PP

                                       ..EEEES-HHHHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST...TE CS
                             DUF61  78 svylvrgkaevkvvskilgkereeedelviykpevrelrrklptatqli 126
                                       +vy+vrg  e+++v+ ++g++    ++l++++ ++ elrr l+t+t+++
  gi|320100297|ref|YP_004175889.1|  83 GVYVVRGGVEARAVAAAIGLN-TYSEPLFLSRVQILELRRVLRTTTTIL 130
                                       *********************.899*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1016.96
//
Query:       gi|320100298|ref|YP_004175890.1|  [L=205]
Description: V-type ATPase subunit D [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-37  127.2  12.1    7.8e-37  127.0  12.1    1.0  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
      0.017   14.5   2.4      0.022   14.1   0.0    1.9  2  CorA        CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0  12.1   8.7e-41   7.8e-37       1     196 []      13     197 ..      13     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 8.7e-41
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       eLirlkkrl++  ++ ++L ++  +Li ef+ +l+e    r+++++ +   +   + +   +ge+ i  + +++v+ 
  gi|320100298|ref|YP_004175890.1|  13 ELIRLKKRLQISVKVERILRERLIILINEFMILLRESVSRRQKVAQLITTLSARATVLSGIYGEN-IYDLFEKTVP- 87 
                                       79******************************************************887777676.6667777887. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikkt 154
                                        k  +  + +en++GVk+ ++ + ++++           +  +d+ +e+ ++ +e+++ela+ e++l+++ +ei++t
  gi|320100298|ref|YP_004175890.1|  88 -K-ATCIIGVENIMGVKTKTVMIMKSGEA-------RPVKTPFDDFAEESARFIEEVIELAKAENALKTMGREIRVT 155
                                       .4.7899*************988554333.......344558*********************************** PP

                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 155 nrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                       +rRvNaL++++IPrl++ti+  ++++dE+eree++rlk+vk+
  gi|320100298|ref|YP_004175890.1| 156 KRRVNALDYILIPRLRSTIRMLQMKFDEREREEKARLKRVKA 197
                                       ****************************************95 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.5e-06     0.022     201     268 ..      21      88 ..       6     106 .. 0.84
   2 ?   -0.8   1.4     0.085   7.6e+02     147     202 ..     146     200 ..     121     203 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-06
                              CorA 201 lerllemlealrerleslqdtyssllserlNrvmkvLTvltaiflPlTlitGiyGmNfkglPelewsy 268
                                       l+ +++   +lrerl  l ++++ ll e   r  kv  ++t++   +T+++GiyG N+  l e+  + 
  gi|320100298|ref|YP_004175890.1|  21 LQISVKVERILRERLIILINEFMILLRESVSRRQKVAQLITTLSARATVLSGIYGENIYDLFEKTVPK 88 
                                       55555566789*********************************99************9999887776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.085
                              CorA 147 keilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldele 202
                                       k + re+   +rr+  l  +l p  +   r+l+ ++d+++ +e k +l+++   le
  gi|320100298|ref|YP_004175890.1| 146 KTMGREIRVTKRRVNALDYILIPRLRSTIRMLQMKFDEREREE-KARLKRVKASLE 200
                                       4455666667788999999998887777799996666666555.467777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1560.26
//
Query:       gi|320100299|ref|YP_004175891.1|  [L=117]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 867.68
//
Query:       gi|320100300|ref|YP_004175892.1|  [L=182]
Description: NUDIX hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-17   61.6   0.1    9.7e-17   61.2   0.1    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.1   5.4e-21   9.7e-17       3     103 ..      41     138 ..      39     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 5.4e-21
                                       EEEEEEE.EEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEE CS
                             NUDIX   3 rravgvv.llnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapyd 75 
                                       + av+v+ +l++   v+l+r++++p ++   e P+G v+pgEtpeeAA REleEEtG+ a +l++l +    ++p++
  gi|320100300|ref|YP_004175892.1|  41 PEAVAVLpVLDDG-SVILLRQFRAPLNDtiIEAPAGVVDPGETPEEAAERELEEETGYHAgRLVRLGS----FTPSP 112
                                       5699999556555.7*****997777777557**************************9966666655....44444 PP

                                       EEEEEEEEEEEEEEEEECSGCSSTSTTT CS
                             NUDIX  76 gpygdeheilyvfleevegelepndene 103
                                       g+    + i ++++ ++e + + +++ e
  gi|320100300|ref|YP_004175892.1| 113 GYSS--EVIHFYYATRLEYRGAKPERYE 138
                                       4433..4444555566666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1397.51
//
Query:       gi|320100301|ref|YP_004175893.1|  [L=312]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   95.2   0.0    6.9e-27   94.6   0.0    1.3  1  ABC_tran  ABC transporter
    1.6e-08   34.8   0.0    0.00049   20.0   0.0    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    3.8e-08   33.9   0.1    2.1e-07   31.6   0.0    2.2  2  DUF4162   Domain of unknown function (DUF4162)
    5.7e-05   22.7   0.2    0.00025   20.6   0.1    1.9  2  KdpD      Osmosensitive K+ channel His kinase sensor domain
     0.0033   16.9   0.2        1.9    7.9   0.0    2.4  3  SMC_N     RecF/RecN/SMC N terminal domain
     0.0045   17.4   0.6       0.17   12.3   0.3    2.6  2  AAA       ATPase family associated with various cellular acti
     0.0051   17.3   0.3     0.0092   16.5   0.3    1.3  1  AAA_23    AAA domain
     0.0073   16.0   0.0      0.012   15.3   0.0    1.3  1  NMT1_2    NMT1-like family
     0.0092   15.2   0.5      0.083   12.1   0.5    2.0  1  NB-ARC    NB-ARC domain
  ------ inclusion threshold ------
      0.015   15.0   0.0       0.04   13.6   0.0    1.7  1  AAA_30    AAA domain
      0.018   14.8   0.0      0.037   13.8   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.025   14.2   0.1      0.088   12.4   0.0    1.8  2  SRP54     SRP54-type protein, GTPase domain
      0.044   13.3   0.4        1.7    8.2   0.0    2.3  2  AAA_25    AAA domain
      0.098   12.6   0.4        1.3    8.9   0.4    2.1  1  ATPase_2  ATPase domain predominantly from Archaea
        0.1   12.2   0.0       0.18   11.4   0.0    1.5  1  STAS      STAS 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 !   94.6   0.0   5.8e-30   6.9e-27       2     137 .]      21     164 ..      20     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 5.8e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       ++++l+++ege+ +++G+nG+GK+t l ++a  ++pt+G+i + g+++ + e  ++rk ig+ +q+ + l+ ++  +
  gi|320100301|ref|YP_004175893.1|  21 EDLNLDIREGEVFGLLGPNGSGKTTTLLTVATIYRPTSGDIYVYGHSVVR-EDYIVRKMIGIAFQDpKALWVDK-PY 95 
                                       689**********************************************9.8899***********54444444.45 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +              e+++ + ++++ lgl e +++      ++LSgG +++v+la++l++kp+l +lDEpta
  gi|320100301|ref|YP_004175893.1|  96 DLliwhakvvgysgeEARRVVREVMEALGLWEHRNKYF----YQLSGGTRKKVELAKVLVQKPRLAILDEPTA 164
                                       55888889***998777777************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 !   12.7   0.0   6.7e-05      0.08       2      19 ..      33      50 ..      32      98 .. 0.89
   2 !   20.0   0.0   4.1e-07   0.00049     234     298 ..     133     194 ..     117     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.7e-05
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       +l GpNgsGK++ L + 
  gi|320100301|ref|YP_004175893.1| 33 FGLLGPNGSGKTTTLLTV 50
                                      689**********98765 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 4.1e-07
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +++lS Gt++   l+  l + +   +l ++DEp +  +  + + l++++k+l+r+g+ vil+T +
  gi|320100301|ref|YP_004175893.1| 133 FYQLSGGTRKKVELAKVLVQKP---RLAILDEPTAQVDVLAKHALWDVIKRLKREGVTVILATND 194
                                       89*****************988...**************************************76 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.3   2.7e+03      40      63 ..     164     188 ..     130     192 .. 0.73
   2 !   31.6   0.0   1.7e-10   2.1e-07       1      78 [.     217     302 ..     217     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                                       EEEEE-------------.----EE CS
                           DUF4162  40 lelkledeeaanellkal.tsgvei 63 
                                       +++ +  ++a  +++k+l ++gv++
  gi|320100301|ref|YP_004175893.1| 164 AQVDVLAKHALWDVIKRLkREGVTV 188
                                       4555666778888888886687776 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.7e-10
                                       E-HHHHHTTS.-SSEEEEE...--.-----..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE CS
                           DUF4162   1 GtleeiKrsy.gknrieve...ad.aeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFeee 69 
                                       Gt++e+K+ + g++ +e++   ++ + ++ e  g    ve  +g+l++ le+ ee+  ++ + l ++++ + ++  +
  gi|320100301|ref|YP_004175893.1| 217 GTIDELKDLIpGGDVVEIQvggTGiPVSIMEKLGeYGRVEAGNGSLRIYLEKgEEKVVDIVDLLrRNNIAVSRLMIK 293
                                       9*********9999999**876226888888889899999999********99***********77*********** PP

                                       ---HHHHHH CS
                           DUF4162  70 ePsLndIFi 78 
                                       eP+L+d+F 
  gi|320100301|ref|YP_004175893.1| 294 EPTLDDVFT 302
                                       ********5 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 ?   -1.0   0.0      0.87     1e+03      13      35 ..      39      61 ..      35      73 .. 0.81
   2 !   20.6   0.1   2.1e-07   0.00025      36     123 ..     104     193 ..     101     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.87
                              KdpD 13 pGvGktyamLeeaqelkeegvdv 35
                                      +G Gkt ++L+ a+  + +  d+
  gi|320100301|ref|YP_004175893.1| 39 NGSGKTTTLLTVATIYRPTSGDI 61
                                      599*******9998766666555 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.1e-07
                              KdpD  36 viglvethgrketeallegleviprke...veykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdve 109
                                       v+g+  ++ r+ +++++e l + ++++   ++ +g + ++++l ++l +kp+++++De   + ++   ++  ++ ++
  gi|320100301|ref|YP_004175893.1| 104 VVGYSGEEARRVVREVMEALGLWEHRNkyfYQLSGGTRKKVELAKVLVQKPRLAILDEPTAQ-VDVLAKHALWDVIK 179
                                       8999999999999999999998876542225668999*********************7765.577788899***** PP

                              KdpD 110 elLeagidVittvn 123
                                       +l ++g+ Vi + n
  gi|320100301|ref|YP_004175893.1| 180 RLKREGVTVILATN 193
                                       *********86555 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 !    6.9   0.1    0.0032       3.8      26      39 ..      32      45 ..       2      52 .. 0.78
   2 !    7.9   0.0    0.0015       1.9     136     213 ..     135     207 ..      47     213 .. 0.79
   3 ?   -3.7   0.0       5.3   6.4e+03     106     134 ..     259     287 ..     254     290 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0032
                                      EEEEEESTTSSHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsn 39
                                      +  ++GpNGSGK+ 
  gi|320100301|ref|YP_004175893.1| 32 VFGLLGPNGSGKTT 45
                                      45689*******96 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0015
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                       +LSgG ++ v la ++    v++  l +lDe  a+ D    +++ +++k+ + +  + vi  +++m+e  + + +v 
  gi|320100301|ref|YP_004175893.1| 135 QLSGGTRKKVELAKVL----VQKPRLAILDEPTAQVDVLAKHALWDVIKRLK-REGVTVILATNDMFEAERVCERVA 206
                                       8999999999998874....5566699**********************998.667888889999999887777776 PP

                                       E CS
                                       x RF
                             SMC_N 213 k 213
                                        
  gi|320100301|ref|YP_004175893.1| 207 I 207
                                       5 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.3
                                       TSEEEEEETTEEE-HHHHHHHHHCTT-ST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 106 kgeseykingkevtkkevsellesagisk 134
                                       +g+ ++++++ e +  ++ +ll++ +i  
  gi|320100301|ref|YP_004175893.1| 259 NGSLRIYLEKGEEKVVDIVDLLRRNNIAV 287
                                       55667778888888889999999888865 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.3   0.00014      0.17       3     114 ..      35     197 ..      33     210 .. 0.61
   2 ?   -2.9   0.0       7.1   8.5e+03      37      57 ..     264     284 ..     241     294 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                       EESSTTSSHHHHHHHHHHHHTHE..............................................EEEEETTT CS
                               AAA   3 lyGppGtGKTllakavakelgve..............................................fleisgse 33 
                                       l Gp G GKT++   va+    +                                              +       
  gi|320100301|ref|YP_004175893.1|  35 LLGPNGSGKTTTLLTVATIYRPTsgdiyvyghsvvredyivrkmigiafqdpkalwvdkpydlliwhakV------- 104
                                       78***************99742222222333334444444444444444444444444444444444441....... PP

                                       CSSS..........................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHH CS
                               AAA  34 llsk..........................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeee 83 
                                                                     y+ + +  +r+ ++ ak    kp   ++DE  a +            
  gi|320100301|ref|YP_004175893.1| 105 ---VgysgeearrvvrevmealglwehrnkYFYQLSGGTRKKVELAKVLVqKPRLAILDEPTAQVDVL--------- 169
                                       ...04444444444555555555555555588888888888888887777777888888876666555......... PP

                                       HHHHHHHHHHHHTTTSSSTEEEEEEESSGGG CS
                               AAA  84 rvvnqLlteldgvkkkeskvivigatnrpdk 114
                                        +  +L  +++++k+  + v+vi+atn++ +
  gi|320100301|ref|YP_004175893.1| 170 -AKHALWDVIKRLKR--EGVTVILATNDMFE 197
                                       .67788888888888..35889999988765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.1
                                       SSTTHHHHHHHHHHHHHHHTS CS
                               AAA  37 kyvgesekkirelfkeakeka 57 
                                        y++++e+k+ ++++ +++++
  gi|320100301|ref|YP_004175893.1| 264 IYLEKGEEKVVDIVDLLRRNN 284
                                       377778888888877777666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   7.7e-06    0.0092       7      36 ..      14      47 ..       7      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.7e-06
                            AAA_23  7 frsf...rdqeidF.skgltlItGpNGaGKTTil 36
                                      f+ f   +d ++d  +  ++ + GpNG+GKTT l
  gi|320100301|ref|YP_004175893.1| 14 FGDFtavEDLNLDIrEGEVFGLLGPNGSGKTTTL 47
                                      555555566677777778**************76 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05     0.012     186     240 ..      74     128 ..      71     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                            NMT1_2 186 avaegiGvtaltsqelwkdhPekvlgvredfveknpntaralvkalleAtkwlda 240
                                        v ++iG   ++ + lw d P+  l  ++++v    + ar++v+ ++eA  ++++
  gi|320100301|ref|YP_004175893.1|  74 IVRKMIGIAFQDPKALWVDKPYDLLIWHAKVVGYSGEEARRVVREVMEALGLWEH 128
                                       5899*********************************************988885 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.5   6.9e-05     0.083      22     145 ..      32     199 ..      20     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.9e-05
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE...................................EEESX CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg.rFdsvawv...................................vvskt 62 
                                       v +l G  G+GKtt +  +   +  + g  +   + v                                   vv+ +
  gi|320100301|ref|YP_004175893.1|  32 VFGLLGPNGSGKTTTLLTVATIYRPTSGdIYVYGHSVvredyivrkmigiafqdpkalwvdkpydlliwhakVVGYS 108
                                       67888888888887666666665556554555444446888888888888888888888899999999999988876 PP

                                       .XHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE......EE-SHHH.H.....HHHHC CS
                            NB-ARC  63 .dkseeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlD......DVweeed.wdkigvvlpar 128
                                         + +++++++++ L+l e+  + + +      +k +l ++L +k  l +lD      DV  ++  wd i+   +  
  gi|320100301|ref|YP_004175893.1| 109 gEEARRVVREVMEALGLWEHRNKYFYQLSGgtrKKVELAKVLVQKPRLAILDeptaqvDVLAKHAlWDVIKRL-K-- 182
                                       156689**********9999999888877788899**********99*****888888898888778666543.3.. PP

                                       HTTSEEEEEESBCCCCC CS
                            NB-ARC 129 enrlrvllTTRdeevan 145
                                        +++ v+l T d+  a+
  gi|320100301|ref|YP_004175893.1| 183 REGVTVILATNDMFEAE 199
                                       58999999998864333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.3e-05      0.04      20     121 ..      32     190 ..      24     195 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.g................grviglAptgkaAkvLa..........eelgie 69 
                                       v  l Gp G+GKtt+l +++ +++   g                +++ig+A +   A  +           + +g  
  gi|320100301|ref|YP_004175893.1|  32 VFGLLGPNGSGKTTTLLTVATIYRPTsGdiyvyghsvvredyivRKMIGIAFQDPKALWVDkpydlliwhaKVVGYS 108
                                       77899******************999556666666666666666666666666555555553333333322122222 PP

                            AAA_30  70 astiakllkrlk..........................grarlepgtllivDEagmv....dtkqlaallkaaekag 116
                                       ++   +++++                            +++ +++ +l i DE        + + l +++k+++++g
  gi|320100301|ref|YP_004175893.1| 109 GEEARRVVREVMealglwehrnkyfyqlsggtrkkvelAKVLVQKPRLAILDEPTAQvdvlAKHALWDVIKRLKREG 185
                                       22222222111133344445566666666666666665444455556666666433223334444445555555556 PP

                            AAA_30 117 akvil 121
                                       ++vil
  gi|320100301|ref|YP_004175893.1| 186 VTVIL 190
                                       66655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.037      16      45 ..      22      53 ..      14      61 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                            AAA_29 16 tieidlkg..atlltGpsGsGKSTllDAiqal 45
                                      ++++d ++  ++ l Gp+GsGK+T l  ++++
  gi|320100301|ref|YP_004175893.1| 22 DLNLDIREgeVFGLLGPNGSGKTTTLLTVATI 53
                                      4444444336999**********988666665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.4e-05     0.088       5      29 ..      34      58 ..      31      71 .. 0.81
   2 ?   -1.6   0.0       1.4   1.7e+03      23      41 ..     179     197 ..     169     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.4e-05
                                      EEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkeg 29
                                       l+G++G+GKTttl  +a +++   
  gi|320100301|ref|YP_004175893.1| 34 GLLGPNGSGKTTTLLTVATIYRPTS 58
                                      589***************9998665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                       HHHHHTTS-EEEEEESTSS CS
                             SRP54  23 allkkegkkvllvaaDtfR 41 
                                       ++lk+eg +v+l++ D+f 
  gi|320100301|ref|YP_004175893.1| 179 KRLKREGVTVILATNDMFE 197
                                       678999999******9995 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0014       1.7      30      54 ..      27      51 ..      17      59 .. 0.88
   2 ?    3.1   0.1     0.051        61      71      98 ..     101     140 ..      90     195 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0014
                            AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                      +++ge+  l G+ g+GKtt +l +a
  gi|320100301|ref|YP_004175893.1| 27 IREGEVFGLLGPNGSGKTTTLLTVA 51
                                      57999999***********999887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.051
                            AAA_25  71 qgkVlyvsaEdsedelrrRlravgeal............r 98 
                                       ++kV+ +s+E+++  +r+ ++a+g               +
  gi|320100301|ref|YP_004175893.1| 101 HAKVVGYSGEEARRVVREVMEALGLWEhrnkyfyqlsggT 140
                                       579999*******999999999995531133334333331 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4    0.0011       1.3      25     131 ..      35     199 ..      25     208 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                          ATPase_2  25 iYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..............eeeekkklekal..... 82 
                                       + Gp gsGKt+ l  +++  +  +   iy++  + ++++++ +++                                
  gi|320100301|ref|YP_004175893.1|  35 LLGPNGSGKTTTLLTVATIYRPTS-GDIYVYGHSVVREDYIVRKMIgiafqdpkalwvdkP----------Ydlliw 100
                                       569999999999988888875533.566666666666666665533344644444444440..........144444 PP

                          ATPase_2  83 ...............................................giavpkaeleeilk....eksklvfkaiel 108
                                                                                      +  v+k +l +il+    +   l++ a+ +
  gi|320100301|ref|YP_004175893.1| 101 hakvvgysgeearrvvrevmealglwehrnkyfyqlsggtrkkvelaKVLVQKPRL-AILDeptaQVDVLAKHALWD 176
                                       44444444444455555556777888888888888888888888886555666666.56665554556677788888 PP

                          ATPase_2 109 llekikkkgkkiiiiiDelqkli 131
                                       +++ +k++g  +i+   +++++ 
  gi|320100301|ref|YP_004175893.1| 177 VIKRLKREGVTVILATNDMFEAE 199
                                       88888888888999888888776 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.18      60      87 ..     165     192 ..     111     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                       EE-HHHHHHHHHHHHHHHHTT-EEEEES CS
                              STAS  60 fiDssGvraLkeilkelkrigvevvlvn 87 
                                        +D+ + +aL +++k+lkr gv+v+l+ 
  gi|320100301|ref|YP_004175893.1| 165 QVDVLAKHALWDVIKRLKREGVTVILAT 192
                                       69************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2339.35
//
Query:       gi|320100302|ref|YP_004175894.1|  [L=280]
Description: ABC transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   21.0  26.1    0.00019   20.6  26.1    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
    0.00045   19.6   7.4    0.00045   19.6   7.4    1.8  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0019   18.2  11.6     0.0019   18.2  11.6    1.7  3  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  26.1   3.2e-08   0.00019     158     342 ..      70     265 ..      44     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.2e-08
                   ABC2_membrane_3 158 nvasflvgliliilifitasfiavs..iveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afgl 231
                                       +v ++ + l+ i ++++++++i+++  i+ E   +i e  l+ +v+++ ++l+++lg  l++ +++l ++l+ ++++
  gi|320100302|ref|YP_004175894.1|  70 GVSYYEFYLLGIYVSILYSTSISRGyvIADEFDDGIVEYHLSLPVKRWVLVLGRVLGCSLAATIFTLPMMLVvLLAV 146
                                       45555444444444444444455541179**************************************9999547773 PP

                   ABC2_membrane_3 232 .gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlp....salkwifsi 303
                                        +++  +l+l  l   +f+  ++ ++ ++ + +k+++ + il + +  +l  ++++++pl+ ++     +  +++ +
  gi|320100302|ref|YP_004175894.1| 147 nALSLPGLLLSTLIAYVFSTGVVGFVIFVVTRVKSTDVTDILFGTIDAILVRLSTVFYPLPVIEalgfAPYYYAALL 223
                                       355555666666666666666666666666667777666554444444577777777775444445499999***** PP

                   ABC2_membrane_3 304 iPffapglgllrli...tgdplweil..lsliilalfavvylll 342
                                       +P+++ ++++  +    + +  +++     l++l++f++ +++l
  gi|320100302|ref|YP_004175894.1| 224 NPLTSMADAIRLIFlpeY-V-AYTVSphALLLYLVGFSLGMMVL 265
                                       **********77766642.3.44555114445555555555555 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 !   19.6   7.4   7.6e-08   0.00045      96     166 ..      96     174 ..      76     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.6e-08
                   ABC2_membrane_2  96 aiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvll.......alaiilalgivlaledllll 164
                                       +ia+E ++g ++  Ls+Pv R+ ++lg ++g ++++ + ++ ++l+++l+       +l+++    +v++++ + ++
  gi|320100302|ref|YP_004175894.1|  96 VIADEFDDGIVEYHLSLPVKRWVLVLGRVLGCSLAATIfTLPMMLVVLLAvnalslpGLLLSTLIAYVFSTGVVGFV 172
                                       79*********************************888788888888666554444433333333333333332222 PP

                   ABC2_membrane_2 165 vv 166
                                       ++
  gi|320100302|ref|YP_004175894.1| 173 IF 174
                                       22 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 !   18.2  11.6   3.1e-07    0.0019       8     161 ..      35     179 ..      28     197 .. 0.73
   2 ?    1.9   1.3     0.031   1.9e+02     105     156 ..     158     209 ..     153     222 .. 0.64
   3 ?   -3.8   0.1       1.8   1.1e+04     109     120 ..     253     264 ..     245     271 .. 0.46

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-07
                   ABC2_membrane_4   8 KlkrskivwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknL 84 
                                        lk +++++++ l+ +++++++++    l  ++l   ++y ++ +g+  ++ +   + i  +y+i +E++++ + + 
  gi|320100302|ref|YP_004175894.1|  35 RLKSQRVFLAMRLSWFIIQVFIFARAISLIVRQLTGVSYYEFYLLGI--YVSILYSTSISRGYVIADEFDDGIVEYH 109
                                       57778889999999999999998887777788999999***988885..556666777789**************** PP

                   ABC2_membrane_4  85 ltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvll 161
                                       l +Pv+r  l+l+ ++ + l + +++l  +l+++l+   +  +g+  +    l+  ++ +g++ f+    i++++ +
  gi|320100302|ref|YP_004175894.1| 110 LSLPVKRWVLVLGRVLGCSLAATIFTLPMMLVVLLAVNALSLPGLLLS---TLIAYVFSTGVVGFV----IFVVTRV 179
                                       ********************9999998866655555444444444333...333333344444442....2233444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.031
                   ABC2_membrane_4 105 lsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpii 156
                                       + +++++ t ++ +++ ++    +++v+ +l+     +++ l ++f  lp+i
  gi|320100302|ref|YP_004175894.1| 158 TLIAYVFSTGVVGFVIFVVTRVKSTDVTDILFGTIDAILVRLSTVFYPLPVI 209
                                       3344444444555555566666667778888877788888888888888887 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.8
                   ABC2_membrane_4 109 lmlvtflitvlf 120
                                       l+lv f + +++
  gi|320100302|ref|YP_004175894.1| 253 LYLVGFSLGMMV 264
                                       222322222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2013.83
//
Query:       gi|320100303|ref|YP_004175895.1|  [L=255]
Description: ABC transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-19   68.0  16.7    7.6e-19   68.0  16.7    1.3  2  ABC2_membrane    ABC-2 type transporter
      2e-05   24.0  13.3      2e-05   24.0  13.3    1.3  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0012   18.0  20.5     0.0017   17.5  20.5    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.34   10.4  12.7       0.98    8.9  12.7    2.0  1  ABC2_membrane_5  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 !   68.0  16.7   1.7e-22   7.6e-19       5     209 ..      10     219 ..       7     220 .. 0.91
   2 ?   -3.7   0.3       1.4   6.4e+03      53      63 ..     232     242 ..     225     246 .. 0.43

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.7e-22
                     ABC2_membrane   5 allkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.....pgllffsvlflafsaltsvapvfe 76 
                                       ++ +r++ ++wr + + l+ ++++ l  +++fg++f ++ n + + ++     pg+l  s++  + +++    + +e
  gi|320100303|ref|YP_004175895.1|  10 LIAQRDLARFWRYK-YWLAGQVAMNLADIFIFGLIFRGMVNPALIPDYikfitPGILSLSIFISS-FSIGRE-VGVE 83 
                                       5789**********.777*******************8654444444477799************.444444.799* PP

                     ABC2_membrane  77 rergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rfflflllllltalaasslgllis 152
                                        +r+v   + + p+ ++ + v++++l+ l+++l+  l fl+++ +l+g++   +++++l+++ll+a  +s+l++ +s
  gi|320100303|ref|YP_004175895.1|  84 LRREVTLYLVSLPV-KRTVLVAGRILGGLLRGLIYQLGFLFFAALLLGIPNPsKWIIILYTTLLLAASMSGLSISLS 159
                                       **************.************************************9999********************** PP

                     ABC2_membrane 153 alapsfedasqlaslvllpllllsGffipidsm..p.kwlqwiaylnPltyavealrsnl 209
                                       +++++f   +++ sl + +l+++s +f+p + +    ++   + +++Pl+ a++++r+++
  gi|320100303|ref|YP_004175895.1| 160 TVTRDFNLQATIRSLTYNVLFFVSNIFYPESVVkaRlGFAAPVVKYSPLSMATSIYRWGF 219
                                       ******************************999863469999**************9875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.4
                     ABC2_membrane  53 pgllffsvlfl 63 
                                       +gll+ s++ l
  gi|320100303|ref|YP_004175895.1| 232 VGLLMWSIIIL 242
                                       33333333333 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 !   24.0  13.3   4.5e-09     2e-05     109     285 ..      92     251 ..      89     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.5e-09
                   ABC2_membrane_2 109 lLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllS 185
                                       l s+Pv R  +++g ++ggl+      +++  +   +l++ + l   ++ ++++++++ ++ll++   + +l++ lS
  gi|320100303|ref|YP_004175895.1|  92 LVSLPVKRTVLVAGRILGGLLR----GLIYQLG---FLFFAALLLGIPNPSKWIIILYTTLLLAA--SMSGLSISLS 159
                                       679*******************....4444455...55566666677788889999999999999..88******** PP

                   ABC2_membrane_2 186 svarssreaaalalglfvvlailvpivlyg.vaellagpavpqeindflsllsptsayntllneilagsdlnalgst 261
                                       +v+r+++ +a++    + vl+++++i+  + v ++ +g+a+       +  +sp s+ + ++++ ++ ++       
  gi|320100303|ref|YP_004175895.1| 160 TVTRDFNLQATIRSLTYNVLFFVSNIFYPEsVVKARLGFAA------PVVKYSPLSMATSIYRWGFNYTG---DVDV 227
                                       ************98888888666666643346777777777......45556788888888887777664...3688 PP

                   ABC2_membrane_2 262 atnllilllllavllvlgyvlFkr 285
                                        +n++ ll + ++ l+++  l+ r
  gi|320100303|ref|YP_004175895.1| 228 LFNAVGLLMWSIIILAVACKLYLR 251
                                       99999************9999887 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 !   17.5  20.5   3.8e-07    0.0017     157     335 ..      54     245 ..      21     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-07
                   ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afg 230
                                       +++  f+ + il ++ifi++++i +++  E ++ +   +++ +v+++ ++ ++ilg +l +l+  l +l++   ++g
  gi|320100303|ref|YP_004175895.1|  54 PDYIKFITPGILSLSIFISSFSIGREVGVELRREVTLYLVSLPVKRTVLVAGRILGGLLRGLIYQLGFLFFaalLLG 130
                                       5678899999*****************9999999****************************998777664444999 PP

                   ABC2_membrane_3 231 lgipfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlp....salkwifs 302
                                         ip    ++++l   ll + +++ l+  ls+++++  + q+ i  ++   ++f+ ++f  e++     ++++ +  
  gi|320100303|ref|YP_004175895.1| 131 --IPNPsKWIIILYTTLLLAASMSGLSISLSTVTRDF-NLQATIRSLTYNVLFFVSNIFYPESVVkarlGFAAPVVK 204
                                       ..****8999999999999999999999999997764.444444344443455555555544433356799999999 PP

                   ABC2_membrane_3 303 iiPffapglgllrlitgd.plwe........illsliilalf 335
                                       + P++    +++r ++++   ++        +++s+iila+ 
  gi|320100303|ref|YP_004175895.1| 205 YSPLSMA-TSIYRWGFNYtGDVDvlfnavglLMWSIIILAVA 245
                                       9999875.5566888655233455555544444555555443 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 ?    8.9  12.7   0.00022      0.98      39     130 ..      60     151 ..      30     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00022
                   ABC2_membrane_5  39 i...fsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgnvt 112
                                       i   ++ ls++is++ i   +  + + ++  yl++LPv+r  +V+ + l++l+ +li+ l +l+++++   i ++  
  gi|320100303|ref|YP_004175895.1|  60 ItpgILSLSIFISSFSIGREVGVELRREVTLYLVSLPVKRTVLVAGRILGGLLRGLIYQLGFLFFAALLLGIPNPSK 136
                                       333366789999999999999*************************************9999999887666666644 PP

                   ABC2_membrane_5 113 isevllsiliglvialif 130
                                       +  +l++    l++a  +
  gi|320100303|ref|YP_004175895.1| 137 WIIILYT---TLLLAASM 151
                                       3333333...22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1847.06
//
Query:       gi|320100304|ref|YP_004175896.1|  [L=180]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   49.9  16.2    3.4e-13   49.6  16.2    1.0  1  DUF998          Protein of unknown function (DUF998)
  ------ inclusion threshold ------
      0.051   13.5   4.0        1.7    8.6   0.2    3.0  2  Deltameth_res   Deltamethrin resistance
      0.067   12.6   7.4      0.015   14.7   2.8    1.9  1  NQR2_RnfD_RnfE  NQR2, RnfD, RnfE family
        0.1   12.8   6.5        3.2    8.0   0.1    3.3  3  SpoIIIAC        Stage III sporulation protein AC/AD protein f
        0.4   10.5  10.0       0.25   11.1   4.1    2.1  2  DUF2157         Predicted membrane protein (DUF2157)
        1.3    9.0   9.2      0.065   13.2   3.1    1.8  2  SLATT_1         SMODS and SLOG-associating 2TM effector domai
        2.6    8.4   5.5       0.55   10.6   1.3    2.0  2  ASFV_L11L       African swine fever virus (ASFV) L11L protein


Domain annotation for each model (and alignments):
>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6  16.2   1.3e-16   3.4e-13       2     175 ..       9     165 ..       7     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.3e-16
                            DUF998   2 aaallalavilaaallrpgydplrhaiSeLgaeg.gpggwlfnaglvllgllvlalavgllraargragragrllla 77 
                                       a +++ l++i++aall + ++pl++a+S+Lg +  +  + +fn+glv  gll+  +av      ++  +r    lla
  gi|320100304|ref|YP_004175896.1|   9 ASVAVPLSSIAIAALLSNWFNPLENALSDLGHAArSSVAAVFNGGLVFGGLLTYTVAV-----TSRQTRRSYNMLLA 80 
                                       456677788**********************98889999******************9.....99999********* PP

                            DUF998  78 vaglglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwll 154
                                       + +++l+l+gv+ +  g         +H ++s+++f++ ++ ++ ++    +   +++r++++ all+ +aa++  +
  gi|320100304|ref|YP_004175896.1|  81 LTAVFLILIGVYDEIYGR--------LHFAVSVAFFTGTMIFMAWIT---VKETSKVIRAYSVSALLIELAAWIIYF 146
                                       ***************996........******************999...889999999999999999888888888 PP

                            DUF998 155 aaaldgslllGlaerllvlai 175
                                             + +++++e ++v+ +
  gi|320100304|ref|YP_004175896.1| 147 MY--RIPRGAAIPELISVASF 165
                                       77..67778888888888766 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00067       1.7      16      33 ..      70      87 ..      67      92 .. 0.89
   2 ?    5.1   0.2    0.0082        21      24      39 ..     100     115 ..      96     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00067
                     Deltameth_res 16 akqrkYNavLaaGivili 33
                                      + +r YN+ La+  v+li
  gi|320100304|ref|YP_004175896.1| 70 QTRRSYNMLLALTAVFLI 87
                                      6799*********99997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0082
                     Deltameth_res  24 vLaaGiviligTiala 39 
                                       ++a++++++ gT++++
  gi|320100304|ref|YP_004175896.1| 100 HFAVSVAFFTGTMIFM 115
                                       799**********997 PP

>> NQR2_RnfD_RnfE  NQR2, RnfD, RnfE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.8   5.8e-06     0.015     188     272 ..       9     103 ..       5     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.8e-06
                    NQR2_RnfD_RnfE 188 iswripvsvlatvavlsllfn..........llaapplfhllsGglllgafFmatdpvtspitkkGklifglliGll 254
                                       +s+ +p+s +a +a+ls  fn           +a + ++ ++ Ggl++g +   t  vts +t++   +  +l +++
  gi|320100304|ref|YP_004175896.1|   9 ASVAVPLSSIAIAALLSNWFNplenalsdlgHAARSSVAAVFNGGLVFGGLLTYTVAVTSRQTRRSYNMLLALTAVF 85 
                                       688999***********9999*****99998667789*****************************99999999999 PP

                    NQR2_RnfD_RnfE 255 tvliRvfgaypeGvafai 272
                                        +li v+ ++     fa+
  gi|320100304|ref|YP_004175896.1|  86 LILIGVYDEIYGRLHFAV 103
                                       999999887666666665 PP

>> SpoIIIAC  Stage III sporulation protein AC/AD protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0013       3.2       8      42 ..      58      91 ..      55      99 .. 0.86
   2 ?    1.9   0.4       0.1   2.6e+02      25      41 ..     100     116 ..      94     120 .. 0.82
   3 ?    5.0   0.1     0.011        27      27      45 ..     134     152 ..     129     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                          SpoIIIAC  8 giiaalladilkdageeeiAslielagkiiillla 42
                                      g+++   a+  +++++ ++ +l+ l ++ +il+ +
  gi|320100304|ref|YP_004175896.1| 58 GLLTYTVAVTSRQTRR-SYNMLLALTAVFLILIGV 91
                                      67777788999*****.***************966 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.1
                          SpoIIIAC  25 eiAslielagkiiilll 41 
                                        +A+ + ++++++i++ 
  gi|320100304|ref|YP_004175896.1| 100 HFAVSVAFFTGTMIFMA 116
                                       68999**********97 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.011
                          SpoIIIAC  27 Aslielagkiiilllalpl 45 
                                       A+liela+ ii +++ +p+
  gi|320100304|ref|YP_004175896.1| 134 ALLIELAAWIIYFMYRIPR 152
                                       89************99987 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.032        82      69     112 ..      10      62 ..       3      72 .. 0.65
   2 ?   11.1   4.1   9.8e-05      0.25      44     120 ..      78     151 ..      74     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.032
                           DUF2157  69 lllvllllslllg.avlwrdr........rvpprlgeallllaalllgaaial 112
                                        ++v+l   ++++ +  w ++         + +r + a+++ ++l++g+++ +
  gi|320100304|ref|YP_004175896.1|  10 SVAVPLSSIAIAAlLSNWFNPlenalsdlGHAARSSVAAVFNGGLVFGGLLTY 62 
                                       33344444444444444444488888888777788888888888888887765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.8e-05
                           DUF2157  44 lllglGlilfvAanWqglsrlvkfllllvllllslllg.avlwrdrrvpprlgeallllaalllgaaialvgqifql 119
                                       ll +++++l+  ++++++   + f++ ++ + ++++++ +++ +  + +++++   + ++all+  a +++  ++ +
  gi|320100304|ref|YP_004175896.1|  78 LLALTAVFLILIGVYDEIYGRLHFAVSVAFFTGTMIFMaWITVK--ETSKVIRA--YSVSALLIELAAWIIYFMYRI 150
                                       899***********************************777666..56666664..445666666666766667766 PP

                           DUF2157 120 s 120
                                        
  gi|320100304|ref|YP_004175896.1| 151 P 151
                                       5 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4      0.65   1.7e+03      32      65 ..      13      46 ..       4      51 .. 0.53
   2 ?   13.2   3.1   2.5e-05     0.065      21      86 ..      68     135 ..      61     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.65
                           SLATT_1 32 illellalllaalrafgelsvdlvgvlaavaaal 65
                                      + l+ +a+++ + + f+ l+ +l ++  a+ +++
  gi|320100304|ref|YP_004175896.1| 13 VPLSSIAIAALLSNWFNPLENALSDLGHAARSSV 46
                                      3344455555555566666665555555555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.5e-05
                           SLATT_1  21 eraakrwrlllillellalllaalr..afgelsvdlvgvlaavaaallaWlelkqyeelaaaYslaae 86 
                                       +r+++r   +l++l+++ l+l+ +   ++g l++++  ++ +    ++aW+ +k+++++++aYs  a 
  gi|320100304|ref|YP_004175896.1|  68 SRQTRRSYNMLLALTAVFLILIGVYdeIYGRLHFAVSVAFFTGTMIFMAWITVKETSKVIRAYSVSAL 135
                                       45566666666666666666655544788889997777778888889*****************9886 PP

>> ASFV_L11L  African swine fever virus (ASFV) L11L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00021      0.55       5      42 ..      78     115 ..      75     119 .. 0.92
   2 ?   -2.1   0.2         2     5e+03      28      36 ..     158     166 ..     135     175 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                         ASFV_L11L   5 llvmapiplvliflysyfkiklhklitialflgclffi 42 
                                       ll ++ + l+li +y  +  +lh  +++a+f g ++f+
  gi|320100304|ref|YP_004175896.1|  78 LLALTAVFLILIGVYDEIYGRLHFAVSVAFFTGTMIFM 115
                                       7889999***************************9996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                         ASFV_L11L  28 klitialfl 36 
                                        li++a f 
  gi|320100304|ref|YP_004175896.1| 158 ELISVASFT 166
                                       444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1299.24
//
Query:       gi|320100305|ref|YP_004175897.1|  [L=791]
Description: heavy metal translocating P-type ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-43  148.6   0.4    3.1e-43  147.4   0.4    1.7  1  E1-E2_ATPase  E1-E2 ATPase
    5.7e-31  108.4   0.0    1.1e-30  107.5   0.0    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
    3.5e-10   40.2   0.0    6.2e-07   29.8   0.0    2.7  2  HMA           Heavy-metal-associated domain
    6.2e-06   26.1   0.0     0.0089   15.8   0.0    2.2  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.052   13.9   0.2        1.7    9.0   0.0    2.7  2  HAD           haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.4   8.6e-47   3.1e-43       4     180 ..     278     456 ..     275     457 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 8.6e-47
                                       --EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-..G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   4 pptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvek..ekgdmvfsGtvvvs 78 
                                        ++++v++dg++ee+ a+ +  + i+++kag+++ +Dg++v+g   vdes  TGE  pv k  e++d+v +Gt+ +s
  gi|320100305|ref|YP_004175897.1| 278 NSKVRVVEDGRVEEVSADAVSLNSIIEVKAGEKILVDGIVVDGWGYVDESTFTGEPIPVLKssENRDRVLAGTILTS 354
                                       689**********************************************************76799*********** PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralall 155
                                       g ++++Vt+ g+dt l  + ++++ea   ++ +q+ +dk ++ l+++v++ al++++ ++++ ++++ +ll+a ++l
  gi|320100305|ref|YP_004175897.1| 355 GYIRVRVTRKGRDTALYNLLASAREAVLHRPGFQQLADKAVGKLTWIVTASALVTVFSWYIYSGDIFLSLLFAASVL 431
                                       ***************************************************************************** PP

                                       HHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 156 vaaiPcaLplavplalalgarrlak 180
                                        +++Pc L++a+p+++++g+ ++++
  gi|320100305|ref|YP_004175897.1| 432 AVSCPCPLGIAIPMVVSIGVIKASR 456
                                       ********************99987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   3.1e-34   1.1e-30       2     209 ..     474     690 ..     473     690 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 3.1e-34
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHHHHHH...HHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.. RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakarsgal...tgfatfigrg.. 67 
                                       + +++Dk+GT+t g+ps++ v+     ++ +++ ++      sehp+++a+ +++ + + ++   + f++++g g  
  gi|320100305|ref|YP_004175897.1| 474 NILLLDKTGTITVGKPSLKGVVTLGGYSREEIMKYVcsveqrSEHPLARAISNYCRDAGVSVedpEFFEHLPGLGvl 550
                                       6799******************************************************77776667788899999** PP

                                       ......HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTT CS
                                       ......xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ......ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaag 134
                                             ++ +g+  +++ l  +i++  +  i++  + g t +l+   +++ av++i d+  v+++a  +v+++k+ g
  gi|320100305|ref|YP_004175897.1| 551 gvvmgkRVGVGSINLVKGLgvEINSGTQTLIDEIGRSGGTPVLVviGDEVAAVLEIRDE--VREDALNVVKYFKSVG 625
                                       ********************************************9988***********..**************** PP

                                       EEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 135 ievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       ++v++++gd +e+++++ ++lG            +   ++  pe+k ++i  +qg +++v+ VGDgvnDa al aA
  gi|320100305|ref|YP_004175897.1| 626 FKVGIASGDIEENVKHVGKELG-----------LDFfYSGLRPEDKGRLIHGIQGGGQRVLYVGDGVNDAIALSAA 690
                                       **********************...........444599**********************************998 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.7e-10   6.2e-07       3      62 .]       9      67 ..       8      67 .. 0.96
   2 !    7.6   0.0    0.0015       5.3      15      45 ..      87     117 ..      85     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.7e-10
                               HMA  3 rvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                       + g++C  C  ++++ L+ l g+ + + d+  + +++e+d+e ++l++i  ai++agy+
  gi|320100305|ref|YP_004175897.1|  9 EIIGVDCSTCIYAIKRRLADLRGNVKLESDFL-GNAVIEYDDEYVSLSEIYHAIRDAGYD 67
                                      577*****************************.**************************7 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                               HMA  15 kvekvLselpgVesvkvdlatktvtVegdae 45 
                                       +vek + +lpg+ +v vd  t +  V++++ 
  gi|320100305|ref|YP_004175897.1|  87 AVEKEIRRLPGILDVRVDTLTCRILVRFNPR 117
                                       69****************9998888887665 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00058       2.1      14      58 ..     608     652 ..     602     656 .. 0.89
   2 !   15.8   0.0   2.5e-06    0.0089     203     241 ..     671     709 ..     662     714 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00058
                                       S---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  14 kkisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                        ++ e + +++k++k+ g+kv iA+G   ++v++v +elgld ++
  gi|320100305|ref|YP_004175897.1| 608 DEVREDALNVVKYFKSVGFKVGIASGDIEENVKHVGKELGLDFFY 652
                                       578889999********************************9765 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.5e-06
                                       GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSE CS
                       Hydrolase_3 203 leeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdy 241
                                        ++v+ +GDg ND   L+aa +g+A+gna++ + +  d 
  gi|320100305|ref|YP_004175897.1| 671 GQRVLYVGDGVNDAIALSAAFVGIAVGNATDIARESGDA 709
                                       578999*************************98876665 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.098   3.5e+02      77     110 ..     374     405 ..     354     410 .. 0.81
   2 ?    9.0   0.0   0.00047       1.7      84     130 ..     609     654 ..     593     691 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.098
                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgg 110
                                       +a++++  l++pg+ +l +  +a G  +++v+++
  gi|320100305|ref|YP_004175897.1| 374 LASAREAVLHRPGFQQLAD--KAVGKLTWIVTAS 405
                                       45555666999********..89999******98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00047
                               HAD  84 klldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlat 130
                                          +++al +++  ++ G++v + Sg ++++v+ + +elg d +++ 
  gi|320100305|ref|YP_004175897.1| 609 E-VREDALNVVKYFKSVGFKVGIASGDIEENVKHVGKELGLDFFYSG 654
                                       2.4588999999888*************************5444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (791 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.26s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 5579.36
//
Query:       gi|320100306|ref|YP_004175898.1|  [L=56]
Description: YHS domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-20   71.8   2.2    3.9e-20   71.7   2.2    1.0  1  YHS              YHS domain
     0.0013   19.0   1.8     0.0019   18.5   1.8    1.5  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
       0.01   15.7   1.3      0.017   15.0   1.2    1.4  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
      0.044   13.3   0.0      0.049   13.1   0.0    1.0  1  FAP206           Domain of unknown function
      0.085   12.8   0.8       0.28   11.2   0.5    1.8  2  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 !   71.7   2.2   1.1e-23   3.9e-20       2      47 ..       4      49 ..       3      50 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 1.1e-23
                               YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYata 47
                                       dPvcgm+vd+ k+++k+ YkG+ YyFcS +Ck++Fe++Pe Y+++
  gi|320100306|ref|YP_004175898.1|  4 VDPVCGMRVDPSKSKHKTLYKGRIYYFCSSRCKEEFERNPEYYLSH 49
                                      59*****************************************986 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.8   5.2e-07    0.0019      17      35 ..      23      41 ..       8      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.2e-07
                   Arc_trans_TRASH 17 lknkvYyvCCktCkselkk 35
                                      +k ++Yy+C + Ck+e+ +
  gi|320100306|ref|YP_004175898.1| 23 YKGRIYYFCSSRCKEEFER 41
                                      678*************975 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 ?   15.0   1.2   4.8e-06     0.017      15      41 .]      17      39 ..      15      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
                            zf-FCS 15 gkpeftyvlendgvvgqFCStsCldsY 41
                                       k++    + ++g +++FCS+ C+ ++
  gi|320100306|ref|YP_004175898.1| 17 SKHK----TLYKGRIYYFCSSRCKEEF 39
                                      6777....99*************9988 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.049     227     254 ..      22      49 ..      12      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                            FAP206 227 kykdkyyaFsseeaareFaadpdrfiea 254
                                        yk++ y F s ++  eF+ +p++++ +
  gi|320100306|ref|YP_004175898.1|  22 LYKGRIYYFCSSRCKEEFERNPEYYLSH 49 
                                       599**********************986 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 ?   -0.4   0.0      0.32   1.1e+03       7      16 ..       6      15 ..       5      22 .. 0.73
   2 ?   11.2   0.5   7.7e-05      0.28      19      31 ..      30      42 ..      26      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.32
                           DUF2116  7 ivCGkaIpld 16
                                      +vCG  +++ 
  gi|320100306|ref|YP_004175898.1|  6 PVCGMRVDPS 15
                                      5888877665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.7e-05
                           DUF2116 19 fCsekCqeeyekk 31
                                      fCs +C+ee+e++
  gi|320100306|ref|YP_004175898.1| 30 FCSSRCKEEFERN 42
                                      9*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 425.51
//
Query:       gi|320100307|ref|YP_004175899.1|  [L=278]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-81  272.2   0.1    3.6e-81  272.1   0.1    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr
  ------ inclusion threshold ------
      0.068   13.3   0.0       0.14   12.3   0.0    1.4  1  TcpA             Toxin-coregulated pilus subunit TcpA


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 !  272.1   0.1     4e-85   3.6e-81       1     234 [.       6     265 ..       6     266 .. 0.90

  Alignments for each domain:
  == domain 1  score: 272.1 bits;  conditional E-value: 4e-85
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       i+LlTDFG++dpyvg+mkgvi+si+p a+ivD+tH ++++++ eaa++L  +++yfp gt++++vVDpgvg+erral
  gi|320100307|ref|YP_004175899.1|   6 IALLTDFGYRDPYVGVMKGVIKSINPAAEIVDLTHGVTRHSIVEAAVVLLVSAKYFPHGTIFVVVVDPGVGSERRAL 82 
                                       89*************************************************************************** PP

                                       EEEETTSEEEEESSSTTHHHH...SEEEEEEGSSCC.....--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGGS CS
                   SAM_adeno_trans  78 vveakggyfvgPDNGlltlal...lleeaveieeee.....ssatFhgrDvFapvaarlaagvsleelgeeldpeel 146
                                       vve+++++++gPDNG l+l++   ++++a++i++++     +s+tFhgrDvFapvaa ++ gv+lee+g e++  +l
  gi|320100307|ref|YP_004175899.1|  83 VVETNNYILLGPDNGCLSLLAardGVKRAFDISNTRfklrdTSHTFHGRDVFAPVAAWISLGVPLEEVGVEVPAGSL 159
                                       ******************88888877*******99999*9999*******************************999 PP

                                       -SSS....E...CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE..............EEEEESSGGGSTTTS CS
                   SAM_adeno_trans 147 vrle....e...derlegevlyvDrFGNvitniskelleelekerkva..............klkkvetyaevaege 202
                                         l+    +   d+++eg+v+y+D +GN++tni  +  +e++     +              ++++ ++++ va+ge
  gi|320100307|ref|YP_004175899.1| 160 RMLDieapRvggDHSVEGSVIYIDVYGNIMTNIGPAEITEAGFL---QgdklkvvgptgvtgTCVFTTSFSLVAPGE 233
                                       777776763567899******************94444433332...12334456778888866677********** PP

                                       EEEEE-TTSEEEEEETTC-HHHHHT--TT-EE CS
                   SAM_adeno_trans 203 llalvnssglleiavnkgsaaellglkvgdev 234
                                       l +++ns g+le+avn+g+aa++lg++ g+++
  gi|320100307|ref|YP_004175899.1| 234 LACYMNSWGYLEVAVNMGDAARMLGVAQGSRI 265
                                       ****************************9987 PP

>> TcpA  Toxin-coregulated pilus subunit TcpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.5e-05      0.14      73     107 ..       6      40 ..       2      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                                       GGGG--TTTS--BGGG-SEEEE-SSTT-B---TT- CS
                              TcpA  73 vadlgdfetvvadaaksvGviksikgGaktldltn 107
                                       +a l df + ++      Gviksi++ a+ +dlt 
  gi|320100307|ref|YP_004175899.1|   6 IALLTDFGYRDPYVGVMKGVIKSINPAAEIVDLTH 40 
                                       6778999**************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 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 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2079.49
//
Query:       gi|320100308|ref|YP_004175900.1|  [L=520]
Description: NADH-ubiquinone/plastoquinone (complex I) oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  174.2  20.8    3.5e-51  174.2  20.8    2.0  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0051   16.9   1.4     0.0051   16.9   1.4    3.8  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
      0.091   13.0   0.0       0.22   11.8   0.0    1.6  1  Tgi2PP           Effector immunity protein Tgi2PP


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.2      0.19   1.2e+03     116     163 ..      82     128 ..      80     131 .. 0.70
   2 !  174.2  20.8   5.8e-55   3.5e-51       2     292 ..     131     440 ..     130     441 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.19
                   Proton_antipo_M 116 vsallAatlvkagvlllirlllllavssneisqlllilaiismllgsl 163
                                       vsall a++  + + ++++ +  ++v ++   ++ l+l++ s +lg +
  gi|320100308|ref|YP_004175900.1|  82 VSALL-ALTTSLVMTIIMAYSAEYIVDEGYPWYVTLMLGAFSGMLGVI 128
                                       89999.666677777777788888866666667777777777777765 PP

  == domain 2  score: 174.2 bits;  conditional E-value: 5.8e-55
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal...... 72 
                                       +d++ l++ lE++++++y L+ ++++k+ s+ ++lk+++++++g  + Ll+++l+yn  g+l++ +ls+ +      
  gi|320100308|ref|YP_004175900.1| 131 SDVFNLFVMLEVTGVSSYGLVMYYRSKAGSIVSGLKYAFIGAMGTTLYLLALALIYNTYGSLNLVDLSLKIhgypgs 207
                                       68999***************************************************************9999***** PP

                   Proton_antipo_M  73 .....elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.... 140
                                            ++g++ + + ++++l l ++ +Ks+++p h+Wlpda+ +aP+pvsa+l++++v++g+++l ++l ++     
  gi|320100308|ref|YP_004175900.1| 208 sitleDAGYSVISAGIIMVLALWTFSIKSGVFPNHFWLPDAHPAAPAPVSAMLSGLVVNVGAIGLYKVLYMMYggtl 284
                                       **99999999999999999***********************************************99998876655 PP

                   Proton_antipo_M 141 .....vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfk 212
                                             +   +s l++  +++s+++g+l+   q d+Kr++AyS++   Gy+++ l+v ++ g+ a + h ++h+l k
  gi|320100308|ref|YP_004175900.1| 285 parvtPVRDLASLLVVSTGMVSAIIGALLMGIQQDVKRIIAYSTVMNTGYIFMSLGVLNAGGLLAFLYHTVVHSLAK 361
                                       554444566788999999*********************************************************** PP

                   Proton_antipo_M 213 allFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavva 289
                                       ++lFl + +v  +   tr i++++g+    P+  +++ v +l+laG+Pp+ gFlsk+l+ ea+++++++++++++va
  gi|320100308|ref|YP_004175900.1| 362 STLFLGI-GVLVRYAGTRRINELAGFGRIHPLPGIAIGVSVLTLAGIPPLPGFLSKLLMYEALFNYNPVFAIAMIVA 437
                                       *******.6668888**********************************************************9998 PP

                   Proton_antipo_M 290 svl 292
                                       s++
  gi|320100308|ref|YP_004175900.1| 438 SAI 440
                                       887 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 !   16.9   1.4   8.5e-07    0.0051      14      56 ..      75     116 ..      71     118 .. 0.89
   2 ?   -2.0   1.0      0.67     4e+03      19      34 ..     132     147 ..     127     154 .. 0.77
   3 ?   -0.8   0.1      0.28   1.7e+03      16      36 ..     424     444 ..     418     446 .. 0.83
   4 ?   -3.1   0.0       1.5   8.7e+03      21      35 ..     471     485 ..     465     492 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.5e-07
                   Proton_antipo_N  14 igfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56 
                                       i++ lD +sal +l+ ++v ++++ YS +Y   degy+ + ++
  gi|320100308|ref|YP_004175900.1|  75 ITYTLDMVSALLALTTSLVMTIIMAYSAEYIV-DEGYPWYVTL 116
                                       7889***************************9.6699888765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.67
                   Proton_antipo_N  19 Dklsalmllvvtfvsl 34 
                                       D + + ++l vt+vs+
  gi|320100308|ref|YP_004175900.1| 132 DVFNLFVMLEVTGVSS 147
                                       6677889999***997 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.28
                   Proton_antipo_N  16 fllDklsalmllvvtfvsllv 36 
                                       f  +++ a+ ++v + ++ll 
  gi|320100308|ref|YP_004175900.1| 424 FNYNPVFAIAMIVASAIGLLA 444
                                       667888999******999985 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.5
                   Proton_antipo_N  21 lsalmllvvtfvsll 35 
                                        sal + ++ +v   
  gi|320100308|ref|YP_004175900.1| 471 ASALTASLILLVVGA 485
                                       455555555555444 PP

>> Tgi2PP  Effector immunity protein Tgi2PP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05      0.22       7      34 ..     393     421 ..     392     422 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                                       TTEEEE--B--.TSS-SSTTEEEEEEEE- CS
                            Tgi2PP   7 pGvfIevDlqD.aGkpylpGYadFlvlye 34 
                                       pG+ I v +   aG+p+lpG+ + l+ ye
  gi|320100308|ref|YP_004175900.1| 393 PGIAIGVSVLTlAGIPPLPGFLSKLLMYE 421
                                       899999999999**********9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3892.62
//
Query:       gi|320100309|ref|YP_004175901.1|  [L=161]
Description: cation antiporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  118.6   1.6    2.1e-34  118.4   1.6    1.0  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   1.6   1.2e-38   2.1e-34       2     146 .]       9     159 ..       8     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 1.2e-38
                              MNHE   2 lllflvWllltgs..lgelllGlllallvalllrrll.......lplrrvllrllayllvflweivkanldVakrvl 69 
                                       ll+f++++l++gs  + ++++G+++a ++ +++ r+l       l++ r+l++ll++l ++ +  +ka++dV+kr++
  gi|320100309|ref|YP_004175901.1|   9 LLVFIIYILIAGSltPYDIATGVIVASVAGWVTGRYLvrnpgklLQPSRLLVSLLYFLKYMTVIEFKAHMDVVKRIF 85 
                                       789******************************99989999888888888999999999998888************ PP

                              MNHE  70 rpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldv.edeeeeareeikgrlErrlle 145
                                       +  ++irpgivkvp+++ sd+a++l+ansit tPGT++vd  e ++ +yv ++dv ++e+ +ar  i++++Er++ +
  gi|320100309|ref|YP_004175901.1|  86 N--MNIRPGIVKVPVTVVSDYARLLVANSITNTPGTVVVD--ERDGFFYVNWIDVsTTEPWQARLLISEEFERYASK 158
                                       *..*************************************..8999*********88889999999********987 PP

                              MNHE 146 i 146
                                       i
  gi|320100309|ref|YP_004175901.1| 159 I 159
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1342.35
//
Query:       gi|320100310|ref|YP_004175902.1|  [L=134]
Description: NADH-ubiquinone oxidoreductase subunit 4L [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   68.4   4.2    4.4e-19   68.0   4.2    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.017   15.5   1.1      0.026   15.0   1.1    1.3  1  AzlC         AzlC protein


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 !   68.0   4.2   4.9e-23   4.4e-19       2     103 ..      11     123 ..      10     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 4.9e-23
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC...........................TTS CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi..............tnpatefadp 64 
                                       ll++++l  li++yg+++rr+l+k+li+l ++s  v+++++++g++      +              +  +++ +dp
  gi|320100310|ref|YP_004175902.1|  11 LLIVLVLNALISIYGIVYRRSLVKKLISLTMLSDTVFVVFIMIGYRLVY---PsippilveltpenlEYVKQHGVDP 84 
                                       678889999************************************9943...234588*******9999999***** PP

                                       CGGHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  65 lpqalvLtaivigaaetavgLallvrlyreygtddvqel 103
                                       lpqalvLt ivig+a+ a++   ++++yr +gt+d + l
  gi|320100310|ref|YP_004175902.1|  85 LPQALVLTGIVIGMAVNALIAFGIIQAYRLKGTTDARRL 123
                                       **********************************98766 PP

>> AzlC  AzlC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.1   2.9e-06     0.026      51     132 ..       5     100 ..       1     111 [. 0.67

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-06
                              AzlC  51 asllaivlttllvNlRhllyglslapklkklsrlkrlllaflltDetfalas....ar...............klsr 108
                                       a  ++++l++l++N+   +yg+ +++ l      k+l+ + +l+D++f++++    +                +l+ 
  gi|320100310|ref|YP_004175902.1|   5 AFTWSLLLIVLVLNALISIYGIVYRRSL-----VKKLISLTMLSDTVFVVFImigyRLvypsippilveltpeNLEY 76 
                                       56799***********************.....6898888***********53554104444445555444332223 PP

                              AzlC 109 ayflglglllylawvlgtllGall 132
                                           g+  l +++  +g ++G+++
  gi|320100310|ref|YP_004175902.1|  77 VKQHGVDPLPQALVLTGIVIGMAV 100
                                       333455555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 975.69
//
Query:       gi|320100311|ref|YP_004175903.1|  [L=244]
Description: Na+/H+ antiporter MnhB subunit-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   65.3  12.6    6.1e-18   65.3  12.6    2.2  2  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter
  ------ inclusion threshold ------
      0.071   12.6   0.1       0.15   11.6   0.1    1.6  1  DUF2106   Predicted membrane protein (DUF2106)


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.9      0.23   2.1e+03      83      83 ..      49      49 ..       4      90 .. 0.53
   2 !   65.3  12.6   6.8e-22   6.1e-18       1     122 [.     104     227 ..     104     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.23
                              MnhB 83 l 83
                                      +
  gi|320100311|ref|YP_004175903.1| 49 Y 49
                                      0 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 6.8e-22
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafglee..lekllrvklaprileglgllla 75 
                                       i rt ++++ ++i+  s++++l+Gh++PGGGFqgG +l++a++ll+ ++++ +   + +++ kl   ++ gl+l+ +
  gi|320100311|ref|YP_004175903.1| 104 IARTSTKIVSVMIIGASASIALHGHLTPGGGFQGGSTLGVAFLLLIPVYSVYAvlSKGVTSEKL--IAVRGLALASI 178
                                       789**************************************************96666667774..59********* PP

                              MnhB  76 vltgllglllg..fltslflelelllgevelgtallfdlgVylvVvggl 122
                                        +++ll+++ g  + +++ ++ + + g    g+++l++++ y++V++g+
  gi|320100311|ref|YP_004175903.1| 179 GIVALLPVFKGleLASNTRFYPSHVAGMLISGSLFLYNFFEYIAVAAGF 227
                                       ***********9655555555544556666****************997 PP

>> DUF2106  Predicted membrane protein (DUF2106)
   #    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     118     142 ..      57      81 ..      33      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                           DUF2106 118 ideilyytrGldtvlessillvafv 142
                                       +  i++  rGldtv e++++++a v
  gi|320100311|ref|YP_004175903.1|  57 VTAIVWDYRGLDTVYETAVFFLAIV 81 
                                       45799999*************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1867.31
//
Query:       gi|320100312|ref|YP_004175904.1|  [L=83]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-10   38.6   8.5    8.9e-10   38.6   8.5    1.8  2  DUF4040   Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
      0.064   11.5   6.8      0.064   11.5   6.8    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   2.1    0.0032        28      20      37 ..       4      21 ..       1      22 [. 0.88
   2 !   38.6   8.5   9.9e-14   8.9e-10       2      67 .]      14      79 ..      13      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0032
                           DUF4040 20 villgvvGllvallfvll 37
                                       +ll+++G l++l+fv+l
  gi|320100312|ref|YP_004175904.1|  4 TLLLIILGSLLSLVFVYL 21
                                      6899************97 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 9.9e-14
                           DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlpr 67
                                      l +++++++v+ rd+l+av +++ +++++++l  ++ A D+ lT++av  g+  +ll++++++++r
  gi|320100312|ref|YP_004175904.1| 14 LSLVFVYLTVTERDLLKAVGFSAGQSIAYTILLHVFAATDIVLTYIAVSVGIYSALLVYVVSKTER 79
                                      77999**********************************************************986 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.8   7.1e-06     0.064     105     177 ..       6      78 ..       1      83 [] 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-06
                           DUF2070 105 vlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfivvvdr 177
                                       +l +  ++   ++v+++v++++llkav  ++ q++++ +ll ++ +++ +l ++++s+ ++ a+++++v  + 
  gi|320100312|ref|YP_004175904.1|   6 LLIILGSLLSLVFVYLTVTERDLLKAVGFSAGQSIAYTILLHVFAATDIVLTYIAVSVGIYSALLVYVVSKTE 78 
                                       44445566777899999***************************76666677777777777777776665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); 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):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 667.14
//
Query:       gi|320100313|ref|YP_004175905.1|  [L=118]
Description: MnhG/PhaG subunit monovalent cation/proton antiporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   69.6  11.4    2.6e-19   69.2  11.4    1.2  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
  ------ inclusion threshold ------
      0.032   13.6   5.3      0.044   13.1   5.3    1.4  1  ExoD            Exopolysaccharide synthesis, ExoD
      0.052   13.2   8.5      0.059   13.0   8.5    1.1  1  Virul_fac_BrkB  Virulence factor BrkB
      0.069   13.6   0.0      0.092   13.2   0.0    1.2  1  FAM163          FAM163 family


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2  11.4   5.9e-23   2.6e-19       1      79 []      13      99 ..      13      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 5.9e-23
                    PhaG_MnhG_YufB  1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaa.......slkllliilfllltaPvaa 71
                                      ll+ G++f l++aigllr+p++y Rlhaat+++  G+++ l+G++l +  +         ++ +++++++l++ aPv++
  gi|320100313|ref|YP_004175905.1| 13 LLFTGGVFDLIAAIGLLRFPNFYVRLHAATIGAIYGAVFPLIGVALIAlGTPEldgrfiiAGGAFATAIILMIIAPVGS 91
                                      7899******************************************88555559************************* PP

                    PhaG_MnhG_YufB 72 hliaraay 79
                                      h++a+aa+
  gi|320100313|ref|YP_004175905.1| 92 HVLAYAAH 99
                                      ******97 PP

>> ExoD  Exopolysaccharide synthesis, ExoD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.3   9.9e-06     0.044     141     179 ..      48      86 ..      22      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-06
                              ExoD 141 tntlpalailllalGllerDGllvllglllallavalla 179
                                       + ++p ++++l+alG+ e DG ++++g ++a++++++++
  gi|320100313|ref|YP_004175905.1|  48 GAVFPLIGVALIALGTPELDGRFIIAGGAFATAIILMII 86 
                                       567999**********************99999988775 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   8.5   1.3e-05     0.059     159     243 ..       7      93 ..       1     105 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                    Virul_fac_BrkB 159 lqllrwlvallllv.lafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYG.slgaliil 233
                                       + l+++l+ ++ ++ l+ a+    +pn  vrl+aa++Ga+ +a++ l++  l++l      +++ i G ++++ iil
  gi|320100313|ref|YP_004175905.1|   7 FWLGSILLFTGGVFdLIAAIGLLRFPNFYVRLHAATIGAIYGAVFPLIGVALIALGTPELDGRFIIAGgAFATAIIL 83 
                                       4555555555555413344446778************************************99999999******** PP

                    Virul_fac_BrkB 234 llWlylsali 243
                                       ++   + + +
  gi|320100313|ref|YP_004175905.1|  84 MIIAPVGSHV 93 
                                       *966555555 PP

>> FAM163  FAM163 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05     0.092       4      30 ..      68      94 ..      66     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                            FAM163  4 GtvvitGGilatviLLciiavLCyCRL 30
                                      G  +i+GG +at i+L+iia +    L
  gi|320100313|ref|YP_004175905.1| 68 GRFIIAGGAFATAIILMIIAPVGSHVL 94
                                      6789***************96655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 951.19
//
Query:       gi|320100314|ref|YP_004175906.1|  [L=92]
Description: multiple resistance and pH regulation protein F [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-10   40.3   4.1    3.2e-10   40.3   4.1    1.9  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6     0.081   1.4e+03      28      39 ..      14      25 ..       7      27 .. 0.60
   2 !   40.3   4.1   1.8e-14   3.2e-10       1      52 [.      34      85 ..      34      86 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.081
                         MrpF_PhaF 28 payldvalvlAl 39
                                      p+y+ +++++ l
  gi|320100314|ref|YP_004175906.1| 14 PLYIAAIVLYTL 25
                                      556666666554 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 1.8e-14
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                      +D v+A+D++++ l+++lal+a+++++p+++   ++lAl++++  + +++ l
  gi|320100314|ref|YP_004175906.1| 34 PDIVLAIDCIAYDLAVFLALIALYYRSPLMITPSMLLALWAYLLDIFISKHL 85
                                      799**********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 701.54
//
Query:       gi|320100315|ref|YP_004175907.1|  [L=1132]
Description: pullulanase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-78  261.9   0.0    1.1e-77  261.5   0.0    1.1  1  Glyco_hydro_57  Glycosyl hydrolase family 57
    2.1e-70  236.7   1.8    4.5e-70  235.6   0.7    2.1  3  Glucodextran_C  C-terminal binding-module, SLH-like, of gluco
      0.004   17.1  29.3     0.0087   16.1  29.3    1.5  1  Mucin           Mucin-like glycoprotein
  ------ inclusion threshold ------
      0.038   13.2   2.5       0.07   12.4   2.5    1.3  1  Med13_C         Mediator complex subunit 13 C-terminal domain
       0.05   13.5   5.4      0.092   12.7   5.4    1.4  1  TMEM154         TMEM154 protein family
       0.53    9.4   2.7       0.85    8.7   2.7    1.2  1  SPESP1          Sperm equatorial segment protein 1
       0.76    7.9  24.3        1.3    7.2  24.3    1.2  1  SSP160          Special lobe-specific silk protein SSP160
        0.8    7.8   8.7        1.2    7.2   8.7    1.1  1  FSA_C           Fragile site-associated protein C-terminus
        1.9    8.7  15.8        3.3    7.9  15.8    1.3  1  AJAP1_PANP_C    AJAP1/PANP C-terminus


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.5   0.0   5.4e-81   1.1e-77       1     319 [.      34     459 ..      34     466 .. 0.92

  Alignments for each domain:
  == domain 1  score: 261.5 bits;  conditional E-value: 5.4e-81
                                       EEEEEE-----TTS-SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-H...HHHHH... CS
                    Glyco_hydro_57   1 afvfhqHqplykkpgkgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylnge...kksyl... 71 
                                       a+v+h Hqp+y++ ++ +++lpwvr+ha+ +Y+k+a il k+p++ vtf++sgsL++qL ++++ +       +   
  gi|320100315|ref|YP_004175907.1|  34 AIVWHYHQPWYYSADESYLVLPWVRMHAVGNYYKMAYILSKYPDIRVTFTFSGSLLEQLTDMVENNkmdA---Reii 107
                                       79*************************************************************9996433...3357 PP

                                       ....................................HHHHHHHHHHHHHHHH---HH.................... CS
                    Glyco_hydro_57  72 ....................................pateellelieeglerctelk.................... 92 
                                                                           p  +el  l ++++++c  +                     
  gi|320100315|ref|YP_004175907.1| 108 awkivngtvtredvfrmlqipggffdinwgriidnsPRFRELRSLAQSAWSNCSTITrseselmscvvdsftggnlt 184
                                       ************************************888888888888899999998999999999999999999** PP

                                       ....HHHHHHHHHHHHHHHHH...............................HHHHT.TT-HHHHHHHHHHCTSEEE CS
                    Glyco_hydro_57  93 ....ldlavlfnlaisgplle...............................qiqkwlnkevlelfrelqesgqvEl 134
                                           +dlavlfnl +++p +                                 +++++  +v +++r+l+ +gqvEl
  gi|320100315|ref|YP_004175907.1| 185 gqnvIDLAVLFNLLWIDPQVAkekypdiyslmekaysqskpsyttsdlravlLVHRDILANVVPAYRDLVSRGQVEL 261
                                       ****************************************************899999******************* PP

                                       EEE-TT-B-GGG-S-...HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C.....- CS
                    Glyco_hydro_57 135 ltspyyHpllpllpd...sedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftde.....l 203
                                       + +py+Hpl+p++ d   sed+e ++ ++  l+++yf+++P g+w++E+av++e+l++++ +G ++++tde      
  gi|320100315|ref|YP_004175907.1| 262 IPVPYSHPLAPIVADlgfSEDLEIHISESMRLFKKYFNVTPAGVWPAEQAVNEEVLAAFKRAGVNWTITDEsilgkA 338
                                       *************************************************************************7432 PP

                                       -----------TTS-EE-TTS...-EEEE--CHH-TTTSGGG-............TTSB............-TT--- CS
                    Glyco_hydro_57 204 aeiledkskespyrpyllkngg..iavffRdreLsddigFryseqypleavddfinwlkkvkka..ksevvtialdg 276
                                          ++ +  + +  p++++ ++  i+v+fR +eLs++i+F+ys+++  +av+d++n++ ++  +   +++++ialdg
  gi|320100315|ref|YP_004175907.1| 339 --GVNTADVNMLGTPWYIDLQAgrIYVVFRSTELSNLISFQYSGRSYVDAVNDLVNRILSLRASvnGPRMIVIALDG 413
                                       ..3333333455566666655566***********************************9977799*********** PP

                                       TT.T--BB-TT-S---HHHHHHHHHHH...HHHHHHHHHHHHHHSS- CS
                    Glyco_hydro_57 277 En.wghypetgkkeFleklyeeleeng...lielvtpsefikklkpk 319
                                       En w++y++ g++ Fl +ly++l+e +    +e+ tp  fi +++++
  gi|320100315|ref|YP_004175907.1| 414 ENpWENYEKFGDL-FLNELYKRLSELQsqgQVETTTPGAFIARYPDT 459
                                       ************9.*******666655555***********998876 PP

>> Glucodextran_C  C-terminal binding-module, SLH-like, of glucodextranase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   3.4e+03      54      92 ..     413     454 ..     408     463 .. 0.77
   2 ?   -2.5   0.0       1.4   2.8e+03      14      46 ..     702     734 ..     702     745 .. 0.81
   3 !  235.6   0.7   2.3e-73   4.5e-70       1     226 [.     815    1053 ..     815    1055 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                    Glucodextran_C  54 genpwngpngFs.lqlvqiY..iddtkeggstrtdtpGlnvt 92 
                                       genpw+  + F  l+l ++Y  +++ +++g+++t+tpG+ ++
  gi|320100315|ref|YP_004175907.1| 413 GENPWENYEKFGdLFLNELYkrLSELQSQGQVETTTPGAFIA 454
                                       689999999996367778886667888999999999998665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                    Glucodextran_C  14 pGeytYPtdevfkpgvfDlvkfkvlekgdkvvf 46 
                                       pG+ +YP+ +  + g + ++++ v+ ++ +v++
  gi|320100315|ref|YP_004175907.1| 702 PGYQVYPRGNRVDLGIYLVKEVLVEVSSASVTL 734
                                       79999******9999999999999988877665 PP

  == domain 3  score: 235.6 bits;  conditional E-value: 2.3e-73
                    Glucodextran_C    1 ifelkDPvgDDkGpGeytYPtdevfkpgvfDlvkfkvlekgdkvvfevkfaelgenpwngpngFslqlvqiYidd 75  
                                        +f+++DPvgDD+GpG + YPt++vfkpgvfD++ f+v+++gdkvvf+++f++lg+npw+gpng+s+q+v+iYi++
  gi|320100315|ref|YP_004175907.1|  815 VFKMNDPVGDDDGPGGFKYPTNAVFKPGVFDMTGFTVIDQGDKVVFKITFRDLGGNPWSGPNGWSMQQVHIYIHT 889 
                                        799************************************************************************ PP

                    Glucodextran_C   76 tkeggstrtdtpGlnvtlaeespWdkavlis.gwesa........gklvvqeeaketed.svkveadqvkntivv 140 
                                        t +gg+++  t Gln+++a+ ++W++a++++ gw+++          ++ ++++  t+d ++kv+adq++n+i++
  gi|320100315|ref|YP_004175907.1|  890 TLNGGNSS--TIGLNAAIAQGYEWHMALILApGWGNDpipvgersALYYYDKDTPVTQDgDFKVYADQASNSIIA 962 
                                        **987666..89***********************999***9986556666666666669*************** PP

                    Glucodextran_C  141 evpkslL.dgeniakwgyvvlvgsqdgygpdkiRkvseeagewrfgggs....aidagvaPkviDllapegetQe 210 
                                        ev+k++L d++n +kw ++v+v+s+dg+g+++iR +s   gew++ + s    a+ a+v P+++D+lap+ ++Q+
  gi|320100315|ref|YP_004175907.1|  963 EVSKKVLyDSGNLDKWVFTVAVTSHDGFGTNRIRGFSIGGGEWQVNVPSnysvAMLANVIPYILDVLAPTPQEQY 1037
                                        ************************************************9999999******************** PP

                    Glucodextran_C  211 evLssydvsakklAtl 226 
                                        ++L+s+d++++++A l
  gi|320100315|ref|YP_004175907.1| 1038 QMLTSFDAANGRQALL 1053
                                        ***********99976 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  29.3   4.4e-06    0.0087      50      95 ..    1057    1095 ..    1017    1103 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.4e-06
                             Mucin   50 tttkppttttttttasttittkttkattttttttttttateaPsda 95  
                                         +t p+tttttttt++tt+tt+tt++tt       ttt+t  P+++
  gi|320100315|ref|YP_004175907.1| 1057 GATPPSTTTTTTTTTTTTTTTTTTTTTT-------TTTTTSTPQTT 1095
                                        3333333333333222222222222222.......22222222222 PP

>> Med13_C  Mediator complex subunit 13 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.5   3.5e-05      0.07     110     204 ..     971    1094 ..     964    1113 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                           Med13_C  110 ghgelkaWssllskknlqk....................psilsacLvsvepdpsLrlmpdavtpd.srfgqsss 163 
                                        + g l+ W  +++ +++                      ps+ s+++++  +   L +++++++++ +++++  +
  gi|320100315|ref|YP_004175907.1|  971 DSGNLDKWVFTVAVTSHDGfgtnrirgfsigggewqvnvPSNYSVAMLANVIPYILDVLAPTPQEQyQMLTSFDA 1045
                                        567777777777755555578888888888888888888999999999999999999997777777666663333 PP

                           Med13_C  164 ............stplstPqdsscthilvfptsattqstpttfasedanaedt 204 
                                                         tP ++++t+ ++++t+ tt++t+tt++++++++++t
  gi|320100315|ref|YP_004175907.1| 1046 angrqallrgygA----TPPSTTTTTTTTTTTTTTTTTTTTTTTTTTTSTPQT 1094
                                        6677778855554....444444443333333333333333333333333332 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   5.4   4.6e-05     0.092       9      83 ..    1058    1127 ..    1049    1132 .] 0.52

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                           TMEM154    9 dtaletatleeesadatsaasteseslkqeeakeslssaelsnesdqlelvlmiiiPlvllillllvviiliqkk 83  
                                         t+ +t+t++++++++  ++ t++ +  ++++  s++++ + +  ++  +    ++P  + +++  +v il+   
  gi|320100315|ref|YP_004175907.1| 1058 ATPPSTTTTTTTTTTT--TTTTTTTTTTTTTTTTSTPQTTITQPGQEGGM---PLLPVAVAVVVAASVSILVYLL 1127
                                        4444444443333333..33333444445666667777777666666653...4456666666666666666444 PP

>> SPESP1  Sperm equatorial segment protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.7   0.00043      0.85     103     183 ..    1005    1092 ..    1001    1102 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00043
                            SPESP1  103 Wsik.PnnvsvvLhte.ePyiek..ePepepePelepeveeeeskqlsea........sesstspavtsakpsvv 165 
                                        W+++ P+n sv + ++  Pyi     P p+ + ++++  + ++ +q            ++++t++++t+++ +++
  gi|320100315|ref|YP_004175907.1| 1005 WQVNvPSNYSVAMLANvIPYILDvlAPTPQEQYQMLTSFDAANGRQALLRgygatppsTTTTTTTTTTTTTTTTT 1079
                                        5554499***97666526***997788888888888888766666654334655444322222222222223333 PP

                            SPESP1  166 tlkkstdldvsteseDvP 183 
                                        t++++t+  +       P
  gi|320100315|ref|YP_004175907.1| 1080 TTTTTTTTTT-----STP 1092
                                        3333333333.....333 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  24.3   0.00063       1.3     671     705 ..    1057    1093 ..    1035    1113 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00063
                            SSP160  671 gsvpdeattttssttttttttttaaptt..tttkaan 705 
                                        g+ p ++tttt++tttttttttt++ tt  ttt + +
  gi|320100315|ref|YP_004175907.1| 1057 GATPPSTTTTTTTTTTTTTTTTTTTTTTttTTTSTPQ 1093
                                        6666555555555544444444443333003333333 PP

>> FSA_C  Fragile site-associated protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.7   0.00061       1.2     561     596 ..    1058    1094 ..    1007    1113 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00061
                             FSA_C  561 siaiattasavelnda.tsstiasaatasslsstkst 596 
                                        ++  +tt+++++  ++ t++t+++++t+++++st+ t
  gi|320100315|ref|YP_004175907.1| 1058 ATPPSTTTTTTTTTTTtTTTTTTTTTTTTTTTSTPQT 1094
                                        3333333332222222022222222233333333322 PP

>> AJAP1_PANP_C  AJAP1/PANP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  15.8    0.0017       3.3      23      64 ..    1056    1098 ..    1041    1125 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                      AJAP1_PANP_C   23 tlstkasrtttvatttstttrltqrtltvvttpepr.rlstte 64  
                                        +++t  s+ttt++ttt+ttt++t++t+t++tt++++ + + t+
  gi|320100315|ref|YP_004175907.1| 1056 YGATPPSTTTTTTTTTTTTTTTTTTTTTTTTTTTSTpQTTITQ 1098
                                        5556666444444444444333333333333332220222233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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):               9  [number of targets reported over threshold]
# CPU time: 0.87u 0.33s 00:00:01.20 Elapsed: 00:00:00.48
# Mc/sec: 7104.88
//
Query:       gi|320100316|ref|YP_004175908.1|  [L=74]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 556.80
//
Query:       gi|320100317|ref|YP_004175909.1|  [L=411]
Description: ORC complex protein Cdc6/Orc1 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-17   63.7   1.3    4.7e-17   61.7   0.7    2.2  2  Cdc6_C       CDC6, C terminal winged helix domain
    8.5e-10   39.3   0.5    2.2e-08   34.7   0.1    2.8  2  AAA_16       AAA ATPase domain
    9.1e-10   38.9   0.0    3.5e-09   37.0   0.0    1.9  2  AAA_22       AAA domain
    2.9e-05   24.1   0.0    5.4e-05   23.2   0.0    1.4  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
     0.0012   18.6   0.0     0.0026   17.5   0.0    1.6  1  AAA_24       AAA domain
     0.0052   17.2   0.0      0.012   16.1   0.0    1.6  1  AAA          ATPase family associated with various cellular a
     0.0092   16.2   1.1      0.018   15.3   0.1    2.0  2  AAA_28       AAA domain
     0.0096   15.3   0.3       0.19   11.1   0.1    2.6  3  ATPase       KaiC
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.028   14.8   0.0    1.6  2  AAA_19       AAA domain
      0.045   14.1   0.3       0.13   12.6   0.3    1.8  1  AAA_assoc_2  AAA C-terminal domain
       0.05   13.0   0.0      0.087   12.2   0.0    1.3  1  TniB         Bacterial TniB protein
      0.054   13.4   0.0      0.097   12.6   0.0    1.5  1  NACHT        NACHT domain
      0.054   13.6   0.3         16    5.7   0.1    3.1  3  TIP49_C      TIP49 AAA-lid domain
      0.083   12.1   0.0       0.21   10.8   0.0    1.6  1  NB-ARC       NB-ARC domain
       0.11   11.6   0.0       0.19   10.8   0.0    1.3  1  T2SSE        Type II/IV secretion system protein
       0.14   12.1   0.0       0.34   10.8   0.0    1.8  1  NTPase_1     NTPase
       0.14   11.3   0.1       0.38    9.9   0.0    1.8  2  DUF815       Protein of unknown function (DUF815)


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 ?   -0.9   0.0       1.6   1.7e+03      27      50 ..     271     294 ..     270     295 .. 0.90
   2 !   61.7   0.7   4.4e-20   4.7e-17       1      80 [.     315     393 ..     315     397 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                                       HHHHHTT-----HHHHHHHHHHHH CS
                            Cdc6_C  27 slCesegvdpltqrevsdllseLe 50 
                                       +++e+eg++ lt + v++ +s+L+
  gi|320100317|ref|YP_004175909.1| 271 DIAEREGARRLTVEHVRKAISRLS 294
                                       6899*************9999985 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 4.4e-20
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+++v+llr+++ + v +gev+e+Y+ lC+ +g +p+ +++ ++++++L  lgi+++++++   r grt+ is+ + 
  gi|320100317|ref|YP_004175909.1| 315 LLSIVRLLRRRNVKGVEMGEVEEEYRLLCNTYGETPRRHTQLYEYVRNLRRLGIVDTTVKNVENR-GRTTIISIPYG 390
                                       89**********************************************************99775.********998 PP

                                       CHH CS
                            Cdc6_C  78 pdd 80 
                                       p +
  gi|320100317|ref|YP_004175909.1| 391 PLE 393
                                       865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.1   2.1e-11   2.2e-08       2     150 ..      34     161 ..      33     187 .. 0.67
   2 ?   -0.2   0.0       1.1   1.1e+03      56      58 ..     293     295 ..     196     351 .. 0.61

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.1e-11
                            AAA_16   2 lvGReeeleqLlsalervrsgrp...elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysa.la 73 
                                       l++R+eel+ L+s+++ + ++ +   + vl++G  G+GK++lvr++++     g  +++r++ ++l      +   +
  gi|320100317|ref|YP_004175909.1|  34 LPYRDEELRSLASYFRHLVTDPGsiaQRVLVTGGLGTGKTTLVRMFAT-----GfTHVARERGVSL------DYiHV 99 
                                       899*************555554458**********************8.....4445677777777......33367 PP

                            AAA_16  74 qalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade. 149
                                       ++   ++l+  ++d+a++  l        +  +           + +e +  +l++l++++r  ++vlDd++ + + 
  gi|320100317|ref|YP_004175909.1| 100 NCYRSRTLFSIVHDAASQLGLT-------TPSR---------GFSPREIVDMILSFLEENDRYAIMVLDDFHYFASv 160
                                       7776777777777772221111.......1111.........245566666666999999999*********88774 PP

                            AAA_16 150 a 150
                                        
  gi|320100317|ref|YP_004175909.1| 161 V 161
                                       2 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                            AAA_16  56 lrg 58 
                                       l+ 
  gi|320100317|ref|YP_004175909.1| 293 LSR 295
                                       122 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   3.3e-12   3.5e-09       8     128 ..      62     187 ..      58     192 .. 0.90
   2 ?   -1.8   0.0       3.2   3.4e+03      71      91 ..     274     295 ..     234     329 .. 0.63

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3.3e-12
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                       ++vtG  GtGKTtl+r+++  ++ +a  +  + ++++v++  s ++ ++ ++ +++lgl + +++ s +e+++++  
  gi|320100317|ref|YP_004175909.1|  62 VLVTGGLGTGKTTLVRMFATGFTHVARERGVSLDYIHVNCYRSRTLFSIVHDAASQLGLTTPSRGFSPREIVDMILS 138
                                       689*******************98887777999999***************************************** PP

                            AAA_22  85 alraravielliiDEaqhlrs...eealeeLrsllnl..srkgvqliLv 128
                                        l++ ++ +++++D+++++ s    e + ++ ++++   ++  + l+++
  gi|320100317|ref|YP_004175909.1| 139 FLEENDRYAIMVLDDFHYFASvvgRESVYFIARMHEAgdGSRRLNLVFI 187
                                       ******************9735559999999999888777777777765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.2
                            AAA_22  71 erlsseell.ealeqalrarav 91 
                                       er   ++l  e++++a+++ ++
  gi|320100317|ref|YP_004175909.1| 274 EREGARRLTvEHVRKAISRLSR 295
                                       3333444444444444444333 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.1e-08   5.4e-05       5      68 ..      39     112 ..      36     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.1e-08
                                       HHHHHHHHHHHHCH......TEEEEEEESTTSSHHHHHHHHHHHTT--...----TTTTSEEEEEE..SS.EEE CS
                              TsaE   5 eetealgkklakal......gdvilLeGdLGaGKTtlvrglakalgve...evkSPTFtlveeYelekeg.lyH 68 
                                       ee+++l++ + + +      ++ +l +G LG+GKTtlvr +a ++ +    +  S  +  v+ Y++++   ++H
  gi|320100317|ref|YP_004175909.1|  39 EELRSLASYFRHLVtdpgsiAQRVLVTGGLGTGKTTLVRMFATGFTHVareRGVSLDYIHVNCYRSRTLFsIVH 112
                                       56777777777755666444445**********************88446778899999999997643325666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.4e-06    0.0026       2      81 ..      59     161 ..      58     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                            AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie........................swedfld 54 
                                       ++++l++G  g+GKTtl++++   +  +  e+G+ sld +++++ +                        s  +++d
  gi|320100317|ref|YP_004175909.1|  59 AQRVLVTGGLGTGKTTLVRMFATGFTHVARERGV-SLDYIHVNCYRsrtlfsivhdaasqlglttpsrgfSPREIVD 134
                                       579*******************************.999999998888876666666666666666666665566666 PP

                            AAA_24  55 evvelaaeladyktlviDtideleelc 81 
                                        + ++ +e+++y + v+D    + + +
  gi|320100317|ref|YP_004175909.1| 135 MILSFLEENDRYAIMVLDDFHYFASVV 161
                                       666669999999999999876666555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-05     0.012       1      98 [.      62     181 ..      62     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                                       EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS.................STTHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsellsk.................yvgesekkirelfk 51 
                                       vl++G  GtGKT+l++  a+ +         + +++ +++ + +                     g s+++i +++ 
  gi|320100317|ref|YP_004175909.1|  62 VLVTGGLGTGKTTLVRMFATGFthvarergvSLDYIHVNCYRSR-TlfsivhdaasqlglttpSRGFSPREIVDMIL 137
                                       799*****************964444444334667888877777.34777888888888888899999999988887 PP

                                       HHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA  52 eakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                       +  e++ +  i+++D+++ +a+       +e+   ++ + ++ dg ++
  gi|320100317|ref|YP_004175909.1| 138 SFLEENdRYAIMVLDDFHYFASVV----GRESVYFIARMHEAGDGSRR 181
                                       754555356999999999987766....44444555555555555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.7e-05     0.018       1      29 [.      61      89 ..      61     100 .. 0.83
   2 ?   -2.0   0.1       3.6   3.8e+03     103     147 ..     303     348 ..     268     356 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                            AAA_28  1 kivitGgestGKTtlleaLaargypvvpE 29
                                      ++ +tGg +tGKTtl++ +a   + v +E
  gi|320100317|ref|YP_004175909.1| 61 RVLVTGGLGTGKTTLVRMFATGFTHVARE 89
                                      689**************999766666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                            AAA_28 103 aarekrydl.vfllppapeidddgeRredleereaiderlrealre 147
                                       a+r +  +   +ll  +  +++ ++   ++ e e+ +++l++++ e
  gi|320100317|ref|YP_004175909.1| 303 AIRYSPLHElLLLLSIVRLLRRRNVKGVEMGEVEEEYRLLCNTYGE 348
                                       4444444442444444444466666666666777777777777665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00018      0.19      20      41 ..      60      81 ..      50      96 .. 0.84
   2 ?   -1.6   0.0       1.3   1.4e+03     141     163 ..     130     152 ..     110     166 .. 0.85
   3 ?    0.8   0.0      0.25   2.6e+02     156     193 ..     263     299 ..     259     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                            ATPase 20 rvvlitGepGtGKtifalqFli 41
                                      + vl+tG+ GtGKt+++  F+ 
  gi|320100317|ref|YP_004175909.1| 60 QRVLVTGGLGTGKTTLVRMFAT 81
                                      569**************99986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                            ATPase 141 ReilrqlvrvlkklgvTailvse 163
                                       Rei++ ++++l++++  ai+v +
  gi|320100317|ref|YP_004175909.1| 130 REIVDMILSFLEENDRYAIMVLD 152
                                       99999999******999999987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.25
                            ATPase 156 vTailvsekssseeaaggygveefivdgvivLdlkeie 193
                                       +T++lv+    + e+a +  ve+ + + + +L ++ ++
  gi|320100317|ref|YP_004175909.1| 263 LTTLLVAGDIAEREGARRLTVEH-VRKAISRLSREIER 299
                                       79999999999999999999999.77777778755444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.7e-05     0.028      11      53 ..      60     105 ..      53     246 .. 0.86
   2 ?   -2.9   0.0       7.6     8e+03      43      65 ..     278     300 ..     255     328 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiv...allvelggvkpeeillvaftgr 53 
                                       + +lvt+G GtGKT+++++     +++ +++gv+++ i + ++ +r
  gi|320100317|ref|YP_004175909.1|  60 QRVLVTGGLGTGKTTLVRMFAtgfTHVARERGVSLDYIHVNCYRSR 105
                                       6799***********9997651115777777777777776666665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.6
                            AAA_19  43 eeillvaftgrAakelrerlaal 65 
                                       ++ l v   ++A ++l+ +++ +
  gi|320100317|ref|YP_004175909.1| 278 ARRLTVEHVRKAISRLSREIERV 300
                                       55566666677777777766544 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00013      0.13       8      67 ..     238     302 ..     233     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   8 eddalealael......adGDaRkaLnlLElaaeaaeakegkieitledleealqrkalryDkagd 67 
                                       +++ale++ae+       +G aR aL++L +a + ae+ eg +++t e++++a++r ++ +++  d
  gi|320100317|ref|YP_004175909.1| 238 DEEALEFIAEYegvdknGEGNARHALTTLLVAGDIAER-EGARRLTVEHVRKAISRLSREIERVSD 302
                                       666667766652222225799********999999986.9**************999888877666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.2e-05     0.087      20     133 ..      45     159 ..      36     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                              TniB  20 lerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealga 96 
                                        + +++L++ p +   + +l+ G   +GKt++v+ Fa   ++  +e+  +++ ++v++  + +   + +    +lg 
  gi|320100317|ref|YP_004175909.1|  45 ASYFRHLVTDPGSIA-QRVLVTGGLGTGKTTLVRMFATGFTHVARERGVSLDYIHVNCYRSRTLFSIVHDAASQLGL 120
                                       556778888888776.89*********************99999999999999999999999999999999999998 PP

                              TniB  97 plkara.rvskleqqvlrllrelk.vrvLiiDEihnlla 133
                                        + +r  +  ++ +++l++l+e +   ++++D +h + +
  gi|320100317|ref|YP_004175909.1| 121 TTPSRGfSPREIVDMILSFLEENDrYAIMVLDDFHYFAS 159
                                       887776577788999999998764278999999997765 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      97 ..      61     161 ..      60     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-05
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C....CH CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgnarsladllfsqlpepaapvse....vw 73 
                                        v+++G  G GKTtL++ +a+   +   ++g   +++ + + r+++  + +   a +l    p  +  ++e    + 
  gi|320100317|ref|YP_004175909.1|  61 RVLVTGGLGTGKTTLVRMFATGFTHVARERGVsLDYIHVNCYRSRTLFSIVHDAASQLGLTTPSRGFSPREivdmIL 137
                                       689*****************998887766665355555555555555555577777777777777777777666566 PP

                                       HHHCCSCCCEEEEEE-STT-SS-T CS
                             NACHT  74 avllelperlLlilDglDelvtdl 97 
                                       ++l e+ + + ++lD++ ++++  
  gi|320100317|ref|YP_004175909.1| 138 SFLEENDRYAIMVLDDFHYFASVV 161
                                       666677777778888877777655 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.4   2.6e+03      31      52 ..     145     166 ..     141     168 .. 0.88
   2 ?    5.7   0.1     0.016        16      29      60 ..     258     289 ..     223     293 .. 0.75
   3 ?    4.2   0.1     0.044        47      34      63 ..     313     341 ..     297     343 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                           TIP49_C  31 RYaiqLltpasilakkrkkkev 52 
                                       RYai  l   + +a++ ++++v
  gi|320100317|ref|YP_004175909.1| 145 RYAIMVLDDFHYFASVVGRESV 166
                                       9******999999999888877 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                           TIP49_C  29 SLRYaiqLltpasilakkrkkkevevedveev 60 
                                         R a+  l +a  +a+++++++ +ve+v+++
  gi|320100317|ref|YP_004175909.1| 258 NARHALTTLLVAGDIAEREGARRLTVEHVRKA 289
                                       46999999999******************987 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.044
                           TIP49_C  34 iqLltpasilakkrkkkevevedveeveeL 63 
                                       + Ll+++++l ++r+ k ve+ +vee ++L
  gi|320100317|ref|YP_004175909.1| 313 LLLLSIVRLL-RRRNVKGVEMGEVEEEYRL 341
                                       4577777777.6777888********9988 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.21      22     111 ..      61     153 ..      44     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilkeLslseddleekeeveslkrk 95 
                                        v + G  G GKttl++     + +v ++      ++ v   ++ +  +i+++ + +L+l+      ++ +e + ++
  gi|320100317|ref|YP_004175909.1|  61 RVLVTGGLGTGKTTLVRMFATGFTHVARERGvslDYIHVNCYRSRTLFSIVHDAASQLGLT-TPSRGFSPRE-IVDM 135
                                       57889999**********99999999885543134566666788888899999999**999.6666777788.9*** PP

                                       HHHHCCCT.TE.EEEEEE CS
                            NB-ARC  96 lvrlLltk.rf.llvlDD 111
                                       +  +L++  r+ ++vlDD
  gi|320100317|ref|YP_004175909.1| 136 ILSFLEENdRYaIMVLDD 153
                                       ******999774889**9 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.19     128     148 ..      58      78 ..      28      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                             T2SSE 128 erglilvsGgTgsGKttllya 148
                                         + +lv+Gg g+GKttl+ +
  gi|320100317|ref|YP_004175909.1|  58 IAQRVLVTGGLGTGKTTLVRM 78 
                                       45678************9865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00032      0.34       1      21 [.      61      81 ..      61     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                                      EEEEE--TTSSHHHHHHHHHH CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvle 21
                                      +v++TG  G+GKtTlv+  + 
  gi|320100317|ref|YP_004175909.1| 61 RVLVTGGLGTGKTTLVRMFAT 81
                                      689*************87654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00036      0.38      50      79 ..      56      85 ..      32     117 .. 0.76
   2 ?   -2.6   0.2       2.3   2.5e+03      95     117 ..     133     155 ..     131     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00036
                            DUF815 50 glpannvLLwGarGtGKSslvkallneyae 79
                                      g  a+ vL++G  GtGK +lv+   + +++
  gi|320100317|ref|YP_004175909.1| 56 GSIAQRVLVTGGLGTGKTTLVRMFATGFTH 85
                                      7789******************98766554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                            DUF815  95 lpklvellrerperfilfvDDLs 117
                                       ++++++ l+e+++  i+++DD  
  gi|320100317|ref|YP_004175909.1| 133 VDMILSFLEENDRYAIMVLDDFH 155
                                       678999999999999*****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2777.32
//
Query:       gi|320100318|ref|YP_004175910.1|  [L=162]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1140.48
//
Query:       gi|320100319|ref|YP_004175911.1|  [L=843]
Description: nuclease [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   28.9   0.0    3.8e-06   27.3   0.0    1.9  1  SNase       Staphylococcal nuclease homologue
  ------ inclusion threshold ------
       0.22   11.0   3.5        1.1    8.8   3.5    2.3  1  SKG6        Transmembrane alpha-helix 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 !   27.3   0.0   4.2e-10   3.8e-06       1      84 [.      70     155 ..      70     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.2e-10
                                       EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHH.CSSEEEEE-S..SBSTTSEEEEEEEET.....TEEHHHHH CS
                             SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlq.kkvvvleldk..kkDkygrllayvyln.....kknineeL 69 
                                       +vrL++idaPe +         g +A+  l+ l+ q   v +l  d+    D ygr+++ vy+        n+n+ L
  gi|320100319|ref|YP_004175911.1|  70 TVRLADIDAPEIN------TSEGAWAAGNLSILLGQyGPVLYLDIDSvrGVDDYGRIIGVVYIRynsthLLNVNKWL 140
                                       69***********......33367777777666654135666666668889************99999999****** PP

                                       HHTTSSEE---BTTS CS
                             SNase  70 vkeGlArvyevyekn 84 
                                       v +G+A+++++ +++
  gi|320100319|ref|YP_004175911.1| 141 VDNGYAQIVNFTDNE 155
                                       *******99977753 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.5   0.00012       1.1      11      32 ..     819     840 ..     816     841 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00012
                              SKG6  11 aIavaVaVPVaViiivLlaili 32 
                                       a+ ++V+ +VaV+++++l +l+
  gi|320100319|ref|YP_004175911.1| 819 AVSAGVGLGVAVVLAAVLRFLV 840
                                       899**************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (843 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2219  (0.123766); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); 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):               2  [number of targets reported over threshold]
# CPU time: 1.27u 0.34s 00:00:01.61 Elapsed: 00:00:00.53
# Mc/sec: 4776.98
//
Query:       gi|320100320|ref|YP_004175912.1|  [L=89]
Description: 30S ribosomal protein S25 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   43.8   0.0    2.5e-11   43.7   0.0    1.0  1  Ribosomal_S25   S25 ribosomal protein
      0.008   15.5   0.0     0.0088   15.3   0.0    1.0  1  EAP30           EAP30/Vps36 family
  ------ inclusion threshold ------
      0.046   13.9   0.1      0.062   13.5   0.1    1.2  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.083   12.8   0.3       0.14   12.1   0.3    1.4  1  MarR_2          MarR family
        0.1   12.7   0.0       0.12   12.5   0.0    1.2  1  PapA_C          Phthiocerol/phthiodiolone dimycocerosyl trans


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   6.9e-15   2.5e-11      20      99 ..       3      86 ..       1      88 [. 0.90

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 6.9e-15
                     Ribosomal_S25 20 kkKKwskgkvkdklnnavlfd..ketydkllkevpky..klitpsvvserlkingslArraLreleekgliklvskhra 94
                                      +kKK + ++  +k ++a +f+  ++++++l + v k   k+ tp+++++ l+i++s+Ar++Lre e++g++kl+s  r+
  gi|320100320|ref|YP_004175912.1|  3 EKKKPAPQTPSEKGARANIFEpsEDLLKRLKTAVSKQgvKYYTPYTLAQELNIRISVARKLLREAEKRGIVKLYSGGRR 81
                                      69999999999999999999644789********996669*************************************** PP

                     Ribosomal_S25 95 qviYt 99
                                        +Y 
  gi|320100320|ref|YP_004175912.1| 82 APVYI 86
                                      ***96 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.5e-06    0.0088     183     232 ..      28      73 ..      10      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-06
                             EAP30 183 vakrlvsllaekssgggvtaselaeeeenlgwsvarakeaLeelereGll 232
                                       ++krl++ + +++  ++ t   la+e   l++ +++a++ L+e+e++G++
  gi|320100320|ref|YP_004175912.1|  28 LLKRLKTAVSKQGV-KYYTPYTLAQE---LNIRISVARKLLREAEKRGIV 73 
                                       44555444444444.89******999...*******************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 ?   13.5   0.1   1.7e-05     0.062      17      53 ..      37      74 ..      21      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                                      HH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 17 se.ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      s+ + k+ ++  la++Ln++ s + + l++ ek G v+
  gi|320100320|ref|YP_004175912.1| 37 SKqGVKYYTPYTLAQELNIRISVARKLLREAEKRGIVK 74
                                      345789999**************************997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   3.9e-05      0.14      23      61 ..      45      81 ..      37      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      t+  la++l++  s + ++l++++++G v   +g   +R
  gi|320100320|ref|YP_004175912.1| 45 TPYTLAQELNIRISVARKLLREAEKRGIVKLYSG--GRR 81
                                      66789************************98876..666 PP

>> PapA_C  Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05      0.12      75     117 ..      31      73 ..       6      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                                       EEEEEBSS---EEEEEEEETTEEEEEEECS.....-SSCHHHH CS
                            PapA_C  75 aapapaasrevviylvstfngrLsIellhssgtfsdaaaarll 117
                                       +  ++ +++ v+ y+ +t+++ L+I++ + ++  ++a+ + ++
  gi|320100320|ref|YP_004175912.1|  31 RLKTAVSKQGVKYYTPYTLAQELNIRISVARKLLREAEKRGIV 73 
                                       5667788899*******************99999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 662.17
//
Query:       gi|320100321|ref|YP_004175913.1|  [L=138]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  103.6   0.0    8.6e-30  103.3   0.0    1.1  1  CTP-dep_RFKase  Domain of unknown function DUF120
    0.00057   19.8   0.0      0.021   14.8   0.0    2.5  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


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 !  103.3   0.0   9.6e-34   8.6e-30       1     121 []      17     129 ..      17     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 9.6e-34
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       V++GlgeG +y+sl  y++++++ lg+epypGTLN++l ++ +    +++  ++i++   e+++ ++g+v +++a i
  gi|320100321|ref|YP_004175913.1|  17 VIEGLGEGCRYISL--YRDAIRRALGIEPYPGTLNIELIDPPV---FNINMGEAIRV---ESPGPEYGDVLAVKAWI 85 
                                       89************..**********************99944...45666778877...59*************** PP

                                       CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                    CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                       ++i++++++p +t+++ +++E++++++LR++l+++ gd +e++v
  gi|320100321|ref|YP_004175913.1|  86 NSIPVYIIRPVKTRHPASIIEVVSQHNLRRSLGIRTGDIIEIQV 129
                                       ******************************************97 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.019   1.7e+02      14      31 ..      34      52 ..      34      57 .. 0.80
   2 !   14.8   0.0   2.3e-06     0.021      15      34 ..     113     132 ..     111     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.019
                                      CCHHHCCEEC.TCEEEEEE CS
                    MazE_antitoxin 14 evrfelgire.Gdevelev 31
                                      ++r++lgi++   ++ +e 
  gi|320100321|ref|YP_004175913.1| 34 AIRRALGIEPyPGTLNIEL 52
                                      68*******9977777765 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.3e-06
                                       CHHHCCEECTCEEEEEECTT CS
                    MazE_antitoxin  15 vrfelgireGdevelevdgd 34 
                                       +r++lgir Gd +e+ v+++
  gi|320100321|ref|YP_004175913.1| 113 LRRSLGIRTGDIIEIQVEEG 132
                                       79***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1107.96
//
Query:       gi|320100322|ref|YP_004175914.1|  [L=81]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 576.57
//
Query:       gi|320100323|ref|YP_004175915.1|  [L=608]
Description: tungsten-dependent formaldehyde:ferredoxin oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-110  369.9   0.4   1.8e-110  369.6   0.4    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.7e-73  246.7   0.1    2.6e-73  246.1   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 !  369.6   0.4    2e-114  1.8e-110       3     382 .]     220     594 ..     218     594 .. 0.96

  Alignments for each domain:
  == domain 1  score: 369.6 bits;  conditional E-value: 2e-114
                                       HHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EE CS
                            AFOR_C   3 gkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgr 79 
                                        +++++++ +s+  ++ + + GT++++++++++++lpt n++eg++e +e+isg+ +e+  +++++gC +C+++Cg+
  gi|320100323|ref|YP_004175915.1| 220 SEEAYRKLLESE-GYDYWIRQGTMATIQWSQQNSVLPTMNYREGVWELYETISGDLMEK-LKTDRRGCPYCNMQCGN 294
                                       567788888888.677999****************************************.9999989********** PP

                                       EEE......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS-- CS
                            AFOR_C  80 evkveegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdgle 156
                                       ++  + g++   +  +ye++a+lGsn+  +dl  + ++n+++d+lGlDtis+Gn+i+f+me++e+Gl+ +       
  gi|320100323|ref|YP_004175915.1| 295 VIADDAGEE---SELDYENVAMLGSNILLEDLRRVGEVNKMADKLGLDTISLGNAIGFYMEASERGLVRE------R 362
                                       ***988886...667*****************************************************99......8 PP

                                       --TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT..-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-S CS
                            AFOR_C 157 lefgdaeallellekiAkregigdllAeGvkrlaeklg..aeelamhvkGlelpaydprgakgmalaYatsnrGacH 231
                                       le+gd +a++e++ ++A+r+g+g+ +AeGv r++  lg  a ++amhvkGle++ay++++++gmalaYats+ Ga+H
  gi|320100323|ref|YP_004175915.1| 363 LEWGDFKAVREIVVDTAYRRGLGAFIAEGVMRMSTSLGgeALDFAMHVKGLEVSAYNCHTTPGMALAYATSSIGAHH 439
                                       9*************************************9999*********************************** PP

                                       GGG-THHHHS---TT--.HHHHHHHHHHHH.HHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHH CS
                            AFOR_C 232 lraylialeekvdplet.egkaelvkwfqd.ltalvdslglCkftseaeerldlelyakllsavtGidvteeellka 306
                                        +a+ i+ e k+d+ ++ ++k+e +++ q+ +  +++sl++C++++ +e  l++e y+k+lsavtG++++ +++ ++
  gi|320100323|ref|YP_004175915.1| 440 KDAWIISYEVKTDRTSYsREKVERLIFLQNiRGGMFESLTTCRLPW-VELGLNIEYYPKMLSAVTGLEWSINDMHTV 515
                                       *****************99***********8899************.8999************************** PP

                                       HHHHHHHHHHHHHHH..T--HHHS---HHHHHS---SSTTTT---...-HHHHHHHHHHHHT--TTS---HHHHHHC CS
                            AFOR_C 307 GeRiynleRlfnlre..Gltrkddtlperlleeplkegpakgkvl.edeleemldeyYelrGWdetGvPtketlkrL 380
                                       ++Riy+l R+f++re  G +r+ d  p+r+++ pl++gp +g++l   ++e+ml++yYe+rGW+e+G+P +etl +L
  gi|320100323|ref|YP_004175915.1| 516 ADRIYTLIRAFWIREhsGWSRSMDYPPARWFKHPLTKGPYAGHHLdPLRYEKMLEAYYEMRGWNENGIPRRETLLKL 592
                                       ***************55566888*********************97777**************************** PP

                                       T- CS
                            AFOR_C 381 gL 382
                                       gL
  gi|320100323|ref|YP_004175915.1| 593 GL 594
                                       *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 !  246.1   0.1   2.9e-77   2.6e-73       1     198 []       6     205 ..       6     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.1 bits;  conditional E-value: 2.9e-77
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gk+l vdL++ k+++  l++e++++y+Ggrgla++ll+d vppg+dplsp n lv+a Gpl+g p+p+sg+lvv++k
  gi|320100323|ref|YP_004175915.1|   6 GKVLLVDLTRMKTREIILDPETYRSYIGGRGLAVRLLWDLVPPGADPLSPYNALVVASGPLSGLPLPSSGKLVVASK 82 
                                       79*************************************************************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTSEEE. CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgdkva. 153
                                       sPlt+++g+ n+G  ++++lk++G+daiv++G+++kpvy+++e++kve+++ae+lwgldt++t+++l +e+g+++  
  gi|320100323|ref|YP_004175915.1|  83 SPLTNGYGDGNIGTMASHHLKHSGFDAIVVTGASRKPVYIYVENEKVEVRSAEHLWGLDTFTTEDKLVREHGRNIGi 159
                                       *************************************************************************6655 PP

                                       .EE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                            AFOR_N 154 .viGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                         iGpaGe++v++A+++ ++gr+ gr G+GavmgsK+lkaivv+gt
  gi|320100323|ref|YP_004175915.1| 160 lEIGPAGEHMVKYATVISQKGRSGGRPGIGAVMGSKRLKAIVVKGT 205
                                       5***************777*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4256.65
//
Query:       gi|320100324|ref|YP_004175916.1|  [L=431]
Description: phosphoadenosine phosphosulfate reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-36  124.2   0.0    7.5e-36  123.8   0.0    1.2  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   4.2e-40   7.5e-36       2     173 ..     212     384 ..     211     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 4.2e-40
                                       EEEE--SSCTCHHHHHHHHHHCTTH..EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-T CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv..pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgss 76 
                                       ++vs+sgG+ds+++l La ++ +p+   vv+vdtg   p + e+ +++  r+g++  v+++  +  ++i+  + +++
  gi|320100324|ref|YP_004175916.1| 212 IAVSYSGGADSTATLMLAGRVIDPGrlIVVYVDTGMDLPGVKEYSMRVLGRLGVNPYVVSSGLDPLAEIASRGLPTR 288
                                       789*********************7446************************************************* PP

                                       HHHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT- CS
                       PAPS_reduct  77 lyeeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilreni 153
                                         ++ + ri K+epl++ +++++ ++++ GaR  es+ ra++p + ++  ++ ++rv+P+ +W+   v+ y+ +e++
  gi|320100324|ref|YP_004175916.1| 289 ENRW-CTRILKLEPLRRFYSEHGVKLVIEGARSRESSGRAATPRIGENPLIPGVIRVLPIKHWSRLLVQLYLISEGV 364
                                       ****.************************************************************************ PP

                                       -B-CCCCTT-SS--BCTTB- CS
                       PAPS_reduct 154 pynpLydqgfrsiGcvpctg 173
                                       ++npLyd+gf+++Gc+ c++
  gi|320100324|ref|YP_004175916.1| 365 ELNPLYDEGFTRLGCILCPA 384
                                       *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3071.11
//
Query:       gi|320100325|ref|YP_004175917.1|  [L=298]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.064   12.8   0.0       0.11   12.0   0.0    1.3  1  Dam           DNA N-6-adenine-methyltransferase (Dam)
      0.074   12.4   0.0        3.8    6.7   0.0    2.1  2  Amidohydro_1  Amidohydrolase family
       0.14   11.5   0.0       0.22   10.9   0.0    1.3  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> Dam  DNA N-6-adenine-methyltransferase (Dam)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.9e-05      0.11      99     129 ..      10      40 ..       5      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                               Dam  99 staWfkealedadevafitrgRisFisaetk 129
                                       s+ Wf+     ++  +fi++gRi+Fi ++ +
  gi|320100325|ref|YP_004175917.1|  10 SNLWFPVKTGVVKGCIFIEKGRIGFIGEHPE 40 
                                       889***999****************987655 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.005        30      12      77 ..      60     127 ..      58     146 .. 0.82
   2 ?    6.7   0.0   0.00064       3.8     278     343 ..     198     270 ..     164     271 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.005
                                       ECETTECSSS...GHHHHH......STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEE CS
                      Amidohydro_1  12 Hleqsllrga...tledwl......vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplgl 77 
                                       H++++ ++++   +l  ++      ++ ++++ ++e g+  a+++G+t+ + ++     + ea  eaa+el  g+
  gi|320100325|ref|YP_004175917.1|  60 HGFST-IVDVveyPLRRLRvgdlsvLSRDELKTVAEVGLINAVSNGITMPIIHSD----HSEAAVEAAREL--GV 127
                                       66544.566677777777788888999999******************9999999....899999999996..54 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00064
                                       CHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.CT.........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 278 gglslkealrmaTingAkalglddkvGsievGkdADlvvvdl.di.........laafvglkkdgnvkkvivkGkl 343
                                       +g+++++++r+ T  + + +g     G ++ G  ADl vvdl ++            +   ++  +++ v + G++
  gi|320100325|ref|YP_004175917.1| 198 AGVDAARLYRILTE-PYRLIGA--GEGYVDRGETADLQVVDLrNPvkasiirgeEDFWSTASRFTSPDLVLIHGEV 270
                                       66888888888885.8899998..78****************9556556677753333333344445666666655 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.7e-05      0.22      73      94 ..     116     137 ..      86     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHHHHTBSEEEEEBCCG CS
                      AP_endonuc_2  73 kraielaaaLGapllvlhpGta 94 
                                       + a+e+a++LG+pl+v+h G a
  gi|320100325|ref|YP_004175917.1| 116 EAAVEAARELGVPLIVIHGGEA 137
                                       6799**************9953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2185.52
//
Query:       gi|320100326|ref|YP_004175918.1|  [L=194]
Description: CDP-alcohol phosphatidyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-12   47.3   3.1    2.5e-12   47.3   3.1    2.6  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
        7.6    5.6   7.0         16    4.6   7.0    1.5  1  Bac_export_2     FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   3.1   2.8e-16   2.5e-12       2      66 .]      26      90 ..      25      90 .. 0.94
   2 ?   -0.7   4.5      0.29   2.6e+03      10      39 ..     149     174 ..     101     184 .. 0.64

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.8e-16
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                       P a+T++++l  ++ ++++++++ ++l ++++ ++s++DalDG +AR ++ +s++G++lDs +D
  gi|320100326|ref|YP_004175918.1| 26 SPHALTVSSMLVLLVGVFVFAYTSNTLLYLIFIAASSMLDALDGTVARVTGRTSRFGAFLDSTVD 90
                                      699*********9999999999999***************************999*******998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHGGGS-H.....HHHHHHHHHHHH CS
                   CDP-OH_P_transf  10 rlllsvlailllltyyp...lvlailllliasl 39 
                                       +++l    illl+        ++ illl++a+l
  gi|320100326|ref|YP_004175918.1| 149 GIVL----ILLLY---NasiHLAEILLLILAIL 174
                                       2232....32221...12323444444444443 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   7.0    0.0017        16      25     157 ..      30     186 ..      23     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0017
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................XXXXXXXXXXXXXXXXXX CS
                      Bac_export_2  25 kelssalvllaglllllllgpslveelaellrevlsa......................lelllelllallllllpl 79 
                                         +ss+lvll+g++++++++++l+  +  + +++l+a                      ++ ++++++   l +l +
  gi|320100326|ref|YP_004175918.1|  30 LTVSSMLVLLVGVFVFAYTSNTLLYLIFIAASSMLDAldgtvarvtgrtsrfgafldstVDRVNDAAMIWSLSILGF 106
                                       56788899999999999999888888888888888888999999999999998888777667788888888888888 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXX CS
                      Bac_export_2  80 llvlllaallanllqvgflfstkalkpklsklnplkglkrifslrslvellksllkvvlvgavaylvlks..eleel 154
                                         + +++ l++++l   +    ++l  +l  +  ++  +ri+++  ++ l  + + ++ +++++  +l++   l+++
  gi|320100326|ref|YP_004175918.1| 107 NQTYIVLLLVSSMLVSYVRARGESLGAQLMGIGLIERPERILGIVLILLLYNASIHLAEILLLILAILSAatVLQRI 183
                                       88999999999999999999999999999999999999999999888888887777766666655555542244555 PP

                                       XXX CS
                      Bac_export_2 155 lal 157
                                       l++
  gi|320100326|ref|YP_004175918.1| 184 LQV 186
                                       554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1468.81
//
Query:       gi|320100327|ref|YP_004175919.1|  [L=339]
Description: phosphoesterase RecJ domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0029   17.8   0.0     0.0046   17.2   0.0    1.3  1  DHH       DHH family
  ------ inclusion threshold ------
      0.046   14.1   0.6       0.17   12.3   0.4    2.0  2  DHHA1     DHHA1 domain
        3.9    7.7   5.0         10    6.4   0.1    3.0  3  DD_K      Dermaseptin


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 !   17.2   0.0   7.8e-07    0.0046       2      79 ..       8     152 ..       7     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.8e-07
                                       EEEE-ECSSSHHHHHH.HHHHHH...................................................... CS
                                       xxxxxxxxxxxxxxxx.xxxxxx...................................................... RF
                               DHH   2 ilivghknpDtDsigS.aialan...................................................... 23 
                                       +++   ++ D+D++ + a+ ++                                                       
  gi|320100327|ref|YP_004175919.1|   8 VFV--AGDWDADGVIAaALIVYSqekagqypleskavvdktpldpdrakyflanfkggydvavfldipysehlgnai 82 
                                       455..89*********5555555899999999999999999999999999999988888888888888888888888 PP

                                       ............CECS--TCGGCGCCHHCCCSEEEEEEE-S---S.....S---SS--EEEE-SSS-HHHHHH CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  24 ............llvDhneksqavegeakeeaedviiiDHHrlge.....efetlapilflnepvgstaeiva 79 
                                                   + vDh+ +s ++++   ++ +dv  iDH  +       e+++  + + +++ + s +e+v 
  gi|320100327|ref|YP_004175919.1|  83 kmmrnhfgvskiIFVDHHVTSLQKAK-ELQSIVDVALIDHRMPTAglvleELNR--RGISVHQRLRSFVEVVK 152
                                       8888888888888******9998877.688999*******98876665432222..23344455555555555 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.37   2.2e+03      39      76 ..      62      98 ..      44     115 .. 0.74
   2 ?   12.3   0.4   2.8e-05      0.17       9      83 ..     210     280 ..     206     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.37
                                      TCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEE CS
                             DHHA1 39 gvkvlvaevgeewdagalgiaadklksklkkpvivfva 76
                                      g   +++++ +      lg+a+ +++++++   i+fv 
  gi|320100327|ref|YP_004175919.1| 62 GGYDVAVFL-DIPYSEHLGNAIKMMRNHFGVSKIIFVD 98
                                      444445555.6667788999999999988887777765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEE CS
                             DHHA1   9 kelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdkv 83 
                                       ++++  +e  ++++ + ka el   a ++ g+  ++ +  ++w+++ +  +a+kl + lk pvi+++ ++++   
  gi|320100327|ref|YP_004175919.1| 210 SKVKAVIE-ERDKEVAEKAVELAVGAIKI-GDFRFIDAR-NKWKKRGVTALASKLSTILKAPVILLAGTNRE-YF 280
                                       55666664.55555556666777777777.888888888.8****************8888******99998.44 PP

>> DD_K  Dermaseptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.027   1.6e+02       1       6 [.     185     190 ..     185     191 .. 0.93
   2 ?    6.4   0.1    0.0017        10       1      13 [.     207     227 ..     207     233 .. 0.91
   3 ?   -2.2   0.2       0.8   4.8e+03       4       8 ..     262     266 ..     261     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.027
                              DD_K   1 GLWstI 6  
                                       +LWs+I
  gi|320100327|ref|YP_004175919.1| 185 ALWSKI 190
                                       7****9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0017
                              DD_K   1 GLWstIL.......Kevg.kA 13 
                                       +LWs+ +       Kev+ kA
  gi|320100327|ref|YP_004175919.1| 207 ALWSKVKavieerdKEVAeKA 227
                                       7*****************998 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.8
                              DD_K   4 stILK 8  
                                       stILK
  gi|320100327|ref|YP_004175919.1| 262 STILK 266
                                       9***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2677.35
//
Query:       gi|320100328|ref|YP_004175920.1|  [L=344]
Description: histone deacetylase superfamily protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-50  172.2   0.0    2.5e-50  171.7   0.0    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.0   1.4e-54   2.5e-50       1     301 [.      20     301 ..      20     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 1.4e-54
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHH...TTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeel...lkvHskeYlelleslsnelkkkeeakekeleeias 74 
                                       hpenp R+ +i+esl++s + +d + l  ++   t+e l   +++Hs++Y+ ++ +++ +   +             
  gi|320100328|ref|YP_004175920.1|  20 HPENPGRIPRIVESLRRS-S-IDYEWL-ESSVLNTREALeiaTRIHSRSYVGKILEMAGRAPLN------------- 80 
                                       9****************7.3.433322.222222233332259***********9988665443............. PP

                                       TSSSSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-.BTTB-B.....TTBSS-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxx RF
                     Hist_deacetyl  75 klldddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHa.kaseas.....GFClvNnvaiaikyl 145
                                          d+dt++s+++++ al + g + +++ +  +g     f ++rPpgHHa  +++a      GFC++Nn++ a+k  
  gi|320100328|ref|YP_004175920.1|  81 --IDEDTYISKDSVELALETLGESYRLALQQGNG---VVFYIARPPGHHAgVRGRATgartqGFCIFNNAVAAVKGF 152
                                       ..4689****************999987666655...899999*******988886666677*************** PP

                                       HHCC-SS-EEEEE-SSS--HHHHHHCTT-TTEEEEEEEE-..CCTSTT.SS--TT---SGGGTTSEEEEEE-TT-BH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 146 qakhelkrvailDvDvHhGnGteeafysdpdvltlSiHry..egifyP.gtgaledlgegkgkgfnlnvpleegtgd 219
                                        +  +l +va+lD+D+H+GnG  e++y  ++vl +++H+   +  ++P   g+   +g+g+g gf++ +ple+gtgd
  gi|320100328|ref|YP_004175920.1| 153 MD-RGLGKVAVLDFDAHYGNGSMEILYG-ARVLQVDLHQDtrTIPVFPlLPGS---VGSGEGYGFKVGIPLEPGTGD 224
                                       99.789********************96.89********95447889955555...58899**************** PP

                                       HHHHHHHHHCHHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 220 eeylkvfeeilrpvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnleal 296
                                       ++y++v+e +  +v+e+++P++ +vsaGfD+ +gd l +l l++  +++l ++++ l     ++v++leGGY+   l
  gi|320100328|ref|YP_004175920.1| 225 DSYVEVLEAVW-RVIERYNPEAFVVSAGFDGFRGDGLTDLVLTEYTFHRLGEMIRGLGV---PTVVVLEGGYSS-GL 296
                                       *******9988.899*******************************************9...89********96.55 PP

                                       HHHHH CS
                                       xxxxx RF
                     Hist_deacetyl 297 aravt 301
                                        ++v+
  gi|320100328|ref|YP_004175920.1| 297 DKGVA 301
                                       55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.42
# Mc/sec: 2469.83
//
Query:       gi|320100329|ref|YP_004175921.1|  [L=202]
Description: adenylyl cyclase CyaB [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-21   77.6   0.0    1.3e-21   77.3   0.0    1.1  1  CYTH      CYTH domain


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   7.3e-26   1.3e-21       3     152 ..      14     163 ..      12     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 7.3e-26
                                       EEEEEEEE-HHHHHHHHHH.HHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEE....EETTTEEEEEEEEECSS CS
                              CYTH   3 EvEvKflvsaaeyedlelr.laelrakeettveqrdtYydtpdrdlartdeaLRiR....raegdgeeltlKgpgvd 74 
                                       E+EvK++++++    +e + l + ++ +++    rd+Y+ +p+rdl+ +dea+R+R    r +g++ +lt+Kgp  +
  gi|320100329|ref|YP_004175921.1|  14 ETEVKLRITGDPGI-VE-EnLLSHGFIKVDECVERDIYFKHPCRDLSLSDEAVRLRyrscRNSGEHLVLTYKGPRIS 88 
                                       99******844433.33.458999999999999************************99877677777*******99 PP

                                       STEEEEEEEEC.CCEEECCCC..HHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEES CS
                              CYTH  75 gereevegevs.reEyeepls..daaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiEleve 148
                                       +e     g ++ r E+e+ l+  +   +++ll+  g+  +as++k+R +++ +g+e+++D+  ++ g ++E+El+  
  gi|320100329|ref|YP_004175921.1|  89 RE-----GVLKaRMEVEARLQpgEIHSMVKLLEYIGFPKLASFTKKRFIFHKDGLEATIDELMGV-GFFLEVELKKP 159
                                       95.....55555777777777677778999***********************************.********998 PP

                                       SHHH CS
                              CYTH 149 deee 152
                                       d  +
  gi|320100329|ref|YP_004175921.1| 160 DAVK 163
                                       8755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1441.37
//
Query:       gi|320100330|ref|YP_004175922.1|  [L=215]
Description: CRISPR-associated protein Cas4 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-06   27.6   0.0    5.4e-06   26.8   0.0    1.4  1  PDDEXK_3     PD-(D/E)XK nuclease superfamily
    1.5e-05   25.1   0.8      0.037   13.9   0.1    2.9  2  PDDEXK_1     PD-(D/E)XK nuclease superfamily
    0.00016   21.8   0.6    0.00041   20.5   0.6    1.6  1  Cas_Cas4     Domain of unknown function DUF83
     0.0032   17.7   0.0     0.0089   16.3   0.0    1.8  1  Tox-REase-9  Restriction endonuclease fold toxin 9
  ------ inclusion threshold ------
       0.18   11.6   0.0       0.32   10.8   0.0    1.5  1  Dna2         DNA replication factor Dna2


Domain annotation for each model (and alignments):
>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.5e-09   5.4e-06      28     108 ..      69     154 ..      61     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.5e-09
                          PDDEXK_3  28 ekaLaveLkkrglkveeqvelpvvYkgkevgeeyrlDllv.eekvivElKaveel....keeheaqllnYlkltklk 99 
                                       +k L+  Lk +g +ve+ ve+pv+ +g +   + r+D +    + +vE+K+ ++     k++h +ql  Yl++++++
  gi|320100330|ref|YP_004175922.1|  69 HKGLEEVLKGEGYEVEKSVEVPVEIDGARYIVKGRVDAYNpGTRTVVEIKSSRTSrgipKPHHVEQLNIYLNIMDVE 145
                                       7889999********************999888*****9977899*****97664223478999************* PP

                          PDDEXK_3 100 lGlliNFnk 108
                                        G+l+   +
  gi|320100330|ref|YP_004175922.1| 146 SGILVYVTS 154
                                       ****97665 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00079       2.8      10      49 ..      38      77 ..      34      87 .. 0.80
   2 !   13.9   0.1     1e-05     0.037     121     255 .]      91     199 ..      78     199 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00079
                          PDDEXK_1 10 fleCplrfflryllglre.eeeleap.dlGtlvHaaleefye 49
                                      + +C  ++++r   +++e +  +e++  lG+l+H+ lee+ +
  gi|320100330|ref|YP_004175922.1| 38 LVACSHKYHMR--RKYPElTIGFEPSmVLGELLHKGLEEVLK 77
                                      67899999996..56677889999988***********9987 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1e-05
                          PDDEXK_1 121 lefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkegl.QlllYllalaegeelkeegepagalylr 196
                                       +e++g ++ +kGr+D    + g+ ++++ K+++   +s       +++ Ql +Yl ++  +         + ++y+ 
  gi|320100330|ref|YP_004175922.1|  91 VEIDGARYIVKGRVDAY--NPGTRTVVEIKSSR---TSRGI-PKPHHVeQLNIYLNIMDVE--------SGILVYVT 153
                                       23335667799999995..56668999999999...44442.2456668999999999877........55555555 PP

                          PDDEXK_1 197 leepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskkCeyCpyksvCr 255
                                                ++v+++  ++ e    + ++  l+++ l+  +++r + +CeyC ++++C+
  gi|320100330|ref|YP_004175922.1| 154 S-------DKIVEYV-IPR-E----RVDVTGLVRNTLGNLVHPRYEWECEYCVFRRLCP 199
                                       5.......5666666.222.2....23444555555666779999999**********7 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.6   1.1e-07   0.00041       6     160 ..      36     198 ..      31     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                          Cas_Cas4   6 qyyliCkrklwlish..eitleensetvelGkllhe........esyerekkevel.se........sikiDvveke 63 
                                         ++ C  k  +  +  e+t+  + ++v  G+llh+        e ye e k+ve+  e        ++++D  +  
  gi|320100330|ref|YP_004175922.1|  36 TDLVACSHKYHMRRKypELTIGFEPSMVL-GELLHKgleevlkgEGYEVE-KSVEVpVEidgaryivKGRVDAYN-- 108
                                       55666666666666555566666655555.*****977777666444443.333332234569999999****99.. PP

                          Cas_Cas4  64 keklvvvEvKkskkk....eeaaklQllyYlllLekkgveikeGvleypkekkreevelteelreelekaikeieei 136
                                       +++ +vvE+K+s+      ++ +  Ql  Yl +++     +++G+l y+++ k +e  + +e+ +    ++  +++ 
  gi|320100330|ref|YP_004175922.1| 109 PGTRTVVEIKSSRTSrgipKPHHVEQLNIYLNIMD-----VESGILVYVTSDKIVEYVIPRERVD----VTGLVRNT 176
                                       9************997887778899*******998.....5667888888888887777444332....22233333 PP

                          Cas_Cas4 137 issekppkvkkkkiCkkCayaelC 160
                                       + +    ++ ++  C+ C ++ lC
  gi|320100330|ref|YP_004175922.1| 177 LGN--LVHPRYEWECEYCVFRRLC 198
                                       322..3334555666666666666 PP

>> Tox-REase-9  Restriction endonuclease fold toxin 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.5e-06    0.0089      15      79 ..      80     148 ..      58     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                       Tox-REase-9  15 dykaekvlg.vgrekEfklpsgkRiDfvdfetkiiyELKPn.npraikr..GlkqlevYkqeleseyGk 79 
                                        y++ek+ +  +++   + + + R+D+ +++t++++E+K   + r+i +   + ql+ Y + ++ e+G 
  gi|320100330|ref|YP_004175922.1|  80 GYEVEKSVEvPVEIDGARYIVKGRVDAYNPGTRTVVEIKSSrTSRGIPKphHVEQLNIYLNIMDVESGI 148
                                       35544444434555556667788****************752789998622578*******99999885 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     9e-05      0.32      60     108 ..      35      84 ..      31     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9e-05
                              Dna2  60 vanslsClRravLqerl.kvsgesskamliGtilHelfqkalleeeldke 108
                                       v++ + C+ +  ++ ++ + +   + +m++G++lH+ ++++l+ e ++ e
  gi|320100330|ref|YP_004175922.1|  35 VTDLVACSHKYHMRRKYpELTIGFEPSMVLGELLHKGLEEVLKGEGYEVE 84 
                                       888999*********9988888899*****************98766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1547.71
//
Query:       gi|320100331|ref|YP_004175923.1|  [L=411]
Description: major facilitator superfamily protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-25   90.4  58.1    7.9e-16   57.9  19.1    2.0  2  MFS_1       Major Facilitator Superfamily
    7.3e-12   44.8  29.6    1.2e-06   27.7  18.6    2.1  2  MFS_1_like  MFS_1 like family
     0.0003   19.3  29.7    0.00048   18.7  10.0    2.1  2  MFS_3       Transmembrane secretion effector
  ------ inclusion threshold ------
          2    8.2   5.7       0.37   10.6   1.0    2.1  2  Pam17       Mitochondrial import protein Pam17


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 !   57.9  19.1   1.8e-19   7.9e-16       2     220 ..      23     233 ..      22     235 .. 0.80
   2 !   37.9  34.2   2.1e-13   9.6e-10       2     172 ..     229     403 ..     226     408 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.8e-19
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.ll 77 
                                       +++ fl++l+ +++ p+++ ++a++lg+   ei  + ++ +++ +v+++++G l+dr+Gr +++l+g ll +l+ ++
  gi|320100331|ref|YP_004175923.1|  23 AISWFLYGLSGALVQPFFS-LYAKSLGAGDLEIAVVKSIGMVVLGVFTVVGGLLTDRVGRVKMILAGTLLVSLTqFA 98 
                                       567799*************.999***************************************************555 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...W 150
                                       ++l   ++w  l+v++v+  ++  ++ pa  a+i d  p ++  +++  l+++ s+  ++ p++gg l++ +g    
  gi|320100331|ref|YP_004175923.1|  99 YAL--VGSWsQLAVVWVIDEAAH-FYQPALTAIIMDSIPSRKELKGFIALNVFPSIPWLFMPVIGGRLYDIYGvqgI 172
                                       555..67788************6.*************************************************5555 PP

                             MFS_1 151 ravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllff 220
                                       r+ f++ +++sl++++l       +++    +    +    g+++lv+ +++l++ + +  ++li l+++f
  gi|320100331|ref|YP_004175923.1| 173 RYGFLVSGVLSLMVLLL--RARALKETLTVAN----R----GGFNLVKDLTELFRFKMMKhVILIYLFTGF 233
                                       55577777777777444..3333333333333....3....344444435555555533333566665555 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 2.1e-13
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslpl.GrlsdrfGrrrvlllglllfalgll 77 
                                       l+++f++ la+s+ ++  +++  + lg+s +e g++ t+ ++ +++asl+l +++s+++    v++++ +l+a++ +
  gi|320100331|ref|YP_004175923.1| 229 LFTGFIAPLASSVWNTYGSIYSVRILGVSNTEWGIVSTVGTASSIIASLILaSVISENY--VAVMVTTSVLSAAS-Y 302
                                       6899999****999999988999*******************99999999956667777..77999999999999.3 PP

                             MFS_1  78 lllfa.......sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllass 147
                                       l++ a       s++++l+++ v  ++g++++ p++ a+++++ p e rgra g+     ++G +l+  +ggll+ +
  gi|320100331|ref|YP_004175923.1| 303 LFF-AsptlmgvSPMTALVAGSVSGAIGGALMGPVISAMLTRILPVELRGRAAGIQRFIENMGWALASYIGGLLYVW 378
                                       333.2233445688889************************************************************ PP

                             MFS_1 148 lgWravfyilaivsllafvlfllll 172
                                       lg  ++ ++  ++s+ af+  +l++
  gi|320100331|ref|YP_004175923.1| 379 LGAVGSLLASSVLSVAAFIYLYLVF 403
                                       *****************99766655 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   6.5   4.6e-08    0.0002     225     318 ..      17     113 ..       6     130 .. 0.87
   2 !   27.7  18.6   2.7e-10   1.2e-06     132     379 ..     125     381 ..     105     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.6e-08
                        MFS_1_like 225 peviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayi 301
                                        +v+++ +  ++ g s ++++ F++lY k+lga    + ++  +g+v   ++ +++  l++++G vk+++++ l++ 
  gi|320100331|ref|YP_004175923.1|  17 GNVLVMAISWFLYGLSGALVQPFFSLYAKSLGAGDLEIAVVKSIGMVVLGVFTVVGGLLTDRVGRVKMILAGTLLVS 93 
                                       5789999999*************************************9999999*********************99 PP

                        MFS_1_like 302 lrfllyaii...enawlvlp 318
                                       l+ + ya++   +++ +v +
  gi|320100331|ref|YP_004175923.1|  94 LTQFAYALVgswSQLAVVWV 113
                                       99999999866544444444 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 2.7e-10
                        MFS_1_like 132 ldaatlkel..gedrkdyGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvl.ilnetek 205
                                       l a+++  +  +++ k +    +f s+ +  + +i G l d y v+ ++y   ++v  +l +++ll+ + +l+et  
  gi|320100331|ref|YP_004175923.1| 125 LTAIIMDSIpsRKELKGFIALNVFPSIPWLFMPVIGGRLYDIYGVQGIRY--GFLVSGVLSLMVLLLRArALKETLT 199
                                       4566777776556667799999***********************98776..7888777777777763213444444 PP

                        MFS_1_like 206 esklkvtksl...qvllnilknpeviifllva.lilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplf 277
                                         + + ++     ++l++  ++++vi++ l++ +i   ++++ +++ ++Y    lg snt +G++ ++g++++i+  
  gi|320100331|ref|YP_004175923.1| 200 VANRGGFNLVkdlTELFRFKMMKHVILIYLFTgFIAPLASSVWNTYGSIYSvRILGVSNTEWGIVSTVGTASSIIAS 276
                                       4444334333333666666677887765554438888999**********9999********************998 PP

                        MFS_1_like 278 ffaeklleklGhvklliiallayilrfllyaii...enawlvlpievLhgisfgllwaaaveyv.skiapksleatg 350
                                       ++   ++    + +++++++l+ +  ++  + +    ++  +l++   +g+  g+l + +++ +  +i p +l+++ 
  gi|320100331|ref|YP_004175923.1| 277 LILASVISENYVAVMVTTSVLSAASYLFFASPTlmgVSPMTALVAGSVSGAIGGALMGPVISAMlTRILPVELRGRA 353
                                       887777777778888888888888888877776699999******9999998888888777655389********** PP

                        MFS_1_like 351 qgllsglyfglGralGsliGGllwdlksa 379
                                        g+   +   +G al s+iGGll+ + +a
  gi|320100331|ref|YP_004175923.1| 354 AGIQRFI-ENMGWALASYIGGLLYVWLGA 381
                                       **97655.99*************987666 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  10.0   1.1e-07   0.00048      39     238 ..      46     242 ..      28     279 .. 0.78
   2 !    4.1  14.9    0.0028        13      62     181 ..     277     394 ..     252     408 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-07
                             MFS_3  39 disasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligi 115
                                       ++ a +l +A+v+  + + + +++++ G l+D + r k++la+ ll+ l     t + a+ l+  w+ la+  +i+ 
  gi|320100331|ref|YP_004175923.1|  46 SLGAGDLEIAVVKSIGMVVLGVFTVVGGLLTDRVGRVKMILAGTLLVSL-----TQF-AYALVGSWSQLAVVWVIDE 116
                                       678999************************************9987543.....333.45688899*********** PP

                             MFS_3 116 GaalndPaWqAsvgelvk.rrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaa...lafavn.alsylalivall 187
                                        a + +Pa  A++ + ++ r++++  +aLn     i     P +gG l  + G     + f v  +ls ++l++   
  gi|320100331|ref|YP_004175923.1| 117 AAHFYQPALTAIIMDSIPsRKELKGFIALNVF-PSIPWLFMPVIGGRLYDIYGVQgirYGFLVSgVLSLMVLLLRAR 192
                                       **************998637789999999965.57999999*****9988877642114555542445555555555 PP

                             MFS_3 188 rwkrevrksslprEkllealraglRftaasreikavlvRaalFglsasavl 238
                                       + k + +  +    +l++ l++ +Rf  + + i   l  +++  l++s v+
  gi|320100331|ref|YP_004175923.1| 193 ALKETLTVANRGGFNLVKDLTELFRFKMMKHVILIYLFTGFIAPLASS-VW 242
                                       556666666666779999***************999999999888655.44 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0028
                             MFS_3  62 silaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvp 138
                                        ila ++++n+    v++++ +l a++ ++ ++ +++g+    +l+a ++  +iG al+ P  +A++  +++ +   
  gi|320100331|ref|YP_004175923.1| 277 LILASVISENYV--AVMVTTSVLSAASYLFFASPTLMGVSPMTALVAGSVSGAIGGALMGPVISAMLTRILPVELRG 351
                                       367888888885..688888888888888889999999999999******************************999 PP

                             MFS_3 139 aAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsyla 181
                                        A  ++    n+  +    +gG+l  ++Ga+ +  + ++  +a
  gi|320100331|ref|YP_004175923.1| 352 RAAGIQRFIENMGWALASYIGGLLYVWLGAVGSLLASSVLSVA 394
                                       ************************9888887665544333222 PP

>> Pam17  Mitochondrial import protein Pam17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3      0.62   2.8e+03      34      85 ..      54     103 ..      47     105 .. 0.72
   2 ?   10.6   1.0   8.3e-05      0.37      40      96 ..     283     341 ..     271     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.62
                             Pam17  34 ielvasivtallglllgaavlstleidptqqilglDplvvlglatlasgalG 85 
                                       i++v si + +lg+++ +  l t ++  +++i  l   ++++l+ +a + +G
  gi|320100331|ref|YP_004175923.1|  54 IAVVKSIGMVVLGVFTVVGGLLTDRVGRVKMI--LAGTLLVSLTQFAYALVG 103
                                       56778888888888888888888888888888..444555556666666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.3e-05
                             Pam17  40 ivtallglllgaavlstleidp..tqqilglDplvvlglatlasgalGwllGpvlgsav 96 
                                       i    ++++++++vls+ +     + +++g+ p+++l+++ ++ ++ G l+Gpv+  ++
  gi|320100331|ref|YP_004175923.1| 283 ISENYVAVMVTTSVLSAASYLFfaSPTLMGVSPMTALVAGSVSGAIGGALMGPVISAML 341
                                       4456677788888887744333238899**************************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3054.43
//
Query:       gi|320100332|ref|YP_004175924.1|  [L=506]
Description: family 1 extracellular solute-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-31  109.1   0.9    5.9e-31  108.3   0.9    1.4  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    2.5e-24   86.8   2.9    4.3e-24   86.0   2.9    1.3  1  SBP_bac_1  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.24   11.4  19.3       0.54   10.2  19.3    1.5  1  Mucin      Mucin-like glycoprotein
          1    7.5  14.6        1.6    6.9  14.6    1.2  1  SSP160     Special lobe-specific silk protein SSP160
        6.1    6.8  14.4         14    5.7  14.4    1.5  1  DUF3439    Domain of unknown function (DUF3439)


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.9   1.6e-34   5.9e-31       2     270 ..     115     423 ..     114     435 .. 0.79

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.6e-34
                                       HHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---S........EE.EEE-HHHHHHHHHTTSB--GGGSTTHH CS
                         SBP_bac_8   2 lakefekkt.gvkvnvvtaasndleqklkaalaagtapd........idvvwanedalatlaeeglladlsdldnld 69 
                                       +++ f+ ++ g++v  v +++ d+     +a+a+ +  +        +d++++++d+++ +a++g++ +l+++  +d
  gi|320100332|ref|YP_004175924.1| 115 IISMFKNEYpGIEVVEVAYSGMDVLKSQISAIATLSPEQrsnyigkvPDLFTWAHDWIGSFADKGYILPLEEVLSSD 191
                                       677788888888888777766666666666688877665777666666999********************877777 PP

                                       H.........-HHHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-....SE..GG CS
                         SBP_bac_8  70 d.........ltdalaavgydgklygvPyasetpyvliynkdllekaedpktwdellaaakklkgkf....gl..pd 131
                                                 l+ al av+y+ k+yg+Pya et  +li+nk l++ + +p+++de+l++ k +++++    gl   +
  gi|320100332|ref|YP_004175924.1| 192 TiindiapnlLPIALSAVTYNLKTYGLPYAGET-IALIVNKNLVP-N-PPASFDEMLQVMKSFTNRNtgsyGLsyQA 265
                                       776677666555599999**************8.9**********.6.***********998865554444552256 PP

                                       ---GGGGGGTHHETTEE---H.......HHH.HHHHHHHHHHH.HTT-EE-S...--SSTTTTTSBSEEEE-TTHHH CS
                         SBP_bac_8 132 pasgwlqaallakdgksldddg.....gkdglkealellkklk.dngktydtg.adavsefanGevaftingswdia 201
                                       ++++ + +   + +g+++d+ +     ++ g+k+ ++++ + + +++++ d g + ++++f nG+  ++i+g+w+ia
  gi|320100332|ref|YP_004175924.1| 266 DPYHLYPFVTAF-GGYYYDEATksigvNSTGTKQGIKFYIQNVlPYVDVSDLGlTYQTNLFLNGKTPMMITGPWNIA 341
                                       777888888888.8888877767889999999******999777****99766455567****************** PP

                                       HHH-T.T.TSEEEE.--S--.....EEEEEEEEEE..BTTS-HHHH..HHHHHHHHH.TTSHHHHHHHHHH---BS- CS
                         SBP_bac_8 202 aaqka.g.kklgai.vpkqg.....sfaggkglav..pknaknedl..aAldFlkwl.tspenqaalaektgyipvn 265
                                       +++k  g  +++++ +p+ g     +f+g+ g+++  ++n + +++  a++ F  ++ +++ + + l++k +y+pv 
  gi|320100332|ref|YP_004175924.1| 342 TINKSlGlSNIAIApLPNIGdkvpkPFSGYRGIYItlMANVGGRERlyASVLFTLYVaLNDNALKILVDKNNYVPVK 418
                                       ***9978559999955754444445*******99877777666655599****9888357778888999*******9 PP

                                       S-TTT CS
                         SBP_bac_8 266 ksaal 270
                                        ++ +
  gi|320100332|ref|YP_004175924.1| 419 NTMIT 423
                                       88764 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 !   86.0   2.9   1.2e-27   4.3e-24       3     286 ..     107     371 ..     104     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.2e-27
                                       SHHHHHHHHHHHHHHHHHHHTTEEEE.EEEECHHHHHHHHHHHHHTTS........SSCSEEEECGGHHHHHHHTTS CS
                         SBP_bac_1   3 sltegaalqalvakafekehpgikVe.iesvgsgslaqkltlaiaaGd........gpaDviavdndwiarlakagl 70 
                                       ++++  a+q ++   f+ e+pgi+V+ + ++g + l+ ++++    +         +++D++++++dwi+ +a++g+
  gi|320100332|ref|YP_004175924.1| 107 NERK--AFQDII-SMFKNEYPGIEVVeVAYSGMDVLKSQISAIATLSPeqrsnyigKVPDLFTWAHDWIGSFADKGY 180
                                       5566..888888.88*********9999999*******8888888888999*****777****************** PP

                                       BECCHHHHHHTTECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHH CS
                         SBP_bac_1  71 llpldpyvkaylapgvkdaadklsssvlpkilds.kv...ly.vPlya.argliYNkdlfekagldppwtWdelvea 141
                                        lpl +++  +++    d a +     lp  l + ++    y +P+ + + +li+Nk l+     +pp ++de + +
  gi|320100332|ref|YP_004175924.1| 181 ILPLEEVLSSDTIIN--DIAPN----LLPIALSAvTYnlkTYgLPYAGeTIALIVNKNLVP----NPPASFDEMLQV 247
                                       ***********6555..44555....45556666677999*******66************....6788******** PP

                                       HHHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTT CS
                         SBP_bac_1 142 akklkekgkkpiggarggsasgtayyfalalakslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgk 216
                                        k ++  + +      +g   +   y ++++   +gg+++d+  +  g+++++ ++ ++++   +        l+ +
  gi|320100332|ref|YP_004175924.1| 248 MKSFTNRNTGS-----YGLSYQADPYHLYPFVTAFGGYYYDEATKsiGVNSTGTKQGIKFYIQNV--------LPYV 311
                                       ******99999.....6666667778889**************9998888888888888888888........9*** PP

                                       EEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.EEE CS
                         SBP_bac_1 217 gaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.lga 286
                                       ++++ + +  ++lf +G+++m+i g+w +           + ++k+    ++++aplP + ++ p+   g+
  gi|320100332|ref|YP_004175924.1| 312 DVSDLGLTYQTNLFLNGKTPMMITGPWNI-----------ATINKSLGLSNIAIAPLPNIGDKVPKPfSGY 371
                                       ***************************94...........4444444456788888888888888775333 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  19.3   0.00015      0.54      45      78 ..      34      66 ..      23      89 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                             Mucin 45 ltttttttkppttttttttasttittkttkattt 78
                                      ++++tttt p tttttt t++tt tt tt++++ 
  gi|320100332|ref|YP_004175924.1| 34 SQSSTTTTPPLTTTTTTGTTTTTATT-TTTTPAG 66
                                      44444444444444444433333222.2222222 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  14.6   0.00044       1.6     677     706 ..      37      68 ..      12      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00044
                            SSP160 677 atttt..ssttttttttttaaptttttkaana 706
                                       +tttt   +ttttt tttt+a ttttt a n+
  gi|320100332|ref|YP_004175924.1|  37 STTTTppLTTTTTTGTTTTTATTTTTTPAGNT 68 
                                       23333113566666677778888888888775 PP

>> DUF3439  Domain of unknown function (DUF3439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  14.4    0.0038        14      47      69 ..      45      67 ..      29      94 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0038
                           DUF3439 47 ttttttttttttmpttttlpttt 69
                                      tttttt ttttt  tttt p+  
  gi|320100332|ref|YP_004175924.1| 45 TTTTTTGTTTTTATTTTTTPAGN 67
                                      45555556666777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1226  (0.0683808); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
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 0.26s 00:00:00.88 Elapsed: 00:00:00.40
# Mc/sec: 3790.44
//
Query:       gi|320100333|ref|YP_004175925.1|  [L=481]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   55.9  14.8    4.3e-15   55.9  14.8    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.017   14.9   0.4      0.043   13.6   0.4    1.6  1  Git3          G protein-coupled glucose receptor regulating G
      0.093   12.9   0.2       0.27   11.4   0.2    1.8  1  TM_PBP2_N     N-terminal of TM subunit in PBP-dependent ABC t
       0.69    9.8   5.1        1.5    8.7   5.1    1.5  1  CoatB         Bacteriophage coat protein B


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 ?    0.2   0.2      0.12   5.5e+02     162     174 ..      17      29 ..       4      87 .. 0.55
   2 !   55.9  14.8   9.6e-19   4.3e-15       3     179 ..     266     472 ..     264     476 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.12
                      BPD_transp_1 162 viavlllnlvadi 174
                                       +ia ++l ++++i
  gi|320100333|ref|YP_004175925.1|  17 AIASIVLYFFFNI 29 
                                       2222222222222 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 9.6e-19
                      BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf............vilsilghlilpviillllsa 64 
                                       llGi +a     +   ++++lr+l  ++++lP ++ ++ + ++f             ++++ ++++l   +  ++ a
  gi|320100333|ref|YP_004175925.1| 266 LLGIGLAffySTPLIYGRRVLRGLALAPWALPLLLSGLTWRFLFspsgqlgrlfgiQLFTDEWQAFLVYNLFEAWLA 342
                                       67777776555666678******************88888777788888888855433455555666666677899* PP

                      BPD_transp_1  65 apyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtll 141
                                        p+++ ++ +al+ ++++ +ea++++Gas wq++r+vvlP++  p++  +il+ g++l +++++++l ++ G ++++
  gi|320100333|ref|YP_004175925.1| 343 YPFIMTVTMGALSGVSREVIEASYIDGASLWQRLRHVVLPLVSKPLMLAAILTTGASLQAFMVPLLLNGG-GPTRVI 418
                                       *******************************************************************966.566666 PP

                      BPD_transp_1 142 leailgydyseis................nggvlalviavlllnlvadilqrll 179
                                       + ++ g+ + + +                +g+++a+ ++v+l++ v+ ++  ++
  gi|320100333|ref|YP_004175925.1| 419 TVPYFGSKTGNVNemiilfgynraitdkeWGYAAATYLIVVLIIMVYVAVWMYV 472
                                       666666666666666679999999999998888877777777777776655555 PP

>> Git3  G protein-coupled glucose receptor regulating Gpa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   9.5e-06     0.043     177     198 ..     454     475 ..     440     478 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.5e-06
                              Git3 177 rYiivvaivaiyisiyiyvrre 198
                                        Y+ivv i+++y+++++yv+r+
  gi|320100333|ref|YP_004175925.1| 454 TYLIVVLIIMVYVAVWMYVSRR 475
                                       7*******************98 PP

>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2     6e-05      0.27       1      22 [.      22      43 ..      22      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                         TM_PBP2_N  1 llLlvfqvfpvlyTistafTNy 22
                                      +l ++f+++p++++i +afTN 
  gi|320100333|ref|YP_004175925.1| 22 VLYFFFNIWPLAFSIGMAFTNA 43
                                      57799****************5 PP

>> CoatB  Bacteriophage coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.1   0.00033       1.5      28      44 ..     458     474 ..     451     475 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00033
                             CoatB  28 aVLvvlVgvavfkWvRR 44 
                                        VL+++V vav+++v R
  gi|320100333|ref|YP_004175925.1| 458 VVLIIMVYVAVWMYVSR 474
                                       59*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3468.45
//
Query:       gi|320100334|ref|YP_004175926.1|  [L=283]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   42.8  15.2    4.5e-11   42.8  15.2    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.64   10.5  11.8       0.11   12.9   4.8    2.4  2  DUF805        Protein of unknown function (DUF805)


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 ?   -6.4  12.5         2   1.8e+04      53     170 ..      14     137 ..       4     140 .. 0.56
   2 !   42.8  15.2     5e-15   4.5e-11      11     177 ..      99     270 ..      90     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: -6.4 bits;  conditional E-value: 2
                      BPD_transp_1  53 ilpviillllsaapyvrlirraalrslpkdlveaaralGasrwq.ifrkvvlPnalppiitglilafggllggavll 128
                                        + + +l+l+ ++ +v++i+ + ++s p+  +   +alG+ +++  +r v+ P  ++ i ++l++++  +l   v++
  gi|320100334|ref|YP_004175926.1|  14 LTVAGFLVLFALLYPVFFIVLQSFYSKPSLIEDPVKALGMLTIEnYVRAVASPEFASAIQMSLLISLLTVLVSVVVI 90 
                                       55566778888888888888888888888888888888887776144555555555555555555555555444444 PP

                      BPD_transp_1 129 eflgswpGlgtllleailgydyseis.........nggvlalviavlllnl 170
                                          + +  ++++ +    +  y   +         +g+v++++++++ll+l
  gi|320100334|ref|YP_004175926.1|  91 TPAA-YA-FSRFHFKGRDMVLYI--YlilsqagggFGVVAVIALLMFLLVL 137
                                       3333.21.333333333333333..24477777555555555555555554 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 5e-15
                      BPD_transp_1  11 nrnkkldkllrpliivll.......slPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslp 80 
                                       ++++k++++++ ++ +l+        + +++l+++l++ ++  ++  +++  + +++  +++p+ +++ ++++++lp
  gi|320100334|ref|YP_004175926.1|  99 RFHFKGRDMVLYIYLILSqagggfgVVAVIALLMFLLV-LSSYGVPAYGWHVLPLIYSAGLVPFQTWLLKSYFDNLP 174
                                       55555555555555555558777766666777777663.3444444444444667899999**************** PP

                      BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis... 154
                                       ++l eaa ++Ga   +i++++vlP++ p +i   ++af++++g+++++ +l  ++ +g  +  +  g          
  gi|320100334|ref|YP_004175926.1| 175 RELDEAAFIDGADWGTIIYRIVLPSSRPAVIIITLFAFMSAWGEFFIANLLRVNT-IGAYIYMTAFGER----Glqd 246
                                       ***********************************************99998444.4444443333333....1334 PP

                      BPD_transp_1 155 ....nggvlalviavlllnlvadilqr 177
                                           ++++l++++ ++++  va   qr
  gi|320100334|ref|YP_004175926.1| 247 psvyAALSLIYAFPIIVIYMVA---QR 270
                                       3333455555555555555554...44 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.8   1.2e-05      0.11      17     102 ..      21     146 ..       6     149 .. 0.66
   2 ?    1.4   0.6     0.047   4.2e+02      37      83 ..     218     264 ..     187     276 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                            DUF805  17 vlfllllvivlallaavlaa.................................aavasalsvvlallllvpslavtv 60 
                                       vlf ll  +++ +l +++ +                                 + +  +l +vl+ +++++ +a ++
  gi|320100334|ref|YP_004175926.1|  21 VLFALLYPVFFIVLQSFYSKpsliedpvkalgmltienyvravaspefasaiqMSLLISLLTVLVSVVVITPAAYAF 97 
                                       5555555555556666665577888899999999999999999999866654433333333444444444449999* PP

                            DUF805  61 RRlHDtgrsgwllllllvp.......lialllllvllllpgtpgenryG 102
                                        R+H  gr  +l+++l++        ++a+++ll++ll  ++ g   yG
  gi|320100334|ref|YP_004175926.1|  98 SRFHFKGRDMVLYIYLILSqagggfgVVAVIALLMFLLVLSSYGVPAYG 146
                                       ***********87766663444444455666677777666766666666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.047
                            DUF805  37 aavasalsvvlallllvpslavtvRRlHDtgrsgwllllllvplial 83 
                                         ++++l  v ++ +++   a+  R l D    + l l+++ p+i++
  gi|320100334|ref|YP_004175926.1| 218 EFFIANLLRVNTIGAYIYMTAFGERGLQDPSVYAALSLIYAFPIIVI 264
                                       44455555556666666667777777777777777777777775442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2036.96
//
Query:       gi|320100335|ref|YP_004175927.1|  [L=289]
Description: transcription factor TFIIB cyclin-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   50.9   0.0    1.1e-08   35.0   0.0    2.3  2  TFIIB            Transcription factor TFIIB repeat
    3.6e-10   39.2   1.4    6.6e-10   38.3   1.4    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
      3e-05   23.6   0.8    4.9e-05   22.9   0.8    1.3  1  Ribosomal_S27e   Ribosomal protein S27
      0.005   17.2   0.8       0.01   16.2   0.8    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
       0.01   15.5   0.8       0.02   14.6   0.8    1.4  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.011   15.6   0.8      0.022   14.7   0.8    1.4  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.04   13.9   0.4      0.069   13.1   0.4    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.043   13.9   0.0          1    9.5   0.0    2.1  2  Cyclin_C         Cyclin, C-terminal domain
      0.044   13.8   0.3      0.086   12.9   0.3    1.5  1  DZR              Double zinc ribbon
      0.065   12.9   2.2       0.11   12.2   2.2    1.4  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.067   12.9   0.0        1.9    8.2   0.0    2.1  2  OmpA_membrane    OmpA-like transmembrane domain
       0.14   12.1   0.8       0.32   11.0   0.8    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.16   11.8   1.0       0.27   11.0   1.0    1.3  1  PADR1            PADR1 (NUC008) domain
       0.16   12.3   1.0       0.35   11.2   1.0    1.5  1  C1_2             C1 domain
       0.17   12.2   0.7       0.98    9.8   0.8    2.3  2  DUF3268          zinc-finger-containing domain
       0.17   11.4   1.4        8.9    5.9   0.2    2.5  2  zf-ribbon_3      zinc-ribbon domain
       0.21   11.3   1.9        5.1    7.0   0.5    2.5  2  zinc_ribbon_2    zinc-ribbon domain
       0.22   11.4   0.9       0.53   10.1   0.9    1.6  1  Cys_rich_CPCC    Cysteine-rich CPCC
       0.41   10.8   2.2        1.6    8.9   2.2    1.9  1  Zn-ribbon_8      Zinc ribbon domain
        3.1    7.6   5.2        6.8    6.5   0.3    2.4  2  Rubredoxin_2     Rubredoxin metal binding 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 !   13.8   0.0     5e-05     0.045      11      68 ..     115     172 ..     105     175 .. 0.91
   2 !   35.0   0.0   1.2e-11   1.1e-08       6      70 ..     207     271 ..     202     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                                       -HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--S CS
                             TFIIB  11 pekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVse 68 
                                       p  V++ A  l+++a+++k+ k      i+ A++y+  + ++  r+ k ++s l++++
  gi|320100335|ref|YP_004175927.1| 115 PTPVRETAALLVREAVKDKNFKENTVRKIIVAAIYLSYKINKQPRSAKVFCSELNIED 172
                                       6689************************************************999876 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 1.2e-11
                                       HHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
                             TFIIB   6 daleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70 
                                        +l+ p  V+  A+ +a  a + ++l+G+ pa++aAA++y+A   ++ kr q e+++++  +++ 
  gi|320100335|ref|YP_004175927.1| 207 HRLNAPPVVETLANSIASSAESYGFLSGKNPASLAAASVYLAGIISNNKRNQLEVAETIGLTDVA 271
                                       68899999*************************************************99988775 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   1.4   7.4e-13   6.6e-10       1      37 [.       1      37 [.       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 7.4e-13
                                      EEETTTTCEECHEETSTTCEEESSSSBEEEECCCCCC CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVlednsideg 37
                                      ++CP Cg +++++D +++++vC  CG+V++++++  g
  gi|320100335|ref|YP_004175927.1|  1 MRCPHCGRDTVIFDSDSNTYVCQVCGAVVDERPAYQG 37
                                      79*****************************987655 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.8   5.5e-08   4.9e-05       9      36 ..       2      29 ..       1      33 [. 0.92

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.5e-08
                                      E-TTTS-EEEEESS-SS-EEESSSTCEE CS
                    Ribosomal_S27e  9 kCpdCenetvvFshaatvvkCisCgkvL 36
                                      +Cp C++ tv+F++ +    C+ Cg v+
  gi|320100335|ref|YP_004175927.1|  2 RCPHCGRDTVIFDSDSNTYVCQVCGAVV 29
                                      8*************999999*****998 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 !   16.2   0.8   1.1e-05      0.01       6      37 ..       3      28 ..       1      46 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCgas 37
                                      CP+Cg + v++ s ++++       C+ Cga+
  gi|320100335|ref|YP_004175927.1|  3 CPHCGRDTVIFDSDSNTY------VCQVCGAV 28
                                      *************99987......8*99***3 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.8   2.2e-05      0.02       6      30 ..       3      28 ..       2      29 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                     A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                      C  Cg++ ++  s+++ +vC+ Cga+
  gi|320100335|ref|YP_004175927.1|  3 CPHCGRDTVIFdSDSNTYVCQVCGAV 28
                                      777*****9999************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 ?   14.7   0.8   2.4e-05     0.022       6      31 ..       2      26 ..       2      30 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                    Zn_ribbon_SprT  6 rCtgCgreythhlsirrhnYrCrrCk 31
                                      rC++Cgr  t+++ ++  +Y C+ C+
  gi|320100335|ref|YP_004175927.1|  2 RCPHCGRD-TVIFDSDSNTYVCQVCG 26
                                      8*****99.****************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 ?   13.1   0.4   7.7e-05     0.069      20      44 ..       2      26 ..       1      28 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-05
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCr 44
                                      +CPhCg +++++ ++   + C+ C+
  gi|320100335|ref|YP_004175927.1|  2 RCPHCGRDTVIFDSDSNTYVCQVCG 26
                                      7*****9999999999********8 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.17   1.5e+02       4      90 ..     102     186 ..     100     201 .. 0.75
   2 ?    9.5   0.0    0.0011         1      30      89 ..     222     282 ..     202     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                                       HHHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHH CS
                          Cyclin_C   4 lsFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedlk 80 
                                       l++l+ +lk  d      +r  a  l+  ++ d +f +     i  aa++l+ ++ ++p   + + + + ++   l 
  gi|320100335|ref|YP_004175927.1| 102 LQWLNEYLKLLDP--PTPVRETAALLVREAVKDKNFKENTVRKIIVAAIYLSYKINKQPRSAKVFCSELNIEDGYLW 176
                                       6899999999555..447999999999999********99999999*****99997666655555555555555555 PP

                                       HHHHHHHHHH CS
                          Cyclin_C  81 pcvelilell 90 
                                       + ++li e++
  gi|320100335|ref|YP_004175927.1| 177 EGIRLIREAV 186
                                       5555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                                       HHHHHCSCCHCC.S-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                          Cyclin_C  30 leltlldydfls.yppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                       +++++  y fls   p  +Aaa+++la  + n++  + ++ + +g++   +++ +  il +
  gi|320100335|ref|YP_004175927.1| 222 IASSAESYGFLSgKNPASLAAASVYLAGIISNNKRNQLEVAETIGLTDVAIRNAYDSILRN 282
                                       455666777776578999************9999999**********99999999999876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   9.6e-05     0.086       1      27 [.       3      34 ..       3      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-05
                               DZR  1 CpqCgee.....lppdarfCseCgtklkavaa 27
                                      Cp+Cg++      +++  +C+ Cg+ +++ +a
  gi|320100335|ref|YP_004175927.1|  3 CPHCGRDtvifdSDSNTYVCQVCGAVVDERPA 34
                                      9*****9999777888889*****99986655 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 ?   12.2   2.2   0.00013      0.11       5      31 ..       1      29 [.       1      30 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                           zf-RRN7  5 ppCgvCgc..rsftlddGfyyCrrChtqe 31
                                      ++C+ Cg   + f++d  +y+C+ C+ ++
  gi|320100335|ref|YP_004175927.1|  1 MRCPHCGRdtVIFDSDSNTYVCQVCGAVV 29
                                      69*******99***************985 PP

>> OmpA_membrane  OmpA-like transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11     1e+02      83     118 ..      62      97 ..      38     106 .. 0.83
   2 ?    8.2   0.0    0.0022       1.9      27      73 ..     134     190 ..     121     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                       EEEEEESSSSEEEEEEEEEEEEEEEEESSSSB.... CS
                     OmpA_membrane  83 lklsyellddldvYakvGvalvradykvkedkkske 118
                                       + ++ e++  + ++ + G  +vra++++k+dk+ ++
  gi|320100335|ref|YP_004175927.1|  62 GVGGTEIAGSFKAHLRRGRSWVRANSEIKVDKRDRK 97 
                                       6678899*******************9999987655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0022
                                       CSS-SSSSSEEEEEEEEEEEEETT..........EEEEEEEEEEEESSS-SS---S- CS
                     OmpA_membrane  27 ekkknierdsvtagvFgGYqinnq..........lalElGYdylGrakakgkkkvvk 73 
                                       + k n+ r  ++a +++ Y+in+q          l +E GY++ G    ++++k vk
  gi|320100335|ref|YP_004175927.1| 134 NFKENTVRKIIVAAIYLSYKINKQprsakvfcseLNIEDGYLWEGIRLIREAVKDVK 190
                                       4567778888999******************9999**********877777766555 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 ?   11.0   0.8   0.00035      0.32      30      57 ..       2      30 ..       1      32 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                    OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgfead 57
                                      +C++Cg+     + +++t++C+ Cg++ d
  gi|320100335|ref|YP_004175927.1|  2 RCPHCGRDTVIfDSDSNTYVCQVCGAVVD 30
                                      6******999999************9876 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0    0.0003      0.27      15      34 ..       2      23 ..       1      26 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                             PADR1 15 kCpeCkegqlvfdss..gYkCt 34
                                      +Cp+C++ +++fds+  +Y+C+
  gi|320100335|ref|YP_004175927.1|  2 RCPHCGRDTVIFDSDsnTYVCQ 23
                                      6*************999****7 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   0.00039      0.35      20      45 ..       2      32 ..       1      32 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                              C1_2 20 nCsaCgrk..idgff...YsCseCdfslhvr 45
                                      +C  Cgr+  i++++   Y C+ C  ++++r
  gi|320100335|ref|YP_004175927.1|  2 RCPHCGRDtvIFDSDsntYVCQVCGAVVDER 32
                                      7999****9955555667***99**999986 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.8    0.0011      0.98       3      52 ..       1      41 [.       1      61 [. 0.67
   2 ?   -2.5   0.0       7.1   6.4e+03      63      80 ..     190     207 ..     181     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCdayvgvhkgtkiplGt 52
                                      +rCp+CG+ +++ +++         + +y+C+ C+a v  ++  +   G 
  gi|320100335|ref|YP_004175927.1|  1 MRCPHCGRDTVIFDSD---------SNTYVCQVCGAVVDERPAYQGTEGF 41
                                      5899999887655543.........3459********9988777666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.1
                           DUF3268  63 keahaaFdklwksgalsr 80 
                                       k +h+++d+ +  g +++
  gi|320100335|ref|YP_004175927.1| 190 KLTHEHYDPRYYIGFITH 207
                                       568999999888887754 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0099       8.9      19      23 ..       3       7 ..       1      10 [. 0.64
   2 ?    4.0   0.1     0.037        34       2      14 ..      19      31 ..      18      32 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0099
                       zf-ribbon_3 19 CpyCG 23
                                      Cp+CG
  gi|320100335|ref|YP_004175927.1|  3 CPHCG 7 
                                      55555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.037
                       zf-ribbon_3  2 tvrCPnCGaplss 14
                                      t+ C  CGa++++
  gi|320100335|ref|YP_004175927.1| 19 TYVCQVCGAVVDE 31
                                      78899****8887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5    0.0056       5.1       1       7 [.       2       8 ..       2      10 .. 0.80
   2 ?    3.0   0.0     0.099        89      15      21 ..      20      27 ..      15      32 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0056
                     zinc_ribbon_2 1 fCpnCGa 7
                                     +Cp+CG+
  gi|320100335|ref|YP_004175927.1| 2 RCPHCGR 8
                                     5999997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.099
                     zinc_ribbon_2 15 F.CpyCGt 21
                                      + C  CG+
  gi|320100335|ref|YP_004175927.1| 20 YvCQVCGA 27
                                      45666665 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.9   0.00059      0.53       2      25 ..       2      26 ..       1      39 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00059
                     Cys_rich_CPCC  2 qCpcCgyltl..eeeegsydiCpvCf 25
                                      +Cp Cg  t+  +++ +++ +C+vC 
  gi|320100335|ref|YP_004175927.1|  2 RCPHCGRDTVifDSD-SNTYVCQVCG 26
                                      7******99865555.5555*****5 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.2    0.0017       1.6       7      34 ..       2      27 ..       1      33 [. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgs 34
                                      rC  Cg++  ++ s s   +t  C  Cg+
  gi|320100335|ref|YP_004175927.1|  2 RCPHCGRDTVIFDSDS---NTYvCQVCGA 27
                                      8*****8888887533...6777****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 ?    2.9   0.8      0.11        95      16      21 ..       2       7 ..       2      10 .. 0.79
   2 ?    6.5   0.3    0.0075       6.8       1       9 [.      20      28 ..      20      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                      Rubredoxin_2 16 rCpsCg 21
                                      rCp+Cg
  gi|320100335|ref|YP_004175927.1|  2 RCPHCG 7 
                                      788887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0075
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      YvC+ CG++
  gi|320100335|ref|YP_004175927.1| 20 YVCQVCGAV 28
                                      9******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1907.48
//
Query:       gi|320100336|ref|YP_004175928.1|  [L=87]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-07   29.6   0.1    5.5e-07   29.5   0.1    1.1  1  Gar1      Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
      0.041   14.0   0.9       0.05   13.7   0.8    1.4  1  PRC       PRC-barrel domain
      0.076   13.2   0.0      0.097   12.9   0.0    1.3  1  CSD2      Cold shock domain


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   9.3e-11   5.5e-07      23      83 ..       4      63 ..       1      79 [. 0.75

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 9.3e-11
                                      EEEEEEEETT.EEEEEE---S--B--B.TT-EEEETT--EEEE--EEES-SSS-EEEEE--GG CS
                              Gar1 23 iGtvssiven.evviksttsgekkvld.fnsilflenktqiGkVdEifGpvnepyysVklnss 83
                                      +G v+  + +  +v+k   s   +vl+  ns +++ n + iG+V +++G+v +p + Vkl+++
  gi|320100336|ref|YP_004175928.1|  4 LGIVEASTRDgFIVVKPV-S--RDVLKlVNSSVYDDNYRRIGRVVDVIGRVDDPRVIVKLENK 63
                                      666666555515666666.4..3899845*******************************932 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8   8.3e-06      0.05       8      31 ..      27      50 ..      20      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.3e-06
                                      --TT-EEEETTSSEEEEEEEEEEE CS
                               PRC  8 dliGkeVytedGeklGkVkDvvid 31
                                      +l++ +Vy+++ +++G+V Dv+  
  gi|320100336|ref|YP_004175928.1| 27 KLVNSSVYDDNYRRIGRVVDVIGR 50
                                      68999****************533 PP

>> CSD2  Cold shock 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      35      60 ..      33      58 ..      11      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                              CSD2 35 eypdkknpeGevievLGkkgdpgvei 60
                                       y+d+++ +G+v++v+G+ +dp v +
  gi|320100336|ref|YP_004175928.1| 33 VYDDNYRRIGRVVDVIGRVDDPRVIV 58
                                      45666668**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 626.65
//
Query:       gi|320100337|ref|YP_004175929.1|  [L=99]
Description: signal recognition particle subunit SRP19 (srp19) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-21   75.6   0.1      6e-21   75.2   0.1    1.2  1  SRP19     SRP19 protein
  ------ inclusion threshold ------
      0.044   13.8   0.0      0.065   13.2   0.0    1.3  1  COX5A     Cytochrome c oxidase subunit Va


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 !   75.2   0.1   6.7e-25     6e-21       1      92 [.      11      91 ..      11      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 6.7e-25
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCCEEEEEC-..........SS- CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanpGrVrvklkedgkevnekikn 79
                                      v+YP Y+dskk+r+eGR++  + av nP ++ei ea+++lgl+ v e ek+yPr    +GrV v++k           +
  gi|320100337|ref|YP_004175929.1| 11 VVYPSYIDSKKSRREGRKIRLSDAVPNPGIDEILEACRRLGLNPVHE-EKQYPRIHGLRGRVLVDKK----------MS 78
                                      69********************************************9.*****************85..........45 PP

                                      CHHHHHHHHHHHH CS
                             SRP19 80 kkellkkiaellk 92
                                      k + l+++a+++k
  gi|320100337|ref|YP_004175929.1| 79 KLSTLIAVAREIK 91
                                      6666666666655 PP

>> COX5A  Cytochrome c oxidase subunit Va
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.3e-06     0.065      20      55 ..      16      50 ..       4      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.3e-06
                             COX5A 20 diDlfelrrglnnlfayDlvPepkvieaalracrrv 55
                                       iD+ + rr   ++   D+vP+p + ++ l+acrr+
  gi|320100337|ref|YP_004175929.1| 16 YIDSKKSRREGRKIRLSDAVPNPGI-DEILEACRRL 50
                                      68999999***************96.89*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 747.65
//
Query:       gi|320100338|ref|YP_004175930.1|  [L=129]
Description: 30S ribosomal protein S8 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-27   95.5   0.6    3.8e-27   95.1   0.6    1.1  1  Ribosomal_S8e  Ribosomal protein S8e
     0.0044   16.4   0.6     0.0052   16.2   0.6    1.0  1  Spiralin       Spiralin


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 !   95.1   0.6   4.2e-31   3.8e-27       5     137 .]       4     126 ..       1     126 [. 0.95

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 4.2e-31
                                       XXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEES.SHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEE CS
                     Ribosomal_S8e   5 rdskhkrkltGgkakllrkkrkielgrkekatklg.aervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlg 80 
                                        ++++ rk +Gg +   r krk+elg ++++t l+ +e    vr+ gG++k+++ ++ + nv+ p ek++kk+kIl+
  gi|320100338|ref|YP_004175930.1|   4 YQGNDLRKPSGGLKGEKRGKRKHELGSPPTNTTLSnSEEKVFVRTLGGNMKVKLKKALYINVALPGEKTAKKVKILD 80 
                                       688999****************************75666667899******************************** PP

                                       EECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  81 VkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       V+++psn++ +r ++++Kg++++++++             +vtsrPgq+G++n+vl+
  gi|320100338|ref|YP_004175930.1|  81 VVETPSNPQNTRFKIISKGTVVKTELGL-----------VKVTSRPGQHGVLNGVLV 126
                                       **************************99...........89**************95 PP

>> Spiralin  Spiralin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   5.8e-07    0.0052      96     172 ..      35     113 ..      25     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.8e-07
                          Spiralin  96 vnleagkvevyvqitpakdktvviGksgyikvtlpkasevkkvdisdvt...vpeqtveikvadpkavtkdeleavn 169
                                         l  ++ +v+v+     +  v + k+ yi v+lp +   kkv i dv+    + q    k+ +  +v k+el +v 
  gi|320100338|ref|YP_004175930.1|  35 TTLSNSEEKVFVRTLG-GNMKVKLKKALYINVALPGEKTAKKVKILDVVetpSNPQNTRFKIISKGTVVKTELGLVK 110
                                       5666677777777444.45568899*******************999983223568999**************9998 PP

                          Spiralin 170 kda 172
                                         +
  gi|320100338|ref|YP_004175930.1| 111 VTS 113
                                       654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 954.91
//
Query:       gi|320100339|ref|YP_004175931.1|  [L=188]
Description: chromate transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  142.2  16.6    1.8e-41  141.9  16.6    1.0  1  Chromate_transp  Chromate transporter


Domain annotation for each model (and alignments):
>> Chromate_transp  Chromate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.9  16.6   9.8e-46   1.8e-41       2     155 ..      10     178 ..       9     180 .. 0.93

  Alignments for each domain:
  == domain 1  score: 141.9 bits;  conditional E-value: 9.8e-46
                   Chromate_transp   2 elflfflkiGllifGGgyavipllreevverkgwlteeefldglalaqalPGPiavnlatfvGylil.gvlGaliat 77 
                                       elf +flkiG+++fGGgy+ i+l+++e+ve k+w++eeefl++l++a+++PGPia+n at +Gy  l g++G++iat
  gi|320100339|ref|YP_004175931.1|  10 ELFVEFLKIGFFMFGGGYGGIALMYKELVEIKKWVSEEEFLELLGVAESTPGPIAINSATWIGYS-LgGLPGSIIAT 85 
                                       79****************************999********************************.66********* PP

                   Chromate_transp  78 lgfflPsfllilllaplleklrknplvkaaleglnaavvglilaaalslakk...............iallafllll 139
                                       +g+++P++l+i++++  l+ +  + +vk +++g+naavv+lil a++++a++               i+++af+ll+
  gi|320100339|ref|YP_004175931.1|  86 IGVVMPAYLVIMAIVTSLKPYMGSDAVKIMFRGINAAVVALILYALIKVARSvliasggalnlvavaIFVTAFILLY 162
                                       ********************988************************988888989999999988766677777777 PP

                   Chromate_transp 140 lfkvspilvillaall 155
                                       + + +pi+vil++a++
  gi|320100339|ref|YP_004175931.1| 163 VGDQHPIVVILVSAAV 178
                                       77889*****999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1437.08
//
Query:       gi|320100340|ref|YP_004175932.1|  [L=466]
Description: CoA-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-53  180.8   2.4    9.8e-53  177.7   0.7    2.7  3  Succ_CoA_lig     Succinyl-CoA ligase like flavodoxin domain
    1.6e-28   99.5   0.0    4.7e-27   94.8   0.0    2.6  2  CoA_binding_2    CoA binding domain
    1.5e-13   51.2   0.0    4.1e-13   49.8   0.0    1.8  1  CoA_binding      CoA binding domain
  ------ inclusion threshold ------
      0.028   15.2   0.0         14    6.5   0.0    3.4  3  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.035   14.5   0.1       0.47   10.9   0.0    2.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
       0.09   13.4   0.0        7.5    7.2   0.0    3.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.7   0.7   3.3e-56   9.8e-53       2     138 .]     158     296 ..     157     296 .. 0.98
   2 ?   -0.6   0.0      0.35   1.1e+03       4      27 ..     307     330 ..     304     333 .. 0.86
   3 ?    0.8   0.0      0.13   3.8e+02      75      99 ..     402     428 ..     383     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 177.7 bits;  conditional E-value: 3.3e-56
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsird..grkflsaar 76 
                                       G +a+isqSGa+a+al+dw+a +++g+s++vs+Gn++dvd  d+leyla+d++t+vil+ylE+++d  gr+fl+aar
  gi|320100340|ref|YP_004175932.1| 158 GYVAFISQSGAFASALMDWMAYNNIGVSRAVSYGNKVDVDDVDILEYLASDEKTRVILIYLEGLKDgrGRAFLEAAR 234
                                       88****************************************************************7779******* PP

                      Succ_CoA_lig  77 raarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       +++  kpv+++k+G++ +g+ aaasht+alag++ v+++af+qaG+++v+s++e++da+++l
  gi|320100340|ref|YP_004175932.1| 235 KVSTVKPVLIFKAGKTGRGSLAAASHTAALAGDYSVYKSAFKQAGIVEVESFDEMMDAVRIL 296
                                       **********************************************************9875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.35
                      Succ_CoA_lig   4 ialisqSGalalalldwaasrglg 27 
                                       + +i+  G+++++l d+++s+g++
  gi|320100340|ref|YP_004175932.1| 307 VYIITDAGGVGVMLTDALTSQGFE 330
                                       77999*************999865 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.13
                      Succ_CoA_lig  75 arraark..kpvvvlksGrseagaraa 99 
                                       + +a++k  kp++++  G +ea + a 
  gi|320100340|ref|YP_004175932.1| 402 LIEAKKKygKPIIAVSIGGEEAVKIAR 428
                                       555666668*********988876654 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   1.6e-30   4.7e-27       2     113 ..      12     135 ..      11     137 .. 0.97
   2 ?    1.7   0.0      0.12   3.5e+02      54     106 ..     378     438 ..     361     442 .. 0.62

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 1.6e-30
                                       -EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeal 76 
                                       ++aV+Ga +++gk g+ +l+++ +  +g +v+pVnp ++eilg k+y+s+ + pe++dl+++++p+  +pe+++e++
  gi|320100340|ref|YP_004175932.1|  12 SVAVIGATPREGKVGRVILENFTKryRG-RVYPVNPGYDEILGLKCYRSIRDLPEAPDLAVIAIPAPGVPEVLRELG 87 
                                       79*********************99999.**********************647*********************** PP

                                       HH--SEEEE-TT...........---HHHHHHHHHTT-EEE.ES-HHH CS
                     CoA_binding_2  77 algakavwlqpg...........sedeeaaelaeeagirvvgdrCilv 113
                                       ++g+ka+++ +g             ++e+ e+a ++gir++g++Ci++
  gi|320100340|ref|YP_004175932.1|  88 EKGCKAAIIISGgfretgtpegeRLENEVKEIALKYGIRIIGPNCIGI 135
                                       ***********************99*********************98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                                       .T--EEEE-S-HHH...HGGGHHHHHHH.....--SEEEE-TT---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  54 epvdlvdvftppea...tpeivkealal.....gakavwlqpgsedeeaaelaeeagirvv 106
                                       ++vd+v+v+  p++     ++v++++++     ++  ++   g+e  ++a++++e+gi+v 
  gi|320100340|ref|YP_004175932.1| 378 GDVDAVVVVALPQVpgiKGSLVEYLIEAkkkygKPIIAVSIGGEEAVKIARRLQENGITVF 438
                                       5666555555554411134556666555333434777777777888888888888888876 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   1.4e-16   4.1e-13       3      94 ..      10      98 ..       8     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.4e-16
                                      TEEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  3 dtkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80
                                      +++v+viGa+ ++++++ +  ++  k+    v++vnp+  ++e+lgl++y s+++l+e   +d avi++Pa+ + e+  
  gi|320100340|ref|YP_004175932.1| 10 PSSVAVIGATPREGKVGrVILENFTKRYRGRVYPVNPG--YDEILGLKCYRSIRDLPEA--PDLAVIAIPAPGVPEVLR 84
                                      689**************6666666666666********..*******************..****************** PP

                                      HHHHTT-SEEEEES CS
                       CoA_binding 81 elveagikgiviit 94
                                      el e+g k ++ii+
  gi|320100340|ref|YP_004175932.1| 85 ELGEKGCKAAIIIS 98
                                      ***********997 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 ?    6.5   0.0    0.0047        14      46      87 ..      52      91 ..      38      97 .. 0.81
   2 ?    0.5   0.0      0.35     1e+03      39      72 ..     187     220 ..     160     266 .. 0.73
   3 ?    3.4   0.0     0.042   1.3e+02      54     115 ..     371     436 ..     347     440 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0047
                                      TTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT- CS
                      GFO_IDH_MocA 46 fgveaysdleelladpeidavivatpngtheelakaaleagk 87
                                      +g+++y ++++l++  ++d++++a+p+    e+ +++ e+g+
  gi|320100340|ref|YP_004175932.1| 52 LGLKCYRSIRDLPE--APDLAVIAIPAPGVPEVLRELGEKGC 91
                                      6899**********..99********9766666666666666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.35
                                       HHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G CS
                      GFO_IDH_MocA  39 aeavaesfgveaysdleelladpeidavivatpn 72 
                                       a    ++ +v+ ++ le+l++d++ +++++    
  gi|320100340|ref|YP_004175932.1| 187 AVSYGNKVDVDDVDILEYLASDEKTRVILIYLEG 220
                                       444456666667777999***9999999998764 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.042
                                       HHHHHTCTTESEEEE-S-G...GGHHHHHHHHHHTT-EEEEESSS-S...SHHHHHHHHHHHHHHTS- CS
                      GFO_IDH_MocA  54 leelladpeidavivatpn...gtheelakaaleagkhvllEKPlat...tveeakelvelaekkgkl 115
                                       le++l   ++dav+v+  +   g    l++ ++ea+k+    KP+ +     eea +++++++++g +
  gi|320100340|ref|YP_004175932.1| 371 LEKVLPRGDVDAVVVVALPqvpGIKGSLVEYLIEAKKKY--GKPIIAvsiGGEEAVKIARRLQENGIT 436
                                       788888889**9998887757767999999999999985..688877655557777777777777655 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 ?    0.2   0.1      0.31   9.2e+02      95     114 ..      69      91 ..      66     100 .. 0.84
   2 ?   10.9   0.0   0.00016      0.47      76     132 ..     384     452 ..     332     454 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.31
                                       -EEEE-TGGGTTT--...TTSSE CS
                   Glyco_trans_1_4  95 lpvVatdvggiaevv...gengl 114
                                       l+v+a +++g++ev+   ge g+
  gi|320100340|ref|YP_004175932.1|  69 LAVIAIPAPGVPEVLrelGEKGC 91 
                                       79***********9998888886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00016
                                       EEE--...---SHHHHHHH.....HTT-EEEE-TGGGTTT--......TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  76 fvaPs...egfglkllEam.....aaglpvVatdvggiaevv......gengllvppgdpealaeailrLl 132
                                       +v+ +    g++ +l+E++      +g+p++a ++gg +e+v      +eng+ v  ++pe  a+a+  L+
  gi|320100340|ref|YP_004175932.1| 384 VVVALpqvPGIKGSLVEYLieakkKYGKPIIAVSIGG-EEAVkiarrlQENGITVF-ESPERAAKALKVLY 452
                                       33333435588888888874433459*********88.8888787666699*8883.48999999998876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0025       7.5      60      93 ..      65      98 ..      49     100 .. 0.89
   2 ?    2.3   0.0     0.085   2.6e+02       7      42 ..     419     447 ..     395     462 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                                      HH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored 60 eeadvvvlavkpedveevlselakdalkgklvis 93
                                      e  d  v+a++   v+evl+el ++  k  ++is
  gi|320100340|ref|YP_004175932.1| 65 EAPDLAVIAIPAPGVPEVLRELGEKGCKAAIIIS 98
                                      67799********************9***99998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.085
                                       TSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHH CS
                     F420_oxidored   7 aGnmgealasgllaagaqpheivvansrnpekaeel 42 
                                       +G+ +  +a++l+++g     i+v    +pe+a+++
  gi|320100340|ref|YP_004175932.1| 419 GGEEAVKIARRLQENG-----ITVF--ESPERAAKA 447
                                       3444555555555555.....3322..334444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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:                         6  (0.000334653); expected 0.2 (1e-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 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3266.99
//
Query:       gi|320100341|ref|YP_004175933.1|  [L=232]
Description: acetyl-CoA synthetase (ADP-forming) subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-80  269.4   0.3    2.3e-80  269.2   0.3    1.0  1  ATP-grasp_5  ATP-grasp domain
    5.5e-06   26.1   0.1    1.1e-05   25.1   0.0    1.5  2  ATP-grasp_2  ATP-grasp domain
  ------ inclusion threshold ------
      0.065   12.7   0.1       0.14   11.6   0.1    1.5  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.2   0.3   3.8e-84   2.3e-80       1     222 []       9     229 ..       9     229 .. 0.99

  Alignments for each domain:
  == domain 1  score: 269.2 bits;  conditional E-value: 3.8e-84
                       ATP-grasp_5   1 kalaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeev 77 
                                       +al+egr  L e+ea +l++ ygip +e  +++s+eeav++a+++gyp++lKivspdi+hK+dvgGv+l+l+++eev
  gi|320100341|ref|YP_004175933.1|   9 NALKEGRYKLLEHEAFQLIKHYGIPSPEVVVVKSPEEAVALADKVGYPIALKIVSPDISHKSDVGGVKLGLRSREEV 85 
                                       589************************************************************************** PP

                       ATP-grasp_5  78 raaaeeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstla 154
                                        +a++e+le+v +++p+ari gvl  +ma+ +g E+i+g  +D+vFGpv++fGlGG+ vevlkdv++++ p+++++a
  gi|320100341|ref|YP_004175933.1|  86 GKAVKEMLETVPRRAPSARIVGVLMYNMAP-QGLEVIIGGVRDSVFGPVVMFGLGGIFVEVLKDVSFRVSPVSKEDA 161
                                       ******************************.********************************************** PP

                       ATP-grasp_5 155 reliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarirl 222
                                         +++++k++ +l+g+rg++++d +a++e++v+ ++L++d peI+++d+nP++++++g++a+Dari l
  gi|320100341|ref|YP_004175933.1| 162 LTMLKEIKSASILEGYRGQPPVDKDAIAEMIVKTARLMEDNPEIESIDLNPVMAYSKGAIAVDARIIL 229
                                       *****************************************************************976 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.8e-09   1.1e-05       1      78 [.      17      95 ..      17     121 .. 0.87
   2 ?   -2.7   0.0       0.6   3.6e+03     174     199 ..     186     212 ..     158     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.8e-09
                                      BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE.--SSSTCCCTTCEEE.ESSHHHHHHHHHCCTT CS
                       ATP-grasp_2  1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKa.QvlaGGRGKagGvkl.vkskeeakeaakellg 77
                                      +l E++a +++++yg+++pe  v++s+eea + a+k+g    ++K     +  +   gGvkl  +s ee+ +a+ke+l 
  gi|320100341|ref|YP_004175933.1| 17 KLLEHEAFQLIKHYGIPSPEVVVVKSPEEAVALADKVGYPI-ALKIvSPDISHKSDVGGVKLgLRSREEVGKAVKEMLE 94
                                      589**********************************9987.666413345666777****956899**********97 PP

                                      S CS
                       ATP-grasp_2 78 k 78
                                      +
  gi|320100341|ref|YP_004175933.1| 95 T 95
                                      5 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHHHHHHHT.TEEEEEEEE CS
                       ATP-grasp_2 174 kkaakiikklyklfvel.datlvEiNP 199
                                       + +a++i+k  +l+ +  + + +++NP
  gi|320100341|ref|YP_004175933.1| 186 DAIAEMIVKTARLMEDNpEIESIDLNP 212
                                       445555666666655432555555565 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.4e-05      0.14      12      44 ..      27      60 ..      16      64 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                                      TT-BBSSEECSS.BSSHHHHHHHHHHH-SSEEEE CS
                       CPSase_L_D2 12 invpvvpssaap.vetleealaiakeigyPviik 44
                                      i+   +ps +++ v++ eea+a+a+++gyP+ +k
  gi|320100341|ref|YP_004175933.1| 27 IKHYGIPSPEVVvVKSPEEAVALADKVGYPIALK 60
                                      44444555555447*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1702.96
//
Query:       gi|320100342|ref|YP_004175934.1|  [L=301]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   36.5  37.4    1.3e-09   36.2  37.4    1.0  1  DUF3584          Protein of unknown function (DUF3584)
    8.6e-08   32.3   9.6    7.9e-05   22.8   0.8    4.1  4  DUF948           Bacterial protein of unknown function (DUF94
    1.5e-05   25.0   9.4    6.5e-05   23.0   1.7    2.9  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    2.4e-05   24.6   5.0      0.083   13.3   0.1    4.5  4  LPP              Lipoprotein leucine-zipper
    2.6e-05   22.6  36.4    7.3e-05   21.1  17.1    2.3  2  EzrA             Septation ring formation regulator, EzrA
    0.00013   21.4  53.6    0.00097   18.5  10.4    3.4  3  GAS              Growth-arrest specific micro-tubule binding
    0.00017   22.0  16.5      0.026   15.0   4.4    4.9  5  NPV_P10          Nucleopolyhedrovirus P10 protein
    0.00018   21.9   7.3    0.00018   21.9   7.3    4.3  4  Snapin_Pallidin  Snapin/Pallidin
    0.00059   20.0   0.3    0.00059   20.0   0.3    3.0  1  WXG100           Proteins of 100 residues with WXG
    0.00062   19.8  55.0       0.11   12.5  15.2    4.6  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    0.00078   19.5  25.9     0.0012   18.9   3.9    4.1  4  DUF1664          Protein of unknown function (DUF1664)
     0.0012   17.9  22.1     0.0012   17.9  22.1    2.2  2  IFT57            Intra-flagellar transport protein 57
     0.0016   18.5  45.5     0.0083   16.2  15.1    4.1  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0017   18.1   5.3     0.0017   18.1   5.3    5.1  4  SKA2             Spindle and kinetochore-associated protein 2
     0.0024   17.2   5.3     0.0024   17.2   5.3    3.1  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
      0.003   17.4  19.9      0.003   17.4  19.9    3.5  3  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.004   16.5   7.6      0.004   16.5   7.6    3.9  5  DUF3450          Protein of unknown function (DUF3450)
     0.0043   16.0  49.0      0.018   13.9  21.4    3.7  3  Spc7             Spc7 kinetochore protein
     0.0045   17.4   5.4     0.0045   17.4   5.4    5.6  4  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
     0.0052   17.2  13.4     0.0052   17.2  13.4    4.7  4  KELK             KELK-motif containing domain of MRCK Ser/Thr
     0.0068   16.6  11.3     0.0068   16.6  11.3    4.7  4  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
  ------ inclusion threshold ------
      0.012   15.4  34.4       0.15   11.7   6.7    2.8  2  SHE3             SWI5-dependent HO expression protein 3
      0.012   15.4   1.0      0.012   15.4   1.0    2.0  1  DUF2937          Protein of unknown function (DUF2937)
      0.014   15.3   3.8      0.014   15.3   3.8    3.4  3  CK2S             Casein Kinase 2 substrate
      0.014   15.2  11.5      0.045   13.6   1.1    2.9  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      0.015   15.5  43.4      0.092   13.0  20.1    3.2  2  ATG16            Autophagy protein 16 (ATG16)
      0.016   15.9   0.6      0.016   15.9   0.6    4.5  3  Occludin_ELL     Occludin homology domain
      0.019   14.2  44.7      0.026   13.7  44.7    1.1  1  Taxilin          Myosin-like coiled-coil protein
      0.021   14.5   7.6      0.021   14.5   7.6    3.2  3  Laminin_I        Laminin Domain I
      0.022   15.2  16.6      0.022   15.2  16.6    2.6  2  Fez1             Fez1
      0.024   14.7   0.3      0.024   14.7   0.3    6.5  5  bZIP_1           bZIP transcription factor
       0.03   13.2  50.7       0.14   11.0  24.8    2.9  2  DUF812           Protein of unknown function (DUF812)
      0.032   14.6   3.2      0.032   14.6   3.2    4.1  2  HrpB7            Bacterial type III secretion protein (HrpB7)
      0.035   14.4  40.5       0.52   10.6   4.4    4.8  4  DUF5082          Domain of unknown function (DUF5082)
       0.04   14.0  40.6       0.94    9.6   7.8    3.9  4  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.043   13.9   9.2       0.83    9.8   1.1    3.7  3  MbeD_MobD        MbeD/MobD like
      0.058   13.5  42.9      0.026   14.6  17.9    3.5  4  ADIP             Afadin- and alpha -actinin-Binding
      0.083   12.2  35.2      0.052   12.8   3.9    3.7  3  DUF4763          Domain of unknown function (DUF4763)
       0.09   10.9  45.3       0.16   10.1  44.9    1.4  1  HOOK             HOOK protein
      0.099   13.3   0.6      0.099   13.3   0.6    4.8  4  AKNA             AT-hook-containing transcription factor
        0.1   12.7  47.6      0.035   14.2  19.4    3.2  3  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.12   12.3  43.2       0.21   11.5  10.8    4.0  4  YscO             Type III secretion protein YscO
       0.14   12.4  51.5      0.085   13.1   6.4    5.4  5  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.14   12.3   6.4        2.2    8.5   0.7    3.2  2  PI_PP_I          Phosphoinositide phosphatase insertion domai
       0.15   10.7  35.3       0.25    9.9  30.4    2.5  2  AAA_13           AAA domain
       0.15   12.5  64.3       0.36   11.3   4.5    6.2  6  ZapB             Cell division protein ZapB
       0.17   12.4  31.3       0.62   10.6   8.1    3.7  3  Spectrin         Spectrin repeat
       0.19   11.7  20.0       0.92    9.5   0.3    5.3  5  DUF4298          Domain of unknown function (DUF4298)
       0.26   11.8  13.2      0.026   15.0   5.5    2.7  3  T3SSipB          Type III cell invasion protein SipB
       0.26   11.1  22.8        1.2    8.9   6.7    4.2  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.27   11.1  20.2       0.15   12.0   6.3    3.9  4  Sec34            Sec34-like family
       0.28   11.1   1.9        8.4    6.4   0.0    3.8  4  Surfac_D-trimer  Lung surfactant protein D coiled-coil trimer
       0.28   10.4  29.2       0.03   13.6   9.8    2.9  3  TMPIT            TMPIT-like protein
       0.29   10.4  37.9        1.9    7.7  17.6    2.9  2  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
       0.34   11.2   8.6       0.06   13.6   3.1    2.6  1  GlcNAc-1_reg     Putative GlcNAc-1 phosphotransferase regulat
       0.38   10.5  41.3       0.23   11.2  13.4    3.6  2  FAM184           Family with sequence similarity 184, A and B
       0.41   11.3  42.6       0.59   10.8   0.6    5.0  5  YabA             Initiation control protein YabA
       0.43   11.1  53.2         20    5.7  20.6    4.1  2  APG6_N           Apg6 coiled-coil region
       0.45   10.4   3.2        7.2    6.5   0.3    3.5  2  DASH_Dam1        DASH complex subunit Dam1
       0.62    9.7  57.7        8.5    6.0  32.6    3.5  2  Lebercilin       Ciliary protein causing Leber congenital ama
       0.71   10.6   7.0       0.48   11.2   0.5    2.7  2  DUF4326          Domain of unknown function (DUF4326)
       0.72    9.9  55.3      0.026   14.6   7.7    4.4  4  DHR10            Designed helical repeat protein 10 domain
       0.83   10.0  30.8          1    9.7   6.1    5.2  5  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.84    9.0   3.8        2.2    7.6   0.6    2.6  3  TraF_2           F plasmid transfer operon, TraF, protein
       0.85    8.2  45.2      0.039   12.6  15.5    2.9  3  FapA             Flagellar Assembly Protein A
       0.87    8.0   6.6        4.1    5.8   6.1    1.9  2  FUSC             Fusaric acid resistance protein family
       0.92    8.8  25.3       0.54    9.5   8.9    2.3  2  CorA             CorA-like Mg2+ transporter protein
       0.97    8.7  26.1       0.88    8.9  10.7    2.4  2  DUF4407          Domain of unknown function (DUF4407)
          1    9.0  40.2        1.8    8.1   7.3    4.4  3  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
          1    8.7  31.5       0.49    9.7   4.5    3.3  3  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
          1    8.9  44.1       0.95    9.0  21.6    3.3  3  Filament         Intermediate filament protein
          1    9.0  56.0        2.9    7.6  13.6    3.7  3  DUF4201          Domain of unknown function (DUF4201)
        1.6    8.7  13.0        2.5    8.1   1.1    3.8  2  Med10            Transcription factor subunit Med10 of Mediat
        1.8    8.6  32.9       0.09   12.8   5.0    4.1  2  Laminin_II       Laminin Domain II
        2.1    7.9  38.0        6.7    6.3   9.7    3.0  2  DUF4795          Domain of unknown function (DUF4795)
        2.3    7.7  19.5       0.24   10.9   5.0    3.0  4  Allexi_40kDa     Allexivirus 40kDa protein
        2.3    8.6  17.4         68    3.8   1.0    3.3  2  T4SS             Type IV secretion system proteins
        2.6    6.4   6.4        4.3    5.6   6.0    1.5  1  Hemagglutinin    Haemagglutinin
        2.8    8.5  32.8        2.2    8.9   7.9    4.5  3  Syntaxin-6_N     Syntaxin 6, N-terminal
        3.1    8.3  39.6        1.9    9.0   6.6    3.5  3  FlgN             FlgN protein
        3.1    8.5  32.8       0.27   11.9   1.1    6.1  7  SlyX             SlyX
        3.3    7.6  12.5          6    6.8   0.7    4.4  3  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
        3.6    7.3  24.7       0.66    9.7   8.4    3.3  3  DUF745           Protein of unknown function (DUF745)
        3.8    7.6  22.9       0.06   13.4  12.5    2.4  2  GldM_N           GldM N-terminal domain
        4.6    6.4  47.9        5.2    6.2   7.3    3.5  2  HAP1_N           HAP1 N-terminal conserved region
        4.9    7.6  32.6        1.1    9.7   0.6    5.6  5  FlaC_arch        Flagella accessory protein C (FlaC)
          5    6.5  50.9         28    4.0  27.7    2.6  2  HMMR_N           Hyaluronan mediated motility receptor N-term
        6.3    6.3  37.9        0.6    9.6   8.6    3.9  2  PspA_IM30        PspA/IM30 family
        6.4    5.8  50.2       0.62    9.1  24.5    3.2  2  Atg14            Vacuolar sorting 38 and autophagy-related su
        6.6    4.5  34.1       0.61    7.9  10.3    2.8  4  V_ATPase_I       V-type ATPase 116kDa subunit family
          7    4.7  30.2      0.041   12.1   9.5    3.2  3  COG6             Conserved oligomeric complex COG6
        7.4    4.7  12.3        1.9    6.7   4.4    2.1  2  SpecificRecomb   Site-specific recombinase
          8    6.3  50.3       0.36   10.6   6.3    6.8  7  DivIC            Septum formation initiator
        9.1    5.8  18.0        3.5    7.2   8.3    3.1  2  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
        9.5    6.7  33.9       0.24   11.8   9.3    3.9  3  Syntaxin_2       Syntaxin-like protein


Domain annotation for each model (and alignments):
>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2  37.4   7.1e-12   1.3e-09     636     913 ..       6     283 ..       2     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 7.1e-12
                           DUF3584 636 leeakravaeaatalknardtlerlqnekesekdklekaiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedls 712
                                       +ee++r++++a t++ + r++++ l++++ ++  +l+  + e kq+  + ++ l++ l  ++e++++++ee ++ ++
  gi|320100342|ref|YP_004175934.1|   6 IEELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGE-KQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAE 81 
                                       8999************************99999999988765.6677789999******************999998 PP

                           DUF3584 713 eer..lekkakwqevvgeldeqlaelkkaieaartqakarlkeleeaykreLkskdvDpetvkelkrkieeLekkie 787
                                       e+r  +e+ ++++ev +e+++ +++++k++    +  + +++ le   ++++ s   ++ +++++kr ++ L +k e
  gi|320100342|ref|YP_004175934.1|  82 ERRskIEELKALREVLAEKKNTIQSMSKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTA-LLEKAE 157
                                       88722567789*******************************************9999999999999888.88889* PP

                           DUF3584 788 riekrreevreYraflqetwlkvdslaeerpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqld 864
                                       + +k+r+ev+e raf+ +   +v +l ++ + l e+  +l ++  +l+q+l++  ++++   + +e ++++ ++  +
  gi|320100342|ref|YP_004175934.1| 158 KLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSK 234
                                       ***************************************************************************** PP

                           DUF3584 865 qldenlrklrdllsklaelkldadaeqaegelaerlaaleelkrkrerl 913
                                       +++e+  +l+ l +k+++l+ + +++++   l+ + + + e k+ ++rl
  gi|320100342|ref|YP_004175934.1| 235 EIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKKRL 283
                                       *****************99999998888877777777777777777776 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1       1.6     3e+02      21      48 ..       6      33 ..       2      51 .. 0.67
   2 !   10.7   0.1    0.0026      0.49      34      87 ..      54     107 ..      48     109 .. 0.91
   3 ?   -0.6   0.0       8.5   1.6e+03      38      55 ..     146     162 ..     126     169 .. 0.53
   4 !   22.8   0.8   4.2e-07   7.9e-05      23      87 ..     182     246 ..     172     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.6
                            DUF948 21 llklkktldeaaatieelekqvdpilke 48
                                      + +l++ +++a+++i e++++++ + ++
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLLKDQ 33
                                      4556667777777777777766666665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0026
                            DUF948  34 tieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                        i++l++++++i +e ++l+++ ++l+e+ ++k+e++++l e +a+  ++++++
  gi|320100342|ref|YP_004175934.1|  54 DIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSM 107
                                       6899***********************************999999988888876 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 8.5
                            DUF948  38 lekqvdpilkevedllak 55 
                                       + k+++++l+++e+l ++
  gi|320100342|ref|YP_004175934.1| 146 I-KRLTALLEKAEKLRKE 162
                                       2.2333444444444444 PP

  == domain 4  score: 22.8 bits;  conditional E-value: 4.2e-07
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                        l+  l+++++ i +l+++ d + +++e++++k + l + ++ k ++v+++ +++++l++ ++el
  gi|320100342|ref|YP_004175934.1| 182 DLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEEL 246
                                       56778999****************************************************99998 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.0      0.11        20      10      91 ..      15      91 ..       6     146 .. 0.57
   2 !   23.0   1.7   3.5e-07   6.5e-05      13     109 ..     164     258 ..     153     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.11
                      Baculo_PEP_C 10 gggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLt 88
                                      + ++q  ++ + +  ++ q  +++++l+t   + ++ Ln++   lk+ l     ++++   +L +   +l+++ r++++
  gi|320100342|ref|YP_004175934.1| 15 NATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRV-LKERLR----KIKEERRQLIEEYRRLAEERRSKIE 88
                                      6667777777777777777778788888777777777777654.443333....3444444444444444444444444 PP

                      Baculo_PEP_C 89 nln 91
                                       l+
  gi|320100342|ref|YP_004175934.1| 89 ELK 91
                                      333 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 3.5e-07
                      Baculo_PEP_C  13 nqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtn 89 
                                       n+ l++    ++++ q   ++++l++l ++i + L++  ++lk+ l+e+ ++ + l + ++++ n+++ ++++e++ 
  gi|320100342|ref|YP_004175934.1| 164 NEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGK-LTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVN-EVSKEIEE 238
                                       677888888899999999999999999999976.9999999999999999999999999999999999.68888888 PP

                      Baculo_PEP_C  90 lnsiltnLlssvtNinstLn 109
                                       l + l +L  +v N+n  L+
  gi|320100342|ref|YP_004175934.1| 239 LSARLEELREKVNNLNRELE 258
                                       88888888888888887764 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         8   1.5e+03       4      22 ..       8      26 ..       3      36 .. 0.44
   2 ?    0.3   0.1       5.1   9.6e+02      10      27 ..      56      73 ..      49     113 .. 0.56
   3 ?    8.8   0.2     0.011       2.1      11      51 ..     175     215 ..     171     227 .. 0.70
   4 !   13.3   0.1   0.00044     0.083       2      34 ..     229     261 ..     228     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 8
                               LPP  4 eLssqVsqLkskvdqlssd 22
                                      eL  ++++  +++ ++ ++
  gi|320100342|ref|YP_004175934.1|  8 ELQREIENATTQIGEIREK 26
                                      3333333333333333333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 5.1
                               LPP 10 sqLkskvdqlssdvnsak 27
                                        Lk+   +++++  ++ 
  gi|320100342|ref|YP_004175934.1| 56 RVLKERLRKIKEERRQLI 73
                                      555555555555443333 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.011
                               LPP  11 qLkskvdqlssdvnsakaaaqaakeEAaRANqRlDNiaqsY 51 
                                       +Lk +v  ls +++s+++ + +  +E  R  q l+ ++++Y
  gi|320100342|ref|YP_004175934.1| 175 SLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKY 215
                                       56666666666666666666666666666666666666666 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00044
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaak 34 
                                       ++e+s+++++L++  ++l ++vn+++ ++++ak
  gi|320100342|ref|YP_004175934.1| 229 VNEVSKEIEELSARLEELREKVNNLNRELEKAK 261
                                       7899**********************9999997 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1  11.5     0.007       1.3     270     360 ..      17     101 ..       3     131 .. 0.67
   2 !   21.1  17.1   3.9e-07   7.3e-05      75     204 ..     144     274 ..     129     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.007
                                       T--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTH CS
                              EzrA 270 eleledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeelekl 346
                                       ++++ +++e+++ ++++  +L   l++E   k+++ + ++ lke+l +++++ ++l ee++rl ++ + + eel+ l
  gi|320100342|ref|YP_004175934.1|  17 TTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKAL 93 
                                       34667788888888888888999999999999999999999999999999999999999998877644444444444 PP

                                       HHHHHHHHHHHHHH CS
                              EzrA 347 relekelkelekdy 360
                                       re+ +e      + 
  gi|320100342|ref|YP_004175934.1|  94 REVLAE------KK 101
                                       443322......22 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.9e-07
                                       HHTHHHHHT-GGGT--S-.SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHH CS
                              EzrA  75 kklpeieellfeaeelld.kykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrk 150
                                       +k+++++ ll++ae+l + + ++ ++++  ++l+ ++ ++  k+++++e++ +lt+   + +++ e++ +kY+ l++
  gi|320100342|ref|YP_004175934.1| 144 QKIKRLTALLEKAEKLRKeRNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKN 220
                                       378999999999999875156799***************************************************** PP

                                       T--TTTTHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHH CS
                              EzrA 151 kllanrfsygealeelekqleniekefsefeeltengdyveakeilkkleeeid 204
                                       +++a++++  e+ +e+e+  + +e+  ++ ++l+ + +  +   +l++ ++ei 
  gi|320100342|ref|YP_004175934.1| 221 SIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEIL 274
                                       *********************************999988888888888887775 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 ?    4.6  16.9     0.095        18      44     155 ..       8     126 ..       3     139 .. 0.63
   2 !   18.5  10.4   5.1e-06   0.00097      51     134 ..     141     227 ..     135     229 .. 0.78
   3 !   10.3  13.8    0.0017      0.33      38     106 ..     218     285 ..     216     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.095
                               GAS  44 rnekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqsl....knlkarlkelekelkdlkwehevl.eqrf 115
                                       + ++e+++++++  +++e+++ ++ ++ +L  +lk+ + +kq++    + lk+rl++ ++e ++l +e++ l e+r 
  gi|320100342|ref|YP_004175934.1|   8 ELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYlndiRVLKERLRKIKEERRQLIEEYRRLaEERR 84 
                                       56677777777777777777777777777777777666666553111155777777777777777777766524455 PP

                               GAS 116 ekvek..erdelykkfeaaiqevqqktglknllLekklkalq 155
                                       +k+e+  +  e+ ++ +++iq +++++   + +L   +++l+
  gi|320100342|ref|YP_004175934.1|  85 SKIEElkALREVLAEKKNTIQSMSKEARTPSNILRGEIERLE 126
                                       555544444555556666677777777777777766666665 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 5.1e-06
                               GAS  51 eisqenkrlkepLkkaee...eveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerde 124
                                        i q+ krl+  L+kae+   e++e  +  ++y++ k + + l  +l++l +++ +l+ e + l+q++e+v k+++ 
  gi|320100342|ref|YP_004175934.1| 141 RIIQKIKRLTALLEKAEKlrkERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQG 217
                                       45677777777776665511155555556679999999999999999999999999999999999999999999999 PP

                               GAS 125 lykkfeaaiq 134
                                       l+++ ea+ +
  gi|320100342|ref|YP_004175934.1| 218 LKNSIEAKQN 227
                                       9999888765 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0017
                               GAS  38 lkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       lk+  e++++ ++e+s+e ++l+  L++++e+v++L+++l++  k  + l++ k+++ e ++  k+l+ 
  gi|320100342|ref|YP_004175934.1| 218 LKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKA-KLGMMLNAKKQEILEKKQDKKRLTI 285
                                       67788999********************************986.6688999999999999999998876 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.97   1.8e+02      36      59 ..       5      28 ..       2      34 .. 0.79
   2 ?    4.4   0.1      0.28        53      10      66 ..      52     109 ..      49     117 .. 0.82
   3 ?    3.7   0.2      0.45        84      19      60 ..     148     189 ..     127     199 .. 0.65
   4 ?    7.5   0.2      0.03       5.7       8      57 ..     168     214 ..     163     222 .. 0.66
   5 !   15.0   4.4   0.00014     0.026       9      65 ..     190     257 ..     187     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.97
                           NPV_P10 36 dvtelnekLdaqsaqLaeletkve 59
                                       ++el+ ++++ ++q+ e+ +k+ 
  gi|320100342|ref|YP_004175934.1|  5 PIEELQREIENATTQIGEIREKIR 28
                                      578999999999999999998886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.28
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdv.telnekLdaqsaqLaeletkvenIqdiLn 66 
                                       ++di+ +++++  ++++  ++ e+ + + +e  +k++++ a  + l +k ++Iq++  
  gi|320100342|ref|YP_004175934.1|  52 LNDIRVLKERLRKIKEERRQLIEEYRRLaEERRSKIEELKALREVLAEKKNTIQSMSK 109
                                       7899999999999999999999988876256788999999999999999999999966 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.45
                           NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       +++al ++ ++++++ ++v e+ +   ++  q+ +l+ k+++
  gi|320100342|ref|YP_004175934.1| 148 RLTALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQS 189
                                       456666666666666666666666666666666666555554 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.03
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletk 57 
                                        Ira  + ++ +V  l+ ++++++e++ +   l+++ d++ +qL+e+ +k
  gi|320100342|ref|YP_004175934.1| 168 EIRAFYSSLKIQVRDLSGKLQSLREKIGK---LTDERDRLKQQLEEVVKK 214
                                       56666666777777777777777776655...667777777777776655 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 0.00014
                           NPV_P10   9 IradikavddkVdalqqqv...........ddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                        r+ i ++ d  d l+qq+           ++++++ ++v+e++++++++sa L+el +kv+n +  L
  gi|320100342|ref|YP_004175934.1| 190 LREKIGKLTDERDRLKQQLeevvkkyqglkNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNREL 257
                                       566666666666666666666666667776999999**************************998766 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   3.1     0.008       1.5       9      71 ..       7      68 ..       1      81 [. 0.87
   2 ?    0.7   0.8       3.7     7e+02      38      77 ..      71     109 ..      67     115 .. 0.75
   3 ?    2.2   0.8       1.3   2.5e+02      36      76 ..     136     170 ..     116     177 .. 0.67
   4 !   21.9   7.3   9.3e-07   0.00018       6      89 ..     171     253 ..     170     254 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.008
                   Snapin_Pallidin  9 ellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkr 71
                                      e l+ ++++ ++++ e+r++ + L++q  +l  +Lk +e+ +++++l+d++  +++L++ik +
  gi|320100342|ref|YP_004175934.1|  7 EELQREIENATTQIGEIREKIRLLKDQRFKLIGELK-TERGEKQKYLNDIRVLKERLRKIKEE 68
                                      568899*****************************8.66666679***************987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 3.7
                   Snapin_Pallidin  38 rlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslne 77 
                                       +l e++++l+e+   + +++lk  ++ L++ k+ ++s+++
  gi|320100342|ref|YP_004175934.1|  71 QLIEEYRRLAEERR-SKIEELKALREVLAEKKNTIQSMSK 109
                                       67777777777777.6788888888888888888888776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 1.3
                   Snapin_Pallidin  36 ldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmssln 76 
                                       ++++n+ ++++++++       l e a+KL++ ++++ ++ 
  gi|320100342|ref|YP_004175934.1| 136 IEEENRIIQKIKRLTA------LLEKAEKLRKERNEVLEIR 170
                                       4444444444444444......6666777777777777665 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 9.3e-07
                   Snapin_Pallidin   6 gllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       ++++ l+ ++++l  kl++lr++  +L+++ drl+++L+e+ +  +  + + ++  ++ ++++ k++++l+ rl++l
  gi|320100342|ref|YP_004175934.1| 171 AFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQ-GLKNSIEAKQNTVNEVSKEIEELSARLEEL 246
                                       68999**********************************9988777.689*************************** PP

                   Snapin_Pallidin  83 kkRaekL 89 
                                       ++++++L
  gi|320100342|ref|YP_004175934.1| 247 REKVNNL 253
                                       ******9 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 !   20.0   0.3   3.1e-06   0.00059       2      84 ..     176     260 ..     175     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.1e-06
                                       HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTH..HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsG..aaadafqaefeewkqaaqklvdaLeeisealkq 76 
                                       +k++  +l  + ++++++ ++l+de +rlk++++++  +++G  ++ +a q++ +e+ +++++l + Lee++e++++
  gi|320100342|ref|YP_004175934.1| 176 LKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGlkNSIEAKQNTVNEVSKEIEELSARLEELREKVNN 252
                                       5777888888889999*************************8556889***************************** PP

                                       HHHHHHHH CS
                            WXG100  77 aanafeda 84 
                                        ++++e+a
  gi|320100342|ref|YP_004175934.1| 253 LNRELEKA 260
                                       *9999875 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 ?    0.6  17.9       2.7   5.1e+02      20     116 ..      14     103 ..       1     126 [. 0.36
   2 !   12.5  15.2   0.00059      0.11      17     111 ..     124     230 ..      97     232 .. 0.78
   3 !   10.8  13.6    0.0019      0.36      30     111 ..     219     300 ..     210     301 .] 0.61

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.7
                    CENP-F_leu_zip  20 dsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqerv 96 
                                       ++   ++ ++   +  ++ ++ k+i e  t++ e ++  + i+ l+e+lr+++ +  +l +e   L    ++ ++++
  gi|320100342|ref|YP_004175934.1|  14 ENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRL---AEERRSKI 87 
                                       222222222222223333333333333333333333333333333333333333333333333333...34445555 PP

                    CENP-F_leu_zip  97 seLeslnsslenlleekEqe 116
                                       +eL++l++    +l ek + 
  gi|320100342|ref|YP_004175934.1|  88 EELKALRE----VLAEKKNT 103
                                       55554433....33333333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00059
                    CENP-F_leu_zip  17 rkadsLkdkvenLerelemsee..nqekvileaEtskaevet..........lkeeieelaeelreleldLvalrse 81 
                                       r +  L+ +v+++e e  ++++   ++++   aE+ ++e ++          lk +++ l+ +l+ l+ ++ +l+ e
  gi|320100342|ref|YP_004175934.1| 124 RLEWILQTRVLSIEEENRIIQKikRLTALLEKAEKLRKERNEvleirafyssLKIQVRDLSGKLQSLREKIGKLTDE 200
                                       5555677777777777777665213445555677777766666667777777************************* PP

                    CENP-F_leu_zip  82 keeLekelqkkqervseLeslnsslenlle 111
                                       ++ L+++l++  ++ + L+++ +  +n+++
  gi|320100342|ref|YP_004175934.1| 201 RDRLKQQLEEVVKKYQGLKNSIEAKQNTVN 230
                                       **********99999999988777777665 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0019
                    CENP-F_leu_zip  30 erelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr.......sekeeLekelqkkqervseL 99 
                                       +  +e  ++  ++v  e E+  a +e+l+e++++l++el++        +       + +e Lek+  kk+ +++eL
  gi|320100342|ref|YP_004175934.1| 219 KNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKA-------KlgmmlnaKKQEILEKKQDKKRLTIDEL 288
                                       444444444444444555555555555555555555555554.......4555555499999999999********* PP

                    CENP-F_leu_zip 100 eslnsslenlle 111
                                       + +  + e +le
  gi|320100342|ref|YP_004175934.1| 289 KIIYGEPEDFLE 300
                                       998877777776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.2      0.56   1.1e+02      63     120 ..       8      65 ..       3      71 .. 0.50
   2 ?    2.5   3.0      0.77   1.5e+02      53     103 ..      61     111 ..      43     139 .. 0.62
   3 ?    7.1   3.9     0.027       5.2      62     121 ..     140     198 ..      91     200 .. 0.89
   4 !   18.9   3.9   6.1e-06    0.0012      56     119 ..     196     259 ..     195     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.56
                           DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       +L+++i++  +++ e  e ++ +k++  ++ ++l++ + + ++  + ++ l+++l++i
  gi|320100342|ref|YP_004175934.1|   8 ELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKI 65 
                                       4444555555555555555555555555555555555555554444555555555444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.77
                           DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                          ++++ +r+L ++  r+ ++  + +e  k+++e ++e ++ +++++++ 
  gi|320100342|ref|YP_004175934.1|  61 RLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEA 111
                                       344566666666666666666555555555555555555555555555554 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.027
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +++ ++i+r+ + l++ +++ ke ++ev e+r   s+++ +v+ ++   ++l +k+ ++ 
  gi|320100342|ref|YP_004175934.1| 140 NRIIQKIKRLTALLEKAEKLRKE-RNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLT 198
                                       56889999999999998888776.899****************************99885 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 6.1e-06
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       +l++ +++L++++++v kk +  k+ +++ ++ v+ev+++++e++  +e+++e v++l+ +le+
  gi|320100342|ref|YP_004175934.1| 196 KLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEK 259
                                       578899****************************************************999875 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7  12.7      0.52        98     247     347 ..       6     110 ..       2     113 .. 0.67
   2 !   17.9  22.1   6.4e-06    0.0012     177     325 ..     101     261 ..      80     279 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.52
                             IFT57 247 lkklhedisktlekies.rEky..lnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqe 320
                                       +++l+++i+++ ++i + rEk+  l  q  +l+ e+++ + e ++  ++++ l+e++ + ++e +++ ee++++ +e
  gi|320100342|ref|YP_004175934.1|   6 IEELQREIENATTQIGEiREKIrlLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEE 82 
                                       56777777777777754366633367777888888888888888888888888888888888888888888888777 PP

                             IFT57 321 meergssmtDgsp.lvkikkaltklkkE 347
                                         ++ +++   +  l + k++++++ kE
  gi|320100342|ref|YP_004175934.1|  83 RRSKIEELKALREvLAEKKNTIQSMSKE 110
                                       7777766655544134555566666666 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 6.4e-06
                             IFT57 177 ekkee......kekekeeeiieskvdaaeWklEleRvlpqLkvtikadakdWrahleqmkkhkk......sieeslp 241
                                       +   +      ke  ++++i+  +++  eW l ++    + +++i ++ k   a le+ +k++k      +i++ ++
  gi|320100342|ref|YP_004175934.1| 101 K---NtiqsmsKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKAEKLRKernevlEIRAFYS 174
                                       1...122244578899999***********99766555566666667777777777777777766666667777778 PP

                             IFT57 242 etksqlkklhedisktlekies...rEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseele 315
                                       ++k q+++l+ +++   eki +      +l +qlee +++y+ +++++++ ++ ++++s++++el+  l+e+ e+++
  gi|320100342|ref|YP_004175934.1| 175 SLKIQVRDLSGKLQSLREKIGKltdERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVN 251
                                       88888888888888877777762214579************************************************ PP

                             IFT57 316 kvkqemeerg 325
                                       ++ +e+e+ +
  gi|320100342|ref|YP_004175934.1| 252 NLNRELEKAK 261
                                       *****99865 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 ?    2.9   0.3      0.57   1.1e+02      99     125 ..       7      33 ..       4      34 .. 0.53
   2 !   11.8   9.2     0.001      0.19       9      83 ..      40     114 ..      34     127 .. 0.89
   3 !   15.0  17.5   0.00011      0.02      10     127 ..     139     258 ..     135     260 .. 0.84
   4 !   16.2  15.1   4.4e-05    0.0083       3      99 ..     180     278 ..     178     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.57
                        TPR_MLP1_2  99 eelekelselekriedlneqNklLhdQ 125
                                       eel++e+++++++i ++ e+ +lL dQ
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKIRLLKDQ 33 
                                       345555555555555555555555444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.001
                        TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesa 83 
                                       e+k+ + ek+++ ++++ l+e l+k +e+ ++  + Y r   +  + ++el+alre l+e k++i+++ +ea + 
  gi|320100342|ref|YP_004175934.1|  40 ELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEARTP 114
                                       6677778999999********************************************************999875 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 0.00011
                        TPR_MLP1_2  10 ikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakae 86 
                                        +++ +++++++a l+k+ e+l+k+++++ e    Y++  ++  + + +lq+lre++ +l++e+  lk+++e++ ++
  gi|320100342|ref|YP_004175934.1| 139 ENRIIQKIKRLTALLEKA-EKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKK 214
                                       555666666666666655.6799999999999999****************************************** PP

                        TPR_MLP1_2  87 leeseesweeqke...elekelselekriedlneqNklLhdQlE 127
                                        +  ++s+e +++   e  ke++el +r+e+l e+ + L   lE
  gi|320100342|ref|YP_004175934.1| 215 YQGLKNSIEAKQNtvnEVSKEIEELSARLEELREKVNNLNRELE 258
                                       ********998862225679************999888877777 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 4.4e-05
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       ++ l  +++sl+e++ +++++   l+++le+  + ++  +++ e   +  +e +ke+++l ++l+el++++++l+ e
  gi|320100342|ref|YP_004175934.1| 180 VRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRE 256
                                       56778899999999999999999999999999999999999999999999999999999999999999999999999 PP

                        TPR_MLP1_2  80 aesakae..leeseesweeqke 99 
                                       +e+ak    l+++++++ e+k+
  gi|320100342|ref|YP_004175934.1| 257 LEKAKLGmmLNAKKQEILEKKQ 278
                                       9999975225555555555554 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 ?    0.7   0.1       2.3   4.2e+02      47      69 ..       6      28 ..       4      45 .. 0.71
   2 !   18.1   5.3   8.9e-06    0.0017      37      98 ..      49     116 ..      34     126 .. 0.83
   3 ?    1.9   9.1         1   1.9e+02      42      99 ..     189     228 ..     123     244 .. 0.68
   4 ?    1.5   5.1       1.3   2.4e+02      29      63 ..     224     259 ..     218     282 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.3
                              SKA2 47 lkkvkeelqaLkeqceellaekk 69
                                      ++++++e+++  +q+ e+ ++ +
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIR 28
                                      67888888888888888876544 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.9e-06
                              SKA2  37 a...eNpvkLlerlkkvkeelqaLkeqceellaekk...elidkirttlvanrellqqLqasaelppl 98 
                                       +   ++ ++L erl+k+kee  +L e+ + l++e++   e  +++r  l++ ++++q++ ++a +p++
  gi|320100342|ref|YP_004175934.1|  49 QkylNDIRVLKERLRKIKEERRQLIEEYRRLAEERRskiEELKALREVLAEKKNTIQSMSKEARTPSN 116
                                       3455678999**************************66666678899**************9987765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1
                              SKA2  42 kLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasaelppls 99 
                                        L e++ k+++e   Lk+q+ee+ ++ + l ++i++                  ++++
  gi|320100342|ref|YP_004175934.1| 189 SLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEA------------------KQNT 228
                                       455556666666666666666666665555554444..................3333 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 1.3
                              SKA2  29 fqqsypdna.eNpvkLlerlkkvkeelqaLkeqcee 63 
                                       ++q++ ++  ++  +L +rl++++e++++L++++e+
  gi|320100342|ref|YP_004175934.1| 224 AKQNTVNEVsKEIEELSARLEELREKVNNLNRELEK 259
                                       555555555677788888888888888888877765 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 ?   -0.2   8.5       2.6   4.9e+02      34      96 ..      52     111 ..       2     171 .. 0.61
   2 !   17.2   5.3   1.3e-05    0.0024      23     102 ..     173     249 ..     166     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.6
                              HemX  34 taevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqql 96 
                                         ++  l+++l +++++  q   + e+  +l+e+ + + e+l+al++ l+++++ +++++++ 
  gi|320100342|ref|YP_004175934.1|  52 LNDIRVLKERLRKIKEERRQ---LIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEA 111
                                       22223333333333333333...3334444444444555555555555555555555555554 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.3e-05
                              HemX  23 yylgqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskv 99 
                                       y   + qv +l+ + ++l++++ +l ++ ++   +k+q +e+ +++q l++++ea+++++++ +k++eel+++l+++
  gi|320100342|ref|YP_004175934.1| 173 YSSLKIQVRDLSGKLQSLREKIGKLTDERDR---LKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEEL 246
                                       5555677777888888899999999888888...9999999*********************************998 PP

                              HemX 100 sga 102
                                         +
  gi|320100342|ref|YP_004175934.1| 247 REK 249
                                       776 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 ?    4.9  17.4      0.11        21      66     188 ..      10     129 ..       2     132 .. 0.70
   2 !   17.4  19.9   1.6e-05     0.003      58     183 ..     142     259 ..     135     265 .. 0.80
   3 ?    3.6   4.6      0.28        52      99     155 ..     245     301 .]     244     301 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.11
                          KASH_CCD  66 eeEleelkalvkeleEkrarlkaqnkql.......ekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeL 135
                                       + E+e++ + + e+ Ek + lk q+ +l         e+q     i  L+e+++k++ e+ +l +  + L++e+   
  gi|320100342|ref|YP_004175934.1|  10 QREIENATTQIGEIREKIRLLKDQRFKLigelkteRGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER--- 83 
                                       55555555555555555555555544332222221558999999999999999999999999999999999998... PP

                          KASH_CCD 136 kkqlheleellaekealleektkqieeLkltieEyssiieeLraeksrLeeql 188
                                       ++++   eel+a +e l  ek++ i+++    +E ++  + Lr e++rLe  l
  gi|320100342|ref|YP_004175934.1|  84 RSKI---EELKALREVL-AEKKNTIQSMS---KEARTPSNILRGEIERLEWIL 129
                                       6666...8888889865.55666677665...788999999999999998665 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.6e-05
                          KASH_CCD  58 alqkaklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekae 134
                                        +qk k l   le + +l ke +E   ++ a  + l+     L+ k++sL e++ kl+ e+d lk++l+e +k+ + 
  gi|320100342|ref|YP_004175934.1| 142 IIQKIKRLTALLEKAEKLRKERNEVL-EIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQG 217
                                       56777888888888888777777765.577778889999999*********************************** PP

                          KASH_CCD 135 LkkqlheleellaekealleektkqieeLkltieEyssiieeLraeksr 183
                                       Lk+ +         k+++++e  k+ieeL +++eE++  +++L  e ++
  gi|320100342|ref|YP_004175934.1| 218 LKNSI-------EAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEK 259
                                       **999.......4566667777777777777777777777777665544 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.28
                          KASH_CCD  99 sLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekeallee 155
                                        L++k+++L+ e++k +     ++kk + L k++++ +  ++el+ + +e e +lee
  gi|320100342|ref|YP_004175934.1| 245 ELREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKKRLTIDELKIIYGEPEDFLEE 301
                                       6999*****************999999999999999999999999999999988875 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.0      0.38        72      46      98 ..      10      62 ..       2      65 .. 0.53
   2 ?    6.8   7.3     0.019       3.7      35      90 ..      58     113 ..      39     125 .. 0.84
   3 ?    7.3   4.1     0.014       2.7      48     110 ..     154     216 ..     125     223 .. 0.70
   4 !   16.5   7.6   2.1e-05     0.004      33      98 ..     188     253 ..     175     263 .. 0.90
   5 !    8.3   9.5    0.0067       1.3      16      91 ..     206     283 ..     205     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.38
                           DUF3450 46 kqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98
                                      ++e+++  +++ e  e++++ ++q  +l+ ++++e+ + ++ +++i+ ++++l
  gi|320100342|ref|YP_004175934.1| 10 QREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERL 62
                                      22222222333333455555566666667777777777777777776666655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.019
                           DUF3450  35 sqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                         ++  k+++e+++l +eyr+l ee  s   + + l++++a+ +++i+s+ ++   
  gi|320100342|ref|YP_004175934.1|  58 LKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEART 113
                                       56788899999999999999999999999999999999999999999999988765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.014
                           DUF3450  48 ellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLe 110
                                       e ++++r+ ++e+ +++++ + l+ +v+++  +++sl+e+i +++  +++l++ le+++++++
  gi|320100342|ref|YP_004175934.1| 154 EKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQ 216
                                       344566666666777777777788888888888888888888888888888888887777665 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 2.1e-05
                           DUF3450  33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98 
                                       ++  +ki kl+de++ l+++++++ ++ + l+   e  ++ v+++ +ei++l  ++ee++e  ++l
  gi|320100342|ref|YP_004175934.1| 188 QSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNL 253
                                       56789****************************************************998766665 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0067
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevy..neqlerlvasqeqeiasleeqiee 90 
                                       ++l+++ k+ +   ++ ++ q+ ++++++e +el+a++++l+e++++l+ +  +++l  ++++ +qei + ++++++
  gi|320100342|ref|YP_004175934.1| 206 QQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNREleKAKLGMMLNAKKQEILEKKQDKKR 282
                                       78999999***************************************987611556789999999999999998876 PP

                           DUF3450  91 i 91 
                                       +
  gi|320100342|ref|YP_004175934.1| 283 L 283
                                       5 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.8      0.11        21     214     251 ..       5      42 ..       2      50 .. 0.78
   2 ?    6.7  14.6     0.015       2.8     150     264 ..      40     150 ..      30     152 .. 0.77
   3 !   13.9  21.4   9.5e-05     0.018     147     261 ..     148     261 ..     146     291 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeia 251
                                        iee+++e+++ ++q+ e++eki  lk+q+ +l  e++
  gi|320100342|ref|YP_004175934.1|   5 PIEELQREIENATTQIGEIREKIRLLKDQRFKLIGELK 42 
                                       58899999999999999999999999998877766655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.015
                              Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelq 226
                                       +l++++ + +k  + +  l+++l++ k+e ++ +e+ ++ aee   ++ eeL++lre lae k++i+    + +e +
  gi|320100342|ref|YP_004175934.1|  40 ELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEE-RRSKIEELKALREVLAEKKNTIQ---SMSKEAR 112
                                       5666666666777777777777777777777777777766655.66899999999999999999999...7888889 PP

                              Spc7 227 eqleeleekieelkeqkseleeeiaeaervleeckgws 264
                                       +  + l+ +ie l+   ++    i+e++r++++ k+ +
  gi|320100342|ref|YP_004175934.1| 113 TPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLT 150
                                       99999999999999999999999999999999988765 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 9.5e-05
                              Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkela 223
                                       +l++l e +e+L k+++e+ e+   +++ k ++++   klq+ +e++ +++  e   l+++l+e+ ++++ +k+ ++
  gi|320100342|ref|YP_004175934.1| 148 RLTALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTD-ERDRLKQQLEEVVKKYQGLKNSIE 223
                                       6778888888899988888777666666666655555555555555555443.335566666666666666666666 PP

                              Spc7 224 elqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                        +q+ ++e++++ieel+++ +el+e++++ +r le+ k
  gi|320100342|ref|YP_004175934.1| 224 AKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAK 261
                                       66666666666666666666666666666666666555 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 ?    0.9   0.2       3.4   6.5e+02      17      41 ..       6      30 ..       3      43 .. 0.64
   2 ?    2.9   5.2      0.83   1.6e+02      13      71 ..      58     104 ..      55     109 .. 0.51
   3 !   17.4   5.4   2.4e-05    0.0045      11      75 ..     188     254 ..     178     255 .. 0.88
   4 ?    5.8   6.9       0.1        19      17      68 ..     229     282 ..     226     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 3.4
                       Cep57_MT_bd 17 lkeLedEfehlklelqelaaqynal 41
                                      ++eL+ E+e    +  e +++++ l
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLL 30
                                      5666666666666666666666555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.83
                       Cep57_MT_bd  13 LaevlkeLedEfehlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEaKadqI 71 
                                       L+e l       +++k e+ +l ++y+ l      ++R++  eel++l + l +K++ I
  gi|320100342|ref|YP_004175934.1|  58 LKERL-------RKIKEERRQLIEEYRRLA-----EERRSKIEELKALREVLAEKKNTI 104
                                       44444.......555555555555555555.....555555555555555555555555 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 2.4e-05
                       Cep57_MT_bd  11 eaLaevlkeLedEfehlklelqelaaqynaldpsl..gkrkRkdLaeeleelvkrlEaKadqIykLy 75 
                                       ++L e + +L+dE + lk +l+e+ ++y+ l  s+   ++  +++ +e+eel  rlE+  +++ +L 
  gi|320100342|ref|YP_004175934.1| 188 QSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIeaKQNTVNEVSKEIEELSARLEELREKVNNLN 254
                                       567788999*************************9656666789***************99999886 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.1
                       Cep57_MT_bd  17 lkeLedEfehlklelqelaaqynaldpslgkrkRkdL.aeelee.lvkrlEaKa 68 
                                       ++e  +E+e+l+++l+el+++ n+l+  l+k+k   + +++ +e l k+ ++K 
  gi|320100342|ref|YP_004175934.1| 229 VNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMlNAKKQEiLEKKQDKKR 282
                                       578899********************9997766443313333330334555555 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.6      0.82   1.6e+02      12      34 ..       9      31 ..       4      48 .. 0.68
   2 ?    4.4   9.8      0.28        53       2      51 ..      55     107 ..      54     126 .. 0.82
   3 ?    0.2   0.8       5.6   1.1e+03       6      18 ..     153     165 ..     129     184 .. 0.55
   4 !   17.2  13.4   2.8e-05    0.0052       1      72 [.     186     257 ..     186     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.82
                              KELK 12 lkqEkeelqkelaeaqErlksqk 34
                                      l++E e+++ ++ e++E+++  k
  gi|320100342|ref|YP_004175934.1|  9 LQREIENATTQIGEIREKIRLLK 31
                                      66677777777777777766543 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.28
                              KELK   2 lkeLekqlrllkqEkeelqkelaeaqErlksqkkeLk...daisqrklamqef 51 
                                       ++ L+++lr +k+E+ +l  e+  + E  +s+ +eLk   + ++ +k ++q +
  gi|320100342|ref|YP_004175934.1|  55 IRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKalrEVLAEKKNTIQSM 107
                                       799************************99999988762225666677666655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 5.6
                              KELK   6 ekqlrllkqEkee 18 
                                        ++ + l++E++e
  gi|320100342|ref|YP_004175934.1| 153 LEKAEKLRKERNE 165
                                       2222223333333 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 2.8e-05
                              KELK   1 klkeLekqlrllkqEkeelqkelaeaqErlksqkkeLkdaisqrklamqefsevneklselrsqkqklsRql 72 
                                       kl++L +++  l+ E++ l+++l+e+  +++  k  +   ++  + + +e +e++ +l+elr++++ l R+l
  gi|320100342|ref|YP_004175934.1| 186 KLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNREL 257
                                       789*******************************************************************98 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 ?    4.2   1.0      0.25        48      10      48 ..       2      40 ..       1      50 [. 0.87
   2 ?    5.4   8.4      0.11        20      52     103 ..     152     210 ..     115     211 .. 0.62
   3 !   16.6  11.3   3.6e-05    0.0068      15      97 ..     174     253 ..     171     262 .. 0.65
   4 ?    2.5  10.5      0.89   1.7e+02       8      66 ..     223     281 ..     218     301 .] 0.54

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.25
                       TMF_TATA_bd 10 svqlverlsseirrlEgElaslkeelerleaerdearee 48
                                      s++ +e+l+ ei    +++ +++e++  l+ +r ++  e
  gi|320100342|ref|YP_004175934.1|  2 SSTPIEELQREIENATTQIGEIREKIRLLKDQRFKLIGE 40
                                      678899*********************999999887666 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.11
                       TMF_TATA_bd  52 lmkeneelkelkkeleelek.......eleelqeryetlLellGeksEeveELraDvaD 103
                                       l+++ e+l+++ +e+ e+++       ++++l+ ++++l e +G+ ++e + L++ +++
  gi|320100342|ref|YP_004175934.1| 152 LLEKAEKLRKERNEVLEIRAfysslkiQVRDLSGKLQSLREKIGKLTDERDRLKQQLEE 210
                                       44444444444444444444555555577777777777777777777777777777665 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 3.6e-05
                       TMF_TATA_bd  15 erlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeks 91 
                                       ++l+ ++r l g l+sl+e++ +l+ erd++++++ +++k+ + l   k+++e  ++ ++e++++ e+l   l e  
  gi|320100342|ref|YP_004175934.1| 174 SSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGL---KNSIEAKQNTVNEVSKEIEELSARLEELR 247
                                       5788899**********************9999887777655444...33444444444444444444444444444 PP

                       TMF_TATA_bd  92 EeveEL 97 
                                       E+v+ L
  gi|320100342|ref|YP_004175934.1| 248 EKVNNL 253
                                       444444 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.89
                       TMF_TATA_bd   8 gpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkel 66 
                                       ++++++v++ s+ei +l + l++l+e++++l++e ++a+  ++   k+ e l++++++ 
  gi|320100342|ref|YP_004175934.1| 223 EAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKK 281
                                       44555556666666666666666666666666655555555555554444444444443 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 ?   11.7   6.7   0.00082      0.15      90     189 ..       7     112 ..       2     130 .. 0.78
   2 ?    7.7  20.1     0.014       2.6      63     158 ..     160     259 ..     123     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00082
                                       HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXX CS
                              SHE3  90 kqlkkrlenssaseteleeelerlkvqYdalv...dsqkeYkehYqqeieeLkesleklklenekqleelqerissn 163
                                       ++l+ ++en + +  e +e++  lk q   l+   ++++  k++Y ++i  Lke+l k k+e+++ +ee+ +   + 
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKIRLLKDQRFKLIgelKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER 83 
                                       578889999999999999999999999888873224566679**********************9999999998888 PP

                                       X.XXXXX..X.XXXXXXXXXXXXXXXXXX CS
                              SHE3 164 dkdidtk..l.dsynnkkknlesieeekn 189
                                         +i+++  l + + +kk++++s+++e+ 
  gi|320100342|ref|YP_004175934.1|  84 RSKIEELkaLrEVLAEKKNTIQSMSKEAR 112
                                       88887532231446778888887777654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.014
                                       HHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHH CS
                              SHE3  63 RKer.rlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqYdal...vdsqkeYkehYqqei 135
                                       RKer  ++++   +s+lk +v +l+ + + l++++ +++++  +l+++le++  +Y+ l   ++++++  +  ++ei
  gi|320100342|ref|YP_004175934.1| 160 RKERnEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLknsIEAKQNTVNEVSKEI 236
                                       7887459999999999**9**9**99999***********99*********99999999555667777778899999 PP

                                       HHHHHHHHHHHHHHHSSSXXXXX CS
                              SHE3 136 eeLkesleklklenekqleelqe 158
                                       eeL+ +le+l++  ++ + el++
  gi|320100342|ref|YP_004175934.1| 237 EELSARLEELREKVNNLNRELEK 259
                                       99999999999877765555543 PP

>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.0   6.3e-05     0.012      30     119 ..     182     276 ..     180     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.3e-05
                           DUF2937  30 rLeghldelkrqlagfqatAkrffkgdlealiahyr......qsedpvvradaesiqalverlerLeqelqalqqas 100
                                        L+g+l++l++++ ++ ++ +r ++  le+++++y+      + + + v++  ++i++l +rle+L++++++l+++ 
  gi|320100342|ref|YP_004175934.1| 182 DLSGKLQSLREKIGKLTDERDRLKQ-QLEEVVKKYQglknsiEAKQNTVNEVSKEIEELSARLEELREKVNNLNREL 257
                                       599**********************.*********9332222234567999999*********************88 PP

                           DUF2937 101 llerlvvllraadaeilee 119
                                         ++l ++l+a + eile+
  gi|320100342|ref|YP_004175934.1| 258 EKAKLGMMLNAKKQEILEK 276
                                       8889999999999999875 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   3.1      0.83   1.6e+02      25      94 ..      50     119 ..       7     131 .. 0.68
   2 ?   15.3   3.8   7.4e-05     0.014      22     111 ..     141     226 ..     136     233 .. 0.85
   3 ?    2.0   4.3      0.91   1.7e+02      55      94 ..     223     268 ..     218     289 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.83
                              CK2S  25 slleslsnlaeqlqalqnvklygtplrdfpdlqerLrekq..lealeevlakLrekleelqkvrdsleklvr 94 
                                       + l+    l e+l+ +++ +++    +++  l e+ r k+  l+al evla+ +++++++ k +++ ++++r
  gi|320100342|ref|YP_004175934.1|  50 KYLNDIRVLKERLRKIKEERRQ--LIEEYRRLAEERRSKIeeLKALREVLAEKKNTIQSMSKEARTPSNILR 119
                                       4555556666777777777755..466666666655555522335555555555555555555555555554 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 7.4e-05
                              CK2S  22 eseslleslsnlaeqlqalqnvklygtplrdfpdlqerLrekqlealeevlakLrekleelqkvrdsleklvrdalq 98 
                                       +  + ++ l+ l+e+ + l + +++  + r+f    +  ++ q   l   l++Lrek+ +l + rd+l+++++++++
  gi|320100342|ref|YP_004175934.1| 141 RIIQKIKRLTALLEKAEKLRKERNEVLEIRAF---YSS-LKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVK 213
                                       66678888999999999999999887777777...444.56788899999*************************** PP

                              CK2S  99 lyeekadklslke 111
                                        y++ ++++++k+
  gi|320100342|ref|YP_004175934.1| 214 KYQGLKNSIEAKQ 226
                                       *******998886 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.91
                              CK2S  55 dlqerLrekqlealeevlakLrekleelqkvrdsleklv......r 94 
                                       + +++++ +  +++ee+ a+L+e  e++++++++lek++       
  gi|320100342|ref|YP_004175934.1| 223 EAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKlgmmlnA 268
                                       5677788888899999999999999999999999999875555441 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       3.4   6.5e+02      98     115 ..       9      26 ..       2      63 .. 0.62
   2 ?    6.0   2.2     0.049       9.3      75     151 ..      74     150 ..      71     171 .. 0.78
   3 ?   13.6   1.1   0.00024     0.045     102     168 ..     180     246 ..     156     265 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 3.4
                                       ............HHHHHH CS
                         MCPsignal  98 iqkeindsvesleetrqr 115
                                       +q+ei+++++ + e r++
  gi|320100342|ref|YP_004175934.1|   9 LQREIENATTQIGEIREK 26 
                                       222222222222222222 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                       +E r+LAe+   + +e++al + + ++ n+  ++ +e+r+  +    ++e+ +  l++ v +++e + ++q i++ +
  gi|320100342|ref|YP_004175934.1|  74 EEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLT 150
                                       799****************9954555555555555667777777778899999999999999999999999988654 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00024
                                       ........HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 102 indsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveev 168
                                       + d    l++ r+++ + +++ ++ +++l+e+v++ + ++++++  + +++e s+ iee +  +ee+
  gi|320100342|ref|YP_004175934.1| 180 VRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEEL 246
                                       4444444444444444444444444444444444444444444444444444444444444444333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  17.3      0.15        28      68     159 ..      19     121 ..       2     145 .. 0.79
   2 ?   13.0  20.1   0.00049     0.092      26     180 ..     151     256 ..     135     280 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.15
                             ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                       +  + ++ki  l++++++l  el++   ++++  + ++ l+e l+k +e+ ++  e+ ++l +er++  ++lk ++e
  gi|320100342|ref|YP_004175934.1|  19 QIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALRE 95 
                                       3556678999999**************************************************************** PP

                             ATG16 145 elrekeklvq...........dlqDE 159
                                        l+ek++++q           +l+ E
  gi|320100342|ref|YP_004175934.1|  96 VLAEKKNTIQsmskeartpsnILRGE 121
                                       **********5555555555555555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00049
                             ATG16  26 rLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaq 102
                                        Ll+++++l                                                  + r+e+ e     + l+ 
  gi|320100342|ref|YP_004175934.1| 151 ALLEKAEKL-------------------------------------------------RKERNEVLEIRAFYSSLKI 178
                                       233333333.................................................3333333333333334444 PP

                             ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklek 179
                                       ++++l+ +lq l+ek+ + + + ++l+++ +++ +k++ +++ ++ k+++v+++  E++ L  +l+ + ek ++l++
  gi|320100342|ref|YP_004175934.1| 179 QVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNR 255
                                       44444444444444444444444444444444444444444444444444444444444444444444444444444 PP

                             ATG16 180 E 180
                                       E
  gi|320100342|ref|YP_004175934.1| 256 E 256
                                       3 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   3.6       0.8   1.5e+02       9      93 ..      75     160 ..      71     165 .. 0.73
   2 ?   15.9   0.6   8.5e-05     0.016      24      76 ..     173     225 ..     168     230 .. 0.92
   3 ?    6.5   3.7     0.071        13      30      84 ..     228     282 ..     223     291 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.8
                      Occludin_ELL   9 qrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegsk.eykkieeeilqeykklkkdpeyqekkkrcey 84 
                                       +++r  +e +++ +e k+l + l+e +++++ +++e ++ ++  + e++++e  ++ +  +++++++  +k kr++ 
  gi|320100342|ref|YP_004175934.1|  75 EYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEARTPSNILRgEIERLEWILQTRVLSIEEENRIIQKIKRLTA 151
                                       44555555566667777777777777777777777777766665578888888888899999999999999999999 PP

                      Occludin_ELL  85 LkekLshiK 93 
                                       L ek + ++
  gi|320100342|ref|YP_004175934.1| 152 LLEKAEKLR 160
                                       988877665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 8.5e-05
                      Occludin_ELL  24 YkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyq 76 
                                       Y++l+ +++++s k++ L++++ +l++++++ k+  ee++++y+ lk++ e +
  gi|320100342|ref|YP_004175934.1| 173 YSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAK 225
                                       999*******************************************9987655 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.071
                      Occludin_ELL  30 eleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrcey 84 
                                        ++evsk+++eL+++l+el+e+ ++ ++  e+         k++e +ekk+  + 
  gi|320100342|ref|YP_004175934.1| 228 TVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKKR 282
                                       5566666666666666666666665444444433333333445555555554444 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  44.7   0.00014     0.026      17     299 ..      10     289 ..       2     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00014
                           Taxilin  17 eekleaLvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekL...cRelqkqnkklkees 90 
                                       + ++e  ++ + e+ e+ + l+ q +k      +l+ e+ + q+ l++   +k++L k+    R+l ++ ++l ee 
  gi|320100342|ref|YP_004175934.1|  10 QREIENATTQIGEIREKIRLLKDQRFK---LIGELKTERGEKQKYLNDIRVLKERLRKIkeeRRQLIEEYRRLAEER 83 
                                       556666667777777777777777777...56677777777777888888888888888777899999999999999 PP

                           Taxilin  91 kqrareeeekrkelaekfqakLkdiqaqieekserneklreenaelteKlkslieqyelreehfekllktkelelql 167
                                       + +++e ++ r+ laek     + iq++ +e +++++ lr e ++l+  l++ +   e  +  ++k+ +   l  + 
  gi|320100342|ref|YP_004175934.1|  84 RSKIEELKALREVLAEKK----NTIQSMSKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKA 156
                                       999999998888888775....56999999*************************************9999888777 PP

                           Taxilin 168 aeaKlqqad.allkeeqekkkrekeyllkeakeltkkvkalketekelkeqlnlYaeKfeefqdtLakSnelFatFk 243
                                        + + ++ + +++++     k +   l  +++ l++k+ +l++++  lk+ql+  ++K++ ++++++   ++ ++  
  gi|320100342|ref|YP_004175934.1| 157 EKLRKERNEvLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVS 233
                                       7776655541567788888888999999************************************************* PP

                           Taxilin 244 kEmekmtkktkklEketnlwkskfektnkallemaeertekkkeieklkkkiqkLe 299
                                       kE+e+++  +++l ++ n++ +  ek++   +  a++++  +k+ +k++  i++L+
  gi|320100342|ref|YP_004175934.1| 234 KEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKKRLTIDELK 289
                                       ****************************************************9997 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6  13.8      0.96   1.8e+02      84     190 ..       6     105 ..       2     145 .. 0.77
   2 ?    4.9   2.7       0.1        19      22      94 ..     123     197 ..     103     200 .. 0.54
   3 ?   14.5   7.6   0.00011     0.021      17      79 ..     197     259 ..     192     265 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.96
                         Laminin_I  84 akeLaekikkladnikeilekvatlneneealpssklseelaeaqrlLeelrsRdftkqleeaeaelkaAqkLLsrv 160
                                       ++eL+ +i++   +i ei ek+  l  + ++l  ++l+ e  e q+ L+ +  R +++ l++  +e    ++L ++ 
  gi|320100342|ref|YP_004175934.1|   6 IEELQREIENATTQIGEIREKIRLLKDQRFKL-IGELKTERGEKQKYLNDI--RVLKERLRKIKEER---RQLIEEY 76 
                                       789*******************8888877777.678***************..77777777765554...6788888 PP

                         Laminin_I 161 qtllqklqeenkaLkealrdsLaeyeakLs 190
                                       + l ++ + + + L +alr+ Lae ++  +
  gi|320100342|ref|YP_004175934.1|  77 RRLAEERRSKIEEL-KALREVLAEKKNTIQ 105
                                       88888888888888.888888888777654 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.1
                         Laminin_I  22 edltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvl...akaqkvnaesertlnnakeLaekikkl 94 
                                       e l+  Lq ++  ++++++ i+   k l+ L + +e+L k+ ++vl   a  + ++ ++ + +++ ++L eki kl
  gi|320100342|ref|YP_004175934.1| 123 ERLEWILQTRVLSIEEENRIIQKI-KRLTALLEKAEKLRKERNEVLeirAFYSSLKIQVRDLSGKLQSLREKIGKL 197
                                       555555555555555555555555.556666666666666555554111233455555555555555555555544 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 0.00011
                         Laminin_I  17 inanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaeser 79 
                                       +  + + l+++L+e ++k++  k  ie ++++++++ +e+eeL  ++++ ++k +++n+e e+
  gi|320100342|ref|YP_004175934.1| 197 LTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEK 259
                                       444556677777777777777777777777777777777777777777777777777777665 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  19.5      0.67   1.3e+02      19     144 ..      41     163 ..       4     173 .. 0.76
   2 ?   15.2  16.6   0.00012     0.022      13     121 ..     174     280 ..     170     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.67
                              Fez1  19 Lkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleee 95 
                                       Lk  + e  + l++i  lk +lr ++++ ++  ee ++l e++++k +el+ + + l++kk++ + +++   ++ ++
  gi|320100342|ref|YP_004175934.1|  41 LKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSK---EARTP 114
                                       788888888889999999999999999999999999999999999999999999999999988877776...56666 PP

                              Fez1  96 lkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeL 144
                                        + lr e+++l+   ++ +l+ +e +   q+ ++l++l ++ e+lr+e 
  gi|320100342|ref|YP_004175934.1| 115 SNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKAEKLRKER 163
                                       6667776666665555555555554555555666777777777777654 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 0.00012
                              Fez1  13 slLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekv 89 
                                       s LK Q +d    + +  + i +l  +   l+++lee  ++ + l++s+e k++ ++++ +e+++ +++ e lrekv
  gi|320100342|ref|YP_004175934.1| 174 SSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKV 250
                                       77999999999999888888888888888899999999999999999999999999999999999999999999999 PP

                              Fez1  90 ekleeelkelreelselsleeeeaalesdeak 121
                                       ++l++el++ +  +  ++  +++++le+++ k
  gi|320100342|ref|YP_004175934.1| 251 NNLNRELEKAKLGMMLNA--KKQEILEKKQDK 280
                                       999999999887655533..333333333322 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1       0.2        39      28      59 ..       6      37 ..       4      42 .. 0.89
   2 ?    1.0   7.2       2.4   4.6e+02      26      59 ..      53      86 ..      44      91 .. 0.81
   3 ?    3.3   2.0      0.46        86      31      58 ..     129     155 ..     120     166 .. 0.73
   4 ?   14.7   0.3   0.00013     0.024      29      63 ..     174     208 ..     170     209 .. 0.92
   5 ?    7.0   5.2     0.034       6.4      24      60 ..     225     261 ..     216     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.2
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekL 59
                                      ieeL+r+ +  +++  + ++++  lk+++ kL
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLLKDQRFKL 37
                                      799************************98887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2.4
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 26 aeieeLerrvkaLekeNksLkseleelkkevekL 59
                                        i  L++r  ++++e  +L++e  +l++e+ ++
  gi|320100342|ref|YP_004175934.1| 53 NDIRVLKERLRKIKEERRQLIEEYRRLAEERRSK 86
                                      446789**********************998754 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  31 LerrvkaLekeNksLkseleelkkevek 58 
                                       L++rv  +e+eN   ++++++l+   ek
  gi|320100342|ref|YP_004175934.1| 129 LQTRVLSIEEENR-IIQKIKRLTALLEK 155
                                       8999********9.66667666654443 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  29 eeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       + L+ +v  L+++ +sL++++++l++e++ Lk+++
  gi|320100342|ref|YP_004175934.1| 174 SSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQL 208
                                       578999***************************97 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  24 KqaeieeLerrvkaLekeNksLkseleelkkevekLk 60 
                                       Kq  ++e +++ ++L++  ++L++++++l+ e ek k
  gi|320100342|ref|YP_004175934.1| 225 KQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAK 261
                                       7888888888888888888888888888888888766 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  17.9     0.028       5.3     360     468 ..       6     114 ..       3     127 .. 0.72
   2 ?   11.0  24.8   0.00074      0.14     319     455 ..     154     292 ..     128     301 .] 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.028
                            DUF812 360 ikqveeeleeekeeneelekevk.lkkktlellpdaeeniekLqa...lveasaqrlvelakqWekhRvplieeyre 432
                                       i++++ e+e+  ++  e  ++++ lk + ++l+ + ++   + q+   ++   ++rl     + ++ R++lieeyr+
  gi|320100342|ref|YP_004175934.1|   6 IEELQREIENATTQIGEIREKIRlLKDQRFKLIGELKTERGEKQKylnDIRVLKERLR----KIKEERRQLIEEYRR 78 
                                       5677777777777766554444415777777776655555444440004444555554....55678999******* PP

                            DUF812 433 lkesksekekeaerkleeikklrekmkevaeelrqk 468
                                       l e+ ++k +e +   e +++ +++++ +++e+r+ 
  gi|320100342|ref|YP_004175934.1|  79 LAEERRSKIEELKALREVLAEKKNTIQSMSKEARTP 114
                                       ********************************9985 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00074
                            DUF812 319 eteeelkkkreeele......elqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktle 389
                                       e+ e l+k+r+e le      +l+ q+ +l+ k+++l+e+i kl+++  +++++lee  ++ + l+++++ k+ t++
  gi|320100342|ref|YP_004175934.1| 154 EKAEKLRKERNEVLEirafysSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVN 230
                                       4555666666655533333339999**************************************************99 PP

                            DUF812 390 llpdaeeniekLqalveasaqrlvelakqWekhRvplieeyrelkesksekekeaerkleeikklr 455
                                        +    + ie+L a +e+ ++++ +l ++ ek++  ++ + + ++e  ++k+++ +  ++e+k + 
  gi|320100342|ref|YP_004175934.1| 231 EV---SKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAK-KQEILEKKQDKKRLTIDELKIIY 292
                                       88...899*************************998887643.45566667777777899998776 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 ?    0.8   0.2         3   5.6e+02     109     135 ..       6      32 ..       3      37 .. 0.78
   2 ?   14.6   3.2   0.00017     0.032      81     140 ..     201     260 ..     198     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 3
                             HrpB7 109 vaatarkiaRndaqidacrerierlrr 135
                                       +++ +r+i  +  qi  +re+i+ l++
  gi|320100342|ref|YP_004175934.1|   6 IEELQREIENATTQIGEIREKIRLLKD 32 
                                       677788888888888888888887765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.00017
                             HrpB7  81 rdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaera 140
                                       rd l+++++++ ++ + +++ ++a+++ v+++ ++i  + a+++  re+++ l+r++e+a
  gi|320100342|ref|YP_004175934.1| 201 RDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKA 260
                                       68899999999999999***************************************9987 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.0    0.0039      0.74       3      65 ..       4      67 ..       2      69 .. 0.84
   2 ?   10.6   4.4    0.0027      0.52       3      55 ..      64     116 ..      62     117 .. 0.91
   3 ?    7.3  12.2     0.028       5.3       2     118 ..      98     222 ..      97     224 .. 0.86
   4 ?    5.0   5.7      0.15        28       2      45 ..     219     259 ..     213     286 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0039
                           DUF5082  3 tkisklqaqiaelrseiaaleekIerLkeaktklsde.keslkqkkkklekplnssesWkGkee 65
                                      t i++lq++i+ +  +i  + ekI+ Lk  + kl +e k +  +k+k+l+++ + +e +++ +e
  gi|320100342|ref|YP_004175934.1|  4 TPIEELQREIENATTQIGEIREKIRLLKDQRFKLIGElKTERGEKQKYLNDIRVLKERLRKIKE 67
                                      56999***********************999998655277788999999999988888887654 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0027
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekpln 55 
                                       + ++++++ i+e+r  ++   +kIe+Lk+ ++ l ++k+++++  k+ ++p n
  gi|320100342|ref|YP_004175934.1|  64 KIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEARTPSN 116
                                       557889999*********************************99999988865 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.028
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLk...eaktklsdekeslkqkkkklekplnssesWkGkeennydgirs.. 73 
                                        +k+++ q+   e+r   + l   IerL+   +++    +e++++ qk+k l+  l + e ++++ +n++ +ir+  
  gi|320100342|ref|YP_004175934.1|  98 AEKKNTIQSMSKEARTPSNILRGEIERLEwilQTRVLSIEEENRIIQKIKRLTALLEKAEKLRKE-RNEVLEIRAfy 173
                                       5799*************************98888888899*******************999975.66777777767 PP

                           DUF5082  74 .nlessyqtyvdkldelid...aieeEIerLenqiseaqgvldtlqsql 118
                                        +l+ +++    kl +l     ++ +E  rL++q++e  ++ + l++++
  gi|320100342|ref|YP_004175934.1| 174 sSLKIQVRDLSGKLQSLREkigKLTDERDRLKQQLEEVVKKYQGLKNSI 222
                                       79999****9999988866111568999*********999999999988 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.15
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkq 45 
                                       k++i++ q+ + e ++ei+ l+  +e+L   ++k+   + +l++
  gi|320100342|ref|YP_004175934.1| 219 KNSIEAKQNTVNEVSKEIEELSARLEEL---REKVNNLNRELEK 259
                                       3333333333333333333333333333...3333333333333 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 ?   -1.1   0.1       9.9   1.9e+03      57      83 ..       7      33 ..       3      45 .. 0.50
   2 ?    9.6   7.8     0.005      0.94      15      78 ..      49     112 ..      40     126 .. 0.86
   3 ?    6.6   6.9     0.041       7.8      33     105 ..     136     209 ..     116     210 .. 0.75
   4 ?    9.3  13.6     0.006       1.1      25     109 ..     190     275 ..     186     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 9.9
                             Mod_r 57 eelrselqekleelkelekefeekeqe 83
                                      eel+ e++++  ++ e++++ + ++ +
  gi|320100342|ref|YP_004175934.1|  7 EELQREIENATTQIGEIREKIRLLKDQ 33
                                      444444444444444444444444443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.005
                             Mod_r  15 eeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefe 78 
                                       +++l+ +    ++++++kee+ +l++e ++lae+  s+ +el+ lr+ l+ek +++++++ke +
  gi|320100342|ref|YP_004175934.1|  49 QKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEAR 112
                                       456666654558899******************************************9999865 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.041
                             Mod_r  33 eekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd.allarLqtava 105
                                        e e+ + + ++ + + l++ ++l+++r+e+ e +  + +l+ +++++  +l++l +k ++    ++rL+++++
  gi|320100342|ref|YP_004175934.1| 136 IEEENRIIQKIKRLTALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLtDERDRLKQQLE 209
                                       34444455666666889******************************999999999887765235666666655 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.006
                             Mod_r  25 l.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspdallarL 100
                                       l +++ +l++e++ l ++ e++ +k   l++++e +++ ++e  +e++el++++ee+ ++ ++l +++ ++ l + L
  gi|320100342|ref|YP_004175934.1| 190 LrEKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMML 266
                                       44667889999999999999999999999999999999999999999999999999999999999999999999999 PP

                             Mod_r 101 qtavaeaee 109
                                       +++ +e+ e
  gi|320100342|ref|YP_004175934.1| 267 NAKKQEILE 275
                                       998888655 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       5.5     1e+03      14      45 ..      71     102 ..      56     126 .. 0.72
   2 ?    6.6   0.1     0.043       8.1      46      69 ..     175     198 ..     154     199 .. 0.84
   3 ?    9.8   1.1    0.0044      0.83      20      69 ..     205     254 ..     201     260 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 5.5
                         MbeD_MobD  14 qLQqdYeqrlqeWesafaelqrmfeltqrena 45 
                                       qL ++Y +  +e  s  +el+++ e+ + ++ 
  gi|320100342|ref|YP_004175934.1|  71 QLIEEYRRLAEERRSKIEELKALREVLAEKKN 102
                                       56677777777777888888887777665544 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.043
                         MbeD_MobD  46 aLseqvtgLsqQVesLseqvrRls 69 
                                        L+ qv +Ls   +sL e++ +l+
  gi|320100342|ref|YP_004175934.1| 175 SLKIQVRDLSGKLQSLREKIGKLT 198
                                       7999***************99987 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0044
                         MbeD_MobD  20 eqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqvrRls 69 
                                       +q+l+e    ++ l++ +e +q      s+ +++Ls   e+L e+v+ l 
  gi|320100342|ref|YP_004175934.1| 205 KQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLN 254
                                       56777777777777777777777777666666666666666666666553 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   1.1     0.079        15      75     125 ..       5      55 ..       2      59 .. 0.86
   2 ?    6.6  11.0     0.041       7.8      57     132 ..      36     111 ..      31     115 .. 0.92
   3 ?    1.5  10.2       1.5   2.9e+02      58     129 ..      58     133 ..      56     153 .. 0.68
   4 ?   14.6  17.9   0.00014     0.026      32     141 ..     163     273 ..     145     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.079
                              ADIP  75 kierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                        ie l+++ e  ++++    +k r l+ +  +l+  lk+e+ e q+  n++
  gi|320100342|ref|YP_004175934.1|   5 PIEELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDI 55 
                                       588999999999999999999999999999999999999999999988877 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.041
                              ADIP  57 slnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqy 132
                                       +l  ++++ + e+++  ++i+ lk++l + + e  ++ ++ r l  + ++ ++ lk ++e l+  kn++q++++ +
  gi|320100342|ref|YP_004175934.1|  36 KLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEA 111
                                       566778999**************************************************************98765 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.5
                              ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvq....akerqlekklktleqklknekeelqrlknalqqik 129
                                       l+e++rk++ e  +l  +++rl ++  ++  el+++     +k+++++   k++ +  ++++ e++rl+ +lq++ 
  gi|320100342|ref|YP_004175934.1|  58 LKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALRevlaEKKNTIQSMSKEARTPSNILRGEIERLEWILQTRV 133
                                       5678888888888888888888888777777777555011144445555555555556678888888888887765 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 0.00014
                              ADIP  32 eniaaiinviysLlqardrdle.qreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktl 107
                                       +n +  i   ys l+ + rdl    +sl e+i kl+ e +rl+++ e + ++++ l++ +++ q++ ++  k++++l
  gi|320100342|ref|YP_004175934.1| 163 RNEVLEIRAFYSSLKIQVRDLSgKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEEL 239
                                       45555566778889999999861569*************************************************** PP

                              ADIP 108 eqklknekeelqrlknalqqiktqyahelkkkdr 141
                                       ++ l +++e+++ l++ l++ k  ++   kk+++
  gi|320100342|ref|YP_004175934.1| 240 SARLEELREKVNNLNRELEKAKLGMMLNAKKQEI 273
                                       **********************999999999986 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  11.1      0.02       3.8      45     152 ..      14     112 ..       2     119 .. 0.74
   2 ?   12.8   3.9   0.00028     0.052      90     154 ..     154     218 ..     145     226 .. 0.90
   3 ?    3.4   5.4      0.22        41      38      74 ..     222     259 ..     212     290 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.02
                           DUF4763  45 eeeeldLdeiydelekiKqrvlelrskLalnvpecPeidecvdedlelelltseqpeileLqrnnhkLrqqlaelqq 121
                                       e+  +++ ei +++  +K +  +l ++L+          e  ++++ l++++  +  +++++ +  +L  + ++l++
  gi|320100342|ref|YP_004175934.1|  14 ENATTQIGEIREKIRLLKDQRFKLIGELK---------TERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAE 81 
                                       34444555555555555555555555555.........3455666666667767899******************** PP

                           DUF4763 122 hlkasrkslkelreslcqekkrlrklqkrln 152
                                        +++  ++lk+lre l ++k+++++++k++ 
  gi|320100342|ref|YP_004175934.1|  82 ERRSKIEELKALREVLAEKKNTIQSMSKEAR 112
                                       ****************************976 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00028
                           DUF4763  90 lelelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlnel 154
                                       +++e+l++e  e+le++   + L+ q+++l+ +l++ r+++ +l++++ ++k++l++  k+ + l
  gi|320100342|ref|YP_004175934.1| 154 EKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGL 218
                                       567888999********************************************999888877655 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.22
                           DUF4763  38 lpaeqe.eeeeeldLdeiydelekiKqrvlelrskLal 74 
                                       ++a+q+   e + +++e  + le+++++v+ l+++L  
  gi|320100342|ref|YP_004175934.1| 222 IEAKQNtVNEVSKEIEELSARLEELREKVNNLNRELEK 259
                                       44445545555678899999999999999999998874 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  44.9   0.00084      0.16     343     588 ..      11     257 ..       6     283 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00084
                              HOOK 343 veleeelkkanalrsqlelykkqvqelhkklseeskkadklefelkkleeklealqkekerllaerdaL....ketn 415
                                       +e+e+   +  ++r ++ l+k q   l   l++e    +k  ++++ l+e+l  ++ e+ +l++e   L    +  +
  gi|320100342|ref|YP_004175934.1|  11 REIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLaeerRSKI 87 
                                       567788888999*****************************************************999933334467 PP

                              HOOK 416 eELkcaq.lqqkelsqadalaskssssgenlaaellpaev..reklirLqhENKmL....klkqegseeekltelqe 485
                                       eELk  + + +++ ++ ++++++  ++++ l  e+   e   + +++ +++EN+++    +l+   ++ ekl +  +
  gi|320100342|ref|YP_004175934.1|  88 EELKALReVLAEKKNTIQSMSKEARTPSNILRGEIERLEWilQTRVLSIEEENRIIqkikRLTALLEKAEKLRKERN 164
                                       99987441333332444455555557777777777777643377777777777666111111222222233322222 PP

                              HOOK 486 lledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqkkkeqlee 562
                                       +  + +   ++L+ + r    ++++L++++  l+ +             lk++lee ++k + +++ ++ k+++++e
  gi|320100342|ref|YP_004175934.1| 165 EVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDER----------DRLKQQLEEVVKKYQGLKNSIEAKQNTVNE 231
                                       2222344444555555555555555555555544444..........445555555555555555555555555555 PP

                              HOOK 563 lepklssnkqkieeleeaLkkkdedl 588
                                       +++++++ + + eel+e+ ++ +++l
  gi|320100342|ref|YP_004175934.1| 232 VSKEIEELSARLEELREKVNNLNREL 257
                                       55555555555555555444433333 PP

>> AKNA  AT-hook-containing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3       7.9   1.5e+03      47      67 ..      54      74 ..      35      89 .. 0.74
   2 ?    0.4   0.1       5.7   1.1e+03      15      80 ..      89     115 ..      75     131 .. 0.54
   3 ?    4.9   1.0      0.21        40      42      75 ..     181     214 ..     174     217 .. 0.87
   4 ?   13.3   0.6   0.00053     0.099      37      73 ..     225     261 ..     215     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 7.9
                              AKNA 47 eIyqlgqrleeLkdqtdqlkq 67
                                       I  l++rl ++k+   ql +
  gi|320100342|ref|YP_004175934.1| 54 DIRVLKERLRKIKEERRQLIE 74
                                      577789999999998777644 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 5.7
                              AKNA  15 ylkglrsetlaqklssskgqpgkfdpsreleaeIyqlgqrleeLkdqtdqlkqkveefskdiaqds 80 
                                        lk+lr                                       +     k+ ++++sk+ + +s
  gi|320100342|ref|YP_004175934.1|  89 ELKALR---------------------------------------EVLAEKKNTIQSMSKEARTPS 115
                                       334443.......................................444444445555555444444 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.21
                              AKNA  42 releaeIyqlgqrleeLkdqtdqlkqkveefskd 75 
                                       r l  ++  l++++ +L d  d lkq+ ee+ k+
  gi|320100342|ref|YP_004175934.1| 181 RDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKK 214
                                       6788888999999****************98775 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00053
                              AKNA  37 kfdpsreleaeIyqlgqrleeLkdqtdqlkqkveefs 73 
                                       k +   e+ +eI  l  rleeL++++++l ++ e++ 
  gi|320100342|ref|YP_004175934.1| 225 KQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAK 261
                                       5556678999**********************99875 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 ?    5.1  13.7      0.11        21      65     154 ..      17     107 ..       3     124 .. 0.45
   2 ?   14.2  19.4   0.00019     0.035      66     186 ..     138     257 ..     116     259 .. 0.61
   3 ?   10.4  11.5    0.0027       0.5      67     124 ..     219     285 ..     214     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.11
                           UPF0242  65 l.ekskleekeaklteld..................eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqL 122
                                       + +  ++ ek+++l++++                  ++                     +   +e l++ kee  qL
  gi|320100342|ref|YP_004175934.1|  17 TtQIGEIREKIRLLKDQRfkligelktergekqkylND---------------------IRVLKERLRKIKEERRQL 72 
                                       22566666666666666633333333333333333333.....................444444444444444444 PP

                           UPF0242 123 qekleaiae...dfeelkleleeqLaekqellqey 154
                                        e+    ae      e +++l e Laek++ +q +
  gi|320100342|ref|YP_004175934.1|  73 IEEYRRLAEerrSKIEELKALREVLAEKKNTIQSM 107
                                       44444333322211122233344444444444433 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00019
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklelee 142
                                       e++ + +k++ lt+l     +k+e+l++ ++e  e +  +++ + +++ l  + q+L+ek  +   + ++lk++lee
  gi|320100342|ref|YP_004175934.1| 138 EENRIIQKIKRLTALL----EKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEE 210
                                       3334444444444443....445555555555555555577777777777777777777777777777777777777 PP

                           UPF0242 143 qLaekqel...lqeyqetieeqrsvlekrqdqieqLeskVrDlnyEi 186
                                        +++ q l   ++  q+t++e  +++e+  ++ e+L  kV+ ln E+
  gi|320100342|ref|YP_004175934.1| 211 VVKKYQGLknsIEAKQNTVNEVSKEIEELSARLEELREKVNNLNREL 257
                                       77766544222555677777777777777777777777777777776 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0027
                           UPF0242  67 kskleekeaklteldeglktkeealeelqeeeeeLkee.........ldakeeelerlkeenqqLqe 124
                                       k+ +e+k++ + e ++++++    leel+e+ ++L++e         l+ak++e+ + k++++ L +
  gi|320100342|ref|YP_004175934.1| 219 KNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRElekaklgmmLNAKKQEILEKKQDKKRLTI 285
                                       6789***********99999999**************99999****9***************99986 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  10.0     0.014       2.6      65     138 ..      10      83 ..       7      92 .. 0.94
   2 ?    4.7  14.7      0.14        27      42     136 ..     130     227 ..      85     232 .. 0.84
   3 ?   11.5  10.8    0.0011      0.21      53     140 ..     171     259 ..     166     262 .. 0.88
   4 ?    7.9   4.1     0.015       2.8      66      93 ..     234     261 ..     232     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  65 lkelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrqqerk 138
                                       ++e+e++  q++  rek + l++q  ++  +l+ er ++++  + ++  +  + K++e+ r++ +e +r++e +
  gi|320100342|ref|YP_004175934.1|  10 QREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER 83 
                                       89*******************************************************************99865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHTTT--HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  42 dyrawraqeearlyaeiigklvllkelekvk...qqvalLrekeaelekqveeakqqleaerealrqarkelqearr 115
                                       + r ++++ee+r++++i++ ++ll+  ek++   ++v   r+   +l+ qv ++  +l+  re+  ++ +e    ++
  gi|320100342|ref|YP_004175934.1| 130 QTRVLSIEEENRIIQKIKRLTALLEKAEKLRkerNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQ 206
                                       6788999***********************988889999************************99999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                              YscO 116 aveKfaelarlvraeasrqqe 136
                                       ++e++++  + ++ + +++q 
  gi|320100342|ref|YP_004175934.1| 207 QLEEVVKKYQGLKNSIEAKQN 227
                                       999999888877777766665 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0011
                                       HHHHHHHTTT--HH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  53 rlyaeiigklvllk.elekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvr 128
                                       + y+++++++ +l+  l  ++++++ L ++  +l++q+ee+ +++++  +  +++++ + e +++ e++ +  + +r
  gi|320100342|ref|YP_004175934.1| 171 AFYSSLKIQVRDLSgKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELR 247
                                       567777777776653589999******************************************************** PP

                                       HHHHHHHHHHHH CS
                              YscO 129 aeasrqqerkEe 140
                                       +  +++ + +E 
  gi|320100342|ref|YP_004175934.1| 248 EKVNNLNRELEK 259
                                       **9999999886 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  66 kelekvkqqvalLrekeaelekqveeak 93 
                                       ke+e++ +++  Lrek+++l  ++e+ak
  gi|320100342|ref|YP_004175934.1| 234 KEIEELSARLEELREKVNNLNRELEKAK 261
                                       89************************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 ?    7.9   6.4     0.018       3.4      45     100 ..      24      79 ..       3      82 .. 0.77
   2 ?    5.0   6.5      0.14        27      10      65 ..      54     110 ..      52     116 .. 0.74
   3 ?    8.6  10.2     0.011         2       5     101 ..     116     212 ..     114     216 .. 0.77
   4 ?   13.1   6.4   0.00045     0.085      38     103 ..     173     242 ..     164     243 .. 0.71
   5 ?    4.8   7.3      0.17        32      37      87 ..     235     284 ..     234     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  45 leelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                        e+++  + +  k Ig++k +  ++++ +++++ lke+l ++++e ++l +e   l
  gi|320100342|ref|YP_004175934.1|  24 REKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRL 79 
                                       45555566777799999999999**********************99998887665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.14
                                       -HHHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCT CS
                      Seryl_tRNA_N  10 npeavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkk 65 
                                       ++  +ke+l+k + e  ++++e+  l e+rr+ + el +l++   e  ++I++++k+
  gi|320100342|ref|YP_004175934.1|  54 DIRVLKERLRKIKeERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKE 110
                                       556677777775557778888888888888888888888888777777777776664 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.011
                                       HHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHH CS
                      Seryl_tRNA_N   5 klirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelk 80 
                                       +++r ++e ++  l++R  + ++  ++++  ++  +l  ++e+l++erNe+ + I     +   +  +l  + ++l 
  gi|320100342|ref|YP_004175934.1| 116 NILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKAEKLRKERNEVLE-IRAFYSSLkIQVRDLSGKLQSLR 191
                                       678999999999999999999999**************************964.44444443356666777777777 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  81 eelkaleaelkeleaelekll 101
                                       e++ +l++e + l+++le+++
  gi|320100342|ref|YP_004175934.1| 192 EKIGKLTDERDRLKQQLEEVV 212
                                       777777777777777776665 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  38 rrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekllla 103
                                         +l++++ +l  +  +l ++Igk+ ++     ++ ee++++ + lk+ ++a++++++e+++e+e+l ++
  gi|320100342|ref|YP_004175934.1| 173 YSSLKIQVRDLSGKLQSLREKIGKLTDERdrlkQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSAR 242
                                       455555555555555555555555555555555778999*************************998765 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHH CS
                      Seryl_tRNA_N  37 krrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkale 87 
                                       + +el ++leel+++ N+l++e +kak      ++ ++e+ e k++ k+l+
  gi|320100342|ref|YP_004175934.1| 235 EIEELSARLEELREKVNNLNRELEKAKLGM-MLNAKKQEILEKKQDKKRLT 284
                                       56789999****************999754.66666666666666666655 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 ?    5.4   0.1      0.11        21      12      59 ..      48      95 ..      40     128 .. 0.76
   2 ?    8.5   0.7     0.012       2.2       7      58 ..     207     261 ..     204     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.11
                                      HHHHHHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHC CS
                           PI_PP_I 12 qqaYflnleskeaslkklkqdlnqfllkWeeikktslsLeedLnkian 59
                                      +q Y+  ++  ++ l+k+k +  q++ +++ + ++  s  e+L+++++
  gi|320100342|ref|YP_004175934.1| 48 KQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALRE 95
                                      588888888888999999999999999998888888877778777655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.012
                                       CS-HHHHHH..H.HC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHH CS
                           PI_PP_I   7 kLeeyqqaY..f.lnleskeaslkklkqdlnqfllkWeeikktslsLeedLnkia 58 
                                       +Lee+ + Y  +  ++e k+++++++ +++ ++  + ee++++  +L+ +L+k +
  gi|320100342|ref|YP_004175934.1| 207 QLEEVVKKYqgLkNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAK 261
                                       677777777332135999*********************************9865 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  10.9     0.042         8     363     466 ..       5     110 ..       2     113 .. 0.86
   2 ?    9.9  30.4    0.0013      0.25     293     469 ..      49     259 ..      36     287 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.042
                            AAA_13 363 kiesikklvaeineliakhNekvanleeekeeakkklelhlv..eeleseldeykkkykklekaieklekelkeeea 437
                                        ie+++ +++++ ++i +  ek+  l++++ ++  +l+  +   +++ +++  +k+ ++k++++  +l +e +  ++
  gi|320100342|ref|YP_004175934.1|   5 PIEELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGekQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAE 81 
                                       57889999999999999999999999999999988887766522677789999999999999999999999999999 PP

                            AAA_13 438 elkkleeeikeLekqlrdekpaaeeinke 466
                                       e + + ee k+L++ l ++k++++ + ke
  gi|320100342|ref|YP_004175934.1|  82 ERRSKIEELKALREVLAEKKNTIQSMSKE 110
                                       99999999999999999999999999876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                            AAA_13 293 ekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkaki..... 364
                                       +k++++++ l+e+l ++ +e +   +  e++  l +e +   e+Lk+l+++l +K++ + +  +  ++ ++i     
  gi|320100342|ref|YP_004175934.1|  49 QKYLNDIRVLKERLRKIKEERR---QLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEARTPSNIlrgei 122
                                       5555555555566655555433...3334555555555555666777777777777655553333333333333333 PP

                            AAA_13 365 esikklvaeineliakhNekvanleeekeeakk..klelhlv..............................eeles 409
                                       e+++ ++++   +i++ N++++++++ ++ ++k  kl++ +                                +l++
  gi|320100342|ref|YP_004175934.1| 123 ERLEWILQTRVLSIEEENRIIQKIKRLTALLEKaeKLRKERNevleirafysslkiqvrdlsgklqslrekiGKLTD 199
                                       67777777777777777777777776666444311455544355666777744444444444444444444445555 PP

                            AAA_13 410 eldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                       e d++k++++++ k+ + l+++++++++ ++++ +ei+eL ++l++ ++ ++++n+eL++
  gi|320100342|ref|YP_004175934.1| 200 ERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEK 259
                                       555566666666666666666666666666666666666666666666666666666655 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.5    0.0051      0.97       6      64 ..       6      64 ..       1      65 [. 0.85
   2 ?    7.1  10.6     0.039       7.3      14      56 ..      49      98 ..      47     107 .. 0.73
   3 ?    4.8   1.6       0.2        37      24      54 ..      84     114 ..      84     125 .. 0.77
   4 ?    2.6   5.5      0.99   1.9e+02      23      59 ..     129     167 ..     117     170 .. 0.64
   5 ?   11.3   4.5    0.0019      0.36      12      54 ..     186     228 ..     174     234 .. 0.59
   6 ?    4.1  18.9      0.34        64       7      64 ..     202     259 ..     202     289 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0051
                              ZapB  6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64
                                       e+L+  i++a ++i + +++i+ Lk +  +l  e +  + e ++  ++   ++erl+k
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRK 64
                                      68999999999999999999999999999999988888888888888888899999887 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.039
                              ZapB 14 qkaidtitlLqmeieeLkeeneelkeenrele.......eeneqlkeere 56
                                      qk ++ i+ L++++++ kee ++l ee r+l        ee+++l+e  +
  gi|320100342|ref|YP_004175934.1| 49 QKYLNDIRVLKERLRKIKEERRQLIEEYRRLAeerrskiEELKALREVLA 98
                                      67788899999999999999999999999999777755566666665444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.2
                              ZapB  24 qmeieeLkeeneelkeenreleeeneqlkee 54 
                                       + +ieeLk+  e l+e+++ +++  ++ ++ 
  gi|320100342|ref|YP_004175934.1|  84 RSKIEELKALREVLAEKKNTIQSMSKEARTP 114
                                       579***************9999777766655 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.99
                              ZapB  23 LqmeieeLkeeneelkeenrele.........eeneqlkeereawq 59 
                                       Lq ++   +een+         +         e+ e+l++er+++ 
  gi|320100342|ref|YP_004175934.1| 129 LQTRVLSIEEENRII-------QkikrltallEKAEKLRKERNEVL 167
                                       555555556666333.......222233345599999999999876 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.0019
                              ZapB  12 kiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkee 54 
                                       k q++ ++i +L  e ++Lk++ ee  ++ + l+ ++e+ +++
  gi|320100342|ref|YP_004175934.1| 186 KLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNT 228
                                       5566666666666666666666666666666666555555544 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.34
                              ZapB   7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                       ++L ++ ++ + +++ L++ ie+ +  ++e ++e++el++ +e+l+e  +++++ l+k
  gi|320100342|ref|YP_004175934.1| 202 DRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEK 259
                                       6899999999************************************999999999987 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   8.1    0.0035      0.66      17      94 ..      23      99 ..       6     106 .. 0.86
   2 ?    4.8   7.4      0.21        40      37     104 ..     167     230 ..     122     231 .. 0.68
   3 ?   10.6   8.1    0.0033      0.62      15      89 ..     188     257 ..     179     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0035
                                      HHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin 17 ieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLke 94
                                      i+ek +ll+++++ k + e+++   + + + ++++  +er+++++e  ++l++e    +ee ++++eel    e L e
  gi|320100342|ref|YP_004175934.1| 23 IREKIRLLKDQRF-KLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAE 99
                                      7888999999999.*************************************999999999999999999887777655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  37 qallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLe 104
                                        +    +  l+ ++++  +++++l e   kl+de     ++++++lee+ ++++ Lk  +++++++++
  gi|320100342|ref|YP_004175934.1| 167 LEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDE----RDRLKQQLEEVVKKYQGLKNSIEAKQNTVN 230
                                       4444444555555666677777777777777777....688999999999999999999999988765 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHH CS
                          Spectrin  15 eWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerW 89 
                                       + ++ek  +l++e+  +  +++++ +kk+++l++ ++a+q+ v+++ +  e+l ++     ee++e++++ln+  
  gi|320100342|ref|YP_004175934.1| 188 QSLREKIGKLTDERD-RLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSAR----LEELREKVNNLNREL 257
                                       567888888854444.8889999999***************************777....488888888888754 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       1.4   2.7e+02      11      36 ..       6      31 ..       3      35 .. 0.82
   2 ?    0.7   0.5       2.8   5.3e+02       5      36 ..      49      80 ..      46      99 .. 0.69
   3 ?    9.5   0.3    0.0049      0.92       2      42 ..     137     176 ..     136     188 .. 0.84
   4 ?    5.4   0.3     0.097        18       3      32 ..     193     222 ..     185     226 .. 0.80
   5 ?    5.9   0.6     0.067        13       4      36 ..     222     254 ..     220     262 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHHHHHTHHHHHHHH CS
                           DUF4298 11 isallqqLeealeqwkklqkklakLd 36
                                      i++l++++e+a  q+ ++ +k++ L+
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLLK 31
                                      67888999999999999998888775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.8
                                      HHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHH CS
                           DUF4298  5 ekildeisallqqLeealeqwkklqkklakLd 36
                                      +k l++i  l + L +  e+ ++l ++++ L 
  gi|320100342|ref|YP_004175934.1| 49 QKYLNDIRVLKERLRKIKEERRQLIEEYRRLA 80
                                      56666666666666666666666666666654 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTSH CS
                           DUF4298   2 eemekildeisallqqLeealeqwkklqkklakLdeYYqse 42 
                                       ee + i+++i++l++ Le+a e+++k  +++ +++++Y+s 
  gi|320100342|ref|YP_004175934.1| 137 EEENRIIQKIKRLTALLEKA-EKLRKERNEVLEIRAFYSSL 176
                                       66678899999999888876.99***************985 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.097
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTHHHH CS
                           DUF4298   3 emekildeisallqqLeealeqwkklqkkl 32 
                                       ++ k++de  +l qqLee++++++ l++ +
  gi|320100342|ref|YP_004175934.1| 193 KIGKLTDERDRLKQQLEEVVKKYQGLKNSI 222
                                       556778888889999999999999887665 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHH CS
                           DUF4298   4 mekildeisallqqLeealeqwkklqkklakLd 36 
                                       +e++ + ++++ +++ee+ +++++l +k+++L+
  gi|320100342|ref|YP_004175934.1| 222 IEAKQNTVNEVSKEIEELSARLEELREKVNNLN 254
                                       566667777777777777777777777776664 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       9.4   1.8e+03      71      93 ..       8      30 ..       3      82 .. 0.71
   2 ?    0.5   0.4       4.1   7.8e+02      46      87 ..      67     108 ..      50     168 .. 0.59
   3 ?   15.0   5.5   0.00014     0.026      40     113 ..     186     256 ..     171     289 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 9.4
                                      HHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB 71 qaksaadaatkkvdeaqkrlkeL 93
                                      +++ ++++at ++ e+ +++  L
  gi|320100342|ref|YP_004175934.1|  8 ELQREIENATTQIGEIREKIRLL 30
                                      56777777888888877777666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 4.1
                                       STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB  46 delqtalseakgatddleaaiekadqaksaadaatkkvdeaq 87 
                                       +e +++++e + ++++   +ie+++ +  +  + ++ ++   
  gi|320100342|ref|YP_004175934.1|  67 EERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMS 108
                                       444445555555555555555555444444444443333333 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 0.00014
                                       TT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH.. CS
                           T3SSipB  40 aasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa 113
                                       +++ l +++ ++++e + ++++le+ ++k++ +k  ++a ++ v+e+ k ++eL   +    +l+++++ ++  
  gi|320100342|ref|YP_004175934.1| 186 KLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEEL---SARLEELREKVNNLNRE 256
                                       556778899999999999999999999999999999999999999999977777...33333333333333322 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.4     0.038       7.2      96     166 ..      44     110 ..       4     138 .. 0.66
   2 ?    3.2   0.7      0.37        70     106     167 ..     148     208 ..     118     211 .. 0.62
   3 ?    8.9   6.7    0.0064       1.2      97     162 ..     205     275 ..     189     287 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.038
                      Bacillus_HBL  96 dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqne 166
                                       + ++k++ l+++  L+e + ++++e +qli+e ++l+++  ++ +++    + l ++la ++ +i+ + +e
  gi|320100342|ref|YP_004175934.1|  44 ERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEEL----KALREVLAEKKNTIQSMSKE 110
                                       56677777777777777777777777777777766655544444433....34445555555555444444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.37
                      Bacillus_HBL 106 llekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqnei 167
                                       +l++L e++ +  ke ++ + e++++ ++l+  +++++ +++ l + ++    + + l++++
  gi|320100342|ref|YP_004175934.1| 148 RLTALLEKAEKLRKE-RNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQL 208
                                       344444444444443.3455567777777777777777777776666655555555555555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0064
                      Bacillus_HBL  97 kkdkaellellekLqeeiqqnqkevkqlikeLkklklkl...akdsknFktdvdelt..silagdsgvisq 162
                                       k++ +e++++++ L+++i  +q++v++++ke+++l  +l    ++++n++ ++++++   +l++++ +i +
  gi|320100342|ref|YP_004175934.1| 205 KQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLeelREKVNNLNRELEKAKlgMMLNAKKQEILE 275
                                       45668999999999999999999999999988888766511156788888777544311566666666554 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.7     0.069        13      20      65 ..      49      94 ..      37     105 .. 0.63
   2 ?    0.2   0.2       3.2     6e+02      46      64 ..     148     166 ..      94     185 .. 0.60
   3 ?    8.6   1.1    0.0085       1.6      11      67 ..     158     214 ..     134     217 .. 0.76
   4 ?   12.0   6.3   0.00079      0.15       4      87 ..     186     272 ..     183     284 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.069
                             Sec34 20 dealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65
                                      ++ l++++ l+e+ ++++e+ ++l e+  +l ee+++  e  ++++
  gi|320100342|ref|YP_004175934.1| 49 QKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALR 94
                                      4556666667777777777777777777777776665554444444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 3.2
                             Sec34  46 aceqlleeqkrleelaeei 64 
                                       +   lle+ ++l++  +e+
  gi|320100342|ref|YP_004175934.1| 148 RLTALLEKAEKLRKERNEV 166
                                       2233444444444444444 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0085
                             Sec34  11 ecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                       ++++  +++ e+    ++l+ ++++ s k +sl+e+  +l++e++rl++  ee+ +k
  gi|320100342|ref|YP_004175934.1| 158 KLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKK 214
                                       333334455556667889999999999999999999999999999999988888665 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00079
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe.eldpit. 78 
                                       +L+s +e++ +l ++ d++++qLee+ +k++  +++ ++ +++ +++ +e ++l+   ee++ek++  + el++++ 
  gi|320100342|ref|YP_004175934.1| 186 KLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNrELEKAKl 262
                                       68888899999999999999999999999998888888888888888888888888888888877654324554432 PP

                             Sec34  79 .rkLnspgss 87 
                                         +Ln+++ +
  gi|320100342|ref|YP_004175934.1| 263 gMMLNAKKQE 272
                                       2455555555 PP

>> Surfac_D-trimer  Lung surfactant protein D coiled-coil trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       3.8   7.3e+02       9      21 ..     116     128 ..     112     131 .. 0.83
   2 ?    6.4   0.0     0.044       8.4       3      19 ..     175     191 ..     173     196 .. 0.88
   3 ?   -1.0   0.1       8.9   1.7e+03       4      20 ..     204     220 ..     202     223 .. 0.68
   4 ?   -0.7   0.0       7.1   1.3e+03       3      16 ..     245     258 ..     243     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHH CS
                   Surfac_D-trimer   9 eaLeGklqrLqna 21 
                                       ++L G++ rL+ +
  gi|320100342|ref|YP_004175934.1| 116 NILRGEIERLEWI 128
                                       6899*****9865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHHHHH CS
                   Surfac_D-trimer   3 aLrQrveaLeGklqrLq 19 
                                       +L+ +v+ L Gklq L 
  gi|320100342|ref|YP_004175934.1| 175 SLKIQVRDLSGKLQSLR 191
                                       899***********997 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 8.9
                                       HHHHHHHHHHHHHHHHH CS
                   Surfac_D-trimer   4 LrQrveaLeGklqrLqn 20 
                                       L+Q++e    k q L+n
  gi|320100342|ref|YP_004175934.1| 204 LKQQLEEVVKKYQGLKN 220
                                       88888877666666665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 7.1
                                       HHHHHHHHHHHHHH CS
                   Surfac_D-trimer   3 aLrQrveaLeGklq 16 
                                        Lr +v++L+ +l 
  gi|320100342|ref|YP_004175934.1| 245 ELREKVNNLNRELE 258
                                       59*******98876 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.3     0.082        15       8      86 ..      17     108 ..       6     119 .. 0.44
   2 ?    4.4   6.3     0.097        18       3      62 ..      54     137 ..      52     176 .. 0.64
   3 ?   13.6   9.8   0.00016      0.03       4      82 ..     187     264 ..     176     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.082
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.............eeeeeeveel 71 
                                       ++++ e++e+ + +k +  +l    ++ + e +k  ++++ lk++l+k+k++ +             +++ ee++ l
  gi|320100342|ref|YP_004175934.1|  17 TTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRqlieeyrrlaeerRSKIEELKAL 93 
                                       33333333333333333333333333333333333333444455555555543334444445554444444555555 PP

                             TMPIT  72 keelkerkkvlkeve 86 
                                       +e l+e+k+++++++
  gi|320100342|ref|YP_004175934.1|  94 REVLAEKKNTIQSMS 108
                                       566666666666665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.097
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.................. 61 
                                       +++ l++++++++e+ ++++++ ++l++   +  +e+k  ++ l e k+++++++k+++                  
  gi|320100342|ref|YP_004175934.1|  54 DIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEARtpsnilrgeierlewilq 130
                                       56667778888888888888888888888888888888888888888888888877755444444444433334443 PP

                             TMPIT  62 ......e 62 
                                             e
  gi|320100342|ref|YP_004175934.1| 131 trvlsiE 137
                                       4433333 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00016
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       +++l++++ +l ++ +++kq+lee+ k  + ++++i+ +++ ++e+++++++l++++ ee +e+v++l++el+++k 
  gi|320100342|ref|YP_004175934.1| 187 LQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARL-EELREKVNNLNRELEKAKL 262
                                       678899999999999999999999999999999999999999999999999999997.6889999999999999885 PP

                             TMPIT  81 vl 82 
                                        +
  gi|320100342|ref|YP_004175934.1| 263 GM 264
                                       43 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  17.6      0.01       1.9     102     247 ..      20     167 ..       2     177 .. 0.70
   2 ?    2.8  26.2      0.31        58     104     242 ..      99     256 ..      84     294 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.01
                    ALIX_LYPXL_bnd 102 lqenkedlelLsgpeeeleaalpssssaaasesveeqirklrsllekldelkaereqllkdlkekaendDitpkl.. 176
                                       + e++e+++lL+ ++ +l   l ++       + ++ ++++r l e+l ++k+er+ql+++ +  ae+   ++k+  
  gi|320100342|ref|YP_004175934.1|  20 IGEIREKIRLLKDQRFKLIGELKTE-----RGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER--RSKIee 89 
                                       4455666666654444444444422.....46888999999999999***********99996655555..444333 PP

                    ALIX_LYPXL_bnd 177 ltekkr............diaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskksdseqsqr 241
                                       l+++++              +a   +++++ e+e ++ + +    s++++++++++i+++ + +e++ k ++     
  gi|320100342|ref|YP_004175934.1|  90 LKALREvlaekkntiqsmSKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKAEKLRK----- 161
                                       222222444444488888556667789*******999888777799************99999999977655..... PP

                    ALIX_LYPXL_bnd 242 qreevl 247
                                       +r+evl
  gi|320100342|ref|YP_004175934.1| 162 ERNEVL 167
                                       555554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.31
                    ALIX_LYPXL_bnd 104 enkedlelLsgpeeeleaalpssssa.......................aasesveeqirklrsllekldelkaere 157
                                       e k++++ +s++++           +                       + ++   ++i++l  llek ++l++er+
  gi|320100342|ref|YP_004175934.1|  99 EKKNTIQSMSKEAR-----------TpsnilrgeierlewilqtrvlsiEEENRIIQKIKRLTALLEKAEKLRKERN 164
                                       33333333333222...........1222233333334444433333332367788889999999999999999999 PP

                    ALIX_LYPXL_bnd 158 qllkdl....kekaendDitpkl..ltekkr..diaanefealfeeelekydplqeqleqslakqeellkeiqeane 226
                                       ++l+        k++  D + kl  l+ek    + + +  ++ +ee ++ky+ l++ +e++ +  +e+ kei+e+ +
  gi|320100342|ref|YP_004175934.1| 165 EVLEIRafysSLKIQVRDLSGKLqsLREKIGklTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSA 241
                                       98875444543478889999999664444445533445667778999999999999999999999999999999999 PP

                    ALIX_LYPXL_bnd 227 efeqskksdseqsqrq 242
                                       ++e+ +++ ++  +r+
  gi|320100342|ref|YP_004175934.1| 242 RLEELREKVNNL-NRE 256
                                       999999998854.333 PP

>> GlcNAc-1_reg  Putative GlcNAc-1 phosphotransferase regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.1   0.00032      0.06      20      78 ..     233     290 ..     220     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00032
                      GlcNAc-1_reg  20 fketnelkskLeeklaekvkllelylekrvalldlndfkdldeLlkddkknvtidndel 78 
                                        ke +el ++Lee l+ekv+ l+  lek    + ln  k+  +  k+dkk +tid+ ++
  gi|320100342|ref|YP_004175934.1| 233 SKEIEELSARLEE-LREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKKRLTIDELKI 290
                                       5778899999976.9*************9999999888876666778*******98655 PP

>> 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 ?    1.0  20.0       1.7   3.2e+02      27     201 ..       9     161 ..       6     172 .. 0.46
   2 ?   11.2  13.4    0.0012      0.23      31     141 ..     180     292 ..     170     301 .] 0.64

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.7
                            FAM184  27 iqqilaetrekilqykskveeeldlkqkiaeleesleqhekekrqalaefeqykrrveerelkleaehsqkvvelsr 103
                                       +q+ ++++  +i ++++k+     lk ++ +l  +l++   e                      ++++ + +  l++
  gi|320100342|ref|YP_004175934.1|   9 LQREIENATTQIGEIREKIRL---LKDQRFKLIGELKTERGE----------------------KQKYLNDIRVLKE 60 
                                       444444444444444444332...222223333333344444......................4455555555555 PP

                            FAM184 104 eveevkrkFeeklrqfaqlqeqle..qekekaLeelrkkhreeveeLlkeqeaqsekllkeqekleekhkaeveklk 178
                                        + ++k++  + ++++  l+e+     e+ kaL e+ ++ ++ ++++ ke ++ s+ l  e e+le  ++++v +++
  gi|320100342|ref|YP_004175934.1|  61 RLRKIKEERRQLIEEYRRLAEERRskIEELKALREVLAEKKNTIQSMSKEARTPSNILRGEIERLEWILQTRVLSIE 137
                                       55555555555555555555443333456666666666666666666666666666666666666666666666666 PP

                            FAM184 179 eeveelekekkklve..eyEeklak 201
                                       ee   ++k  k+l++  e+ ekl k
  gi|320100342|ref|YP_004175934.1| 138 EENRIIQKI-KRLTAllEKAEKLRK 161
                                       544333332.222220022223333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0012
                            FAM184  31 laetrekilqykskveeeldlkqki.aeleesleqhekekrqalaefeqykrrvee.relkle.aehsqkvvelsre 104
                                       +++ + k++ +++k+++ +d + ++ ++lee +++++  k+   a+ ++  + ++e +el+++ +e ++kv +l+re
  gi|320100342|ref|YP_004175934.1| 180 VRDLSGKLQSLREKIGKLTDERDRLkQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEiEELSARlEELREKVNNLNRE 256
                                       67889999999999999999987753689999999998888776665555444433122332225677777777777 PP

                            FAM184 105 veevkrkFeeklrqfaqlqeqleqekekaLeelrkkh 141
                                       +e++k       ++ +++ e+++  k+  ++el+  +
  gi|320100342|ref|YP_004175934.1| 257 LEKAKLGMMLNAKK-QEILEKKQDKKRLTIDELKIIY 292
                                       77776554433333.2222333334445577777665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.6       0.3        57      11      41 ..       7      37 ..       3      54 .. 0.53
   2 ?    7.1   6.5     0.045       8.5       3      67 ..      48     112 ..      46     120 .. 0.71
   3 ?    1.2   0.9         3   5.6e+02      23      47 ..     142     165 ..     117     177 .. 0.54
   4 ?   10.8   0.6    0.0031      0.59       4      43 ..     181     220 ..     178     227 .. 0.83
   5 ?    7.1   9.3     0.046       8.7       8      79 ..     220     294 ..     216     295 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.3
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA 11 eeleeqleelleeleelkeelaelleenaeL 41
                                      eel++++e+ +++++e++e++  l ++  +L
  gi|320100342|ref|YP_004175934.1|  7 EELQREIENATTQIGEIREKIRLLKDQRFKL 37
                                      4555555555555555555555444444333 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXX CS
                              YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkels 67 
                                       k++ ++ ++ l+e+l++++ee ++l ee  +l ee ++   e + lre l+e++++ ++ +ke +
  gi|320100342|ref|YP_004175934.1|  48 KQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEAR 112
                                       66667777788888888888888888888888888777777799999999766666555555444 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  23 eleelkeelaelleenaeLelenek 47 
                                        ++++k +l++lle+ ++L+ e ++
  gi|320100342|ref|YP_004175934.1| 142 IIQKIK-RLTALLEKAEKLRKERNE 165
                                       222222.233344444444444333 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLel 43 
                                       ++l  kl++l e++++l++e ++lk++l+e++++ + L+ 
  gi|320100342|ref|YP_004175934.1| 181 RDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKN 220
                                       6788899999999999999999999999999999988874 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHH.XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLelenek..lrerl.eeeekkekekkkelsegkenLarlYee 79 
                                       +++e+ +++++e+++e+eel ++l+el e+ ++L+ e ek  l  +l +++++  ++k+ +++ + ++L+ +Y e
  gi|320100342|ref|YP_004175934.1| 220 NSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKakLGMMLnAKKQEILEKKQDKKRLTIDELKIIYGE 294
                                       667777888999999999999999999999999987755500555554333344455555566677888888865 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  20.6      0.11        20      34     127 ..       8      98 ..       3     145 .. 0.74
   2 ?    3.5  26.7      0.52        99      16     124 ..     157     262 ..     134     289 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.11
                            APG6_N  34 klkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelql 110
                                       +l++e +++    +++ e++e+++ l++++ +l+ eLk    e+++  ++++ l+e l++++ee ++ ++ey+ l+ 
  gi|320100342|ref|YP_004175934.1|   8 ELQREIENA---TTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAE 81 
                                       555554443...35777777777777777777777777777777777777777777777777777777777777777 PP

                            APG6_N 111 elleleeeldsleaqye 127
                                       e  ++ eel++l   ++
  gi|320100342|ref|YP_004175934.1|  82 ERRSKIEELKALREVLA 98 
                                       77777777776654444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.52
                            APG6_N  16 kqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                       ++l++ ++e  + ++f + lk + ++      +l++l+e++ kl +e+++l ++L+e+ k+ + l++ ++a +++ +
  gi|320100342|ref|YP_004175934.1| 157 EKLRKERNEVLEIRAFYSSLKIQVRD---LSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVN 230
                                       34444444445555566666655444...346788888888888888888888888888888888888888888888 PP

                            APG6_N  93 aleeeeerfwreynelqlelleleeeldslea 124
                                       ++ +e e+   +  el+ ++++l+ el++ + 
  gi|320100342|ref|YP_004175934.1| 231 EVSKEIEELSARLEELREKVNNLNRELEKAKL 262
                                       88888888888777777777777777766554 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   0.0      0.75   1.4e+02       2      19 ..     191     208 ..     175     223 .. 0.56
   2 ?    6.5   0.3     0.038       7.2       6      30 ..     230     254 ..     225     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.75
                         DASH_Dam1   2 epafaeLaDsletLdknl 19 
                                       ++++ +L+D+ + L+++l
  gi|320100342|ref|YP_004175934.1| 191 REKIGKLTDERDRLKQQL 208
                                       233333444444444333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.038
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLs 30 
                                       +e ++++e+L+++le+L +  ++L+
  gi|320100342|ref|YP_004175934.1| 230 NEVSKEIEELSARLEELREKVNNLN 254
                                       6667777777776666666555555 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  32.6     0.045       8.5      13     188 ..       6     189 ..       2     193 .. 0.75
   2 ?    0.1  30.7       2.9   5.5e+02      24     174 ..     130     282 ..     129     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.045
                        Lebercilin  13 ikeLqnelaelqskleelrkEnklLkrlqkrqekaL.......skyedteaeLpqllarhneEvrvlrerlRksqek 82 
                                       i+eLq e++++  ++ e+r+  +lLk++ ++   +L       +ky ++   L + l++ +eE r l e++R++ e+
  gi|320100342|ref|YP_004175934.1|   6 IEELQREIENATTQIGEIREKIRLLKDQRFKLIGELktergekQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEE 82 
                                       89***************************998888822222223555555556666666666666666666666666 PP

                        Lebercilin  83 erelekklkekeaellrlkdklkklkk.LsedknL..aereeLqkkLeeleakleekeekikeLerkleleeksfrr 156
                                        r+  ++lk   + l + k++++ ++k      n    e e+L+  L++    +ee+++ i++ +r   l+ek+   
  gi|320100342|ref|YP_004175934.1|  83 RRSKIEELKALREVLAEKKNTIQSMSKeARTPSNIlrGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKA--E 157
                                       6666666666666666666666666664333344422477777777999999999****************997..5 PP

                        Lebercilin 157 qlaaekkktkeaqeevkalqeeierlkqklke 188
                                       +l++e++ + e+++  ++l+ ++++l+ kl+ 
  gi|320100342|ref|YP_004175934.1| 158 KLRKERNEVLEIRAFYSSLKIQVRDLSGKLQS 189
                                       799***********************999985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.9
                        Lebercilin  24 qskleelrkEnklLkrlqkr.....qekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekea 95 
                                       q ++  +++En++++++++       +++L+k  ++  e+    ++ +  vr l  +l  ++ek  +l  +  +  +
  gi|320100342|ref|YP_004175934.1| 130 QTRVLSIEEENRIIQKIKRLtalleKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQ 206
                                       66777788999999888654111113445666666666777778899999999999999999999999999999999 PP

                        Lebercilin  96 ellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkleleeksfrrqlaaekkktkeaqeev 172
                                       +l+++ +k++ lk+  e+k+ +  +e++k++eel+a+lee +ek+++L+r+le    +   +l+a+k+ + e +++ 
  gi|320100342|ref|YP_004175934.1| 207 QLEEVVKKYQGLKNSIEAKQ-NTVNEVSKEIEELSARLEELREKVNNLNRELEK--AKLGMMLNAKKQEILEKKQDK 280
                                       99999999999999887777.58999***********************97764..455556666666665555555 PP

                        Lebercilin 173 ka 174
                                       k+
  gi|320100342|ref|YP_004175934.1| 281 KR 282
                                       54 PP

>> DUF4326  Domain of unknown function (DUF4326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5    0.0026      0.48      30      65 ..      60     100 ..      22     104 .. 0.81
   2 ?    2.2   1.2       1.6     3e+02      33      65 ..     207     249 ..     136     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0026
                           DUF4326  30 e.....lgereevvekyreyleeraekdeelkaaleeLrgk 65 
                                       e      +er++ +e+yr+ +eer++k eelka +e L++k
  gi|320100342|ref|YP_004175934.1|  60 ErlrkiKEERRQLIEEYRRLAEERRSKIEELKALREVLAEK 100
                                       345555689***************************99965 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 1.6
                           DUF4326  33 ereevvekyreyleer..........aekdeelkaaleeLrgk 65 
                                       + eevv+ky+   ++           +++ eel a leeLr+k
  gi|320100342|ref|YP_004175934.1| 207 QLEEVVKKYQGLKNSIeakqntvnevSKEIEELSARLEELREK 249
                                       5567777776554443334444444455566666666666654 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 ?    0.1  16.6       4.3   8.1e+02      29     110 ..       7      89 ..       3      95 .. 0.90
   2 ?   -0.3  14.4       5.8   1.1e+03      39     116 ..      35     112 ..      32     113 .. 0.91
   3 ?   14.6   7.7   0.00014     0.026      39     103 ..     146     210 ..     121     212 .. 0.87
   4 ?    9.2  13.7    0.0064       1.2      50     104 ..     206     260 ..     206     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 4.3
                             DHR10  29 qvvekdlrsciklleeieaelakleeak.kklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeek 104
                                       ++++++++++++++ ei ++++ l++++ k + el+ +  ek++ l+++   +erl++  e  ++ +e +r+ aee+
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKIRLLKDQRfKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER 83 
                                       67899*******************999835569*******************************************9 PP

                             DHR10 105 reaaka 110
                                       r + ++
  gi|320100342|ref|YP_004175934.1|  84 RSKIEE 89 
                                       988764 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 5.8
                             DHR10  39 iklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleel 115
                                       +kl+ e+++e  + ++   ++  l+++l + ++e+r+l  + +rl     ++ e+l  lre  +ek++  ++  +e+
  gi|320100342|ref|YP_004175934.1|  35 FKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEA 111
                                       7899999999999999999999999********************999999999*******9999999999988887 PP

                             DHR10 116 r 116
                                       r
  gi|320100342|ref|YP_004175934.1| 112 R 112
                                       7 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 0.00014
                             DHR10  39 iklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaee 103
                                       ik l  + ++ +kl++++ ++ e r+ +++++i++r+l+ k + l+ ++ + +++ +rl++q ee
  gi|320100342|ref|YP_004175934.1| 146 IKRLTALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEE 210
                                       5556666777889*************************************************987 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0064
                             DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeek 104
                                       ++lee+ kk + l++ +e k+++++e+++++e l  +le  +ek + l ++ e+ 
  gi|320100342|ref|YP_004175934.1| 206 QQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKA 260
                                       5678888888888888888888888888888888888888888888887776654 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3      0.56     1e+02      53      78 ..       6      31 ..       2      37 .. 0.84
   2 ?    1.5   0.2         2   3.8e+02      50      79 ..      38      67 ..      34      74 .. 0.83
   3 ?    5.1   3.4      0.15        27      25      73 ..      62     110 ..      49     116 .. 0.85
   4 ?    4.5   3.1      0.22        41      37      87 ..     150     200 ..     123     218 .. 0.58
   5 ?    9.7   6.1    0.0053         1      13      85 ..     206     254 ..     192     262 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.56
                           BLOC1_2 53 lnekyeelqpylqqidqiekqvteLe 78
                                      ++e++ e+++  +qi +i ++++ L+
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLLK 31
                                      6788889*************998876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 2
                           BLOC1_2 50 leklnekyeelqpylqqidqiekqvteLee 79
                                      + +l+ +  e q+yl+ i  +++++++++e
  gi|320100342|ref|YP_004175934.1| 38 IGELKTERGEKQKYLNDIRVLKERLRKIKE 67
                                      567888888999999999999999998765 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.15
                           BLOC1_2  25 LeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekq 73 
                                       L k+ e+  + ++++++ a++ ++k+e+l+++ e l+++++ i+ + k+
  gi|320100342|ref|YP_004175934.1|  62 LRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKE 110
                                       667777777888999999999999*************999999988775 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.22
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                                       ++l ++a++l+k+ +++ e  +  ++++ q+ ++  ++++L e + +L   
  gi|320100342|ref|YP_004175934.1| 150 TALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDE 200
                                       445555555555555555555555555555555555555555555555332 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0053
                           BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                                       +                        +l++v+++ +   + +++k++++++  ++i+++ ++++eL e v+ L+
  gi|320100342|ref|YP_004175934.1| 206 Q------------------------QLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLN 254
                                       3........................344444444444444444455555555555555555555555555443 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.8   3.4e+02      15      73 ..      32      92 ..      26     113 .. 0.69
   2 ?    0.3   0.0         2   3.7e+02      28      81 ..     134     193 ..     121     198 .. 0.74
   3 ?    7.6   0.6     0.012       2.2      35      82 ..     196     250 ..     186     273 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.8
                            TraF_2 15 eddvglllplsvgvevgdvdnlvDkiDdlsdildgleaavnaasad......etqvdeaaddlna 73
                                      ++++ l++   +  e g++++ +++i  l+++l ++++   +++++      e    +++++l+a
  gi|320100342|ref|YP_004175934.1| 32 DQRFKLIG--ELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEyrrlaeE--RRSKIEELKA 92
                                      45888777..4899999999999999999999999999999999986554331..2333333333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2
                            TraF_2  28 vevgdvdnlvDkiDdlsdildgleaavnaasad.....etq.vdeaaddlnalLedlggd 81 
                                       +++++ + ++ ki +l++ l+++e+  ++ ++       ++ ++ +++dl + L++l+++
  gi|320100342|ref|YP_004175934.1| 134 LSIEEENRIIQKIKRLTALLEKAEKLRKERNEVleiraFYSsLKIQVRDLSGKLQSLREK 193
                                       577888999999999999999888777665555777763335777788888888877765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.012
                            TraF_2  35 nlvDkiDdlsdild....gleaavnaasad..etq..vdeaaddlnalLedlggdg 82 
                                       +l+D+ D+l+++l+    ++++  n+ +a+  + +  v++++++l a Le+l+++ 
  gi|320100342|ref|YP_004175934.1| 196 KLTDERDRLKQQLEevvkKYQGLKNSIEAKqnT-VneVSKEIEELSARLEELREKV 250
                                       566777755555554444555555554444432.2357777777777777776654 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  14.0     0.019       3.6     333     439 ..       7     112 ..       2     120 .. 0.62
   2 ?    1.7  15.8       0.4        76     340     429 ..     140     234 ..      94     240 .. 0.60
   3 ?   12.6  15.5    0.0002     0.039     334     422 ..     182     276 ..     168     297 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                              FapA 333 pelkeklkeleeeleeleeeleklkkk.ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                        el++++++  +++ e++e+++ lk++ +k++ +lk e   +++ ++++  l+e + k+kee ++l ee+ +l ee 
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKIRLLKDQrFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER 83 
                                       34555555666666666666666665564444444444444556666666666666666666666666666666666 PP

                              FapA 409 eskkeeakikvnkeiypgvkikigkkkliik 439
                                       +sk   +++k+ +e+  + k +i++++++ +
  gi|320100342|ref|YP_004175934.1|  84 RSK--IEELKALREVLAEKKNTIQSMSKEAR 112
                                       666..55888888888888888887777665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.4
                              FapA 340 keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk..... 411
                                       +++ +++++l + lek +k  k+ ++  +  ++ s  k q+  l  ++++l+e++ +l++e+++lk++le+      
  gi|320100342|ref|YP_004175934.1| 140 NRIIQKIKRLTALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVvkkyq 216
                                       44444444443333333333222222222333455667777777777788888888888877777777777765553 PP

                              FapA 412 keeakikvnkeiypgvki 429
                                         +++i++++  +++v  
  gi|320100342|ref|YP_004175934.1| 217 GLKNSIEAKQNTVNEVSK 234
                                       223356665555555544 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.0002
                              FapA 334 elkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                       +l  kl+ l+e++ +l +e ++lk++++++ k+ +  k+  + k+++++++ ++ e+l+ +leel+e+ ++l+ ele
  gi|320100342|ref|YP_004175934.1| 182 DLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQgLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELE 258
                                       45555666666666666666666666665555444445555667899999999999999999999999999999999 PP

                              FapA 410 sk.....keeakikvnke 422
                                       +       +++k ++ ++
  gi|320100342|ref|YP_004175934.1| 259 KAklgmmLNAKKQEILEK 276
                                       884444322224344333 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.0      0.46        87     259     330 ..      37     106 ..       3     126 .. 0.55
   2 ?    5.8   6.1     0.022       4.1     189     330 ..      93     231 ..      56     280 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.46
                              FUSC 259 llaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaa 330
                                       l+ el++  ++  ++++  +++ l +rlr++++++ +  +  ++l+++ ++ ++el +l++ l++ ++ i++
  gi|320100342|ref|YP_004175934.1|  37 LIGELKT--ERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQS 106
                                       3333333..555666666677777777777777666666666666666666666666666555555555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                              FUSC 189 ararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaa 265
                                        r+ la++ ++++++++ a++ s+ +r ++++l  +l+  +  +   + + +  +rl a  ++a++ l++   e+ +
  gi|320100342|ref|YP_004175934.1|  93 LREVLAEKKNTIQSMSKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKAEK-LRKERNEVLE 168
                                       566666666666666666666666666666666666555555555555555555555555555532.4444444444 PP

                              FUSC 266 leaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaa 330
                                       +  +a+ + l+ +++ l  +l++lr+   + +d +++l ++l e++++++ l  s++a ++   +
  gi|320100342|ref|YP_004175934.1| 169 I--RAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNE 231
                                       2..34566666666666666666666666666666666666666666666666666666655544 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   8.4     0.066        13     121     228 ..       7     110 ..       3     117 .. 0.84
   2 ?    9.5   8.9    0.0029      0.54     120     222 ..     146     257 ..     137     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.066
                              CorA 121 drlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdl 197
                                       ++l +++e+  +++ e+ + + +  k++ ++ + +l+++ ++ +++l++ r +  ++l+    k++ ++  e +r+l
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKI-RLLKDQRFKLIGELKTERGEKQKYLNDIRVLK-ERLR--KIKEERRQLIEEYRRL 79 
                                       667788888888888888888.77888888999999************998777.6666..4777777777779*** PP

                              CorA 198 ldelerllemlealrerleslqdtyssllse 228
                                        +e ++ +e+l+alre+l   ++t++s++ e
  gi|320100342|ref|YP_004175934.1|  80 AEERRSKIEELKALREVLAEKKNTIQSMSKE 110
                                       ******************9999999998765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0029
                              CorA 120 vdrlfellekleeeldeledel........edstkkeilrelaqlrrrlvkl...rralapnrevlkrllakaddkl 185
                                       ++rl +llek e+ ++e  + l         + + +++ ++l  lr++++kl   r+ l+++ e + + ++ ++++ 
  gi|320100342|ref|YP_004175934.1| 146 IKRLTALLEKAEKLRKERNEVLeirafyssLKIQVRDLSGKLQSLREKIGKLtdeRDRLKQQLEEVVKKYQ-GLKNS 221
                                       66777788888888887777777788999999999*****************7776666655555545555.78888 PP

                              CorA 186 lddedkeylrdlldelerllemlealrerleslqdty 222
                                       +++++ +  ++++ e+e l+  le lre++++l+ ++
  gi|320100342|ref|YP_004175934.1| 222 IEAKQ-NTVNEVSKEIEELSARLEELREKVNNLNREL 257
                                       88776.88*************************9876 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  15.9     0.073        14     147     249 ..      60     224 ..       3     224 .. 0.53
   2 ?    8.9  10.7    0.0047      0.88     115     223 ..     155     261 ..     144     289 .. 0.45

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.073
                           DUF4407 147 aeidaaearldalraeaqkeldgtk.............gtgttgvaGkgpaake....................... 187
                                       + +++ ++++++l +e+++ ++  +              ++ + ++   ++a++                       
  gi|320100342|ref|YP_004175934.1|  60 ERLRKIKEERRQLIEEYRRLAEERRskieelkalrevlAEKKNTIQSMSKEARTpsnilrgeierlewilqtrvlsi 136
                                       33333333333333333333222111111111111111111111222222222233333333333334444444444 PP

                           DUF4407 188 ........kkaqldaaqaelaelkakld.........................atarlaalraelaeleaerakera 231
                                               k + l+a+ ++        +                          + +l++lr+++ +l++er++ ++
  gi|320100342|ref|YP_004175934.1| 137 eeenriiqKIKRLTALLEKA-------EklrkernevleirafysslkiqvrdLSGKLQSLREKIGKLTDERDRLKQ 206
                                       43333222222222222222.......133335557777888999******************************** PP

                           DUF4407 232 asqaaaaaddGllarlea 249
                                       + ++  ++ +Gl   +ea
  gi|320100342|ref|YP_004175934.1| 207 QLEEVVKKYQGLKNSIEA 224
                                       *******99999776665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0047
                           DUF4407 115 eqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaq 191
                                       ++++  ke +e l+   +a ++ l+ q+++l+++++++++++ +l++e ++ l+++  +  ++ +G   + ++k++ 
  gi|320100342|ref|YP_004175934.1| 155 KAEKLRKERNEVLE--IRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDR-LKQQLEEVVKKYQGLKNSIEAKQNT 228
                                       44444444444444..55555555555555555555555555555444442.2222333333344455555555555 PP

                           DUF4407 192 ldaaqaelaelkakld.atarlaalraelaele 223
                                        ++ ++e++el+a+l+  ++++++l++el++++
  gi|320100342|ref|YP_004175934.1| 229 VNEVSKEIEELSARLEeLREKVNNLNRELEKAK 261
                                       555555555555554443333333333333322 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 ?   -1.6  18.4       9.5   1.8e+03      43     127 ..       9      92 ..       2     168 .. 0.77
   2 ?    1.1  20.5       1.4   2.7e+02      17     126 ..      53     223 ..      48     229 .. 0.73
   3 ?    8.1   7.3    0.0098       1.8      75     120 ..     221     266 ..     217     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 9.5
                     PI3K_P85_iSH2  43 iseeiqlkrqaleaFneaikmFeeq.iklqekfskeaqehEieklqenleqlksrlkelhsskekLeedlkqqkeee 118
                                       ++ ei+   +++   +e i+++++q  kl+ +++ e  + E++k  + ++ lk+rl ++++++++L e+ +  +ee 
  gi|320100342|ref|YP_004175934.1|   9 LQREIENATTQIGEIREKIRLLKDQrFKLIGELKTE--RGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER 83 
                                       567788888888888888888888755777776554..678888888888888888888888888888877777777 PP

                     PI3K_P85_iSH2 119 releReina 127
                                       r+   e+ a
  gi|320100342|ref|YP_004175934.1|  84 RSKIEELKA 92 
                                       754444444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.4
                     PI3K_P85_iSH2  17 eklrevskqlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaq.............. 79 
                                       ++ r +++ l + ++e+ ql eey ++ ee   +r ++e  +   +++ e+ +++ ++skea               
  gi|320100342|ref|YP_004175934.1|  53 NDIRVLKERLRKIKEERRQLIEEYRRLAEE---RRSKIEELKALREVLAEKKNTIQSMSKEARtpsnilrgeierle 126
                                       455666677777788888888999988887...55555555666667889999999999999445555566666777 PP

                     PI3K_P85_iSH2  80 ..................................................ehEieklqenleqlksrlkelhsskek 106
                                                                                         +  +++l+  l+ l++++ +l +++++
  gi|320100342|ref|YP_004175934.1| 127 wilqtrvlsieeenriiqkikrltallekaeklrkernevleirafysslKIQVRDLSGKLQSLREKIGKLTDERDR 203
                                       77777778777777888888888888888888888888888888888887777778888888888888888888888 PP

                     PI3K_P85_iSH2 107 LeedlkqqkeeereleRein 126
                                       L+++l++ +++++ l  +i 
  gi|320100342|ref|YP_004175934.1| 204 LKQQLEEVVKKYQGLKNSIE 223
                                       88888888877777665554 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0098
                     PI3K_P85_iSH2  75 skeaqehEieklqenleqlksrlkelhsskekLeedlkqqkeeere 120
                                       s ea+++ ++++++ +e+l +rl+el+++ ++L+ +l++ k   ++
  gi|320100342|ref|YP_004175934.1| 221 SIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMML 266
                                       6789999999****************************99876664 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   9.1      0.65   1.2e+02     151     255 ..      32     134 ..       5     139 .. 0.67
   2 ?    9.7   4.5    0.0026      0.49     179     240 ..     154     216 ..     129     224 .. 0.79
   3 ?    8.0   4.3    0.0084       1.6     181     239 ..     219     271 ..     210     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.65
                   Phlebovirus_NSM 151 eekdktisr.ktkesEediknqvlhseieqlknelqkkRndikrgqekrdakklveesmArvkdlkeelkiltdels 226
                                       +++ k+i   kt+  E+    q   ++i  lk++l+k + +  r q  ++ ++l ee   +++    elk l + l 
  gi|320100342|ref|YP_004175934.1|  32 DQRFKLIGElKTERGEK----QKYLNDIRVLKERLRKIKEE--RRQLIEEYRRLAEERRSKIE----ELKALREVLA 98 
                                       44445554435555555....77778888888888888888..88888888888888888887....5566777777 PP

                   Phlebovirus_NSM 227 qikseiqilrkkikdfetvvpA.......llsvAll 255
                                       + k+ iq++ k  +    ++         +l + +l
  gi|320100342|ref|YP_004175934.1|  99 EKKNTIQSMSKEARTPSNILRGeierlewILQTRVL 134
                                       888888888888877777766655555555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0026
                   Phlebovirus_NSM 179 qlknelqkkRndikrgqe.krdakklveesmArvkdlkeelkiltdelsqikseiqilrkkik 240
                                        + ++l+k Rn++   +    + k  v+++  + + l+e+  +ltde +++k++++   kk +
  gi|320100342|ref|YP_004175934.1| 154 EKAEKLRKERNEVLEIRAfYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQ 216
                                       4567899*****88776525788999***************************9998877765 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0084
                   Phlebovirus_NSM 181 knelqkkRndikrgqekrdakklveesmArvkdlkeelkiltdelsqikseiqilrkki 239
                                       kn ++ k n        +++ k +ee+ Ar ++l+e+   l  el+++k  +    kk 
  gi|320100342|ref|YP_004175934.1| 219 KNSIEAKQN------TVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQ 271
                                       333333333......3567889999************************9998887776 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.3    0.0092       1.7     216     288 ..       4      79 ..       1      81 [. 0.77
   2 ?    0.3   2.8       2.3   4.3e+02     212     275 ..      84     147 ..      79     153 .. 0.71
   3 ?    9.0  21.6     0.005      0.95      32     137 ..     154     261 ..     131     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0092
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 216 eeitelrrqiqsleieleslkkqkasleaqlaeleerleael...eklqeklseleeelaeireemarqlreYqeL 288
                                       + i+el+r+i++ ++++ +++++ + l++q   l  +l++e+   +k+ + ++ l e l++i+ee  + ++eY++L
  gi|320100342|ref|YP_004175934.1|   4 TPIEELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERgekQKYLNDIRVLKERLRKIKEERRQLIEEYRRL 79 
                                       5689999999999999999999999999987777666665551105555667778999999999999999999987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.3
                                       XX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 212 rsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeir 275
                                       rs  ee++ lr  + +++  ++s+ k++++  + l+   erle  l++   +++e ++ +++i+
  gi|320100342|ref|YP_004175934.1|  84 RSKIEELKALREVLAEKKNTIQSMSKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIK 147
                                       5556777888888888888888888888877777777777777777777777777777777766 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.005
                                       XXXXXXXXXX..XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  32 akieeleekk..saevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelk 106
                                        k e+l++++    e++  ++  + ++++l  +l++l ++  +l  e+d+l+++le++ kky+   n+ e+  ++++
  gi|320100342|ref|YP_004175934.1| 154 EKAEKLRKERneVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVN 230
                                       22222222211122333444444557888888888888888888888888888888888888888888888888888 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 107 alrkdldeatlarvdLekkvesLkeelaflk 137
                                       ++ k+++e++ +  +L +kv+ L+ el+  k
  gi|320100342|ref|YP_004175934.1| 231 EVSKEIEELSARLEELREKVNNLNRELEKAK 261
                                       8888888888888888888888888887655 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  16.0       1.1   2.1e+02      45     133 ..       7      95 ..       6     103 .. 0.91
   2 ?    6.6  16.2     0.031       5.8       7     136 ..      89     216 ..      84     222 .. 0.77
   3 ?    7.6  13.6     0.016       2.9      46     111 ..     224     289 ..     218     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.1
                           DUF4201  45 eqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkler 121
                                       e lq+e+++ +++I e  +++  lk++  k + +l++++   + + +  + lk++l++++e++++l +e  ++ +er
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER 83 
                                       67999********************************************************************9999 PP

                           DUF4201 122 dklrkqneklkq 133
                                           ++ + l++
  gi|320100342|ref|YP_004175934.1|  84 RSKIEELKALRE 95 
                                       888888887776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.031
                           DUF4201   7 elsklrlklislkhqlakiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkktt..ktvhalth 81 
                                       el++lr  l+++k++++ ++++ ++  ++       + e l+   q+ +  Iee n  ++++k+ t+   +  +l  
  gi|320100342|ref|YP_004175934.1|  89 ELKALREVLAEKKNTIQSMSKEARTPSNI----LRGEIERLEWILQTRVLSIEEENRIIQKIKRLTAllEKAEKLRK 161
                                       55555666666666665555555554443....23355666666777888899999999999988764467788888 PP

                           DUF4201  82 lkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136
                                       +++   ++++ +s lk + +++  +l++lr+++ k+  erd+l++q e++ ++ +
  gi|320100342|ref|YP_004175934.1| 162 ERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQ 216
                                       888888*******************************************998865 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.016
                           DUF4201  46 qlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklr 111
                                         q+ +++ +k+Iee ++ L++l++k+++   +l+  k  ++ ++++++ l+k+ ++k  ++++l+
  gi|320100342|ref|YP_004175934.1| 224 AKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKKRLTIDELK 289
                                       67999*****************************99999999999999999998888888887775 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 ?    8.1   1.1     0.013       2.5      77     107 ..      70     100 ..       7     113 .. 0.88
   2 ?    1.9   5.8       1.1   2.1e+02       2      52 ..     206     253 ..     101     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Med10  77 refvelvrrkNqlmkGkmeafkkfrdvLaee 107
                                       r+++e+ rr  ++ + k+e +k +r+vLae+
  gi|320100342|ref|YP_004175934.1|  70 RQLIEEYRRLAEERRSKIEELKALREVLAEK 100
                                       899**************************97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHS--TT.S-TTHHHHHHHHHHHHHHHHHHHHH.. CS
                             Med10   2 qqlkeviqsllelgvqvsdydenessqevlaqklktlvesLqelsktaskl 52 
                                       qql+ev+++   l+  +++ ++   + +++++++++l+++L+el ++ ++l
  gi|320100342|ref|YP_004175934.1| 206 QQLEEVVKKYQGLKNSIEAKQN---TVNEVSKEIEELSARLEELREKVNNL 253
                                       5555555555555555555554...67778888888888888887776654 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.1     0.045       8.5      10      92 ..     141     222 ..     134     227 .. 0.54
   2 ?   12.8   5.0   0.00048      0.09       2      45 ..     219     262 ..     218     287 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.045
                                       XXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  10 etakevleqlapls..qnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                        +++++++ +a l+  ++l ++++++ ei++     + +v+d++  +++ r+++ kL+ + ++L ++l+e+ ++ ++
  gi|320100342|ref|YP_004175934.1| 141 RIIQKIKRLTALLEkaEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQG 217
                                       55555555444443113455555555566665556666666666666666666666666666666666666666555 PP

                                       ...HHHHH CS
                        Laminin_II  85 ssslsdni 92 
                                          l+++i
  gi|320100342|ref|YP_004175934.1| 218 ---LKNSI 222
                                       ...33333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00048
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetne 45 
                                       k+ +++ ++t++ev + +++ls++le+++ek++++nr++e+ + 
  gi|320100342|ref|YP_004175934.1| 219 KNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKL 262
                                       67788888999999999999999999999999999999887653 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  22.5      0.15        29      12     170 ..      41     209 ..       6     226 .. 0.74
   2 ?    6.3   9.7     0.036       6.7       6      66 ..     226     286 ..     214     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.15
                           DUF4795  12 lq..........eaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaeka..dkea 76 
                                       l+          ++i+ l+e+l k++e+ ++l ++ +++ ++  +  +++++l++v a+k+++ + ++  a  + + 
  gi|320100342|ref|YP_004175934.1|  41 LKtergekqkylNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEArtPSNI 117
                                       3366666667778999*******************999999999999999999999888888888876655448899 PP

                           DUF4795  77 Latkvsrdq..fDeakkeLekmleellekleeqeealkkaldtLqeelkekldrlelepLkeqleerlkelqkelqe 151
                                       L+  ++r +  +++++  +e+  + +++k++   + l+ka ++L+   ke++++le+  + + l+ +++ l+ +lq+
  gi|320100342|ref|YP_004175934.1| 118 LRGEIERLEwiLQTRVLSIEEE-NRIIQKIKRLTALLEKA-EKLR---KERNEVLEIRAFYSSLKIQVRDLSGKLQS 189
                                       ******9999999998888887.45777777666666555.6666...66777777777777777777777777776 PP

                           DUF4795 152 amekedk.edeaaglrkkLl 170
                                         ek+ k +de   l+++L 
  gi|320100342|ref|YP_004175934.1| 190 LREKIGKlTDERDRLKQQLE 209
                                       66666666556666666653 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.036
                           DUF4795   6 aellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeevee 66 
                                       +++++++ ++ie+l+++le+l ekv++l+ +le+ +  +    k+ e lek+ ++k  + +
  gi|320100342|ref|YP_004175934.1| 226 QNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKKRLTID 286
                                       5568889999999999999999999999999999999999999999999998888765555 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.4      0.15        28      77     144 ..      17      86 ..       4     119 .. 0.46
   2 ?    0.4   0.7         2   3.8e+02      81     133 ..     109     162 ..      90     175 .. 0.60
   3 ?    1.9   0.5      0.71   1.3e+02      81     137 ..     140     197 ..     122     201 .. 0.53
   4 ?   10.9   5.0    0.0013      0.24      75     145 ..     189     261 ..     176     287 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.15
                      Allexi_40kDa  77 ttlLselrdalrtltkl.ldklksvekklelsaetasdskllk.klesietsleelhakldelsssetse 144
                                       tt++ e+r+++r l+++ ++ + +++++  ++++  +d ++lk +l  i+++ ++l ++ ++l+++  s+
  gi|320100342|ref|YP_004175934.1|  17 TTQIGEIREKIRLLKDQrFKLIGELKTERGEKQKYLNDIRVLKeRLRKIKEERRQLIEEYRRLAEERRSK 86 
                                       5556666666666654313333333333333333333333322134444444444444444444333333 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2
                      Allexi_40kDa  81 selrdalrtltklldklksvekklelsaetasd.skllkklesietsleelhak 133
                                        e r+ ++ l+ ++++l+ + ++  ls+e+++   + +k+l+++ ++ e+l ++
  gi|320100342|ref|YP_004175934.1| 109 KEARTPSNILRGEIERLEWILQTRVLSIEEENRiIQKIKRLTALLEKAEKLRKE 162
                                       356666777777777777777776666655443135556666666666666554 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.71
                      Allexi_40kDa  81 selrdalrtltklldklksvekklelsae.tasdskllkklesietsleelhakldel 137
                                       +++ +++++lt ll+k +++ k+ ++  e +a+ s+l  ++  +  +l++l +k+ +l
  gi|320100342|ref|YP_004175934.1| 140 NRIIQKIKRLTALLEKAEKLRKERNEVLEiRAFYSSLKIQVRDLSGKLQSLREKIGKL 197
                                       4455555555555555555544444333313334444445556666666666666555 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.0013
                      Allexi_40kDa  75 sqttlLselrdalrtltklldklksvekklels..aetasdskllkklesietsleelhakldelsssetses 145
                                       s   ++ +l d+  +l+++l+++ ++ + l++s  a++++ +++ k++e +  +leel +k+++l ++ ++++
  gi|320100342|ref|YP_004175934.1| 189 SLREKIGKLTDERDRLKQQLEEVVKKYQGLKNSieAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAK 261
                                       2333344444444455555555544444433330033334445556666666666666666666655555544 PP

>> T4SS  Type IV secretion system proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.0      0.36        68     128     194 ..       7      75 ..       2      78 .. 0.75
   2 ?    2.3   2.5         1   1.9e+02     118     150 ..     220     252 ..     202     279 .. 0.39

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.36
                              T4SS 128 eqaydkankrlkqiqkLadqinnatDp..KeiaDLqaRiqaeqallqneqiqlqllqklaeaeeklaeq 194
                                       e++++++++ ++qi +++++i   +D+  K i +L+     +q +l+   +  + l+k  e++++l e+
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKIRLLKDQrfKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEE 75 
                                       789999999999999999999999998445667777777777777777777777777777777776665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 1
                              T4SS 118 nkaaqdkalaeqaydkankrlkqiqkLadqinn 150
                                       n+  +++ + +++ +++++  +++++L++++nn
  gi|320100342|ref|YP_004175934.1| 220 NSIEAKQNTVNEVSKEIEELSARLEELREKVNN 252
                                       222223333333333333333333333333333 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.0     0.023       4.3     381     439 ..     219     277 ..     198     294 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.023
                                       HHHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Hemagglutinin 381 nsliekenkqleavgkelnelekrieeldkkvddgfldvityniellvllenerildfe 439
                                          ie +++ ++ v+ke++el  r+eel +kv+++  ++   +  +++  + + il+ +
  gi|320100342|ref|YP_004175934.1| 219 KNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEILEKK 277
                                       33456666678889999999999999999999988887776666666655666666654 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 ?    3.3   2.8      0.65   1.2e+02      44      92 ..       7      56 ..       2      75 .. 0.74
   2 ?    6.3   3.3     0.073        14       9      85 ..     141     215 ..     135     223 .. 0.82
   3 ?    8.9   7.9     0.012       2.2      16      89 ..     207     286 ..     196     290 .. 0.47

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.65
                      Syntaxin-6_N 44 teLrkalrsiewdledLeetvriveknpsk.fkidekelsrrrafveevr 92
                                      +eL+++++++ +++ +++e +r ++ ++ k  +  ++e  +++++++++r
  gi|320100342|ref|YP_004175934.1|  7 EELQREIENATTQIGEIREKIRLLKDQRFKlIGELKTERGEKQKYLNDIR 56
                                      6999*****************99998665555555555555555555544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.073
                      Syntaxin-6_N   9 eVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrr 85 
                                        + ++++++++l+++ e+l+++ ++    e++   + L+ ++r+++ +l+ L+e ++ +  ++++ k + +e+ ++ 
  gi|320100342|ref|YP_004175934.1| 141 RIIQKIKRLTALLEKAEKLRKERNE--VLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKY 215
                                       5667889999999999998888876..58999999999999999999999999999999999888888888887665 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.012
                      Syntaxin-6_N  16 kaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivek...........npskfkidekel 81 
                                       ++e+++++++ l++     + e  ++t +e+ k++++++  le+L+e v+ +++           n +k +i ek+ 
  gi|320100342|ref|YP_004175934.1| 207 QLEEVVKKYQGLKN-----SIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRelekaklgmmlNAKKQEILEKKQ 278
                                       33333333333222.....2455556666666666666666666666664444422223333333444444444444 PP

                      Syntaxin-6_N  82 srrrafve 89 
                                       +++r  ++
  gi|320100342|ref|YP_004175934.1| 279 DKKRLTID 286
                                       44444444 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.6    0.0098       1.9      39     115 ..      12      88 ..       6      91 .. 0.85
   2 ?    2.6   9.7      0.95   1.8e+02      35     111 ..      88     164 ..      79     175 .. 0.84
   3 ?    8.4   8.4     0.016         3      44     118 ..     184     262 ..     177     269 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0098
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN  39 aLeelleekqellekleqleqkrakllaelglsaeeatlsellak..eedeelkelwqelkelleelkelnelNgrl 113
                                       ++e+ ++++ e+ ek++ l+++r kl+ el+++  + + ++ l+     +e+l+++ +e ++l+ee ++l+e  ++ 
  gi|320100342|ref|YP_004175934.1|  12 EIENATTQIGEIREKIRLLKDQRFKLIGELKTE--RGEKQKYLNDirVLKERLRKIKEERRQLIEEYRRLAEERRSK 86 
                                       78999****************************..55555555555569*****************99999877666 PP

                                       HH CS
                              FlgN 114 ie 115
                                       ie
  gi|320100342|ref|YP_004175934.1|  87 IE 88 
                                       65 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.95
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN  35 gdieaLeelleekqellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqelkelleelkelnelNg 111
                                       ++++aL e+l ek+ +++ +++++++ +++l    ++ e+   +++l+ ee++++ ++ ++l++lle++ +l +  +
  gi|320100342|ref|YP_004175934.1|  88 EELKALREVLAEKKNTIQSMSKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKAEKLRKERN 164
                                       6889***************************999999777777777777******************9988765544 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHHTT--.SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHH CS
                              FlgN  44 leekqellekleqleqkrakllaelgls.aeeatlsellak..eedeelkelwqelkelleelke.lnelNgrlieq 116
                                         + q+l ek+ +l ++r++l ++l+++ ++ ++l++ +++  ++ +e+ +  +el+++leel+e +n lN++l ++
  gi|320100342|ref|YP_004175934.1| 184 SGKLQSLREKIGKLTDERDRLKQQLEEVvKKYQGLKNSIEAkqNTVNEVSKEIEELSARLEELREkVNNLNRELEKA 260
                                       55667777888888888888888888888777777888877788888888888888888888886357888887666 PP

                                       CC CS
                              FlgN 117 sl 118
                                        l
  gi|320100342|ref|YP_004175934.1| 261 KL 262
                                       65 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.9     0.064        12      19      47 ..       6      34 ..       3      51 .. 0.73
   2 ?    0.7   0.8       4.4   8.2e+02      40      55 ..      55      70 ..      36      89 .. 0.61
   3 ?    1.9   0.3       1.9   3.5e+02      19      41 ..      90     112 ..      81     131 .. 0.77
   4 ?   -0.2   0.6       8.4   1.6e+03      24      47 ..     141     156 ..     118     171 .. 0.51
   5 ?    2.8   0.7         1   1.9e+02      27      55 ..     167     195 ..     142     202 .. 0.74
   6 ?    6.3   3.1      0.08        15      15      53 ..     183     221 ..     160     227 .. 0.54
   7 ?   11.9   1.1    0.0015      0.27      17      55 ..     220     258 ..     214     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.064
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                              SlyX 19 ieeLndvvaeqqqqidrlqrqlrllaerl 47
                                      ieeL++++ +   qi ++++++rll+++ 
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLLKDQR 34
                                      77888888888888888888888887764 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 4.4
                                      HHHHHHT-XXXXXXXX CS
                              SlyX 40 lrllaerlkeleessg 55
                                      +r l+erl++++e+ +
  gi|320100342|ref|YP_004175934.1| 55 IRVLKERLRKIKEERR 70
                                      3444444444444322 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  19 ieeLndvvaeqqqqidrlqrqlr 41 
                                       +++L +v+ae   +i+ + ++ r
  gi|320100342|ref|YP_004175934.1|  90 LKALREVLAEKKNTIQSMSKEAR 112
                                       56677788888888877777655 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 8.4
                                       HHHHHHHHHHHHHHHHHHHHHHT- CS
                              SlyX  24 dvvaeqqqqidrlqrqlrllaerl 47 
                                       +++ +  +  + l        e+ 
  gi|320100342|ref|YP_004175934.1| 141 RIIQKIKRLTALL--------EKA 156
                                       3333333332222........222 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  27 aeqqqqidrlqrqlrllaerlkeleessg 55 
                                        e +   + l+ q+r l  +l++l+e+ g
  gi|320100342|ref|YP_004175934.1| 167 LEIRAFYSSLKIQVRDLSGKLQSLREKIG 195
                                       55555666788888888888888887754 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  15 qedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                       +   +++L + + +  ++ drl++ql++++++ + l++s
  gi|320100342|ref|YP_004175934.1| 183 LSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQGLKNS 221
                                       333445555555555556666666666666666555555 PP

  == domain 7  score: 11.9 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  17 dtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       + ie+ +++v e  ++i++l ++l++l+e++++l+ + +
  gi|320100342|ref|YP_004175934.1| 220 NSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELE 258
                                       678888999**********************99887765 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 ?    0.7   0.2       2.7     5e+02      22      33 ..     144     155 ..     140     165 .. 0.82
   2 ?    4.8   0.9      0.13        25      22      44 ..     199     221 ..     177     222 .. 0.84
   3 ?    6.8   0.7     0.032         6      18      41 ..     230     253 ..     227     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHH CS
                    Matrilin_ccoil  22 seiqaLtqkLea 33 
                                       ++i++Lt+ Le 
  gi|320100342|ref|YP_004175934.1| 144 QKIKRLTALLEK 155
                                       689*****9997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                    Matrilin_ccoil  22 seiqaLtqkLeavtkRlealEnk 44 
                                       +e ++L q+Le+v k+ + l n 
  gi|320100342|ref|YP_004175934.1| 199 DERDRLKQQLEEVVKKYQGLKNS 221
                                       555678888*******9999886 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                    Matrilin_ccoil  18 tkVeseiqaLtqkLeavtkRleal 41 
                                       ++V++ei+ L+++Le+  +++  l
  gi|320100342|ref|YP_004175934.1| 230 NEVSKEIEELSARLEELREKVNNL 253
                                       6899************99999877 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.9      0.81   1.5e+02      64     152 ..       6      91 ..       3      95 .. 0.61
   2 ?    5.5   0.7     0.066        13      52     125 ..      92     165 ..      90     172 .. 0.89
   3 ?    9.7   8.4    0.0035      0.66      66     134 ..     196     264 ..     182     285 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.81
                            DUF745  64 veqleqelreaeavvqeekkslqssean.akaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektq 139
                                       +e+l++e+++a +++ e+ ++++  + +  k+  + +++  ++    ++ l+ ++   e++++++++  q ++e + 
  gi|320100342|ref|YP_004175934.1|   6 IEELQREIENATTQIGEIREKIRLLKDQrFKLIGELKTERGEK----QKYLNDIRVLKERLRKIKEERRQLIEEYRR 78 
                                       5778888888888888888877765543144444444433333....444555555556666666666777777777 PP

                            DUF745 140 lleaAkkRveeLk 152
                                       l e+ ++++eeLk
  gi|320100342|ref|YP_004175934.1|  79 LAEERRSKIEELK 91 
                                       7777777777765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.066
                            DUF745  52 AAeAaLaGKqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeq 125
                                       A   +La K+  ++++ +e r  +++++ e + l+   ++  +  +  + + q++++l+all++a++  ++ ++
  gi|320100342|ref|YP_004175934.1|  92 ALREVLAEKKNTIQSMSKEARTPSNILRGEIERLEWILQTRVLSIEEENRIIQKIKRLTALLEKAEKLRKERNE 165
                                       556699*****************************999999999999999*************99987666555 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0035
                            DUF745  66 qleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqel 134
                                       +l++e    +++++e+ k++q  +++++a +++++++ +++e l+a l++ +e+++n+++  ++a+  +
  gi|320100342|ref|YP_004175934.1| 196 KLTDERDRLKQQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGM 264
                                       456666666666777777777777777777777777777777777777777777766666666655433 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.7       7.7   1.4e+03      89      89 ..      64      64 ..       4     123 .. 0.46
   2 ?   13.4  12.5   0.00032      0.06      19     152 ..     141     280 ..     135     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 7.7
                            GldM_N 89 n 89
                                      +
  gi|320100342|ref|YP_004175934.1| 64 K 64
                                      2 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00032
                            GldM_N  19 nasekNaalyaslea..kaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkded.......vgeika 86 
                                       ++ +k ++l a le+  k++++++++ e+ + +  +k +  +l   +++l+e+i k ++++d         v++++ 
  gi|320100342|ref|YP_004175934.1| 141 RIIQKIKRLTALLEKaeKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLkqqleevVKKYQG 217
                                       55677777777777655788888888889999999999999999999999999999999884434445555899999 PP

                            GldM_N  87 kdnldaaselmlaegksgkGkeLkkkineyreellklvndlakdaklieselstedpkkkkkkegk 152
                                        +n+ +a++  ++e  s++ +eL ++++e re++++l ++l+k    + + l++++++  +kk+ k
  gi|320100342|ref|YP_004175934.1| 218 LKNSIEAKQNTVNEV-SKEIEELSARLEELREKVNNLNRELEKA--KLGMMLNAKKQEILEKKQDK 280
                                       9***********777.***********************84443..47888888887444443333 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   7.3     0.027       5.2     233     303 ..       7      77 ..       2      81 .. 0.83
   2 ?    1.3  40.9      0.87   1.6e+02      92     298 ..      52     260 ..      49     301 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                            HAP1_N 233 erqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaevegmLheaqeevk 303
                                       e+ q+ei++ ++qi ++++k++ l+ ++ +l  +L+ ++  +++  ++++ l+e+ + +++  ++  ee +
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYR 77 
                                       56799999999999999999999999999999999999999999999999999998887776666666655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.87
                            HAP1_N  92 lkrNsvLternekLeeqLesareeiaqlrhelslkddLLqlysdseeeseeeseeseelreeesleslqklvqld.l 167
                                       l+  +vL+er  k+ e+ ++  ee+ +l  e   k + L+ + +   e+++  ++ +++ ++ s  ++ ++ +l+ +
  gi|320100342|ref|YP_004175934.1|  52 LNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEARTPSNILRGEIERLEwI 128
                                       666689*************************9999888888888866666666555566777777788888899957 PP

                            HAP1_N 168 LqeklreLeeeNekLreeasqLkt..etdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqqeeissL 242
                                       Lq ++ ++eeeN+ ++ + ++L+   e  +   kE++ vl++ +  s+ + q+ +ls +l++ +e++ +  +e  +L
  gi|320100342|ref|YP_004175934.1| 129 LQTRVLSIEEENRIIQ-KIKRLTAllEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRL 204
                                       9***********9875.44555441144444469999999**999999***************************** PP

                            HAP1_N 243 laqivdlqqklkelgveneelkqhL.aaskeaqrqLtaELqdlqekyaevegmLhea 298
                                       + q+ ++ +k + l+   e  ++   ++ske++ +L a L++l+ek ++ +  L+ a
  gi|320100342|ref|YP_004175934.1| 205 KQQLEEVVKKYQGLKNSIEAKQNTVnEVSKEIE-ELSARLEELREKVNNLNRELEKA 260
                                       *******99999999999988877725788887.99999999999999998888766 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   0.3     0.078        15       2      26 ..       6      30 ..       2      39 .. 0.52
   2 ?    0.3   0.6       5.2   9.7e+02      31      42 ..      63      74 ..      33     103 .. 0.59
   3 ?    9.7   0.6    0.0057       1.1       8      44 ..     179     215 ..     174     220 .. 0.88
   4 ?    9.4   5.1    0.0071       1.3       5      40 ..     218     253 ..     214     259 .. 0.79
   5 ?    1.6   0.2         2   3.9e+02       1      23 [.     249     273 ..     249     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.078
                         FlaC_arch  2 idelEnklsklsteletvkkeneel 26
                                      i+el+ ++++  t+++ +++++  l
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLL 30
                                      3444444444444444444444333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 5.2
                         FlaC_arch 31 eelkenVkdlls 42
                                       ++ke+ ++l++
  gi|320100342|ref|YP_004175934.1| 63 RKIKEERRQLIE 74
                                      333333333332 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0057
                         FlaC_arch   8 klsklsteletvkkeneelsksveelkenVkdllsLY 44 
                                       ++ +ls +l+++++++ +l ++ ++lk++ +++++ Y
  gi|320100342|ref|YP_004175934.1| 179 QVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKY 215
                                       67889999999****************9999999877 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0071
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       l n ++  + +++ v ke+eels  +eel e+V++l
  gi|320100342|ref|YP_004175934.1| 218 LKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNL 253
                                       667778888888889999999999999998888765 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 2
                         FlaC_arch   1 ridelEnklsklst..eletvkken 23 
                                       ++++l  +l+k +   +l+  k+e+
  gi|320100342|ref|YP_004175934.1| 249 KVNNLNRELEKAKLgmMLNAKKQEI 273
                                       7999999999877642555544444 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4  24.9       6.6   1.2e+03     190     295 ..      12     121 ..       4     171 .. 0.45
   2 ?    4.0  27.7      0.15        28     204     333 ..     148     278 ..     123     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.6
                            HMMR_N 190 klqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseql.ekykldiaqleellkekndeie 265
                                       +++ + +++ e ++k++ Lk++  +l  e + e+ e +k l+ i  l++  +++ e  ++ i++++ l++e+ ++ie
  gi|320100342|ref|YP_004175934.1|  12 EIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIkEERRQLIEEYRRLAEERRSKIE 88 
                                       22233333333333333333333333333333333444433333333333333322223333333333444333333 PP

                            HMMR_N 266 s...LkssLeekeqelskqvkdlnekcklleke 295
                                       +   L++ L ek+++++   k++ +  + l  e
  gi|320100342|ref|YP_004175934.1|  89 ElkaLREVLAEKKNTIQSMSKEARTPSNILRGE 121
                                       200044555555555555555555555555544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.15
                            HMMR_N 204 kvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLee...keqe 277
                                       ++++L ek    ek+  +e+ e+ +  +  + l+   + l   + ++++l+e + +  de   Lk++Lee   k q 
  gi|320100342|ref|YP_004175934.1| 148 RLTALLEKA---EKL-RKERNEVLEIRAFYSSLKIQVRDL---SGKLQSLREKIGKLTDERDRLKQQLEEvvkKYQG 217
                                       233333333...333.334555555555555555555555...8899999999999999999999999874435566 PP

                            HMMR_N 278 lskqvkdlnekckllekekeel...vreeeekeqtlsaEleelk..eklklkeqeaqklqq 333
                                       l++ ++ +++ ++++ ke eel   ++e +ek ++l+ Ele+ k    l+ k+qe+ + +q
  gi|320100342|ref|YP_004175934.1| 218 LKNSIEAKQNTVNEVSKEIEELsarLEELREKVNNLNRELEKAKlgMMLNAKKQEILEKKQ 278
                                       8888888888899998888876555778899999*******98832567778888766666 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2  13.5       6.5   1.2e+03      55     164 ..       8     117 ..       4     139 .. 0.77
   2 ?    9.6   8.6    0.0032       0.6      92     153 ..     207     268 ..     203     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6.5
                         PspA_IM30  55 qlerkleeqkeqakklekkAkaALtkgeeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieel 131
                                       +l+r++e+++ q+ +  +k + +L+ ++ +L+ e+ +e+ + +k +++ + + +++r+  e+ r+ +e+  +  ee 
  gi|320100342|ref|YP_004175934.1|   8 ELQREIENATTQIGEIREKIR-LLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRLAEER 83 
                                       678888889999999888876.5888888899888888777777777777777777777777777777777777888 PP

                         PspA_IM30 132 kakkellka.rekaakaqeavqkslgklstesat 164
                                       ++k+e+lka re  a  ++++q+ +++++t+s++
  gi|320100342|ref|YP_004175934.1|  84 RSKIEELKAlREVLAEKKNTIQSMSKEARTPSNI 117
                                       8888888764666777777888888887777765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0032
                         PspA_IM30  92 eikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqk 153
                                       ++++  k+ ++l+ + +  + +v ++ k++e+l +++eel++k++ l   ++ ak  + +++
  gi|320100342|ref|YP_004175934.1| 207 QLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNA 268
                                       45555566677788888889999999999999999999999999999999999998877776 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1  18.2       1.8   3.5e+02      23     123 ..      19     109 ..       2     132 .. 0.50
   2 ?    9.1  24.5    0.0033      0.62      22     134 ..     140     259 ..     129     289 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.8
                             Atg14  23 rlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeiee 99 
                                       ++ e re+++ lk +++ l ++++ +  +k+   +  ++i+ +k++l+++k ++++l e+ ++l + +++  +e+++
  gi|320100342|ref|YP_004175934.1|  19 QIGEIREKIRLLKDQRFKLIGELKTERGEKQ---KYLNDIRVLKERLRKIKEERRQLIEEYRRLAEERRSKIEELKA 92 
                                       4444444444444444444444443322222...3344444444444444444444444444444444444444444 PP

                             Atg14 100 kkkklaklsdklkkRrsdleslqn 123
                                        ++ la++++++       +s+++
  gi|320100342|ref|YP_004175934.1|  93 LREVLAEKKNTI-------QSMSK 109
                                       444444444444.......33333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0033
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegke.......eaeqledkiknkkakleelksliadlrerlqelkdkls 91 
                                       +r++++ +rl+ l+++ e l+k+ ++ le +        ++ +l+ k++++++k+ +l  ++ +l+++l+e+ +k +
  gi|320100342|ref|YP_004175934.1| 140 NRIIQKIKRLTALLEKAEKLRKERNEVLEIRAfysslkiQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQ 216
                                       47888888888888888888888888888888888888855555555555555555555555555555555555555 PP

                             Atg14  92 qlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqia 134
                                        lk +ie+k++++ + s+++ +  ++le l++++++  +++ +
  gi|320100342|ref|YP_004175934.1| 217 GLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEK 259
                                       5555555555555555555554444444444444443333222 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   9.8     0.019       3.6      19     120 ..       7     108 ..       3     133 .. 0.70
   2 ?    0.8   4.0      0.46        87      75     119 ..     139     183 ..     102     211 .. 0.50
   3 ?    1.2  12.6      0.35        65      32      98 ..     180     256 ..     130     261 .. 0.44
   4 ?    7.9  10.3    0.0032      0.61      31     121 ..     197     279 ..     170     290 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
                        V_ATPase_I  19 nafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenlekl 95 
                                       +++qr+  +   ++ e+ +k+r+l+++  kl  +  +    e+ ++++  +++  l+e+l+k++ee ++l e++++l
  gi|320100342|ref|YP_004175934.1|   7 EELQREIENATTQIGEIREKIRLLKDQRFKLIGELKT----ERGEKQKYLNDIRVLKERLRKIKEERRQLIEEYRRL 79 
                                       5788999999999999999999999998883333333....356778888889999999999999999999999999 PP

                        V_ATPase_I  96 kkelnelvel....kavlekakefleeee 120
                                        +e+++ +e+    ++vl + k+ +++ +
  gi|320100342|ref|YP_004175934.1|  80 AEERRSKIEElkalREVLAEKKNTIQSMS 108
                                       88877666650000445555555554332 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.46
                        V_ATPase_I  75 eeelekleeelkelnenleklkkelnelvelkavlekakefleee 119
                                       e+++ ++ ++l+ l e++ekl+ke+ne++e +a +++ k  +++ 
  gi|320100342|ref|YP_004175934.1| 139 ENRIIQKIKRLTALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDL 183
                                       344444445555555555555555555555555555554444332 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.35
                        V_ATPase_I  32 cdemerklrfleeeieklekavikeeea..........eesleapeekeldeleeelekleeelkelnenleklkke 98 
                                       + +++ kl+ l+e+i kl+++  + +++           +++ ++++++++e+++e+e+l ++l+el+e+ ++l++e
  gi|320100342|ref|YP_004175934.1| 180 VRDLSGKLQSLREKIGKLTDERDRLKQQleevvkkyqgLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRE 256
                                       33333333333333333222222222222222222322333333333334444444444444444444444444433 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0032
                        V_ATPase_I  31 rcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelka 107
                                        +de +r  + lee ++k++          +++ ++++++++e+++e+e+l ++l+el+e+ ++l++el++++    
  gi|320100342|ref|YP_004175934.1| 197 LTDERDRLKQQLEEVVKKYQG--------LKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMM 265
                                       223333333444444444333........445555555666666666666666666666666666666666666666 PP

                        V_ATPase_I 108 vlekakefleeeee 121
                                       +  k +e+le++++
  gi|320100342|ref|YP_004175934.1| 266 LNAKKQEILEKKQD 279
                                       66666666654422 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.3     0.022       4.1      34     101 ..       8      76 ..       6      79 .. 0.89
   2 ?   -0.1   3.6       1.1     2e+02      33      94 ..     146     207 ..     103     211 .. 0.74
   3 ?   12.1   9.5   0.00022     0.041      30     120 ..     206     296 ..     198     301 .] 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                              COG6  34 efleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkle.lkqkllkaf 101
                                       e  +e +++ +q+ +i++++  l++   ++  +l++ + e +++l+++  Lke+++k++ ++++l++++
  gi|320100342|ref|YP_004175934.1|   8 ELQREIENATTQIGEIREKIRLLKDQRFKLIGELKTERGEKQKYLNDIRVLKERLRKIKeERRQLIEEY 76 
                                       566789999*********************************************999962577777765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                              COG6  33 eefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelk 94 
                                        + l ++ + ae+L++ +++v ++ + ++++k +++  + + ++l e++ +L+ e+++l+++
  gi|320100342|ref|YP_004175934.1| 146 IKRLTALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQ 207
                                       34455555556677778888888888888888888888888888888888888888877776 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00022
                              COG6  30 kineefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllkaflkkFt 106
                                       ++ ee+++++q +++++++ +++v++ ++ ++e++ +l++ +e+ ++l++e e+ k       +kq++l++ ++k  
  gi|320100342|ref|YP_004175934.1| 206 QQLEEVVKKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLGMMLNAKKQEILEKKQDKKR 282
                                       45689************************************************************************ PP

                              COG6 107 LseeEeaaLtsgee 120
                                       L+ +E+++++ ++e
  gi|320100342|ref|YP_004175934.1| 283 LTIDELKIIYGEPE 296
                                       *********99984 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.0      0.17        32     177     230 ..      59     112 ..      47     126 .. 0.87
   2 ?    6.7   4.4      0.01       1.9     120     231 ..     145     259 ..     130     269 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                    SpecificRecomb 177 espFlalqrelealleayeaaledeeeaeedlkhlrvlldqcreavdrvrkhle 230
                                       ++   ++++e  +l+e+y++ +e+++++ e+lk lr +l++ +++++++ k++ 
  gi|320100342|ref|YP_004175934.1|  59 KERLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEKKNTIQSMSKEAR 112
                                       55666788999999******99************************99999875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                    SpecificRecomb 120 tlarLlelleeeeeeeeeaaeklreellealevlsvqiaalglepelrrrlpeleeeespFlalqrelealleayea 196
                                       +++rL++lle++e+ ++e  e l+   +    + s +i+  +l+ +l ++ +++ + +    +l+++le+++++y+ 
  gi|320100342|ref|YP_004175934.1| 145 KIKRLTALLEKAEKLRKERNEVLEIRAF----YSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEEVVKKYQG 217
                                       6788888993333333333333333322....334555566888888888888888888888888888888888887 PP

                    SpecificRecomb 197 .......aledeeeaeedlkhlrvlldqcreavdrvrkhlee 231
                                              ++++ +e +++ ++l++ l++ re v+++ ++le+
  gi|320100342|ref|YP_004175934.1| 218 lknsieaKQNTVNEVSKEIEELSARLEELREKVNNLNRELEK 259
                                       444444355555566666667778888888888888888776 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.018       3.5      26      54 ..       6      33 ..       4      39 .. 0.73
   2 ?    3.0   4.5      0.45        85      23      52 ..      52      81 ..      41      89 .. 0.81
   3 ?    1.6   1.1       1.2   2.4e+02      24      47 ..      88     111 ..      82     125 .. 0.77
   4 ?   -0.3   1.0       4.8     9e+02      38      54 ..     147     163 ..     128     171 .. 0.46
   5 ?   10.2   1.5    0.0026       0.5      19      56 ..     173     210 ..     170     216 .. 0.81
   6 ?   10.6   6.3    0.0019      0.36      17      52 ..     213     248 ..     207     267 .. 0.70
   7 ?   -0.7   1.2       6.6   1.2e+03      23      39 ..     270     284 ..     257     290 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.018
                                      HHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                             DivIC 26 iaalqaelaklkaeneeLeaevkdLksde 54
                                      i++lq+e+++ + ++ e  +++++Lk d+
  gi|320100342|ref|YP_004175934.1|  6 IEELQREIENATTQIGEIREKIRLLK-DQ 33
                                      67788888888888888888888884.55 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.45
                                      HHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC 23 kqeiaalqaelaklkaeneeLeaevkdLks 52
                                       ++i  l++ l k+k+e+++L +e ++L  
  gi|320100342|ref|YP_004175934.1| 52 LNDIRVLKERLRKIKEERRQLIEEYRRLAE 81
                                      578999999***************999943 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  24 qeiaalqaelaklkaeneeLeaev 47 
                                       +e++al + la++k++++++ +e 
  gi|320100342|ref|YP_004175934.1|  88 EELKALREVLAEKKNTIQSMSKEA 111
                                       677778888888888888877776 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHCC-XXXX CS
                             DivIC  38 aeneeLeaevkdLksde 54 
                                       ++  +L ++ ++L++++
  gi|320100342|ref|YP_004175934.1| 147 KRLTALLEKAEKLRKER 163
                                       22222222333333322 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                             DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksdedy 56 
                                       y++lk ++ +l  +l++l++++ +L++e ++Lk++ + 
  gi|320100342|ref|YP_004175934.1| 173 YSSLKIQVRDLSGKLQSLREKIGKLTDERDRLKQQLEE 210
                                       67888899999999999999999999999999875444 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 0.0019
                                       XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  17 laykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                        +y+ lk+ i+a+q++++++++e+eeL a++++L+ 
  gi|320100342|ref|YP_004175934.1| 213 KKYQGLKNSIEAKQNTVNEVSKEIEELSARLEELRE 248
                                       567788888888888888888888888888888864 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 6.6
                                       HHHHHHHHHHHHHHHHH CS
                             DivIC  23 kqeiaalqaelaklkae 39 
                                       kq  + l+++ +k++ +
  gi|320100342|ref|YP_004175934.1| 270 KQ--EILEKKQDKKRLT 284
                                       22..2334444444444 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   2.5       1.2   2.2e+02     201     251 ..      40     100 ..       3     126 .. 0.42
   2 ?    7.2   8.3     0.019       3.5     165     253 ..     178     255 ..     107     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.2
                         Phage_GPO 201 eavelvAeev......kelsekveall....aleaelaalkkeveklkaeleaLkekLskt 251
                                       e  ++  e++      + l+e++++ +    +l +e   l +e +++ +el+aL+e L ++
  gi|320100342|ref|YP_004175934.1|  40 ELKTERGEKQkylndiRVLKERLRKIKeerrQLIEEYRRLAEERRSKIEELKALREVLAEK 100
                                       3333333333111111111111111111111333333333333333333444444444433 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.019
                         Phage_GPO 165 feeeeeeeegeslferikallskkkksddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkael 241
                                       ++ +       +l  ++++l +k  k +d+r   +++ +e+v ++ + l++++e   a+++ +++++ke+e+l+a+l
  gi|320100342|ref|YP_004175934.1| 178 IQVR-------DLSGKLQSLREKIGKLTDER-DRLKQQLEEVVKKYQGLKNSIE---AKQNTVNEVSKEIEELSARL 243
                                       3333.......33334444433333333333.3455556666666666666666...44555555555555555555 PP

                         Phage_GPO 242 eaLkekLsktda 253
                                       e+L+ek+++ ++
  gi|320100342|ref|YP_004175934.1| 244 EELREKVNNLNR 255
                                       555555444332 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   6.9       2.8   5.3e+02      27      66 ..      47     100 ..       4     112 .. 0.43
   2 ?   11.8   9.3    0.0013      0.24       7      99 ..     138     228 ..     133     230 .. 0.72
   3 ?    6.4   4.4     0.062        12      31      76 ..     218     263 ..     217     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.8
                        Syntaxin_2  27 d..............teelreklhelieeinelikktnellkklsqldnsssds 66 
                                       +               ++++e+ ++liee ++l+++  +++++l++l + +  +
  gi|320100342|ref|YP_004175934.1|  47 EkqkylndirvlkerLRKIKEERRQLIEEYRRLAEERRSKIEELKALREVLAEK 100
                                       122222222222222333335555666666666666666666666655555443 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0013
                        Syntaxin_2   7 kinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssdsqqkl..qkekLkkdfke 81 
                                       + n+ ++++++l+  L+++   ++ r+++ e++   + l  ++ +l  kl++l ++      kl  ++++Lk++++e
  gi|320100342|ref|YP_004175934.1| 138 EENRIIQKIKRLTALLEKAEKLRKERNEVLEIRAFYSSLKIQVRDLSGKLQSLREKI----GKLtdERDRLKQQLEE 210
                                       557788999999999999977777777666666555555555555555555555544....3444599********* PP

                        Syntaxin_2  82 alqeFqkiqrqyaekekq 99 
                                       +++++q + ++++ k++ 
  gi|320100342|ref|YP_004175934.1| 211 VVKKYQGLKNSIEAKQNT 228
                                       **************9986 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.062
                        Syntaxin_2  31 lreklhelieeinelikktnellkklsqldnsssdsqqklqkekLk 76 
                                       l+++++  ++ +ne++k+++el  +l++l ++ ++ ++ l+k+kL 
  gi|320100342|ref|YP_004175934.1| 218 LKNSIEAKQNTVNEVSKEIEELSARLEELREKVNNLNRELEKAKLG 263
                                       6778888899999999999999999999999888888888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3113  (0.173629); expected 358.6 (0.02)
Passed bias filter:                      892  (0.0497518); expected 358.6 (0.02)
Passed Vit filter:                       290  (0.0161749); expected 17.9 (0.001)
Passed Fwd filter:                       215  (0.0119917); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              95  [number of targets reported over threshold]
# CPU time: 2.60u 0.41s 00:00:03.01 Elapsed: 00:00:00.64
# Mc/sec: 1420.33
//
Query:       gi|320100343|ref|YP_004175935.1|  [L=280]
Description: undecaprenyl pyrophosphate synthetase [Desulfurococcus mucosus DSM 2162]
Scores for 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-75  252.2   0.0    4.9e-75  251.9   0.0    1.1  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 !  251.9   0.0   2.7e-79   4.9e-75       1     224 []      56     279 ..      56     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 251.9 bits;  conditional E-value: 2.7e-79
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGG.S-HHHHHHHHHHHHHHHHH.HH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfk.Rskeevdalmellkeellk.ee 75 
                                       i DGNrRwA++ g+ ++  Gh  G+e++ke+l+++ +lg+++vt+Ya+SteN+k Rs+ e ++l++l+++ l + +e
  gi|320100343|ref|YP_004175935.1|  56 IPDGNRRWARRLGFDPSL-GHIYGYERMKEVLKWIWDLGIRYVTIYAMSTENCKyRSNGEREHLFNLARKGLRElRE 131
                                       78***********99998.**********************************7699***********854433135 PP

                                       HHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGH CS
                      Prenyltransf  76 lkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eei 151
                                       l+++++++vrv+v+G l+l+p+d+ e ++++e++t+k ++ ++lnia++Yg+r+ei++av+++v+++++ k + ++i
  gi|320100343|ref|YP_004175935.1| 132 LRDIHERKVRVKVFGTLDLVPSDIVELAKELEKETEKYDS-YQLNIALCYGGRQEILDAVKAVVRDVIDGKITvDDI 207
                                       78**********************************6666.**************************9888875677 PP

                                       SHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 152 deetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                       +ee+++k+lyt++a pdpDl+iRtsGeeR+SnFllwq+ayselyf+dv+WP+f+k d+++a+++yq rerrfg
  gi|320100343|ref|YP_004175935.1| 208 SEEAFSKYLYTSEA-PDPDLIIRTSGEERISNFLLWQSAYSELYFCDVYWPEFRKIDFWRAIRSYQMRERRFG 279
                                       8**********877.********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2069.42
//
Query:       gi|320100344|ref|YP_004175936.1|  [L=230]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-38  129.2  11.1    9.3e-38  128.8  11.1    1.2  1  CdvA           CdvA-like coiled-coil domain
    4.5e-05   23.7  12.1    0.00099   19.4   4.0    2.6  2  BLOC1_2        Biogenesis of lysosome-related organelles comp
     0.0012   19.3   3.9     0.0033   17.9   3.7    1.9  2  Syntaxin-6_N   Syntaxin 6, N-terminal
     0.0021   18.1   2.0     0.0042   17.1   2.0    1.5  1  Imm3           Immunity protein Imm3
     0.0027   17.6   3.3     0.0035   17.2   3.3    1.1  1  PIN_8          PIN like domain
     0.0031   17.0   3.4     0.0042   16.6   3.4    1.1  1  Golgin_A5      Golgin subfamily A member 5
     0.0052   16.8   1.3     0.0095   16.0   0.2    1.9  2  PRC            PRC-barrel domain
  ------ inclusion threshold ------
      0.016   14.1   6.4      0.015   14.1   4.1    1.8  2  Fmp27_WPPW     RNA pol II promoter Fmp27 protein domain
      0.022   15.2   2.3       0.05   14.1   2.2    1.6  1  FlgN           FlgN protein
      0.029   14.4   0.1      0.095   12.7   0.0    1.8  2  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
       0.13   11.5   3.0       0.14   11.4   1.0    1.9  2  DUF4763        Domain of unknown function (DUF4763)
       0.14   12.1   1.6       0.72    9.8   0.3    2.4  3  GIT_CC         GIT coiled-coil Rho guanine nucleotide exchang
       0.14   12.3   6.2       0.16   12.2   2.3    2.0  2  Fib_alpha      Fibrinogen alpha/beta chain family
       0.23   11.5   3.4       0.29   11.2   1.0    2.3  2  DUF2433        Protein of unknown function (DUF2433)
       0.26   11.9   3.7       0.11   13.1   1.0    1.7  1  DUF883         Bacterial protein of unknown function (DUF883)
       0.32   11.5   6.2        1.2    9.7   6.2    2.0  1  DUF16          Protein of unknown function DUF16
       0.39   10.8   5.7       0.82    9.8   5.5    1.7  1  DivIVA         DivIVA protein
       0.47    9.3   2.5       0.57    9.0   2.5    1.1  1  LMBR1          LMBR1-like membrane protein
       0.51    9.5   8.1       0.94    8.6   3.1    2.0  2  ISG65-75       Invariant surface glycoprotein
       0.54    9.8   5.9       0.45   10.0   1.9    2.5  2  Fzo_mitofusin  fzo-like conserved region
       0.65   10.4   8.1       0.26   11.6   4.5    1.9  2  Uso1_p115_C    Uso1 / p115 like vesicle tethering protein, C 
        0.8    9.3   8.8        3.1    7.4   4.5    2.1  2  DUF4795        Domain of unknown function (DUF4795)
        1.8    9.0   6.6        3.1    8.2   6.6    1.3  1  PGBA_C         Plasminogen-binding protein pgbA C-terminal
        2.8    8.5  12.3        3.8    8.0   7.1    2.1  2  APG6_N         Apg6 coiled-coil region
        3.2    7.8   9.4         11    6.1   9.4    1.8  1  UPF0242        Uncharacterised protein family (UPF0242) N-ter
        3.8    6.8   6.6        4.9    6.4   6.6    1.2  1  FAM76          FAM76 protein
        7.3    7.3   7.3        1.1    9.9   0.8    2.1  2  YabA           Initiation control protein YabA
        8.9    6.8  12.7         13    6.3   8.1    2.4  2  ZapB           Cell division protein ZapB
        9.2    6.5   9.9       0.77   10.0   4.2    2.0  3  Med21          Subunit 21 of Mediator complex


Domain annotation for each model (and alignments):
>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8  11.1   1.5e-40   9.3e-38       1     120 [.      88     207 ..      88     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 1.5e-40
                              CdvA   1 krkkALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidE 77 
                                       kr  ALeeL s+++ip +tyee+k+kl+e+l klke+ak +ke+l+kr++e+ed i +leka++++k+sy+sGEi+E
  gi|320100344|ref|YP_004175936.1|  88 KRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITAVKVSYISGEIPE 164
                                       89*************************************************************************** PP

                              CdvA  78 eaYksaieairellesaleekeeikklleklskleleeeevee 120
                                       +aYk++++++r++l+ +++ek+++kk+l+k+++le+ ++++++
  gi|320100344|ref|YP_004175936.1| 165 KAYKASMDHLRRNLDILNSEKASVKKHLDKIEALENLPVDAAV 207
                                       ***********************************99887765 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 !   19.4   4.0   1.6e-06   0.00099      10      83 ..      78     152 ..      73     155 .. 0.91
   2 !    9.1   0.4    0.0025       1.5      38      72 ..     166     200 ..     164     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.6e-06
                           BLOC1_2  10 yleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpyl.qqidqiekqvteLeeavse 83 
                                       +le+ le +++ +  Le+lN + +  ++ +++  ++l ++l kl+e+ + +++ l ++i +ie+ + eLe+a+ +
  gi|320100344|ref|YP_004175936.1|  78 LLENRLERVKKRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELrKRIHEIEDMIVELEKAITA 152
                                       789999*******************************************998766267*************9875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0025
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiek 72 
                                       ++k ++++l+++l+ ln+++++++++l++i+++e+
  gi|320100344|ref|YP_004175936.1| 166 AYKASMDHLRRNLDILNSEKASVKKHLDKIEALEN 200
                                       5788999*************************986 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 ?   -0.2   0.1       2.5   1.5e+03      47      72 ..      80      98 ..      69     116 .. 0.51
   2 !   17.9   3.7   5.3e-06    0.0033      20      96 ..     106     189 ..      79     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.5
                      Syntaxin-6_N 47 rkalrsiewdledLeetvriveknps 72
                                      ++        le  ++ v+++e+ +s
  gi|320100344|ref|YP_004175936.1| 80 ENR-------LERVKKRVAALEELNS 98
                                      333.......3333333333333333 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 5.3e-06
                      Syntaxin-6_N  20 lyrrwerlledtsss.......tseeldetrteLrkalrsiewdledLeetvrivek......npsk.fkidekels 82 
                                       +y+++++       +        +ee +  ++eLrk +++ie  + +Le+++ +v+        p+k +k + + l+
  gi|320100344|ref|YP_004175936.1| 106 TYEEFKK-------KldeslikLKEEAKGVKEELRKRIHEIEDMIVELEKAITAVKVsyisgeIPEKaYKASMDHLR 175
                                       3444433.......0333344489****************************9885544444456676888888887 PP

                      Syntaxin-6_N  83 rrrafveevreevk 96 
                                       r  +++++ +  vk
  gi|320100344|ref|YP_004175936.1| 176 RNLDILNSEKASVK 189
                                       77777766666665 PP

>> Imm3  Immunity protein Imm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.0   6.8e-06    0.0042       4      97 ..     106     198 ..     103     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.8e-06
                              Imm3   4 eYqeLldaineeyeeykaeerslseaiartsdefenveklgeiekvvvdvaigeialk.hakvfvklkegiikrLss 79 
                                        Y+e  +++ e+  ++k+e ++ +e + + + e e+   + e+ek++  v ++ i+ + ++k ++   +++ ++L+ 
  gi|320100344|ref|YP_004175936.1| 106 TYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIED--MIVELEKAITAVKVSYISGEiPEKAYKASMDHLRRNLDI 180
                                       69999999**************************99..899999999998888887653689*************** PP

                              Imm3  80 lnleelkgelteeeikdl 97 
                                       ln e+++ +  +++i+ l
  gi|320100344|ref|YP_004175936.1| 181 LNSEKASVKKHLDKIEAL 198
                                       ******999888888876 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.3   5.7e-06    0.0035      21     131 ..      87     196 ..      78     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.7e-06
                             PIN_8  21 kdllkvlekladrlwvPhqvalEfqrnresviskekkayedlekeleklkkaaekkle..ealkkwakkkaldteel 95 
                                       k+ +++le+l+++  +P ++ +Ef ++ ++ + k k+ ++ +++el+k ++++e+ +   e++ +  k  +++ e  
  gi|320100344|ref|YP_004175936.1|  87 KKRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVelEKAITAVKVSYISGEIP 163
                                       666789**********************9999999999999999996666666654330134455666666778999 PP

                             PIN_8  96 rkelkkqleelkeelkaeleelkksskadkeedpil 131
                                       +k++k+++++l+++l   l++ k s+k++   d+i+
  gi|320100344|ref|YP_004175936.1| 164 EKAYKASMDHLRRNL-DILNSEKASVKKHL--DKIE 196
                                       999999999999999.33333333333333..5554 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.4   6.8e-06    0.0042      88     205 ..      83     197 ..      76     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.8e-06
                         Golgin_A5  88 aeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatlqsrikdrekeieklrnqlttkslssss 164
                                        e ++++++ lee  ++++   +++e+  ++l+e l  l+ee + +k++l++ri++ e++i +l++ +t  + s  s
  gi|320100344|ref|YP_004175936.1|  83 LERVKKRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITAVKVSYIS 159
                                       56677888888887776666677777778899******************************************999 PP

                         Golgin_A5 165 eselesRlkqLtesLiqKQtvlEalsteknslvlQLeRleq 205
                                        +  e+  k+ ++ L     +l+ l++ek s+   L+++e+
  gi|320100344|ref|YP_004175936.1| 160 GEIPEKAYKASMDHL---RRNLDILNSEKASVKKHLDKIEA 197
                                       999999999999998...45899999999999999999885 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.5e-05    0.0095       6      59 ..       9      58 ..       5      75 .. 0.86
   2 ?   -1.6   0.1       4.8     3e+03      24      42 ..     138     155 ..     133     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                                      S---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEG CS
                               PRC  6 asdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPf 59
                                      + +  Gk+V +  G+++G +  ++ d  +g v++l++s ++f +   k v +++
  gi|320100344|ref|YP_004175936.1|  9 IDEYLGKPVNDPYGRRVGYIIGFYSDA-DGNVTSLEISFNEFGF---KQVTVDM 58
                                      67899******************9997.*************977...7777765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.8
                                       EEEEEEEETTTTEEEEEEE CS
                               PRC  24 kVkDvvidekegrvralvv 42 
                                       +++D++++  e  ++a++v
  gi|320100344|ref|YP_004175936.1| 138 EIEDMIVEL-EKAITAVKV 155
                                       789998888.888888877 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 ?    1.9   1.1      0.13        80     174     220 ..      77     126 ..      71     132 .. 0.65
   2 ?   14.1   4.1   2.5e-05     0.015     156     244 ..     113     203 ..      89     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.13
                        Fmp27_WPPW 174 elleeRleeleeqiekleekleelelkseke...deelkeeieelekeik 220
                                        lle+Rle+++++++ lee  ++ e   ++    +++l+e + +l++e+k
  gi|320100344|ref|YP_004175936.1|  77 ILLENRLERVKKRVAALEELNSKKEIPVHTYeefKKKLDESLIKLKEEAK 126
                                       58899999999999988888777777777743344444444444444444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.5e-05
                        Fmp27_WPPW 156 ktHdCilgkendpervqkelleeRleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefl 229
                                       k  + +++ +++ + v++e l++R++e+e+ i +le+++  ++ +  +    ++++k+ +++l+++++ l++++  +
  gi|320100344|ref|YP_004175936.1| 113 KLDESLIKLKEEAKGVKEE-LRKRIHEIEDMIVELEKAITAVKVSYISGeipEKAYKASMDHLRRNLDILNSEKASV 188
                                       4556777776666666655.699*********************99999999************************* PP

                        Fmp27_WPPW 230 etlledlkeseesse 244
                                       ++ l+++++ e+   
  gi|320100344|ref|YP_004175936.1| 189 KKHLDKIEALENLPV 203
                                       *******99887544 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.2   8.1e-05      0.05      35     132 ..      88     185 ..      78     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.1e-05
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHH...HH CS
                              FlgN  35 gdieaLeelleekqellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqelkelleelkel...ne 108
                                       + ++aLeel+ +k+  + + e++++k++++l +l+++   ++++e l+ +   e++++  el++++ ++k      e
  gi|320100344|ref|YP_004175936.1|  88 KRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEE--AKGVKEELR-KRIHEIEDMIVELEKAITAVKVSyisGE 161
                                       4689*********************************..456665555.5999999999999999998887522258 PP

                                       HHHHHHHHCCHHHHHHHHHCCHXX CS
                              FlgN 109 lNgrlieqslefnqrllnllqgaa 132
                                       + +++ ++s+++++r l++l++ +
  gi|320100344|ref|YP_004175936.1| 162 IPEKAYKASMDHLRRNLDILNSEK 185
                                       899999999999999999999876 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015     0.095      57     105 ..     106     154 ..      74     159 .. 0.71
   2 ?   -1.5   0.0       3.9   2.4e+03      79      89 ..     181     194 ..     164     208 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                      Baculo_PEP_C  57 llaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNin 105
                                         +e++++ld++l +L++  + ++++lr+++  ++  + +L   +t ++
  gi|320100344|ref|YP_004175936.1| 106 TYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITAVK 154
                                       3445556999***********************************9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.9
                      Baculo_PEP_C  79 lq...dtlrneLtn 89 
                                       l+    +++++L+ 
  gi|320100344|ref|YP_004175936.1| 181 LNsekASVKKHLDK 194
                                       22111222222222 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   0.00023      0.14     191     242 ..      89     140 ..      78     142 .. 0.85
   2 ?   -0.8   0.0       1.2   7.6e+02      62      87 ..     168     193 ..     160     202 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                           DUF4763 191 slrtkmeeslkklvplreykqdrrdaskelkelkkflkklhdelverfdkle 242
                                       ++ +  e   kk +p + y++ ++++ ++l++lk+ +k + +el +r++++e
  gi|320100344|ref|YP_004175936.1|  89 RVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIE 140
                                       4455555678999************************************998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                           DUF4763  62 KqrvlelrskLalnvpecPeidecvd 87 
                                       K+ +++lr++L +   e+ + ++++d
  gi|320100344|ref|YP_004175936.1| 168 KASMDHLRRNLDILNSEKASVKKHLD 193
                                       44445555555444444444444444 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 ?   -2.2   0.0       6.3   3.9e+03      15      29 ..      79      94 ..      76      96 .. 0.69
   2 ?    9.8   0.3    0.0012      0.72       8      57 ..      96     147 ..      93     154 .. 0.89
   3 ?    0.1   0.0       1.2   7.7e+02      46      65 ..     171     190 ..     166     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.3
                            GIT_CC 15 leeyle.lKkalaase 29
                                      le+ le +Kk +aa e
  gi|320100344|ref|YP_004175936.1| 79 LENRLErVKKRVAALE 94
                                      5556655888888877 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                            GIT_CC   8 L.sdgpVtleeylelKkalaaseakiqq.LlkvNtslsdelrlLQskvqkLq 57 
                                       L s+  ++++ y e Kk+l  s  k+++  + v+++l + ++++  ++ +L+
  gi|320100344|ref|YP_004175936.1|  96 LnSKKEIPVHTYEEFKKKLDESLIKLKEeAKGVKEELRKRIHEIEDMIVELE 147
                                       557889********************987888**********9999998886 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                            GIT_CC  46 lrlLQskvqkLqaeNaqlrd 65 
                                       + +L ++++ L++e a++++
  gi|320100344|ref|YP_004175936.1| 171 MDHLRRNLDILNSEKASVKK 190
                                       6789999*******999986 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.3   0.00025      0.16      34     111 ..      80     157 ..      75     163 .. 0.79
   2 ?   10.2   3.3    0.0011      0.65      22     110 ..     114     201 ..     111     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                       +++le+++++++ +++ +++ e  v++ ++  ++  +s  + ++  k +++el+++i ++++ i++ e+ i + +  
  gi|320100344|ref|YP_004175936.1|  80 ENRLERVKKRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITAVKVS 156
                                       688999999999999988877666665555555555555556999999*****************999999988765 PP

                                       H CS
                         Fib_alpha 111 l 111
                                       +
  gi|320100344|ref|YP_004175936.1| 157 Y 157
                                       5 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketid 98 
                                       l + l k +++ k   e+l+++++ei+++  e e+ ++++k s+ + +  +k  +  + +++++l+   +  k++++
  gi|320100344|ref|YP_004175936.1| 114 LDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITAVKVSYISGEIPEKAYKASMDHLRRNLD-ILNSEKASVK 189
                                       56678888888888889******************************9999999999999999999.7777888999 PP

                                       CCHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnv 110
                                       ++  +i++L n+
  gi|320100344|ref|YP_004175936.1| 190 KHLDKIEALENL 201
                                       999******987 PP

>> DUF2433  Protein of unknown function (DUF2433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.6     1e+03       3      18 ..      44      60 ..      42      65 .. 0.78
   2 ?   11.2   1.0   0.00047      0.29      12      60 ..     105     155 ..      97     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.6
                           DUF2433  3 ssyNefsvnp.sleayr 18
                                      +s+Nef +++ +++ +r
  gi|320100344|ref|YP_004175936.1| 44 ISFNEFGFKQvTVDMFR 60
                                      89*****9763677776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00047
                           DUF2433  12 psleayrsklakskakfaevwetvkkeveaaid..eaqrklLenalevvek 60 
                                       +++e++++kl +s  k++e  + vk+e+ + i+  e++   Le+a+  v+ 
  gi|320100344|ref|YP_004175936.1| 105 HTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHeiEDMIVELEKAITAVKV 155
                                       689*****************************9999999******998865 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 ?   13.1   1.0   0.00017      0.11       8      63 ..      87     141 ..      79     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                            DUF883   8 eslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaae 63 
                                       ++ +a leel  ++++   +++ee +++l+e+l +++e+++ ++e++++r++e+ +
  gi|320100344|ref|YP_004175936.1|  87 KKRVAALEELN-SKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIED 141
                                       55567777776.6667899*********************************9876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   6.2    0.0019       1.2      13     103 ..     102     196 ..      45     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                                       .X.XTTB-BHHHHHHB-..BHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHHHHH.......HHHHHH.. CS
                             DUF16  13 iPvkteYVTrkqlnefkdsnkqrLkkieakvd....klgeqinkleqkvekqgekikelkve.......qkaqgeel 78 
                                       iPv+t       ++efk+  ++ L+k++++ +     l ++i+++e+ + ++++ i+  kv         ka ++++
  gi|320100344|ref|YP_004175936.1| 102 IPVHT-------YEEFKKKLDESLIKLKEEAKgvkeELRKRIHEIEDMIVELEKAITAVKVSyisgeipEKAYKASM 171
                                       44444.......34566666666666655555444444445555555555555555544443111112268999999 PP

                                       .....HHHHHHHHHHHHHHHHHHHC CS
                             DUF16  79 nkvdetleliletLqkinkRlDsie 103
                                       +++ + l+++    ++++k lD+ie
  gi|320100344|ref|YP_004175936.1| 172 DHLRRNLDILNSEKASVKKHLDKIE 196
                                       9***********************9 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.5    0.0013      0.82      33      86 ..      82     135 ..      78     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  33 dyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakke 86 
                                        +e++ k++++l+e  +++e  +  y+e +++L ++l+  +e a+ vk++ +k 
  gi|320100344|ref|YP_004175936.1|  82 RLERVKKRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKR 135
                                       6899********************************************987765 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.5   0.00092      0.57     185     289 ..     101     197 ..      83     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00092
                             LMBR1 185 elPrslwreiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaek 261
                                       e+P +++ e+k++lde l kl+ ea+ +++e+ +  +e+ed+  e++k+ + +   +     ++ i  ++Pe++ + 
  gi|320100344|ref|YP_004175936.1| 101 EIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITAV---K-----VSYISGEIPEKAYKA 169
                                       7999*************************999999999997777776665555...4.....566888999988888 PP

                             LMBR1 262 lksnenkteeslaklekqlikalqkrer 289
                                          +   +++ l++++ +++k l k e 
  gi|320100344|ref|YP_004175936.1| 170 SMDHLRRNLDILNSEKASVKKHLDKIEA 197
                                       7777777888888888777777766554 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.1    0.0015      0.94      58     129 ..      71     138 ..      62     156 .. 0.65
   2 ?    3.2   0.2     0.072        44      47      84 ..     162     199 ..     154     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                          ISG65-75  58 etkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaeka 129
                                       e ++++  +en +e+v+++v  le+l  +    +++   + e+ kk ++e + k k++ + +k++l+k  + 
  gi|320100344|ref|YP_004175936.1|  71 EWEYTAILLENRLERVKKRVAALEELNSK----KEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHE 138
                                       6677888899*************888777....555555555556666666655555555555555443332 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.072
                          ISG65-75  47 vreetadyllketkdklayienakekvdyyveklesll 84 
                                       + e++ +  +++ +++l+ ++++k++v+++++k+e+l 
  gi|320100344|ref|YP_004175936.1| 162 IPEKAYKASMDHLRRNLDILNSEKASVKKHLDKIEALE 199
                                       55666677788899999999999999999999998875 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.26   1.6e+02     117     153 ..      79     115 ..      68     117 .. 0.80
   2 ?   10.0   1.9   0.00073      0.45      94     139 ..     109     154 ..      92     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.26
                     Fzo_mitofusin 117 leeeikelekeiekleevqkkakllrnkaslleseLe 153
                                       le+++++++k++++lee+++k ++  +  ++++++L+
  gi|320100344|ref|YP_004175936.1|  79 LENRLERVKKRVAALEELNSKKEIPVHTYEEFKKKLD 115
                                       89999************99998877676666666665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00073
                     Fzo_mitofusin  94 qvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkak 139
                                         +++l++ + +l+++ + +++el+++i+e+e  i +le++++  k
  gi|320100344|ref|YP_004175936.1| 109 EFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITAVK 154
                                       5679999*********************************998877 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.5   0.00043      0.26      17      87 ..      76     144 ..      71     148 .. 0.87
   2 ?   -0.6   0.1       2.7   1.7e+03      48      63 ..     179     194 ..     151     201 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                       Uso1_p115_C  17 neklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEldDLLl 87 
                                       +  l+++l+  +k++  le+   + + e   +++e+ +kkl + l kl++e+k  ke+ ++   E++D+ +
  gi|320100344|ref|YP_004175936.1|  76 AILLENRLERVKKRVAALEEL--NSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIV 144
                                       56799999999*999999999..666777799********************999999998899***9987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.7
                       Uso1_p115_C  48 keleaenkklekelek 63 
                                       + l++e+ +++k l+k
  gi|320100344|ref|YP_004175936.1| 179 DILNSEKASVKKHLDK 194
                                       2233333344443333 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.5     0.005       3.1     114     146 ..      92     140 ..      73     150 .. 0.51
   2 ?    6.3   0.4     0.011       6.6      10      60 ..     137     187 ..     136     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.005
                           DUF4795 114 aldtLq..........eelkekld......rlelepLkeqleerlkelq 146
                                       al++L+          ee k+kld      + e + +ke+l +r++e++
  gi|320100344|ref|YP_004175936.1|  92 ALEELNskkeipvhtyEEFKKKLDesliklKEEAKGVKEELRKRIHEIE 140
                                       2233334444444444555555555555555555555555555555555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                           DUF4795  10 kklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkad 60 
                                       ++++++i++l++ +  ++ +  + e  +++++ ++++l+  ++ l+++ka 
  gi|320100344|ref|YP_004175936.1| 137 HEIEDMIVELEKAITAVKVSYISGEIPEKAYKASMDHLRRNLDILNSEKAS 187
                                       578889999999999999999999999999999**************9964 PP

>> PGBA_C  Plasminogen-binding protein pgbA C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.6     0.005       3.1      14      74 ..      87     148 ..      80     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.005
                            PGBA_C  14 kknapvlkenaakkevnkpnskeekrrlkeekkkakaeqrarefeqrarehqerde.kelee 74 
                                       kk    l e ++kke++     e k++l e   k k e +  + e r r h+  d   ele+
  gi|320100344|ref|YP_004175936.1|  87 KKRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMiVELEK 148
                                       45555699********************************9999999999987664246665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.1    0.0062       3.8      47     114 ..      81     148 ..      62     155 .. 0.86
   2 ?    3.3   0.2      0.18   1.1e+02      27      62 ..     166     198 ..     154     208 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0062
                            APG6_N  47 eeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelle 114
                                       + le+ ++++++le+  ++++      e+ +++l++ l +l+ee++ ++ee ++ ++e  +  +el++
  gi|320100344|ref|YP_004175936.1|  81 NRLERVKKRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEK 148
                                       56788999999999999999999999999999999999999999999999999999998888888765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.18
                            APG6_N  27 aYeeflkklkkekkeeekqdeeleeleeelekleke 62 
                                       aY++ +++l+++ +  +   +e ++ ++ l+k+e+ 
  gi|320100344|ref|YP_004175936.1| 166 AYKASMDHLRRNLDILN---SEKASVKKHLDKIEAL 198
                                       45555555555544433...3444444444444443 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   9.4     0.018        11      88     160 ..      80     152 ..      55     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.018
                           UPF0242  88 eealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetiee 160
                                       e+ le ++++   L+e  ++ke  ++ ++e +++L e l + +e+ + +k el ++++e +  + e+++ i+ 
  gi|320100344|ref|YP_004175936.1|  80 ENRLERVKKRVAALEELNSKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITA 152
                                       4567777777777777777777777777777777777777777777777777777777777777777777664 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.6    0.0079       4.9     198     294 ..      98     194 ..      73     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0079
                             FAM76 198 eekesnetskksldsnssdhlvavtqLkeeia.slkkqleqkdqellekdkkitelkaellekekelreklkeleke 273
                                       ++ke   ++ ++ +++  + l+++++  + ++ +l+k++++ + +++e +k it++k+  ++ e   ++ +k++  +
  gi|320100344|ref|YP_004175936.1|  98 SKKEIPVHTYEEFKKKLDESLIKLKEEAKGVKeELRKRIHEIEDMIVELEKAITAVKVSYISGEIP-EKAYKASMDH 173
                                       344444445567888888899998887777753799**********************99987754.3445555666 PP

                             FAM76 274 akekieklekkirellkevae 294
                                        +++++ l+++ ++++k++ +
  gi|320100344|ref|YP_004175936.1| 174 LRRNLDILNSEKASVKKHLDK 194
                                       777888888888888777655 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.8       1.1   6.9e+02      22      58 ..      81     120 ..      71     134 .. 0.52
   2 ?    9.9   0.8    0.0018       1.1       3      67 ..     129     193 ..     127     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHXXXXXX CS
                              YabA  22 eeleelkeelaelleenaeLele...neklrerleeeekk 58 
                                       ++le++k+++a+l e n++ e+     e+++++l+e+  k
  gi|320100344|ref|YP_004175936.1|  81 NRLERVKKRVAALEELNSKKEIPvhtYEEFKKKLDESLIK 120
                                       5677777777777777766665522333444444222222 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXX CS
                              YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkels 67 
                                       k+el ++++e+e+ + el + ++++k +  +    +++ ++  ++lr++l+  ++++++ kk+l+
  gi|320100344|ref|YP_004175936.1| 129 KEELRKRIHEIEDMIVELEKAITAVKVSYISGEIPEKAYKASMDHLRRNLDILNSEKASVKKHLD 193
                                       68999***********************9999999999************554444444444333 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.1     0.021        13      22      70 ..      78     140 ..      75     141 .. 0.91
   2 ?    1.7   5.2      0.59   3.7e+02       7      64 ..     130     194 ..     113     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
                              ZapB  22 lLqmeieeLkeeneelkeenrele..............eeneqlkeereawqerlkkLLgkle 70 
                                       lL +++e++k+++++l+e n + e              e++ +lkee + ++e l+k + ++e
  gi|320100344|ref|YP_004175936.1|  78 LLENRLERVKKRVAALEELNSKKEipvhtyeefkkkldESLIKLKEEAKGVKEELRKRIHEIE 140
                                       79999*************99999999*9**99999999******************9888776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.59
                              ZapB   7 eqLEskiqkaidtitlLqmeieeLkeen.......eelkeenreleeeneqlkeereawqerlkk 64 
                                       e+L ++i++  d+i +L + i ++k          +++k  ++ l++ ++ l  e+++++++l+k
  gi|320100344|ref|YP_004175936.1| 130 EELRKRIHEIEDMIVELEKAITAVKVSYisgeipeKAYKASMDHLRRNLDILNSEKASVKKHLDK 194
                                       45666666666666666666666666665555555555555555557777777888888888887 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.2   1.4e+03     105     138 ..      84     117 ..      68     121 .. 0.55
   2 ?   10.0   4.2    0.0012      0.77     101     143 ..     112     154 ..     106     155 .. 0.90
   3 ?   -1.9   0.1       5.7   3.5e+03     105     130 ..     169     194 ..     162     202 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.2
                             Med21 105 erikeLeeelreveeereekvkekeellkkveel 138
                                       er+k+  + l+e ++++e  v+  ee  kk++e 
  gi|320100344|ref|YP_004175936.1|  84 ERVKKRVAALEELNSKKEIPVHTYEEFKKKLDES 117
                                       3333333345555556666667777777777665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                             Med21 101 eeqeerikeLeeelreveeereekvkekeellkkveellrava 143
                                       ++ +e++ +L+ee + v+ee++++++e e +  ++e++++av+
  gi|320100344|ref|YP_004175936.1| 112 KKLDESLIKLKEEAKGVKEELRKRIHEIEDMIVELEKAITAVK 154
                                       556788889******************************9996 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.7
                             Med21 105 erikeLeeelreveeereekvkekee 130
                                       ++++ L ++l+  ++e++ + k  ++
  gi|320100344|ref|YP_004175936.1| 169 ASMDHLRRNLDILNSEKASVKKHLDK 194
                                       56667777777777776666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1638  (0.0913604); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); expected 358.6 (0.02)
Passed Vit filter:                       158  (0.00881254); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 1479.58
//
Query:       gi|320100345|ref|YP_004175937.1|  [L=175]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1301.74
//
Query:       gi|320100346|ref|YP_004175938.1|  [L=290]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   12.7   0.1       0.12   11.9   0.1    1.3  1  DUF1897   Domain of unknown function (DUF1897)


Domain annotation for each model (and alignments):
>> DUF1897  Domain of unknown function (DUF1897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.4e-06      0.12      15      30 ..     256     271 ..     256     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-06
                           DUF1897  15 aeYYrsiGmheeAeai 30 
                                       +eYYr+iG ++ A  +
  gi|320100346|ref|YP_004175938.1| 256 IEYYRRIGSERPASTV 271
                                       8*********999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2220.89
//
Query:       gi|320100347|ref|YP_004175939.1|  [L=74]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 542.47
//
Query:       gi|320100348|ref|YP_004175940.1|  [L=252]
Description: diphthine synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-21   76.7   0.2    2.8e-21   76.5   0.2    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 !   76.5   0.2   1.5e-25   2.8e-21       1     212 [.       1     218 [.       1     219 [. 0.83

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.5e-25
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsr......aleilldllaeeleleapmgkekepleeayeeiaea 71 
                                       +l ++G+G  ++ +lT++ l++l++a+ ++ d+ +       +e+++d  +            +++++ + ++i ++
  gi|320100348|ref|YP_004175940.1|   1 MLAFIGIGY-SRRHLTQESLELLRSAEKIYIDT-YtsmyedGYEWIRDVNPS------AEIIVARRRDLEGDAITRI 69 
                                       689******.88*****************8777.223345599999998765......455558889999999**** PP

                      TP_methylase  72 laealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl...lpg 145
                                       + e +r+   V+++++GDP+ ++t++++   ++a ++g+ev+v  G+s+++++ +r+g+  + +g++++++     +
  gi|320100348|ref|YP_004175940.1|  70 VEESVRKN--VAIVCAGDPFTATTHDAIR--VEALKRGVEVRVATGISIVSLVHSRIGLQAYRFGKIVTLVypdNFK 142
                                       ******97..******************8..555559**********************************999777 PP

                      TP_methylase 146 lakeeereleallangdtlvllkaprk......laelaelL...kea.lyddttpvavveragtedervvrgtleel 212
                                       ++   e+ +++l+ n +tl+ll+ + +      ++e++e+L    ++ l  d+   ++v+r+g+  e v  g+++el
  gi|320100348|ref|YP_004175940.1| 143 PYSVVETIYDNLSRNLHTLILLDLRLEegvamtIPEAVEILgglDDKgLILDQ-VGVAVARLGWSSELVKAGRVREL 218
                                       788999****************3333346667799999999554333566655.5577899***9999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1832.70
//
Query:       gi|320100349|ref|YP_004175941.1|  [L=349]
Description: periplasmic-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-16   59.4   0.0    5.6e-16   58.8   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   3.1e-20   5.6e-16       1     202 [.      46     252 ..      46     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 3.1e-20
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG.--GGGGGGT.......TS-BSBESSSB-H..HHHHHH--SEEEE-GGG CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdttt.sdpldadklee.....aivevgadgeidv..EklaalkPDlvilskgl 69 
                                       i+slsps+te+l+ lG +d vvg d  + sd+++           ++++vg+++   +  E+++a+ PDlv++ kg 
  gi|320100349|ref|YP_004175941.1|  46 IVSLSPSITETLAYLGGLDTVVGADSLSlSDEWFNIS--TilrarNVTDVGGYWWSAIrsEEILAASPDLVLAEKGA 120
                                       9*********************988755255555553..135668999999999777777***************** PP

                                       ...GGGHHHHHHHS-EEE----TTS...HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEE CS
                      Peripla_BP_2  70 gltdedeellksgiptvivessntg...eslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvf 143
                                         +    ++ k+   tv++ ++ +    +++   + +++ +l++++   ++  +++ ++++ ++ +++  +   ++f
  gi|320100349|ref|YP_004175941.1| 121 --HIPLLDFFKNYNVTVVYLEGGASrsiQDVLSDMYTVALILNKTSLLAEFSGKLEAEFQKYRELVAERYKGVSILF 195
                                       ..888888888888888888888777889999*************************************77777777 PP

                                       EETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH CS
                      Peripla_BP_2 144 ggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr 202
                                         +  gg+ vag ++yi d+++ lg+ n+  +    ++ +is E  ++ +pdvi+v+++
  gi|320100349|ref|YP_004175941.1| 196 VIDLTGGIWVAGKGTYIDDIVERLGLVNACRD--IYSWTSISLEKAVELNPDVIVVASM 252
                                       7778899**********************999..79*********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2657.30
//
Query:       gi|320100350|ref|YP_004175942.1|  [L=311]
Description: transport system permease [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-59  199.9  34.9    6.1e-59  199.5  34.9    1.1  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
      0.037   13.5  22.7      0.068   12.6  22.7    1.6  1  ABC-3     ABC 3 transport family
       0.22   11.9   2.6       0.54   10.7   0.1    2.7  3  PEN-2     Presenilin enhancer-2 subunit of gamma secretase


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 !  199.5  34.9     1e-62   6.1e-59      36     311 ..      32     306 ..       5     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 199.5 bits;  conditional E-value: 1e-62
                             FecCD  36 eivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissgaalgavlalllllgslslfalplaaflgal 112
                                         +l++r+ rvl all+Ga++++aG+llQ+ +rNpL+d +++G+ sga ++  +++l+  ++  +   +++++lg++
  gi|320100350|ref|YP_004175942.1|  32 PALLDYRFNRVLSALLSGAIIGLAGVLLQSSLRNPLVDHYVIGVGSGALVFTYIFILW--TGGYTLNASFFSMLGGF 106
                                       3689****************************************************99..567777999******** PP

                             FecCD 113 lalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGslsgaswskvllllvlllll 189
                                       +a++l++lla ++ + s ++ iLaGi +++++s+l+ ll ++   +++ ++   l+Gs+  a+ +k+ +ll++l+++
  gi|320100350|ref|YP_004175942.1| 107 TAMVLTILLA-EKLSGSATSYILAGIGMNSVFSGLSILLSYV-AVREYPYVHALLVGSFIVATAEKTQVLLIVLAVS 181
                                       **********.99999999*********************99.889******************************* PP

                             FecCD 190 lllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvg.adhrkll 265
                                       ll+++l+a++l+ l+++de +   G n++ +rl+ ++l+ + t++++++ G igF+GL+ Phiar++ g +d+r + 
  gi|320100350|ref|YP_004175942.1| 182 LLTVFLIAKPLNTLEVSDEFSMVAGFNPRLTRLASVVLAGASTSIVTSMYGLIGFIGLVTPHIARYVSGtSDNRVVA 258
                                       ***************************************************************************** PP

                             FecCD 266 plsallGallllladllarllls..ptelpvgivtaliGapffiylll 311
                                       pl++l+++++l l+d+++r l++    e+p+g+v +liGap+fiyll+
  gi|320100350|ref|YP_004175942.1| 259 PLAMLTSSAVLYLTDFISRRLFAvmWGEVPAGAVASLIGAPIFIYLLV 306
                                       *********************9976779******************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 ?   12.6  22.7   1.1e-05     0.068      56     255 ..      93     305 ..      36     308 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                             ABC-3  56 lllgailvglia...avalell.krk.t.klkedtaigivlsvfla.lglvlvslikkskvdldsyLfGniltisqe 125
                                       ++l a ++++++   a++l++l ++k +    + ++ gi + ++++ l+++l   + +    +++ L G+ +  + e
  gi|320100350|ref|YP_004175942.1|  93 YTLNASFFSMLGgftAMVLTILlAEKlSgSATSYILAGIGMNSVFSgLSILLSYVAVREYPYVHALLVGSFIVATAE 169
                                       44444444443311122222221222021223345678877766652666665555558899***********9999 PP

                             ABC-3 126 dliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaat 202
                                          +++i+ av ll+++l+ k+l  + ++ e+++v+g++++l +l  ++l +++ +++  + G+i  i l ++P ++
  gi|320100350|ref|YP_004175942.1| 170 KTQVLLIVLAVSLLTVFLIAKPLNTLEVSDEFSMVAGFNPRLTRLASVVLAGASTSIVTSMYGLIGFIGL-VTPHIA 245
                                       99999***********************************************************999986.678765 PP

                             ABC-3 203 Arrl.trslesllivAillglvsvvaGlllSyyl......dlatGavivlvatllfllal 255
                                        +   t++ + ++ +A+l++   +++  ++S  l      ++++Gav  l+ + +f+  l
  gi|320100350|ref|YP_004175942.1| 246 RYVSgTSDNRVVAPLAMLTSSAVLYLTDFISRRLfavmwgEVPAGAVASLIGAPIFIYLL 305
                                       554414455566679999999888888888854323333358999999999998888755 PP

>> PEN-2  Presenilin enhancer-2 subunit of gamma secretase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   9.1e-05      0.54      44      82 ..      65     103 ..      57     113 .. 0.83
   2 ?   -2.4   0.0       1.1   6.5e+03      64      64 ..     168     168 ..     149     205 .. 0.53
   3 ?   -0.5   0.1      0.29   1.7e+03      52      66 ..     292     306 ..     270     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.1e-05
                             PEN-2  44 qkeirkyvilSaiGalvwlvvllaWalvfqikraewgev 82 
                                       ++ + +yvi    Galv++ +++ W+  ++++ + +  +
  gi|320100350|ref|YP_004175942.1|  65 NPLVDHYVIGVGSGALVFTYIFILWTGGYTLNASFFSML 103
                                       566889***********************9998777655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                             PEN-2  64 v 64 
                                       +
  gi|320100350|ref|YP_004175942.1| 168 A 168
                                       2 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.29
                             PEN-2  52 ilSaiGalvwlvvll 66 
                                       ++S+iGa +++ +l+
  gi|320100350|ref|YP_004175942.1| 292 VASLIGAPIFIYLLV 306
                                       789******999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2282.82
//
Query:       gi|320100351|ref|YP_004175943.1|  [L=249]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-20   73.7   0.0    2.5e-20   73.4   0.0    1.1  1  ABC_tran    ABC transporter
    4.2e-13   49.8   0.1    5.8e-06   26.3   0.1    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    5.4e-05   23.1   0.0     0.0032   17.2   0.0    2.1  2  AAA_15      AAA ATPase domain
    0.00017   21.1   0.0       0.16   11.4   0.0    2.4  2  SMC_N       RecF/RecN/SMC N terminal domain
    0.00031   21.3   0.0    0.00048   20.7   0.0    1.2  1  AAA_23      AAA domain
    0.00063   20.2   0.0     0.0011   19.4   0.0    1.4  1  AAA_16      AAA ATPase domain
     0.0015   18.9   0.0       0.01   16.2   0.0    2.0  1  AAA         ATPase family associated with various cellular ac
     0.0016   18.1   0.0     0.0033   17.1   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.021   14.4   0.0      0.035   13.7   0.0    1.3  1  AAA_27      AAA domain
      0.023   15.3   0.0      0.037   14.6   0.0    1.7  1  AAA_18      AAA domain
      0.025   14.4   0.0        0.1   12.3   0.0    2.0  1  DEAD        DEAD/DEAH box helicase
      0.027   14.5   0.0       0.36   10.9   0.0    2.2  2  AAA_14      AAA domain
      0.027   13.3   0.0      0.064   12.0   0.0    1.6  1  ABC_ATPase  Predicted ATPase of the ABC class
      0.052   13.3   0.0      0.073   12.8   0.0    1.3  1  AAA_30      AAA domain
        0.1   12.8   0.0       0.26   11.4   0.0    1.7  2  AAA_33      AAA domain
        0.1   12.8   0.0       0.19   12.0   0.0    1.7  1  AAA_22      AAA domain
       0.14   11.0   0.0        0.2   10.4   0.0    1.1  1  DLIC        Dynein light intermediate chain (DLIC)
       0.17   11.9   0.0       0.33   11.0   0.0    1.4  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
       0.36    8.3   0.1       0.46    7.9   0.1    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 !   73.4   0.0   2.7e-23   2.5e-20       4     136 ..      21     160 ..      18     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.7e-23
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                        s+++  ++++ ++G+n +GK+tLl+++a+l++   G+il+dg + ++ +l +l+k +++ + +  +    l+vre 
  gi|320100351|ref|YP_004175943.1|  21 ASFQIPGNKVTCLMGPNASGKTTLLRAVARLVE-YRGSILIDGLEASRMPLAVLSKILSYGSPTsVSTSLSLRVREI 96 
                                       799*****************************8.7*************9***********98885555555667777 PP

                                       ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                  + ++ +e+a  +l+++ l d+ v     +LS G+ qrv++a al+k+p+ lllDEp 
  gi|320100351|ref|YP_004175943.1|  97 lemalyplkniDVEKAVEEASMELDITMLLDRYV----GELSSGELQRVVIASALVKNPRYLLLDEPD 160
                                       999**99664444444666666666666666666....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.5e-07   0.00014       1      22 [.      30      51 ..      30      72 .. 0.80
   2 !   26.3   0.1   6.1e-09   5.8e-06     220     301 ..     116     193 ..      59     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.5e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      +++l GpN+sGK++LL+a   l
  gi|320100351|ref|YP_004175943.1| 30 VTCLMGPNASGKTTLLRAVARL 51
                                      699****************776 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 6.1e-09
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvilt 295
                                        ++ l+ +   ++ + elS+G ++   ++++ l  ++  + ll+DEp+++ +  + + l ++l +++++  + ++++
  gi|320100351|ref|YP_004175943.1| 116 ASMELDITMLLDRYVGELSSGELQR-VVIASALVKNP--RYLLLDEPDAHVDVGFKPVLSRVLrRRAAS--STIVVA 187
                                       55666666677788999*****999.66777776666..88**********************655555..9***** PP

                            AAA_21 296 THSpll 301
                                       TH+p++
  gi|320100351|ref|YP_004175943.1| 188 THDPVF 193
                                       ****96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.4e-06    0.0032      17      43 ..      23      48 ..      18      55 .. 0.84
   2 ?    3.6   0.0     0.046        43     324     368 ..     151     193 ..     105     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.4e-06
                            AAA_15 17 veidlseeltvliGkNnsGKSsileal 43
                                      ++i+ ++ +t+l G+N+sGK+++l+a 
  gi|320100351|ref|YP_004175943.1| 23 FQIPGNK-VTCLMGPNASGKTTLLRAV 48
                                      6677566.****************985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.046
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       +  ll++EP+ah    ++ vl + l++ a ++   +++ TH p +
  gi|320100351|ref|YP_004175943.1| 151 PRYLLLDEPDAHVDVGFKPVLSRVLRRRAASST--IVVATHDPVF 193
                                       45599************************9996..*******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 !   11.4   0.0   0.00017      0.16      22      44 ..      27      48 ..      13      57 .. 0.80
   2 !    7.4   0.0    0.0028       2.6     137     202 ..     133     193 ..      68     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                      TTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 22 fsksftaivGpNGSGKsnlldAi 44
                                        +++t+++GpN SGK+ ll A+
  gi|320100351|ref|YP_004175943.1| 27 G-NKVTCLMGPNASGKTTLLRAV 48
                                      3.469***************998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0028
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                       LS Ge +     +++A   vk     llDe da+ D      ++++l+++  ++ ++v +++   +
  gi|320100351|ref|YP_004175943.1| 133 LSSGELQ----RVVIASALVKNPRYLLLDEPDAHVDVGFKPVLSRVLRRRAASSTIVVATHDPV-F 193
                                       5555544....23444445555556689***********999**99999997776666666544.3 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.1e-07   0.00048      18      39 ..      27      48 ..      17      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.1e-07
                            AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                      ++++t++ GpN +GKTT+l+A+
  gi|320100351|ref|YP_004175943.1| 27 GNKVTCLMGPNASGKTTLLRAV 48
                                      799*****************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.2e-06    0.0011      25     162 ..      29     178 ..      14     187 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekl 101
                                        ++ l G+ ++GK++l+r+++r +e +g i++ g   +    +p+++l ++l          +  ++++  + re l
  gi|320100351|ref|YP_004175943.1|  29 KVTCLMGPNASGKTTLLRAVARLVEYRGSILIDGLEASR---MPLAVLSKIL-S----YGSPTSVSTSLSLRVREIL 97 
                                       67789*****************99999988888888887...6665555555.2....2223333333666666666 PP

                            AAA_16 102 eealaavpelagaea...................srllellkrll.allsrderplvlvlDdlq.wadeaslqllaa 157
                                       e al + ++++ ++a                   +    +l+r + a +   + p +l+lD+ +  +d +   +l+ 
  gi|320100351|ref|YP_004175943.1|  98 EMALYPLKNIDVEKAveeasmelditmlldryvgELSSGELQRVViASALV-KNPRYLLLDEPDaHVDVGFKPVLSR 173
                                       666664444444444444334433435555555566666666666444443.6678888887665555555555666 PP

                            AAA_16 158 Llrll 162
                                        lr++
  gi|320100351|ref|YP_004175943.1| 174 VLRRR 178
                                       66555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05      0.01       2      71 ..      32     163 ..      31     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                                       EEESSTTSSHHHHHHHHHHHHTHE..................................................... CS
                               AAA   2 llyGppGtGKTllakavakelgve..................................................... 25 
                                       +l+Gp   GKT+l +ava+ ++ +                                                     
  gi|320100351|ref|YP_004175943.1|  32 CLMGPNASGKTTLLRAVARLVEYRgsilidgleasrmplavlskilsygsptsvstslslrvreilemalyplknid 108
                                       79******************865555555556666667777777777777777777777777777777777755555 PP

                                       ........EEEEETTTCSSSSTTH..HHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                               AAA  26 ........fleisgsellskyvge..sekkirelfkeakekakpsilfiDEidala 71 
                                                +e++ + ll+ yvge  s +  r ++++a  k+ p  l++DE da +
  gi|320100351|ref|YP_004175943.1| 109 vekaveeaSMELDITMLLDRYVGElsSGELQRVVIASALVKN-PRYLLLDEPDAHV 163
                                       555555555555555555559888424455666666676666.8999999988876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.5e-06    0.0033      18      45 ..      24      51 ..      16      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.5e-06
                            AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqal 45
                                      +i  + +t l+Gp+ sGK+Tll A++ l
  gi|320100351|ref|YP_004175943.1| 24 QIPGNKVTCLMGPNASGKTTLLRAVARL 51
                                      4543449***************999876 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.7e-05     0.035      21      49 ..      23      51 ..      19      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                            AAA_27 21 fsaeeadlhliyGpNEAGKstalrAisdl 49
                                      f+   ++++ ++GpN +GK+t+lrA+ +l
  gi|320100351|ref|YP_004175943.1| 23 FQIPGNKVTCLMGPNASGKTTLLRAVARL 51
                                      5666889999****************987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.9e-05     0.037       2      40 ..      32      71 ..      32     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf.gvnlrdvakengllle 40
                                      +l+G+ ++GKttl ++++++ ++ g +l+d +  +++ l 
  gi|320100351|ref|YP_004175943.1| 32 CLMGPNASGKTTLLRAVARLVEYrGSILIDGLEASRMPLA 71
                                      799**************99988898888877776666655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011       0.1     106     150 ..     136     179 ..      19     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                       HHHHHHH.HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 106 grlddll.stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       g l++++  +    +++ r+l lDE d   d gf++ ++r+l++ +
  gi|320100351|ref|YP_004175943.1| 136 GELQRVViASAL--VKNPRYLLLDEPDAHVDVGFKPVLSRVLRRRA 179
                                       444443322222..8999***********************99874 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00038      0.36       2      24 ..      28      50 ..      27      79 .. 0.86
   2 ?    1.3   0.0      0.35   3.3e+02      55      89 ..     141     177 ..     105     189 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                            AAA_14  2 rkilvitGaRrvGKTtllkqlik 24
                                      +k+ +++G+  +GKTtll+ +++
  gi|320100351|ref|YP_004175943.1| 28 NKVTCLMGPNASGKTTLLRAVAR 50
                                      6899**************99874 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.35
                            AAA_14  55 lilek.lkeekktylflDEiqev..pewekalkslvde 89 
                                       ++ ++ l  ++ +yl+lDE       +++ +l +++++
  gi|320100351|ref|YP_004175943.1| 141 VVIASaLV-KNPRYLLLDEPDAHvdVGFKPVLSRVLRR 177
                                       33333233.47899****96544224456666665555 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 ?   12.0   0.0   6.8e-05     0.064     244     266 ..      28      50 ..      23      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.8e-05
                                       SSEEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAlek 266
                                       ++vt ++G+++ GK+TLL+A+++
  gi|320100351|ref|YP_004175943.1|  28 NKVTCLMGPNASGKTTLLRAVAR 50 
                                       459*****************986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.8e-05     0.073      17      46 ..      27      56 ..      21     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag 46
                                      g++v++l Gp  +GKtt+l+a+++++e +g
  gi|320100351|ref|YP_004175943.1| 27 GNKVTCLMGPNASGKTTLLRAVARLVEYRG 56
                                      56799********************99887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00028      0.26       2      21 ..      31      50 ..      30      67 .. 0.85
   2 ?   -2.3   0.0       4.7   4.4e+03      19      34 ..     147     162 ..     143     190 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                            AAA_33  2 vllvGlpGsGKstlaerllk 21
                                      + l G+++sGK+tl++ +++
  gi|320100351|ref|YP_004175943.1| 31 TCLMGPNASGKTTLLRAVAR 50
                                      6789************9875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.7
                            AAA_33  19 llkklgavllssdtlr 34 
                                       l+k+  + ll++++++
  gi|320100351|ref|YP_004175943.1| 147 LVKNPRYLLLDEPDAH 162
                                       5655557777777644 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.19       6      30 ..      29      53 ..      26     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                      ++++++G+  +GKTtllr +++  +
  gi|320100351|ref|YP_004175943.1| 29 KVTCLMGPNASGKTTLLRAVARLVE 53
                                      6899****************99864 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00022       0.2      17      45 ..      20      48 ..      17      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                              DLIC 17 rsssklPsgksvlvlGedgsGkttliakl 45
                                      ++s ++P +k   ++G ++sGkttl+  +
  gi|320100351|ref|YP_004175943.1| 20 KASFQIPGNKVTCLMGPNASGKTTLLRAV 48
                                      567899*******************8765 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   0.00035      0.33      18      45 ..      25      54 ..      13      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                                      H..TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglakalgv 45
                                      +  ++v +L G+  +GKTtl r++a+ +++
  gi|320100351|ref|YP_004175943.1| 25 IpgNKVTCLMGPNASGKTTLLRAVARLVEY 54
                                      2456789*****************998765 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00049      0.46      20      37 ..      31      48 ..      24      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00049
                           DUF3584 20 tnieGtNaaGKTtLlrLi 37
                                      t + G Na+GKTtLlr +
  gi|320100351|ref|YP_004175943.1| 31 TCLMGPNASGKTTLLRAV 48
                                      6789************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1717.94
//
Query:       gi|320100352|ref|YP_004175944.1|  [L=189]
Description: isochorismatase hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-45  152.9   0.0      1e-44  152.8   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 !  152.8   0.0   5.7e-49     1e-44       2     167 ..       4     164 ..       3     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 5.7e-49
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgael 78 
                                       al+++Dm ++fv +g+ +s+e+++++++i++ +  ar +gipvi+  d h       d +   + ph  +g +++++
  gi|320100352|ref|YP_004175944.1|   4 ALLIVDMLKEFV-HGRLKSPEATQIIPAISRIASIARSKGIPVIYLADHHY----PFDHELSIWGPHAMQGDPESDI 75 
                                       9***********.**************************************....88889999************** PP

                   Isochorismatase  79 vpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspel 155
                                       ++el+p +gd+v+ K+ +s+f +t+ld iL+ lg++t++l+Gi+t++CV++ta+da+ + y+++vv+DAv+a+++ +
  gi|320100352|ref|YP_004175944.1|  76 IDELKPGPGDIVLYKRSYSGFRETGLDYILRDLGVDTVILTGIHTHICVLHTAIDAFYNRYKIIVVEDAVSAFNKGD 152
                                       ***************************************************************************** PP

                   Isochorismatase 156 hdaalkrlkqaf 167
                                       h++al+ ++   
  gi|320100352|ref|YP_004175944.1| 153 HEWALNYMRTVL 164
                                       ********9544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1330.93
//
Query:       gi|320100353|ref|YP_004175945.1|  [L=195]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1468.07
//
Query:       gi|320100354|ref|YP_004175946.1|  [L=89]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-06   27.9   0.2    3.6e-06   27.6   0.2    1.1  1  MJ1316    MJ1316 RNA cyclic group end recognition domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2     2e-10   3.6e-06       4      76 .]       8      80 ..       6      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2e-10
                            MJ1316  4 aqdvlnRirWdkeldkskfvvgyldR.fkgikevpleeiswied....flleeeegelaIPlHRiryikrk.gevvWdR 76
                                       +++l Ri +  +  +s+++v++  R ++g   +p+   s ied    ++++ +e    IPlHR+++i+   +++v++R
  gi|320100354|ref|YP_004175946.1|  8 LENWLRRIVFGGR--RSDYTVYVRFRtENGEVLKPIP-GSLIEDfrggYIYTRDE---VIPLHRVEEIRDShDTLVYRR 80
                                      5789*********..9**********75555444444.55556644576666666...7**********9769999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 643.91
//
Query:       gi|320100355|ref|YP_004175947.1|  [L=426]
Description: glutamate dehydrogenase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-75  251.7   0.4      1e-74  251.3   0.4    1.1  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    3.6e-50  169.2   0.0    8.2e-50  168.0   0.0    1.6  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
    7.8e-05   22.1   0.5    0.00015   21.1   0.2    1.6  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0069   16.8   0.1      0.014   15.8   0.1    1.4  1  NAD_binding_7    Putative NAD(P)-binding
     0.0074   16.4   1.6      0.074   13.1   0.4    2.2  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
     0.0084   13.7   0.0      0.011   13.2   0.0    1.1  1  Bac_GDH          Bacterial NAD-glutamate dehydrogenase
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.023   14.0   0.1    1.3  1  ThiF             ThiF family
      0.014   15.1   0.0      0.077   12.7   0.0    2.0  2  DUF3158          Protein of unknown function (DUF3158)
      0.098   11.8   0.0       0.19   10.8   0.0    1.4  1  CoA_transf_3     CoA-transferase family III


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.3   0.4   5.1e-78     1e-74       1     243 []     187     424 ..     187     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: 251.3 bits;  conditional E-value: 5.1e-78
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldie 77 
                                       GG  +r  +Tg+Gv+ +++e++kk  +  legk+va+ G+Gnvg yaa+ l+e+ga+vvavsDssG+iydp+Gld+e
  gi|320100355|ref|YP_004175947.1| 187 GGLYARVVSTGYGVALTAREAAKKWIGG-LEGKTVAVHGFGNVGMYAAKYLAEWGARVVAVSDSSGYIYDPKGLDVE 262
                                       999*********************6666.************************************************ PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       e +++ke +++v++yk   ++++++ +n+ ellel+vdilvP+Atq++i++en++ +ik  +k++ EgAN+ptt+eA
  gi|320100355|ref|YP_004175947.1| 263 EAIRVKETTGKVTNYK---KGDVKVSANHMELLELPVDILVPAATQDVITKENVN-KIK--AKVISEGANGPTTPEA 333
                                       ****************...56899999999*************************.999..**************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T..HHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe..lvkgani 229
                                       ++il+e+gv++vpd++aN+GGVt+S +E++ n ++   t+ee  ++l+k m+  f++v +  +++  +  ++++a++
  gi|320100355|ref|YP_004175947.1| 334 EKILHEKGVIIVPDILANSGGVTMSWIEWSHNRMGCWLTDEEALSRLDKMMSVNFERVFNDWRKRFSThpMRTAAYA 410
                                       ***************************************************************9766667******* PP

                                       HHHHHHHHHHHHCT CS
                     ELFV_dehydrog 230 agfekvaeamkaqG 243
                                       +++++v++amk +G
  gi|320100355|ref|YP_004175947.1| 411 IAVDRVVKAMKLRG 424
                                       ***********998 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.0   0.0   4.1e-53   8.2e-50       1     130 []      41     169 ..      41     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.0 bits;  conditional E-value: 4.1e-53
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       pe+ +qv+++++rdnG+le++ g+r+qh+salgP+kGG+R+ ++v+  ev aL+++mt+K++l+++p+GG+kggv++
  gi|320100355|ref|YP_004175947.1|  41 PEKLVQVKITIRRDNGKLETYLGWRSQHNSALGPYKGGVRYGEDVTPGEVVALSMWMTWKTSLAGIPYGGGKGGVRV 117
                                       8999************************************************************************* PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       +pk ls++ele++ r+f   +a k +Gp++D+pApDv+t++++maw +dey+k
  gi|320100355|ref|YP_004175947.1| 118 NPKALSQRELEELSRKFFAGIA-KDVGPDVDIPAPDVYTNPQTMAWYFDEYSK 169
                                       **********************.777*************************85 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   7.7e-08   0.00015      32      68 ..     213     249 ..     191     268 .. 0.86
   2 ?   -3.7   0.0       3.2   6.4e+03     104     121 ..     303     320 ..     299     322 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.7e-08
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68 
                                         l+gktv++ G+G++G  +ak+l+++g++v+a++ s
  gi|320100355|ref|YP_004175947.1| 213 GGLEGKTVAVHGFGNVGMYAAKYLAEWGARVVAVSDS 249
                                       4699*****************************9876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.2
                                       TTTTSBSHHHHHCSTTTE CS
                      2-Hacid_dh_C 104 etrhlinaeelakmkkga 121
                                       +t+++i++e+ +k+k ++
  gi|320100355|ref|YP_004175947.1| 303 ATQDVITKENVNKIKAKV 320
                                       678888888888888766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.9e-06     0.014       5      54 ..     215     271 ..     214     327 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.9e-06
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.......elvklaeee 54 
                                       l+gk+v v G G+v++  ++ l+e ga+v+ v+  + ++ +       e ++++e++
  gi|320100355|ref|YP_004175947.1| 215 LEGKTVAVHGFGNVGMYAAKYLAEWGARVVAVSDSSGYIYDpkgldveEAIRVKETT 271
                                       689******************************998444444455455444444333 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 !   13.1   0.4   3.7e-05     0.074      21      50 ..     215     244 ..     207     249 .. 0.92
   2 ?    1.9   0.0      0.11   2.2e+02      79     105 ..     296     321 ..     284     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEE CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvi 50 
                                       l Gk++ v G+G+vG  +a+ l + Garv+
  gi|320100355|ref|YP_004175947.1| 215 LEGKTVAVHGFGNVGMYAAKYLAEWGARVV 244
                                       579*************************97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                                       -SEEEE-SSSSSSB-HHHHCCS-TTEE CS
                     AdoHcyase_NAD  79 adivvtttGnkdiitlehlkkmkddai 105
                                       +di+v +  ++d+it+e+++k+k ++i
  gi|320100355|ref|YP_004175947.1| 296 VDILVPA-ATQDVITKENVNKIKAKVI 321
                                       6777765.579************9987 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.7e-06     0.011    1050    1099 ..     312     361 ..     305     363 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-06
                           Bac_GDH 1050 ngkelrakvvgEGgNLGltQlgRiEyalkggrintDaiDNsaGVdcSDhE 1099
                                        n ++++akv++EG+N   t  +     +kg+ i  D + Ns+GV +S  E
  gi|320100355|ref|YP_004175947.1|  312 NVNKIKAKVISEGANGPTTPEAEKILHEKGVIIVPDILANSGGVTMSWIE 361 
                                        66899*****************9999*******************99655 PP

>> ThiF  ThiF 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     0.023      16      49 ..     215     248 ..     196     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                       HHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  16 LrdskvllvGaGglGsellknLalsGvgkltlvD 49 
                                       L+ ++v++ G G +G +++k+La +G + + + D
  gi|320100355|ref|YP_004175947.1| 215 LEGKTVAVHGFGNVGMYAAKYLAEWGARVVAVSD 248
                                       88899**********************9999888 PP

>> DUF3158  Protein of unknown function (DUF3158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.9e-05     0.077      37      92 ..      17      74 ..       6      92 .. 0.80
   2 ?   -0.8   0.0      0.56   1.1e+03      71      94 ..     348     371 ..     335     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-05
                           DUF3158 37 qckalr..delialaqevlaqareypfsllpveli.dqttsaGttFLRWrkldrsrmGv 92
                                       +k+lr  ++l+ l +ev++  r +p +l++v+++  +  +   t+L Wr++++s++G 
  gi|320100355|ref|YP_004175947.1| 17 AVKQLReaASLLGLPDEVVEVLR-HPEKLVQVKITiRRDNGKLETYLGWRSQHNSALGP 74
                                      34444411679999999998766.5*********989999999*************996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.56
                           DUF3158  71 qttsaGttFLRWrkldrsrmGval 94 
                                         +++G+  + W + +++rmG  l
  gi|320100355|ref|YP_004175947.1| 348 ILANSGGVTMSWIEWSHNRMGCWL 371
                                       567899***************866 PP

>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.7e-05      0.19       1      35 [.     215     249 ..     215     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.7e-05
                      CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEpp 35 
                                       L+G +V   +   +G +a+++LA++GA+V+ v ++
  gi|320100355|ref|YP_004175947.1| 215 LEGKTVAVHGFGNVGMYAAKYLAEWGARVVAVSDS 249
                                       56667777777778*****************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2937.71
//
Query:       gi|320100356|ref|YP_004175948.1|  [L=78]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   15.9   0.7      0.011   15.8   0.7    1.0  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
      0.068   13.4   1.4       0.07   13.3   1.4    1.1  1  DPM3             Dolichol-phosphate mannosyltransferase subun
        3.1    7.8  10.4        0.2   11.6   4.2    2.0  2  SecE             SecE/Sec61-gamma subunits of protein translo
        7.7    6.9   7.3        2.8    8.3   4.8    1.5  1  Nodulin_late     Late nodulin protein


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.7   2.4e-06     0.011      35     106 ..       7      76 ..       2      78 .] 0.58

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-06
                   Phage_holin_3_6  35 sgagllgaagvlallalllllvalalalaa..lwlaalivaavllvlagvlalvglkklkkakplpertieelk 106
                                        ga+l+ +++vla l   l++++ +       + +  l v ++++vl + l +vg+  +k +  +pe+  +el 
  gi|320100356|ref|YP_004175948.1|   7 AGALLISGTVVLATLYTYLVFFTPI----SiqATVLKLTVYVFVMVLLLSLFIVGYTLFKTNFFPPEEVERELS 76 
                                       3344444444433333333333332....122445577888999999999999999988885558887777765 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.4   1.6e-05      0.07       8      70 ..      12      69 ..       1      78 [] 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                              DPM3  8 lalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGayslatlgygvltfndcpea 70
                                      ++ +++l++l+++l++ +     +   +  v+ l +++ v++ + sl+ +gy +++ n  p +
  gi|320100356|ref|YP_004175948.1| 12 ISGTVVLATLYTYLVFFT-----PISIQATVLKLTVYVFVMVLLLSLFIVGYTLFKTNFFPPE 69
                                      333344444444444332.....5567788899999999999*************98866544 PP

>> 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 ?   -0.7   0.4      0.31   1.4e+03      32      43 ..      15      26 ..       9      30 .. 0.58
   2 ?   11.6   4.2   4.4e-05       0.2      21      42 ..      36      57 ..      34      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.31
                                      HHHHHHHHHHHH CS
                              SecE 32 fvvimglflflv 43
                                      +vv+ +l+ +lv
  gi|320100356|ref|YP_004175948.1| 15 TVVLATLYTYLV 26
                                      345555555544 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                              SecE 21 EllkttvvVlvfvvimglflfl 42
                                       +lk tv V+v+v++++lf+ +
  gi|320100356|ref|YP_004175948.1| 36 TVLKLTVYVFVMVLLLSLFIVG 57
                                      689****************976 PP

>> Nodulin_late  Late nodulin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.8   0.00063       2.8       5      20 ..      41      56 ..      35      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00063
                      Nodulin_late  5 lkfvYalilflslflv 20
                                      + +v++++l+lslf+v
  gi|320100356|ref|YP_004175948.1| 41 TVYVFVMVLLLSLFIV 56
                                      559************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1209  (0.0674327); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
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: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 598.47
//
Query:       gi|320100357|ref|YP_004175949.1|  [L=367]
Description: polyprenyl synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-53  180.2   0.0    5.3e-53  179.7   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.7   0.0   2.9e-57   5.3e-53       5     242 ..      45     301 ..      42     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 179.7 bits;  conditional E-value: 2.9e-57
                                       HHHHHHHHHSSS--HHHHHHHHHHHHHS.CGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HH..... CS
                   polyprenyl_synt   5 eealeylveagGKrlRpllvllaaealk.eeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcah..... 75 
                                       e a++y++ +gGKrlR+ l+l  +   +   + + +   +l+  +ell+++ LvhDD+mD +e+RRG p++h     
  gi|320100357|ref|YP_004175949.1|  45 EIASDYTL-RGGKRLRAFLTLVGYWSKEwG-SGDPSLITSLMTGIELLQSYLLVHDDVMDRDEIRRGGPTVHswfrd 119
                                       55788999.*******99998776555532.3467999**********************************99999 PP

                                       ...........HCTCHHHHHHHHHHHHHHHHHHHHHHH.STT..HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC. CS
                   polyprenyl_synt  76 ...........rlvGnklAindgdfllarafellaklf.eks..lellelfsevllqtveGqlldleeekdddlskf 138
                                                   ++G ++Ai +gdfl+a+a+e++++   +++   +ll +++  l +++ Gq+ld+  +   +l + 
  gi|320100357|ref|YP_004175949.1| 120 kcirefktgdcTHYGDSQAITVGDFLEATAVEYVSRAGiNGEvlSKLLGTYAAGLRKVAYGQYLDVLFSY-RSLHEV 195
                                       9999988888777***********************9884444689*******************96664.778888 PP

                                       SHHHHHHHHHHHTH.HHCHHHHHHHHHHTTHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHT CS
                   polyprenyl_synt 139 sleeyleivkyKTa.ylfalpvalaallagasd.eelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqe 213
                                       s+ + l +++ KTa y+++lp+ ++a+++g  + + l +l++++ + G+aFQ++DD++ l+gdp ++gKp+g+D++e
  gi|320100357|ref|YP_004175949.1| 196 SERDVLLVHRLKTAsYTIELPLHMGAIASGKYNeRLLGELSSYAIPAGIAFQLRDDIIGLYGDPRQTGKPVGSDVKE 272
                                       8*****************************6552667**************************************** PP

                                       T---HHHHHHHHCT-HHHHHHHHHHTTSS CS
                   polyprenyl_synt 214 gkctlpilkalelaspeqrkvlkeilgkk 242
                                        k tl+++ka+el s+e +++l ei+   
  gi|320100357|ref|YP_004175949.1| 273 RKKTLLVVKAYELGSEEVKRRLSEIYDAP 301
                                       **************************843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2861.07
//
Query:       gi|320100358|ref|YP_004175950.1|  [L=217]
Description: 3-hexulose-6-phosphate synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   86.0   0.8    3.4e-24   85.7   0.8    1.1  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    0.00053   19.2   0.1     0.0011   18.1   0.1    1.6  1  NanE            Putative N-acetylmannosamine-6-phosphate epim
     0.0025   17.3   0.3     0.0037   16.8   0.3    1.4  1  His_biosynth    Histidine biosynthesis protein
      0.008   15.6   0.8       0.01   15.2   0.8    1.5  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.031   13.6   0.2      0.044   13.1   0.2    1.4  1  TMP-TENI        Thiamine monophosphate synthase
      0.031   14.0   0.2      0.095   12.5   0.2    1.9  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
       0.28   10.2   3.8       0.32   10.0   3.8    1.2  1  FMN_dh          FMN-dependent dehydrogenase


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 !   85.7   0.8   1.3e-27   3.4e-24       3     225 .]       5     211 ..       3     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 1.3e-27
                                       EEEEE-SSSHHHHHHHHHHHGGGS....SEEEEEHHHHHHHTHH.HHTHHHHHHHHHT.SEEEEEEEE-S-HHHHHH CS
                         OMPdecase   3 LclalDvatarelleladkvgpsi....vvlKthydlvegwgfegtgaklaalarkhg.flifeDrKfaDIGntvek 74 
                                       L++alD+++  e++e+a k+ ++     ++l+++++l+++wg       ++++++    + +++D K++D+++++  
  gi|320100358|ref|YP_004175950.1|   5 LQVALDLTKLPEAVEIATKIASHTscrnIWLEVGTPLLKAWG-----LIAVKAVKNLSnCFVVVDTKTMDVPAIEGG 76 
                                       9******************99854122258************.....66666666665589**************** PP

                                       HHHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTT CS
                         OMPdecase  75 qatagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedf 151
                                       +        +++ d++tv +va++++vk+++e+a++ g  +l++ + +s+++ l+++  + +   v+ +  h     
  gi|320100358|ref|YP_004175950.1|  77 ML------LDAGGDAFTVLGVADDDVVKEAVETARARG--KLVVADLISHPDPLKRAV-ELDRLGVDVVLYHV---- 140
                                       *9......7***************************98..9************99999.55666666666665.... PP

                                       ESEEECCCHTHHHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                         OMPdecase 152 vmGfvaqetlnateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                         G+ +q+ +  t ++   ++  l++ + +   ++++g+++ ++++li  +gadi++vG +I+ka++pv+ +er+
  gi|320100358|ref|YP_004175950.1| 141 --GISVQRSRRVTVAQlLREIEGLRRNVSA-RIAVAGGIKPGDVKGLIA-SGADIVVVGGAITKAENPVQVVERI 211
                                       ..9999998884455567899999999998.*****************9.88********************996 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 !   18.1   0.1   4.4e-07    0.0011      82     184 ..      98     206 ..      92     217 .] 0.66

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.4e-07
                                       HHHHHHHHHH--EEEEE-.SSHH...HHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHH....HTT--EEEE CS
                              NanE  82 eelikkikekyqllmaDi.stle...eglvakklGvdivGttlsGytkeeekaepDfalvkals....eaglkviae 150
                                       +e +++ + +++l++aD+ s  +    ++  ++lGvd+v   + G   + ++     +l++++     +   ++ + 
  gi|320100358|ref|YP_004175950.1|  98 KEAVETARARGKLVVADLiSHPDplkRAVELDRLGVDVVLYHV-GISVQRSRRVTVAQLLREIEglrrNVSARIAVA 173
                                       5677788888999999961444311146667889999997654.666666666777788777652111223345566 PP

                                       S---SHHHHHHHHTT--SEEEE-HHHH-HHHHHH CS
                              NanE 151 GrintPekakkaieiGvdavvvGsaitrleeiak 184
                                       G i  P   k  i +G+d vvvG+ait+ e+ ++
  gi|320100358|ref|YP_004175950.1| 174 GGI-KPGDVKGLIASGADIVVVGGAITKAENPVQ 206
                                       666.5999*******************9875333 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   1.4e-06    0.0037      30     119 ..     120     215 ..      88     217 .] 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                                       SHHHHHHHHHHHT-SE.EEEEEHHHHCTTHHHHHHHHHH...HHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEES CS
                      His_biosynth  30 dpvelakryeeegade.lhvvDldaakegreanldlvee...iaeevfipvqvGGGIrsledveelleagadkviig 102
                                       dp++ a ++++ g+d  l+ v ++  ++ r +  +l++e   ++++v++ + v GGI+  + v+ l+ +gad v++g
  gi|320100358|ref|YP_004175950.1| 120 DPLKRAVELDRLGVDVvLYHVGISVQRSRRVTVAQLLREiegLRRNVSARIAVAGGIKPGD-VKGLIASGADIVVVG 195
                                       666666666666666424566666666666666666555222689************9887.*************** PP

                                       HHHHH-...THHHHHHHHHH CS
                      His_biosynth 103 taavkn...pelikelaekf 119
                                        a  k     +++++++e++
  gi|320100358|ref|YP_004175950.1| 196 GAITKAenpVQVVERILEEM 215
                                       87554311146677777665 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 !   15.2   0.8     4e-06      0.01     154     197 ..     160     198 ..      46     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-06
                                       HHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 154 kkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                       + +r+     +++ +i v GG+k   ++ +++ gad++V+g a+
  gi|320100358|ref|YP_004175950.1| 160 EGLRR-----NVSARIAVAGGIKPGDVKGLIASGADIVVVGGAI 198
                                       33333.....46679**************************997 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   1.7e-05     0.044     137     181 .]     154     198 ..      97     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                          TMP-TENI 137 lgleglkelaealeiPvvaiGGitlenvaevleagadgvavvsai 181
                                       + l  ++ l+++++  + + GGi++ +v+ ++++gad v v  ai
  gi|320100358|ref|YP_004175950.1| 154 QLLREIEGLRRNVSARIAVAGGIKPGDVKGLIASGADIVVVGGAI 198
                                       556778888999999************************997776 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 ?   12.5   0.2   3.7e-05     0.095     113     161 ..     151     201 ..      91     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHHHH..HHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB CS
                         QRPTase_C 113 elkkaveelk..eknkrvlievSGgvtlenveeyaksgvdvisvgalthsv 161
                                       ++++ + e++  ++n + +i v+Gg++  +v+ +  sg d++ vg +++++
  gi|320100358|ref|YP_004175950.1| 151 TVAQLLREIEglRRNVSARIAVAGGIKPGDVKGLIASGADIVVVGGAITKA 201
                                       444444444311445559*************************99877766 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.8   0.00013      0.32     224     304 ..     116     199 ..      50     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                                       E-SHHHHHHHHHTTESEE.EE--GGGTSSTT-..--HHHCHHHH...HHHH..SS-EEEESS--SHHHHHHHHHTT- CS
                            FMN_dh 224 vltaedakraveaGvdgi.vvSNHGGRqldga..patidvLpei...veavggrievlvDgGirrGsDvlkAlalGA 294
                                       + +++  krave+   g+ vv  H G ++  +  ++  + L ei   +++v  ++ + v gGi+ G Dv   +a GA
  gi|320100358|ref|YP_004175950.1| 116 ISHPDPLKRAVELDRLGVdVVLYHVGISVQRSrrVTVAQLLREIeglRRNV--SARIAVAGGIKPG-DVKGLIASGA 189
                                       466777788888777777344568775544431145556677773334444..5899999***999.9*99****** PP

                                       SEEEESHHHH CS
                            FMN_dh 295 davllGRpfl 304
                                       d+v++G ++ 
  gi|320100358|ref|YP_004175950.1| 190 DIVVVGGAIT 199
                                       ******9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1714.07
//
Query:       gi|320100359|ref|YP_004175951.1|  [L=255]
Description: ribonuclease HII [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-36  125.2   0.0    3.2e-36  125.0   0.0    1.0  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.0   0.0   1.8e-40   3.2e-36       1     195 [.       9     210 ..       9     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 1.8e-40
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH...SEEEEEEE-HHHHH.HHTTT CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik...kkiekrklvaeeikyasene 74 
                                       iG+DEaGrGp +G +v+++v+ + +  e l  +g+kDSK L + +r+eL+ +i      i +  ++   i++ ++ne
  gi|320100359|ref|YP_004175951.1|   9 IGVDEAGRGPFVGDMVIVGVIGPSRVFESLVSIGLKDSKALEPVARRELFWEILssnVDIVAWLVSPFTIDRGNMNE 85 
                                       8*************************************************999976666777777777777777777 PP

                                       S-HHHHHHHHHH.HHHHHHHHTCEECCECCCE--SS.HHHHHHHHHHHHC..CEEEEETTGGGT-HHHHHHHHHHHH CS
                         RNase_HII  75 inlneikaaltl.aviklleklgvkvdeilvdgvtt.peslkkkleqiik..ikvtvekkadekyllvaaASiiAkv 147
                                       ++ + i   l+l    +l + +  +   i+vd v+   es+ +  + i +  ++v++e  ad++y++v+aAS+iAkv
  gi|320100359|ref|YP_004175951.1|  86 LEYIRICRILKLlSYSRLARSKPGNSLRIYVDEVKGyGESVRECAMRIYGehVEVVMEPEADARYPAVSAASVIAKV 162
                                       777776655544144446666677777*****9999555666666667779999*********************** PP

                                       HHHHHHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTS CS
                         RNase_HII 148 erdeelellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsf 195
                                        rd +++ l +  g    gsGy+sd+++ra+l        k+p + r+s+
  gi|320100359|ref|YP_004175951.1| 163 IRDRNIDVLGKITG--GLGSGYPSDPASRAWLATIYGRwdKPPVFIRRSW 210
                                       ************76..99**************988777678999****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 2111.69
//
Query:       gi|320100360|ref|YP_004175952.1|  [L=386]
Description: small GTP-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   74.4   0.0    1.1e-20   73.6   0.0    1.4  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
    3.2e-20   71.9   0.1    6.4e-20   71.0   0.1    1.5  1  TGS            TGS domain
    4.1e-16   59.1   0.0    8.6e-16   58.0   0.0    1.5  1  MMR_HSR1       50S ribosome-binding GTPase
    1.4e-10   40.9   0.0    7.1e-09   35.4   0.0    2.3  2  FeoB_N         Ferrous iron transport protein B
    3.1e-05   24.1   0.4     0.0052   16.9   0.0    2.6  2  YchF-GTPase_C  Protein of unknown function (DUF933)
      4e-05   23.3   0.1       0.49    9.9   0.1    3.9  2  GTP_EFTU       Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.017   15.0   0.0        6.4    6.6   0.0    2.5  2  RsgA_GTPase    RsgA GTPase
      0.026   14.0   0.0      0.055   12.9   0.0    1.5  1  SRPRB          Signal recognition particle receptor beta subu
      0.048   13.7   0.1        1.8    8.6   0.0    2.7  3  Dynamin_N      Dynamin family
      0.087   13.2   0.1        3.3    8.0   0.1    2.8  1  AAA_16         AAA ATPase domain
       0.21   11.0   0.0       0.48    9.8   0.0    1.5  2  Mg_chelatase   Magnesium chelatase, subunit ChlI


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 !   73.6   0.0   6.6e-24   1.1e-20       2     106 .]     203     311 ..     202     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 6.6e-24
                      MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlis..leeldel 76 
                                        Gi++t   kl + + ++v+++l+ey+ihna+v+i ++vt+Dd+ +++ +n++Y+p+++++NK+Dl+s  +e ++ l
  gi|320100360|ref|YP_004175952.1| 203 QGIRFTLMGKLLNATLDDVRRLLEEYRIHNAHVKIYGEVTLDDVEQALFENTTYKPSVVFVNKVDLVSgvDEVVKVL 279
                                       6999999999999999**************************************************76435666777 PP

                      MMR_HSR1_Xtn  77 arep..nsvviSaekelnldeLkekiweeLnL 106
                                        +++   ++  Sa ++l+l+++ e+++ +L+L
  gi|320100360|ref|YP_004175952.1| 280 GEKSglPVIAGSAFTGLGLNKVGEALFTQLEL 311
                                       77643478889*******************97 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.1   3.9e-23   6.4e-20       1      59 [.     312     383 ..     312     384 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 3.9e-23
                                       EEEEE.TTSSEEE.....EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd.....lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       irvyt  +   p      l++gat++D+A +Ihr+++k+f+yA+V+G       +rvgl+hv+edgd+veI 
  gi|320100360|ref|YP_004175952.1| 312 IRVYTkSPNTDPSskplvLRKGATIRDVAESIHRDFVKNFVYAKVWGksvhypgERVGLEHVVEDGDIVEIH 383
                                       678886444444568888****************************************************96 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   5.3e-19   8.6e-16       1     101 [.      83     179 ..      83     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 5.3e-19
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.T CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.a 76 
                                       +v+++G pN+GKS L+n+ltg++  ++d+p+ T++++ g +k+++  i+l+Dtp  ++   ++ gl +++  l + a
  gi|320100360|ref|YP_004175952.1|  83 QVVVLGPPNTGKSMLVNKLTGARTVIADYPFSTTQPVPGMLKYEDIYIQLIDTPP-LS---RGSGLINKIIGLARnA 155
                                       599****************************************99**********.54...488*******988879 PP

                                       SEEEEEEETTTTCSHHHHHHHHHHH CS
                          MMR_HSR1  77 dlillvvdaseeklkpldeeleell 101
                                       d +l+v+da+++ + ++ eel  ll
  gi|320100360|ref|YP_004175952.1| 156 DGLLIVLDATRD-IIADFEELRGLL 179
                                       ********8854.444446665555 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 !   35.4   0.0   4.4e-12   7.1e-09       2      55 ..      83     136 ..      82     166 .. 0.93
   2 ?    3.3   0.0     0.032        52     106     154 ..     257     303 ..     247     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 4.4e-12
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE-- CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlP 55 
                                       +v+++G pn+Gk++l+n+ltga++ ++ +p  t +   g lk+++  ++++D P
  gi|320100360|ref|YP_004175952.1|  83 QVVVLGPPNTGKSMLVNKLTGARTVIADYPFSTTQPVPGMLKYEDIYIQLIDTP 136
                                       7999*************************************************9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.032
                                       SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                            FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                       +p v+ +n++d ++  g++  +k L ek g+pv++ sa ++ g++++ +
  gi|320100360|ref|YP_004175952.1| 257 KPSVVFVNKVDLVS--GVDEVVKVLGEKSGLPVIAGSAFTGLGLNKVGE 303
                                       789999*****997..55555789*****************99998865 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 !   16.9   0.0   3.2e-06    0.0052      16      44 ..     329     357 ..     311     363 .. 0.87
   2 ?    4.8   0.1      0.02        33      67      82 ..     368     383 ..     364     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
                     YchF-GTPase_C  16 tikkgttapqaAgviHsDfekgFiraevi 44 
                                        ++kg+t+ + A  iH Df k+F+ a+v 
  gi|320100360|ref|YP_004175952.1| 329 VLRKGATIRDVAESIHRDFVKNFVYAKVW 357
                                       689***********************995 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                     YchF-GTPase_C  67 egkdyvvqdgDiilfk 82 
                                        g ++vv+dgDi++++
  gi|320100360|ref|YP_004175952.1| 368 VGLEHVVEDGDIVEIH 383
                                       6889********9876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0069        11      66     113 ..     124     174 ..      81     186 .. 0.63
   2 !    9.9   0.1    0.0003      0.49     123     192 ..     257     309 ..     240     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0069
                                       TCSSEEEEEEEESSSGG...GHHHHHHHHHT-SEEEEEEETTTBSTHHHHH CS
                          GTP_EFTU  66 etkkylinliDtPGHvd...FskevirglrvlDgavlvvdaveGvepqtee 113
                                       ++++  i+liDtP        ++++i  +r +Dg ++v+da++++ +  ee
  gi|320100360|ref|YP_004175952.1| 124 KYEDIYIQLIDTPPLSRgsgLINKIIGLARNADGLLIVLDATRDIIADFEE 174
                                       466677777777755442224555555577777777777777776666555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0003
                                       TEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                          GTP_EFTU 123 vpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvell 192
                                        p +vf+NK+D +       v+ev + l          gek+    pv+ gSa++g g++++ eal++ l
  gi|320100360|ref|YP_004175952.1| 257 KPSVVFVNKVDLVS-----GVDEVVKVL----------GEKS--GLPVIAGSAFTGLGLNKVGEALFTQL 309
                                       34899999999874.....344444444..........4443..589**********9999999988765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0039       6.4     100     122 ..      82     104 ..      50     116 .. 0.83
   2 ?    5.8   0.0    0.0074        12      43     100 ..     252     308 ..     239     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0039
                                       SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpe 122
                                         +v++G+   GKS L+n+l++ 
  gi|320100360|ref|YP_004175952.1|  82 VQVVVLGPPNTGKSMLVNKLTGA 104
                                       567899**************986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0074
                                       HHTT-EE.EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTS CS
                       RsgA_GTPase  43 eekgiep.vivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdk 100
                                       e++  +p v+ +nK+Dl++  +  e +k   e+ g++v++ sa t+ gl+++ e+l  +
  gi|320100360|ref|YP_004175952.1| 252 ENTTYKPsVVFVNKVDLVSGVD--EVVKVLGEKSGLPVIAGSAFTGLGLNKVGEALFTQ 308
                                       444454416678*********9..778888899999***99999999999998888666 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 ?   12.9   0.0   3.4e-05     0.055       5      86 ..      83     165 ..      79     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                                       EEEEE-STTSSHHHHHHHHHHSS---B-..--SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG.EEE CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktv..tSqessaalkvksekgskltliDfPGheklrqklleklkakss.lkg 78 
                                       +v+++G+ ++GK +l ++Lt   +  +    S  + +   + + ++  ++liD P   +  + l++k++  ++ + g
  gi|320100360|ref|YP_004175952.1|  83 QVVVLGPPNTGKSMLVNKLTGARTVIADypFSTTQPV-PGMLKYEDIYIQLIDTPPLSR-GSGLINKIIGLARnADG 157
                                       6999***************988443332013332222.22235599*********9877.56677777765544999 PP

                                       EEEEEETT CS
                             SRPRB  79 lvfvvDSt 86 
                                       l+ v+D+t
  gi|320100360|ref|YP_004175952.1| 158 LLIVLDAT 165
                                       99999998 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3   2.2e+03      62      82 ..      50      70 ..      23      74 .. 0.77
   2 ?    8.6   0.0    0.0011       1.8       1      25 [.      84     108 ..      84     120 .. 0.83
   3 ?    1.7   0.0      0.15   2.4e+02     103     151 ..     130     176 ..     121     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                                      B--CHHHHHHHHHHHHHHHTS CS
                         Dynamin_N 62 ledfsevreeieketekiaga 82
                                       + + e+r+eie++++k++g+
  gi|320100360|ref|YP_004175952.1| 50 TRRLAELRDEIEERRKKKTGR 70
                                      567889999999999998865 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                                       EEEEEBTTTTHHHHHHHHHTS--S- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilp 25 
                                       ++v+G  + GKS ++n+L+g++   
  gi|320100360|ref|YP_004175952.1|  84 VVVLGPPNTGKSMLVNKLTGARTVI 108
                                       79******************98655 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.15
                                       EEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-CHHHHH CS
                         Dynamin_N 103 ltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdlsnsealfla 151
                                       + l+D+P l +      + +  ++++ad +l v++a  d+  ++ ++l+
  gi|320100360|ref|YP_004175952.1| 130 IQLIDTPPLSRGSGLI-NKIIGLARNADGLLIVLDATRDII-ADFEELR 176
                                       7899999999966555.777788899**********99998.6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1     0.002       3.3      26      45 ..      83     102 ..      70     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.002
                            AAA_16  26 lvllsGesGvGKsslvrell 45 
                                        v++ G++ +GKs lv++l 
  gi|320100360|ref|YP_004175952.1|  83 QVVVLGPPNTGKSMLVNKLT 102
                                       6899************9986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00029      0.48      20      44 ..      79     103 ..      64     115 .. 0.87
   2 ?   -3.4   0.0       3.2   5.3e+03     111     139 ..     161     188 ..     149     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00029
                      Mg_chelatase  20 aGgHnlllvGppGsGKtmlakrlps 44 
                                        G  +++++Gpp +GK+ml ++l++
  gi|320100360|ref|YP_004175952.1|  79 EGDVQVVVLGPPNTGKSMLVNKLTG 103
                                       5788999*************99975 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.2
                      Mg_chelatase 111 fLDElpefkrkvlevLRePledgevtisr 139
                                       +LD + ++ ++ +e LR  led  v++s+
  gi|320100360|ref|YP_004175952.1| 161 VLDATRDIIAD-FEELRGLLEDSGVVLSK 188
                                       46666666554.57899999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2820.05
//
Query:       gi|320100361|ref|YP_004175953.1|  [L=112]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 849.26
//
Query:       gi|320100362|ref|YP_004175954.1|  [L=120]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   1.7       0.09   12.8   0.1    2.3  2  HisKA     His Kinase A (phospho-acceptor) domain
        0.5   10.8   2.8       0.63   10.5   0.0    2.4  3  HHH_8     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     1e-05      0.09      31      64 ..      47      78 ..       5      81 .. 0.79
   2 ?    0.5   0.1     0.069   6.2e+02      44      60 ..     100     116 ..      78     119 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                      .T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
                             HisKA 31 gklteelkeyletiesearrldhlvedlLdlsri 64
                                      +  teel+e le   s+++ ++++ved   lsr+
  gi|320100362|ref|YP_004175954.1| 47 IGFTEELREILEEKASGGESIEDIVEDA--LSRL 78
                                      5679***********************9..6666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.069
                                       HHHHHHHHHHHHHHHHH CS
                             HisKA  44 iesearrldhlvedlLd 60 
                                       +++++  l +l+e+l++
  gi|320100362|ref|YP_004175954.1| 100 LREGSVELMDLLEELRE 116
                                       44444445555555543 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     7e-05      0.63      11      33 ..       2      24 ..       1      26 [. 0.84
   2 ?   -2.3   0.1      0.66   5.9e+03      13      16 ..      55      58 ..      49      73 .. 0.58
   3 ?   -0.9   0.3      0.25   2.2e+03       3      14 ..     106     117 ..     105     119 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7e-05
                                      HHHHHHHCT--CCCHHHHHHHHC CS
                             HHH_8 11 ladllelkgedpfrvraYrrAar 33
                                      + dl e+ +++ f+v aYr A r
  gi|320100362|ref|YP_004175954.1|  2 ISDLAEFLRRHGFKVIAYRDALR 24
                                      567888888889*********87 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.66
                                      HHHH CS
                             HHH_8 13 dlle 16
                                      ++le
  gi|320100362|ref|YP_004175954.1| 55 EILE 58
                                      2222 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHH CS
                             HHH_8   3 eiadaLeeladl 14 
                                       e+ d+Leel + 
  gi|320100362|ref|YP_004175954.1| 106 ELMDLLEELREE 117
                                       466777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 859.19
//
Query:       gi|320100363|ref|YP_004175955.1|  [L=456]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-44  149.3   0.0    1.1e-43  148.3   0.0    1.6  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.4e-24   84.2   0.0    3.3e-23   82.2   0.0    2.1  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.6e-21   76.0   0.0      6e-21   74.8   0.0    1.6  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.7e-12   46.3   0.1    1.1e-11   44.7   0.1    1.8  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
  ------ inclusion threshold ------
       0.12   12.5   0.0        2.7    8.2   0.0    2.9  4  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su


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 !  148.3   0.0     3e-47   1.1e-43       2     136 ..       5     135 ..       4     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 3e-47
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fgt+G+Rg+v+ +el+pelv +lg ai++ + +   +++++v++D+R+ ++ +++++a  l+++Gv+v+++gl+p
  gi|320100363|ref|YP_004175955.1|   5 RLFGTDGVRGVVN-EELNPELVVRLGLAIGSFFDK---GSRILVAMDSRAGGELIKNIVAGALMSTGVKVYDAGLAP 77 
                                       68***********.77******************9...8************************************** PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-E CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeee 136
                                       tPa+++a+++ ++d+g+m+taSHnppeyngiKv+ s+G+++++++ee+Ie+ + ++++
  gi|320100363|ref|YP_004175955.1|  78 TPALQYAVKSNGFDGGVMVTASHNPPEYNGIKVIGSHGIEVDRDEEEAIEELYWENRF 135
                                       ***************************************************9998876 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 !   82.2   0.0   9.3e-27   3.3e-23       1     103 []     155     256 ..     155     256 .. 0.99
   2 ?   -3.3   0.0       4.1   1.5e+04      32      48 ..     287     303 ..     269     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 9.3e-27
                                       .HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHH CS
                        PGM_PMM_II   1 eaYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealklliel 77 
                                       e+Y++a+++ vd++ ik+++ ++++dp++ +g+ +++ + +elgv+++ +n + dp f+++ p+p+  e+l++ ++l
  gi|320100363|ref|YP_004175955.1| 155 EEYVKAVVSHVDRDLIKSRNYRLLVDPANSVGSLTTPLIARELGVKPIVVNGTLDPLFSGRLPEPTV-ENLAETSKL 230
                                       58*****************************************************************.********* PP

                                       GGGGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  78 vkkegadlglafDgDaDRlgvvderG 103
                                       v++ g  lg+a+D DaDR++++de+G
  gi|320100363|ref|YP_004175955.1| 231 VREVGVALGVAHDADADRVIMIDEKG 256
                                       ************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.1
                                       THHHHHHHHHHTT-EEE CS
                        PGM_PMM_II  32 ggeilkellkelgvdvv 48 
                                       ++ i++e+l+ l++dvv
  gi|320100363|ref|YP_004175955.1| 287 SSVIVEEVLRPLNIDVV 303
                                       45688899998888886 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 !   74.8   0.0   1.7e-24     6e-21       2     113 ..     261     370 ..     260     371 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.7e-24
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTT.ECEEEETTCEEEET CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeeg.avlGgEeSghiifl 77 
                                       gd+++alla+yl+e+   +g  v + v++s ++e+v++ l+i +v  kvG+  ++  m+++g a++G+Ee+g+++++
  gi|320100363|ref|YP_004175955.1| 261 GDRTAALLARYLREK-GLKGR-VYTAVSSSVIVEEVLRPLNIDVVWLKVGSVDIAHTMRRNGdALCGFEENGGFMYP 335
                                       9***********996.44465.**************************************988************** PP

                                       TTBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHHH CS
                       PGM_PMM_III  78 deattkDGilaallvleilaetgkslselleellkk 113
                                        +++ +DG ++ +l+le+la+ g + s+l e+l+ k
  gi|320100363|ref|YP_004175955.1| 336 PHQYVRDGGMTTALFLEMLATYGVPASQLFESLP-K 370
                                       ******************************7665.3 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.1   3.1e-15   1.1e-11       8      70 ..     382     447 ..     374     451 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.1e-15
                                       C-TT....EECCCCCTTH..HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHH CS
                        PGM_PMM_IV   8 ekak..vvaalaallkva..sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeeva 70 
                                       ++ +  vv+++++++ ++   +++g+k++  d + l vRpSGTepllrv++Eak+ e+l+++ + v+
  gi|320100363|ref|YP_004175955.1| 382 RESAlaVVEKVKEAFRNErlITIDGVKVVSSDYWLL-VRPSGTEPLLRVMIEAKTIERLDEVSQLVD 447
                                       433334455555555555999***************.*******************99999877665 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 ?   -0.2   0.0      0.31   1.1e+03      25      45 ..      81     101 ..      74     114 .. 0.79
   2 ?   -3.4   0.0         3   1.1e+04      24      42 ..     268     286 ..     265     296 .. 0.58
   3 ?    8.2   0.0   0.00076       2.7      13      31 ..     338     356 ..     332     368 .. 0.88
   4 ?   -3.1   0.0       2.6   9.4e+03      34      43 ..     404     413 ..     394     428 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.31
                       FrhB_FdhB_N  25 lkylLeegiidgvivvapskd 45 
                                       l+y+ +++  dg + v++s +
  gi|320100363|ref|YP_004175955.1|  81 LQYAVKSNGFDGGVMVTASHN 101
                                       8899999999*9999998833 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3
                       FrhB_FdhB_N  24 llkylLeegiidgvivvap 42 
                                       l+ yl e+g+   v ++ +
  gi|320100363|ref|YP_004175955.1| 268 LARYLREKGLKGRVYTAVS 286
                                       4555555555555554444 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00076
                       FrhB_FdhB_N  13 kkaqsGGivtallkylLee 31 
                                       ++  +GG++tal+ ++L +
  gi|320100363|ref|YP_004175955.1| 338 QYVRDGGMTTALFLEMLAT 356
                                       6788*************87 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.6
                       FrhB_FdhB_N  34 idgvivvaps 43 
                                       idgv vv ++
  gi|320100363|ref|YP_004175955.1| 404 IDGVKVVSSD 413
                                       8999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3140.60
//
Query:       gi|320100364|ref|YP_004175956.1|  [L=143]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   49.9   1.7      5e-13   49.4   1.7    1.2  1  Trm112p         Trm112p-like protein
  ------ inclusion threshold ------
      0.014   15.5   1.2      0.049   13.8   1.2    2.0  1  zf-RING_7       C4-type zinc ribbon domain
      0.047   13.1   4.3        1.4    8.4   0.1    3.2  3  zf-ribbon_3     zinc-ribbon domain
       0.11   12.5   2.7       0.35   11.0   0.1    2.1  2  zf-RRPl_C4      Putative ribonucleoprotein zinc-finger pf C4 
       0.51   10.4   7.3        1.7    8.7   7.3    1.8  1  DZR             Double zinc ribbon
        2.3    8.2   6.1         11    6.1   0.2    2.7  3  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        2.6    8.9   8.1        7.8    7.3   8.1    1.8  1  zinc_ribbon_15  zinc-ribbon family


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 !   49.4   1.7   1.9e-16     5e-13       5      68 .]       7      88 ..       4      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.9e-16
                                      CCC-B-TTTHH.C--HHHHHHHHH.TT---S-SS----S................CHHTTEECCCCEEEETTTTEEEEE CS
                           Trm112p  5 lniLaCpackg.pLdwealvevaa.lglnelpkekpedy................ellleldieegeLvCpncgraYpI 65
                                      l++L+C +ck+ pL++ ++  +++    +++ ++ +++y                 ++l+  i +g+L+Cpncgr+YpI
  gi|320100364|ref|YP_004175956.1|  7 LDVLVCVHCKHhPLELTVIESEEQsIDVEKVEAPVCKEYcgylrekidrnkaypcRECLRKGIRTGVLYCPNCGRWYPI 85
                                      79**********************999999999999999****************99********************** PP

                                      ETT CS
                           Trm112p 66 kdG 68
                                      k+G
  gi|320100364|ref|YP_004175956.1| 86 KNG 88
                                      **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 ?   13.8   1.2   1.9e-05     0.049      17      32 ..      69      82 ..      60      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                                      HCCSTB-EE-TTT--E CS
                         zf-RING_7 17 lragdevvtCpeCGRI 32
                                      +r g  v +Cp+CGR+
  gi|320100364|ref|YP_004175956.1| 69 IRTG--VLYCPNCGRW 82
                                      3334..9********6 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.014        36       5      12 ..      12      20 ..       9      23 .. 0.83
   2 ?    0.3   0.1       0.2     5e+02      17      24 ..      40      48 ..      36      49 .. 0.65
   3 ?    8.4   0.1   0.00054       1.4       4       9 ..      75      80 ..      69      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.014
                       zf-ribbon_3  5 CPnCGa.pl 12
                                      C +C++ pl
  gi|320100364|ref|YP_004175956.1| 12 CVHCKHhPL 20
                                      999*99776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
                       zf-ribbon_3 17 nvCp.yCGt 24
                                      +vC+ yCG+
  gi|320100364|ref|YP_004175956.1| 40 PVCKeYCGY 48
                                      566548887 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00054
                       zf-ribbon_3  4 rCPnCG 9 
                                      +CPnCG
  gi|320100364|ref|YP_004175956.1| 75 YCPNCG 80
                                      677776 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.6      0.12   2.9e+02      54      85 ..      11      44 ..       4      59 .. 0.64
   2 ?   11.0   0.1   0.00014      0.35       3      34 ..      60      89 ..      58      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                        zf-RRPl_C4 54 LCtkCkeknekekeircetfeeylkklk..lCke 85
                                       C +Ck++  + + i++e+ +  ++k++  +Cke
  gi|320100364|ref|YP_004175956.1| 11 VCVHCKHHPLELTVIESEEQSIDVEKVEapVCKE 44
                                      5777877777766677776666666665555544 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00014
                        zf-RRPl_C4  3 kCkyClskklknlnetvyCeaCeiyfkvknek 34
                                       C+ Cl+k + +    +yC++C  ++ +kn+ 
  gi|320100364|ref|YP_004175956.1| 60 PCRECLRKGIRT--GVLYCPNCGRWYPIKNGV 89
                                      6999****9998..9***********999975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   7.3   0.00067       1.7       1      49 []      12      80 ..       8      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00067
                               DZR  1 CpqCgee....................lppdarfCseCgtklkavaaedrCpsCgek.vdpearfCpeCG 49
                                      C +C++                      p  +++C++ ++k++  ++++ C +C +k +  +  +Cp+CG
  gi|320100364|ref|YP_004175956.1| 12 CVHCKHHpleltvieseeqsidvekveAPVCKEYCGYLREKID-RNKAYPCRECLRKgIRTGVLYCPNCG 80
                                      6666666666666666666666666556777778888888886.5669*********9999********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 ?    6.1   0.2    0.0042        11      18      27 ..       8      17 ..       3      18 .. 0.89
   2 ?   -3.1   0.3       3.3   8.4e+03      22      25 ..      61      64 ..      58      65 .. 0.64
   3 ?    5.1   0.0    0.0088        23      18      26 ..      72      80 ..      70      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0042
                    PhnA_Zn_Ribbon 18 allvCpeCah 27
                                      ++lvC +C+h
  gi|320100364|ref|YP_004175956.1|  8 DVLVCVHCKH 17
                                      89******99 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                    PhnA_Zn_Ribbon 22 CpeC 25
                                      C eC
  gi|320100364|ref|YP_004175956.1| 61 CREC 64
                                      5555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0088
                    PhnA_Zn_Ribbon 18 allvCpeCa 26
                                       +l Cp+C+
  gi|320100364|ref|YP_004175956.1| 72 GVLYCPNCG 80
                                      5899**997 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   8.1     0.003       7.8      64      86 .]      38      80 ..       7      80 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.003
                    zinc_ribbon_15 64 e...................kkeCknC.gkeveeefkyCpkCg 86
                                      e                   ++ C++C +k +   + yCp+Cg
  gi|320100364|ref|YP_004175956.1| 38 EapvckeycgylrekidrnkAYPCREClRKGIRTGVLYCPNCG 80
                                      13445555555555555555999****44569999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1020.56
//
Query:       gi|320100365|ref|YP_004175957.1|  [L=462]
Description: amidohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-46  158.7   0.0    2.6e-46  158.5   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
    4.2e-18   66.1   0.0    4.4e-14   52.8   0.1    2.3  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5   0.0     3e-50   2.6e-46       1     343 [.      60     418 ..      60     419 .. 0.89

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 3e-50
                                       EEEE-EEEEEEECETTECSSS..........GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga..........tledwl..........vppetaaealesgiktalksGtttvadmga 57 
                                       +v+PGl +aH+H+++ ll g           ++++ l          ++ e+a++ + +g   + ksG+t + d + 
  gi|320100365|ref|YP_004175957.1|  60 VVTPGLMCAHTHFYGLLLTGSpwfskiepptDFQQNLqriwwaldveLTYEDAYASALIGSILFAKSGVTNFFDNIS 136
                                       69***********9888877798888887765555559999999********************************* PP

                                       SSTHHHHHHHHHHHT..SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHH CS
                      Amidohydro_1  58 ttstgiealleaaee..lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsd 131
                                         +++i+ +l+ +e+    +g+r ++++    r+s e      ++ ++ +  ++  + +g++   a++ h+ ++++d
  gi|320100365|ref|YP_004175957.1| 137 S-PNAIDGVLDYIEKgvNEVGIRGIVSFEATQRRSLEEGVRGLRENERFI--VKNNRDPGRLVkGAIYLHASFTVTD 210
                                       6.458899988888877446999999988888877776666666666666..556666677777************* PP

                                       HHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHH CS
                      Amidohydro_1 132 eelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellke 208
                                       e+ k a + a k+++ +aiH++e   +v + ++ +g    +  ++e++++lg+l++ ++ l+h v +t +e+ ++ke
  gi|320100365|ref|YP_004175957.1| 211 ELFKLAHETAGKYGALIAIHTAEGLVDVYHNIERYG---LR--PVERMKKLGFLGS-NVHLVHAVNITEDELHIIKE 281
                                       ************************************...88..*************.9999999999999******* PP

                                       HHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHH CS
                      Amidohydro_1 209 rlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye.deegglslke 284
                                          ++ vah p sn+  + g++++ ++l+ Gv+vg+g D    g +++ +e +r  +++++  l++ d+++ l++++
  gi|320100365|ref|YP_004175957.1| 282 T--GVHVAHNPLSNMLNAVGVARVPEMLRLGVNVGIGND----GYVFDQFENMRATYLIHK--LWNrDPRV-LTPLQ 349
                                       *..************************************....9***************99..55548888.***** PP

                                       HHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.CT.........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 285 alrmaTingAkalglddkvGsievGkdADlvvvdl.di.........laafvglkkdgnvkkvivkGkl 343
                                       +++m+T n A+ + ++ ++GsievGk+ADlvv+ +  +           ++v++ +++ v++viv+G++
  gi|320100365|ref|YP_004175957.1| 350 VFEMSTVNVARMFHVEGELGSIEVGKKADLVVLRPeAPstpvnsqtvMGHIVNSFSSRDVDTVIVDGRI 418
                                       *********************************88822456888999********************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   2.6e-05      0.23       1      32 [.      52      84 ..      52      99 .. 0.75
   2 !   52.8   0.1   4.9e-18   4.4e-14     320     473 .]     248     420 ..     204     420 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.6e-05
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnl.rllr 32
                                      e+i+ +Gr+v+PG+  +HtH +g  +    +++
  gi|320100365|ref|YP_004175957.1| 52 ETINGRGRVVTPGLMCAHTHFYGLLLTGsPWFS 84
                                      68999***************9998766655555 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 4.9e-18
                      Amidohydro_3 320 sqiervaalq.vaagvqpvfnf....edelldsrlgperargs..........tpvkellnagvkvalgsDapvgpf 381
                                       +++er+++l+ +   v++v++     ++ ++++++g + a++           ++v e+l+ gv+v  g+D  + +f
  gi|320100365|ref|YP_004175957.1| 248 RPVERMKKLGfLGSNVHLVHAVniteDELHIIKETGVHVAHNPlsnmlnavgvARVPEMLRLGVNVGIGND--GYVF 322
                                       55666666662344556555556666555666666644444444566666777******************..999* PP

                      Amidohydro_3 382 dpwprigaa.vmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppel 457
                                       d +  ++a+ + +k +      r+ + l+  +++ + T + A++++ e + G++evG++ADlvvl+ ++   + +  
  gi|320100365|ref|YP_004175957.1| 323 DQFENMRATyLIHKLW-----NRDPRVLTPLQVFEMSTVNVARMFHVEGELGSIEVGKKADLVVLRPEAPSTPVNS- 393
                                       ****998762666666.....579******************************************7777777763. PP

                      Amidohydro_3 458 aear.............vrltvvdGrvvy 473
                                        + +             v  ++vdGr+++
  gi|320100365|ref|YP_004175957.1| 394 -Q-TvmghivnsfssrdVDTVIVDGRIIV 420
                                       .3.2366899****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3214.95
//
Query:       gi|320100366|ref|YP_004175958.1|  [L=777]
Description: HAD superfamily P-type ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  169.1   1.1    6.8e-50  169.1   1.1    2.7  4  E1-E2_ATPase     E1-E2 ATPase
    9.6e-27   94.6   0.0    1.9e-26   93.7   0.0    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.6e-09   37.9   0.1    4.2e-06   26.7   0.1    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    1.8e-09   37.2   0.0    5.4e-09   35.6   0.0    1.8  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    0.00012   21.8   8.7    0.00012   21.8   8.7    2.3  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.8   6.5e+03     106     140 ..      27      61 ..      25      77 .. 0.65
   2 !  169.1   1.1   1.9e-53   6.8e-50       5     180 ..      97     271 ..      92     272 .. 0.97
   3 ?   -2.1   0.0      0.65   2.3e+03      13      34 ..     294     315 ..     285     317 .. 0.80
   4 ?   -4.7   0.7       4.2   1.5e+04     125     135 ..     747     757 ..     720     768 .. 0.51

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                                       ----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STT CS
                      E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflialll 140
                                       +k++ l+ +++kl +  + ++ ++a++ f++  ++
  gi|320100366|ref|YP_004175958.1|  27 KKESTLKIFVKKLQGLTAYTIEAAAVISFILGRYI 61 
                                       56667777777777777777777777777766544 PP

  == domain 2  score: 169.1 bits;  conditional E-value: 1.9e-53
                                       -EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EE CS
                      E1-E2_ATPase   5 ptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgea 81 
                                         +k +rdg++++i+++ +vpGD+v+++ gd++paDg+++eg+  vdes LTGEs+pvek+ gd v++Gt v +gea
  gi|320100366|ref|YP_004175958.1|  97 IVVKALRDGEWRDIPSEYIVPGDVVKVRLGDIIPADGVVLEGHLLVDESTLTGESMPVEKNPGDPVYAGTAVARGEA 173
                                       567888*********************************************************************** PP

                                       EEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHH CS
                      E1-E2_ATPase  82 kavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaa 158
                                       ++++tatg  t++g+ ++lve+  + +  ++++ ++++++l +v +++++lv++ +l+++ ++++al ++l+ll+a+
  gi|320100366|ref|YP_004175958.1| 174 IIRITATGPRTRYGRTVELVEAG-KPRLLIEEITSSITRWLLAVDVFFVVLVVVRLLITQTPVVDALPFTLTLLIAS 249
                                       **********************9.8999************************************************* PP

                                       S-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 159 iPcaLplavplalalgarrlak 180
                                       iP+aLp++++++lalg  +la+
  gi|320100366|ref|YP_004175958.1| 250 IPIALPAMTTITLALGSVELAR 271
                                       *******************998 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.65
                                       TS-EEEEGGG--TTSEEEEETT CS
                      E1-E2_ATPase  13 gteeeidakelvpGDivllkag 34 
                                       +++ +i  ++lv+ Di+ l++g
  gi|320100366|ref|YP_004175958.1| 294 DKTGTITENKLVVKDIIPLREG 315
                                       5667888999*********998 PP

  == domain 4  score: -4.7 bits;  conditional E-value: 4.2
                                       HHHHHHHHHHH CS
                      E1-E2_ATPase 125 vvlliallvfl 135
                                       v+l++++++++
  gi|320100366|ref|YP_004175958.1| 747 VILIAFVYTVA 757
                                       22222222222 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   5.2e-30   1.9e-26       1     210 []     288     542 ..     288     542 .. 0.81

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 5.2e-30
                                       SSEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHH..HHCHHHHHHHHHHHHH.....HHHHHHHHHET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx..xxxxxxxxxxxxxxxx.....xxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa......alalaaaletg..sehpigkalvaaakar.....sgaltgfatfi 64 
                                       ++++++Dk+GT+t+ + +v+d+i+ +      ++ l aal+     + pi ka+ ++a ++     s ++ +f  f 
  gi|320100366|ref|YP_004175958.1| 288 MEVICLDKTGTITENKLVVKDIIPLRegftehDVILYAALASEpdGRDPIDKAILEKAGELgvdlgSVSVMEFKPFS 364
                                       579***********************99999999999999999*9****************9998877778888876 PP

                                       TTE..............HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..................TTHHHH CS
                                       xxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxx RF
                         Hydrolase  65 grg..............ayaigkpewltaldippdlgaaigsaqsqgrtvall..................qarala 109
                                        +               ++ +g p+ l +          ++++ ++   +a+                   + r+ +
  gi|320100366|ref|YP_004175958.1| 365 PESkrsealvsmggrilKAVKGAPQVLVDV---------DTTLDRERFNEAVRtlgdrgmrplavgveengSLRVIG 432
                                       666788876666666675566666655555.........4444444444444455555666666699998878**** PP

                                       HHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT........GGGE.SEEEEHHCES....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxx.xxxxxxxxxx....... RF
                         Hydrolase 110 vftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG........ddyf.daviasdiet....... 170
                                       ++ i d+  ++++   +++++k++g++ v++tgdn   a+++a+ +G        +    +        +       
  gi|320100366|ref|YP_004175958.1| 433 LIGIYDK--PREDSQRFIEEIKSMGVKPVMVTGDNYYVAKSIARSVGiegrvvslKGVPrE--------Eladllds 499
                                       *******..**************************************86554444222222........24555566 PP

                                       ...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 171 ...vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                          +a++ pe+k +++r +q k++ v m GDgvnDa+al++A+
  gi|320100366|ref|YP_004175958.1| 500 agvFAEVVPEDKYEIVRLYQSKGKVVGMTGDGVNDAPALKQAD 542
                                       799***************************************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 !    9.0   0.0   0.00029         1      16      63 ..     440     487 ..     433     489 .. 0.91
   2 !   26.7   0.1   1.2e-09   4.2e-06     199     245 ..     518     564 ..     512     574 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGG CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNG 63 
                                         e +++ i+++k+ g+k v  TG +++ ++++++++g++  v++l G
  gi|320100366|ref|YP_004175958.1| 440 PREDSQRFIEEIKSMGVKPVMVTGDNYYVAKSIARSVGIEGRVVSLKG 487
                                       5678999*********************************99998877 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.2e-09
                                       CT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE-- CS
                       Hydrolase_3 199 lnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtks 245
                                       ++ + + v   GDg ND + L++a+lgvA+ na++ +k++A+ v ++
  gi|320100366|ref|YP_004175958.1| 518 YQSKGKVVGMTGDGVNDAPALKQADLGVAVSNATDIAKSVASVVLTK 564
                                       55555666678*******************************99875 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 !   35.6   0.0   1.5e-12   5.4e-09      19      69 .]       5      54 ..       3      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.5e-12
                   Cation_ATPase_N 19 nGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      +GL+++e++e l+ yG N++ ++kk+s +++++k+++ ++ +  ++aa++s
  gi|320100366|ref|YP_004175958.1|  5 TGLSSSEVEEKLRIYGFNTV-PEKKESTLKIFVKKLQGLTAYTIEAAAVIS 54
                                      7*******************.****************************98 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   4.4       2.5     9e+03     131     173 ..     219     257 ..     200     267 .. 0.61
   2 !   21.8   8.7   3.4e-08   0.00012       4     176 ..     614     764 ..     611     776 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.5
                   Cation_ATPase_C 131 aillslllqvlivyvpglnavfgtaplsleewlialllalvvl 173
                                        +++ +++ +li+++p    v +  p +l+ ++ ++++al  +
  gi|320100366|ref|YP_004175958.1| 219 FFVVLVVVRLLITQTP----VVDALPFTLTLLIASIPIALPAM 257
                                       3444446666677777....55555666666666666666554 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.4e-08
                   Cation_ATPase_C   4 lsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrri.liqgllqalvtllvffltlllfgis 79 
                                       l++++++++ +++D++  l+++++   ++    +P+      ++ + l+++ +i gl+ ++  +l+++l+l   + +
  gi|320100366|ref|YP_004175958.1| 614 LTPTHMILMLFLYDFV-TLSISTDRLRPS---SKPE-----KWNVRRLVKVsVILGLVKIAELFLALYLGLHVLSLQ 681
                                       6777777777777777.666666666532...2333.....27777788888***************9999988888 PP

                   Cation_ATPase_C  80 ekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtap 156
                                        ++       a+t++F+tl  s +fn+ln r    + ++ ++ + +k++ +a++  +l   +i++    +++++  p
  gi|320100366|ref|YP_004175958.1| 682 LEQ-------ARTFVFYTLLTSGLFNILNFRE---TGWF-WHSKPSKVMTIALTTDILAGTIIAWK---GWIIQPIP 744
                                       877.......**********************...7777.8899999*******999766666665...89999999 PP

                   Cation_ATPase_C 157 lsleewlialllalvvllvd 176
                                       +++   + +  +a+ ++l d
  gi|320100366|ref|YP_004175958.1| 745 PPVILIAFVYTVAVTLILTD 764
                                       98888877766666665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (777 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 5228.01
//
Query:       gi|320100367|ref|YP_004175959.1|  [L=297]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-24   86.7  38.6    3.9e-13   49.7  15.7    2.0  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3  14.8   2.1e-15   3.8e-11       2     136 ..      14     145 ..      13     146 .. 0.93
   2 !   49.7  15.7   2.2e-17   3.9e-13       2     136 ..     153     282 ..     152     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2.1e-15
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +gi  +++a+++w+++f+++k  + +++plt+++ r+l+a +ll +++l k+ +  +++  ++    ++  ++ +l+
  gi|320100367|ref|YP_004175959.1|  14 MGIASLVAATVLWGSSFPFIKLSVMDIEPLTYAATRSLVAILLLTPLLLAKATRG-VIHTGSLYR-GVIIGVAYLLG 88 
                                       69999**************************************************.888887555.55555899999 PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        +l+  +  +t++s+ ++it l  v + ++ +l+ +++ ++++ ++++l++ G+++++
  gi|320100367|ref|YP_004175959.1|  89 LYLQAAGTVYTTPSISAFITGLNSVHVHVYIALV-KKSYSVMDGVALLLAVSGLYVLT 145
                                       9*****************************9999.*******************9985 PP

  == domain 2  score: 49.7 bits;  conditional E-value: 2.2e-17
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +g+ll++l+++ wa+ ++l  ++ ++ s ++l+  +fl +++ + ++   + +     sl+ + ++++l++ +tv a
  gi|320100367|ref|YP_004175959.1| 153 IGVLLVFLGSIAWAAQILLVSRF-NSSSIMELLYGMFLPGAL-MYPLVSASTEGV---SLRVLVYIAYLAAACTVGA 224
                                       79******************885.666666666656655555.555555555555...69***************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        +l++++++++s+ +a+li++lePvf+l++s +   e ++ ++l+g +li+++++l +
  gi|320100367|ref|YP_004175959.1| 225 TFLQVWGQRYVSPLTAALIFLLEPVFALFFSLIMGLEEPEPYKLVGGGLIVASTYLAS 282
                                       ******************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 2046.59
//
Query:       gi|320100368|ref|YP_004175960.1|  [L=325]
Description: carbamate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-29  102.7   0.0    3.4e-29  102.2   0.0    1.3  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 !  102.2   0.0   1.9e-33   3.4e-29       2     240 ..       9     305 ..       8     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.9e-33
                                       EEEEEE-TTCCCCTCC........HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH......TCCCCCHHHC. CS
                         AA_kinase   2 rvVvKlGGssltdkee........aslrrlaeqiaalkesgnklvvVhGggsftdgllal......ksglssgelaa 64 
                                       ++V++lGG+++ +k++         +   +a+ i +l+e+++ +vv hG+g+++  +++       +++++     +
  gi|320100368|ref|YP_004175960.1|   9 TIVIALGGNAFQTKGDkgtaeeywRNAYTAADLIVRLVEEKYGVVVTHGNGPQVGIIAEWmslglkNKNIP-----P 80 
                                       79**********77777****9999999**************************99999985555555555.....3 PP

                                       .................E..HHHHHHHHHHHHHHHHHHHHHHHHHTTH....GEEEE-GGGTCEECCCE........ CS
                         AA_kinase  65 ..............glrstleeagevatrdalaslgerlvaallaagl....pavglsaaaldateagr........ 115
                                                     g  ++++  +++a++ +l+sl + +v+ + + ++    pa++ + +++++  ++         
  gi|320100368|ref|YP_004175960.1|  81 mpldvagamsqgwlGYMLQQALYNKLAEKKLLGSLVKGVVTVITQTLVdrndPAFKDPTKYIGPWYEKDeaeklske 157
                                       55555999999999888889999999999999999987776666666666667777777777766666677778888 PP

                                       .................HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE........EEEE-HHHHHHHHHH CS
                         AA_kinase 116 ...............degsdgnvesvdaeaieelleagvvpvltgfigldeege........lgrgssDtiaallAe 169
                                                       + s++++ +v+++ai++l+e+g++++  g++g+++  +         +++++D  a   A 
  gi|320100368|ref|YP_004175960.1| 158 lgwvfkpdprggyrrVVASPDPIGQVEIDAIKTLVEQGFIVIADGGGGIPVYRGddgllhgvEAVIDKDLGAERMAS 234
                                       888888889**************************************99999999999999988************* PP

                                       HCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                         AA_kinase 170 algAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvIt 240
                                       al+Ad l+iltdV+  y + +    +a++l+ ++v+ea++   ++++  g+m +k++a ++++++gg  +vI+
  gi|320100368|ref|YP_004175960.1| 235 ALEADVLLILTDVEKAYLNYGTP--NAKPLDVLRVSEALKyyREGHFKPGSMGPKILAGVRFVQNGGKMAVIA 305
                                       *******************9855..6****************************************8777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2376.98
//
Query:       gi|320100369|ref|YP_004175961.1|  [L=244]
Description: FeS assembly ATPase SufC [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-19   69.5   0.0    5.1e-19   69.1   0.0    1.1  1  ABC_tran     ABC transporter
    2.8e-09   37.2   0.0    0.00074   19.4   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.7e-08   32.2   0.0    3.9e-07   29.7   0.0    1.9  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0015   18.3   0.0     0.0062   16.2   0.0    1.9  2  AAA_29       P-loop containing region of AAA domain
     0.0044   16.8   0.0       0.15   11.7   0.0    2.1  2  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.023   14.6   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
      0.017   15.2   0.0      0.026   14.7   0.0    1.4  1  AAA_33       AAA domain
      0.018   14.6   0.0      0.025   14.2   0.0    1.3  1  AAA_25       AAA domain
      0.018   13.7   0.0       0.96    8.0   0.0    2.0  2  AAA_13       AAA domain
      0.019   15.4   0.0      0.029   14.8   0.0    1.4  1  AAA_16       AAA ATPase domain
      0.022   15.2   0.0      0.076   13.4   0.0    1.8  2  AAA          ATPase family associated with various cellular a
      0.032   14.7   0.0       0.05   14.1   0.0    1.2  1  AAA_23       AAA domain
      0.039   13.7   0.0      0.058   13.1   0.0    1.2  1  AAA_24       AAA domain
      0.065   13.1   0.1       0.15   12.0   0.0    1.7  2  NACHT        NACHT domain
      0.078   13.1   0.0       0.19   11.8   0.0    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
        0.1   12.9   0.0       0.45   10.8   0.0    1.9  2  AAA_28       AAA domain
       0.21   11.3   0.1       0.75    9.5   0.0    1.8  2  IstB_IS21    IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   4.9e-22   5.1e-19       2     136 ..      18     172 ..      17     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 4.9e-22
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpelt 75 
                                       + v++++ +g++va++G+nG+GK++L+ +l+g+      eG++ +dg d +    +e++ + +  ++q+p   p++t
  gi|320100369|ref|YP_004175961.1|  18 NGVDVEVAAGRVVALMGPNGSGKTSLVYALMGHPAYriVEGSVMIDGVDYTLkPAHERALAGVFLVFQNPVDLPGVT 94 
                                       7899****************************9766669*******99998867889999****************8 PP

                                       HHHH.........HHHTC..........HHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                       xxxx.........xxxxx..........xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren.........esdee..........iekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllll 132
                                       ++               +           e+++s+ +l++lk++ + ++    +SgG+k+r ++ +a + +pk l+l
  gi|320100369|ref|YP_004175961.1|  95 LEALiksslnkrlG---KgdlsgnipglSERVRSEAKLIGLKEELLARDLnVGFSGGEKKRSEILQARILRPKYLIL 168
                                       77778876655550...055556677779999999999999999987766799************************ PP

                                       ESTT CS
                                       xxxx RF
                          ABC_tran 133 DEpt 136
                                       DEp 
  gi|320100369|ref|YP_004175961.1| 169 DEPD 172
                                       **95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.5e-06    0.0069       2      19 ..      30      47 ..      29      76 .. 0.79
   2 !   19.4   0.0     7e-07   0.00074     255     302 ..     163     207 ..      95     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.5e-06
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       +l GpNgsGK++L +al
  gi|320100369|ref|YP_004175961.1| 30 VALMGPNGSGKTSLVYAL 47
                                      6899*************9 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7e-07
                            AAA_21 255 lkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                       +   + l++DEp++gL+   +r +++ ++e  + g+ v+l TH+p+ll
  gi|320100369|ref|YP_004175961.1| 163 P---KYLILDEPDSGLDVDGVRIVADYVREVVDSGGGVLLITHNPTLL 207
                                       2...559***************************************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 !   29.7   0.0   3.7e-10   3.9e-07      25     204 ..      28     209 ..       9     221 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.7e-10
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsis 100
                                       ++ a++GpNGSGK++l+ A+   +G+ +++ +  + + d + +  k  ++   a v ++f+n+ +  +  + e  i+
  gi|320100369|ref|YP_004175961.1|  28 RVVALMGPNGSGKTSLVYAL---MGHPAYRIVEGSVMIDGVDYtLKPAHERALAGVFLVFQNPVDL-PGVTLEALIK 100
                                       5889****************...**999988888888888888667777788899******99998.3333333343 PP

                                       EEEET...TSEEEEEETTEEE-HHHHHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkr...kgeseykingkevtkkevsellesagiske........lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                        ++ +   kg+ +  i g +   + v++  +  g+++e         +SgGek+ + +   +  +  +p+ l +lDe
  gi|320100369|ref|YP_004175961.1| 101 SSLNKrlgKGDLSGNIPGLS---ERVRSEAKLIGLKEEllardlnvGFSGGEKKRSEI---LQARILRPKYL-ILDE 170
                                       33333111333344443322...2333333333333333333344469*****98764...55566667654.79** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                        d+ LD   v++va++++e  ++   ++ i+++ ++l+ 
  gi|320100369|ref|YP_004175961.1| 171 PDSGLDVDGVRIVADYVREVVDSgGGVLLITHNPTLLRY 209
                                       ******************988775789999999887765 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   0.0   5.9e-06    0.0062      14      42 ..      19      47 ..      15      50 .. 0.81
   2 ?   -1.6   0.0       2.2   2.3e+03      36      51 ..      59      74 ..      59      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.9e-06
                            AAA_29 14 ghtieidlkg.atlltGpsGsGKSTllDAi 42
                                      g ++e+  +g ++ l+Gp+GsGK++l+ A+
  gi|320100369|ref|YP_004175961.1| 19 GVDVEVA-AGrVVALMGPNGSGKTSLVYAL 47
                                      5677787.4559**************9776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                            AAA_29 36 STllDAiqalLvpakk 51
                                      S ++D + + L pa++
  gi|320100369|ref|YP_004175961.1| 59 SVMIDGVDYTLKPAHE 74
                                      789******9999984 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00014      0.15      18      43 ..      23      47 ..      20      49 .. 0.83
   2 ?    3.0   0.0     0.065        68     324     368 ..     163     206 ..     149     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                            AAA_15 18 eidlseeltvliGkNnsGKSsileal 43
                                      e+     +  l G+N+sGK+s+++al
  gi|320100369|ref|YP_004175961.1| 23 EVAAGR-VVALMGPNGSGKTSLVYAL 47
                                      555556.8899*************98 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.065
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       ++ l+++EP+  L  +  ++++++ +e+++++   v++ TH+p +
  gi|320100369|ref|YP_004175961.1| 163 PKYLILDEPDSGLDVDGVRIVADYVREVVDSGG-GVLLITHNPTL 206
                                       566899**************************8.9*******986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.1e-05     0.023      96     127 ..      24      55 ..       3      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                       HCTTSEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpelelkt 127
                                       + ++++++l+G+ G GK++L+ al+++   ++
  gi|320100369|ref|YP_004175961.1|  24 VAAGRVVALMGPNGSGKTSLVYALMGHPAYRI 55 
                                       44569*******************99877665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.5e-05     0.026       1      43 [.      29      71 ..      29     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqq 43
                                      +v l G++GsGK+ l+  l+ + ++ +++  ++++ + +t ++
  gi|320100369|ref|YP_004175961.1| 29 VVALMGPNGSGKTSLVYALMGHPAYRIVEGSVMIDGVDYTLKP 71
                                      7899****************99989999998888888776665 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   2.4e-05     0.025      31      58 ..      25      52 ..      14     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                            AAA_25 31 pagelallaGapgtGKttlaldlalava 58
                                      +ag +++l+G+ g+GKt l++ l+ + a
  gi|320100369|ref|YP_004175961.1| 25 AAGRVVALMGPNGSGKTSLVYALMGHPA 52
                                      689******************9987755 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.019        20      22      36 ..      33      47 ..      20      60 .. 0.85
   2 ?    8.0   0.0   0.00091      0.96     523     578 ..     159     211 ..     153     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.019
                            AAA_13 22 YGwNGaGKTtLSrll 36
                                       G NG+GKT+L  +l
  gi|320100369|ref|YP_004175961.1| 33 MGPNGSGKTSLVYAL 47
                                      69********97655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00091
                            AAA_13 523 eigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                       +i   k  ++D P S LD + + iv+ ++++++   ++   +++ THn +++++v+
  gi|320100369|ref|YP_004175961.1| 159 RILRPKYLILDEPDSGLDVDGVRIVADYVREVV---DSGGGVLLITHNPTLLRYVN 211
                                       566677889***********************9...9999*************997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.8e-05     0.029      21      47 ..      26      50 ..      19     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellra 47
                                      +g  ++v l G+ G+GK+slv +l+ +
  gi|320100369|ref|YP_004175961.1| 26 AG--RVVALMGPNGSGKTSLVYALMGH 50
                                      44..79***************888755 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 ?   13.4   0.0   7.2e-05     0.076       2      28 ..      31      57 ..      30      86 .. 0.83
   2 ?   -1.0   0.0       2.1   2.2e+03      41      69 ..     147     173 ..     115     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-05
                                      EEESSTTSSHHHHHHHHHHHHTHEEEE CS
                               AAA  2 llyGppGtGKTllakavakelgvefle 28
                                       l+Gp G GKT+l+ a++ +   +++e
  gi|320100369|ref|YP_004175961.1| 31 ALMGPNGSGKTSLVYALMGHPAYRIVE 57
                                      699**************9986555554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHTSTSEEEEEETGGG CS
                               AAA  41 esekkirelfkeakekakpsilfiDEida 69 
                                        +ekk +e+++ a+  + p+ l++DE d+
  gi|320100369|ref|YP_004175961.1| 147 GGEKKRSEILQ-ARILR-PKYLILDEPDS 173
                                       55666667775.46776.99999999886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-05      0.05      21      39 ..      29      47 ..      18      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                      ++++ GpNG+GKT+++ A+
  gi|320100369|ref|YP_004175961.1| 29 VVALMGPNGSGKTSLVYAL 47
                                      67899**********9987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.5e-05     0.058       3      33 ..      28      58 ..      26      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpkplfidtek 33
                                      + ++++Gp+g+GKT+l++ l  +p++  +e+
  gi|320100369|ref|YP_004175961.1| 28 RVVALMGPNGSGKTSLVYALMGHPAYRIVEG 58
                                      6799**************9988887766665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.15       1      21 [.      28      48 ..      28      62 .. 0.91
   2 ?   -2.7   0.0       4.7   4.9e+03      86      99 ..      61      74 ..      53     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      SCEEEEC-TTTCHHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqkla 21
                                      r+v+l G++GsGKT L+  l+
  gi|320100369|ref|YP_004175961.1| 28 RVVALMGPNGSGKTSLVYALM 48
                                      799*************99887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.7
                                      EEE-STT-SS-TCH CS
                             NACHT 86 ilDglDelvtdlgq 99
                                       +Dg+D++ +  ++
  gi|320100369|ref|YP_004175961.1| 61 MIDGVDYTLKPAHE 74
                                      58888887765544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.19       2      56 ..      30      93 ..      29     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                      EEEEESTTSSHHHHHHHHHTS.......TEEESSSTTSSSSEEEEEEEETTEEE...EEEECGGC CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.......kaivsdkpgtTrdinegrvklkgkei...elvDtpGl 56
                                      va++G   +GK++L+ al+g         + + d    T+++ ++r    g  +   + vD+pG+
  gi|320100369|ref|YP_004175961.1| 30 VALMGPNGSGKTSLVYALMGHpayriveGSVMIDGVDYTLKPAHERAL-AGVFLvfqNPVDLPGV 93
                                      89*****************96322111122223444667777666653.2211112256888884 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00042      0.45       2      27 ..      30      56 ..      29      62 .. 0.87
   2 ?   -1.1   0.0       1.8   1.9e+03      22      38 ..     178     194 ..     173     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv 27
                                      ++++G+ ++GKT+l+ aL  +  y++v
  gi|320100369|ref|YP_004175961.1| 30 VALMGPNGSGKTSLVYALMGHpAYRIV 56
                                      89****************988777777 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                            AAA_28  22 rgypvvpEaareileek 38 
                                       +g+++v++++re+++++
  gi|320100369|ref|YP_004175961.1| 178 DGVRIVADYVREVVDSG 194
                                       58999*******99875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00071      0.75      47      71 ..      27      52 ..      18      62 .. 0.81
   2 ?   -1.3   0.0       1.4   1.5e+03      98     116 ..     152     170 ..     138     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00071
                         IstB_IS21 47 kenivllGpsGvGKshlaial.gvea 71
                                         ++l+Gp G GK+ l  al g+ a
  gi|320100369|ref|YP_004175961.1| 27 GRVVALMGPNGSGKTSLVYALmGHPA 52
                                      56799*************99635555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                         IstB_IS21  98 klaralkrllkvdllilDd 116
                                       + +  ++r+l+++ lilD+
  gi|320100369|ref|YP_004175961.1| 152 RSEILQARILRPKYLILDE 170
                                       4455678999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1776.35
//
Query:       gi|320100370|ref|YP_004175962.1|  [L=468]
Description: Iron-regulated ABC transporter membrane component SufB [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-67  225.1   0.4    9.7e-67  224.8   0.4    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.8   0.4   5.4e-71   9.7e-67       2     218 .]     212     437 ..     211     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 224.8 bits;  conditional E-value: 5.4e-71
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       qfe+t++v++eg+e+t+i   +gc            g+ve++++++A++++v+vqnws+++vn+++kr   +++a +
  gi|320100370|ref|YP_004175962.1| 212 QFEHTVVVADEGSEITFI---EGCsaprlkkfsfhdGMVELYAHKEARVNFVTVQNWSRNIVNFNNKRGIAEENAVI 285
                                       89****************...666666666666777*********************************999***** PP

                           UPF0051  67 elttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkik 143
                                       e++++s+g+k+t+++p++ lkg+ga++  + + +++g+   dt++kv+h++p tssri+sk+++  ++ +v+rg i+
  gi|320100370|ref|YP_004175962.1| 286 EWIEGSIGSKVTVTYPTTILKGRGARTASTVIGISNGDTVKDTGSKVIHAAPSTSSRIVSKSISGRGGVNVYRGLIQ 362
                                       ***************************************************************************** PP

                           UPF0051 144 vrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       v+kga+++++++++++L+l++k++++t P++ + ++d+ ++H+At+ ++ ++qlfYL sRGlse+eA +liv gf
  gi|320100370|ref|YP_004175962.1| 363 VNKGASNSKSYTQCDSLILDEKSSSSTYPIIHVMEEDADIGHEATTIRVTDDQLFYLASRGLSEKEALSLIVLGF 437
                                       *************************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3709.59
//
Query:       gi|320100371|ref|YP_004175963.1|  [L=335]
Description: SufBD protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-19   70.6   0.0      2e-19   70.2   0.0    1.1  1  UPF0051      Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
       0.11   12.9   0.1       0.63   10.5   0.0    2.4  2  Pea-VEAacid  Pea-VEAacid family


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 !   70.2   0.0   2.2e-23     2e-19      26     218 .]     121     313 ..      93     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 2.2e-23
                           UPF0051  26 gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrkepsvelkgegaeaelnglylak 102
                                         ++i+v+++ + ++v + +  +dav ls+ ++e+g  ++l+lt++   g+l    +    +g+g+ ++ ++++ a+
  gi|320100371|ref|YP_004175963.1| 121 TGLRIIVADGVSHEVVILYESLRDAVDLSEIKVEQGDSSRLTLTAFFKPGSLMHV-VAESRSGKGSALSKTMIIDAA 196
                                       5678999999999***9999999**********************9999996666.5555589************** PP

                           UPF0051 103 gkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnLllsdkaradtiPeleidad 179
                                        +++++++   + n p++s +  +k+ l +++ a  rgk  v++ga  ++     ++L+ + +++++  P lei+++
  gi|320100371|ref|YP_004175963.1| 197 SGSRVELEDSSRINTPGSSVESYIKARLGGGSIAALRGKGVVARGAVDSKVVYGIESLITDTESKVYMHPFLEINTN 273
                                       ***************************************************************************** PP

                           UPF0051 180 dvk.asHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                        v  a H A    i  +++fY+ +RGl+  eA+ l++rgf
  gi|320100371|ref|YP_004175963.1| 274 RVAeARHYARNYIITLDKVFYMGTRGLDPGEATMLLIRGF 313
                                       **99***********************************9 PP

>> Pea-VEAacid  Pea-VEAacid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.46   4.1e+03       1       7 [.     161     171 ..     161     175 .. 0.60
   2 ?   10.5   0.0   7.1e-05      0.63       4      15 .]     211     222 ..     210     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.46
                       Pea-VEAacid   1 LdLT....PGS 7  
                                       L+LT    PGS
  gi|320100371|ref|YP_004175963.1| 161 LTLTaffkPGS 171
                                       66764444777 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.1e-05
                       Pea-VEAacid   4 TPGSHVDSYVEA 15 
                                       TPGS V SY+ A
  gi|320100371|ref|YP_004175963.1| 211 TPGSSVESYIKA 222
                                       9********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2624.07
//
Query:       gi|320100372|ref|YP_004175964.1|  [L=75]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   13.1   0.0      0.094   12.8   0.0    1.2  1  WhiA_N    WhiA N-terminal LAGLIDADG-like domain
       0.15   11.8   0.0       0.16   11.7   0.0    1.0  1  DUF1131   Protein of unknown function (DUF1131)


Domain annotation for each model (and alignments):
>> WhiA_N  WhiA N-terminal LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05     0.094      26      59 ..      31      64 ..      21      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                            WhiA_N 26 vlevqtenaaiARriykllkelYgieaellvrkk 59
                                       lev+t ++ i R + ++l + Yg+++e++v++ 
  gi|320100372|ref|YP_004175964.1| 31 ELEVKTRSNIIPRALAEMLGDKYGYKVEVSVVNG 64
                                      699****************************986 PP

>> DUF1131  Protein of unknown function (DUF1131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.8e-05      0.16      16      62 ..      21      69 ..      14      75 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                           DUF1131 16 slevseqGvgeitast..alteeaieealdgdyrlrsGmetenGkivsi 62
                                       + v ++Gvge++ +t  ++  +a++e l+++y ++  +++ nG+ v +
  gi|320100372|ref|YP_004175964.1| 21 LIAVLKEGVGELEVKTrsNIIPRALAEMLGDKYGYKVEVSVVNGEEVVY 69
                                      578999****9988772257799********************985554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 559.43
//
Query:       gi|320100373|ref|YP_004175965.1|  [L=122]
Description: adenosylmethionine decarboxylase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-35  119.5   0.0    8.1e-35  119.3   0.0    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase
  ------ inclusion threshold ------
       0.19   10.4   0.0       0.22   10.3   0.0    1.1  1  DUF935     Protein of unknown function (DUF935)


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 !  119.3   0.0   9.1e-39   8.1e-35       1     105 [.      13     117 ..      13     118 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 9.1e-39
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftc 77 
                                       h++ +ly+cdpe+l d e+l++i+++aae+ g t+l+v+ +k++p Gvsvv ++ eSh+siHtwpe+++a++Dv+tc
  gi|320100373|ref|YP_004175965.1|  13 HVYGELYECDPEILMDMEKLINIVEKAAEIGGFTLLDVKAWKINP-GVSVVGIVLESHISIHTWPEYSFATVDVYTC 88 
                                       99*****************************************97.******************************* PP

                                       ST.HHHHHHHHHHHHHHT-SEEEEEEEEE CS
                         AdoMet_dc  78 ge.ispekaleylieafkadrvtvdelkR 105
                                       g   +p ka++y+++a+ka+r+t++++ R
  gi|320100373|ref|YP_004175965.1|  89 GVkGDPVKAFKYIVHALKARRHTLKVASR 117
                                       *************************9998 PP

>> DUF935  Protein of unknown function (DUF935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.4e-05      0.22     132     198 ..      43     110 ..      23     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.4e-05
                            DUF935 132 kGfsvlEil.Wetsggqwvpralewrdprwfqfdredrrelrlrdeteegeelppfkfvvhrhkaksg 198
                                        Gf+ l+++ W+ + g  v+  +   + +  ++ + +  ++ + + + +g +++ fk++vh  ka+  
  gi|320100373|ref|YP_004175965.1|  43 GGFTLLDVKaWKINPGVSVVGIVLESHISIHTWPEYSFATVDVYTCGVKGDPVKAFKYIVHALKARRH 110
                                       58888888669999999998888889999999999999***************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 969.16
//
Query:       gi|320100374|ref|YP_004175966.1|  [L=391]
Description: monooxygenase FAD-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-08   33.8   0.0    3.1e-08   33.1   0.0    1.3  1  Lycopene_cycl  Lycopene cyclase protein
      7e-06   25.9   1.1    0.00041   20.0   0.2    2.1  2  DAO            FAD dependent oxidoreductase
    0.00014   21.3   0.1     0.0002   20.7   0.1    1.3  1  FAD_binding_3  FAD binding domain
    0.00087   18.6   0.0     0.0027   17.0   0.0    1.9  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0038   16.5   0.1     0.0065   15.7   0.1    1.3  1  Thi4           Thi4 family
     0.0071   16.6   0.1      0.027   14.7   0.1    2.0  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.015   14.5   0.2      0.026   13.8   0.2    1.3  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.054   12.2   0.1      0.085   11.5   0.1    1.3  1  HI0933_like    HI0933-like protein
       0.23   10.5   0.5       0.54    9.3   0.1    1.8  2  FAD_binding_2  FAD binding domain


Domain annotation for each model (and alignments):
>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.6e-11   3.1e-08       1     290 [.       5     285 ..       5     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.6e-11
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieas.psllfpnnyvWsdefedlgaleecvehsW..sgtivylddgkk 74 
                                       Dv ++GaGpAgls+A +l   k + +vv+ e + p++  p   +     e +  +e+ v+ +   s  +vy++++ +
  gi|320100374|ref|YP_004175966.1|   5 DVCIVGAGPAGLSVASHL---KLRDAVVIEEHGkPGI--PKHCSGLVGVETARLIEKYVGRVVdsSYNTVYFNAFGR 76 
                                       9*****************...7777777666551445..44444444434333355555554411345799999988 PP

                     Lycopene_cycl  75 illgraYg.....rvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslkk 146
                                        ++   Y+      v++  l+e+l   +  +g +   + v++ + ++      +l+gg++ ++ + + a g  +  +
  gi|320100374|ref|YP_004175966.1|  77 LYKV-SYRddfvfHVNRPLLEEKLSSLVERKGHRVSYGVVARPRGVDS-----ILAGGVEFKCNTLLIAEG--AVGR 145
                                       7776.6653333357888888877665556666666666666666666.....9*****************..5668 PP

                     Lycopene_cycl 147 arrlglQtfyGvevevdnppfdldkmvlMDfr..veqklkgltFlYalPldsdrllvEeTelaskpeLpadalkkrl 221
                                        rr  +  + G  + ++   f + +++ MD     + ++    F +++Pld+d++l+    + + +   a +++k+ 
  gi|320100374|ref|YP_004175966.1| 146 FRRFFVNPYSGFIIGIQSL-FRVRNIE-MDSIyiYYSEFTPGFFSWIIPLDQDTALIGGG-FTRVD---AGLVEKAT 216
                                       8999************998.9998766.8866557777788889*************865.55555...67888888 PP

                     Lycopene_cycl 222 aaylralglkvkevveeEqgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasai 290
                                       ++ ++a g++   vve   g+iP+    + p ++ k +  G    l++P TG  +    + +++la  i
  gi|320100374|ref|YP_004175966.1| 217 RRVVEAYGVRLGGVVERFGGIIPMQRPIPDPVIAGKAVFHGDSVPLIKPYTGGGLHYIFKLSERLARHI 285
                                       8889999*****************888888899999999*************88777777777666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   2.1e-07   0.00041       1      38 [.       5      44 ..       5      52 .. 0.82
   2 ?    4.5   0.0     0.011        22     188     321 ..     128     251 ..      80     276 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.1e-07
                                      EEEEECTSHHHHHHHHHHHHTTEEEEESSSSTT..SSGGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrgVtllekgdiag..sgaSg 38
                                      dv+i+G+G +Gls+A +L  r  +++e +  +g  +++Sg
  gi|320100374|ref|YP_004175966.1|  5 DVCIVGAGPAGLSVASHLKLRDAVVIEEHGKPGipKHCSG 44
                                      9*****************9989888888867664445554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                                       EEEEEEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEEEECCTHSTGS.GCSEEEEEEEETTTTEEEEEETTSEE CS
                               DAO 188 gendaadavVnaaGawsdllgllkeldlpispvrgqvlvlkplseklvsp.aailpvpetdddgrgvyvtprkdgrv 263
                                       g +++++++ +a Ga    +   +++   + p  g ++ ++ l +  + + + i+ ++   ++g+   ++p  +++ 
  gi|320100374|ref|YP_004175966.1| 128 GVEFKCNTLLIAEGAVG-RF---RRF--FVNPYSGFIIGIQSLFRVRNIEmDSIYIYYSEFTPGFFSWIIPLDQDTA 198
                                       33334577777777663.23...444..6788888888887766632222124444444777788889999888999 PP

                                       EEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGG.GCGEEEEEEEEEEE..TTSSEEEEE CS
                               DAO 264 lvGgtadeesgdddpevdeedidellealrklfPq.lgdvlrkwaGlrpl..pdglplige 321
                                       l+Gg         + +vd+  +++  +++ + +   lg v++++ G+ p+  p  +p+i  
  gi|320100374|ref|YP_004175966.1| 199 LIGGGF-------T-RVDAGLVEKATRRVVEAYGVrLGGVVERFGGIIPMqrPIPDPVIAG 251
                                       999964.......4.799999999999999999554899999*******533444777755 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1     1e-07    0.0002       2      35 ..       4      35 ..       3      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      +dV+IVGaGpaGl+ a+ L+ +  + v++e + +
  gi|320100374|ref|YP_004175966.1|  4 ADVCIVGAGPAGLSVASHLKLR--DAVVIEEHGK 35
                                      79*******************9..9999999976 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.3e-06    0.0027       2     156 ..       5     208 ..       4     234 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE......TTHCHHHCSHHHHCHHHHHHHHHHHHH............... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve......legtclnggcllskallgvaedaeias............... 57 
                                       dv+++G+GpAGl++a +l+    + +++e        ++c +         +gv+ ++ i++               
  gi|320100374|ref|YP_004175966.1|   5 DVCIVGAGPAGLSVASHLKLR--DAVVIEehgkpgIPKHCSGL--------VGVETARLIEKyvgrvvdssyntvyf 71 
                                       8*****************984..44455323333344444443........33333333333444444445777555 PP

                                       .........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC................. CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2  58 .........................evvkklnqgielllgeevvkidpgkkkvklekkke................. 92 
                                                                e       ++                        +                 
  gi|320100374|ref|YP_004175966.1|  72 nafgrlykvsyrddfvfhvnrplleE-------KLS-----------------------Slverkghrvsygvvarp 118
                                       54444444433333332222221110.......111.......................122233444445555566 PP

                                       .......TCEEEEEESEEEE---E..EE-BC...TCTTC...TTBEECCSEC..HHHHHHCCSS-T..........S CS
                                       .......xxxxxxxxxxxxxxxxx..xxxxx...xxxxx..xxxxxxxxxxx..xxxxxxxxxxxx..........x RF
                       Pyr_redox_2  93 .......gdeekiaydklvlAtGs..sprdl...gipGv..aenvgklvrtl..dsaealklkllp..........k 143
                                                + ++++++l++A G+  + r++   +  G   + +  + vr++  ds   + ++ +p          +
  gi|320100374|ref|YP_004175966.1| 119 rgvdsilAGGVEFKCNTLLIAEGAvgRFRRFfvnPYSGFiiGIQSLFRVRNIemDSIYIYYSEFTPgffswiipldQ 195
                                       66667886777899999999999876444443455555555333334444431145555566666688888888888 PP

                                       EEEEES-SHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvE 156
                                       +++ +GgG++ v+
  gi|320100374|ref|YP_004175966.1| 196 DTALIGGGFTRVD 208
                                       8899999988666 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.3e-06    0.0065      16      52 ..       2      35 ..       1      46 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.3e-06
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvs 52
                                      +++Dv ivGaG++GL+ a  l  +     +++e++  
  gi|320100374|ref|YP_004175966.1|  2 VKADVCIVGAGPAGLSVASHLKLR---DAVVIEEHGK 35
                                      689****************99888...5677777655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.4e-05     0.027       1      32 [.       8      37 ..       8      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      IvGaG +Gl+ A++L+ +  d +++e + ++G
  gi|320100374|ref|YP_004175966.1|  8 IVGAGPAGLSVASHLKLR--DAVVIEEHGKPG 37
                                      9**************996..889999988887 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 ?   13.8   0.2   1.3e-05     0.026       2      30 ..       8      33 ..       7      37 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                      I+GaGPaGl++a +lk  +    +++E +
  gi|320100374|ref|YP_004175966.1|  8 IVGAGPAGLSVASHLKLRDA---VVIEEH 33
                                      9*************998776...667654 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.3e-05     0.085       2      36 ..       5      37 ..       4      45 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.3e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      dv ++G+G+AGl  A +++ r+   +++e+  k+g
  gi|320100374|ref|YP_004175966.1|  5 DVCIVGAGPAGLSVASHLKLRD--AVVIEEHGKPG 37
                                      89**************995554..44555555555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00027      0.54       1      28 [.       5      30 ..       5      46 .. 0.78
   2 ?   -2.1   0.0      0.77   1.5e+03     348     376 ..     236     271 ..     201     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00027
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEE CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavv 28
                                      Dv ++G+G AGL+ A  ++ + +  +v+
  gi|320100374|ref|YP_004175966.1|  5 DVCIVGAGPAGLSVASHLKLRDA--VVI 30
                                      99*************98887776..333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.77
                                       .S-TTTSEEE..............EEEEEEEES-EE CS
                     FAD_binding_2 348 gidpadrpip.......gpfyavkvvpaqhytmgGv 376
                                       gi p +rpip       + f+ + v    +yt gG+
  gi|320100374|ref|YP_004175966.1| 236 GIIPMQRPIPdpviagkAVFHGDSVPLIKPYTGGGL 271
                                       688999999988888877777777777778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3026.04
//
Query:       gi|320100375|ref|YP_004175967.1|  [L=429]
Description: glutamine synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-88  296.8   0.0    2.4e-88  296.4   0.0    1.1  1  Gln-synt_C  Glutamine synthetase, catalytic domain
      1e-09   38.0   0.0    2.3e-09   36.8   0.0    1.5  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.4   0.0   2.7e-92   2.4e-88       3     336 ..      90     416 ..      88     423 .. 0.93

  Alignments for each domain:
  == domain 1  score: 296.4 bits;  conditional E-value: 2.7e-92
                                       -HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCE...SSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHH CS
                        Gln-synt_C   3 dPRsvlkralarlaeeGltvvvgpElEFflfdkeedke...asksllevdseekgrpaekggyfsvapvdeaedlrr 76 
                                       dPRs++ ++++++ e+G+ + +g+ElEF++  k+ +      ++ l+++ +     +  k++y+s  p+ e+e+ ++
  gi|320100375|ref|YP_004175967.1|  90 DPRSIAGKTVEKAWENGYVFRAGCELEFYITGKVGFYLgrrRQGLLVSASKGGVAGQVVKSHYVSEIPL-EVEEALS 165
                                       9*********************************99766434444444444455566677777777777.89999** PP

                                       HHHHHHHHTT--EECCEEECCCT.EEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEE CS
                        Gln-synt_C  77 eivealealgieveashhEvatg.QvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHv 152
                                       +++++l + gi+v ++h E +   Q+E++l++ d+l   D++++    vk v ++hg +  FmpKp+++d Gsg+H+
  gi|320100375|ref|YP_004175967.1| 166 DVIRVLGNNGISVSKIHRENGFLnQYELSLSHRDPLGLGDSILLSVASVKRVLNTHGFNGVFMPKPFADDYGSGLHI 242
                                       *********************988***************************************************** PP

                                       EEEEEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEE CS
                        Gln-synt_C 153 hlSlwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRi 229
                                       h+S+w   ++n+f+d +   +l++ +r+figG+l+ha++lta+t+p+vnS++Rl++g+eaPv+++wg  NRs+++R+
  gi|320100375|ref|YP_004175967.1| 243 HVSMW-IGDRNIFFDGG---ELTDAGRYFIGGILDHARSLTAFTNPSVNSFRRLIEGFEAPVYISWGIGNRSTMVRV 315
                                       *****.888*******8...7******************************************************** PP

                                       E-TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTHTSS-B--SSHHHHHHHHHC CS
                        Gln-synt_C 230 paskekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeerkgieelPasleeAlealee 306
                                       p    ++ r+E+R+pdas+NPYL ++a+l AgldG+++k +pg pv+ ++y+ +++     ++lP+sleeA+e+l +
  gi|320100375|ref|YP_004175967.1| 316 PL---NGGRIEVRTPDASMNPYLGISAILLAGLDGLRKKTDPGSPVDYNMYDKPSTS----SRLPRSLEEAVESLLS 385
                                       **...99***********************************************987....68************** PP

                                       S.HHHCCSS-HHHHHHHHHHHHHCHHHHHCT CS
                        Gln-synt_C 307 d.ellkevlgeevieaylalkraEleeleee 336
                                       d e+lk ++ ++++e y +lk  E ++ ++ 
  gi|320100375|ref|YP_004175967.1| 386 DhEYLKPLFPRDMLEYYAELKLREARRNRSI 416
                                       ************************9987765 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 !   36.8   0.0   2.6e-13   2.3e-09       5      63 ..       6      64 ..       3      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.6e-13
                                      EEEEEE-SSS-EEEEEEEHHHHHHHTTT.T-EEEETTSSTTT------EEEEEEEGGGEE CS
                        Gln-synt_N  5 vdlqFtDikgklkhvtipadelsedale.egvsFDGSsiegfaeieeSDmlLkPdlstav 63
                                      +++ FtDi g +++v+i++d +  ++le    ++DGSsi g+ +ie SD+++ P  st+v
  gi|320100375|ref|YP_004175967.1|  6 LHILFTDIAGVHRQVSIAVDGV-PETLEgIRAGIDGSSIPGYGRIERSDLFVEPASSTIV 64
                                      6788******************.777772566***********************88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3314.12
//
Query:       gi|320100376|ref|YP_004175968.1|  [L=152]
Description: AsnC family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-16   57.5   0.3    1.2e-15   56.8   0.3    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    9.6e-15   54.3   0.3    1.7e-14   53.5   0.3    1.4  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    2.5e-13   49.6   2.7      4e-13   49.0   2.7    1.3  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.3e-05   24.9   0.1    2.2e-05   24.2   0.1    1.3  1  HTH_IclR         IclR helix-turn-helix domain
      4e-05   23.4   0.1      7e-05   22.6   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00016   21.3   0.1    0.00031   20.4   0.1    1.6  1  HTH_38           Helix-turn-helix domain
     0.0002   21.0   0.1    0.00039   20.1   0.1    1.4  1  HTH_23           Homeodomain-like domain
    0.00078   19.9   0.1      0.002   18.5   0.1    1.7  1  HTH_27           Winged helix DNA-binding domain
    0.00094   19.2   0.1     0.0017   18.4   0.1    1.3  1  HTH_20           Helix-turn-helix domain
    0.00096   19.5   0.0     0.0017   18.7   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
     0.0014   18.1   1.0     0.0025   17.3   1.0    1.4  1  Sigma70_r4       Sigma-70, region 4
     0.0031   17.3   0.1     0.0054   16.6   0.1    1.3  1  MarR_2           MarR family
      0.009   15.9   0.1      0.022   14.7   0.1    1.7  2  HTH_11           HTH domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.029   14.2   0.0    1.4  1  RuvB_C           RuvB C-terminal winged helix domain
      0.022   14.7   0.0      0.048   13.6   0.0    1.5  1  MarR             MarR family
      0.025   14.8   0.0      0.091   13.0   0.0    1.9  1  DUF4777          Domain of unknown function (DUF4777)
      0.032   13.9   0.1      0.065   12.9   0.1    1.5  1  HTH_50           Helix-turn-helix domain
      0.035   13.8   0.3      0.079   12.6   0.3    1.7  1  Sigma70_r4_2     Sigma-70, region 4
      0.059   13.5   0.1       0.13   12.4   0.0    1.7  2  AsnC_trans_reg2  AsnC-like ligand binding domain
      0.064   13.1   0.1       0.13   12.2   0.1    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
      0.075   12.6   0.0       0.13   11.8   0.0    1.4  1  HTH_47           winged helix-turn-helix
       0.12   12.5   0.0       0.27   11.5   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin


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 !   56.8   0.3   1.5e-18   1.2e-15       1      48 []       6      53 ..       6      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.5e-18
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +de+dr++L++Lq+++r s r +Aerlg ++stv++r++rL+++G++k
  gi|320100376|ref|YP_004175968.1|  6 MDELDREVLKALQEDSRQSLRSIAERLGRPVSTVHERVRRLIDKGVLK 53
                                      8********************************************986 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 !   53.5   0.3   2.1e-17   1.7e-14       1      75 []      72     142 ..      72     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.1e-17
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       +l++++++h   + ++e+++ ++p+V+ +y +tG++d  +++v++ +++l++f++  + ++p v++t+tsiv++t
  gi|320100376|ref|YP_004175968.1|  72 ILMNVDGKH---IIDVERHVSQHPNVLVVYDITGEFDVAVIAVFKEIRELDEFIKW-ILQNPYVKQTRTSIVFRT 142
                                       678999999...*****************************************988.***************986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   2.7   4.9e-16     4e-13       1      41 [.       6      46 ..       6      47 .. 0.99

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.9e-16
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      +De+Dr  L+aLqed+R s + +Aer+G   stv++RvrrL
  gi|320100376|ref|YP_004175968.1|  6 MDELDREVLKALQEDSRQSLRSIAERLGRPVSTVHERVRRL 46
                                      9***************************************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 !   24.2   0.1   2.7e-08   2.2e-05       8      49 ..      13      53 ..      12      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.7e-08
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +L+al e  +  +l+ +A+r+g p Stvh  ++ L+  G ++
  gi|320100376|ref|YP_004175968.1| 13 VLKALQEDSRQ-SLRSIAERLGRPVSTVHERVRRLIDKGVLK 53
                                      99********8.************************999886 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   8.6e-08     7e-05       8      51 ..       8      51 ..       2      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.6e-08
                                      HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
                              TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGl 51
                                      e + +v +aL +  + + + iae+lg+p s+v e +r+L+dkG+
  gi|320100376|ref|YP_004175968.1|  8 ELDREVLKALQEDSRQSLRSIAERLGRPVSTVHERVRRLIDKGV 51
                                      78899**************************************7 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   3.8e-07   0.00031       4      43 ..       5      45 ..       2      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.8e-07
                            HTH_38  4 hLsleeReeIerllaeG.lslreIArrLgrspsTIsRElkR 43
                                      ++   +Re++ +l +    slr IA rLgr  sT++  ++R
  gi|320100376|ref|YP_004175968.1|  5 KMDELDREVLKALQEDSrQSLRSIAERLGRPVSTVHERVRR 45
                                      566779*******98777*****************877776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   4.7e-07   0.00039       9      40 ..      12      45 ..      11      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.7e-07
                            HTH_23  9 rillllae..GlsvreIAreLgvsrrTvy.rwlkr 40
                                      ++l++l+e  ++s r IA++Lg++ +Tv  r+ +r
  gi|320100376|ref|YP_004175968.1| 12 EVLKALQEdsRQSLRSIAERLGRPVSTVHeRV-RR 45
                                      5899999999*******************555.54 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 !   18.5   0.1   2.5e-06     0.002       4      49 ..       9      53 ..       6      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.5e-06
                            HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                      +++ vL  ++ ++ r++l+ +++rl +  s++++ +++L+ kG+++
  gi|320100376|ref|YP_004175968.1|  9 LDREVLKALQ-EDSRQSLRSIAERLGRPVSTVHERVRRLIDKGVLK 53
                                      68899999**.********************************994 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   2.1e-06    0.0017      12      55 ..      10      53 ..       6      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                       r++l+aL ++  +++  +aerl+ + +t++ ++r L + g ++
  gi|320100376|ref|YP_004175968.1| 10 DREVLKALQEDSRQSLRSIAERLGRPVSTVHERVRRLIDKGVLK 53
                                      589**********************************9998876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.1e-06    0.0017       3      52 ..       8      53 ..       6      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-06
                                      -S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-E CS
                   Penicillinase_R  3 elEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKglls 52
                                      el++ev+++l e ++++ +++ e+l ++     sTV+  +rrL +Kg+l+
  gi|320100376|ref|YP_004175968.1|  8 ELDREVLKALQEDSRQSLRSIAERLGRP----VSTVHERVRRLIDKGVLK 53
                                      6789************************....9***************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.0   3.1e-06    0.0025       5      47 ..       6      49 ..       4      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-06
                                      S-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4  5 Lpererevlelrf.geglTleEIgerlgiSrerVrqiekrAlrk 47
                                      ++e +revl+    +  ++l  I+erlg + ++V+ + +r ++k
  gi|320100376|ref|YP_004175968.1|  6 MDELDREVLKALQeDSRQSLRSIAERLGRPVSTVHERVRRLIDK 49
                                      68899********99999*********************99876 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   6.6e-06    0.0054       8      51 ..      11      52 ..       6      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      + vL aL    +   + + +a+rlg + s+v+ +++rL ++G +
  gi|320100376|ref|YP_004175968.1| 11 REVLKALQEDSR--QSLRSIAERLGRPVSTVHERVRRLIDKGVL 52
                                      567777777776..8999***********************975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.7e-05     0.022       4      54 ..      12      66 ..      10      67 .. 0.86
   2 ?   -2.7   0.0       7.4     6e+03      24      40 ..     103     119 ..      90     123 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgr.GY 54
                                       +l+ L ++++  s   +Ae+L++  +tv+ ++++L ++g    + +  + gr GY
  gi|320100376|ref|YP_004175968.1| 12 EVLKAL-QEDSRQSLRSIAERLGRPVSTVHERVRRLIDKGvlkgFTVLVDYGRlGY 66
                                      578888.888889***************************8888777777777777 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.4
                            HTH_11  24 eLnvSrrtvrrdIkaLe 40 
                                       e++v   +v + I++L 
  gi|320100376|ref|YP_004175968.1| 103 EFDVAVIAVFKEIRELD 119
                                       55555556666666665 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 ?   14.2   0.0   3.6e-05     0.029       4      44 ..       6      43 ..       5      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTT CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedvi 44
                                      +deld+++Lk+l+   +++  +l+++a+ lg + +t+ + +
  gi|320100376|ref|YP_004175968.1|  6 MDELDREVLKALQ---EDSRQSLRSIAERLGRPVSTVHERV 43
                                      799*********9...79******************99876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.9e-05     0.048       8      47 ..      13      52 ..      11      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      +L  l e   +s+  +a++lg   stv + ++rL++kG +
  gi|320100376|ref|YP_004175968.1| 13 VLKALQEDSRQSLRSIAERLGRPVSTVHERVRRLIDKGVL 52
                                      67777888889999***********************965 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.091      28      56 ..      27      55 ..      24      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                           DUF4777 28 rvaerydlseeelkkvVkntLeaAvrhGF 56
                                      ++aer++++ + + + V+++ +++v +GF
  gi|320100376|ref|YP_004175968.1| 27 SIAERLGRPVSTVHERVRRLIDKGVLKGF 55
                                      69**************************9 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     8e-05     0.065       9      46 ..       7      45 ..       4      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8e-05
                            HTH_50  9 eefErelikkaye.kYpStRklAkrLGvShtaianklrk 46
                                      +e +re++k++ e + +S R +A+rLG   +++  ++r+
  gi|320100376|ref|YP_004175968.1|  7 DELDREVLKALQEdSRQSLRSIAERLGRPVSTVHERVRR 45
                                      78899999999873568********************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 ?   12.6   0.3   9.7e-05     0.079      27      49 ..      23      45 ..       5      49 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-05
                                      --HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 27 lsykEIAellgisegtVksrlsR 49
                                       s + IAe+lg +++tV  r++R
  gi|320100376|ref|YP_004175968.1| 23 QSLRSIAERLGRPVSTVHERVRR 45
                                      47889*************99988 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 ?   -2.2   0.0       5.8   4.7e+03      61      65 ..      26      30 ..       8      49 .. 0.58
   2 ?   12.4   0.0   0.00016      0.13       1      37 [.      63      99 ..      63     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.8
                   AsnC_trans_reg2 61 aeiaa 65
                                      + ia+
  gi|320100376|ref|YP_004175968.1| 26 RSIAE 30
                                      33333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00016
                   AsnC_trans_reg2  1 klGfkanalvawkvpeerveevaevvaelpevtHcYe 37
                                      +lG++  al+ ++v+ +++ +v + v+++p+v  +Y 
  gi|320100376|ref|YP_004175968.1| 63 RLGYTVKALILMNVDGKHIIDVERHVSQHPNVLVVYD 99
                                      69*****************************988876 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 ?   12.2   0.1   0.00016      0.13       5      45 ..      11      52 ..       7      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +++Lk+L+e + ++   +ae lg + stv +  ++L + G++
  gi|320100376|ref|YP_004175968.1| 11 REVLKALQEdSRQSLRSIAERLGRPVSTVHERVRRLIDKGVL 52
                                      689******556*****************9999999998875 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.13      44      77 ..      20      53 ..       5      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                      EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 44 DGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      D ++sL  iAer+g p+ +v + +r+L ++g+l+
  gi|320100376|ref|YP_004175968.1| 20 DSRQSLRSIAERLGRPVSTVHERVRRLIDKGVLK 53
                                      77899**************************996 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.27      16      52 ..      16      52 ..       5      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                                      HHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 16 lseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      +  e +  +   +aerL+   s+V e +++L ++G +
  gi|320100376|ref|YP_004175968.1| 16 ALQEDSRQSLRSIAERLGRPVSTVHERVRRLIDKGVL 52
                                      555555666778*******************999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1137.10
//
Query:       gi|320100377|ref|YP_004175969.1|  [L=483]
Description: sulfide dehydrogenase (flavoprotein) subunit SudA [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-42  142.7   0.1    5.4e-42  142.1   0.1    1.3  1  Fer4_20         Dihydroprymidine dehydrogenase domain II, 4Fe
    1.5e-39  136.0   0.0    2.4e-39  135.3   0.0    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.5e-16   58.5   3.4    5.9e-08   33.2   0.2    3.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      2e-12   47.0   0.9    0.00028   20.3   0.0    3.8  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.7e-09   37.1   0.3    1.1e-08   35.1   0.0    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.9e-08   32.3   0.0      0.004   16.5   0.0    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    9.7e-06   24.5   0.4    0.00015   20.6   0.1    2.1  2  HI0933_like     HI0933-like protein
    1.5e-05   24.5   0.2     0.0022   17.4   0.0    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    4.1e-05   23.0   0.2    0.00017   21.0   0.0    1.9  2  FAD_binding_3   FAD binding domain
    6.5e-05   22.2   5.1    0.00016   20.9   0.3    2.9  3  FAD_binding_2   FAD binding domain
    0.00031   20.2   0.5     0.0066   15.8   0.1    2.6  3  Amino_oxidase   Flavin containing amine oxidoreductase
    0.00038   20.9   0.1       0.59   10.6   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
    0.00053   19.3   0.8    0.00086   18.6   0.1    1.7  2  Thi4            Thi4 family
    0.00061   19.0   1.0      0.027   13.6   0.2    2.4  3  GIDA            Glucose inhibited division protein A
    0.00068   20.2   0.1        0.2   12.3   0.0    2.6  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0022   17.6   0.6      0.043   13.4   0.1    2.8  3  DAO             FAD dependent oxidoreductase
     0.0056   16.3   0.0       0.16   11.6   0.0    2.2  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0077   16.1   0.0       0.93    9.4   0.0    2.3  2  YjeF_N          YjeF-related protein N-terminus
     0.0087   15.4   0.1       0.68    9.3   0.0    2.5  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.019   15.0   0.5        5.3    7.1   0.0    3.3  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.037   13.2   0.0        1.5    7.9   0.0    2.3  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.042   14.1   0.1        6.9    7.0   0.0    2.6  2  TrkA_N          TrkA-N domain
      0.071   11.9   1.1       0.09   11.6   0.1    1.6  2  Trp_halogenase  Tryptophan halogenase
       0.15   12.0   2.9        0.2   11.7   0.2    2.4  3  NAD_binding_9   FAD-NAD(P)-binding
        0.2   10.7   0.2       0.36    9.8   0.2    1.4  1  Lycopene_cycl   Lycopene cyclase protein
       0.45   10.7   3.1       0.86    9.8   3.1    1.5  1  Fer4_10         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.1   0.1   7.8e-45   5.4e-42       1     112 [.      23     135 ..      23     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 7.8e-45
                                       HTTS-S-SB----HHHHHHHHTT----T..T-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS CS
                           Fer4_20   1 raknfkevalglteeealeeAsRClqCk..kapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvC 75 
                                       r+++f+ev lg+t e+a+eeAsRClqC    apcvkgCPv+++ip+f++k++eg++++a++ii+etn+lp ++grvC
  gi|320100377|ref|YP_004175969.1|  23 RIRDFNEVVLGYTLEQAMEEASRCLQCPlnFAPCVKGCPVHVNIPGFLRKLREGDVKGALEIIMETNPLPGITGRVC 99 
                                       5789***********************654799******************************************** PP

                                       -GGGTGCCS-GGGTTB.----HHHHHHHHHHHHHHT- CS
                           Fer4_20  76 pqeelCegaCvlekkgkepvaigklerfvadaareeg 112
                                       pqee+Ce++C++++ g + ++igklerfvad+ar++g
  gi|320100377|ref|YP_004175969.1| 100 PQEEQCERNCIMGRIG-DRINIGKLERFVADYARKHG 135
                                       ************9888.9***************9986 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 !  135.3   0.0   3.5e-42   2.4e-39       1     294 []     148     454 ..     148     454 .. 0.82

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 3.5e-42
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCCHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgielllgee 74 
                                       k+++++G+GpAGl+aa +l++ g++v ++   ++++  g +l + + +++ ++ei++   e ++k+  g+e l++  
  gi|320100377|ref|YP_004175969.1| 148 KKIAIVGSGPAGLTAAAELRKMGHEVRVF---EALHEPGGVLVYGIPEFRLPKEIVRyelEYLSKI--GVEILTD-- 217
                                       589**************************...778888899999*********9999744222222..3444444.. PP

                                       CEEEEESCEEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC.........TTBEECCSECHHHHHHCCSS-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  75 vvkidpgkkkvklekkkegdeekiaydklvlAtGs.sprdlgipGv........aenvgklvrtldsaealklkllp 142
                                          +  gk ++ l+++        +yd+++l tG+ +p+ l+ipGv        +e       +l++a  +     p
  gi|320100377|ref|YP_004175969.1| 218 ---VVVGK-TLSLRDL------LTEYDAVFLGTGAgTPNFLNIPGVnclniysaNEFL--TRVNLMKAYLF-----P 277
                                       ...66666.7888554......479*********7588888*****665555322222..22355555555.....3 PP

                                       .........SEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEE CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 .........krivvvGgGyiGvElAaalaklgke.vtlveardrllraldkelsaaleealekeGvevklgtsvkei 209
                                                +r++v+GgG+++++ A  + +lg++ v+++++r++ l      ++++  e  e+eGv++++  s++e+
  gi|320100377|ref|YP_004175969.1| 278 eydtpikkpNRVAVIGGGNTAMDAARSALRLGSReVYVLYRRTKEL----MTARQEEVENAEEEGVKFMFLVSPVEF 350
                                       555559999**********************9977*********99....67888888999**************** PP

                                       EETTE.......EEEEEETTSCE...............EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS CS
                                       xxxxx.......xxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 210 dgnge.......klevvledgee...............idadlvvvavGvrpstelleeklglelderggivvdefl 264
                                         +++        +++ l++  +               +++d v++a+G +p++ l+++   l+l+e+g ivvde++
  gi|320100377|ref|YP_004175969.1| 351 VCDDKgrvkavrLIKMRLGEPGRdgrprpipipgsefeLEVDAVIIAIGQTPNRILFKDIPELKLTEKGTIVVDEKY 427
                                       *9999988755444466666666899***************************999878899*************** PP

                                       BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       rt+v+g++a GD +   +g  ++++A+  G
  gi|320100377|ref|YP_004175969.1| 428 RTTVKGVFAGGDAI---RGESTVVKAMGDG 454
                                       ************99...8999999998766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   9.8e-08   6.8e-05       1      63 [.     149     220 ..     149     224 .. 0.81
   2 !   33.2   0.2   8.6e-11   5.9e-08       1      78 [.     288     363 ..     288     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.8e-08
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS..TT.......SSHHHHHHHHHHHHHTTEEEECSEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll..rl.......lDeeaskilqeklekngievllntkv 63 
                                       k+++vG+G  gl +A++l+++g++V v+e+  ++    +       l++e+ ++  e+l+k g+e+l++ +v
  gi|320100377|ref|YP_004175969.1| 149 KIAIVGSGPAGLTAAAELRKMGHEVRVFEALHEPGgvLVygipefrLPKEIVRYELEYLSKIGVEILTDVVV 220
                                       79*****************************99984311222333368999999999999999999987665 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 8.6e-11
                                       EEEEECSSHHHHHHHHHHHHTTS.EEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgk.kVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.ves 75 
                                       +v+v+GgG++++++A  + +lg+ +V+v+ r+ k l     +a+++  e+ e++g+++++  +++e++ +++g v++
  gi|320100377|ref|YP_004175969.1| 288 RVAVIGGGNTAMDAARSALRLGSrEVYVLYRRTKEL----MTARQEEVENAEEEGVKFMFLVSPVEFVCDDKGrVKA 360
                                       79********************659****9998877....79**********************************9 PP

                                       EEE CS
                         Pyr_redox  76 vkl 78 
                                       v+l
  gi|320100377|ref|YP_004175969.1| 361 VRL 363
                                       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 !   14.5   0.1   2.2e-05     0.015       2      28 ..     152     177 ..     151     183 .. 0.89
   2 !   20.3   0.0     4e-07   0.00028     163     198 ..     285     321 ..     231     343 .. 0.76
   3 !    7.7   0.0    0.0026       1.8     259     305 .]     392     438 ..     383     438 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilE 28 
                                       I+G GPaGl+aa el+k+g  ++ + E
  gi|320100377|ref|YP_004175969.1| 152 IVGSGPAGLTAAAELRKMGH-EVRVFE 177
                                       9******************9.577777 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4e-07
                       Pyr_redox_3 163 agqkvvViGgknSavDaAlelvrkga.eVtvvtrgse 198
                                       + ++v+ViGg+n+a+DaA    r g+ eV v++r+++
  gi|320100377|ref|YP_004175969.1| 285 KPNRVAVIGGGNTAMDAARSALRLGSrEVYVLYRRTK 321
                                       4579********************9736****99874 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0026
                       Pyr_redox_3 259 ddvvlatGykpdlsflkk.slfeldedgrpvlteeteetnvpglflaG 305
                                       d v++a+G +p+  ++k+ + ++l+e+g++v++e+   t v+g+f  G
  gi|320100377|ref|YP_004175969.1| 392 DAVIIAIGQTPNRILFKDiPELKLTEKGTIVVDEKYRTT-VKGVFAGG 438
                                       78999***********9999************9887655.*****876 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 !   35.1   0.0   1.6e-11   1.1e-08       1      35 [.     152     186 ..     152     215 .. 0.85
   2 ?   -1.0   0.1         3   2.1e+03       1      18 [.     291     308 ..     291     320 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.6e-11
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35 
                                       IvG+G +Gl+aA++L+k g++v ++e+ + +GG +
  gi|320100377|ref|YP_004175969.1| 152 IVGSGPAGLTAAAELRKMGHEVRVFEALHEPGGVL 186
                                       9*******************************965 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                                       EE--SHHHHHHHHHHHCC CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLaka 18 
                                       ++G+G +++ aA+ + + 
  gi|320100377|ref|YP_004175969.1| 291 VIGGGNTAMDAARSALRL 308
                                       89***9999999775554 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   4.5e-05     0.031      29      59 ..     148     178 ..     139     182 .. 0.88
   2 !   16.5   0.0   5.8e-06     0.004       5      64 ..     261     323 ..     257     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-05
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDv 59 
                                        k+ ++G G aGl A+a  +++g +V+v++ 
  gi|320100377|ref|YP_004175969.1| 148 KKIAIVGSGPAGLTAAAELRKMGHEVRVFEA 178
                                       589*************************985 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 5.8e-06
                                       HHHHCSCGCTSEEETTCEETC..B---EEEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHH CS
                       AlaDh_PNT_C   5 aakalekffggkgtlaGgvpg..vepakvlviGgGvaGlqAiatakglga.kVtvlDvrparl 64 
                                       a ++l++ + +k  l         +p +v viGgG   + A++ a +lg  +V+vl  r++ l
  gi|320100377|ref|YP_004175969.1| 261 ANEFLTRVNLMKAYLFPEYDTpiKKPNRVAVIGGGNTAMDAARSALRLGSrEVYVLYRRTKEL 323
                                       556666777777777665443224899**********************73688887666544 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.2e-07   0.00015       2      36 ..     149     183 ..     148     188 .. 0.93
   2 ?    1.9   0.0       0.1        71       2      29 ..     288     316 ..     287     323 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.2e-07
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +++++G G+AGl aA++++k g++V ++e+ +++g
  gi|320100377|ref|YP_004175969.1| 149 KIAIVGSGPAGLTAAAELRKMGHEVRVFEALHEPG 183
                                       799**************************988877 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.1
                                       SEEEE--SHHHHHHHHHHHHTT.--EEEE CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrg.krVlll 29 
                                       +v+viGgG   + aA sa + g ++V +l
  gi|320100377|ref|YP_004175969.1| 288 RVAVIGGGNTAMDAARSALRLGsREVYVL 316
                                       69**************9966551556665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.1e-06    0.0022       2      41 ..     150     189 ..     149     206 .. 0.94
   2 ?    5.0   0.1     0.018        13       2      24 ..     289     311 ..     288     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg 41 
                                       + +vG+gpaG++AA    ++G +v + e     GG l  g
  gi|320100377|ref|YP_004175969.1| 150 IAIVGSGPAGLTAAAELRKMGHEVRVFEALHEPGGVLVYG 189
                                       78*********************************99876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.018
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGak 24 
                                       v V+GGg   + AA +A r G +
  gi|320100377|ref|YP_004175969.1| 289 VAVIGGGNTAMDAARSALRLGSR 311
                                       89*******************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 !   21.0   0.0   2.4e-07   0.00017       4      33 ..     150     179 ..     148     183 .. 0.91
   2 ?   -0.8   0.0       1.1   7.3e+02       4      41 ..     289     327 ..     287     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       ++IVG+GpaGl++a +L++ G +v++ e  
  gi|320100377|ref|YP_004175969.1| 150 IAIVGSGPAGLTAAAELRKMGHEVRVFEAL 179
                                       78***********************99876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                       EEEE--SHHHHHHHHHHHHTTHH.EEEEESSSSSCCSSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvr.vvlvekrsttvvlpr 41 
                                       V+++G+G + + +a+   + G r v ++ +r+++  + r
  gi|320100377|ref|YP_004175969.1| 289 VAVIGGGNTAMDAARSALRLGSReVYVLYRRTKELMTAR 327
                                       99********99999988888885667777777666655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   2.3e-07   0.00016       2      36 ..     150     184 ..     149     189 .. 0.89
   2 ?    0.0   0.3       0.5   3.4e+02       2      28 ..     289     316 ..     288     327 .. 0.85
   3 ?    1.3   0.0      0.21   1.4e+02     151     223 ..     334     432 ..     319     454 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.3e-07
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                       + ++GsG AGL+AA+e+++ G++v v e  +e gg
  gi|320100377|ref|YP_004175969.1| 150 IAIVGSGPAGLTAAAELRKMGHEVRVFEALHEPGG 184
                                       67**************************9988776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.5
                                       EEEE--SHHHHHHHHHHHHTTT.-EEEE CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvavv 28 
                                       v ViG+G   + AA +a + G  +v v+
  gi|320100377|ref|YP_004175969.1| 289 VAVIGGGNTAMDAARSALRLGSrEVYVL 316
                                       89************99999888667665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.21
                                       HHTCTEEEEESEEEEEEEECTT.EEEEEEEEET...............TTTCEEEEEESEEEE-----GG....... CS
                     FAD_binding_2 151 arkagvdfqerteadeLivedg.rvtGavvenp...............esgrevrirakavvlatgGfgr....... 204
                                       a++ gv+f++  + +e++ +d+ rv  + + ++                 g+e++++ +av++a g  ++       
  gi|320100377|ref|YP_004175969.1| 334 AEEEGVKFMFLVSPVEFVCDDKgRVKAVRLIKMrlgepgrdgrprpipIPGSEFELEVDAVIIAIGQTPNrilfkdi 410
                                       44555777777777777775444777777776677777777777777777777777777777777777775555555 PP

                                       .............GSSSBSSGT CS
                     FAD_binding_2 205 ...allkellgaaaeaettnap 223
                                          +l ++ +  + e++ t+++
  gi|320100377|ref|YP_004175969.1| 411 pelKLTEKGTIVVDEKYRTTVK 432
                                       5553333333333333333333 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   9.6e-06    0.0066       2      28 ..     158     184 ..     157     187 .. 0.96
   2 ?   -0.9   0.0       1.1   7.5e+02     250     272 ..     386     409 ..     382     418 .. 0.77
   3 ?    1.0   0.0       0.3     2e+02     414     451 ..     427     461 ..     422     462 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.6e-06
                                       HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                       aGL+aA +L   G++V v+Ea   +GG
  gi|320100377|ref|YP_004175969.1| 158 AGLTAAAELRKMGHEVRVFEALHEPGG 184
                                       9*************************9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                                       EE..EESEEEE-S-HHHHHSSEEES CS
                     Amino_oxidase 250 vv..eaDaVvvTvplgvlkailfsP 272
                                       ++  e+DaV++++ +   + ilf+ 
  gi|320100377|ref|YP_004175969.1| 386 EFelEVDAVIIAIGQTPNR-ILFKD 409
                                       55559********999988.88876 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.3
                                       HCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 414 akpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                       +++  ++++f  G+++     +tv +A+  G++aA+ i
  gi|320100377|ref|YP_004175969.1| 427 YRT-TVKGVFAGGDAIR--GESTVVKAMGDGWKAARSI 461
                                       566.799********99..99**************976 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0055       3.8       6      36 ..     146     176 ..     144     220 .. 0.92
   2 !   10.6   0.0   0.00086      0.59       8      59 ..     287     339 ..     284     418 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0055
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvv 36 
                                       +gkk+ +vG G+ +++ +  l + g +v v 
  gi|320100377|ref|YP_004175969.1| 146 TGKKIAIVGSGPAGLTAAAELRKMGHEVRVF 176
                                       699*************************996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00086
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleag.akvtvvapevkeeleelvklaeeelekd....l 59 
                                        +v v+GgG+ A+  +r+ l+ g  +v v+  +    ++el+++++ee+e+     +
  gi|320100377|ref|YP_004175969.1| 287 NRVAVIGGGNTAMDAARSALRLGsREVYVLYRR----TKELMTARQEEVENAeeegV 339
                                       689******************995568887777....67888888888753322222 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.2e-06   0.00086      19      64 ..     149     193 ..     145     242 .. 0.83
   2 ?   -3.4   0.1       6.5   4.5e+03      20      35 ..     289     304 ..     287     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf 64 
                                        ++ivG+G++GLtaa  l k  + +v ++e+   pGG    G   f
  gi|320100377|ref|YP_004175969.1| 149 KIAIVGSGPAGLTAAAELRKM-GHEVRVFEALHEPGGVLVYGIPEF 193
                                       589****************99.*************99887776555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.5
                                       EEEE--SHHHHHHHHH CS
                              Thi4  20 vvivGaGssGLtaayy 35 
                                       v+++G+G + + aa+ 
  gi|320100377|ref|YP_004175969.1| 289 VAVIGGGNTAMDAARS 304
                                       7899999999999985 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   3.9e-05     0.027       1      28 [.     149     176 ..     149     192 .. 0.88
   2 ?    3.6   0.0     0.043        30       2      24 ..     289     311 ..     288     330 .. 0.82
   3 ?   -3.2   0.0       4.7   3.2e+03     354     388 ..     430     465 ..     422     467 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi 28 
                                       ++ ++G G AG+ AA+++ ++G++v  +
  gi|320100377|ref|YP_004175969.1| 149 KIAIVGSGPAGLTAAAELRKMGHEVRVF 176
                                       588**********************987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.043
                                       EEEE-SSHHHHHHHHHHHHTT-- CS
                              GIDA   2 viViGgGhAGceAAlaaarlGak 24 
                                       v ViGgG   + AA  a rlG +
  gi|320100377|ref|YP_004175969.1| 289 VAVIGGGNTAMDAARSALRLGSR 311
                                       89******************986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.7
                                       SSBTEEE-CG.GGTB-SHHHHHHHHHHHHHHHHHHH CS
                              GIDA 354 kvkgLflAGq.inGteGYeEaaaqGllAGinaarka 388
                                       +vkg+f+ G+ i G +  + a++ G+ A++ +  ++
  gi|320100377|ref|YP_004175969.1| 430 TVKGVFAGGDaIRGESTVVKAMGDGWKAARSIDEYL 465
                                       488999999768899999999999999998887665 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 ?    5.2   0.0     0.046        32       1      30 [.     149     175 ..     149     181 .. 0.92
   2 !   12.3   0.0   0.00029       0.2       1      47 [.     288     332 ..     288     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.046
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEE CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivv 30 
                                       ki+i+G+G  g + a  l + g   he++v
  gi|320100377|ref|YP_004175969.1| 149 KIAIVGSGPAGLTAAAELRKMG---HEVRV 175
                                       7*********************...**996 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00029
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47 
                                       ++++iG+Gn +   a+ +l+ g   +e++v  +r++e +++ +ee++
  gi|320100377|ref|YP_004175969.1| 288 RVAVIGGGNTAMDAARSALRLG--SREVYVLYRRTKELMTARQEEVE 332
                                       69********************..9******9999999888888775 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   6.3e-05     0.043       1      33 [.     149     183 ..     149     185 .. 0.88
   2 ?   -0.6   0.0       1.1   7.8e+02     155     207 ..     206     248 ..     196     274 .. 0.62
   3 ?    0.4   0.0      0.57   3.9e+02       1      29 [.     288     319 ..     288     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       +++i+G+G +Gl++A eL + g  V ++e+ +++g
  gi|320100377|ref|YP_004175969.1| 149 KIAIVGSGPAGLTAAAELRKMGheVRVFEALHEPG 183
                                       59****************66689******988887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                       HHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HH CS
                               DAO 155 aaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.ll 207
                                        + + Gveil+   v+g       +  +        +++dav + +Ga++  +l
  gi|320100377|ref|YP_004175969.1| 206 YLSKIGVEILTD-VVVGKTLS---LRDL--L-----TEYDAVFLGTGAGTPnFL 248
                                       555666666666.44443121...2333..1.....236777777777776544 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.57
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekg 29 
                                       +v++iGGG + + +A+ + r g   V +l ++
  gi|320100377|ref|YP_004175969.1| 288 RVAVIGGGNTAMDAARSALRLGsreVYVLYRR 319
                                       59******999999999988787888887665 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00023      0.16       4      32 ..     147     175 ..     145     182 .. 0.92
   2 ?    2.2   0.0      0.17   1.2e+02       5      48 ..     287     338 ..     283     347 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                       TS-EEEES-SHHHHHHHHHHHHTT--EEE CS
                              IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvv 32 
                                       gkkia++G G  G + a +lr  g +v v
  gi|320100377|ref|YP_004175969.1| 147 GKKIAIVGSGPAGLTAAAELRKMGHEVRV 175
                                       8************************9987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.17
                                       S-EEEES-SHHHHHHHH.HHHHTT--EEEEE-TT-.......HHHHHHHHTT CS
                              IlvN   5 kkiaviGyGsqGhaqal.nlrdsgldvvvglregs.......ksvkkAkeeg 48 
                                        ++aviG G+ +   a+  lr    +v v  r+++       + v++A+eeg
  gi|320100377|ref|YP_004175969.1| 287 NRVAVIGGGNTAMDAARsALRLGSREVYVLYRRTKelmtarqEEVENAEEEG 338
                                       689******9998777525777777888777766634444333455555555 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0013      0.93      37      59 ..     154     182 ..     127     227 .. 0.76
   2 ?    4.5   0.0     0.043        29      25      87 ..     284     343 ..     263     371 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                            YjeF_N  37 nnGgdglaaArhLaqegakVtv......l 59 
                                        +G  gl aA++L+++g++V+v       
  gi|320100377|ref|YP_004175969.1| 154 GSGPAGLTAAAELRKMGHEVRVfealheP 182
                                       5799******************5544440 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.043
                            YjeF_N  25 aekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggkvve 87 
                                       ++++ + ++G+gn+  d+   A  L +++  V v l+++ ++l    ++++e++++ g+k+  
  gi|320100377|ref|YP_004175969.1| 284 KKPNRVAVIGGGNTAMDAARSALRLGSRE--VYV-LYRRTKELMTARQEEVENAEEEGVKFMF 343
                                       56777889999999999888888884444..555.4577778888889999999999988765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00099      0.68      21      67 ..     134     178 ..     120     193 .. 0.83
   2 ?    3.4   0.0     0.063        43      37      77 ..     287     328 ..     278     367 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00099
                                       TCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                      2-Hacid_dh_C  21 gewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                       +    + ++++   +gk+++i+G G  G ++a  l+++g +v +++ 
  gi|320100377|ref|YP_004175969.1| 134 HGI--RPEVKIPPSTGKKIAIVGSGPAGLTAAAELRKMGHEVRVFEA 178
                                       444..5666777789***************************98876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.063
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHH CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeee 77 
                                        +v++iG G+ +  +a+ +  +g + +++  +++ke  ++++
  gi|320100377|ref|YP_004175969.1| 287 NRVAVIGGGNTAMDAARSALRLGSREVYVLYRRTKELmTARQ 328
                                       689********************9555544443433323333 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.25   1.7e+02      10      37 ..     145     172 ..     139     177 .. 0.81
   2 ?    1.4   0.0      0.45   3.1e+02      68      88 ..     225     245 ..     212     251 .. 0.84
   3 ?    7.1   0.0    0.0077       5.3      12      48 ..     286     322 ..     280     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.25
                                       .TT-EEEEES-SHHHHHHHHHHHCCT-C CS
                      Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvk 37 
                                        ++kk+ ++G G  +  +a  L + g +
  gi|320100377|ref|YP_004175969.1| 145 STGKKIAIVGSGPAGLTAAAELRKMGHE 172
                                       5789*************99999887655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.45
                                       GHHHHHHT-SEEEE-SSSSS- CS
                      Shikimate_DH  68 elkellaeadvvisataseep 88 
                                       +l++ll e+d v+  t++ +p
  gi|320100377|ref|YP_004175969.1| 225 SLRDLLTEYDAVFLGTGAGTP 245
                                       68899***********99887 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0077
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHH CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtler 48 
                                        ++v +iG G++a  +a+  l+ g ++v v+ R  + 
  gi|320100377|ref|YP_004175969.1| 286 PNRVAVIGGGNTAMDAARSALRLGSREVYVLYRRTKE 322
                                       579***************************9875544 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 ?    2.8   0.0     0.074        51       5      32 ..     150     175 ..     141     181 .. 0.69
   2 ?    7.9   0.0    0.0022       1.5     188     224 ..     283     318 ..     231     334 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.074
                       K_oxygenase   5 ligiGiGpsnLsLailleevkkelkalf 32 
                                       ++++G Gp+ L+ a+ l+++    ++++
  gi|320100377|ref|YP_004175969.1| 150 IAIVGSGPAGLTAAAELRKMG--HEVRV 175
                                       567777777777777777777..33444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0022
                       K_oxygenase 188 llakkriaVvGsGqSaaeifedllrrqkkvelklvtr 224
                                        ++++r+aV+G+G +a + ++ +lr  +  e+ ++ r
  gi|320100377|ref|YP_004175969.1| 283 IKKPNRVAVIGGGNTAMDAARSALRLGS-REVYVLYR 318
                                       68999**************999998765.34444444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0      0.01       6.9       1      29 [.     150     178 ..     150     182 .. 0.88
   2 ?    4.4   0.0     0.061        42       1      43 [.     289     332 ..     289     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidk 29 
                                       i+i+G G  G + a eL++ g+ +v v + 
  gi|320100377|ref|YP_004175969.1| 150 IAIVGSGPAGLTAAAELRKmGH-EVRVFEA 178
                                       79*****************777.5999875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.061
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle 43 
                                       +++iG G++++  a+   + g+++v+v  ++ + + ++r+e++e
  gi|320100377|ref|YP_004175969.1| 289 VAVIGGGNTAMDAARSALRlGSREVYVLYRRTKELMTARQEEVE 332
                                       68**************9998988899999999999998888765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.09       1      32 [.     149     177 ..     149     185 .. 0.86
   2 ?   -3.3   0.1       4.3   2.9e+03       1      20 [.     288     307 ..     288     316 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlve 32 
                                       ki ivG G+aG +aAa l+k++   +ev + e
  gi|320100377|ref|YP_004175969.1| 149 KIAIVGSGPAGLTAAAELRKMG---HEVRVFE 177
                                       79******************99...5566555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.3
                                       EEEEE--SHHHHHHHHHHHH CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalak 20 
                                       ++ ++GGG  +  aA    +
  gi|320100377|ref|YP_004175969.1| 288 RVAVIGGGNTAMDAARSALR 307
                                       589*****999888865544 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00028       0.2       1      40 [.     151     186 ..     151     191 .. 0.86
   2 ?   -2.0   0.1       4.7   3.2e+03       1      19 [.     290     308 ..     290     316 .. 0.81
   3 ?   -1.1   0.0       2.4   1.7e+03     143     155 ..     388     400 ..     384     401 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagr 40 
                                       aivG Gp+Gl+++++L +       +e+ +f+  +epg   
  gi|320100377|ref|YP_004175969.1| 151 AIVGSGPAGLTAAAELRKM-----GHEVRVFEAlHEPGGVL 186
                                       8***************888.....599999**999998444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.7
                     NAD_binding_9   1 aivGaGprGlavlerLlar 19 
                                       a++G+G +++ +++  l+ 
  gi|320100377|ref|YP_004175969.1| 290 AVIGGGNTAMDAARSALRL 308
                                       79*****999998887765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.4
                     NAD_binding_9 143 slaadaVvLAlGh 155
                                       +l++daV++A+G+
  gi|320100377|ref|YP_004175969.1| 388 ELEVDAVIIAIGQ 400
                                       589********97 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00052      0.36       2      32 ..     150     178 ..     149     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvliea 32 
                                       ++++G+GpAgl  Aa+l   k+g +v + ea
  gi|320100377|ref|YP_004175969.1| 150 IAIVGSGPAGLTAAAEL--RKMGHEVRVFEA 178
                                       79***************..888888777765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.1    0.0012      0.86       5      55 ..      42     109 ..      38     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                           Fer4_10   5 dddtCirCg....kCvkaCPadl............tsvgakgeaseeeavrk.kvekCtgcgaCveaC 55 
                                       ++++C++C      Cvk CP+++            + +ga ++++e ++  +     C++ ++C + C
  gi|320100377|ref|YP_004175969.1|  42 EASRCLQCPlnfaPCVKGCPVHVnipgflrklregDVKGALEIIMETNPLPGiTGRVCPQEEQCERNC 109
                                       6789****98899********99999999999887777777777777777775556688888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3410.80
//
Query:       gi|320100378|ref|YP_004175970.1|  [L=281]
Description: sulfide dehydrogenase (flavoprotein) subunit SudB [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-12   47.0   3.2      5e-12   45.4   3.1    1.9  2  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    5.3e-05   23.5   0.0    8.7e-05   22.8   0.0    1.4  1  FAD_binding_6    Oxidoreductase FAD-binding domain
    0.00073   20.2   0.0     0.0018   18.9   0.0    1.7  1  NAD_binding_1    Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
      0.067   13.2   0.1       0.12   12.4   0.1    1.4  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
       0.18   10.9   0.0       0.28   10.3   0.0    1.2  1  DUF815           Protein of unknown function (DUF815)
        8.4    6.4   9.7          2    8.3   4.6    2.5  2  Rep_1B           Replicase polyprotein 1ab


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 ?   -1.8   0.0      0.92   2.8e+03      33      41 ..     190     198 ..     188     199 .. 0.84
   2 !   45.4   3.1   1.7e-15     5e-12       2      42 .]     215     251 ..     214     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.92
                                       -CEEECCCB CS
                   DHODB_Fe-S_bind  33 GPvFdadev 41 
                                       GPv+ +++v
  gi|320100378|ref|YP_004175970.1| 190 GPVIMMKKV 198
                                       9***99988 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 1.7e-15
                                       ---SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB. CS
                   DHODB_Fe-S_bind   2 erMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadevd 42 
                                        +M++G+G+C++C+v+++g     ++++C+dGP Fda++vd
  gi|320100378|ref|YP_004175970.1| 215 PIMVDGTGMCGACRVTVEGR----TVFACVDGPDFDAHKVD 251
                                       68***************775....8**************96 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.9e-08   8.7e-05       3      96 ..       5      93 ..       3      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                                      EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHC CS
                     FAD_binding_6  3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLde 81
                                      ++t+k+++ + +  fr++ p  +   +  +Gq+v++rl+ kge    + t++  + ++G++el+v+ +  Gk ++ + +
  gi|320100378|ref|YP_004175970.1|  5 VITAKRKLAPRVNWFRIQAPLIAR--RAQPGQFVIVRLHEKGE--RIPLTLFDWNANEGFIELVVQEV--GKTTMEMGR 77
                                      678889999999999999887666..7889*********7777..5599****************976..********* PP

                                      S-TT-E.EEEEEEE-S CS
                     FAD_binding_6 82 lkigdt.leikGPlGk 96
                                       ++gd+ l+i+GPlG+
  gi|320100378|ref|YP_004175970.1| 78 YNVGDHvLNITGPLGN 93
                                      ****87269*****97 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.1e-07    0.0018       2     108 ..     106     199 ..     105     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.1e-07
                                       EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHH CS
                     NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvq 78 
                                       ++gG+G a ++ v +a+ e+    +kv+ + G rt+e ++++ee++++    +++  +v++    ++g+ g kg+ +
  gi|320100378|ref|YP_004175970.1| 106 VCGGVGSAVCYPVAKALRER---GNKVISIIGFRTRELVILEEEFRRI----SDE-VIVTT----DDGSYGVKGFTT 170
                                       8***************9997...789**********************....443.35555....7888899***** PP

                                       HHHHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                     NAD_binding_1  79 dalleellslkkeethvyvCGppgMikavr 108
                                       dal+  l+s   +  +vy +Gp  M+k v+
  gi|320100378|ref|YP_004175970.1| 171 DALRSLLES-GVKPGLVYTAGPVIMMKKVA 199
                                       ***777777.8999*************986 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     4e-05      0.12      54      73 ..     221     240 ..     197     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                            Fer2_3  54 egiCGscavainGkptlaCt 73 
                                        g+CG+c v+++G++  aC 
  gi|320100378|ref|YP_004175970.1| 221 TGMCGACRVTVEGRTVFACV 240
                                       79*****************6 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.2e-05      0.28      67     137 ..     112     182 ..     101     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.2e-05
                            DUF815  67 SslvkallneyaeegLrlievekedlkelpklvellrerperfilfvDDLsFeeeeeeyksLksvLeGsle 137
                                       S+++  + ++++e+g ++i +   + +el  l e+ r+ + ++i+  DD s+  +  +  +L+s+Le +++
  gi|320100378|ref|YP_004175970.1| 112 SAVCYPVAKALRERGNKVISIIGFRTRELVILEEEFRRISDEVIVTTDDGSYGVKGFTTDALRSLLESGVK 182
                                       77778888999999999999999999999999999999*****************************9986 PP

>> Rep_1B  Replicase polyprotein 1ab
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.6   0.00068         2       7      49 ..      63     115 ..      58     119 .. 0.66
   2 ?   -1.2   0.2      0.65   1.9e+03      33      45 ..     230     242 ..     225     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00068
                                       EEBBT.TEECSSSEEEESSSSEEEEE-........-TSSEEEBSS-.SCEEEE CS
                            Rep_1B   7 lvvad.GrttsPPGrykvGhkvvavva........dvGGnivfGcG.PGshia 49 
                                       lvv + G+tt   Gry vG  v+ +          d+ G +v  cG  Gs + 
  gi|320100378|ref|YP_004175970.1|  63 LVVQEvGKTTMEMGRYNVGDHVLNITGplgnpthiDMYGVVVIVCGgVGSAVC 115
                                       6776559***************9987511222222555667777752466555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.65
                                       -TSSEEEBSS-SC CS
                            Rep_1B  33 dvGGnivfGcGPG 45 
                                        v G  vf c  G
  gi|320100378|ref|YP_004175970.1| 230 TVEGRTVFACVDG 242
                                       5789999999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2118.97
//
Query:       gi|320100379|ref|YP_004175971.1|  [L=320]
Description: putative signal transduction protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-47  157.9  12.9    3.3e-14   53.0   0.8    4.1  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   4.3e-11   7.7e-07       5      55 ..      44      93 ..      38      95 .. 0.84
   2 !   38.1   1.3   8.6e-14   1.5e-09       2      56 ..     120     174 ..     119     175 .. 0.94
   3 !   42.9   0.0   2.7e-15   4.9e-11       1      55 [.     183     236 ..     183     238 .. 0.93
   4 !   53.0   0.8   1.9e-18   3.3e-14       1      55 [.     258     312 ..     258     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.3e-11
                                      SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT.BEEEEEEHHHHHHHH CS
                               CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedg.klvGivtlrDllral 55
                                       +r++ +v+p+ttl +ale+m    ++r ++V ++g +l G++tl D++++l
  gi|320100379|ref|YP_004175971.1| 44 ARRNPRVVYPSTTLLKALEEMSL--YGRSLIVSDSGrRLRGLLTLGDIVSYL 93
                                      678999***************43..5544499778867************98 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 8.6e-14
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                         im ++++ ++ d+tl  +le m+ +g++ +PV+d dg + Gi+t++Dl+r+l 
  gi|320100379|ref|YP_004175971.1| 120 DTIMVKNPIHLYVDDTLTRVLESMIIHGIGVVPVLDRDGAVYGIITEHDLVRYLY 174
                                       569*********************999**888*********************95 PP

  == domain 3  score: 42.9 bits;  conditional E-value: 2.7e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V++ m+r+vvt+  d++l++ale+m+ +g++rlPV+ +d+ + G++t +D++++ 
  gi|320100379|ref|YP_004175971.1| 183 VAEAMSRPVVTIGIDASLKKALEKMTTYGFRRLPVTSGDN-VAGMLTAMDVVKYF 236
                                       6789*********************9999*******7677.**********9985 PP

  == domain 4  score: 53.0 bits;  conditional E-value: 1.9e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+++m+r++vtv+p ++l+ a+++m +k+vs+++VVd++g l Gi+t+rD+l al
  gi|320100379|ref|YP_004175971.1| 258 VEELMSRELVTVKPGDDLATAIQEMMDKDVSSVLVVDDEGVLQGILTERDVLYAL 312
                                       899*********************88**************888*********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2540.67
//
Query:       gi|320100380|ref|YP_004175972.1|  [L=275]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-30  105.7   1.9      2e-08   34.6   0.0    4.2  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   2.8e-06      0.05       3      56 ..       5      65 ..       3      66 .. 0.78
   2 !   34.6   0.0   1.1e-12     2e-08       1      54 [.      79     131 ..      79     134 .. 0.91
   3 !   20.8   0.0   2.2e-08   0.00039      17      54 ..     155     192 ..     142     194 .. 0.76
   4 !   32.8   0.2   3.9e-12     7e-08       1      56 [.     214     268 ..     214     269 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-06
                                      HHSBSSCEEEETTSBHHHHHHHHH.HHTSSEEEEEETTTB........EEEEEEHHHHHHHHH CS
                               CBS  3 dimtrdvvtvppdttleealelmr.ekgvsrlPVVdedgk........lvGivtlrDllrall 56
                                      ++  +d+++v+ +++l+  l+l+  +++  ++ V+ e+ +        + G+vt rD+l +++
  gi|320100380|ref|YP_004175972.1|  5 EFIDPDPLVVDKNDSLSTYLRLLSkRENDKAV-VM-ENRRingrqvktVAGVVTGRDILGKIV 65
                                      677899*****************633446677.88.45544555778788*********9875 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1.1e-12
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+ +m+++++t++pd+++++al  m++k ++ lPVVd+ + + G v +r ll++
  gi|320100380|ref|YP_004175972.1|  79 VSGFMSTQPFTIKPDASIRDALTAMASKSIGILPVVDGFN-FKGAVYRRSLLKL 131
                                       6779*********************9999*888***8777.**********986 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2.2e-08
                                       BHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  17 tleealelmrekg..vsrlPVVdedgklvGivtlrDllra 54 
                                       +l  + + m e+g  + ++ VVd++gk++G++t +Dl+ a
  gi|320100380|ref|YP_004175972.1| 155 SLLMLRQSMLESGegF-AV-VVDDEGKPCGYITVMDLAYA 192
                                       5555666687877334.55.78***************866 PP

  == domain 4  score: 32.8 bits;  conditional E-value: 3.9e-12
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+d+ +rd+++v++d+ l+ ++e++ ek+ ++++V+ e g +vG+v ++Dl+++l+
  gi|320100380|ref|YP_004175972.1| 214 VRDYYRRDLPVVKEDAELGRVAETLYEKRSRGVLVTGERG-VVGVVREHDLISYLA 268
                                       78999*******************99***99**9*99999.*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2177.62
//
Query:       gi|320100381|ref|YP_004175973.1|  [L=183]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-44  151.5   0.0    1.9e-44  151.3   0.0    1.0  1  Mut7-C    Mut7-C RNAse domain
    2.5e-05   23.9   0.0    4.1e-05   23.3   0.0    1.3  1  DUF5615   Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
      0.081   12.9   0.1       0.16   11.9   0.1    1.5  1  zf_CopZ   Zinc binding 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 !  151.3   0.0   3.1e-48   1.9e-44       2     145 ..       7     152 ..       6     153 .. 0.97

  Alignments for each domain:
  == domain 1  score: 151.3 bits;  conditional E-value: 3.1e-48
                            Mut7-C   2 rfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlrev 76 
                                       +f++Damlg+la++LR+lGyd++y s++ed  +l++a+ e+ri+lTrdr+L+++a ++    +ll+ +d+++ l++v
  gi|320100381|ref|YP_004175973.1|   7 KFIVDAMLGSLARWLRILGYDTVYGSRMEDWLILRRAELEGRIILTRDRGLHHKALKRGLksILLQDDDLASMLAKV 83 
                                       8*****************************************************99886688999************ PP

                            Mut7-C  77 iarlglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveel 145
                                           g++l ++ e +rC + n++l++v+keevk++vp++vy+++++f+ C++C+kv+W G+hw+ +e++
  gi|320100381|ref|YP_004175973.1|  84 SGLTGVRLYVDYERTRCPEDNTPLRKVDKEEVKDKVPPRVYSMHEDFWVCPRCGKVYWVGNHWKMIESI 152
                                       ****************************************************************99876 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   6.8e-09   4.1e-05       2      63 ..       7      62 ..       6      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.8e-09
                           DUF5615  2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFgelll 63
                                      k+++D+ l  +l+++lr +g+d+++      ++++D  il++A+ e+rii+T+D+  ++ +l
  gi|320100381|ref|YP_004175973.1|  7 KFIVDAMLG-SLARWLRILGYDTVYG-----SRMEDWLILRRAELEGRIILTRDRGLHHKAL 62
                                      899999999.9**********98887.....5689*******************98776644 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.7e-05      0.16       2      48 ..      98     140 ..      97     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                       -B-TTT--B-EEE-HHHHHHHB-GGGGGG--S-EE.E---TT-SEEE CS
                           zf_CopZ   2 kkCPvCgkkGkkVkliTvkhllkpellekvkeedYylCknedCdVvY 48 
                                       ++CP  ++  +kV+++ vk  + p + +    ed+++C+   C  vY
  gi|320100381|ref|YP_004175973.1|  98 TRCPEDNTPLRKVDKEEVKDKVPPRVYS--MHEDFWVCP--RCGKVY 140
                                       68**********************9887..577899**5..566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1429.76
//
Query:       gi|320100382|ref|YP_004175974.1|  [L=223]
Description: AMMECR1 domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-45  153.9   0.0    3.3e-45  153.7   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 !  153.7   0.0   1.8e-49   3.3e-45       1     166 []      18     197 ..      18     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 1.8e-49
                                       HHHHHHHHHHHTTSS-S-H...H---HHHHSEEEEEEEEE..EE......CCECCCECEEEEEEHHHHHHHHHHHHH CS
                           AMMECR1   1 lklareaieealkeekkle...eeakeelkekaglFVtlk..ekkg....eLRGCiGtleperpLaeevaenAlaaA 68 
                                       +k+ar+aie++++++++++    +  e+l +++ +F t++     +    +LRGCiG+l+p ++L+e+ +e A++aA
  gi|320100382|ref|YP_004175974.1|  18 VKIARDAIEAYVTRGERIDvsmYRLGEKLLRPGMTFTTIErlD--EsgrpHLRGCIGFLAPLQSLVESTVESAIEAA 92 
                                       689***************987767777999**********653..23578*************************** PP

                                       HT-TTS----HHHHTTEEEEEEEE---EE-...-....GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHH CS
                           AMMECR1  69 feDpRFspvtaeElpeleveVsvLtepepi...v....ledlevgkhGliiekgsrsatlLPqvaveqgwdkeefla 138
                                       ++DpRF+pv++ El++l +eV+vL++p+ +   +    ++ + +g+hGl+ ekg +++tlLP v+ve+ wd+e+fla
  gi|320100382|ref|YP_004175974.1|  93 VNDPRFNPVEPWELDKLIIEVTVLSQPSIVdvgDrwvlPSLIIIGRHGLVAEKGWFKGTLLPVVPVEYCWDEETFLA 169
                                       ***************************99955514555777************************************ PP

                                       HHHHHHTS-TTCCCSTTSEEEEE-EEEE CS
                           AMMECR1 139 sllrKaglrpdewkdseikltryevekf 166
                                       +++ Kaglrpd+w d+++k+  ye+++f
  gi|320100382|ref|YP_004175974.1| 170 ETCVKAGLRPDCWLDKSTKIHLYEGRVF 197
                                       ************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1643.19
//
Query:       gi|320100383|ref|YP_004175975.1|  [L=276]
Description: NH(3)-dependent NAD(+) synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-71  237.8   0.0    1.1e-70  237.6   0.0    1.0  1  NAD_synthase   NAD synthase
    4.3e-05   22.5   0.0     0.0012   17.8   0.0    2.1  2  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.046   13.2   0.0       0.18   11.3   0.0    1.8  2  QueC           Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.6   0.0   1.8e-74   1.1e-70       3     242 .]      19     261 ..      17     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 237.6 bits;  conditional E-value: 1.8e-74
                                       HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE CS
                      NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievkt 78 
                                       e++v flk+y + aga+++v+GlSGG+DSs++ +l v+alg ++v+a ++P + v+++ed++da +la +lg+e+  
  gi|320100383|ref|YP_004175975.1|  19 ETIVGFLKSYFAGAGAEKAVVGLSGGLDSSVTLRLLVDALGANKVTAAIMPdTRVTPPEDTRDAAELAGSLGVEYFI 95 
                                       67899**********************************************999*********************** PP

                                       ---HHHHHHHHH..HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTT CS
                      NAD_synthase  79 idikpivrafeq..elkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiae 153
                                       i+i+ +v +++    + +a + la+gNl+aRiRm+ily+ian+ln +v+gTg++sEl++GyfTkyGDg++d++p+a 
  gi|320100383|ref|YP_004175975.1|  96 IPIDTVVDSYSVipGF-DAGNRLATGNLRARIRMNILYYIANRLNGIVVGTGDRSELLLGYFTKYGDGGVDVLPLAC 171
                                       ***********97444.5557******************************************************** PP

                                       S-HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHH CS
                      NAD_synthase 154 llKtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekie 229
                                       l+Kt+v+eL ++l+ P r+l kp s +L++g   eee+g++Y+ +D ++  l++ + s  e ++ ++lp ev+e++ 
  gi|320100383|ref|YP_004175975.1| 172 LYKTQVRELGRRLGLPARILGKPSSPRLWKGHLAEEEIGLSYEAVDLVFYsLIDLGLSISEAVDATGLPVEVFERVL 248
                                       ************************************************999************************** PP

                                       HHHHHTGGGGSSS CS
                      NAD_synthase 230 klvkksehKrklp 242
                                       +l ++s+hKr+lp
  gi|320100383|ref|YP_004175975.1| 249 SLHRRSRHKRRLP 261
                                       ***********98 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.9e-07    0.0012       2      67 ..      36      95 ..      35     105 .. 0.79
   2 !    2.7   0.0    0.0075        45     165     187 ..     166     190 ..     164     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-07
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplev 67
                                      k vv+lSgG DSsv++ ll ++     +v+ +++ +     ++ +  ed++da + a  lg+++ +
  gi|320100383|ref|YP_004175975.1| 36 KAVVGLSGGLDSSVTLRLLVDALG-ANKVTAAIMPD-----TRVTPPEDTRDAAELAGSLGVEYFI 95
                                      679****************98764.44566666666.....24567899************99865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0075
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla..v 187
                                       ++Pl++l K++vr++ ++ gl+  +
  gi|320100383|ref|YP_004175975.1| 166 VLPLACLYKTQVRELGRRLGLParI 190
                                       68***************99998444 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.9e-05      0.18       1      62 [.      36      99 ..      36     106 .. 0.61
   2 ?   -1.0   0.0      0.17     1e+03     156     176 ..     167     187 ..     164     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                                      EEEEE--SSHHHHHHHHHHHHH-..SEEEEEEE.ESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC  1 kavvllSGGlDSttvlalakkeg..kevealtf.dYgqrhkkeleaakkiakelgveehkildld 62
                                      kavv lSGGlDS++ l l  ++   ++v+a  + d      ++++ a+++a +lgv e  i+ +d
  gi|320100383|ref|YP_004175975.1| 36 KAVVGLSGGLDSSVTLRLLVDALgaNKVTAAIMpDTRVTPPEDTRDAAELAGSLGV-EYFIIPID 99
                                      79***********9987766654224444332202222245556666666666666.66666555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.17
                                       -TTTT--HHHHHHHHHHTTHH CS
                              QueC 156 aPlidlsKaeivklgkelgvp 176
                                        Pl  l K+++ +lg +lg+p
  gi|320100383|ref|YP_004175975.1| 167 LPLACLYKTQVRELGRRLGLP 187
                                       59****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2169.62
//
Query:       gi|320100384|ref|YP_004175976.1|  [L=142]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1147.26
//
Query:       gi|320100385|ref|YP_004175977.1|  [L=175]
Description: ABC-type thiamin-like transport system, permease 1 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.9e-35  119.4   9.3    8.9e-35  119.4   9.3    1.9  2  ABC_cobalt  ABC-type cobalt transport system, permease compon


Domain annotation for each model (and alignments):
>> ABC_cobalt  ABC-type cobalt transport system, permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   9.3     5e-39   8.9e-35       1     119 [.       7     125 ..       7     127 .. 0.98
   2 ?   -0.1   0.6     0.053   9.5e+02       3      21 ..     146     163 ..     144     173 .. 0.63

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 5e-39
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-GGG.GGGGGGGGGHHHHHHHHHH-STTHHHHHHHHHHHHHHHTT- CS
                        ABC_cobalt   1 kdiilvavigvvfGviflawglvynalsaaltPlgaealllGlWllagvlaaliirkpgaallaellaAlvemllgs 77 
                                       +di+++ vi++++Gv+f +w+ vy+a++a+ +P++a+ +++GlW+++++laa +irkpg+a+l+e+l Al+e+++ +
  gi|320100385|ref|YP_004175977.1|   7 VDILVLGVIAAIYGVLFYIWWDVYYAVKAVGGPVAARLVTYGLWFMPAPLAASLIRKPGSAVLGEVLPALLESIIPT 83 
                                       69*************************************************************************** PP

                                       TTTTHHHHHHHHHHHHHHHHHHHTTT---SHHHHHHHHHHHH CS
                        ABC_cobalt  78 qwGastllsglvqGlgaElafaltrYrrftllvlllsgalaa 119
                                       + G+++l++g++qG+++E+ +a + Y+++ ll+++l+gal a
  gi|320100385|ref|YP_004175977.1|  84 PGGLTNLIYGVAQGVFSEASYAGFLYKKYGLLQAILAGALPA 125
                                       **************************************9865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.053
                                       HHHHHHHHHHHHHHHHHHH CS
                        ABC_cobalt   3 iilvavigvvfGviflawg 21 
                                       +i+v++i+v  G+++ a+ 
  gi|320100385|ref|YP_004175977.1| 146 VIVVSAIAVS-GALYGAIA 163
                                       7888888876.66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1405.35
//
Query:       gi|320100386|ref|YP_004175978.1|  [L=281]
Description: TatD-like deoxyribonuclease [Desulfurococcus mucosus DSM 2162]
Scores for 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   69.4   0.0    3.5e-19   69.2   0.0    1.0  1  TatD_DNase  TatD related DNase


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 !   69.2   0.0     2e-23   3.5e-19       2     254 ..       5     277 ..       4     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 2e-23
                                       EEEE-TTS.CCCTTTHHHHHHHHHHTTEEEEEEE-SSG.................GGHHHHHHHHTT.TTTEEEEE- CS
                        TatD_DNase   2 DaHcHlds.kefeedreeileraeeagvaavvvvgtss.................kdskavlelakkypnkvyavlG 60 
                                       DaH H++  k +   + ++ er++++g+  ++ v + +                 +  ++  ++a+++  +v   +G
  gi|320100386|ref|YP_004175978.1|   5 DAHLHTNPvKGM--GASRVSERFKREGGWFMALVALPPyhygieevgvdsyrrvlEILNREAQVARSHGLRVARLMG 79 
                                       9*******7776..555555***********977777777777777777788877788899999999********** PP

                                       --GGGGGC............C.CCHHHHHHHH..HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHT CS
                        TatD_DNase  61 iHPnevde............asedlleelkel..anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkel 123
                                       +HP+e+de            +   l   + +l  + +k     +iGe+G+ +y ++ +     e+v+ + l++ +e+
  gi|320100386|ref|YP_004175978.1|  80 LHPAEIDEyyrrgvkgrklyE---LASSVLDLirSALKAGLLDGIGEVGRQHYATSVERIVLSEMVMMNALEISREY 153
                                       ********9999987764431...3344433334448***************99999999***************** PP

                                       TEEEEEEEES...-HHHHHHHHHHCGGCCS.EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS- CS
                        TatD_DNase 124 klplviHlrk...aeedlleilkeaaeaka.kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavp 196
                                       + ++ +Hl++     +  +e l+++  +++ k+vlH+ s++   a++ l  g+  +++     k    ++e +++  
  gi|320100386|ref|YP_004175978.1| 154 DVVIHLHLEQggwVTAFSVERLRRLLVPGHgKIVLHHSSSETVLAAEEL--GLAYTIPV----K---GFDEKLASRR 221
                                       **********998777888999999999999******444444444444..44444443....3...3889999999 PP

                                       GGGEEE---TTSSEECCCTT.SE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 197 ldrlLiETDaPyltpkpyrg.krnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                         + ++E+D  ++++ p r+ ++ +p+ +++v++   e   +++e +++i+ eN+ r++
  gi|320100386|ref|YP_004175978.1| 222 PVNAMVESD--FIDD-PERPgAAAYPWEIPRVLKGQLERGVIDEEYVYRIMVENITRYY 277
                                       9999*****..8988.99999***********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2154.26
//
Query:       gi|320100387|ref|YP_004175979.1|  [L=87]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   27.8  25.7     0.0034   17.5   8.2    3.9  4  zf-B_box       B-box zinc finger
     0.0001   22.1   4.8     0.0001   22.1   4.8    4.7  3  zf-HIT         HIT zinc finger
  ------ inclusion threshold ------
      0.079   13.1   1.7      0.079   13.1   1.7    4.1  4  zf-AN1         AN1-like Zinc finger
       0.26   11.5  32.8        3.5    7.8   6.2    4.1  2  FYVE           FYVE zinc finger
        4.5    7.8  25.5      7e+02    0.8  25.5    2.5  1  zf-CHY         CHY zinc finger


Domain annotation for each model (and alignments):
>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.3   1.9e-06    0.0068       4      28 ..       1      25 [.       1      25 [. 0.94
   2 !    9.6   2.4   0.00027      0.97      16      29 ..      32      45 ..      28      49 .. 0.84
   3 !   17.5   8.2   9.4e-07    0.0034       3      31 ..      39      67 ..      37      72 .. 0.88
   4 ?    3.1   0.4      0.03   1.1e+02      15      21 ..      73      79 ..      69      83 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                          zf-B_box  4 tkCpeHknkpatlfCedCqqplCee 28
                                      +kC+++++++a + C+ C+  +C +
  gi|320100387|ref|YP_004175979.1|  1 MKCEICGEREAVYTCRLCGRRVCGD 25
                                      58*********************85 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00027
                          zf-B_box 16 lfCedCqqplCeeC 29
                                        C++C++ +Ce C
  gi|320100387|ref|YP_004175979.1| 32 GVCKVCSEAMCEIC 45
                                      57************ PP

  == domain 3  score: 17.5 bits;  conditional E-value: 9.4e-07
                          zf-B_box  3 etkCpeHknkpatlfCedCqqplCeeCst 31
                                      e +C++++++ a+ +C+ C+   Ce+C+ 
  gi|320100387|ref|YP_004175979.1| 39 EAMCEICGRQLAIGYCKYCGRIGCEDCLI 67
                                      679************************43 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.03
                          zf-B_box 15 tlfCedC 21
                                      ++ C+dC
  gi|320100387|ref|YP_004175979.1| 73 EYVCKDC 79
                                      5666666 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   4.8   2.8e-08    0.0001       4      24 ..       2      23 ..       1      24 [. 0.95
   2 ?    1.4   0.7     0.084     3e+02       3       9 ..      32      38 ..      31      41 .. 0.79
   3 ?   -9.4  15.7         5   1.8e+04       5      19 ..      42      57 ..      38      84 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.8e-08
                                      B-TTT-S.B-SEE-TTT--EES CS
                            zf-HIT  4 lCgvCgf.pakYkCpkCntryC 24
                                      +C++Cg+ +a Y+C+ C+ r+C
  gi|320100387|ref|YP_004175979.1|  2 KCEICGErEAVYTCRLCGRRVC 23
                                      7********************* PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.084
                                      -B-TTT- CS
                            zf-HIT  3 klCgvCg 9 
                                      ++C vC 
  gi|320100387|ref|YP_004175979.1| 32 GVCKVCS 38
                                      5799997 PP

  == domain 3  score: -9.4 bits;  conditional E-value: 5
                                      -TTT-S.B-SEE-TTT CS
                            zf-HIT  5 CgvCgf.pakYkCpkC 19
                                      C++Cg   a   C  C
  gi|320100387|ref|YP_004175979.1| 42 CEICGRqLAIGYCKYC 57
                                      7777764333333333 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.7   2.2e-05     0.079       1      25 [.       3      24 ..       2      26 .. 0.88
   2 ?    3.1   1.5      0.03   1.1e+02      12      25 ..      30      43 ..      25      47 .. 0.80
   3 ?    0.8  10.6      0.16   5.8e+02       1      27 [.      42      65 ..      34      70 .. 0.77
   4 ?    4.2   3.2     0.014        50       1      27 [.      62      87 .]      61      87 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                            zf-AN1  1 CsfksCkkkdflpfkCryCgkvFCl 25
                                      C++  C++++  +++Cr Cg++ C 
  gi|320100387|ref|YP_004175979.1|  3 CEI--CGEREA-VYTCRLCGRRVCG 24
                                      775..**9997.8***********7 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.03
                            zf-AN1 12 lpfkCryCgkvFCl 25
                                      + + C+ C++  C+
  gi|320100387|ref|YP_004175979.1| 30 VKGVCKVCSEAMCE 43
                                      5578****999997 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.16
                            zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkH 27
                                      C++  C++++  ++ C+yCg+  C+++
  gi|320100387|ref|YP_004175979.1| 42 CEI--CGRQLA-IGYCKYCGRIGCEDC 65
                                      443..666664.79*******999876 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.014
                            zf-AN1  1 CsfksCkkkdflp.fkCryCgkvFClkH 27
                                      C+  +C  +++++ + C++C  ++ lkH
  gi|320100387|ref|YP_004175979.1| 62 CE--DCLIQVSTVeYVCKDCAFKYRLKH 87
                                      44..6777777777*******9998888 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.2   0.00098       3.5      11      37 ..       2      24 ..       1      32 [. 0.81
   2 ?    2.5  18.4     0.044   1.6e+02      10      46 ..      40      72 ..      28      85 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00098
                                      B-TTT--B--SSS--EE-TTT--EE-S CS
                              FYVE 11 kCeiCakkFsllrrrhhCrlCGkvvCe 37
                                      kCeiC ++  +    + CrlCG+ vC 
  gi|320100387|ref|YP_004175979.1|  2 KCEICGEREAV----YTCRLCGRRVCG 24
                                      68888887766....78*********6 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.044
                                      SB-TTT--B--SSS--EE-TTT--EE-STTS-EEE.E CS
                              FYVE 10 kkCeiCakkFsllrrrhhCrlCGkvvCekCssklval 46
                                      + CeiC ++  +     +C+ CG++ Ce+C  + +++
  gi|320100387|ref|YP_004175979.1| 40 AMCEICGRQLAI----GYCKYCGRIGCEDCLIQVSTV 72
                                      345555555544....69************9776644 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8  25.5       0.2     7e+02      12      73 ..       2      80 ..       1      82 [. 0.59

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                            zf-CHY 12 rapcCkk...lyaCreCHeeledhelerl.....evkevlcllCeteqekavlCkkCkk..........efaeyfCpiC 72
                                      +++ C +   +y+Cr C ++++ ++ + +       +e +c  C + q +   Ck C++          ++ ey+C+ C
  gi|320100387|ref|YP_004175979.1|  2 KCEICGEreaVYTCRLCGRRVCGDDYDSVkgvckVCSEAMCEICGR-QLAIGYCKYCGRigcedcliqvSTVEYVCKDC 79
                                      56666544449*******7655554444311111334455666665.45556677776677777777766777778877 PP

                            zf-CHY 73 k 73
                                       
  gi|320100387|ref|YP_004175979.1| 80 A 80
                                      6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 593.49
//
Query:       gi|320100388|ref|YP_004175980.1|  [L=331]
Description: AIR synthase-like protein domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-17   62.7   1.4    8.3e-17   61.7   1.4    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.1e-12   48.4   1.0    5.5e-12   46.2   0.3    2.1  2  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   1.4   9.3e-21   8.3e-17       1     155 [.     150     307 ..     150     308 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 9.3e-21
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHH...HTTECEEEE--TTHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaal...kglvkaahDvTgGGLl 73 
                                       ++Gd ++ +g +G  gag   ++   ++e+l +  +v++    + +  iy + +   +   k+ v+ +hD T+GG++
  gi|320100388|ref|YP_004175980.1| 150 REGDHVVIIGRIGGEGAG-VIAW---DFEDLLLGkGVPENIIKRAKGFIYDVSIVKTAlavKDYVNTMHDATEGGVI 222
                                       689********9999999.4445...455555556888999999999999998888888889*************** PP

                                       HHHHHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEE CS
                            AIRS_C  74 galaemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGev 145
                                        al e+a asg  + +d+d+ +i +e+e      +  +l+  +sG  + +vpp + da+l+ l+  g+  ++v+G+v
  gi|320100388|ref|YP_004175980.1| 223 QALREVASASGKDIIVDADAFQIEKEVEeisqrIGVNPLRLLSSGCIVASVPPGNLDALLSRLRGLGV-GFSVVGHV 298
                                       *******************9999999999999999*********************************.6******* PP

                                       EESSSEEEEE CS
                            AIRS_C 146 takeelsviv 155
                                       ++++ ++viv
  gi|320100388|ref|YP_004175980.1| 299 VKGG-GRVIV 307
                                       **97.55555 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 !   46.2   0.3   6.1e-16   5.5e-12       1      93 [.      34     138 ..      34     139 .. 0.83
   2 ?    0.2   0.0      0.14   1.2e+03      18      60 ..     210     254 ..     191     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 6.1e-16
                                       SSSEE........EEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHH CS
                              AIRS   1 dDaav........vvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevv 59 
                                       +Daav        v+++d      +     +    +G++av+v+ +D+a+ G  P++++ +  +p      ++ee++
  gi|320100388|ref|YP_004175980.1|  34 EDAAVlrlrdgflVAHVD-----PIT----TgvrkAGYLAVHVAGNDIAVRGVAPRWFMPVTLIPahyseaDVEELF 101
                                       588843333333355555.....333....244447************************99999************ PP

                                       HHHHHHHHHTT-EEEEEEEEEESS...EEEEEEEEEE CS
                              AIRS  60 rglaeaaeelgvplvgGdtsfsne...ptisvtavGl 93 
                                       r++++a++e+g   +gG+t+++++   p+i++ta+G 
  gi|320100388|ref|YP_004175980.1| 102 RDMGAALREIGGVAIGGHTEVTPGldrPIIAMTAIGY 138
                                       *********************999999********96 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                                       CTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHH CS
                              AIRS  18 vepvhfiGakavavnlsDlaamGArPlalllslalp...wleevvr 60 
                                       v+ +h +++ +v ++l+ +a+  ++ +  +++ a++   ++ee+ +
  gi|320100388|ref|YP_004175980.1| 210 VNTMHDATEGGVIQALREVASASGKDII-VDADAFQiekEVEEISQ 254
                                       3444446777999999999988888885.66666655577777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2513.22
//
Query:       gi|320100389|ref|YP_004175981.1|  [L=170]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.032   14.8   0.1        7.1    7.3   0.0    2.1  2  Syntaxin-6_N   Syntaxin 6, N-terminal
      0.048   13.1   0.1       0.12   11.8   0.1    1.7  1  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller


Domain annotation for each model (and alignments):
>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0023        21      11      66 ..       9      63 ..       3      82 .. 0.73
   2 ?    7.3   0.0   0.00079       7.1      36      56 ..     139     159 ..      99     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0023
                      Syntaxin-6_N 11 qkslnkaeslyrrwe.rlledtssstseeldetrteLrkalrsiewdledLeetvri 66
                                        +++++++l r+ + r+  ++s++   +  +t + L + ++si   l+ Le+  ++
  gi|320100389|ref|YP_004175981.1|  9 DRAVKSLNTLSRNIRsRV--LGSQELDAKTASTASHLVEIIESIAVSLQRLENKLKT 63
                                      567777777777774243..3334457889999999999999999999999987755 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00079
                      Syntaxin-6_N  36 seeldetrteLrkalrsiewd 56 
                                        ++++  r+eL++alrs+e+ 
  gi|320100389|ref|YP_004175981.1| 139 IDDYKAKRNELKNALRSLEKV 159
                                       6789999***********975 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 ?   11.8   0.1   1.4e-05      0.12      12      44 ..      70     100 ..      69     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                                       EEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEE CS
                     DNA_gyraseA_C  12 vkrfplselpeqgRgakGvkgiklkegdklvsv 44 
                                       v+r+  +++  +gRg  Gv +++++++  + sv
  gi|320100389|ref|YP_004175981.1|  70 VVRLAPYTYVITGRG--GVVLMRTRPEYIILSV 100
                                       789999*********..*******998766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1265.31
//
Query:       gi|320100390|ref|YP_004175982.1|  [L=208]
Description: conserved protein implicated in secretion [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00066   19.3   1.9     0.0018   17.9   1.9    1.8  1  Snf7          Snf7
  ------ inclusion threshold ------
      0.027   14.1   0.7      0.044   13.4   0.7    1.3  1  DUF4125       Protein of unknown function (DUF4125)
      0.051   13.3   0.3       0.16   11.6   0.0    2.0  2  Sigma70_r4_2  Sigma-70, region 4
      0.059   13.6   0.1       0.13   12.4   0.1    1.6  1  DUF5388       Family of unknown function (DUF5388)
        0.1   12.6   0.8        0.2   11.6   0.8    1.4  1  HisK_N        Histidine kinase N terminal
       0.15   12.1   0.9       0.35   10.9   0.4    1.9  2  LOH1CR12      Tumour suppressor protein
        1.2    9.5   3.7        1.4    9.3   0.1    2.4  2  DUF2175       Uncharacterized protein conserved in archaea (D


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.9     7e-07    0.0018       4      98 ..      34     135 ..      32     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                              Snf7   4 rsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaien.... 76 
                                        ++++a+ +++++ e+l ++  +l + + +   k+++ ra+ ++K+  +++k  +ql ++++ le ++l++e+    
  gi|320100390|ref|YP_004175982.1|  34 YRIKTAIGRISNYLEKLSDRDRELFEMIVESLTKKDELRAKMYAKEVAEIRKVSKQLLTVQYALEHAALKLETfiiy 110
                                       5899*******************************************************************973322 PP

                                       ...HHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7  77 ...lksnkevlnamkqgakamkamn 98 
                                           +    v+  m+++ +++k + 
  gi|320100390|ref|YP_004175982.1| 111 ggaVNEVAPVIGVMREAVNILKGVA 135
                                       2223555666777777777777665 PP

>> DUF4125  Protein of unknown function (DUF4125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   1.7e-05     0.044      66     133 ..      23      89 ..       8      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                           DUF4125  66 NllteKYarmmestapeeyekiedllpelseekeeliekIvkiqvewqeelakkYPklakkarklese 133
                                       + + eK a + ++  ++++ +i ++l++ls++ +el e Iv+  ++  e  ak Y+k ++++rk+ ++
  gi|320100390|ref|YP_004175982.1|  23 DPM-EKKAIIAQYRIKTAIGRISNYLEKLSDRDRELFEMIVESLTKKDELRAKMYAKEVAEIRKVSKQ 89 
                                       554.666888899999********************************************99998765 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 ?   11.6   0.0   6.3e-05      0.16       3      25 ..      42      63 ..      40      69 .. 0.84
   2 ?   -1.5   0.1      0.84   2.1e+03      30      41 ..      78      89 ..      77     104 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                                      HHHHHHTTS-HHHHHHHHHHHTS CS
                      Sigma70_r4_2  3 alrealaeLperqreifllryle 25
                                      ++ + l++L+ r+re f+++  e
  gi|320100390|ref|YP_004175982.1| 42 RISNYLEKLSDRDRELFEMIV-E 63
                                      67889**************84.4 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.84
                                      HHHHHHHT--HH CS
                      Sigma70_r4_2 30 kEIAellgiseg 41
                                      kE+Ae+ ++s +
  gi|320100390|ref|YP_004175982.1| 78 KEVAEIRKVSKQ 89
                                      788888777765 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.2e-05      0.13      42      69 ..      43      70 ..      29      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                           DUF5388 42 veslidsLsesdkkrfkkqleiLEekDa 69
                                      +++++++Ls+ d++ f+ ++e L +kD+
  gi|320100390|ref|YP_004175982.1| 43 ISNYLEKLSDRDRELFEMIVESLTKKDE 70
                                      4789***********************7 PP

>> HisK_N  Histidine kinase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   7.7e-05       0.2      11      70 ..      26      84 ..      22      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.7e-05
                                      CHHHHHHHHHCCS---TT-TTHHHHHHHHHHHHHHHHHHHTTSS-GGGGHHHHHHHHHHH CS
                            HisK_N 11 ekekfleewkkkilisdkDpykeevkeNgealfelviellkeeiseedlkelaekiakeR 70
                                      ek++++++++ k +i    +y e++    ++lfe+++e+l+++ +    k  a+ +a+ R
  gi|320100390|ref|YP_004175982.1| 26 EKKAIIAQYRIKTAIGRISNYLEKLSDRDRELFEMIVESLTKKDE-LRAKMYAKEVAEIR 84
                                      6889************************************98755.56688888888877 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00014      0.35      68     112 ..      61     106 ..      27     109 .. 0.77
   2 ?   -1.5   0.0      0.96   2.5e+03      64      84 ..     171     193 ..     151     198 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                          LOH1CR12  68 llaelrekqkqy.asyaealskvnelsdqlsriqiiledivpllEt 112
                                       ++++l +k +   + ya+++++++++s+ql  +q  le+    lEt
  gi|320100390|ref|YP_004175982.1|  61 IVESLTKKDELRaKMYAKEVAEIRKVSKQLLTVQYALEHAALKLET 106
                                       334445555544156***********************98888776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.96
                          LOH1CR12  64 kiitllae..lrekqkqyasyae 84 
                                       + +++l+e  ++++qk  +++ae
  gi|320100390|ref|YP_004175982.1| 171 EAKKVLEEarIVAEQKMKEKFAE 193
                                       44445543114566666666665 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.9      0.34   8.7e+02      58      89 ..      70     101 ..      32     109 .. 0.55
   2 ?    9.3   0.1   0.00055       1.4      45      91 ..     143     189 ..     129     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.34
                           DUF2175  58 eivklkelervaedeevkkvleqkrkelEkaa 89 
                                       e+  +  +++vae ++v k l +++  lE+aa
  gi|320100390|ref|YP_004175982.1|  70 ELRAKMYAKEVAEIRKVSKQLLTVQYALEHAA 101
                                       23333334444454555555555555666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00055
                           DUF2175  45 aaaLleleevlneeivklkelervaedeevkkvleqkrkelEkaaak 91 
                                       + a++ele+ + +++v l     v  d e+kkvle++r+ +E+++ +
  gi|320100390|ref|YP_004175982.1| 143 QYAVRELETAVGAGVVDLTTDIGVGMDSEAKKVLEEARIVAEQKMKE 189
                                       5678999*****************999***************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1229  (0.0685482); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1554.39
//
Query:       gi|320100391|ref|YP_004175983.1|  [L=100]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 786.41
//
Query:       gi|320100392|ref|YP_004175984.1|  [L=228]
Description: GTP cyclohydrolase III [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   18.1   0.0       0.12   11.6   0.0    2.1  2  GCH_III   GTP cyclohydrolase III


Domain annotation for each model (and alignments):
>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   6.9e-06      0.12      22     112 ..      26     117 ..       5     190 .. 0.74
   2 !    5.1   0.0   0.00064        12      83     117 ..     192     226 ..     179     228 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.9e-06
                                       HHHHHHHHHHHHHHHHHHHTTT-EEE-TTSS.EEEEE-TT--HHHHHHHHHHHHHHSSS-EEEEEEEESSHHHHHHH CS
                           GCH_III  22 adlqalqarlyadlqkelaardGlvfatRfD.nllaitngidleehkRiqesirnrypvtvsmgigaaetPldalea 97 
                                         l  l +r+   l+++l  ++G++f t  +   +a+tng+d e+h  ++ ++    p  v++++  a +P+ al  
  gi|320100392|ref|YP_004175984.1|  26 RRLNELFSRVEELLNNTLEPYGGIAFNTGVEgEYIALTNGVDREQHLDLLFKLDWETPHGVRVASLKASNPVVALLS 102
                                       45677777777788999999******99987479****************************************999 PP

                                       HHHHHHHH--TT-TT CS
                           GCH_III  98 aseaLreagsaqdee 112
                                        s+  r+ +  + ee
  gi|320100392|ref|YP_004175984.1| 103 SSSYFRRGERFLFEE 117
                                       888888766555554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.00064
                                       EEEEEESSHHHHHHHHHHHHHHH--TT-TT----E CS
                           GCH_III  83 mgigaaetPldaleaaseaLreagsaqdeeRkevl 117
                                       +gig +++ l+a ++a +aL++  +   eeR  vl
  gi|320100392|ref|YP_004175984.1| 192 VGIGVSQRGLNAYRNAVKALQRLLDGVAEERVCVL 226
                                       7899999999***********99999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1922.13
//
Query:       gi|320100393|ref|YP_004175985.1|  [L=606]
Description: glutamine--fructose-6-phosphate transaminase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-41  139.9   0.6    1.7e-26   92.6   0.7    2.3  2  SIS       SIS domain
    1.3e-13   51.3   0.0    2.6e-13   50.3   0.0    1.5  1  GATase_6  Glutamine amidotransferase domain
    2.4e-11   43.6   0.0    5.9e-11   42.3   0.0    1.6  1  GATase_7  Glutamine amidotransferase domain
    0.00094   19.2   1.3      0.002   18.2   0.9    1.7  1  SIS_2     SIS domain
  ------ inclusion threshold ------
       0.01   14.7   0.0      0.015   14.2   0.0    1.2  1  GATase_4  Glutamine amidotransferases class-II


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 !   92.6   0.7   4.8e-30   1.7e-26       2     130 ..     288     416 ..     287     417 .. 0.97
   2 !   44.9   0.0   2.7e-15   9.5e-12       8     126 ..     468     585 ..     466     588 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 4.8e-30
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelake 78 
                                       ++ a+ iy+++ G+s ++++ + ++++e++gi v  ++a+e+ ++vl +++ + ++i++s+sget+d+++++++ak+
  gi|320100393|ref|YP_004175985.1| 288 IHGARDIYIVANGSSLHAGMVATYYFNELAGISVTPVSAAEFPYSVLETVSTGSVIIAVSQSGETSDVINSVKQAKQ 364
                                       67899************************************************************************ PP

                                       TTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  79 rgakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                       rga i+++T++ gs la e+ + l i a+pe+ v++tks++a+ +a  +la+
  gi|320100393|ref|YP_004175985.1| 365 RGAVIVGVTNNVGSRLALESNVYLPIGAGPEIAVPATKSFSATVVAMLLLAM 416
                                       ********************999999999999*************9999875 PP

  == domain 2  score: 44.9 bits;  conditional E-value: 2.7e-15
                                       EEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEE.SSSHHHHHHHHHH.HHHHTTSE CS
                               SIS   8 iyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilis.fsgetkdlvaaae.lakergak 82 
                                        yv G+G  y+ia+e+alkl+e + i++e+ + +el+hg+l l+ ++ +vili  f + +k+l + +  + ++r+a 
  gi|320100393|ref|YP_004175985.1| 468 TYVAGSGITYPIALEGALKLKEAALIHAEGMQLGELRHGPLTLVGRGFPVILIEpFEDSAKSLYLKVArEIANRDAV 544
                                       69****************************************************999999998777777******** PP

                                       EEEEESSTTSHHHHHSSEEEEEEEECHC.SSSHCHHHHHHHHHHH CS
                               SIS  83 iiaITdskgsplareadlalyinaepet.lvastksltaqlaald 126
                                       ++aI  ++g    r     +yi +++   l++ + +l++ql+a+ 
  gi|320100393|ref|YP_004175985.1| 545 LLAISTESGPREGRG----IYIEVPARRhLYPVIVALPLQLLAYR 585
                                       ****96555444443....55555555556999999999999885 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   7.1e-17   2.6e-13      12     102 ..      66     165 ..      51     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 7.1e-17
                          GATase_6  12 devalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllalleelG... 85 
                                       ++++laH+R a++g ++ e  +P+   +gr+++v  G i+ny++ r++l++ +g+ +rsr+Dtev ++lle++    
  gi|320100393|ref|YP_004175985.1|  66 SNMVLAHTRYASRGWPVYENTHPLLDCTGRIAVVGDGIIDNYEDYRARLEK-EGHVLRSRTDTEVAAHLLEKYYrie 141
                                       569*************88777******************************.*****************94433333 PP

                          GATase_6  86 ....eevle...rlrGmfafaiwd 102
                                           ++vl+   +l+G ++ a++ 
  gi|320100393|ref|YP_004175985.1| 142 gdwlKAVLRvgaELKGLYSLAFMV 165
                                       345455553445888888777665 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.6e-14   5.9e-11      12     119 ..      85     196 ..      73     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.6e-14
                          GATase_7  12 gaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea......ewgeeal...erlnGmfA 79 
                                       +  P++ + +gr+++v +G i Ny++ r++Le++gh  r+++Dtev ++lle+      +w++++l    +l+G ++
  gi|320100393|ref|YP_004175985.1|  85 NTHPLL-DCTGRIAVVGDGIIDNYEDYRARLEKEGHVLRSRTDTEVAAHLLEKyyriegDWLKAVLrvgAELKGLYS 160
                                       567999.689*************************************************888888744479****** PP

                          GATase_7  80 faiwdeeekrlllaRDrlGikPLyygedkgdallfaSelk 119
                                       +a +    + +l +++    +PL +g  + + ++++S + 
  gi|320100393|ref|YP_004175985.1| 161 LAFMVLGVDGILFVQN---GQPLVIGMGS-HCVFLSSDIP 196
                                       9999877777777777...4788888885.5777777765 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.9   5.5e-07     0.002      97     137 ..     335     373 ..     325     374 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.5e-07
                                       HHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2  97 rlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                       +   +++g v++ +S+sG+   v++ +++ak+rg+ ++++t
  gi|320100393|ref|YP_004175985.1| 335 ET--VSTGSVIIAVSQSGETSDVINSVKQAKQRGAVIVGVT 373
                                       44..899*********************************9 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.3e-06     0.015      62     117 ..      57     110 ..      31     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-06
                          GATase_4  62 elvreypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpk 117
                                       + v   +i s++v+aH R a++G   +enthp      gr  +   +G +++y+++
  gi|320100393|ref|YP_004175985.1|  57 KQVDLEDIPSNMVLAHTRYASRGWPVYENTHPLLD-CTGRIAVV-GDGIIDNYEDY 110
                                       333334699***********************864.44554443.35555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4326.36
//
Query:       gi|320100394|ref|YP_004175986.1|  [L=368]
Description: tryptophanyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-46  157.9   0.0    7.8e-46  156.7   0.0    1.4  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.058   12.3   0.0       0.25   10.2   0.0    2.0  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.7   0.0   8.7e-50   7.8e-46       3     291 ..      63     342 ..      61     343 .. 0.88

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 8.7e-50
                                       HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHT CS
                      tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakg 79 
                                        ++++v++G++P+g++HlG  ++ + l+ lq+ g +v ++iaD++A+i++ +  e  ++ kr  ++ +     +a g
  gi|320100394|ref|YP_004175986.1|  63 GEKVAVLTGFMPSGRPHLGTAMVYEELRFLQSLGAHVKIVIADAEAYIVRRE--ERSDVVKRGVDFIAH---AIAWG 134
                                       57899***********************************************..677788888888888...9**** PP

                                       CHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.... CS
                      tRNA-synt_1b  80 ldpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.... 152
                                       +dpekae+++q+++ +  e+  l++++++ +s+++m ++     +l      + g +   l qaaDil+l+ d    
  gi|320100394|ref|YP_004175986.1| 135 IDPEKAEFYYQTAMDN--EYYRLIQMFSRKISMAEMEAIYG---EL------TPGKIVASLTQAADILHLQLDkygg 200
                                       ***********98765..67777777777777777766666...23......3344444455777777777777777 PP

                                       ....EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHC CS
                      tRNA-synt_1b 153 ....lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqka 225
                                           +vp+G DQ+ +++l+rdla+rf+++  +k p++++++ll gldG  KmSKS ++ aI Ldd+++ ++kk  +a
  gi|320100394|ref|YP_004175986.1| 201 yrhvVVPVGADQDPHLRLTRDLADRFEQELGLKRPSSIYHKLLRGLDGN-KMSKSRPEFAIHLDDDPDLAEKKLLNA 276
                                       7777*********************************************.*************************** PP

                                       HCSTTC..SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 226 vtdsde..evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnel 291
                                       +t  ++  + ++ l + +  +  ++e + +++  ++ +e+ e++ e+vt++v +g++k+++ e l+++
  gi|320100394|ref|YP_004175986.1| 277 LTGGRAtaDEQRRLGGEPWKCS-IYELYVYHLVGDD-SELREVYDECVTGRVLCGQCKRRAVERLKRR 342
                                       ****998888888888888888.9999999999998.9***********************9998876 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   2.8e-05      0.25      21      43 ..      62      84 ..      56     198 .. 0.70
   2 ?   -1.3   0.0      0.09   8.1e+02     260     288 ..     229     257 ..     218     279 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.8e-05
                      tRNA-synt_1f 21 ekdevvvesGispSGliHiGnlr 43
                                      + ++v v +G  pSG++H+G++ 
  gi|320100394|ref|YP_004175986.1| 62 HGEKVAVLTGFMPSGRPHLGTAM 84
                                      457999**************963 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.09
                      tRNA-synt_1f 260 ilggeaPekvvYelillkggekmssSkGn 288
                                        lg ++P ++   l+    g+kms+S+ +
  gi|320100394|ref|YP_004175986.1| 229 ELGLKRPSSIYHKLLRGLDGNKMSKSRPE 257
                                       578899999999999888888*****865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2624.67
//
Query:       gi|320100395|ref|YP_004175987.1|  [L=137]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0012   19.0   0.0     0.0016   18.6   0.0    1.2  1  HSP20       Hsp20/alpha crystallin family
     0.0063   16.1   0.0      0.021   14.4   0.0    1.8  2  ArsA_HSP20  HSP20-like domain found in ArsA


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 !   18.6   0.0   1.8e-07    0.0016       4      88 ..      43     130 ..      40     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-07
                                       SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..--.-TT----SS---EEEEEE--STTB-TTT.-EEEE.E CS
                             HSP20   4 eeeeefevkldvpglkkeelkvkvednrvlvkgeheeeee.dekglikerssrkFsrkftLPenvdadk.vkasl.k 77 
                                       + ++++ev +d+p  + + l v+++d+r++v+   +e+   ++  ++++ + r ++ +++LP +v +++ v  +  +
  gi|320100395|ref|YP_004175987.1|  43 QYPDRYEVIIDMPLADLSVLSVSIRDQRLTVECALREKIRfERWSVHRSVEHRAYRLELRLPPDVIPEEaVVEKSeA 119
                                       56899***************************9998444404444455578899*********98665414333346 PP

                                       TTEEEEEEEBS CS
                             HSP20  78 dGvLtvtvpkk 88 
                                       + + +v +p++
  gi|320100395|ref|YP_004175987.1| 120 KSMIRVRIPRR 130
                                       67777777765 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 !   14.4   0.0   2.3e-06     0.021       2      33 ..      46      87 ..      45     114 .. 0.81
   2 ?   -0.2   0.0     0.085   7.6e+02       4      20 ..      97     114 ..      94     130 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-06
                        ArsA_HSP20  2 deyvlkldLPfvdkeeidlsrsgdeLtIkig..........n 33
                                      d+y++ +d+P +d + +++s++++ Lt+++           +
  gi|320100395|ref|YP_004175987.1| 46 DRYEVIIDMPLADLSVLSVSIRDQRLTVECAlrekirferwS 87
                                      89***************************9877777666663 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.085
                        ArsA_HSP20   4 yvlkldLP.fvdkeeidl 20 
                                       y+l l+LP  v +ee  +
  gi|320100395|ref|YP_004175987.1|  97 YRLELRLPpDVIPEEAVV 114
                                       888888872345555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1060.20
//
Query:       gi|320100396|ref|YP_004175988.1|  [L=260]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  109.3   0.1    3.1e-31  109.1   0.1    1.1  1  PAC2         PAC2 family
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.29   10.8   0.0    1.4  1  DNase-RNase  Bifunctional nuclease


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 !  109.1   0.1   3.4e-35   3.1e-31       1     209 [.      31     233 ..      31     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 3.4e-35
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEE.TTT.SEEEEEEE.E CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyak.dsgsrdllvlqg.r 75 
                                       Lil fp++G+V ++a ++L+ s ++  vgeid ++ l      ++ +v++gr ++p+++y++    sr l+vl   +
  gi|320100396|ref|YP_004175988.1|  31 LILSFPDTGLVSSIAGRHLVVSEGFSIVGEIDAPS-LS-----HISVVHNGRAVSPIQIYYSeA--SRILMVLSEvP 99 
                                       89*********************************.99.....99999999********99954..45555555575 PP

                                       -HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHH.HHH..HCT-CEEEEHHHHH CS
                              PAC2  76 epilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeell.eel..eeseyggivgitgl 149
                                        p +    +++ +l ++  lg + vv+++gl+  +r    + ++  v++ +t e +  +el  ee ++g+i+g+ ++
  gi|320100396|ref|YP_004175988.1| 100 LPLGIMHPLIDSILTYLHGLGMENVVTVSGLAVPNRF---ELEKPNVFLLSTGEWRGlKELgfEELKEGFITGPYAA 173
                                       55555558************************99884...44455899999888777566644477*********** PP

                                       HHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHH CS
                              PAC2 150 LlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeql 209
                                       L+++a++rg++a+++++e+   +pdP++aa+ l++lsk++glevd+++L+++ae l+ ++
  gi|320100396|ref|YP_004175988.1| 174 LMKEARRRGVNALVIFVESFYDIPDPESAAVGLQALSKVTGLEVDVSRLISEAELLKLKM 233
                                       ******************************************************998766 PP

>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.2e-05      0.29      22      69 ..      74     122 ..      65     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                                       TSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHT.TEEEE CS
                       DNase-RNase  22 egrrvlpIwigaaeaqaialalegeeppRPlthDLlaslleal.gakve 69 
                                       +gr v pI i  +ea+ i + l++++ p  + h L+ s+l+ l g+ +e
  gi|320100396|ref|YP_004175988.1|  74 NGRAVSPIQIYYSEASRILMVLSEVPLPLGIMHPLIDSILTYLhGLGME 122
                                       567789*********************************9987344555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2063.98
//
Query:       gi|320100397|ref|YP_004175989.1|  [L=132]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for 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  168.4   2.8    5.9e-50  168.2   2.8    1.0  1  DUF2153   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
       0.12   12.4   1.4       0.75    9.9   0.2    2.4  2  VPR       VPR/VPX protein


Domain annotation for each model (and alignments):
>> DUF2153  Uncharacterized protein conserved in archaea (DUF2153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.2   2.8   6.6e-54   5.9e-50       1     117 [.       7     123 ..       7     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 6.6e-54
                           DUF2153   1 nLeeWvkeqkelletlkkvekkveeaDRLdlilasraafqhmmrtlkaFdqWLqdPviishmpremLldvketlrei 77 
                                       nL++Wvk+q+++ e +k +e+++ee DRL li+ sr+afqhm +t++aFdqWL+dP+i+shmpremL++++++lr i
  gi|320100397|ref|YP_004175989.1|   7 NLDSWVKRQNTVREMFKRAEQNYEELDRLALITLSRLAFQHMEKTIEAFDQWLKDPMITSHMPREMLVELWSRLRVI 83 
                                       79*************************************************************************** PP

                           DUF2153  78 lekllelDieHtsevrelleklskegklnpllalekeaee 117
                                       l++l+elDi+Hts+++e+l+kl+ e+ +npl+a+eke +e
  gi|320100397|ref|YP_004175989.1|  84 LYELIELDIDHTSKFSEHLKKLAAENAINPLFAFEKEEKE 123
                                       **********************************996655 PP

>> VPR  VPR/VPX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.046   4.1e+02      10      33 ..      14      36 ..       6      52 .. 0.46
   2 ?    9.9   0.2   8.3e-05      0.75      12      48 ..      49      79 ..      43      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.046
                               VPR 10 ieepqrEpfdeWleetleeikeeA 33
                                       +++ rE f +  e+  ee+++ A
  gi|320100397|ref|YP_004175989.1| 14 RQNTVREMF-KRAEQNYEELDRLA 36
                                      344444444.33333334443333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.3e-05
                               VPR 12 epqrEpfdeWleetleeikeeAvkHfprelliavwny 48
                                      e + E+fd+Wl++ +         H+pre+l+++w +
  gi|320100397|ref|YP_004175989.1| 49 EKTIEAFDQWLKDPM------ITSHMPREMLVELWSR 79
                                      56779*******977......468***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1055.05
//
Query:       gi|320100398|ref|YP_004175990.1|  [L=158]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   16.7   0.0     0.0098   16.1   0.0    1.3  1  DapH_N    Tetrahydrodipicolinate succinyltransferase N-termin


Domain annotation for each model (and alignments):
>> DapH_N  Tetrahydrodipicolinate succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.5e-07    0.0098      31      77 ..     107     153 ..      95     158 .] 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.5e-07
                                       C----TTSEEEE-SSEEEEEEEHHHHHHHHHHTTTTEEEEEEEE--B CS
                            DapH_N  31 elefpeevkvfgsedsgvvfGdwkeieevleenkdkiedyevendrR 77 
                                       +l  + + k f ++++g++ Gd+++i+++ ++ k ki  ++ve+d +
  gi|320100398|ref|YP_004175990.1| 107 KLVATGSGKEFLDSHMGIIGGDAENIRKLFNDLKPKIAPLDVEVDVK 153
                                       33334677899***************************999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1192.42
//
Query:       gi|320100399|ref|YP_004175991.1|  [L=273]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2051.06
//
Query:       gi|320100400|ref|YP_004175992.1|  [L=450]
Description: TBP-interacting protein TIP49 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-142  472.8   0.8   9.8e-142  472.3   0.8    1.2  1  TIP49            TIP49 P-loop domain
    3.2e-27   94.5   1.6    1.3e-26   92.5   1.3    2.3  1  TIP49_C          TIP49 AAA-lid domain
      2e-12   47.7   2.0    4.7e-09   36.8   0.1    2.9  2  AAA              ATPase family associated with various cellul
    2.6e-09   37.0   0.8    8.9e-07   28.8   0.1    2.9  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.5e-08   32.7   0.2    0.00038   20.7   0.0    2.7  2  AAA_22           AAA domain
    5.8e-07   30.1   1.1    6.7e-06   26.6   1.1    2.4  1  AAA_16           AAA ATPase domain
    3.7e-05   23.7   0.1    0.00025   21.0   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00014   22.4   0.0    0.00051   20.6   0.0    2.0  1  AAA_18           AAA domain
    0.00015   21.8   0.3      0.036   14.1   0.1    2.5  2  TFIID-31kDa      Transcription initiation factor IID, 31kD su
    0.00018   21.1   0.0     0.0023   17.5   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
    0.00028   20.5   0.7     0.0015   18.1   0.2    2.1  2  AAA_25           AAA domain
     0.0005   19.5   0.6      0.002   17.5   0.1    2.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00059   19.3   0.0      0.002   17.5   0.0    1.8  2  DnaB_C           DnaB-like helicase C terminal domain
     0.0007   19.4   0.1     0.0015   18.3   0.1    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0015   18.8   1.6       0.03   14.7   1.6    2.3  1  AAA_19           AAA domain
      0.004   17.4   0.1      0.015   15.6   0.1    2.0  1  AAA_28           AAA domain
     0.0043   17.2   0.1     0.0089   16.2   0.1    1.7  1  AAA_33           AAA domain
     0.0052   16.5   0.2       0.19   11.5   0.1    2.3  2  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.024   14.6   0.0    1.5  1  NACHT            NACHT domain
      0.016   14.7   0.1      0.033   13.6   0.1    1.6  1  PhoH             PhoH-like protein
      0.017   15.6   0.1      0.099   13.1   0.0    2.3  2  AAA_17           AAA domain
      0.019   15.4   0.0      0.038   14.4   0.0    1.5  1  RNA_helicase     RNA helicase
      0.025   14.4   0.0      0.052   13.3   0.0    1.5  1  AAA_11           AAA domain
      0.026   13.8   0.0      0.056   12.7   0.0    1.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.026   13.8   0.0      0.055   12.7   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.027   14.2   0.4       0.46   10.2   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
      0.041   14.4   0.0      0.083   13.4   0.0    1.5  1  ABC_tran         ABC transporter
      0.044   13.8   0.0      0.092   12.8   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.053   13.5   0.1       0.56   10.2   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
      0.055   13.6   0.1       0.19   11.8   0.0    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.063   13.0   0.1        0.6    9.8   0.1    2.5  3  AAA_24           AAA domain
      0.088   11.6   1.3        7.6    5.2   0.3    2.3  2  AAA_32           AAA domain
       0.13   12.3   0.0        2.9    7.9   0.0    2.4  2  AAA_14           AAA domain
       0.13   11.4   0.1       0.37    9.8   0.0    1.8  2  Parvo_NS1        Parvovirus non-structural protein NS1
        2.2    8.6   4.8       0.94    9.7   0.2    2.9  2  PCP_red          Proto-chlorophyllide reductase 57 kD subunit


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 !  472.3   0.8  1.9e-144  9.8e-142       1     350 [.      13     362 ..      13     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 472.3 bits;  conditional E-value: 1.9e-144
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49   1 rislhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelged 77 
                                       ris+hshi gLGlde+g+a+ + +glvGq++areaag++v++i+e+++aGr++Ll+Gp+gtGktala+ai++elge+
  gi|320100400|ref|YP_004175992.1|  13 RISAHSHIMGLGLDEKGKAKMVGDGLVGQTEAREAAGIVVKMIREGRIAGRGILLVGPPGTGKTALAVAIARELGEE 89 
                                       89*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-...TTS--EEEEEE-SS-E CS
                             TIP49  78 vpfvalsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenpls.kekkikevkitlktakee 153
                                       +pfv++sgsevys+e kkte+l++alrk++gv+++e ++v+eG v e+++ +a++p+  + +   e++i+l t +ee
  gi|320100400|ref|YP_004175992.1|  90 TPFVIMSGSEVYSTEKKKTEILMEALRKALGVKLREVRKVYEGVVKEVKIRRARHPMVpYLTVPVEARIVLATRDEE 166
                                       ********************************************************99899999************* PP

                                       EEEEE-HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS..------S--------S---S----XXXXXXXXX CS
                             TIP49 154 kklklgskiaeellkekvkegDviviekesGkvkklGrsear..akefDiekdefvelPkGevekkkevvqevtLhd 228
                                         l++ +++++++l+  v++gDvi i++e+G+v+++Grs++   a+++D+e++++ve+PkG v+k+ke+v+ +tLhd
  gi|320100400|ref|YP_004175992.1| 167 LALTVPEEVTQQILEIGVRKGDVIWIDAETGRVHRVGRSREVegARTYDVETKRIVEVPKGPVKKEKEIVNVLTLHD 243
                                       ***************************************97622689****************************** PP

                                       XXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 229 lDvanarpqdllslllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnralese 305
                                       lD++ a +++++s +     + ++ei +++r++++++v+k+++e kaei+pGvlfiD++hmlDie+fs+l ra+ese
  gi|320100400|ref|YP_004175992.1| 244 LDAIYAAQRSMISFF---GLTFEREIPSEVRRQVDETVKKWIDEKKAEIIPGVLFIDDAHMLDIEAFSFLTRAMESE 317
                                       ***************...4556789**************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 306 laPivilatnrgiakirGtdiisphGipvDlldrlliiktekytk 350
                                       +aPi+ilatnrgia+irGtdi+sphG+p+Dlldrllii t++yt 
  gi|320100400|ref|YP_004175992.1| 318 FAPILILATNRGIARIRGTDIESPHGMPLDLLDRLLIIPTRPYTP 362
                                       *******************************************86 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   1.3   2.6e-29   1.3e-26       1      66 []     368     433 ..     368     433 .. 1.00

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 2.6e-29
                           TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                       I+kiRa eE+v++++eAl++L++ig++tSLRYa+qLl+pa+i+a+ r++++++vedve++ +LF+D
  gi|320100400|ref|YP_004175992.1| 368 IIKIRASEEEVNISSEALEKLVEIGSKTSLRYAVQLLEPARIIAEERGSDRIDVEDVEKARKLFID 433
                                       9****************************************************************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 !   36.8   0.1   9.2e-12   4.7e-09       1      38 [.      65     118 ..      65     140 .. 0.74
   2 !    9.2   0.1    0.0029       1.5      27     111 ..     255     328 ..     244     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 9.2e-12
                                       EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS..............S CS
                               AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellsk..............y 38 
                                       +ll+GppGtGKT+la a+a+elg  ++f+ +sgse+ s                
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIARELGeeTPFVIMSGSEVYSTekkkteilmealrkA 118
                                       69********************76799**********44233333333333333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0029
                                       EEEETTTCSSSSTTHHHHHHHHHHHH.HHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                               AAA  27 leisgsellskyvgesekkirelfke.akeka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                       +++ g ++  ++ +e  +++ e++k+ + ek+    p +lfiD+++ l  +             + L ++++ +   
  gi|320100400|ref|YP_004175992.1| 255 ISFFGLTFEREIPSEVRRQVDETVKKwIDEKKaeiIPGVLFIDDAHMLDIEA-----------FSFLTRAMESEFA- 319
                                       4455555555566677777777777744444446788*********995555...........8888888888877. PP

                                       SSTEEEEEEESS CS
                               AAA 100 eskvivigatnr 111
                                           i+i+atnr
  gi|320100400|ref|YP_004175992.1| 320 ---PILILATNR 328
                                       ...388888888 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   1.7e-09   8.9e-07       9      61 ..      38      90 ..      31     126 .. 0.88
   2 ?   -2.1   0.0       5.5   2.8e+03      82      99 ..     184     205 ..     169     235 .. 0.75
   3 ?    5.6   0.0     0.024        12      87     117 ..     293     323 ..     286     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.7e-09
                            RuvB_N  9 yigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl 61
                                       +gq++ +e   i+++  ++ + a   +ll+GpPG Gkt+la  ia+elg + 
  gi|320100400|ref|YP_004175992.1| 38 LVGQTEAREAAGIVVKMIREGRIAGRGILLVGPPGTGKTALAVAIARELGEET 90
                                      79***********************************************9764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.5
                            RuvB_N  82 leekdvlfid....eihrlsra 99 
                                       ++++dv++id     +hr+ r+
  gi|320100400|ref|YP_004175992.1| 184 VRKGDVIWIDaetgRVHRVGRS 205
                                       6789999999533336776554 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.024
                            RuvB_N  87 vlfideihrlsraveevlysamedfrldivi 117
                                       vlfid+ h l+ ++  +l  ame     i+i
  gi|320100400|ref|YP_004175992.1| 293 VLFIDDAHMLDIEAFSFLTRAMESEFAPILI 323
                                       9**********************87666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   7.4e-07   0.00038       8      71 ..      65     130 ..      60     193 .. 0.79
   2 !    9.3   0.0    0.0026       1.3      80     128 ..     276     325 ..     236     333 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.4e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdllrellralglelka....e 71 
                                       ++++G++GtGKT l+  ++++l ee       p v+    +v+ +++++ + l+++l +alg++l +    +
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIARELGEE------TPFVImsgsEVYSTEKKKTEILMEALRKALGVKLREvrkvY 130
                                       799*******************876......8888899988888888888888*********9998855551 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0026
                            AAA_22  80 ealeqalrarav...ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                       e++ + ++++++   +++l iD+a+ l   ea+++L + ++ s++   liL+
  gi|320100400|ref|YP_004175992.1| 276 ETVKKWIDEKKAeiiPGVLFIDDAHML-DIEAFSFLTRAME-SEFAPILILA 325
                                       5555555666668889***********.9*****9965555.3555444444 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   1.1   1.3e-08   6.7e-06       3      78 ..      39     116 ..      37     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.3e-08
                            AAA_16   3 vGReeeleqLlsalervrsgrp..elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqal 76 
                                       vG  e +e+   +++++r+gr   + +ll+G++G+GK++l+ +++r+l ++  ++ ++g  + ++++    +l +al
  gi|320100400|ref|YP_004175992.1|  39 VGQTEAREAAGIVVKMIREGRIagRGILLVGPPGTGKTALAVAIARELGEETPFViMSGSEVYSTEKKKTEILMEAL 115
                                       666666666677888999999999***************************85553555555554443333344444 PP

                            AAA_16  77 ar 78 
                                        r
  gi|320100400|ref|YP_004175992.1| 116 -R 116
                                       .3 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 !   21.0   0.0     5e-07   0.00025       2      40 ..      65     105 ..      64     145 .. 0.83
   2 ?   -1.0   0.0       3.2   1.6e+03      65      90 ..     290     315 ..     260     320 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5e-07
                                       EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHH CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal..nreveyvqltrdtteed 40 
                                       +lLvGppGtgK+ la  +a+ l  +++++++ +++ +++e+
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIARELgeETPFVIMSGSEVYSTEK 105
                                       89********************9888888888887776665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.2
                                       G-SEEEEESGGG--HHHHHHHHHHHH CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslle 90 
                                        + +l++D+ ++++ e+++ L + +e
  gi|320100400|ref|YP_004175992.1| 290 IPGVLFIDDAHMLDIEAFSFLTRAME 315
                                       67899999999999888888877766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   9.9e-07   0.00051       1     106 [.      65     167 ..      65     169 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.9e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss.aleegkn 76 
                                       Ill G+pG+GKt la +++++l  g++  +v+  +  +++ +++   ++++l e  +++l  +l+e ++  ++  k 
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIAREL--GEETPFVIMSGSEVYSTEKK---KTEILMEALRKALGVKLREVRKvYEGVVKE 136
                                       99*******************9..77777777775555555444...677777777777766777665532222222 PP

                            AAA_18  77 lvidghlaeleseaakdikk......vvLtaspeel 106
                                       + i   +  ++++      +      +vL +++eel
  gi|320100400|ref|YP_004175992.1| 137 VKIRRARHPMVPYL-----TvpvearIVLATRDEEL 167
                                       22333333333333.....23344467777777776 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 ?    5.1   0.0     0.043        22      42      72 ..      94     124 ..      92     145 .. 0.81
   2 !   14.1   0.1     7e-05     0.036       5      81 ..     362     446 ..     359     450 .] 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.043
                       TFIID-31kDa  42 vLedAkvlaehakkkevslddvrlAiqsrle 72 
                                       +++ ++v+++++kk+e+ ++++r A+  +l 
  gi|320100400|ref|YP_004175992.1|  94 IMSGSEVYSTEKKKTEILMEALRKALGVKLR 124
                                       7899*********************887776 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7e-05
                       TFIID-31kDa   5 PrdarlihliLaslgvteyeerVvlqLldfay....rytssvLedAkvlaehakkkevslddvrlA....iqsrlek 73 
                                       P + r i +i as +  +++++ +++L+++      ry +++Le A+++ae++++++++++dv+ A    i   +++
  gi|320100400|ref|YP_004175992.1| 362 PEEIREIIKIRASEEEVNISSEALEKLVEIGSktslRYAVQLLEPARIIAEERGSDRIDVEDVEKArklfIDVSVST 438
                                       666666666666666667777778888888666666***************************99966666666666 PP

                       TFIID-31kDa  74 qfkepppk 81 
                                       ++ ++ +k
  gi|320100400|ref|YP_004175992.1| 439 EYLKQYEK 446
                                       66666655 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 !   17.5   0.0   4.5e-06    0.0023      33      88 ..      62     117 ..      52     123 .. 0.86
   2 ?    0.6   0.0      0.66   3.4e+02     103     117 ..     293     307 ..     284     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-06
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklek 88 
                                       ++ +llvGp GtGKt+++  + ++l +e+  +++     + + ++  +i+++ l k
  gi|320100400|ref|YP_004175992.1|  62 GRGILLVGPPGTGKTALAVAIARELGEETPFVIMSGSEVYSTEKKKTEILMEALRK 117
                                       5779**********************777777777777888888888999999988 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.66
                             AAA_7 103 vvFvDDlnmpakeky 117
                                       v+F+DD +m   e +
  gi|320100400|ref|YP_004175992.1| 293 VLFIDDAHMLDIEAF 307
                                       79*******998876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   2.9e-06    0.0015      27      65 ..      57      94 ..      50     193 .. 0.73
   2 ?    0.5   0.0      0.75   3.8e+02      67      94 ..     182     209 ..     166     254 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-06
                            AAA_25 27 kgllpagelallaGapgtGKttlaldlalavatGkpwlg 65
                                      +g  +ag  +ll+G+pgtGKt+la+ +a ++ +  p+  
  gi|320100400|ref|YP_004175992.1| 57 EGR-IAGRGILLVGPPGTGKTALAVAIARELGEETPFVI 94
                                      455.489999******************99888887755 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.75
                            AAA_25  67 vapeqgkVlyvsaEdsedelrrRlravg 94 
                                       + +++g V++++aE ++ +   R r+v 
  gi|320100400|ref|YP_004175992.1| 182 IGVRKGDVIWIDAETGRVHRVGRSREVE 209
                                       55799*********99955445555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.9e-06     0.002      21      68 ..      61     108 ..      36     118 .. 0.72
   2 ?   -0.6   0.0       1.4   6.9e+02     108     133 ..     292     317 ..     287     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.9e-06
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkke 68 
                                        g  +llvGppG+GKt la +++  l + +   ++  ++++s  +kk+
  gi|320100400|ref|YP_004175992.1|  61 AGRGILLVGPPGTGKTALAVAIARELGEETPFVIMSGSEVYSTEKKKT 108
                                       34679******************9999999999999999999887443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledg 133
                                       GvLf+D++  ++ +++  L + +e++
  gi|320100400|ref|YP_004175992.1| 292 GVLFIDDAHMLDIEAFSFLTRAMESE 317
                                       9********99999999999999876 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 !   17.5   0.0   3.8e-06     0.002      20      81 ..      63     128 ..      53     157 .. 0.78
   2 ?   -1.8   0.0         3   1.5e+03      92     127 ..     282     317 ..     251     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
                                       XEEEEEEXTTSSHHHHHHHHHHHHHHCSTSE....EEEEESSSXHHHHHHHHHHHHHTXXHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  20 dliiiAarpsmGktalalniaenaavkeklp....vavfslemsaeqlvqRllsseaeidskklrt 81 
                                         i++ + p++Gktala+ ia++  +++         v+s e +++++++  l +  +++++++r+
  gi|320100400|ref|YP_004175992.1|  63 RGILLVGPPGTGKTALAVAIARELGEETPFVimsgSEVYSTEKKKTEILMEALRKALGVKLREVRK 128
                                       5588999***************9997554322223789*********************9988875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                       HHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  92 lteaieelseaklfiddtpaltvseirskarrlkke 127
                                       + e+ +e+    lfidd   l ++     +r +++e
  gi|320100400|ref|YP_004175992.1| 282 IDEKKAEIIPGVLFIDDAHMLDIEAFSFLTRAMESE 317
                                       444555666677999999999999998888888665 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   2.9e-06    0.0015      48      71 ..      63      86 ..      47     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.9e-06
                         IstB_IS21 48 enivllGpsGvGKshlaialgvea 71
                                       +i+l+Gp+G+GK+ la+a+++e 
  gi|320100400|ref|YP_004175992.1| 63 RGILLVGPPGTGKTALAVAIAREL 86
                                      5799****************9986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.6   5.8e-05      0.03       9     126 ..      61     314 ..      53     324 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.8e-05
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaft.grAakelrerlaalgae................ 68 
                                       + + +l++++pGtGKT + ++i ++l e++     +   v  t ++ ++ l e+l+++++                 
  gi|320100400|ref|YP_004175992.1|  61 AGRGILLVGPPGTGKTALAVAIARELGEETPFVIMSGSEVYSTeKKKTEILMEALRKALGVklrevrkvyegvvkev 137
                                       567799****************9999998865543333333330334444455553322223555555555556666 PP

                            AAA_19  69 ..............................atTiHrlal...................................... 77 
                                                                     a       l                                      
  gi|320100400|ref|YP_004175992.1| 138 kirrarhpmvpyltvpvearivlatrdeelA-------Ltvpeevtqqileigvrkgdviwidaetgrvhrvgrsre 207
                                       6655555555555555555555444444441.......155555555555555566666666666666666666777 PP

                            AAA_19  78 ................................................................ldfddlltealel 90 
                                                                                                        ++d++++++   
  gi|320100400|ref|YP_004175992.1| 208 vegartydvetkrivevpkgpvkkekeivnvltlhdldaiyaaqrsmisffgltfereipsevrRQVDETVKKWI-- 282
                                       777777777777777777777777777777777777777888888888888866666666443333333332222.. PP

                            AAA_19  91 leeaeeekklqeeellivDEfqdvdelqyrLlkall 126
                                         ++++ + +    +l++D + ++d  ++++l + +
  gi|320100400|ref|YP_004175992.1| 283 --DEKKAEII--PGVLFIDDAHMLDIEAFSFLTRAM 314
                                       ..32333344..558888888888866666666555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.9e-05     0.015       2      49 ..      65     114 ..      64     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpwv 49 
                                       i ++G+++tGKT l+ a+a++   ++p v  ++ e+++ + +k+e  l ++
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIARElgeETPFVIMSGSEVYSTEKKKTEI-LMEA 114
                                       789****************988888999999999999999888775.4443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.7e-05    0.0089       2      32 ..      65      99 ..      65     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg....avllssdt 32
                                      +llvG+pG+GK+ la  ++++lg    +v+ s  +
  gi|320100400|ref|YP_004175992.1| 65 ILLVGPPGTGKTALAVAIARELGeetpFVIMSGSE 99
                                      689*******************9888655555444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00036      0.19      21      46 ..      65      90 ..      52     197 .. 0.78
   2 ?    2.9   0.0      0.15        76      71     117 ..     276     319 ..     240     326 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                            AAA_30 21 avltGpAGtGKttalkalreaweaag 46
                                       +l+Gp+GtGKt +  a+++ + ++ 
  gi|320100400|ref|YP_004175992.1| 65 ILLVGPPGTGKTALAVAIARELGEET 90
                                      589*********99888855444443 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                            AAA_30  71 stiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekaga 117
                                       +t++k++++ k+  ++ p  +l +D a m+d++ +  l++a+e++ a
  gi|320100400|ref|YP_004175992.1| 276 ETVKKWIDEKKA--EIIP-GVLFIDDAHMLDIEAFSFLTRAMESEFA 319
                                       678888866552..3333.5899************999999987655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.7e-05     0.024       3      30 ..      65      92 ..      63     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.7e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      ++l G++G GKT+L+  +a+++ e++++
  gi|320100400|ref|YP_004175992.1| 65 ILLVGPPGTGKTALAVAIARELGEETPF 92
                                      799*******************999865 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.5e-05     0.033      22      44 ..      65      87 ..      47     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                                      EEEE--TTSSTTHHHHHHHHHHH CS
                              PhoH 22 vfaiGpaGtGKtylavalaveal 44
                                      +  +Gp GtGKt lava+a e+ 
  gi|320100400|ref|YP_004175992.1| 65 ILLVGPPGTGKTALAVAIARELG 87
                                      5689*************997765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00019     0.099       1      65 [.      68     137 ..      68     187 .. 0.75
   2 ?   -1.2   0.0       4.9   2.5e+03      48      80 ..     265     294 ..     253     325 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00019
                                       EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaeki 65 
                                       +G+PG GK+ ++  +++++     f ++s +++   e k+ +   +a  +   ++l+e +++ + + +++
  gi|320100400|ref|YP_004175992.1|  68 VGPPGTGKTALAVAIARELgeetPFVIMSGSEVYSTEKKKTEIlMEALRKALGVKLREVRKVYEGVVKEV 137
                                       7***************988554468888866666677666664244444444556666666655555544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.9
                                       TSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                            AAA_17  48 klpleekkelqkeaaekiaeeakkkgvlvdghp 80 
                                       + p e+++++++++++ i e+++    ++ g  
  gi|320100400|ref|YP_004175992.1| 265 EIPSEVRRQVDETVKKWIDEKKA---EIIPGVL 294
                                       44566666666666666666542...2443333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.5e-05     0.038       1      40 [.      65     107 ..      65     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.5e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..klkkkdsvys.rnpe 40 
                                       i+l+Gp+g+GK+ la  +a++l ++      + ++vys  +++
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIARELGEETpfVIMSGSEVYStEKKK 107
                                       689*******************977756566667777744444 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0    0.0001     0.052      20      57 ..      65     110 ..      51     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                            AAA_11  20 tliqGPPGtgKTktivellsqllsr........rkseeeksakpri 57 
                                        l+ GPPGtgKT   v++ ++l ++        ++   ++++k +i
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIARELGEEtpfvimsgSEVYSTEKKKTEI 110
                                       5899****************99643455554432244445555555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.056       5      54 ..      66     122 ..      63     170 .. 0.64
   2 ?   -2.9   0.0       5.8     3e+03     163     182 ..     265     284 ..     226     290 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                           DUF2075   5 lVtGvaGtGKtvvllnllael.......eddeeertavylsvNhplvlvlrealakk 54 
                                       l  G +GtGKt ++++++ el        ++ +e +++   + + l+++lr+al  k
  gi|320100400|ref|YP_004175992.1|  66 LLVGPPGTGKTALAVAIARELgeetpfvIMSGSEVYSTEKKKTEILMEALRKALGVK 122
                                       55699****************655544433333333333333333333444433333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                           DUF2075 163 hLksqfRvaaseaviewvda 182
                                       +  s +R + +e+v +w+d+
  gi|320100400|ref|YP_004175992.1| 265 EIPSEVRRQVDETVKKWIDE 284
                                       56678899999999999985 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.055      19      53 ..      65      99 ..      62     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                      ill+G pG GK++la ++++el+++  +v +++ +
  gi|320100400|ref|YP_004175992.1| 65 ILLVGPPGTGKTALAVAIARELGEETPFVIMSGSE 99
                                      89********************9999999887665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0009      0.46      20      57 ..      60      96 ..      39     111 .. 0.77
   2 ?    0.9   0.0      0.62   3.2e+02      95     119 ..     292     316 ..     285     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0009
                                      TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavn 57
                                           +l++G  GtGK+ la ai ++   +e+pfv + 
  gi|320100400|ref|YP_004175992.1| 60 IAGRGILLVGPPGTGKTALAVAIARELG-EETPFVIMS 96
                                      445679*****************98766.667888765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.62
                                       SEEEEETGGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqe 119
                                       G+lf+D+ + l++e+ + L r++++
  gi|320100400|ref|YP_004175992.1| 292 GVLFIDDAHMLDIEAFSFLTRAMES 316
                                       9*************99999999886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00016     0.083      11      61 ..      62     112 ..      58     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkei 61 
                                       g+ + +vG+ G+GK+ L+ ++a++l  +   + + g ++ ++e+++++  +
  gi|320100400|ref|YP_004175992.1|  62 GRGILLVGPPGTGKTALAVAIARELGEETPFVIMSGSEVYSTEKKKTEILM 112
                                       67789*******************999888887777777774444443333 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00018     0.092      18      46 ..      55      89 ..      40     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                                      H......TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 18 l......gdvilLeGdLGaGKTtlvrglakalgve 46
                                      +      g+ ilL G+ G+GKT+l+ ++a++lg e
  gi|320100400|ref|YP_004175992.1| 55 IregriaGRGILLVGPPGTGKTALAVAIARELGEE 89
                                      2332233455**********************975 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 ?   10.2   0.0    0.0011      0.56      26      67 ..      64     101 ..      41     143 .. 0.77
   2 ?    1.0   0.0      0.75   3.9e+02     134     146 ..     283     304 ..     210     325 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                                       EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHH CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprksll 67 
                                        +l++ + GtGKT +a++++++l ++ +    +++  + +++
  gi|320100400|ref|YP_004175992.1|  64 GILLVGPPGTGKTALAVAIARELGEETP----FVIMSGSEVY 101
                                       678999****************998633....5555555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.75
                                       S.........EEEEETGGGTTS CS
                            ResIII 134 d.........viiiDEaHrlga 146
                                       d         v++iD aH l  
  gi|320100400|ref|YP_004175992.1| 283 DekkaeiipgVLFIDDAHMLDI 304
                                       12234566789*******8876 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00037      0.19       6      60 ..      65     117 ..      63     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHT CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligap 60 
                                       ill+gp g+Gkt la a+a+ l   +e +++++  se+   e+ ++ + ++   +
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIARELG--EETPFVIMSGSEVYSTEKKKTEILMEALRK 117
                                       799*******************6..899*****9999999888888777766555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0012       0.6       4      27 ..      64      92 ..      61     120 .. 0.80
   2 ?   -1.7   0.0       3.8     2e+03      24      47 ..     319     342 ..     314     375 .. 0.82
   3 ?   -1.0   0.0       2.3   1.2e+03      23      47 ..     404     428 ..     392     447 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                            AAA_24  4 kiliyGpsgiGKTtlakel.....gpkpl 27
                                       il++Gp+g+GKT la  +     +++p+
  gi|320100400|ref|YP_004175992.1| 64 GILLVGPPGTGKTALAVAIarelgEETPF 92
                                      599***********998776666545554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.8
                            AAA_24  24 pkplfidtekGlksldadkfpdie 47 
                                         +l++ t++G +++ ++++++++
  gi|320100400|ref|YP_004175992.1| 319 APILILATNRGIARIRGTDIESPH 342
                                       568999***********9998876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.3
                            AAA_24  23 gpkplfidtekGlksldadkfpdie 47 
                                        + + +i  e+G++++d+ ++++++
  gi|320100400|ref|YP_004175992.1| 404 LEPARIIAEERGSDRIDVEDVEKAR 428
                                       56677888899*******9998776 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.019       9.9       8      56 ..      36      88 ..      31      93 .. 0.81
   2 ?    5.2   0.3     0.015       7.6     475     508 ..     395     428 ..     364     430 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                            AAA_32  8 eeiigqeRAvealefglkikkk....gYNifvlGesgtGrttlvkrlleeiak 56
                                      ++++gq  A ea  + +k+ ++    g  i ++G++gtG+t l+  + +e  +
  gi|320100400|ref|YP_004175992.1| 36 DGLVGQTEAREAAGIVVKMIREgriaGRGILLVGPPGTGKTALAVAIARELGE 88
                                      67899999***999999997762222579*************99998887655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                            AAA_32 475 trfseiadllrEAdywakkegaevveaehVekAl 508
                                       t+++  ++ll+ A ++a+++g++ ++ e+VekA 
  gi|320100400|ref|YP_004175992.1| 395 TSLRYAVQLLEPARIIAEERGSDRIDVEDVEKAR 428
                                       45566799************************95 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0057       2.9       5      58 ..      65     117 ..      61     133 .. 0.78
   2 ?    1.6   0.0       0.5   2.5e+02      38      90 ..     262     317 ..     244     332 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0057
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelile 58 
                                       ++++G+  +GKT l+  +++el  ++  ++ ++  +   ++++++e l+e++++
  gi|320100400|ref|YP_004175992.1|  65 ILLVGPPGTGKTALAVAIARELG-EETPFVIMSGSEVYSTEKKKTEILMEALRK 117
                                       7899***************9999.888888888888777776666555555554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.5
                            AAA_14  38 ldderdkkladp.e.kllelileklkeekktylflDEiqev.pewekalkslvdeg 90 
                                       +++e  ++ + + + ++ + i ek  e    +lf+D ++++  e++++l + ++++
  gi|320100400|ref|YP_004175992.1| 262 FEREIPSEVRRQvDeTVKKWIDEKKAEIIPGVLFIDDAHMLdIEAFSFLTRAMESE 317
                                       444444433322011344444444222234679******99448999999988876 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00072      0.37      98     137 ..      46      85 ..      40      90 .. 0.78
   2 ?   -3.5   0.0       8.3   4.2e+03      81     104 ..     231     254 ..     229     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00072
                         Parvo_NS1  98 evgqvllawlskqlgkrntvwfyGpantGktnlaeaIaka 137
                                       e++ ++++++++       ++++Gp+ tGkt la aIa+ 
  gi|320100400|ref|YP_004175992.1|  46 EAAGIVVKMIREGRIAGRGILLVGPPGTGKTALAVAIARE 85 
                                       6666666666666666667999***************975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.3
                         Parvo_NS1  81 eenriykllslngynpvevgqvll 104
                                       +e+ i+ +l l++++ ++++q ++
  gi|320100400|ref|YP_004175992.1| 231 KEKEIVNVLTLHDLDAIYAAQRSM 254
                                       67899999**********999776 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 ?   -2.1   0.1       9.2   4.7e+03      11      24 ..     265     278 ..     264     290 .. 0.69
   2 ?    9.7   0.2    0.0018      0.94      28      45 .]     411     428 ..     408     428 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 9.2
                                       TS-HHHHHHHHHHH CS
                           PCP_red  11 kiPffvRkkaRraa 24 
                                       +iP  vR+++  ++
  gi|320100400|ref|YP_004175992.1| 265 EIPSEVRRQVDETV 278
                                       78888998875555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0018
                                       HHHHT-SEE-HHHHHHHH CS
                           PCP_red  28 ArerGleeVtvevveaAk 45 
                                       A+erG ++++ve ve+A+
  gi|320100400|ref|YP_004175992.1| 411 AEERGSDRIDVEDVEKAR 428
                                       9***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2825.32
//
Query:       gi|320100401|ref|YP_004175993.1|  [L=381]
Description: pyridoxal-dependent decarboxylase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-22   77.6   0.0    4.1e-21   75.1   0.0    2.1  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    2.8e-12   46.3   0.0    6.5e-11   41.8   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
    5.3e-11   42.3   0.0    1.7e-10   40.7   0.0    1.7  1  Beta_elim_lyase  Beta-eliminating lyase
    1.4e-10   40.9   0.0    0.00027   20.2   0.0    2.1  2  Aminotran_1_2    Aminotransferase class I and II
    3.5e-05   23.3   0.0    6.2e-05   22.5   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.077   11.7   0.0       0.18   10.4   0.0    1.7  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
       0.14   10.8   0.0       0.27    9.9   0.0    1.6  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain


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 !   75.1   0.0   1.6e-24   4.1e-21      74     355 ..      59     308 ..      39     326 .. 0.73

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 1.6e-24
                                       SHHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEE CS
                     Pyridoxal_deC  74 sPaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlyt 150
                                       +P++ e   ++++ ++ llg+          g+ ++g++es++lal   r+        +g+e           +++
  gi|320100401|ref|YP_004175993.1|  59 YPVVEEASRILIEGVGALLGAE--------HGIHTSGGTESNILALYIGRRIS------RGRE--------N-TVVA 112
                                       5555555555555555555555........36777777777777766555422......2322........2.2445 PP

                                       ETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHC CS
                     Pyridoxal_deC 151 sdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdiceky 227
                                        + +h+s++ka l++g +l  ip+d+   + +  le+ + +       pf vv+t+Gtt  g  d +ke g+i e++
  gi|320100401|ref|YP_004175993.1| 113 PSSVHRSIDKACLLMGCRLVKIPVDPLKPVDPGVLEEYVRK-----HKPFAVVVTAGTTEAGVVDPVKEAGEIAEEH 184
                                       5569*********************9554555555555532.....359**************************** PP

                                       T-EEEEE-TTGGGGGGSGGGGG......GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT. CS
                     Pyridoxal_deC 228 dlwlHvDAAyaGsaficpeirh......llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLeh 298
                                       ++ lHvDAAy+G  ++ p+          l+  + + Si+v  hK + +++  s l++  +  +++a  +e+eY+ +
  gi|320100401|ref|YP_004175993.1| 185 GVFLHVDAAYGG--LLIPFLHRrgylaeDLRMYPGVSSISVDMHKNGCAPIPSSILFLSRRDYIEEAC-FEMEYMPR 258
                                       ************..666665444887766777899*****************9999998888877776.9****994 PP

                                       TTTTTSEECCCGSSSSSG..HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                     Pyridoxal_deC 299 edsdvaadlgtkaiplsr..rvrilklwfvlralGveglqnqirksvelakyleklirk 355
                                                    +   r    +i+    v+ + G +g+++   +++e+a yl++++ +
  gi|320100401|ref|YP_004175993.1| 259 GR--------SCGLLGTRpgGAVIAAA-AVFMTIGAKGYEENAVRMMENALYLHENLSH 308
                                       44........34444444433333333.3333479999999999999999999988765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   2.5e-14   6.5e-11      52     177 ..      73     193 ..      49     201 .. 0.83
   2 ?    2.4   0.0     0.024        62     251     302 ..     266     317 ..     244     323 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.5e-14
                                       HHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSE.EEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCB CS
                       Aminotran_5  52 vaelinaeseeeiiftsGtteainlvalslarslkpgde.ivvteaehhanlvpwqelakrtgakvkvipldeegel 127
                                       v +l++ae     i tsG+te++ l+++   r++++g+e  vv  +  h     + +++   g ++++ip+d+ + +
  gi|320100401|ref|YP_004175993.1|  73 VGALLGAEH---GIHTSGGTESNILALYIG-RRISRGREnTVVAPSSVHRS---IDKACLLMGCRLVKIPVDPLKPV 142
                                       566666664...699*****9876666655.66666665144444444433...47888899*************** PP

                                       EGGGHHHH--.TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 128 dldeleklln.ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                       d+  le++++ +k+ +v +t+  ++ G+++pv+e g++a ++g++++vDaa
  gi|320100401|ref|YP_004175993.1| 143 DPGVLEEYVRkHKPFAVVVTAGTTEAGVVDPVKEAGEIAEEHGVFLHVDAA 193
                                       ********9769**************************************9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.024
                                       SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES. CS
                       Aminotran_5 251 GTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygp 302
                                       GT +  ++i+ +a++  + + g+e+ + +  e a yl+e l+ lp ++ y+p
  gi|320100401|ref|YP_004175993.1| 266 GTRPGGAVIAAAAVFMTIGAKGYEENAVRMMENALYLHENLSHLPMITSYKP 317
                                       8999999**************************************9999875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   6.6e-14   1.7e-10      37     250 ..      69     297 ..      50     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 6.6e-14
                                       HHHHHHHHTT-SEEEEES-HHHHHHHHH..HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-H CS
                   Beta_elim_lyase  37 LedavaelfgkeaalfvpqGtaAnsill..killqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdl 111
                                       L + v +l+g+e+++ +  Gt +n ++l     + rg e  v  p+ +h+   +a   l g +l++++ +    +d+
  gi|320100401|ref|YP_004175993.1|  69 LIEGVGALLGAEHGIHTSGGTESNILALyiGRRISRGRENTVVAPSSVHRSIDKAC-LLMGCRLVKIPVDPLKPVDP 144
                                       4455566********************95555679***************999998.567788************** PP

                                       HHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH........HHHTS CS
                   Beta_elim_lyase 112 ekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa........kslge 180
                                         le+ +++     ++ ++++++ T+++  G v   + ++e+ +ia+++g+ lh+D+A                l+e
  gi|320100401|ref|YP_004175993.1| 145 GVLEEYVRK--H--KPFAVVVTAGTTEA--GVV---DPVKEAGEIAEEHGVFLHVDAAY--GGLlipflhrrGYLAE 210
                                       *********..4..6799999999*997..765...66789999*************94..3334577766577777 PP

                                       -CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH....HHHHHHHHHHHHT---SSTHHHHH............... CS
                   Beta_elim_lyase 181 ivkemfsyvDsvtmslkKdllanvG.gvlafrddeledylaerveqrkylggglrqagvlaa............... 241
                                       +++ m+ +v s+++ + K+++a++  ++l+++++   dy++e++  ++y+  g r+ g+l+                
  gi|320100401|ref|YP_004175993.1| 211 DLR-MYPGVSSISVDMHKNGCAPIPsSILFLSRR---DYIEEACFEMEYMPRG-RSCGLLGTrpggaviaaaavfmt 282
                                       775.8899****************9789999999...*******999998766.44677666555555555555555 PP

                                       ........HHHHHHH CS
                   Beta_elim_lyase 242 ......leagirale 250
                                             +e ++r +e
  gi|320100401|ref|YP_004175993.1| 283 igakgyEENAVRMME 297
                                       555554444444444 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.1e-07   0.00027      58     194 ..      78     198 ..      54     212 .. 0.87
   2 !   18.7   0.0   3.1e-07    0.0008     258     363 .]     276     374 ..     258     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                                       CTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E..EEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-H CS
                     Aminotran_1_2  58 grseklklkreaavvvgsGagaliealifllklnpgde..ilvpdptyasyknilrlsggevvryplyseedfhldl 132
                                       g        +e  + +++G+ ++i al    ++ +g+e  +++p+ ++ s+++++ l+g+ +v++p++  +   +d 
  gi|320100401|ref|YP_004175993.1|  78 G--------AEHGIHTSGGTESNILALYIGRRISRGREntVVAPSSVHRSIDKACLLMGCRLVKIPVD--PLKPVDP 144
                                       3........888999************9999999888777**************************88..8889*** PP

                                       HHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCB CS
                     Aminotran_1_2 133 ealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfv 194
                                         lee ++++     k+  ++v+      G+v + +e  ++   a++++++l vD aY+g+ 
  gi|320100401|ref|YP_004175993.1| 145 GVLEEYVRKH-----KPFAVVVTAGTTEAGVVDPVKEAGEI---AEEHGVFLHVDAAYGGLL 198
                                       *****99996.....34455555556678************...**************9986 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.1e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH..CHHHHHHHHHHTCTEEE CS
                     Aminotran_1_2 258 aavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae..takelskkLleevgvyv 332
                                       aa++ ++      ++  ee++ r+ +++ +l+++L    l++++s   +++l +++    t +el+k+Ll++ ++yv
  gi|320100401|ref|YP_004175993.1| 276 AAAVFMTIG----AKGYEENAVRMMENALYLHENL--SHLPMITSYKPILPLNVFKSTiyTYEELFKALLDR-KLYV 345
                                       333333333....34789*****************..57*********************************.**** PP

                                       EEGGGGTSTTEEEEEC.TTS-HHHHHHHHHHH CS
                     Aminotran_1_2 333 tpgtsftvpgrlRitv.Aglteeeleelveal 363
                                        +  s+ +++ lR+ v +++ ++ l++l++al
  gi|320100401|ref|YP_004175993.1| 346 YK--SPSLQA-LRVVVmPHVEKAHLDRLINAL 374
                                       **..889888.*****************9986 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   2.4e-08   6.2e-05      32     146 ..      73     193 ..      53     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.4e-08
                                       HHHHHT-SEEEEESSHHHHHHHHHHH...TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCG CS
                   DegT_DnrJ_EryC1  32 faaylgvkhaiavssGtaAlhlaLra...lgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaie 105
                                       + a lg++h i +s Gt+++ laL     ++ g++++V+ ps    +  +a l +g + v + vdp    +dp  +e
  gi|320100401|ref|YP_004175993.1|  73 VGALLGAEHGIHTSGGTESNILALYIgrrISRGRENTVVAPSSVHRSIDKACLLMGCRLVKIPVDPLK-PVDPGVLE 148
                                       67899*******************9996677778999****************************876.79****** PP

                                       GG--TTEEEEEEB-G....GGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 106 aaitertkaIlpVhl....yGqvadmdalkaiaakhglkvieDaA 146
                                       + + +     ++V +    +G v  +++  +ia++hg+ +  DaA
  gi|320100401|ref|YP_004175993.1| 149 EYVRKHKPFAVVVTAgtteAGVVDPVKEAGEIAEEHGVFLHVDAA 193
                                       *****9955555544223368888999999**************9 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.2e-05      0.18     104     195 ..     110     195 ..      93     316 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.2e-05
                                       CEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEE.EHHHHHHHHHHCCTCCCEEEEEECSSTTTTB----HHHHHH CS
                           SepSecS 104 viwvridekSslkavelaGleialvekvlegDeli.tdvedveeiiekkreevilavlstlsffaprspDdvkeiak 179
                                       v+ +   ++S  ka  l+G +++ ++     D l+ +d+   ee ++k++   + av+ t  +    + D+vke  +
  gi|320100401|ref|YP_004175993.1| 110 VVAPSSVHRSIDKACLLMGCRLVKIP--V--DPLKpVDPGVLEEYVRKHK---PFAVVVTAGTTEAGVVDPVKEAGE 179
                                       55555555555555555554443333..2..3332278888888887733...445555555556668899****** PP

                                       HHHCCT--EEEEGCCC CS
                           SepSecS 180 iCaeydvPhlvNgAYa 195
                                       i +e++v + v +AY+
  gi|320100401|ref|YP_004175993.1| 180 IAEEHGVFLHVDAAYG 195
                                       ***************8 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 ?    9.9   0.0    0.0001      0.27     160     270 ..     147     257 ..      76     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0001
                                       HHHSTTTGSESEEEEESS-.TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS-BTTBEEEE. CS
                          OKR_DC_1 160 ikevpdakaprlavitnsT.YdGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllaenendpgilv. 234
                                       ++e+  +++p  +v+t +T   Gv+  +ke+ + +e+ ++ +++D A++g   +ip+ +    l  + +  pg+   
  gi|320100401|ref|YP_004175993.1| 147 LEEYVRKHKPFAVVVTAGTtEAGVVDPVKEAGEIAEEHGVFLHVDAAYGGL--LIPFLHRRGYLAEDLRMYPGVSSi 221
                                       456666666666777776516799999**********************96..689998888888886666766541 PP

                                       EEEHCCCCS--TT-EEEEEES-BT--HHHHHHHHHH CS
                          OKR_DC_1 235 tqSvHKllaalsqaSlihvkeelivneerlneafmm 270
                                          +HK   a   +S++ +     ++e  ++  +m 
  gi|320100401|ref|YP_004175993.1| 222 SVDMHKNGCAPIPSSILFLSRRDYIEEACFEMEYMP 257
                                       456899999988888888877777888888877774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2733.25
//
Query:       gi|320100402|ref|YP_004175994.1|  [L=294]
Description: Non-specific serine/threonine protein kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-44  150.7   0.0    4.9e-44  150.2   0.0    1.2  1  RIO1             RIO1 family
    1.8e-21   76.2   0.6    3.6e-21   75.2   0.6    1.5  1  Rio2_N           Rio2, N-terminal
    1.2e-07   31.9   0.1     0.0012   18.8   0.0    2.4  3  APH              Phosphotransferase enzyme family
     0.0018   18.0   0.0      0.003   17.2   0.0    1.2  1  WaaY             Lipopolysaccharide core biosynthesis protein
     0.0062   15.4   0.0     0.0074   15.1   0.0    1.1  1  Pkinase_fungal   Fungal protein kinase
  ------ inclusion threshold ------
      0.018   14.4   0.0       0.24   10.7   0.0    2.1  1  Kdo              Lipopolysaccharide kinase (Kdo/WaaP) family
       0.02   14.3   0.0      0.076   12.4   0.0    1.8  1  Pkinase          Protein kinase domain
      0.032   13.5   0.0       0.17   11.1   0.0    2.0  2  Fructosamin_kin  Fructosamine 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 !  150.2   0.0   2.2e-47   4.9e-44       2     186 ..     109     284 ..     108     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 2.2e-47
                                       EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpiel 78 
                                       +y + +  g +va+K+ ++++t+F++ k  +s  +r      ++++ + +kl+ae+Ef++Lk+l++ ++ vP pi +
  gi|320100402|ref|YP_004175994.1| 109 IYLGLAPGGLKVAVKVLRIGRTSFRRTKLLRSWSSR-----PHMSWYDESKLAAEREFKALKALSSVNALVPVPIGY 180
                                       77788888889*******************999999.....589********************************* PP

                                       ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTEEE CS
                              RIO1  79 krhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQave 154
                                       +rhv+v e+++  gv++++  d++      e+++ ++e++ k+y+++g+vH+DLSeyN++v+ d k++iID++Q+v 
  gi|320100402|ref|YP_004175994.1| 181 NRHVVVVEYVE--GVELYTRPDLS---RPGEVLDLIVETIGKAYRDVGIVHGDLSEYNIIVTADeKPYIIDWPQYVY 252
                                       ***********..***********...8999********************************99************ PP

                                       TTSTTHHHHHHHHHHHHHHHHHTTC-----HH CS
                              RIO1 155 ldhpnalefLerDveniikfFrrkgvekvdee 186
                                        d+pna ++L+rD+++i++fF++ +  +vd+e
  gi|320100402|ref|YP_004175994.1| 253 RDEPNAVTLLRRDLSYIARFFSKVYGLHVDVE 284
                                       ***********************998877766 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.6   1.6e-24   3.6e-21       2      80 ..       9      89 ..       8      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.6e-24
                            Rio2_N  2 ryLskedfrvLtavEmg.mrnhevVptelieeisrlkeeevkkrlsrllkaklisr.ktakydGYkLtyeGyDyLALkt 78
                                      r+L+++df+vL avE g +r  e+Vp e++e+is+l+ee++   l +l++ kl++r +   y+ Y+Lty+GyD+LA ++
  gi|320100402|ref|YP_004175994.1|  9 RSLTSDDFKVLAAVEKGvSRGREYVPLEMLEKISGLHEEKLVLILGKLHELKLVKRkTISGYKAYRLTYMGYDMLAFRA 87
                                      89*************9856889**********************************55568*****************9 PP

                            Rio2_N 79 lv 80
                                      lv
  gi|320100402|ref|YP_004175994.1| 88 LV 89
                                      96 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.1   9.1e+03      75     108 ..      31      59 ..      12      66 .. 0.61
   2 !   10.7   0.0   0.00016      0.37      33     103 ..     153     216 ..     102     218 .. 0.82
   3 !   18.8   0.0   5.3e-07    0.0012     167     193 ..     223     247 ..     217     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.1
                                       E----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH CS
                               APH  75 eyvpgrsllrklsaaqlpellealgeflaalhqv 108
                                       eyvp + l+      +++   e+l+  l++lh++
  gi|320100402|ref|YP_004175994.1|  31 EYVPLEMLEK-----ISGLHEEKLVLILGKLHEL 59 
                                       4444444444.....5555556666666666655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                                       -HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHC CS
                               APH  33 aaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgefla 103
                                       ++  ++re++ l++L+  ++ vP+++        + ++++++eyv+g  l+++++ +  +e+l+ ++e+++
  gi|320100402|ref|YP_004175994.1| 153 SKLAAEREFKALKALSSVNALVPVPIG-------YNRHVVVVEYVEGVELYTRPDLSRPGEVLDLIVETIG 216
                                       456678888899999988889999999.......56689*************9999999999999888876 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 5.3e-07
                                       EEE-SS-SGGGEEEC..TTEEEEE--- CS
                               APH 167 vllHgDlhpgNllvdpddgrvtGviDf 193
                                       +++HgDl+  N++v++d+ +  ++iD+
  gi|320100402|ref|YP_004175994.1| 223 GIVHGDLSEYNIIVTADEKP--YIIDW 247
                                       79*************77666..5**** PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.3e-06     0.003     118     177 ..     183     246 ..     176     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                              WaaY 118 yimiieyiegielvdmpeid..devkakikqsiek.lhqlgmvsgdphrgnfivkkdev.riid 177
                                       +++++ey+eg+el   p+++   ev + i ++i k   + g+v gd    n+iv  de   iid
  gi|320100402|ref|YP_004175994.1| 183 HVVVVEYVEGVELYTRPDLSrpGEVLDLIVETIGKaYRDVGIVHGDLSEYNIIVTADEKpYIID 246
                                       799***************9733689999999997615679**************9987524555 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.3e-06    0.0074     287     351 ..     183     242 ..     119     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-06
                    Pkinase_fungal 287 hrrlvispvGkpiekaespkellealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkg 351
                                       h+++v    G+++++  + ++  e+l   +++  + +++ gi+H D Se+Ni++t      ++k 
  gi|320100402|ref|YP_004175994.1| 183 HVVVVEYVEGVELYTRPDLSRPGEVLDLIVETIGKAYRDVGIVHGDLSEYNIIVTA-----DEKP 242
                                       45555555677777766666666677777777788899*****************4.....4444 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.24      51     174 ..     149     255 ..     123     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                               Kdo  51 fk.lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwae.laeelkrallk 125
                                       +   +++ a rEf++lk+L ++   vp p+ ++        r ++++e +eg++    l+++ +   ++e+   +++
  gi|320100402|ref|YP_004175994.1| 149 WYdESKLAAEREFKALKALSSVNALVPVPIGYN--------RHVVVVEYVEGVE----LYTRPDLsRPGEVLDLIVE 213
                                       44477889999*********9999999999876........4567888888875....3343111245666666666 PP

                               Kdo 126 avgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr 174
                                        +g++ +   ++g+ H+dl   ni + ++e    + ++iD  +   r  
  gi|320100402|ref|YP_004175994.1| 214 TIGKAYR---DVGIVHGDLSEYNIIVTADE----KPYIIDWPQYVYRDE 255
                                       6666655...47999999999999999998....888888776666655 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.4e-05     0.076       5     142 ..      99     247 ..      96     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                                       EEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH...........HHHHHHHHHHHHHSCTTB--EEEEEEE. CS
                           Pkinase   5 eklGeGsfGkVykaveketgkivAvKkikkekakkkke...........kkvlrEikilkklkhpnivrlyevfee. 69 
                                        ++G G+ +++y ++ +  g +vAvK+++  +++ +++            +   E k+ ++ + + +  l +v    
  gi|320100402|ref|YP_004175994.1|  99 DRIGVGKESEIYLGL-APGGLKVAVKVLRIGRTSFRRTkllrswssrphMSWYDESKLAAEREFKALKALSSVNALv 174
                                       578999999999999.7899999999988776665555567777777774455555555555544444444443335 PP

                                       .....SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-S CS
                           Pkinase  70 .....kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitD 141
                                             ++ ++v+eyveg el ++     s + e +  i+++i ++ +   + gi+H Dl   Ni++  +++  i+D
  gi|320100402|ref|YP_004175994.1| 175 pvpigYNRHVVVVEYVEGVELYTRPD--LSRPGEVLDLIVETIGKAYR---DVGIVHGDLSEYNIIVTADEKPYIID 246
                                       555556777889*****998877664..45666677777777777755...789****************9999999 PP

                                       G CS
                           Pkinase 142 F 142
                                       +
  gi|320100402|ref|YP_004175994.1| 247 W 247
                                       8 PP

>> Fructosamin_kin  Fructosamine kinase
   #    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      73     117 ..      17      59 ..      10      77 .. 0.76
   2 ?   11.1   0.0   7.4e-05      0.17     174     221 ..     208     256 ..     196     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.26
                   Fructosamin_kin  73 rvPkvlavGelkdasfLvleyLelklekkesaaelgqqLaklHra 117
                                       +v  ++  G ++ ++++ le Le    +  + ++l   L+klH+ 
  gi|320100402|ref|YP_004175994.1|  17 KVLAAVEKGVSRGREYVPLEMLEKI--SGLHEEKLVLILGKLHEL 59 
                                       5566778899999999999999988..335667888889999984 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.4e-05
                   Fructosamin_kin 174 vervaellskhqpkpsllHGdLWsgNaaltkdgepvifd.PaayygdrE 221
                                       ++ + e++ k      ++HGdL + N+ +t+d++p+i+d P   y d+ 
  gi|320100402|ref|YP_004175994.1| 208 LDLIVETIGKAYRDVGIVHGDLSEYNIIVTADEKPYIIDwPQYVYRDEP 256
                                       55566667777778899**********************8888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2149.43
//
Query:       gi|320100403|ref|YP_004175995.1|  [L=636]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-44  151.0   0.4    3.2e-44  150.0   0.4    1.5  1  DUF460         Protein of unknown function (DUF460)
      0.003   17.9   0.8      0.017   15.4   0.2    2.3  2  DUF641         Plant protein of unknown function (DUF641)
     0.0064   16.4   0.6      0.017   15.0   0.6    1.7  1  Spc29          Spindle Pole Component 29
     0.0097   16.1   0.9      0.028   14.6   0.0    2.1  3  Fib_alpha      Fibrinogen alpha/beta chain family
  ------ inclusion threshold ------
      0.012   14.8   1.1      0.024   13.8   1.1    1.4  1  DUF4686        Domain of unknown function (DUF4686)
      0.015   14.9   0.2      0.031   13.9   0.2    1.5  1  DUF2229        CoA enzyme activase uncharacterised domain (DU
      0.027   14.4   2.7        6.1    6.9   0.1    2.9  3  TMF_DNA_bd     TATA element modulatory factor 1 DNA binding
      0.038   14.5   0.2       0.34   11.4   0.2    2.4  2  DUF16          Protein of unknown function DUF16
       0.16   12.3   1.5       0.38   11.1   0.5    2.2  2  BLOC1_2        Biogenesis of lysosome-related organelles comp
          1    9.5   5.0       0.15   12.2   0.5    1.8  2  Tropomyosin_1  Tropomyosin like
        1.9    8.6   4.8        1.7    8.8   0.9    2.8  2  DUF1192        Protein of unknown function (DUF1192)
        6.4    6.7   7.8        2.8    7.9   1.8    3.1  2  PKcGMP_CC      Coiled-coil N-terminus of cGMP-dependent prote
          9    6.8   8.0       0.53   10.8   0.2    2.8  3  ZapB           Cell division protein ZapB


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 !  150.0   0.4   2.3e-47   3.2e-44       2     141 .]     214     352 ..     213     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 2.3e-47
                            DUF460   2 vkskdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpv 78 
                                       ++ k+v++ +++ +++++  + + +k++ ++ivG+DPG+ +g+avl ldg +l ++s+++ dr++v+ ++selG+p+
  gi|320100403|ref|YP_004175995.1| 214 FRYKNVRIMIKPYRSRRLLEVGE-EKTRIPVIVGVDPGMGIGVAVLTLDGVPLLVTSMKSPDRDDVVAAVSELGRPI 289
                                       57899*******99999887666.999************************************************** PP

                            DUF460  79 ivAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                       ivAtDvs+ppetv kla++l+avly+P++d+sv++K+++a++++++++v++ d H RDalaAA
  gi|320100403|ref|YP_004175995.1| 290 IVATDVSRPPETVVKLAAMLNAVLYAPDQDMSVDDKNRIAREYMDRYSVDIPDAHARDALAAA 352
                                       **************************************************************9 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 !   15.4   0.2   1.3e-05     0.017      51     122 ..     389     462 ..     372     468 .. 0.85
   2 ?    0.4   0.0      0.57   7.9e+02      87     118 ..     472     503 ..     462     512 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                            DUF641  51 kklselkrlyrkkqkkkase..aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksn 122
                                       + lse+ + y+k++  ++++  +e+ + ++   ++r+++ ++e+ v++l ++++++ds i  L+ +L+ +++++
  gi|320100403|ref|YP_004175995.1| 389 RPLSEVLEEYFKRNIPRRQPivEEKPTTQQGCGKLREKVSALEALVRRLIEDVEKRDSYIRDLELELRLMRSRK 462
                                       5699999999999887766456888899999999******************************9998877766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.57
                            DUF641  87 lktyeitvkkleaelkakdseieeLkekLeea 118
                                       + ++   +++l++ ++ kd+ i eL  kL ++
  gi|320100403|ref|YP_004175995.1| 472 ISSLIEEIEALRRRIDDKDAVIRELYGKLLTL 503
                                       44444556778888888888888888777665 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.6   1.2e-05     0.017     112     163 ..     458     509 ..     421     520 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                             Spc29 112 iyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkr 163
                                       ++s+   ++e e+k+ +  +eI++L+r ++++ +v++eL  k+  le ++ +
  gi|320100403|ref|YP_004175995.1| 458 MRSRKPGVEEYERKISSLIEEIEALRRRIDDKDAVIRELYGKLLTLEGNIVK 509
                                       56666677899***********************************998855 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 ?   -2.5   0.0       3.9   5.4e+03      77      90 ..     354     367 ..     326     378 .. 0.56
   2 !   14.6   0.0     2e-05     0.028      33     121 ..     423     510 ..     417     514 .. 0.94
   3 ?   -3.7   0.1       8.8   1.2e+04      53      72 ..     612     631 ..     590     634 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHCC CS
                         Fib_alpha  77 nvikksskeleeei 90 
                                       ++++k+++++ee  
  gi|320100403|ref|YP_004175995.1| 354 KAYNKYRNTIEEAK 367
                                       34444444444322 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2e-05
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqn 109
                                       ++++++ le  ++++ +  ++ ++++++++  lr   + k++ +++ +k+s+ +e ei+ l+++id++   ir+L +
  gi|320100403|ref|YP_004175995.1| 423 LREKVSALEALVRRLIEDVEKRDSYIRDLELELRLMRSRKPGVEEYERKISSLIE-EIEALRRRIDDKDAVIRELYG 498
                                       67899************************************99************.*******************99 PP

                                       HHHHHHHHHHHH CS
                         Fib_alpha 110 vlesneqkiqkL 121
                                        l ++e +i kL
  gi|320100403|ref|YP_004175995.1| 499 KLLTLEGNIVKL 510
                                       999999998887 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 8.8
                                       HHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  53 eaeelvkeikdslrekqksk 72 
                                       + e++ + i+d+ r++ k++
  gi|320100403|ref|YP_004175995.1| 612 KHERILRMIEDYQRSRLKKQ 631
                                       33445556666666666555 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.1   1.7e-05     0.024     290     356 ..     434     496 ..     421     510 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                           DUF4686 290 kelllkeveqrderikqLeneiailksqsekekefqkqviaeNekLllekrkLleqlseqeeliknn 356
                                         +l+++ve+rd++i++Le e+++++s++   +e+ +++     +L++e   L +++ +++ +i++ 
  gi|320100403|ref|YP_004175995.1| 434 VRRLIEDVEKRDSYIRDLELELRLMRSRKPGVEEYERKIS----SLIEEIEALRRRIDDKDAVIREL 496
                                       56899*********************************96....69999999999999999998865 PP

>> DUF2229  CoA enzyme activase uncharacterised domain (DUF2229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.3e-05     0.031     118     185 ..     320     391 ..     300     407 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                           DUF2229 118 ldledkkelakqlleel..giskkeikkAvekAleaqkafkeelrkkgeelleeleee...gkkgivllGrpY 185
                                       ++++dk+++a+++++++  +i  + ++ A+++A++a++++++++++++   l+ +++    +  + vl Grp 
  gi|320100403|ref|YP_004175995.1| 320 MSVDDKNRIAREYMDRYsvDIPDAHARDALAAAVKAYNKYRNTIEEAKS-KLAGIRDVdryQLIAEVLRGRPL 391
                                       55667778999999866559***********************887765.55545554111444578888886 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 ?   -2.5   0.0         4   5.5e+03      29      42 ..     357     370 ..     347     373 .. 0.64
   2 ?    6.5   0.1    0.0058         8      37      71 ..     422     456 ..     417     459 .. 0.92
   3 ?    6.9   0.1    0.0045       6.1       9      52 ..     467     510 ..     464     513 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
                        TMF_DNA_bd  29 lklnntikkLrkkn 42 
                                       +k +nti + ++k+
  gi|320100403|ref|YP_004175995.1| 357 NKYRNTIEEAKSKL 370
                                       45566666665554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0058
                        TMF_DNA_bd  37 kLrkknkelekeikelkkkleklekeleeleerlk 71 
                                       kLr+k++ le  +++l + +ek ++ +  le +l+
  gi|320100403|ref|YP_004175995.1| 422 KLREKVSALEALVRRLIEDVEKRDSYIRDLELELR 456
                                       9************************9999998876 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0045
                        TMF_DNA_bd   9 eKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikel 52 
                                       e + +I  L eE e+L+   ++  + i +L  k+  le +i +l
  gi|320100403|ref|YP_004175995.1| 467 EYERKISSLIEEIEALRRRIDDKDAVIRELYGKLLTLEGNIVKL 510
                                       55778999999999999999999999999999999999888777 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00025      0.34      29     101 ..     413     488 ..     392     491 .. 0.79
   2 ?    5.6   0.0     0.015        21      32      74 ..     461     503 ..     456     518 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                       -..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHHHHH CS
                             DUF16  29 kdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgee...lnkvdetleliletLqkinkRlDs 101
                                       k  ++q   k+ +kv++l+  + +l + vek +  i++l+ e    + +   +++ ++ + +++e ++++  R+D 
  gi|320100403|ref|YP_004175995.1| 413 KPTTQQGCGKLREKVSALEALVRRLIEDVEKRDSYIRDLELELRLMRSRkpgVEEYERKISSLIEEIEALRRRIDD 488
                                       344888899999****************************998766653112669999999999*********996 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                                       BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaq 74 
                                        k  +++ e k+++l e+i++l   ++ +++ i+el  +  + 
  gi|320100403|ref|YP_004175995.1| 461 RKPGVEEYERKISSLIEEIEALRRRIDDKDAVIRELYGKLLTL 503
                                       5666788999999999999999999999999999997766555 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 ?   -2.8   0.0       5.9   8.1e+03      35      49 ..     355     369 ..     346     377 .. 0.41
   2 ?   11.1   0.5   0.00027      0.38      19      92 ..     424     497 ..     415     501 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.9
                           BLOC1_2  35 kykklkdvaaslekk 49 
                                        y+k+++ ++++++k
  gi|320100403|ref|YP_004175995.1| 355 AYNKYRNTIEEAKSK 369
                                       233333333333332 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                           BLOC1_2  19 vedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       +e+++ Le+l ++ +e ++k ++ + +le +l  +++++  +++y ++i  + ++++ L   ++  D+ ++eL 
  gi|320100403|ref|YP_004175995.1| 424 REKVSALEALVRRLIEDVEKRDSYIRDLELELRLMRSRKPGVEEYERKISSLIEEIEALRRRIDDKDAVIRELY 497
                                       6789999****************************************************999999999988885 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00011      0.15      32      98 ..     422     488 ..     404     510 .. 0.85
   2 ?   -2.5   0.3       3.9   5.3e+03      74      97 ..     596     618 ..     593     625 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                     Tropomyosin_1  32 ekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeeleesdkkLke 98 
                                       +  ++++ L+  ++ l e+vek ++ +++ + ++    ++k   e+++rki  L ee+e   +++ +
  gi|320100403|ref|YP_004175995.1| 422 KLREKVSALEALVRRLIEDVEKRDSYIRDLELELRLMRSRKPGVEEYERKISSLIEEIEALRRRIDD 488
                                       56678899999999999*****************************************998877765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.9
                     Tropomyosin_1  74 nnealtrkiqlLEeeleesdkkLk 97 
                                       ++e+l r+i+ L  ele+ ++ L+
  gi|320100403|ref|YP_004175995.1| 596 KAEELWRRINELV-ELEKHERILR 618
                                       5677778877774.4666666555 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       1.1   1.5e+03      21      47 ..     419     445 ..     403     449 .. 0.76
   2 ?    8.8   0.9    0.0012       1.7      21      48 ..     464     491 ..     462     493 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                           DUF1192  21 SveELeerIalLeaEIaRleaaiakkk 47 
                                       +   L+e +++Lea + Rl + ++k++
  gi|320100403|ref|YP_004175995.1| 419 GCGKLREKVSALEALVRRLIEDVEKRD 445
                                       56679999******9999998888875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                           DUF1192  21 SveELeerIalLeaEIaRleaaiakkka 48 
                                       +veE e  I+ L +EI+ l++ i++k+a
  gi|320100403|ref|YP_004175995.1| 464 GVEEYERKISSLIEEIEALRRRIDDKDA 491
                                       699***********************98 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4      0.53   7.2e+02       6      18 ..     444     456 ..     441     458 .. 0.77
   2 ?    7.9   1.8     0.002       2.8       8      31 ..     477     500 ..     467     500 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.53
                         PKcGMP_CC   6 KDERIRELEkrla 18 
                                        D  IR+LE  l+
  gi|320100403|ref|YP_004175995.1| 444 RDSYIRDLELELR 456
                                       5777****99886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.002
                         PKcGMP_CC   8 ERIRELEkrlaekdeEIqELrskL 31 
                                       E I  L +r+ +kd++I EL  kL
  gi|320100403|ref|YP_004175995.1| 477 EEIEALRRRIDDKDAVIRELYGKL 500
                                       55777999************7776 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.7   2.4e+03      23      39 ..     423     439 ..     416     456 .. 0.55
   2 ?   10.8   0.2   0.00038      0.53       7      29 ..     466     488 ..     465     510 .. 0.87
   3 ?   -2.6   0.1       5.8     8e+03      18      32 ..     595     609 ..     592     622 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                              ZapB  23 LqmeieeLkeeneelke 39 
                                       L++++++L++ ++ l e
  gi|320100403|ref|YP_004175995.1| 423 LREKVSALEALVRRLIE 439
                                       33333333333333322 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00038
                              ZapB   7 eqLEskiqkaidtitlLqmeiee 29 
                                       e+ E ki+++i++i++L+ +i++
  gi|320100403|ref|YP_004175995.1| 466 EEYERKISSLIEEIEALRRRIDD 488
                                       56699***************986 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.8
                              ZapB  18 dtitlLqmeieeLke 32 
                                       ++ ++L  +i eL e
  gi|320100403|ref|YP_004175995.1| 595 EKAEELWRRINELVE 609
                                       444455555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      799  (0.0445647); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.42
# Mc/sec: 4530.45
//
Query:       gi|320100404|ref|YP_004175996.1|  [L=414]
Description: methionine adenosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-170  567.3   0.9   1.7e-170  567.1   0.9    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.1   0.9  9.6e-175  1.7e-170       1     395 [.       7     409 ..       7     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: 567.1 bits;  conditional E-value: 9.6e-175
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       rni++e l+  +v++++vE+vErKG+GHPD+iaD+++ea+sralsk+yl++fg+ilhhn+Dk+llv+G+s+p+fgGG
  gi|320100404|ref|YP_004175996.1|   7 RNIEIELLRMASVSSMKVELVERKGVGHPDYIADSASEAASRALSKYYLKEFGTILHHNLDKTLLVGGQSNPRFGGG 83 
                                       79*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.....EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS. CS
                   AdoMet_Synthase  78 eviepieillsgratkev....egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkke 150
                                        ++epi+i+++grat+ev    +  kip+++i++ea+ke++k+n+r+ld+ek+vivd++++kgsadL+ vfe+ k++
  gi|320100404|ref|YP_004175996.1|  84 ILLEPIYIVVAGRATTEVrtedGLVKIPFGRIIVEAVKEWIKKNMRYLDPEKHVIVDYMVRKGSADLVTVFEAGKSS 160
                                       ******************65544568*************************************************** PP

                                       .-BESSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHH CS
                   AdoMet_Synthase 151 vplaNDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYl 227
                                       vplaNDtS+gvgyapls+leklvl+ erllns e+k+k+p+vGeD+KvmglR++k+i lT+a+a++dr v+d+ eYl
  gi|320100404|ref|YP_004175996.1| 161 VPLANDTSIGVGYAPLSSLEKLVLQSERLLNSPEFKSKVPAVGEDVKVMGLRRGKEIVLTIAAAIIDREVRDKYEYL 237
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--T CS
                   AdoMet_Synthase 228 evkeeikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaa 304
                                       +vke+i e+v++l +k+  +++v+++vNtaD +e++s+yltvtGtsaE+gDdG++GRGNR+nGli+p+rp+slEA+a
  gi|320100404|ref|YP_004175996.1| 238 KVKEDIVEAVSDLSSKIVPDYNVRIHVNTADIPERDSFYLTVTGTSAEHGDDGATGRGNRANGLIPPMRPISLEATA 314
                                       ***************************************************************************** PP

                                       TS-TTT-HHHHHHHHHHHHHHHHHHH-TT.EEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---H...HSHHHHHHH CS
                   AdoMet_Synthase 305 GKNPvsHvGKiYnvlaneiakeiveeveg.vkevyvrllsqiGkpidePlvasvqvilekgvsle...evekeveei 377
                                       GKNPv+HvGKiYnv+a++ia++++e ++g  +++yv+llsqiGkpid+Plvas+++i++++  +e   ++++e++ i
  gi|320100404|ref|YP_004175996.1| 315 GKNPVNHVGKIYNVVARRIAERVYEIYNGvFSDIYVELLSQIGKPIDQPLVASIKLIPSDSSMTEipgHIKSEINGI 391
                                       ****************************9559**************************877655433389******* PP

                                       HHHHHT-HHHHHHHHTTT CS
                   AdoMet_Synthase 378 ideelekieeiteelieg 395
                                       +deel++i+++te+++++
  gi|320100404|ref|YP_004175996.1| 392 ADEELANIKRVTEMVLND 409
                                       ***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3047.12
//
Query:       gi|320100405|ref|YP_004175997.1|  [L=665]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-32  110.5   0.0    1.2e-31  110.0   0.0    1.3  1  FbpA             Fibronectin-binding protein A N-terminus (Fb
    2.9e-22   79.4   0.0      7e-22   78.1   0.0    1.7  1  NFACT-R_1        NFACT protein RNA binding domain
  ------ inclusion threshold ------
      0.012   16.0   3.2      0.017   15.6   0.3    2.2  2  DUF16            Protein of unknown function DUF16
      0.033   14.2   4.1       0.38   10.8   0.0    2.6  3  DUF1664          Protein of unknown function (DUF1664)
      0.048   14.0   3.5       0.21   11.9   0.4    2.2  2  OmpH             Outer membrane protein (OmpH-like)
      0.072   13.0   0.1         17    5.4   0.0    2.7  2  Phage_NinH       Phage NinH protein
       0.12   10.5   3.5       0.26    9.5   2.4    1.8  1  Cast             RIM-binding protein of the cytomatrix active
       0.25   11.8   0.3        5.1    7.6   0.0    2.5  2  NPV_P10          Nucleopolyhedrovirus P10 protein
        0.4    9.9   1.6        1.9    7.7   0.6    2.0  2  FmiP_Thoc5       Fms-interacting protein/Thoc5
       0.45   10.4   3.0       0.61   10.0   1.3    1.9  2  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
        0.7    9.4   4.3       0.18   11.3   0.9    1.6  2  ASD2             Apx/Shroom domain ASD2
        1.3    9.2   3.6        1.3    9.2   0.7    2.1  2  CREPT            Cell-cycle alteration and expression-elevate
        3.2    6.6   5.4        3.7    6.4   0.4    2.1  2  Spc7             Spc7 kinetochore protein
        3.8    7.4   5.6        3.7    7.4   0.5    2.2  2  DASH_Spc19       Spc19
        4.3    6.7   8.3       0.29   10.5   1.1    2.0  2  DUF3523          Domain of unknown function (DUF3523)
        4.9    7.4   8.3         19    5.5   0.2    2.6  2  THOC7            Tho complex subunit 7
        9.8    6.3   6.9        3.2    7.8   0.9    2.4  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding


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 !  110.0   0.0   1.2e-34   1.2e-31      33     347 ..      38     345 ..       9     433 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 1.2e-34
                                       EEEEEETTEEEEEEEEXXTTTXEEEEXXX.XXXXXSSXXHHHHHHHHHHTTXEEEEEEEXTTSSEEEEEEEEEXTTS CS
                              FbpA  33 vltlranrgrhkLllsahpsyarihltek.pkenpkeppnFcmlLRkyLkgarivsieqlgfdRivelsiekrdElg 108
                                       +l+lr   g   L ++    + rihl++  p+  +k+   F+ +LR +++ +ri s++q+ ++Riv l+   r    
  gi|320100405|ref|YP_004175997.1|  38 ILKLRCPSGVTHLKIEP---AVRIHLSQSiPE--EKDIDGFTRFLRSRVRDSRILSVRQPWWERIVVLETGAR---- 105
                                       67788667777899999...99****998555..788889*********************************.... PP

                                       XEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS CS
                              FbpA 109 deeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYelPpsqdklnPleaeeleefkellskk 185
                                        e+  + ++E+  r +  ++ d++++Ii + +  + +   +R i p e+Y++Pp  ++ +P ++ +l+   ++l++ 
  gi|320100405|ref|YP_004175997.1| 106 -EKPLRHYIEVVPR-GQWVVADPSDRIIYSTRFTEYR---DRVIKPSETYKPPPF-KGSDPWDSATLR---DRLKE- 172
                                       .888999*******.***************9998777...9**********9999.******988856...44443. PP

                                       .XXXHHHHHHHBTTXXHHHHHHHHTTXS..SSH...............HHHHHHHHTXXX....XXEE......XSS CS
                              FbpA 186 ekdlvkaLvkafqGlspllaeellerag..ldketsakelseedlerlyealqelleeleeekfepqlvlkee.kpe 259
                                        +dlv+aLv+a  Gl +++aee+l+rag   +k+++++e+ + d+erl e++ ++++e +++     lv+  e + +
  gi|320100405|ref|YP_004175997.1| 173 GRDLVRALVTAW-GLPGHIAEEILYRAGllEAKNKRVSEIPSPDVERLIEEYGSIVREASTG--MGYLVYSGEnTLD 246
                                       49*********9.***************7778999************************954..4456666663444 PP

                                       SEESSX...XTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHCCG CS
                              FbpA 260 efsvvp...lkslselekesfdslsealdeyYakkaerdrveqkrsdlekr...veneleklekklkklekelekae 330
                                        ++ ++   ++   + + ++++++++a+d+y+++ + + + +++  +l+     +e++++++e+ +  +++e+ek  
  gi|320100405|ref|YP_004175997.1| 247 IYTSYNpllFRDVYNNSVKQVEDINTAIDAYFTEYEAELERQRRLDELAAAvkeIEARIKRQEEVIRGYREEVEKIG 323
                                       444444686666557888*************98876665555555555544444********************998 PP

                                       GH.....HHHHCCHH------- CS
                              FbpA 331 ka.....enyrligelltayly 347
                                               ny  ++e l + ++
  gi|320100405|ref|YP_004175997.1| 324 RIlqliyGNYASVNEALECARS 345
                                       8777777788888887777655 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 !   78.1   0.0   6.6e-25     7e-22       2     109 .]     447     555 ..     446     555 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 6.6e-25
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia. 77 
                                       ++w  + +g+l i+G+D+++ne++++kyl ++dv++h+d+++++ v+l+ s+g     + e + +a  la+++S+a 
  gi|320100405|ref|YP_004175997.1| 447 FHWLFTRNGFLAIGGRDQSQNEMVVRKYLGDNDVFIHADIHGGSAVVLK-SRGL---HSVEDVVDASYLAACYSRAw 519
                                       99***********************************************.5555...56677889************ PP

                         NFACT-R_1  78 gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       ++ +s ++v++vp s++skt+p    l++G+++++g
  gi|320100405|ref|YP_004175997.1| 520 RAGFSFIEVFWVPGSQVSKTPPsgeyLPRGAFMIYG 555
                                       *********************************986 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.3   1.6e-05     0.017      23      99 ..     265     340 ..     258     343 .. 0.87
   2 ?    0.4   0.2      0.89   9.4e+02      36      55 ..     404     423 ..     379     442 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                       HHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHH CS
                             DUF16  23 kqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRl 99 
                                       kq ++     ++ +++ ea+++ ++ ++++l+ +v++ +++ik++++ +   +ee++k+++ l+li    +++n+ l
  gi|320100405|ref|YP_004175997.1| 265 KQVEDINTAIDAYFTEYEAELE-RQRRLDELAAAVKEIEARIKRQEEVIRGYREEVEKIGRILQLIYGNYASVNEAL 340
                                       6666666667889999999999.7789***************************************99888888765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.89
                                       HHHHHHHHH...HHHHHHHH CS
                             DUF16  36 Lkkieakvdklgeqinkleq 55 
                                       + kie  v++l+e   +l++
  gi|320100405|ref|YP_004175997.1| 404 VGKIESAVKVLEEMRRQLNE 423
                                       12233333333322222222 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036      0.38      37     111 ..     265     341 ..     247     346 .. 0.80
   2 ?    4.1   0.4     0.042        45      48      96 ..     387     428 ..     379     442 .. 0.55
   3 ?   -3.4   0.1       8.8   9.2e+03      15      34 ..     512     531 ..     508     533 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                           DUF1664  37 rslsdavesvskqleqvseslaatkr..hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       +  +d  + +    ++  ++l++++r  +L++ +++++++++ q+e+++  +eev+++ + l+ i  +  sv+ea e
  gi|320100405|ref|YP_004175997.1| 265 KQVEDINTAIDAYFTEYEAELERQRRldELAAAVKEIEARIKRQEEVIRGYREEVEKIGRILQLIYGNYASVNEALE 341
                                       55566666666777777788888885558999999999999999999999999999999999999999999998865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.042
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredl 96 
                                       k l++   +l++ + +L  +i++  k l+e+       +++++e+++ +
  gi|320100405|ref|YP_004175997.1| 387 KGLDKQVVELEKKRGELVGKIESAVKVLEEM-------RRQLNEASSTM 428
                                       4555555555555555555555555555555.......44444444444 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 8.8
                           DUF1664  15 avgYgyvwwkGwklsdlmfv 34 
                                       a+ Y   w  G+++ ++++v
  gi|320100405|ref|YP_004175997.1| 512 AACYSRAWRAGFSFIEVFWV 531
                                       6789999999****999988 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4    0.0002      0.21      10      72 ..     259     322 ..     256     342 .. 0.71
   2 ?    2.4   0.2      0.17   1.8e+02      23      56 ..     395     428 ..     382     439 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                       HHHHS.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH....HHHHHHHH CS
                              OmpH  10 ilees.pegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqe....lqkkeqel 72 
                                       ++++s ++ +++++ ++++f++++aele +++ l++l+++ ++  ++  + ++++e    ++++++++
  gi|320100405|ref|YP_004175997.1| 259 VYNNSvKQVEDINTAIDAYFTEYEAELE-RQRRLDELAAAVKEI-EA--RIKRQEEvirgYREEVEKI 322
                                       667776999******************9.777788888888522.22..4455555544555555555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS CS
                              OmpH  23 qlekkfkklqaeleakekelqklqeelqkkakkl 56 
                                       +lekk+ +l  ++e+  k l++++++l+++++++
  gi|320100405|ref|YP_004175997.1| 395 ELEKKRGELVGKIESAVKVLEEMRRQLNEASSTM 428
                                       7888888888888888888999988888666655 PP

>> Phage_NinH  Phage NinH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.016        17       4      32 ..     318     346 ..     315     350 .. 0.91
   2 ?    4.6   0.0     0.028        30      29      49 ..     467     487 ..     461     498 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                        Phage_NinH   4 svktiPdlLvetyGnqtEvARrlkcsRat 32 
                                       +v  i  +L + yGn   v   l+c R+t
  gi|320100405|ref|YP_004175997.1| 318 EVEKIGRILQLIYGNYASVNEALECARST 346
                                       57788999*******************98 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.028
                        Phage_NinH  29 sRatvRkYvrDkeakqHAivn 49 
                                       +   vRkY+ D +   HA + 
  gi|320100405|ref|YP_004175997.1| 467 NEMVVRKYLGDNDVFIHADIH 487
                                       55679************9665 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.4   0.00025      0.26      88     171 ..     250     330 ..     226     423 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00025
                              Cast  88 dlnqllqqerqesnssgeekeldkelteenflrlqseheRqakeleLLrktleelelRieaqkqtlgardesikkLl 164
                                         n ll ++  +++ + + + ++++  +  f+  ++e eRq + l  L  +++e+e Ri+ q + +    e + k+ 
  gi|320100405|ref|YP_004175997.1| 250 SYNPLLFRDVYNNSVK-QVEDINTA-IDAYFTEYEAELERQRR-LDELAAAVKEIEARIKRQEEVIRGYREEVEKIG 323
                                       5566666663333333.33333333.477899********977.5557899*****************999999999 PP

                              Cast 165 emlqskg 171
                                        +lq   
  gi|320100405|ref|YP_004175997.1| 324 RILQLIY 330
                                       9998643 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0048       5.1      13      65 ..     264     326 ..     257     337 .. 0.68
   2 ?    1.2   0.1      0.48   5.1e+02      17      65 ..     390     428 ..     383     442 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0048
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet..............kvenIqdiL 65 
                                       +k+v+d  +a+++  ++ +++l+     + +Ld+++a+++e+e+              +ve+I  iL
  gi|320100405|ref|YP_004175997.1| 264 VKQVEDINTAIDAYFTEYEAELER----QRRLDELAAAVKEIEArikrqeevirgyreEVEKIGRIL 326
                                       566666666666666666666666....677888888888888755555555555555777777777 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.48
                           NPV_P10  17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       d++V  l+++            el  k+++  + L+e+  ++++ ++++
  gi|320100405|ref|YP_004175997.1| 390 DKQVVELEKK-------RG---ELVGKIESAVKVLEEMRRQLNEASSTM 428
                                       4444444433.......22...244444444444444444444444443 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.24   2.5e+02     105     153 ..     292     340 ..     273     354 .. 0.61
   2 ?    7.7   0.6    0.0018       1.9     100     142 ..     382     424 ..     380     436 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.24
                        FmiP_Thoc5 105 kelaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqeal 153
                                        ela+++ke+e++ k  e+ i+  +++ +++   L+ +  + + ++eal
  gi|320100405|ref|YP_004175997.1| 292 DELAAAVKEIEARIKRQEEVIRGYREEVEKIGRILQLIYGNYASVNEAL 340
                                       2455555666666666666666666666666666655555555555555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                        FmiP_Thoc5 100 EleqRkelaeqlkeleekkkkleqeieekkkfLssLppkLksl 142
                                       El  Rk l++q+ ele+k+ +l  +ie+  k L+++  +L++ 
  gi|320100405|ref|YP_004175997.1| 382 ELSIRKGLDKQVVELEKKRGELVGKIESAVKVLEEMRRQLNEA 424
                                       9999***********************************9875 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 ?   10.0   1.3   0.00058      0.61       5      79 ..     261     331 ..     257     339 .. 0.82
   2 ?   -1.1   0.0       1.5   1.6e+03       3      28 ..     406     431 ..     388     444 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHCHHHHHHHHHHHHHHHHHHHCTHHHH-..-----EE-SS- CS
                      Phage_Mu_Gam   5 nwalrkiaelkreleeieaeaneeiaaik..ekleaeleplkkeieylesllkqYaeankdeLfkdgktKslklpfG 79 
                                       n+ ++++ ++++ ++ + +e+++e ++ +   +l+a++++++++i+  e+ ++ Y e+ +      +  + l+l++G
  gi|320100405|ref|YP_004175997.1| 261 NNSVKQVEDINTAIDAYFTEYEAELERQRrlDELAAAVKEIEARIKRQEEVIRGYREEVE------KIGRILQLIYG 331
                                       66789999999999999998888777666559*************************988......34556666666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Phage_Mu_Gam   3 eanwalrkiaelkreleeieaeanee 28 
                                       ++++a++ + e++r+l+e+ + +  e
  gi|320100405|ref|YP_004175997.1| 406 KIESAVKVLEEMRRQLNEASSTMSIE 431
                                       67788888888888888888877655 PP

>> ASD2  Apx/Shroom domain ASD2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.4   2.6e+03     153     283 ..     297     310 ..     260     343 .. 0.52
   2 ?   11.3   0.9   0.00017      0.18     112     154 ..     393     435 ..     378     439 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                              ASD2 153 evealvkevckpnelekyrmFigDlekvvsLLLsLSgRLarvenaLssldeeadaeekksLeekrklLleQledAke 229
                                       +v                                                                           
  gi|320100405|ref|YP_004175997.1| 297 AV--------------------------------------------------------------------------- 298
                                       22........................................................................... PP

                              ASD2 230 LKenldrRervvseiLakyLseeqlqdYehFvkmKaaLlieqreLeekiklgee 283
                                                                                 +e+e +ik  ee
  gi|320100405|ref|YP_004175997.1| 299 ------------------------------------------KEIEARIKRQEE 310
                                       ..........................................222222222222 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00017
                              ASD2 112 dldlkekkeeLieslskklevLkeeqealleeikanealgeev 154
                                         +l++k+ eL+ ++++ ++vL+e +++l e++++++   ++v
  gi|320100405|ref|YP_004175997.1| 393 VVELEKKRGELVGKIESAVKVLEEMRRQLNEASSTMSIEDKTV 435
                                       369****************************999887666655 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 ?    9.2   0.7    0.0012       1.3      49     111 ..     263     324 ..     257     335 .. 0.87
   2 ?    0.1   0.1      0.76     8e+02      43      69 ..     397     423 ..     382     433 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                             CREPT  49 llkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvks 111
                                        +kqve+  ++++ Y +  eaele  ++l   l++ ++ + ++++++ee ++ ++e +ek+  
  gi|320100405|ref|YP_004175997.1| 263 SVKQVEDINTAIDAYFTEYEAELERQRRLD-ELAAAVKEIEARIKRQEEVIRGYREEVEKIGR 324
                                       57999******************8666665.6788889999*****************99975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.76
                             CREPT  43 keeaekllkqveealellaeYnkrLea 69 
                                       +++  +l+ ++e+a+++l+e   +L++
  gi|320100405|ref|YP_004175997.1| 397 EKKRGELVGKIESAVKVLEEMRRQLNE 423
                                       455667888888888888888888875 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.4    0.0035       3.7     188     255 ..     279     345 ..     254     356 .. 0.58
   2 ?    2.3   0.6     0.059        62     141     182 ..     386     427 ..     375     439 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0035
                              Spc7 188 eaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                                       +++e  e   + +L el  +++e++a i+++++ +   +e++e++   ++ +  ++++++e+++ a++
  gi|320100405|ref|YP_004175997.1| 279 TEYE-AELERQRRLDELAAAVKEIEARIKRQEEVIRGYREEVEKIGRILQLIYGNYASVNEALECARS 345
                                       3222.233346667777777777777777777777777777777777777777777777776665554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.059
                              Spc7 141 kegleenlegleedkelLekqeeeldellpeleeekaeleee 182
                                       ++gl++++ +le+ + +L  + e + ++l+e++++ +e +++
  gi|320100405|ref|YP_004175997.1| 386 RKGLDKQVVELEKKRGELVGKIESAVKVLEEMRRQLNEASST 427
                                       445555555555555555555555555555555544444444 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5    0.0036       3.7      56     105 ..     265     313 ..     257     324 .. 0.83
   2 ?    2.1   0.6      0.16   1.6e+02      72     113 ..     389     430 ..     381     441 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0036
                                       HHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                        DASH_Spc19  56 slaeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskk 105
                                       +  e+i+ +i+  +++ e+ele+ +rr ++L a ++  e r++++e+  +
  gi|320100405|ref|YP_004175997.1| 265 KQVEDINTAIDAYFTEYEAELER-QRRLDELAAAVKEIEARIKRQEEVIR 313
                                       567899***************98.699*****************877655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XX CS
                        DASH_Spc19  72 aekeleklerreetLkaklelqegrlsnaesskkeeeesees 113
                                       ++k++ +le+++ +L  k+e   + l++++++ +e++++ + 
  gi|320100405|ref|YP_004175997.1| 389 LDKQVVELEKKRGELVGKIESAVKVLEEMRRQLNEASSTMSI 430
                                       7899999*************9999999986666655555443 PP

>> DUF3523  Domain of unknown function (DUF3523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   0.00028      0.29      90     138 ..     265     313 ..     257     350 .. 0.83
   2 ?   -0.0   1.0      0.44   4.6e+02     112     163 ..     386     434 ..     382     439 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                           DUF3523  90 rktlqeetkqkqqraqyedeLarkryqdeleaqrkrneellkkqeesvl 138
                                       +++   +t  ++   +ye+eL+r+r  del+a  k+ e  +k+qee ++
  gi|320100405|ref|YP_004175997.1| 265 KQVEDINTAIDAYFTEYEAELERQRRLDELAAAVKEIEARIKRQEEVIR 313
                                       566666778888899******************************9764 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.44
                           DUF3523 112 rkryqdeleaqrkrneellkkqeesvlrqEairiqeqrrkteeeeaeleret 163
                                       rk ++++  +  k++ el+ k e +v+  E++r   ++ ++    + +e +t
  gi|320100405|ref|YP_004175997.1| 386 RKGLDKQVVELEKKRGELVGKIESAVKVLEEMR---RQLNEASSTMSIEDKT 434
                                       677788888888999999999999999999999...4444555555666555 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.9      0.05        53      44     107 ..     286     349 ..     216     351 .. 0.72
   2 ?    5.5   0.2     0.018        19      67     103 ..     390     426 ..     384     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.05
                             THOC7  44 dllldfaafelsierlqllakanerereryeaekeeieseieavreeieelkaqLeearatran 107
                                       + + ++ ++  +++ +++  k  e+ ++ y +e e+i + ++ +  + ++ ++ Le ar tra 
  gi|320100405|ref|YP_004175997.1| 286 ERQRRLDELAAAVKEIEARIKRQEEVIRGYREEVEKIGRILQLIYGNYASVNEALECARSTRAV 349
                                       3344455555666677777777777888888888888899999999999999999999988875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.018
                             THOC7  67 erereryeaekeeieseieavreeieelkaqLeeara 103
                                        +++ ++e+++ e+  +ie++ +  ee++ qL ea  
  gi|320100405|ref|YP_004175997.1| 390 DKQVVELEKKRGELVGKIESAVKVLEEMRRQLNEASS 426
                                       68999****************************9975 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.6      0.43   4.5e+02      35      64 ..     291     320 ..     280     324 .. 0.54
   2 ?    7.8   0.9    0.0031       3.2      34      73 ..     385     424 ..     367     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                        TMF_DNA_bd  35 ikkLrkknkelekeikelkkkleklekele 64 
                                       +++L + +ke e  ik++++ ++ + +e+e
  gi|320100405|ref|YP_004175997.1| 291 LDELAAAVKEIEARIKRQEEVIRGYREEVE 320
                                       455555555555555555554444444443 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0031
                        TMF_DNA_bd  34 tikkLrkknkelekeikelkkkleklekeleeleerlkea 73 
                                       + k L+k++ elek+  el  k+e+ +k lee+++ l ea
  gi|320100405|ref|YP_004175997.1| 385 IRKGLDKQVVELEKKRGELVGKIESAVKVLEEMRRQLNEA 424
                                       5577999999*******************99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (665 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      977  (0.0544927); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); 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: 0.81u 0.28s 00:00:01.09 Elapsed: 00:00:00.43
# Mc/sec: 4683.01
//
Query:       gi|320100406|ref|YP_004175998.1|  [L=91]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 679.04
//
Query:       gi|320100407|ref|YP_004175999.1|  [L=210]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  136.1   0.0    1.3e-39  135.9   0.0    1.0  1  RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
  ------ inclusion threshold ------
       0.18   11.4   0.1        4.1    7.1   0.0    2.5  2  zf_C2H2_13    Zinc finger domain
        0.2   11.6   0.9       0.28   11.1   0.2    1.6  2  Tudor-knot    RNA binding activity-knot of a chromodomain


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 !  135.9   0.0   2.2e-43   1.3e-39       2     195 ..      11     197 ..      10     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 2.2e-43
                      RNA_Me_trans   2 yviEhleeelseWvllEYrhiakevgaenliltslskasleslpeelkslaklelekesveellkelkevkkekvcl 78 
                                       +v+Ehlee ls+W+llEYrh+++ +g++ +++t+++ + ++++    +     +   es+ +++++   v++e v++
  gi|320100407|ref|YP_004175999.1|  11 VVVEHLEEGLSPWILLEYRHLSSIYGSQCVVFTNMPLR-YHRIM---A--RYGKPVAESIVDMVDRG-LVRREDVIV 80 
                                       69**********************************95.55452...2..233455679*****997.89******* PP

                      RNA_Me_trans  79 LDpkaekelspedaeefdvflfGGIlGddpprdRTselrkkg...fegRrLGpvqmttDtAvrvtklvvedkvklee 152
                                       LDp++++el+ +d +++ ++++GGIlGd+ppr RT+el +++   +++ ++G+ q+++D+Av+  + +   ++ ++ 
  gi|320100407|ref|YP_004175999.1|  81 LDPASPRELTYRDLSTARYVVVGGILGDHPPRRRTWELLTSRltgARAFNIGSGQYSIDGAVYYIHYMYL-NKGVDG 156
                                       ****************************************9965556668**************999998.899*** PP

                      RNA_Me_trans 153 ieyvdepelkfnkkesvempfrYvkdeegkpllpegmlellkk 195
                                        +yvd + +++ +   v++pfrY+   +gkpl++ +++ ++ +
  gi|320100407|ref|YP_004175999.1| 157 YRYVDGVSIETPEG-VVRLPFRYPL-VDGKPLISGDLVYYIVN 197
                                       **********9987.8*********.9*******999998865 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00068       4.1      22      38 ..       5      18 ..       4      21 .. 0.85
   2 ?    1.3   0.0     0.044   2.6e+02      18      34 ..      51      66 ..      44      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00068
                        zf_C2H2_13 22 kCGkPisleaivdHLen 38
                                       CGkP+   ++v+HLe+
  gi|320100407|ref|YP_004175999.1|  5 GCGKPV---VVVEHLEE 18
                                      6****9...689**997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.044
                        zf_C2H2_13 18 RvCnkCGkPisleaivd 34
                                      R+    GkP++ e+ivd
  gi|320100407|ref|YP_004175999.1| 51 RIMARYGKPVA-ESIVD 66
                                      777778***97.78888 PP

>> Tudor-knot  RNA binding activity-knot of a chromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   4.6e-05      0.28      31      45 ..     141     155 ..     113     164 .. 0.85
   2 ?   -3.4   0.0       1.5   9.3e+03      37      44 ..     193     200 ..     192     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.6e-05
                                       EEEEEEETTS-CCC- CS
                        Tudor-knot  31 yeYYVHYeefNkRlD 45 
                                         YY+HY  +Nk  D
  gi|320100407|ref|YP_004175999.1| 141 AVYYIHYMYLNKGVD 155
                                       67**********877 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                                       ETTS-CCC CS
                        Tudor-knot  37 YeefNkRl 44 
                                       Y   NkRl
  gi|320100407|ref|YP_004175999.1| 193 YYIVNKRL 200
                                       44568887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1491.97
//
Query:       gi|320100408|ref|YP_004176000.1|  [L=148]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.12   12.3   0.1         12    5.8   0.0    2.1  2  APS_kinase  Adenylylsulphate kinase


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0014        25      40      73 ..      18      51 ..      15      66 .. 0.88
   2 ?    5.8   0.0   0.00067        12      51      79 ..     104     132 ..      85     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0014
                                      HHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHT CS
                        APS_kinase 40 nvRhgLnkdLgfseedRkenirrvaevakllada 73
                                       +R  L  +Lg+ + +R    r ++  ++ la+ 
  gi|320100408|ref|YP_004176000.1| 18 AIRDALGDELGYIDVERVRCYRSIGARTRALARI 51
                                      79***********************999988875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00067
                                       SSHHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                        APS_kinase  51 fseedRkenirrvaevaklladaglivlv 79 
                                          + R  n rrva + ++l+++g + ++
  gi|320100408|ref|YP_004176000.1| 104 LRPHGRYVNNRRVASLYRRLVEKGGVKII 132
                                       5667899****************999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1138.06
//
Query:       gi|320100409|ref|YP_004176001.1|  [L=277]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-50  171.1   0.1    2.8e-50  170.8   0.1    1.1  1  NucS      Endonuclease NucS


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 !  170.8   0.1   1.5e-54   2.8e-50       3     214 ..      30     240 ..      28     254 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 1.5e-54
                              NucS   3 avlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppksslt.aevedgslilksirrkpee 78 
                                       + ++v+ +C+v+yeGr +srL +g+r+++ik dG++lvh+   + PvnWqp  s +  +  e+g+l + ++r kp+e
  gi|320100409|ref|YP_004176001.1|  30 NTVIVIGECSVEYEGRSTSRLGKGDRVLMIKQDGSVLVHRPTGYSPVNWQPDTSVIEaWINERGELSILAVRSKPRE 106
                                       6789**************************************************997256689************** PP

                              NucS  79 eLkveieevehasayeledveelvldGseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivel 155
                                        L++  + v+ +    l+d+ e+++   eae++ +++ +p+Lie Gf+ v+ e  + +G  di g d+eg+ vivel
  gi|320100409|ref|YP_004176001.1| 107 VLNISFSRVDSVIIARLRDDAEFTMYLDEAEMKRVLVGNPELIEPGFRVVEDEKRLGSGQADIYGVDKEGRPVIVEL 183
                                       ***************************************************************************** PP

                              NucS 156 krrkaevdaveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeldpp 214
                                       kr  a  dav qL  yv+ ++  ++ ++ rG+l+aps  + a + l   +le++++d  
  gi|320100409|ref|YP_004176001.1| 184 KRITASRDAVLQLYGYVKAYEATYG-KRPRGILIAPSFSPSAIETLLRLQLEYRQVD-L 240
                                       *************************.778****************9999*****998.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1984.36
//
Query:       gi|320100410|ref|YP_004176002.1|  [L=192]
Description: type 11 methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   61.0   0.0    2.7e-16   60.0   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    2.7e-14   53.6   0.0    1.1e-13   51.7   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    1.4e-08   34.8   0.0    1.8e-08   34.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    5.4e-08   33.5   0.0    1.4e-07   32.1   0.0    1.7  2  Methyltransf_12  Methyltransferase domain
    7.7e-07   29.0   0.0    1.1e-06   28.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    0.00021   20.7   0.0    0.00026   20.4   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0061   16.4   0.0      0.016   15.1   0.0    1.7  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.047   13.0   0.0      0.094   12.0   0.0    1.5  1  CMAS             Mycolic acid cyclopropane synthetase
       0.11   12.9   0.1       0.19   12.1   0.1    1.4  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   1.3e-19   2.7e-16       1      96 []      53     150 ..      53     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.3e-19
                                       EEET-TTSHHHHHHHHTT....SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg....arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhh 73 
                                       Ld+GcGtG+l+e+la+rg    ar++++D+s  m+ + +ek ++ +  v  vv+ ae++p++d+s+D+vvs  ++ +
  gi|320100410|ref|YP_004176002.1|  53 LDAGCGTGLLVEYLAERGldryARYICLDPSVGMISRLSEKPVDYR--VIPVVGYAEEIPLRDSSIDIVVSVTAWSN 127
                                       8**************7777777*************88877777776..5559************************* PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                       +   ++a +e++Rv   gGl+++
  gi|320100410|ref|YP_004176002.1| 128 IGGKREATREFKRVTGRGGLIIV 150
                                       *999****************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   5.5e-17   1.1e-13       2      97 .]      53     146 ..      52     146 .. 0.92
   2 ?   -0.8   0.0       1.3   2.6e+03      68      92 ..     149     174 ..     148     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 5.5e-17
                                       EEET-TTSHHHHHHHCTS..TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrl..gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       Ld+GcGtG l+++la+r+    a+++++D+s +m+ +  e+    +++v  v+g ae++p+ d+s+D+vvs+ a++ 
  gi|320100410|ref|YP_004176002.1|  53 LDAGCGTGLLVEYLAERGldRYARYICLDPSVGMISRLSEKPV--DYRVIPVVGYAEEIPLRDSSIDIVVSVTAWSN 127
                                       9****************87549******************994..459***********************988888 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       +     ++a +e++rv+  gG
  gi|320100410|ref|YP_004176002.1| 128 IG--GKREATREFKRVTGRGG 146
                                       77..6679*********9998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                                       EEEESTGGG.SSHHHHHHHHHHHHHH CS
                   Methyltransf_25  68 vvssgalhh.lsdedlekalkeiarv 92 
                                       +vss++ hh ++++  ++++k+ia++
  gi|320100410|ref|YP_004176002.1| 149 IVSSHVKHHsTPPALFDACFKKIAEH 174
                                       67766766646666678899988876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   8.8e-12   1.8e-08      16     143 ..      42     175 ..      25     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 8.8e-12
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengf....svtgvDlspeaveiae...kakkaqkdqfdeqeaaepqgkfdl 85 
                                       ll++   ++ +Ld GcGtG l e+l+e+g      ++  D+s  ++++++    ++  +++  +++e++  + ++d+
  gi|320100410|ref|YP_004176002.1|  42 LLTRYMDSATLLDAGCGTGLLVEYLAERGLdryaRYICLDPSVGMISRLSekpVDYRVIPVVGYAEEIPLRDSSIDI 118
                                       5555667899*****************99665679**************9999999999****************** PP

                   Methyltransf_23  86 IvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhi 143
                                       +v+     ++    e+ r +++ +  gG++++s + + ++++  +l  ++  +  +hi
  gi|320100410|ref|YP_004176002.1| 119 VVSVTAWSNIGGKREATREFKRVTGRGGLIIVSSHVK-HHSTPPALFDACFKKIAEHI 175
                                       ***********************************75.57776666666666655666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   7.1e-11   1.4e-07       1      98 [.      53     147 ..      53     148 .. 0.82
   2 ?   -1.5   0.0       2.2   4.3e+03      70      80 ..     149     169 ..     147     185 .. 0.56

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 7.1e-11
                   Methyltransf_12   1 LeiGcGtGsllrallekl..pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnv 75 
                                       L+ GcGtG l+++l+e+   + ++y+++D+s  +i + +ek  +++     +v + ++    +d  ss D+vv+  +
  gi|320100410|ref|YP_004176002.1|  53 LDAGCGTGLLVEYLAERGldRYARYICLDPSVGMISRLSEKPVDYR--VIPVVGYAEEIP-LRD--SSIDIVVSVTA 124
                                       89*********************************55555544444..455555554444.444..4********** PP

                   Methyltransf_12  76 lhhlkdirevldnirklLkpgGr 98 
                                        +++  +re+ ++++++   gG 
  gi|320100410|ref|YP_004176002.1| 125 WSNIGGKREATREFKRVTGRGGL 147
                                       *****************999997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                   Methyltransf_12  70 vvasnvlhhl..........k 80 
                                       +v+s+v hh           k
  gi|320100410|ref|YP_004176002.1| 149 IVSSHVKHHStppalfdacfK 169
                                       677788888644433332233 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   5.5e-10   1.1e-06       5     116 ..      50     157 ..      47     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.5e-10
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgp.kaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                        ++lD+GCGtG l+  lae+  +  a+++ +D s  +i++  e    + +d +v   +g +ee++  l d+++D+++
  gi|320100410|ref|YP_004176002.1|  50 ATLLDAGCGTGLLVEYLAERGLDrYARYICLDPSVGMISRLSE----KPVDyRVIPVVGYAEEIP--LRDSSIDIVV 120
                                       579***************955554799***********99888....46666788899*******..99******** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedprlla 116
                                       s  +   +  + ++ +e +rv   gg ++++++  + 
  gi|320100410|ref|YP_004176002.1| 121 SVTAWSNIGGKREATREFKRVTGRGGLIIVSSHVKHH 157
                                       **999***************************99333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.3e-07   0.00026      33     153 ..      34     152 ..      16     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHH.EEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TT CS
                   Ubie_methyltran  33 rlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekg.kvvvlDinenmLkvgekklkeegkinieflqanae 108
                                        ++   v  l+    +a++lD  +Gtg l   l++   +++ + + lD +  m++   +k  +   +++  +++ ae
  gi|320100410|ref|YP_004176002.1|  34 SKYGVLVALLTRYMDSATLLDAGCGTGLLVEYLAERGLDRYaRYICLDPSVGMISRLSEKPVD---YRVIPVVGYAE 107
                                       444445555555667889***********999998765554389999******9866665544...5788899**** PP

                                       T-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 109 eLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                       e+p  d s D+v       n+  k +a +e  rv   GG ++v  
  gi|320100410|ref|YP_004176002.1| 108 EIPLRDSSIDIVVSVTAWSNIGGKREATREFKRVTGRGGLIIVSS 152
                                       ***********9999999*********************987743 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.1e-06     0.016     102     157 ..      93     151 ..      24     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.1e-06
                                       S-SSTTEEES-T..TS-S--TT-EEEEEEES..---SS-HHHHHHHHHHHEEEEEEEEEE CS
                    Methyltransf_8 102 vavnervvacdl..akvPledesvdvavfcl..slmgtnladflkeanrvlkvGGllkva 157
                                       ++v+ rv++      ++Pl d+s+d++v     s +g   ++ ++e +rv   GGl+ v+
  gi|320100410|ref|YP_004176002.1|  93 KPVDYRVIPVVGyaEEIPLRDSSIDIVVSVTawSNIGG-KREATREFKRVTGRGGLIIVS 151
                                       5677778765322389**********987651155554.5789*************9886 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.7e-05     0.094      48     172 ..      33     158 ..      19     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHTTT.T--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG CS
                              CMAS  48 laKldlilekl.elkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyed 123
                                       ++K+ +++  l +  +  tlLd GcG G lv + +er + +  +  +  +    +  r+ e  + + + + + +y +
  gi|320100410|ref|YP_004176002.1|  33 YSKYGVLVALLtRYMDSATLLDAGCGTGLLVEYLAER-GLDRYARYICLDPSVGMISRLSEKPV-DYRVIPVVGYAE 107
                                       5555555555423456789**************9999.77766666666666666666666553.344566667754 PP

                                       ...---.--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--H CS
                              CMAS 124 ...lde.kvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitslhk 172
                                          l++  +d vvsv a   +g ++ +t  +++k+++ ++Gl+++ + ++ h+
  gi|320100410|ref|YP_004176002.1| 108 eipLRDsSIDIVVSVTAWSNIGGKREAT--REFKRVTGRGGLIIVSSHVKHHS 158
                                       33355579999*******9999988765..77888888999998888777665 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.3e-05      0.19      59      85 ..      49      75 ..      21      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-05
                      AdoMet_MTase 59 etsfvdvgcgngllvyvlaaegykgyg 85
                                        ++ d gcg gllv  la  g   y 
  gi|320100410|ref|YP_004176002.1| 49 SATLLDAGCGTGLLVEYLAERGLDRYA 75
                                      46789**************99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1504.81
//
Query:       gi|320100411|ref|YP_004176003.1|  [L=93]
Description: LSM family small nuclear ribonucleoprotein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-18   64.1   0.0    7.9e-18   63.9   0.0    1.1  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.043   13.9   0.3      0.063   13.4   0.3    1.2  1  LSM14     Scd6-like 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 !   63.9   0.0   8.8e-22   7.9e-18       2      66 ..      16      80 ..      15      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 8.8e-22
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                       lk+  +++++v+ k+g e++GtL  +D  mN+vL+d++e++ ++k + ++g+++iRG+++ +is
  gi|320100411|ref|YP_004176003.1| 16 VLKSAEGQIILVRIKGGYEYIGTLDLIDGTMNIVLSDCTEYSSEGKPTSRYGRIIIRGSHVEFIS 80
                                      6999*****************************************99999***********9997 PP

>> LSM14  Scd6-like Sm domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3     7e-06     0.063       4      67 ..      22      76 ..      21      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-06
                             LSM14  4 GskislisksdirYeGilceinledstiaLqnvrsfGtegrkdneqippskevyeyivFrgsDi 67
                                      G+ i + +k +  Y G+l  i+    +i L++ + +  eg+++++        y  i+ rgs +
  gi|320100411|ref|YP_004176003.1| 22 GQIILVRIKGGYEYIGTLDLID-GTMNIVLSDCTEYSSEGKPTSR--------YGRIIIRGSHV 76
                                      88999*****************.8899*************76443........56666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 697.17
//
Query:       gi|320100412|ref|YP_004176004.1|  [L=291]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-11   44.1   1.3    2.8e-10   40.5   0.1    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
    2.7e-09   36.8   0.0    7.7e-09   35.4   0.0    1.7  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.027   13.9   0.0      0.042   13.3   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 !   40.5   0.1   4.7e-14   2.8e-10       7      89 ..      31     116 ..      27     165 .. 0.82
   2 ?    2.7   0.1     0.018   1.1e+02     134     197 .]     190     262 ..     185     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 4.7e-14
                                       EEEEEE.....ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B   7 nsylie.....gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                        syl+      g + ++L+DtG+ +ea +    +  lgl  +dvd+++l+H H+DH+ gl+ l ++++ +  +  ++
  gi|320100412|ref|YP_004176004.1|  31 VSYLVKatmeeGSEVTVLFDTGYNGEAVLRN--MEVLGLSFDDVDYIVLSHNHYDHANGLPTLLKTAGRKRLVPVIV 105
                                       6777777777788999*************85..8********************************99888888888 PP

                                       HHCCHCHHHHH CS
                       Lactamase_B  79 apalfmeeadd 89 
                                       ++ +f++ +  
  gi|320100412|ref|YP_004176004.1| 106 GKGFFHRSVAL 116
                                       88888777754 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.018
                                       CEEEEEETTCCEEEECTTTSSHHCCCCCC...........TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 134 ghgvveygggkvlftGDallagetgridl..........tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       +++ v+++ g +l++G+  +    +               ++g++  d+++++ ++ ++  l++l +e++v+gH
  gi|320100412|ref|YP_004176004.1| 190 VSLAVRSRKGILLLVGCSHPGVASIARKAssvlgdrihmVMGGFHLVDADEHRIAR-TIQALRELGVEKVVAGH 262
                                       55666666777777777777444444444577788888999999999******999.9***************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 !   35.4   0.0   1.3e-12   7.7e-09       3      67 ..      47     110 ..      46     180 .. 0.71
   2 ?   -1.5   0.1      0.25   1.5e+03     182     200 ..     244     262 ..     219     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.3e-12
                                       EEES--TTHHHH.HTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EE..EEEEEEHHHH CS
                     Lactamase_B_2   3 iLiDagpdlrqq.alralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkk..lplyapkgvl 67 
                                       +L+D+g +  +   lr     e l  +++++d ++l+h+HyDH +gl+tl +++++k  +p+++ kg  
  gi|320100412|ref|YP_004176004.1|  47 VLFDTGYN--GEaVLRN---MEvLGLSFDDVDYIVLSHNHYDHANGLPTLLKTAGRKrlVPVIVGKGFF 110
                                       78999998..2212333...355788999***********************66666679998665543 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.25
                                       TSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 182 eeaveaaadlgakrlvliH 200
                                         +++a+++lg++++v  H
  gi|320100412|ref|YP_004176004.1| 244 ARTIQALRELGVEKVVAGH 262
                                       6789999999999999888 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 ?   13.3   0.0     7e-06     0.042       6      61 ..      44      97 ..      39     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7e-06
                     Lactamase_B_6  6 nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfks 61
                                      +v++L D G +++ v   + ++ l    ++vd i+Lsh   +h  +++ l++++++
  gi|320100412|ref|YP_004176004.1| 44 EVTVLFDTGYNGEAV--LRNMEVLGLSFDDVDYIVLSHNHYDHANGLPTLLKTAGR 97
                                      799********9855..45788888899********************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2081.00
//
Query:       gi|320100413|ref|YP_004176005.1|  [L=280]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-09   37.5   0.0    9.3e-09   35.9   0.0    1.9  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.27   11.0   0.0    1.4  1  GATase       Glutamine amidotransferase class-I


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 !   35.9   0.0     1e-12   9.3e-09       3     162 ..      16     169 ..      14     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1e-12
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESS.TGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilggg.epllypdfvellerlaklavpgi 78 
                                       ++ +C l+C+fC  ++     ++  +ls ++  e+++ l +e gv++++++gg +   y +++ +++ l+  + +++
  gi|320100413|ref|YP_004176005.1|  16 TGSACWLNCRFCRGKY----LRHMTHLSRDRAGEILRGL-YESGVRGILVSGGfTREGYLPIEGFIDVLRDAR-RKY 86 
                                       6789***********6....9******************.799988888887736788999999999999984.455 PP

                                       EEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd.eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                        + + +  +l + +  le+l+   +d+v       ++  + k+++  + ++e++le+l+++ +ag+++v + ++ +p
  gi|320100413|ref|YP_004176005.1|  87 GFIYNAHLGLQRdRSTLEALRGI-IDVVDYEFTLSNY--IAKYVRgLPVNVEAYLESLKLMSDAGLHVVPHLYLWHP 160
                                       55555555554478888888885.5999999866666..899999988***************************** PP

                                       TTSHHHHHH CS
                                       xxxxxxxxx RF
                       Radical_SAM 154 Gendeelee 162
                                       G+++e ++ 
  gi|320100413|ref|YP_004176005.1| 161 GFSKEVFRR 169
                                       **9997665 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     3e-05      0.27      39      69 ..      51      84 ..      29      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3e-05
                                      THHSTSEEEEEEESSCTT...TTTHHHHHHHHCT CS
                            GATase 39 llknpdgilvsgGpgspg...vegkieaikeare 69
                                       ++++ gilvsgG+   g   +eg i++++ ar 
  gi|320100413|ref|YP_004176005.1| 51 YESGVRGILVSGGFTREGylpIEGFIDVLRDARR 84
                                      47899*************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2016.52
//
Query:       gi|320100414|ref|YP_004176006.1|  [L=307]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   31.7   2.5    1.9e-05   25.1   0.6    3.0  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 !   25.1   0.6   1.1e-09   1.9e-05      76     162 ..     106     190 ..      34     194 .. 0.63
   2 ?    0.1   0.1     0.051   9.1e+02       9      33 ..     263     291 ..     262     303 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-09
                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr..vvdriv 150
                                       + + i++ + ++   + +le+++elgv  + +gl++a+ e + k+  +++t+e ++  +e++ e+ + r  v++ ++
  gi|320100414|ref|YP_004176006.1| 106 SRLPISLAITPVP--KGVLEEFKELGVSELGVGLDTATRELFAKWG-KPYTWEIYWSFIENAVEV-FGRgrVYVHLI 178
                                       4445555444444..779**********************999999.77****************.77779665555 PP

                                       EBTTTSHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeelee 162
                                       ++ Ge  +e ++
  gi|320100414|ref|YP_004176006.1| 179 VGLGERLREAVD 190
                                       566666555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.051
                                       S--TTTSCCTT....HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxx....xxxxxxxxxxxxxx RF
                       Radical_SAM   9 lrCsfCarpet....vrregrgrslsvee 33 
                                       ++C+ C+rp+     ++ + ++  +++e+
  gi|320100414|ref|YP_004176006.1| 263 RGCPGCNRPFYtdlpSSIYNYPSRRTLEK 291
                                       68*******98888844444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2116.30
//
Query:       gi|320100415|ref|YP_004176007.1|  [L=252]
Description: biotin/lipoate A/B protein ligase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   45.1   0.0    1.4e-11   44.5   0.0    1.3  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   7.6e-16   1.4e-11       2     130 ..      50     163 ..      49     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 7.6e-16
                                       EEEES-HHHHHH..GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHH CS
                     BPL_LplA_LipB   2 gevikstntllkeslnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavl 76 
                                       g+++k +     es+ +    s+g++v+rr +gG  v+h++ ge+ty ++l ++   + ++v e y  +++  +  l
  gi|320100415|ref|YP_004176007.1|  50 GYFQKVE-----ESVDLGYASSRGIDVTRRISGGGSVYHDASGEVTYGIVLPARG--VFSDVRESYeaICRGLVESL 119
                                       5666665.....77777888999*****************************886..44466666666666666555 PP

                                       HHH......HHTT-TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEE CS
                     BPL_LplA_LipB  77 ealgyrdskpgiegipvfikwpnDlyvngrKlaGiavtstrgktlhhivigvgv 130
                                       + l       g   + +     nD++vngrK++G+a+ +++g  l+h++++  +
  gi|320100415|ref|YP_004176007.1| 120 RIL-------GVDAAFAP---VNDIVVNGRKISGSAQARRKGFLLQHGTMMYAT 163
                                       555.......55555555...9**************************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1858.73
//
Query:       gi|320100416|ref|YP_004176008.1|  [L=96]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-07   29.5   0.1    1.2e-06   28.4   0.0    1.5  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus


Domain annotation for each model (and alignments):
>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   6.5e-11   1.2e-06      16      57 ..      12      55 ..       9      71 .. 0.87
   2 ?   -1.4   0.0      0.13   2.3e+03      48      65 ..      67      86 ..      55      90 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6.5e-11
                                      EEEEEEEEETTEEEEEEEEESBSS.SSHC.HHHHHHHTTSBSSH CS
                    Lip_prot_lig_C 16 tvevrldvekgiIkdikiyGDffg.pkdi.eeleekLigvkyek 57
                                      tve++++v++ +Ik++ ++GDff  p+d+ e+lee+L+++  ++
  gi|320100416|ref|YP_004176008.1| 12 TVEIEVEVSDCRIKRVVFSGDFFAyPDDVvEKLEEALKDCGSDE 55
                                      79*********************7688877********997665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.13
                                      HHHTTSBSS..HHHHHHHHH CS
                    Lip_prot_lig_C 48 ekLigvkye..keaieeale 65
                                      + Ligv+++  ++++++al+
  gi|320100416|ref|YP_004176008.1| 67 ALLIGVEWDvlENEVRNALK 86
                                      56777766533566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 740.18
//
Query:       gi|320100417|ref|YP_004176009.1|  [L=246]
Description: zinc/iron permease [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-11   43.3   7.2    2.8e-11   43.3   7.2    2.6  2  Zip         ZIP Zinc transporter
  ------ inclusion threshold ------
      0.054   12.9   7.4        0.3   10.4   2.9    2.5  2  ThrE        Putative threonine/serine exporter
        9.2    5.8   5.9       0.55    9.8   0.4    1.8  2  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   5.2    0.0072        43     282     332 ..      43      82 ..      18      83 .. 0.73
   2 !   43.3   7.2   4.6e-15   2.8e-11     182     328 ..     104     238 ..      88     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0072
                               Zip 282 llalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmlll 332
                                        l++s+G+++ v++  l   El           s ++l+++++Gfa+m ll
  gi|320100417|ref|YP_004176009.1|  43 SLGFSGGVMIAVSFSMLYEGEL-----------SAYKLVFFTAGFAVMWLL 82 
                                       4689999999888754444333...........446699999999999887 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 4.6e-15
                               Zip 182 lkvraiilllglilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkav...llnllfa 253
                                       +  +a+++ +++ilH++++GLA+G  +  +   g+s+ +A+ +  ++e++  g++ + +g + +  +   +++l+ a
  gi|320100417|ref|YP_004176009.1| 104 RLKIAWLIAFSMILHNVPEGLAVGssTVRNPVLGFSVAVAIGVQDVVEGFMAGLPYVITGDRGRAFLlslIAALAEA 180
                                       4457*********************99999********************999998888876666666777777778 PP

                               Zip 254 ltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfal 328
                                       l+++ + ++Gi+            + + l  +s+G ++ +   e++p E ++e+       s  + +g+llG++ 
  gi|320100417|ref|YP_004176009.1| 181 LASLGAGFLGIV---------EAGALAPLTCFSSGAMVFIVSHEIIP-ETHREH-------SSESTAGFLLGVMA 238
                                       888888888888.........566677899*****************.******.......67777777777765 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1    0.0039        23     115     147 ..      49      82 ..      34      94 .. 0.75
   2 ?   10.4   2.9   5.1e-05       0.3     114     176 ..     180     242 ..     165     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0039
                              ThrE 115 aglaaaafallfggdwidflvaflagll.ggllr 147
                                         ++a++f++l +g++ +  ++f+++++ +++l 
  gi|320100417|ref|YP_004176009.1|  49 GVMIAVSFSMLYEGELSAYKLVFFTAGFaVMWLL 82 
                                       568899********99999877776665155554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.1e-05
                              ThrE 114 aaglaaaafallfggdwidflvaflagllggllrlllakrglnsfvleavaaflasllallav 176
                                       a + ++a+f  +++++ ++ l +f  g++++++++ +   ++ +  +e +a+fl +++a++++
  gi|320100417|ref|YP_004176009.1| 180 ALASLGAGFLGIVEAGALAPLTCFSSGAMVFIVSHEIIPETHREHSSESTAGFLLGVMAATVL 242
                                       3344456777778**********************************************8876 PP

>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.9         1   6.3e+03       8      35 ..      21      48 ..      16      58 .. 0.69
   2 ?    9.8   0.4   9.1e-05      0.55      33      54 ..     137     158 ..     103     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1
                                      HHHHHHHHHHHTTT--SCCHHHHHHHHH CS
                        MS_channel  8 iivvgilivlsllgvnvsallavlGalg 35
                                        +vgil vl  +  +v  + a+lG+ g
  gi|320100417|ref|YP_004176009.1| 21 SSIVGILPVLAGFKPPVRWIDASLGFSG 48
                                      4577888888888888888888888866 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 9.1e-05
                                       HHHHHHHHHHCHHHHHHHHHHH CS
                        MS_channel  33 alglalglalkdlisnlvaGii 54 
                                         ++a++++++d++++++aG+ 
  gi|320100417|ref|YP_004176009.1| 137 GFSVAVAIGVQDVVEGFMAGLP 158
                                       3589****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1958.44
//
Query:       gi|320100418|ref|YP_004176010.1|  [L=273]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2065.91
//
Query:       gi|320100419|ref|YP_004176011.1|  [L=122]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-21   75.0   0.0    5.1e-21   74.8   0.0    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   2.9e-25   5.1e-21       3      94 ..      14     108 ..      12     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 2.9e-25
                                       SCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSS..CSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSE CS
                     Nitro_FeMo-Co   3 srvdqhFGrapyFaiyeveegevkivenrveeaadaeg..ggggklaqllaeegvdvvivgkiGpralakleaagie 77 
                                       + v+ hFG+apyFa+yev++ ++k ++ + +++a+ ++  ++g+++a+ l ++gv++vi+ ++Gp+a+++l+++gi+
  gi|320100419|ref|YP_004176011.1|  14 NYVSLHFGKAPYFAFYEVSDTGFKQLSLERNPFATMGSgsSKGQAIARYLVSKGVEAVIAYEVGPGAFQHLRDHGIR 90 
                                       5799********************88888444444444459999********************************* PP

                                       EEES.-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  78 vykg.aggtveealkevl 94 
                                       v+++    ++eealk ++
  gi|320100419|ref|YP_004176011.1|  91 VFVVeKTLPIEEALKLFI 108
                                       ****99*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 956.10
//
Query:       gi|320100420|ref|YP_004176012.1|  [L=80]
Description: FeoA family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   63.6   0.2    1.6e-17   63.5   0.2    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.2   9.1e-22   1.6e-17       1      73 [.       3      73 ..       3      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 9.1e-22
                                      EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      ++L+ +++G r++i++i ++ +    rL ++G+ pG  +evv ++ ++gp+v+rv++++v+Lg+++A++I Ve
  gi|320100420|ref|YP_004176012.1|  3 TTLDSAPPGSRVRISSILHH-GGWVHRLYQLGVFPGVIVEVV-HNEGRGPVVIRVNGSEVVLGKGLARRIVVE 73
                                      69***************999.99*******************.79***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 602.67
//
Query:       gi|320100421|ref|YP_004176013.1|  [L=695]
Description: small GTP-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-47  158.4   0.2      2e-46  157.3   0.2    1.5  1  FeoB_N       Ferrous iron transport protein B
    2.2e-23   82.6  26.1    1.2e-18   67.5   7.2    3.2  3  Gate         Nucleoside recognition
    9.3e-20   70.8   0.1    1.8e-19   69.9   0.1    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
    1.8e-09   38.0   0.1    3.6e-09   37.0   0.1    1.4  1  FeoB_Cyto    FeoB cytosolic helical domain
    2.9e-05   23.7   0.5    2.9e-05   23.7   0.5    3.3  3  FeoB_C       Ferrous iron transport protein B C terminus
    0.00014   21.5   0.0    0.00027   20.6   0.0    1.4  1  Ras          Ras family
    0.00028   20.4   0.1    0.00058   19.4   0.1    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
    0.00061   19.4   0.1     0.0034   16.9   0.1    2.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0011   18.5   0.1     0.0023   17.4   0.1    1.6  1  Arf          ADP-ribosylation factor family
     0.0065   16.4   0.8        3.5    7.5   0.1    2.3  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.032   14.5   0.0    1.5  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.034   13.8   0.0      0.061   12.9   0.0    1.3  1  SRP54        SRP54-type protein, GTPase domain
      0.037   13.4   0.0      0.059   12.7   0.0    1.3  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
        0.1   11.7   0.1       0.15   11.0   0.1    1.2  1  IIGP         Interferon-inducible GTPase (IIGP)


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 !  157.3   0.2   1.6e-49     2e-46       2     156 .]       7     161 ..       6     161 .. 0.99

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 1.6e-49
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       +v ++G+pnvGk+++fn +t+++ +vgNwpG+tv  ++g++++kg+++ ++DlPGiY +++ ++ee var+ +l e+
  gi|320100421|ref|YP_004176013.1|   7 KVLFIGQPNVGKSSIFNMVTKSHVEVGNWPGKTVAVNKGEVSFKGYKLILYDLPGIYGFTTLTQEELVAREAILLEK 83 
                                       7999************************************************************************* PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                       pdvvv vvd+t  er++ L +q+lel+ +vvl++ ++d a+ +gi+i+ + ++++L+vpvv++s  ++ ++e+ll++
  gi|320100421|ref|YP_004176013.1|  84 PDVVVVVVDSTIPERTMNLAIQVLELTGRVVLVFSKTDLAHGRGIHINYEGVARELNVPVVPVSIVSGFEVERLLDE 160
                                       **************************************************************************987 PP

                                       H CS
                            FeoB_N 156 i 156
                                       i
  gi|320100421|ref|YP_004176013.1| 161 I 161
                                       6 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3       2.1   2.7e+03       7      37 ..     296     351 ..     286     364 .. 0.50
   2 !   25.1   5.2   1.3e-08   1.7e-05       2     110 ..     375     468 ..     374     470 .. 0.92
   3 !   67.5   7.2     9e-22   1.2e-18       2     109 ..     538     661 ..     537     664 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.1
                              Gate   7 iillasiliwflss.........................ssllgrigkllepvfap 37 
                                       i l +++l+  l+                          s+l+++   +l+ ++ p
  gi|320100421|ref|YP_004176013.1| 296 IYLSIFMLVFTLNTgfplntilsamgfenaasiveeyslSGLVEKSFTALTSMLEP 351
                                       33333333333333555555555555555555555544444444444444444444 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.3e-08
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       l ++p+i++++i+  + ++s+l+ r++ +   +f+++g  l++ a+ ++++gf+   ++v+++  ++         +
  gi|320100421|ref|YP_004176013.1| 375 LVFLPLIIVMVIVQVIVEDSGLAPRLAVASHSFFSKMG--LSGHAFFPFMLGFG---CNVPAVLATR---------T 437
                                       67899*********************************..**************...******9998.........8 PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrelg 110
                                         + +++l +ll++++ +pc a+l+v+  +++
  gi|320100421|ref|YP_004176013.1| 438 NPNSVERLRLLLTLSF-IPCQARLVVLLAFTS 468
                                       8888999999999999.69******9988765 PP

  == domain 3  score: 67.5 bits;  conditional E-value: 9e-22
                              Gate   2 lkagpiillasiliwflss............ssllgrigkllepvfaplg..qeldwkatvslltgfaakevvvgtl 64 
                                       ++ag +i+++s+++wf++s             s+++++++ l+ + aplg      w ++ s++tgf+ake+vv+tl
  gi|320100421|ref|YP_004176013.1| 538 KRAGLVIFAGSMFVWFITSfttsltytgnmdESIASIASRGLQFITAPLGitGGNAWIIALSIITGFIAKELVVSTL 614
                                       89*************************************************999*********************** PP

                              Gate  65 gtly..tsalgellqgfdtpksalafllfvllytpcvatlavivrel 109
                                        +     +  g+++    +  + +++ +f++ly+pc+at+a+i++e+
  gi|320100421|ref|YP_004176013.1| 615 LVATgsDTVRGAMSVLGLSDLQLFSLAVFTTLYMPCLATVATIYSES 661
                                       7776667889**********************************997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.1   1.4e-22   1.8e-19       1      97 [.       7     106 ..       7     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.4e-22
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee 75 
                                       +v+++G+pNvGKS+++n  t+++++v+++pg+T  +n+g+v++kg +++l+D+pG++   +  +e+ ++++   le+
  gi|320100421|ref|YP_004176013.1|   7 KVLFIGQPNVGKSSIFNMVTKSHVEVGNWPGKTVAVNKGEVSFKGYKLILYDLPGIYGftTLTQEELVAREAILLEK 83 
                                       589****************************************************9855444455555555555788 PP

                                       TSEEEEEEETT..TTCSHHHHHHH CS
                          MMR_HSR1  76 adlillvvdas..eeklkpldeel 97 
                                        d++++vvd++  e    +l  ++
  gi|320100421|ref|YP_004176013.1|  84 PDVVVVVVDSTipE-RTMNLAIQV 106
                                       9********55532.222333333 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   2.8e-12   3.6e-09       6      89 ..     183     267 ..     180     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.8e-12
                         FeoB_Cyto   6 EkaiekleellkesnlkaklppRwlAlklLegDeelleelk..edpelraeveearkeleaelgedledvIvdaryk 80 
                                        + +++lee+l+ s   +++p+Rw+A++lLegD+ l+e +k   + +  ++vee+  e ++ +g  + + I++ar+k
  gi|320100421|ref|YP_004176013.1| 183 NEYVDSLEEMLSRSGRLKEYPARWVAVRLLEGDSVLEEVVKstLSSDEFKRVEELLGEARRLIGVPA-ERITEARFK 258
                                       577899********9999**********************955337999999999999999998765.579****** PP

                         FeoB_Cyto  81 fiegilrev 89 
                                       +i++i+++ 
  gi|320100421|ref|YP_004176013.1| 259 LINAIASKH 267
                                       *****9986 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.7       9.1   1.2e+04       9      15 ..     296     302 ..     290     317 .. 0.50
   2 !   23.7   0.5   2.3e-08   2.9e-05       2      50 ..     480     529 ..     479     531 .. 0.89
   3 ?   -1.3   0.5       1.5   1.9e+03       8      21 ..     595     608 ..     593     613 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9.1
                            FeoB_C   9 ilvallv 15 
                                       i + +++
  gi|320100421|ref|YP_004176013.1| 296 IYLSIFM 302
                                       3333322 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.3e-08
                            FeoB_C   2 fslYllgilvallvalllkktt.lkgepspfvmELPpYrlPslknvlikt 50 
                                       +s Yll ++v+l+v ++l k+     +++ ++mE P  ++P ++ v  kt
  gi|320100421|ref|YP_004176013.1| 480 LSSYLLAVAVFLVVNYVLYKLSrSDAKEPQLLMEVPAFHRPLARVVYWKT 529
                                       789***************9975555666******************9998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.5
                            FeoB_C   8 gilvallvalllkk 21 
                                        i++ +++++++k 
  gi|320100421|ref|YP_004176013.1| 595 IIALSIITGFIAKE 608
                                       6899999**99987 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.1e-07   0.00027       1     158 [.       7     163 ..       7     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                       EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEE CS
                               Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegill 77 
                                       K++++G+ +vGK+s+ +  +k++ +    +       +++ ev+ k +kl ++D  G   f++l++  +   e+ill
  gi|320100421|ref|YP_004176013.1|   7 KVLFIGQPNVGKSSIFNMVTKSHVEVGNWPGK--TVAVNKGEVSFKGYKLILYDLPGIYGFTTLTQEELVAREAILL 81 
                                       899**************999999887777644..55777778888999***************************97 PP

                                       .....EEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTH CS
                               Ras  78 .....vyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenv 149
                                            v  + +++  e+  ++  ++ + +     +vLv  K+Dl++ r ++ +  e +a+el+++ + +S  +  +v
  gi|320100421|ref|YP_004176013.1|  82 ekpdvVVVVVDSTIPERTMNLAIQVLELTG---RVVLVFSKTDLAHGRGIHINY-EGVARELNVPVVPVSIVSGFEV 154
                                       544425555566666667788888888887...59***************9987.679******************* PP

                                       HHHHHHHHH CS
                               Ras 150 eeafeellr 158
                                       e +++e+++
  gi|320100421|ref|YP_004176013.1| 155 ERLLDEIIN 163
                                       **9999987 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   4.5e-07   0.00058       5      92 ..       7     100 ..       4     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.5e-07
                                       EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG....GGTT-SEEEETT-GCCSHHHHHHHHHHGGEE... CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkv.ksekgskltliDfPGheklrqklleklkaksslk... 77 
                                       +vl++G  + GK s+f+ +t+ +v+      ++ a++k   s kg kl l D+PG   + +   e+l+a++ +    
  gi|320100421|ref|YP_004176013.1|   7 KVLFIGQPNVGKSSIFNMVTKSHVEVGNWPGKTVAVNKGeVSFKGYKLILYDLPGIYGFTTLTQEELVAREAILlek 83 
                                       69********************999888877666666654688************9999888888888777743222 PP

                                       ..EEEEEEETTS-HHHH CS
                             SRPRB  78 ..glvfvvDStidpkev 92 
                                          +v vvDSti ++ +
  gi|320100421|ref|YP_004176013.1|  84 pdVVVVVVDSTIPERTM 100
                                       326999******99876 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 !   16.9   0.1   2.7e-06    0.0034      53     191 ..      37     164 ..       4     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                                       TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHH........HHT-SEEEEEEETTTBSTHHHHHHHHHHHHT CS
                          GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFskevirg........lrvlDgavlvvdaveGvepqteevlrlalke 121
                                       g T+ ++  +++   k y++ l D PG   F+  + +         l++ D++v+vvd++  + ++t +++ ++l++
  gi|320100421|ref|YP_004176013.1|  37 GKTVAVNKGEVS--FKGYKLILYDLPGIYGFTTLTQEElvareailLEKPDVVVVVVDST--IPERTMNLAIQVLEL 109
                                       677888888888..99***************98877665555677888999999999998..99************* PP

                                       TTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 122 gvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                         +++++  K D + +  +    e v ++l                +vpvv++S ++g++v+ ll+ +++ 
  gi|320100421|ref|YP_004176013.1| 110 TGRVVLVFSKTDLAhGRGIHINYEGVAREL----------------NVPVVPVSIVSGFEVERLLDEIINV 164
                                       **************6666666677777777................599*****************99986 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.8e-06    0.0023      13     101 ..       4     103 ..       1     124 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                       TEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSS..SSSEEEEEEEETTEEEEEEEE-S........SGGGGGGGGGG CS
                               Arf  13 kelrilllGLDnaGKtTilkklkleelvt.tvP..TigfnveeleiknlkftvwDvGG........qeklRplWknY 78 
                                       k +++l++G  n GK+ i +++++ +++    P  T+  n  e+++k++k+ ++D+ G        qe+l       
  gi|320100421|ref|YP_004176013.1|   4 KVIKVLFIGQPNVGKSSIFNMVTKSHVEVgNWPgkTVAVNKGEVSFKGYKLILYDLPGiygfttltQEELVAREAIL 80 
                                       789*******************99988765566558999999**************984445444455555555667 PP

                                       CTTESEEEEEEETT-CTTHHHHH CS
                               Arf  79 fektdavifvvDsadreRleeak 101
                                       +ek d+v+ vvDs+  eR ++  
  gi|320100421|ref|YP_004176013.1|  81 LEKPDVVVVVVDSTIPERTMNLA 103
                                       88999999999999999876655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0027       3.5     102     127 ..       8      32 ..       3      50 .. 0.84
   2 !    6.9   0.0    0.0041       5.2      28      96 ..      93     160 ..      70     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0027
                                       EEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpelelkt 127
                                       ++++Gq  vGKS++ n+++ + ++++
  gi|320100421|ref|YP_004176013.1|   8 VLFIGQPNVGKSSIFNMVTKS-HVEV 32 
                                       579*************99876.4444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0041
                                       TT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                       RsgA_GTPase  28 pelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkel 96 
                                        ++ +++++ ++  + e   ++v+v++K+Dl++ +    +++   ++l+++v+ vs  ++ ++e+l ++
  gi|320100421|ref|YP_004176013.1|  93 STIPERTMNLAIQ-VLELTGRVVLVFSKTDLAHGRGIHINYEGVARELNVPVVPVSIVSGFEVERLLDE 160
                                       4444444444433.34455689*************9788899999**********99999888888665 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 ?   14.5   0.0   2.5e-05     0.032       1      74 [.       7      70 ..       7     122 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                                      EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-H CS
                               Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhp 74
                                      Kv+++G+ +vGK+s+++ +++++++  + +   v + + ev ++kg         +kl ++D+ G   f +l++
  gi|320100421|ref|YP_004176013.1|  7 KVLFIGQPNVGKSSIFNMVTKSHVEVGNWPGKTVAVNKGEV-SFKG---------YKLILYDLPGIYGFTTLTQ 70
                                      99*******************99987766555555544444.3444.........3455555555444444333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.8e-05     0.061      78     173 ..      46     146 ..      23     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-05
                                       HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH..SSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTS CS
                             SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvv..kpdevllvldattgqeavkqakaFkeavgitgviltklDg 152
                                       +   +++ ++l D  G     +   eel + + ++  kpd v++v+d+t+ + +++ a +  e +g   ++++k D 
  gi|320100421|ref|YP_004176013.1|  46 EVSFKGYKLILYDLPGIYGFTTLTQEELVAREAILleKPDVVVVVVDSTIPERTMNLAIQVLELTGRVVLVFSKTDL 122
                                       45557899999999999999999999**999999899**************************************** PP

                                       SSSTTHHHH...HHHHHTS-EEEE CS
                             SRP54 153 dakgGaals...iaaelklPikfi 173
                                           G+ ++   +a+el++P++ +
  gi|320100421|ref|YP_004176013.1| 123 AHGRGIHINyegVARELNVPVVPV 146
                                       *****9997555788899998765 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.6e-05     0.059       1      88 [.       7      95 ..       7     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                         Gtr1_RagA  1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafv...eeylssqkeeifrn 76
                                      kvL++G+ + GK+s+ +++ +  +       g t+ v+k ev f +  +l l D++G   f    +e l   ++ ++++
  gi|320100421|ref|YP_004176013.1|  7 KVLFIGQPNVGKSSIFNMVTKSHVEVG-NWPGKTVAVNKGEVSF-KGYKLILYDLPGIYGFTtltQEELVAREAILLEK 83
                                      8*************9998876655443.45699*********65.567999*****98766511156777778888899 PP

                         Gtr1_RagA 77 vgvliyVfDves 88
                                       +v++ V+D++ 
  gi|320100421|ref|YP_004176013.1| 84 PDVVVVVVDSTI 95
                                      99*****99983 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00012      0.15      34     152 ..       4     121 ..       1     125 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                       --EEEEEEESTTSSHHHHHHHHTT--TTSTTS--SSCHSHHTS-EEEE-SS-TTEEEEEE--G.GGSSSSHHHHH.. CS
                              IIGP  34 aklkiavtGdsGnGkssFinaLRliGheeedsAptGvvettkkrtpYssskfPnvvlWDLPGl.GatafsvesYl.. 107
                                       +++k+  +G+   Gkss  n +    h e +  p  +v + k +  ++  k    +l+DLPG+ G t  + e+ +  
  gi|320100421|ref|YP_004176013.1|   4 KVIKVLFIGQPNVGKSSIFNMVT-KSHVEVGNWPGKTVAVNKGEVSFKGYK---LILYDLPGIyGFTTLTQEELVar 76 
                                       68999************999875.5899999999999*9999999998765...69******9899******99944 PP

                                       HHTTGGG-SEEEEEESSS--HHHHHHHHHHHHTT-EEEEEEE-HH CS
                              IIGP 108 eemkfseyDlfiiiaserFssndvklakaiqrmrkrFYvvrtKlD 152
                                       e + + + D+++++  +   +  ++la+++ ++  r  +v  K D
  gi|320100421|ref|YP_004176013.1|  77 EAILLEKPDVVVVVVDSTIPERTMNLAIQVLELTGRVVLVFSKTD 121
                                       5678899**************************999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4492.62
//
Query:       gi|320100422|ref|YP_004176014.1|  [L=337]
Description: phosphate uptake regulator PhoU [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   37.8   2.0    2.8e-08   34.1   0.4    2.5  2  PhoU             PhoU domain
    4.6e-08   32.8   0.0    1.3e-06   28.2   0.0    2.5  2  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
  ------ inclusion threshold ------
      0.087   12.8   0.0       0.74    9.8   0.0    2.4  3  Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-termin


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 !   34.1   0.4   4.6e-12   2.8e-08       1      88 [.     140     228 ..     140     229 .. 0.85
   2 ?    2.8   0.1     0.026   1.6e+02      41      86 ..     274     318 ..     247     320 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 4.6e-12
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH.....HHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae.....dlrellsllria 72 
                                       lr+m+++v  m++d+ +++ ++  e   ++ erd  id+l+    r+ l++++++  l e      + e++s+ ++ 
  gi|320100422|ref|YP_004176014.1| 140 LRKMGRLVPAMMRDVESSITSGT-E--LDIEERDSLIDKLYLYSVRQ-LNMVMQGRLLLEktglkSMGEAISIANLL 212
                                       799****************9986.4..69******************.6666664433334666789999******* PP

                                       HHHHHHHHHHHHHHHH CS
                              PhoU  73 rdlERigDhavniaer 88 
                                       + lER+gDha+++ ++
  gi|320100422|ref|YP_004176014.1| 213 KILERMGDHAAQLYRW 228
                                       **********988765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHGG-SH...HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  41 ekeiersllealakrqplae...dlrellsllriardlERigDhavnia 86 
                                       e+ i +   ++l  ++++++   d   ++sl ri+ +l  ++  +++i+
  gi|320100422|ref|YP_004176014.1| 274 EDTIMEL--RIL--EDKVRKpglDPSLVISLTRIIAYLRDVAEVVTDIV 318
                                       4444222..333..33333344478999999999999999999999885 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 !   28.2   0.0   2.2e-10   1.3e-06       6      40 ..      13      48 ..       9      49 .. 0.95
   2 ?    1.8   0.0     0.041   2.5e+02      19      41 ..     155     177 ..     147     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.2e-10
                                      EEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCC CS
                    MazE_antitoxin  6 sgavriPkevrfelgireGdevelevdgd.kiilrp 40
                                      s+ v++Pk + +   +++Gdev +ev +d  +++rp
  gi|320100422|ref|YP_004176014.1| 13 SLGVSLPKKWLRHYRLKQGDEVDIEVLPDyTLLIRP 48
                                      899**************************9999998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.041
                                       C.CEECTCEEEEEECTTCCCCCCC CS
                    MazE_antitoxin  19 l.gireGdevelevdgdkiilrpl 41 
                                          i  G+e+ +e+ + ++i++++
  gi|320100422|ref|YP_004176014.1| 155 EsSITSGTELDIEERD-SLIDKLY 177
                                       357899******9987.8888875 PP

>> Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2   7.2e+03      39      54 ..      92     107 ..      90     109 .. 0.81
   2 ?   -1.3   0.0      0.36   2.2e+03      19      32 ..     135     148 ..     135     153 .. 0.85
   3 ?    9.8   0.0   0.00012      0.74      33      64 ..     237     268 ..     234     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                       HHCCHHHHCCCCCCCC CS
                   Phe_tRNA-synt_N  39 GkliNelKqeieeale 54 
                                       G   N  K++i   le
  gi|320100422|ref|YP_004176014.1|  92 GSTCNSFKEKIYRLLE 107
                                       8889999999987776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.36
                                       CCCCCCCTTTTCCC CS
                   Phe_tRNA-synt_N  19 eltellkelgklpp 32 
                                       +l+e+l+++g l p
  gi|320100422|ref|YP_004176014.1| 135 PLSEVLRKMGRLVP 148
                                       5899******9866 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00012
                                       CTTTHHHHCCHHHHCCCCCCCCCHHHCCHCCH CS
                   Phe_tRNA-synt_N  33 eeRkeaGkliNelKqeieealeerkeeleaae 64 
                                       + R+eaG l+ e+++++e+ l e  ++le+ e
  gi|320100422|ref|YP_004176014.1| 237 DSRREAGLLLGEVRAAAEKILGEYLAALENPE 268
                                       78**************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2416.82
//
Query:       gi|320100423|ref|YP_004176015.1|  [L=373]
Description: phosphate ABC transporter substrate-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-54  183.3   0.0    9.7e-54  182.9   0.0    1.0  1  PBP_like_2  PBP superfamily domain
    1.1e-06   28.8   0.2    4.3e-06   26.9   0.0    1.9  2  SBP_bac_1   Bacterial extracellular solute-binding protein
    3.7e-05   22.9   0.0    0.00026   20.2   0.0    2.1  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 !  182.9   0.0   1.6e-57   9.7e-54       9     280 ..      43     341 ..      29     342 .. 0.91

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 1.6e-57
                        PBP_like_2   9 vgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggl 85 
                                       v  ++gaGst  ap + ++a  f++a +g+ v+y+++GSgag++++ ng++ fa sd pl ++++++ +    +g+ 
  gi|320100423|ref|YP_004176015.1|  43 V--LNGAGSTLAAPQVIEWARSFKEA-TGIVVEYSPVGSGAGRAMFFNGTAVFAVSDPPLDKETYLE-Y----KGRV 111
                                       3..99***************99****.8********************************9998753.2....4678 PP

                        PBP_like_2  86 iqvpvaigaialvvnkd.....nplnlsreaLakIfsgkItnWnd.........vlglpadgpIkvvhrsdgsgttf 148
                                        q+pv+ ga+++ +n +     + lnl+ e+La I++g+++ W d         v+gl++d+ I vvhrsd+sgtt+
  gi|320100423|ref|YP_004176015.1| 112 LQFPVLAGAVVVTYNLPeipsgTRLNLTGEVLALIYKGEVSRWCDeriksinpaVAGLLPDKEIIVVHRSDSSGTTR 188
                                       ***************777**988999*************************************************** PP

                        PBP_like_2 149 lfstalaeq.................gpwtasgigasgsegvasav.snngaigyvsvaywlavkgysladvtngag 207
                                       +f+ +l+++                  ++t +g+g +g+egvas++ +n++ igyv+++y+l   g+++a + n+ag
  gi|320100423|ref|YP_004176015.1| 189 VFTGYLHKVapdiwgsklvgftvewpVDATGRGLGGKGNEGVASIIkANPYSIGYVEASYALYT-GMPIARLMNKAG 264
                                       *******9999999999999999977666788999999*******99***************88.************ PP

                        PBP_like_2 208 kfvlptaataasalkvakias.......nplawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldy 277
                                        + +p+ + + sa++ +   +       ++ ++ l+ + +++++g+yP+++f+y+ vy +y +++ +a ++ +F+ y
  gi|320100423|ref|YP_004176015.1| 265 FYTEPSKEAVLSAINSVVD-QlpdtplgDFSSV-LDALLDAPGSGSYPIVTFSYMFVYRDY-GDPYTARALGEFIRY 338
                                       ******9999888887332.3577889877788.888999*******************98.55788********** PP

                        PBP_like_2 278 lls 280
                                       +l+
  gi|320100423|ref|YP_004176015.1| 339 ILT 341
                                       986 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 !   26.9   0.0   7.2e-10   4.3e-06      17     204 ..      60     248 ..      46     259 .. 0.79
   2 ?   -2.0   0.1      0.44   2.6e+03      79     119 ..     278     320 ..     271     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 7.2e-10
                                       H..HHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEECGGHHHHHHHT..TSBECCHHHHHHTTECTT CS
                         SBP_bac_1  17 a..fekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviavdndwiarlaka..glllpldpyvkaylapgv 86 
                                       a  f++  +gi Ve+ +vgsg+++    ++t+++a +d+p D  +       +++    +++   +++v+ y+ p+ 
  gi|320100423|ref|YP_004176015.1|  60 ArsFKE-ATGIVVEYSPVGSGAGRAmffNGTAVFAVSDPPLDKETY-----LEYKGRvlQFPVLAGAVVVTYNLPEI 130
                                       366866.9*****************999999999999999554444.....44444468999999999999999998 PP

                                       CCTEEEEHHHHTHHHHCEEEESEEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCT...HCCHCCE CS
                         SBP_bac_1  87 kdaadklsssvlpkildskvlyvPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkp...iggargg 159
                                       + ++  +                   + + +liY      k +++    W +  ++  ++  +g  p   i++++++
  gi|320100423|ref|YP_004176015.1| 131 PSGTRLNLT-----------------GeVLALIY------KGEVS---RWCDERIKSINPAVAGLLPdkeIIVVHRS 181
                                       887776422.................22668999......33333...99999999999999999999********* PP

                                       EHHHHHHHHHHHHHHHHTGGGEECCCT....................HHCSHHHHS..HHHHHHHHH CS
                         SBP_bac_1 160 sasgtayyfalalakslggkvfdkdgg....................gldnpegvt..aatylvkly 204
                                       + sgt+ +f+ +l k+++  +++k +g                    g+++ +  +  +++y++++y
  gi|320100423|ref|YP_004176015.1| 182 DSSGTTRVFTGYLHKVAPDIWGSKLVGftvewpvdatgrglggkgneGVASIIKANpySIGYVEASY 248
                                       ***********************99999999999999999996666666666666666666666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.44
                                       HHTTECTTCCTEEEEHHHHTHHHHCE.EE.ESEEEEE.EEEEEE CS
                         SBP_bac_1  79 kaylapgvkdaadklsssvlpkilds.kv.lyvPlya.argliY 119
                                       ++  +++ +d  + ++ssvl++ ld+ +   y P+ + +++++Y
  gi|320100423|ref|YP_004176015.1| 278 INSVVDQLPDTPLGDFSSVLDALLDApGSgSY-PIVTfSYMFVY 320
                                       55667778888999999999999998554666.77788888888 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.4e-08   0.00026       3     149 ..      62     243 ..      60     265 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.4e-08
                                       HHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH.....................HCCCCCEEEEEE CS
                          PBP_like   3 elaeknpgvrvavanvGsggGlkalrageadiagshlldketee.....................ynapalrkaldg 58 
                                        ++e+  g+ v+++ vGsg+G +++ +g+a  a s+ + +++ +                     y       +l++
  gi|320100423|ref|YP_004176015.1|  62 SFKEA-TGIVVEYSPVGSGAGRAMFFNGTAVFAVSDPPLDKE-TyleykgrvlqfpvlagavvvtY-------NLPE 129
                                       56664.8999***************************86533.22454444433333322222222.......3333 PP

                                       EEEEEE-CC-HCHCCCCHCCHHH.....S--BGGGC.....-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT..... CS
                          PBP_like  59 ievvlvnlarreqglvvakgnpk.....kitnwkdl.....adaplrlvnRetGSGtrdlfdellkkegisk..... 120
                                       i+     +++ e   +++kg+       +i++++       +d+++ +v R  +SGt  +f+  l+k   ++     
  gi|320100423|ref|YP_004176015.1| 130 IPSGTRLNLTGEVLALIYKGEVSrwcdeRIKSINPAvagllPDKEIIVVHRSDSSGTTRVFTGYLHKV--APdiwgs 204
                                       33333444444555555555333234442333332234445************************665..5556888 PP

                                       ..........E-SSTTSEEESSHHHHHCCHCCETTCCEC CS
                          PBP_like 121 ..........ssikgyaqearshlavaaaVaagradvgv 149
                                                  + +g +   + +  va++++a++  +g+
  gi|320100423|ref|YP_004176015.1| 205 klvgftvewpVDATGRGLGGKGNEGVASIIKANPYSIGY 243
                                       888888888867777777788888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2786.30
//
Query:       gi|320100424|ref|YP_004176016.1|  [L=302]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  20.8    1.2e-05   25.2  20.8    2.8  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 ?   -5.0   7.5         1   1.8e+04      17      34 ..      65      82 ..       7      88 .. 0.52
   2 !   25.2  20.8   6.5e-10   1.2e-05      19     176 ..      67     289 ..      58     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: -5.0 bits;  conditional E-value: 1
                      BPD_transp_1 17 dkllrpliivllslPsfv 34
                                        ll++li vl ++P+ +
  gi|320100424|ref|YP_004176016.1| 65 GTLLTGLISVLIATPISL 82
                                      234444444444444444 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 6.5e-10
                      BPD_transp_1  19 llrpliivllslPsfvlaillvlvf.................................................... 43 
                                       ll++li vl ++P+ + +++l+                                                       
  gi|320100424|ref|YP_004176016.1|  67 LLTGLISVLIATPISLSLMFLIGDMlpspasrilhrlleamgslptviyglwggfalsqilrdsiylpihaylgfip 143
                                       67777777777777776666664446777777777777777777777777777777788888888888888888998 PP

                      BPD_transp_1  44 ..vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilaf 118
                                         +     g++i+ + i+l ls++py+  +  ++ rslp  +veaa+alG  r++++r  +   ++p +++ ++l++
  gi|320100424|ref|YP_004176016.1| 144 lfSCRPLSGQSIMTAGIVLGLSMTPYASSLLVNGYRSLPGKYVEAAYALGFYRFETYR-LIAGVMKPLVVAAAMLSL 219
                                       887777889**********************************************999.999*************** PP

                      BPD_transp_1 119 ggllggavlleflgswpG............lgtllleailgydyseis.......nggvlalviavlllnlvadilq 176
                                        ++lg+++++ + +++              +       + +   ++ s         +++++v++v++l+lv+  + 
  gi|320100424|ref|YP_004176016.1| 220 SRALGETTIVALSIGNAYlaspcvfnpgttV-------SAWIVNQFESsfiypgaSSALYTGVLVVMALSLVLSYIG 289
                                       ********99999955447788855444441.......333333333345556552555555555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2356.08
//
Query:       gi|320100425|ref|YP_004176017.1|  [L=282]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-11   43.8  12.6    2.2e-11   43.8  12.6    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 ?   -1.2   7.5     0.078   1.4e+03     111     173 ..      12      92 ..       7      97 .. 0.55
   2 !   43.8  12.6   1.3e-15   2.2e-11       4     177 ..      91     278 ..      88     282 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.078
                      BPD_transp_1 111 itglilafggllggavlleflgswpGlgtllleailgydyseis..................nggvlalviavllln 169
                                       + ++++a++g +g a+ll++l s  + g++ l  + ++ ++                     ++++++++++ lll+
  gi|320100425|ref|YP_004176017.1|  12 AGLAAVAVVGGIGVASLLSLLYSVVANGLPPLLMEGASFITGLPatpmgssiggiapaligtIASSAIATVLALLLS 88 
                                       44455555555666666666665555555555555555555444888888877755555555555555555555555 PP

                      BPD_transp_1 170 lvad 173
                                       l++ 
  gi|320100425|ref|YP_004176017.1|  89 LFTS 92 
                                       5554 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 1.3e-15
                      BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslp 80 
                                       +++++  ++ +++  ++  ++ ++ ++P++v  ++ + + ++      ++l++ i+l++  +p++ +  ++alrs++
  gi|320100425|ref|YP_004176017.1|  91 TSLFTREYPYSRTAGFIEAVVRAFNGVPTIVASMFTYTI-IVVRMGRPSVLAASIALFIAVLPTAHYYLSSALRSVE 166
                                       55666678899999*****************66664443.333444478888999999999**************** PP

                      BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis... 154
                                       + ++eaa  lG +r++++r++ l  a + +++g++++f+++ g+++ l+f++     g l+ ++ +g d + ++   
  gi|320100425|ref|YP_004176017.1| 167 ERYREAAFSLGFRRIHVLRYIYLGIARRQVASGVLMTFIRATGETAPLLFTM-----GFLTNTVFQGLDQPGNAvsl 238
                                       ****************************************************.....88888888888888777788 PP

                      BPD_transp_1 155 .................nggvlalviavlllnlvadilqr 177
                                                        ++++l l++avl   l++ +l+r
  gi|320100425|ref|YP_004176017.1| 239 lifnyalspysnyheaaWAASLLLLLAVLTPALAIEFLMR 278
                                       9999999999999999999999999999988888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2210.79
//
Query:       gi|320100426|ref|YP_004176018.1|  [L=250]
Description: phosphate ABC transporter ATP-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for 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  103.8   0.0    1.3e-29  103.4   0.0    1.1  1  ABC_tran     ABC transporter
    4.8e-12   46.3   0.1    3.6e-06   27.0   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.8e-07   30.8   0.0    0.00056   19.4   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00014   22.1   0.0    0.00041   20.6   0.0    1.8  1  AAA_22       AAA domain
    0.00038   20.1   0.1    0.00089   19.0   0.1    1.6  1  AAA_29       P-loop containing region of AAA domain
    0.00046   19.1   0.1     0.0012   17.8   0.1    1.5  2  Adeno_IVa2   Adenovirus IVa2 protein
    0.00053   19.8   0.0      0.068   12.9   0.0    2.0  2  AAA_15       AAA ATPase domain
    0.00079   19.4   0.1     0.0016   18.3   0.0    1.7  2  RsgA_GTPase  RsgA GTPase
     0.0027   18.1   0.0     0.0049   17.3   0.0    1.7  1  AAA_16       AAA ATPase domain
     0.0062   16.3   0.0      0.012   15.4   0.0    1.4  1  AAA_30       AAA domain
     0.0067   17.0   0.0      0.012   16.1   0.0    1.3  1  AAA_23       AAA domain
     0.0095   15.9   0.0      0.017   15.1   0.0    1.4  1  ATPase_2     ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.024   14.1   0.0        2.6    7.4   0.0    2.3  2  TniB         Bacterial TniB protein
      0.025   14.5   0.0        0.3   11.0   0.0    2.1  2  Rad17        Rad17 P-loop domain
      0.026   14.5   0.0      0.064   13.3   0.0    1.6  1  Kelch_5      Kelch motif
      0.033   13.9   0.0       0.13   12.0   0.0    1.9  2  AAA_24       AAA domain
      0.059   12.9   0.0        0.1   12.2   0.0    1.3  1  AAA_27       AAA domain
      0.071   13.7   0.0       0.15   12.6   0.0    1.7  1  AAA_18       AAA domain
       0.11   12.5   0.0       0.27   11.2   0.0    1.6  2  AAA_5        AAA domain (dynein-related subfamily)
       0.17   11.8   0.0       0.29   11.0   0.0    1.3  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 !  103.4   0.0   1.5e-32   1.3e-29       1     137 []      20     176 ..      20     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.5e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqepqlfp 72 
                                       l+n+++ +k +++ +i+G++G+GKStLl+++ +l +       +G +++ ++dl e +  +lr+++  ++qep+ fp
  gi|320100426|ref|YP_004176018.1|  20 LSNLDIGVKSNTISVIMGPSGSGKSTLLRVFNRLIDLnpeaeVSGVVRIMNRDLYEWNPYELRRHVVLVQQEPTPFP 96 
                                       68999*****************************9887788889********************************* PP

                                       TSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       +l++ +n               e ++ ++ al+++ l +  ++++++ p+ LSgGqkqr+++aral+ +p++lllDE
  gi|320100426|ref|YP_004176018.1|  97 NLSIFDNvalparlnkvagsrgELERLVKWALESVMLWDEVKDRLEKPPTILSGGQKQRLCMARALALRPEILLLDE 173
                                       **************9999988888888******************9999**************************** PP

                                       TTT CS
                                       xxx RF
                          ABC_tran 135 pta 137
                                       pta
  gi|320100426|ref|YP_004176018.1| 174 PTA 176
                                       *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 !   17.7   0.0   2.8e-06    0.0025       1      26 [.      32      57 ..      32      83 .. 0.79
   2 !   27.0   0.0   4.1e-09   3.6e-06     220     299 ..     131     206 ..      70     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarld 26
                                      + v+ Gp gsGKS+LL+ +  l +l+
  gi|320100426|ref|YP_004176018.1| 32 ISVIMGPSGSGKSTLLRVFNRLIDLN 57
                                      679****************9997652 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 4.1e-09
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                        + + e +d+ e p++ lS G+k+ l+++ al+ ++    +ll+DEp ++++P+ + ++ e lk+l++ ++ +il+T
  gi|320100426|ref|YP_004176018.1| 131 VMLWDEVKDRLEKPPTILSGGQKQRLCMARALALRP---EILLLDEPTANIDPANTVKIEESLKALKN-DVTIILVT 203
                                       677788888888899999***************999...9**************************99.******** PP

                            AAA_21 297 HSp 299
                                       H p
  gi|320100426|ref|YP_004176018.1| 204 HMP 206
                                       *76 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   0.2   0.00061      0.54      23      41 ..      29      47 ..      22      53 .. 0.86
   2 !   19.4   0.0   6.2e-07   0.00056     136     205 ..     147     212 ..      54     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00061
                                      TSSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnll 41
                                      s+ +++i+Gp GSGKs ll
  gi|320100426|ref|YP_004176018.1| 29 SNTISVIMGPSGSGKSTLL 47
                                      56789***********987 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 6.2e-07
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                        LSgG+k+ + +a  +A++   p+ + llDe  a++D +n+ k+ e lk+ ++++ +i +++  ++ +++
  gi|320100426|ref|YP_004176018.1| 147 ILSGGQKQRLCMARALALR---PE-ILLLDEPTANIDPANTVKIEESLKALKNDVTIILVTHMPHQAARV 212
                                       8*******99999888874...44.789*********************************988776655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.6e-07   0.00041       4      61 ..      29      86 ..      25     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.6e-07
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrell 61
                                      + +i v++G+sG+GK+tllr + +  d  ++a  e ++vv++    +   ++ +l+r+++
  gi|320100426|ref|YP_004176018.1| 29 SNTISVIMGPSGSGKSTLLRVFNRLIDLNPEA--EVSGVVRIMNRDLYewNPYELRRHVV 86
                                      67899***************999998765555..44555544444444344444444444 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   0.1   9.9e-07   0.00089      19      39 ..      27      47 ..      19      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.9e-07
                            AAA_29 19 idlkgatlltGpsGsGKSTll 39
                                      ++ + + +++GpsGsGKSTll
  gi|320100426|ref|YP_004176018.1| 27 VKSNTISVIMGPSGSGKSTLL 47
                                      55555899************8 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.3e-06    0.0012      79     119 ..      21      60 ..      12      70 .. 0.82
   2 ?   -2.3   0.0       1.7   1.5e+03     286     320 ..     192     227 ..     187     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                        Adeno_IVa2  79 sslnyg.lqPviGviyGPtGsGksqllrnlissklisPiPet 119
                                       s l++g +   i vi GP GsGks llr    ++li+  Pe+
  gi|320100426|ref|YP_004176018.1|  21 SNLDIGvKSNTISVIMGPSGSGKSTLLRV--FNRLIDLNPEA 60 
                                       66666623568*****************5..59999999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                        Adeno_IVa2 286 glskdlavllkaifefleqk.srysfilynvePvre 320
                                        l +d++++l + + +++ +  +y +ily    v+e
  gi|320100426|ref|YP_004176018.1| 192 ALKNDVTIILVTHMPHQAARvGDYVYILYGGRVVEE 227
                                       577788777777777766552689999997665555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   7.6e-05     0.068      16      50 ..      22      57 ..      19     103 .. 0.78
   2 ?    5.2   0.0     0.016        15     324     367 ..     166     207 ..     155     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.6e-05
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      + +i ++++ ++v+ G+ +sGKS++l++++ +++ +
  gi|320100426|ref|YP_004176018.1| 22 NLDIGVKSNtISVIMGPSGSGKSTLLRVFNRLIDLN 57
                                      566667777799******************999966 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       + ill++EP a++ p +   + ++lk l nd    +i+ TH ph
  gi|320100426|ref|YP_004176018.1| 166 PEILLLDEPTANIDPANTVKIEESLKALKNDVT--IILVTHMPH 207
                                       679*****************************6..******998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.8e-06    0.0016      99     121 ..      30      52 ..      11      91 .. 0.84
   2 ?   -3.4   0.0       8.5   7.6e+03       9      19 ..     171     181 ..     167     202 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                                       TSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                       + +sv++G+SG GKStL+ +++ 
  gi|320100426|ref|YP_004176018.1|  30 NTISVIMGPSGSGKSTLLRVFNR 52 
                                       489**************977654 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.5
                                       TTTTEES--EE CS
                       RsgA_GTPase   9 vrpkvaNvdql 19 
                                       ++++ aN+d +
  gi|320100426|ref|YP_004176018.1| 171 LDEPTANIDPA 181
                                       55666666654 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   5.4e-06    0.0049      25      49 ..      31      55 ..      19     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.4e-06
                            AAA_16 25 elvllsGesGvGKsslvrellrale 49
                                       + ++ G+sG+GKs+l+r + r + 
  gi|320100426|ref|YP_004176018.1| 31 TISVIMGPSGSGKSTLLRVFNRLID 55
                                      56789*************9998655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05     0.012      17      45 ..      29      57 ..      24      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa 45
                                      ++ ++v+ Gp G+GK+t+l++ +++++ +
  gi|320100426|ref|YP_004176018.1| 29 SNTISVIMGPSGSGKSTLLRVFNRLIDLN 57
                                      4569*****************99987655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-05     0.012      17      37 ..      27      48 ..      16      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                            AAA_23 17 F.skgltlItGpNGaGKTTild 37
                                        s+ + +I Gp G+GK+T+l+
  gi|320100426|ref|YP_004176018.1| 27 VkSNTISVIMGPSGSGKSTLLR 48
                                      3578899*************97 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05     0.017      19      40 ..      29      50 ..      24      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkei 40
                                      +n+i +i Gp gsGK++Ll+ +
  gi|320100426|ref|YP_004176018.1| 29 SNTISVIMGPSGSGKSTLLRVF 50
                                      689****************976 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0029       2.6      39      64 ..      34      59 ..      26      94 .. 0.84
   2 ?    4.7   0.0     0.019        17     106     159 ..     152     203 ..     117     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0029
                              TniB 39 llvGdsnnGKtmivekFarlhppekd 64
                                      +++G+s  GK+++++ F rl   +++
  gi|320100426|ref|YP_004176018.1| 34 VIMGPSGSGKSTLLRVFNRLIDLNPE 59
                                      79***************997655544 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.019
                              TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       ++++ +++   +l++++L++DE    +     +  ++ ++lk L+n++ i +v+
  gi|320100426|ref|YP_004176018.1| 152 QKQRLCMARALALRPEILLLDEPTANI--DPANTVKIEESLKALKNDVTIILVT 203
                                       5666667777789999******76544..5556666667788888998888775 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00033       0.3      45      67 ..      30      52 ..      19      70 .. 0.83
   2 ?    1.1   0.0      0.35   3.1e+02     117     144 ..     181     208 ..     174     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                             Rad17 45 kriLLisGPsGCgkstvvkvLsk 67
                                      + i +i GPsG gkst ++v  +
  gi|320100426|ref|YP_004176018.1| 30 NTISVIMGPSGSGKSTLLRVFNR 52
                                      45889*************99876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.35
                             Rad17 117 akylklqklGddlrtdkklilvedlPnk 144
                                       a+  k++   + l+ d  +ilv  +P +
  gi|320100426|ref|YP_004176018.1| 181 ANTVKIEESLKALKNDVTIILVTHMPHQ 208
                                       6677888889999*************87 PP

>> Kelch_5  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.1e-05     0.064       8      37 ..     207     236 ..     206     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-05
                           Kelch_5   8 hcavtvsekiYv.yGGkvgrdgsvsddvyvL 37 
                                       h a+ v++++Y+ yGG+v  ++++ +dv+++
  gi|320100426|ref|YP_004176018.1| 207 HQAARVGDYVYIlYGGRV-VEEGPVNDVFIH 236
                                       89999*************.5********996 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   0.00014      0.13       6      29 ..      34      56 ..      29      91 .. 0.84
   2 ?   -0.8   0.0       1.2   1.1e+03      29      58 ..     169     199 ..     158     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                            AAA_24  6 liyGpsgiGKTtlakelgpkplfi 29
                                      +i+Gpsg+GK+tl++ + ++ + +
  gi|320100426|ref|YP_004176018.1| 34 VIMGPSGSGKSTLLRVF-NRLIDL 56
                                      8*************999.766555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                            AAA_24  29 idtekGlksldadkfpdie.swedfldevve 58 
                                       + +++ ++++d+++ ++ie s+++++++v+ 
  gi|320100426|ref|YP_004176018.1| 169 LLLDEPTANIDPANTVKIEeSLKALKNDVTI 199
                                       5556666677777777666666666666554 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   0.00011       0.1      17      49 ..      21      53 ..       9      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            AAA_27 17 rsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      ++ld++ +++ + +i+Gp  +GKst+lr +++l
  gi|320100426|ref|YP_004176018.1| 21 SNLDIGVKSNTISVIMGPSGSGKSTLLRVFNRL 53
                                      67999999*******************988776 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   0.00016      0.15       2      25 ..      34      60 ..      34     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf...g 25
                                      +++G++G+GK+tl +  +++  +    
  gi|320100426|ref|YP_004176018.1| 34 VIMGPSGSGKSTLLRVFNRLIDLnpeA 60
                                      599***********9998875334541 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   0.0    0.0003      0.27       3      24 ..      34      57 ..      33      77 .. 0.80
   2 ?   -3.2   0.0       8.7   7.8e+03      65      73 ..     165     173 ..     153     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                                      EEE--SSSSHHHHHHHGGGGB..S CS
                             AAA_5  3 lLvGppGtgKselaerlaaal..n 24
                                      ++ Gp+G+gKs+l + + +++  n
  gi|320100426|ref|YP_004176018.1| 34 VIMGPSGSGKSTLLRVFNRLIdlN 57
                                      579****************99653 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.7
                                       G-SEEEEES CS
                             AAA_5  65 egeilvlDE 73 
                                       ++eil+lDE
  gi|320100426|ref|YP_004176018.1| 165 RPEILLLDE 173
                                       667777777 PP

>> NACHT  NACHT 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       3      20 ..      33      50 ..      31      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      +++ G++GsGK+tLl+ +
  gi|320100426|ref|YP_004176018.1| 33 SVIMGPSGSGKSTLLRVF 50
                                      789************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 00:00:00.43
# Mc/sec: 1740.44
//
Query:       gi|320100427|ref|YP_004176019.1|  [L=201]
Description: PhoU family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-15   55.3   3.4    4.1e-08   33.6   1.0    2.2  2  PhoU           PhoU domain
     0.0057   16.0   0.1       0.01   15.2   0.1    1.3  1  PhoU_div       Protein of unknown function DUF47
  ------ inclusion threshold ------
      0.058   13.0   0.0      0.084   12.4   0.0    1.1  1  Lipoprotein_2  Borrelia lipoprotein


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 !   22.0   0.1   2.7e-08   0.00016       6      85 ..      17      99 ..      12     101 .. 0.85
   2 !   33.6   1.0   6.8e-12   4.1e-08       7      86 ..     124     196 ..     120     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.7e-08
                                      HHHHHHHHHHHHHHHCT-H..HHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  6 eiveemlddalealeekdt..ela.revierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81
                                        +   ++d+ ++le +d    +  +e+ e+ + +   ++e+ +s+l  +a++qpl+ +l e+++ll +++d++R +++
  gi|320100427|ref|YP_004176019.1| 17 LEAVGLVRDLSRLLEPGDSvrGMMdEEIHEKTEILFISCNELFNSVLVFIARNQPLGPELVEASNLLYLVYDIYRYARY 95
                                      55667788899999999854577778888888888888999******99****************************** PP

                                      HHHH CS
                              PhoU 82 avni 85
                                      a++i
  gi|320100427|ref|YP_004176019.1| 96 AREI 99
                                      **98 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 6.8e-12
                                       HHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   7 iveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhav 83 
                                       i+ e++++a++a++e+ te ++e+ ++ +e drl+++  ++     + r+  a        +l + r++ERi Dha+
  gi|320100427|ref|YP_004176019.1| 124 IAVEAMEKAYKAYFEDCTECVEELKRLGEESDRLYMAQLEKTSANTMLRNTDAI-------ALLVLRHIERIVDHAE 193
                                       8899*********************************98885544466666554.......899************* PP

                                       HHH CS
                              PhoU  84 nia 86 
                                       +i+
  gi|320100427|ref|YP_004176019.1| 194 RIS 196
                                       *97 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.7e-06      0.01     132     205 ..     124     196 ..     117     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-06
                          PhoU_div 132 evieeleklletalskk.diveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedva 205
                                        ++e++ek     ++   + vee+++l +e+D l+   ++k   +    n+ ++ llv   +++e ++d ae+++
  gi|320100427|ref|YP_004176019.1| 124 IAVEAMEKAYKAYFEDCtECVEELKRLGEESDRLYMAQLEKTSANTMLRNTDAIALLV--LRHIERIVDHAERIS 196
                                       579999998888888658**************************99999999999886..8************98 PP

>> Lipoprotein_2  Borrelia lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.4e-05     0.084      10      85 ..     116     195 ..     114     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                     Lipoprotein_2  10 dlvsdvLGlkveskkskvgkyfkkvgetvesvkt....kLnkivaelkeekkknaegteksveklvegkldkivega 82 
                                       ++v+ +LG+ ve+  +  ++yf++  e ve++k+         +a l+++++ +    + ++  lv   +++iv+ a
  gi|320100427|ref|YP_004176019.1| 116 EIVAPALGIAVEAMEKAYKAYFEDCTECVEELKRlgeeSDRLYMAQLEKTSANTMLRNTDAIALLVLRHIERIVDHA 192
                                       78999**************************9962111334456666666666666555557778888888888877 PP

                     Lipoprotein_2  83 kka 85 
                                         +
  gi|320100427|ref|YP_004176019.1| 193 ERI 195
                                       665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1435.76
//
Query:       gi|320100428|ref|YP_004176020.1|  [L=238]
Description: Ala-tRNA(Pro) hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-12   45.3   0.1    1.2e-11   44.5   0.1    1.4  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
      2e-09   36.5   0.1      3e-09   35.9   0.1    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)


Domain annotation for each model (and alignments):
>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.1   1.4e-15   1.2e-11       1      44 []     190     233 ..     190     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.4e-15
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +r+v+i  +++++ gG+Hv++T+eIg +k+l+ e+++k+  R+y
  gi|320100428|ref|YP_004176020.1| 190 LRIVEIPGVDIQADGGPHVRHTSEIGVIKLLRTENKGKNKKRLY 233
                                       69****558*********************************98 PP

>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   3.4e-13     3e-09     473     552 .]      13      93 ..       5      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.4e-13
                                       SEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEET..TEEEEEXSS.XSXXXTTSEEEEE CS
                      tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkak..gvvlhkgkleegklkvgdkvkae 547
                                       ke  + ve+++ + v LdrT+f + sGG ++D+G+i + + ++rv +v   k  g v h+++    ++++g +vk+ 
  gi|320100428|ref|YP_004176020.1|  13 KECDAVVEAVQGNKVFLDRTVFHPRSGGVENDTGFIIAGDVRVRVLNVYYDKetGDVAHEVDDA-SSITIGSRVKLL 88 
                                       5667889999*************************************9755434899****996.9*********** PP

                                       EXHHH CS
                      tRNA-synt_2c 548 vdeer 552
                                       +d++r
  gi|320100428|ref|YP_004176020.1|  89 LDWDR 93 
                                       *9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1843.57
//
Query:       gi|320100429|ref|YP_004176021.1|  [L=531]
Description: CTP synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-120  399.8   0.1   6.7e-120  399.3   0.1    1.2  1  CTP_synth_N    CTP synthase N-terminus
    9.6e-45  152.7   0.0    2.2e-44  151.5   0.0    1.6  1  GATase         Glutamine amidotransferase class-I
    8.6e-12   45.3   0.0    1.7e-11   44.3   0.0    1.4  1  Peptidase_C26  Peptidase C26
     0.0022   18.0   0.0     0.0032   17.5   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
       0.02   14.1   0.0       0.16   11.1   0.0    2.0  2  ArsA_ATPase    Anion-transporting ATPase
       0.13   11.8   0.0       0.26   10.8   0.0    1.5  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


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 !  399.3   0.1  2.2e-123  6.7e-120       1     265 []       3     266 ..       3     266 .. 0.99

  Alignments for each domain:
  == domain 1  score: 399.3 bits;  conditional E-value: 2.2e-123
                                       EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHH CS
                       CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfl 77 
                                       ky++vtGGv+SglGkG++aas+g llks g++vt++k+DPYlnvdagt++p+ hGEvfv++dG+etDlD+G+YeRfl
  gi|320100429|ref|YP_004176021.1|   3 KYVFVTGGVLSGLGKGVVAASTGLLLKSLGYRVTAVKVDPYLNVDAGTMNPYMHGEVFVTEDGGETDLDIGHYERFL 79 
                                       8**************************************************************************** PP

                                       T----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHH CS
                       CTP_synth_N  78 dikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfle 154
                                       +++l+++nnit+G+iy++vi+kerrG+ylG++vq+iphvt+eikeri+++a+++ advviveigGtvgdie+lpfle
  gi|320100429|ref|YP_004176021.1|  80 GVELSRRNNITSGQIYHEVISKERRGEYLGQCVQIIPHVTNEIKERIRETAREQGADVVIVEIGGTVGDIEGLPFLE 156
                                       ****************************************************999********************** PP

                                       HHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--G CS
                       CTP_synth_N 155 airqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvek 231
                                       a rq+++e g++n+l++hv+l pvl a+ge+ktkp+qhs++elr++Giqpd +v+rs+++l+ee++ k+alf n++ 
  gi|320100429|ref|YP_004176021.1| 157 AARQMRFEEGSSNTLFLHVALAPVL-ASGEVKTKPVQHSIQELRRIGIQPDAVVVRSSRTLDEEARYKVALFGNIPV 232
                                       *************************.6************************************************** PP

                                       GGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 232 eavisvkdvesiyevpllleeqglaelileklkl 265
                                       eav+s++d++ iy+vpl+l+++gl+++++++l l
  gi|320100429|ref|YP_004176021.1| 233 EAVFSNPDIDLIYRVPLILHREGLTRYVASRLGL 266
                                       *****************************99975 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   0.0   7.3e-48   2.2e-44       2     190 .]     301     527 ..     300     527 .. 0.89

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 7.3e-48
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH....THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-E CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile....llknpdgilvsgGpgspgvegkieaikearenkiPi 74 
                                       + D+y s++e+l ha++  +v+ve+ +++a+  e ++       ++dgi+v +G+g +g egki +ik are+++P+
  gi|320100429|ref|YP_004176021.1| 301 VRDSYISIVEALRHAGIWSDVRVELQWFEATEIEADKsltsRVLEADGIIVLPGFGRRGSEGKIHVIKAAREAGKPL 377
                                       67***************************977777566754499********************************* PP

                                       EEETHHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTS CS
                            GATase  75 LGICLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglkn 120
                                       LGIC+GmQl++ e +r++                        +++  +++ggt rlg+++           +yg+ +
  gi|320100429|ref|YP_004176021.1| 378 LGICFGMQLMTVEAARNLAglenansteldpatphpvidllpEQRGIGQLGGTLRLGARKIiiepgslaWSIYGT-R 453
                                       ****************555555555556666666666699997777************777*******98999*9.* PP

                                       EEEEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T..EEEESSBTTSTTSTTHHHHHHHHHHHH CS
                            GATase 121 evierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p..fvgvQFHPEststpegpellfnflika 190
                                       ev+erhrHry +npk    le+agl+vt++se++   +eiie+k+ +  ++g+Q HPE++s+p +p+++ + +i+a
  gi|320100429|ref|YP_004176021.1| 454 EVYERHRHRYGLNPKyidILEKAGLRVTGWSEEG--HAEIIELKEgKvfYYGTQAHPEFKSKPLKPSPVYKRFIEA 527
                                       *****************8889999*******998..688888888766799********************99975 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   5.5e-15   1.7e-11      94     216 .]     363     509 ..     357     509 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 5.5e-15
                     Peptidase_C26  94 elaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe.............q.....saashavk 152
                                       ++ +i+aa e+g+P+lgiC G+ql+ v    +l+   +++s++ d   ++             q        ++++ 
  gi|320100429|ref|YP_004176021.1| 363 KIHVIKAAREAGKPLLGICFGMQLMTVEAARNLAGLENANSTELDPATPHpvidllpeqrgigQlggtlRLGARKII 439
                                       57899**********************99999987666656666655555688888887666626667788899*** PP

                     Peptidase_C26 153 vekgsllaellgseeievnslHhqaike......laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       +e+gsl  +++g++e+     H+ +++          +lrv+ ++e g  E ie++e k+f++g Q HPE
  gi|320100429|ref|YP_004176021.1| 440 IEPGSLAWSIYGTREVYERHRHRYGLNPkyidilEKAGLRVTGWSEEGHAEIIELKEGKVFYYGTQAHPE 509
                                       *************************9988888866789*******************************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 !   17.5   0.0   1.1e-06    0.0032       8      48 ..      13      50 ..       6     425 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                      TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  8 GGvGKTtlaanLaralarrglrVllvDaDpqannlailegl 48
                                      +G GK ++aa+ + +l+  g+rV +v++Dp  n +a   g+
  gi|320100429|ref|YP_004176021.1| 13 SGLGKGVVAASTGLLLKSLGYRVTAVKVDPYLNVDA---GT 50
                                      89****************************999887...33 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   0.0   5.5e-05      0.16       2     131 ..       3     141 ..       2     162 .. 0.73
   2 ?    0.7   0.0     0.081   2.4e+02     212     249 ..     180     219 ..     172     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.5e-05
                                       EEEEEEES..TTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HH...... CS
                       ArsA_ATPase   2 kvilvgGK..GGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpe...... 70 
                                       k+++v+G    G GK  v+a+t++ l   g++v  + +DP  ++     +   + +  v+e    +++d+       
  gi|320100429|ref|YP_004176021.1|   3 KYVFVTGGvlSGLGKGVVAASTGLLLKSLGYRVTAVKVDPYLNVDAGTMNPYMHGEVFVTEDGGETDLDIGhyerfl 79 
                                       78999985347*****************************9998766666677888888877777777766777777 PP

                                       .HHHHHHHCCHH.GGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEE CS
                       ArsA_ATPase  71 .veleeakqevq.keeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlD 131
                                        vel++ ++ ++ + +++++  e   + l + ++++P + + +  e++ +  +e+  dvv++ 
  gi|320100429|ref|YP_004176021.1|  80 gVELSRRNNITSgQIYHEVISKERRGEYLGQCVQIIPHVTNEIK-ERIRETAREQGADVVIVE 141
                                       76666655544413445555666667777777777777765443.566666667777777765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.081
                                       EEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE..E-TTC CS
                       ArsA_ATPase 212 VvipEklslkEteRaikeLkkygikvdavivNk..llpee 249
                                       V+ + ++  k  + +i+eL ++gi+ dav+v     l+ee
  gi|320100429|ref|YP_004176021.1| 180 VLASGEVKTKPVQHSIQELRRIGIQPDAVVVRSsrTLDEE 219
                                       556666667778899***************9754466665 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 ?   10.8   0.0   8.8e-05      0.26      66      92 ..     365     391 ..     358     441 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.8e-05
                          GATase_3  66 eaikeaaeaggpvlgiCGGlqmLGeei 92 
                                         ik+a eag+p+lgiC G+q++  e 
  gi|320100429|ref|YP_004176021.1| 365 HVIKAAREAGKPLLGICFGMQLMTVEA 391
                                       569999****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 4208.12
//
Query:       gi|320100430|ref|YP_004176022.1|  [L=180]
Description: phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-21   77.0   0.0    1.3e-21   76.7   0.0    1.1  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.0   7.5e-26   1.3e-21      11     155 ..      15     152 ..       6     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 7.5e-26
                                       EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-.EE-EEEEEE-TTT--EE........EE----T CS
                      Pribosyltran  11 ildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevp.layvrkvkyrpdgseeaargssdesrlledpa 86 
                                       +    ++la +i++   ++pd+++++a+gG+++a il d L+v+ +  ++++ y + g    ++ ++    +l+ ++
  gi|320100430|ref|YP_004176022.1|  15 LHGLLRDLATRINSG--YRPDIIIAVAKGGLIPARILVDLLGVEeMGLIEVKFYKGVGEAREKPYVTFT--ALPPID 87 
                                       556788999999999..************************9985667777777777777777777775..****** PP

                                       TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE-SE CS
                      Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvgfe 155
                                       gkk l+VDDi d+G+Tl+ +++ L + +   +r+a+l+ kp +++ +d++   v     +++v++++++
  gi|320100430|ref|YP_004176022.1|  88 GKKLLVVDDIADSGRTLQVVADVLSRFKYMDLRFATLYVKPWSTIMPDYYGEIVE----EWIVFPWEIC 152
                                       ***********************************************99777776....9****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1351.56
//
Query:       gi|320100431|ref|YP_004176023.1|  [L=268]
Description: photosystem I assembly BtpA [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-72  244.2   0.0    1.7e-72  244.0   0.0    1.1  1  BtpA            BtpA family
    0.00015   20.7   0.2    0.00025   20.0   0.2    1.3  1  Trp_syntA       Tryptophan synthase alpha chain
  ------ inclusion threshold ------
      0.066   12.6   0.0          3    7.2   0.0    2.4  2  Bac_luciferase  Luciferase-like monooxygenase
      0.088   12.7   0.0       0.15   12.0   0.0    1.4  1  Nre_C           Archaeal Nre, C-terminal
       0.12   12.0   0.0       0.94    9.1   0.0    2.3  2  DUF1580         Protein of unknown function (DUF1580)
       0.17   11.8   0.8       0.49   10.3   0.2    2.1  2  DUF3933         Protein of unknown function (DUF3933)


Domain annotation for each model (and alignments):
>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.0   0.0   5.6e-76   1.7e-72       2     252 ..       5     263 ..       4     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 244.0 bits;  conditional E-value: 5.6e-76
                              BtpA   2 ekpvigvvHLkpLPgsaeykanleevidkAvkeakaleegGvDavilenygdaPflke.vdpetvaamtvivkevks 77 
                                        k vigv+HL+ LP+     ++le+v+++Av+ea++lee G+ +v++enygd P+ k+  dp+t++am+++v+ev +
  gi|320100431|ref|YP_004176023.1|   5 SKFVIGVIHLPRLPSTLYRAEGLEQVVERAVSEAMTLEELGFSGVLVENYGDYPYEKRvLDPLTISAMSIVVREVVK 81 
                                       689***********8766666*************************************67***************** PP

                              BtpA  78 dvsiplGvnvLrndavaalaiAkavgakFiRvnvltgvalsdeGilegkaaellrykkllesrvkiladvavkhavp 154
                                        vsip+G+n+Lrn   +a+aiA a+ga FiRvn lt++ ++d Gile++a  llr  +    +++++ dv+ kh v 
  gi|320100431|ref|YP_004176023.1|  82 SVSIPVGLNLLRNSGREAYAIAIATGARFIRVNALTETLVTDSGILEPEAP-LLRVLRANYPGISVFGDVMCKHGVS 157
                                       *************************************************95.78888888999************99 PP

                              BtpA 155 lve........rdlesavkdtvergladavilsGkatGgevdleelklaketvkvkvlvgsGvseenlekllsiadG 223
                                       l +          +  av+d verg ad v+++G +tG+++ l+ + l+k+  + +v++gsG +  nl  lls+adG
  gi|320100431|ref|YP_004176023.1| 158 LNTvlyagtreDAVRVAVEDLVERGGADYVVVTGARTGEAPGLDMVSLVKRYSSRPVVIGSGSNPGNLGALLSVADG 234
                                       965222221113567788999******************************************************** PP

                              BtpA 224 vivgtsikkdGkianaiDkervrkivela 252
                                       vivg++i+ +G++ n++D +r+r+++++ 
  gi|320100431|ref|YP_004176023.1| 235 VIVGSYIRVGGRAGNPLDPARARAYISAF 263
                                       ************************99986 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   8.5e-08   0.00025     175     229 ..     189     241 ..     158     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.5e-08
                                       -SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHH CS
                         Trp_syntA 175 vTgaenavaaevdelverlkkltavPvavGFGistkeqvkqvakvadGvivGSal 229
                                       vTga++  a  +d +v+ +k+++  Pv +G G s++ +  ++ +vadGvivGS +
  gi|320100431|ref|YP_004176023.1| 189 VTGARTGEAPGLD-MVSLVKRYSSRPVVIGSG-SNPGNLGALLSVADGVIVGSYI 241
                                       8999999888886.89****************.999*****************86 PP

>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.001         3      19      61 ..      25      72 ..       9      76 .. 0.76
   2 ?    2.8   0.0     0.021        63     164     193 ..     210     239 ..     186     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                    Bac_luciferase 19 s...aslrylvelaraaEelGfdavwvaehhggpgga..ldaftllaa 61
                                      +   + ++++v  a ++EelGf +v+v      p+ +  ld++t+ a+
  gi|320100431|ref|YP_004176023.1| 25 EgleQVVERAVSEAMTLEELGFSGVLVENYGDYPYEKrvLDPLTISAM 72
                                      3355688999999*************9766666666699999998876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.021
                    Bac_luciferase 164 qgpiPvyvaaas.paglelaarhadglllag 193
                                       +  +Pv+++++s p +l    ++adg+++ +
  gi|320100431|ref|YP_004176023.1| 210 SS-RPVVIGSGSnPGNLGALLSVADGVIVGS 239
                                       33.7888888888888988888888888766 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.1e-05      0.15      33      67 ..      70     104 ..      62     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.1e-05
                             Nre_C  33 qakvivlreitpeYwaPvGvWqvReavrkalekkp 67 
                                       +a  iv+re+ +   +PvG   +R++ r+a++   
  gi|320100431|ref|YP_004176023.1|  70 SAMSIVVREVVKSVSIPVGLNLLRNSGREAYAIAI 104
                                       7899*************************998544 PP

>> DUF1580  Protein of unknown function (DUF1580)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00031      0.94      28      54 ..     153     180 ..     146     182 .. 0.84
   2 ?   -1.0   0.0      0.47   1.4e+03      16      27 ..     203     214 ..     195     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00031
                           DUF1580  28 rHGvkLetwriGgrRlTsve.AVrryik 54 
                                       +HGv L+t+++ g R  +v  AV + ++
  gi|320100431|ref|YP_004176023.1| 153 KHGVSLNTVLYAGTREDAVRvAVEDLVE 180
                                       9**************9999657777665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.47
                           DUF1580  16 vstilRWslkpn 27 
                                       vs + R+s +p+
  gi|320100431|ref|YP_004176023.1| 203 VSLVKRYSSRPV 214
                                       788889999997 PP

>> DUF3933  Protein of unknown function (DUF3933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.94   2.8e+03      34      46 ..     103     115 ..      98     118 .. 0.79
   2 ?   10.3   0.2   0.00016      0.49      19      52 ..     163     200 ..     157     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.94
                           DUF3933  34 GLrtGerYvvvsa 46 
                                        + tG r++ v a
  gi|320100431|ref|YP_004176023.1| 103 AIATGARFIRVNA 115
                                       5679999998877 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                           DUF3933  19 Yaetkqeaieka.eLLGLrtGerYvvvsak...eaeGL 52 
                                       Ya t+ +a+  a e L  r G  Yvvv+     ea GL
  gi|320100431|ref|YP_004176023.1| 163 YAGTREDAVRVAvEDLVERGGADYVVVTGArtgEAPGL 200
                                       9********9877999***********95322266665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2091.43
//
Query:       gi|320100432|ref|YP_004176024.1|  [L=315]
Description: transcription initiation factor IIB (TFIIB) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-38  129.0   0.5    1.1e-19   70.3   0.1    2.3  2  TFIIB            Transcription factor TFIIB repeat
    4.3e-11   42.2   0.1    7.5e-11   41.4   0.1    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
    3.5e-07   30.3   0.0      0.022   14.9   0.0    2.2  2  Cyclin_C         Cyclin, C-terminal domain
    9.8e-05   21.7   0.2     0.0023   17.3   0.0    2.7  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
    0.00038   20.4   1.7      0.045   13.8   0.7    2.4  2  TFIIB_C_1        Transcription factor IIB C-terminal module 1
    0.00044   19.7   0.1    0.00044   19.7   0.1    3.2  3  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.013   15.1   1.2      0.059   13.1   0.1    2.7  4  Sigma70_r4_2     Sigma-70, region 4
       0.02   14.7   0.4      0.075   12.9   0.1    2.2  2  HTH_23           Homeodomain-like domain
      0.028   14.2   0.2       0.18   11.6   0.0    2.5  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.035   14.1   0.0      0.059   13.4   0.0    1.3  1  RB_B             Retinoblastoma-associated protein B domain
      0.081   13.0   0.4        2.1    8.5   0.0    3.0  3  HTH_3            Helix-turn-helix
       0.12   12.8   0.2         14    6.1   0.0    2.6  2  Rrf2             Transcriptional regulator
       0.12   12.6   0.1       0.25   11.5   0.1    1.5  1  Ribonucleas_3_3  Ribonuclease-III-like


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 !   70.3   0.1   7.7e-23   1.1e-19       2      71 .]     136     205 ..     135     205 .. 0.97
   2 !   57.0   0.0   1.1e-18   1.5e-15       1      71 []     229     299 ..     229     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 7.7e-23
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        r+ad l+Lp +V+++A  ++++a++++++ Grs ++++AA++y+Acr  +v r++ ei   +++  k+i
  gi|320100432|ref|YP_004176024.1| 136 DRLADVLNLPSYVKEEAARIYREAVDRGLVRGRSIESVIAAAIYLACREMKVPRSLDEITRHTRIGRKEI 205
                                       689**************************************************************99987 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 1.1e-18
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++r++  l+Lp +  + A e++++a+e +v+ G+ pag+aAA++y+A+ + ++k+tqkei+ ++ V+e+t+
  gi|320100432|ref|YP_004176024.1| 229 VPRIVHGLGLPGQAVKLAIEIINTAKEHGVTGGKDPAGLAAAAVYMAAERLGEKKTQKEIAHIAGVTEVTV 299
                                       6799999**************************************************************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 !   41.4   0.1   5.4e-14   7.5e-11       4      43 .]      22      61 ..      22      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.4e-14
                                      TTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  4 PnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      P+C  +++v+D+++ge+vC d G+V+e+  ide+pewr+f
  gi|320100432|ref|YP_004176024.1| 22 PKCPQDKIVYDAAHGEYVCQDTGEVIEEKVIDERPEWRAF 61
                                      8999999*******************************98 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   5.8e-05      0.08      45      90 ..     172     216 ..     169     226 .. 0.84
   2 !   14.9   0.0   1.6e-05     0.022      44      90 ..     264     310 ..     259     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                                       HHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                          Cyclin_C  45 SliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                       S+iAaa +l++r + + p   ++++ +t++  +++  c++l+l  l
  gi|320100432|ref|YP_004176024.1| 172 SVIAAAIYLACREM-KVPRSLDEITRHTRIGRKEIARCYRLLLREL 216
                                       88888777777777.99*9**********************99766 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                          Cyclin_C  44 pSliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                       p  +Aaaa+++a   l++++ ++++ h+ g+++  +++ ++ ++++l
  gi|320100432|ref|YP_004176024.1| 264 PAGLAAAAVYMAAERLGEKKTQKEIAHIAGVTEVTVRNRYKELAKVL 310
                                       6669***************************************9987 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.15   2.1e+02      18      40 ..     176     201 ..     174     210 .. 0.77
   2 !   17.3   0.0   1.7e-06    0.0023      16      51 ..     271     306 ..     265     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.15
                      HTH_Tnp_ISL3  18 ayilellles...rsvkavArqlgvS 40 
                                       a+i+ +++e+   rs  ++ r+++++
  gi|320100432|ref|YP_004176024.1| 176 AAIYLACREMkvpRSLDEITRHTRIG 201
                                       67888888888779999999999987 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.7e-06
                      HTH_Tnp_ISL3  16 leayilelllesrsvkavArqlgvSwtTVwrildry 51 
                                       + ++++e+l e ++ k++A + gv++ TV+++++++
  gi|320100432|ref|YP_004176024.1| 271 AVYMAAERLGEKKTQKEIAHIAGVTEVTVRNRYKEL 306
                                       6799****************************9976 PP

>> 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 !   13.8   0.7   3.3e-05     0.045       6      71 ..     132     194 ..     128     219 .. 0.86
   2 ?    5.2   0.0     0.015        21      25      77 ..     241     294 ..     232     314 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                         TFIIB_C_1   6 rnalevllklsrrdeavleealelakrfvGkrrergervekqeevaaaclmlaaerlrqPvPLael 71 
                                        n l+ l +  + +  v+eea  + ++ v +   rg+ +e    v+aa++ la+ +++ P  L e+
  gi|320100432|ref|YP_004176024.1| 132 MNELDRLADVLNLPSYVKEEAARIYREAVDRGLVRGRSIE---SVIAAAIYLACREMKVPRSLDEI 194
                                       5789999999999******************999999887...69***************999997 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                         TFIIB_C_1  25 ealelakrfvGkrrergervekqe.evaaaclmlaaerlrqPvPLaelrvldps 77 
                                       +a++la + + + +e g+   k     aaa++ +aaerl++    +e+ ++++ 
  gi|320100432|ref|YP_004176024.1| 241 QAVKLAIEIINTAKEHGVTGGKDPaGLAAAAVYMAAERLGEKKTQKEIAHIAGV 294
                                       5777888888888888887777651568999********998888888887764 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.18   2.5e+02       4      22 ..     100     118 ..      99     119 .. 0.91
   2 ?   -0.9   0.3      0.89   1.2e+03      20      49 ..     188     217 ..     180     217 .. 0.80
   3 !   19.7   0.1   3.2e-07   0.00044      16      43 ..     278     305 ..     271     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.18
                                       HS-HHHHHHHHHHHTTT-- CS
                        Sigma70_r4   4 sLpererevlelrfgeglT 22 
                                       +L+e+  e ++lr ++ +T
  gi|320100432|ref|YP_004176024.1| 100 RLTEKKHELVKLRKWQART 118
                                       79***********999887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.89
                                       T--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        Sigma70_r4  20 glTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                       +++l EI ++  i r  + +  +  lr LR
  gi|320100432|ref|YP_004176024.1| 188 PRSLDEITRHTRIGRKEIARCYRLLLRELR 217
                                       689999999999988888777777777776 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 3.2e-07
                                       HHTTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  16 rfgeglTleEIgerlgiSrerVrqiekr 43 
                                       r ge+ T++EI+ + g+++ +Vr + k+
  gi|320100432|ref|YP_004176024.1| 278 RLGEKKTQKEIAHIAGVTEVTVRNRYKE 305
                                       669**********************987 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         4   5.6e+03      10      25 ..     100     115 ..      99     117 .. 0.85
   2 ?   -3.0   0.0       4.3   5.9e+03      42      53 ..     123     134 ..     122     135 .. 0.70
   3 ?   13.1   0.1   4.3e-05     0.059      27      48 ..     283     304 ..     278     310 .. 0.91
   4 ?    0.3   0.0       0.4   5.5e+02      29      38 ..     303     312 ..     302     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4
                                       TS-HHHHHHHHHHHTS CS
                      Sigma70_r4_2  10 eLperqreifllryle 25 
                                       +L+e+  e + lr ++
  gi|320100432|ref|YP_004176024.1| 100 RLTEKKHELVKLRKWQ 115
                                       7999999999999876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHHH CS
                      Sigma70_r4_2  42 tVksrlsRArkk 53 
                                       +V+++l++A+  
  gi|320100432|ref|YP_004176024.1| 123 SVERNLAQAMNE 134
                                       688888888755 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 4.3e-05
                                       --HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  27 lsykEIAellgisegtVksrls 48 
                                       +++kEIA + g++e+tV++r++
  gi|320100432|ref|YP_004176024.1| 283 KTQKEIAHIAGVTEVTVRNRYK 304
                                       799*****************96 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.4
                                       HHHHHHHHT- CS
                      Sigma70_r4_2  29 ykEIAellgi 38 
                                       ykE A++lg+
  gi|320100432|ref|YP_004176024.1| 303 YKELAKVLGV 312
                                       9*******98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.2     1e+04      20      26 ..     202     208 ..     195     210 .. 0.74
   2 ?   12.9   0.1   5.4e-05     0.075       8      39 ..     269     304 ..     267     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.2
                            HTH_23  20 vreIAre 26 
                                       ++eIAr 
  gi|320100432|ref|YP_004176024.1| 202 RKEIARC 208
                                       7899986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.4e-05
                            HTH_23   8 lrillllae....GlsvreIAreLgvsrrTvyrwlk 39 
                                       + +++++ae    +++++eIA + gv++ Tv++  k
  gi|320100432|ref|YP_004176024.1| 269 AAAVYMAAErlgeKKTQKEIAHIAGVTEVTVRNRYK 304
                                       6799999988999*******************5544 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.7   2.4e+03       9      25 ..     191     207 ..     191     218 .. 0.77
   2 ?   11.6   0.0   0.00013      0.18      19      41 ..     284     306 ..     281     307 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
                     HTH_AsnC-type   9 LeaLqedaRisyaeLAe 25 
                                       L+++ +  Ri  +e+A+
  gi|320100432|ref|YP_004176024.1| 191 LDEITRHTRIGRKEIAR 207
                                       56677888888888887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                     HTH_AsnC-type  19 syaeLAervGlSestvlrRvrrL 41 
                                       + +e+A   G++e tv++R++ L
  gi|320100432|ref|YP_004176024.1| 284 TQKEIAHIAGVTEVTVRNRYKEL 306
                                       679*****************988 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 ?   13.4   0.0   4.3e-05     0.059      10      94 ..     128     210 ..     120     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                              RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqp 86 
                                       +  a+  l +L + L+l s ++e++  + ++++  ++ l++ R ++ ++ +a+Y  ++  k  +s+ ei ++ r   
  gi|320100432|ref|YP_004176024.1| 128 LAQAMNELDRLADVLNLPSYVKEEAARIYREAV--DRGLVRGRSIESVIAAAIYLACREMKVPRSLDEITRHTRIGR 202
                                       566788899999999999999999999888887..578********************************9999877 PP

                              RB_B  87 qasskvyr 94 
                                       ++ ++ yr
  gi|320100432|ref|YP_004176024.1| 203 KEIARCYR 210
                                       77777666 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.5   2.1e+03      39      51 ..     133     145 ..     121     147 .. 0.76
   2 ?    8.5   0.0    0.0015       2.1       3      27 ..     276     300 ..     274     302 .. 0.89
   3 ?    1.0   0.0      0.33   4.6e+02      13      21 ..     304     312 ..     300     315 .] 0.65

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHTSE CS
                             HTH_3  39 etlkklakaLgvs 51 
                                         l +la++L+++
  gi|320100432|ref|YP_004176024.1| 133 NELDRLADVLNLP 145
                                       5688899999876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                                       HHHHHTTHHHHHHHHHHTSSHHHHH CS
                             HTH_3   3 elRkqlglsqeeLAeklGvsrstis 27 
                                       + R+  + +q+e+A  +Gv+  t++
  gi|320100432|ref|YP_004176024.1| 276 AERLGEKKTQKEIAHIAGVTEVTVR 300
                                       6799999*************99996 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.33
                                       HHHHHHHTS CS
                             HTH_3  13 eeLAeklGv 21 
                                       +eLA++lGv
  gi|320100432|ref|YP_004176024.1| 304 KELAKVLGV 312
                                       566666665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.05        69       8      50 ..     171     213 ..     165     221 .. 0.86
   2 ?    6.1   0.0      0.01        14      13      51 ..     270     308 ..     266     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHH CS
                              Rrf2   8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLr 50 
                                       e ++ a +yLa +e + p s++ei +++ i ++ +++  + L 
  gi|320100432|ref|YP_004176024.1| 171 ESVIAAAIYLACREMKVPRSLDEITRHTRIGRKEIARCYRLLL 213
                                       6678899***********************9999999887775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                                       HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHH CS
                              Rrf2  13 allyLakeeeeepvsseeiaerqnispsylekilakLrk 51 
                                       a +y+a+e+ +e+ + +eia+  ++ ++ ++   ++L+k
  gi|320100432|ref|YP_004176024.1| 270 AAVYMAAERLGEKKTQKEIAHIAGVTEVTVRNRYKELAK 308
                                       4578999888889******************99999986 PP

>> Ribonucleas_3_3  Ribonuclease-III-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00018      0.25      47     110 ..     116     181 ..      98     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                   Ribonucleas_3_3  47 kdegeltklraslvs.eeslaeiAkelgLgkvlrlrkgeeetegsgrekvladaleAliG.Aiyld 110
                                       +++ +lt++ ++l +  ++l+++A  l+L ++++ +      e+ +r  v++  +e++i+ Aiyl 
  gi|320100432|ref|YP_004176024.1| 116 ARTRILTSVERNLAQaMNELDRLADVLNLPSYVKEEAARIYREAVDRGLVRGRSIESVIAaAIYLA 181
                                       4555677777788775679***************988888899999999*********97369985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2244.45
//
Query:       gi|320100433|ref|YP_004176025.1|  [L=444]
Description: transposase, IS605 OrfB family [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-22   77.3   0.1    1.3e-21   76.3   0.1    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00014   21.3   1.2       0.03   13.8   0.1    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.011   15.7   2.3      0.018   15.1   1.3    1.7  2  DZR             Double zinc ribbon
      0.013   15.8   0.8      0.025   14.8   0.8    1.5  1  OrfB_IS605      Probable transposase
      0.036   14.2   1.7      0.082   13.1   1.7    1.6  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.069   13.0   0.1       0.14   12.0   0.1    1.5  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.085   12.9   2.0        6.1    7.0   0.1    3.1  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.15   11.9   0.0        0.3   11.0   0.0    1.4  1  VasL            Type VI secretion system, EvfB, or VasL
       0.32   11.1   1.7         15    5.8   0.1    2.6  2  Zn-ribbon_8     Zinc ribbon domain
        0.4   11.0   3.3       0.65   10.3   0.3    2.4  2  zinc_ribbon_9   zinc-ribbon
       0.97    9.1   3.4       0.89    9.3   1.2    2.1  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        2.9    8.2   5.1         27    5.1   0.1    3.0  3  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
        3.4    7.2   7.4        4.4    6.9   4.5    2.4  2  zf-ribbon_3     zinc-ribbon domain
        6.9    6.5   8.5        7.6    6.4   1.5    2.7  4  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1     1e-24   1.3e-21       1      69 []     300     367 ..     300     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +r+l  +l ++++++G++ + v+p++TS+tC+ Cgs++ e +  r++kCpnCgfeadrD++A++Ni ++
  gi|320100433|ref|YP_004176025.1| 300 YRRLGYWLDWQCEKHGVPHIAVDPRNTSSTCPLCGSRLIE-NGYRRMKCPNCGFEADRDTVAVLNIRRK 367
                                       789999**********************************.*************************985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   2.4e-05      0.03       2      27 ..     310     335 ..     309     342 .. 0.90
   2 !    6.2   0.2    0.0058       7.5       1       7 [.     345     351 ..     345     359 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                       EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                       +C ++g +++ +Dp ++  +C+ CG+
  gi|320100433|ref|YP_004176025.1| 310 QCEKHGVPHIAVDPRNTSSTCPLCGS 335
                                       69999********************8 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0058
                                       EEETTTT CS
                      TF_Zn_Ribbon   1 ykCPnCg 7  
                                       +kCPnCg
  gi|320100433|ref|YP_004176025.1| 345 MKCPNCG 351
                                       79****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.3   1.4e-05     0.018      10      41 ..     325     357 ..     310     359 .. 0.81
   2 ?   -2.5   0.0       4.4   5.6e+03      17      23 ..     391     397 ..     390     408 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                               DZR  10 pdarfCseCgtklkavaa.edrCpsCgekvdpe 41 
                                       + + +C+ Cg++l +      +Cp+Cg ++d +
  gi|320100433|ref|YP_004176025.1| 325 NTSSTCPLCGSRLIENGYrRMKCPNCGFEADRD 357
                                       56789********966558999*****988765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.4
                               DZR  17 eCgtklk 23 
                                       +Cg++++
  gi|320100433|ref|YP_004176025.1| 391 RCGEPVN 397
                                       5777665 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.8     2e-05     0.025      48     102 ..     205     264 ..     164     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                        OrfB_IS605  48 sdykylakeiaelqsklkkskn.....ykkasrklarlhrkrsrrrkhllhklathlikt 102
                                       ++  ++++   +lq+k++         ++  + +++r h+k + ++ + ++k++++++ t
  gi|320100433|ref|YP_004176025.1| 205 EKAVRYRELAERLQRKYSNGSYrawlrRRGIRDRVRRFHEKARSIIEDWARKVSREIALT 264
                                       455677777777888876665578888899**************************9866 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.7   6.4e-05     0.082      15      40 .]     327     351 ..     326     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-05
                     Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCvaCd 40 
                                       ++tCp Cg+ L ++ +  ++ C++C+
  gi|320100433|ref|YP_004176025.1| 327 SSTCPLCGSRLIEN-GYRRMKCPNCG 351
                                       789**********9.56899*****6 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 ?   12.0   0.1   0.00011      0.14      10      38 ..     326     354 ..     318     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       S--B-TTT-SB--SSSS-EEEETTT--EE CS
                              C1_1  10 qptfCkhCgeflwgkekqglkCswCkllv 38 
                                        +++C  Cg+ l + +++ +kC +C++ +
  gi|320100433|ref|YP_004176025.1| 326 TSSTCPLCGSRLIENGYRRMKCPNCGFEA 354
                                       6789********99***********9875 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0047       6.1       1      10 [.     329     338 ..     329     341 .. 0.87
   2 ?    3.5   0.1     0.057        73       1      11 [.     346     356 ..     346     361 .. 0.81
   3 ?   -0.7   0.0       1.1   1.5e+03       5      14 ..     392     401 ..     391     412 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0047
                    DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                       +CP CGs ++
  gi|320100433|ref|YP_004176025.1| 329 TCPLCGSRLI 338
                                       7******997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.057
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP CG ++ R
  gi|320100433|ref|YP_004176025.1| 346 KCPNCGFEADR 356
                                       6*****87755 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                    DNA_ligase_ZBD   5 CGsavvReeg 14 
                                       CG +v R+ g
  gi|320100433|ref|YP_004176025.1| 392 CGEPVNRPKG 401
                                       *****99865 PP

>> VasL  Type VI secretion system, EvfB, or VasL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023       0.3      36      84 ..     245     293 ..     240     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                              VasL  36 avkaltrqWqqqlearalpaeslsgweqartqlqqLsdkLlelerqrgk 84 
                                       +++ + + W++++++++   +  +g+  ar+ l+ L + L +l rq ++
  gi|320100433|ref|YP_004176025.1| 245 KARSIIEDWARKVSREIALTARRDGYAVAREDLTYLVESLRRLPRQHKT 293
                                       67788899*************************************9886 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        15       7      35 ..     310     336 ..     308     339 .. 0.62
   2 ?    3.7   0.1     0.053        68      28      37 ..     346     355 ..     342     358 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgse 35 
                                       +Ce++g  + ++ +  ++   +CP Cgs+
  gi|320100433|ref|YP_004176025.1| 310 QCEKHGVPHIAVDP--RNTSSTCPLCGSR 336
                                       56666644444443..445678*****95 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.053
                       Zn-ribbon_8  28 aCPeCgsevr 37 
                                       +CP+Cg e+ 
  gi|320100433|ref|YP_004176025.1| 346 KCPNCGFEAD 355
                                       4777776555 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00051      0.65      11      33 ..     318     339 ..     311     340 .. 0.89
   2 ?    0.3   0.2       0.7   8.9e+02      22      28 ..     346     351 ..     342     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00051
                     zinc_ribbon_9  11 fVsvspdedsdvlCPhCgggFVE 33 
                                       ++ v p+++s + CP Cg+  +E
  gi|320100433|ref|YP_004176025.1| 318 HIAVDPRNTSST-CPLCGSRLIE 339
                                       688999999999.******9887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.7
                     zinc_ribbon_9  22 vlCPhCg 28 
                                       + CP+Cg
  gi|320100433|ref|YP_004176025.1| 346 K-CPNCG 351
                                       4.****7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.2   0.00069      0.89       6      28 ..     330     351 ..     326     353 .. 0.90
   2 ?   -2.1   0.0       2.6   3.3e+03       8      13 ..     391     396 ..     391     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00069
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCg 28 
                                       C+ CG++ + + g + + Cp+Cg
  gi|320100433|ref|YP_004176025.1| 330 CPLCGSRLIEN-GYRRMKCPNCG 351
                                       *******8765.99********9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                     zf-NADH-PPase   8 rCGapt 13 
                                       rCG p+
  gi|320100433|ref|YP_004176025.1| 391 RCGEPV 396
                                       8**996 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 ?   -3.0   0.2       7.2   9.3e+03      10      20 ..     234     245 ..     234     247 .. 0.82
   2 ?    5.1   0.1     0.021        27       4      12 ..     328     336 ..     325     337 .. 0.87
   3 ?    4.5   0.1     0.033        42       2      10 ..     343     351 ..     342     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.2
                                       T-TTTEE.ETT. CS
                    Prim_Zn_Ribbon  10 GGrDrFr.fddk 20 
                                       G rDr r f +k
  gi|320100433|ref|YP_004176025.1| 234 GIRDRVRrFHEK 245
                                       5599*9999997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                                       E--TTTT-T CS
                    Prim_Zn_Ribbon   4 spCPvCGGr 12 
                                       s CP CG+r
  gi|320100433|ref|YP_004176025.1| 328 STCPLCGSR 336
                                       78*****97 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.033
                                       EEE--TTTT CS
                    Prim_Zn_Ribbon   2 khspCPvCG 10 
                                       ++  CP+CG
  gi|320100433|ref|YP_004176025.1| 343 RRMKCPNCG 351
                                       5678****9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.5    0.0034       4.4       4      24 ..     329     352 ..     327     353 .. 0.83
   2 ?   -2.6   0.0       3.3   4.2e+03       7      11 ..     391     395 ..     390     396 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0034
                       zf-ribbon_3   4 rCPnCGa.plssd..dnvCpyCGt 24 
                                       +CP CG+ +++ +   ++Cp+CG 
  gi|320100433|ref|YP_004176025.1| 329 TCPLCGSrLIENGyrRMKCPNCGF 352
                                       69999999999863368******6 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.3
                       zf-ribbon_3   7 nCGap 11 
                                       +CG+p
  gi|320100433|ref|YP_004176025.1| 391 RCGEP 395
                                       69986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.076        97      12      22 ..     326     336 ..     324     337 .. 0.72
   2 ?    5.5   5.5     0.011        14       2      22 ..     330     353 ..     329     354 .. 0.86
   3 ?    6.4   1.5    0.0059       7.6       1       8 [.     346     353 ..     346     359 .. 0.77
   4 ?   -1.4   0.1       1.7   2.2e+03      18      22 ..     391     395 ..     390     397 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.076
                     zinc_ribbon_2  12 nakFCpyCGtp 22 
                                       ++  Cp CG+ 
  gi|320100433|ref|YP_004176025.1| 326 TSSTCPLCGSR 336
                                       56779999976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                     zinc_ribbon_2   2 CpnCGael.qdnakF..CpyCGtp 22 
                                       Cp CG  l +++ +   Cp+CG++
  gi|320100433|ref|YP_004176025.1| 330 CPLCGSRLiENGYRRmkCPNCGFE 353
                                       999999998889999999999975 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0059
                     zinc_ribbon_2   1 fCpnCGae 8  
                                       +CpnCG e
  gi|320100433|ref|YP_004176025.1| 346 KCPNCGFE 353
                                       78999876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.7
                     zinc_ribbon_2  18 yCGtp 22 
                                       +CG+p
  gi|320100433|ref|YP_004176025.1| 391 RCGEP 395
                                       46655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3283.14
//
Query:       gi|320100434|ref|YP_004176026.1|  [L=105]
Description: translation initiation factor 1 (eIF-1/SUI1) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-20   71.0   0.2      1e-19   70.8   0.2    1.1  1  SUI1      Translation initiation factor SUI1
  ------ inclusion threshold ------
        0.1   12.9   0.1       0.12   12.7   0.1    1.3  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
       0.14   12.3   0.0       0.16   12.1   0.0    1.1  1  DUF809    Protein of unknown function (DUF809)


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.2   1.7e-23     1e-19       2      77 .]      25      97 ..      24      97 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 1.7e-23
                              SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygvp 77
                                      ++ ++irl++r+ +K vT+v gl +++  lk++ak+lk+k+a++g+  k+g   i++QGd+r++v+++L+e++g+p
  gi|320100434|ref|YP_004176026.1| 25 QSLVKIRLDTRKFGKAVTIVDGLPNDKEFLKQVAKALKTKLATGGTF-KEG--RIELQGDHRHRVKQILIEDFGIP 97
                                      6789******************************************8.888..8*******************997 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 ?   12.7   0.1   2.1e-05      0.12      39      77 ..      52      92 ..      20      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                              Img2 39 alredLrkaleelvkvne....vtgkieikGdrveevkkfLes 77
                                      ++ ++++kal++  k+ +    ++g+ie++Gd++++vk++L +
  gi|320100434|ref|YP_004176026.1| 52 EFLKQVAKALKT--KLATggtfKEGRIELQGDHRHRVKQILIE 92
                                      455555555553..3333455599***************9975 PP

>> DUF809  Protein of unknown function (DUF809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.7e-05      0.16      63     119 ..      30      87 ..      17      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                            DUF809  63 yefqygwlgvkitiksnvpnd.evtkkvspiikgeiegkeekkegkgeiegkeekkeg 119
                                         ++   +g  +ti   +pnd e  k+v+  +k ++      keg+ e++g + ++  
  gi|320100434|ref|YP_004176026.1|  30 IRLDTRKFGKAVTIVDGLPNDkEFLKQVAKALKTKLATGGTFKEGRIELQGDHRHRVK 87 
                                       55556678999*********96789*************************98876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 880.98
//
Query:       gi|320100435|ref|YP_004176027.1|  [L=49]
Description: DNA-directed RNA polymerase subunit P [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-05   22.9   1.3    8.4e-05   22.6   1.3    1.2  1  Zn-ribbon_8      Zinc ribbon domain
     0.0001   21.9   6.8    0.00065   19.3   6.8    2.0  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
    0.00091   19.2   2.6      0.018   15.0   0.1    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0014   18.5   4.0       0.14   12.1   0.3    2.3  2  zinc_ribbon_4    zinc-ribbon domain
     0.0017   17.8   1.3       0.26   10.8   0.1    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0059   16.6   3.7      0.052   13.6   0.5    2.1  2  Rubredoxin       Rubredoxin
     0.0082   15.9   5.1       0.07   12.9   0.5    2.2  2  zinc_ribbon_5    zinc-ribbon domain
     0.0098   16.1   0.8      0.013   15.7   0.8    1.2  1  zf-RING_7        C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.015   15.2   1.3      0.024   14.6   1.3    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.016   15.6   2.5       0.27   11.8   0.3    2.2  2  zf-C2H2          Zinc finger, C2H2 type
      0.017   15.2   0.2      0.017   15.2   0.2    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.029   14.5   0.0      0.038   14.1   0.0    1.3  1  VirDNA-topo-I_N  Viral DNA topoisomerase I, N-terminal
      0.034   13.9   2.2        1.9    8.3   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.039   14.3   0.3      0.047   14.1   0.3    1.1  1  DUF4379          Probable Zinc-ribbon domain
      0.053   13.2   0.2      0.057   13.1   0.2    1.2  1  TackOD1          Thaumarchaeal output domain 1
      0.077   12.4   2.5        1.5    8.4   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.092   13.2   2.6        4.9    7.7   0.1    2.2  2  zf-H2C2_2        Zinc-finger double domain
        0.1   12.2   1.9       0.88    9.2   0.1    2.0  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.15   11.4   0.3       0.17   11.2   0.3    1.0  1  Rtf2             Rtf2 RING-finger
       0.15   12.1   5.2          1    9.5   0.6    2.2  2  UPF0547          Uncharacterised protein family UPF0547
       0.18   11.6   3.6        2.8    7.7   0.9    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.21   12.5   1.5        4.8    8.3   0.1    2.2  2  zf-C2H2_4        C2H2-type zinc finger
       0.31   10.9   5.7          6    6.8   0.6    2.6  3  TFIIS_C          Transcription factor S-II (TFIIS)
       0.51   10.3   5.4        2.7    7.9   0.4    2.1  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        1.1    9.5   5.7        1.5    9.0   0.5    2.1  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
        2.3    7.7   5.7         11    5.6   0.5    2.1  2  Mu-like_Com      Mu-like prophage protein Com


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.3   1.2e-07   8.4e-05       6      33 ..       4      32 ..       3      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-07
                       Zn-ribbon_8  6 YrCeeCghefe..vlqsisdapltaCPeCg 33
                                      Y+C +Cg +f+  ++ +i+   +++CP+C 
  gi|320100435|ref|YP_004176027.1|  4 YKCGRCGYVFDdeEMKRIF-GRQVKCPNCT 32
                                      ***********88888777.44788****5 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   6.8   9.4e-07   0.00065       1      30 [.       4      38 ..       4      39 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.4e-07
                                      -B-SSS--B----S.....SS----SSS-----B- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevslkk.....gdpiRCkeCGhRilYK 30
                                      Y+Cg+Cg  + +++     g +++C +C++ i+YK
  gi|320100435|ref|YP_004176027.1|  4 YKCGRCGYVFDDEEmkrifGRQVKCPNCTYEIVYK 38
                                      9*****9655544422244789************9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4     0.049        34      37      45 ..       3      11 ..       2      12 .. 0.86
   2 !   15.0   0.1   2.6e-05     0.018      13      35 ..      20      42 ..      18      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.049
                     Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                      +++C +C++
  gi|320100435|ref|YP_004176027.1|  3 KYKCGRCGY 11
                                      699****97 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.6e-05
                     Zn_Tnp_IS1595 13 lrWpngfvCPhCgsrkayriktr 35
                                      ++++  + CP+C ++ +y+i+++
  gi|320100435|ref|YP_004176027.1| 20 RIFGRQVKCPNCTYEIVYKIARP 42
                                      67888899************984 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2   0.00074      0.51      24      35 ..       2      13 ..       1      14 [. 0.87
   2 !   12.1   0.3    0.0002      0.14      12      32 ..      11      32 ..      11      36 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00074
                     zinc_ribbon_4 24 vkvrCskCghvF 35
                                      vk +C +Cg vF
  gi|320100435|ref|YP_004176027.1|  2 VKYKCGRCGYVF 13
                                      6789*******9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                     zinc_ribbon_4 12 yeiddeklp.akgvkvrCskCg 32
                                      y +dde ++   g+ v+C++C 
  gi|320100435|ref|YP_004176027.1| 11 YVFDDEEMKrIFGRQVKCPNCT 32
                                      67788887756799*******6 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00038      0.26      22      33 ..       6      17 ..       3      22 .. 0.86
   2 !    6.4   0.2    0.0089       6.1       2       7 ..      27      32 ..      26      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                                      ESSSSBEEEECC CS
                      TF_Zn_Ribbon 22 CtdCGlVledns 33
                                      C++CG+V +d+ 
  gi|320100435|ref|YP_004176027.1|  6 CGRCGYVFDDEE 17
                                      *********985 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0089
                                      EETTTT CS
                      TF_Zn_Ribbon  2 kCPnCg 7 
                                      kCPnC 
  gi|320100435|ref|YP_004176027.1| 27 KCPNCT 32
                                      899995 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.5   7.6e-05     0.052       1      15 [.       3      17 ..       3      20 .. 0.91
   2 ?    4.5   0.2     0.053        37      36      41 ..      27      32 ..      24      38 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.6e-05
                                      EEEETTT-BEEETTT CS
                        Rubredoxin  1 kyeCkvCgyvYdpak 15
                                      ky+C  Cgyv+d+++
  gi|320100435|ref|YP_004176027.1|  3 KYKCGRCGYVFDDEE 17
                                      7***********985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.053
                                      BBTTTB CS
                        Rubredoxin 36 vCPdCg 41
                                      +CP+C 
  gi|320100435|ref|YP_004176027.1| 27 KCPNCT 32
                                      688886 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.5    0.0001      0.07      24      36 ..       2      14 ..       1      15 [. 0.91
   2 ?    6.3   0.3     0.012       8.1      17      31 ..      16      31 ..      14      35 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                     zinc_ribbon_5 24 kkVrCakCaevFd 36
                                      +k +C++C+ vFd
  gi|320100435|ref|YP_004176027.1|  2 VKYKCGRCGYVFD 14
                                      688*********8 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                     zinc_ribbon_5 17 sklKk.sgkkVrCakC 31
                                      +++K   g  V+C  C
  gi|320100435|ref|YP_004176027.1| 16 EEMKRiFGRQVKCPNC 31
                                      5565524788999888 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 !   15.7   0.8   1.9e-05     0.013       1      29 [.       5      31 ..       5      32 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                                      EETTT--B--CCHHHHHCCSTB-EE-TTT CS
                         zf-RING_7  1 tCgGChmelppqvlselragdevvtCpeC 29
                                      +Cg C+ + + ++ +++ +    v+Cp+C
  gi|320100435|ref|YP_004176027.1|  5 KCGRCGYVFDDEEMKRIFGR--QVKCPNC 31
                                      7*****************99..6****** 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 ?   14.6   1.3   3.5e-05     0.024      30      55 ..       5      34 ..       3      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke....alsgrtfkCpnCgfe 55
                                      +C +Cg++ ++    +  gr++kCpnC +e
  gi|320100435|ref|YP_004176027.1|  5 KCGRCGYVFDDeemkRIFGRQVKCPNCTYE 34
                                      7*******9988899999*********987 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3    0.0004      0.27       1      13 [.       4      16 ..       4      20 .. 0.86
   2 ?    4.2   0.1     0.097        67       2       8 ..      27      33 ..      26      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                                      EEETTTTEEESSH CS
                           zf-C2H2  1 ykCpdCgksFkrk 13
                                      ykC+ Cg++F + 
  gi|320100435|ref|YP_004176027.1|  4 YKCGRCGYVFDDE 16
                                      9*********876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.097
                                      EETTTTE CS
                           zf-C2H2  2 kCpdCgk 8 
                                      kCp C++
  gi|320100435|ref|YP_004176027.1| 27 KCPNCTY 33
                                      8****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 ?   15.2   0.2   2.4e-05     0.017      69      95 ..       2      34 ..       1      46 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                                      -EEEETTTS-EEECHH..HHH.....S-TTTSSS CS
                              HypA 69 vkvrCreCgkefelee..kal.....rCpkCgsa 95
                                      vk++C +Cg+ f+ ee  + +     +Cp+C  +
  gi|320100435|ref|YP_004176027.1|  2 VKYKCGRCGYVFDDEEmkR-IfgrqvKCPNCTYE 34
                                      6899********9776431.245555*****865 PP

>> VirDNA-topo-I_N  Viral DNA topoisomerase I, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.6e-05     0.038       8      34 ..      12      42 ..       7      49 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-05
                                      EESSTTS-....SB--TT-THHHHHHH---- CS
                   VirDNA-topo-I_N  8 lfvDkelt....nrVsddNptYeilkkvkiP 34
                                       f D+e++    ++V++ N tYei+ k+  P
  gi|320100435|ref|YP_004176027.1| 12 VFDDEEMKrifgRQVKCPNCTYEIVYKIARP 42
                                      56777766222258***********999766 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     0.018        13      16      21 ..       6      11 ..       2      16 .. 0.71
   2 ?    8.3   0.1    0.0027       1.9       1       9 [.      27      35 ..      24      36 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|320100435|ref|YP_004176027.1|  6 CGRCGY 11
                                      667765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0027
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +CpnC +e+
  gi|320100435|ref|YP_004176027.1| 27 KCPNCTYEI 35
                                      688886665 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   6.8e-05     0.047      28      56 .]       2      31 ..       1      31 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-05
                           DUF4379 28 vwWkCakCgheWeasvsnrtkgssk.CpkC 56
                                      v  kC +Cg+ +  +  +r+ g++  Cp C
  gi|320100435|ref|YP_004176027.1|  2 VKYKCGRCGYVFDDEEMKRIFGRQVkCPNC 31
                                      678****************9555546**** PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   8.2e-05     0.057     105     133 ..       5      35 ..       1      47 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-05
                           TackOD1 105 hhftCgnvgpeeef..lkegkleCpkCktkL 133
                                       ++ +Cg+v   ee     + +++Cp+C  ++
  gi|320100435|ref|YP_004176027.1|   5 KCGRCGYVFDDEEMkrIFGRQVKCPNCTYEI 35 
                                       6889999988888754679999999999876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.037        26      18      25 ..       5      12 ..       3      16 .. 0.80
   2 ?    8.4   0.2    0.0021       1.5      16      22 ..      25      31 ..      23      35 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +C  CG++
  gi|320100435|ref|YP_004176027.1|  5 KCGRCGYV 12
                                      58888887 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0021
                       zf-ribbon_3 16 dnvCpyC 22
                                      +++Cp+C
  gi|320100435|ref|YP_004176027.1| 25 QVKCPNC 31
                                      6677777 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4     0.026        18      15      24 ..       4      13 ..       2      15 .. 0.90
   2 ?    7.7   0.1    0.0072       4.9      14      22 ..      25      33 ..      18      37 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
                         zf-H2C2_2 15 yeCplCdkaF 24
                                      y+C  C+++F
  gi|320100435|ref|YP_004176027.1|  4 YKCGRCGYVF 13
                                      9********9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0072
                         zf-H2C2_2 14 pyeCplCdk 22
                                       ++Cp C +
  gi|320100435|ref|YP_004176027.1| 25 QVKCPNCTY 33
                                      479****98 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0013      0.88       2      17 ..       3      18 ..       2      19 .. 0.88
   2 ?    2.9   0.2      0.12        83       2      11 ..      25      34 ..      24      36 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                            zf_UBZ  2 tylCerCgkeipesel 17
                                       y C rCg  + ++e+
  gi|320100435|ref|YP_004176027.1|  3 KYKCGRCGYVFDDEEM 18
                                      599*****99999887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                            zf_UBZ  2 tylCerCgke 11
                                      ++ C+ C  e
  gi|320100435|ref|YP_004176027.1| 25 QVKCPNCTYE 34
                                      579****765 PP

>> Rtf2  Rtf2 RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00024      0.17     135     158 ..       8      33 ..       4      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                              Rtf2 135 kCGcVfsekalkevk..sevClvCgk 158
                                        CG Vf ++ +k +   + +C++C+ 
  gi|320100435|ref|YP_004176027.1|   8 RCGYVFDDEEMKRIFgrQVKCPNCTY 33 
                                       6*************655889****86 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.6    0.0015         1      16      25 ..       5      14 ..       4      15 .. 0.86
   2 ?    5.0   0.3     0.039        27       2       8 ..      27      33 ..      26      35 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                           UPF0547 16 fCphCGyvFq 25
                                      +C  CGyvF+
  gi|320100435|ref|YP_004176027.1|  5 KCGRCGYVFD 14
                                      6978*****6 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.039
                           UPF0547  2 vCPeCea 8 
                                      +CP C  
  gi|320100435|ref|YP_004176027.1| 27 KCPNCTY 33
                                      5777754 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9    0.0041       2.8       1      10 [.       4      13 ..       4      15 .. 0.89
   2 ?    4.9   0.1     0.032        22      16      20 ..      27      31 ..      16      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0041
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y C +CG+++
  gi|320100435|ref|YP_004176027.1|  4 YKCGRCGYVF 13
                                      99*****975 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.032
                      Rubredoxin_2 16 rCpsC 20
                                      +Cp+C
  gi|320100435|ref|YP_004176027.1| 27 KCPNC 31
                                      7**** 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 ?    8.3   0.1    0.0069       4.8       1      13 [.       4      16 ..       4      20 .. 0.80
   2 ?    3.9   0.1      0.19   1.3e+02       2      10 ..      27      33 ..      26      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0069
                         zf-C2H2_4  1 fkCpiCgksFssk 13
                                      +kC  Cg +F + 
  gi|320100435|ref|YP_004176027.1|  4 YKCGRCGYVFDDE 16
                                      89********654 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.19
                         zf-C2H2_4  2 kCpiCgksF 10
                                      kCp C  ++
  gi|320100435|ref|YP_004176027.1| 27 KCPNC--TY 33
                                      8****..66 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 ?    6.8   0.6    0.0088         6      27      38 ..       2      13 ..       1      14 [. 0.85
   2 ?   -1.1   0.0       2.5   1.7e+03      22      29 ..      15      22 ..      13      23 .. 0.82
   3 ?    6.6   0.2      0.01       7.1       2      13 ..      27      38 ..      24      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0088
                           TFIIS_C 27 vfykCtkCghrW 38
                                      v ykC  Cg+ +
  gi|320100435|ref|YP_004176027.1|  2 VKYKCGRCGYVF 13
                                      679******987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                           TFIIS_C 22 DEpmtvfy 29
                                      DE+m +++
  gi|320100435|ref|YP_004176027.1| 15 DEEMKRIF 22
                                      99998875 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.01
                           TFIIS_C  2 kCpkCgsreayf 13
                                      kCp+C  + +y 
  gi|320100435|ref|YP_004176027.1| 27 KCPNCTYEIVYK 38
                                      899998887775 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 ?    7.9   0.4    0.0039       2.7      22      32 ..       4      14 ..       1      18 [. 0.80
   2 ?    5.4   0.8     0.024        17      22      30 ..      26      34 ..      14      35 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0039
                                      EEESSSS-EEE CS
                    RNA_POL_M_15KD 22 feCrqCgYeep 32
                                      + C  CgY++ 
  gi|320100435|ref|YP_004176027.1|  4 YKCGRCGYVFD 14
                                      78*******96 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                                      EEESSSS-E CS
                    RNA_POL_M_15KD 22 feCrqCgYe 30
                                      + C +C Ye
  gi|320100435|ref|YP_004176027.1| 26 VKCPNCTYE 34
                                      78******8 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.095        65      37      44 ..       5      12 ..       2      20 .. 0.82
   2 ?    9.0   0.5    0.0022       1.5      35      48 ..      25      38 ..      13      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.095
                    zinc_ribbon_13 37 sCknCgYt 44
                                       C +CgY+
  gi|320100435|ref|YP_004176027.1|  5 KCGRCGYV 12
                                      59999996 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0022
                    zinc_ribbon_13 35 tvsCknCgYtelYk 48
                                       v C nC Y  +Yk
  gi|320100435|ref|YP_004176027.1| 25 QVKCPNCTYEIVYK 38
                                      599*********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 ?    5.6   0.5     0.016        11      24      31 ..       3      10 ..       1      18 [. 0.84
   2 ?    5.1   0.5     0.022        15      24      30 ..      25      31 ..      21      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.016
                       Mu-like_Com 24 tiKCPRCG 31
                                      + KC RCG
  gi|320100435|ref|YP_004176027.1|  3 KYKCGRCG 10
                                      679****9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.022
                       Mu-like_Com 24 tiKCPRC 30
                                      ++KCP C
  gi|320100435|ref|YP_004176027.1| 25 QVKCPNC 31
                                      89***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 414.31
//
Query:       gi|320100436|ref|YP_004176028.1|  [L=290]
Description: agmatinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-58  196.2   0.0    1.1e-57  195.6   0.0    1.1  1  Arginase  Arginase family
  ------ inclusion threshold ------
       0.13   12.0   0.0        2.6    7.7   0.0    2.2  2  CHASE2    CHASE2 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 !  195.6   0.0   1.3e-61   1.1e-57       4     277 ..      24     280 ..      22     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 195.6 bits;  conditional E-value: 1.3e-61
                                       EEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHH CS
                          Arginase   4 allGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavaei 79 
                                       +l+GvP+d + +++pG+rf+P+++r+a  ++e    y+l +g+ +e+  ++dlg++ ++p+d e +l+ i + v+ +
  gi|320100436|ref|YP_004176028.1|  24 VLVGVPMDYTSTYKPGSRFAPDSVRNAACNIEF---YSLATGRlMENEGLIDLGNIVLPPGDVEGSLRIIGDVVKGV 97 
                                       79**************************99998...999999999999***************************** PP

                                       HHT..TCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEE CS
                          Arginase  80 lka..gklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvq 154
                                       +++  g l  +lGG+H i+++i++al+  ++   +++ fDAH+D+r ++  gs+ +h++++rr + e+ +   ++++
  gi|320100436|ref|YP_004176028.1|  98 VDEypGMLLGFLGGEHLITYPIVKALKSSVD---TLVVFDAHLDMRGEY-LGSRVNHASFLRRLV-EDGV---RVIH 166
                                       **98888899*******************98...59*************.8**************.4555...59** PP

                                       EEE-STCSHHHHHH.HHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B- CS
                          Arginase 155 iGirsvdneeyela.kelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGlt 230
                                       iG r+++ +e e++ k+  ++v+++ e  +  l      +l  +    +++y+S+D+Dvl p++aPG+G pep Glt
  gi|320100436|ref|YP_004176028.1| 167 IGSRAYSGDELEFLkKTRDVTVYSILEALKGPL------ALGDL----GKTYISIDMDVLEPSYAPGVGNPEPFGLT 233
                                       **************6666666666666644333......34444....589************************** PP

                                       HHHHHHHHHH.HHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 231 lrellallre.laeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                       +  ll+ll++ ++++ +++g+D+vEvnP  d ++  t+++a +lv+el
  gi|320100436|ref|YP_004176028.1| 234 PLHLLELLKRiVEASSRVIGFDIVEVNPLVDVND-VTSIMAGKLVFEL 280
                                       **********77889*****************66.***********95 PP

>> CHASE2  CHASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.018   1.6e+02      47      71 ..     141     165 ..     129     169 .. 0.81
   2 ?    7.7   0.0   0.00029       2.6      54      76 ..     235     257 ..     177     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.018
                            CHASE2  47 grwpwsravlarllerLeaagakai 71 
                                       g++  sr  +a +l+rL + g+++i
  gi|320100436|ref|YP_004176028.1| 141 GEYLGSRVNHASFLRRLVEDGVRVI 165
                                       66666999****************9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00029
                            CHASE2  54 avlarllerLeaagakaiglDil 76 
                                        +l +ll+r+ +a  ++ig+Di+
  gi|320100436|ref|YP_004176028.1| 235 LHLLELLKRIVEASSRVIGFDIV 257
                                       56789*****************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2140.64
//
Query:       gi|320100437|ref|YP_004176029.1|  [L=582]
Description: glycyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-25   87.2   0.2    1.5e-24   85.9   0.2    1.7  1  HGTP_anticodon  Anticodon binding domain
    4.6e-12   46.3   0.0    5.9e-11   42.7   0.0    2.4  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
       0.08   13.4   1.2         41    4.9   0.0    3.4  3  zf-C2H2         Zinc finger, C2H2 type
       0.19   11.8   0.2       0.64   10.1   0.2    1.9  1  ADK_lid         Adenylate kinase, active site lid


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 !   85.9   0.2   3.4e-28   1.5e-24       1      93 [.     480     575 ..     480     576 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 3.4e-28
                                       SEEEEESSSS....HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEE CS
                    HGTP_anticodon   1 qvvviplnek....aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrd 73 
                                       +v+v pl  +      ++ e+a++++++L ++g+r+ +d +++sig+++++ad++g+pfav+v++++le+gtvtvrd
  gi|320100437|ref|YP_004176029.1| 480 HVAVFPLVAGrrpeHARIVEVARDIYRRLVKKGFRAIYD-DDGSIGRRYARADEVGVPFAVTVDYQTLEDGTVTVRD 555
                                       6999999999999877799***************88886.79*********************************** PP

                                       TTTCEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  74 rdtreqervsldelveklke 93 
                                       rdt  qervs+d l+e++ e
  gi|320100437|ref|YP_004176029.1| 556 RDTALQERVSVDRLEEYFLE 575
                                       *****************987 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 !   42.7   0.0   1.3e-14   5.9e-11      12     178 ..     165     459 ..     159     460 .. 0.76
   2 ?   -3.3   0.0       1.7   7.8e+03      84     117 ..     498     532 ..     493     573 .. 0.51

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.3e-14
                                       EE-SSSHHHHHHHHHHHEEEB.GG.SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  12 iLkPtneetfvelirdevlrs.kr.LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlika 86 
                                       +L+P+n +++   + +  lr  ++ LPl ++q++++ R+E s  +GLlR+reF+  + + f  ++++  + +++i++
  gi|320100437|ref|YP_004176029.1| 165 YLRPENAQGMFINFANV-LRMmRNkLPLGIAQVGRVARNEISPRQGLLRLREFTIMEFEFFFDPEEASKESAEYIRE 240
                                       89*******99999977.8776556****************9566******************999*********** PP

                                       HHHHHHHTT.SCEEEEEEGTTSC...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                      tRNA-synt_2b  87 isriferlglefraiielmsaks...................................................... 109
                                       +++   r++ ++  ++++ +  +                                                      
  gi|320100437|ref|YP_004176029.1| 241 VEDRKVRVLTSEARLKGVEEPAEytvrelvekgivktpwlaywmgvgeafveslgvprekvrfiekhpherahyslq 317
                                       **999999998877777766544555666666677788888888888888887777777777777777777666666 PP

                                       ................BTTSEEEEEEEEETT.............................................. CS
                                       ................xxxxxxxxxxxxxxx.............................................. RF
                      tRNA-synt_2b 110 ................adykdkkefeavses.............................................. 124
                                                       a                                                            
  gi|320100437|ref|YP_004176029.1| 318 tfdqevytekygwievA-------------Gyayrttydlsrhmqyskadltffkryekpvertvskaypdparigv 381
                                       55555555555555552.............04444444444444667777777777788888888888888888888 PP

                                       .........................TSEEEEEEEEEEEETHHHHHTTE..EEECTTSSEEEEEEEEEEEEHHHHHHH CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 125 .........................ltkgieigtiqklgtrlserlga..tvldennreksvimicaaigveRllsa 174
                                                                ++kg   + +++     ++++ +  +v + ++++  ++++  ++gveRll +
  gi|320100437|ref|YP_004176029.1| 382 lygegrarimeklasrtpedlyrelSGKGY--VEVEGV-RIPPDAFIVkqEVERVHGEKIIPHVVEPSFGVERLLYV 455
                                       888888888888888888888776555655..666666.56678887765777778888899999999999999999 PP

                                       HHHH CS
                                       xxxx RF
                      tRNA-synt_2b 175 ileq 178
                                       +le+
  gi|320100437|ref|YP_004176029.1| 456 VLEH 459
                                       9997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHTT..SCEEEEEEGTTSCBTTSEEEE CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  84 ikaisriferlgl.efraiielmsaksadykdkke 117
                                       ++++ +i++rl    frai  + + +   y+   e
  gi|320100437|ref|YP_004176029.1| 498 VEVARDIYRRLVKkGFRAIYDDDGSIGRRYARADE 532
                                       56677777777652356666664444433433333 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.045     2e+02       2      17 ..      94     108 ..      93     109 .. 0.84
   2 ?    2.9   0.1      0.04   1.8e+02       2      12 ..     134     148 ..     133     154 .. 0.83
   3 ?    4.9   0.0    0.0091        41       7      21 ..     335     349 ..     335     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.045
                                       EETTTTEEESSHHHHH CS
                           zf-C2H2   2 kCpdCgksFkrksnLk 17 
                                       +C +Cg+ + r ++L 
  gi|320100437|ref|YP_004176029.1|  94 ECLKCGRIY-RADHLI 108
                                       699******.888876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.04
                                       EETTTT....EEESS CS
                           zf-C2H2   2 kCpdCg....ksFkr 12 
                                       kCp+Cg    k+F +
  gi|320100437|ref|YP_004176029.1| 134 KCPECGgdlgKPFYT 148
                                       8*****999999876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0091
                                       TEEESSHHHHHHHHH CS
                           zf-C2H2   7 gksFkrksnLkrHir 21 
                                       g+ +++ ++L rH++
  gi|320100437|ref|YP_004176029.1| 335 GYAYRTTYDLSRHMQ 349
                                       5789**********7 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 ?   10.1   0.2   0.00014      0.64       4      31 ..      95     142 ..      93     144 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                                       -TTT--EE...ETTTB--S.....................STTB-TTT--.- CS
                           ADK_lid   4 CpkCGrsY...hvvfnpPk.....................veglCDkCGepL 31 
                                       C kCGr+Y   h++    k                        +C +CG++L
  gi|320100437|ref|YP_004176029.1|  95 CLKCGRIYradHLI----KeaagvevegwspeemrkviveHGIKCPECGGDL 142
                                       9*******555333....3233444444444455555654556899999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4141.47
//
Query:       gi|320100438|ref|YP_004176030.1|  [L=130]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0028   17.6   0.0     0.0039   17.2   0.0    1.2  1  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0066   16.3   0.0      0.026   14.5   0.0    2.0  2  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a


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 !   17.2   0.0   4.3e-07    0.0039      27      93 ..      54     118 ..      39     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-07
                                       SSS-EEEEEHHHHHHHT--TT-EEEE.EETTEEEEEEEEEESSB-TTEEEEESSHCC.....S-GHCT CS
                   Molydop_binding  27 pepevveinpedAaalGikdGdlVev.esrrGsvevrakvtervrpGvvfmpfgwweagekggnaNal 93 
                                        ep v++i  + A+ l+ik +d+Ve+    r ++ ++a+v e+  + +v+++  + e  ++g++ N++
  gi|320100438|ref|YP_004176030.1|  54 NEP-VARIPSALASMLDIKSDDTVEIvVAGRKKFLFKAVVFESTDENTVYIYPKEVE--KNGVADNSI 118
                                       345.99******************96257788*******************998877..666666655 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 !   14.5   0.0   2.9e-06     0.026      10      34 ..      59      83 ..      57      87 .. 0.91
   2 ?   -2.9   0.0       0.8   7.1e+03      12      17 ..     105     110 ..     100     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-06
                                      EE-CCCHHHCCEECTCEEEEEECTT CS
                    MazE_antitoxin 10 riPkevrfelgireGdevelevdgd 34
                                      riP +++  l+i+  d+ve++v g 
  gi|320100438|ref|YP_004176030.1| 59 RIPSALASMLDIKSDDTVEIVVAGR 83
                                      9*******************99765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.8
                                       -CCCHH CS
                    MazE_antitoxin  12 Pkevrf 17 
                                       Pkev +
  gi|320100438|ref|YP_004176030.1| 105 PKEVEK 110
                                       777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1007.51
//
Query:       gi|320100439|ref|YP_004176031.1|  [L=125]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1028.71
//
Query:       gi|320100440|ref|YP_004176032.1|  [L=528]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-11   44.5   2.0    1.8e-10   41.5   1.8    2.7  1  Radical_SAM  Radical SAM superfamily
    1.1e-08   35.2   0.0      2e-08   34.3   0.0    1.5  1  B12-binding  B12 binding domain
     0.0063   16.8   0.1      0.024   15.0   0.1    1.9  2  DUF5413      Family of unknown function (DUF5413)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   1.8     3e-14   1.8e-10      10     150 ..     229     390 ..     183     407 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 3e-14
                                       --TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.TTHHHHHHHHHHTC........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx........... RF
                       Radical_SAM  10 rCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.pdfvellerlakla........... 74 
                                       +C fC++p+   + g++rs+s+e+i++ev+el +e+g++ ++l+  + l+y +    l+e                 
  gi|320100440|ref|YP_004176032.1| 229 GCGFCSVPS---MFGPARSRSIESIVREVEEL-VEHGARRIVLSAPDFLDYgR--DLLVEGVLTHPceppaninaie 299
                                       5*******8...8*******************.9**********998888742..2333333333344666666644 PP

                                       ..............CCTEEEEEEECSSCHG..............HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT CS
                                       ..............xxxxxxxxxxxxxxxx..............xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 ..............vpgiritvetngtlpd..............eeklerllelg.vdrvslgleaaddekvlklmn 122
                                                                                   e++++ l ++   + +++gle+++d  + +++ 
  gi|320100440|ref|YP_004176032.1| 300 gllsgisslgpvsqG--------------KvvvmienikaclvnEDVARVLGRYLrGTPIHIGLETGNDV-FNERVL 361
                                       444444455665531..............0333333333345556777777777689************9.777776 PP

                                       .CTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 123 .rghtfeevlealeklreagikrvvdriv 150
                                        ++  + +vlea+++l+ +g+++ v+ + 
  gi|320100440|ref|YP_004176032.1| 362 gKPVRVRHVLEAVRLLKGHGLRPYVYLMH 390
                                       688999****************9666665 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   3.4e-12     2e-08      55     120 ..      59     121 ..      22     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.4e-12
                       B12-binding  55 vglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       + +S+ ++s l a  +lv  ++r++p +kvv+GG++ s+ ++ +l +  g+d+v+vge+e +l+++
  gi|320100440|ref|YP_004176032.1|  59 LFISI-MSSDLGALDRLVTYARRVNPSLKVVAGGPA-SFQYASLLME-HGVDYVIVGEAEIPLPRF 121
                                       67899.****************************85.9999888887.9***********999987 PP

>> DUF5413  Family of unknown function (DUF5413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     4e-06     0.024      51     104 ..      56     108 ..      51     122 .. 0.88
   2 ?   -2.3   0.0       0.9   5.4e+03      63      94 ..     295     326 ..     291     331 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                           DUF5413  51 ysylfgllpalmlaaiddillhvrrvgpvlrlllvglvafvatallygsrgads 104
                                        sylf  + +  l+a+d ++++ rrv p+l+++ +g  +f  ++ll  ++g d+
  gi|320100440|ref|YP_004176032.1|  56 ASYLFISIMSSDLGALDRLVTYARRVNPSLKVVAGGPASFQYASLLM-EHGVDY 108
                                       69***********************************9999998875.456555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.9
                           DUF5413  63 laaiddillhvrrvgpvlrlllvglvafvata 94 
                                       + ai+ +l  +  +gpv +  +v ++  + ++
  gi|320100440|ref|YP_004176032.1| 295 INAIEGLLSGISSLGPVSQGKVVVMIENIKAC 326
                                       67899999999999999887777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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 0.23s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 4206.83
//
Query:       gi|320100441|ref|YP_004176033.1|  [L=145]
Description: tRNA intron endonuclease [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   0.1    1.6e-25   89.0   0.1    1.2  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    9.2e-07   28.4   0.0    1.7e-06   27.6   0.0    1.5  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
     0.0079   16.4   0.1      0.046   13.9   0.0    2.1  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 !   89.0   0.1   2.6e-29   1.6e-25       1      83 [.      54     135 ..      54     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 2.6e-29
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                       f++ yavyrdLr++G+++r GlkFG+d++vY+++p+ +h+ + V+v++ +e +d+ +l++ +rl hsv+Kkl++ai 
  gi|320100441|ref|YP_004176033.1|  54 FEELYAVYRDLRRRGLIPRRGLKFGCDYLVYRHGPGIDHAPFGVQVFRVNEIVDPVELVRMGRLLHSVRKKLVIAIY 130
                                       7889************************************************************************9 PP

                                       TTTSCE CS
                     tRNA_int_endo  78 daegdv 83 
                                        +eg v
  gi|320100441|ref|YP_004176033.1| 131 -NEGAV 135
                                       .55555 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 !   27.6   0.0   2.9e-10   1.7e-06      31      66 ..       8      43 ..       3      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.9e-10
                                      CCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHH CS
                   tRNA_int_endo_N 31 lidepLqLslvEAlYLlekGklevvkggeplsfeel 66
                                        ++pL+Lsl+EAlYL+e +++ v +g++ l   el
  gi|320100441|ref|YP_004176033.1|  8 SVNAPLELSLIEALYLVEMNRVAVLQGDRQLAQGEL 43
                                      5789***********************999987766 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 !   13.9   0.0   7.6e-06     0.046      49      70 ..      10      31 ..       2      33 .. 0.85
   2 ?   -0.3   0.0      0.21   1.3e+03      12      25 ..     122     134 ..     112     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.6e-06
                   tRNA_int_end_N2 49 rgrlwLlpeEaLYLvErGsldi 70
                                      +  l+L   EaLYLvE++++ +
  gi|320100441|ref|YP_004176033.1| 10 NAPLELSLIEALYLVEMNRVAV 31
                                      566899************9876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                   tRNA_int_end_N2  12 skslvraiwfprdr 25 
                                        k+lv+ai++ +++
  gi|320100441|ref|YP_004176033.1| 122 RKKLVIAIYN-EGA 134
                                       6899999997.344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1236.13
//
Query:       gi|320100442|ref|YP_004176034.1|  [L=222]
Description: putative phosphate transport regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-09   35.5   5.9    9.1e-09   35.0   5.9    1.3  1  PhoU_div  Protein of unknown function DUF47
  ------ inclusion threshold ------
      0.012   16.1   9.0       0.03   14.8   0.8    2.4  2  PhoU      PhoU domain
        1.4    8.8   6.4         12    5.8   0.1    2.6  3  DUF1759   Protein of unknown function (DUF1759)


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 !   35.0   5.9   1.5e-12   9.1e-09      41     211 ..      45     214 ..      10     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.5e-12
                          PhoU_div  41 kveellkeiselEreADeikreirlklekglflPvdRedllelveslDeildvlediamlvtl...rkvefpeelkd 114
                                       ++e+  ++   + + + e+k      l k   + +  +  +e+v  +D  +  + ++a ++ +    ++++  +lk 
  gi|320100442|ref|YP_004176034.1|  45 DIEKTYEKMRLIKQRGEETKIMLMEYLVKNSEVMMYSSSYIEMVRTIDRFIQHADSVAYRLVIaskNNIGIRGDLKS 121
                                       56666666666666666666555544444444445567789*****************9876622246889****** PP

                          PhoU_div 115 eflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnplevlllveii 191
                                        ++ +l++  + + ++ +++ +l++    +++    v e+ +lEd++D + r+li k ++   a ++ + ++l+++i
  gi|320100442|ref|YP_004176034.1| 122 TLDSMLQRIRQQVDLIRDALAKLSTHPRRSID---HVDEVLKLEDDVDRVFRELIFKVYE-TYAGSVTGLMVLKDLI 194
                                       ************************97777777...8***********************9.66799*********** PP

                          PhoU_div 192 eklenvsdraedvadrisii 211
                                       e +e++sd  + ++++i+ +
  gi|320100442|ref|YP_004176034.1| 195 EYVEELSDLLKYLGEEIRYL 214
                                       ****************9976 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.9    0.0039        23       3      88 ..      21     104 ..      14     105 .. 0.76
   2 ?   14.8   0.8   5.1e-06      0.03       1      80 [.     123     202 ..     123     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHHHHHHHHCT-H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   3 rmaeiveemlddalealeekdt.elarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                        m +i ++ ++++  +  ++ t   +++ +e+ + i +  +e +  l+e l k++++ +   + +s+++++r + R 
  gi|320100442|ref|YP_004176034.1|  21 NMMSILSDEVSLLTALMNQYSTgTDIEKTYEKMRLIKQRGEETKIMLMEYLVKNSEVMM---YSSSYIEMVRTIDRF 94 
                                       55666665565555555555543667888899999999999999999999977777766...4568*********** PP

                                       HHHHHHHHHH CS
                              PhoU  79 gDhavniaer 88 
                                         ha ++a r
  gi|320100442|ref|YP_004176034.1|  95 IQHADSVAYR 104
                                       9999999865 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHHHHHHHHHHHHHCT-H......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdt......elarevierddeidrlekeiersllealakrqplaedlrellsllri 71 
                                       l++m + +++++d+  +al++  t      + ++ev++++d++dr ++e++ +++e +a   +++     l+ l ++
  gi|320100442|ref|YP_004176034.1| 123 LDSMLQRIRQQVDLIRDALAKLSThprrsiDHVDEVLKLEDDVDRVFRELIFKVYETYAG--SVTG----LMVLKDL 193
                                       679****************88886667777999*************99997777777743..2222....2223334 PP

                                       HHHHHHHHH CS
                              PhoU  72 ardlERigD 80 
                                       + + E  +D
  gi|320100442|ref|YP_004176034.1| 194 IEYVEELSD 202
                                       455555444 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.2    0.0056        33      24     119 ..      12     101 ..       8     116 .. 0.53
   2 ?    5.8   0.1    0.0021        12      57     109 ..     120     172 ..     116     191 .. 0.90
   3 ?   -1.5   0.0      0.36   2.2e+03      94     117 ..     189     212 ..     170     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0056
                           DUF1759  24 eLskvqkfnYLkSlLkgeAanvvahlalseenYeaaveaLkkrYdnkrkiirell.nelmklpslkeedasqlrriv 99 
                                       eL+ ++ +n + S+L +e   + a ++      +++ + ++k Y++ r i++    +++m ++ l   ++s++   +
  gi|320100442|ref|YP_004176034.1|  12 ELTAIEYLNNMMSILSDEVSLLTALMN-----QYSTGTDIEKTYEKMRLIKQRGEeTKIMLMEYL--VKNSEVMMYS 81 
                                       677777888888999998776655543.....344445556666666666654430334444442..2223333333 PP

                           DUF1759 100 davneivralealgeeadky 119
                                           e+vr++++  ++ad +
  gi|320100442|ref|YP_004176034.1|  82 SSYIEMVRTIDRFIQHADSV 101
                                       44444555555555544433 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0021
                           DUF1759  57 eaaveaLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivral 109
                                       +++++ + +r  ++  +ir+ l +l   p  + + ++++ ++ d v+++ r l
  gi|320100442|ref|YP_004176034.1| 120 KSTLDSMLQRIRQQVDLIRDALAKLSTHPRRSIDHVDEVLKLEDDVDRVFREL 172
                                       578899999999**************************************998 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.36
                           DUF1759  94 qlrrivdavneivralealgeead 117
                                       +l+ +++ v+e+   l+ lgee +
  gi|320100442|ref|YP_004176034.1| 189 VLKDLIEYVEELSDLLKYLGEEIR 212
                                       567777778888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 1826.77
//
Query:       gi|320100443|ref|YP_004176035.1|  [L=145]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1231.42
//
Query:       gi|320100444|ref|YP_004176036.1|  [L=194]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-23   82.7   0.0    3.4e-23   82.1   0.0    1.2  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   1.9e-27   3.4e-23       3     125 ..       6     173 ..       4     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.9e-27
                                       EEEEE-SSCGGGCHHHHHH...HHHHTTEEEEEEESCHHHHCCHHG.GS................TCSSHHHHHHCT CS
                      Flavoprotein   3 illgiTGsvaaikalelle...kLkkegievqvvltkaAkkfiske.klklaa............redpilhielrr 63 
                                       +++++TG++++i+al+lle    Lk++  e++v+ t +A k++ +e +l+l              r          +
  gi|320100444|ref|YP_004176036.1|   6 LIIAMTGASGIIYALRLLErssLLKSKYREIHVIYTSNAVKVALHEeNLDLPGflskatgvdavyR----------D 72 
                                       799***************955446779***************998855666556665666555541..........1 PP

                                       .............TESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTH CS
                      Flavoprotein  64 .............wadllviaPasantlakianGiadnll..............................tlilrat 97 
                                                        +vi+Pas+nt+akianGi+dnl+                              +  l   
  gi|320100444|ref|YP_004176036.1|  73 ddltsrlasssnlVSTDMVIVPASMNTVAKIANGIQDNLVtrvadsilrlrnrlivvfretplsaidlfnLYRL--- 146
                                       344445555666678889********************************************999887553344... PP

                                       CCTTEEEEE.--HHCCTCSTCHHHHHHH CS
                      Flavoprotein  98 akkpiliaPamnpamyenpqtlknlekl 125
                                       a  +++++P ++p +y +p ++++l+++
  gi|320100444|ref|YP_004176036.1| 147 ALSGAIVVP-ASPGFYIRPGSVEDLVDF 173
                                       568******.*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.35
# Mc/sec: 1648.90
//
Query:       gi|320100445|ref|YP_004176037.1|  [L=100]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0085   16.1   0.0     0.0099   15.9   0.0    1.0  1  DUF4947   Domain of unknown function (DUF4947)
  ------ inclusion threshold ------
      0.025   14.4   0.0       0.04   13.8   0.0    1.4  1  DUF2642   Protein of unknown function (DUF2642)


Domain annotation for each model (and alignments):
>> DUF4947  Domain of unknown function (DUF4947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-06    0.0099      26     101 ..      12      87 ..       8      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                           DUF4947  26 lpkdaneakkdkiyatgdekvaYssegdqieaqipDykgYtkekvkeiLGePekvvtdsseiqesleekelenika 101
                                       l+   ne +++ ++a+     +    ++ + a +  y g++++  + i G+P+ v+t+ +++   l++   e + +
  gi|320100445|ref|YP_004176037.1|  12 LNAMVNELRRNGLWAERHSYSIRIMYNGVFIASLHLYPGFNEAVLRLISGDPDAVSTARNTVVGVLKKYLPEYVVK 87 
                                       6667799999999999887777777789********************************9998888765555555 PP

>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-06      0.04      15      47 ..      57      89 ..      48      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                           DUF2642 15 qsllgqevvvqttrgsvrGiLkdvkPDHivvei 47
                                      + + g+  +v t r++v G+Lk+ +P ++v e+
  gi|320100445|ref|YP_004176037.1| 57 RLISGDPDAVSTARNTVVGVLKKYLPEYVVKEV 89
                                      556677789********************9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 859.73
//
Query:       gi|320100446|ref|YP_004176038.1|  [L=357]
Description: translation factor SUA5 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-57  191.6   0.0    1.1e-56  191.1   0.0    1.2  1  Sua5_yciO_yrdC  Telomere recombination
    1.2e-28  100.3   0.0    1.7e-28   99.9   0.0    1.2  1  SUA5            Putative GTP-binding controlling metal-bindin


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.1   0.0   1.2e-60   1.1e-56       3     179 .]      24     198 ..      22     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.1 bits;  conditional E-value: 1.2e-60
                                       HHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCE CS
                    Sua5_yciO_yrdC   3 lrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpit 79 
                                       l + g+va+ptetvYgL++ a+ e+av +++++K rp d+pl+++v+sl++l+++a+  +++ a++l+e+fwPGp+t
  gi|320100446|ref|YP_004176038.1|  24 LLNRGLVAFPTETVYGLGAVAYYEDAVLKVFKAKMRPPDNPLIIHVSSLDMLNEVAT-GIPDDAYRLIEKFWPGPLT 99 
                                       566689**************************************************8.******************* PP

                                       EEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS-- CS
                    Sua5_yciO_yrdC  80 lllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildgge 156
                                       l+l+r+ + +p++v++gl+tv+vr+P +p+a++L++a+g+p++a+San+sg+ps+t+ e+v ++l ++vd+i+d+ge
  gi|320100446|ref|YP_004176038.1| 100 LILPRHPS-IPRVVTGGLDTVAVRMPGHPVALKLIDATGRPVAAPSANISGRPSPTTGEHVIRDLMGRVDAIIDAGE 175
                                       ****8766.******************************************************************** PP

                                       -SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 157 iavgvdstVvdltegkpkilRrG 179
                                       +  gv+stVv+++e++p +lR+G
  gi|320100446|ref|YP_004176038.1| 176 TFFGVESTVVNILEDPPVLLRPG 198
                                       *********************98 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0   1.9e-32   1.7e-28       4     134 .]     203     348 ..     200     348 .. 0.73

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.9e-32
                                       HHHHHHS-..-..-..........-------------S-SSEEEEE--GGGHHHH.......HHHHHTTS-EEEEEE CS
                              SUA5   4 eeleevld..a..vek......keekpraPGmkyrHYaPkapvvlveaeeeeeaake..ekleekkksgkkvgvlat 68 
                                       ee+e++l+  +    +       +e   aPGmkyrHY+P+a+++lveae + e  +    +++++     ++ v+++
  gi|320100446|ref|YP_004176038.1| 203 EEVEKALGkkIviP-EfarglaYSEIALAPGMKYRHYSPEAKLILVEAEGSYEYIAGrvIEAARSLGGVGELCVISS 278
                                       66777763221220.1223444456779******************9998776655455555555555555666666 PP

                                       GGGTGG.....TSEEEEE......E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHTT CS
                              SUA5  69 seskea.....assvlsls....lgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAAg 134
                                       se+++      +      +    lgsr +l e+arnLF++Lr +De+g+++++ e++pe+g+glAvmnRLrkA++
  gi|320100446|ref|YP_004176038.1| 279 SETMHYyrslsNV-----KavftLGSRVNLYEVARNLFKVLRLVDEAGCRVVFSESFPETGIGLAVMNRLRKASS 348
                                       6666657654211.....134459*************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2572.08
//
Query:       gi|320100447|ref|YP_004176039.1|  [L=264]
Description: circadian clock protein KaiC [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-54  184.5   0.0    2.1e-54  184.3   0.0    1.0  1  ATPase     KaiC
    2.7e-08   33.6   0.0    4.6e-08   32.9   0.0    1.3  1  AAA_25     AAA domain
    7.1e-06   25.5   0.1    1.3e-05   24.6   0.0    1.6  1  Rad51      Rad51
    9.4e-06   25.3   0.0    1.4e-05   24.7   0.0    1.2  1  RecA       recA bacterial DNA recombination protein
    0.00018   21.4   0.0    0.00032   20.6   0.0    1.4  1  MEDS       MEDS: MEthanogen/methylotroph, DcmR Sensory domain
    0.00036   19.3   0.9     0.0056   15.4   0.9    2.0  1  GvpD       GvpD gas vesicle protein
      0.002   17.9   0.0     0.0035   17.1   0.0    1.4  1  IstB_IS21  IstB-like ATP binding protein
     0.0036   16.7   0.0     0.0052   16.1   0.0    1.2  1  DnaB_C     DnaB-like helicase C terminal domain
     0.0084   15.9   0.0      0.015   15.0   0.0    1.5  1  AAA_24     AAA domain
  ------ inclusion threshold ------
      0.019   14.1   0.0       0.12   11.5   0.0    1.9  2  PAXNEB     PAXNEB protein
       0.03   14.6   0.0      0.046   14.0   0.0    1.3  1  AAA_22     AAA domain
      0.059   12.6   0.0       0.11   11.7   0.0    1.3  1  DUF2075    Uncharacterized conserved protein (DUF2075)
       0.13   12.6   0.0       0.16   12.3   0.0    1.3  1  AAA_16     AAA ATPase domain
       0.16   11.5   0.0       0.26   10.8   0.0    1.3  1  AAA_7      P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   0.0   1.7e-57   2.1e-54       1     227 [.       6     232 ..       6     236 .. 0.97

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 1.7e-57
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       +++g++glDe+++gGip+g +v ++GepGtGKt ++ qF+ kg+e+ g++ v+vt+ee+ e++ ++a+++ + l+ +
  gi|320100447|ref|YP_004176039.1|   6 IPSGVPGLDELIDGGIPRGFMVAVVGEPGTGKTAMSIQFIAKGLET-GDKAVYVTTEESRESILRQAERFNIGLKPY 81 
                                       699****************************************999.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlk 152
                                        eeg+l+++da + + ++  + ++ d+eel++++ ea k ++    r+v+Ds +++   +k+a+aR++  +++rvl+
  gi|320100447|ref|YP_004176039.1|  82 IEEGRLVVVDALMGEYGDVWSLKELDVEELVSTVIEAKKYLGPghARLVVDSMSAF-WLDKPAMARKYSYHVKRVLS 157
                                       *****************99999*******************98889**********.******************** PP

                            ATPase 153 klgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvl 227
                                       k+g T + +s+  ++ +   g+g+e+ ++dgvi+L++  +++ l+R l i kmR t+h+++++++e+ +  g++v 
  gi|320100447|ref|YP_004176039.1| 158 KWGFTMLVTSQYAVTTQLGFGFGIEH-VADGVIRLRKSVVKGFLKRFLVIEKMRLTNHDQRVFEIEVVDgVGVRVN 232
                                       **************999999******.***************************************9998899885 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   3.6e-11   4.6e-08      17     158 ..       8     141 ..       2     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.6e-11
                            AAA_25  17 apppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlra 92 
                                       +  p ++ l++g +p+g  ++++G pgtGKt++ ++  ++ + tG+           k +yv +E+s++ + r +++
  gi|320100447|ref|YP_004176039.1|   8 SGVPGLDELIDGGIPRGFMVAVVGEPGTGKTAMSIQFIAKGLeTGD-----------KAVYVTTEESRESILRQAER 73 
                                       55688999****************************9888886665...........89**********99999999 PP

                            AAA_25  93 vgeal...rddarllvld.lagveslpLfakdrggtlltadvdaleaaieev.egvrlvviDplsralggd 158
                                           l    + +rl v+d l+g+   ++++++  +  +++ v  +++a ++  +g + +v+D++s+++   
  gi|320100447|ref|YP_004176039.1|  74 FNIGLkpyIEEGRLVVVDaLMGE-YGDVWSLK--ELDVEELVSTVIEAKKYLgPGHARLVVDSMSAFWLDK 141
                                       88777656667888888724444.44444433..2224455555555544432336668899999988665 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     1e-08   1.3e-05      19     101 ..       6      80 ..       2     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1e-08
                                       E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHT CS
                             Rad51  19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaery 95 
                                       +  G   lDel++GGi+ g +  ++Ge ++Gkt ++ ++        +   + +kavy+ te +   e +++ aer+
  gi|320100447|ref|YP_004176039.1|   6 IPSGVPGLDELIDGGIPRGFMVAVVGEPGTGKTAMSIQFIA------KGLETGDKAVYVTTEES--RESILRQAERF 74 
                                       6678889**************************98877632......222345799******97..46789999999 PP

                                       T--HHH CS
                             Rad51  96 kldkee 101
                                       ++  + 
  gi|320100447|ref|YP_004176039.1|  75 NIGLKP 80 
                                       886655 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.1e-08   1.4e-05      31      94 ..       3      65 ..       1      79 [. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                      --EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS---- CS
                              RecA 31 vetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehald 94
                                       e i+sG  +ld  +  GG+p+G ++ + G   +Gkt+++++ ia+  ++g  a+++ +e + +
  gi|320100447|ref|YP_004176039.1|  3 TERIPSGVPGLDELID-GGIPRGFMVAVVGEPGTGKTAMSIQFIAKGLETGDKAVYVTTEESRE 65
                                      67899*******9887.****************************************9998755 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 !   20.6   0.0   2.5e-07   0.00032      15      68 ..      39      92 ..      35     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.5e-07
                              MEDS 15 ealvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleilda 68
                                      ++ ++fi++gl+ g+k +yv+++++++ ++++ ++ ++ +  + e+g+l ++da
  gi|320100447|ref|YP_004176039.1| 39 AMSIQFIAKGLETGDKAVYVTTEESRESILRQAERFNIGLKPYIEEGRLVVVDA 92
                                      56789********************************************99986 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.9   4.4e-06    0.0056      13     208 ..      27     226 ..      20     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.4e-06
                              GvpD  13 llikGaPGtGktlftlrgld.vlrresdvlyvstrvddetvseay....fsgeaeldktalldllkdpleldldvdv 84 
                                       + + G+PGtGkt + ++++   l+  ++ +yv+t    e++        +  +  +++  l  ++ d+l  +   + 
  gi|320100447|ref|YP_004176039.1|  27 VAVVGEPGTGKTAMSIQFIAkGLETGDKAVYVTTEESRESILRQAerfnIGLKPYIEEGRL--VVVDALMGEYGDVW 101
                                       5688**************96269999999*****999999865432323233334444333..56788888888888 PP

                              GvpD  85 Piekldlesllefvdeiaaiatkliialdswelvyeylaery.dsPediktvkndlvvlaresgvrlvlvletaans 160
                                        +++ld+e l++ v        k  +     +lv++ +++ + d+P   +    ++  +  + g  +++ ++ a   
  gi|320100447|ref|YP_004176039.1| 102 SLKELDVEELVSTVI-----EAKKYLGPGHARLVVDSMSAFWlDKPAMARKYSYHVKRVLSKWGFTMLVTSQYAVTT 173
                                       999999999988776.....344555556667777777654426666666666666555556666666555555555 PP

                              GvpD 161 rl......eyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftladG 208
                                       +l      e+++dGv+ l+     +g l+r l +ek+r  + ++r++   + dG
  gi|320100447|ref|YP_004176039.1| 174 QLgfgfgiEHVADGVIRLRKS-VVKGFLKRFLVIEKMRLTNHDQRVFEIEVVDG 226
                                       433333339999***999744.44899**********99888888877766666 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.7e-06    0.0035      50     115 ..      27      91 ..      20     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.7e-06
                         IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkv.dllilD 115
                                       ++++G +G+GK+ ++i +  ++ ++g + ++v++e+  e++ r  + ++++  lk +++  +l+++D
  gi|320100447|ref|YP_004176039.1|  27 VAVVGEPGTGKTAMSIQFIAKGLETGDKAVYVTTEESRESILR--QAERFNIGLKPYIEEgRLVVVD 91 
                                       899*******************************998776543..4445555555555444666666 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 !   16.1   0.0   4.1e-06    0.0052       2      64 ..       6      68 ..       5      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.1e-06
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlv 64
                                      +++g   LD+l+  G+ +g ++ + + p++Gkta+ ++++++  ++ ++ v ++  e s+e+++
  gi|320100447|ref|YP_004176039.1|  6 IPSGVPGLDELIDgGIPRGFMVAVVGEPGTGKTAMSIQFIAKGLETGDKAV-YVTTEESRESIL 68
                                      6889999**99862688999999***************9998887666555.556666777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-05     0.015       4      38 ..      26      67 ..      23     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksl 38
                                      +++++G++g+GKT +  ++       g+k++++ te++  s+
  gi|320100447|ref|YP_004176039.1| 26 MVAVVGEPGTGKTAMSIQFiakgletGDKAVYVTTEESRESI 67
                                      799****************99999999999999999977665 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.5e-05      0.12      21      84 ..       8      70 ..       4      72 .. 0.87
   2 ?    0.1   0.0      0.28   3.5e+02     209     281 ..     127     191 ..     108     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.5e-05
                            PAXNEB 21 tGtpsLDklLgGGLplGsil.lieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlre 84
                                      +G+p LD+l+ GG+p G ++ ++ E gt + a+ +   F+A G+ ++ + ++++ ++++e++lr+
  gi|320100447|ref|YP_004176039.1|  8 SGVPGLDELIDGGIPRGFMVaVVGEPGTGKTAMSI--QFIAKGLETGDKAVYVTTEESRESILRQ 70
                                      9****************876266799998877766..7*****************9999999986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.28
                            PAXNEB 209 lRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieL 281
                                        R+v+ s+ s  + d      kp    k+ + ++ +l++   ++l+t    +   + ++   ie+++D+vi+L
  gi|320100447|ref|YP_004176039.1| 127 ARLVVDSM-SAFWLD------KPAMARKYSYHVKRVLSKWGFTMLVTSQYAVT-TQLGFGFGIEHVADGVIRL 191
                                       56666665.344423......55666666677788888888888888888887.888899999*******999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-05     0.046       7      55 ..      26      66 ..      23     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                            AAA_22  7 ilvvtGesGtGKT.tllrrlleqldeeakaeeerpevvfvtlpsstsskd 55
                                      +++v+Ge+GtGKT ++++ +++ l+        +++ v+vt  +s   ++
  gi|320100447|ref|YP_004176039.1| 26 MVAVVGEPGTGKTaMSIQFIAKGLET-------GDKAVYVTTEESR--ES 66
                                      679**********4466777777654.......7777777776665..33 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.6e-05      0.11       4      49 ..      27      70 ..      25      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
                           DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlre 49
                                      v V G++GtGKt + ++++a+    e + +avy++  ++   +lr+
  gi|320100447|ref|YP_004176039.1| 27 VAVVGEPGTGKTAMSIQFIAKG--LETGDKAVYVTTEESRESILRQ 70
                                      6799***************998..8888899998888877777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.16      25      63 ..      25      66 ..      13     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_16 25 elvllsGesGvGKsslv.rellralekd.g.giflrgkcdql 63
                                       +v ++Ge+G+GK+++  + +++ le+  + +++++++ +++
  gi|320100447|ref|YP_004176039.1| 25 FMVAVVGEPGTGKTAMSiQFIAKGLETGdKaVYVTTEESRES 66
                                      5799***********974555555544432255555555555 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 ?   10.8   0.0    0.0002      0.26      30      58 ..      21      50 ..      13      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                             AAA_7 30 lknkkpvllvGptGtGKtviikd.llkkld 58
                                      + ++  v +vG+ GtGKt++  + + k l+
  gi|320100447|ref|YP_004176039.1| 21 IPRGFMVAVVGEPGTGKTAMSIQfIAKGLE 50
                                      55677899************9995666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2018.14
//
Query:       gi|320100448|ref|YP_004176040.1|  [L=814]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  180.8   0.0    4.8e-53  179.6   0.0    1.6  2  Helicase_RecD    Helicase
      1e-42  146.1   0.0    2.8e-29  102.2   0.0    2.2  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
      1e-28   99.1   0.0    4.6e-28   97.0   0.0    2.1  2  DUF1726          Domain of unknown function (DUF1726)
    0.00013   21.7   0.0    0.00025   20.8   0.0    1.4  1  tRNA_bind_2      Possible tRNA binding domain
    0.00027   21.2   0.0    0.00056   20.1   0.0    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0011   19.4   0.0     0.0057   17.0   0.0    2.2  2  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         3   9.1e+03      15      46 ..      17      49 ..      15      56 .. 0.76
   2 !  179.6   0.0   1.6e-56   4.8e-53       1     177 []     262     441 ..     262     441 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                     Helicase_RecD 15 Glalaaliaegk.snilvtapskenvktlfefl 46
                                      G+a+ +l++++    i+++  s+e++++l ++l
  gi|320100448|ref|YP_004176040.1| 17 GKAAGKLVKHRVrGMIVISGSSPEKLASLSARL 49
                                      677777777766567899999999999887766 PP

  == domain 2  score: 179.6 bits;  conditional E-value: 1.6e-56
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk.....snilvtapskenvktlfeflakglealglkeeekkkkaekaelrvr 72 
                                       vl+AdRGRGKS a+G+ +  li+  +      +ilvtap++ n+++l++ + + l++lg+++e  k+++  +elr++
  gi|320100448|ref|YP_004176040.1| 262 VLIADRGRGKSCAIGIGAVGLIHLLRkikpkPRILVTAPEPGNIQSLMALAMRVLDKLGYRYEVIKREGYVIELRSD 338
                                       799*****************999888888989********************************************* PP

                     Helicase_RecD  73 kqrieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrel 149
                                       k +iey++p ++ + +   d+++vDEAA i++pll k++e+++r+v+++T+hGYEG+Grgfs++flk++k+++++ l
  gi|320100448|ref|YP_004176040.1| 339 KFSIEYWEPLAIPRING--DVVIVDEAAGIHVPLLYKIWESHRRIVFSSTIHGYEGAGRGFSVRFLKKIKSDENTIL 413
                                       *************9875..********************************************************** PP

                     Helicase_RecD 150 releleepiRyaegdplEkwlndlLlLd 177
                                        e+e++epiRy+ gdp+E+w +++LlLd
  gi|320100448|ref|YP_004176040.1| 414 YEYEMTEPIRYNYGDPIEEWQFKTLLLD 441
                                       **************************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 !  102.2   0.0   9.3e-33   2.8e-29       2     123 ..     480     594 ..     479     598 .. 0.93
   2 !   42.7   0.0   1.4e-14   4.2e-11     177     226 ..     597     646 ..     590     647 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 9.3e-33
                   GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlip 78 
                                       l++++v +HY+n+P+DL +++DaP+h++ +  +++       +++c+vq+a EG i++e++ + l+++ +  G++ip
  gi|320100448|ref|YP_004176040.1| 480 LFGIYVLAHYRNEPDDLGMIADAPHHTVRAVKTSSG------RIVCAVQIAREGPIDDETALELLKGS-KIPGNIIP 549
                                       899**************************9988665......8****************999888765.99****** PP

                   GNAT_acetyltr_2  79 wtlsqqfqdeefaslsGaRivRiAvhpelqkmGYGsralelleky 123
                                       + + ++ +  +fa+ +G RivRiA+hp++q++G Gs +l +++++
  gi|320100448|ref|YP_004176040.1| 550 DRFLKHLRYMDFAKTTGWRIVRIATHPAVQGKGIGSWVLGKIKEE 594
                                       **************************************9999876 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 1.4e-14
                   GNAT_acetyltr_2 177 pekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                          ld++g +fG+ ++Ll+FW ++g++pv+++  +n ++GE+++++++++
  gi|320100448|ref|YP_004176040.1| 597 ELGLDWVGSGFGVNEQLLRFWVKNGYVPVHISPDRNPVSGEYTVLVIQPI 646
                                       4579*******************************************987 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0   1.5e-31   4.6e-28       1      93 []     104     195 ..     104     195 .. 0.98
   2 ?   -1.4   0.0      0.75   2.2e+03      70      92 ..     392     414 ..     369     415 .. 0.76

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 1.5e-31
                           DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplteevkkrfnk 77 
                                       y++s+k+LG t+++lv+dl+++l+Pn+lgrl+++V+GGG+iill+pp++++++ +t f+ +l+v+++  e ++ f+k
  gi|320100448|ref|YP_004176040.1| 104 YEKSDKYLGATVSVLVMDLTHDLKPNDLGRLIGIVEGGGIIILLTPPWDKWDEAKTIFKMNLTVPQY-PEPRHIFIK 179
                                       89*****************************************************************.6******** PP

                           DUF1726  78 rfirklkehegilivd 93 
                                       + ++ l e +gi i+d
  gi|320100448|ref|YP_004176040.1| 180 WVKKHLLEFDGIGIYD 195
                                       ************9987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.75
                           DUF1726  70 evkkrfnkrfirklkehegiliv 92 
                                          + f  rf++k+k+ e+++++
  gi|320100448|ref|YP_004176040.1| 392 GAGRGFSVRFLKKIKSDENTILY 414
                                       45567999*******99998876 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 !   20.8   0.0   8.4e-08   0.00025      54     126 ..     694     766 ..     658     776 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.4e-08
                                       --------HHHHHHHHHHHHS---HHHHHSSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHHH CS
                       tRNA_bind_2  54 eeldellspfDlkRLesYannllDYhvilDllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddlek 126
                                       e+  +l++p  l RL  Y++  + ++   D++ +la++++    +++ kL+ +q+ +Lla  LQ  + d+l+ 
  gi|320100448|ref|YP_004176040.1| 694 EKPLHLFTPVTLDRLWTYCQGPMTFEAAADIMFKLARIHWLISPESRPKLTRLQEVVLLAKALQGLTWDELHG 766
                                       333478***********************************************************99999875 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.9e-07   0.00056      55      96 ..     550     602 ..     455     622 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                                       T...........TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESE CS
                    Acetyltransf_1  55 d...........ekggvayieslaVspeyrgkGlGsaLlealeerareegikk 96 
                                       d            k+  + i ++a +p+ +gkG+Gs  l ++ e+a e g++ 
  gi|320100448|ref|YP_004176040.1| 550 DrflkhlrymdfAKTTGWRIVRIATHPAVQGKGIGSWVLGKIKEEAAELGLDW 602
                                       2444445555567888999*****************************99854 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   5.3e+03      26      38 ..     479     491 ..     457     492 .. 0.69
   2 !   17.0   0.0   1.9e-06    0.0057      25      75 ..     567     623 ..     540     624 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                                       CTEEEEE-GGGTT CS
                    Acetyltransf_7  26 eitrlaVdpeyrg 38 
                                       ++ +++V+ +yr+
  gi|320100448|ref|YP_004176040.1| 479 QLFGIYVLAHYRN 491
                                       33449******97 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.9e-06
                                       TCTEEEEE-GGGTTSSHHHHHHHH...TT.........SEEEEE.EEEETHHHHHHHHHHTTEE CS
                    Acetyltransf_7  25 aeitrlaVdpeyrgkGiGraLlea...ae.........kgiile.qlelnaekaikfYeklGFe 75 
                                         i r+a++p+ +gkGiG+  l     ++         +g+    +      + ++f+ k+G++
  gi|320100448|ref|YP_004176040.1| 567 WRIVRIATHPAVQGKGIGSWVLGKikeEAaelgldwvgSGF--GvNE-----QLLRFWVKNGYV 623
                                       45677*****************6423311332222322221..1112.....448899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (814 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.40
# Mc/sec: 6103.39
//
Query:       gi|320100449|ref|YP_004176041.1|  [L=746]
Description: AAA ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-99  329.3   0.0    3.2e-50  170.0   0.0    2.6  2  AAA              ATPase family associated with various cellul
    1.3e-36  124.2   4.3    1.8e-18   66.1   0.2    2.8  2  AAA_lid_3        AAA+ lid domain
    1.9e-27   95.2   0.1    7.4e-27   93.4   0.1    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      4e-17   61.7   0.3    2.4e-16   59.3   0.1    2.5  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    5.1e-16   58.8   0.0    3.2e-08   33.5   0.0    3.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      1e-13   52.0   0.0      9e-07   29.4   0.0    2.8  2  AAA_16           AAA ATPase domain
    1.8e-13   51.0   0.0    2.2e-07   31.2   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.1e-12   46.9   0.2    3.5e-05   23.2   0.0    2.8  3  TIP49            TIP49 P-loop domain
    3.8e-12   46.7   0.6    0.00068   19.9   0.1    4.3  2  AAA_22           AAA domain
    1.6e-11   44.4   1.6      2e-05   24.6   0.1    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    5.5e-11   42.8   0.0    0.00016   21.9   0.0    2.5  2  AAA_33           AAA domain
    2.2e-09   37.4   0.0    0.00012   22.1   0.0    2.4  2  AAA_14           AAA domain
    3.6e-09   36.5   0.0     0.0063   16.5   0.0    3.1  2  Vps4_C           Vps4 C terminal oligomerisation domain
    9.1e-09   35.3   0.0     0.0064   16.2   0.0    2.9  3  IstB_IS21        IstB-like ATP binding protein
    1.1e-08   35.7   0.0     0.0017   18.9   0.0    2.9  2  AAA_18           AAA domain
    6.5e-08   33.0   0.0     0.0039   17.4   0.0    2.5  2  AAA_28           AAA domain
      2e-07   31.3   0.0     0.0046   17.3   0.0    2.7  2  RNA_helicase     RNA helicase
    2.6e-07   30.4   4.6       0.51    9.9   0.0    4.7  4  AAA_25           AAA domain
    3.9e-07   29.7   1.1      0.018   14.4   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.8e-06   27.8   0.0       0.02   14.6   0.0    2.6  2  AAA_24           AAA domain
    8.7e-06   25.7   0.1      0.078   13.0   0.0    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.3e-05   24.7   3.8       0.25   10.6   0.0    4.1  4  ATPase           KaiC
    1.8e-05   24.1   0.0       0.22   10.8   0.0    2.5  2  Zeta_toxin       Zeta toxin
    2.6e-05   24.8   0.0       0.21   12.1   0.0    2.5  2  ABC_tran         ABC transporter
    3.4e-05   23.4   0.0       0.17   11.4   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    3.6e-05   23.6   0.0       0.14   12.0   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    3.8e-05   23.4   0.1       0.44   10.2   0.0    3.2  2  Sigma54_activat  Sigma-54 interaction domain
    3.9e-05   22.9   0.1      0.048   12.7   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    5.9e-05   23.1   0.1      0.019   14.9   0.0    2.8  2  ATPase_2         ATPase domain predominantly from Archaea
    7.9e-05   22.6   0.0     0.0065   16.3   0.0    2.6  2  Bac_DnaA         Bacterial dnaA  protein
    8.7e-05   21.8   0.0       0.34   10.0   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    0.00013   21.5   1.3       0.28   10.6   0.1    2.6  2  PhoH             PhoH-like protein
    0.00029   20.2   0.0      0.083   12.1   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00029   20.8   1.1        0.7    9.8   0.1    3.3  3  NACHT            NACHT domain
     0.0018   18.2   0.0        1.9    8.4   0.0    3.1  3  Rad17            Rad17 P-loop domain
     0.0019   18.0   0.4        2.3    7.9   0.0    3.1  3  AAA_30           AAA domain
     0.0022   18.4   0.1          2    8.8   0.0    3.0  2  AAA_17           AAA domain
     0.0028   16.8   0.0        1.2    8.1   0.0    2.6  2  T2SSE            Type II/IV secretion system protein
     0.0032   17.3   0.0        1.5    8.5   0.0    2.3  2  AAA_11           AAA domain
     0.0049   15.9   0.0       0.15   11.0   0.0    2.5  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0054   16.8   0.0        2.5    8.2   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0057   16.1   0.4        2.5    7.4   0.1    2.4  2  IPT              Isopentenyl transferase
     0.0076   16.3   0.2      0.029   14.4   0.0    2.0  1  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
       0.01   15.5   0.1        2.8    7.6   0.0    2.4  2  Cytidylate_kin   Cytidylate kinase
      0.013   15.9   3.5          6    7.2   0.1    3.3  3  AAA_19           AAA domain
      0.019   14.7   0.0        4.6    7.0   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.021   14.0   0.0        5.2    6.2   0.0    2.5  2  NB-ARC           NB-ARC domain
      0.033   14.3   0.0          4    7.5   0.0    2.5  2  SKI              Shikimate kinase
      0.056   12.9   0.0         12    5.3   0.0    3.3  3  TniB             Bacterial TniB protein
      0.056   12.3   0.0         11    4.8   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
      0.062   13.0   0.2         43    3.7   0.0    3.8  4  Guanylate_kin    Guanylate kinase
      0.066   13.0   0.0         14    5.6   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      0.068   12.4   0.0        2.2    7.5   0.0    2.4  2  KAP_NTPase       KAP family P-loop domain
      0.086   12.7   1.0        0.2   11.5   0.1    2.1  1  eIF-1a           Translation initiation factor 1A / IF-1
       0.11   12.5   0.0         22    5.0   0.0    2.7  3  ResIII           Type III restriction enzyme, res subunit
       0.12   12.5   0.3        1.2    9.2   0.0    2.6  2  DUF1905          Domain of unknown function (DUF1905)
       0.12   12.2   4.0         23    4.9   0.0    4.0  3  NTPase_1         NTPase
       0.18   11.5   0.0        3.9    7.2   0.0    2.1  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.26   11.5   0.3        6.5    7.0   0.1    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.0     1e-52   3.2e-50       1     131 [.     225     354 ..     225     355 .. 0.98
   2 !  156.6   0.0   1.4e-48   4.2e-46       1     131 [.     501     630 ..     501     631 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 1e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +llyGppGtGKTllaka+a+e+g++f++i+g+e++sk+ gese+++r++f+ea+++a p ++fiDEid++a++r++ 
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGAYFITINGPEIMSKFYGESEERLRKIFEEAQANA-PAVIFIDEIDSIAPKREEV 300
                                       69******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt +dg+k++ +kvivigatnrpd +dpal+r gRfdr+iei+
  gi|320100449|ref|YP_004176041.1| 301 TGEVEKRVVAQLLTLMDGLKER-GKVIVIGATNRPDAIDPALRRpGRFDREIEIP 354
                                       *********************6.77***************************997 PP

  == domain 2  score: 156.6 bits;  conditional E-value: 1.4e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +ll+GppGtGKTllakava+e+g++f+ i g+e+lsk+vgesek ir++f++a+  a p ++f+DEid++a+ r ++
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGANFIAIRGPEVLSKWVGESEKAIRQIFRRARMVA-PAVVFFDEIDSIAGVRGSD 576
                                       69******************************************************9.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        s++++r+vnq+lteldg +   +kv+vi+atnrpd ldpallr gRfdr i+++
  gi|320100449|ref|YP_004176041.1| 577 PSGVTDRIVNQMLTELDGIQPL-RKVVVIAATNRPDLLDPALLRpGRFDRLIYVP 630
                                       *********************6.77***************************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 !   58.6   0.6   1.2e-18   3.8e-16       1      34 [.     377     420 ..     377     441 .. 0.74
   2 !   66.1   0.2   5.9e-21   1.8e-18       1      45 []     653     705 ..     653     705 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.2e-18
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr..........g 34 
                                       dvdl+++A +T+Gy+GAD+aal +eAa++Alrr          +
  gi|320100449|ref|YP_004176041.1| 377 DVDLDKIADMTHGYTGADIAALAKEAAMNALRRfmkeegieieK 420
                                       9********************************55555555440 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 5.9e-21
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr........gikeitmedfee 45 
                                       dv+l+eLA++TeGy+GAD+aa+creA++ Alr+        + ++i+m++f++
  gi|320100449|ref|YP_004176041.1| 653 DVNLEELARKTEGYTGADIAAVCREASMIALREnyaatgrlDVTKIGMSHFMK 705
                                       9********************************555555444778*****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 !   93.4   0.1   2.4e-29   7.4e-27       1      83 [.      12      95 ..      12      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 2.4e-29
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkV 78
                                      +LrVaea+q+d gr+i+rid+e+m++lg++ gd++e++g k + +++vw+a+pedeg g Ir+dg++R+ +gvs Gd V
  gi|320100449|ref|YP_004176041.1| 12 KLRVAEARQRDIGRKIARIDRETMAKLGVSLGDFIEVTGpKGSEIVKVWQAYPEDEGSGLIRIDGFVRRKIGVSPGDYV 90
                                      69*************************************9999************************************ PP

                                      EEEEE CS
                           CDC48_N 79 tVrka 83
                                      tV+++
  gi|320100449|ref|YP_004176041.1| 91 TVKPV 95
                                      ***97 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.1   7.9e-19   2.4e-16       1      63 [.     112     174 ..     112     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 7.9e-19
                                       ..SCCCCH.HHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   1 ridgdema.ylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       +++gd +a ylk+q+lg pv  Gd+v  + +g+ ++++V+st+P  +v ite+T +e+ t+pv+
  gi|320100449|ref|YP_004176041.1| 112 PVYGD-LApYLKKQLLGNPVKRGDIVEAPIFGMLLRFAVTSTQPPSVVYITENTHVEVKTEPVR 174
                                       57899.777*****************************************************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 !   33.5   0.0   1.1e-10   3.2e-08      34     104 ..     223     301 ..     215     348 .. 0.82
   2 !   22.0   0.0   3.7e-07   0.00011      33      94 ..     498     567 ..     472     618 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.1e-10
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                         +llyGpPG Gkt lak +a+e+g+ + +  gP +      e +  l  ++ + +++   v+fidei  ++++ ee
  gi|320100449|ref|YP_004176041.1| 223 KGILLYGPPGTGKTLLAKALANEIGAYFITINGPEImskfygESEERLRKIFEEAQANapAVIFIDEIDSIAPKREE 299
                                       569*******************************994433333456799999887765337*************999 PP

                            RuvB_N 103 vl 104
                                       v 
  gi|320100449|ref|YP_004176041.1| 300 VT 301
                                       85 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 3.7e-07
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaallt..nleekdvlfideih 94 
                                          +ll+GpPG Gkt lak +a+e g+++ +  gP +      e ++ +  ++   ++ +  v+f dei 
  gi|320100449|ref|YP_004176041.1| 498 PKGILLFGPPGTGKTLLAKAVATESGANFIAIRGPEVlskwvgESEKAIRQIFRraRMVAPAVVFFDEID 567
                                       5679**************************9999965222222233444445431134455667777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0     3e-09     9e-07      24     139 ..     222     327 ..     212     333 .. 0.76
   2 !   19.4   0.0   3.7e-06    0.0011      24     132 ..     498     597 ..     489     605 .. 0.57

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3e-09
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr.e 99 
                                       p  +ll+G++G+GK+ l+++l++++    ++f++ +  +      +s +      ee lr++ +ea++++++    +
  gi|320100449|ref|YP_004176041.1| 222 PKGILLYGPPGTGKTLLAKALANEIG---AYFITINGPEI-----MSKFYGES--EERLRKIFEEAQANAPAVIFiD 288
                                       589*******************9777...88****99999.....44444444..4677777777666555554404 PP

                            AAA_16 100 kleealaavpelagaeasrllellkrllallsrderplvl 139
                                       ++++ +    e++g+ ++r+ ++l  l++ l+++++ +++
  gi|320100449|ref|YP_004176041.1| 289 EIDSIAPKREEVTGEVEKRVVAQLLTLMDGLKERGK-VIV 327
                                       55555558888888888***********99999888.443 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 3.7e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p  +ll G++G+GK+ l+++++++  ++ +i++rg  + +        ++     e+ +rq+ ++a+  +++     
  gi|320100449|ref|YP_004176041.1| 498 PKGILLFGPPGTGKTLLAKAVATESGAN-FIAIRGPEVLS-------KWVGES--EKAIRQIFRRARMVAPAVVFFD 564
                                       4899******************877777.55555555444.......344444..3677777776443333332222 PP

                            AAA_16 101 leealaavpelagaea....srllellkrllallsr 132
                                         ++   ++ ++g+++     r+ +++   l+ +++
  gi|320100449|ref|YP_004176041.1| 565 EIDS---IAGVRGSDPsgvtDRIVNQMLTELDGIQP 597
                                       2222...22233333333355555555555555555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   7.2e-10   2.2e-07       6     105 ..     225     318 ..     220     323 .. 0.83
   2 !   17.0   0.0   1.6e-05     0.005       6     100 ..     501     589 ..     497     596 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7.2e-10
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt+lakala+ + +     +i+++  e++     + + ++++  ++   +a+ +   ++++DEid i
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGA----YFITINGPEIMS----KFYGESEERLRKIFEEAQANApaVIFIDEIDSI 293
                                       8999******************96....************....66666666666666666666667********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+ + +v +  V+  LL +++g
  gi|320100449|ref|YP_004176041.1| 294 APKrEEVTGEVEK-RVVAQLLTLMDG 318
                                       **97777777766.577778999987 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.6e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...EEEEETGGG CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...ivllDEidK 79 
                                       ill gp g+Gkt+laka+a    +    ++i +   e+l      + v + + a   + +++      +v++DEid 
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGA----NFIAIRGPEVLS-----KWVGESEKAIRQIFRRARMVapaVVFFDEIDS 568
                                       7899****************9995....999999999999.....55555555555555555554566********* PP

                                       -------------..HHHHHHHH CS
                             AAA_2  80 ihpkessgadvSr..egVqrdLL 100
                                       i+     g+d S+  + +++ +L
  gi|320100449|ref|YP_004176041.1| 569 IAG--VRGSDPSGvtDRIVNQML 589
                                       **9..666676642234444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     9e-07   0.00027      51      94 ..     223     264 ..     219     277 .. 0.87
   2 ?    1.4   0.0      0.49   1.5e+02     253     288 ..     257     291 ..     256     296 .. 0.90
   3 !   23.2   0.0   1.1e-07   3.5e-05      51     107 ..     499     554 ..     491     559 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevk 94 
                                       +++Ll Gp+gtGkt la a+++e+g    f++++g e+ s    
  gi|320100449|ref|YP_004176041.1| 223 KGILLYGPPGTGKTLLAKALANEIG--AYFITINGPEIMSKFYG 264
                                       89***********************..78*********997555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.49
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 253 eiteklreeinkkvakyveegkaeivpGvlfiDevh 288
                                       ei +k   e ++ + k  ee +a+  p v+fiDe+ 
  gi|320100449|ref|YP_004176041.1| 257 EIMSKFYGESEERLRKIFEEAQAN-APAVIFIDEID 291
                                       89999999999***********99.59*******86 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.1e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksi 107
                                       +++Ll Gp+gtGkt la a++ e g    f+a+ g ev s  v  +e ++ q +r++ 
  gi|320100449|ref|YP_004176041.1| 499 KGILLFGPPGTGKTLLAKAVATESG--ANFIAIRGPEVLSKWVGESEkAIRQIFRRAR 554
                                       89********************988..78**************9998578999**985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.3e-06   0.00068       8     117 ..     225     317 ..     220     337 .. 0.54
   2 !   16.7   0.1   2.3e-05    0.0069       8      35 ..     501     528 ..     495     604 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                       ++++G++GtGKT+l++ l+++            + +f+t+++++    +++++  +          s+e+l++ +e+
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEI-----------GAYFITINGPE----IMSKFYGE----------SEERLRKIFEE 276
                                       89******************87...........44455555554....22222222..........23334444444 PP

                            AAA_22  85 alraravielliiDEaqhlr..s........eealeeLrslln 117
                                       a  ++ +  ++ iDE++ +   +        ++++ +L +l++
  gi|320100449|ref|YP_004176041.1| 277 AQANAPA--VIFIDEIDSIApkReevtgeveKRVVAQLLTLMD 317
                                       3333333..5555555555543123333444445555555554 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.3e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeaka 35 
                                       ++++G++GtGKT+l++ ++ +  +   a
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGANFIA 528
                                       89****************9987443333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   6.6e-08     2e-05       2     136 ..     225     343 ..     224     344 .. 0.73
   2 !   15.3   0.2     5e-05     0.015       2      78 ..     501     570 ..     500     620 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 6.6e-08
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       +lL GppGtgK+ la+ la  +++ + ++++++ +++  + g+ e     ++l++     +a+ ++++++DE++ + 
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGAYFITINGPEIMSK--FYGESE-----ERLRKIFEEAQANAPAVIFIDEIDSIA 294
                                       89*******************************8865..555555.....33333333334559**********998 PP

                                       ...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  79 ...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                           ev++++ +    + l l++g ++ ++        + vi+++n++d     ++palr+
  gi|320100449|ref|YP_004176041.1| 295 pkrEEVTGEVEKRVVAQLLTLMDGLKERGK--------VIVIGATNRPD----AIDPALRR 343
                                       222356666655555555555555555544........99999999999....88898886 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5e-05
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+ la+ +a   ++++  + +++      ++ ++    g+ +     + r ar   ++++++DE++ 
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGANFIAIRGPE------VLSKWV---GESEKAIRQIFRRARmvAPAVVFFDEIDS 568
                                       89****************999999988888876......455555...22223333333344445777777777775 PP

                                       -- CS
                             AAA_5  77 ae 78 
                                       + 
  gi|320100449|ref|YP_004176041.1| 569 IA 570
                                       54 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.1e-07   0.00016       2      79 ..     225     332 ..     225     391 .. 0.72
   2 !   18.6   0.0   5.5e-06    0.0017       2      78 ..     501     607 ..     501     641 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.1e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       +ll G+pG+GK+ la+ l+++ g  +++++ ++++++ +g+ +++++                              
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGayFITINGPEIMSKFYGESEERLRkifeeaqanapavifideidsiapkreeVT 301
                                       6789*******************99999*****99999998888777667777777777777777777777655433 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatn 79 
                                        +v++r+ ++l  l +   ++g+ +++ atn
  gi|320100449|ref|YP_004176041.1| 302 GEVEKRVVAQLLTLMDGLKERGKVIVIGATN 332
                                       3466666666666665545555555556665 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5.5e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       +ll G+pG+GK+ la+ ++ + g  ++ ++ ++++++ +g+ ++ ++                            d+
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGanFIAIRGPEVLSKWVGESEKAIRqifrrarmvapavvffdeidsiagvrgsDP 577
                                       6899*******************99999*****88888887776666455555555555555555555555555555 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildat 78 
                                       + v+dr+ +++   ++  +  ++ v++ at
  gi|320100449|ref|YP_004176041.1| 578 SGVTDRIVNQMLTELDGIQPLRKVVVIAAT 607
                                       555666555555555555555555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.9e-07   0.00012       5     102 ..     225     332 ..     222     355 .. 0.79
   2 !   12.8   0.0   0.00031     0.093       5      79 ..     501     572 ..     498     588 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.9e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT l+k l++e       ++ in  +   k + ++e+ l+ i+e+++++   ++f+DEi  +     
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIG---AYFITINGPEIMSKFYGESEERLRKIFEEAQANAPAVIFIDEIDSIapkre 298
                                       7899***************8888...89999999998887666665555555555555699***********99999 PP

                            AAA_14  77 .......pewekalkslvd.egknldvivtGSns 102
                                              +++   l  l+d  +++++viv G  +
  gi|320100449|ref|YP_004176041.1| 299 evtgeveKRVVAQLLTLMDgLKERGKVIVIGATN 332
                                       9999888888888888888533678898888765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00031
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpew 79 
                                       +++ G+  +GKT l+k ++ e+     +++ i   +   k   ++ek ++ i+++  +     ++f+DEi  + ++
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESG---ANFIAIRGPEVLSKWVGESEKAIRQIFRRaRM-VAPAVVFFDEIDSIAGV 572
                                       7899***************9999...99999999998888877777666666665233.37899******988765 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 !   16.5   0.0   2.1e-05    0.0063      19      45 ..     424     450 ..     413     453 .. 0.90
   2 !   16.4   0.0   2.3e-05    0.0069      24      55 ..     693     724 ..     677     729 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-05
                            Vps4_C  19 ipsdkllePpvtlkDflkalkkarptV 45 
                                       ip++kl + +vt++Dfl a+k+++p+ 
  gi|320100449|ref|YP_004176041.1| 424 IPAEKLEKLKVTMEDFLVAMKSVQPSL 450
                                       99***********************95 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.3e-05
                            Vps4_C  24 llePpvtlkDflkalkkarptVskeDLekhee 55 
                                       l   ++ +++f+kal+k  p+ s +D+e +e+
  gi|320100449|ref|YP_004176041.1| 693 LDVTKIGMSHFMKALEKIPPSLSRSDIEMYER 724
                                       5566899**********************997 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 !   16.2   0.0   2.1e-05    0.0064      45      70 ..     220     245 ..     207     328 .. 0.86
   2 !   15.7   0.0     3e-05    0.0091      47      71 ..     498     522 ..     492     567 .. 0.84
   3 ?   -2.0   0.0       8.5   2.6e+03      29     100 ..     665     739 ..     642     743 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgve 70 
                                       e  ++i+l Gp+G+GK+ la al+ e
  gi|320100449|ref|YP_004176041.1| 220 EPPKGILLYGPPGTGKTLLAKALANE 245
                                       556789*****************976 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                        ++i+l+Gp+G+GK+ la a+++e 
  gi|320100449|ref|YP_004176041.1| 498 PKGILLFGPPGTGKTLLAKAVATES 522
                                       5789****************99875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8.5
                         IstB_IS21  29 sldkrkvkeL.atlsfiekkenivllGp...sGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgkla 100
                                       ++  + ++++ ++ s i+ +en + +G    + +G sh+  al +       +      e+L +elkr  + g+++
  gi|320100449|ref|YP_004176041.1| 665 GYTGADIAAVcREASMIALRENYAATGRldvTKIGMSHFMKALEKIPPSLS-RSDIEMYERLARELKRVSGSGSFK 739
                                       445555555446777888888888888633356677888887754222111.111222356666666666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.6e-06    0.0017       1      66 [.     225     318 ..     225     333 .. 0.61
   2 !   13.5   0.0   0.00025     0.077       1      22 [.     501     522 ..     501     568 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.6e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe..........aldes 49 
                                       Ill G+pG+GKt lak+L+++  ++                  ++lr+++ e +   +   +            + +
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIgAYfitingpeimskfygesEERLRKIFEEAQANAPAVIFideidsiapkREEVT 301
                                       99****************99985558888877777777777755555555555555444444444444444333344 PP

                            AAA_18  50 krldedkldklldalee 66 
                                        ++++ ++++ll+++++
  gi|320100449|ref|YP_004176041.1| 302 GEVEKRVVAQLLTLMDG 318
                                       44444444455555544 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00025
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       Ill G+pG+GKt lak+++ + 
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATES 522
                                       99***************98775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-05    0.0039       2      48 ..     225     276 ..     224     309 .. 0.76
   2 !   13.0   0.0    0.0003     0.092       2      36 ..     501     536 ..     500     563 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpw 48 
                                       i + G+++tGKT l++aLa++    + ++  pE++ +++ e  ++ +++ ++
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEigaYFITIngPEIMSKFYGESEERLRKIFEE 276
                                       7899***************888433334467777777776666665555444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0003
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareile 36 
                                       i ++G+++tGKT l++a a + g + ++  + e+l+
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATEsGANFIAIRGPEVLS 536
                                       789****************76666655433333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.5e-05    0.0046       1      31 [.     225     255 ..     225     301 .. 0.79
   2 !   11.4   0.0    0.0011      0.33       1      26 [.     501     526 ..     501     608 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkk 31 
                                       i+lyGp+g+GK++lak La+++   + +++ 
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGAYFITING 255
                                       789******************9977744443 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0011
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i+l+Gp+g+GK++lak +a++   ++
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGANF 526
                                       689**************988766554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0017      0.51      36      54 ..     225     243 ..     219     247 .. 0.89
   2 ?    6.2   0.0     0.022       6.8     128     176 ..     268     316 ..     254     343 .. 0.85
   3 !    8.1   0.2    0.0059       1.8      36      54 ..     501     519 ..     495     535 .. 0.88
   4 ?    3.8   0.0      0.12        38     128     172 ..     544     588 ..     539     605 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt la  la
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALA 243
                                       69************98887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.022
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                       + ++++ +++++ + ++++ iD ++++ +  e+   +v +++v++l  + 
  gi|320100449|ref|YP_004176041.1| 268 ERLRKIFEEAQA-NAPAVIFIDEIDSIAPKREEVTGEVeKRVVAQLLTLM 316
                                       557889999999.77***************99999998899999987665 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0059
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt la  +a
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVA 519
                                       69***********997665 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.12
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galveal 172
                                        +++++ ++++ v+ +++v +D ++++ g    + s v +++v+++
  gi|320100449|ref|YP_004176041.1| 544 KAIRQIFRRARMVA-PAVVFFDEIDSIAGVRGSDPSGVtDRIVNQM 588
                                       68999*******87.**************97777777666666654 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   0.1   5.9e-05     0.018      25      43 ..     225     243 ..     222     249 .. 0.90
   2 !   13.2   0.1   0.00014     0.044      25      43 ..     501     519 ..     498     521 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.9e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+l+
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALA 243
                                       89**************996 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00014
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVA 519
                                       89*************9875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.7e-05      0.02       5      24 ..     225     245 ..     222     306 .. 0.62
   2 !   10.5   0.0    0.0012      0.36       5      22 ..     501     518 ..     498     570 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.7e-05
                            AAA_24   5 iliyGpsgiGKTtlakel.gp 24 
                                       il+yGp+g+GKT lak l  +
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALaNE 245
                                       89**************99533 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       il++Gp+g+GKT lak  
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAV 518
                                       89*************987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00026     0.078      19      50 ..     222     255 ..     191     268 .. 0.75
   2 !    9.7   0.1    0.0026      0.79      20      49 ..     499     530 ..     471     534 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00026
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..---- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkS 50 
                                        + ilL+G+ G+GKT l+++la+++g    +++ 
  gi|320100449|ref|YP_004176041.1| 222 PKGILLYGPPGTGKTLLAKALANEIGAYfiTING 255
                                       3449*******************99976555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0026
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evk 49 
                                       + ilL G+ G+GKT l++++a + g +  +++
  gi|320100449|ref|YP_004176041.1| 499 KGILLFGPPGTGKTLLAKAVATESGANfiAIR 530
                                       349******************99988755555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00097       0.3      13      38 ..     216     241 ..     209     254 .. 0.85
   2 ?    1.5   0.1      0.51   1.6e+02     108     153 ..     267     318 ..     259     333 .. 0.66
   3 ?   -2.5   0.0       8.5   2.6e+03      71     112 ..     392     437 ..     386     446 .. 0.65
   4 !   10.6   0.0   0.00084      0.25      14      40 ..     493     519 ..     465     533 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00097
                            ATPase  13 kgGipegrvvlitGepGtGKtifalq 38 
                                       + Gi   + +l++G pGtGKt++a+ 
  gi|320100449|ref|YP_004176041.1| 216 HLGIEPPKGILLYGPPGTGKTLLAKA 241
                                       568888899**************975 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.51
                            ATPase 108 ieelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkk 153
                                        e+l+++ +e +a     + iD i+++    +e + +v ++ + ql++ + +
  gi|320100449|ref|YP_004176041.1| 267 EERLRKIFEEAQAnapAVIFIDEIDSIapkREEVTGEVEKRVVAQLLTLMDG 318
                                       5677777777777555678888888883213333444556667777777754 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.5
                            ATPase  71 Gwdlekleeegklaiidasesaeesaee....kdkedleelieela 112
                                       G d+ +l +e  ++ +  ++++e+++ e       e+le+l+ +++
  gi|320100449|ref|YP_004176041.1| 392 GADIAALAKEAAMNALRRFMKEEGIEIEkgqpIPAEKLEKLKVTME 437
                                       7788888888888888888888887777333333444444444444 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00084
                            ATPase  14 gGipegrvvlitGepGtGKtifalqFl 40 
                                        Gi   + +l+ G pGtGKt++a+  +
  gi|320100449|ref|YP_004176041.1| 493 MGIEPPKGILLFGPPGTGKTLLAKAVA 519
                                       78999999**************98755 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00086      0.26      14      51 ..     220     255 ..     213     277 .. 0.88
   2 !   10.8   0.0   0.00072      0.22      14      50 ..     496     530 ..     490     534 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00086
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       e Pk ill G pG GK+ la++l++e+  +  ++++++
  gi|320100449|ref|YP_004176041.1| 220 EPPKGILLYGPPGTGKTLLAKALANEI--GAYFITING 255
                                       56999*********************9..677777765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00072
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       e Pk ill G pG GK+ la+++++e   + n++ + 
  gi|320100449|ref|YP_004176041.1| 496 EPPKGILLFGPPGTGKTLLAKAVATES--GANFIAIR 530
                                       6699**********************8..88888875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00071      0.21       7      70 ..     218     279 ..     216     326 .. 0.80
   2 !   10.1   0.0    0.0029       0.9       7      66 ..     494     551 ..     492     603 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00071
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepql 70 
                                        +++ + + + G+ G+GK+ L+k+la++       i+++g ++ ++   +++++++ +++e+q 
  gi|320100449|ref|YP_004176041.1| 218 GIEPPKGILLYGPPGTGKTLLAKALANEIGA--YFITINGPEIMSKFYGESEERLRKIFEEAQA 279
                                       677778899*****************99865..5567788888887788888888888887655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0029
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpq 66 
                                        +++ + + ++G+ G+GK+ L+k++a ++   +  i ++g ++ ++   +++k i+ ++ 
  gi|320100449|ref|YP_004176041.1| 494 GIEPPKGILLFGPPGTGKTLLAKAVATESG--ANFIAIRGPEVLSKWVGESEKAIRQIFR 551
                                       567777899****************99875..4566667666666666666666666655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00055      0.17      32      58 ..     221     247 ..     209     302 .. 0.78
   2 !    9.2   0.0    0.0027      0.82      33      56 ..     498     521 ..     488     530 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00055
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkld 58 
                                         k +ll+Gp GtGKt+++k l +++ 
  gi|320100449|ref|YP_004176041.1| 221 PPKGILLYGPPGTGKTLLAKALANEIG 247
                                       56789***************9999876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0027
                             AAA_7  33 kkpvllvGptGtGKtviikdllkk 56 
                                        k +ll Gp GtGKt+++k + ++
  gi|320100449|ref|YP_004176041.1| 498 PKGILLFGPPGTGKTLLAKAVATE 521
                                       6789*************9986654 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00047      0.14       2      31 ..     225     254 ..     224     317 .. 0.80
   2 !    9.2   0.0    0.0035       1.1       2      31 ..     501     530 ..     500     612 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00047
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       +ll g PG++ktll+kala+ +++ f  i 
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGAYFITIN 254
                                       7999*******************9997775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0035
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       +ll g PG++ktll+ka+a+  +++f  i+
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGANFIAIR 530
                                       78999***************9999998775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0014      0.44      24      60 ..     224     257 ..     214     334 .. 0.83
   2 !    9.0   0.0    0.0034         1      23      47 ..     499     523 ..     490     534 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0014
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTT CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaa 60 
                                        +l+ G  GtGK+lla+a+ ++     + f+++n  +
  gi|320100449|ref|YP_004176041.1| 224 GILLYGPPGTGKTLLAKALANEIG---AYFITINGPE 257
                                       69****************987654...6677777655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0034
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                         +l+ G  GtGK+lla+a+ ++s 
  gi|320100449|ref|YP_004176041.1| 499 KGILLFGPPGTGKTLLAKAVATESG 523
                                       569****************987764 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 !   12.7   0.0   0.00016     0.048     117     141 ..     225     249 ..     220     254 .. 0.90
   2 !    7.9   0.0    0.0049       1.5     117     136 ..     501     520 ..     494     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                       +++yGp+ tGkt la+a+a+ +  y
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGAY 249
                                       89*****************988766 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0049
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       ++++Gp+ tGkt la+a a+
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVAT 520
                                       899*************8876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   6.2e-05     0.019      15     122 ..     217     328 ..     211     338 .. 0.73
   2 ?    4.8   0.0     0.074        23      19      43 ..     497     521 ..     490     529 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.2e-05
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal......... 82 
                                       l  ep + +++YGp g GKt L k ++++         y+i +++ +i ++     ee+ +k +e+a          
  gi|320100449|ref|YP_004176041.1| 217 LGIEPPKGILLYGPPGTGKTLLAKALANEI------GAYFITINGPEIMSKFYGESEERLRKIFEEAQanapavifi 287
                                       5567788899***************99998......45666666666666665522444444444444777777888 PP

                          ATPase_2  83 .giavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                         i+    + ee+  e  k v +++  l++ +k++gk i+i
  gi|320100449|ref|YP_004176041.1| 288 dEIDSIAPKREEVTGEVEKRVVAQLLTLMDGLKERGKVIVI 328
                                       85555555566777789999999999999999999997776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.074
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiien 43 
                                       p + ++++Gp g GKt L k ++++
  gi|320100449|ref|YP_004176041.1| 497 PPKGILLFGPPGTGKTLLAKAVATE 521
                                       6666899***********9998876 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.2e-05    0.0065      37     184 ..     225     372 ..     220     413 .. 0.79
   2 ?    3.3   0.0      0.21        64      37      62 ..     501     526 ..     495     570 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-05
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       +++yg+ G Gkt L ka++ne+ + +     + +++ e ++++    +++  + f e   ++  v+ iD+i  +a k
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGAYF-----ITINGPEIMSKFYGESEERLRKIFEEAQANApAVIFIDEIDSIAPK 296
                                       79*****************9997665.....668999999999999999999999998886626788*******988 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                                                 ++  +l+++++ l e gk +v+ +   P +++    r   rf++   ++i ppd+  r +il  +  
  gi|320100449|ref|YP_004176041.1| 297 ReevtgevekRVVAQLLTLMDGLKERGKVIVIGATNRPDAIDPAL-RRPGRFDR--EIEIPPPDKRARKEILAVHT- 369
                                       52222211113445789999999***************9987654.33578876..68999**********97443. PP

                                       HTT- CS
                          Bac_DnaA 181 aekl 184
                                         ++
  gi|320100449|ref|YP_004176041.1| 370 -RNM 372
                                       .344 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.21
                                       EEEE-SSSSSHHHHHHHHHHHHHHHS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlena 62 
                                       ++++g+ G Gkt L ka++ e  +n+
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGANF 526
                                       799***************98876665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0011      0.34      50      81 ..     219     250 ..     168     331 .. 0.78
   2 !    9.2   0.0     0.002      0.61      23      83 ..     459     528 ..     443     567 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                            DUF815  50 glpannvLLwGarGtGKSslvkallneyaeeg 81 
                                        +p + +LL+G  GtGK  l kal ne+ +  
  gi|320100449|ref|YP_004176041.1| 219 IEPPKGILLYGPPGTGKTLLAKALANEIGAYF 250
                                       467789********************987665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                            DUF815  23 devklddLvgidkqkealventeqfle.........glpannvLLwGarGtGKSslvkallneyaeegLr 83 
                                        +v++dd+ g+d+ k++l e +e  ++          +p + +LL+G  GtGK  l ka+ +e  ++ ++
  gi|320100449|ref|YP_004176041.1| 459 PNVRWDDIGGLDDVKQELREAIEWPMKypgvfekmgIEPPKGILLFGPPGTGKTLLAKAVATESGANFIA 528
                                       567777777777777777777764332111111111468899******************9998877643 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1     0.003      0.91      23      40 ..     226     243 ..     218     248 .. 0.86
   2 !   10.6   0.1   0.00093      0.28      23      42 ..     502     521 ..     494     528 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.003
                                       EEE--TTSSTTHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavala 40 
                                          Gp GtGKt+la ala
  gi|320100449|ref|YP_004176041.1| 226 LLYGPPGTGKTLLAKALA 243
                                       578***********9998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00093
                                       EEE--TTSSTTHHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalave 42 
                                         +Gp GtGKt+la a+a e
  gi|320100449|ref|YP_004176041.1| 502 LLFGPPGTGKTLLAKAVATE 521
                                       679*************9976 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00027     0.083       4      55 ..     225     270 ..     222     309 .. 0.68
   2 ?    5.9   0.0     0.021       6.2       6      25 ..     503     522 ..     499     551 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakke 55 
                                       +l  G +GtGKt+++ +l++e+        a +++ N+p+++ + + + +++ 
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEI-------GAYFITINGPEIMsKFYGESEERL 270
                                       6789******************.......566666666654435555555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                           DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                         G +GtGKt+++ ++++e 
  gi|320100449|ref|YP_004176041.1| 503 LFGPPGTGKTLLAKAVATES 522
                                       5699*********9999886 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0023       0.7       3      24 ..     225     246 ..     223     251 .. 0.90
   2 ?   -0.2   0.0       2.7   8.3e+02      66     124 ..     267     325 ..     256     369 .. 0.55
   3 ?    7.2   0.1     0.015       4.5       3      23 ..     501     521 ..     499     525 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0023
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       ++l G++G GKT L++ la ++
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEI 246
                                       7899**************9886 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.7
                                       -SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEE CS
                             NACHT  66 aapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasll 124
                                       +++ ++++++ ++++  + + +D +D ++ + ++   + +++v   L +l+ +  l+e   +
  gi|320100449|ref|YP_004176041.1| 267 EERLRKIFEEAQANAPAV-IFIDEIDSIAPKREEvtgEVEKRVVAQLLTLMDG--LKERGKV 325
                                       555555444444444444.4568888888877778774444444444466666..3333333 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.015
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT L++ +a++
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATE 521
                                       6789************99976 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0063       1.9      44      75 ..     221     252 ..     192     269 .. 0.73
   2 ?   -0.0   0.0       2.3   7.1e+02     140     178 ..     257     293 ..     250     299 .. 0.76
   3 ?    5.4   0.0     0.052        16      48      79 ..     501     532 ..     490     571 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0063
                             Rad17  44 kkriLLisGPsGCgkstvvkvLskelgiklre 75 
                                       + + +L+ GP+G gk+   k L+ e g  ++ 
  gi|320100449|ref|YP_004176041.1| 221 PPKGILLYGPPGTGKTLLAKALANEIGAYFIT 252
                                       44557889*****************9987664 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2.3
                             Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                                       ++ +kfy++s ++lr++  ++       p ++ i ei+s+
  gi|320100449|ref|YP_004176041.1| 257 EIMSKFYGESeERLRKIFEEAQANA---PAVIFIDEIDSI 293
                                       6779999999889999888775443...568888999875 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.052
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                       +L+ GP+G gk+   k ++ e g +++    p
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGANFIAIRGP 532
                                       5778****************999988776655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0075       2.3      21      40 ..     225     244 ..     212     256 .. 0.82
   2 ?   -2.2   0.0       9.1   2.8e+03     101     124 ..     305     330 ..     259     339 .. 0.53
   3 ?    6.5   0.1      0.02       6.1      22      39 ..     502     519 ..     495     531 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0075
                            AAA_30  21 avltGpAGtGKttalkalre 40 
                                        +l Gp+GtGKt + kal++
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALAN 244
                                       5789**********999976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.1
                            AAA_30 101 dtkqlaallkaaek..agakvilvGD 124
                                         + +a+ll+ ++   +  kvi++G 
  gi|320100449|ref|YP_004176041.1| 305 EKRVVAQLLTLMDGlkERGKVIVIGA 330
                                       44444444444443212566666665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.02
                            AAA_30  22 vltGpAGtGKttalkalr 39 
                                       +l Gp+GtGKt + ka++
  gi|320100449|ref|YP_004176041.1| 502 LLFGPPGTGKTLLAKAVA 519
                                       578*********999986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0066         2       1      24 [.     228     251 ..     228     303 .. 0.83
   2 ?    6.4   0.0     0.036        11       1      24 [.     504     527 ..     504     555 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0066
                                       EE-TTSSHHHHHHHHHHHHTEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                       +G+PG GK+ +++ l+ ++g  ++
  gi|320100449|ref|YP_004176041.1| 228 YGPPGTGKTLLAKALANEIGAYFI 251
                                       7*****************986655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.036
                                       EE-TTSSHHHHHHHHHHHHTEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                       +G+PG GK+ +++ ++ + g  ++
  gi|320100449|ref|YP_004176041.1| 504 FGPPGTGKTLLAKAVATESGANFI 527
                                       6***********999998876554 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 !    8.1   0.0    0.0041       1.2     129     163 ..     222     253 ..     150     259 .. 0.83
   2 ?    5.9   0.0     0.019       5.9      37     152 ..     393     521 ..     375     529 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0041
                             T2SSE 129 rglilvsGgTgsGKttllyallkeinksderivtv 163
                                        + il+ G+ g+GKt l+ al +ei ++   ++t+
  gi|320100449|ref|YP_004176041.1| 222 PKGILLYGPPGTGKTLLAKALANEIGAY---FITI 253
                                       4679********************9887...5555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                             T2SSE  37 reveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvagealviR..kksakeltlddlgae 111
                                       ++++ l k+a++  ++r++   + +i++ +p+   +l++ +v ++  l+ +   +   iR    ++ +++ dd+g  
  gi|320100449|ref|YP_004176041.1| 393 ADIAALAKEAAMNALRRFMKEEGIEIEKGQPIPAEKLEKLKVTMEDFLVAMKSVQPSLIRevFVEVPNVRWDDIGGL 469
                                       56667777777777777777777777777777777777555555555555555566667754445556677777777 PP

                             T2SSE 112 ealkekiaevlrkavr...........erglilvsGgTgsGKttllyallke 152
                                        ++k++++e+++ +++             + il+ G+ g+GKt l+ a+ +e
  gi|320100449|ref|YP_004176041.1| 470 DDVKQELREAIEWPMKypgvfekmgiePPKGILLFGPPGTGKTLLAKAVATE 521
                                       77776666666555431111110000034569************99998765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0049       1.5      20      41 ..     225     246 ..     216     285 .. 0.76
   2 ?    6.3   0.0     0.024       7.2      20      37 ..     501     518 ..     479     555 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0049
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                        l+ GPPGtgKT    +l +++
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEI 246
                                       5899********8887777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.024
                            AAA_11  20 tliqGPPGtgKTktivel 37 
                                        l+ GPPGtgKT    ++
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAV 518
                                       5889********655444 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00049      0.15      37      69 ..     227     259 ..     219     293 .. 0.91
   2 ?    1.9   0.0       0.3        90      37      63 ..     503     529 ..     495     566 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                             AAA_6  37 paGpagtGKtEtvkdLakalakqvvvfncsdql 69 
                                       ++Gp gtGKt   k La++++ +++ +n  + +
  gi|320100449|ref|YP_004176041.1| 227 LYGPPGTGKTLLAKALANEIGAYFITINGPEIM 259
                                       68************************9977655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.3
                             AAA_6  37 paGpagtGKtEtvkdLakalakqvvvf 63 
                                       + Gp gtGKt   k +a + +  ++ +
  gi|320100449|ref|YP_004176041.1| 503 LFGPPGTGKTLLAKAVATESGANFIAI 529
                                       68********99999999888777655 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 !    8.2   0.0    0.0083       2.5      24      47 ..     225     248 ..     220     301 .. 0.65
   2 ?    5.8   0.0     0.045        14      24      47 ..     501     524 ..     496     569 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0083
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       ++l G++G+gk+l A++L+++ g 
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGA 248
                                       799***************997654 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.045
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       ++l G++G+gk+l A++ + +sg 
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGA 524
                                       799**************9998876 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.019       5.7       5      31 ..     226     252 ..     223     255 .. 0.90
   2 !    7.4   0.1    0.0083       2.5       5      31 ..     502     528 ..     499     531 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++G+ +tGKt  a +la+e ga  i+
  gi|320100449|ref|YP_004176041.1| 226 LLYGPPGTGKTLLAKALANEIGAYFIT 252
                                       89******************9987775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0083
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l+fG+ +tGKt  a ++a e ga  i+
  gi|320100449|ref|YP_004176041.1| 502 LLFGPPGTGKTLLAKAVATESGANFIA 528
                                       89********************99987 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   9.5e-05     0.029      29      64 ..      24      60 ..       5      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.5e-05
                                      S.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEE CS
                   Molydop_binding 29 p.evveinpedAaalGikdGdlVevesrrGsvevrak 64
                                      + + ++i  e++a+lG++ Gd +ev+ ++Gs  v+++
  gi|320100449|ref|YP_004176041.1| 24 GrKIARIDRETMAKLGVSLGDFIEVTGPKGSEIVKVW 60
                                      24699**************************999997 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    0.0094       2.8       3      27 ..     227     251 ..     225     255 .. 0.89
   2 ?    5.5   0.0      0.04        12       3      27 ..     503     527 ..     501     529 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0094
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+ala+++g+ ++
  gi|320100449|ref|YP_004176041.1| 227 LYGPPGTGKTLLAKALANEIGAYFI 251
                                       67******************99886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.04
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a+a++ g++++
  gi|320100449|ref|YP_004176041.1| 503 LFGPPGTGKTLLAKAVATESGANFI 527
                                       56*****************999987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.024       7.2      11      30 ..     223     242 ..     219     252 .. 0.81
   2 ?   -0.5   0.0       4.8   1.5e+03      94     125 ..     273     304 ..     261     317 .. 0.69
   3 ?    7.2   0.1      0.02         6      11      30 ..     499     518 ..     495     532 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.024
                            AAA_19  11 kvllvtaGpGtGKTrvlkhi 30 
                                       k +l+ ++pGtGKT + k+ 
  gi|320100449|ref|YP_004176041.1| 223 KGILLYGPPGTGKTLLAKAL 242
                                       56899*********887765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 4.8
                            AAA_19  94 aeeekklqeeellivDEfqdvdelqyrLlkal 125
                                         ee + ++ +++++DE+  + +   ++  ++
  gi|320100449|ref|YP_004176041.1| 273 IFEEAQANAPAVIFIDEIDSIAPKREEVTGEV 304
                                       445556656679******99987766665555 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.02
                            AAA_19  11 kvllvtaGpGtGKTrvlkhi 30 
                                       k +l+ ++pGtGKT + k++
  gi|320100449|ref|YP_004176041.1| 499 KGILLFGPPGTGKTLLAKAV 518
                                       56899*********877665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.015       4.6       2      28 ..     223     249 ..     222     254 .. 0.86
   2 ?    5.1   0.0     0.058        18       2      23 ..     499     520 ..     498     523 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.015
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkY 28 
                                       k ill G+ g+GKt L++al +e   Y
  gi|320100449|ref|YP_004176041.1| 223 KGILLYGPPGTGKTLLAKALANEIGAY 249
                                       6699****************9986555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.058
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkg 23 
                                       k ill+G+ g+GKt L++a+  
  gi|320100449|ref|YP_004176041.1| 499 KGILLFGPPGTGKTLLAKAVAT 520
                                       679***************9876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.017       5.2      23      43 ..     225     245 ..     211     251 .. 0.83
   2 ?    4.9   0.0     0.041        12      23      43 ..     501     521 ..     491     527 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       + l+G +G GKt lak   n+
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANE 245
                                       789************998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.041
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       + l G +G GKt lak +  +
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATE 521
                                       6789************99876 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.013         4       1      24 [.     231     254 ..     231     280 .. 0.81
   2 ?    4.3   0.0      0.13        41       1      21 [.     507     527 ..     507     553 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.013
                                       TTSSHHHHHHHHHHHHTSEEEEHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlD 24 
                                       +G+GK+ ++k+lA+++g  fi + 
  gi|320100449|ref|YP_004176041.1| 231 PGTGKTLLAKALANEIGAYFITIN 254
                                       69******************9874 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                                       TTSSHHHHHHHHHHHHTSEEE CS
                               SKI   1 mGaGKstvGkllAkklglefi 21 
                                       +G+GK+ ++k++A + g +fi
  gi|320100449|ref|YP_004176041.1| 507 PGTGKTLLAKAVATESGANFI 527
                                       69****************998 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.039        12      25      56 ..     212     243 ..     199     250 .. 0.85
   2 ?   -1.8   0.0       5.6   1.7e+03     119     132 ..     281     294 ..     262     336 .. 0.71
   3 ?    3.1   0.0      0.18        56      35      56 ..     498     519 ..     473     528 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.039
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFa 56 
                                       eL+e+   + ++ +ll+G++ +GKt +++  a
  gi|320100449|ref|YP_004176041.1| 212 ELFEHLGIEPPKGILLYGPPGTGKTLLAKALA 243
                                       6888888888999************9998765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.6
                              TniB 119 kvrvLiiDEihnll 132
                                        + v+ iDEi+++ 
  gi|320100449|ref|YP_004176041.1| 281 APAVIFIDEIDSIA 294
                                       45689999999886 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.18
                              TniB  35 mpnlllvGdsnnGKtmivekFa 56 
                                       ++ +ll+G++ +GKt +++  a
  gi|320100449|ref|YP_004176041.1| 498 PKGILLFGPPGTGKTLLAKAVA 519
                                       5789************998766 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.038        12      59      79 ..     219     239 ..     189     246 .. 0.86
   2 ?    4.8   0.0     0.036        11      58      79 ..     494     515 ..     468     521 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.038
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                                        ep++g+ l+G+ G GKt l 
  gi|320100449|ref|YP_004176041.1| 219 IEPPKGILLYGPPGTGKTLLA 239
                                       589***************985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.036
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                         ep++g+ l G+ G GKt l 
  gi|320100449|ref|YP_004176041.1| 494 GIEPPKGILLFGPPGTGKTLLA 515
                                       568****************985 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.14        43       4      30 ..     224     250 ..     222     258 .. 0.86
   2 ?    0.5   0.0       1.4   4.2e+02      75      95 ..     259     279 ..     252     298 .. 0.79
   3 ?    2.9   0.0      0.25        77       4      30 ..     500     526 ..     498     535 .. 0.86
   4 ?   -0.8   0.0       3.6   1.1e+03      76      96 ..     536     556 ..     528     577 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        + l gp g+Gk  l kaL +e   +f
  gi|320100449|ref|YP_004176041.1| 224 GILLYGPPGTGKTLLAKALANEIGAYF 250
                                       6899***************99988877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.4
                                       TTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                        ++ yg+s e  ++++e+++ 
  gi|320100449|ref|YP_004176041.1| 259 MSKFYGESEERLRKIFEEAQA 279
                                       5789************99876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.25
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        + l gp g+Gk  l ka+ +e   +f
  gi|320100449|ref|YP_004176041.1| 500 GILLFGPPGTGKTLLAKAVATESGANF 526
                                       6899**************999988877 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.6
                                       TEEEEEEHHHHHHHHHTTSEE CS
                     Guanylate_kin  76 gnlygtsveaieevlekgkiv 96 
                                       ++  g+s +ai++++  ++ v
  gi|320100449|ref|YP_004176041.1| 536 SKWVGESEKAIRQIFRRARMV 556
                                       567799**********99985 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.094        29      21      39 ..     222     239 ..     213     244 .. 0.77
   2 ?    5.6   0.0     0.045        14      19      42 ..     497     518 ..     486     520 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.094
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|320100449|ref|YP_004176041.1| 222 PKG-ILLYGPPGTGKTLLA 239
                                       456.9**********8765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.045
                            AAA_29  19 idlkgatlltGpsGsGKSTllDAi 42 
                                         +kg +ll Gp G+GK+ l  A+
  gi|320100449|ref|YP_004176041.1| 497 P-PKG-ILLFGPPGTGKTLLAKAV 518
                                       3.366.9**********8776555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.31        93      19      44 ..     221     246 ..     211     249 .. 0.86
   2 ?    7.5   0.0    0.0071       2.2     159     196 ..     268     304 ..     253     311 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.31
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledel 44 
                                       +p  + Lyg+ G+GK+ l + l +e+
  gi|320100449|ref|YP_004176041.1| 221 PPKGILLYGPPGTGKTLLAKALANEI 246
                                       566799*************9999886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0071
                        KAP_NTPase 159 elladmektLdalqkrlVvviDdLDrceteevlqllea 196
                                       e l +++++ +a + + V++iD++D++ +++   + e+
  gi|320100449|ref|YP_004176041.1| 268 ERLRKIFEEAQA-NAPAVIFIDEIDSIAPKREEVTGEV 304
                                       455555555555.99************99987776666 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 ?   11.5   0.1   0.00066       0.2      22      51 ..      65      94 ..      46     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00066
                                      SSSSBEEEEE-HHHHCT----TT-EEEEEE CS
                            eIF-1a 22 dngkevlaeipgkfRnkiwikrGdyVlVel 51
                                      +++   l +i g  R+ki + +GdyV+V++
  gi|320100449|ref|YP_004176041.1| 65 EDEGSGLIRIDGFVRRKIGVSPGDYVTVKP 94
                                      456677999*******************98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.072        22      21      47 ..     219     245 ..     190     251 .. 0.73
   2 ?   -1.6   0.0       7.7   2.3e+03     113     140 ..     261     289 ..     244     297 .. 0.77
   3 ?    3.9   0.0      0.15        47      22      45 ..     496     519 ..     443     531 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.072
                                       ..TTSEEEEEESTTSTHHHHHHHHHHH CS
                            ResIII  21 skrdkrglikmaTGtGKTlvaaklier 47 
                                       ++  k +l+  + GtGKTl+a +l+ +
  gi|320100449|ref|YP_004176041.1| 219 IEPPKGILLYGPPGTGKTLLAKALANE 245
                                       3778899999**********9887765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.7
                                       HHHHTH.........HHHTTT-SEEEEET CS
                            ResIII 113 sldadseee.eeeseellrdrfdviiiDE 140
                                       +++ +see+ ++  ee++ ++  vi+iDE
  gi|320100449|ref|YP_004176041.1| 261 KFYGESEERlRKIFEEAQANAPAVIFIDE 289
                                       45555544466677788888888*****9 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.15
                                       .TTSEEEEEESTTSTHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaakli 45 
                                       +  k +l+  + GtGKTl+a +++
  gi|320100449|ref|YP_004176041.1| 496 EPPKGILLFGPPGTGKTLLAKAVA 519
                                       7778899999********995544 PP

>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       4.4   1.3e+03      56      81 ..      24      49 ..      10      49 .. 0.82
   2 ?    9.2   0.0    0.0041       1.2      52      80 ..      64      92 ..      59      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 4.4
                                      T-EEEEE-HHHHHHHT--TTSEEEEE CS
                           DUF1905 56 ggyiLpvkaavrkaigkeaGdtvtve 81
                                      g+ i  ++++ ++++g++ Gd ++v+
  gi|320100449|ref|YP_004176041.1| 24 GRKIARIDRETMAKLGVSLGDFIEVT 49
                                      66667899999**********99996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0041
                                      ESSTT-EEEEE-HHHHHHHT--TTSEEEE CS
                           DUF1905 52 pmgkggyiLpvkaavrkaigkeaGdtvtv 80
                                      p+++g+ ++ ++  vr++ig+++Gd vtv
  gi|320100449|ref|YP_004176041.1| 64 PEDEGSGLIRIDGFVRRKIGVSPGDYVTV 92
                                      677799999*******************9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.075        23       2      24 ..     225     247 ..     224     261 .. 0.82
   2 ?    1.2   0.1         1     3e+02      82     119 ..     267     305 ..     260     333 .. 0.74
   3 ?    4.4   0.0       0.1        31       2      22 ..     501     521 ..     500     537 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.075
                                       EEEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                       +++ GppG+GKt l k +++++ 
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIG 247
                                       6788**********999999885 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1
                                       HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHH CS
                          NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkfkeave 119
                                       ee   +++++a+ + + vi iDEi ++  k +++  +ve
  gi|320100449|ref|YP_004176041.1| 267 EERLRKIFEEAQaNAPAVIFIDEIDSIAPKREEVTGEVE 305
                                       55556666777645666*******777666666655555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.1
                                       EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                       +++ GppG+GKt l k v+ +
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATE 521
                                       6788********999988865 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.44   1.3e+02       4      30 ..     228     256 ..     225     294 .. 0.59
   2 ?    7.2   0.0     0.013       3.9       3      71 ..     503     566 ..     501     571 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.44
                   Viral_helicase1   4 hGvpGcGKStlirkllrts..liltvnrp 30 
                                        G pG GK+ l + l+++   + +t+n p
  gi|320100449|ref|YP_004176041.1| 228 YGPPGTGKTLLAKALANEIgaYFITINGP 256
                                       588*************9966544444444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                   Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                         G pG GK+ l + ++ +s  ++ ++r   e+l++++ ++++     ++ + m +       ++++DE+
  gi|320100449|ref|YP_004176041.1| 503 LFGPPGTGKTLLAKAVATESgANFIAIRG-PEVLSKWVGESEKAIRQIFRRARMVAP-----AVVFFDEI 566
                                       5688*************999*99999999.9*******9999998888998888654.....48999997 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 ?    7.0   0.1     0.021       6.5       2      31 ..     225     254 ..     224     261 .. 0.93
   2 ?    2.3   0.0      0.57   1.7e+02       2      30 ..     501     529 ..     500     534 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.021
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                       i++ G+P +GKt  a +La + +a ++ti 
  gi|320100449|ref|YP_004176041.1| 225 ILLYGPPGTGKTLLAKALANEIGAYFITIN 254
                                       7889********************999996 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.57
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       i++ G+P +GKt  a ++a + +a +++i
  gi|320100449|ref|YP_004176041.1| 501 ILLFGPPGTGKTLLAKAVATESGANFIAI 529
                                       7789***************9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        59  (0.00329076); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              59  [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:00.42
# Mc/sec: 5354.94
//
Query:       gi|320100450|ref|YP_004176042.1|  [L=249]
Description: circadian clock protein KaiC [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-88  294.9   0.1    3.7e-88  294.8   0.1    1.0  1  ATPase     KaiC
    1.5e-07   31.2   0.1    3.1e-07   30.2   0.1    1.5  1  AAA_25     AAA domain
    3.5e-05   22.6   0.0    4.9e-05   22.1   0.0    1.2  1  GvpD       GvpD gas vesicle protein
    8.5e-05   21.9   0.2     0.0048   16.2   0.0    2.2  2  Rad51      Rad51
    0.00029   20.4   0.2      0.051   13.0   0.0    2.4  2  RecA       recA bacterial DNA recombination protein
    0.00045   19.6   0.9      0.014   14.7   0.2    2.1  2  DUF2075    Uncharacterized conserved protein (DUF2075)
     0.0041   17.5   0.0     0.0064   16.9   0.0    1.4  1  AAA_16     AAA ATPase domain
     0.0079   15.3   0.0      0.014   14.4   0.0    1.4  1  T2SSE      Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.017   14.5   0.0      0.031   13.6   0.0    1.6  1  DnaB_C     DnaB-like helicase C terminal domain
      0.019   15.3   1.4      0.065   13.6   1.2    2.1  1  AAA_19     AAA domain
      0.028   14.1   0.4       0.24   11.1   0.3    2.4  2  AAA_24     AAA domain
      0.038   14.4   0.9      0.085   13.3   0.9    1.9  1  AAA        ATPase family associated with various cellular act
      0.044   13.7   0.6        3.2    7.6   0.1    2.4  2  FliM       Flagellar motor switch protein FliM
      0.055   13.3   0.0       0.12   12.2   0.0    1.6  1  MEDS       MEDS: MEthanogen/methylotroph, DcmR Sensory domain
        0.1   12.3   0.0        0.2   11.4   0.0    1.5  2  IstB_IS21  IstB-like ATP binding protein
       0.13   12.6   0.1       0.31   11.3   0.1    1.7  1  AAA_22     AAA domain
       0.13   12.3   0.0       0.24   11.4   0.0    1.5  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 !  294.8   0.1   3.5e-91   3.7e-88       1     230 [.       5     237 ..       5     238 .. 0.99

  Alignments for each domain:
  == domain 1  score: 294.8 bits;  conditional E-value: 3.5e-91
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       vktg++glDeil+gGip+++vvl++G+pGtGKti+alqFl++g++  gepg++v++ee+++++r n++ +Gwd++++
  gi|320100450|ref|YP_004176042.1|   5 VKTGVPGLDEILNGGIPRRNVVLLSGGPGTGKTILALQFLWSGLQL-GEPGIYVALEEHPVQVRVNMRGFGWDTRQF 80 
                                       79*****************************************888.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaee......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlv 148
                                       e+egk+a+ida++ ++++a++      k+++++eeli+ l++ai+e++a+rvv+Ds+++l y  k++ aR+ + ql+
  gi|320100450|ref|YP_004176042.1|  81 EQEGKFAVIDAFTGGIGEAAKrekyvvKETDSVEELIDVLRTAIREVNAQRVVVDSVSTL-YLLKPSIARNVVLQLK 156
                                       *****************9999999**99********************************.**************** PP

                            ATPase 149 rvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       +vl+++g+T++lvs++s++e+++gg+gve+ ++dg+i+Ldl+e+++elvR+++i+kmRgt+hs+k+h++eIt++gi+
  gi|320100450|ref|YP_004176042.1| 157 KVLSGMGTTSLLVSQVSVTERGFGGPGVEH-AADGIIRLDLDEVDGELVRSIIIWKMRGTSHSMKRHVMEITDKGIV 232
                                       ******************************.********************************************** PP

                            ATPase 226 vleek 230
                                       v+++k
  gi|320100450|ref|YP_004176042.1| 233 VHPDK 237
                                       **986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   2.9e-10   3.1e-07      16     158 ..       6     144 ..       2     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.9e-10
                            AAA_25  16 aapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlr 91 
                                       ++  p ++ ++ g +p+  ++ll G pgtGKt lal+   + + +G+           + +yv++E+   ++r  +r
  gi|320100450|ref|YP_004176042.1|   6 KTGVPGLDEILNGGIPRRNVVLLSGGPGTGKTILALQFLWSGLqLGE-----------PGIYVALEEHPVQVRVNMR 71 
                                       55668889999999*************************99996666...........5699999999999999999 PP

                            AAA_25  92 avgeal...rddarllvld.........lagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralg 156
                                         g +    ++ ++ +v+d         + ++e+  +    ++   +++ +d l+ ai+ev+ ++ vv+D++s ++ 
  gi|320100450|ref|YP_004176042.1|  72 GFGWDTrqfEQEGKFAVIDaftggigeaA-KREKYVV----KETDSVEELIDVLRTAIREVN-AQRVVVDSVSTLYL 142
                                       88844444544555555554444443321.1111111....223337889999*******86.*********99876 PP

                            AAA_25 157 gd 158
                                         
  gi|320100450|ref|YP_004176042.1| 143 LK 144
                                       55 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   4.7e-08   4.9e-05      12     195 ..      25     216 ..      12     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.7e-08
                              GvpD  12 tllikGaPGtGktlftlrgldv.lrresdvlyvstrvddetvseay.........fsgeaeldktalldllkdplel 78 
                                        +l+ G PGtGkt+++l++l + l+  ++ +yv+       v             f++e+   k a++d +  +++ 
  gi|320100450|ref|YP_004176042.1|  25 VVLLSGGPGTGKTILALQFLWSgLQLGEPGIYVALEEHPVQVRVNMrgfgwdtrqFEQEG---KFAVIDAFTGGIGE 98 
                                       57899***************6549999******988776666543346555444444443...7899********98 PP

                              GvpD  79 dldvdvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPed.iktvkndlvvlaresgvrlvlvl 154
                                         +++  +   + +s+ e +d +  +a +    +++ ++v++ +++ y   ++  + v  +l  +  + g   +lv+
  gi|320100450|ref|YP_004176042.1|  99 AAKREKYV-VKETDSVEELID-VLRTAIRE---VNAQRVVVDSVSTLYLLKPSiARNVVLQLKKVLSGMGTTSLLVS 170
                                       88877666.667889999999.44444444...45567899999999988887346777888777777777666666 PP

                              GvpD 155 etaansr......leyivdGvvtlnvkeddrgrlrrdlrleklrGvr 195
                                       +    +r      +e+ +dG++ l++ e   g l+r++ + k+rG +
  gi|320100450|ref|YP_004176042.1| 171 QVSVTERgfggpgVEHAADGIIRLDLDEV-DGELVRSIIIWKMRGTS 216
                                       66555543444459************987.7**************87 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.6e-06    0.0048      18      57 ..       4      43 ..       1      52 [. 0.91
   2 ?    3.8   0.0     0.027        28     113     145 ..     109     141 ..      91     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.6e-06
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                      ++ tG   lDe+L+GGi+  ++  + G  ++Gkt l+ ++
  gi|320100450|ref|YP_004176042.1|  4 RVKTGVPGLDEILNGGIPRRNVVLLSGGPGTGKTILALQF 43
                                      689*******************************998875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.027
                                       STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGG CS
                             Rad51 113 tiehqeellqqaaallaedkfallivDsvtaly 145
                                       ++++ eel++ + + + e + + ++vDsv +ly
  gi|320100450|ref|YP_004176042.1| 109 ETDSVEELIDVLRTAIREVNAQRVVVDSVSTLY 141
                                       5689999999999999*************9999 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   4.9e-05     0.051      31      88 ..       2      58 ..       1      79 [. 0.84
   2 ?    5.0   0.1     0.014        14     106     143 ..     103     140 ..      87     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                                      --EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                              RecA 31 vetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafid 88
                                      ve + +G  +ld  l  GG+p+  ++ + G   +Gkt lal+ + +  + g    ++ 
  gi|320100450|ref|YP_004176042.1|  2 VERVKTGVPGLDEILN-GGIPRRNVVLLSGGPGTGKTILALQFLWSGLQLGEPGIYVA 58
                                      78899********998.*************************9877766666666555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                                       GG-EEE--SSHHHHHHHHHHHHTTT--SEEEEE-TTT- CS
                              RecA 106 dellvsqpdtGeqaleiadalvrsgaidlivvdsvaal 143
                                       ++ +v + d+ e+ ++++ + +r    + +vvdsv++l
  gi|320100450|ref|YP_004176042.1| 103 EKYVVKETDSVEELIDVLRTAIREVNAQRVVVDSVSTL 140
                                       67889999***************************987 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.3e-05     0.014       2      23 ..      24      45 ..      23      70 .. 0.83
   2 ?    3.7   0.0     0.028        30     169     230 ..      78     135 ..      58     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                           DUF2075  2 avvlVtGvaGtGKtvvllnlla 23
                                      +vvl +G++GtGKt+++l++l 
  gi|320100450|ref|YP_004176042.1| 24 NVVLLSGGPGTGKTILALQFLW 45
                                      799***************9875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.028
                           DUF2075 169 Rvaaseaviewvdalldgkkekakplssqenfdirvfddleelkkalkeknkesgrsrlvat 230
                                       R++ +e   + +da++ g  e+ak    +e++ ++ +d++eel + l++  +e +  r+v+ 
  gi|320100450|ref|YP_004176042.1|  78 RQFEQEGKFAVIDAFTGGIGEAAK----REKYVVKETDSVEELIDVLRTAIREVNAQRVVVD 135
                                       777778888888888866666654....569**********************999999975 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     6e-06    0.0064      24     106 ..      21     101 ..      12     168 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                            AAA_16  24 p..elvllsGesGvGKsslvrellr...alekdggif.lrgkcdqlesaipysalaqalareellrqlldeaesael 94 
                                       p  ++vllsG +G+GK+ l+ ++l    +l + g+++ l+++ +q +      +  + + +    rq ++e + a  
  gi|320100450|ref|YP_004176042.1|  21 PrrNVVLLSGGPGTGKTILALQFLWsglQLGEPGIYVaLEEHPVQVR------VNMRGFGW--DTRQFEQEGKFAVI 89 
                                       24499***************999965678888898887888888872......23444422..44455555444444 PP

                            AAA_16  95 eawrekleeala 106
                                       +a+   + ea++
  gi|320100450|ref|YP_004176042.1|  90 DAFTGGIGEAAK 101
                                       444444444444 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 !   14.4   0.0   1.4e-05     0.014     117     146 ..      11      40 ..       3      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttll 146
                                        ++e+l+  + +r ++l+sGg g+GKt+l+
  gi|320100450|ref|YP_004176042.1|  11 GLDEILNGGIPRRNVVLLSGGPGTGKTILA 40 
                                       57899**********************987 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 ?   13.6   0.0   2.9e-05     0.031       2      42 ..       5      46 ..       4     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaen 42
                                      ++tg   LD++++ G+ + +++++ + p++Gkt lal++  +
  gi|320100450|ref|YP_004176042.1|  5 VKTGVPGLDEILNgGIPRRNVVLLSGGPGTGKTILALQFLWS 46
                                      7899999**9876268999******************98755 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.2   6.2e-05     0.065      10      27 ..      23      40 ..      14     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.2e-05
                            AAA_19 10 ekvllvtaGpGtGKTrvl 27
                                      ++v+l+ +GpGtGKT + 
  gi|320100450|ref|YP_004176042.1| 23 RNVVLLSGGPGTGKTILA 40
                                      6799***********765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00023      0.24       3      23 ..      24      60 ..      22     150 .. 0.51
   2 ?   -1.9   0.0       2.3   2.4e+03     158     177 ..     182     213 ..     171     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                            AAA_24  3 lkiliyGpsgiGKTtlakel................g 23
                                      + +l+ G +g+GKT la+++                +
  gi|320100450|ref|YP_004176042.1| 24 NVVLLSGGPGTGKTILALQFlwsglqlgepgiyvalE 60
                                      57899**************977777764333333332 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.3
                            AAA_24 158 nelkeevDlvlranlkred............k 177
                                       + +++ +D ++r++l+++d             
  gi|320100450|ref|YP_004176042.1| 182 PGVEHAADGIIRLDLDEVDgelvrsiiiwkmR 213
                                       56889999999999988776655555555441 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9     8e-05     0.085       1      18 [.      26      43 ..      26     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-05
                                      EEEESSTTSSHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakav 18
                                      vll+G pGtGKT+la + 
  gi|320100450|ref|YP_004176042.1| 26 VLLSGGPGTGKTILALQF 43
                                      79************9765 PP

>> FliM  Flagellar motor switch protein FliM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1     0.003       3.2      86     129 ..      85     126 ..      78     130 .. 0.81
   2 ?    4.3   0.1     0.032        34       5      40 ..     128     163 ..     127     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.003
                                       HHHHHHHHTTS-S---S.TT----HHHHHHHHHHHHHHHHHHHH CS
                              FliM  86 vfsivdrllGGdgraaakegrefteiErkvierllkvvledlke 129
                                        f+++d + GG g+aa+   +++   E+  +e+l++v    ++e
  gi|320100450|ref|YP_004176042.1|  85 KFAVIDAFTGGIGEAAK--REKYVVKETDSVEELIDVLRTAIRE 126
                                       599************99..6778888888899998877666666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.032
                                       XXXX--HHHHHHHHHHHHHHHHHHHHHHHHHHTS-E CS
                              FliM   5 rqdrvskerlrtleliherlaRllttslsallrkiv 40 
                                       +++rv+ + + tl l++  +aR++  +l+ +l+ + 
  gi|320100450|ref|YP_004176042.1| 128 NAQRVVVDSVSTLYLLKPSIARNVVLQLKKVLSGMG 163
                                       5799*************************9998765 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 ?   12.2   0.0   0.00011      0.12      17      68 ..      40      91 ..      37     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                              MEDS 17 lvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleilda 68
                                      +++f+ +gl+ ge+ +yva +++  ++r  +r  g d  +++++g++ ++da
  gi|320100450|ref|YP_004176042.1| 40 ALQFLWSGLQLGEPGIYVALEEHPVQVRVNMRGFGWDTRQFEQEGKFAVIDA 91
                                      689********************************************99997 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019       0.2      46      84 ..      22      60 ..      17      89 .. 0.80
   2 ?   -3.3   0.0       6.1   6.5e+03      82     101 ..     112     131 ..      94     142 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                         IstB_IS21 46 kkenivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                      +++ ++l G++G+GK+ la  +  ++ + g   ++v +e
  gi|320100450|ref|YP_004176042.1| 22 RRNVVLLSGGPGTGKTILALQFLWSGLQLGEPGIYVALE 60
                                      67778899***********99888777777666666655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.1
                         IstB_IS21  82 rvedLveelkrarrdgklar 101
                                       +ve+L+  l++a r+ +++r
  gi|320100450|ref|YP_004176042.1| 112 SVEELIDVLRTAIREVNAQR 131
                                       45666666666655555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00029      0.31       5      98 ..      23     135 ..      21     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlpsst.sskdllrellralglelka... 70 
                                       ++++++ G +GtGKT l+ ++l +  +  +          e+p +v+v++ + + + +++ +e   a+ +   +   
  gi|320100450|ref|YP_004176042.1|  23 RNVVLLSGGPGTGKTILALQFLWSGLQLGE--PgiyvaleEHPVQVRVNMRGFGwDTRQFEQEGKFAVIDA-FTggi 96 
                                       67899************9999876544333..144788887888888888888774444433322222211.11233 PP

                            AAA_22  71 ............erlsseellealeqalraravielliiD 98 
                                                   e++s eel++ l+ a+r+  + + +++D
  gi|320100450|ref|YP_004176042.1|  97 geaakrekyvvkETDSVEELIDVLRTAIREVNA-QRVVVD 135
                                       344666777777777777777777777777777.666666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.24       2     102 ..      23     138 ..      22     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderd...............kkladpe.....kllelile 58 
                                       r++++++G   +GKT l+ q++ + l   e  +y++l++++                      e      +++++  
  gi|320100450|ref|YP_004176042.1|  23 RNVVLLSGGPGTGKTILALQFLWSGLQLGEPGIYVALEEHPVqvrvnmrgfgwdtrqF-----EqegkfAVIDAFTG 94 
                                       67999****************999887789999*****99986666665555543220.....12233345555555 PP

                            AAA_14  59 klke.ekktylflDEiqevpewekalkslvdegknldvivtGSns 102
                                        + e  k++  +  E   v+e+ ++l+  ++e  n + +v  S s
  gi|320100450|ref|YP_004176042.1|  95 GIGEaAKREKYVVKETDSVEELIDVLRTAIREV-NAQRVVVDSVS 138
                                       532253444456789999999999999999988.44444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 1835.17
//
Query:       gi|320100451|ref|YP_004176043.1|  [L=115]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   0.1       0.13   11.9   0.1    1.1  1  DUF4988   Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.4e-06      0.13      42      78 ..      27      63 ..       9      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.4e-06
                           DUF4988 42 veensdgsyvltlsdgktitltqgkdgeakaPvigvd 78
                                      ve++s   ++++ls g +i l  + d+e+ +P i ++
  gi|320100451|ref|YP_004176043.1| 27 VESVSHAVKTIELSSGAKIRLEIMRDNEVVYPTIKIN 63
                                      6777888899************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 925.86
//
Query:       gi|320100452|ref|YP_004176044.1|  [L=238]
Description: LuxR family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-05   23.3  16.5    7.6e-05   22.8  16.2    1.5  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    5.3e-05   22.3   4.6    6.4e-05   22.0   4.6    1.1  1  DUF812           Protein of unknown function (DUF812)
      9e-05   22.8  14.7    0.00033   21.0  14.7    1.8  1  ATG16            Autophagy protein 16 (ATG16)
      9e-05   21.9   0.2    0.00033   20.1   0.0    1.9  1  GerE             Bacterial regulatory proteins, luxR family
    0.00015   21.3   0.0    0.00065   19.3   0.0    2.1  1  Sigma70_r4_2     Sigma-70, region 4
    0.00027   20.3   2.7    0.00039   19.8   2.7    1.2  1  DUF3450          Protein of unknown function (DUF3450)
    0.00028   21.4   2.8    0.00028   21.4   2.8    2.2  2  DUF16            Protein of unknown function DUF16
    0.00039   20.1   0.1     0.0011   18.6   0.1    1.8  1  HTH_38           Helix-turn-helix domain
     0.0004   20.1   0.0     0.0015   18.3   0.0    1.9  1  HTH_23           Homeodomain-like domain
    0.00053   18.8   3.0    0.00073   18.3   3.0    1.4  1  AAA_13           AAA domain
    0.00061   18.5   4.2    0.00072   18.3   4.2    1.1  1  Macoilin         Macoilin family
    0.00067   19.7   9.7    0.00067   19.7   9.7    1.9  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    0.00068   19.7  10.3    0.00068   19.7  10.3    2.2  2  DHR10            Designed helical repeat protein 10 domain
    0.00073   20.0   3.0     0.0066   16.9   3.0    2.5  1  HTH_40           Helix-turn-helix domain
    0.00073   19.8   3.1     0.0017   18.6   3.1    1.6  1  KxDL             Uncharacterized conserved protein
    0.00076   17.8   4.1    0.00098   17.4   4.1    1.2  1  EzrA             Septation ring formation regulator, EzrA
    0.00077   17.7   7.0    0.00098   17.4   7.0    1.2  1  HOOK             HOOK protein
      0.001   19.5   0.3       0.39   11.2   0.0    3.0  2  NPV_P10          Nucleopolyhedrovirus P10 protein
     0.0013   18.7   0.0     0.0039   17.2   0.0    1.8  1  HTH_29           Winged helix-turn helix
     0.0018   17.0   4.8     0.0023   16.6   4.8    1.1  1  FapA             Flagellar Assembly Protein A
      0.002   18.7  10.1     0.0031   18.0  10.1    1.4  1  APG6_N           Apg6 coiled-coil region
     0.0022   17.7  10.0     0.0042   16.7   9.4    1.6  1  Filament         Intermediate filament protein
     0.0025   17.0   6.5     0.0037   16.4   6.5    1.3  1  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0027   16.7   3.2     0.0034   16.4   3.2    1.3  1  IFT57            Intra-flagellar transport protein 57
     0.0033   15.7   6.6     0.0041   15.4   6.6    1.1  1  FPP              Filament-like plant protein, long coiled-coi
     0.0034   16.9   0.0     0.0034   16.9   0.0    2.8  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0037   16.0   5.3     0.0043   15.8   5.3    1.2  1  GOLGA2L5         Putative golgin subfamily A member 2-like pr
     0.0039   17.5   6.8      0.011   16.0   4.8    2.4  2  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0043   17.5   1.8     0.0079   16.6   1.0    1.8  1  DUF3037          Protein of unknown function (DUF3037)
     0.0044   16.8   4.0     0.0044   16.8   4.0    1.7  1  TACC_C           Transforming acidic coiled-coil-containing p
     0.0046   16.4   3.2     0.0059   16.0   3.2    1.2  1  DUF4407          Domain of unknown function (DUF4407)
     0.0053   16.6   5.1     0.0053   16.6   5.1    1.8  2  DUF724           Protein of unknown function (DUF724)
     0.0056   16.8  11.6     0.0056   16.8  11.6    2.2  2  Tropomyosin_1    Tropomyosin like
      0.006   16.0   6.5      0.011   15.1   6.5    1.4  1  GAS              Growth-arrest specific micro-tubule binding
     0.0063   16.4   0.1      0.053   13.4   0.0    2.3  2  HTH_5            Bacterial regulatory protein, arsR family
     0.0064   16.6  10.3      0.015   15.4   9.8    1.5  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0069   16.4   2.7     0.0069   16.4   2.7    1.8  1  Laminin_II       Laminin Domain II
     0.0081   16.1   0.1      0.031   14.2   0.0    2.0  1  HTH_11           HTH domain
     0.0084   16.4   8.7      0.015   15.6   5.0    2.4  2  DUF641           Plant protein of unknown function (DUF641)
      0.009   14.9  14.1      0.016   14.1  14.1    1.4  1  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.012   15.5   2.6      0.012   15.5   2.6    3.4  3  PKcGMP_CC        Coiled-coil N-terminus of cGMP-dependent pro
      0.013   15.1   7.3      0.028   14.0   7.3    1.5  1  DUF4795          Domain of unknown function (DUF4795)
      0.014   15.0   4.8      0.018   14.7   4.8    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.014   15.9   2.5      0.068   13.7   2.5    1.9  1  T3SSipB          Type III cell invasion protein SipB
      0.015   12.9   7.0      0.018   12.6   7.0    1.1  1  DUF3584          Protein of unknown function (DUF3584)
      0.016   15.4   5.0      0.024   14.8   2.9    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
      0.019   14.3   6.1       0.19   11.0   6.6    1.9  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.02   14.0   3.4      0.024   13.7   3.4    1.1  1  AIP3             Actin interacting protein 3
      0.024   14.8   9.0      0.025   14.7   6.8    1.9  2  ADIP             Afadin- and alpha -actinin-Binding
      0.025   14.9   1.2        3.9    7.8   0.1    3.1  3  V-SNARE_C        Snare region anchored in the vesicle membran
      0.026   14.7   0.0      0.073   13.2   0.0    1.8  1  HTH_28           Helix-turn-helix domain
      0.028   14.4   1.8       0.88    9.6   0.5    2.5  2  HisKA            His Kinase A (phospho-acceptor) domain
      0.032   13.8   8.9      0.038   13.6   5.2    2.1  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.032   14.3   0.4       0.14   12.3   0.0    2.3  1  HTH_20           Helix-turn-helix domain
      0.034   14.6   4.8      0.074   13.5   4.8    1.6  1  Snapin_Pallidin  Snapin/Pallidin
      0.039   13.5   5.8       0.16   11.5   1.4    2.4  2  Fzo_mitofusin    fzo-like conserved region
       0.04   13.7   0.0       0.11   12.2   0.0    1.7  1  HTH_DeoR         DeoR-like helix-turn-helix domain
       0.04   13.4   3.3      0.052   13.1   0.0    2.8  1  Sigma70_r4       Sigma-70, region 4
      0.042   14.0  10.2        0.2   11.7   4.3    2.9  2  COG2             COG (conserved oligomeric Golgi) complex com
      0.042   13.2   3.3      0.053   12.9   3.3    1.1  1  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
      0.046   13.7   1.1       0.22   11.5   0.2    2.5  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.054   13.5   3.3      0.086   12.9   2.2    2.0  1  DUF1515          Protein of unknown function (DUF1515)
      0.057   12.5   1.1      0.088   11.9   1.0    1.3  1  Poty_PP          Potyviridae polyprotein
      0.066   12.5   0.4       0.16   11.3   0.6    1.5  1  ATPase           KaiC
      0.066   13.6  10.9      0.079   13.3   8.5    2.2  2  V-SNARE          Vesicle transport v-SNARE protein N-terminus
      0.073   13.3   1.5        4.7    7.5   0.0    3.4  2  DnaB_bind        DnaB-helicase binding domain of primase
      0.075   12.7   6.5      0.037   13.7   2.5    2.4  2  RPW8             Arabidopsis broad-spectrum mildew resistance
      0.076   10.8  18.2       0.14    9.9  18.2    1.4  1  Myosin_tail_1    Myosin tail
      0.077   13.1   0.7      0.077   13.1   0.7    4.0  2  T3SS_needle_E    Type III secretion system, cytoplasmic E com
      0.083   12.3   0.1        0.2   11.1   0.0    1.7  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.083   12.9   4.3        0.7    9.9   3.7    2.3  2  DUF1664          Protein of unknown function (DUF1664)
      0.096   12.3   9.2       0.16   11.6   9.2    1.5  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.11   11.8   4.2        0.2   11.0   4.2    1.4  1  CASP_C           CASP C terminal
       0.11   13.0   4.8       0.14   12.8   3.4    1.7  1  ING              Inhibitor of growth proteins N-terminal hist
       0.12   11.9  11.8       0.94    9.0   8.7    2.2  2  PspA_IM30        PspA/IM30 family
       0.13   12.1   6.4       0.34   10.7   2.4    2.2  2  Phage_GP20       Phage minor structural protein GP20
       0.13   12.7   0.7        0.3   11.5   0.7    1.7  1  L31              Mitochondrial ribosomal protein L31
       0.14   11.8  12.7      0.041   13.6   9.4    1.6  1  YkyA             Putative cell-wall binding lipoprotein
       0.16   12.2   8.3        2.9    8.2   1.0    2.5  2  DUF5082          Domain of unknown function (DUF5082)
       0.17   11.6   6.9       0.13   12.0   5.3    1.6  1  DUF745           Protein of unknown function (DUF745)
       0.17    9.8   4.6        0.2    9.5   4.6    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.17   11.0  12.0       0.25   10.5  12.0    1.1  1  HAP1_N           HAP1 N-terminal conserved region
       0.17   12.2   9.8       0.57   10.5   5.9    2.2  2  HrpB7            Bacterial type III secretion protein (HrpB7)
       0.18   12.2  12.1       0.68   10.4   2.7    3.2  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.18   12.0  14.6       0.18   12.1  10.4    2.3  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.19   11.6   4.6          1    9.2   3.8    2.1  1  Spc29            Spindle Pole Component 29
       0.19   11.7   8.7        3.6    7.5   0.4    2.7  3  Prefoldin        Prefoldin subunit
       0.22   10.7   7.2       0.13   11.4   5.2    1.6  2  TMPIT            TMPIT-like protein
       0.22   11.4  11.1      0.082   12.8   3.7    2.4  2  Wtap             WTAP/Mum2p family
       0.22   11.2  11.1       0.47   10.2  10.9    1.7  1  DUF4201          Domain of unknown function (DUF4201)
       0.22   11.4  14.3       0.16   12.0   6.1    2.3  2  YscO             Type III secretion protein YscO
       0.23   11.3   3.7        1.8    8.4   0.2    2.4  3  DASH_Duo1        DASH complex subunit Duo1
       0.24   11.2   2.8       0.86    9.4   2.7    2.0  1  USP8_interact    USP8 interacting
       0.24   11.5   3.4       0.89    9.7   3.4    2.0  1  DUF2730          Protein of unknown function (DUF2730)
       0.26   10.7  11.9       0.27   10.7  10.8    1.4  1  Golgin_A5        Golgin subfamily A member 5
       0.28   11.5   2.5        1.8    8.8   2.5    2.5  1  DUF948           Bacterial protein of unknown function (DUF94
       0.29   10.8   4.8       0.35   10.5   2.5    2.0  2  Med4             Vitamin-D-receptor interacting Mediator subu
       0.29   10.3   6.9       0.84    8.8   6.5    2.0  1  DLP_helical      Dynamin-like helical domain
       0.31   11.5  13.0       0.24   11.8  11.6    1.5  1  Fez1             Fez1
       0.31   11.1   8.0        2.1    8.4   0.8    3.1  2  Bcr-Abl_Oligo    Bcr-Abl oncoprotein oligomerisation domain
       0.32   10.7   3.9       0.45   10.3   0.5    2.2  2  Lectin_N         Hepatic lectin, N-terminal domain
       0.36   10.2  18.7       0.36   10.2  16.0    1.8  1  Tropomyosin      Tropomyosin
       0.38    9.5   5.9       0.43    9.4   5.6    1.3  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
       0.43   11.1  10.3       0.18   12.3   7.6    1.7  1  FlgN             FlgN protein
       0.47   10.8  12.8       0.42   11.0  11.2    1.8  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
       0.47   10.7  11.3       0.12   12.6   8.1    1.7  1  FliJ             Flagellar FliJ protein
       0.59    9.9   7.7       0.88    9.4   5.2    2.3  2  SKA1             Spindle and kinetochore-associated protein 1
       0.63    9.3   8.1        1.3    8.2   5.3    2.0  2  FmiP_Thoc5       Fms-interacting protein/Thoc5
       0.67   10.5  11.8        0.3   11.6   9.0    1.9  1  Spectrin         Spectrin repeat
       0.67   10.5   6.9       0.91   10.1   4.3    2.4  2  Syntaxin-6_N     Syntaxin 6, N-terminal
        0.7   11.0   9.0        7.4    7.7   1.4    3.0  2  DUF5320          Family of unknown function (DUF5320)
       0.77   10.3   8.9        3.7    8.1   7.8    2.3  1  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
       0.77   10.0  10.8       0.58   10.4   7.6    1.9  2  zf-C4H2          Zinc finger-containing protein
       0.78    9.6   4.1       0.71    9.7   2.0    2.1  1  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
        0.8    9.8   9.4        2.3    8.3   9.4    1.9  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.87    9.5   5.5         11    5.9   0.3    2.4  2  Sec8_exocyst     Sec8 exocyst complex component specific doma
       0.89    9.9  10.5        1.2    9.5   8.9    1.9  1  OmpH             Outer membrane protein (OmpH-like)
       0.91    7.4   4.2        1.2    7.0   3.5    1.4  2  Prominin         Prominin
       0.93    9.9   4.7         68    3.9   0.1    3.3  3  NBD94            Nucleotide-Binding Domain 94 of RH
       0.97    8.9   9.2        4.8    6.7   1.4    2.2  2  Vps5             Vps5 C terminal like
        1.1   10.0   9.4        1.1    9.9   2.7    2.6  2  SlyX             SlyX
        1.3    8.9  11.7        2.2    8.1   6.4    2.6  2  DivIC            Septum formation initiator
        1.5    8.7   4.5        5.5    6.9   1.0    2.0  2  Sec34            Sec34-like family
        1.6    9.5   6.6        3.7    8.3   6.6    1.8  1  DUF2203          Uncharacterized conserved protein (DUF2203)
        1.8    8.9   8.6         36    4.7   2.2    3.2  2  Rx_N             Rx N-terminal domain
        2.2    7.7  16.1          1    8.8  11.8    2.1  2  HMMR_N           Hyaluronan mediated motility receptor N-term
        2.5    8.8  16.0          2    9.1  10.5    2.7  1  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        2.5    8.5   6.7          2    8.8   1.0    3.2  2  TSC22            TSC-22/dip/bun family
        2.6    8.3  10.2        5.2    7.4   9.9    1.8  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        2.6    8.8   5.9          2    9.2   3.1    2.1  1  Occludin_ELL     Occludin homology domain
        2.7    8.7  10.4       0.97   10.1   6.7    2.2  1  YabA             Initiation control protein YabA
        2.7    7.6  10.0        5.9    6.5   9.2    1.8  2  GrpE             GrpE
        2.7    7.3  16.0        3.9    6.8  15.6    1.5  1  DUF3552          Domain of unknown function (DUF3552)
        2.7    8.9   5.7        1.1   10.3   2.9    1.7  1  CSN5_C           Cop9 signalosome subunit 5 C-terminal domain
          3    8.4  15.6         51    4.4   1.1    2.6  2  ZapB             Cell division protein ZapB
        3.1    7.9   9.1        6.2    6.9   1.9    2.1  2  Nup54            Nucleoporin complex subunit 54
        3.7    7.7   9.3        9.1    6.5   0.7    2.8  3  Med9             RNA polymerase II transcription mediator com
        4.3    7.2  14.0        1.3    8.9   3.0    3.4  3  CdvA             CdvA-like coiled-coil domain
        4.6    7.5  11.3        6.3    7.1   3.7    2.8  2  Spc24            Spc24 subunit of Ndc80
        4.7    7.4  13.1         20    5.4  11.3    2.6  2  Cnn_1N           Centrosomin N-terminal motif 1
          5    7.3  20.7       0.95    9.6  16.3    2.0  1  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
        5.2    6.8  17.9         11    5.7  17.9    1.7  1  ERM              Ezrin/radixin/moesin family
        5.6    7.4  12.6         20    5.6   5.3    2.8  2  Csm1_N           Csm1 N-terminal domain
        5.6    7.5   9.2    3.1e+02    1.9   8.7    2.6  1  DUF4140          N-terminal domain of unknown function (DUF41
        5.9    7.1   9.9         18    5.5   5.3    2.2  2  CREPT            Cell-cycle alteration and expression-elevate
        5.9    6.0   6.2       0.93    8.6   2.5    1.5  1  Tho2             Transcription factor/nuclear export subunit 
        6.1    7.3  18.4       0.74   10.2   3.6    3.4  2  CLZ              C-terminal leucine zipper domain of cyclic n
        8.3    6.4   8.8        9.8    6.1   1.1    2.4  2  DUF4446          Protein of unknown function (DUF4446)
        8.3    6.7  13.6       0.73   10.1   3.0    3.0  3  XhlA             Haemolysin XhlA
        8.4    6.6  17.1        1.8    8.7   2.5    3.6  2  Exonuc_VII_S     Exonuclease VII small subunit
        8.6    6.8  11.8        9.8    6.6   8.7    2.1  2  CENP-H           Centromere protein H (CENP-H)
        9.3    6.3  19.7       0.51   10.4  13.4    2.2  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding


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 !   22.8  16.2   6.5e-07   7.6e-05      36     123 ..     143     227 ..     115     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.5e-07
                    CENP-F_leu_zip  36 seenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenllee 112
                                        ee+  +++ e E++++ +++l+++i el+e  ++ e +++ lrs  e L++el+   erv+eLes++s + ++ + 
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELE---ERVKELESCRSNVDSMRKT 216
                                       5777888999********************************************8...59***********999999 PP

                    CENP-F_leu_zip 113 kEqekvqmkee 123
                                       +E+  + ++e+
  gi|320100452|ref|YP_004176044.1| 217 LEDAARLLQEA 227
                                       99987777665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   4.6   5.5e-07   6.4e-05     289     389 ..     104     218 ..      66     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.5e-07
                            DUF812 289 setdslktkgsrfthaeklqftke..........ela......kkaeteeelkkkreeeleelqeqieeleskieel 349
                                       +++ ++ktk+ ++ h+   +++k           + +      + +  e el+k+r+  l+el+ +i+el + +++ 
  gi|320100452|ref|YP_004176044.1| 104 RSHLNMKTKAGKLVHETYEKLKKGelklvvpfirT-PvagceeQVKALEGELEKQRN-RLKELEAKISELTEAVKQR 178
                                       23334556666666665556655566666666650.244555344555667766666.89***************** PP

                            DUF812 350 eeeikklessikqveeeleeekeeneelekevklkkktle 389
                                       eeei+ l+s  + ++ elee+ +e e   ++v+ ++ktle
  gi|320100452|ref|YP_004176044.1| 179 EEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       **************************99999999999987 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0  14.7   2.8e-06   0.00033     107     186 ..     143     225 ..     137     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.8e-06
                             ATG16 107 lneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklr...klekE 180
                                        +e++++le +l+++++rl+elea++++l++++k+reee+++++   ++l+ El+    +l++  ++ +   k+ ++
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDsmrKTLED 219
                                       6899**************************************************98776665543333322266666 PP

                             ATG16 181 NkeLve 186
                                       ++ L++
  gi|320100452|ref|YP_004176044.1| 220 AARLLQ 225
                                       666666 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   0.0   2.8e-06   0.00033      15      38 ..      84     107 ..      81     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-06
                                       CTTS-HHHHHHHHTS-HHHHHHHH CS
                              GerE  15 aeGksnkeIAeelniSekTVkvhk 38 
                                        +G+ + +IAeel+ Se+T+++h+
  gi|320100452|ref|YP_004176044.1|  84 KAGLPVSQIAEELGRSETTIRSHL 107
                                       58*********************8 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.5e-06   0.00065      26      47 ..      86     107 ..      83     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.5e-06
                                       ---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2  26 glsykEIAellgisegtVksrl 47 
                                       gl+  +IAe+lg se+t++s+l
  gi|320100452|ref|YP_004176044.1|  86 GLPVSQIAEELGRSETTIRSHL 107
                                       899******************9 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.7   3.3e-06   0.00039      13     105 ..     142     234 ..     131     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.3e-06
                           DUF3450  13 alaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqie 89 
                                       ++++++++++ e ek  +  ++ ++ki++l++  ++ ++e++ l++ +e+l+ + e+  + ++s +++++s+++ +e
  gi|320100452|ref|YP_004176044.1| 142 GCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       338999999999***************************************************************** PP

                           DUF3450  90 eieeierelvpllekm 105
                                       ++ ++ +e   +l+ +
  gi|320100452|ref|YP_004176044.1| 219 DAARLLQEALSMLQHV 234
                                       ****999999998875 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       7.7   9.1e+02      34      66 ..      94     126 ..      89     133 .. 0.74
   2 !   21.4   2.8   2.3e-06   0.00028      33      99 ..     151     217 ..     136     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 7.7
                                       HHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH CS
                             DUF16  34 qrLkkieakvdklgeqinkleqkvekqgekike 66 
                                       ++L ++e++++++ +   k  + v++  ek+k+
  gi|320100452|ref|YP_004176044.1|  94 EELGRSETTIRSHLNMKTKAGKLVHETYEKLKK 126
                                       567788888888887777777777777777765 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHH CS
                             DUF16  33 kqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRl 99 
                                       + +L+k  ++++ l+ +i++l+++v++ +e+i+ l+   +a ++el++  + le+    ++++ k l
  gi|320100452|ref|YP_004176044.1| 151 EGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTL 217
                                       5578999999999999999999999999999999999999999999988888888888888888876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   9.7e-06    0.0011      17      38 ..      83     104 ..      79     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.7e-06
                            HTH_38  17 laeGlslreIArrLgrspsTIs 38 
                                        ++Gl +++IA +Lgrs +TI 
  gi|320100452|ref|YP_004176044.1|  83 MKAGLPVSQIAEELGRSETTIR 104
                                       589******************6 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-05    0.0015      15      35 ..      81     104 ..      74     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-05
                            HTH_23  15 ae...GlsvreIAreLgvsrrTvy 35 
                                       a+   Gl+v++IA+eLg+s+ T++
  gi|320100452|ref|YP_004176044.1|  81 ARmkaGLPVSQIAEELGRSETTIR 104
                                       44446*****************98 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.0   6.2e-06   0.00073     365     469 ..      90     198 ..      36     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.2e-06
                            AAA_13 365 esikklvaeineliakhNekvanleeekeeakkklelhlv....eeleseldeykkkykklekaieklekelkeeea 437
                                       ++i +++ + +++i++h ++ ++  + + e  +kl++ ++      ++  +   ++++k+le ++ek  ++lke ea
  gi|320100452|ref|YP_004176044.1|  90 SQIAEELGRSETTIRSHLNMKTKAGKLVHETYEKLKKGELklvvPFIRTPVAGCEEQVKALEGELEKQRNRLKELEA 166
                                       48888888889999999888888888888888888877662223345566667777777777777777777777777 PP

                            AAA_13 438 elkkleeeikeLekqlrdekpaaeeinkeLka 469
                                       ++ +l e +k+ e++++  + +ae + +eL++
  gi|320100452|ref|YP_004176044.1| 167 KISELTEAVKQREEEIQGLRSGAEALKRELEE 198
                                       77777777777777777777777777777764 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   4.2   6.1e-06   0.00072     400     483 ..     142     225 ..      71     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.1e-06
                          Macoilin 400 rLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklhelvsakqkdkqtlqqlekrLk 476
                                         e+++k L  eL+++r+  +el+ kis lt++ ++  +e+q l+   + l+  l+e v++    + ++ ++ k L+
  gi|320100452|ref|YP_004176044.1| 142 GCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       5699***********************************************************************98 PP

                          Macoilin 477 eekeara 483
                                       + ++  +
  gi|320100452|ref|YP_004176044.1| 219 DAARLLQ 225
                                       7665444 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 !   19.7   9.7   5.7e-06   0.00067      20     109 ..     143     232 ..     136     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.7e-06
                        TPR_MLP1_2  20 aeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswee 96 
                                        e+++++l+ +lekq++++ke + k ++     ++  +e+q lr+ ++ lk e++e  +e+es +++++  ++ +e 
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLED 219
                                       58999999999999999999999999998888899999999999999999999999999999999999999999999 PP

                        TPR_MLP1_2  97 qkeelekelsele 109
                                           l++ ls l+
  gi|320100452|ref|YP_004176044.1| 220 AARLLQEALSMLQ 232
                                       9999999999886 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 !   19.7  10.3   5.8e-06   0.00068      56     116 ..     144     204 ..     140     205 .. 0.96
   2 ?    0.4   0.1       5.5   6.4e+02      12      31 ..     215     234 ..     207     237 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.8e-06
                             DHR10  56 kkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleelr 116
                                       ++++k+l+ +le+++++l+ele+k++ l+  +++ ee+++ lr  ae+ +++ ++r++el+
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELE 204
                                       6799*******************************************************97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 5.5
                             DHR10  12 aelErkarelqakidalqvv 31 
                                       + lE  ar lq+ + +lq v
  gi|320100452|ref|YP_004176044.1| 215 KTLEDAARLLQEALSMLQHV 234
                                       45677777777777777766 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.0   5.6e-05    0.0066       6      44 ..      80     117 ..      76     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.6e-05
                            HTH_40   6 lelleeglsieeIAkerglkesTIegHLaelieegeeid 44 
                                       +  ++ gl + +IA+e g +e+TI +HL    ++g+ + 
  gi|320100452|ref|YP_004176044.1|  80 YARMKAGLPVSQIAEELGRSETTIRSHLNMKTKAGK-LV 117
                                       556799**********************99999985.22 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   3.1   1.4e-05    0.0017      11      80 ..     150     219 ..     146     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-05
                              KxDL  11 ldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                       l+  l +Q++ +++l++k  eL+e  ++ +e+ + lr+  +  ++ l e  k+Les++++++s++++l++
  gi|320100452|ref|YP_004176044.1| 150 LEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLED 219
                                       566689************************************************************9985 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   4.1   8.3e-06   0.00098      94     170 ..     152     228 ..      89     235 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.3e-06
                                       HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHH CS
                              EzrA  94 ykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekql 170
                                        ++ k +++l+ele++++e+ e +k+  ee++ l++  e  + e e+  ++ +++r ++ + r+++++a+  l++ l
  gi|320100452|ref|YP_004176044.1| 152 GELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEAL 228
                                       23344445555555555555555555555555555555555555555555555555555555555555555555544 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   7.0   8.3e-06   0.00098     491     570 ..     144     227 ..      90     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.3e-06
                              HOOK 491 nrrkneLetenrlanqrileLeaqveelqkalqeqgskaed....ssllkkkleehleklkevqeelqkkkeqleel 563
                                       +++++ Le e  ++++r++eLea++ el++a ++ + + +     + +lk++lee++++l++  +++ + +++le+ 
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGlrsgAEALKRELEERVKELESCRSNVDSMRKTLEDA 220
                                       678899**********************999887777666555447899**************************98 PP

                              HOOK 564 epklssn 570
                                       +  l+++
  gi|320100452|ref|YP_004176044.1| 221 ARLLQEA 227
                                       7766655 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0033      0.39       9      58 ..     136     182 ..     131     190 .. 0.69
   2 ?    4.1   0.1      0.53        62      22      54 ..     195     227 ..     190     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0033
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                       Ir+ ++  +++V+al+ ++++ ++ l++   l++k+ ++++++++ e+++
  gi|320100452|ref|YP_004176044.1| 136 IRTPVAGCEEQVKALEGELEKQRNRLKE---LEAKISELTEAVKQREEEI 182
                                       7777777778888887776666665555...7777777777777666665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.53
                           NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLael 54 
                                        l+++v+++++   +v+ + + L++ +  L+e 
  gi|320100452|ref|YP_004176044.1| 195 ELEERVKELESCRSNVDSMRKTLEDAARLLQEA 227
                                       477888888888888888988888888887764 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.3e-05    0.0039       6      34 ..      81     108 ..      77     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.3e-05
                            HTH_29   6 lllaeGvstvsqiAkllglsrrtvyrwlk 34 
                                       + ++ G++ vsqiA+ lg s++t++ +l+
  gi|320100452|ref|YP_004176044.1|  81 ARMKAGLP-VSQIAEELGRSETTIRSHLN 108
                                       67899**9.****************9875 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   4.8   1.9e-05    0.0023     277     411 ..      93     217 ..      76     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.9e-05
                              FapA 277 ekqilnslikaggkiivngrkgkivggnikalkevkakklGselgtkteiev.gldepelkeklkeleeeleeleee 352
                                       ++++  s+ + + +++ + + gk+v ++++ lk+ ++k      +  +++ v g +     e++k+le ele+ +++
  gi|320100452|ref|YP_004176044.1|  93 AEELGRSETTIRSHLNMKTKAGKLVHETYEKLKKGELK----LVVPFIRTPVaGCE-----EQVKALEGELEKQRNR 160
                                       55566677777788888777799999999999999999....56778888887777.....8889999999999999 PP

                              FapA 353 leklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                       l++l++ki++l +  a kq e+e++     ++  k +l+e+++ele ++ +++++ ++ 
  gi|320100452|ref|YP_004176044.1| 161 LKELEAKISELTE--AVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTL 217
                                       9999999999998..45566777777777777777777777777777777777766665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0  10.1   2.6e-05    0.0031      48     132 ..     139     223 ..      94     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-05
                            APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldslea 124
                                        ++  ee++++le e e+  + Lkele++ +el +++++ eee + l    e+  re  e   el+++    ds+  
  gi|320100452|ref|YP_004176044.1| 139 PVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRK 215
                                       45566778888888888888888888888888888888888888888888888888888888888888888888887 PP

                            APG6_N 125 qyehaqnq 132
                                        +e+a + 
  gi|320100452|ref|YP_004176044.1| 216 TLEDAARL 223
                                       77777655 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   9.4   3.5e-05    0.0042     185     262 ..     157     233 ..     141     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 185 nreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklq 261
                                       +r+ ++e  ++k++el+ea+++ +e+++  ++  + l+r+++++  eles +++ +s++++l+++   l+++l++lq
  gi|320100452|ref|YP_004176044.1| 157 QRNRLKE-LEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEALSMLQ 232
                                       3333332.366777777777777777777777777777777777777777777777777777777777777777766 PP

                                       H CS
                          Filament 262 e 262
                                       +
  gi|320100452|ref|YP_004176044.1| 233 H 233
                                       5 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 !   16.4   6.5   3.1e-05    0.0037      47     121 ..     148     220 ..      91     236 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.1e-05
                             Atg14  47 kalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdlesl 121
                                       kaleg+   e++++++k + ak++el   + + +e++q l+   + lk+e+ee+ k+l+++++++  +r++le +
  gi|320100452|ref|YP_004176044.1| 148 KALEGEL--EKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDA 220
                                       1222222..444455555555555555555555555555555555555555555555555555555555544444 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.2   2.9e-05    0.0034     269     340 ..     144     216 ..      92     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.9e-05
                             IFT57 269 nsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDg.splvkikka 340
                                       ++q++ l  e+++++++l+e++ k+++l+e v+++++e + +    e++k+e+eer +++    s++ +++k+
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCrSNVDSMRKT 216
                                       4566666666667777777777777777777777777777777777777777777766553321333344444 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   6.6   3.5e-05    0.0041     683     803 ..     107     232 ..      68     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-05
                               FPP 683 neskkeenkllkeeleelkseken.....levelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlk 754
                                        ++k++  kl +e +e+lk    +     + + ++ ++e++++l   l+++ + l+el++++++l e+ ++ e++++
  gi|320100452|ref|YP_004176044.1| 107 LNMKTKAGKLVHETYEKLKKGELKlvvpfIRTPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQ 183
                                       34444555555555555554444400111456678899*************************************** PP

                               FPP 755 cmkesyesletrateleaelnelkqkieaLeveLeeekksheeleakck 803
                                             e l   ++e  +el++ +++++++ + Le+  +  +e+++  +
  gi|320100452|ref|YP_004176044.1| 184 GLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEALSMLQ 232
                                       ******************************************9987665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-05    0.0034      16      46 ..      85     115 ..      81     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-05
                            HTH_24  16 prisqreLAerlglSpstvnrrlkrLeeeGl 46 
                                       ++++ +++Ae+lg S +t++ +l+  +++G 
  gi|320100452|ref|YP_004176044.1|  85 AGLPVSQIAEELGRSETTIRSHLNMKTKAGK 115
                                       7999*********************999995 PP

>> GOLGA2L5  Putative golgin subfamily A member 2-like protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   5.3   3.7e-05    0.0043      35     118 ..     144     222 ..      98     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          GOLGA2L5  35 seqvkllkeekeksvsqvqeLeaslaeLknqaavkpaeeeaq.ppagPseeeqrlqeeleqLqkekealagqlqaqv 110
                                        eqvk l+ e ek+ ++++eLea+++eL +++  k+ eee q   +g     ++l+e++++L+  ++++ + +++ +
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAV--KQREEEIQgLRSGAEALKRELEERVKELESCRSNVDS-MRKTL 217
                                       79**************************9875..5555555524667666666666666666554444332.33333 PP

                                       XXXXXXXX CS
                          GOLGA2L5 111 rDneqLsr 118
                                        D    +r
  gi|320100452|ref|YP_004176044.1| 218 ED---AAR 222
                                       33...333 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.0    0.0011      0.13      51      86 ..     145     180 ..     100     188 .. 0.87
   2 !   16.0   4.8   9.4e-05     0.011      13      93 ..     138     219 ..     132     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0011
                           BLOC1_2  51 eklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                       e++++++ el+++ ++++++e++++eL+eav++ +e
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREE 180
                                       56666777***********************98555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.4e-05
                           BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDeys 88 
                                         +++  e++k Le   e++ ++ k+l+ ++++l++ +++ +e+ + l++  + ++ ++e++v+eLe+  s +D++ 
  gi|320100452|ref|YP_004176044.1| 138 TPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKrELEERVKELESCRSNVDSMR 214
                                       556677889999999999999********************************99747******************* PP

                           BLOC1_2  89 keLEa 93 
                                       k LE+
  gi|320100452|ref|YP_004176044.1| 215 KTLED 219
                                       *9997 PP

>> DUF3037  Protein of unknown function (DUF3037)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.0   6.7e-05    0.0079      24      92 ..     144     210 ..     138     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.7e-05
                           DUF3037  24 skkegflkvrleldeaRlralfpeldlealeeelkaleeicegekaagpiakldlaerfrwltaprstv 92 
                                       +++ + l+ +le++++Rl++l   +++ +l e++k+ ee ++g +++ ++ k++l+er+++l++ rs+v
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELE--AKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNV 210
                                       66788899999**********9..578******************9999999***************98 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.0   3.7e-05    0.0044      68     141 ..     145     218 ..     136     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-05
                            TACC_C  68 keiqkvleekeqlladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahae 141
                                       ++++ +  e e+  + l+++e ++s+l + ++++ e ++g+++  e+lk++ ee ++ ++      ++++++ e
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       56667777888888888888888888888888888888888888888888888888888777777777766554 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.2     5e-05    0.0059     130     208 ..     127     217 ..      89     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-05
                           DUF4407 130 a........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqae 198
                                                 ++ +a  e+q++al++e++++++rl++l+a+   el+ + +++++ ++G    a++ k++l+++ +e
  gi|320100452|ref|YP_004176044.1| 127 GelklvvpfIRTPVAGCEEQVKALEGELEKQRNRLKELEAKIS-ELTEAVKQREEEIQGLRSGAEALKRELEERVKE 202
                                       1555555556666677777777888888888888888877777.666666666677778888888888888888888 PP

                           DUF4407 199 laelkakld.....a 208
                                       l++ ++++d      
  gi|320100452|ref|YP_004176044.1| 203 LESCRSNVDsmrktL 217
                                       887777755322220 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       7.6     9e+02     106     145 ..      91     130 ..      88     134 .. 0.79
   2 !   16.6   5.1   4.5e-05    0.0053     105     179 ..     141     222 ..     135     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 7.6
                            DUF724 106 klleerkklekkieeeesekrkleeeidelekkilelerq 145
                                       +++ee+ + e  i+ + + k+k+ + ++e+ +k ++ e +
  gi|320100452|ref|YP_004176044.1|  91 QIAEELGRSETTIRSHLNMKTKAGKLVHETYEKLKKGELK 130
                                       7888999999999999999999999998888887776655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.5e-05
                            DUF724 105 tklleerkklekkieeeesekrkleeeidelekkilelerqlallk.......ekkeaadkeiarlkseaekleeel 174
                                       + ++e+ k+le ++e+++++ ++le++i+el +++++ e++ + l+       ++ e+  ke+ + +s++++++++l
  gi|320100452|ref|YP_004176044.1| 141 AGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRsgaealkRELEERVKELESCRSNVDSMRKTL 217
                                       5689999**********************999999999999999997776544555555556666666666666666 PP

                            DUF724 175 edveq 179
                                       ed+ +
  gi|320100452|ref|YP_004176044.1| 218 EDAAR 222
                                       66655 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2         8   9.5e+02      92     106 ..     113     127 ..      89     131 .. 0.59
   2 !   16.8  11.6   4.8e-05    0.0056      19     106 ..     143     234 ..     137     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 8
                     Tropomyosin_1  92 sdkkLkettekLret 106
                                       + k ++et ekL++ 
  gi|320100452|ref|YP_004176044.1| 113 AGKLVHETYEKLKKG 127
                                       334456666666655 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.8e-05
                     Tropomyosin_1  19 leekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekae....esekkktnnealtrkiqlLEeelee 91 
                                       +ee+vK+le e +++ + +k+L+ k+++l e v + ee+++  ++ ae    e e++ ++ e+    ++ +   le+
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEalkrELEERVKELESCRSNVDSMRKTLED 219
                                       899*************************************998877762111344555667799999********** PP

                     Tropomyosin_1  92 sdkkLkettekLret 106
                                       + + L+e++  L+++
  gi|320100452|ref|YP_004176044.1| 220 AARLLQEALSMLQHV 234
                                       *******99999875 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   6.5   9.5e-05     0.011      68     153 ..     145     230 ..     134     237 .. 0.41

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.5e-05
                               GAS  68 eeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaa...iqevqqktg 141
                                       e+v+ L+ +l   ek++++lk+l+a+++el++ +k+ ++e + l+   e++++e +e  k+ e++   ++ +++  +
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGEL---EKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCrsnVDSMRKTLE 218
                                       3333333333...2333344444444444444444444444444444444444333333333332222333333334 PP

                               GAS 142 lknllLekklka 153
                                         + lL+  l+ 
  gi|320100452|ref|YP_004176044.1| 219 DAARLLQEALSM 230
                                       444444433333 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00045     0.053      18      38 ..      89     109 ..      83     114 .. 0.91
   2 ?   -0.1   0.0       7.7     9e+02      11      26 ..     161     176 ..     159     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00045
                                       HHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  18 vcelaeelglsqstvShHLkk 38 
                                       v+++aeelg s+ t++ HL++
  gi|320100452|ref|YP_004176044.1|  89 VSQIAEELGRSETTIRSHLNM 109
                                       9******************85 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 7.7
                                       HTTSSEEHHHHHHHHT CS
                             HTH_5  11 Laegelcvcelaeelg 26 
                                       L e e++++el+e+++
  gi|320100452|ref|YP_004176044.1| 161 LKELEAKISELTEAVK 176
                                       5566899*****9987 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   5.0   0.00027     0.032     103     178 ..     105     188 ..      89     196 .. 0.65
   2 !   15.4   9.8   0.00013     0.015      65     135 ..     154     226 ..     144     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00027
                           UPF0242 103 eeldakeeelerlkeenqqLqekleaiae........dfeelkleleeqLaekqellqeyqetieeqrsvlekrqdq 171
                                        +l+ k+++ +  +e  ++L++   + +           ee+ ++le +L++++++l+e++++i+e+ + +++r+++
  gi|320100452|ref|YP_004176044.1| 105 SHLNMKTKAGKLVHETYEKLKKGELKLVVpfirtpvaGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEE 181
                                       55555544444444444444432222222344445557889999999999999999999999999999999999999 PP

                           UPF0242 172 ieqLesk 178
                                       i+ L s 
  gi|320100452|ref|YP_004176044.1| 182 IQGLRSG 188
                                       9988765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 0.00013
                           UPF0242  65 l..ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfee 135
                                       l  + + l+e eak++el e +k+ ee+++ l++  e Lk+el+++ +ele  + +  ++++ le++a+  +e
  gi|320100452|ref|YP_004176044.1| 154 LekQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQE 226
                                       2226777777788888888888888888888888888888888888888888888888888888887775554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.7   5.8e-05    0.0069      13     100 ..     141     225 ..     129     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.8e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HH CS
                        Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasssls 89 
                                       +  +eq+++l+ +le+ ++ l+e+++++ e +e vk+  + i+  r+    L++++   ++++kel+  +++  s+ 
  gi|320100452|ref|YP_004176044.1| 141 AGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKREL---EERVKELESCRSNVDSMR 214
                                       556899************************************99999999999875...578888888888877777 PP

                                       HHHHHHHHHHH CS
                        Laminin_II  90 dniseikelIa 100
                                       + ++    l +
  gi|320100452|ref|YP_004176044.1| 215 KTLEDAARLLQ 225
                                       77766555555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   0.00026     0.031      16      36 ..      87     107 ..      80     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00026
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdI 36 
                                       ++ +++AeeL++S++t+r ++
  gi|320100452|ref|YP_004176044.1|  87 LPVSQIAEELGRSETTIRSHL 107
                                       7899**************986 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 !   15.6   5.0   0.00013     0.015      70     120 ..     144     194 ..     111     201 .. 0.81
   2 ?    3.1   0.4      0.92   1.1e+02      98     118 ..     200     220 ..     187     229 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 0.00013
                            DUF641  70 eaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaek 120
                                       e++ ++le e+++qr+ lk +e+ +++l + +k++++ei+ L++  e++++
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKR 194
                                       388999************************************986555444 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.92
                            DUF641  98 eaelkakdseieeLkekLeea 118
                                        +el++ +s++++++++Le+a
  gi|320100452|ref|YP_004176044.1| 200 VKELESCRSNVDSMRKTLEDA 220
                                       234444455555555555555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  14.1   0.00014     0.016     196     280 ..     147     233 ..      88     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00014
                              Spc7 196 id..keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsr 270
                                       ++  + eLe+ r++l+el+a+i+e+ + +++++e+++ l++  e+lk + +e  +e+++ ++ ++  ++  e+  + 
  gi|320100452|ref|YP_004176044.1| 147 VKalEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARL 223
                                       22225688888888888888888888888888888888888888888888888888888888888888888888888 PP

                              Spc7 271 lkeevkalee 280
                                       l+e +++l++
  gi|320100452|ref|YP_004176044.1| 224 LQEALSMLQH 233
                                       8888888876 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.0         6   7.1e+02       7      28 ..     144     165 ..     144     167 .. 0.64
   2 ?   15.5   2.6    0.0001     0.012       7      29 ..     165     187 ..     159     188 .. 0.91
   3 ?    2.8   0.8      0.89   1.1e+02       7      14 ..     197     204 ..     193     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 6
                         PKcGMP_CC   7 DERIRELEkrlaekdeEIqELr 28 
                                       +E ++ LE  l+++    +EL 
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELE 165
                                       5677777777777766666664 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 0.0001
                         PKcGMP_CC   7 DERIRELEkrlaekdeEIqELrs 29 
                                       + +I EL +++++++eEIq Lrs
  gi|320100452|ref|YP_004176044.1| 165 EAKISELTEAVKQREEEIQGLRS 187
                                       579*******************8 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.89
                         PKcGMP_CC   7 DERIRELE 14 
                                       +ER++ELE
  gi|320100452|ref|YP_004176044.1| 197 EERVKELE 204
                                       78888887 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   7.3   0.00024     0.028     100     198 ..     106     227 ..      89     235 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00024
                           DUF4795 100 llekleeqeealkkaldtLq......................eelkekldrlelepLkeqle...erlkelqkelqe 151
                                        l++ +++ + +++ +++L+                      ++l+  l     e+ +++l+    ++ el +++++
  gi|320100452|ref|YP_004176044.1| 106 HLNMKTKAGKLVHETYEKLKkgelklvvpfirtpvagceeqvKALEGEL-----EKQRNRLKeleAKISELTEAVKQ 177
                                       4555557777777777777777777777777777766543333333333.....33333332222555566655555 PP

                           DUF4795 152 amekedk.edeaaglrkkLlerfdcI.SCdrpvemkegtlpksk.slpsr 198
                                       + e ++     a++l+++L er++ + SC  +v+ + +tl+++   l + 
  gi|320100452|ref|YP_004176044.1| 178 REEEIQGlRSGAEALKRELEERVKELeSCRSNVDSMRKTLEDAArLLQEA 227
                                       55555446667888888888888888888888887766666655455444 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 ?   14.7   4.8   0.00015     0.018     132     251 ..      90     226 ..      79     237 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00015
                      Exonuc_VII_L 132 taaAelvvpdkaeleeqleeler..rlekaikrlleekkqr.........leklasrlkspeellerkrqrldelee 197
                                       +++Ae + +++++++++l+  ++  +l +++ ++l++ + +         +  +++++k  e  le++r+rl+ele+
  gi|320100452|ref|YP_004176044.1|  90 SQIAEELGRSETTIRSHLNMKTKagKLVHETYEKLKKGELKlvvpfirtpVAGCEEQVKALEGELEKQRNRLKELEA 166
                                       56677777666666666654433223333333333222222333333333444456666667777777777777777 PP

                      Exonuc_VII_L 198 rleralkkqlkkkrerleelkerlk...ekleekkerlkklkerle....lleekkerlee 251
                                       ++++ l++++k+++e+++ l++  +   ++lee+ ++l++ +++++    +le++ + l+e
  gi|320100452|ref|YP_004176044.1| 167 KISE-LTEAVKQREEEIQGLRSGAEalkRELEERVKELESCRSNVDsmrkTLEDAARLLQE 226
                                       7777.77777777777777774443233333333333333333333222222222222222 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.5   0.00057     0.068      54     142 ..     146     232 ..     141     236 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00057
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH...HHHHHHHHHHHHHHHH CS
                           T3SSipB  54 eakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa.adalqadealqKklda 129
                                       + k++  +le++ ++++++++++ ++t++v++  + +++L     +  +l+++ +   +      +    + K+l+ 
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGL---RSGAEALKRELEERVKElESCRSNVDSMRKTLED 219
                                       6777888899999999999999999999999999999999...4444444444433333312333333446788877 PP

                                       HHHHHHHHHHHHH CS
                           T3SSipB 130 asklsekakakek 142
                                       a +l ++a ++ +
  gi|320100452|ref|YP_004176044.1| 220 AARLLQEALSMLQ 232
                                       7777777766655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   7.0   0.00015     0.018     611     706 ..     136     233 ..     104     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                           DUF3584 611 leealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiae...rkqqaee 684
                                       + + ++  e++ k++e el++ ++ l+e++++++e  +a+k+++++++ l++  e++k++le+ ++e    ++++  
  gi|320100452|ref|YP_004176044.1| 136 IRTPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKElesCRSNVDS 212
                                       55555666777788888888888888888888888888888888888888888888888888776651113444444 PP

                           DUF3584 685 qlqkldaqlkqleeqqkaalee 706
                                        +++l+ ++ +l ++  ++l++
  gi|320100452|ref|YP_004176044.1| 213 MRKTLEDAARLL-QEALSMLQH 233
                                       444444444443.444455555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.4    0.0011      0.13      66     131 ..     108     174 ..      89     195 .. 0.65
   2 ?   14.8   2.9    0.0002     0.024      33     108 ..     143     218 ..     135     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHH.HHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  66 rekqkskkdndnvikkssk.eleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqkerk 131
                                       + k k  k   ++++k++k el+  +  ++  +   e+++++L + le++++++++Le +i++++++
  gi|320100452|ref|YP_004176044.1| 108 NMKTKAGKLVHETYEKLKKgELKLVVPFIRTPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEA 174
                                       4344443333445555543356655666777777777888888888888888888888888877664 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 0.0002
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLq 108
                                        +++++ le ele+ +n+ ke e  ++e+++ +++++++ ++  +  + +++elee++ +l+   ++  s  + L 
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       5789*************************************999999999****9998888754333323333343 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 ?    0.7   0.0       2.1   2.5e+02     280     318 ..      96     134 ..      91     148 .. 0.90
   2 ?   11.0   6.6    0.0016      0.19      42     121 ..     145     229 ..     135     236 .. 0.54

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.1
                              HemX 280 LeevstwvrsyFdtddeavkaflkeldeLaeqsvsvdvP 318
                                       L + +t++rs  +++++a k + ++ ++L++ + ++ vP
  gi|320100452|ref|YP_004176044.1|  96 LGRSETTIRSHLNMKTKAGKLVHETYEKLKKGELKLVVP 134
                                       6677899***********************999999988 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0016
                              HemX  42 qqlaaleqqlaq....veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga.erkdWlLaeAd 113
                                       +q++ale +l++    +++++++ +el+e+++q +e+++ l++  e+l+++lee  ++l+   ++ ++    L +A 
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKqrnrLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNvDSMRKTLEDAA 221
                                       44444443333322225555555556666666666666666666666666666666666655555555555566666 PP

                              HemX 114 fLlklAgr 121
                                        Ll+ A+ 
  gi|320100452|ref|YP_004176044.1| 222 RLLQEALS 229
                                       66655554 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.4    0.0002     0.024      84     168 ..     139     234 ..      91     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0002
                                       XXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX....................XXXXXXXXXXXXXX CS
                              AIP3  84 slaslskelkelkssiesqkaslqevserqeeaakekasesla...........kkelkaqlkevqslrrdLavlrq 149
                                        +a +++++k l+ ++e+q+++l+e++++ +e ++  +++  +           k+el++++ke++s r ++ ++r+
  gi|320100452|ref|YP_004176044.1| 139 PVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEiqglrsgaealKRELEERVKELESCRSNVDSMRK 215
                                       444445555555555555555555444333333222222222233455555555899******************** PP

                                       XXXXXXXXXXXXXXXXXXX CS
                              AIP3 150 lysefkseikeslselrek 168
                                       + ++  + ++e ls l++ 
  gi|320100452|ref|YP_004176044.1| 216 TLEDAARLLQEALSMLQHV 234
                                       *******999999988765 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.8   0.00021     0.025      80     137 ..     144     201 ..     138     205 .. 0.92
   2 ?    9.9   2.2    0.0064      0.75      58     114 ..     171     227 ..     170     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00021
                              ADIP  80 ktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqyahelk 137
                                       ++q+++le el+ + +++++le+k+ +l++++k+  ee+q l++ ++++k  ++  +k
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVK 201
                                       79*********************************************99998877666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0064
                              ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklkne 114
                                       l+e +++ e ei+ l+s  e lk++le+  +el++  ++  +++k+l+++ + l++ 
  gi|320100452|ref|YP_004176044.1| 171 LTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEA 227
                                       78999*******************************************999988875 PP

>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.97   1.1e+02      45      61 ..      89     105 ..      88     111 .. 0.91
   2 ?    7.8   0.1     0.033       3.9      29      52 ..     152     175 ..     141     178 .. 0.87
   3 ?    0.5   0.1       6.3   7.5e+02      35      58 ..     207     230 ..     200     236 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.97
                         V-SNARE_C  45 lhnvanrlgksnsiLrs 61 
                                       ++++a++lg+s +++rs
  gi|320100452|ref|YP_004176044.1|  89 VSQIAEELGRSETTIRS 105
                                       5799***********96 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.033
                         V-SNARE_C  29 edLhsQretLkrarsklhnvanrl 52 
                                       ++L +Qr++Lk   +k++++++++
  gi|320100452|ref|YP_004176044.1| 152 GELEKQRNRLKELEAKISELTEAV 175
                                       5899**************998876 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 6.3
                         V-SNARE_C  35 retLkrarsklhnvanrlgksnsi 58 
                                       r++  + r++l ++a  l  + s 
  gi|320100452|ref|YP_004176044.1| 207 RSNVDSMRKTLEDAARLLQEALSM 230
                                       555555555555555444444444 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00062     0.073       8      33 ..      82     107 ..      76     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00062
                            HTH_28   8 llaaGhsvreaArelgisrrtvyrWi 33 
                                       +++aG +v+++A+elg s++t+++ +
  gi|320100452|ref|YP_004176044.1|  82 RMKAGLPVSQIAEELGRSETTIRSHL 107
                                       466799*****************976 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.62        74      13      53 ..     136     173 ..     136     183 .. 0.70
   2 ?    9.6   0.5    0.0075      0.88      19      58 ..     184     220 ..     182     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHH CS
                             HisKA  13 LrtPLsailgnaeaLkregklteelkeyletiesearrldh 53 
                                       +rtP+++    ++aL+ e    e+++  l+ +e  +  l++
  gi|320100452|ref|YP_004176044.1| 136 IRTPVAGCEEQVKALEGE---LEKQRNRLKELEAKISELTE 173
                                       79*************884...45666666555555555544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0075
                                       HHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  19 ailgnaeaLkregklteelkeyletiesearrldhlvedl 58 
                                       +++  aeaLkr  +l e++ke le+ +s+++ +++ +ed 
  gi|320100452|ref|YP_004176044.1| 184 GLRSGAEALKR--ELEERVKE-LESCRSNVDSMRKTLEDA 220
                                       567779*****..47777777.999999999999999986 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.2   0.00032     0.038      41     132 ..     101     196 ..      89     202 .. 0.85
   2 ?    3.4   0.8      0.43        51      91     123 ..     194     226 ..     189     234 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00032
                     PI3K_P85_iSH2  41 nkiseeiqlkrqaleaFnea.ikmFeeqiklqekfskea...qehEieklqenleqlksrlkelhsskekLeedlkq 113
                                       + i++ +++k  a +   e+ +k+ + ++kl   f++ +   +e+ ++ l+  le+ ++rlkel+++ ++L e++kq
  gi|320100452|ref|YP_004176044.1| 101 TTIRSHLNMKTKAGKLVHETyEKLKKGELKLVVPFIRTPvagCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQ 177
                                       56788888888777766665478888888888889998888889999****************************** PP

                     PI3K_P85_iSH2 114 qkeeereleReinalkpel 132
                                       + ee + l     alk el
  gi|320100452|ref|YP_004176044.1| 178 REEEIQGLRSGAEALKREL 196
                                       ******9999999999988 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.43
                     PI3K_P85_iSH2  91 eqlksrlkelhsskekLeedlkqqkeeereleR 123
                                       ++l++r+kel+s++++++   k+  +  r+l+ 
  gi|320100452|ref|YP_004176044.1| 194 RELEERVKELESCRSNVDSMRKTLEDAARLLQE 226
                                       568889999999998888766666666666654 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0011      0.14      21      46 ..      83     108 ..      54     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0011
                                       TCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  21 raegltaselaerldlskntlsyHLr 46 
                                        ++gl +s++ae+l+ s +t++ HL+
  gi|320100452|ref|YP_004176044.1|  83 MKAGLPVSQIAEELGRSETTIRSHLN 108
                                       689*********************97 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   4.8   0.00063     0.074       9      82 ..     148     220 ..     143     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00063
                   Snapin_Pallidin   9 ellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       + le +l++ +++lkel+++ +eL+e +++  e+++ l+  +e ++  +l+e +k L +++ ++ s+ ++l+ +
  gi|320100452|ref|YP_004176044.1| 148 KALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAE-ALKRELEERVKELESCRSNVDSMRKTLEDA 220
                                       6789999********************************9999.8899*******************9999865 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.4    0.0014      0.16      72     148 ..     121     203 ..     109     206 .. 0.71
   2 ?    5.3   0.9      0.11        13      96     136 ..     193     236 ..     189     238 .] 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0014
                     Fzo_mitofusin  72 fveyatekLrlivslt...sancshqvqq...elsstfarlcqqvdetekeleeeikelekeiekleevqkkak.ll 141
                                       + +  + +L+l+v +     a c++qv+    el++  +rl++  +   +el+e +k+ e+ei+ l +  + +k  l
  gi|320100452|ref|YP_004176044.1| 121 YEKLKKGELKLVVPFIrtpVAGCEEQVKAlegELEKQRNRLKE-LEAKISELTEAVKQREEEIQGLRSGAEALKrEL 196
                                       6666777888888765223688999998666689999999875.566677899999999999998887666654246 PP

                     Fzo_mitofusin 142 rnkasll 148
                                        ++ ++l
  gi|320100452|ref|YP_004176044.1| 197 EERVKEL 203
                                       6666555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.11
                     Fzo_mitofusin  96 qqelsstfarl...cqqvdetekeleeeikelekeiekleevqk 136
                                       ++el++ +++l   +++vd ++k+le+  + l++ +++l++v +
  gi|320100452|ref|YP_004176044.1| 193 KRELEERVKELescRSNVDSMRKTLEDAARLLQEALSMLQHVAN 236
                                       56666666665222357888888888888888888888877765 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 ?   12.2   0.0   0.00097      0.11      15      44 ..      87     116 ..      81     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00097
                          HTH_DeoR  15 lsveelvellgvSeaTiRRDLneLeeqgll 44 
                                       l v +++e+lg Se+TiR  Ln  +++g+l
  gi|320100452|ref|YP_004176044.1|  87 LPVSQIAEELGRSETTIRSHLNMKTKAGKL 116
                                       5689******************99999986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00044     0.052      19      41 ..      85     107 ..      80     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00044
                                       TT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4  19 eglTleEIgerlgiSrerVrqie 41 
                                        gl+ ++I+e+lg S+ ++r+++
  gi|320100452|ref|YP_004176044.1|  85 AGLPVSQIAEELGRSETTIRSHL 107
                                       6899****************975 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.6    0.0029      0.34      65     117 ..     141     193 ..     136     197 .. 0.87
   2 ?   11.7   4.3    0.0017       0.2      64     123 ..     161     221 ..     160     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0029
                              COG2  65 vglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellk 117
                                        g +e+++ +e +l++ r++++++++k+se  e+v+++ ee + l++  e lk
  gi|320100452|ref|YP_004176044.1| 141 AGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALK 193
                                       589999999*********************99999999999888888777766 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0017
                              COG2  64 Lvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellk.lllkld 123
                                       L+ l+++++e++  +++  ++++ +r+  ++ ++e+e++++e ++ +++  +++  l + +
  gi|320100452|ref|YP_004176044.1| 161 LKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRkTLEDAA 221
                                       88999***************************************99998855540344444 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.3   0.00045     0.053     168     248 ..     136     226 ..      90     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00045
                   Phlebovirus_NSM 168 iknqvl..hseieqlknelqkkRndikrgqek.....rdakklveesm...Arvkdlkeelkiltdelsqikseiqi 234
                                       i++ v+   ++++ l++el+k+Rn +k  + k     + +k++ ee +    + + lk el     el+  +s++ +
  gi|320100452|ref|YP_004176044.1| 136 IRTPVAgcEEQVKALEGELEKQRNRLKELEAKiseltEAVKQREEEIQglrSGAEALKRELEERVKELESCRSNVDS 212
                                       556665224568899*********96655544211115555555554311145555666666666999999999999 PP

                   Phlebovirus_NSM 235 lrkkikdfetvvpA 248
                                       +rk   d   +++ 
  gi|320100452|ref|YP_004176044.1| 213 MRKTLEDAARLLQE 226
                                       99988887776664 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.047       5.6      75     104 ..     146     178 ..      87     196 .. 0.58
   2 ?   11.5   0.2    0.0019      0.22      39     109 ..     146     218 ..     128     237 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.047
                      Baculo_PEP_C  75 alnalq...dtlrneLtnlnsiltnLlssvtNi 104
                                       +++al+   ++ rn+L+ l++++++L+  v   
  gi|320100452|ref|YP_004176044.1| 146 QVKALEgelEKQRNRLKELEAKISELTEAVKQR 178
                                       233333333333333333333333333333332 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0019
                      Baculo_PEP_C  39 lldaietqLnalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLtnlnsiltnLlssvtNinstLn 109
                                       +++a+e++L++  ++lk+l a    ++++l++++++   ++q      ++l+ eL+   ++l +  s+v  + +tL+
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGELEKQRNRLKELEA----KISELTEAVKQREEEIQglrsgaEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       444444444444444444333....3333333333333333333366666666666666666666666666666665 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.2   0.00073     0.086       9      60 ..     160     211 ..     149     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00073
                           DUF1515   9 qlgtllaevkelredlkrsedrsdasrakmyrkmdelvervtalegsvvklk 60 
                                       +l++l a++ el e++k+ e+  +  r+       el erv+ le++ ++++
  gi|320100452|ref|YP_004176044.1| 160 RLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVD 211
                                       68899***************************9************9988765 PP

>> Poty_PP  Potyviridae polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   0.00075     0.088     139     236 ..     123     221 ..     112     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00075
                           Poty_PP 139 kvtavnvskiAlklstdeksvgrtlliveelLveerskleqlkhlvsesvgsylvgilalnyclrary.akdrveen 214
                                       k+++++++ +   ++t  +  +  +   e +L+++r+ l +l+  +se ++  +    +++  + +    k  +ee 
  gi|320100452|ref|YP_004176044.1| 123 KLKKGELKLVVPFIRTPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEaLKRELEER 199
                                       566667777777788888888888889999**************999999996666655555444444245679*** PP

                           Poty_PP 215 ievLenvrsqleefsvvsdkde 236
                                       ++ Le  rs++  ++++ +++ 
  gi|320100452|ref|YP_004176044.1| 200 VKELESCRSNVDSMRKTLEDAA 221
                                       ***************9988764 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6    0.0013      0.16      57     144 ..     144     228 ..     119     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0013
                            ATPase  57 eepaedlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglay 133
                                       ee+ ++l  + ++    l++le++    + +a++++ee + +  ++ +e+l++el+e +ke++  r  +Ds      
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAK-ISELTEAVKQREE-EIQGLRSGAEALKRELEERVKELESCRSNVDSMRKT-L 217
                                       555666666666666667777777.4455666666655.445999**************************9988.6 PP

                            ATPase 134 eekeavaReil 144
                                       e+ + ++ e l
  gi|320100452|ref|YP_004176044.1| 218 EDAARLLQEAL 228
                                       66666655555 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   8.5   0.00067     0.079      14      77 ..     146     217 ..     141     219 .. 0.79
   2 ?    3.0   1.5       1.1   1.3e+02       5      42 ..     193     232 ..     190     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00067
                           V-SNARE  14 rlsslag..eerkaalreiekkldeaeelldqMelEvrnlps...serasykaklre...ykselkklkkel 77 
                                       +++ l+g  e+++  l+e+e+k+ e+ e ++q e E+++l s   + + ++ ++++e   ++s++++++k l
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGelEKQRNRLKELEAKISELTEAVKQREEEIQGLRSgaeALKRELEERVKElesCRSNVDSMRKTL 217
                                       56667774469999**************************55577999999999876222566666666666 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 1.1
                           V-SNARE   5 laeiksklarlsslag..eerkaalreiekkldeaeelld 42 
                                         e++++++ l s  +  ++ +++l ++ + l+ea ++l+
  gi|320100452|ref|YP_004176044.1| 193 KRELEERVKELESCRSnvDSMRKTLEDAARLLQEALSMLQ 232
                                       5566666677776555446888888888888888888886 PP

>> DnaB_bind  DnaB-helicase binding domain of primase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0      0.04       4.7      30      48 ..      56      74 ..      55      78 .. 0.89
   2 ?    2.8   0.0       1.1   1.3e+02      15      36 ..     215     236 ..     203     238 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.04
                                      HHTTSSSHHHHHHHHHHHH CS
                         DnaB_bind 30 llaripdpieRdlYirrlA 48
                                      +l  i+dp+eR+ +++ lA
  gi|320100452|ref|YP_004176044.1| 56 ILELIRDPVERSTWVDSLA 74
                                      6889***********9998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 1.1
                                       TSHHHHHHHHHHHHHHHTTSSS CS
                         DnaB_bind  15 stpegkaravrealpllaripd 36 
                                       +t e+ ar+++eal +l+ +++
  gi|320100452|ref|YP_004176044.1| 215 KTLEDAARLLQEALSMLQHVAN 236
                                       567999*********9987776 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.0      0.26        31      35      73 ..     159     197 ..     142     201 .. 0.55
   2 ?   13.7   2.5   0.00032     0.037       9      81 ..     164     233 ..     162     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.26
                              RPW8  35 krLestleritPvvkeieklnkeldrpreeieeLkklLe 73 
                                       +rL++   +i+ + + +++ ++e++  r+  e Lk++Le
  gi|320100452|ref|YP_004176044.1| 159 NRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELE 197
                                       444444444555555555555555555555555555555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00032
                              RPW8   9 lgaalgellkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLekaekLVek 81 
                                       l+a ++el +a+++ +++    +s  + L++ le+    vke+e+++ ++d++r+ +e+  +lL++a ++++ 
  gi|320100452|ref|YP_004176044.1| 164 LEAKISELTEAVKQREEEIQGLRSGAEALKRELEE---RVKELESCRSNVDSMRKTLEDAARLLQEALSMLQH 233
                                       789999************************98887...89***************************999876 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  18.2    0.0012      0.14     134     229 ..     141     233 ..      90     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                     Myosin_tail_1 134 kkleedilvledqnnklskekklleeRiaeltsnlaeeeeksksLsklknkheavisdledRlkkeektRqelekak 210
                                          ee++  le + +k +   k le +i+elt+ + + ee    ++ l++  ea+  +le+R+k  e  R +++ ++
  gi|320100452|ref|YP_004176044.1| 141 AGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEE---IQGLRSGAEALKRELEERVKELESCRSNVDSMR 214
                                       55788888888888888888899************999986...67889**************************** PP

                     Myosin_tail_1 211 Rklegessdlqeqiadlqa 229
                                       + le  +  lqe ++ lq 
  gi|320100452|ref|YP_004176044.1| 215 KTLEDAARLLQEALSMLQH 233
                                       *******99**99998886 PP

>> T3SS_needle_E  Type III secretion system, cytoplasmic E component of needle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   2.4       4.7   5.5e+02      11      32 ..     143     163 ..     139     194 .. 0.76
   2 ?   13.1   0.7   0.00066     0.077       4      43 ..     196     237 ..     195     238 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 4.7
                                       CCTHHHHHHHHHHHHHHHHHHH CS
                     T3SS_needle_E  11 apgeqakelqdrLeaArarLkq 32 
                                       ++ eq+k+l  +Le+ r+rLk+
  gi|320100452|ref|YP_004176044.1| 143 CE-EQVKALEGELEKQRNRLKE 163
                                       56.7888888888888888875 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00066
                                       HHHH...HCCCCTHHHHHHHHHHHHHHHHHHHHHCCTSSHHHH CS
                     T3SS_needle_E   4 LEdr...LrhapgeqakelqdrLeaArarLkqalsspqspeeY 43 
                                       LE+r   L  ++ + +++++++Le+A++ L++als +q ++++
  gi|320100452|ref|YP_004176044.1| 196 LEERvkeLESCR-SNVDSMRKTLEDAARLLQEALSMLQHVANH 237
                                       666511155566.9************************99986 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 ?   11.1   0.0    0.0017       0.2      14      45 ..      73     104 ..      72     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0017
                      HTH_Tnp_ISL3  14 lrleayilelllesrsvkavArqlgvSwtTVw 45 
                                       l+ +a ++++++ + +v+++A++lg S+tT++
  gi|320100452|ref|YP_004176044.1|  73 LAVAAGAYARMKAGLPVSQIAEELGRSETTIR 104
                                       56778899999*******************98 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.074       8.8      81     121 ..     132     172 ..      88     174 .. 0.79
   2 ?    9.9   3.7     0.006       0.7      65     112 ..     158     205 ..     143     236 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.074
                           DUF1664  81 iskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +   i+  v+  +e++++++ ++e+ ++  ++le+k++++ 
  gi|320100452|ref|YP_004176044.1| 132 VVPFIRTPVAGCEEQVKALEGELEKQRNRLKELEAKISELT 172
                                       55567888999999999999999999999999999999985 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.006
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                        +r++++++k+ e +e+ k+ +ee++ +r++ +++++++e+  +  e+
  gi|320100452|ref|YP_004176044.1| 158 RNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELES 205
                                       345566666666666666666666666666666666555443333333 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   9.2    0.0013      0.16      56     154 ..     136     235 ..      91     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0013
                      HAUS-augmin3  56 ie.psdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklke 131
                                       i  p  + +e+v++le +le++++ l++Le++++eL +  +  +++ + L   a +l++el+++ +e ++ + ++  
  gi|320100452|ref|YP_004176044.1| 136 IRtPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDS 212
                                       44555666689999999999999999999999999999999999999999999999999999999999999999999 PP

                      HAUS-augmin3 132 aqeelraenaetnavLqqlteea 154
                                         + l+ +   ++++L++l+  a
  gi|320100452|ref|YP_004176044.1| 213 MRKTLEDAARLLQEALSMLQHVA 235
                                       99999999988888888888755 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.2    0.0017       0.2      90     148 ..     155     213 ..     144     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0017
                            CASP_C  90 tsQRDRFrk...rnaeLEeelrkqeetvsslraeiaslqkDNlkLYEkvRYlqsYnrgskas 148
                                        +QR R ++   +++eL e +++ ee+++ lr+ +++l++   +L E+v+ l+s +++  + 
  gi|320100452|ref|YP_004176044.1| 155 EKQRNRLKEleaKISELTEAVKQREEEIQGLRSGAEALKR---ELEERVKELESCRSNVDSM 213
                                       5899999954449999999999999999999999999998...6999999999999887654 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.4    0.0012      0.14       7      89 ..     145     233 ..     141     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0012
                                       TSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......TS..S-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING   7 dsvenLPlelqrnltelreiDakvqellkeidskiekfl......kngslqknekeeelsriqeelkeaqelldeKi 77 
                                       ++v++L  el+++  +l+e++ak++el++ ++++ e+        ++ + + +e+ +el++ +++++ + + l++  
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQglrsgaEALKRELEERVKELESCRSNVDSMRKTLEDAA 221
                                       6899************************9995555554455587744455556666666677777777777777777 PP

                                       HHHHHHHHHHHH CS
                               ING  78 qlaqqaldlvdk 89 
                                        l q+al ++++
  gi|320100452|ref|YP_004176044.1| 222 RLLQEALSMLQH 233
                                       777777777665 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.7     0.008      0.94      47     146 ..      93     193 ..      89     205 .. 0.73
   2 ?    3.4   0.1      0.41        48      10      33 ..     206     229 ..     199     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.008
                         PspA_IM30  47 aqviarqkqlerkleeqkeqakklekkAkaALtkgeeeLArealae.ikslekqaealetqlaqqrsaveqlrkqle 122
                                       a+ ++r   + r   + k +a kl  +  + L+kge +L   +++   +  e+q++ale +l++qr   ++l+++++
  gi|320100452|ref|YP_004176044.1|  93 AEELGRSETTIRSHLNMKTKAGKLVHETYEKLKKGELKLVVPFIRTpVAGCEEQVKALEGELEKQRNRLKELEAKIS 169
                                       55555555566666666777777777788888888888888887652567888888888888888888888888888 PP

                         PspA_IM30 123 aletkieelkakkellkarekaak 146
                                       +l   +++ +++++ l + ++a k
  gi|320100452|ref|YP_004176044.1| 170 ELTEAVKQREEEIQGLRSGAEALK 193
                                       888888888888888777666554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.41
                         PspA_IM30  10 lraniselldkaeDPekileqair 33 
                                        r+n+ ++  ++eD+ ++l++a+ 
  gi|320100452|ref|YP_004176044.1| 206 CRSNVDSMRKTLEDAARLLQEALS 229
                                       689999999999999999999875 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.4    0.0029      0.34      31      73 ..     144     183 ..     119     191 .. 0.62
   2 ?    4.8   1.3      0.19        22      31      71 ..     172     209 ..     170     235 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0029
                        Phage_GP20  31 keqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeye 73 
                                       +eq+k+ +++   L+k+ +  +eL+++i el++++k+ ++e +
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGE---LEKQRNRLKELEAKISELTEAVKQREEEIQ 183
                                       3444444443...344445566666666666666666666654 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.19
                        Phage_GP20  31 keqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakae 71 
                                       +e +k+r++++++L     ++e+L++++ee  ++++   ++
  gi|320100452|ref|YP_004176044.1| 172 TEAVKQREEEIQGLRS---GAEALKRELEERVKELESCRSN 209
                                       5566666666666633...3555555555544444443333 PP

>> L31  Mitochondrial ribosomal protein L31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7    0.0026       0.3      22      65 ..     156     199 ..     151     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0026
                               L31  22 rqrkRlkavDevieavkeslkkkgvslkalekakaelpkesems 65 
                                       +qr+Rlk++++ i++++e++k+++ +++ l++  + l +e e  
  gi|320100452|ref|YP_004176044.1| 156 KQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEER 199
                                       89*********************999999988777777666544 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   9.4   0.00035     0.041      11      94 ..     145     227 ..     143     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00035
                              YkyA  11 eeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefeki 87 
                                       e++++lE e+e+q + L+ele+k  el e + ++  +e + + + ++ +   +eeR ++le+ + ++++ ++ +e++
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAV-KQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDA 220
                                       67888999*******************9999.568888999********************************9999 PP

                              YkyA  88 keeieei 94 
                                          ++e 
  gi|320100452|ref|YP_004176044.1| 221 ARLLQEA 227
                                       9888775 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.5      0.11        13       5      42 ..     147     184 ..     143     193 .. 0.71
   2 ?    8.2   1.0     0.024       2.9      13      54 ..     187     228 ..     175     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.11
                           DUF5082   5 isklqaqiaelrseiaaleekIerLkeaktklsdekes 42 
                                        ++l+ + ++ r++++ le kI++L ea ++ ++e + 
  gi|320100452|ref|YP_004176044.1| 147 VKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQG 184
                                       55677788888889999999999998887766666554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.024
                           DUF5082  13 aelrseiaaleekIerLkeaktklsdekeslkqkkkklekpl 54 
                                       + +++  + lee +++L++ ++ +++  ++l+++ + l++ l
  gi|320100452|ref|YP_004176044.1| 187 SGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEAL 228
                                       556677899*************************99999865 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   5.3    0.0011      0.13      87     160 ..     149     222 ..     137     236 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0011
                            DUF745  87 sseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkeark 160
                                       + e  ++  ++  k+ +++++ l++++k+ +e+++ +++ a+  ++el+e+ + le+ ++ v++++k l++a +
  gi|320100452|ref|YP_004176044.1| 149 ALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAAR 222
                                       44444555555556666666666666666666666666666666666666666666666666666666666544 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 ?    9.5   4.6    0.0017       0.2      59     135 ..     126     212 ..      91     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                        V_ATPase_I  59 a.........eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee.eeeeee 125
                                       +          +++ a  e++++ le elek  ++lkel+++ ++l++ +++ +e+ + l++ +e l++e ee+ +e
  gi|320100452|ref|YP_004176044.1| 126 KgelklvvpfIRTPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRElEERVKE 202
                                       14444445557778888889999999999999999999999999999999999999999999999998774444443 PP

                        V_ATPase_I 126 eeseeeeeek 135
                                        es +++ ++
  gi|320100452|ref|YP_004176044.1| 203 LESCRSNVDS 212
                                       3332222222 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  12.0    0.0021      0.25     181     298 ..     108     227 ..     104     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0021
                            HAP1_N 181 kLreeasqLktetd.tlEekEqqLvldcveq.lseanqqiaelseelarkleelerqqeeissLlaqivdlqqklke 255
                                       +++++a +L +et  +l + E +Lv  +++  ++  ++q++ l+ el+++++ l++   +is+L+  + + ++ ++ 
  gi|320100452|ref|YP_004176044.1| 108 NMKTKAGKLVHETYeKLKKGELKLVVPFIRTpVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQG 184
                                       689*********96257888*****99886538999****************************************9 PP

                            HAP1_N 256 lgveneelkqhLaaskeaqrqLtaELqdlqekyaevegmLhea 298
                                       l +  e lk +L+      ++ ++ +  +++  ++   +L+ea
  gi|320100452|ref|YP_004176044.1| 185 LRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEA 227
                                       9999999999998765555577777777777777777777776 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 ?   10.5   5.9    0.0049      0.57      84     140 ..     143     199 ..     135     202 .. 0.81
   2 ?    9.3   5.3     0.011       1.4      82     140 ..     169     227 ..     165     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0049
                             HrpB7  84 legrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaera 140
                                        e++v+a+e el++ r++l++ e+++++  +++   + +i+  r  +e+l+r++e++
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEER 199
                                       578888888888888888888888888888888888888888888888888888765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.011
                             HrpB7  82 dvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaera 140
                                       ++l++ v++ e+e++ +r   +a +++++++ +++ + ++++d +r+++e ++r +++a
  gi|320100452|ref|YP_004176044.1| 169 SELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEA 227
                                       68999999999999999999999999999999999999999999999999999988876 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.7    0.0058      0.68       8      38 ..     146     176 ..     140     185 .. 0.57
   2 ?    7.5   1.2     0.047       5.5       6      39 ..     179     212 ..     175     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0058
                         FlaC_arch   8 klsklsteletvkkeneelsksveelkenVk 38 
                                       +++ l+ ele  ++ ++el+ ++ el e Vk
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGELEKQRNRLKELEAKISELTEAVK 176
                                       5555555555555555555555555555554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.047
                         FlaC_arch   6 EnklsklsteletvkkeneelsksveelkenVkd 39 
                                       E++++ l +  e +k+e+ee  k++e    nV  
  gi|320100452|ref|YP_004176044.1| 179 EEEIQGLRSGAEALKRELEERVKELESCRSNVDS 212
                                       7788888888888888888888888887777744 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 ?   12.1  10.4    0.0015      0.18      56     115 .]     144     203 ..     138     203 .. 0.95
   2 ?    7.7   6.0     0.033       3.8      16      73 ..     170     227 ..     169     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0015
                       TMF_TATA_bd  56 neelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaDlKemykeqveql 115
                                        e++k+l++ele+++++l+el+ + ++l e  ++++Ee++ Lr   + lK  ++e v++l
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKEL 203
                                       699*************************************************99999986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.033
                       TMF_TATA_bd  16 rlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekel 73 
                                       +l  +++++E E++ l++  e l++e +e  +e+ +  +++++++++ ++ + l +e 
  gi|320100452|ref|YP_004176044.1| 170 ELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEA 227
                                       688999********************99999999999999999998888777766553 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.8    0.0086         1     129     164 ..     143     178 ..     129     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0086
                             Spc29 129 qkleIkeLkreleqqrtvnseLqekvaeleeevkrl 164
                                        ++++k+L+ ele+qr   +eL  k+ el e vk+ 
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQR 178
                                       578999999999999999999999999999999542 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.0     0.042         5      89     118 ..     143     172 ..     135     174 .. 0.84
   2 ?    7.4   1.1     0.033       3.9      82     119 ..     164     201 ..     164     202 .. 0.92
   3 ?    7.5   0.4     0.031       3.6      13      35 ..     194     218 ..     187     237 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  89 lekqlekleeeleklkdqittleanlaqly 118
                                        e+q++ le elek ++++++lea++++l+
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELT 172
                                       689999999999999999999999999876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                       l+ k++el++++++ eee++ l++ ++ l ++l+++++
  gi|320100452|ref|YP_004176044.1| 164 LEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVK 201
                                       5679****************************999876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHHHHHHHHHTT... CS
                         Prefoldin  13 aqlkeaieelektletlktlkk..e 35 
                                       ++l+e+ +ele++++++++++k  e
  gi|320100452|ref|YP_004176044.1| 194 RELEERVKELESCRSNVDSMRKtlE 218
                                       4455555555555555555555321 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.7      0.15        17      25      89 ..      93     168 ..      88     175 .. 0.69
   2 ?   11.4   5.2    0.0011      0.13       8      91 ..     144     226 ..     137     236 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.15
                             TMPIT  25 leelsklqskcskeikkqkkrlkelksslkklkksvk...........eeeeeeveelkeelkerkkvlkevesll 89 
                                        eel +++++++++++ ++k  k ++++ +klkk              +  ee+v+ l+ el+++++ lke+e+ +
  gi|320100452|ref|YP_004176044.1|  93 AEELGRSETTIRSHLNMKTKAGKLVHETYEKLKKGELklvvpfirtpvAGCEEQVKALEGELEKQRNRLKELEAKI 168
                                       5666677777777777777777777777777776633466677777766777888888888888888888887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0011
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84 
                                       e+++k+le + ++ +++l+el++ +s++++++k+ +++++ l+s  + lk+++ ee+ +e+e+ ++++++++k+l++
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKREL-EERVKELESCRSNVDSMRKTLED 219
                                       56666666666666666666666666666666666666666666666666664.35555555555555555555555 PP

                             TMPIT  85 vesllpk 91 
                                        + ll +
  gi|320100452|ref|YP_004176044.1| 220 AARLLQE 226
                                       5555443 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.7   0.00069     0.082     112     154 ..     145     187 ..     143     189 .. 0.94
   2 ?    5.4   1.3      0.14        16      54     105 ..     181     231 ..     180     238 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00069
                              Wtap 112 grvakLeselalqkkfveelkkaleeleelleeleeevevlqs 154
                                       ++v+ Le+el++q++ ++el+ + +el e +++ eee+ +l s
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRS 187
                                       67999*********************************99875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.14
                              Wtap  54 vfsrlrkeleeaenkleeaqeeLqalkftpdsqtGkrLmakcrvLeqENeEL 105
                                       +++ lr+  e+ +++lee  +eL++++ + ds + k L    r+L++    L
  gi|320100452|ref|YP_004176044.1| 181 EIQGLRSGAEALKRELEERVKELESCRSNVDS-MRKTLEDAARLLQEALSML 231
                                       68888999999999999999999999999998.6677777777777765555 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  10.9     0.004      0.47      89     175 ..     143     224 ..     107     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.004
                           DUF4201  89 leselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLr 165
                                        e+++++l+ el+++ +rl++l+++++++ +  ++ +++ + l++       +aL ++ +++++++e+ r+ v+++r
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGA-----EALKRELEERVKELESCRSNVDSMR 214
                                       56777778888888888888888888888877777777777776543.....4577778888888888888888888 PP

                           DUF4201 166 rkvkilemrl 175
                                       ++++++++ l
  gi|320100452|ref|YP_004176044.1| 215 KTLEDAARLL 224
                                       8888877655 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   7.5     0.089        11      78     140 ..     136     198 ..     127     199 .. 0.86
   2 ?   12.0   6.1    0.0013      0.16      69     125 ..     176     232 ..     171     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.089
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  78 LrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrqqerkEe 140
                                        r  +a  e+qv+ ++ +le+ r++l+++++++ e   av+  +e+ + +r+ a+++++ +Ee
  gi|320100452|ref|YP_004176044.1| 136 IRTPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEE 198
                                       677788999999999999999999999999999998888888888999999999999999998 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  69 ekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelar 125
                                        +  ++++ Lr   + l+ ++ee  ++le +r ++++ rk l+ a r +++     +
  gi|320100452|ref|YP_004176044.1| 176 KQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEALSMLQ 232
                                       344599*****************************************9888655555 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.9       1.3   1.6e+02      10      39 ..     148     177 ..     145     182 .. 0.58
   2 ?    3.0   0.9      0.73        86       2      32 ..     154     184 ..     153     193 .. 0.85
   3 ?    8.4   0.2     0.016       1.8      15      46 ..     195     226 ..     179     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 1.3
                         DASH_Duo1  10 rkinevienviesLkkaksniervketves 39 
                                       + +   +e+ ++ Lk+ + +i++++e+v++
  gi|320100452|ref|YP_004176044.1| 148 KALEGELEKQRNRLKELEAKISELTEAVKQ 177
                                       555555666666666666666666666654 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.73
                         DASH_Duo1   2 LekEleqLrkinevienviesLkkaksnier 32 
                                       Lek+ + L+++ + i+ ++e+ k+ +++i+ 
  gi|320100452|ref|YP_004176044.1| 154 LEKQRNRLKELEAKISELTEAVKQREEEIQG 184
                                       8999999999999999999999999888875 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.016
                         DASH_Duo1  15 vienviesLkkaksniervketvestntLLdk 46 
                                        +e  +++L++++sn++++ +t+e++ +LL++
  gi|320100452|ref|YP_004176044.1| 195 ELEERVKELESCRSNVDSMRKTLEDAARLLQE 226
                                       56778899999999999999999999999986 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.7    0.0073      0.86       1      48 [.     170     217 ..     128     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0073
                     USP8_interact   1 eLrelvqkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrstn 48 
                                       eL e v++++++i+ l++ ++  k++l+e+ +ele  ++ + ++r+t 
  gi|320100452|ref|YP_004176044.1| 170 ELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTL 217
                                       567777777777777777777777777777777777777777777664 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.4    0.0075      0.89      34      87 ..     146     197 ..     141     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0075
                           DUF2730  34 dleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevr 87 
                                       +++ l+ ++e++++rl+ele+k+++L  a  +++ + ++++lr   +al++e++
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGELEKQRNRLKELEAKISELTEA--VKQREEEIQGLRSGAEALKRELE 197
                                       67788889999999999999999999654..56667777777777777776665 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  10.8    0.0023      0.27      61     172 ..     145     221 ..     135     234 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0023
                         Golgin_A5  61 eelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatl 137
                                       e++++l++++e+ r+ l++lea+     ++l e +++ ee+++  r+  e+++ ele+  +el++ ++++   ++tl
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKI----SELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTL 217
                                       344444444444444444444443....3334444444444444444444444444444444444444444444444 PP

                         Golgin_A5 138 qsrikdrekeieklrnqlttkslsssseselesRl 172
                                       +                                  
  gi|320100452|ref|YP_004176044.1| 218 EDA-------------------------------A 221
                                       433...............................3 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 ?    8.8   2.5     0.016       1.8      25      85 ..     158     218 ..      72     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.016
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       ++ l+e++a i el++ v++  +e+++l + +++l  +++e+++++++  ++v  + ++++
  gi|320100452|ref|YP_004176044.1| 158 RNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       6778889999999999999999999999999999999999999998888888877776655 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 ?    1.9   0.3       1.3   1.6e+02      39      62 ..     141     164 ..     136     174 .. 0.68
   2 ?   10.5   2.5    0.0029      0.35      12      62 ..     162     213 ..     161     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 1.3
                              Med4  39 eslDekikeivksLkeyekeLkav 62 
                                       +  +e++k ++++L + ++ Lk++
  gi|320100452|ref|YP_004176044.1| 141 AGCEEQVKALEGELEKQRNRLKEL 164
                                       556788888888888888777765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0029
                              Med4  12 delskslkelee.hqknearilqLraeveslDekikeivksLkeyekeLkav 62 
                                       +el+++++el e  +++e++i+ Lr  +e+l +++ e vk+L ++++ + ++
  gi|320100452|ref|YP_004176044.1| 162 KELEAKISELTEaVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSM 213
                                       688999999866268999****************************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 ?    8.8   6.5    0.0071      0.84      72     127 ..     150     205 ..     104     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0071
                       DLP_helical  72 lerqlpeaeerleelekevekleesakriekelaelkkeieearielreelkayfs 127
                                       le +l++ ++rl+ele+++ +l e++k+ e+e++ l++  e  ++el+e++k+++s
  gi|320100452|ref|YP_004176044.1| 150 LEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELES 205
                                       66788888999999999999999999999999999999999999999999999875 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  11.6     0.002      0.24      18     107 ..     146     221 ..     125     237 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.002
                              Fez1  18 QLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekveklee 94 
                                       Q k    e+ ++ + + +l a++ el+++++++eeei+ l++ +e  ++ele+  +el+  +s+++ +r+       
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRK------- 215
                                       4444444444444444444444444444444444444444444444444444444444444444444443....... PP

                              Fez1  95 elkelreelsels 107
                                              +l++++
  gi|320100452|ref|YP_004176044.1| 216 -------TLEDAA 221
                                       .......333322 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 ?    8.4   0.8     0.018       2.1      25      49 ..     146     170 ..     134     178 .. 0.87
   2 ?    5.4   0.4      0.16        19      29      48 ..     199     218 ..     188     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.018
                     Bcr-Abl_Oligo  25 svedieqeLerCkaslrrLekelne 49 
                                        v+++e eLe+ ++ l++Le +++e
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGELEKQRNRLKELEAKISE 170
                                       6899999999999999999998876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.16
                     Bcr-Abl_Oligo  29 ieqeLerCkaslrrLekeln 48 
                                         +eLe C+ ++  ++k l+
  gi|320100452|ref|YP_004176044.1| 199 RVKELESCRSNVDSMRKTLE 218
                                       558**********9999886 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 ?   10.3   0.5    0.0038      0.45      85     124 ..     143     185 ..     128     192 .. 0.82
   2 ?    2.9   0.7      0.74        87      55     107 ..     180     228 ..     169     236 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0038
                          Lectin_N  85 lsekvtsleaklekkq...qdlkadhselllhvkqlvkdLrtL 124
                                       ++e+v+ le +lek++   ++l+a  sel+  vkq  ++++ L
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRnrlKELEAKISELTEAVKQREEEIQGL 185
                                       6899**********993334566889999*****999988876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.74
                          Lectin_N  55 reLetLketfsnfssstlaeiqalssqggslsekvtsleaklekkqqdlkadh 107
                                       +e++ L+   + +  + +  +++l+s    +  +v s++ +le   + l++  
  gi|320100452|ref|YP_004176044.1| 180 EEIQGLRSGAEALKRELEERVKELES----CRSNVDSMRKTLEDAARLLQEAL 228
                                       34444444444444444444444444....44445555555555554444444 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  16.0     0.003      0.36     119     197 ..     144     222 ..     140     234 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.003
                       Tropomyosin 119 arklvvvesdLeraeeraeaaeskiveLeeeLkvvgnnlksLevseekasere.deyeeeirtLeekLkeaeeRaee 194
                                       +++++ +e++Le+ ++r ++ e+ki+eL e +k   ++++ L  s ++a +re +e  +e+++  ++   + +  e+
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLR-SGAEALKRElEERVKELESCRSNVDSMRKTLED 219
                                       4456666666666666666666666666666666666666666.333444444133333344444444444444444 PP

                       Tropomyosin 195 AEr 197
                                       A r
  gi|320100452|ref|YP_004176044.1| 220 AAR 222
                                       444 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 ?    9.4   5.6    0.0036      0.43     174     239 ..     155     220 ..     115     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0036
                        Fmp27_WPPW 174 elleeRleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlkes 239
                                       e  ++Rl+ele++i++l+e++++ e++ +      e+lk+e   le+ +kel++ ++ ++++ + l+  
  gi|320100452|ref|YP_004176044.1| 155 EKQRNRLKELEAKISELTEAVKQREEEIQGLrsgAEALKRE---LEERVKELESCRSNVDSMRKTLEDA 220
                                       556899***************99999988874444444444...4444445555555555554444433 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   7.6    0.0015      0.18      43     134 ..     150     237 ..     141     238 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
                              FlgN  43 lleekqellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqelkelleelkelnelNgrlieqsle 119
                                       l  e +++ ++l++le k+++l+++++++  e++++ l +   +e+lk   +e  + le ++   ++ ++++e++ +
  gi|320100452|ref|YP_004176044.1| 150 LEGELEKQRNRLKELEAKISELTEAVKQR--EEEIQGLRS--GAEALKRELEERVKELESCRSNVDSMRKTLEDAAR 222
                                       45556677788899999999999999999..788888877..88888888888888889999999999999999999 PP

                                       HHHHHHHHCCHXXXX CS
                              FlgN 120 fnqrllnllqgaank 134
                                        +q++l++lq+ an+
  gi|320100452|ref|YP_004176044.1| 223 LLQEALSMLQHVANH 237
                                       999999999998876 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   6.6       0.2        24      44      79 ..     144     179 ..      91     183 .. 0.48
   2 ?   11.0  11.2    0.0036      0.42       3      72 ..     147     221 ..     144     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.2
                       Uso1_p115_C  44 esqakeleaenkklekeleklraelkeekekekekq 79 
                                       e+q k le e +k +++l++l+a+++e  e  k+ +
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQRE 179
                                       333344444444444444444444444444333223 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0036
                       Uso1_p115_C   3 aseleseaaslkdeneklkaelqslskalesleqk..eakkaaesqakeleaenkklek...eleklraelkeek 72 
                                        ++le e +++++  ++l+a++++l++a+++ e++       ae+ ++ele+++k+le+   +++ +r++l++++
  gi|320100452|ref|YP_004176044.1| 147 VKALEGELEKQRNRLKELEAKISELTEAVKQREEEiqGLRSGAEALKRELEERVKELEScrsNVDSMRKTLEDAA 221
                                       5789999****************************8666667788888888888888887777777777777665 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   8.1     0.001      0.12       3      87 ..     143     222 ..     142     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.001
                              FliJ   3 aareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekar 79 
                                       +++++++ + el++++++l ele  ++e+ +  +++      +e++ +++  +al++++++  +el+  + +v+  r
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQRE-----EEIQGLRSGAEALKRELEERVKELESCRSNVDSMR 214
                                       5778888999999999999999999999999999999.....99999999999999999999999999999999999 PP

                              FliJ  80 eewqearq 87 
                                       + +  a +
  gi|320100452|ref|YP_004176044.1| 215 KTLEDAAR 222
                                       98877655 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       8.2   9.7e+02      33      68 ..      90     125 ..      85     149 .. 0.70
   2 ?    9.4   5.2    0.0075      0.88      14      77 ..     150     213 ..     125     237 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 8.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                              SKA1  33 saleellnklkkelqeeeeaikklkkeieaslkqqe 68 
                                       s++ e l + ++++++  +++ k+ k++ +++++ +
  gi|320100452|ref|YP_004176044.1|  90 SQIAEELGRSETTIRSHLNMKTKAGKLVHETYEKLK 125
                                       566666666777777777777777777777765443 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0075
                                       ..........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXX CS
                              SKA1  14 inqdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenl 77 
                                       ++ + + +++ l+++ea++s+l+e +++ ++e+q  ++  + lk e+e+ +k+ e+     + +
  gi|320100452|ref|YP_004176044.1| 150 LEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSM 213
                                       3444555567778888888888888888888888888888888877777775544433333333 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.3     0.011       1.3     114     155 ..     143     184 ..     138     204 .. 0.77
   2 ?    3.8   1.4      0.24        28     108     156 ..     179     227 ..     176     237 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.011
                        FmiP_Thoc5 114 leekkkkleqeieekkkfLssLppkLkslkkatkplqealgl 155
                                       +ee++k+le e e+++++L++L+ k+++l +a+k+ +e+++ 
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQG 184
                                       68999******************************9999843 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.24
                        FmiP_Thoc5 108 aeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglp 156
                                       +e+++ l +  ++l+ e ee+ k+L+s  ++++s+ k+++   + l+  
  gi|320100452|ref|YP_004176044.1| 179 EEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEA 227
                                       6777788888888899999999999999998887776666555544433 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   9.0    0.0025       0.3      41     104 ..     145     204 ..     139     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  41 kkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLe 104
                                       ++ kale el+ q++r+k+l++  ++l+++     ++ ee +++l++  e+Lk+ ++er ++Le
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAV----KQREEEIQGLRSGAEALKRELEERVKELE 204
                                       7889999999999999999999999998884....78888888999999999999999999997 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.3    0.0077      0.91      34      99 .]     132     214 ..      71     214 .. 0.71
   2 ?    5.9   1.1      0.16        19       8      63 ..     180     234 ..     176     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0077
                      Syntaxin-6_N  34 s..........tseeldetrteL...rkalrsiewdledLeetvriveknp....skfkidekelsrrrafveevre 93 
                                                   +e+++ ++ eL   r+ l+++e ++++L e+v+  e++     s  +  ++el++r + +e++r+
  gi|320100452|ref|YP_004176044.1| 132 VvpfirtpvagCEEQVKALEGELekqRNRLKELEAKISELTEAVKQREEEIqglrSGAEALKRELEERVKELESCRS 208
                                       155555555554555555555552226789999***********877774422215577778999999999999999 PP

                      Syntaxin-6_N  94 evkemk 99 
                                       +v++m+
  gi|320100452|ref|YP_004176044.1| 209 NVDSMR 214
                                       999995 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.16
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwe.rlledtssstseeldetrteLrkalrsiewdledLeet 63 
                                       ee+q   + ae+l r+ e r++e++  s ++++d+ r+ L+ a r +++ l+ L+++
  gi|320100452|ref|YP_004176044.1| 180 EEIQGLRSGAEALKRELEeRVKELE--SCRSNVDSMRKTLEDAARLLQEALSMLQHV 234
                                       5566666666777777752333332..458899999999999999999999988876 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1      0.15        18      79      99 .]     144     164 ..     137     164 .. 0.93
   2 ?    7.7   1.4     0.063       7.4      66      98 ..     173     205 ..     165     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.15
                           DUF5320  79 eeqaeaLeeeleaikkrlkel 99 
                                       eeq +aLe ele+ ++rlkel
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKEL 164
                                       89*****************97 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.063
                           DUF5320  66 taeaskeeekelLeeqaeaLeeeleaikkrlke 98 
                                        a ++ eee++ L++ aeaL++ele+  k+l++
  gi|320100452|ref|YP_004176044.1| 173 EAVKQREEEIQGLRSGAEALKRELEERVKELES 205
                                       5567899*******************9999986 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 ?    8.1   7.8     0.032       3.7      17      66 ..     147     205 ..     143     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.032
                       Cep57_MT_bd  17 lkeLedEfehlklelqelaaqynaldpsl........gkrk.RkdLaeeleelvkrlEa 66 
                                       +k+Le E+e+ + +l+el+a++ +l+ ++        g r+  ++L++elee vk+lE+
  gi|320100452|ref|YP_004176044.1| 147 VKALEGELEKQRNRLKELEAKISELTEAVkqreeeiqGLRSgAEALKRELEERVKELES 205
                                       79*************************99443333332222135788888888888886 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       6.1   7.2e+02      56      91 ..      91     126 ..      87     144 .. 0.82
   2 ?   10.4   7.6    0.0049      0.58       6      85 ..     155     234 ..     149     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 6.1
                           zf-C4H2  56 lIhaDinalEsvikeaeeekekslekakklyeeykk 91 
                                       +I + + + E++i++  + k+k+ + ++++ye++kk
  gi|320100452|ref|YP_004176044.1|  91 QIAEELGRSETTIRSHLNMKTKAGKLVHETYEKLKK 126
                                       788888888999999999999999888888888765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0049
                           zf-C4H2   6 rektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekeksleka 82 
                                        ++ ++l++l++k+++  ea+++ e+ ++  ++  e L++E ++ v eL   ++ ++++ +++++a    +++l++ 
  gi|320100452|ref|YP_004176044.1| 155 EKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEALSML 231
                                       5666788999999999999999999***************************************9998888888877 PP

                           zf-C4H2  83 kkl 85 
                                       +++
  gi|320100452|ref|YP_004176044.1| 232 QHV 234
                                       765 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 ?    9.7   2.0    0.0061      0.71       5      73 ..     158     222 ..     140     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0061
                              ACCA   5 ekpiaeleekieelkklaeesevdlseeieklekkleklkkeiyknltpwqkvqlaRhpeRpktldyie 73 
                                        ++++ele+ki+el+++ ++     +eei+ l++ +e+lk+e+ +++++++  +    + R ++ d  +
  gi|320100452|ref|YP_004176044.1| 158 RNRLKELEAKISELTEAVKQ----REEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAAR 222
                                       46789999999998777555....467899999999999999988888888877777777777766655 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 ?    8.3   9.4      0.02       2.3      51     109 ..     148     205 ..      90     236 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.02
                             Mod_r  51 sl.epeleelrselqekleelkelekefeekeqeldellqkfspdallarLqtavaeaee 109
                                       +  e ele++r++l+e   ++ el +++++ e+e + l    + +al++ L++ v+e e 
  gi|320100452|ref|YP_004176044.1| 148 KAlEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLR--SGAEALKRELEERVKELES 205
                                       332555555555555555555555555555555554443..4445555555555555443 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.1      0.16        19      83     127 ..     142     186 ..     135     199 .. 0.80
   2 ?    5.9   0.3     0.091        11      78     113 ..     200     235 ..     195     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.16
                      Sec8_exocyst  83 esqekvselKesleeakkklstkkkeLkelnarsakykevieiLd 127
                                        ++e+v++l  +le+ ++ l++ +++++el +  ++ +e i+ L 
  gi|320100452|ref|YP_004176044.1| 142 GCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLR 186
                                       578888888889999999998888888888888888888887775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.091
                      Sec8_exocyst  78 lssiqesqekvselKesleeakkklstkkkeLkeln 113
                                       ++ +++++++v  +++ le+a + l++  ++L+ ++
  gi|320100452|ref|YP_004176044.1| 200 VKELESCRSNVDSMRKTLEDAARLLQEALSMLQHVA 235
                                       7899**********************9999999876 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   8.9      0.01       1.2      21      88 ..     147     218 ..     134     237 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS......-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  21 qeqlekkfkklqaeleakekelqklqeelqkkakkle.....keekeqelqkkeqelqqkqqqkaqelqkkqq 88 
                                        + le + +k ++ l+++e+++ +l e+ ++++++ +      e+ ++el+++++el+   + +   ++k  +
  gi|320100452|ref|YP_004176044.1| 147 VKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQglrsgAEALKRELEERVKELES-CRSNVDSMRKTLE 218
                                       33444444444444444444444444444322222223444555555556666666665.3322233333332 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.5     0.018       2.2     645     710 ..     111     184 ..      86     204 .. 0.63
   2 ?    7.0   3.5      0.01       1.2     625     705 ..     153     232 ..     118     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.018
                          Prominin 645 knlkqslkneaqdlraiqqelvlp.lessvkklkksvkklde.......ensdlqesikkllaaveraenflkk 710
                                       +++++ +++++++l++ + +lv+p +++ v+  +++vk+l+        + ++l+++i++l++av++ e++++ 
  gi|320100452|ref|YP_004176044.1| 111 TKAGKLVHETYEKLKKGELKLVVPfIRTPVAGCEEQVKALEGelekqrnRLKELEAKISELTEAVKQREEEIQG 184
                                       67777777788888888777777754455666666666666655444335566888888888888888888874 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
                          Prominin 625 nletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaav 701
                                       +le+  ++l+el  ++s+  +++ ++ ++e q lr+  + l  +le+ vk+l++   ++d+  ++l+++ + l +a+
  gi|320100452|ref|YP_004176044.1| 153 ELEKQRNRLKELEAKISEL-TEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEAL 228
                                       4555555566666665555.556666666666666666666666666666666666666666666666665555555 PP

                          Prominin 702 erae 705
                                       + ++
  gi|320100452|ref|YP_004176044.1| 229 SMLQ 232
                                       5444 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 ?    3.7   0.0      0.67        79      48      73 ..      80     105 ..      67     126 .. 0.86
   2 ?    1.9   1.0       2.5     3e+02      61      89 ..     151     179 ..     145     182 .. 0.76
   3 ?    3.9   0.1      0.58        68      64      90 ..     193     219 ..     189     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.67
                             NBD94  48 YgrsLikllvqkIdeekkkaenliee 73 
                                       Y+r+   l v +I ee  ++e++i++
  gi|320100452|ref|YP_004176044.1|  80 YARMKAGLPVSQIAEELGRSETTIRS 105
                                       8888889999*************987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 2.5
                             NBD94  61 deekkkaenlieeiekyienideikkkls 89 
                                       + e +k +n ++e+e+ i ++ e+ k+ +
  gi|320100452|ref|YP_004176044.1| 151 EGELEKQRNRLKELEAKISELTEAVKQRE 179
                                       567789999999***99999977666554 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.58
                             NBD94  64 kkkaenlieeiekyienideikkklse 90 
                                       k+  e+ ++e+e++  n+d+++k l++
  gi|320100452|ref|YP_004176044.1| 193 KRELEERVKELESCRSNVDSMRKTLED 219
                                       55667889*************998765 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.4     0.041       4.8     113     195 ..      93     177 ..      82     183 .. 0.73
   2 ?    6.6   1.3     0.044       5.1      35      74 ..     195     234 ..     187     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.041
                              Vps5 113 ideylrligsvksvfeqRvklwqkwqsaeqelskkkeql....eKlekaaksqqdklqqlkkeveelerkvqeaeke 185
                                       ++e  r+   ++s ++  +k+++ +++  ++l+k   +l     ++  a    ++++++l+ e+e+ +++++e+e +
  gi|320100452|ref|YP_004176044.1|  93 AEELGRSETTIRSHLNMKTKAGKLVHETYEKLKKGELKLvvpfIRTPVA--GCEEQVKALEGELEKQRNRLKELEAK 167
                                       5556666667777778888888877777777777665541111233333..5578999******************* PP

                              Vps5 186 Feeisetikk 195
                                        +e++e +k+
  gi|320100452|ref|YP_004176044.1| 168 ISELTEAVKQ 177
                                       *****99996 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.044
                              Vps5  35 slesqLkkLykaiellvsqrkelasataelakslesLasl 74 
                                       +le++ k+L++  ++++s rk+l  a+  l ++l++L ++
  gi|320100452|ref|YP_004176044.1| 195 ELEERVKELESCRSNVDSMRKTLEDAARLLQEALSMLQHV 234
                                       79*********************************99766 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.7    0.0095       1.1      13      55 ..     141     183 ..     137     191 .. 0.82
   2 ?    3.2   0.7       1.2   1.4e+02       1      38 [.     196     233 ..     189     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0095
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  13 afqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       a  e+++++L  ++ +q+ ++++l++++ +l+e +k++ee+ +
  gi|320100452|ref|YP_004176044.1| 141 AGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQ 183
                                       5568899999999999999999999999999999999888755 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   1 leerleeLEiklafqedtieeLndvvaeqqqqidrlqr 38 
                                       leer++eLE+  +  + + ++L d+    q+ ++ lq+
  gi|320100452|ref|YP_004176044.1| 196 LEERVKELESCRSNVDSMRKTLEDAARLLQEALSMLQH 233
                                       58888888888888888888888887777777777775 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.4     0.019       2.2      23      51 ..     144     172 ..     141     183 .. 0.87
   2 ?    1.9   1.8       1.6   1.9e+02      34      46 ..     190     199 ..     173     232 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLk 51 
                                       +++++al+ el+k++++ +eLea++++L+
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELT 172
                                       79************************996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHH CS
                             DivIC  34 aklkaeneeLeae 46 
                                       ++lk e   Le++
  gi|320100452|ref|YP_004176044.1| 190 EALKRE---LEER 199
                                       333222...2222 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.0     0.047       5.5      17      69 ..     145     197 ..     141     198 .. 0.87
   2 ?    1.7   0.1       1.8   2.1e+02       3      38 ..     201     236 ..     199     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.047
                             Sec34  17 eqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       eq+++++ +Le+ +++ k+ ++k s+l ea +q  ee + l++ ae+++ +L+
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELE 197
                                       58888999999999999999999999999999999999999999999888875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.8
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvse 38 
                                       ++Les ++++d++ + +++a ++L+e  +  ++v++
  gi|320100452|ref|YP_004176044.1| 201 KELESCRSNVDSMRKTLEDAARLLQEALSMLQHVAN 236
                                       689999999999999999999999999888888865 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.6     0.031       3.7      14      83 ..     153     217 ..      88     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.031
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleagl 83 
                                       +l+++ ++l++l++++ el e++++ ++e      + l++  e+l+ e+ee v+e+e+   +v ++++ l
  gi|320100452|ref|YP_004176044.1| 153 ELEKQRNRLKELEAKISELTEAVKQREEE-----IQGLRSGAEALKRELEERVKELESCRSNVDSMRKTL 217
                                       33333344444444444444444444443.....555566666666666666666665555554444444 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.2       0.3        36      20      62 ..     140     183 ..     112     192 .. 0.77
   2 ?    4.3   3.8      0.42        50       8      36 ..     170     198 ..     164     236 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.3
                              Rx_N  20 lkgvkeeleklkdeLesiqavLedaeerqi.kdeavkeWlkelr 62 
                                       + g +e+++ l+ eLe+ +  L++ e +     eavk+  +e++
  gi|320100452|ref|YP_004176044.1| 140 VAGCEEQVKALEGELEKQRNRLKELEAKISeLTEAVKQREEEIQ 183
                                       56788999999999999999999999865535677776665555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.42
                              Rx_N   8 kLadllaeeakllkgvkeeleklkdeLes 36 
                                        L++ ++++ + ++g+++  e lk+eLe 
  gi|320100452|ref|YP_004176044.1| 170 ELTEAVKQREEEIQGLRSGAEALKRELEE 198
                                       56666666665555555555555555553 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       4.9   5.8e+02      84     116 ..     100     132 ..      88     138 .. 0.81
   2 ?    8.8  11.8    0.0085         1     190     300 ..     146     218 ..     137     237 .. 0.40

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 4.9
                            HMMR_N  84 EkeiRsLvqergeqdkrlqaleeelkkveakLl 116
                                       E  iRs ++ +++  k +++  e+lkk e kL 
  gi|320100452|ref|YP_004176044.1| 100 ETTIRSHLNMKTKAGKLVHETYEKLKKGELKLV 132
                                       677888888999999999999999999888886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0085
                            HMMR_N 190 klqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeies 266
                                       ++++++ +Le+                                       +++l   + +i +l e +k++++ei+ 
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGELEK--------------------------------------QRNRLKELEAKISELTEAVKQREEEIQG 184
                                       33333333333......................................3333333344444444444444444444 PP

                            HMMR_N 267 LkssLeekeqelskqvkdlnekckllekekeelv 300
                                       L+s  e+ + el+++vk+l++  + +++ ++ l 
  gi|320100452|ref|YP_004176044.1| 185 LRSGAEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       4444444444444444444433333333332222 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  10.5     0.017         2      30      88 ..     162     223 ..     147     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.017
                    HIP1_clath_bdg  30 keleeelerlke...eaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssq 88 
                                       kele ++ +l+e   ++e++++  ++  e+Lkrele++ +el++ +s ++s  ++ e+ +  
  gi|320100452|ref|YP_004176044.1| 162 KELEAKISELTEavkQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDAARL 223
                                       4555555555541004444555667889*********************9998887766554 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0     0.017         2      17      44 ..     162     189 ..     153     194 .. 0.86
   2 ?    1.0   0.6       4.7   5.5e+02      25      35 ..     195     205 ..     190     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.017
                             TSC22  17 evLkekIkeLeernseleeENslLkala 44 
                                        +L  kI eL+e +++ eeE + L++ a
  gi|320100452|ref|YP_004176044.1| 162 KELEAKISELTEAVKQREEEIQGLRSGA 189
                                       578899***************9999865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 4.7
                             TSC22  25 eLeernselee 35 
                                       eLeer++ele+
  gi|320100452|ref|YP_004176044.1| 195 ELEERVKELES 205
                                       55666665553 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 ?    7.4   9.9     0.044       5.2      35     100 ..     144     213 ..     115     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  35 dekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       +e+ ++l+ ele+ +++ +el ++I+++ ++     e+++ l+  +++lk el++  +el+  +++++++
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVkqreEEIQGLRSGAEALKRELEERVKELESCRSNVDSM 213
                                       6778888888888888888888888777655445568888888888888888888888888777777665 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.1     0.017         2       8      92 ..     145     231 ..     142     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.017
                      Occludin_ELL   8 eqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqek..kkrc 82 
                                       eq ++ + e +k+ ++ kel+a+++e+++ +++ e+e++ l+ g +  k+  ee ++e+++++++ + ++k  +   
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKtlEDAA 221
                                       56666666777788888999999999999999999999999999997766666668999999885555444114556 PP

                      Occludin_ELL  83 eyLkekLshi 92 
                                       + L+e Ls++
  gi|320100452|ref|YP_004176044.1| 222 RLLQEALSML 231
                                       6666666665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   6.7    0.0082      0.97       9      72 ..     153     216 ..     140     236 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0082
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXX CS
                              YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegken 72 
                                       +le+  ++l+el ++++el e++++  ee + L+   e l+++lee+ k+ ++ ++++++ ++ 
  gi|320100452|ref|YP_004176044.1| 153 ELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKT 216
                                       4444455555566666666666666666666666666666666655554444444444444443 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   9.2      0.05       5.9       5      58 ..     145     198 ..     141     219 .. 0.73
   2 ?    3.2   1.9      0.54        64      11      52 ..     179     220 ..     176     235 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.05
                                       ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHH CS
                              GrpE   5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakk 58 
                                       e+ +++e e+e+++++l+ele+++ el+e++++ ++e++ lr  +e  k e+++
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEE 198
                                       566777778888888888888888888888888888888777665544444433 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.54
                                       HHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHH CS
                              GrpE  11 edeeeeleeeleelekevkelkekllrllaefenlrkrteke 52 
                                       e+e++ l++  e+l++e++e  ++l+  + +++ +rk +e+ 
  gi|320100452|ref|YP_004176044.1| 179 EEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLEDA 220
                                       344444444444444444444444444444444444444433 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  15.6     0.033       3.9      69     149 ..     143     226 ..     118     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.033
                           DUF3552  69 lekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleel...veeqrqeLer 142
                                       +e+ +k  + el+++ +Rl++ e ++ + +e+++++ee+++  ++  ++ +++lee+ +ele+    v + r+ Le+
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCrsnVDSMRKTLED 219
                                       57777778888888888888888888888888888888888877777777777777777776542225566777887 PP

                           DUF3552 143 isgLtke 149
                                        + L +e
  gi|320100452|ref|YP_004176044.1| 220 AARLLQE 226
                                       7777665 PP

>> CSN5_C  Cop9 signalosome subunit 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.9    0.0089       1.1      14      75 ..     159     228 ..     155     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0089
                            CSN5_C  14 kqisDLaeKlekaessvsrsrsaagtlseeaseaeekkk........kkkedsqLakvvkdstkiaseaq 75 
                                       +++++L++K+++ +++v++++++++ l + a+  +++ +         +++ +++ k  +d+ ++ +ea 
  gi|320100452|ref|YP_004176044.1| 159 NRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEervkelesCRSNVDSMRKTLEDAARLLQEAL 228
                                       5789999**********99999996666555444444335677777778888899999999999988876 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.1      0.43        51      45      65 ..     130     164 ..     102     164 .. 0.72
   2 ?    4.0  16.2      0.57        68       6      53 ..     161     208 ..     144     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.43
                              ZapB  45 e..............eeneqlkeereawqerlkkL 65 
                                       +              e++++l+ e e++++rlk L
  gi|320100452|ref|YP_004176044.1| 130 KlvvpfirtpvagceEQVKALEGELEKQRNRLKEL 164
                                       3456666677777779999*************987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.57
                              ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlke 53 
                                       L++LE+ki+++ + +++  +ei+ L+   e+lk+e +e  +e+e  + 
  gi|320100452|ref|YP_004176044.1| 161 LKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRS 208
                                       677777777777777777777777777777777755555555555444 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.9     0.052       6.2      36     132 ..     145     178 ..      90     184 .. 0.66
   2 ?    4.4   0.8      0.32        37      30      75 ..     188     232 ..     185     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHH CS
                             Nup54  36 kRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeel 112
                                       + vka + e++++r+rlke++ +++el +                                                
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTE------------------------------------------------ 173
                                       34444455555555555555555555553................................................ PP

                                       HHHHHHHHHHHS-HHH.HHH CS
                             Nup54 113 rarletleaqlndpaqlkgr 132
                                                       +k+r
  gi|320100452|ref|YP_004176044.1| 174 ---------------AVKQR 178
                                       ...............33444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.32
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  30 GFedLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrle 75 
                                       G e+L++ ++   ke++ +r+ ++++++ le+ + +  +e+++ l+
  gi|320100452|ref|YP_004176044.1| 188 GAEALKRELEERVKELESCRSNVDSMRKTLEDAA-RLLQEALSMLQ 232
                                       78999999**********************9999.55555555555 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.7     0.077       9.1      52      79 ..     140     167 ..     122     168 .. 0.85
   2 ?    2.8   7.5       1.1   1.3e+02      28      70 ..     147     193 ..     133     202 .. 0.62
   3 ?    3.3   3.1      0.73        86      40      75 ..     180     219 ..     164     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.077
                              Med9  52 veeqeaeieeleeqlakKrelLkkyknr 79 
                                       v+  e+++++le +l+k+r+ Lk++  +
  gi|320100452|ref|YP_004176044.1| 140 VAGCEEQVKALEGELEKQRNRLKELEAK 167
                                       5566899****************99876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 1.1
                              Med9  28 tgelrhkLkkarelirelpg....idrsveeqeaeieeleeqlakKr 70 
                                       + +l   L+k r+ ++el+     + + v+++e+ei+ l+   ++ +
  gi|320100452|ref|YP_004176044.1| 147 VKALEGELEKQRNRLKELEAkiseLTEAVKQREEEIQGLRSGAEALK 193
                                       33344444444444444444444488888888888888887666554 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.73
                              Med9  40 elirelpg.......idrsveeqeaeieeleeqlakKrelLkk 75 
                                       e i+   g       + r  ee+ +e+e+ + +++  r+ L++
  gi|320100452|ref|YP_004176044.1| 180 EEIQ---GlrsgaeaLKRELEERVKELESCRSNVDSMRKTLED 219
                                       2222...133345557788888888888888888777777765 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   5.1      0.48        56      25      52 ..     155     182 ..     111     184 .. 0.81
   2 ?    8.9   3.0     0.011       1.3      23      61 ..     174     212 ..     169     220 .. 0.82
   3 ?    3.9   0.7      0.37        44       5      39 ..     195     229 ..     193     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.48
                              CdvA  25 ekleealkklkekakelkeklkkrlkel 52 
                                       ek ++ lk+l++k +el e +k+r +e+
  gi|320100452|ref|YP_004176044.1| 155 EKQRNRLKELEAKISELTEAVKQREEEI 182
                                       4556667777777777777777777776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.011
                              CdvA  23 ikekleealkklkekakelkeklkkrlkeledqikslek 61 
                                         ++ ee+++ l+  a++lk +l++r+kele+  +++++
  gi|320100452|ref|YP_004176044.1| 174 AVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDS 212
                                       5577899***********************998777766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.37
                              CdvA   5 ALeeLvsegdipkstyeeikekleealkklkekak 39 
                                        Lee v+e +  +s ++++++ le+a + l+e  +
  gi|320100452|ref|YP_004176044.1| 195 ELEERVKELESCRSNVDSMRKTLEDAARLLQEALS 229
                                       57777888888888888888888888888887665 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.7     0.053       6.3      16      48 ..     143     175 ..     136     186 .. 0.65
   2 ?    3.4   4.0      0.74        87       9      44 ..     171     209 ..     169     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.053
                             Spc24  16 leselesleselaelkeeleeleeeseekeser 48 
                                        e+++++le el++ +++l+ele + +e ++++
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAV 175
                                       577778888888888888888888777733332 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.74
                             Spc24   9 iakelsdleselesleselaelkeeleeleeesee...k 44 
                                       +++++++ e+e++ l+s  + lk+elee  +e e+   +
  gi|320100452|ref|YP_004176044.1| 171 LTEAVKQREEEIQGLRSGAEALKRELEERVKELEScrsN 209
                                       567788889999999988888888888877766664331 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 ?    2.6   5.4       1.3   1.5e+02      19      72 ..     129     181 ..     117     182 .. 0.70
   2 ?    5.4  11.3      0.17        20       6      71 ..     144     215 ..     143     229 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 1.3
                            Cnn_1N  19 LKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkllreaeka 72 
                                       LKL + f +  +   + eq+++l+ e+ + + ++++l+ ++ e+++ +++ e++
  gi|320100452|ref|YP_004176044.1| 129 LKLVVPFIRTPVAGCE-EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEE 181
                                       4444444444444333.5888888899999999999999999999998888876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.17
                            Cnn_1N   6 eeqidkLkKENFdLKLriyfLeerleklse......eqkeellkenielkveveslqkelkekkkllreaek 71 
                                       eeq+++L+ E    + r+++Le ++ +l+e      e+++ l +    lk e+e+  kel++++  ++++ k
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEavkqreEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRK 215
                                       566666666666667777777777666666666666455555555555555555555555555555554444 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  16.3    0.0081      0.95      33      96 ..     146     209 ..     142     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0081
                            CENP-Q  33 ekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaearerkeklkkehvllqe 96 
                                       + +ale +L+ ++  l++Lea i+++ +a ++ +e+++ L   a+a++re +e+ k+++    +
  gi|320100452|ref|YP_004176044.1| 146 QVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSN 209
                                       6799**********************************************88888884443333 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  17.9     0.096        11      11      87 ..     144     224 ..      91     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.096
                               ERM  11 eerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaea....eeeiqrlkesaekeeeekeklerk 83 
                                       ee+ k l+ e ek+++ L+e e ++ +L e  ++ eee + L   a+++    ee  ++l+  +++ ++ ++ le+ 
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALkrelEERVKELESCRSNVDSMRKTLEDA 220
                                       44555555555555555555555555555555555555555444333331111333333333333333333333333 PP

                               ERM  84 lrea 87 
                                       +r  
  gi|320100452|ref|YP_004176044.1| 221 ARLL 224
                                       3333 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.3      0.17        20      32      62 ..     150     180 ..     141     185 .. 0.60
   2 ?    5.3   0.7      0.22        26      31      60 ..     191     220 ..     187     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.17
                            Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkelee 62 
                                       L+ +le++ +++++L++++ el e vk+ ee
  gi|320100452|ref|YP_004176044.1| 150 LEGELEKQRNRLKELEAKISELTEAVKQREE 180
                                       4445566666666666666666666665554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.22
                            Csm1_N  31 vLsqkletkdqeiesLkeqlaeleekvkel 60 
                                        L+++le + +e+es + +++++++ ++++
  gi|320100452|ref|YP_004176044.1| 191 ALKRELEERVKELESCRSNVDSMRKTLEDA 220
                                       589999**************9999988776 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 ?    1.9   8.7       2.6   3.1e+02      55      84 ..     155     185 ..     126     232 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 2.6
                           DUF4140  55 ervpnreaeeee.lkalraeleeledelaal 84 
                                       e++ nr +e e+ +++l++++++ e+e++ l
  gi|320100452|ref|YP_004176044.1| 155 EKQRNRLKELEAkISELTEAVKQREEEIQGL 185
                                       3333333333322333333333333333333 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 ?    5.5   5.3      0.15        18      53     118 ..     136     198 ..     115     203 .. 0.77
   2 ?    3.7   9.9      0.54        63      57     114 ..     161     218 ..     143     237 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.15
                             CREPT  53 veealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelks 118
                                       +++ ++  +e +k Le ele+ ++  k le+ ++ + e++++ ee+++ l++ +e +k    el++
  gi|320100452|ref|YP_004176044.1| 136 IRTPVAGCEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKR---ELEE 198
                                       56667777889999*****9998888999999999999999999999888877665554...4444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.54
                             CREPT  57 lellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrk 114
                                       l+ l+   + L++ +++R++  + l++  ea+k +l++  ++le++++ ++ +++  +
  gi|320100452|ref|YP_004176044.1| 161 LKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKTLE 218
                                       2333333445666666676666667776677766666666666666666665555443 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 ?    8.6   2.5    0.0079      0.93      29      93 ..     152     216 ..     136     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0079
                              Tho2  29 keieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekks 93 
                                        e+ek +++++el+ + s+ ++a k++++e++ l++ +e+L++E++e  ++ e +++   + +k+
  gi|320100452|ref|YP_004176044.1| 152 GELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELESCRSNVDSMRKT 216
                                       46777777788887666777999****************************99999988877765 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 ?   10.2   3.6    0.0062      0.74      29      67 ..     143     181 ..     137     185 .. 0.92
   2 ?    2.4   0.2       1.8   2.1e+02      24      45 ..     212     233 ..     206     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0062
                               CLZ  29 leekverLessLeaLqtrlarLlaeyessqrkLkqRitk 67 
                                        ee+v+ Le++Le   +rl+ L a+ ++  +  kqR ++
  gi|320100452|ref|YP_004176044.1| 143 CEEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEE 181
                                       69*********************************9665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 1.8
                               CLZ  24 aeqkeleekverLessLeaLqt 45 
                                       + +k+le+ ++ L+++L +Lq 
  gi|320100452|ref|YP_004176044.1| 212 SMRKTLEDAARLLQEALSMLQH 233
                                       5678999999999999999985 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.2       0.2        24      38      76 ..     145     183 ..     136     187 .. 0.83
   2 ?    6.1   1.1     0.083       9.8      38      81 ..     187     230 ..     175     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.2
                           DUF4446  38 kdgksleellkekleeveelkeeseelekeieeleeklk 76 
                                       ++ k le  l+++ ++++el+++ +el++ +++ ee+++
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQ 183
                                       466888999999999999999999999999998888776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.083
                           DUF4446  38 kdgksleellkekleeveelkeeseelekeieeleeklkkslqk 81 
                                       + ++ l++ l+e+++e+e+ ++++++++k++e+  + l+++l+ 
  gi|320100452|ref|YP_004176044.1| 187 SGAEALKRELEERVKELESCRSNVDSMRKTLEDAARLLQEALSM 230
                                       46789999***********************9999988887765 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.3       8.4   9.9e+02       2      35 ..      92     125 ..      91     131 .. 0.74
   2 ?   10.1   3.0    0.0062      0.73       3      45 ..     144     186 ..     142     196 .. 0.63
   3 ?    2.4   0.2       1.5   1.8e+02      16      38 ..     196     218 ..     194     234 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 8.4
                              XhlA   2 ikerlerietkldnlee.rvdkleekaaeaeekik 35 
                                       i e+l r et + ++ + + +k  +   e++ek+k
  gi|320100452|ref|YP_004176044.1|  92 IAEELGRSETTIRSHLNmK-TKAGKLVHETYEKLK 125
                                       8899999999999998844.677777777777766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0062
                              XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkle 45 
                                       +e ++ +e++l++  +r+++le k +e  e +k+ ee++  l 
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLR 186
                                       4566666666666666666666666666666666666666555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 1.5
                              XhlA  16 leervdkleekaaeaeekiknle 38 
                                       leerv++le   +++++  k le
  gi|320100452|ref|YP_004176044.1| 196 LEERVKELESCRSNVDSMRKTLE 218
                                       34444444444444444444443 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 ?    6.6   0.2     0.067       7.9      10      50 ..      91     131 ..      89     133 .. 0.94
   2 ?    8.7   2.5     0.015       1.8       6      46 ..     194     234 ..     190     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.067
                      Exonuc_VII_S  10 eIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkv 50 
                                       +I+e+L   e+++   l++  ++ kL+ e  +kL++ e k+
  gi|320100452|ref|YP_004176044.1|  91 QIAEELGRSETTIRSHLNMKTKAGKLVHETYEKLKKGELKL 131
                                       899**********************************9986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.015
                      Exonuc_VII_S   6 aeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdea 46 
                                        eLee v++LEs    ++ + k  e +++Ll+e+ ++L+ +
  gi|320100452|ref|YP_004176044.1| 194 RELEERVKELESCRSNVDSMRKTLEDAARLLQEALSMLQHV 234
                                       58999999999999999999999999999999999998865 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 ?    5.5   0.5      0.18        21      33      83 ..     103     162 ..      89     164 .. 0.73
   2 ?    6.6   8.7     0.083       9.8      20      89 ..     145     217 ..     137     225 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.18
                            CENP-H  33 ekenlrlkrknrelaael.lelakekesek..........eklkeelekleaelkksrqrwr 83 
                                        ++ l++k+k  +l+ e  ++l+k +   k             +e++++le el+k+r+r +
  gi|320100452|ref|YP_004176044.1| 103 IRSHLNMKTKAGKLVHETyEKLKKGEL--KlvvpfirtpvAGCEEQVKALEGELEKQRNRLK 162
                                       456788888999999998334444443..3469999887755899**************976 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.083
                            CENP-H  20 qelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksrqrwrvvknva 89 
                                       +++++l+ el++ +   ++l++k  el++ + + ++e +  +   e lk+ele+  +el+  r+++  +++++
  gi|320100452|ref|YP_004176044.1| 145 EQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRsgaEALKRELEERVKELESCRSNVDSMRKTL 217
                                       4455555555555555555555555555555333333333335666677777777777777777777777665 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 ?   10.4  13.4    0.0043      0.51      11      71 ..     144     204 ..     136     213 .. 0.89
   2 ?    2.6   1.2       1.2   1.4e+02      52      69 ..     192     209 ..     190     232 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0043
                        TMF_DNA_bd  11 DeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                       +eq+++L  E+ek +    +l+++i++L + +k+ e+ei+ l +  e l +elee  ++l+
  gi|320100452|ref|YP_004176044.1| 144 EEQVKALEGELEKQRNRLKELEAKISELTEAVKQREEEIQGLRSGAEALKRELEERVKELE 204
                                       89*****************************************888888888888777765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 1.2
                        TMF_DNA_bd  52 lkkkleklekeleeleer 69 
                                       lk++le+ +kele+ ++ 
  gi|320100452|ref|YP_004176044.1| 192 LKRELEERVKELESCRSN 209
                                       444444444444443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1989  (0.110938); expected 358.6 (0.02)
Passed bias filter:                     1262  (0.0703888); expected 358.6 (0.02)
Passed Vit filter:                       359  (0.0200234); expected 17.9 (0.001)
Passed Fwd filter:                       162  (0.00903564); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             152  [number of targets reported over threshold]
# CPU time: 1.15u 0.35s 00:00:01.50 Elapsed: 00:00:00.48
# Mc/sec: 1499.52
//
Query:       gi|320100453|ref|YP_004176045.1|  [L=90]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 700.21
//
Query:       gi|320100454|ref|YP_004176046.1|  [L=239]
Description: TatD-like deoxyribonuclease [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-41  141.1   0.0    4.5e-41  140.9   0.0    1.0  1  TatD_DNase  TatD related DNase


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 !  140.9   0.0   2.5e-45   4.5e-41       1     254 [.       3     237 ..       3     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 2.5e-45
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHH CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleel 77 
                                       iDaH+H+++  +     ++l+r +  g   +v+v+ ++++s+a+lela++y++ v +++GiHP++v+++  ++l   
  gi|320100454|ref|YP_004176046.1|   3 IDAHIHCHE--L---GRDELSRYA--GRYILVCVSDDPASSRATLELAEEYKG-VTPCIGIHPWNVKNHGLSDL--- 68 
                                       8*******9..4...566776665..555667899999**************9.*************8744444... PP

                                       HHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCS.EE CS
                        TatD_DNase  78 kel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeaka.kv 152
                                       ++l +++ +  v ++Ge+GLD+ +  ++  ++q e+F+e    A+e++ +l iH+  a++++ e +   +   + kv
  gi|320100454|ref|YP_004176046.1|  69 RSLlKEAVERGVKCLGEVGLDK-RFTPESFSRQLEFFREIAGYAREYGFALNIHAAGAWREVFEEVYGRD---LdKV 141
                                       44444478889***********.777899*******************************9998776654...337* PP

                                       EETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHH CS
                        TatD_DNase 153 vlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvve 229
                                        +H+++g  + + ++++ gyy++l+ + +   + ++re++++vpl+++L+E+DaPy       g +  p++++ ++e
  gi|320100454|ref|YP_004176046.1| 142 YFHWYTGPLDLLNNIVEAGYYVGLNPAWRL--QAKHREVIASVPLRNVLTESDAPYEYR----GLKMTPEMITGSLE 212
                                       **************************9888..669********************9877....9************* PP

                                       HHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 230 klaelkaltleelaeitaeNakrlf 254
                                        la ++++++ee++ +++ N+ +++
  gi|320100454|ref|YP_004176046.1| 213 LLASIHGVSVEEVESTIWGNYVKIL 237
                                       *********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1981.98
//
Query:       gi|320100455|ref|YP_004176047.1|  [L=181]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.7   0.0       0.17   11.2   0.0    1.2  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.7e-06      0.17      64      90 ..     103     129 ..      96     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.7e-06
                                       SHHHHHHHHHHHHHT-EEEEEEETTS- CS
                              PALP  64 GNhgralAaaaallGlkvtivvpadas 90 
                                       GN+gr lA+a +l+G+  ++v+++d  
  gi|320100455|ref|YP_004176047.1| 103 GNAGRLLALALRLAGYTPIVVFDDDIA 129
                                       ****************99999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1346.89
//
Query:       gi|320100456|ref|YP_004176048.1|  [L=224]
Description: haloacid dehalogenase domain-containing protein hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-11   44.0   0.0      5e-11   43.0   0.0    1.5  1  HAD_2           Haloacid dehalogenase-like hydrolase
    0.00041   20.4   0.0    0.00069   19.6   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.057   13.8   0.0      0.074   13.4   0.0    1.2  1  HAD             haloacid dehalogenase-like hydrolase
      0.061   13.6   0.0      0.083   13.2   0.0    1.2  1  Hydrolase       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 !   43.0   0.0   1.1e-14     5e-11       2     178 .]       7     186 ..       6     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.1e-14
                             HAD_2   2 iFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkev 78 
                                       ++D D  ++      ++a+  +l++yg + +s +e+ +l++ +   l +++    +eee +  ++r+y++++     
  gi|320100456|ref|YP_004176048.1|   7 VMDYDLSMVYNLSDFYEAYSGALKSYGGGFISFDEFLNLLNEDR--LSERIPGGVREEEFWLLFRRIYVSRHP---- 77 
                                       56666666666677778888888888777666666666665555..444444444444456666555555544.... PP

                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsk..sreaveekleqlgiesyFdvivtsedvekk.........KPdpevieka 144
                                        p+dgv +lL  Lk+  +k+++v+ +  s e ++++l+ lg+++y d ++t +d ++          K    +i  +
  gi|320100456|ref|YP_004176048.1|  78 IPMDGVVDLLRLLKSLPVKIAVVSGRetSGEYIWRDLRMLGLDEYVDEVYTVSDLQRLngleeylfdK--SWIISYI 152
                                       6***********************99667899**********************99865666667667..99***** PP

                             HAD_2 145 leklklkkeeviyvGDsptDieaakkagikviav 178
                                       l+k ++ + +++ +GD +tD+ +++k+gi +i+v
  gi|320100456|ref|YP_004176048.1| 153 LRKHGVAPCNALCIGDFTTDLLSCRKLGIPFIGV 186
                                       *******************************987 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.5e-07   0.00069       9      72 ..     148     208 ..     145     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEE CS
                    Hydrolase_like   9 mydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddl 72 
                                       ++ ++l+++g++p + l iGD   tD+++ ++ G+ ++ V    +r   l+  + ++++v+++l
  gi|320100456|ref|YP_004176048.1| 148 IISYILRKHGVAPCNALCIGDF-TTDLLSCRKLGIPFIGVNKDEYRGMLLK--KRGAAIVVKNL 208
                                       567899****************.***********************96655..67888899887 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    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      59     184 ..      53     173 ..      13     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                               HAD  59 eallagls.eelaaelerfvaevirpklldpgalellaahraaGdrvvvvSgg...lrplvepllaelgadevlate 131
                                       e++ +g + ee+   ++r++   ++p   + g+++ll+  ++  ++++vvSg      +++++ l+ lg de +++ 
  gi|320100456|ref|YP_004176048.1|  53 ERIPGGVReEEFWLLFRRIYV-SRHPI-PMDGVVDLLRLLKSLPVKIAVVSGRetsG-EYIWRDLRMLGLDEYVDEV 126
                                       455556666778888888883.33443.446*********************98845.55555556***99999998 PP

                               HAD 132 levdd..rltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDl 184
                                       + v d  rl+g    e+ +  +    +++ + +  +++g ++++   +GD  +Dl
  gi|320100456|ref|YP_004176048.1| 127 YTVSDlqRLNGL---EEYLFDK----SWIIS-YILRKHGVAPCNALCIGDFTTDL 173
                                       888877666666...7777777....77777.78888888889999999988887 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.083     111     208 ..      71     178 ..      47     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                                       HHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEH..HHHHHHHHHTT.GGGESEEEEHHCES.STTT......SHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxx.xxxx......xxx RF
                         Hydrolase 111 ftiadplkvkpeaaeavasLkaagievvlltgdnp..etaeraanqlG.ddyfdaviasdiet.vakp......spe 177
                                       + ++    ++++++++++ Lk+  +++++++g +   e  +r ++ lG d+y+d v+++++     +       + +
  gi|320100456|ref|YP_004176048.1|  71 IYVSRHPIPMDGVVDLLRLLKSLPVKIAVVSGRETsgEYIWRDLRMLGlDEYVDEVYTVSDLQrLNGLeeylfdKSW 147
                                       666777789**********************9999888999*******9999999999999998444455577788* PP

                                       HHHHHHHHHTSTGGGEEEEESSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 178 gkvaaireLqgkpeevamVGDgvnDaaalaa 208
                                       +  +++r+ ++ p + + +GD  +D+   ++
  gi|320100456|ref|YP_004176048.1| 148 IISYILRKHGVAPCNALCIGDFTTDLLSCRK 178
                                       *********************9999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1636.27
//
Query:       gi|320100457|ref|YP_004176049.1|  [L=93]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   14.8   0.2      0.039   14.2   0.2    1.4  1  ALS_ss_C    Small subunit of acetolactate synthase
       0.04   14.1   0.0       0.56   10.4   0.0    2.1  2  Stork_head  Winged helix Storkhead-box1 domain
      0.044   13.5   0.1       0.38   10.4   0.0    2.0  2  DUF4423     Domain of unknown function (DUF4423)
      0.089   13.2   0.1       0.11   12.9   0.1    1.3  1  YtzH        YtzH-like protein
        0.1   13.2   0.0       0.14   12.8   0.0    1.3  1  RPA_C       Replication protein A C terminal
        0.1   12.5   0.0       0.18   11.7   0.0    1.3  1  TBPIP       TBPIP/Hop2 winged helix domain
       0.11   12.4   0.1       0.19   11.6   0.1    1.4  1  DUF4574     Ubiquinol-cytochrome-c reductase complex assembly


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 ?   14.2   0.2   1.5e-05     0.039      14      60 ..       5      53 ..       1      65 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS...-GGGE CS
                          ALS_ss_C 14 erseileiaeifrakivdvspdsliieltgteekidaliell...kpfgi 60
                                      +++ei+e+a++ r ki+   ++ +++  + +ee+++++i++l   kp+++
  gi|320100457|ref|YP_004176049.1|  5 SEEEIEELARRVRLKILHEDEE-VVLMTAPNEEQLEEIIKELlgyKPMNL 53
                                      689**************96655.67888999***********55445544 PP

>> Stork_head  Winged helix Storkhead-box1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.1   2.6e+02      46      62 ..      30      46 ..      19      51 .. 0.86
   2 ?   10.4   0.0   0.00022      0.56      48      76 ..      63      91 ..      50      93 .] 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.1
                        Stork_head 46 iqiPseeviydaLgsLi 62
                                      ++ P+ee +++++ +L+
  gi|320100457|ref|YP_004176049.1| 30 MTAPNEEQLEEIIKELL 46
                                      88999999999999997 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00022
                        Stork_head 48 iPseeviydaLgsLikerkiYhtgeGYfi 76
                                      i se+ i++aL sL+  +  Y t++G  i
  gi|320100457|ref|YP_004176049.1| 63 IASEDKIRRALNSLLDRGEAYITSDGRYI 91
                                      6699*********************9655 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.1   2.7e+02      37      53 ..       7      23 ..       1      31 [. 0.58
   2 ?   10.4   0.0   0.00015      0.38      25      79 ..      41      93 .]      34      93 .] 0.93

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.1
                           DUF4423 37 adpeelakrlrpkisae 53
                                      +++eela+r+r ki  e
  gi|320100457|ref|YP_004176049.1|  7 EEIEELARRVRLKILHE 23
                                      45666666666555444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                           DUF4423 25 virellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqt 79
                                      +i ell  k+   + +e+   l + +s++++++al+ Ll+ g +  + dg+y +t
  gi|320100457|ref|YP_004176049.1| 41 IIKELLGYKPM--NLREIHTVLSGIASEDKIRRALNSLLDRGEAYITSDGRYIST 93
                                      68899999999..9************************************99875 PP

>> YtzH  YtzH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.4e-05      0.11      13      55 ..      20      63 ..       8      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
                              YtzH 13 iLkeqqadccgtvseceQierlvksllaneev.dedvkqvLeei 55
                                      iL+e ++   +t  + eQ+e+++k ll  + +  +++++vL+ i
  gi|320100457|ref|YP_004176049.1| 20 ILHEDEEVVLMTAPNEEQLEEIIKELLGYKPMnLREIHTVLSGI 63
                                      8999999999*****************98888568999999888 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05      0.14      50     102 ..      34      87 ..      19      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                                       HHHHHHHHHHH.SXSTTTEEHHHHHHHS..TSXHHHHHHHHHHHHHTTSEEESSS CS
                             RPA_C  50 laqqvlnlikqspeseeGvhvdeiaqkl..rlsvndvkqavdeLsneGiiYsTiD 102
                                       +++q+ ++ik+   + + ++++ei   l    s+ ++++a+++L++ G  Y T D
  gi|320100457|ref|YP_004176049.1|  34 NEEQLEEIIKE-LLGYKPMNLREIHTVLsgIASEDKIRRALNSLLDRGEAYITSD 87 
                                       56666667776.777777999999999985569999*****************99 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.1e-05      0.18       3      46 ..      39      80 ..      36      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
                             TBPIP  3 eelvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdeg 46
                                      ee+++e+l   ++P++  ++ + l +  +   + +aL++L d g
  gi|320100457|ref|YP_004176049.1| 39 EEIIKELL--GYKPMNLREIHTVLSGIASEDKIRRALNSLLDRG 80
                                      57777777..49****************************9987 PP

>> DUF4574  Ubiquinol-cytochrome-c reductase complex assembly factor 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.6e-05      0.19      25      52 ..      28      55 ..      24      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.6e-05
                           DUF4574 25 fvLvtPgeerkqeilkempeqdpqrrde 52
                                       ++++P+ee+ +ei ke+ + +p++  e
  gi|320100457|ref|YP_004176049.1| 28 VLMTAPNEEQLEEIIKELLGYKPMNLRE 55
                                      6899**************9999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      812  (0.0452898); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 700.05
//
Query:       gi|320100458|ref|YP_004176050.1|  [L=435]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   87.1   0.1    5.9e-24   85.3   0.0    1.9  2  Radical_SAM     Radical SAM superfamily
    3.1e-08   33.7   0.1    6.9e-08   32.6   0.1    1.6  1  B12-binding     B12 binding domain
  ------ inclusion threshold ------
      0.086   13.0   0.2         14    5.9   0.0    2.5  2  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.61   3.6e+03      29      45 ..      37      52 ..      17      93 .. 0.68
   2 !   85.3   0.0   9.8e-28   5.9e-24       1     167 []     176     356 ..     176     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.61
                                      HHHHHHHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxx RF
                       Radical_SAM 29 lsveeileevkelkaek 45
                                       ++ +++eev+e++ ++
  gi|320100458|ref|YP_004176050.1| 37 DTPGRLMEEVEEAS-RN 52
                                      45555666666654.22 PP

  == domain 2  score: 85.3 bits;  conditional E-value: 9.8e-28
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS..............TTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly..............pdf 63 
                                       v+vtrgC+++Cs+C+++++   +  +r++s+ +i+  v+el a+ gv+   +   + l y              +++
  gi|320100458|ref|YP_004176050.1| 176 VEVTRGCPYGCSYCQVSYM--HGAFYRHRSIGRIVYYVREL-ARLGVRDYRFITPDSLSYglstvrrepdvgliDEL 249
                                       689***************8..9999****************.8**********999999999999999777654444 PP

                                       HHHHHHHHHTCCCTEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  64 vellerlaklavpgiritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevleal 134
                                          l + a+  + g ri++ + +  ++      e ++ l+++     + +g+++++d+ vl +++rgh++++vl+a+
  gi|320100458|ref|YP_004176050.1| 250 LSSLHEVAR--DVGGRIFYGSFPSEVRpehvtGEAVRVLRRYVsNREIIVGAQSGSDR-VLSMVRRGHSVDDVLNAV 323
                                       444444444..499999999999999999*****************************.****************** PP

                                       HHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 135 eklreagikrvvdrivglpGendeeleellell 167
                                       + + e+g+ ++vd+i+g+pGe++e+ ee+l+l+
  gi|320100458|ref|YP_004176050.1| 324 RVISENGFTPSVDVILGIPGETREDQEETLRLI 356
                                       *****************************9986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   1.2e-11   6.9e-08      19     120 ..      21     125 ..      14     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.2e-11
                       B12-binding  19 vlaaalrdagfeVqllganven.edivaairaekpdvvglSalltsqleav..kelvel..lkrirprvkvvvGGah 90 
                                       ++aaa r  g++V++ +      e++++a r ++  vvg S+ lt+ l +    ++++    ++++ +  +++GG+h
  gi|320100458|ref|YP_004176050.1|  21 LIAAADRVPGVRVEVADTPGRLmEEVEEASRNREKCVVGYSL-LTTMLVDEsfLNTLKTilHHAESHGCLTIAGGPH 96 
                                       45555555688898888887778*******************.66655433226666667656666799******** PP

                       B12-binding  91 psldpeetleaklgiddvvvgegedaleal 120
                                       +s dp  +l+  lg+ +v +ge+e++++++
  gi|320100458|ref|YP_004176050.1|  97 ASGDPVGVLRS-LGFKVVFIGEAEETIREF 125
                                       **********9.**************9987 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0023        14       1      69 [.      12      87 ..      12     109 .. 0.72
   2 ?    4.3   0.3    0.0067        40      94     137 ..     186     228 ..     183     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0023
                    Acetyltransf_6  1 skrRknlrrkrrkleelgevrfrvatdpedleallelfraqwarr.......pdvfadpltraflrdllaalaarg 69
                                      +k+R++++  +  ++++ +vr++va++p  l + +e  ++ +++        + +  d+ +   l+ +l++ +++g
  gi|320100458|ref|YP_004176050.1| 12 KKTRYSVNALIAAADRVPGVRVEVADTPGRLMEEVEEASRNREKCvvgysllTTMLVDESFLNTLKTILHHAESHG 87
                                      699************************9998887777766555445565555555555555555555555555555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0067
                    Acetyltransf_6  94 rlyywlggydpel.aklspgllllweliedaaeeGlrrfdlgggd 137
                                       + y++++ ++ ++ ++ s+g++++   ++++a+ G+r + + ++d
  gi|320100458|ref|YP_004176050.1| 186 CSYCQVSYMHGAFyRHRSIGRIVY--YVRELARLGVRDYRFITPD 228
                                       678999999999669******986..59***********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3113.70
//
Query:       gi|320100459|ref|YP_004176051.1|  [L=144]
Description: putative AsnC family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   33.3   0.0      6e-08   32.5   0.0    1.4  1  MarR_2          MarR family
    2.2e-07   30.7   0.1    4.3e-07   29.8   0.0    1.6  2  MarR            MarR family
    2.9e-05   23.8   0.3    6.2e-05   22.8   0.2    1.6  2  HTH_5           Bacterial regulatory protein, arsR family
    4.9e-05   23.6   0.1    7.9e-05   22.9   0.1    1.3  1  Rrf2            Transcriptional regulator
    6.3e-05   23.1   0.1    0.00015   21.9   0.1    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    7.5e-05   22.5   0.5    7.5e-05   22.5   0.5    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    9.9e-05   21.8   0.2    0.00028   20.4   0.1    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00019   21.4   0.0    0.00028   20.8   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00049   20.2   0.0    0.00066   19.8   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
    0.00053   20.0   0.0     0.0011   19.0   0.0    1.5  1  DprA_WH         DprA winged helix domain
    0.00062   19.7   0.0      0.001   19.0   0.0    1.4  1  HTH_36          Helix-turn-helix domain
     0.0013   18.6   0.1     0.0026   17.6   0.1    1.5  1  TFIIE_alpha     TFIIE alpha subunit
     0.0018   18.2   0.1     0.0027   17.6   0.1    1.3  1  HTH_11          HTH domain
     0.0025   17.3   1.6      0.056   12.8   0.1    2.0  2  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
     0.0028   17.2   0.0      0.019   14.6   0.0    2.0  2  GntR            Bacterial regulatory proteins, gntR family
     0.0069   16.4   0.0      0.018   15.1   0.0    1.7  2  Trans_reg_C     Transcriptional regulatory protein, C termina
     0.0076   16.3   0.0      0.017   15.2   0.0    1.6  1  HTH_20          Helix-turn-helix domain
     0.0084   16.1   0.0      0.013   15.6   0.0    1.3  1  z-alpha         Adenosine deaminase z-alpha domain
  ------ inclusion threshold ------
      0.015   14.1   0.0      0.016   14.1   0.0    1.0  1  HTH_micro       HTH-like
      0.026   14.1   0.0      0.038   13.5   0.0    1.2  1  HTH_CodY        CodY helix-turn-helix domain
      0.082   12.7   0.0       0.13   12.1   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.092   13.3   0.0       0.16   12.5   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   7.4e-11     6e-08       8      56 ..      11      59 ..       8      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.4e-11
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                        +L +L  + g+++ +++l ++lg+++  vsril +L++aG ver+p 
  gi|320100459|ref|YP_004176051.1| 11 TALLKYLLKHSGQEIYQSQLSKELGVDPKVVSRILIKLEKAGVVERTPV 59
                                      67899999999999********************************986 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   5.3e-10   4.3e-07      11      53 ..      17      60 ..       7      66 .. 0.86
   2 ?   -2.7   0.0       7.1   5.8e+03      37      45 ..      76      84 ..      75      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5.3e-10
                                      HHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                              MarR 11 ilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                      +l+++g+ +++s+L k lgv++  v+r+l +Lek+G +eR++ +
  gi|320100459|ref|YP_004176051.1| 17 LLKHSGQeIYQSQLSKELGVDPKVVSRILIKLEKAGVVERTPVT 60
                                      5667777799******************************9855 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.1
                                      HHHHHHHTT CS
                              MarR 37 vldrLekkG 45
                                      +++++e+ G
  gi|320100459|ref|YP_004176051.1| 76 LVKAMEDSG 84
                                      789999988 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   7.7e-08   6.2e-05       7      46 ..      13      55 ..       8      56 .. 0.92
   2 ?   -2.3   0.0       5.2   4.2e+03       2      13 ..      71      82 ..      70      92 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.7e-08
                                      HHHHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  7 ILklLae...gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +Lk+L +   +e + ++l++elg+ +  vS+ L kL++aG+Ve
  gi|320100459|ref|YP_004176051.1| 13 LLKYLLKhsgQEIYQSQLSKELGVDPKVVSRILIKLEKAGVVE 55
                                      688888889889999***************************7 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.2
                                      HHHHHHHHHHTT CS
                             HTH_5  2 ptRlkILklLae 13
                                      p R k++k++++
  gi|320100459|ref|YP_004176051.1| 71 PVRDKLVKAMED 82
                                      666677777776 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   9.7e-08   7.9e-05       1      56 [.       1      55 [.       1      58 [. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.7e-08
                                      X---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  1 MklsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      M+ ++ +e  + +l yL k++++e +  ++++++ ++ p+++++il kL+kag+v+
  gi|320100459|ref|YP_004176051.1|  1 MSDKTASEKETALLKYLLKHSGQE-IYQSQLSKELGVDPKVVSRILIKLEKAGVVE 55
                                      5556666667778999******99.9999*************************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 !   21.9   0.1   1.9e-07   0.00015      14      55 ..      16      57 ..      13      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-07
                                      HHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 14 YtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                      Y l+ +++ + +++l+++L+v p  Vs  l kLek+G ve  
  gi|320100459|ref|YP_004176051.1| 16 YLLKHSGQEIYQSQLSKELGVDPKVVSRILIKLEKAGVVERT 57
                                      556668888999*************************99865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.5   9.2e-08   7.5e-05       7      59 ..       7      64 ..       7      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.2e-08
                                      HHHCCCHCHHHHHHCCCHHC..HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST...T CS
                              TrmB  7 seyEakvYlaLlklgpatad..eiaeelgvprskvYevLrsLedkGlVerekgr...p 59
                                      se E    ++Llk+   +++  ++++elgv+   v ++L +Le++G+Ver + +   +
  gi|320100459|ref|YP_004176051.1|  7 SEKETALLKYLLKHSGQEIYqsQLSKELGVDPKVVSRILIKLEKAGVVERTPVTyegR 64
                                      6889999999**88887765227***************************99885552 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   0.1   3.5e-07   0.00028       5      48 .]      10      55 ..       7      55 .. 0.85
   2 ?   -1.5   0.0       2.3   1.9e+03      38      46 ..      77      85 ..      75      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.5e-07
                            HTH_24  5 drkILelLqknpr..isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + ++L++L k+++  i q++L+++lg+ p  v+r l +Le++G+++
  gi|320100459|ref|YP_004176051.1| 10 ETALLKYLLKHSGqeIYQSQLSKELGVDPKVVSRILIKLEKAGVVE 55
                                      56778888885544588***************************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                            HTH_24 38 lkrLeeeGl 46
                                      +k +e++G+
  gi|320100459|ref|YP_004176051.1| 77 VKAMEDSGI 85
                                      899***997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.5e-07   0.00028      22      54 ..      25      57 ..      11      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.5e-07
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisrg 54
                                      + q +l+  lG+ +  vsril +L+++g+++r 
  gi|320100459|ref|YP_004176051.1| 25 IYQSQLSKELGVDPKVVSRILIKLEKAGVVERT 57
                                      5799**************************964 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 !   19.8   0.0     8e-07   0.00066      19      62 ..      25      64 ..       8      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8e-07
                    B-block_TFIIIC 19 itqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksi 62
                                      i qs+L+ke++ dp+ +  +l +Lek g +++ ++    t+ + 
  gi|320100459|ref|YP_004176051.1| 25 IYQSQLSKELGVDPKVVSRILIKLEKAGVVERTPV----TYEGR 64
                                      78******************************999....55554 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.3e-06    0.0011       9      59 ..       5      58 ..       1      58 [. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                           DprA_WH  9 plddlerrvLaaL...gpePvhvDqLvrrtglpaaevsaaLleLELaGlverlp 59
                                      ++++ e ++L  L   + + +   qL++++g+++ +vs++L+ LE aG ver p
  gi|320100459|ref|YP_004176051.1|  5 TASEKETALLKYLlkhSGQEIYQSQLSKELGVDPKVVSRILIKLEKAGVVERTP 58
                                      5677777777777776667788889***************************88 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.3e-06     0.001       5      53 ..       8      52 ..       7      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                            HTH_36  5 psaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlG 53
                                       ++ +ll +l+++++++ +    q+ l+k lg++ + vsr++ +Le++G
  gi|320100459|ref|YP_004176051.1|  8 EKETALLKYLLKHSGQEIY----QSQLSKELGVDPKVVSRILIKLEKAG 52
                                      57999*********88888....*************************9 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.2e-06    0.0026      13      58 ..       8      55 ..       3      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.2e-06
                                      HHHHHHHHHHHCTT..SEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 13 eeavlvldvLlekg..evteedlakelkidlnelrklLnrLyearlvk 58
                                      e+    l+ Ll+++  e+   +l+kel++d++++ ++L +L +a++v+
  gi|320100459|ref|YP_004176051.1|  8 EKETALLKYLLKHSgqEIYQSQLSKELGVDPKVVSRILIKLEKAGVVE 55
                                      5667788999988766899**************************996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.3e-06    0.0027       2      44 ..      10      53 ..       9      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                            HTH_11  2 llqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ++++l+ Ll++ g+ i  ++L++eL+v  ++v r + +Le++gv
  gi|320100459|ref|YP_004176051.1| 10 ETALLKYLLKHSGQeIYQSQLSKELGVDPKVVSRILIKLEKAGV 53
                                      5789**************************************93 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 ?    4.6   0.1     0.022        18      84     147 ..       6      68 ..       2      70 .. 0.75
   2 !   12.8   0.1   6.9e-05     0.056     302     335 ..      96     129 ..      52     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.022
                                       SXHHHH.HHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEEE CS
                     RNA_pol_Rpc34  84 lsedes.lVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiYl 147
                                        se+e  l     + sG+e I + ++ + l+   +vv ++L  Le+ + + ++ +v +  +k +l
  gi|320100459|ref|YP_004176051.1|   6 ASEKETaLLKYLLKHSGQE-IYQSQLSKELGVDPKVVSRILIKLEKAGVV-ERTPVTYEGRKTFL 68 
                                       4445543666667778877.999999999***********9999987766.67788888777765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.9e-05
                                       STTXXSSXSSSSSXXTSSSSSSSSSSTTSSSSXX CS
                     RNA_pol_Rpc34 302 glveapcgecpvfdlceeggavspkncvYlkeWl 335
                                        +   pc +cp + +c egg   p +c +l+e+l
  gi|320100459|ref|YP_004176051.1|  96 TVADIPCVKCPYIYKCYEGGYYDPATCQWLTEYL 129
                                       56789*************************9987 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.4e-05     0.019      21      57 ..      22      57 ..      16      59 .. 0.91
   2 ?    0.0   0.0      0.84   6.9e+02      34      46 ..      83      95 ..      74     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                                      TSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 21 GdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                      G+ +  +++L++e+gV+  +v + L++Le +g+ver 
  gi|320100459|ref|YP_004176051.1| 22 GQEI-YQSQLSKELGVDPKVVSRILIKLEKAGVVERT 57
                                      6777.7899**************************96 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.84
                                      HTS-HHHHHHHHH CS
                              GntR 34 fgVsrttvReALr 46
                                       g++  t+ReA +
  gi|320100459|ref|YP_004176051.1| 83 SGIDPYTLREAFD 95
                                      5788899***976 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 !   15.1   0.0   2.2e-05     0.018       6      38 ..       6      38 ..       2      46 .. 0.85
   2 ?   -2.9   0.0       9.5   7.8e+03      50      60 ..      69      79 ..      67      85 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                                      -SHHHHHHHHHHHHTTTSEEEHHHHHHHHTTTT CS
                       Trans_reg_C  6 ltpkefklLelLlenpgrvvsreeLleevwged 38
                                       ++ke++lL++Ll+++g+ + + +L +e+  + 
  gi|320100459|ref|YP_004176051.1|  6 ASEKETALLKYLLKHSGQEIYQSQLSKELGVDP 38
                                      689***********************9987655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.5
                                      HHHHHHHHHTT CS
                       Trans_reg_C 50 isrLRkkLedd 60
                                      ++ +R+kL ++
  gi|320100459|ref|YP_004176051.1| 69 VKPVRDKLVKA 79
                                      66678888764 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.1e-05     0.017      15      58 ..      13      58 ..       5      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                      HHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 15 ilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +l++L  +++++   s+l ++l+++++ +s+ L +Le+ag ve++ 
  gi|320100459|ref|YP_004176051.1| 13 LLKYLlkHSGQEIYQSQLSKELGVDPKVVSRILIKLEKAGVVERTP 58
                                      677788999999999****************************986 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05     0.013       3      53 ..       7      56 ..       5      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEE CS
                           z-alpha  3 qeqaekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyr 53
                                       e++   l++L + + ++   + +l+ +L+ + + + r+L++le+ g v r
  gi|320100459|ref|YP_004176051.1|  7 SEKETALLKYLLKHS-GQEIYQSQLSKELGVDPKVVSRILIKLEKAGVVER 56
                                      57888999***9999.9******************************9987 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     2e-05     0.016      95     139 ..      12      57 ..       2      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                         HTH_micro  95 kivdflvkak.dyvkaaelraklnidpKklfYvikkLakkglieqk 139
                                        ++ +l+k + + + +++l ++l +dpK ++ ++ kL+k g++e  
  gi|320100459|ref|YP_004176051.1|  12 ALLKYLLKHSgQEIYQSQLSKELGVDPKVVSRILIKLEKAGVVERT 57 
                                       5788999988799******************************954 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.7e-05     0.038       8      57 ..      28      80 ..      22      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                          HTH_CodY  8 skiaDriGitrsvivnaLrkLesaGiiesrsL...GmkGtYlkvlnekflkeL 57
                                      s+++ ++G+   v+   L kLe aG++e   +   G k   +k + +k++k +
  gi|320100459|ref|YP_004176051.1| 28 SQLSKELGVDPKVVSRILIKLEKAGVVERTPVtyeGRKTFLVKPVRDKLVKAM 80
                                      888999**********************8776222444445677777777766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.13      12      52 .]      18      58 ..      10      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      l + +qe   s+l++++g+ +  v+R+L  L++ G ve+ +
  gi|320100459|ref|YP_004176051.1| 18 LKHSGQEIYQSQLSKELGVDPKVVSRILIKLEKAGVVERTP 58
                                      5667777899****************************975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0002      0.16      18      62 ..      24      68 ..       8      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                            HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62
                                      +  +++l++ l v+   +s +l kL+++G+vert+   ++r +++
  gi|320100459|ref|YP_004176051.1| 24 EIYQSQLSKELGVDPKVVSRILIKLEKAGVVERTPVTYEGRKTFL 68
                                      4456999***************************99888988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 00:00:00.42
# Mc/sec: 1018.83
//
Query:       gi|320100460|ref|YP_004176052.1|  [L=216]
Description: translin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-11   42.9   0.0      4e-09   36.8   0.0    2.1  1  Translin  Translin family
  ------ inclusion threshold ------
      0.088   13.4   0.7       0.94   10.1   0.7    2.4  1  ADSL_C    Adenylosuccinate lyase C-terminus
      0.095   12.8   0.4       0.24   11.6   0.0    1.8  2  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   6.7e-13     4e-09       2     191 ..      25     185 ..      24     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.7e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHHHGGGTH.H CS
                          Translin   2 rreriikasrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayrYqrqisgg 78 
                                       +re+ ++++r++t++s  ii+l+hr + ++      + +  + a++ ++++++ll       ++++   Y  ++ +g
  gi|320100460|ref|YP_004176052.1|  25 VREEAYRLVRELTRSSGDIIVLVHRGMGRE------AGSRLEAARNLVRRLNELL-------REHPDIYYTGMVYNG 88 
                                       699**********************88322......2222355666666666666.......7788899******** PP

                                       HHHHHHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHH CS
                          Translin  79 lqeliealsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplq 155
                                       l e+ ea +f+    +++  ++ e++               ++   Yl Gl dL+gEL R+ +  + +g  + ++++
  gi|320100460|ref|YP_004176052.1|  89 LSEYAEAELFYGITVEGRAPSWRELE---------------IPYVPYLQGLGDLVGELRRYVVELLDKGLID-EARK 149
                                       ***********988888888887765...............44456*********************99987.9*** PP

                                       HHHHHHHHHHHHHTS----HH....HHHHHTTHHHHH CS
                          Translin 156 ilkflrelragfellnlknds.akdlrkKldvlkqsv 191
                                         + ++e++ +++ l+ + d+ +  lr+K+dv +  v
  gi|320100460|ref|YP_004176052.1| 150 YFNVMEEVYINLRRLDYP-DAlTPGLRHKVDVASRLV 185
                                       ******************.553669******987655 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7   0.00016      0.94      16      46 ..      24      79 ..      18      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                      H-HHHHHHHHHHHHHHHHHC.........................HHHHHHT-HHH CS
                            ADSL_C 16 lgReeAyelVqeaamkawee.........................llelLaadpev 46
                                        ReeAy+lV+e+++ + +                          l elL+++p++
  gi|320100460|ref|YP_004176052.1| 24 AVREEAYRLVRELTRSSGDIivlvhrgmgreagsrleaarnlvrrLNELLREHPDI 79
                                      56************999866777777777777777777777777777777777765 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.6   3.6e+03       6      20 ..      53      67 ..      51      75 .. 0.72
   2 ?   11.6   0.0   3.9e-05      0.24      55     112 ..     123     192 ..     112     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.6
                                      HHHHHHHHHHHHHHH CS
                              HEPN  6 rrAeedleaAellle 20
                                      r+A ++leaA++l +
  gi|320100460|ref|YP_004176052.1| 53 REAGSRLEAARNLVR 67
                                      567777777777654 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.9e-05
                                       HHHHHHCCHHHT.........-HHHHHHHHHHHCCCHHCC...CTSS--S...--HHHHHHHHHHHHHHH CS
                              HEPN  55 dlreLleelkkelke......seelreeleeLekayiesr...Ypdakee...yteedaeealkdaeevl 112
                                       +l +L++el+++  e      ++e r++++++e+ yi+ r   Ypda ++    + + a ++++d++ ++
  gi|320100460|ref|YP_004176052.1| 123 GLGDLVGELRRYVVElldkglIDEARKYFNVMEEVYINLRrldYPDALTPglrHKVDVASRLVEDTRILI 192
                                       5666666666666666666779***************987333666655599888899999999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1649.01
//
Query:       gi|320100461|ref|YP_004176053.1|  [L=235]
Description: DNA-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   18.7   0.4     0.0046   17.3   0.4    1.8  1  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0086   16.3   0.2      0.013   15.7   0.2    1.2  1  Fib_alpha        Fibrinogen alpha/beta chain family
  ------ inclusion threshold ------
      0.014   15.7   0.3      0.028   14.7   0.3    1.5  1  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.014   15.0   0.4      0.027   14.1   0.4    1.4  1  DUF4795          Domain of unknown function (DUF4795)
      0.017   15.1   0.1      0.027   14.5   0.1    1.2  1  Laminin_II       Laminin Domain II
      0.027   14.1   0.3       0.04   13.5   0.3    1.2  1  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
      0.052   13.4   0.9      0.073   12.9   0.9    1.3  1  Selenoprotein_S  Selenoprotein S (SelS)
      0.053   13.2   2.7      0.079   12.6   2.7    1.3  1  Lebercilin       Ciliary protein causing Leber congenital ama
      0.064   13.0   0.3       0.13   12.1   0.3    1.5  1  SKA2             Spindle and kinetochore-associated protein 2
      0.073   13.1   1.1       0.14   12.1   1.1    1.6  1  Phasin           Poly(hydroxyalcanoate) granule associated pr
       0.11   12.3   2.9       0.26   11.1   2.9    1.7  1  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
       0.12   12.4   0.1       0.19   11.8   0.1    1.4  1  DUF1664          Protein of unknown function (DUF1664)
       0.25   11.9   6.5       0.55   10.8   6.5    1.5  1  APG6_N           Apg6 coiled-coil region
        1.1    8.1   5.7       0.23   10.3   2.5    1.4  2  Spc7             Spc7 kinetochore protein


Domain annotation for each model (and alignments):
>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   3.6e-06    0.0046       7      40 ..      69     102 ..      54     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                         FlaC_arch   7 nklsklsteletvkkeneelsksveelkenVkdl 40 
                                        +++k    letv+++ +el + veel+e+Vk l
  gi|320100461|ref|YP_004176053.1|  69 DEINKGLAPLETVRRQVSELVQRVEELEEKVKAL 102
                                       6777777789*********************976 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2     1e-05     0.013      51     131 ..      28     105 ..      16     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  51 tkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidq 127
                                       ++  ++++++i++ l ek  ++++ +  ++k++ +le     ++++i++    ++  +  +++++q++++Le+++++
  gi|320100461|ref|YP_004176053.1|  28 ERGFRDVSSYITELLSEKTLQQPGREGDLEKIRARLE---RFVQDEINKGLAPLETVRRQVSELVQRVEELEEKVKA 101
                                       5667889999***************************...7899********************************* PP

                                       HHHH CS
                         Fib_alpha 128 kerk 131
                                       +e++
  gi|320100461|ref|YP_004176053.1| 102 LEQQ 105
                                       9987 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   2.2e-05     0.028      57      94 ..      68     105 ..      51     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                           BLOC1_2  57 yeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       ++e+++ l  ++ + +qv+eL + v+eL+e +k+LE++
  gi|320100461|ref|YP_004176053.1|  68 QDEINKGLAPLETVRRQVSELVQRVEELEEKVKALEQQ 105
                                       35777778888888888888888888888888888865 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   2.1e-05     0.027      74     155 ..       7     104 ..       5     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                           DUF4795  74 keaLatkvsrdq.fDeakkeLekmleellekle...........eqeealkkaldtLq....eelkekldrlelepL 134
                                       k+ +++ v+++  ++  kk+Le++++++ + ++           + e +l+k+   L+    +e+++ l    le +
  gi|320100461|ref|YP_004176053.1|   7 KREVRILVDEELyMELEKKALERGFRDVSSYITellsektlqqpGREGDLEKIRARLErfvqDEINKGLA--PLETV 81 
                                       6788999999989************9999998888889999999**************555555555555..45555 PP

                           DUF4795 135 keqle...erlkelqkelqeamek 155
                                       + q+    +r++el+++++  +e+
  gi|320100461|ref|YP_004176053.1|  82 RRQVSelvQRVEELEEKVKA-LEQ 104
                                       55555444444444444442.122 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.1e-05     0.027      25      84 ..      55     108 ..      35     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  25 nlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       +le++++ l+++ ++      ++++    ++ +rr+v++L + +++L++k+k l+q+ e 
  gi|320100461|ref|YP_004176053.1|  55 DLEKIRARLERFVQD------EINKGLAPLETVRRQVSELVQRVEELEEKVKALEQQGER 108
                                       445555555555544......566667778999***********************9886 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   3.1e-05      0.04     159     262 ..      16     113 ..       7     125 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                         Phage_GPO 159 vetalefeeeeeeeegeslferikallskkkksddarfadveeavelvAeevk.elsekveallaleaelaalkkev 234
                                       +e  +e+e+++ e+  +++ + i++lls+k+ ++  r  d+e+   ++ + v+ e+++ ++        l++++++v
  gi|320100461|ref|YP_004176053.1|  16 EELYMELEKKALERGFRDVSSYITELLSEKTLQQPGREGDLEKIRARLERFVQdEINKGLA-------PLETVRRQV 85 
                                       567789999998888999****************999999999866666655413444444.......455555555 PP

                         Phage_GPO 235 eklkaeleaLkekLsktdakekqrpeat 262
                                       ++l +++e+L+ek+++ +++ ++rp  t
  gi|320100461|ref|YP_004176053.1|  86 SELVQRVEELEEKVKALEQQGERRPAET 113
                                       5555555555555555555555554433 PP

>> Selenoprotein_S  Selenoprotein S (SelS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   5.7e-05     0.073      76     138 ..      69     130 ..      34     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                   Selenoprotein_S  76 dvvvkrqealeaaRlrmqeeldakaekfkekkkqleeekRrqkiemWesmkeGksykgkakla 138
                                       d++ k    le  R+++  el  ++e+ +ek k le    r+  e++   + Gk yk+   + 
  gi|320100461|ref|YP_004176053.1|  69 DEINKGLAPLETVRRQVS-ELVQRVEELEEKVKALEQQGERRPAETYGEARTGKPYKSGIERL 130
                                       555555666777777765.6889**********************************986655 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.7   6.2e-05     0.079      93     148 ..      52     107 ..      20     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                        Lebercilin  93 keaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkle 148
                                       +e +l++++  l++  +   +k La  e++ ++++el +++ee eek+k Le++ e
  gi|320100461|ref|YP_004176053.1|  52 REGDLEKIRARLERFVQDEINKGLAPLETVRRQVSELVQRVEELEEKVKALEQQGE 107
                                       68899************99*********************************9865 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 ?   12.1   0.3   9.8e-05      0.13      16      60 ..      54     105 ..      44     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-05
                              SKA2  16 sdLdyvqhrLekefqqsypdna.......eNpvkLlerlkkvkeelqaLkeq 60 
                                        dL+ +  rLe+ +q++ ++         + + +L++r++++ e+++aL++q
  gi|320100461|ref|YP_004176053.1|  54 GDLEKIRARLERFVQDEINKGLapletvrRQVSELVQRVEELEEKVKALEQQ 105
                                       69*********99999999987666677777778888888888888888776 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 ?   12.1   1.1   0.00011      0.14      77     125 ..      56     103 ..       6     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                            Phasin  77 aeeqwdklekafdervakaLsrlgvpsredveaLsarvdeLtkelekla 125
                                       +e+   +le+ +++ ++k L  l+   r+ v++L +rv+eL++++++l+
  gi|320100461|ref|YP_004176053.1|  56 LEKIRARLERFVQDEINKGLAPLETV-RRQVSELVQRVEELEEKVKALE 103
                                       44555699****************87.567***************9886 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 ?   11.1   2.9   0.00021      0.26      26      59 ..      70     103 ..      52     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                     TRAF_BIRC3_bd  26 EverssttieaverqrrldqekieaLekKvrqLe 59 
                                       E+++  + +e v+rq  +  + +e Le+Kv++Le
  gi|320100461|ref|YP_004176053.1|  70 EINKGLAPLETVRRQVSELVQRVEELEEKVKALE 103
                                       9999999**************************9 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00015      0.19      81     122 ..      63     104 ..      22     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                           DUF1664  81 iskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       + + +++e+++    l++++++v+++ + ve+le+k++ +e+
  gi|320100461|ref|YP_004176053.1|  63 LERFVQDEINKGLAPLETVRRQVSELVQRVEELEEKVKALEQ 104
                                       4556789999999999***********************996 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.5   0.00043      0.55      22     101 ..      28     109 ..      15     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                            APG6_N  22 ekerdaYeeflkklkkekkeeek.qdeeleeleeelek.lekeeeelleeLkelekereeleaelaaleeelealee 96 
                                       e+  ++ +++  +l +ek+ ++   + +le+++ +le+ +++e ++ l+ L+ + ++ +el + +++lee+ +ale+
  gi|320100461|ref|YP_004176053.1|  28 ERGFRDVSSYITELLSEKTLQQPgREGDLEKIRARLERfVQDEINKGLAPLETVRRQVSELVQRVEELEEKVKALEQ 104
                                       44444555566666666554433678899******99978999999******************************* PP

                            APG6_N  97 eeerf 101
                                       + er 
  gi|320100461|ref|YP_004176053.1| 105 QGERR 109
                                       99875 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.5   0.00018      0.23     178     249 ..      33     105 ..       6     120 .. 0.56
   2 ?   -3.3   0.1       2.6   3.3e+03     129     150 ..     176     197 ..     175     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                              Spc7 178 eleeeleklqeaaeeles.idkeeLeelreelae.lkaeieekkkelaelqeqleeleekieelkeqkseleee 249
                                       ++++ +++l ++++ l++   + +Le++r +l++ ++ ei++  + l+++++q+ el +++eel+e+ + le++
  gi|320100461|ref|YP_004176053.1|  33 DVSSYITELLSEKT-LQQpGREGDLEKIRARLERfVQDEINKGLAPLETVRRQVSELVQRVEELEEKVKALEQQ 105
                                       33333333333222.22212355666666666653455666666666666666666666666666666666554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                              Spc7 129 WYeWRmqllegLkegleenleg 150
                                       W e++ +l+ ++k++ ee+l+ 
  gi|320100461|ref|YP_004176053.1| 176 WREFKEKLFGEVKSNSEEELKR 197
                                       7788888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1266  (0.0706119); expected 358.6 (0.02)
Passed bias filter:                      969  (0.0540465); expected 358.6 (0.02)
Passed Vit filter:                       180  (0.0100396); 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 0.28s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 1715.27
//
Query:       gi|320100462|ref|YP_004176054.1|  [L=127]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.24   11.4   0.0    1.2  1  Gag_p17   gag gene protein p17 (matrix protein)


Domain annotation for each model (and alignments):
>> Gag_p17  gag gene protein p17 (matrix protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.3e-05      0.24      40      94 ..      63     120 ..      58     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
                           Gag_p17  40 lerfavdeglleteeGckkileql...epalktGseglrslyntvavllcvhqeikvk 94 
                                        + f vd++ l+ eeGc++ ++ +   +p  + G  gl  l +t++v+   +++ kv+
  gi|320100462|ref|YP_004176054.1|  63 ADVFDVDPDTLNDEEGCREFMDLVirwDPDANRGWLGLWRLGDTIVVVAAEYNDEKVE 120
                                       5789**************9887542338999999999999999998888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 958.66
//
Query:       gi|320100463|ref|YP_004176055.1|  [L=359]
Description: RNA procession exonuclease-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-08   34.1   0.0    3.3e-08   33.3   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
          1    9.3   7.1       0.85    9.6   3.1    2.6  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   3.7e-12   3.3e-08      35     177 ..      40     173 ..      29     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.7e-12
                                       E-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT..TTEEEEEE-TTSEEEECSTTEEEEEEE CS
                     Lactamase_B_2  35 llthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee..pavnvheldwgesfelgdggleitatp 109
                                       ++thaH+DHl+gl    ++++   ++++++ +l+ +ea   y  ++     +++++++ ++e ++++ g+ ++ + p
  gi|320100463|ref|YP_004176055.1|  40 VVTHAHIDHLKGLEESIRFSK---TIVGTAVTLDLVEALN-YVGRDLLpyYRLKRKPIGLNECMSIE-GD-RMCLLP 110
                                       79***********99999876...6999999999999995.44444445999**************7.45.799999 PP

                                       E-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH......HHT CS
                     Lactamase_B_2 110 arhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemir......hmg 177
                                       a+h  g          + + +e +g ++ y+gD +  ++ +   ++g+d l++++t+ +++  +       +m 
  gi|320100463|ref|YP_004176055.1| 111 ASHIPGS---------AQVYVEHEGFKLGYTGDFKLGEGTVV--MKGLDALVIEATYGNPKHRRPfkdvvpEML 173
                                       9999999.........99999*****************9987..************999977443555555555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.1   9.5e-05      0.85      49      76 ..      40      67 ..      17     170 .. 0.62
   2 ?   -1.7   0.1      0.28   2.5e+03      13      39 ..     308     334 ..     304     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 9.5e-05
                                      E-SBSSHHHHTTGGGCTTHHCCEETCCE CS
                       Lactamase_B 49 ilTHlHlDHiGglgglveatdvpvgava 76
                                      ++TH+H+DH  gl++ ++  +  vg   
  gi|320100463|ref|YP_004176055.1| 40 VVTHAHIDHLKGLEESIRFSKTIVGTAV 67
                                      67***********987765555544444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                                       ETTCEEEES--SCHHHHHHHHHHHHHT CS
                       Lactamase_B  13 gdggviLiDtGtsteaaraalelaalg 39 
                                       gd g++++D+  +++a+ ++++l ++g
  gi|320100463|ref|YP_004176055.1| 308 GDPGLVVVDASRDGDAWSLRDALVDKG 334
                                       677899999999999998888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2418.21
//
Query:       gi|320100464|ref|YP_004176056.1|  [L=370]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   85.2   0.0      6e-24   84.5   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-12   48.5   0.0    1.6e-12   48.0   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.1e-10   41.8   0.8    5.6e-09   36.2   0.1    2.9  2  Glyco_transf_4   Glycosyltransferase Family 4
     0.0073   16.7   0.0       0.03   14.7   0.0    2.0  2  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   1.3e-27     6e-24      12     170 ..     182     344 ..     174     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 1.3e-27
                                       TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES......STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.....ngeeekelkklaeelelsdnviflgevsr 83 
                                        e++ ++lsv+r+++eK v+++i ++++l  +   + ++v+aG     n+++ + l++la   ++ d v+f  +v r
  gi|320100464|ref|YP_004176056.1| 182 TEREAMVLSVARISPEKHVERVIYVARELSTR-GVKPRFVVAGslskyNKDYYEGLRELAVREGVDDIVEFKVNVAR 257
                                       588999***********************887.******************************************** PP

                                       SSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  84 edleellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairkllede 159
                                       ++l el++++ i+++p  +E+fGi+++EAmaag+p+++   +g  +++    ++Gl  +  ++ +++ a+r lled+
  gi|320100464|ref|YP_004176056.1| 258 NELVELYRRSMIYLHPTPREHFGISIVEAMAAGTPAVIPLdSGSWRDIAM-CDKGLALPYRSIGEASSAVRMLLEDS 333
                                       ***********************************999883666666555.555**********************9 PP

                                       HHHHHHHHHHH CS
                   Glycos_transf_1 160 elrerlgenar 170
                                        l  +l++++ 
  gi|320100464|ref|YP_004176056.1| 334 SLWMHLSRAGA 344
                                       99888888775 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   3.6e-16   1.6e-12       3     134 .]     187     332 ..     185     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 3.6e-16
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---.......HHHHHHH.T.T-T.TEEEE---..THHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rp....eeleela.a.gleerveftGfv..edlae 68 
                                        +l v r++ ++k v+ ++  + +l  +  + r+v++G+ +  +    e l+ela + g+++ vef   v  ++l e
  gi|320100464|ref|YP_004176056.1| 187 MVLSVARIS-PEKHVERVIYVARELSTRgvKPRFVVAGSLSkYNkdyyEGLRELAvReGVDDIVEFKVNVarNELVE 262
                                       588999995.55999999999988887743379*****6433223566677776644899988*******9888*** PP

                                       HHHH-SEEEE--..---SHHHHHHHHTT-EEEE-.TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  69 llaaadvfvaPs..egfglkllEamaaglpvVat.dvggiaevv.gengllvppgdpealaeailrLled 134
                                       l++++ +++ P+  e fg++++Eamaag+p V   d g ++++   + gl +p ++  +   a+  Lled
  gi|320100464|ref|YP_004176056.1| 263 LYRRSMIYLHPTprEHFGISIVEAMAAGTPAVIPlDSGSWRDIAmCDKGLALPYRSIGEASSAVRMLLED 332
                                       *************99***************9998788889998887889999999999999999999987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.1   1.2e-12   5.6e-09       1     169 [.      18     171 ..      18     172 .. 0.83
   2 ?    0.7   0.0       0.1   4.6e+02       8      32 ..     203     227 ..     200     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.2e-12
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvv..tpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkrekpD 74 
                                       +GG e ++le a a+arrG+ V++   t +++ +l e    ++  ++ v++++l++++ ++  +      +  ++ D
  gi|320100464|ref|YP_004176056.1|  18 PGGSEYVTLETALAFARRGFTVYIDsvTLHTPSRLKELIhHYGLKPGEVRRVGLGDPGGDPLLIVNTSGDILSGRSD 94 
                                       59******************988876644444444444455999********************************* PP

                    Glyco_transf_4  75 vvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrer 151
                                       v+  h+p +l              +   + g +     +   k +s l+  +  +++r++++ ia+S +ta  +r++
  gi|320100464|ref|YP_004176056.1|  95 VLYLHYPSFLSHEF----------YYPGLNGVF-----ELAGKTYSLLNSIVFPFVMRKVKAYIANSSFTASFFRRY 156
                                       **999977763332..........222344555.....466777899999999999********************* PP

                    Glyco_transf_4 152 ygvppekitVipnGvDle 169
                                       yg++p   +Vi ++v+++
  gi|320100464|ref|YP_004176056.1| 157 YGIEP---HVITPPVNTD 171
                                       ****9...********98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.1
                    Glyco_transf_4   8 vleLaraLarrGheVtvvtpgddgp 32 
                                       v ++ar+L  rG++ ++v+ g+  +
  gi|320100464|ref|YP_004176056.1| 203 VIYVARELSTRGVKPRFVVAGSLSK 227
                                       7789*********999996554443 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.5   6.6e+03      47      69 ..      47      69 ..      36      70 .. 0.81
   2 !   14.7   0.0   6.7e-06      0.03       1      78 [.     269     348 ..     269     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                   Glyco_trans_1_2 47 edleelaekiryllanpeerrai 69
                                      +++  l e i ++   p+e r++
  gi|320100464|ref|YP_004176056.1| 47 HTPSRLKELIHHYGLKPGEVRRV 69
                                      56778899999999999999876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.7e-06
                   Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltdda.egleel..ftpgkevilfedleelaekiryllanpeerraiaeaar 74 
                                       i+L+p+ +e +   ++Ea+a+G++a+      + +++   ++g  ++ +++  e+  ++r ll++  ++  +++a+ 
  gi|320100464|ref|YP_004176056.1| 269 IYLHPTPREHFGISIVEAMAAGTPAVIPLDsGSWRDIamCDKG-LALPYRSIGEASSAVRMLLEDSSLWMHLSRAGA 344
                                       678888889999999***********99445566665214555.788899**************************9 PP

                   Glyco_trans_1_2  75 ervl 78 
                                        r++
  gi|320100464|ref|YP_004176056.1| 345 TRAR 348
                                       9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2769.82
//
Query:       gi|320100465|ref|YP_004176057.1|  [L=230]
Description: cobalt transport protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-08   32.3   4.8    1.1e-07   31.7   4.8    1.2  1  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
       0.12   11.4   3.3       0.34    9.9   3.3    1.8  1  PHO4      Phosphate transporter family


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 !   31.7   4.8   1.2e-11   1.1e-07      12     208 ..       9     198 ..       2     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.2e-11
                                       HHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE.......EECTTEEE CS
                              CbiQ  12 vkliwlfllllalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlittegefvfaggg 88 
                                       +++ ++ ++l a+ +   l+++   ++++ + ++++   r+ +  l+l+ + l   +l +l+  +  +g++v+  g 
  gi|320100465|ref|YP_004176057.1|   9 TFMYAVVMTLAAFLVKKPLWLA--AASAVSISIGFAYGGRRMLYLLALASIGLAGVFLNALV--FANTGNVVLESGF 81 
                                       5555555555555555555555..56667777777666655555555444433333333333..5669********* PP

                                       ...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHC.CCSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  89 qisitseGllrglllalRiltllslllllalTTppeeltssl.erlgvPlelalillLayRfiflLleevqrikqAq 164
                                        i + +  +    +++lR l +  +   +alT +  e++ +l +++g P  +al+++ a+R i+l++  +++i+  +
  gi|320100465|ref|YP_004176057.1|  82 -IVVRKHAVEEFTVVSLRLLLIAGAGGVFALTHSSSEIARGLvREIGLPYHVALAVSYALRSIPLIKRDLDEIMFMR 157
                                       .*******************99999999***********9973679******************************* PP

                                       HHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS CS
                              CbiQ 165 klRlgdsklgirrslrslgkliaalflralkraervalAmeaRG 208
                                       k R+      i  + r +  ++ +l+   + ra     + e+RG
  gi|320100465|ref|YP_004176057.1| 158 KQRGYGR---IPLTPRGVSSVLTPLLSINYTRAVWGGVSAEVRG 198
                                       ***9766...6666777777777777777777766666666666 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.3   3.8e-05      0.34     218     256 ..      12      51 ..       6     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.8e-05
                              PHO4 218 aalisiykask.evplwvlllgglaialGlllgGkrvikt 256
                                        a+++++ a   + plw+ ++ +++i++G++ gG+r+   
  gi|320100465|ref|YP_004176057.1|  12 YAVVMTLAAFLvKKPLWLAAASAVSISIGFAYGGRRMLYL 51 
                                       44444443322257**********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1552.74
//
Query:       gi|320100466|ref|YP_004176058.1|  [L=463]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-40  139.3   0.0    5.1e-19   69.2   0.0    2.4  2  ABC_tran        ABC transporter
    9.2e-24   84.8   8.9    3.1e-10   40.4   0.0    4.1  4  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    4.5e-10   39.3   0.0      0.017   14.6   0.0    4.0  3  SMC_N           RecF/RecN/SMC N terminal domain
    1.6e-09   37.4   0.4    8.9e-05   22.2   0.0    2.4  2  AAA_29          P-loop containing region of AAA domain
    4.5e-08   32.9   0.3     0.0023   17.5   0.0    3.0  3  AAA_25          AAA domain
    3.5e-07   30.1   0.1     0.0014   18.4   0.0    2.7  3  AAA_30          AAA domain
    3.7e-07   30.7   0.3      0.013   15.9   0.0    2.6  2  AAA_16          AAA ATPase domain
    2.5e-06   27.8   0.4      0.012   15.9   0.0    2.8  3  AAA_22          AAA domain
    4.4e-06   26.7   0.0     0.0002   21.2   0.0    2.8  3  AAA_15          AAA ATPase domain
    4.7e-06   27.3   0.0     0.0028   18.2   0.0    2.2  2  AAA_23          AAA domain
    5.2e-06   26.7   0.1     0.0034   17.6   0.0    2.6  2  AAA_33          AAA domain
    6.8e-05   22.1   0.0       0.41    9.7   0.0    2.6  2  T2SSE           Type II/IV secretion system protein
    0.00012   22.1   0.9        0.3   11.0   0.1    2.4  2  NACHT           NACHT domain
    0.00012   21.7   0.1       0.25   10.8   0.0    2.2  2  AAA_7           P-loop containing dynein motor region
    0.00012   21.8   0.0        2.2    8.0   0.0    3.8  4  IstB_IS21       IstB-like ATP binding protein
    0.00016   21.5   0.1       0.52   10.0   0.1    2.3  2  AAA_24          AAA domain
    0.00022   20.7   0.3       0.46    9.8   0.0    2.4  2  Mg_chelatase    Magnesium chelatase, subunit ChlI
    0.00031   20.7   0.1        0.1   12.5   0.0    2.4  2  RsgA_GTPase     RsgA GTPase
    0.00055   19.9   2.8       0.43   10.5   0.1    3.0  3  NTPase_1        NTPase
    0.00068   20.0   0.3        1.6    9.1   0.1    2.6  2  AAA_19          AAA domain
     0.0009   19.7   0.2       0.84   10.1   0.0    3.0  3  AAA             ATPase family associated with various cellula
     0.0012   19.1   0.0       0.84   10.1   0.0    2.4  2  RNA_helicase    RNA helicase
     0.0015   18.6   0.0       0.52   10.4   0.0    3.1  3  AAA_14          AAA domain
     0.0017   18.0   2.6       0.75    9.4   0.2    2.7  3  cobW            CobW/HypB/UreG, nucleotide-binding domain
     0.0017   18.9   0.3       0.56   10.8   0.0    2.9  2  AAA_18          AAA domain
     0.0026   17.8   1.3       0.39   10.7   0.1    2.5  2  AAA_5           AAA domain (dynein-related subfamily)
     0.0032   17.4   0.1        3.5    7.7   0.0    2.3  2  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
     0.0038   17.2   0.0       0.22   11.4   0.0    2.2  2  Rad17           Rad17 P-loop domain
     0.0053   16.3   1.0       0.27   10.7   0.2    2.2  2  Pox_A32         Poxvirus A32 protein
     0.0062   16.2   0.8       0.14   11.8   0.1    2.3  2  SRP54           SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.016   14.6   0.1          3    7.1   0.0    2.5  2  FtsK_SpoIIIE    FtsK/SpoIIIE family
      0.018   14.8   0.0        3.8    7.2   0.0    2.6  2  PRK             Phosphoribulokinase / Uridine kinase family
      0.026   14.5   0.0        7.2    6.4   0.0    2.3  2  ATPase_2        ATPase domain predominantly from Archaea
      0.031   14.1   0.5        2.4    7.9   0.0    2.5  2  ATP_bind_1      Conserved hypothetical ATP binding protein
      0.036   13.2   0.1       0.85    8.7   0.0    2.2  2  NB-ARC          NB-ARC domain
       0.04   13.4   0.1        4.4    6.7   0.0    2.4  2  PhoH            PhoH-like protein
      0.041   13.9   0.1        1.8    8.6   0.1    2.3  2  Dynamin_N       Dynamin family
      0.062   13.2   0.2        6.3    6.7   0.0    2.7  2  APS_kinase      Adenylylsulphate kinase
       0.07   12.9   0.1       0.38   10.5   0.0    2.0  2  Cytidylate_kin  Cytidylate kinase
      0.077   12.2   0.1        2.9    7.0   0.0    2.1  2  PIF1            PIF1-like helicase
      0.088   13.0   2.8       0.66   10.2   0.2    2.7  2  AAA_28          AAA domain
       0.11   12.3   0.0        4.7    6.9   0.0    2.5  2  AAA_11          AAA domain
       0.15   12.0   0.9         14    5.6   0.1    2.6  2  MobB            Molybdopterin guanine dinucleotide synthesis 
       0.15   11.4   0.2         13    5.1   0.1    2.2  2  ATPase          KaiC
       0.24   10.5   0.6        4.5    6.4   0.1    2.7  3  TIP49           TIP49 P-loop domain
       0.28   10.1   0.1        1.7    7.5   0.0    1.9  2  AAA_10          AAA-like domain
       0.46   10.6   2.4       0.92    9.6   0.2    2.4  2  MMR_HSR1        50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   3.1e-21   1.2e-18       5     137 .]      26     174 ..      22     174 .. 0.89
   2 !   69.2   0.0   1.3e-21   5.1e-19       2     136 ..     267     393 ..     266     394 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 3.1e-21
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkp.....teGeilld.gkdlkeqeleslrkeigvlpqe..pqlfpe 73 
                                        l+   ge   ++G++G+GK+ +l  ++g lk       eGe++l+  ++l+++e  +l   +g++ q+   q+ + 
  gi|320100466|ref|YP_004176058.1|  26 RLEAWSGEACMLTGPSGSGKTVFLLSITGILKHllngvVEGEVRLKgLNPLHRDEYARLPGFLGFVMQDpeRQIIYP 102
                                       577789**************************999999********6677777****************66445555 PP

                                       SBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + + e             e+++++ ++l+ lgl +++ ++v    ++LSgG+++r+a+  +++ +p++++lDEp+a
  gi|320100466|ref|YP_004176058.1| 103 TPLDEAiavleargysyeEAERKAIQVLDALGLRGKAGEHV----ENLSGGERKRLAITLSIIHDPDIIILDEPSA 174
                                       545555888899****9999999************999999....*****************************75 PP

  == domain 2  score: 69.2 bits;  conditional E-value: 1.3e-21
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       +n ++++++ge+va+vG+nG+GKSt+lk+lag lkp  Ge+              + + + + pq+ +++f + +vr
  gi|320100466|ref|YP_004176058.1| 267 ENADIHIRRGEVVALVGPNGSGKSTILKTLAGFLKPLGGEV------------INAARGLFYAPQNpDTVFIHGSVR 331
                                       688999***********************************............346788999999998999999999 PP

                                       HH..HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx..xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++  +++++   a ++l   +   ++vk      LS+Gq++ +++  a +  ++l+llDEpt
  gi|320100466|ref|YP_004176058.1| 332 REleDASRRTRVAFEELASMYPWYERVKGLHpLRLSHGQRRWLSILVAYAYGRDLMLLDEPT 393
                                       99988888899999999888877666654434*****************************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 ?    6.6   0.2     0.015       5.8       4      27 ..      37      57 ..      36      75 .. 0.80
   2 !   17.3   0.0   8.3e-06    0.0032     236     294 ..     145     199 ..     114     202 .. 0.85
   3 !   23.6   0.5   1.1e-07     4e-05       2      24 ..     279     301 ..     278     333 .. 0.75
   4 !   40.4   0.0   8.2e-13   3.1e-10     235     303 .]     364     429 ..     322     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                            AAA_21  4 liGpNgsGKSnLLdaldllarldr 27
                                      l+Gp gsGK+ +L  + ++   ++
  gi|320100466|ref|YP_004176058.1| 37 LTGPSGSGKTVFLLSITGI---LK 57
                                      99***********999887...44 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 8.3e-06
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvil 294
                                       +lS G ++ la+ ++++ ++   +++++DEp ++L+P+ +  + +l+ +e+sr  + vil
  gi|320100466|ref|YP_004176058.1| 145 NLSGGERKRLAITLSIIHDP---DIIILDEPSASLDPAGIGFIRRLVsREKSR--GRVIL 199
                                       6899***999*******999...**************9998888999444444..55554 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 1.1e-07
                            AAA_21   2 nvliGpNgsGKSnLLdaldllar 24 
                                        +l+GpNgsGKS++L++l ++  
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLAGFLK 301
                                       68****************88743 PP

  == domain 4  score: 40.4 bits;  conditional E-value: 8.2e-13
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpllld 303
                                         lS G++r+l +l+a+++ +   +l l+DEp +gL+++l + l++l++el+ +g  ++l+TH+p l++
  gi|320100466|ref|YP_004176058.1| 364 LRLSHGQRRWLSILVAYAYGR---DLMLLDEPTTGLDHALYSGLVKLVNELRGRGRSILLSTHDPRLVA 429
                                       56899*************999...9****************************************9985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   9.4e-05     0.036      28     213 ..      36     220 ..      24     225 .. 0.63
   2 !   14.6   0.0   4.4e-05     0.017      25      44 ..     277     296 ..     266     302 .. 0.84
   3 ?    3.6   0.0     0.098        37     136     210 ..     365     437 ..     341     445 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-05
                                       EEEESTTSSHHHHHHHH....HHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAi....lFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                       +++Gp GSGK+ +l +i    +++L      ++r + l+ l     ++ +   + +  +++++++++   ++  +  
  gi|320100466|ref|YP_004176058.1|  36 MLTGPSGSGKTVFLLSItgilKHLLNGVVEGEVRLKGLNPLHR---DEYARLPGFLGFVMQDPERQIIYPTPLDEAI 109
                                       5667777777766666511113444333333555555555533...3444455556666666666655555555555 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                         ++  g s  + ++k ++  +   l  +ag + e+LSgGe++ +a+ L   i  ++   + +lDe  a LD + + 
  gi|320100466|ref|YP_004176058.1| 110 AVLEARGYSYEEAERKAIQVLDALGLRGKAGEHVENLSGGERKRLAITLS--I--IHDPDIIILDEPSASLDPAGIG 182
                                       55555555555666666666777777777788889*******98777665..3..3445589*************** PP

                                       HHHHHHHHHCTTSEEEEE-.SSHHHCCC-.SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxx RF
                             SMC_N 178 kvaellkeksknaQfivis.lreemleka.dklvgvtk 213
                                        + +l+ +++++  +i  + ++ + +++  dk + v+k
  gi|320100466|ref|YP_004176058.1| 183 FIRRLVSREKSRGRVILLTeHKGGYFADLvDKAYAVRK 220
                                       ******99888888887662444555444466666665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.4e-05
                                       SEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                       ++ a+vGpNGSGKs +l  +
  gi|320100466|ref|YP_004176058.1| 277 EVVALVGPNGSGKSTILKTL 296
                                       5789************9876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.098
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka.dklvg 210
                                        LS G++  ++  +l+A      + l+llDe    LD++  + +++l++e + +   ++  +++ ++++++ d+++ 
  gi|320100466|ref|YP_004176058.1| 365 RLSHGQRRWLS--ILVAYA--YGRDLMLLDEPTTGLDHALYSGLVKLVNELRGRgRSILLSTHDPRLVADVaDRVYV 437
                                       67777777544..444433..344699**********************9998834455566666666544244444 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   0.1   0.00018     0.067      23      42 ..      32      52 ..      24      57 .. 0.79
   2 !   22.2   0.0   2.3e-07   8.9e-05      15      49 ..     269     303 ..     265     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                            AAA_29 23 g.atlltGpsGsGKSTllDAi 42
                                      g a++ltGpsGsGK+ +l +i
  gi|320100466|ref|YP_004176058.1| 32 GeACMLTGPSGSGKTVFLLSI 52
                                      4589***********988555 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 2.3e-07
                            AAA_29  15 htieidlkgatlltGpsGsGKSTllDAiqalLvpa 49 
                                        +i+i++ +++ l+Gp+GsGKST+l  ++  L p 
  gi|320100466|ref|YP_004176058.1| 269 ADIHIRRGEVVALVGPNGSGKSTILKTLAGFLKPL 303
                                       578888667***************98777766665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00037      0.14      32      53 ..      31      52 ..       8      55 .. 0.84
   2 ?   -1.0   0.0         3   1.1e+03     121     152 ..     142     173 ..     112     178 .. 0.76
   3 !   17.5   0.0     6e-06    0.0023      23      82 ..     263     331 ..     252     394 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                            AAA_25 32 agelallaGapgtGKttlaldl 53
                                       ge ++l+G++g+GKt+++l++
  gi|320100466|ref|YP_004176058.1| 31 SGEACMLTGPSGSGKTVFLLSI 52
                                      4999***************986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                            AAA_25 121 rggtlltadvdaleaaieevegvrlvviDpls 152
                                       + ++l  ++ ++l+ ++  +++++ +++D  s
  gi|320100466|ref|YP_004176058.1| 142 HVENLSGGERKRLAITLSIIHDPDIIILDEPS 173
                                       445556677788888999999*******9765 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 6e-06
                            AAA_25  23 rwlvkg...llpagelallaGapgtGKttlaldlalava.tGkpwlg.....pvapeqgkVlyvsaEds 82 
                                       + lv++   ++++ge+++l+G+ g+GK+t++  la  +  +G ++        +ap++  ++++++  +
  gi|320100466|ref|YP_004176058.1| 263 EPLVENadiHIRRGEVVALVGPNGSGKSTILKTLAGFLKpLGGEVINaarglFYAPQNPDTVFIHGSVR 331
                                       44555545599*******************999987776644444444555544555555555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0038       1.5      20      45 ..      34      59 ..      27      79 .. 0.82
   2 ?   -2.1   0.0       6.9   2.6e+03      81      99 ..     151     174 ..      92     204 .. 0.58
   3 !   18.4   0.0   3.6e-06    0.0014      17      54 ..     275     312 ..     268     320 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0038
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa 45
                                       ++ltGp G+GKt  l +++ ++++ 
  gi|320100466|ref|YP_004176058.1| 34 ACMLTGPSGSGKTVFLLSITGILKHL 59
                                      689************99999888776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.9
                            AAA_30  81 k.....grarlepgtllivDEagm 99 
                                       +         +++ +++i DE + 
  gi|320100466|ref|YP_004176058.1| 151 RkrlaiTLSIIHDPDIIILDEPSA 174
                                       234443212234458888888765 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 3.6e-06
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAp 54 
                                       +  v++l+Gp G+GK+t+lk+l+  ++  gg+vi +A 
  gi|320100466|ref|YP_004176058.1| 275 RGEVVALVGPNGSGKSTILKTLAGFLKPLGGEVINAAR 312
                                       44599*****************************9985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   0.00033      0.12      23      45 ..      31      53 ..      22     200 .. 0.79
   2 !   15.9   0.0   3.5e-05     0.013      22      51 ..     274     303 ..     265     391 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00033
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                      ++e+++l+G+sG+GK+  + ++ 
  gi|320100466|ref|YP_004176058.1| 31 SGEACMLTGPSGSGKTVFLLSIT 53
                                      5689************9986665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.5e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekd 51 
                                        r+e+v l+G+ G+GKs+++++l+  l+  
  gi|320100466|ref|YP_004176058.1| 274 RRGEVVALVGPNGSGKSTILKTLAGFLKPL 303
                                       56699***************9998655444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.3    0.0054       2.1       7      23 ..      34      50 ..      31      60 .. 0.84
   2 ?   -1.6   0.0       7.9     3e+03      85     115 ..     157     187 ..     110     202 .. 0.55
   3 !   15.9   0.0   3.2e-05     0.012       5     103 ..     276     396 ..     272     425 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0054
                            AAA_22  7 ilvvtGesGtGKTtllr 23
                                       +++tG+sG+GKT+ l 
  gi|320100466|ref|YP_004176058.1| 34 ACMLTGPSGSGKTVFLL 50
                                      5789*********9875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.9
                            AAA_22  85 alrarav...ielliiDEaqh.lrseealeeLrsl 115
                                        l+       + ++i+DE    l  ++ + ++r+l
  gi|320100466|ref|YP_004176058.1| 157 TLS---IihdPDIIILDEPSAsL-DPAGIGFIRRL 187
                                       222...13335788888865556.44444445444 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 3.2e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee................erpevvfvtlpsstsskdllrellralg 65 
                                         +++++G+ G+GK+t l++l+  l+                       ++p++vf+  ++  +++d  r+   a++
  gi|320100466|ref|YP_004176058.1| 276 GEVVALVGPNGSGKSTILKTLAGFLK------PlggevinaarglfyapQNPDTVFIHGSVRRELEDASRRTRVAFE 346
                                       66889*****************9994......122346656667777777777777777777766666666666666 PP

                            AAA_22  66 lelka..........erlsseellealeqalrarav.ielliiDEaqh.l 103
                                       + ++            +l++++  ++    l a+a  + l+++DE    l
  gi|320100466|ref|YP_004176058.1| 347 ELASMypwyervkglHPLRLSHGQRRWLSILVAYAYgRDLMLLDEPTTgL 396
                                       54444777775555555555555555555555555577777777755555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       6.4   2.4e+03     320     336 ..     160     176 ..     151     178 .. 0.83
   2 !   21.2   0.0   5.3e-07    0.0002      16      48 ..     268     301 ..     265     326 .. 0.87
   3 ?    1.8   0.0      0.41   1.5e+02     298     368 ..     367     427 ..     364     428 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.4
                            AAA_15 320 keeknvilliEEPEahL 336
                                       +  +++i++++EP a+L
  gi|320100466|ref|YP_004176058.1| 160 IIHDPDIIILDEPSASL 176
                                       66789********9987 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 5.3e-07
                            AAA_15  16 dveidlsee.ltvliGkNnsGKSsilealdlFln 48 
                                       +++i++    +  l+G+N+sGKS+il+ l  Fl+
  gi|320100466|ref|YP_004176058.1| 268 NADIHIRRGeVVALVGPNGSGKSTILKTLAGFLK 301
                                       566676666699*****************99998 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.41
                            AAA_15 298 GsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       ++G++r l++  l ++a  +       ++ l++EP + L   + + l+kl  el   ++  ++++TH p +
  gi|320100466|ref|YP_004176058.1| 367 SHGQRRWLSI--LVAYAYGR-------DLMLLDEPTTGLDHALYSGLVKLVNELRGRGR-SILLSTHDPRL 427
                                       7788886655..45666666.......78**********999************99999.9******9976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.022       8.3      24      43 ..      37      56 ..      33      79 .. 0.88
   2 !   18.2   0.0   7.3e-06    0.0028      20      39 ..     277     296 ..     263     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.022
                            AAA_23 24 ItGpNGaGKTTildAiklaL 43
                                      +tGp G+GKT +l  i+ +L
  gi|320100466|ref|YP_004176058.1| 37 LTGPSGSGKTVFLLSITGIL 56
                                      79**********99999877 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7.3e-06
                            AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                        +++++GpNG+GK+Til  +
  gi|320100466|ref|YP_004176058.1| 277 EVVALVGPNGSGKSTILKTL 296
                                       5889************9866 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.024         9       3      16 ..      36      49 ..      35      63 .. 0.88
   2 !   17.6   0.0   8.8e-06    0.0034       1      33 [.     278     326 ..     278     422 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.024
                            AAA_33  3 llvGlpGsGKstla 16
                                      +l G++GsGK+ ++
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVFL 49
                                      789********986 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 8.8e-06
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklgavllssdt.............l 33 
                                       +v lvG++GsGKst ++ l   lk+lg+++++                +
  gi|320100466|ref|YP_004176058.1| 278 VVALVGPNGSGKSTILKTLagfLKPLGGEVINAARglfyapqnpdtvfI 326
                                       799***************9777888889999876555555555555551 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0013      0.48     132     154 ..      35      57 ..      25      65 .. 0.85
   2 !    9.7   0.0    0.0011      0.41      91     155 ..     214     302 ..     209     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                             T2SSE 132 ilvsGgTgsGKttllyallkein 154
                                        +++G+ gsGKt++l ++  +++
  gi|320100466|ref|YP_004176058.1|  35 CMLTGPSGSGKTVFLLSITGILK 57 
                                       579************98877765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
                             T2SSE  91 ealviRkksakeltlddlgaeealk............................ekiaevlrkavrerglilvsGgTg 139
                                       +a+++Rk+++ el  ++++  e++                             e         +r+  ++ + G+ g
  gi|320100466|ref|YP_004176058.1| 214 KAYAVRKRRVVELAGEEIADYEKMPecretlgssggvlletrglsagyreplvE----NADIHIRRGEVVALVGPNG 286
                                       667777777777766666666666666677777777777777777766642222....333345555778899**** PP

                             T2SSE 140 sGKttllyallkeink 155
                                       sGK+t+l +l  +++ 
  gi|320100466|ref|YP_004176058.1| 287 SGKSTILKTLAGFLKP 302
                                       ********99988875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0024       0.9       3      21 ..      35      53 ..      33      61 .. 0.85
   2 !   11.0   0.1   0.00079       0.3       2      21 ..     278     297 ..     277     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      ++l+G++GsGKT++l ++ 
  gi|320100466|ref|YP_004176058.1| 35 CMLTGPSGSGKTVFLLSIT 53
                                      789************9986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00079
                                       CEEEEC-TTTCHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                       +v+l G++GsGK+t l+ la
  gi|320100466|ref|YP_004176058.1| 278 VVALVGPNGSGKSTILKTLA 297
                                       799**************998 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0033       1.3      33      53 ..      32      52 ..      26      61 .. 0.83
   2 !   10.8   0.0   0.00066      0.25      27      54 ..     270     297 ..     267     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0033
                             AAA_7 33 kkpvllvGptGtGKtviikdl 53
                                      +  ++l+Gp+G+GKtv + ++
  gi|320100466|ref|YP_004176058.1| 32 GEACMLTGPSGSGKTVFLLSI 52
                                      5689************98665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00066
                             AAA_7  27 elllknkkpvllvGptGtGKtviikdll 54 
                                       + +++++  v lvGp G+GK++i+k+l 
  gi|320100466|ref|YP_004176058.1| 270 DIHIRRGEVVALVGPNGSGKSTILKTLA 297
                                       578999999**************99875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.016       6.2      47      66 ..      32      51 ..      27      56 .. 0.85
   2 ?    1.2   0.0      0.69   2.6e+02      97     158 ..     152     212 ..     142     219 .. 0.78
   3 !    8.0   0.0    0.0058       2.2      43      67 ..     272     296 ..     263     302 .. 0.87
   4 ?   -0.3   0.0       2.1   7.9e+02      90     147 ..     364     422 ..     352     427 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                         IstB_IS21 47 kenivllGpsGvGKshlaia 66
                                       e+++l+GpsG GK+ +  +
  gi|320100466|ref|YP_004176058.1| 32 GEACMLTGPSGSGKTVFLLS 51
                                      5889***********87655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.69
                         IstB_IS21  97 gklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewdevl 158
                                        +la +l+ +  +d++ilD+ +   ld a    + +++++   r  +i+ ++ + + + +++
  gi|320100466|ref|YP_004176058.1| 152 KRLAITLSIIHDPDIIILDEPS-ASLDPAGIGFIRRLVSREKSRGRVILLTEHKGGYFADLV 212
                                       5777888899999*******76.579999999999999999988888888777776666655 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0058
                         IstB_IS21  43 fiekkenivllGpsGvGKshlaial 67 
                                       +i++ e ++l+Gp G GKs +  +l
  gi|320100466|ref|YP_004176058.1| 272 HIRRGEVVALVGPNGSGKSTILKTL 296
                                       69999*************9876655 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.1
                         IstB_IS21  90 lkrarrdgklaralkrllkv.dllilDdlgllpldqaeaellfeviekryer.rsiiits 147
                                       l++ +++ +  ++l +++   dl++lD+  ++ ld+a  + l +++++  +r rsi++++
  gi|320100466|ref|YP_004176058.1| 364 LRLSHGQRRWLSILVAYAYGrDLMLLDEP-TTGLDHALYSGLVKLVNELRGRgRSILLST 422
                                       66667777777766666554488899986.567999999999999999887746777776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0022      0.83       5      22 ..      35      52 ..      31     130 .. 0.81
   2 !   10.0   0.1    0.0014      0.52       4      22 ..     278     296 ..     275     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0022
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++++Gpsg+GKT +++++
  gi|320100466|ref|YP_004176058.1| 35 CMLTGPSGSGKTVFLLSI 52
                                      79************9988 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0014
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        ++++Gp+g+GK+t++k+l
  gi|320100466|ref|YP_004176058.1| 278 VVALVGPNGSGKSTILKTL 296
                                       689**************99 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0029       1.1      24      49 ..      34      59 ..      26      69 .. 0.86
   2 !    9.8   0.0    0.0012      0.46      25      50 ..     279     304 ..     263     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppl 49
                                        +l+Gp+GsGKt+    ++++l +l
  gi|320100466|ref|YP_004176058.1| 34 ACMLTGPSGSGKTVFLLSITGILKHL 59
                                      5799****************999876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                      Mg_chelatase  25 lllvGppGsGKtmlakrlpsllppls 50 
                                       + lvGp GsGK+ + k l++ l pl 
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLAGFLKPLG 304
                                       679******************99885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.031        12      95     121 ..      28      54 ..       8      69 .. 0.80
   2 !   12.5   0.0   0.00027       0.1      98     122 ..     275     299 ..     261     313 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.031
                                       HHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallp 121
                                       e+++++ ++l G+SG GK+ ++ ++++
  gi|320100466|ref|YP_004176058.1|  28 EAWSGEACMLTGPSGSGKTVFLLSITG 54 
                                       56788999***********99887776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00027
                                       TTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpe 122
                                       ++++++lvG+ G GKSt++++l++ 
  gi|320100466|ref|YP_004176058.1| 275 RGEVVALVGPNGSGKSTILKTLAGF 299
                                       4599*****************9975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0011      0.43       3      41 ..      36      71 ..      34      74 .. 0.84
   2 ?   -1.0   0.0       3.7   1.4e+03      73     103 ..     141     171 ..     121     172 .. 0.74
   3 !    8.0   0.1    0.0064       2.4       2      27 ..     279     304 ..     278     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                                      EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE--- CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreg 41
                                      ++TGp+G+GKt ++  ++  lk+    ++G++  evr +
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVFLLSITGILKHL---LNGVVEGEVRLK 71
                                      79*******************755...888888888865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.7
                                       TEEE-HHHHHHHHHHHHHHHHHHH-EEEE-- CS
                          NTPase_1  73 kyvvdvesfeelalealrkalseadviviDE 103
                                       + v ++   e+  l++    ++++d+i++DE
  gi|320100466|ref|YP_004176058.1| 141 EHVENLSGGERKRLAITLSIIHDPDIIILDE 171
                                       5555555556666666666678999****99 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0064
                                       EEEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssg 27 
                                       v++ Gp G+GK+T++k ++  lk  g
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLAGFLKPLG 304
                                       7899*************999998665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0041       1.6       9      38 ..      31      60 ..      26     199 .. 0.78
   2 !    8.3   0.0    0.0072       2.8       9      38 ..     275     304 ..     268     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0041
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelg 38
                                      + + +++t++ G+GKT  l  i  +l++l 
  gi|320100466|ref|YP_004176058.1| 31 SGEACMLTGPSGSGKTVFLLSITGILKHLL 60
                                      567899***********9988877776654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0072
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelg 38 
                                       + +v++++++ G+GK+++lk+    l+ lg
  gi|320100466|ref|YP_004176058.1| 275 RGEVVALVGPNGSGKSTILKTLAGFLKPLG 304
                                       578999**************9988777665 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 ?    6.3   0.0     0.033        13       2      22 ..      36      56 ..      35      82 .. 0.85
   2 ?   -1.1   0.0       6.1   2.3e+03      35      66 ..     143     171 ..     105     177 .. 0.70
   3 !   10.1   0.0    0.0022      0.84       2      23 ..     280     301 ..     279     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.033
                                      EEESSTTSSHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel 22
                                      +l+Gp G GKT +  ++   l
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVFLLSITGIL 56
                                      79*********9988877655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 6.1
                                       SSSSTTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  35 lskyvgesekkirelfkeakekakpsilfiDE 66 
                                       ++++ g   k+++ +++ +    +p i+++DE
  gi|320100466|ref|YP_004176058.1| 143 VENLSGGERKRLAITLSIIH---DPDIIILDE 171
                                       34455555555555555543...478999998 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0022
                                       EEESSTTSSHHHHHHHHHHHHT CS
                               AAA   2 llyGppGtGKTllakavakelg 23 
                                        l+Gp G GK+++ k +a  l+
  gi|320100466|ref|YP_004176058.1| 280 ALVGPNGSGKSTILKTLAGFLK 301
                                       69***************98764 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.021       7.9       2      26 ..      36      59 ..      35     117 .. 0.81
   2 !   10.1   0.0    0.0022      0.84       2      43 ..     280     325 ..     279     334 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.021
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      +l+Gpsg GK+++  + ++ +lk+l
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVFLLS-ITGILKHL 59
                                      799**********999.66666666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0022
                      RNA_helicase   2 wlyGpsgeGKStlakeLakall...kklklkkkdsvys.rnpeddf 43 
                                        l+Gp+g GKSt+ k+La  l    +++ +  ++ +y+ +np++ f
  gi|320100466|ref|YP_004176058.1| 280 ALVGPNGSGKSTILKTLAGFLKplgGEVINAARGLFYApQNPDTVF 325
                                       689*************875544333333444456666655655555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.08        31       3      22 ..      33      52 ..      31      69 .. 0.84
   2 ?   -2.0   0.0       9.1   3.5e+03      64      96 ..     163     198 ..     148     201 .. 0.66
   3 !   10.4   0.0    0.0014      0.52       3      25 ..     277     299 ..     275     365 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.08
                            AAA_14  3 kilvitGaRrvGKTtllkql 22
                                      +++++tG+  +GKT++l  +
  gi|320100466|ref|YP_004176058.1| 33 EACMLTGPSGSGKTVFLLSI 52
                                      6789***********99876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 9.1
                            AAA_14  64 kktylflDEiqev..pewekalkslvdeg.knldvi 96 
                                       +  +++lDE + +  p    ++++lv ++ ++++vi
  gi|320100466|ref|YP_004176058.1| 163 DPDIIILDEPSASldPAGIGFIRRLVSREkSRGRVI 198
                                       467899999766544666677777777554556665 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0014
                            AAA_14   3 kilvitGaRrvGKTtllkqlike 25 
                                       ++++++G+  +GK+t+lk+l+  
  gi|320100466|ref|YP_004176058.1| 277 EVVALVGPNGSGKSTILKTLAGF 299
                                       799***************99844 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2     0.002      0.75       3      36 ..      35      68 ..      33      72 .. 0.84
   2 ?   -2.7   0.0       9.7   3.7e+03     103     132 ..      96     123 ..      85     132 .. 0.63
   3 !    7.8   0.3    0.0061       2.3       2      21 ..     278     297 ..     277     308 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                                      EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS- CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglklavivNef 36
                                       +ltG+ GsGKT +l +++   ++l   v+++e+
  gi|320100466|ref|YP_004176058.1| 35 CMLTGPSGSGKTVFLLSITGILKHLLNGVVEGEV 68
                                      689*************999777788888888776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.7
                                       SHHHHHCCCECEEEEEEETTTH.CCHCCHH CS
                              cobW 103 eeelksdltldavvavvDaknleaeeekie 132
                                       e+++  ++ ld  +av++a+ ++   e+ e
  gi|320100466|ref|YP_004176058.1|  96 ERQIIYPTPLDEAIAVLEARGYS--YEEAE 123
                                       56677778889999999997762..22223 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0061
                                       EEEEEESTTCCHHHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll 21 
                                       v+ l+G+ GsGK+t+l++l 
  gi|320100466|ref|YP_004176058.1| 278 VVALVGPNGSGKSTILKTLA 297
                                       6889************9985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.084        32       2      14 ..      36      48 ..      35      74 .. 0.89
   2 !   10.8   0.0    0.0015      0.56       1      19 [.     279     297 ..     279     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.084
                            AAA_18  2 lltGtpGvGKttl 14
                                      +ltG++G+GKt +
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVF 48
                                      69********965 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0015
                            AAA_18   1 IlltGtpGvGKttlakeLs 19 
                                       ++l G+ G+GK+t+ k L+
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLA 297
                                       6899************995 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.039        15       3      22 ..      36      55 ..      34      65 .. 0.78
   2 !   10.7   0.1     0.001      0.39       2      23 ..     279     300 ..     278     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.039
                                      EEE--SSSSHHHHHHHGGGG CS
                             AAA_5  3 lLvGppGtgKselaerlaaa 22
                                      +L Gp+G+gK+ +  ++   
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVFLLSITGI 55
                                      89*********887776655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.001
                                       EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                                       v LvGp G+gKs++ + la +l
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLAGFL 300
                                       579***************9888 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.011       4.4      16      42 ..      29      55 ..      16      65 .. 0.77
   2 !    7.7   0.0    0.0091       3.5      19      42 ..     276     299 ..     261     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                                      HCHTEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE 16 kalgdvilLeGdLGaGKTtlvrglaka 42
                                      +  g++ +L+G+ G+GKT++  ++   
  gi|320100466|ref|YP_004176058.1| 29 AWSGEACMLTGPSGSGKTVFLLSITGI 55
                                      3337789*************8776554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0091
                                       TEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglaka 42 
                                       g+v++L G+ G+GK+t+ + la  
  gi|320100466|ref|YP_004176058.1| 276 GEVVALVGPNGSGKSTILKTLAGF 299
                                       789****************99865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.16        63      47      64 ..      34      51 ..      21      69 .. 0.76
   2 !   11.4   0.0   0.00059      0.22      45      79 ..     276     310 ..     265     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.16
                             Rad17 47 iLLisGPsGCgkstvvkv 64
                                        +++GPsG gk+  +  
  gi|320100466|ref|YP_004176058.1| 34 ACMLTGPSGSGKTVFLLS 51
                                      5689********987655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00059
                             Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                        +++ + GP G gkst++k L+  l +   e +n+
  gi|320100466|ref|YP_004176058.1| 276 GEVVALVGPNGSGKSTILKTLAGFLKPLGGEVINA 310
                                       4578899**************97776665555554 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00071      0.27      17      33 ..      36      52 ..      33      62 .. 0.85
   2 ?    3.9   0.0     0.082        31      16      33 ..     279     296 ..     273     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00071
                           Pox_A32 17 alvGgsGsGktvyLlsL 33
                                       l+G sGsGktv+Lls+
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVFLLSI 52
                                      589************97 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.082
                           Pox_A32  16 lalvGgsGsGktvyLlsL 33 
                                       +alvG  GsGk + L+ L
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTL 296
                                       69*************988 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.24        91       4      18 ..      35      49 ..      33      61 .. 0.81
   2 !   11.8   0.1   0.00036      0.14       3      33 ..     278     308 ..     276     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.24
                                      EEEEESTTSSHHHHH CS
                             SRP54  4 illvGlqGaGKTttl 18
                                      ++l G+ G+GKT  l
  gi|320100466|ref|YP_004176058.1| 35 CMLTGPSGSGKTVFL 49
                                      79**********766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00036
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvl 33 
                                       v++lvG++G+GK t l  La  lk  g +v+
  gi|320100466|ref|YP_004176058.1| 278 VVALVGPNGSGKSTILKTLAGFLKPLGGEVI 308
                                       899*****************99987776665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.048        18      28      57 ..      18      50 ..       8      55 .. 0.78
   2 ?    7.1   0.0    0.0079         3      42      59 ..     279     296 ..     263     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.048
                                      S-EEEEEGGGS-....SEEEE--TTSSHHHHHH CS
                      FtsK_SpoIIIE 28 gnplvldlkkma...shllvaGatgsGKStaln 57
                                      g+p+ +d +  a      ++ G +gsGK+++l 
  gi|320100466|ref|YP_004176058.1| 18 GSPILVDSRLEAwsgEACMLTGPSGSGKTVFLL 50
                                      666666666666666678999**********95 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0079
                                       EEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  42 llvaGatgsGKStalntL 59 
                                       + ++G  gsGKSt l+tL
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTL 296
                                       5689************98 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0      0.01       3.8       4      26 ..      37      59 ..      35      78 .. 0.81
   2 ?    4.9   0.0     0.051        20       1      24 [.     278     301 ..     278     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
                               PRK  4 vagsSGaGkttvarklekifgre 26
                                      ++g+SG+Gkt +   ++ i+++ 
  gi|320100466|ref|YP_004176058.1| 37 LTGPSGSGKTVFLLSITGILKHL 59
                                      79***************999843 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.051
                               PRK   1 vIgvagsSGaGkttvarklekifg 24 
                                       v+++ g+ G+Gk+t+ ++l   ++
  gi|320100466|ref|YP_004176058.1| 278 VVALVGPNGSGKSTILKTLAGFLK 301
                                       78999************9987665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.033        13      21      45 ..      33      57 ..      23      64 .. 0.77
   2 ?    6.4   0.0     0.019       7.2      21      47 ..     277     303 ..     271     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.033
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiienle 45
                                      e  +++Gp gsGKt +l  i   l+
  gi|320100466|ref|YP_004176058.1| 33 EACMLTGPSGSGKTVFLLSITGILK 57
                                      567899**********998876665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledk 47 
                                       e++ + Gp gsGK+++lk ++  l+ +
  gi|320100466|ref|YP_004176058.1| 277 EVVALVGPNGSGKSTILKTLAGFLKPL 303
                                       677889************987766655 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 ?    3.7   0.1      0.12        44       2      21 ..      38      57 ..      37      63 .. 0.85
   2 ?    7.9   0.0    0.0063       2.4       2      23 ..     282     303 ..     281     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                        ATP_bind_1  2 vGpaGsGKttfvgalseile 21
                                      +Gp GsGKt f  +++ il+
  gi|320100466|ref|YP_004176058.1| 38 TGPSGSGKTVFLLSITGILK 57
                                      7**********999887766 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0063
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelr 23 
                                       vGp GsGK+t+ ++l+ +l+  
  gi|320100466|ref|YP_004176058.1| 282 VGPNGSGKSTILKTLAGFLKPL 303
                                       8*************99988766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.26        98      24      40 ..      36      52 ..      27      60 .. 0.84
   2 ?    8.7   0.0    0.0022      0.85      21      39 ..     277     295 ..     263     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                                      EEEESTTSSHHHHHHHH CS
                            NB-ARC 24 alvGmgGvGKttlakqi 40
                                       l G  G+GKt+ + +i
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVFLLSI 52
                                      689*********88766 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0022
                                       EEEEEEESTTSSHHHHHHH CS
                            NB-ARC  21 lvvalvGmgGvGKttlakq 39 
                                        vvalvG  G+GK+t++k 
  gi|320100466|ref|YP_004176058.1| 277 EVVALVGPNGSGKSTILKT 295
                                       49**************986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.011       4.4      22     116 ..      35     138 ..      26     142 .. 0.68
   2 ?    4.0   0.0     0.079        30      16      35 ..     273     292 ..     267     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                                       EEEE--TTSSTT..HHHHHHHHHHHHTTS-SEEEEEE-S--T........T----SS---------TTTHHHHHHHT CS
                              PhoH  22 vfaiGpaGtGKt..ylavalavealkkkkvkriiltrpavea........geelGflpgdleekvdpylrplydaLk 88 
                                       ++ +Gp+G+GKt  +l+++  ++ l ++ v+  + ++                lGf+  d  e+  +y  pl +a+ 
  gi|320100466|ref|YP_004176058.1|  35 CMLTGPSGSGKTvfLLSITGILKHLLNGVVEGEVRLKGLNPLhrdeyarlPGFLGFVMQD-PERQIIYPTPLDEAIA 110
                                       6789********544677777899999998877766644333222222233346666666.4555578888888888 PP

                                       TTS-TTCHHHHHHTTSEEEEEGGGGTT- CS
                              PhoH  89 dllgaekvekllekgkievaplaymRGr 116
                                        l  +    +  e++ i+v++   +RG+
  gi|320100466|ref|YP_004176058.1| 111 VLEARGYSYEEAERKAIQVLDALGLRGK 138
                                       7777777777788888888888888887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.079
                                       HHH-SEEEEE--TTSSTTHH CS
                              PhoH  16 lkkndivfaiGpaGtGKtyl 35 
                                       +++ ++v  +Gp G+GK+ +
  gi|320100466|ref|YP_004176058.1| 273 IRRGEVVALVGPNGSGKSTI 292
                                       667899***********876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.31   1.2e+02      96     134 ..     120     169 ..     106     201 .. 0.77
   2 ?    8.6   0.1    0.0046       1.8       1      21 [.     279     299 ..     279     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.31
                                       EETTS-SEEEEE---B-SSSGTTS...........HHHHHHHSTTEEEEE CS
                         Dynamin_N  96 lsllvkgltlvDlPGldsvnkrdq...........elvkeyikkadiila 134
                                        +  +k + ++D  Gl   + ++            +++ ++i++ dii++
  gi|320100466|ref|YP_004176058.1| 120 EEAERKAIQVLDALGLRGKAGEHVenlsggerkrlAITLSIIHDPDIIIL 169
                                       5677889999********99999999********************9986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0046
                                       EEEEEBTTTTHHHHHHHHHTS CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlge 21 
                                       +a+vG   sGKS++l  L g 
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLAGF 299
                                       799***************996 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.13        50       4      23 ..      34      53 ..      31      76 .. 0.74
   2 ?    6.7   0.0     0.016       6.3       1      30 [.     275     304 ..     275     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                                      EEEEESSTTSSHHHHHHHHH CS
                        APS_kinase  4 vvwltGlsgsGKstianale 23
                                        +ltG sgsGK+     + 
  gi|320100466|ref|YP_004176058.1| 34 ACMLTGPSGSGKTVFLLSIT 53
                                      5689********97655444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT CS
                        APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekg 30 
                                       rg vv l G  gsGKsti ++l+  L+  g
  gi|320100466|ref|YP_004176058.1| 275 RGEVVALVGPNGSGKSTILKTLAGFLKPLG 304
                                       578999************999988777655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.1   7.9e+02       4      12 ..      38      46 ..      36      58 .. 0.82
   2 ?   10.5   0.0   0.00099      0.38       1      21 [.     279     299 ..     279     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.1
                                      E-STTSSHH CS
                    Cytidylate_kin  4 DGPagsGKs 12
                                       GP+gsGK 
  gi|320100466|ref|YP_004176058.1| 38 TGPSGSGKT 46
                                      6*******7 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00099
                                       EEEE-STTSSHHHHHHHHHHH CS
                    Cytidylate_kin   1 iaiDGPagsGKssvaralaek 21 
                                       +a+ GP gsGKs++ ++la  
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLAGF 299
                                       6899**************964 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.14        54      21      48 ..      31      58 ..      22      66 .. 0.81
   2 ?    7.0   0.0    0.0075       2.9      19      57 ..     273     311 ..     265     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                      CTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1 21 kgklfFvtGsgGtgKtflwkallkklrs 48
                                      +g+   +tG +G+gKt ++  ++ +l+ 
  gi|320100466|ref|YP_004176058.1| 31 SGEACMLTGPSGSGKTVFLLSITGILKH 58
                                      6888899**********99999999886 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0075
                                       .HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEE CS
                              PIF1  19 nekgklfFvtGsgGtgKtflwkallkklrsegkivlavA 57 
                                        ++g+++ + G  G+gK+ ++k+l  +l++ g  v++ A
  gi|320100466|ref|YP_004176058.1| 273 IRRGEVVALVGPNGSGKSTILKTLAGFLKPLGGEVINAA 311
                                       57899999**********************999999877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2       0.5   1.9e+02       3      16 ..      36      49 ..      34      66 .. 0.86
   2 ?   10.2   0.2    0.0017      0.66       2      20 ..     279     297 ..     278     350 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.5
                            AAA_28  3 vitGgestGKTtll 16
                                      ++tG++++GKT  l
  gi|320100466|ref|YP_004176058.1| 36 MLTGPSGSGKTVFL 49
                                      79*********865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0017
                            AAA_28   2 ivitGgestGKTtlleaLa 20 
                                       ++++G+ ++GK+t+l+ La
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLA 297
                                       89****************9 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.012       4.7      16      41 ..      32      56 ..      23     130 .. 0.72
   2 ?    2.5   0.0      0.27     1e+02      15      63 ..     274     319 ..     263     343 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                            AAA_11 16 eseitliqGPPGtgKTktivellsql 41
                                       +  +++ GP G+gKT +++++   l
  gi|320100466|ref|YP_004176058.1| 32 GE-ACMLTGPSGSGKTVFLLSITGIL 56
                                      44.499**********7766655444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.27
                            AAA_11  15 seseitliqGPPGtgKT...ktivellsqllsrrkseeeksakpriLvCapS 63 
                                       ++ e++ + GP G+gK+   kt++++l+ l        e  + +r L  ap+
  gi|320100466|ref|YP_004176058.1| 274 RRGEVVALVGPNGSGKStilKTLAGFLKPL------GGEVINAARGLFYAPQ 319
                                       566788999********4444444444443......3444555555555555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.09        34       4      24 ..      37      57 ..      34      63 .. 0.86
   2 ?    5.6   0.1     0.035        14       1      27 [.     278     304 ..     278     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.09
                              MobB  4 ivgksgsGKTtLleklipelk 24
                                      ++g sgsGKT +l  +  +lk
  gi|320100466|ref|YP_004176058.1| 37 LTGPSGSGKTVFLLSITGILK 57
                                      7899*********99888776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.035
                              MobB   1 vlgivgksgsGKTtLleklipelkarg 27 
                                       v+++vg +gsGK t+l+ l   lk  g
  gi|320100466|ref|YP_004176058.1| 278 VVALVGPNGSGKSTILKTLAGFLKPLG 304
                                       6899**************998887665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.033        13      19      37 ..      32      50 ..      29      67 .. 0.81
   2 ?    4.0   0.0     0.072        28      16      35 ..     273     292 ..     268     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.033
                            ATPase 19 grvvlitGepGtGKtifal 37
                                      g++  +tG +G+GKt+f l
  gi|320100466|ref|YP_004176058.1| 32 GEACMLTGPSGSGKTVFLL 50
                                      67889**********9964 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.072
                            ATPase  16 ipegrvvlitGepGtGKtif 35 
                                       i +g+vv ++G  G+GK+++
  gi|320100466|ref|YP_004176058.1| 273 IRRGEVVALVGPNGSGKSTI 292
                                       7899*************987 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.012       4.5      48      71 ..      30      53 ..      17      63 .. 0.85
   2 ?   -1.2   0.0       2.4     9e+02      36      60 ..     181     205 ..     179     210 .. 0.87
   3 ?    0.5   0.0      0.71   2.7e+02      50      67 ..     276     293 ..     263     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                                      XXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 48 laGravLlaGpsgtGktalaiais 71
                                       +G a +l+Gpsg+Gkt   ++i+
  gi|320100466|ref|YP_004176058.1| 30 WSGEACMLTGPSGSGKTVFLLSIT 53
                                      689**************9999886 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.4
                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  36 agvivelikekklaGravLlaGpsg 60 
                                        g+i +l+  +k  Gr++Ll+ ++g
  gi|320100466|ref|YP_004176058.1| 181 IGFIRRLVSREKSRGRVILLTEHKG 205
                                       58999**************997766 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.71
                                       XXXXXXXXXXXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktala 67 
                                       G +v l+Gp+g+Gk+ + 
  gi|320100466|ref|YP_004176058.1| 276 GEVVALVGPNGSGKSTIL 293
                                       88999*********9985 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1         1     4e+02      23      38 ..      34      49 ..      26      63 .. 0.84
   2 ?    7.5   0.0    0.0043       1.7      24      52 ..     279     307 ..     262     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1
                            AAA_10 23 asliiGdlGnGKSvla 38
                                      a++++G+ G GK v+ 
  gi|320100466|ref|YP_004176058.1| 34 ACMLTGPSGSGKTVFL 49
                                      689*********9975 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0043
                            AAA_10  24 sliiGdlGnGKSvlakllvlyisllggka 52 
                                       ++++G+ G GKS + k+l  ++  lgg +
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLAGFLKPLGGEV 307
                                       599****************9999988876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       4.2   1.6e+03       2      21 ..      35      54 ..      34      65 .. 0.86
   2 ?    9.6   0.2    0.0024      0.92       2      21 ..     279     298 ..     278     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.2
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      +++ G + +GK+ ++ ++tg
  gi|320100466|ref|YP_004176058.1| 35 CMLTGPSGSGKTVFLLSITG 54
                                      5799********99999987 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0024
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       va+vG   +GKSt++++l g
  gi|320100466|ref|YP_004176058.1| 279 VALVGPNGSGKSTILKTLAG 298
                                       89***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3093.76
//
Query:       gi|320100467|ref|YP_004176059.1|  [L=540]
Description: amino acid permease [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-17   62.7  48.5    5.7e-17   61.7  48.5    1.4  1  AA_permease_2  Amino acid permease
    7.6e-07   28.1  58.2    3.4e-05   22.6  58.2    3.5  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7  48.5   6.3e-21   5.7e-17       1     404 [.      19     521 ..      19     534 .. 0.69

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 6.3e-21
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn.....laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf 72 
                                       ++++++f+ v+  ++ sg f  +      +++ g  ++   +ia++i++ +v+l+++ ++s lprs   yv ++++ 
  gi|320100467|ref|YP_004176059.1|  19 FTWFDVFLWVVANPVASGLFYYSvsatgEYGYYGG-VVPAAFIAAGIVFAPVALLFMIVASSLPRSASPYVLASRGL 94 
                                       78*********999888887777654444444444.66678888888889*********888*************** PP

                     AA_permease_2  73 gkkvaflsawfnwfayvpvlasil..svaasyllnalgp..dlqgn............twltyliaiaililvalin 133
                                       g +++f++a +++f     l++++  ++ ++ l   l    ++ g+            +  ++l a+ ++++++l  
  gi|320100467|ref|YP_004176059.1|  95 GALPGFIAASLYLFMSGGLLSLGFlaYSSIEVLGDGLTVsgHIAGSsilvglgsavraQPYMLLAAFTLVTVLFLAA 171
                                       ************88766655555422445555633332211333338888888888765566666777777778888 PP

                     AA_permease_2 134 irgikesakiqnilgilkillpliiliilglitvdgggfssl...stetdt.........................f 182
                                        +g k ++ +    + l ++  l  ++ l l+ ++++ f+ +                                   
  gi|320100467|ref|YP_004176059.1| 172 GMGRKSVKALLHASTALPLV--LYAAVMLSLFPFSRSVFTGNwdrL----FnnsysrivdlalnggvvngvsvqplR 242
                                       88888888888888888775..445666788888999999766541....033456666666666666666555433 PP

                     AA_permease_2 183 fpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddei....... 250
                                         + w+g++ ++++++w++ G+e+a+ ++ ev++    + k+ + g ++ + +y+++++a++ v + d +       
  gi|320100467|ref|YP_004176059.1| 243 AVSEWSGTFTVFTMAVWAYLGVENASFIAGEVREpgSSYLKGYIAGYMVLVAMYTVTPVAVTLVAGYDFLsaysyly 319
                                       34477778***********************9998568****************************99997788888 PP

                     AA_permease_2 251 .......anlsnlgsv....aalffeavggkvvaiivvilialsllg....aintavigssrvlealardgvlPrff 312
                                              ++l +   v    a  ++  v   ++ ++ ++l++l++++     ++t +++++r+l+al++d+ +Pr  
  gi|320100467|ref|YP_004176059.1| 320 hhypdvlKTLMG---VnappAPCLATIVSVYTGNMVTSLLFTLAAFLfyfnTMLTSWVSATRILFALGEDRLMPRLT 393
                                       777755433333...255566666666666677777777777766666666999*********************** PP

                     AA_permease_2 313 akvn.kfgspiraiiltaivslillllfllas.....saaynfllsvsslgliisyllliigal......ilrkkrp 377
                                       a+v+ +++ p +a  +++i+s++++ ++ ++      +a++  l++++  +++ + +l++i+ l      + r++ +
  gi|320100467|ref|YP_004176059.1| 394 ARVSrRTHVPGYANLFIYILSIAVVSASPFIRshpsiEASFIRLMTLGYAFFLTITGLALISTLvfaeelYERFTFK 470
                                       ****99***************87777777655566666666666666555555555555555551333332233333 PP

                     AA_permease_2 378 hlkr....pgk.....................ilvaiigalfllfllvalff 404
                                       + kr    +g+                     ilva +g+ ++l+l++a  f
  gi|320100467|ref|YP_004176059.1| 471 D-KRvlypIGFttsvvgfalalssfagisltdILVASTGFSLILLLFIAVTF 521
                                       3.22344433344444445555555555555555555555555555444443 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6  58.2   3.8e-09   3.4e-05       8     388 ..      30     465 ..      23     526 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.8e-09
                       AA_permease   8 ggviGtglfvglgvvlsqaGplga..llayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                       ++ +  glf  + +++++ G  g+    a++ ag+v++ v+l +  +a+  p+s++ y++asr lg   Gf  + +y
  gi|320100467|ref|YP_004176059.1|  30 ANPVASGLFYYSVSATGEYGYYGGvvPAAFIAAGIVFAPVALLFMIVASSLPRSASPYVLASRGLGALPGFIAASLY 106
                                       56666799999*********99997889***************************************9999999998 PP

                       AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvt...................gavflvvlliinlvgvkvygeaef 140
                                       lf++   l l++  a + i+ ++    ++  ++                     a f++v +++  +g+       +
  gi|320100467|ref|YP_004176059.1| 107 LFMSGGLLSLGFL-AYSSIEVLGDGLTVS-GHIAgssilvglgsavraqpymlLAAFTLVTVLFLAAGMGRKSVKAL 181
                                       8888888888844.445566665544444.33335677888999999999988666666666666666666665555 PP

                       AA_permease 141 i...lalikiiaiiafiivg......iillaggkpnkga.gfrflgdngsifknnlppgfakeeegafknfisvfvi 207
                                       +   +al ++++++ ++ ++      + ++++   n+ +  +  l  ng++++   ++  +  + +  ++ + vf  
  gi|320100467|ref|YP_004176059.1| 182 LhasTALPLVLYAAVMLSLFpfsrsvFTGNWDRLFNNSYsRIVDLALNGGVVNGVSVQPLR--AVSEWSGTFTVFTM 256
                                       5555777888888888888854555444444444444447677777777755555555544..334489******** PP

                       AA_permease 208 vvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa............ 272
                                       +v a+ G e+   iagEv++P  s  k+ +   + ++ +Y+   ++++l+ +++ l+  +                 
  gi|320100467|ref|YP_004176059.1| 257 AVWAYLGVENASFIAGEVREPGSSYLKGYIAGYMVLVAMYTVTPVAVTLVAGYDFLSAYSYLYHHypdvlktlmgvn 333
                                       *****************************************999999999999998888855544999999999999 PP

                       AA_permease 273 ....aspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaPkvlkkvs.krgvPlraills 344
                                             +  i+ +++g+ v + l++++ ++  +++++ s +sa+R+l++l +d+l+P+  ++vs + +vP  a l+ 
  gi|320100467|ref|YP_004176059.1| 334 appaPCLATIVSVYTGNMVTSLLFTLAAFLFYFNTMLTSWVSATRILFALGEDRLMPRLTARVSrRTHVPGYANLFI 410
                                       999777889999*********************************************66666651569********* PP

                       AA_permease 345 miisllal...............llaslnlaapivfnfllaisaliglivwlliilsyl 388
                                       +i+s +++               ++  ++l+    ++f+l+i++l+ +++++++   y 
  gi|320100467|ref|YP_004176059.1| 411 YILSIAVVsaspfirshpsieasFIRLMTLG----YAFFLTITGLALISTLVFAEELYE 465
                                       ********88888888888444444444444....777777777777666655444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.44
# Mc/sec: 3691.23
//
Query:       gi|320100468|ref|YP_004176060.1|  [L=553]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 4060.54
//
Query:       gi|320100469|ref|YP_004176061.1|  [L=236]
Description: cytidyltransferase-like domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-19   69.6   0.1    2.7e-19   69.0   0.1    1.3  1  DUF357           Protein of unknown function (DUF357)
    8.4e-13   48.7   0.0    2.8e-12   47.0   0.0    1.7  2  CTP_transf_like  Cytidylyltransferase-like


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 !   69.0   0.1     3e-23   2.7e-19       2      71 ..      19      83 ..      18      85 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 3e-23
                                      HHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS CS
                            DUF357  2 YirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlg 71
                                      Yi+++e+al++v      ++ l+ ++e ++e+a+ Y +Daky+lek+d++++la+++YaeG+LD+++++g
  gi|320100469|ref|YP_004176061.1| 19 YIENVEQALQQVG-----SQGLQPVQEYIVELAREYTSDAKYYLEKNDCFTSLACIAYAEGLLDSLRHQG 83
                                      *************.....99***********************************************998 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.2   1.8e+03      56      87 ..      11      57 ..       7      75 .. 0.70
   2 !   47.0   0.0   3.1e-16   2.8e-12       2     138 ..     103     225 ..     102     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                                      HHHTTCTTEEEEEEESEHH..............HHHHHTTTT.EEEE CS
                   CTP_transf_like 56 elakevdevisvdpweltr..............evlkklkpd.klyl 87
                                      e++++v+  i+  +  l++              e+ +++ +d k+yl
  gi|320100469|ref|YP_004176061.1| 11 EECERVKAYIENVEQALQQvgsqglqpvqeyivELAREYTSDaKYYL 57
                                      56666666666666666666777777777777788888888866665 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 3.1e-16
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltrev 76 
                                       + G+F ++H GH++ll++a +l+   ++v v  d +  ++k  +p++ +++Rl  +e  ++v++++  d+ +  +  
  gi|320100469|ref|YP_004176061.1| 103 VAGSFELLHPGHIHLLRRAWELGR--VYVVVSRDSNFERFKgrRPVVGEKDRLTVVENVRYVSKAVLGDEEDFLK-P 176
                                       68*******************999..57778888888888669*******************************7.* PP

                                       HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHH CS
                   CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSst 138
                                       l++lkpd  ++++g d+  +   + el+++l++++l  v+++        k e r  + Ss+
  gi|320100469|ref|YP_004176061.1| 177 LEELKPD--IVLLGPDQWIS---PGELKKLLEERGLSRVRVE--------KLESRIGEWSSS 225
                                       *******..********999...7999999999999888666........444444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1694.37
//
Query:       gi|320100470|ref|YP_004176062.1|  [L=239]
Description: NADPH-dependent FMN reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-28   98.7   0.0    3.7e-28   98.2   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
      5e-12   46.0   0.0    7.9e-12   45.3   0.0    1.3  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.0   4.1e-32   3.7e-28       1     145 [.       5     160 ..       5     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 4.1e-32
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--....---HCHGHT...CGGSHHHHHHHHHHH CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc..alcdkdlese...gqtsddvaellekia 71 
                                       ++ilvi+GS+rk +++ +l  +aa+ +  ag   e++ l d+ i+pc  ++ d+ + ++     ++dd++ l  k+ 
  gi|320100470|ref|YP_004176062.1|   5 PRILVINGSPRKYGSSMQLSIVAAKGVVDAGGIPEIVSLYDYrIKPCmgCVSDGNKYCRfpcVIKDDDFNTLAGKLL 81 
                                       59*********************************************8766665555559978999*********** PP

                                       H-SCEEEEEEECTTCE-HHHHHHHHCHT-.......SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EE CS
                           FMN_red  72 aadaliivtPeYngsysgllKnalDrlsr......trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaiv 142
                                       +++++ii+tP+Y++ +sg+lKn++Drl        ++g+  l+gK+++++a+g + +g + a + l  v++ +ga+v
  gi|320100470|ref|YP_004176062.1|  82 ESHGVIISTPVYWYAPSGVLKNFIDRLTSmehmifHKGRSLLEGKVAGFIATGLD-SGVMMAISYLAIVMSSMGAHV 157
                                       ***************************99*********************99965.********************* PP

                                       EEC CS
                           FMN_red 143 vpr 145
                                       +p 
  gi|320100470|ref|YP_004176062.1| 158 IPW 160
                                       995 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   8.8e-16   7.9e-12       2     184 ..       6     174 ..       5     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 8.8e-16
                                       EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTT..C.HHHHHHH.HH CS
                      Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeek..p.adveseq.ie 73 
                                       +iL+in++pr+   +s +l   +++++ +ag    +++ Ly+    p +   +++ +  y ++     d + +    
  gi|320100470|ref|YP_004176062.1|   6 RILVINGSPRK-YGSSMQLSIVAAKGVVDAG-GIPEIVSLYDYrIKPCMG--CVSDGNKYCRFpcViKDDDFNTlAG 78 
                                       79********9.6888***************.77899*****85555554..333336677777656777888888* PP

                                       HHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTT.SCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS-S CS
                      Flavodoxin_2  74 kllaadaivlqfPlwwfgvPailKgwiDrvltagf.afyteeggegrgggLkgkkalvivttGgpeesyqerglega 149
                                       kll+++ +++++P++w+  + +lK++iDr  ++ + +f   ++   ++ +L+gk a +i+t   +           +
  gi|320100470|ref|YP_004176062.1|  79 KLLESHGVIISTPVYWYAPSGVLKNFIDRLTSMEHmIF---HK---GRSLLEGKVAGFIATG-LD-----------S 137
                                       *******************************9999455...22...2567778877777665.44...........2 PP

                                       -HHHHHHHHHHHHHHTT-EEEEEEEEESCT.CCCH.H CS
                      Flavodoxin_2 150 amdellpplrgilgfiGikdvepvlvegva.gaed.e 184
                                       ++ +++++l  ++  +G++++++  ++ +  ++++ e
  gi|320100470|ref|YP_004176062.1| 138 GVMMAISYLAIVMSSMGAHVIPWSMAYSHLeDITRdE 174
                                       5778999999999999999999999998544333323 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1840.65
//
Query:       gi|320100471|ref|YP_004176063.1|  [L=175]
Description: NUDIX hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   79.4   0.0    3.1e-22   79.0   0.0    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   1.7e-26   3.1e-22       5     117 ..      19     132 ..      16     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 1.7e-26
                                       EEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd 80 
                                       avg+vll+++  +Llv+r   p  g W+lPgG +epgE + +AArREl+EEtG++ae l +l++l +  +++g    
  gi|320100471|ref|YP_004176063.1|  19 AVGAVLLRGDS-ILLVKRGSPPALGrWSLPGGVIEPGERIGDAARRELREETGIDAEPLGVLWVLNNIVMDRGGRVK 94 
                                       89***999995.*******555556*************999**********************99887776665554 PP

                                       EEEEE..EEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHH CS
                             NUDIX  81 eheil..yvfl.eevegelepndenevsevrwvpleellk 117
                                        h+++  ++f  ++++ge++p+   +  +++w+pl e+l+
  gi|320100471|ref|YP_004176063.1|  95 YHYVIvdVLFNpDSLKGEPKPG--SDAVDLKWFPLGEALR 132
                                       4444433555599999999999..77789********933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1327.57
//
Query:       gi|320100472|ref|YP_004176064.1|  [L=235]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-26   92.3  20.0    6.9e-19   68.5   9.1    2.1  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
  ------ inclusion threshold ------
        4.1    7.4   7.3       0.36   10.8   1.8    2.1  2  DUF1427          Protein of unknown function (DUF1427)


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   9.1   7.7e-23   6.9e-19       3     122 ..       2     116 ..       1     132 [. 0.87
   2 !   29.9   3.1   5.6e-11     5e-07      71     171 ..     136     227 ..     132     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 7.7e-23
                                       .TTHHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHH CS
                   ECF-ribofla_trS   3 stkkvvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapft 79 
                                       +++++v  a+++ lv+++t+++++  p  t+g++nlg++++++aal  Gp+v++++G++G alaDl +gY ++ap t
  gi|320100472|ref|YP_004176064.1|   2 RVRQLVEAAVFTVLVYAATVVLQVYQP-VTGGYFNLGESMIYVAALSSGPLVAGIAGGVGAALADLTTGYQVFAPGT 77 
                                       689***********************9.9999********************************************* PP

                                       HHHHHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS  80 liikgliGlivGliakklkknkengvfkilalvlfaivmvigy 122
                                       l+ik  +G+ +G++a+ l+ ++    ++i++ +++++++ +++
  gi|320100472|ref|YP_004176064.1|  78 LVIKLAEGVAAGYLARALRSRH----WRIAGGLIGSAYAAVFT 116
                                       ******************4444....56666666665555544 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 5.6e-11
                                       S-GGGHHHHHHHHHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHHH CS
                   ECF-ribofla_trS  71 gYgiwapftliikgliGlivGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekvalq 147
                                        Y++w+ + l++   +G+i+ +   + + ++     + +al+ ++++mv+gy++ e ++   + +    p    a+ 
  gi|320100472|ref|YP_004176064.1| 136 VYVPWYIW-LLAGLALGFILVYSLLSGRSSA----GEAIALITSGLIMVAGYFLYEYFV--SNPLTGRPPI--DAVF 203
                                       699*****.9999999999988888884444....5999********************..3333333333..3566 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS 148 sipaniiqavvgaiialpLlkala 171
                                       +ip ni q+v+g+++alp+++ l+
  gi|320100472|ref|YP_004176064.1| 204 EIPVNIGQVVTGIVVALPVAAWLR 227
                                       9*****************998876 PP

>> DUF1427  Protein of unknown function (DUF1427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3      0.61   5.5e+03       2      14 ..      41      53 ..      40      59 .. 0.72
   2 ?   10.8   1.8     4e-05      0.36       5      34 ..     142     173 ..     138     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.61
                           DUF1427  2 lYllslgaGllvG 14
                                      +Y+ +l+ G lv 
  gi|320100472|ref|YP_004176064.1| 41 IYVAALSSGPLVA 53
                                      7999999996663 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4e-05
                           DUF1427   5 lslgaGllvG..viYsllnvrsPaPPvvaLvG 34 
                                       + l aGl +G  ++Ysll+ rs a  ++aL+ 
  gi|320100472|ref|YP_004176064.1| 142 IWLLAGLALGfiLVYSLLSGRSSAGEAIALIT 173
                                       56889999994447****************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1712.14
//
Query:       gi|320100473|ref|YP_004176065.1|  [L=427]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-41  141.5   0.0    2.4e-19   70.2   0.0    2.9  2  ABC_tran         ABC transporter
      2e-17   63.9   0.1      9e-06   25.7   0.0    3.8  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.5e-09   37.4   1.0     0.0012   18.5   0.1    2.4  2  AAA_29           P-loop containing region of AAA domain
    1.5e-08   35.2   0.1    0.00069   20.0   0.0    3.0  3  AAA_16           AAA ATPase domain
    1.3e-07   32.3   0.9      0.013   16.0   0.1    2.1  2  AAA_23           AAA domain
      3e-07   30.3   3.3     0.0042   16.8   0.0    3.1  2  AAA_30           AAA domain
    5.7e-07   29.6   3.1     0.0069   16.3   0.2    3.4  4  NTPase_1         NTPase
    3.1e-06   27.5   0.8     0.0097   16.2   0.1    2.9  3  AAA_22           AAA domain
      5e-06   26.1   0.0       0.48    9.8   0.0    3.7  4  SMC_N            RecF/RecN/SMC N terminal domain
    2.8e-05   24.1   0.2      0.025   14.5   0.0    2.2  2  RsgA_GTPase      RsgA GTPase
    3.6e-05   23.4   2.4       0.69    9.4   0.1    3.7  4  AAA_25           AAA domain
    9.4e-05   23.0   0.8      0.035   14.6   0.0    3.1  3  AAA_18           AAA domain
    0.00026   20.2   0.5     0.0072   15.4   0.1    2.2  2  T2SSE            Type II/IV secretion system protein
    0.00081   19.8   1.1       0.12   12.8   0.1    2.4  2  AAA_19           AAA domain
    0.00082   18.8   0.8      0.097   12.0   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0014   18.6   0.3      0.043   13.7   0.0    2.1  2  Rad17            Rad17 P-loop domain
     0.0016   18.4   3.2        0.3   11.0   0.1    2.5  2  NACHT            NACHT domain
     0.0016   17.7   0.3        1.2    8.3   0.0    2.4  2  Zeta_toxin       Zeta toxin
     0.0017   18.0   6.6       0.05   13.2   0.4    2.3  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0018   18.1   0.3       0.53   10.0   0.0    2.6  2  AAA_24           AAA domain
     0.0019   18.2   1.9        1.3    9.1   0.1    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0019   18.4   2.1       0.18   12.0   0.0    2.8  3  AAA_33           AAA domain
     0.0019   18.2   0.4        1.8    8.7   0.0    2.6  2  MMR_HSR1         50S ribosome-binding GTPase
      0.002   18.0   1.9       0.55   10.1   0.1    2.4  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.002   18.4   3.0       0.67   10.2   0.4    3.2  3  AAA_28           AAA domain
     0.0023   18.1   0.2        5.5    7.3   0.0    3.4  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.003   17.5   0.3       0.21   11.4   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0038   17.0   0.3       0.69    9.6   0.0    2.3  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0061   17.0   2.2       0.96    9.9   0.1    2.5  2  AAA              ATPase family associated with various cellul
     0.0061   16.3   0.0        1.7    8.3   0.0    3.0  3  AAA_15           AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.1   0.1        5.1    6.6   0.0    2.3  2  AAA_27           AAA domain
      0.014   15.5   0.7        1.3    9.0   0.1    2.5  2  AAA_14           AAA domain
      0.014   14.3   0.9        1.9    7.2   0.0    2.1  2  DLIC             Dynein light intermediate chain (DLIC)
      0.015   15.7   0.1        2.4    8.6   0.0    2.3  2  RNA_helicase     RNA helicase
      0.017   14.1   0.6        1.8    7.5   0.0    2.3  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.017   15.1   2.5       0.89    9.6   0.1    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
      0.021   14.3   0.5       0.35   10.3   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
      0.031   13.4   1.1        4.1    6.5   0.1    2.3  2  NB-ARC           NB-ARC domain
      0.032   14.7   1.4        0.1   13.0   0.2    2.4  2  DUF4350          Domain of unknown function (DUF4350)
      0.039   13.9   0.6        1.2    9.0   0.0    2.3  2  APS_kinase       Adenylylsulphate kinase
      0.045   13.5   1.8       0.75    9.5   0.2    2.2  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.051   13.4   0.3         10    5.9   0.1    2.2  2  dNK              Deoxynucleoside kinase
      0.054   13.2   0.4        1.3    8.8   0.0    2.8  3  IstB_IS21        IstB-like ATP binding protein
      0.064   13.0   1.6        2.2    8.0   0.1    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.12   11.8   0.6         13    5.2   0.0    2.3  2  PhoH             PhoH-like protein
       0.15   10.7   0.2        2.3    6.7   0.1    2.0  2  AAA_13           AAA domain
       0.18    9.7   0.1       0.44    8.4   0.0    1.7  2  Herpes_Helicase  Helicase
        0.3   10.2   0.2        8.9    5.4   0.0    2.1  2  PIF1             PIF1-like helicase
       0.42   10.2   4.0        8.6    5.9   0.5    2.4  2  SRP54            SRP54-type protein, GTPase domain
       0.57    7.6   2.2        1.4    6.3   0.3    1.9  2  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 !   67.9   0.0   3.4e-21   1.2e-18       2     136 ..      18     160 ..      17     161 .. 0.88
   2 !   70.2   0.0   6.6e-22   2.4e-19       2     136 ..     257     381 ..     256     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.4e-21
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlkeqeleslrkeigvlpqe.pqlfpe 73 
                                       +n++l ++ ge + ++G++G+GK+tL+++l+g l+       Ge+ +dg++++  e  +  + ++++pqe      +
  gi|320100473|ref|YP_004176065.1|  18 RNLDLRVQDGEALIVTGPSGSGKTTLIRVLTGVLDRiggfLDGEVIIDGQPVSAMEPWRIYELVAYIPQEpWYALIG 94 
                                       799*********************************888888999*********99999999********5344567 PP

                                       SBHHHH......HHHTC.HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx......xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren......esdee.iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +tv+++      +  ++  ++ l+klgl ++ d+       +LS G+ qr+  a+a++++ ++l+lDEp 
  gi|320100473|ref|YP_004176065.1|  95 YTVHSEycyalsQLGVRcDHTSLEKLGLRGKLDSLT----VNLSAGETQRLIWAEAFARRYRVLILDEPL 160
                                       778888997766555555567899999999777777....*****************************6 PP

  == domain 2  score: 70.2 bits;  conditional E-value: 6.6e-22
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       k vs++++++++ +++G+nGaGK+tLlkl+ag lkp +G++             +   +  ++p++    f + t r
  gi|320100473|ref|YP_004176065.1| 257 KGVSFTIEKSSLAGLTGRNGAGKTTLLKLMAGVLKPLKGSV-------------RRFGRATYIPENpLLYFTKPTPR 320
                                       78***************************************.............44455667777733345555566 PP

                                       HH......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e+         + +e+a++ ++l ++ d+++    ++LS G+++r+ala a l   +++l+DEpt
  gi|320100473|ref|YP_004176065.1| 321 EEllyaagGGVDAVEEAVELFNLAGVLDRPL----AKLSSGERRRLALASAYLGGFDIYLVDEPT 381
                                       6666655566666999999999999999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.2e-05     0.019       3      25 ..      31      53 ..      30      76 .. 0.76
   2 ?   -1.1   0.0       3.5   1.3e+03     119     152 ..     160     193 ..     138     230 .. 0.59
   3 !   18.5   0.0     4e-06    0.0014       1      39 [.     268     300 ..     268     318 .. 0.76
   4 !   25.7   0.0   2.5e-08     9e-06     231     299 ..     348     413 ..     335     417 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.2e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                      +++Gp gsGK++L++ l ++ + 
  gi|320100473|ref|YP_004176065.1| 31 IVTGPSGSGKTTLIRVLTGVLDR 53
                                      689**************988643 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.5
                            AAA_21 119 rggvsvfslkelsvsepndlqfgkaltditsraw 152
                                        + ++++ + +  ++ +++l +g+ l+ ++++ w
  gi|320100473|ref|YP_004176065.1| 160 LVYLDDEARGTVAKAAWEALAHGASLVVVDHDPW 193
                                       3333444444444455555555555555555555 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 4e-06
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsgg 39 
                                       l++l+G+Ng+GK++LL+++ ++      +++l+ + +++
  gi|320100473|ref|YP_004176065.1| 268 LAGLTGRNGAGKTTLLKLMAGV------LKPLKGSVRRF 300
                                       578****************665......45555555554 PP

  == domain 4  score: 25.7 bits;  conditional E-value: 2.5e-08
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       ++p+++lS+G +r lal++a+l      +++l+DEp  gL+ +   r+l+ l +l +ng+ v+++TH+ 
  gi|320100473|ref|YP_004176065.1| 348 DRPLAKLSSGERRRLALASAYLGGF---DIYLVDEPTGGLDQANAVRVLDALTRLVENGGTVVVATHDK 413
                                       57999*****************744...**************9999999999888899*********95 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.4e-06    0.0012      16      39 ..      21      44 ..      13      52 .. 0.73
   2 !   17.2   0.1   8.7e-06    0.0031      12      50 ..     256     294 ..     254     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.4e-06
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                      +++++  g a ++tGpsGsGK+Tl+
  gi|320100473|ref|YP_004176065.1| 21 DLRVQD-GeALIVTGPSGSGKTTLI 44
                                      455553.359999***********9 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 8.7e-06
                            AAA_29  12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                       f+g +++i+ ++   ltG++G+GK+Tll  ++ +L p k
  gi|320100473|ref|YP_004176065.1| 256 FKGVSFTIEKSSLAGLTGRNGAGKTTLLKLMAGVLKPLK 294
                                       788889999888999*************88888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.9e-06   0.00069      18      45 ..      23      48 ..      16      88 .. 0.79
   2 ?    0.2   0.0       2.4   8.7e+02      56      89 ..     122     159 ..     109     192 .. 0.64
   3 !   10.8   0.0    0.0013      0.46      28     128 ..     270     401 ..     261     421 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-06
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrell 45
                                      rv +g  e+++++G+sG+GK++l+r l 
  gi|320100473|ref|YP_004176065.1| 23 RVQDG--EALIVTGPSGSGKTTLIRVLT 48
                                      55555..89***************9886 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.4
                            AAA_16  56 lrgkcdqlesa.....ipysalaqalareellrqlldea 89 
                                       lrgk d+l+ +     + ++++a+a+ar ++   +lde+
  gi|320100473|ref|YP_004176065.1| 122 LRGKLDSLTVNlsageTQRLIWAEAFAR-RYRVLILDEP 159
                                       6677777744433344555889999966.7777777772 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0013
                            AAA_16  28 llsGesGvGKsslvrellralekdggiflrgkcdqlesa.....ipysalaqalareellrqlldeaesaeleawre 99 
                                        l+G  G GK++l++  +  + k     l+g  +++++a      p++ +++   reell + +   ++ e +    
  gi|320100473|ref|YP_004176065.1| 270 GLTGRNGAGKTTLLKLMA-GVLKP----LKGSVRRFGRAtyipeNPLLYFTKPTPREELLYAAGGGVDAVEEAVELF 341
                                       589***********8877.56666....6666666655544444455557777777777777777744433333333 PP

                            AAA_16 100 kleeala...............................avpelagaeasrllellkrlla 128
                                        l ++l                                +++ l+ a a r+l++l+rl++
  gi|320100473|ref|YP_004176065.1| 342 NLAGVLDrplaklssgerrrlalasaylggfdiylvdePTGGLDQANAVRVLDALTRLVE 401
                                       333333354445555555555566667788888888888888888888889998888883 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     8e-05     0.029      22      43 ..      30      51 ..       9      58 .. 0.80
   2 !   16.0   0.1   3.7e-05     0.013      17      40 ..     263     287 ..     254     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8e-05
                            AAA_23 22 tlItGpNGaGKTTildAiklaL 43
                                       ++tGp G+GKTT+++ ++ +L
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVLTGVL 51
                                      4789***********9998776 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.7e-05
                            AAA_23  17 F.skgltlItGpNGaGKTTildAik 40 
                                         ++ l  +tG NGaGKTT+l  + 
  gi|320100473|ref|YP_004176065.1| 263 IeKSSLAGLTGRNGAGKTTLLKLMA 287
                                       445578899***********98766 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   1.2e-05    0.0042      19      47 ..      28      60 ..      21     189 .. 0.72
   2 !   11.9   1.3   0.00037      0.13      17      49 ..     265     297 ..     259     417 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaag....g 47
                                         ++tGp G+GKtt++++l+ ++++ g    g
  gi|320100473|ref|YP_004176065.1| 28 EALIVTGPSGSGKTTLIRVLTGVLDRIGgfldG 60
                                      4789*****************999998646662 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00037
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrv 49 
                                       +  +a ltG+ G+GKtt+lk ++ +++  +g+v
  gi|320100473|ref|YP_004176065.1| 265 KSSLAGLTGRNGAGKTTLLKLMAGVLKPLKGSV 297
                                       556899***************999998876554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.3   2.2e+03      37      52 ..       5      20 ..       2      24 .. 0.87
   2 !   16.3   0.2   1.9e-05    0.0069       2      39 ..      30      63 ..      29      70 .. 0.80
   3 !   11.4   0.1   0.00063      0.23       4      25 ..     271     292 ..     269     302 .. 0.86
   4 ?   -1.3   0.0         5   1.8e+03      94     136 ..     370     414 ..     349     424 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.3
                                      EE-------EEEEEET CS
                          NTPase_1 37 evreggrrigFkivdl 52
                                       vr  g r gF+i +l
  gi|320100473|ref|YP_004176065.1|  5 HVRVAGYRDGFTIRNL 20
                                      69999********988 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.9e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                      +++TGp+G+GKtTl++ ++ +l+    ++gGf+  ev 
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVLTGVLD----RIGGFLDGEVI 63
                                      69******************995....67777766665 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00063
                                       EE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlellks 25 
                                       +TG+ G GKtTl+k ++ +lk 
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVLKP 292
                                       8**************9999975 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 5
                                       HHH-EEEE--.-STTGGG.-HHHHHHHHHHHTTTSEEEEE--SS- CS
                          NTPase_1  94 seadviviDE.iGkmElk.skkfkeaveevLksekpvlavihrrk 136
                                        + d++++DE  G +    + ++ +a++++++++  v++  h ++
  gi|320100473|ref|YP_004176065.1| 370 GGFDIYLVDEpTGGLDQAnAVRVLDALTRLVENGGTVVVATHDKR 414
                                       556777777755777654144677888888885555555555553 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.7e-05    0.0097       5      26 ..      27      48 ..      23      54 .. 0.85
   2 ?   -1.4   0.0       7.3   2.6e+03      85      99 ..     146     158 ..     105     189 .. 0.64
   3 !    8.5   0.0    0.0062       2.2       9      26 ..     270     287 ..     263     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrll 26
                                         l+vtG+sG+GKTtl+r l+
  gi|320100473|ref|YP_004176065.1| 27 GEALIVTGPSGSGKTTLIRVLT 48
                                      5679**************9775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 7.3
                            AAA_22  85 alraravielliiDE 99 
                                       a+ +r++  +li+DE
  gi|320100473|ref|YP_004176065.1| 146 AFARRYR--VLILDE 158
                                       2222223..555555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0062
                            AAA_22   9 vvtGesGtGKTtllrrll 26 
                                        +tG  G+GKTtll+ ++
  gi|320100473|ref|YP_004176065.1| 270 GLTGRNGAGKTTLLKLMA 287
                                       589***********9876 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 ?    5.4   0.0     0.029        11      27      44 ..      30      47 ..       6      54 .. 0.79
   2 ?   -0.8   0.0       2.4   8.6e+02     148     183 ..     140     175 ..      96     195 .. 0.78
   3 ?    5.6   0.1     0.026       9.4      25      44 ..     267     286 ..     255     302 .. 0.80
   4 !    9.8   0.0    0.0013      0.48     137     208 ..     354     422 ..     329     426 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.029
                                      EEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAi 44
                                       +++Gp GSGK+ l+  +
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVL 47
                                      5689********998766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                                       HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 148 aLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                        L+ A   +++  + +lDe    LD++ +  va+  
  gi|320100473|ref|YP_004176065.1| 140 RLIWAEAFARRYRVLILDEPLVYLDDEARGTVAKAA 175
                                       456666666777788999999999999999999865 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.026
                                       SEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                       s+  ++G+NG+GK+ ll  +
  gi|320100473|ref|YP_004176065.1| 267 SLAGLTGRNGAGKTTLLKLM 286
                                       56789*********998765 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0013
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadkl 208
                                       LS Ge+      L +A        +yl+De    LD++n  +v + l +  +n   ++v ++++++++  d  
  gi|320100473|ref|YP_004176065.1| 354 LSSGERR----RLALASAYLGGFDIYLVDEPTGGLDQANAVRVLDALTRLVENgGTVVVATHDKRVVSLLDDD 422
                                       5666665....3556778889999************************9999956778888999988877665 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   6.9e-05     0.025      88     122 ..      15      50 ..       2      56 .. 0.80
   2 !    7.5   0.1    0.0098       3.5     100     124 ..     267     291 ..     249     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                        ++++l  +++d +  ++ G+SG GK+tLi +l++ 
  gi|320100473|ref|YP_004176065.1|  15 FTIRNLDLRVQDgEALIVTGPSGSGKTTLIRVLTGV 50 
                                       5677777778877999****************9875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0098
                                       SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpele 124
                                       +++ l G  G+GK+tL++ +++ l+
  gi|320100473|ref|YP_004176065.1| 267 SLAGLTGRNGAGKTTLLKLMAGVLK 291
                                       667799***********99987655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0025       0.9      30      50 ..      24      44 ..      17      49 .. 0.86
   2 ?    2.0   0.0      0.38   1.3e+02      93     149 ..     143     189 ..     132     200 .. 0.69
   3 !    9.4   0.1    0.0019      0.69      15      52 ..     245     285 ..     231     306 .. 0.78
   4 ?   -1.8   0.0       5.5     2e+03     165     187 ..     389     411 ..     382     414 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge  +++G++g+GKttl 
  gi|320100473|ref|YP_004176065.1| 24 VQDGEALIVTGPSGSGKTTLI 44
                                      567999*************96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.38
                            AAA_25  93 vgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviD 149
                                       + ea++++ r+l+ld    e+l  ++++++gt+++a+++al+      +g+ lvv+D
  gi|320100473|ref|YP_004176065.1| 143 WAEAFARRYRVLILD----EPLVYLDDEARGTVAKAAWEALA------HGASLVVVD 189
                                       555666667777776....34545566677777777776555......678888888 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0019
                            AAA_25  15 laapppprrwlvkg...llpagelallaGapgtGKttlald 52 
                                       l  + p  + l+kg    + + +la l+G+ g+GKttl+  
  gi|320100473|ref|YP_004176065.1| 245 LWFKYPGEKPLFKGvsfTIEKSSLAGLTGRNGAGKTTLLKL 285
                                       5556667777777766568999***************9744 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.5
                            AAA_25 165 vgalvealeriarrtgaavllvh 187
                                       + ++++al r+ ++ g  v+++h
  gi|320100473|ref|YP_004176065.1| 389 AVRVLDALTRLVENGGTVVVATH 411
                                       56788888888666555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   9.8e-05     0.035       2      19 ..      31      48 ..      30      79 .. 0.74
   2 ?    4.8   0.3      0.11        38       3      17 ..     271     285 ..     270     300 .. 0.89
   3 ?   -0.7   0.0       5.3   1.9e+03      49      88 ..     381     417 ..     351     425 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-05
                            AAA_18  2 lltGtpGvGKttlakeLs 19
                                      ++tG++G+GKttl + L 
  gi|320100473|ref|YP_004176065.1| 31 IVTGPSGSGKTTLIRVLT 48
                                      79*************993 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.11
                            AAA_18   3 ltGtpGvGKttlake 17 
                                       ltG  G+GKttl k 
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKL 285
                                       89**********986 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 5.3
                            AAA_18  49 skrldedkldklldaleenssaleegknlvidghlaeles 88 
                                       +  ld+ +  ++ldal +     e+g+++v+  h    +s
  gi|320100473|ref|YP_004176065.1| 381 TGGLDQANAVRVLDALTRL---VENGGTVVVATHDKRVVS 417
                                       5567777777777777776...579999999999876665 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 !   15.4   0.1     2e-05    0.0072     122     153 ..      20      51 ..       8      57 .. 0.84
   2 ?    2.8   0.0      0.15        52     134     153 ..     271     290 ..     227     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                             T2SSE 122 lrkavrerglilvsGgTgsGKttllyallkei 153
                                       l   v+    ++v+G+ gsGKttl+ +l   +
  gi|320100473|ref|YP_004176065.1|  20 LDLRVQDGEALIVTGPSGSGKTTLIRVLTGVL 51 
                                       5566788899**************98877665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                             T2SSE 134 vsGgTgsGKttllyallkei 153
                                       ++G  g GKttll  +   +
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVL 290
                                       7999********98776555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00032      0.12      11      39 ..      28      56 ..      22      73 .. 0.87
   2 ?    5.4   0.1     0.062        22      10      38 ..     266     294 ..     259     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00032
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelgg 39
                                      + l+vt++ G+GKT++++    +l ++gg
  gi|320100473|ref|YP_004176065.1| 28 EALIVTGPSGSGKTTLIRVLTGVLDRIGG 56
                                      6789**************99999988775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.062
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelg 38 
                                       +++  +t+  G GKT++lk +  +l+ l+
  gi|320100473|ref|YP_004176065.1| 266 SSLAGLTGRNGAGKTTLLKLMAGVLKPLK 294
                                       5677899***********99988887666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00027     0.097      17      47 ..      22      52 ..      13      57 .. 0.84
   2 ?    4.6   0.4      0.05        18      27      50 ..     271     294 ..     267     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                      Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsllp 47
                                      + +  g  l+++Gp+GsGKt l++ l+++l 
  gi|320100473|ref|YP_004176065.1| 22 LRVQDGEALIVTGPSGSGKTTLIRVLTGVLD 52
                                      555667789******************9996 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.05
                      Mg_chelatase  27 lvGppGsGKtmlakrlpsllppls 50 
                                       l+G  G+GKt l k ++++l pl+
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVLKPLK 294
                                       789*****************9986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00012     0.043      43      67 ..      25      49 ..      16      53 .. 0.82
   2 ?    2.6   0.1       0.3   1.1e+02      47      69 ..     268     290 ..     256     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                             Rad17 43 rkkriLLisGPsGCgkstvvkvLsk 67
                                      +  + L+++GPsG gk+t ++vL+ 
  gi|320100473|ref|YP_004176065.1| 25 QDGEALIVTGPSGSGKTTLIRVLTG 49
                                      445589****************975 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.3
                             Rad17  47 iLLisGPsGCgkstvvkvLskel 69 
                                       +  ++G  G gk+t +k ++  l
  gi|320100473|ref|YP_004176065.1| 268 LAGLTGRNGAGKTTLLKLMAGVL 290
                                       66699************998665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00084       0.3       3      20 ..      30      47 ..      28      53 .. 0.87
   2 ?    7.2   0.8     0.013       4.5       5      20 ..     271     286 ..     267     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00084
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      +i++G++GsGKTtL++ l
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVL 47
                                      79************9866 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                                       EEC-TTTCHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqkl 20 
                                       l+G++G GKTtLl+ +
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLM 286
                                       79***********865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0035       1.2      18      43 ..      29      54 ..      17      62 .. 0.85
   2 !    6.8   0.1      0.01       3.6      21      46 ..     271     296 ..     260     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0035
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerq 43
                                      ++++ G +G+GK++l++ l+  l+r 
  gi|320100473|ref|YP_004176065.1| 29 ALIVTGPSGSGKTTLIRVLTGVLDRI 54
                                      7899*************999888765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnv 46 
                                       l G  GAGK++l++l++  l++ ++ 
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVLKPLKGS 296
                                       7899***********99888755555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.4   0.00014      0.05       2      20 ..      29      47 ..      28      56 .. 0.87
   2 !    7.6   1.0    0.0073       2.6       4      19 ..     270     285 ..     267     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                                      EEEEEESTTCCHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhl 20
                                      ++++tG+ GsGKTtL++ l
  gi|320100473|ref|YP_004176065.1| 29 ALIVTGPSGSGKTTLIRVL 47
                                      579*************976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0073
                                       EEEESTTCCHHHHHHH CS
                              cobW   4 vltGflGsGKTtLlnh 19 
                                       +ltG  G+GKTtLl+ 
  gi|320100473|ref|YP_004176065.1| 270 GLTGRNGAGKTTLLKL 285
                                       79************85 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0015      0.53       5      22 ..      30      47 ..      27     158 .. 0.89
   2 ?    5.5   0.3     0.035        13       7      22 ..     271     286 ..     267     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++++Gpsg+GKTtl++ l
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVL 47
                                      6799**********9877 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.035
                            AAA_24   7 iyGpsgiGKTtlakel 22 
                                       ++G +g+GKTtl+k +
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLM 286
                                       79***********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 !    9.1   0.1    0.0036       1.3      19      40 ..      27      48 ..      14      54 .. 0.79
   2 !    8.0   0.4    0.0075       2.7      21      43 ..     268     290 ..     255     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0036
                                      TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                      g++++ +G+ G+GKTtl+r l 
  gi|320100473|ref|YP_004176065.1| 27 GEALIVTGPSGSGKTTLIRVLT 48
                                      678999************9886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0075
                                       EEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakal 43 
                                       +  L+G  GaGKTtl + +a  l
  gi|320100473|ref|YP_004176065.1| 268 LAGLTGRNGAGKTTLLKLMAGVL 290
                                       56799***********9987655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0    0.0005      0.18       3      20 ..      31      48 ..      30      71 .. 0.84
   2 ?   -1.9   0.0       9.3   3.3e+03      73      86 ..     154     172 ..     124     194 .. 0.52
   3 ?    4.8   0.3     0.084        30       5      20 ..     272     287 ..     268     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0005
                            AAA_33  3 llvGlpGsGKstlaerll 20
                                      ++ G++GsGK+tl++ l 
  gi|320100473|ref|YP_004176065.1| 31 IVTGPSGSGKTTLIRVLT 48
                                      789**********99876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 9.3
                            AAA_33  73 vildatnls..rrer...a 86 
                                       +ild +++    ++r   a
  gi|320100473|ref|YP_004176065.1| 154 LILDEPLVYldDEARgtvA 172
                                       5556664442223332221 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.084
                            AAA_33   5 vGlpGsGKstlaerll 20 
                                        G +G+GK+tl++ ++
  gi|320100473|ref|YP_004176065.1| 272 TGRNGAGKTTLLKLMA 287
                                       6999*******99775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0     0.005       1.8       3      22 ..      31      50 ..      29      69 .. 0.87
   2 ?    7.4   0.1     0.012       4.4       3      21 ..     270     288 ..     268     411 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.005
                                      EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                      ++ G + +GK+tLi+ ltg 
  gi|320100473|ref|YP_004176065.1| 31 IVTGPSGSGKTTLIRVLTGV 50
                                      689**************984 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.012
                                       EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg 21 
                                       ++ Gr  +GK+tL++ + g
  gi|320100473|ref|YP_004176065.1| 270 GLTGRNGAGKTTLLKLMAG 288
                                       799***********99987 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 !   10.1   0.1    0.0015      0.55       2      25 ..      30      53 ..      29      57 .. 0.86
   2 ?    7.1   0.2     0.013       4.8       3      24 ..     270     291 ..     268     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                              MobB  2 lgivgksgsGKTtLleklipelka 25
                                      l ++g sgsGKTtL+  l  +l +
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVLTGVLDR 53
                                      56889***********99999876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                              MobB   3 givgksgsGKTtLleklipelk 24 
                                       g++g++g+GKTtLl+ +  +lk
  gi|320100473|ref|YP_004176065.1| 270 GLTGRNGAGKTTLLKLMAGVLK 291
                                       689***********98887776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.4    0.0019      0.67       3      20 ..      31      48 ..      29      58 .. 0.88
   2 ?    0.7   0.0       1.6   5.7e+02     102     129 ..     144     170 ..      91     195 .. 0.63
   3 ?    5.9   0.0      0.04        14       4      20 ..     271     287 ..     270     322 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0019
                            AAA_28  3 vitGgestGKTtlleaLa 20
                                      ++tG++++GKTtl++ L+
  gi|320100473|ref|YP_004176065.1| 31 IVTGPSGSGKTTLIRVLT 48
                                      79************9886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.6
                            AAA_28 102 aaarekrydlvfllppapeidddgeRre 129
                                       a+a ++ry+  +l +p  ++ dd++R  
  gi|320100473|ref|YP_004176065.1| 144 AEAFARRYRVLILDEPLVYL-DDEARGT 170
                                       23334445444444456666.6666642 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.04
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       +tG  ++GKTtll+ +a
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMA 287
                                       79999********9988 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 ?    7.3   0.0     0.015       5.5      61      86 ..     148     173 ..     111     177 .. 0.82
   2 ?    6.3   0.0     0.031        11      48      89 ..     362     397 ..     342     398 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.015
                           SbcCD_C  61 epalrlvfLDEAFsklDeesiatlle 86 
                                        +++r+++LDE    lD+e + t+ +
  gi|320100473|ref|YP_004176065.1| 148 ARRYRVLILDEPLVYLDDEARGTVAK 173
                                       568999*************9999876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.031
                           SbcCD_C  48 aalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +ala++y         +++ + DE  ++lD+ ++ ++l++l+
  gi|320100473|ref|YP_004176065.1| 362 LALASAYLG------GFDIYLVDEPTGGLDQANAVRVLDALT 397
                                       455555655......59999*****************99986 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   0.00059      0.21      21      41 ..      28      48 ..      17      56 .. 0.81
   2 ?    3.9   0.1      0.12        43      25      44 ..     271     290 ..     262     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00059
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeii 41
                                      e + ++Gp gsGKt+L++ + 
  gi|320100473|ref|YP_004176065.1| 28 EALIVTGPSGSGKTTLIRVLT 48
                                      56789************9875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                          ATPase_2  25 iYGpegsGKtaLlkeiienl 44 
                                       ++G+ g GKt+Llk ++  l
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVL 290
                                       68***********9877655 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0019      0.69       4      25 ..      32      53 ..      30      65 .. 0.90
   2 ?    5.3   0.0     0.042        15       3      24 ..     270     291 ..     268     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                               PRK  4 vagsSGaGkttvarklekifgr 25
                                      v+g+SG+Gktt+ r l+ ++ r
  gi|320100473|ref|YP_004176065.1| 32 VTGPSGSGKTTLIRVLTGVLDR 53
                                      8**************9998875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.042
                               PRK   3 gvagsSGaGkttvarklekifg 24 
                                       g++g  GaGktt+ + +  +++
  gi|320100473|ref|YP_004176065.1| 270 GLTGRNGAGKTTLLKLMAGVLK 291
                                       89***********999988876 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 !    9.9   0.1    0.0027      0.96       2      19 ..      31      48 ..      30      63 .. 0.88
   2 ?    6.4   0.2     0.031        11       3      22 ..     271     290 ..     269     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0027
                                      EEESSTTSSHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakava 19
                                      +++Gp G GKT+l++ + 
  gi|320100473|ref|YP_004176065.1| 31 IVTGPSGSGKTTLIRVLT 48
                                      799***********9886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.031
                                       EESSTTSSHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel 22 
                                       l+G  G GKT+l k +a  l
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVL 290
                                       79************999876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.26        92      24      44 ..      27      48 ..      11      71 .. 0.81
   2 !    8.3   0.0    0.0047       1.7      17      44 ..     261     287 ..     256     305 .. 0.81
   3 ?    1.4   0.0      0.57     2e+02     293     367 ..     350     414 ..     327     416 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.26
                            AAA_15 24 e.ltvliGkNnsGKSsileald 44
                                          ++ G+ +sGK++++++l 
  gi|320100473|ref|YP_004176065.1| 27 GeALIVTGPSGSGKTTLIRVLT 48
                                      4467888***********9996 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0047
                            AAA_15  17 veidlseeltvliGkNnsGKSsileald 44 
                                       ++i+ s+ l  l G+N++GK+++l+++ 
  gi|320100473|ref|YP_004176065.1| 261 FTIEKSS-LAGLTGRNGAGKTTLLKLMA 287
                                       5666555.88899***********9985 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.57
                            AAA_15 293 plnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       pl+k +sG +r l l+   +++          +i+l++EP   L   +   + ++l +l++++   v++ TH   
  gi|320100473|ref|YP_004176065.1| 350 PLAKLSSGERRRLALA--SAYLGGF-------DIYLVDEPTGGLDQANAVRVLDALTRLVENGG-TVVVATHDKR 414
                                       6777777777776554..4445555.......78999999999999999999***********8.9******875 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.014       5.1      14      48 ..      15      49 ..      13      54 .. 0.90
   2 ?    5.8   0.1     0.026       9.2      19      46 ..     259     286 ..     256     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.014
                            AAA_27 14 ftdrsldfsaeeadlhliyGpNEAGKstalrAisd 48
                                      ft r+ld++ ++ +  ++ Gp  +GK+t++r ++ 
  gi|320100473|ref|YP_004176065.1| 15 FTIRNLDLRVQDGEALIVTGPSGSGKTTLIRVLTG 49
                                      88899*****99999**************998775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.026
                            AAA_27  19 ldfsaeeadlhliyGpNEAGKstalrAi 46 
                                       ++f  e+++l  + G N AGK+t+l+ +
  gi|320100473|ref|YP_004176065.1| 259 VSFTIEKSSLAGLTGRNGAGKTTLLKLM 286
                                       4566778999999**********99865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0037       1.3       3      22 ..      28      47 ..      26      53 .. 0.87
   2 ?    4.4   0.1       0.1        36       6      23 ..     270     287 ..     265     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0037
                            AAA_14  3 kilvitGaRrvGKTtllkql 22
                                      ++l++tG+  +GKTtl++ l
  gi|320100473|ref|YP_004176065.1| 28 EALIVTGPSGSGKTTLIRVL 47
                                      789*************9765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.1
                            AAA_14   6 vitGaRrvGKTtllkqli 23 
                                        +tG   +GKTtllk ++
  gi|320100473|ref|YP_004176065.1| 270 GLTGRNGAGKTTLLKLMA 287
                                       689999********9876 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0054       1.9      25      51 ..      27      53 ..      21      58 .. 0.86
   2 ?    5.5   0.1     0.017       6.2      30      55 ..     271     296 ..     258     301 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0054
                              DLIC 25 gksvlvlGedgsGkttliaklqGveee 51
                                      g +++v G +gsGkttli  l Gv + 
  gi|320100473|ref|YP_004176065.1| 27 GEALIVTGPSGSGKTTLIRVLTGVLDR 53
                                      67899******************9876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                              DLIC  30 vlGedgsGkttliaklqGveeekkGr 55 
                                       + G +g+Gkttl+  + Gv ++ kG+
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVLKPLKGS 296
                                       5799********************97 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0067       2.4       2      19 ..      31      48 ..      30      72 .. 0.82
   2 ?    4.8   0.0     0.098        35       3      20 ..     271     288 ..     270     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0067
                      RNA_helicase  2 wlyGpsgeGKStlakeLa 19
                                      +++Gpsg GK+tl++ L+
  gi|320100473|ref|YP_004176065.1| 31 IVTGPSGSGKTTLIRVLT 48
                                      799***********9965 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.098
                      RNA_helicase   3 lyGpsgeGKStlakeLak 20 
                                       l+G++g GK+tl k +a 
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAG 288
                                       68***********98553 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 ?    4.7   0.1     0.035        13      31      57 ..      29      55 ..      17      66 .. 0.84
   2 ?    7.5   0.0     0.005       1.8      13      50 ..     250     287 ..     240     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.035
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrG 57
                                       + +tG  G+Gk tl+  l+  l r G
  gi|320100473|ref|YP_004176065.1| 29 ALIVTGPSGSGKTTLIRVLTGVLDRIG 55
                                      4558*************9998887766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.005
                                       HHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
                              MeaB  13 peakellerllakaGraqvvGltGvPGaGkstlvealg 50 
                                       p  k l++ ++ +  ++   GltG  GaGk tl++ ++
  gi|320100473|ref|YP_004176065.1| 250 PGEKPLFKGVSFTIEKSSLAGLTGRNGAGKTTLLKLMA 287
                                       56677777788888899999*************98665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0025      0.89       2      23 ..      30      51 ..      29      55 .. 0.87
   2 ?    4.7   0.2     0.077        28       4      23 ..     271     290 ..     270     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0025
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                      +++ Gp+G+gK++l++ l  +l
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVLTGVL 51
                                      7999***********9998766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.077
                                       EE--SSSSHHHHHHHGGGGB CS
                             AAA_5   4 LvGppGtgKselaerlaaal 23 
                                       L G  G gK++l + +a +l
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVL 290
                                       89**************9887 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00099      0.35      26      55 ..      20      49 ..      16      54 .. 0.84
   2 ?    1.6   0.1      0.46   1.7e+02      36      53 ..     269     286 ..     259     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00099
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllk 55
                                      l+l ++ +  ++++Gp+G+GKt++i+ l+ 
  gi|320100473|ref|YP_004176065.1| 20 LDLRVQDGEALIVTGPSGSGKTTLIRVLTG 49
                                      5677899999**************987665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.46
                             AAA_7  36 vllvGptGtGKtviikdl 53 
                                         l+G  G GKt+++k +
  gi|320100473|ref|YP_004176065.1| 269 AGLTGRNGAGKTTLLKLM 286
                                       5589*********98865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.011       4.1      22      40 ..      29      47 ..      17      66 .. 0.78
   2 ?    5.4   0.1     0.025         9      22      38 ..     268     284 ..     261     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                                      EEEEEESTTSSHHHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlakqi 40
                                       + + G  G+GKttl++  
  gi|320100473|ref|YP_004176065.1| 29 ALIVTGPSGSGKTTLIRVL 47
                                      57899**********9865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                                       EEEEEESTTSSHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlak 38 
                                       + +l G+ G GKttl+k
  gi|320100473|ref|YP_004176065.1| 268 LAGLTGRNGAGKTTLLK 284
                                       5689**********987 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       5.9   2.1e+03      52      69 .]     172     189 ..     143     189 .. 0.63
   2 ?   13.0   0.2   0.00029       0.1      29      68 ..     366     409 ..     321     410 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.9
                           DUF4350  52 laallewvarGntlvlaa 69 
                                       ++a  e +a+G+ lv+++
  gi|320100473|ref|YP_004176065.1| 172 AKAAWEALAHGASLVVVD 189
                                       445566678999999985 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00029
                           DUF4350  29 dalegedgtllvvapdlrlte....eelaallewvarGntlvla 68 
                                       +a+ g+ + +lv  p++ l++    + l+al ++v++G+t+v+a
  gi|320100473|ref|YP_004176065.1| 366 SAYLGGFDIYLVDEPTGGLDQanavRVLDALTRLVENGGTVVVA 409
                                       34555788999*****99999999999****************8 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0033       1.2       4      30 ..      29      55 ..      26      70 .. 0.77
   2 ?    2.9   0.1      0.25        89       7      26 ..     271     290 ..     265     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0033
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekg 30
                                       + +tG sgsGK+t+ + l   L + g
  gi|320100473|ref|YP_004176065.1| 29 ALIVTGPSGSGKTTLIRVLTGVLDRIG 55
                                      6789*************9999988776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.25
                                       EESSTTSSHHHHHHHHHHHH CS
                        APS_kinase   7 ltGlsgsGKstianalekkL 26 
                                       ltG  g+GK+t+ + ++  L
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVL 290
                                       8**********988777666 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0021      0.75       1      21 [.      32      52 ..      32      56 .. 0.86
   2 ?    3.2   0.1      0.18        63       2      21 ..     272     291 ..     271     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0021
                        ATP_bind_1  1 vvGpaGsGKttfvgalseile 21
                                      v+Gp GsGKtt+++ l+ +l+
  gi|320100473|ref|YP_004176065.1| 32 VTGPSGSGKTTLIRVLTGVLD 52
                                      89***********99987766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                        ATP_bind_1   2 vGpaGsGKttfvgalseile 21 
                                       +G  G+GKtt+ + ++ +l+
  gi|320100473|ref|YP_004176065.1| 272 TGRNGAGKTTLLKLMAGVLK 291
                                       6999********99987766 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.028        10       2      22 ..      31      51 ..      30      59 .. 0.87
   2 ?    5.4   0.0     0.041        15       5      22 ..     273     290 ..     270     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.028
                                      EEEESTTSSHHHHHHHHHCCS CS
                               dNK  2 vveGnIgaGKstlvklLskkl 22
                                       v G+ g+GK+tl+ +L+  l
  gi|320100473|ref|YP_004176065.1| 31 IVTGPSGSGKTTLIRVLTGVL 51
                                      689************998665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.041
                                       ESTTSSHHHHHHHHHCCS CS
                               dNK   5 GnIgaGKstlvklLskkl 22 
                                       G  gaGK+tl+kl++  l
  gi|320100473|ref|YP_004176065.1| 273 GRNGAGKTTLLKLMAGVL 290
                                       778**********99776 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 ?    8.8   0.0    0.0035       1.3      44      64 ..      24      44 ..      15      50 .. 0.86
   2 ?   -1.7   0.0       5.6     2e+03     104     117 ..     146     159 ..     125     185 .. 0.68
   3 ?    0.5   0.1       1.2   4.3e+02      42      63 ..     260     282 ..     254     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0035
                         IstB_IS21 44 iekkenivllGpsGvGKshla 64
                                      +++ e+++++GpsG GK+ l 
  gi|320100473|ref|YP_004176065.1| 24 VQDGEALIVTGPSGSGKTTLI 44
                                      67899*************885 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.6
                         IstB_IS21 104 krllkvdllilDdl 117
                                       +   + ++lilD+ 
  gi|320100473|ref|YP_004176065.1| 146 AFARRYRVLILDEP 159
                                       44557799999984 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.2
                         IstB_IS21  42 sfiekkeniv.llGpsGvGKshl 63 
                                       sf+ +k +++ l+G  G+GK+ l
  gi|320100473|ref|YP_004176065.1| 260 SFTIEKSSLAgLTGRNGAGKTTL 282
                                       565444444439*********87 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0063       2.2       4      23 ..      30      49 ..      28      52 .. 0.88
   2 ?    3.6   0.2      0.14        51       6      22 ..     271     287 ..     269     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0063
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      +++ G++gsGKttL + l+g
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVLTG 49
                                      6899***********99976 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                         PduV-EutP   6 liGkvgsGKttLtqalk 22 
                                       l G+ g+GKttL + + 
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMA 287
                                       679*********98776 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.036        13      19      35 ..      27      43 ..      16      52 .. 0.80
   2 ?    4.5   0.2     0.057        20      15      51 ..     262     299 ..     257     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.036
                                      -SEEEEE--TTSSTTHH CS
                              PhoH 19 ndivfaiGpaGtGKtyl 35
                                       + ++++Gp+G+GKt l
  gi|320100473|ref|YP_004176065.1| 27 GEALIVTGPSGSGKTTL 43
                                      567899********987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.057
                                       HHHH-SEEEEE--TTSSTT.HHHHHHHHHHHHTTS-SE CS
                              PhoH  15 alkkndivfaiGpaGtGKt.ylavalavealkkkkvkr 51 
                                       +++k+++   +G+ G+GKt +l ++++v    k++v+r
  gi|320100473|ref|YP_004176065.1| 262 TIEKSSLAGLTGRNGAGKTtLLKLMAGVLKPLKGSVRR 299
                                       57899999**********82456666776666666655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.21        76      23      39 ..      34      50 ..      31      79 .. 0.78
   2 ?    6.7   0.1    0.0065       2.3      23      39 ..     273     289 ..     271     305 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.21
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G  G+GKTtL r+l  +
  gi|320100473|ref|YP_004176065.1| 34 GPSGSGKTTLIRVLTGV 50
                                      778*********99876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0065
                            AAA_13  23 GwNGaGKTtLSrllrsl 39 
                                       G+NGaGKTtL +l++ +
  gi|320100473|ref|YP_004176065.1| 273 GRNGAGKTTLLKLMAGV 289
                                       9*********9998875 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0012      0.44      60      86 ..      28      54 ..      19      99 .. 0.91
   2 ?   -2.3   0.1       2.2   7.7e+02      64      83 ..     271     290 ..     267     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                   Herpes_Helicase 60 saylitGtAGaGkstsiqalaenldCl 86
                                      +a+++tG  G+Gk+t i +l+ +ld +
  gi|320100473|ref|YP_004176065.1| 28 EALIVTGPSGSGKTTLIRVLTGVLDRI 54
                                      589******************999965 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                   Herpes_Helicase  64 itGtAGaGkstsiqalaenl 83 
                                       +tG  GaGk+t ++ +a +l
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVL 290
                                       69*********998887665 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.025       8.9      20      46 ..      25      51 ..      18      56 .. 0.88
   2 ?    2.6   0.1      0.18        63      21      48 ..     265     292 ..     253     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
                                      HCTS-EEEEESTTSSCHHHHHHHHHHC CS
                              PIF1 20 ekgklfFvtGsgGtgKtflwkallkkl 46
                                      + g+ + vtG +G+gKt l + l+ +l
  gi|320100473|ref|YP_004176065.1| 25 QDGEALIVTGPSGSGKTTLIRVLTGVL 51
                                      679999***************999876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                                       CTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1  21 kgklfFvtGsgGtgKtflwkallkklrs 48 
                                       k+ l  +tG  G+gKt l+k +  +l++
  gi|320100473|ref|YP_004176065.1| 265 KSSLAGLTGRNGAGKTTLLKLMAGVLKP 292
                                       55666689**************999987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.045        16       4      22 ..      30      48 ..      28      56 .. 0.81
   2 ?    5.9   0.5     0.024       8.6       6      26 ..     271     291 ..     266     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.045
                                      EEEEESTTSSHHHHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLa 22
                                      +++ G+ G+GKTt +  L 
  gi|320100473|ref|YP_004176065.1| 30 LIVTGPSGSGKTTLIRVLT 48
                                      6789*********997776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.024
                                       EEESTTSSHHHHHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLaallk 26 
                                       l G +GaGKTt l  +a +lk
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLMAGVLK 291
                                       789*********999988776 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.17        61      22      37 ..      32      47 ..      14      48 .. 0.81
   2 ?    6.3   0.3    0.0039       1.4      22      37 ..     271     286 ..     256     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.17
                           DUF3584 22 ieGtNaaGKTtLlrLi 37
                                      + G  ++GKTtL+r++
  gi|320100473|ref|YP_004176065.1| 32 VTGPSGSGKTTLIRVL 47
                                      67999*********86 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0039
                           DUF3584  22 ieGtNaaGKTtLlrLi 37 
                                       + G N+aGKTtLl+L+
  gi|320100473|ref|YP_004176065.1| 271 LTGRNGAGKTTLLKLM 286
                                       789**********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 3029.20
//
Query:       gi|320100474|ref|YP_004176066.1|  [L=234]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1870.96
//
Query:       gi|320100475|ref|YP_004176067.1|  [L=759]
Description: DEAD/DEAH box helicase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-26   92.2   0.0    9.6e-25   87.3   0.0    2.4  3  DEAD           DEAD/DEAH box helicase
    1.2e-16   61.0   0.0    6.1e-16   58.7   0.0    2.0  2  Helicase_C     Helicase conserved C-terminal domain
    5.4e-13   49.5   0.8    1.6e-12   48.0   0.8    1.9  1  DUF1998        Domain of unknown function (DUF1998)
    1.4e-05   25.2   0.0    4.6e-05   23.5   0.0    1.7  2  ResIII         Type III restriction enzyme, res subunit
     0.0046   16.7   0.0      0.017   14.9   0.0    2.0  1  AAA_30         AAA domain
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.018   15.4   0.0    1.4  1  AAA_19         AAA domain
       0.31   10.5   0.0        0.5    9.8   0.0    1.2  1  UvrD-helicase  UvrD/REP helicase N-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.0   3.8e-28   9.6e-25       2     170 ..      66     232 ..      65     237 .. 0.86
   2 ?    2.0   0.0     0.062   1.6e+02      44     106 ..     283     346 ..     271     361 .. 0.83
   3 ?   -3.3   0.0       2.6   6.7e+03      16      36 ..     563     583 ..     560     595 .. 0.80

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 3.8e-28
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       + Q ea+ +il+g++ +++a TG+GKT+afl+pv+++v+e  +  +p+a+++ Pt++La+++ln++ +++ y  ++ 
  gi|320100475|ref|YP_004176067.1|  66 RFQYEAYRHILNGENTVISAGTGTGKTEAFLLPVIKRVVE-GDGWNPRAMVLYPTKALARDQLNRFIEYTVYPAVSF 141
                                       68*************************************9.666678************************966444 PP

                                       EEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHH.HHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldng.vdivvgtpgrldd.llstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                        +++ g++  + ++++ ++ + i+v++p++l+  l+ + +++   ++  f+V+DE + +     + +i++++++l++
  gi|320100475|ref|YP_004176067.1| 142 -AVYDGDTPVRLRRRIASNpPSIIVSNPDMLHTgLIYSPHVRgfAERADFMVFDELHVYEGV-LGSHIHHLAERLKK 216
                                       .6888888888888886556*************766444444559999*************8.************65 PP

                                       HCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD 152 itcdgklqrqvivlSATlp 170
                                         ++++    +i  SAT+ 
  gi|320100475|ref|YP_004176067.1| 217 SRASKP---VFIGASATIG 232
                                       555444...49******85 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.062
                                       TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEEEHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                              DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvgtpg 106
                                       +++g + ++ + +++Lae   + l+++   +++ v+ + +  + +rd  +kl++g vd vv+tp 
  gi|320100475|ref|YP_004176067.1| 283 SRKGLRFIVFVDSQQLAELLTRILRTRHG-VNVAVHrAGLPADVRRDVEAKLRSGvVDGVVATPT 346
                                       56788999999999999999998888888.566676567889999*******9999*******95 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.6
                                       EEEEEESTTSSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  16 dvlvaaeTGsGKTlaflipvl 36 
                                       d+l++ +TGsG  +a++  vl
  gi|320100475|ref|YP_004176067.1| 563 DILAERRTGSGVRAAYARVVL 583
                                       8899999***98777777766 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.97   2.5e+03      19      60 ..     113     158 ..     104     167 .. 0.70
   2 !   58.7   0.0   2.4e-19   6.1e-16       5     110 ..     277     381 ..     273     382 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.97
                                       EEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHH CS
                        Helicase_C  19 ilifvntidrlek.vklllekk...gikvavlhgelpqnereeile 60 
                                       +++  +t+  + + ++ + e     ++++av++g++p + r++i +
  gi|320100475|ref|YP_004176067.1| 113 AMVLYPTKALARDqLNRFIEYTvypAVSFAVYDGDTPVRLRRRIAS 158
                                       5666666664432323332333567899*********999999876 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 2.4e-19
                                       HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                        Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                       +l+ +l  +++g + ++fv +++ +e  +++l++++g++vav+ + lp++ r+++ ++ ++g +d ++at  +e Gi
  gi|320100475|ref|YP_004176067.1| 277 QLCSIL--SRKGLRFIVFVDSQQLAELlTRILRTRHGVNVAVHRAGLPADVRRDVEAKLRSGVVDGVVATPTLELGI 351
                                       566665..89999**********8877899999999***************************************** PP

                                       TSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       di  ++  ++ ++p ++t+y qr+GR+gR 
  gi|320100475|ref|YP_004176067.1| 352 DIGALDAAVMASPPPSYTKYLQRAGRVGRR 381
                                       *****************************5 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.8   6.2e-16   1.6e-12       1      83 []     641     714 ..     641     714 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 6.2e-16
                           DUF1998   1 lehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCeea 77 
                                       +ehali+a+ +++++   dlg+ ++            i++yda+ gG+G+a+ ++e le+  + a e++++cdC+ +
  gi|320100475|ref|YP_004176067.1| 641 IEHALISAARVVCGSGLTDLGGVSY--------PSGDIVVYDAAVGGSGVAKLLYERLEDAEKVAEEIMSRCDCH-D 708
                                       69**********************9........4678***********************88888888888***8.* PP

                           DUF1998  78 GCpaCl 83 
                                       GCp+C+
  gi|320100475|ref|YP_004176067.1| 709 GCPRCI 714
                                       *****7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.8e-08   4.6e-05      23     169 ..      77     231 ..      59     233 .. 0.73
   2 ?   -1.7   0.0      0.95   2.4e+03      41      68 ..     275     300 ..     273     308 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.8e-08
                                       TTSEEEEEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--. CS
                            ResIII  23 rdkrglikmaTGtGKTlva.aklierllkk.gkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka. 96 
                                       + ++ +i + TGtGKT    + +i+r+ +  g++ ++++l p+k+l    l++f +++  ++     +++gd+  + 
  gi|320100475|ref|YP_004176067.1|  77 NGENTVISAGTGTGKTEAFlLPVIKRVVEGdGWNPRAMVLYPTKALARDQLNRFIEYTVYPAV-SFAVYDGDTPVRl 152
                                       4568899*********9998999999987515566*******************999987743.5556777776668 PP

                                       ........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...TTTHHHHHT---.....SEEEEE CS
                            ResIII  97 .kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..kswreilekfke.....avllgl 165
                                        ++++s+  +i+v++ ++l+  +    + + +   +r d++++DE H + +   +++ +++e +k+      v +g 
  gi|320100475|ref|YP_004176067.1| 153 rRRIASNPPSIIVSNPDMLHTGL--IYSPHVRGFAERADFMVFDELHVYEGVlgSHIHHLAERLKKsraskPVFIGA 227
                                       888999***************99..22334444566777********998865534444433332222233777777 PP

                                       ESS- CS
                            ResIII 166 TATp 169
                                       +AT+
  gi|320100475|ref|YP_004176067.1| 228 SATI 231
                                       7775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.95
                                       HHHHHHHH-S.....-EEEEESSHHHHH CS
                            ResIII  41 aaklierllkkgkeekflflvprkslle 68 
                                        a+l+  l++kg   +f+++v++++l e
  gi|320100475|ref|YP_004176067.1| 275 TAQLCSILSRKGL--RFIVFVDSQQLAE 300
                                       5666777777766..9********9987 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   6.5e-06     0.017       2      63 ..      64     128 ..      63     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.5e-06
                            AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKt..talkalreaweaag..grviglAptgkaAkv.La 63 
                                       l   Q +a +++l++++  +v+ ++ GtGKt  ++l ++++++e +g   r ++l pt++ A++ L+
  gi|320100475|ref|YP_004176067.1|  64 LYRFQYEAYRHILNGEN--TVISAGTGTGKTeaFLLPVIKRVVEGDGwnPRAMVLYPTKALARDqLN 128
                                       5667************8..9***********445688999999999877677777777777765466 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   6.9e-06     0.018       1      61 [.      68     130 ..      68     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.9e-06
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTr.vlkhivallvelggvkpeeillvaftgrAakelrer 61 
                                       q ea +  l+ ++ ++ aG GtGKT+  l  +++ +ve  g++p+ ++l      A ++l+  
  gi|320100475|ref|YP_004176067.1|  68 QYEAYRhILNGENTVISAGTGTGKTEaFLLPVIKRVVEGDGWNPRAMVLYPTKALARDQLNRF 130
                                       567887789999*************83578899*********998887766555666666655 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 ?    9.8   0.0    0.0002       0.5       7      41 ..      70     106 ..      65     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
                                       HHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTS CS
                     UvrD-helicase   7 eaias..lggpilveAsAGsGKTfvlaerilrlikee 41 
                                       ea ++   g++++++A+ G+GKT      +++ + e+
  gi|320100475|ref|YP_004176067.1|  70 EAYRHilNGENTVISAGTGTGKTEAFLLPVIKRVVEG 106
                                       555555467899***********97665555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); 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: 0.63u 0.21s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 5655.47
//
Query:       gi|320100476|ref|YP_004176068.1|  [L=76]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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     0.0029   17.4   0.0    1.0  1  Viral_P18  ssRNA positive strand viral 18kD cysteine rich pro


Domain annotation for each model (and alignments):
>> Viral_P18  ssRNA positive strand viral 18kD cysteine rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-07    0.0029      27      90 ..       4      74 ..       2      76 .] 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-07
                         Viral_P18 27 avcGvs.cGmPaavekvs.vpadteedvymlifvleq.........ycGekhyklsealkdvsddelkldrlear 90
                                      ++cGv+ cG  aa  kvs + a + e+  +l+ +++          y  e hykl   +++  ++e  l+ l ++
  gi|320100476|ref|YP_004176068.1|  4 GKCGVNgCGRDAA-RKVSyLDAKVLEEHGLLLHPVDAapprrpghvYLCEEHYKL---WRKLTKRERLLRDLSRK 74
                                      79***88999999.777736899999**********99********999*****9...66667777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 581.09
//
Query:       gi|320100477|ref|YP_004176069.1|  [L=466]
Description: peptidase U62 modulator of DNA gyrase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-56  191.9   0.1    2.5e-56  191.6   0.1    1.1  1  PmbA_TldD      Putative modulator of DNA gyrase
  ------ inclusion threshold ------
       0.07   13.2   0.0       0.22   11.6   0.0    1.8  2  Ribosomal_L27  Ribosomal L27 protein


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 !  191.6   0.1   2.8e-60   2.5e-56       2     279 .]      22     315 ..      21     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 2.8e-60
                                       EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-... CS
                         PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea... 75 
                                        +vr++e+  +s++++ng ++++++++ +g+gvrvi++g +g+a+t+d+s  +++++ve av++a+   +       
  gi|320100477|ref|YP_004176069.1|  22 IDVRYQEYYHESLSVDNGVLRELTTTRATGIGVRVIVNGLMGYATTNDLSPGSVKRTVEVAVKLARALRSSGMPqdi 98 
                                       69*******************************************9999999*************776655555999 PP

                                       ..................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEE CS
                         PmbA_TldD  76 ..................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldve 134
                                                         e+v+ +ek  ll+++ ka r+ +         ++s+ ++    ++ ++++a+S+G +v 
  gi|320100477|ref|YP_004176069.1|  99 yerpvqrdrvashyvenpEDVDLSEKAGLLLDMYKAGRNIP---------GVSSLTIPFGYERDRRVYASSRGDYVD 166
                                       99********************************9976665.........699999999****************** PP

                                       EEEEEEEEEEEEEE..S.TCS...ETEEEEEEEESSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHH CS
                         PmbA_TldD 135 qtrtrvslslsvia.dd.ggs...gdgmgggsgyedleeedleeiaeeaaekalasleakplppgkypVvlspeavg 206
                                       +tr  +++++ ++a ++ + +     + ++  g+e +e++++ +++ e  + a+++ +a  ++pg+y+Vvl++e vg
  gi|320100477|ref|YP_004176069.1| 167 YTRRMIGIGVRIVAsSGgSHEmlwT-SESRVAGWEFIESFNWLDYVVENSRLAVEAAGAPHVKPGRYDVVLDNEIVG 242
                                       **************55423337542.344455556677788888********************************* PP

                                       HHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 207 sllheavghaleadavlegrSflkdklGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLkny 279
                                       ++lhea+gha ead v +g S+l++++G++vas+l++ivdd++++g  + p+DdEG+p  +t+ +++GvL ++
  gi|320100477|ref|YP_004176069.1| 243 LMLHEAFGHASEADIVEAGGSVLGGRIGSEVASPLVSIVDDGRIEGGVYVPYDDEGTPKLKTYTVRKGVLSSF 315
                                       ***********************88*****************9877788*********************987 PP

>> Ribosomal_L27  Ribosomal L27 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       0.8   7.1e+03      53      69 ..     151     168 ..     148     172 .. 0.76
   2 ?   11.6   0.0   2.5e-05      0.22      15      48 ..     320     355 ..     308     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.8
                     Ribosomal_L27  53 GkdhtlfAlvdG.vVkfe 69 
                                        +d  ++A   G +V ++
  gi|320100477|ref|YP_004176069.1| 151 ERDRRVYASSRGdYVDYT 168
                                       589999999999667776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.5e-05
                     Ribosomal_L27  15 skgkrlGvKkfggqlvk..agnIivrQrgtkfhpGe 48 
                                       + ++rlG++ +g+  +   +++I+vrQ +t + pG+
  gi|320100477|ref|YP_004176069.1| 320 TTARRLGAQPTGNARIMsfRNTILVRQTNTYMEPGD 355
                                       5789*********87752379**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3346.31
//
Query:       gi|320100478|ref|YP_004176070.1|  [L=453]
Description: peptidase U62 modulator of DNA gyrase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-45  155.3   0.1    3.7e-45  154.9   0.1    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.9   0.1   2.1e-49   3.7e-45       1     277 [.      22     315 ..      22     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 2.1e-49
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEE..EE...ESSHHHHHHHHHHHHHHCCS---TT- CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgf..astldtsdealeeaveraveiaklapedpea 75 
                                       e+e++ +es+ +s++++ ++v+++s+s+    g+r   g r+g    ++l+ +     e++ +  +ia  apedp++
  gi|320100478|ref|YP_004176070.1|  22 EVEAYSVESSILSLTVSSNKVKEASRSRIVTTGLRGAIGRRVGGlaLTALNVD---PVEVAGELARIAGAAPEDPYW 95 
                                       6899*******************************665888888642222333...336666688899999****** PP

                                       ....................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEE CS
                         PmbA_TldD  76 ....................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGld 132
                                                           +e+s+ee++e+l+++ +a+rsa     +++  +++ v++sl+   ++ +++nS+G+d
  gi|320100478|ref|YP_004176070.1|  96 pgfptplhgtsralcldkriAELSEEEAVEILLNAMEAMRSAAI-SMHVD--EAVVVEGSLNMGSQRYRVVNSHGVD 169
                                       ******************************97777767666665.22223..6778899****************** PP

                                       EEEEEEEEEEEEEEEE..STCSETEEEEEEEE.....SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HH CS
                         PmbA_TldD 133 veqtrtrvslslsviad.dggsgdgmgggsgy.....edleeedleeiaeeaaekalasleakplppgkypVvlspe 203
                                       +  + t++sl l+  ++ +      +g+ + +     + l+e+ l e  +ea e a    +a+p+++g y+V+l+pe
  gi|320100478|ref|YP_004176070.1| 170 ADAECTFISLWLTLSVKtS------RGSSDKSvftvrRGLDEQYLMERSREAGELAPLFAGARPVESGVYDVILTPE 240
                                       ********99998888323......222222233444333345566689**************************** PP

                                       HHHHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE- CS
                         PmbA_TldD 204 avgsllheavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLk 277
                                        +g++l+ ++ +a++a ++le rS+lk+k+Ge+v s+ lti+ddpt   + gs++fDdEGv t+ +v+ ++Gv+k
  gi|320100478|ref|YP_004176070.1| 241 SAGLILSTLLTPAFSALNILESRSPLKGKVGEEVVSPVLTITDDPTLpLETGSRGFDDEGVGTRMKVILDKGVFK 315
                                       **************************99******************999*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3424.28
//
Query:       gi|320100479|ref|YP_004176071.1|  [L=301]
Description: biotin--acetyl-CoA-carboxylase ligase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-09   36.9   0.5    4.6e-09   36.3   0.5    1.3  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
    5.9e-07   29.3   0.3    1.2e-06   28.2   0.3    1.5  1  BPL_C          Biotin protein ligase C terminal domain
  ------ inclusion threshold ------
      0.035   14.4   0.7      0.063   13.6   0.7    1.4  1  Aim19          Altered inheritance of mitochondria protein 19


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 !   36.3   0.5   7.6e-13   4.6e-09      30     131 .]     102     194 ..      85     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 7.6e-13
                                       EEESS-B..-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TTEEEETTTEEEET CS
                     BPL_LplA_LipB  30 rrqtgGr..nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegipvfikwpnDlyvn 104
                                       + q +Gr   +w++  g+l+ ++  s     + ++v++l+ + + +  +++l      +    + ++ikwpnD++++
  gi|320100479|ref|YP_004176071.1| 102 QVQGKGRhgKTWIGNLGGLWVTFKAS-----VAPQVAQLLPVAIPVLLVRTL------RDKLVVDAEIKWPNDIVYK 167
                                       4555666*9*****999999888777.....468999999999999999***......6889999************ PP

                                       TEEEEEEEEEEEETTS-EEEEEEEEEE CS
                     BPL_LplA_LipB 105 grKlaGiavtstrgktlhhivigvgvn 131
                                       grK+aG++ +  + + +   +igvg+n
  gi|320100479|ref|YP_004176071.1| 168 GRKIAGVLLEGEYVGVSIVSYIGVGLN 194
                                       *************99999999999887 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 !   28.2   0.3   2.1e-10   1.2e-06       1      45 [.     251     294 ..     251     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.1e-10
                                       STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCE CS
                             BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdi 45 
                                       ++G++V++ + +g++ G+a++++++G L+++ + g    ++sG+i
  gi|320100479|ref|YP_004176071.1| 251 TLGRRVIAVTSNGEIKGVARDVSEYGELIIEDERG-SHRLTSGEI 294
                                       69*********************************.999999998 PP

>> Aim19  Altered inheritance of mitochondria protein 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7     1e-05     0.063      73     114 ..      73     113 ..      71     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                             Aim19  73 WSllYllvngkksikslrrgkvvPlaLsalalanavlyGkrf 114
                                       WS lY +v g + +++++  ++++++Ls l +   + +Gk++
  gi|320100479|ref|YP_004176071.1|  73 WSYLYKIVSGSTMVSARQ-MSPWSIVLSELQVQGKGRHGKTW 113
                                       **********99999888.9*********9999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2185.20
//
Query:       gi|320100480|ref|YP_004176072.1|  [L=232]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   32.3   0.2    3.9e-07   30.7   0.2    1.9  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.087   13.1   0.0       0.17   12.2   0.0    1.5  1  PqqD      Coenzyme PQQ synthesis protein D (PqqD)


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 !   30.7   0.2   4.3e-11   3.9e-07       1      73 [.      14     110 ..      14     131 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.3e-11
                          CxxCxxCC   1 eCkeCgaCCk.elkvklteedlerlkaaevaeeeeeskkiak..................adgrCvfldeetklCki 58 
                                       +C +Cg CC+ +    l+ ed+   + a+      +s+  +                   ++grC+fl++   +C i
  gi|320100480|ref|YP_004176072.1|  14 KCPACGLCCTfSPVSILPHEDIVLRTIADALGLPYSSQPGYVifeevnrvnlafsyvmelHNGRCIFLSGS--KCMI 88 
                                       6*********73334445555433333333222222222222356677788888889999***********..8*** PP

                          CxxCxxCC  59 Ye.eRpkicrlfpas......e 73 
                                       +   +p+icr +p +      +
  gi|320100480|ref|YP_004176072.1|  89 HDvYKPLICRSYPYVprhvryN 110
                                       **889********986554441 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.9e-05      0.17      35      67 .]     150     184 ..     138     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHCT--..HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD  35 ivaalaeeydvd..eeeaeadvlafldqLrekgli 67 
                                       ++  l++ey+++   e++++ +l++l++L+++g++
  gi|320100480|ref|YP_004176072.1| 150 VIRYLKKEYNAAveMENIRNTLLSLLSKLWREGIV 184
                                       5777999**777667******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1693.26
//
Query:       gi|320100481|ref|YP_004176073.1|  [L=182]
Description: cytidyltransferase-like domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-10   41.1   0.0      1e-09   38.7   0.0    2.1  2  CTP_transf_like  Cytidylyltransferase-like
    2.6e-05   23.6   0.0     0.0041   16.4   0.1    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   1.1e-13     1e-09       5     141 ..      11     136 ..       7     138 .. 0.70
   2 ?   -2.3   0.0       0.5   4.5e+03      32      59 ..     140     168 ..     137     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.1e-13
                                       --TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHHHHHHHT CS
                   CTP_transf_like   5 tFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.kevdevisvdpweltrevlkkl 80 
                                       +F+p+H+GHl+ +e   +  +e +i+ v  + +++   +++++a eRl m++ a k+       + ++++   l  l
  gi|320100481|ref|YP_004176073.1|  11 RFQPFHYGHLNAIEYCYRNYDE-VIIVVGMASQSHTP-ENPFTAGERLLMIRGAlKWAGH--DLSRYVTVT--LPTL 81 
                                       8*********************.99999999999998.****************776555..444444443..2222 PP

                                       TTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                   CTP_transf_like  81 kpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                       +++  + v+  ++++       ++++++ ++++++ + e  ++v+ ++ k++  +S++ ir
  gi|320100481|ref|YP_004176073.1|  82 EVN-RAAVHFVRQYSP-----PFKSVVTLNPIIQRLFMEEGYEVIPPPVKERDTYSGSAIR 136
                                       221.244555555555.....4666666666666666666666666666666666666666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.5
                                       EESSTHCSST.-SCSSTHHHHHHHHHHHT CS
                   CTP_transf_like  32 vpsdeppkkk.kkplasaeeRlemlelak 59 
                                       +++d++ k+   +p+a   eR+  +e+++
  gi|320100481|ref|YP_004176073.1| 140 LANDPSWKQLvPPPVAEIIERIGGVERIR 168
                                       56777777774488888888887777774 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   4.6e-07    0.0041       6      38 ..       8      40 ..       4      43 .. 0.90
   2 !    5.3   0.0    0.0011       9.5     200     236 ..     126     160 ..     107     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.6e-07
                       HIGH_NTase1  6 iIaEYNPfHnGHlyhlekakeltgadvviavmS 38
                                      +Ia + PfH GHl  +e + +++++ ++++ m 
  gi|320100481|ref|YP_004176073.1|  8 VIARFQPFHYGHLNAIEYCYRNYDEVIIVVGMA 40
                                      8999******************99999999886 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0011
                       HIGH_NTase1 200 eeeiaSAtaiRkalkeekkleelkklvPestleilke 236
                                       e+++ S +aiR+++  +    + k+lvP  ++ei+++
  gi|320100481|ref|YP_004176073.1| 126 ERDTYSGSAIRRMMLAN--DPSWKQLVPPPVAEIIER 160
                                       46789*********555..478**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1404.61
//
Query:       gi|320100482|ref|YP_004176074.1|  [L=125]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.4   0.4      0.095   12.7   0.4    1.3  1  FtsL      Cell division protein FtsL
      0.064   13.3   0.1       0.24   11.5   0.0    2.0  2  DUF1707   Domain of unknown function (DUF1707)


Domain annotation for each model (and alignments):
>> FtsL  Cell division protein FtsL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   1.1e-05     0.095      28      73 ..      57     102 ..      55     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                              FtsL  28 vavvlithqtRqlvselekllserdkLeeewrnLlLEestlsahsr 73 
                                       va+v++    R  v++ ++llse +  +ee++++ +E   +   sr
  gi|320100482|ref|YP_004176074.1|  57 VATVWTKSIERDCVTQVNNLLSEGRLTQEEYKKYRVELVEQCMVSR 102
                                       799********************************99876665555 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.51   4.6e+03      21      38 ..      40      57 ..      26      60 .. 0.57
   2 ?   11.5   0.0   2.7e-05      0.24      11      31 ..      69      89 ..      65     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.51
                           DUF1707 21 eGrLtldEfdeRleaala 38
                                       G +++  +d R   ++ 
  gi|320100482|ref|YP_004176074.1| 40 KGLIEIRQLDPRYPYIYV 57
                                      455666666666555555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.7e-05
                           DUF1707 11 avelLrealaeGrLtldEfde 31
                                       v ++++ l+eGrLt +E+ +
  gi|320100482|ref|YP_004176074.1| 69 CVTQVNNLLSEGRLTQEEYKK 89
                                      567789999**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 907.61
//
Query:       gi|320100483|ref|YP_004176075.1|  [L=142]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1089.06
//
Query:       gi|320100484|ref|YP_004176076.1|  [L=87]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 643.96
//
Query:       gi|320100485|ref|YP_004176077.1|  [L=503]
Description: metal dependent phosphohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   45.6   0.2    1.7e-11   44.4   0.2    1.6  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.2   9.4e-16   1.7e-11       1      78 [.      49     156 ..      49     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 9.4e-16
                                       HHHHHHHHHHHHHHHHHHHHH................HHHHHHHHHHHHHTTTTHHHHTS..HHH...HHH.CTCCH CS
                                HD   1 rleHsleVaklarrlaedlge................eedrellllaaLlHDiGkgpfgdafekk...eee.fekfl 57 
                                       r++Hsl+V++l++  aedl                  e+ +e ++la+LlHD+G+  fg++fe     +++  +++ 
  gi|320100485|ref|YP_004176077.1|  49 RFQHSLGVMHLTGLVAEDLTGklvsihgvdvlegyspETLVEAARLAGLLHDVGHAAFGHSFEYSvlwKKNvLGELS 125
                                       79*****************889*****************************************99998555688899 PP

                                       HHHHHHHHHHHHHHHHHHHH..........H CS
                                HD  58 aHekvgaeilrevekrlgld..........l 78 
                                       +Hek+g ++l+ +++++ l           +
  gi|320100485|ref|YP_004176077.1| 126 NHEKIGLKLLELLLEDRLLEaeerygltglT 156
                                       9**********99999866555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3878.16
//
Query:       gi|320100486|ref|YP_004176078.1|  [L=63]
Description: helix-turn-helix, type 11 domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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    1.1  1  HTH_IclR       IclR helix-turn-helix domain
    9.5e-06   25.6   0.1    1.1e-05   25.4   0.1    1.1  1  HTH_20         Helix-turn-helix domain
    6.5e-05   22.7   0.0    7.6e-05   22.5   0.0    1.2  1  MarR_2         MarR family
    0.00013   22.3   0.0    0.00015   22.1   0.0    1.1  1  FaeA           FaeA-like protein
    0.00014   21.5   0.1    0.00016   21.4   0.1    1.0  1  LexA_DNA_bind  LexA DNA binding domain
    0.00034   20.5   0.1    0.00045   20.1   0.1    1.3  1  HTH_Crp_2      Crp-like helix-turn-helix domain
    0.00069   19.1   0.0    0.00077   19.0   0.0    1.2  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0011   18.5   0.0     0.0013   18.4   0.0    1.0  1  HrcA_DNA-bdg   Winged helix-turn-helix transcription represso
     0.0014   18.2   0.1     0.0025   17.4   0.0    1.4  2  Sigma70_r4_2   Sigma-70, region 4
     0.0015   18.4   0.0     0.0018   18.1   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0015   18.3   0.0     0.0018   18.1   0.0    1.2  1  HTH_5          Bacterial regulatory protein, arsR family
     0.0026   17.4   0.1     0.0033   17.1   0.1    1.3  1  GntR           Bacterial regulatory proteins, gntR family
     0.0031   17.8   0.0     0.0033   17.7   0.0    1.2  1  Rrf2           Transcriptional regulator
     0.0058   16.7   0.0     0.0066   16.5   0.0    1.1  1  DprA_WH        DprA winged helix domain
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.013   15.7   0.1    1.4  1  HTH_28         Helix-turn-helix domain
      0.011   15.8   0.0      0.012   15.7   0.0    1.1  1  DUF2250        Uncharacterized protein conserved in archaea (
      0.018   14.9   0.2      0.033   14.0   0.0    1.5  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.029   14.4   0.0      0.035   14.1   0.0    1.2  1  DUF2089        Protein of unknown function (DUF2089)
      0.031   13.7   0.0      0.051   13.0   0.0    1.4  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
       0.04   13.7   0.0      0.073   12.9   0.0    1.4  1  HTH_23         Homeodomain-like domain
      0.043   13.8   0.0      0.053   13.6   0.0    1.2  1  HTH_29         Winged helix-turn helix
      0.053   13.7   0.0      0.053   13.7   0.0    1.1  1  Rio2_N         Rio2, N-terminal
      0.064   13.4   0.1      0.088   13.0   0.1    1.3  1  AbiEi_4        Transcriptional regulator, AbiEi antitoxin
      0.065   13.2   0.0      0.071   13.1   0.0    1.1  1  HTH_11         HTH domain
        0.1   12.5   0.0       0.12   12.3   0.0    1.1  1  TFIIE_alpha    TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.9e-10   2.1e-07       8      52 .]      11      55 ..      10      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.9e-10
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      + ++l++++ +l  +e++r tgl+  tv+  L+ L ++G+ve+ +
  gi|320100486|ref|YP_004176078.1| 11 LVEFLGSQGKPLMPKEISRLTGLNYNTVRARLHDLRKEGLVERRP 55
                                      6789**************************************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 !   25.4   0.1   1.5e-08   1.1e-05      19      61 .]      15      58 ..       4      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.5e-08
                                      H.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 19 L.araegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      L +++++l ++e+ ++ +l  nt++ +L+ L++ gLve++ eg+
  gi|320100486|ref|YP_004176078.1| 15 LgSQGKPLMPKEISRLTGLNYNTVRARLHDLRKEGLVERRPEGW 58
                                      367899************************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.1e-07   7.6e-05      10      56 ..      11      56 ..       6      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +  +Lg  + + l ++e+ r +gl   +v  +l +L + GLverrp 
  gi|320100486|ref|YP_004176078.1| 11 LVEFLGSQGKP-LMPKEISRLTGLNYNTVRARLHDLRKEGLVERRPE 56
                                      66778888876.99*******************************84 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     2e-07   0.00015       2      49 ..       8      55 ..       7      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-07
                                      HHHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                              FaeA  2 keeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrsp 49
                                      ke ++e+l s + p   +ei   +gl    +R  L  L+keg ++r p
  gi|320100486|ref|YP_004176078.1|  8 KERLVEFLGSQGKPLMPKEISRLTGLNYNTVRARLHDLRKEGLVERRP 55
                                      899*******************************************98 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 !   21.4   0.1   2.3e-07   0.00016       7      60 ..       3      55 ..       1      57 [. 0.95

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.3e-07
                                      HHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                     LexA_DNA_bind  7 rQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdp 60
                                       Qr+v + +++++ ++g p   +ei+r  gl+  ++v  +L+ L++ G++er p
  gi|320100486|ref|YP_004176078.1|  3 EQRTVKERLVEFLGSQGKPLMPKEISRLTGLN-YNTVRARLHDLRKEGLVERRP 55
                                      59999***************************.9******************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 !   20.1   0.1   6.3e-07   0.00045      21      55 ..      21      55 ..       9      63 .] 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.3e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgr 55
                                      pl  +e++++ Gl+  tv   l++L++egl++r+ 
  gi|320100486|ref|YP_004176078.1| 21 PLMPKEISRLTGLNYNTVRARLHDLRKEGLVERRP 55
                                      66678***************************763 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.1e-06   0.00077      21      48 .]      25      52 ..       6      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +e+++ +gl  +tv++rl  L +eGl++
  gi|320100486|ref|YP_004176078.1| 25 KEISRLTGLNYNTVRARLHDLRKEGLVE 52
                                      8*************************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 !   18.4   0.0   1.8e-06    0.0013       5      57 ..       3      55 ..       1      57 [. 0.95

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                      HrcA_DNA-bdg  5 vqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvp 57
                                       q+++ + L+e    +++++  +ei  + + n  tvR  l+ L+  gLve +p
  gi|320100486|ref|YP_004176078.1|  3 EQRTVKERLVEFLGSQGKPLMPKEISRLTGLNYNTVRARLHDLRKEGLVERRP 55
                                      6999*********************************************9876 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.6   6.9e+03      41      47 ..       5      11 ..       4      12 .. 0.68
   2 !   17.4   0.0   3.5e-06    0.0025      30      52 ..      25      47 ..      22      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.6
                                      HHHHHHH CS
                      Sigma70_r4_2 41 gtVksrl 47
                                      +tVk rl
  gi|320100486|ref|YP_004176078.1|  5 RTVKERL 11
                                      6888665 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.5e-06
                                      HHHHHHHT--HHHHHHHHHHHHH CS
                      Sigma70_r4_2 30 kEIAellgisegtVksrlsRArk 52
                                      kEI++l+g++ +tV+ rl+  rk
  gi|320100486|ref|YP_004176078.1| 25 KEISRLTGLNYNTVRARLHDLRK 47
                                      8******************8777 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.5e-06    0.0018      22      57 ..      21      56 ..      12      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      p+  +ei++ +g+ +++v   L  L + GlVer+++
  gi|320100486|ref|YP_004176078.1| 21 PLMPKEISRLTGLNYNTVRARLHDLRKEGLVERRPE 56
                                      67789****************************987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.6e-06    0.0018      14      46 ..      20      52 ..       7      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-06
                                      SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++l   e+++ +gl+  tv+  L  Lr++GLVe
  gi|320100486|ref|YP_004176078.1| 20 KPLMPKEISRLTGLNYNTVRARLHDLRKEGLVE 52
                                      678899**************************8 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   4.5e-06    0.0033      11      59 ..       9      56 ..       4      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.5e-06
                                      HHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 11 edIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      e++++   + G +L   +e++   g + +tvR  L  L  eglverr+ 
  gi|320100486|ref|YP_004176078.1|  9 ERLVEFLGSQGKPL-MPKEISRLTGLNYNTVRARLHDLRKEGLVERRPE 56
                                      55555555678888.8899***************************985 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.6e-06    0.0033      22      58 ..      18      54 ..       5      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.6e-06
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      +++p+  +ei++ ++++ + ++  l+ Lrk+glv+ +
  gi|320100486|ref|YP_004176078.1| 18 QGKPLMPKEISRLTGLNYNTVRARLHDLRKEGLVERR 54
                                      45678899**************************965 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.2e-06    0.0066      13      61 .]       7      57 ..       2      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.2e-06
                           DprA_WH 13 lerrvLaaLgpe..PvhvDqLvrrtglpaaevsaaLleLELaGlverlpGg 61
                                       ++r+++ Lg++  P+   +++r tgl   +v a L  L  +Glver+p g
  gi|320100486|ref|YP_004176078.1|  7 VKERLVEFLGSQgkPLMPKEISRLTGLNYNTVRARLHDLRKEGLVERRPEG 57
                                      568899999987779999******************************976 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.1   1.8e-05     0.013      16      45 ..      25      51 ..       7      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                            HTH_28 16 reaArelgisrrtvyrWikryeegGiagLv 45
                                      +e++r+ g+++ tv+  ++ ++++G+   v
  gi|320100486|ref|YP_004176078.1| 25 KEISRLTGLNYNTVRARLHDLRKEGL---V 51
                                      79*********************775...4 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   1.7e-05     0.012      24      56 ..      23      55 ..       3      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                           DUF2250 24 YaksiakeleipleevrellkkLeelGLlerve 56
                                       +k i++ + ++ + vr  l++L++ GL+er  
  gi|320100486|ref|YP_004176078.1| 23 MPKEISRLTGLNYNTVRARLHDLRKEGLVERRP 55
                                      689***************************975 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         7     5e+03      33      38 ..       6      11 ..       4      13 .. 0.75
   2 ?   14.0   0.0   4.6e-05     0.033      21      42 .]      25      46 ..      22      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7
                     HTH_AsnC-type 33 tvlrRv 38
                                      tv +R+
  gi|320100486|ref|YP_004176078.1|  6 TVKERL 11
                                      888886 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.6e-05
                     HTH_AsnC-type 21 aeLAervGlSestvlrRvrrLe 42
                                      +e+++ +Gl  +tv++R++ L+
  gi|320100486|ref|YP_004176078.1| 25 KEISRLTGLNYNTVRARLHDLR 46
                                      69****************9986 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.9e-05     0.035      53      75 ..      25      47 ..       4      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-05
                           DUF2089 53 kevekelgisYpTvrnrldeile 75
                                      ke+ +  g+ Y+Tvr+rl+++ +
  gi|320100486|ref|YP_004176078.1| 25 KEISRLTGLNYNTVRARLHDLRK 47
                                      899****************9866 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 ?   13.0   0.0   7.2e-05     0.051      31      51 ..      25      45 ..      25      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                      HTH_Tnp_ISL3 31 kavArqlgvSwtTVwrildry 51
                                      k+++r++g++ +TV+ +l+++
  gi|320100486|ref|YP_004176078.1| 25 KEISRLTGLNYNTVRARLHDL 45
                                      78****************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.073      21      46 ..      25      50 ..      23      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                            HTH_23 21 reIAreLgvsrrTvyrwlkryreeGl 46
                                      +eI+r+ g +++Tv+  l+  r+eGl
  gi|320100486|ref|YP_004176078.1| 25 KEISRLTGLNYNTVRARLHDLRKEGL 50
                                      8**************99999899996 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.4e-05     0.053      15      48 ..      24      55 ..      17      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-05
                            HTH_29 15 vsqiAkllglsrrtvyrwlkrfeegGlaalld.rr 48
                                      +++i +l+gl + tv+  l++ +++G   l + r+
  gi|320100486|ref|YP_004176078.1| 24 PKEISRLTGLNYNTVRARLHDLRKEG---LVErRP 55
                                      79************************...666344 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.4e-05     0.053      28      65 ..      25      59 ..       8      63 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.4e-05
                            Rio2_N 28 elieeisrlkeeevkkrlsrllkaklisrktakydGYk 65
                                      ++i+++++l+ + v+ rl++l k++l++r+    +G+ 
  gi|320100486|ref|YP_004176078.1| 25 KEISRLTGLNYNTVRARLHDLRKEGLVERRP---EGWV 59
                                      6799************************975...5655 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00012     0.088       2      44 ..      10      57 ..       9      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                           AbiEi_4  2 rlpelasrqvGlfttrelea.aGispsa....lrrLvrkGwLvrlrrG 44
                                      rl+e++ +q+  +  +e+ +  G+ +++    l+ L+++G+++r + G
  gi|320100486|ref|YP_004176078.1| 10 RLVEFLGSQGKPLMPKEISRlTGLNYNTvrarLHDLRKEGLVERRPEG 57
                                      55556656666666678878888999888999************8876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.9e-05     0.071       3      47 ..       9      52 ..       7      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIe 47
                                      + ++e+L ++ +p+  +e+++ +++   tvr ++ +L++ g  +e
  gi|320100486|ref|YP_004176078.1|  9 ERLVEFLGSQGKPLMPKEISRLTGLNYNTVRARLHDLRKEG-LVE 52
                                      6789999777778***************************9.444 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.12      29      59 ..      23      53 ..       4      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      BHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                       TFIIE_alpha 29 teedlakelkidlnelrklLnrLyearlvky 59
                                         +++++++++ n +r  L +L++++lv+ 
  gi|320100486|ref|YP_004176078.1| 23 MPKEISRLTGLNYNTVRARLHDLRKEGLVER 53
                                      5679************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 469.41
//
Query:       gi|320100487|ref|YP_004176079.1|  [L=288]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.077   13.6   0.0       0.15   12.7   0.0    1.4  1  ACT_4     ACT domain
       0.17   11.7   0.4       0.39   10.5   0.4    1.7  1  ACT       ACT domain


Domain annotation for each model (and alignments):
>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05      0.15       4      57 ..      27      80 ..      25      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                             ACT_4  4 sytvrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVk 57
                                      +y + l++++++ kg++a+i+++i + + +i ++++    +  + ++++ + V+
  gi|320100487|ref|YP_004176079.1| 27 RYFTLLDLIVRNGKGVVARISELILSRGLSIANITTPGLVTRDMDKGRLLILVE 80
                                      5778899***************************98765554455555555555 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   4.4e-05      0.39       3      33 ..      32      62 ..      30      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.4e-05
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEEEE CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieq 33
                                      l + v++ +G+ ar++ ++  rg++i++i++
  gi|320100487|ref|YP_004176079.1| 32 LDLIVRNGKGVVARISELILSRGLSIANITT 62
                                      56789999********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2110.69
//
Query:       gi|320100488|ref|YP_004176080.1|  [L=438]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.13   12.5   0.1       0.24   11.7   0.1    1.3  1  DDE_Tnp_IS240  DDE domain
       0.14   11.2   0.1       0.57    9.2   0.0    1.8  2  Njmu-R1        Mjmu-R1-like protein family


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.6e-05      0.24      11      56 ..      35      80 ..      32     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                     DDE_Tnp_IS240 11 vkikGkwaYlyravDkegrildflvskrRdtkaakaflrkalkkek 56
                                      ++++++++ ++ra+D++  ++ +   +  +++a + f++k  ++ +
  gi|320100488|ref|YP_004176080.1| 35 IQVAEEKQTIWRAIDAQLDTVIVSAVASANKTAYQSFMNKWSSEMQ 80
                                      89*****************9999999999**********9988775 PP

>> Njmu-R1  Mjmu-R1-like protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1     0.064   5.7e+02     165     224 ..       8      67 ..       6      98 .. 0.77
   2 ?    9.2   0.0   6.4e-05      0.57     116     160 ..     112     160 ..      93     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.064
                           Njmu-R1 165 vvkikrvvqllqekltlllhaalsstpvevkesdektkrdiarflkaaslqglvqeestv 224
                                       v+ +   v l+   l +  ++ + +++++v e ++ + r i   l+++ +  +   ++t+
  gi|320100488|ref|YP_004176080.1|   8 VIAVTLLVLLMTTTLLYTTSTLTYYSNIQVAEEKQTIWRAIDAQLDTVIVSAVASANKTA 67 
                                       677777899999999999999999999999999999999999999998888887665543 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 6.4e-05
                           Njmu-R1 116 flGGsekGle....lfrleldkyvqglkssldselenlesevksylsnW 160
                                       f+   e Gl+      +  ld+++qgl+s+l+  l+ + s+v s+l+nW
  gi|320100488|ref|YP_004176080.1| 112 FVCPGECGLNyskpGVNASLDRFIQGLNSTLQFYLNAVSSSVYSALQNW 160
                                       5556677888543336789****************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3081.90
//
Query:       gi|320100489|ref|YP_004176081.1|  [L=129]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 950.27
//
Query:       gi|320100490|ref|YP_004176082.1|  [L=369]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2831.23
//
Query:       gi|320100491|ref|YP_004176083.1|  [L=862]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-14   53.1   0.8      2e-13   50.7   0.0    2.6  2  DUF2341   Domain of unknown function (DUF2341)


Domain annotation for each model (and alignments):
>> DUF2341  Domain of unknown function (DUF2341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.1e-17     2e-13       3      62 ..     203     261 ..     201     266 .. 0.94
   2 ?   -0.7   0.1      0.13   2.3e+03      43      64 ..     379     400 ..     355     433 .. 0.71

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.1e-17
                           DUF2341   3 sdiRfvdsdgtt.LpywieswdantekaliWvkvpsipangnktikiyygnptatstsngd 62 
                                       sd+Rf+dsdg t L y+ie+w   +  aliWvk+p ++a + kti++y gn+ a+++sn+ 
  gi|320100491|ref|YP_004176083.1| 203 SDVRFTDSDGVTpLDYYIEYWGSVN--ALIWVKIPLLKAREVKTIYMYWGNSFAQEKSNPG 261
                                       8*******************97766..9******************************985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                           DUF2341  43 nktikiyygnptatstsngdat 64 
                                        +++ i+ygn + t +  g+ +
  gi|320100491|ref|YP_004176083.1| 379 LSNYTIIYGNWSITGEVTGEGV 400
                                       4566788888887776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 5815.00
//
Query:       gi|320100492|ref|YP_004176084.1|  [L=258]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   15.2   1.1      0.048   14.0   1.1    1.6  1  DUF1270   Protein of unknown function (DUF1270)


Domain annotation for each model (and alignments):
>> DUF1270  Protein of unknown function (DUF1270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.1   2.7e-06     0.048       7      33 ..       9      35 ..       4      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-06
                           DUF1270  7 syllavlCftvlaivlmPllyfttaWs 33
                                      s l+ v  ft la+ l+P+ yf+t  s
  gi|320100492|ref|YP_004176084.1|  9 STLILVGVFTALALALIPYSYFATMSS 35
                                      67899999***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1890.69
//
Query:       gi|320100493|ref|YP_004176085.1|  [L=250]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.9   0.1       0.23   11.4   0.1    1.2  1  Pox_LP_H2  Viral late protein H2


Domain annotation for each model (and alignments):
>> Pox_LP_H2  Viral late protein H2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   1.3e-05      0.23      29      76 ..      11      58 ..       2      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
                         Pox_LP_H2 29 vstliffvlilaisvlllllqvsdnsvlselakyariknavksWkplv 76
                                      v+++i+f++ +ais+ ++++ ++  + ++ l+ y  +k  + +  +++
  gi|320100493|ref|YP_004176085.1| 11 VAAVILFTVAVAISLAVFFYTAFYTDYVKALTEYGHVKTVLWNIADVI 58
                                      6789**********************************9876655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1934.79
//
Query:       gi|320100494|ref|YP_004176086.1|  [L=580]
Description: type II secretion system F domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-19   70.2   3.7    1.6e-11   44.3   0.1    4.0  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 ?   -0.1   0.8     0.049   8.7e+02      94     124 ..      36      66 ..      31      67 .. 0.86
   2 !   34.9   0.9   6.7e-13   1.2e-08       3     121 ..     111     235 ..     109     239 .. 0.90
   3 ?   -6.4   4.3         1   1.8e+04     109     123 ..     294     308 ..     292     317 .. 0.56
   4 !   44.3   0.1   8.7e-16   1.6e-11       1     124 [.     385     511 ..     385     512 .. 0.94
   5 ?   -5.6   2.2         1   1.8e+04     109     124 ..     558     573 ..     553     574 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  94 lrrkllaallepllllvvallvllillaill 124
                                       +  ++ aal++ ++++ +a+ + l +l+ ll
  gi|320100494|ref|YP_004176086.1|  36 MHSEVYAALTGLVFIVSLAASITLTILLALL 66 
                                       56789999***********999999998776 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 6.7e-13
                                       HHHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   3 rqlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqliragee 73 
                                        +l+t++ +G++++ a+e++ + ++ +++ +e  +r +   r  g ++ +a++    rtpss  +e+++ +i+++++
  gi|320100494|ref|YP_004176086.1| 111 SYLSTMVMSGLSPYIAFERILKGSTiFKRTSELAQRFILLNRILGrDPLTAFDelakRTPSSRVKETLSGYIATVKA 187
                                       68**********************998888888888777777766466677777779******************** PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllilla 121
                                       gg++ ++L++ ++ l +e     k+ a +l+ ll++++a+++l ++ +
  gi|320100494|ref|YP_004176086.1| 188 GGDVVDYLNKRSRLLFNEMLVGMKIIADRLGGLLEAYLAMILLTMISF 235
                                       ****************************************99988755 PP

  == domain 3  score: -6.4 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXX CS
                             T2SSF 109 lvvallvllillail 123
                                       +++a ++++ ll+++
  gi|320100494|ref|YP_004176086.1| 294 VFFATFIPITLLLVV 308
                                       555555555555554 PP

  == domain 4  score: 44.3 bits;  conditional E-value: 8.7e-16
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHH....HHHCT-TT.TS.-HHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgsls....ealertpssef.pelvvqlirage 72 
                                       flr l+   ++G+p+++++  l+  + +g++++ l++ia++l+ G++l+    e++++   s++   l+  l+ ++e
  gi|320100494|ref|YP_004176086.1| 385 FLRDLVEVRKTGLPPERSIIELSPRD-YGVFTPHLRKIAMELSIGIPLRritdEVMRKIR-SWIgQVLLFILTDSIE 459
                                       8999**********************.*******************99655547777665.5999************ PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                        gg   evLe+la + e  ++++ +++ +l   +++ +++++++++ +++++
  gi|320100494|ref|YP_004176086.1| 460 VGGGTVEVLENLAWFAESVEAIEDERKRSLRTLMIVPYMGGILSAVTVIYMV 511
                                       ************************************************9998 PP

  == domain 5  score: -5.6 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXXX CS
                             T2SSF 109 lvvallvllillaill 124
                                       +v a+l+ li l+++l
  gi|320100494|ref|YP_004176086.1| 558 VVHAVLLTLITLIVML 573
                                       4555555566655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4337.84
//
Query:       gi|320100495|ref|YP_004176087.1|  [L=558]
Description: type II secretion system protein E [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-49  167.5   0.0    5.2e-49  166.8   0.0    1.2  1  T2SSE          Type II/IV secretion system protein
    0.00011   22.7   0.0     0.0003   21.3   0.0    1.8  1  ABC_tran       ABC transporter
     0.0022   17.7   0.1     0.0059   16.3   0.1    1.7  1  AAA_29         P-loop containing region of AAA domain
     0.0024   17.4   0.1     0.0044   16.6   0.1    1.4  1  AAA_7          P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.011   14.9   0.1      0.018   14.2   0.1    1.2  1  PIF1           PIF1-like helicase
      0.017   15.7   0.4      0.038   14.5   0.4    1.5  1  AAA_23         AAA domain
      0.021   14.7   0.0      0.061   13.2   0.0    1.8  1  RsgA_GTPase    RsgA GTPase
      0.021   15.2   0.0      0.049   14.0   0.0    1.6  1  AAA_16         AAA ATPase domain
      0.022   14.1   0.3      0.072   12.4   0.0    2.0  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.025   14.8   1.8      0.049   13.9   0.1    2.3  3  AAA_28         AAA domain
      0.031   14.0   0.3      0.067   12.9   0.3    1.5  1  AAA_30         AAA domain
       0.04   14.2   2.5       0.42   10.9   2.5    2.3  1  AAA_19         AAA domain
      0.064   12.2   0.6       0.19   10.6   0.6    1.7  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.066   13.3   0.1       0.75    9.9   0.0    2.6  3  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.081   12.7   0.0       0.21   11.3   0.0    1.7  1  DEAD           DEAD/DEAH box helicase


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 !  166.8   0.0   4.3e-52   5.2e-49       5     256 ..     155     416 ..     152     434 .. 0.92

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 4.3e-52
                             T2SSE   5 leallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrl 80 
                                       l+++++d+++ di  +     ++v  r+ +    ++++  ++al+ li ++a++a+++is   p++da lp +++r+
  gi|320100495|ref|YP_004176087.1| 155 LDPIMKDPNIEDISCNGVSIpIFVWHRKYESIPTNIAFTGEEALNELIMKMAHMAGKHISIAYPILDAMLP-EKHRV 230
                                       78899*******************99999999***************************************.77777 PP

                             T2SSE  81 rvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                        +     v +  ++++iRk ++k +++ +++ +++ ++  a+ l   +++ ++++++GgTg+GKtt+l+al  +i+ 
  gi|320100495|ref|YP_004176087.1| 231 AATYSKEVSTkgPSFTIRKFREKPYSIVEVIEQGNIDAVTAAYLWMLLEHGKTFMIAGGTGTGKTTMLNALSMFIKP 307
                                       7666554444359***************************************************************9 PP

                             T2SSE 156 sderivtvEDpvEiqleganqvqlnak..........kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnT 222
                                          +ivt+ED+ E++l ++n vql ++           ++v + dl++ +LR rPD ++vGE+R++e+  + +A+ T
  gi|320100495|ref|YP_004176087.1| 308 G-MKIVTIEDTPELNLPHVNWVQLTSRetyvvgtqslGTSVKLYDLVKLSLRYRPDYVIVGEVRGEEASVLFQAMAT 383
                                       9.********************************99999************************************** PP

                             T2SSE 223 GHlgslsTlHansaagalerLeqlgaeveaaelk 256
                                       GH g  sT+Ha++   a++rL    ++++++ ++
  gi|320100495|ref|YP_004176087.1| 384 GHSG-ASTIHAETLDYAIKRLTSPPMNIPPTYMR 416
                                       ****.****************9877777666554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.5e-07    0.0003       8      49 ..     278     319 ..     274     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.5e-07
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdl 49 
                                       l++g++  i G +G+GK+t+l++l+   kp +  +++++++ 
  gi|320100495|ref|YP_004176087.1| 278 LEHGKTFMIAGGTGTGKTTMLNALSMFIKPGMKIVTIEDTPE 319
                                       789***************************999999997654 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     5e-06    0.0059      18      49 ..     276     308 ..     259     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5e-06
                            AAA_29  18 eidlkg.atlltGpsGsGKSTllDAiqalLvpa 49 
                                       ++ ++g +++++G +G+GK+T+l A+++ + p 
  gi|320100495|ref|YP_004176087.1| 276 MLLEHGkTFMIAGGTGTGKTTMLNALSMFIKPG 308
                                       555677799*****************9887775 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 !   16.6   0.1   3.7e-06    0.0044      23      54 ..     272     302 ..     258     315 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                             AAA_7  23 syllelllknkkpvllvGptGtGKtviikdll 54 
                                          l +ll+++k +++ G tGtGKt++++ l 
  gi|320100495|ref|YP_004176087.1| 272 A-YLWMLLEHGKTFMIAGGTGTGKTTMLNALS 302
                                       3.455899*******************99865 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.5e-05     0.018      19      53 ..     278     312 ..     262     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                       .HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCE CS
                              PIF1  19 nekgklfFvtGsgGtgKtflwkallkklrsegkiv 53 
                                        e+gk+f + G  GtgKt +++al+ ++++  kiv
  gi|320100495|ref|YP_004176087.1| 278 LEHGKTFMIAGGTGTGKTTMLNALSMFIKPGMKIV 312
                                       589***************************99988 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   3.2e-05     0.038      20      40 ..     282     302 ..     264     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                            AAA_23  20 gltlItGpNGaGKTTildAik 40 
                                       + + I G +G+GKTT l+A+ 
  gi|320100495|ref|YP_004176087.1| 282 KTFMIAGGTGTGKTTMLNALS 302
                                       6799***************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.1e-05     0.061      91     120 ..     272     302 ..     244     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinall 120
                                       + l  ll++ kt +++G +G GK+t++nal 
  gi|320100495|ref|YP_004176087.1| 272 AYLWMLLEHgKTFMIAGGTGTGKTTMLNALS 302
                                       45666677779******************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.1e-05     0.049      21     124 ..     279     382 ..     264     392 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                       +++    ++ G  G+GK++++++l   ++    +++++ + + +   +p + ++q+ +re+++    +   ++   +
  gi|320100495|ref|YP_004176087.1| 279 EHG-KTFMIAGGTGTGKTTMLNALSMFIKPGMkIVTIEDTPELN---LPHVNWVQLTSRETYVVGTQSL-GTSVKLY 350
                                       444.67889****************8888875477799999999...9*999*****997777766555.4446677 PP

                            AAA_16  97 wrekleeala....avpelagaeasrllellk 124
                                       +  kl  +++    +v+e++g+eas l+++++
  gi|320100495|ref|YP_004176087.1| 351 DLVKLSLRYRpdyvIVGEVRGEEASVLFQAMA 382
                                       77777777778888999999999988888875 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     6e-05     0.072      41      59 ..     283     301 ..     233     305 .. 0.83
   2 ?   -2.1   0.1       1.6   1.9e+03     110     131 ..     489     513 ..     486     523 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-05
                                       SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  41 hllvaGatgsGKStalntL 59 
                                         ++aG+tg+GK+t+ln+L
  gi|320100495|ref|YP_004176087.1| 283 TFMIAGGTGTGKTTMLNAL 301
                                       579**************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHH...HHHHHTT-SSH CS
                      FtsK_SpoIIIE 110 eeLvkemeery...alfreagvrsi 131
                                       e +v+e+++r+   + +re+g+r+ 
  gi|320100495|ref|YP_004176087.1| 489 EDVVEEVKRRAvvlEWMREEGIRDA 513
                                       6789999999988899999999875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.1e-05     0.049       2      26 ..     284     311 ..     283     319 .. 0.76
   2 ?   -1.5   0.0       2.2   2.7e+03       3      32 ..     336     371 ..     335     404 .. 0.61
   3 ?   -3.2   0.0       7.4   8.8e+03      26      44 ..     491     509 ..     472     525 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                            AAA_28   2 ivitGgestGKTtlleaLa...argypv 26 
                                       ++i Gg +tGKTt+l+aL+   + g+++
  gi|320100495|ref|YP_004176087.1| 284 FMIAGGTGTGKTTMLNALSmfiKPGMKI 311
                                       5799**************9443225554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                            AAA_28   3 vitGgestGKTtlleaLaar......gypvvpEaar 32 
                                       +++G++s G++  l  L +       +y++v E+  
  gi|320100495|ref|YP_004176087.1| 336 YVVGTQSLGTSVKLYDLVKLslryrpDYVIVGEVRG 371
                                       689999999999887777433334566777777654 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 7.4
                            AAA_28  26 vvpEaareileeklakged 44 
                                       vv+E+ r+ +  ++ ++e+
  gi|320100495|ref|YP_004176087.1| 491 VVEEVKRRAVVLEWMREEG 509
                                       5566666666555544444 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   5.6e-05     0.067      15      42 ..     279     305 ..     270     315 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaw 42 
                                       ++g ++ ++ G+ GtGKtt+l+al   +
  gi|320100495|ref|YP_004176087.1| 279 EHG-KTFMIAGGTGTGKTTMLNALSMFI 305
                                       444.58899*************997655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.5   0.00035      0.42      10      35 ..     281     306 ..     276     477 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallv 35 
                                        k++++ +G GtGKT++l++    ++
  gi|320100495|ref|YP_004176087.1| 281 GKTFMIAGGTGTGKTTMLNALSMFIK 306
                                       68899************997654444 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   0.6   0.00016      0.19      17      36 ..     283     302 ..     277     317 .. 0.81
   2 ?   -2.3   0.0       1.3   1.6e+03      15      56 ..     332     374 ..     328     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                     TrwB_AAD_bind  17 hilivGttGsGKtqalekll 36 
                                        ++i+G+tG+GKt++l++l 
  gi|320100495|ref|YP_004176087.1| 283 TFMIAGGTGTGKTTMLNALS 302
                                       589*************9985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                     TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllr.airargdraivlDltGafv 56 
                                        + + +vGt+  G ++ l +l++ ++r r d +iv    G+  
  gi|320100495|ref|YP_004176087.1| 332 SRETYVVGTQSLGTSVKLYDLVKlSLRYRPDYVIVGEVRGEEA 374
                                       578899****************956899999999988888755 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 ?   -1.0   0.0       1.4   1.7e+03     100     127 ..     139     173 ..      82     174 .. 0.72
   2 ?   -1.1   0.0       1.6   1.9e+03      92     124 ..     200     236 ..     191     239 .. 0.70
   3 ?    9.9   0.0   0.00063      0.75       4      97 ..     286     381 ..     284     457 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                                       HHHHC.......TS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxx.......xxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA 100 lkqry.......gvpvlgviprdeavaeapargep 127
                                       lk +y       g  vl+ i +d ++ ++ ++g +
  gi|320100495|ref|YP_004176087.1| 139 LKLMYyiernllGYGVLDPIMKDPNIEDISCNGVS 173
                                       33333342223478888899999999999888865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                                       TCHHHHHHHHHHC...TS-EEE.EEE--CCHCCCCHH CS
                                       xxxxxxxxxxxxx...xxxxxx.xxxxxxxxxxxxxx RF
                              CbiA  92 llkealeelkqry...gvpvlg.viprdeavaeapar 124
                                       +l+  ++    ++   + p+l+ ++p++ +va  +++
  gi|320100495|ref|YP_004176087.1| 200 ELIMKMAHMAGKHisiAYPILDaMLPEKHRVAATYSK 236
                                       444455555555567799****9******99988776 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00063
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHHCCHCCCHHHHHHCHCHHHH...E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiepdlkrllellealgkkkall.lki 76 
                                       +++  G+GKTt++ +L   ++  g +++ +   p+ n+ ++     ++++    + ++l+ +++  + +k  l  ++
  gi|320100495|ref|YP_004176087.1| 286 IAGGTGTGKTTMLNALSMFIKP-GMKIVTIEDTPELNLPHVnwvQLTSRETYVVGTQSLGTSVKLYDLVKLSLrYRP 361
                                       567789**********998887.*******98888888886665555555555588887777744444433336777 PP

                                       EEEEEEEESS...-TTCHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  77 agvvlnrvdgeneetllkeal 97 
                                         v++  v+ge e   l +a+
  gi|320100495|ref|YP_004176087.1| 362 DYVIVGEVRGE-EASVLFQAM 381
                                       78888877777.344455554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.21       9      67 ..     276     328 ..     268     367 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                       HHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   9 plilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnl 67 
                                        l+ +g+ +++a+ TG+GKT++  + +l+ +     k+g k++ +e t eL   ++n +
  gi|320100495|ref|YP_004176087.1| 276 MLLEHGKTFMIAGGTGTGKTTM--LNALSMF----IKPGMKIVTIEDTPELNLPHVNWV 328
                                       45558999************98..7777777....579999999999999987777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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 0.28s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 4106.53
//
Query:       gi|320100496|ref|YP_004176088.1|  [L=245]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1705.33
//
Query:       gi|320100497|ref|YP_004176089.1|  [L=318]
Description: phosphoesterase DHHA1 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-09   37.3   0.1    5.9e-09   36.5   0.1    1.4  1  DHHA1          DHHA1 domain
  ------ inclusion threshold ------
       0.18   12.3   0.0       0.29   11.6   0.0    1.3  1  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   6.5e-13   5.9e-09      28     131 ..     204     292 ..     187     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 6.5e-13
                                       HHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSHSS-HHHHHHHHH CS
                             DHHA1  28 eellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdkvkvsarskkdgvdagelakeaa 104
                                       ++l   ++ev+g  ++vae+++++++     +a++l  +++  v+v++++++    k+s+rs+  gv+++++a +  
  gi|320100497|ref|YP_004176089.1| 204 DGLKTVVREVDGFRICVAESSDTVEN---SFLASYLMGRFNADVAVIASSDG----KLSLRSR--GVNVRDIAVA-- 269
                                       45555556666777777777555555...88899999988888888888754....8******..**********.. PP

                                       HHTTCCEEEETCEEEEEEEHCHHHHHH CS
                             DHHA1 105 aklgggGGGHdlAaGagipaekleeal 131
                                           +gGGGH  A+Ga+ip+     +l
  gi|320100497|ref|YP_004176089.1| 270 ----LGGGGHLTASGARIPIPFKTRLL 292
                                       ....**************966555555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.3e-05      0.29      19     105 ..      20     107 ..       5     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                                       HHHHHHH.HT--EEEESSS-.SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH...--SEEEE-TT-- CS
                     CoA_binding_2  19 vlrylle.hglpvvpVnpke.eeilgekvyaslaedpepvdlvdvftppeatpeivkealal...gakavwlqpgse 90 
                                       +  yl++ ++++v+   p + +e lg+ v +  +     + l d+ ++p +   +v+ +++l   g ++ w+  +++
  gi|320100497|ref|YP_004176089.1|  20 LYIYLNKlEDYRVYFTEPYGlHEALGKAVGKGFT----RIALMDLGVNPPVFNRVVELLGELtggGSRVSWFDHHVW 92 
                                       4455666678999999999889999965555555....899**********999999999998778*********** PP

                                       -HHHHHHHHHTT-EE CS
                     CoA_binding_2  91 deeaaelaeeagirv 105
                                       ++e ++++e  g+ +
  gi|320100497|ref|YP_004176089.1|  93 EDEWVKAVEGSGVVL 107
                                       *********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2546.66
//
Query:       gi|320100498|ref|YP_004176090.1|  [L=181]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   30.8   0.3    1.2e-06   28.5   0.1    2.1  2  DUF429    Protein of unknown function (DUF429)


Domain annotation for each model (and alignments):
>> DUF429  Protein of unknown function (DUF429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   6.7e-11   1.2e-06       1     132 [.       6     117 ..       6     127 .. 0.79
   2 ?   -0.5   0.0      0.05     9e+02     182     201 ..     144     163 ..     129     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.7e-11
                            DUF429   1 GvDla..gcrtgwaavaledgrlrlvdv....eae.eivaalaallaaaeeaavvaiDaPiglperetggRaaDraa 70 
                                       G+Dla  ++++ ++av+   + lr+v +    + + +i+  ++ l     +++v a+DaP+     + g+R  D ++
  gi|320100498|ref|YP_004176090.1|   6 GIDLAgsPRNPSGVAVIEHSRGLRIVFIgllyS-DeDILGLVERL-----KPVVAAVDAPLTP---GRGYRSVDLEL 73 
                                       9******99999999998899999977798733.36*********.....**********975...79********* PP

                            DUF429  71 rkllarrgasvfpvpar.aalaagkglserafgllpklrevdelldarpelrgrvvEvhPeaa 132
                                           +r g +v+p+  r + +  +     ra++l+  +r          +++  vvE+hP  a
  gi|320100498|ref|YP_004176090.1|  74 I---KR-GYRVLPPGWRgMRMLYE-----RAVRLAGIMR----------GMGVEVVETHPRSA 117
                                       5...77.********997555444.....5666555554..........44455666666655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.05
                            DUF429 182 DvlDAvacaltArraarGra 201
                                       D  DA+++  +A +  +G +
  gi|320100498|ref|YP_004176090.1| 144 DEEDALVASIVALKHGEGGV 163
                                       55599999999998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1404.12
//
Query:       gi|320100499|ref|YP_004176091.1|  [L=456]
Description: 2,3-di-O-geranylgeranylglyceryl phosphate reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-11   42.8   1.3    1.3e-05   24.5   0.2    2.7  3  FAD_binding_2   FAD binding domain
    1.7e-09   37.6   0.2    2.8e-09   36.8   0.2    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    2.9e-09   36.4   0.8    3.6e-07   29.6   0.0    2.3  2  Lycopene_cycl   Lycopene cyclase protein
    1.2e-07   31.3   3.2    9.7e-06   25.1   0.1    2.9  2  FAD_binding_3   FAD binding domain
    2.1e-07   30.9   5.2     0.0043   16.7   0.6    2.3  2  DAO             FAD dependent oxidoreductase
    1.7e-06   28.1   0.1     0.0031   17.7   0.1    3.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    6.8e-06   25.2   0.1     0.0059   15.5   0.0    2.8  3  Trp_halogenase  Tryptophan halogenase
    3.5e-05   23.2   1.0    0.00017   20.9   1.1    1.8  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.5e-05   23.4   5.1       0.28   11.8   0.1    3.3  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00013   20.9   0.2     0.0013   17.5   0.0    2.1  2  HI0933_like     HI0933-like protein
    0.00039   19.6   0.4    0.00063   18.9   0.4    1.3  1  GIDA            Glucose inhibited division protein A
     0.0007   18.9   1.1     0.0022   17.3   1.0    1.9  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 !   24.5   0.2   8.5e-09   1.3e-05       1      35 [.       4      38 ..       4      69 .. 0.94
   2 !   16.5   0.0   2.4e-06    0.0035     146     210 ..     100     161 ..      82     177 .. 0.87
   3 ?   -2.4   0.0       1.2   1.9e+03     210     246 ..     277     314 ..     254     319 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.5e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      D++V+G+G+AGL ++l +a +G +va+ve +++ +
  gi|320100499|ref|YP_004176091.1|  4 DAVVVGAGVAGLYSSLILASKGFRVALVESKPASR 38
                                      89***************************999866 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG...... CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkel 210
                                        l+++a++ gv++++++ ++ ++v+d+ v  ++v+ + +g++v+++a + ++a+g+ ++  l+++
  gi|320100499|ref|YP_004176091.1| 100 WLLRQALDKGVELLDQHTVLGVTVKDNTVKSITVK-KVGGGTVELEASGFIDASGAKPA--LRSR 161
                                       58999******************************.99999**************9986..3333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                                       .....GSSSBSSGTT-S-HHHHHHHCTTSS.EES..TT CS
                     FAD_binding_2 210 llgaaaeaettnapavtGdglalalragaa.lnddrme 246
                                       +   + +a+t+n+++  G g +l++++ +a  ++d++e
  gi|320100499|ref|YP_004176091.1| 277 VGVVGDAAYTVNPVHGGGIGSSLEAADIVArHMGDALE 314
                                       45556678888888888888888888777777776666 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.2   1.9e-12   2.8e-09       1     144 [.       4     153 ..       4     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.9e-12
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLve..ergvlGGlltsglvatdignkaeeqvvtgiareflerlrq...rgg 72 
                                       D vVvG+g+aG+   +  a +G +v+Lve  +  ++G  + + + +     ++  +    +++++++ +r     + 
  gi|320100499|ref|YP_004176091.1|   4 DAVVVGAGVAGLYSSLILASKGFRVALVEskPASRIGDKTCGDAIGVHHFEHIGLKPPDSVVDHVYKGVRIyspSER 80 
                                       779**************************555568998888877655555454447788899999999966322222 PP

                      FAD_oxidored  73 arlkkrskwn...tfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.grktirAkvfiDATg 144
                                       ++++ +   +   +  ++  + +l + l++ gv++l ++++ +v++++++++s+tv++   g+ +++A+ fiDA+g
  gi|320100499|ref|YP_004176091.1|  81 YEITVPG--EgvsVNRVKLGQWLLRQALDK-GVELLDQHTVLGVTVKDNTVKSITVKKVGgGTVELEASGFIDASG 153
                                       2333222..133488999999999999988.*****************9*******988855************98 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   2.4e-10   3.6e-07       1     163 [.       4     188 ..       4     200 .. 0.74
   2 !    5.1   0.1    0.0068        10     235     297 ..     255     316 ..     252     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.4e-10
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnn....yvWsdefedlga..leecvehsWsgtivyldd 71 
                                       D vv+GaG Agl     l  a +g +v l+e+ p +  + +       + +fe +g    +++v+h+++g+++y + 
  gi|320100499|ref|YP_004176091.1|   4 DAVVVGAGVAGLYSSLIL--ASKGFRVALVESKPASRIGDKtcgdAIGVHHFEHIGLkpPDSVVDHVYKGVRIYSPS 78 
                                       88**********999999..9**********9998854433111134577888888333578*************97 PP

                     Lycopene_cycl  72 gk.killgraYgrvsskrlkeellerlvengvklle.akvesveeeeageslvvle...ggr.kirarlvvdargla 142
                                       ++ +i++  +  +v++ +l + ll++  ++gv+ll+  +v  v+ ++++ ++++++   gg  +++a+  +da+g+ 
  gi|320100499|ref|YP_004176091.1|  79 ERyEITVPGEGVSVNRVKLGQWLLRQALDKGVELLDqHTVLGVTVKDNTVKSITVKkvgGGTvELEASGFIDASGA- 154
                                       7625566578899*******************998626899998888865555543232344699**********4. PP

                     Lycopene_cycl 143 slk.............karrlglQtfyGvevevd 163
                                       ++              k++++ + ++y  +ve d
  gi|320100499|ref|YP_004176091.1| 155 KPAlrsrlpeawpiseKPYTTDFNIAYREVVEYD 188
                                       4434566666666666666666666666666665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0068
                     Lycopene_cycl 235 vveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres 297
                                       v+++  g++P    ++lp +  + v  +G aa  v P  G  +  sl +a+++a  + +al++ 
  gi|320100499|ref|YP_004176091.1| 255 VIHAGGGIVPT--RRPLPTMVWRnVGVVGDAAYTVNPVHGGGIGSSLEAADIVARHMGDALEQG 316
                                       66777789999..788888776636679***************************999999863 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   6.5e-09   9.7e-06       2     181 ..       3     171 ..       2     186 .. 0.83
   2 !    5.1   0.4    0.0075        11     287     319 ..     278     310 ..     272     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.5e-09
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                       +d ++VGaG aGl ++l+L+++G rv lve         + +g +   +  ++++Gl+      +  + + g   y 
  gi|320100499|ref|YP_004176091.1|   3 YDAVVVGAGVAGLYSSLILASKGFRVALVESKPASRIGDKTCG-DAIGVHHFEHIGLKPPDSVVD--HVYKGVRIYS 76 
                                       6899***************************999999999888.566789999999975444444..4455555565 PP

                                       ECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEE CS
                     FAD_binding_3  79 elsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvra 155
                                       +       ++++e+   p +   ++  +l + L+ +a  +g+++  ++ v++++  +++v++   +k  g + +++a
  gi|320100499|ref|YP_004176091.1|  77 P-------SERYEIT-VPGEGVSVNRVKLGQWLLRQALDKGVELLDQHTVLGVTVKDNTVKSITVKKVGGGTVELEA 145
                                       5.......7778844.5555556677788888888999*************************************** PP

                                       EEEEE--GTT-HHHHHHTGGEEEEEE CS
                     FAD_binding_3 156 kYlvGaDGgrStvrktlgiefegeet 181
                                          + a G++ + r++l+   + +e+
  gi|320100499|ref|YP_004176091.1| 146 SGFIDASGAKPALRSRLPEAWPISEK 171
                                       **************999977655555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0075
                                       EE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHH CS
                     FAD_binding_3 287 flaGDAaHihpPtgGqGlNtaiqDavnLawkLa 319
                                        ++GDAa ++ P++G G+ ++++ a  +a+ ++
  gi|320100499|ref|YP_004176091.1| 278 GVVGDAAYTVNPVHGGGIGSSLEAADIVARHMG 310
                                       579**************9999887766666655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6   2.9e-06    0.0043       1      45 [.       4      52 ..       4      82 .. 0.73
   2 !   16.6   0.4     3e-06    0.0045     135     311 ..      83     264 ..      70     311 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS..SSTTSSGGGSSEEEEE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg..diagsgaSgrnsgllh 45
                                      d v++G+G++Gl   + La +g  V+l+e++  +++g  + g + g+ h
  gi|320100499|ref|YP_004176091.1|  4 DAVVVGAGVAGLYSSLILASKGfrVALVESKpaSRIGDKTCGDAIGVHH 52
                                      78*****************99********99222344555555555555 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3e-06
                                       EEETTEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEE..EEE--GGGHH. CS
                               DAO 135 lfypdtgqv.dpakltaalaraaealGveilegtevtgleeedgkvwgve.rttp.gendaada..vVnaaGawsd. 205
                                       + +p++g+  +  kl ++l+r+a ++Gve+l +++v g+  +d+ v+ +  + +  g +++ +a   + a Ga    
  gi|320100499|ref|YP_004176091.1|  83 ITVPGEGVSvNRVKLGQWLLRQALDKGVELLDQHTVLGVTVKDNTVKSITvK-KVgGGTVELEAsgFIDASGAKPAl 158
                                       5567766666999**************************8887666666432.2223334445556******98542 PP

                                       HHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE...EEETTTTEEEEEETTSEEEE.EESSE....EETT CS
                               DAO 206 llgllkeldlpispvrgqvlvlkplseklvspaailpvpe...tdddgrgvyvtprkdgrvlv.Ggtad....eesg 274
                                             +l         + + +++++ +++++ a   v e   ++++++  y++ ++ ++v++ Gg  +    + sg
  gi|320100499|ref|YP_004176091.1| 159 R----SRL--------PEAWPISEKPYTTDFNIAYREVVEydgSVNEADRDYAVIYL-NTVVApGG--YwwlfPKSG 220
                                       2....222........12222211111222221222222222334444444444444.32222222..223443333 PP

                                       CSS.....TSCSHHHHHHHHHHHHHHS.GGG.CGEEEEEEEEEE CS
                               DAO 275 ddd.....pevdeedidellealrklf.Pql.gdvlrkwaGlrp 311
                                       d++     + v ++ ++  ++   k++ P++ g+v ++  G+ p
  gi|320100499|ref|YP_004176091.1| 221 DGRvvnvgLGVIWNGLHNPRHNYDKYLkPRFpGRVIHAGGGIVP 264
                                       33333334444444555555555555544444555556666555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.1e-06    0.0031       1      29 [.       7      35 ..       7      82 .. 0.87
   2 !    7.2   0.0     0.004         6      13      53 ..     100     149 ..      99     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      +vGaG++Gl+    La +gf+v l+e+ +
  gi|320100499|ref|YP_004176091.1|  7 VVGAGVAGLYSSLILASKGFRVALVESKP 35
                                      8*************************964 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.004
                                       HHHHCC.TEEEEEE-SSSSSSGGG-EECE........TTCEECTS---EE CS
                     NAD_binding_8  13 ylLaka.gfdvlllekrdrlGGraasyev........pgvrvdygahifh 53 
                                       +lL++a ++ v+ll++++ lG  +++++v        +g +v++ a+ f 
  gi|320100499|ref|YP_004176091.1| 100 WLLRQAlDKGVELLDQHTVLGVTVKDNTVksitvkkvGGGTVELEASGFI 149
                                       7899988999*****************99555555544466666666665 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    0.0038       5.6       3      40 ..       6      40 ..       4      57 .. 0.86
   2 !   15.5   0.0     4e-06    0.0059     150     214 ..      91     159 ..      73     182 .. 0.89
   3 ?   -0.2   0.0      0.22   3.3e+02     314     353 ..     274     312 ..     261     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0038
                                      EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---S CS
                    Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlveseeigtvg 40
                                      v+vG+G aG  +  +la  +   ++v lves+   ++g
  gi|320100499|ref|YP_004176091.1|  6 VVVGAGVAGLYSSLILASKG---FRVALVESKPASRIG 40
                                      9****************999...9******98655544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4e-06
                                       EE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT....S-EEE-SEEEE-SGGG-III CS
                    Trp_halogenase 150 hldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled....greveadlfiDcsGfrglli 214
                                       ++++ ++ ++L r a ++Gv+ ++ + v  ++ +d+ v+s+++++      e+ea  fiD+sG +  l 
  gi|320100499|ref|YP_004176091.1|  91 SVNRVKLGQWLLRQALDKGVELLDQHTVLGVTVKDNTVKSITVKKvgggTVELEASGFIDASGAKPALR 159
                                       57899999*********************999************9997445789999******987765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.22
                                       EETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BT CS
                    Trp_halogenase 314 wvknvvalGlasgfvePlestsihliqaalrrLlallpdk 353
                                       w +nv  +G+a+  v+P+ + +i    +a++ +++++ d 
  gi|320100499|ref|YP_004176091.1| 274 W-RNVGVVGDAAYTVNPVHGGGIGSSLEAADIVARHMGDA 312
                                       4.588889************99999999988888888765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.1   1.1e-07   0.00017       1     112 [.       3     157 ..       3     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE..............TTHCHHHCSHHHHCHHHHHHHHHHHHH...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve..............legtclnggcllskallgvaedaeias...... 57 
                                       +d vv+G+G+AGl  +l la +g++v+lve              + g ++++++ l              +      
  gi|320100499|ref|YP_004176091.1|   3 YDAVVVGAGVAGLYSSLILASKGFRVALVEskpasrigdktcgdAIGVHHFEHIGL--------------Kppdsvv 65 
                                       588**************************866666542233333233333333333..............0222234 PP

                                       .....................................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC..TCE CS
                                       .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                       Pyr_redox_2  58 .....................................evvkklnqgielllgeevvkidpgkkkvklekkke..gde 95 
                                                                            +  + l +g+ell +++v+++  +  +vk  + k+  g +
  gi|320100499|ref|YP_004176091.1|  66 dhvykgvriyspseryeitvpgegvsvnrvklgqwllR--QALDKGVELLDQHTVLGVTVKDNTVKSITVKKvgGGT 140
                                       55566666666999999999999999999999999653..4677899999998888888777777776655555777 PP

                                       EEEEESEEEE---EEE- CS
                                       xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  96 ekiaydklvlAtGsspr 112
                                        ++++   + A+G++p 
  gi|320100499|ref|YP_004176091.1| 141 VELEASGFIDASGAKPA 157
                                       88888888888888875 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00019      0.28       2      46 ..       5      48 ..       4      59 .. 0.84
   2 !   11.3   0.4   0.00025      0.38      42      79 ..      97     134 ..      93     138 .. 0.92
   3 ?    0.4   0.1      0.64   9.6e+02       5      26 ..     136     157 ..     135     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskil 46
                                      +vvvG+G+ gl    +la  g +V +ve ++  +   D+++++++
  gi|320100499|ref|YP_004176091.1|  5 AVVVGAGVAGLYSSLILASKGFRVALVESKPASR-IGDKTCGDAI 48
                                      69***************************99887.6677766665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesvklk 79 
                                       ++++l ++  ++g+e+l +++v  ++ ++++v+s+++k
  gi|320100499|ref|YP_004176091.1|  97 LGQWLLRQALDKGVELLDQHTVLGVTVKDNTVKSITVK 134
                                       68999**********************9999****997 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.64
                                       ECSSHHHHHHHHHHHHTTSEEE CS
                         Pyr_redox   5 vGgGyiglElAgalaelgkkVt 26 
                                       vGgG++ lE+ g++ + g+k  
  gi|320100499|ref|YP_004176091.1| 136 VGGGTVELEASGFIDASGAKPA 157
                                       8***********9998887765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.6e-07    0.0013       2      34 ..       4      36 ..       3      76 .. 0.87
   2 ?    0.9   0.0     0.094   1.4e+02     113     162 ..      99     152 ..      93     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.6e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      d +v+G+G AGl+ ++ +a++g rV+l+e++++
  gi|320100499|ref|YP_004176091.1|  4 DAVVVGAGVAGLYSSLILASKGFRVALVESKPA 36
                                      89***************************9753 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.....TTEEEEESEEEE-- CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktk....seeeleadklvlAt 162
                                       + ll+++ ++gv+l  +++v +v+ +++ + ++++k    ++ elea+  + A+
  gi|320100499|ref|YP_004176091.1|  99 QWLLRQALDKGVELLDQHTVLGVTVKDNTVKSITVKkvggGTVELEASGFIDAS 152
                                       578999999**************9999998888884243333455555555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   4.2e-07   0.00063       1      45 [.       4      49 ..       4      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.2e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT--SSSSEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkldtiaelsCnpsig 45
                                      d +V+G+G AG+  +l +a +G++v+L+  +  ++i+   C ++ig
  gi|320100499|ref|YP_004176091.1|  4 DAVVVGAGVAGLYSSLILASKGFRVALVeSKPASRIGDKTCGDAIG 49
                                      579*************************555678999999999998 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.0   1.5e-06    0.0022      17      56 ..       2      40 ..       1     136 [. 0.65
   2 ?   -3.3   0.0       2.9   4.3e+03      41      59 ..     197     215 ..     193     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                      + D v+vGaG +GL ++ +la k +++va++e++ +   G
  gi|320100499|ref|YP_004176091.1|  2 KYDAVVVGAGVAGLYSSLILASK-GFRVALVESKPASRIG 40
                                      6799*******************.********99764332 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                                       TS-EEEEESSSS--TTTTT CS
                              Thi4  41 dlkvailersvspGGGawl 59 
                                       d  v+ l+  v+pGG  wl
  gi|320100499|ref|YP_004176091.1| 197 DYAVIYLNTVVAPGGYWWL 215
                                       66788899999**999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3157.19
//
Query:       gi|320100500|ref|YP_004176092.1|  [L=509]
Description: AMP phosphorylase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   49.8   0.2      2e-12   46.5   0.0    2.6  3  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    7.3e-12   45.4   0.9    1.3e-10   41.3   0.9    2.3  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
      1e-09   38.1   0.0    3.1e-09   36.5   0.0    1.9  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    4.7e-08   33.1   0.5    9.9e-08   32.1   0.5    1.5  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    0.00018   21.5   0.3       0.14   12.2   0.1    2.5  2  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.044   12.7   0.0      0.076   11.9   0.0    1.3  1  TcpF             Vibrio cholerae toxin co-regulated pilus bio
      0.059   11.9   0.0      0.085   11.4   0.0    1.2  1  AstA             Arginine N-succinyltransferase beta subunit


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 ?   -3.5   0.0       3.4   8.7e+03       4      14 ..      28      38 ..      26      40 .. 0.80
   2 ?   -0.5   0.0      0.38   9.6e+02      34      55 ..     151     172 ..     151     174 .. 0.90
   3 !   46.5   0.0     8e-16     2e-12       2      70 ..     433     494 ..     432     498 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.4
                                      EE-HHHHHHHH CS
                            PYNP_C  4 eidareiGlaa 14
                                        dare+G++a
  gi|320100500|ref|YP_004176092.1| 28 TSDARELGVVA 38
                                      56999***998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.38
                                       EEES--TT-EEBTTSEEEEEEE CS
                            PYNP_C  34 ielhkklGdkVkkGeplatiYa 55 
                                       i+ ++++G +V  +e+++ +++
  gi|320100500|ref|YP_004176092.1| 151 IKAMVETGSRVTFEETVYDVHS 172
                                       6778999*************97 PP

  == domain 3  score: 46.5 bits;  conditional E-value: 8e-16
                                       EEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHHH CS
                            PYNP_C   2 vseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklkk 70 
                                       v+ id+ ++ l+a++ GA       p d+++G++lh k+G +V+kG+pl+t+Y+++ ++le av  l++
  gi|320100500|ref|YP_004176092.1| 433 VTHIDNAAVSLIARACGA-------PYDKGAGVRLHAKVGYRVNKGDPLITLYSSSASRLETAVRLLRD 494
                                       899***************.......**************************************998875 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 !   41.3   0.9     5e-14   1.3e-10       3     253 .]     166     395 ..     164     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 5e-14
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHS.EEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevg.vgf 78 
                                        + D+++ GG+  n+  + + + ++vAa G+ ++k + r+++s +G+aD++e l  +++lt++e+ ++ ++v+ v  
  gi|320100500|ref|YP_004176092.1| 166 TVYDVHSIGGVPGNS-KVALLTVPIVAASGLLIPKTSSRAITSPAGTADTMEVL-ARVDLTMDEIVEIARRVKgVLA 240
                                       578********9999.9***********************************99.5789999999999888751555 PP

                                       EEHHSSSSHHH.HHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHH CS
                   Glycos_transf_3  79 lfapeyhkamk.hvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGlde 154
                                        + + ++++++  ++++ r l i            p   ++ + +++sk++a ++  ++ +++v+r++ v+      
  gi|320100500|ref|YP_004176092.1| 241 WGGKLNLAPADdIFVNIERRLSI-----------DP--DQQMVASILSKKIAMGVERLVIDMPVGRGAKVKD--AST 302
                                       55555555555156789999988...........67..6677889***************************..777 PP

                                       HHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHT CS
                   Glycos_transf_3 155 vsllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvla 230
                                       +  la   + ++   g   +++l+   +++++ ++ ale    +e++e+l +    k s++  d  +l+ag +l l+
  gi|320100500|ref|YP_004176092.1| 303 ADKLAGLFIRQAGlLGLSIKVALTYGGQPIGTTAGPALEA---REALEALIER---KGSRSLIDKAVLLAGLVLELS 373
                                       7778888899888899999*******************99...6666665555...5555557999*********** PP

                                       TSSSSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 231 gkadslkegvakaeevidsGkAl 253
                                       g+a+   +g + a+ev  sGkA+
  gi|320100500|ref|YP_004176092.1| 374 GRAQ-PGQGEDIAREVFLSGKAY 395
                                       *776.57899***********95 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.2e-12   3.1e-09       3      63 .]      98     158 ..      97     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.2e-12
                                       HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       ++kk + g+ L++ e++ +i+++++g + +a+iaAfL++     + +eE+  l +Am+e g
  gi|320100500|ref|YP_004176092.1|  98 ALKKRLHGGRLSEGEMKSIIRDVVDGVYGEAEIAAFLVSQLYSELGEEELSYLIKAMVETG 158
                                       58999999**************************************************976 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 !   32.1   0.5   3.9e-11   9.9e-08      10      83 ..      17      90 ..      11      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 3.9e-11
                                      -CSSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE CS
                           CDC48_N 10 edvgrgivridpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrka 83
                                       d  r+ ++++++d +elg+   +vv ++  +++++a v+++e+ ++ +g++++++ t + +gvs GdkV V+++
  gi|320100500|ref|YP_004176092.1| 17 IDLHRNLIIMNTSDARELGVVANNVVLVTLgDKSAYATVVTSETITQ-PGVVALSKQTASALGVSEGDKVGVKPV 90
                                      4788************************98677799*******9977.*************************97 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   5.5e-05      0.14      30      76 ..      22      69 ..      13      71 .. 0.90
   2 !   12.0   0.0   6.2e-05      0.16      24      52 ..      59      87 ..      49      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.5e-05
                                      -EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS.B-TTEEEE CS
                   Molydop_binding 30 evveinpedAaalGikdGdlVevesrrGsvevrakvter.vrpGvvfm 76
                                      + + +n  dA++lG+  +  V v+    s+ + ++++e+  +pGvv++
  gi|320100500|ref|YP_004176092.1| 22 NLIIMNTSDARELGVVANNVVLVTLGDKSAYATVVTSETiTQPGVVAL 69
                                      4899***********************************7799*9987 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.2e-05
                                      HHCSSS-EEEEEHHHHHHHT--TT-EEEE CS
                   Molydop_binding 24 lakpepevveinpedAaalGikdGdlVev 52
                                      +  ++p vv ++ ++A+alG+++Gd+V v
  gi|320100500|ref|YP_004176092.1| 59 ETITQPGVVALSKQTASALGVSEGDKVGV 87
                                      45556679*******************88 PP

>> TcpF  Vibrio cholerae toxin co-regulated pilus biosynthesis protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     3e-05     0.076     124     177 ..     144     199 ..     131     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                                       TTXSXHHHHHHTSSEEEEEEETTEEEEEEESSXXTTSXEEXXX..XEETTTSXXXX CS
                              TcpF 124 egklstalnqeyitgrfltkengrydivnvggvpdntpvklpa..ivskrglmgtt 177
                                       e +ls  ++    tg  +t e+  yd+  +ggvp n+ v l +  iv+  gl+   
  gi|320100500|ref|YP_004176092.1| 144 EEELSYLIKAMVETGSRVTFEETVYDVHSIGGVPGNSKVALLTvpIVAASGLLIPK 199
                                       66778888888889*************************98643378888887544 PP

>> AstA  Arginine N-succinyltransferase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.3e-05     0.085     286     335 ..      37      87 ..       8      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                              AstA 286 eegekllvantkledFravlaeleleeee.lvlsaeaaeaLevsegdkvrv 335
                                         ++ +lv+ ++ + +  v+++ ++++ + ++ls+++a+aL+vsegdkv v
  gi|320100500|ref|YP_004176092.1|  37 VANNVVLVTLGDKSAYATVVTSETITQPGvVALSKQTASALGVSEGDKVGV 87 
                                       4567789999999******99999999999******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3596.51
//
Query:       gi|320100501|ref|YP_004176093.1|  [L=375]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   79.4   0.0    7.7e-19   67.9   0.0    2.2  2  DUF711    Uncharacterised ACR (DUF711)


Domain annotation for each model (and alignments):
>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   2.4e-05      0.44       5      70 ..      26      79 ..      24     104 .. 0.78
   2 !   67.9   0.0   4.3e-23   7.7e-19     224     400 ..     196     360 ..     129     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 2.4e-05
                            DUF711  5 ekldiRtvTlgislldcasedleklaekiyekiikkaaklvktveeieeeyGievvtkRisvtpis 70
                                      e++++R+vT++   +  ++            ++ ++  ++++++ ei++e+G++v tkR+s+ +i+
  gi|320100501|ref|YP_004176093.1| 26 ENIEVRAVTYFAGRHRGIR------------EEYEHGINVLERAVEILREQGLRVFTKRVSMPSIG 79
                                      6778888888866553333............356788899999*******************9998 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 4.3e-23
                            DUF711 224 sleelaeaikktafkitrlgelvarevakrlgvefggiDlSlaPtpavgdSvaeileelglesfGapGtlaalallt 300
                                       s++ l+e +++     ++++el++++    lg ++  iD Sl+P   +++Sva +l +lg + + +pG   al++++
  gi|320100501|ref|YP_004176093.1| 196 SIDGLSESMHRVFKVFNNIAELLEKS----LGYPV-YIDYSLSPW--MERSVAGLLGSLGFSPL-EPGFNYALHVVN 264
                                       45555555555555555555555555....99997.58*******..78*************99.9*********** PP

                            DUF711 301 davkkGGvmasskvgGlsGlflpvsEDaglaeaaeegaltiekLlamsaVCsvGLDmvpipgdtsaetiaaliaDea 377
                                       + +         + +G++ ++lp  ED++l+e   +g l+ ++ l +++ C  G+Dm+ +p   s+e +a l +D  
  gi|320100501|ref|YP_004176093.1| 265 KLIGM--HGDRLRAVGFNEVMLPYAEDSVLVEYGGRGLLRARDFLRYASTCVAGVDMIIVPS--SVEGLARLTLDAY 337
                                       ***88..666789************************************************7..5679********* PP

                            DUF711 378 alavrlnKtlavRliPvpgkkaG 400
                                       +l+ + +++l+ R iPv g+  G
  gi|320100501|ref|YP_004176093.1| 338 SLSRVKSRPLSLRAIPVDGEPGG 360
                                       ******************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2865.94
//
Query:       gi|320100502|ref|YP_004176094.1|  [L=314]
Description: ornithine carbamoyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-56  190.8   0.0    2.1e-56  190.4   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    5.7e-50  169.2   0.2    1.2e-49  168.1   0.1    1.6  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.4   0.0   2.3e-60   2.1e-56       3     156 ..     158     311 ..     156     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.4 bits;  conditional E-value: 2.3e-60
                                       .EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE-- CS
                            OTCace   3 lkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdv 79 
                                       lki+fvGd+  nv++sl+ ++ +lg  +v+++Pkg+ep + v++  ++ a+ +ggs++i+ d+ +av++aDvvytdv
  gi|320100502|ref|YP_004176094.1| 158 LKIVFVGDGGDNVLHSLMLAVGILGGRIVIASPKGYEPHPSVVKLFNEHAAPNGGSYEIERDPFKAVENADVVYTDV 234
                                       79******99******************************************************************* PP

                                       SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                            OTCace  80 wvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                       wvsmg++kere+rl++l++y+vt el+++ak+da+++HcLPa+rgeEv deV+d+  s+v++qaeNr h++kA+l+l
  gi|320100502|ref|YP_004176094.1| 235 WVSMGQDKEREKRLRDLEPYRVTVELMERAKPDAVFMHCLPAHRGEEVVDEVIDGRWSIVWDQAENRKHAQKAVLAL 311
                                       ***************************************************************************98 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 !  168.1   0.1   1.4e-53   1.2e-49       1     148 []       8     149 ..       8     149 .. 0.97
   2 ?   -2.3   0.0      0.44   3.9e+03      88     116 ..     252     285 ..     236     311 .. 0.62

  Alignments for each domain:
  == domain 1  score: 168.1 bits;  conditional E-value: 1.4e-53
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHT.TT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTT CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkk.ekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaed 76 
                                       rh+l+l+++s+ee+  +l++a +lk++  + e+  +ll g++la++Fe+pStRTr+Sfe+A+++lGg++++ls a++
  gi|320100502|ref|YP_004176094.1|   8 RHFLTLAEYSREELLFILETAMQLKQRYLAgERVIPLLVGRHLAMIFEKPSTRTRISFETAMRELGGNAIYLS-ASE 83 
                                       8**************************9998888999************************************.769 PP

                                       SCTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  77 iqlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       +ql      r+E++eDtarvlsryvda+++R++++ ++e+la+y++vpviN++ +d +HP QaL D+lti e
  gi|320100502|ref|YP_004176094.1|  84 LQLA-----RGETIEDTARVLSRYVDAVMARVYEHYKIERLAQYSRVPVINGL-SDLHHPAQALSDVLTIME 149
                                       9998.....77******************************************.****************87 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.44
                                       SCHHHHHHHHHHHT.SEEEEE....ESSHHHHHH CS
                          OTCace_N  88 EsleDtarvlsryv.daiviR....hpgaeelee 116
                                       E+++ t+++++r   da++++    h+g+e ++e
  gi|320100502|ref|YP_004176094.1| 252 EPYRVTVELMERAKpDAVFMHclpaHRGEEVVDE 285
                                       6777788888888888888883333334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2249.83
//
Query:       gi|320100503|ref|YP_004176095.1|  [L=817]
Description: oligosaccharyl transferase STT3 subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-18   64.4  27.7    1.5e-16   60.4  27.7    2.4  1  STT3             Oligosaccharyl transferase STT3 subunit


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 !   60.4  27.7   8.3e-21   1.5e-16      30     474 ..      53     564 ..      28     577 .. 0.68

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 8.3e-21
                                       --SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC...HHHHHHH CS
                              STT3  30 lsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld...vsirevc 103
                                       + efD+Y  y + +++++nG          n+  h  +yP G+ + y ++++ L  + ++ ++h ++    s+++  
  gi|320100503|ref|YP_004176095.1|  53 FFEFDSYIEYWQAKYVYENGLLSWYTLTRDNPATHIFWYPWGRDIIY-SSYPFL-PMWIGSTYHLVEglgLSLKQWG 127
                                       46*******************9988888889999999*****99999.579***.5557889999998977777776 PP

                                       HCCHHHHHHHHCHHHHHHH.HHHS..-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCC CS
                              STT3 104 lwlpallgsLlaIpiyflv.relk..sdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktk 177
                                       + l +++   ++I+  +++ rel   s +aGl+ All a+ P  + rtv+G+   ++ ++v++l+ ++f  k +k+ 
  gi|320100503|ref|YP_004176095.1| 128 I-LQPIIFAAIGIVLAYVTgRELSggSRLAGLFTALLTAVLPAATERTVLGYIEKEGVALVPILLYVYFYSKLVKSI 203
                                       5.566666666777777777***844689****************************************76655555 PP

                                       S.......TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-CCHHHHHHHHHHHHHHH..CCCCC CS
                              STT3 178 s.......nkislaviaaliiflivlaWggyailiyallllfilalLiigrfelklkiavtfsviiaflviaiivll 247
                                       s       +k +++v+++l+++++   Wggy ++i+ ++++f +++ +  r + k   +   + +ia ++  i+vl+
  gi|320100503|ref|YP_004176095.1| 204 SsgqasrlRKTAYMVLSGLFLAMVGWLWGGY-VFILGTMVAFTVVYPVLVRGSVKGEFLAYQFGLIASSM--ILVLP 277
                                       5555***************************.99998888887777555554444444443333333333..33333 PP

                                       CCTTCHHHSTTTCH..HCCCCHHHHHHHHCCCHHC..CCCCCHHCC..CHHTT.HHHHTT--GGGHHHHHHHHHHHH CS
                              STT3 248 flgfqvvavseiig..algifgllqlvafgsvvvlvaelkfyqfis..lfqpgilsevlgligevvtalavlglial 320
                                         + ++   +++ +   lg++  + lv+ + ++vl  e+     ++  l+++ +l  ++ l +  + +  + gl+ +
  gi|320100503|ref|YP_004176095.1| 278 SPANASNLGIYPFNprDLGVALASTLVLPLAYYVLNTEYRRLGLRKplLTKGRYLLLLVVL-VAGGSVAVAQGLVPI 353
                                       3333332322222211234444444444444444445555555555544444433333333.333332222222222 PP

                                       C.........................................................CCCCCTS-----TTHHHHH CS
                              STT3 321 w.........................................................lgilyslldleyaklkiki 340
                                                                                                 +g ly + + e  kl++ i
  gi|320100503|ref|YP_004176095.1| 354 GgrlawalglrfipasplvesiaehqsplssystligmlhswgvypwlffasplvlgvIGSLYFIYRGEADKLYVSI 430
                                       23445567777777777888888888888888888888888899999999999998888888888877777777766 PP

                                       HHHHS---S--CCHHHCCSSST.TTTCCCHHHCHHCCHHCTCHHHHHHH....HHHHHHCCC-SCHCCCCCHHHHHH CS
                              STT3 341 iilvsvwlpvgllaltkglrfl.iftvPlgiifvgllleflavfvkiys....vsqilfsgvvvillmltllpvlal 412
                                       + +++ +  + ++ ++++   + ++++    +f+g l+e+l    +          ++++++  +      ++vlal
  gi|320100503|ref|YP_004176095.1| 431 AFILAFYSYLNAAYMIASAAYFgTLVMG---VFMGRLVEYLLPTRRELEdrrkGRVRYRPAREYR------VVVLAL 498
                                       6666655555444444444333366554...4667777777666666663322444455555555......445555 PP

                                       HCCCHHHHHHHHCCHHHHHHHHH....HHHHHHHHHCT.TTTTHHHTTHHHCHHHHHHHHHHHHHH CS
                              STT3 413 laavkiskifstykdekeakikv....aakavaptksnglkeslewkantnrdsvvitwwdyghil 474
                                       +a   +++ ++ y d +++k +v    a +++ p  s+ ++++ e +   ++ s+vi wwdyg+ +
  gi|320100503|ref|YP_004176095.1| 499 VALALVNTAYAGYVDYVSNKSMVytlkAGVSGLPYYSDSWYKAVEAIRGLPEGSLVIAWWDYGYGI 564
                                       555555555555555555555554432344559******************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (817 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 5667.56
//
Query:       gi|320100504|ref|YP_004176096.1|  [L=180]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   13.6   2.6        1.2    8.8   0.6    2.8  2  RPW8      Arabidopsis broad-spectrum mildew resistance protei
      0.056   13.0   0.0      0.075   12.6   0.0    1.3  1  Snf7      Snf7
       0.22   12.2   1.3        0.4   11.4   0.6    1.8  1  DUF2203   Uncharacterized conserved protein (DUF2203)


Domain annotation for each model (and alignments):
>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.6   0.00021       1.2      44     132 ..      22      98 ..       3     105 .. 0.62
   2 ?   -1.1   0.0      0.23   1.3e+03      68      81 ..     159     172 ..     156     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00021
                              RPW8  44 itPvvkeieklnkel.drpreeieeLkklLekaekLVekcsklkrynvlkkyrYkkklkeLekslrkfvqvelqvqq 119
                                       ++ ++++i++l +++ +r+++ +e+L++l  k+e+ +               rY+ ++ +L+k l +  +v+l v++
  gi|320100504|ref|YP_004176096.1|  22 VRLLRDRIDTLYNRIsERREALFERLTDLESKGERYLA-------------KRYAEEISKLDKLLSRLAAVQLVVEK 85 
                                       44455555555555555555555555555555554332.............36778888888888888888887777 PP

                              RPW8 120 vrdikellakmke 132
                                       v    ++ ++m+e
  gi|320100504|ref|YP_004176096.1|  86 VDLALQYAINMRE 98 
                                       7767777777765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
                              RPW8  68 LkklLekaekLVek 81 
                                        k+ Le+a + V+k
  gi|320100504|ref|YP_004176096.1| 159 VKRILEEAREVVKK 172
                                       68899999999988 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05     0.075      11     105 ..      27     123 ..      17     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7  11 rkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkevlnam 87 
                                       +++d    ++ ++ + l + l +l  kg++  a++++ ++ ++ k+l++l +++  +e+v la++ + ++ e+    
  gi|320100504|ref|YP_004176096.1|  27 DRIDTLYNRISERREALFERLTDLESKGERYLAKRYAEEISKLDKLLSRLAAVQLVVEKVDLALQYAINMREFSGVA 103
                                       445555556666677777788************************************************99999888 PP

                                       HHHHHHHHHHHH..CTCCHH CS
                              Snf7  88 kqgakamkamnk..kvdidk 105
                                        ++ +  k  +k  +++i++
  gi|320100504|ref|YP_004176096.1| 104 SEVSSLVKDLSKlpELNIPD 123
                                       88777777776633455555 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   6.6e-05       0.4       6      81 ..      13      88 ..      11      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                           DUF2203  6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdlea 81
                                       +A + L  ++ l +++ +l +++ e++e+l e  ++ e++++++l+++++e  +++++l++++ ++  +v  ++ 
  gi|320100504|ref|YP_004176096.1| 13 RKALEALYHVRLLRDRIDTLYNRISERREALFERLTDLESKGERYLAKRYAEEISKLDKLLSRLAAVQLVVEKVDL 88
                                      5688899999999999*************9999999999999************************9999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1380.32
//
Query:       gi|320100505|ref|YP_004176097.1|  [L=225]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.5   0.0      0.062   13.5   0.0    1.5  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 ?   13.5   0.0   3.4e-06     0.062      26      84 ..      48     110 ..      33     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-06
                            DUF432  26 seveiyvkvpveigvf.ikskkevel...iDvfslskkkYaLYGspesGviaryvksevysep 84 
                                       s+ e+ + +++++  +  +sk++++    + +  +++ +Y+LY ++e+G + +y+  + +s  
  gi|320100505|ref|YP_004176097.1|  48 SRSEMSMDFEIDLVTVnGSSKDRYRDpekLFLYRVDRGRYTLYNPEEHGELEKYIGVQRVSPA 110
                                       455677778888776667777776543347788889******************988877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1796.07
//
Query:       gi|320100506|ref|YP_004176098.1|  [L=287]
Description: ParA/MinD-like ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-83  279.7   0.0    2.5e-83  279.3   0.0    1.0  1  ParA          NUBPL iron-transfer P-loop NTPase
    7.7e-14   51.8   0.0    2.1e-13   50.4   0.0    1.7  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      7e-07   28.7   0.7      7e-07   28.7   0.7    1.6  2  ArsA_ATPase   Anion-transporting ATPase
    7.9e-07   29.2   0.3    1.3e-05   25.2   0.3    2.2  1  AAA_31        AAA domain
    0.00019   21.0   0.3     0.0017   17.8   0.3    2.2  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    0.00069   19.0   0.1     0.0012   18.1   0.1    1.5  1  MipZ          ATPase MipZ
      0.008   16.0   1.1        1.7    8.4   0.0    2.6  2  AAA_26        AAA domain
     0.0097   15.5   0.0      0.015   14.9   0.0    1.4  1  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.034   13.4   0.0      0.049   12.9   0.0    1.2  1  Zeta_toxin    Zeta toxin
      0.056   12.6   0.1      0.084   12.1   0.1    1.2  1  NB-ARC        NB-ARC domain
       0.07   12.1   0.1       0.12   11.3   0.1    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.11   12.2   0.2       0.57    9.9   0.1    1.9  2  IstB_IS21     IstB-like ATP binding protein
       0.15   11.6   0.1       0.28   10.7   0.1    1.4  1  TF_Zn_Ribbon  TFIIB zinc-binding
       0.16   11.9   0.1        1.3    9.0   0.0    2.0  2  ResIII        Type III restriction enzyme, res subunit
       0.17   11.2   0.1       0.29   10.4   0.1    1.3  1  VirC1         VirC1 protein
       0.18   11.5   0.1        3.3    7.4   0.0    2.2  2  AAA_30        AAA domain
       0.21   11.0   0.2       0.55    9.7   0.2    1.6  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ


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 !  279.3   0.0   2.4e-86   2.5e-83       5     245 ..      30     273 ..      27     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 279.3 bits;  conditional E-value: 2.4e-86
                              ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs.ekkliPvea.kgikvmSig 79 
                                       +i+vlSgKGGVGK+ +++++Al La kg +v++lDaDi+G sip++lgv++ +  +s + +++Pve   g+kv+ ++
  gi|320100506|ref|YP_004176098.1|  30 KIIVLSGKGGVGKTFISSSIALGLALKGRRVAILDADIHGSSIPSMLGVQGMRHYASeNGEILPVEGpLGVKVVAVN 106
                                       799************************************************988888466699***999******** PP

                              ParA  80 fllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkk 155
                                       ++l+s d +vvwrGp++skai++ll++v+wg+ DyL+iD+PPGtgD+++t+aq + +++gaviVt p+ ++ ++v k
  gi|320100506|ref|YP_004176098.1| 107 LMLDSPDLPVVWRGPLVSKAITELLSKVAWGDGDYLVIDMPPGTGDAAITIAQVIpDVTGAVIVTAPNMLTETIVAK 183
                                       *******************************************************889******************* PP

                              ParA 156 aiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepes 232
                                       a++++ + ++++lG+veNms+f+cp cg+  +++g+++ge la+++g++llg+ipldp i+ea+d+g+p++l+ pe 
  gi|320100506|ref|YP_004176098.1| 184 AVNFTARNNIRLLGIVENMSYFKCPVCGSVFNLLGRSTGEYLASKYGTRLLGKIPLDPLINEAVDRGEPYLLAYPEG 260
                                       ***************************************************************************** PP

                              ParA 233 eaakaleeiaekv 245
                                       eaaka++++++++
  gi|320100506|ref|YP_004176098.1| 261 EAAKAVMSMVDEI 273
                                       *********9988 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0     2e-16   2.1e-13       1     127 [.      31     252 ..      31     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2e-16
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i++ s+kGGvGKT+++ ++a  la +g+rV+ +DaD  +++  +  g+++ ++                        
  gi|320100506|ref|YP_004176098.1|  31 IIVLSGKGGVGKTFISSSIALGLALKGRRVAILDADIHGSSIPSMLGVQGMRHYasengeilpvegplgvkvvavnl 107
                                       799**************************************99966666666667779******************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|320100506|ref|YP_004176098.1| 108 mldspdlpvvwrgplvskaitellskvawgdgdylvidmppgtgdaaitiaqvipdvtgavivtapnmltetivaka 184
                                       ******************************************************************99999999999 PP

                                       ......CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ......dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                             + +rll+++e+++  ++    + g v+n  + +       e l+    +yg ++lg+ip d  ++ea+ rg
  gi|320100506|ref|YP_004176098.1| 185 vnftarNNIRLLGIVENMSY-FK--CPVCGSVFNLLGRS-----TGEYLAS---KYGTRLLGKIPLDPLINEAVDRG 250
                                       99999977788888888884.33..89999999998876.....3455555...45********************* PP

                                       S- CS
                                       xx RF
                              CbiA 126 ep 127
                                       ep
  gi|320100506|ref|YP_004176098.1| 251 EP 252
                                       97 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.7   6.6e-10     7e-07       2      38 ..      30      66 ..      29      70 .. 0.94
   2 ?   -2.5   0.1       2.2   2.3e+03     120     137 ..     134     152 ..     126     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.6e-10
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      k+i+++GKGGVGKt +s+++a+ l+ kg++v ++  D
  gi|320100506|ref|YP_004176098.1| 30 KIIVLSGKGGVGKTFISSSIALGLALKGRRVAILDAD 66
                                      89*****************************999877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
                                       HHCSSSSEEEEESBS.CCH CS
                       ArsA_ATPase 120 vkeeeydvvvlDtaP.TGh 137
                                       v   + d++v+D +P TG+
  gi|320100506|ref|YP_004176098.1| 134 VAWGDGDYLVIDMPPgTGD 152
                                       5556679999999996776 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.3   1.2e-08   1.3e-05       4      43 ..      31      70 ..      29     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQan 43
                                      I +   KGGvGKT  s  +a  la +g +v + D+D  ++
  gi|320100506|ref|YP_004176098.1| 31 IIVLSGKGGVGKTFISSSIALGLALKGRRVAILDADIHGS 70
                                      556788******************************8765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   1.6e-06    0.0017       2     218 ..      31     247 ..      30     280 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                         Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGy 78 
                                        i + GkGG+Gk++ s+ ++  la +g++v i+  D    s   +lg + +    + + e+g  e + ve     G 
  gi|320100506|ref|YP_004176098.1|  31 IIVLSGKGGVGKTFISSSIALGLALKGRRVAILDADIHGSSIPSMLGVQGM---RHYASENG--EILPVE-----GP 97 
                                       57889****************************999777776666654332...34444444..333333.....44 PP

                         Fer4_NifH  79 ggvkcve....sGGPepGvGCaGrgvitaielleelgayddlDfvlyDvLGDvvCGGfalPiredkaqev..yivts 149
                                        gvk+v        P+  v   G  v +ai  l  + a+ d D+++ D+      G  a+ i++   +    +ivt 
  gi|320100506|ref|YP_004176098.1|  98 LGVKVVAvnlmLDSPDLPVVWRGPLVSKAITELLSKVAWGDGDYLVIDMPPG--TGDAAITIAQVIPDVTgaVIVTA 172
                                       4444332111145778778888888888887777777888888888887533..45556666654433221133333 PP

                         Fer4_NifH 150 gelmalyaanniakgiekyaksggvrlgGliinsrkvd.....d.....ereliekfaeelgtkvlevvPrdeivrk 216
                                        ++    +   +ak++ +++ ++++rl G++ n    +     +     +r   e +a++ gt++l ++P+d  +++
  gi|320100506|ref|YP_004176098.1| 173 PNM---LTETIVAKAV-NFTARNNIRLLGIVENMSYFKcpvcgSvfnllGRSTGEYLASKYGTRLLGKIPLDPLINE 245
                                       333...3334444554.345556677777777643211111111111113334455666666666666666666666 PP

                         Fer4_NifH 217 ae 218
                                       a 
  gi|320100506|ref|YP_004176098.1| 246 AV 247
                                       65 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.2e-06    0.0012       3      48 ..      31      76 ..      29     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl 48
                                      i++   kGG Gk+ ++  +a  L+ kG rva +d d+   ++   l
  gi|320100506|ref|YP_004176098.1| 31 IIVLSGKGGVGKTFISSSIALGLALKGRRVAILDADIHGSSIPSML 76
                                      556678******************************9888776555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5     0.016        17       3      33 ..      31      61 ..      30      63 .. 0.86
   2 !    8.4   0.0    0.0016       1.7     146     196 ..     182     245 ..     153     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                      i+v +   gvGKT++s  ++  l  kg +v+
  gi|320100506|ref|YP_004176098.1| 31 IIVLSGKGGVGKTFISSSIALGLALKGRRVA 61
                                      677778889***********99999999986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0016
                            AAA_26 146 lltiealrqknvrvlGvilNk..vrnp........e.....nvetlekksgipvlGvvPylpdlea 196
                                       + ++++  ++n+r+lG++ N   +  +        +     + e l +k g+++lG +P +p +++
  gi|320100506|ref|YP_004176098.1| 182 AKAVNFTARNNIRLLGIVENMsyF--KcpvcgsvfNllgrsTGEYLASKYGTRLLGKIPLDPLINE 245
                                       334444556778888888776221..1334444440444448899999999********9998765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05     0.015      35      74 ..      31      60 ..      22     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                            AAA_25 35 lallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkV 74
                                      +++l G +g+GKt++ +++al +a +G+            V
  gi|320100506|ref|YP_004176098.1| 31 IIVLSGKGGVGKTFISSSIALGLAlKGRR-----------V 60
                                      689*********************66664...........3 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.7e-05     0.049      10      62 ..      23      76 ..      15      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                        Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeye 62
                                        ++ r k+i+l+G  G GK+ +++ ++  l+ ++++v  ld+D   + +P   
  gi|320100506|ref|YP_004176098.1| 23 KLQGYRFKIIVLSGKGGVGKTFISSSIALGLAlKGRRVAILDADIHGSSIPSML 76
                                      455677799*********************99999999999*998777777665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.9e-05     0.084       7      41 ..      19      50 ..      14      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                                      HHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC  7 kviekLlekdelqslvvalvGmgGvGKttlakqil 41
                                        + kL     ++  ++ l+G+gGvGKt ++++i 
  gi|320100506|ref|YP_004176098.1| 19 DAKRKLQ-GYRFK--IIVLSGKGGVGKTFISSSIA 50
                                      5566666.55566..9**************99985 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00012      0.12      28      66 ..      28      66 ..      15      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      r + + l G  G+Gk  + + ++l l+ +G+rva+l  D
  gi|320100506|ref|YP_004176098.1| 28 RFKIIVLSGKGGVGKTFISSSIALGLALKGRRVAILDAD 66
                                      55678899********999****************9877 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00054      0.57      49      79 ..      31      61 ..      23      67 .. 0.87
   2 ?   -0.4   0.0      0.78   8.3e+02      33      66 ..     126     158 ..     120     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00054
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvl 79
                                       ivl G  GvGK++++ +++   + +g +v 
  gi|320100506|ref|YP_004176098.1| 31 IIVLSGKGGVGKTFISSSIALGLALKGRRVA 61
                                      5899************999998888888885 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.78
                         IstB_IS21  33 rkvkeLatlsfiekkenivllGpsGvGKshlaia 66 
                                       ++++ L + ++  + + +v+  p+G+G + ++ia
  gi|320100506|ref|YP_004176098.1| 126 AITELLSKVAW-GDGDYLVIDMPPGTGDAAITIA 158
                                       44444455555.567788999999**99988887 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00026      0.28       1      20 [.     205     224 ..     205     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                                       EEETTTTCEECHEETSTTCE CS
                      TF_Zn_Ribbon   1 ykCPnCgstnlveDpergel 20 
                                       +kCP+Cgs + ++  ++ge+
  gi|320100506|ref|YP_004176098.1| 205 FKCPVCGSVFNLLGRSTGEY 224
                                       79******984444566776 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0013       1.3      12      54 ..      17      59 ..      13      65 .. 0.84
   2 ?    0.5   0.0      0.51   5.4e+02      10      44 ..     125     160 ..     124     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                                      HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.... CS
                            ResIII 12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgke 54
                                      i++ + kl+ +r k +++    G+GKT+++ +++  l+ kg++
  gi|320100506|ref|YP_004176098.1| 17 INDAKRKLQGYRFKIIVLSGKGGVGKTFISSSIALGLALKGRR 59
                                      67777888889999999****************9999988764 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.51
                                       HHHHHHT......TTSEEE.EEESTTSTHHHHH.HHH CS
                            ResIII  10 eaienlleklkskrdkrgl.ikmaTGtGKTlva.akl 44 
                                       +ai++ll+k+   +d  +l i m+ GtG   +  a++
  gi|320100506|ref|YP_004176098.1| 125 KAITELLSKVA-WGDGDYLvIDMPPGTGDAAITiAQV 160
                                       57788888887.66666665********877664555 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00027      0.29       5      39 ..      32      66 ..      29      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                             VirC1  5 tfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                       + s kGG Gkt    ++   la +g+rva+++ad
  gi|320100506|ref|YP_004176098.1| 32 IVLSGKGGVGKTFISSSIALGLALKGRRVAILDAD 66
                                      56788********9999999**************9 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0031       3.3      17      52 ..      28      63 ..      18      66 .. 0.83
   2 ?    2.1   0.0      0.13   1.4e+02      17      78 ..     138     197 ..     126     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvigl 52
                                      + ++ vl G  G GKt++ ++++  ++ +g+rv++l
  gi|320100506|ref|YP_004176098.1| 28 RFKIIVLSGKGGVGKTFISSSIALGLALKGRRVAIL 63
                                      5568899***************99999999999875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.13
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllk 78 
                                       +  + v+  p+GtG   +  ++++++ +  g vi+ Ap+      +a++++++a++  +ll 
  gi|320100506|ref|YP_004176098.1| 138 DGDYLVIDMPPGTGDAAI--TIAQVIPDVTGAVIVTAPNMLTETIVAKAVNFTARNNIRLLG 197
                                       444778888999996554..688888888889999999999999999999999998877775 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00053      0.55       2      38 ..      30      65 ..      29      71 .. 0.91
   2 ?   -2.3   0.0       2.4   2.5e+03     109     133 ..     131     156 ..     124     183 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
                          CBP_BcsQ  2 kvlalqGvRGGvGttsllaaLawalhelgesvlviDl 38
                                      k+++l+G +GGvG+t +++++a  l   g +v ++D+
  gi|320100506|ref|YP_004176098.1| 30 KIIVLSG-KGGVGKTFISSSIALGLALKGRRVAILDA 65
                                      6899999.9**************9999*****99997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                          CBP_BcsQ 109 lkelk.eqyrwillDlpagasaltre 133
                                       l++++ ++ +++++D+p g+ + + +
  gi|320100506|ref|YP_004176098.1| 131 LSKVAwGDGDYLVIDMPPGTGDAAIT 156
                                       55555566788999999877655433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2109.21
//
Query:       gi|320100507|ref|YP_004176099.1|  [L=317]
Description: mevalonate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-15   57.3   0.8    1.4e-15   57.3   0.8    1.7  2  GHMP_kinases_N   GHMP kinases N terminal domain
    1.8e-11   44.2   0.5    4.9e-11   42.8   0.5    1.7  1  GHMP_kinases_C   GHMP kinases C terminal
  ------ inclusion threshold ------
      0.093   12.3   0.0       0.18   11.4   0.0    1.5  1  GalKase_gal_bdg  Galactokinase galactose-binding signature


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.8   2.3e-19   1.4e-15       2      66 .]      81     147 ..      80     147 .. 0.94
   2 ?   -2.9   0.0       1.4   8.4e+03      28      55 ..     244     269 ..     237     271 .. 0.58

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.3e-19
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       i+i+s iPvgaG+GSSAA+ v+l+  ll+++g  +  e+  ++a+ +e +++ g++sg+D++ ++yGg
  gi|320100507|ref|YP_004176099.1|  81 IYIDSGIPVGAGMGSSAAVNVSLTHSLLHACGAGFtrEDvSRIAYMGEVEVH-GKPSGIDNTLATYGG 147
                                       89*****************************9886555589***********.**************8 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                                       HHHHTTEHHHHHHHHHHHHHHHHHHHHH CS
                    GHMP_kinases_N  28 llallglsleeaklaleaerlaqggngs 55 
                                       ++++l  ++  + l++ + +l + g+g+
  gi|320100507|ref|YP_004176099.1| 244 VNDYLVHRM--LGLGAYGAKLSGAGRGG 269
                                       455552222..56777777777777766 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 !   42.8   0.5   8.3e-15   4.9e-11       1      84 [.     212     292 ..     212     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 8.3e-15
                    GHMP_kinases_C   1 llealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                       +l+al+++d+ +lgel++ ++   l+   g +  + + l+  ++ lGa+gaklsGaG G+ v++l+ ++++a+++++
  gi|320100507|ref|YP_004176099.1| 212 ALAALRERDVVRLGELMTVNHG--LLFSMGASAWVNDYLVHRMLGLGAYGAKLSGAGRGGIVIGLA-EPARAQAIVE 285
                                       5889******************..89***************************************9.********** PP

                    GHMP_kinases_C  78 alreefe 84 
                                       +l +e++
  gi|320100507|ref|YP_004176099.1| 286 ELEREGV 292
                                       **88775 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 ?   11.4   0.0     3e-05      0.18      16      47 ..       6      37 ..       3      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                                      EEEEEEEE--S-TTTT-EEEEEEEEEEEEEEE CS
                   GalKase_gal_bdg 16 APGRvnLiGEHtDYngGfVlpmAieqdiyiav 47
                                      APG v L GEH    g+  +  A+ +  + +v
  gi|320100507|ref|YP_004176099.1|  6 APGKVILFGEHFVVEGYPAIGLAVGLYASTCV 37
                                      9****************999999987776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2310.41
//
Query:       gi|320100508|ref|YP_004176100.1|  [L=149]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1076.02
//
Query:       gi|320100509|ref|YP_004176101.1|  [L=314]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2236.90
//
Query:       gi|320100510|ref|YP_004176102.1|  [L=364]
Description: egghead protein-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-21   75.5   0.2    8.2e-21   74.8   0.2    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.1e-13   51.6   0.0    1.4e-13   51.3   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0042   16.6   0.0       0.01   15.3   0.0    1.7  2  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.093   13.3   0.0        0.2   12.2   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2


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 !   74.8   0.2   1.8e-24   8.2e-21       1     183 [.     124     318 ..     124     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.8e-24
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwl.eelaalffaedhgkdilvrealgrvvp.svGs 75 
                                       + +++D+D+++  d++++ +  ++     ++ g+ l++++++++ + +  +++ +d +  ++++  lg+++  ++G 
  gi|320100510|ref|YP_004176102.1| 124 WYVFIDDDNLILDDSFLYEIPYYEAKGFVAGNGILLPRPGKSMVsYVMDWIRYIDDLTLYRFFTGLLGKPLIgLHGE 200
                                       789********************98777778888889865554416677778999**************988688** PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc....el.. 146
                                         ++  s+l+e+ g++  ++s++EDf +++ l r+ y++   + + v  ksp+++++ + Qr Rw+ G     +   
  gi|320100510|ref|YP_004176102.1| 201 LLIVKGSVLKEI-GFN--NRSITEDFRFAVELVRRKYKTWQSNTR-VSIKSPNSVKDLMIQRGRWFKGLitdiKYsp 273
                                       ************.888..8************************88.9*********************876551156 PP

                   Glyco_trans_2_3 147 ..eklillvrllgylgsllwsalp......lhlallllfsllala 183
                                         +kli  +r++++  +l++s l+      l l++++l + ++++
  gi|320100510|ref|YP_004176102.1| 274 apMKLIVGFRSFAWVLNLAVSVLFfpilvyLGLVWYILPGSIYYL 318
                                       788889899999999998888877333333333333443333322 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 !   51.3   0.0   3.1e-17   1.4e-13       7     228 ..      44     262 ..      40     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.1e-17
                   Glyco_tranf_2_3   7 lVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvn..arnlgstgksralne 81 
                                       ++++ ++++++ + l + ++++ +r+  +  v+ + a  +++++     l +vr+ vv+    r+l   gk raln 
  gi|320100510|ref|YP_004176102.1|  44 VIVS-KADEKVQRSLIESVKYHVSRFSHITLVVDEGAPLISTLRY----LRGVRLIVVPSgyRRDL--VGKGRALNY 113
                                       5555.8888999999999999889988888888888888999985....55666666655422443..4999***** PP

                   Glyco_tranf_2_3  82 alravk..sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpv.fl.lnrstlvsalgal.efaerhlrflaarr 153
                                        ++++   +++ +++DdD+++ +d++ +  ++++++  g+v ++  +l + ++++vs +++  ++ ++ +  ++++ 
  gi|320100510|ref|YP_004176102.1| 114 FVEHYVspDKWYVFIDDDNLILDDSFLYEIPYYEAK--GFVAGNGiLLpRPGKSMVSYVMDWiRYIDDLTLYRFFTG 188
                                       ***9776788***********************444..555555514425699******877699999999999999 PP

                   Glyco_tranf_2_3 154 alg..vltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwv 228
                                        lg   + l+G+++ +  +vlke+ g+    ++t+D++ +++l r++++t   + + v   +p s+k++  qr+Rw 
  gi|320100510|ref|YP_004176102.1| 189 LLGkpLIGLHGELLIVKGSVLKEI-GFNN-RSITEDFRFAVELVRRKYKTWQSNTR-VSIKSPNSVKDLMIQRGRWF 262
                                       998788******************.7777.9*******************877777.9999***************6 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 ?   -3.1   0.0         1   4.7e+03      28      51 ..      38      61 ..      35      70 .. 0.49
   2 !   15.3   0.0   2.2e-06      0.01     102     172 ..     198     262 ..     111     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                   Glyco_transf_21 28 aakydllvisDsdvrvkpdyLeel 51
                                      a +y+++++s +d  v++  +e++
  gi|320100510|ref|YP_004176102.1| 38 ACNYEIVIVSKADEKVQRSLIESV 61
                                      344555555555555555544444 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.2e-06
                   Glyco_transf_21 102 vGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRqlrWa 172
                                        G  ++++ ++L++i Gf+   + + eD+ ++  l ++ +k+++s++  ++  +++ +s+++l+ +  rW 
  gi|320100510|ref|YP_004176102.1| 198 HGELLIVKGSVLKEI-GFNN--RSITEDFRFAVELVRRKYKTWQSNTR-VS--IKSPNSVKDLMIQRGRWF 262
                                       5889999999*****.7887..8***********************96.43..444569***********6 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-05       0.2      11      85 ..      61     135 ..      54     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                   Glyco_tranf_2_4  11 lahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrq.vellkallary.aeadwvlvvDaDEflv 85 
                                       +++h +  f++i ++ ++   +    l+ l  v+l+ v++ y++   +  ++l+ + ++y ++++w +++D D+++ 
  gi|320100510|ref|YP_004176102.1|  61 VKYHVSR-FSHITLVVDEGA-PLISTLRYLRGVRLIVVPSGYRRDLVGkGRALNYFVEHYvSPDKWYVFIDDDNLIL 135
                                       6666665.788777777777.56778999999**********8765553679***999983568**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2731.83
//
Query:       gi|320100511|ref|YP_004176103.1|  [L=387]
Description: iron-containing alcohol dehydrogenase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-83  279.7   0.3    3.7e-83  279.3   0.3    1.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    8.2e-11   42.1   4.3    3.3e-08   33.6   0.4    2.2  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
       0.55    9.4   4.0      0.094   11.9   0.3    1.6  2  DHQ_synthase  3-dehydroquinate synthase


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 !  279.3   0.3   6.2e-87   3.7e-83       4     349 ..      15     362 ..      13     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 279.3 bits;  conditional E-value: 6.2e-87
                                       EEEETTGG.GGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-T CS
                            Fe-ADH   4 ivfgkgal.eelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalare 79 
                                       ++fg+g+l e+l+e +k +g  +ali+t+k++++ sg+ld+vle+l+++ +e++v+dgv+ np  ++ +ea ++a e
  gi|320100511|ref|YP_004176103.1|  15 LFFGPGVLrEKLAENVKGYG--KALIITSKSAARVSGALDTVLEALKRESVEYVVYDGVKANPYASMADEAGRIAVE 89 
                                       689***985789*******9..******************************************************* PP

                                       T.--EEEEEESHHHHHHHHHHHHHTT....................--EEEEESS-S-S-TT-SEEEEE.-TTSEEE CS
                            Fe-ADH  80 egadvviavGGGsviDtAKaialllanp.evedyl.gegkakkkkalpliaiPTtaGtGsevtplavitdeeegekl 154
                                       +++d+++avGGGsviD++K+++++++ + + +d+  +   + + ++l+lia+  t GtGsev ++av+t + + ek 
  gi|320100511|ref|YP_004176103.1|  90 NRVDLIVAVGGGSVIDVGKLASVIATTGiKAADIAvNPASVSNARRLRLIAVNLTHGTGSEVDRYAVVTIDGTFEKR 166
                                       **************************87668888855555666777***********************99999*** PP

                                       EE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 155 sifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedle 231
                                       +++    +Pd+ + Dp +t tl +++  +t lDa+ ha+Ea +s+ +n l+ +l++ a++ ++ +l+r++ d+++le
  gi|320100511|ref|YP_004176103.1| 167 GMA--VRYPDVGFDDPLYTRTLSREQSLYTSLDAFYHAYEAATSTFSNHLTLTLSRDAVEAVVGSLPRVLGDPGNLE 241
                                       ***..9*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.C.GGGGGS-HHHHHHHHH..........HHHHHHT........ CS
                            Fe-ADH 232 areqmllastlaglafsnaglgavHalahalgalf.giphglanaillpavlrfnaeaaperlaqlaralgge..sd 305
                                        re++l+as++ag+++ ++ ++++Hal+h++++l+ ++phg+++ail p v+ ++ +a pe  a + r l       
  gi|320100511|ref|YP_004176103.1| 242 HREKLLYASMIAGISIDQSMTHLNHALEHSFSGLHpELPHGAGLAILGPMVVYYTHKAVPEASAHVLRPLDPGlkPL 318
                                       *********************************9999***************9999999**********98779999 PP

                                       .T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-T CS
                            Fe-ADH 306 eeaaeeliealrellkelglptsLselgvdeedldklaeaalkd 349
                                       +  ae++ +a++e+ ++lg+  +Ls++gvd  +++k  e++++ 
  gi|320100511|ref|YP_004176103.1| 319 AGDAERAYRAVKEFQSSLGFDERLSDYGVDMGEVEKALEFTMRM 362
                                       99*****************************99*9999999886 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 !   33.6   0.4   5.5e-12   3.3e-08      18      96 ..      32     112 ..      17     129 .. 0.85
   2 !   10.0   0.3   8.2e-05      0.49     171     247 ..     208     283 ..     193     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 5.5e-12
                          Fe-ADH_2  18 elkkvllvadentkka..agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiak 92 
                                       ++ k+l+++++   ++  a + v e+lk++ ++  v++ v++++  + + +  + + e+++dl+vavGgG++iD++k
  gi|320100511|ref|YP_004176103.1|  32 GYGKALIITSKSAARVsgALDTVLEALKRESVEYVVYDGVKANPYASMADEAGRIAVENRVDLIVAVGGGSVIDVGK 108
                                       4569999999999998667789****************99999999999999999999******************* PP

                          Fe-ADH_2  93 yvsa 96 
                                       ++s 
  gi|320100511|ref|YP_004176103.1| 109 LASV 112
                                       *996 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 8.2e-05
                          Fe-ADH_2 171 wklanevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalHGe 247
                                       +  +n+++  l++ +++ v+ ++ +++ d+++ e  e+ll a++++gi+i ++     H + H +  l+  +  HG+
  gi|320100511|ref|YP_004176103.1| 208 STFSNHLTLTLSRDAVEAVVGSLPRVLGDPGNLEHREKLLYASMIAGISIDQSMTHLNHALEHSFSGLH-PELPHGA 283
                                       45566777899999*************************************999999999999999988.6777986 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   1.6e-05     0.094      29      62 ..      90     123 ..      64     129 .. 0.87
   2 ?   -3.8   0.4      0.91   5.4e+03     186     206 ..     265     287 ..     263     300 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                                       -TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEE CS
                      DHQ_synthase  29 eRksllialGGGvvgDlaGfvAatylRGvrfvqv 62 
                                       +R +l++a+GGG v D+  +++ + + G++   +
  gi|320100511|ref|YP_004176103.1|  90 NRVDLIVAVGGGSVIDVGKLASVIATTGIKAADI 123
                                       6999******************999999997665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.91
                                       HHHHHHHHTT..TTS-HHHHHHH CS
                      DHQ_synthase 186 gHaiEallgy..ekllHGeaVai 206
                                        Ha+E+ ++    +l HG + ai
  gi|320100511|ref|YP_004176103.1| 265 NHALEHSFSGlhPELPHGAGLAI 287
                                       68888776543468999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); 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:                         3  (0.000167327); expected 0.2 (1e-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: 2728.33
//
Query:       gi|320100512|ref|YP_004176104.1|  [L=409]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-105  350.4   0.0     1e-104  350.1   0.0    1.1  1  DUF763    Protein of unknown function (DUF763)
  ------ inclusion threshold ------
      0.069   13.1   0.1       0.17   11.8   0.1    1.7  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 !  350.1   0.0  1.1e-108    1e-104       1     312 []       6     354 ..       6     354 .. 0.93

  Alignments for each domain:
  == domain 1  score: 350.1 bits;  conditional E-value: 1.1e-108
                            DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkea 77 
                                       G+adLpLh+g+vP++l+erm+ L+++i+++ive yg+ el++rl dP+wFq+++nv+GmdWdsSGsTtvv+++lk++
  gi|320100512|ref|YP_004176104.1|   6 GVADLPLHNGHVPPYLFERMRVLGGLIARYIVEYYGPGELVRRLGDPFWFQAFNNVIGMDWDSSGSTTVVVYVLKNT 82 
                                       89*************************************************************************** PP

                            DUF763  78 l...kseelgilvaGGkGkksrktpeeleklaeklgldeeklvkasrlvakvdnaalqdgyqlYlhalivsekgkwa 151
                                       +   + ++ gi+v+GGkG++sr + ee +++++  +   e++v asr++ak+d +alqdgy++Y+h+liv+++g++ 
  gi|320100512|ref|YP_004176104.1|  83 FppgSLRDNGIAVLGGKGRDSRAVAEEAKAISDVADY--ERIVGASRMAAKIDGVALQDGYSIYIHSLIVDSDGDML 157
                                       *99999**************************99877..89************************************ PP

                            DUF763 152 viqQGmneeerlARRYhwl..seelesfveephsgiagekkeeevlnlvskeseearkaildlvkekp.ekllkelk 225
                                       v+qQG+ne++ +ARRYh    + +l ++  ephsg+a+  k e  lnl++  s+ear+aild+v+++p  +ll++l 
  gi|320100512|ref|YP_004176104.1| 158 VVQQGLNEDSGMARRYHLPvpKGSLPTTRVEPHSGVAS-MKIELSLNLANPGSREARRAILDIVSSTPpGSLLNSLG 233
                                       *****************7633566778889********.66667********************7665489****** PP

                            DUF763 226 elkallkgekkl...........................klpakhev......lekvlekayelqpedfeellllkg 269
                                       e++++l+ge ++                           +             + k+ +++++l +++f+el+ l+g
  gi|320100512|ref|YP_004176104.1| 234 EANRILRGEPSIlswvtggaqgdtwsrvrqltevcpryyR------PvanlrlVGKAASEIKKLGVREFDELIGLPG 304
                                       ********99999*********999977766666555542......045555599********************** PP

                            DUF763 270 vGpktlraLalvaeliygekasfkDPv.......kysfavGgKdgvPypv 312
                                       vG++t+raLalva+liyg ++s +DP         y++a+GgKdgvPypv
  gi|320100512|ref|YP_004176104.1| 305 VGAETIRALALVADLIYGYRPSLRDPTtsimdpfLYAYAHGGKDGVPYPV 354
                                       *********************************9***************8 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.9e-05      0.17      10      28 ..     296     314 ..     294     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                                       HHHHHTSTT-SHHHHHHHH CS
                               HHH  10 reeLlalPGVGpktAeaIl 28 
                                       ++eL  lPGVG +t +a +
  gi|320100512|ref|YP_004176104.1| 296 FDELIGLPGVGAETIRALA 314
                                       69************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2961.20
//
Query:       gi|320100513|ref|YP_004176105.1|  [L=477]
Description: acetylornithine transaminase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-110  368.4   0.0   4.4e-110  368.1   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 !  368.1   0.0  2.4e-114  4.4e-110       7     406 .]      64     473 ..      58     473 .. 0.93

  Alignments for each domain:
  == domain 1  score: 368.1 bits;  conditional E-value: 2.4e-114
                                       --SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-B.T-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHH CS
                       Aminotran_3   7 dnlllvitkaeGvyltdvdgkrylDlvssiavvnlGh.ahPkvvkavkeqaaklshvsfgaltnepalklaekllkl 82 
                                       ++l+lvi+++eGv+l+dvdg+rylD+ s+i v+nlG+  hP+v kav eq++ l h     ++n  ++ la+kl+++
  gi|320100513|ref|YP_004176105.1|  64 EELPLVIERGEGVWLYDVDGNRYLDFSSAIGVNNLGYpTHPEVKKAVVEQLERLAHAAGTDFFNPYQVMLAKKLAEI 140
                                       45679********************************77*******************99***************** PP

                                       CT-..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEE CS
                       Aminotran_3  83 apkgld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevv 158
                                       ap+g+  kvf+ nsG+eA+e+A+K+ar+      at ++ +iaf g+fHGrt+g+l++t+sk+ +k+l+ p +p+v 
  gi|320100513|ref|YP_004176105.1| 141 APGGVPrKVFFSNSGTEANEAAVKIARQ------ATGRKLFIAFYGGFHGRTMGSLGLTASKSVHKRLVFPWMPGVF 211
                                       ***99889********************......******************************************* PP

                                       EE-TTBGGGTB-HH.......HHHHHHHHHHHHHH...CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHH CS
                       Aminotran_3 159 rlkypdeevlkene.......eeeaalleeleale...kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkh 225
                                       +++yp +++ + +        e  ++++e +e+++    +  +evaA+  EpiqgegG+vv++  f+++l++l++k+
  gi|320100513|ref|YP_004176105.1| 212 HAPYPNPYRNPWHIdgyeepvELVNRVIEFIEEYIlekLAPPEEVAAIFAEPIQGEGGYVVPPRVFFKELKKLADKY 288
                                       ******9999877656653444444555555555586556679********************************** PP

                                       T-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHH CS
                       Aminotran_3 226 dvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgG.lplsavlataevmqalapgshgsTfgGnplacava 301
                                       ++l+ +DEvq G+GrTG +fA+eh+++ pD++ +aKal+gG  p+ a++ + ++     pg h++T+gG  la ++a
  gi|320100513|ref|YP_004176105.1| 289 GILVSIDEVQMGLGRTGRMFAIEHFDIVPDIISMAKALSGGvVPIGATVFRSDLDFKQ-PGIHSNTYGGHALASVAA 364
                                       ****************************************************986555.999*************** PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTE CS
                       Aminotran_3 302 lavleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGv 372
                                       l+++e++e  kll n+++l+  ++e+Le l+++ e++++vRg Gl  ++e++++++ k+      ++i+++a+ +G+
  gi|320100513|ref|YP_004176105.1| 365 LKTIEVVE--KLLPNVNRLEPLFREELEGLKQSVEQVGDVRGIGLAWGVEIVKDKKSKTpdpslrNRIVARALRNGL 439
                                       ******96..7**********************9**********************8889*****99********** PP

                                       E-EEETTTEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 373 lilsaGdnvirllppliitdeeidelleilkkal 406
                                       ++l++G+++irl+ppl+i++ee++ +lei+ ka+
  gi|320100513|ref|YP_004176105.1| 440 VLLPCGKSSIRLIPPLVISEEEAKTGLEIFRKAV 473
                                       ******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3383.71
//
Query:       gi|320100514|ref|YP_004176106.1|  [L=59]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   17.8   3.8      0.044   13.6   0.2    2.2  2  RPAP1_N   RPAP1-like, N-terminal


Domain annotation for each model (and alignments):
>> RPAP1_N  RPAP1-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.8   0.00062        11      23      34 ..      14      25 ..       8      27 .. 0.85
   2 !   13.6   0.2   2.4e-06     0.044       4      25 ..      26      47 ..      24      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00062
                           RPAP1_N 23 reeLlesLdPkl 34
                                       eeLl  LdP+l
  gi|320100514|ref|YP_004176106.1| 14 IEELLRDLDPSL 25
                                      69********98 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.4e-06
                           RPAP1_N  4 deENrarLasMspeEIeeeree 25
                                       eE r+ L+sMsp+E +  r+e
  gi|320100514|ref|YP_004176106.1| 26 REEARRLLESMSPDELAGLRKE 47
                                      58999**********9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 442.19
//
Query:       gi|320100515|ref|YP_004176107.1|  [L=476]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-27   93.4   0.0    2.5e-26   92.0   0.0    1.7  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
      1e-18   67.8   0.0    2.8e-18   66.4   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.1e-12   45.8   0.1    1.6e-11   44.2   0.1    1.8  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    4.2e-06   26.9   0.0    1.3e-05   25.3   0.0    1.9  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
  ------ inclusion threshold ------
      0.079   12.5   0.5       0.23   11.0   0.5    1.8  1  PGM1_C       PGM1 C-terminal domain


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.0     7e-30   2.5e-26       2     131 ..      12     135 ..      11     141 .. 0.94
   2 ?   -2.4   0.0         1   3.7e+03      28      49 ..     268     288 ..     265     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 7e-30
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fgt+G+R +++ +el++  +++lg a++    +    +  ++ +DtRv+s  l  a+aag+aa+G+++ ++gl+p
  gi|320100515|ref|YP_004176107.1|  12 RLFGTAGVRMRYP-DELDAVAAYRLGLAMGVLGLS----SCSYIVYDTRVTSHVLTYAFAAGVAASGMDASIVGLAP 83 
                                       68***********.88**************77776....799999******************************** PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHH CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaii 131
                                       tP++ +a  + +   g+ +taSHnppeyng+K+y+ +G +++++ ee++e+ +
  gi|320100515|ref|YP_004176107.1|  84 TPVAGYAGLR-RGGVGVSVTASHNPPEYNGFKFYDVEGFEFTRSLEERVEELV 135
                                       *********9.67899*********************************9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                       HHHHHHCHHCSTS-EEEEEE-S CS
                         PGM_PMM_I  28 qaiaeylkaeakkkkvvvGrDt 49 
                                       + +a++l +e +k+ vvv+ Dt
  gi|320100515|ref|YP_004176107.1| 268 ALFAKILLEE-RKGVVVVSVDT 288
                                       5678888885.99999999997 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   7.8e-22   2.8e-18       2     100 ..     159     255 ..     158     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 7.8e-22
                                       HHHHHGGGTS-.HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHH CS
                        PGM_PMM_II   2 aYiealkekvd.seaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealklliel 77 
                                       +Y+e+l+e+ + s++ ++   +vv+d+++Ga+ ++++ + ++lg ++v++n+ pd+ fp++ p+p+  ++l++l  +
  gi|320100515|ref|YP_004176107.1| 159 DYVEDLLEASQpSRRAWSP--RVVVDCANGASYHVTPVVVRSLGGIPVTVNCSPDGYFPGRPPEPRR-DVLEKLLPV 232
                                       7999**9999976666666..8*********************************************.********* PP

                                       GGGGG-SEEEEE-TTS-BEEEEE CS
                        PGM_PMM_II  78 vkkegadlglafDgDaDRlgvvd 100
                                        +  +  ++la+DgDaDRl++ d
  gi|320100515|ref|YP_004176107.1| 233 YRGVEPAMVLAHDGDADRLAALD 255
                                       ********************998 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   4.4e-15   1.6e-11      23      69 ..     406     455 ..     385     460 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 4.4e-15
                                       H...HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHH CS
                        PGM_PMM_IV  23 a...sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeev 69 
                                             ++g ++ + d +++ vR SGTep++rvy+Ea+s+e+l+++++ v
  gi|320100515|ref|YP_004176107.1| 406 PvavIDIDGYRFEYSDDSWILVRVSGTEPKIRVYAEARSSERLKEMVDTV 455
                                       344457889999999999999************************99987 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 !   25.3   0.0   3.7e-09   1.3e-05       2     109 ..     263     367 ..     262     370 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.7e-09
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTT...ECEEEETTCEEE CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeeg...avlGgEeSghii 75 
                                        d+llal+ak llee  ++g  vv +v t +++++v+++ g++l +   G  +  e++ke g   +v++gE    +i
  gi|320100515|ref|YP_004176107.1| 263 QDRLLALFAKILLEE--RKGV-VVVSVDTGRVVDEVVEASGGRLERYILGKTH--ERVKELGvgsVVMAGEP-WKLI 333
                                       699*********995..6565.****************************986..45555544459999998.6788 PP

                                       ETTTBSS--HHHHHHHHHHHHHHHTS-HHHHHHH CS
                       PGM_PMM_III  76 fldeattkDGilaallvleilaetgkslsellee 109
                                         +   + DG+  a+l+++++ e+gk+l+ +lee
  gi|320100515|ref|YP_004176107.1| 334 DTSWGPWVDGVRQAALLVKLVVERGKPLARILEE 367
                                       8888999***********************9976 PP

>> PGM1_C  PGM1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   6.4e-05      0.23      17      49 ..     277     318 ..     276     319 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                            PGM1_C  17 treGVVlyt.gtlpgd........grveyliiAesleeAeel 49 
                                        r+GVV+ + +t   +        gr+e  i+++++e++ el
  gi|320100515|ref|YP_004176107.1| 277 ERKGVVVVSvDTGRVVdevveasgGRLERYILGKTHERVKEL 318
                                       69*******9**9999***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3536.77
//
Query:       gi|320100516|ref|YP_004176108.1|  [L=256]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   15.2   0.1      0.018   15.2   0.1    3.7  3  DUF350    Domain of Unknown Function (DUF350)


Domain annotation for each model (and alignments):
>> DUF350  Domain of Unknown Function (DUF350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.3      0.81   1.4e+04       2       7 ..      19      24 ..      14      26 .. 0.51
   2 ?   15.2   0.1     1e-06     0.018       1      33 [.      32      64 ..      32      78 .. 0.88
   3 ?    0.5   2.5     0.037   6.7e+02      34      45 ..     190     201 ..     131     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.81
                            DUF350  2 gvvGiv 7 
                                      g+v++v
  gi|320100516|ref|YP_004176108.1| 19 GLVAVV 24
                                      334444 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1e-06
                            DUF350  1 YgvvGivllllgffvfdllTpgklgelIkqgnn 33
                                      Y +v +++l++g++vf+ll+p++l+  + ++++
  gi|320100516|ref|YP_004176108.1| 32 YIAVDLAVLTAGIVVFTLLFPYHLSTDVTGRRV 64
                                      6777799******************99988876 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.037
                            DUF350  34 Aaaivlagviig 45 
                                       +a++vla+v+++
  gi|320100516|ref|YP_004176108.1| 190 PASLVLAAVDLA 201
                                       899999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1835.68
//
Query:       gi|320100517|ref|YP_004176109.1|  [L=546]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   15.1   0.3       0.22   11.9   0.0    2.5  2  AAA_16    AAA ATPase 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 ?   11.9   0.0   1.2e-05      0.22      18     106 ..       3     114 ..       1     145 [. 0.60
   2 ?   -0.3   0.0     0.067   1.2e+03       3      23 ..     168     188 ..     167     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd.....ggif.lrgkcdqlesa...................ipy 69 
                                       r ++g p +v ++G s +GKss ++ +l +l+++      +++ +++k +++++                    + y
  gi|320100517|ref|YP_004176109.1|   3 RRSEGKPLIVGFIGFSQSGKSSRIENIL-RLTGSetmepAVYTrVYEKGTRHSRHfmpfasvargrtidtvlvtVDY 78 
                                       6788999*********************.677777997656668999999995555444444444444444433333 PP

                            AAA_16  70 ...salaqalareellrqlldeaesaeleawrekleeala 106
                                          ++la +++++++l++l+      +l+a re+l ++l 
  gi|320100517|ref|YP_004176109.1|  79 tghDHLAAYFFTRRILEALEKG----LLGAGREALVRELV 114
                                       5545566666666666666666....33344433333333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.067
                            AAA_16   3 vGReeeleqLlsalervrsgr 23 
                                       ++R+ee++++ ++++++ + +
  gi|320100517|ref|YP_004176109.1| 168 PCRDEEVARVVEYVRQTLRET 188
                                       69***********99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3808.97
//
Query:       gi|320100518|ref|YP_004176110.1|  [L=357]
Description: aspartate/ornithine carbamoyltransferase Asp/Orn-binding region [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-38  130.0   0.0    3.8e-37  127.8   0.0    1.8  2  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.7e-33  115.7   0.0    2.6e-33  115.1   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.12   1.1e+03      10      40 ..      63      94 ..      53     125 .. 0.75
   2 !  127.8   0.0   4.2e-41   3.8e-37       4     156 ..     191     353 ..     189     354 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.12
                                      STTSHHHHHHHHHHHHCT-EEEEES-TT.SSH CS
                            OTCace 10 dkknnvanslikllarlgmdvvlvaPkg.lep 40
                                       k  ++ ns   ++ +lg + ++++P++ + p
  gi|320100518|ref|YP_004176110.1| 63 NKSLRTRNSFQTGVYQLGGQATYISPDQvYAP 94
                                      477899999999999***********998655 PP

  == domain 2  score: 127.8 bits;  conditional E-value: 4.2e-41
                                       EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE-- CS
                            OTCace   4 kiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdv 79 
                                        +a++G+ k+  v+++++ ++a lg+dv++++P+g+e + e ++ akk a+  g++++i +d+ ea++ga +vy++ 
  gi|320100518|ref|YP_004176110.1| 191 SYAYSGGlKPLAVPQDVASMFALLGADVYVAHPPGFELMDEAMQIAKKYAEHWGSEFKIVHDMDEAFEGATIVYPKA 267
                                       5799**99**************************************9999999************************ PP

                                       SSETTC.........CGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTT.BHHHHHHHHH CS
                            OTCace  80 wvsmge.........ekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdspr.svvfeqaeNr 146
                                       w + g          ++  ++   k+k++ vt+e l++a k  +++Hc Pa+rg+EvtdeV ds++ s++fe+aeNr
  gi|320100518|ref|YP_004176110.1| 268 WSPRGFfppynstvdKEGAKAYQDKFKNWIVTMERLEKAGK-PFYMHCGPADRGQEVTDEVLDSYEkSLYFEEAENR 343
                                       **9999****9999555555777899***********9998.89******************99876********** PP

                                       HHHHHHHHHH CS
                            OTCace 147 lhtikAllvl 156
                                       lh++kA++ +
  gi|320100518|ref|YP_004176110.1| 344 LHVQKAVMSM 353
                                       ********86 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 !  115.1   0.0   2.9e-37   2.6e-33       1     145 [.      15     172 ..      15     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 2.9e-37
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHT.TT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTT. CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkk.ekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseae. 75 
                                       ++ ls  d++ +++ ++l+ a+elk+  ++  +k + l+gk+l+l+F+++S+RTr Sf++++++lGg+++++s  + 
  gi|320100518|ref|YP_004176110.1|  15 KDWLSNYDYDIDTVFKVLQAARELKQMYHSgVRKVNWLEGKMLYLIFYNKSLRTRNSFQTGVYQLGGQATYISPDQv 91 
                                       57789999*******************9998899999************************************5556 PP

                                       ...TSCT.TTGGSTTSSCHHHHHHHHHHHTSEEEEE..........ESSHHHHHHHHHHHSSEEEEEEETSSB-HHH CS
                          OTCace_N  76 ...diql.ssvskgrkEsleDtarvlsryvdaiviR..........hpgaeeleelakyasvpviNagdgdgeHPtQ 138
                                          +  l + +   ++E ++D+arvlsry+dai+iR           +g++ ++e+ak+a++pv+N++  d +HP Q
  gi|320100518|ref|YP_004176110.1|  92 yapT--LpEDMVPYQTEAISDVARVLSRYGDAIAIRiygdaakwiiGRGHRIIREFAKWADIPVLNME-DDVWHPFQ 165
                                       6443..2433444457********************6666555554446666****************.999***** PP

                                       HHHHHHH CS
                          OTCace_N 139 aLaDllt 145
                                       +LaD++ 
  gi|320100518|ref|YP_004176110.1| 166 SLADAQA 172
                                       ****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2524.04
//
Query:       gi|320100519|ref|YP_004176111.1|  [L=207]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.7e-41  139.4   0.0      1e-40  139.2   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 !  139.2   0.0   5.6e-45     1e-40       1     162 [.      25     188 ..      25     189 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 5.6e-45
                                       S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET.... CS
                        NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleek 77 
                                       gS+Np+K+++v +af+++f +ve + +s ++g ++qP+g e +++GA++Ra +a e+  e+dy vG+E+G   + ++
  gi|320100519|ref|YP_004176111.1|  25 GSRNPAKIKGVVNAFTRFFGSVEARFTSPETGLPPQPIGLELIIEGARRRAIYAAEKLGECDYSVGVEAGWILVMGD 101
                                       8**************************************************************************** PP

                                       TEEEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT-..-HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHH CS
                        NTPase_I-T  78 lldvawaavvdkegrvsvgrsasfelPeevveevkege..elgevmdelfgtenikqkeGaigllTkglvtRedlye 152
                                       ++d++ a++  ++g  s+g+s+ f++P+ ++e+v +g   el+ev+de +gt++i+ k+G+i+llTkg+v R+dl  
  gi|320100519|ref|YP_004176111.1| 102 YYDLEAAWIHGRNGVDSLGFSPVFKIPRGFAELVVSGArrELEEVVDEHYGTRSIGDKGGFISLLTKGVVVRQDLSF 178
                                       **********************************966555************************************* PP

                                       HHHHHHTHHH CS
                        NTPase_I-T 153 qavilAlipf 162
                                        a+++Alip+
  gi|320100519|ref|YP_004176111.1| 179 MATVMALIPV 188
                                       ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1505.18
//
Query:       gi|320100520|ref|YP_004176112.1|  [L=506]
Description: citrate transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-23   81.8  68.0    4.5e-20   72.0  41.6    2.9  3  CitMHS           Citrate transporter
    0.00016   21.1  31.6     0.0023   17.3  31.6    2.1  1  ArsB             Arsenical pump membrane protein


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 ?   -0.9   2.2     0.085   7.6e+02     223     267 ..      19      73 ..       4      77 .. 0.38
   2 !   72.0  41.6     5e-24   4.5e-20       6     273 ..      77     421 ..      67     423 .. 0.71
   3 !   23.8  18.3   2.4e-09   2.2e-05      18     162 ..     332     493 ..     323     505 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.085
                                       xxxxxxxxxxx.xxxxxxxxxxx...xxxxxxx.......xxxxxxxxxxxxxxxx RF
                            CitMHS 223 fllvgaleqtG.ilealadllga...ggplval.......alvlgliallsafisn 267
                                       f l+ +l  +G +++ +a+++ +   g p + l       a  ++l+ +++++i +
  gi|320100520|ref|YP_004176112.1|  19 FFLMSILHVSGpLGDRIAGMVAEyrgGAP-LDLnslqadvAQSIALTIFFTVIIAT 73 
                                       33345566666655555555422342111.22222111112223333333333332 PP

  == domain 2  score: 72.0 bits;  conditional E-value: 5e-24
                                       xxx.xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   6 lek.lrldvvallvlvllvltiee..alsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllv 79 
                                       +e+ ++ +++ + vl+++ lt+++  ++ +i++ ++++l+g m+++++l e+G+f+rla  l+ ++ +  +ll+ll+
  gi|320100520|ref|YP_004176112.1|  77 MEWrVAAAITGVGVLAITGLTPPQnmIYRAIDWRLLVFLIGSMTLAGILREAGVFNRLAVSLVEKSTSAFRLLLLLG 153
                                       55567777777766666677777779*****************************************8766****** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxx RF
                            CitMHS  80 lltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraa.........arpgl 146
                                       l++alls+++  ++ ++  + +vl+l +    + +  l++  +la n+g++++p+G+p+ + +         + +++
  gi|320100520|ref|YP_004176112.1| 154 LFSALLSMILGEVTSIIYAVLVVLELRRV-LEIDVKpLIVYTVLATNTGSVALPVGNPIGVYIaftanisvaEFLAK 229
                                       **********8899999999999999997.55555559999*****************3333355555555533333 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxx... RF
                            CitMHS 147 slpnllllalllvgllplvllfmfgvalalpvnap....................kvkkqkaiieaiarsllpv... 200
                                       +lp  ll +l+l+ l++ ++l           n+                     ++ + + ++++++r  l +   
  gi|320100520|ref|YP_004176112.1| 230 CLPLSLLEVLVLI-LVYRLVLS----------NYVerlngelkqsreliakltaaRTIDVTPVMARHTRIGLLIlav 295
                                       3333333333333.22322222..........333444555556666666666666666666666666644433333 PP

                                       ..xxxxxxx.................................................xxxxxxxxxxxxxxxxxxx RF
                            CitMHS 201 ..atillla.................................................ykkveWsvlllfaGvfllv 226
                                         +     +                                                   +veW+ +++f  +f+l+
  gi|320100520|ref|YP_004176112.1| 296 ftG-----LvvlneklaeamslatgvpvdpdsllafipylsialallladpssmdkllSSAVEWPSIIFFMSLFILS 367
                                       330.....25555555555555555555555555555666666666677********99****************** PP

                                       xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 227 galeqtGilealadllga.......ggplvalalvlgliallsafisnvavaal 273
                                        al+ tG +  +a  +         +g+++++ ++l+++a+ls++++n +v + 
  gi|320100520|ref|YP_004176112.1| 368 YALSYTGAIAKIAYGIAMfsepgsfTGNMLVVGVLLAASAMLSSVLDNLSVIVA 421
                                       *******7777774442244466543676777888999999*******999754 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 2.4e-09
                                       xxxxx.xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxx.xxxx..xxx RF
                            CitMHS  18 vlvll.vltiee....alsgiaspiillllgamiigaaleetGlfdrlaakll......rlaggkrd.llvl..lvl 80 
                                       ++++l + ++ +    + s++ +p i++++ ++i++ al+ tG++  +a  ++      +++g+  + +  +  l +
  gi|320100520|ref|YP_004176112.1| 332 IALALlLADPSSmdklLSSAVEWPSIIFFMSLFILSYALSYTGAIAKIAYGIAmfsepgSFTGN--MlV--VgvLLA 404
                                       33333333333355578999*********************************99999888888..533..335999 PP

                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                            CitMHS  81 ltallsafvsn.dgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll... 153
                                       ++a+ls++++n  + v+++ p+++ +      ++++  ++l ++   gg  tpiG               n+++   
  gi|320100520|ref|YP_004176112.1| 405 ASAMLSSVLDNlSVIVALTQPVTILVQLG--LSRVS-YLALLYGGVFGGNYTPIGST------------ANIVAvsm 466
                                       ***********666677777777766654..33333.45699***************............66665444 PP

                                       ...............xxxxxxxx...x RF
                            CitMHS 154 ...............lalllvgl...l 162
                                                      +al+ + l   +
  gi|320100520|ref|YP_004176112.1| 467 aerekiavswgewlrIALVSTTLqitV 493
                                       444444444444433333333332221 PP

>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  31.6   2.6e-07    0.0023      22     423 .]      81     502 ..      61     502 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.6e-07
                              ArsB  22 igwsacggavlaliagvvnfhdvltvtgivwnatlafvaiilislildnigffewaalhmakaakgygvrmfvyvsl 98 
                                       +  +  g  vla i+g+   +++     i w   + ++  + ++ il + g+f+  a+ + + +     r+++ + l
  gi|320100520|ref|YP_004176112.1|  81 VAAAITGVGVLA-ITGLTPPQNM-IYRAIDWRLLVFLIGSMTLAGILREAGVFNRLAVSLVEKST-SAFRLLLLLGL 154
                                       333444444554.5666665554.457899999999999999999*********99999887654.5689999**** PP

                              ArsB  99 lgaivaalfandgaaliltpivlamvralhfneklvfpfiiasgfiadttslpfvvsnlvnivsadyfhitfidyas 175
                                       + a+++ ++ +  + +    +vl + r l ++   v p+i+ + + ++t s+ + v n + +  a    i++ ++ +
  gi|320100520|ref|YP_004176112.1| 155 FSALLSMILGEVTSIIYAVLVVLELRRVLEID---VKPLIVYTVLATNTGSVALPVGNPIGVYIAFTANISVAEFLA 228
                                       *****999998888888888899999999776...66999999999*******************99********99 PP

                              ArsB 176 rmvvpylfsllasiivlylffrksipkry.dltevkkpv...eaik..dqn..mf...rlswyil....gllligyf 237
                                       + +   l+ +l  i+v  l++ + + +   +l + ++ +    a +  d    m    r+   il    gl+++   
  gi|320100520|ref|YP_004176112.1| 229 KCLPLSLLEVLVLILVYRLVLSNYVERLNgELKQSRELIaklTAARtiDVTpvMArhtRIGLLILavftGLVVLNEK 305
                                       99988899999988888887777665432123322222200022221121111221112233332222244444444 PP

                              ArsB 238 aseffsipvsv..vags.iaii.fl.iaa...qkspavhtkkvvkeapwaivffsigmyvvvygvrnagltdvlsdv 306
                                        +e +s+   v     s +a i +l ia       p+   k +     w  ++f + ++++ y +  +g    ++  
  gi|320100520|ref|YP_004176112.1| 306 LAEAMSLATGVpvDPDSlLAFIpYLsIALallLADPSSMDKLLSSAVEWPSIIFFMSLFILSYALSYTGAIAKIAYG 382
                                       566666644431022231233322212211113467777888888889*9999999********************* PP

                              ArsB 307 iqaaadqglfagti.gmgfi...aailssimnnlptvmidalaiagtdthgmmrealiyanvigsdlgpkitpigsl 379
                                       i   ++ g f+g +  +g++   +a+lss+++nl  ++  +  ++     g+ r +   a + g  +g + tpigs 
  gi|320100520|ref|YP_004176112.1| 383 IAMFSEPGSFTGNMlVVGVLlaaSAMLSSVLDNLSVIVALTQPVTILVQLGLSRVSY-LALLYGGVFGGNYTPIGST 458
                                       ************75234443222479********99887777777778888888764.4667788899999****** PP

                              ArsB 380 atllwlhvlshkgmkiswgtyfktgiiltiptllitlvglyiwl 423
                                       a ++ + +  ++ + +swg +++  ++ t   + ++l+  y+wl
  gi|320100520|ref|YP_004176112.1| 459 ANIVAVSMAEREKIAVSWGEWLRIALVSTTLQITVALLWSYLWL 502
                                       ************************99999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.42
# Mc/sec: 3603.62
//
Query:       gi|320100521|ref|YP_004176113.1|  [L=203]
Description: phospholipase D/transphosphatidylase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   81.7   0.0    5.8e-23   81.2   0.0    1.1  1  PLDc_2    PLD-like domain
    0.00026   21.0   0.5     0.0017   18.4   0.0    2.2  2  PLDc      Phospholipase D Active site motif
  ------ inclusion threshold ------
      0.067   13.1   0.0        0.3   11.0   0.0    1.9  2  Pox_L5    Poxvirus L5 protein family
       0.41   10.6   2.0       0.86    9.5   2.0    1.5  1  Tail_VII  Inovirus G7P protein


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 !   81.2   0.0   1.3e-26   5.8e-23       3     133 .]      63     194 ..      62     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 1.3e-26
                            PLDc_2   3 qliksAkksidiatyyf........vsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagve 71 
                                       +++ +A++s+++++y +         +  ++l+al++++++gv+v++++d+     +   +  + +++ +  ++g++
  gi|320100521|ref|YP_004176113.1|  63 KALGNAERSVYVIMYVVkydpreagDPVNSLLNALRDLREKGVDVKVVVDD----ETY--RSYRETIDYM-VASGIP 132
                                       5789*************98888877777789*******************8....233..3455666666.99**** PP

                            PLDc_2  72 vrvfetllgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFerlw 133
                                       vr+ e+++++ HaK++++d++t+i+GS+N+t+++l+ n+E+ v++  + l+++  ++F+++w
  gi|320100521|ref|YP_004176113.1| 133 VRLDESASRTTHAKILIVDNSTLILGSHNWTESALTMNHEASVETNCHSLVSKALSYFDSIW 194
                                       **966556899*************************************************99 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.24   1.1e+03      10      17 ..     109     115 ..     109     126 .. 0.85
   2 !   18.4   0.0   3.9e-07    0.0017       4      26 ..     142     164 ..     140     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                                       EEETTTEE CS
                              PLDc  10 vivDdrva 17 
                                       v+vDd+ +
  gi|320100521|ref|YP_004176113.1| 109 VVVDDE-T 115
                                       89***9.3 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.9e-07
                                       EE---EEEETTTEEEEE---SSH CS
                              PLDc   4 thHqKivivDdrvafvGgaNLcd 26 
                                       t H+Ki+ivD+   ++G+ N++ 
  gi|320100521|ref|YP_004176113.1| 142 TTHAKILIVDNSTLILGSHNWTE 164
                                       56*******************97 PP

>> Pox_L5  Poxvirus L5 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.38   1.7e+03       2      23 ..      75      96 ..      75      98 .. 0.84
   2 ?   11.0   0.0   6.7e-05       0.3      28      63 ..     150     184 ..     134     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.38
                            Pox_L5  2 llmlfsrkakiskdpidkllkt 23
                                      +++++++ ++   dp+++ll++
  gi|320100521|ref|YP_004176113.1| 75 IMYVVKYDPREAGDPVNSLLNA 96
                                      6788899999999****99875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.7e-05
                            Pox_L5  28 egdkllilglpnsgtksALaldrkpiviknCealLq 63 
                                        ++  lilg + + t+sAL ++++  v  nC++l +
  gi|320100521|ref|YP_004176113.1| 150 VDNSTLILGSH-NWTESALTMNHEASVETNCHSLVS 184
                                       57889999***.999*****************9986 PP

>> Tail_VII  Inovirus G7P protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.0   0.00019      0.86      13      35 ..       9      30 ..       6      32 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00019
                          Tail_VII 13 iciglVlvWFvLGrlAGsvAGmF 35
                                      +  ++ +v F+ G +AG +AG++
  gi|320100521|ref|YP_004176113.1|  9 GARSILVV-FAVGVVAGLIAGIY 30
                                      56677888.************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1443.85
//
Query:       gi|320100522|ref|YP_004176114.1|  [L=375]
Description: nucleotidyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  131.6   0.0    1.5e-37  129.5   0.0    1.8  2  NTP_transferase  Nucleotidyl transferase
    4.4e-10   40.1   0.0    6.6e-10   39.6   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    1.8e-07   30.6   5.0    7.1e-05   22.4   0.3    4.0  3  Hexapep          Bacterial transferase hexapeptide (six repea
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.042   13.6   0.0    1.5  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
      0.056   13.3   0.0       0.12   12.3   0.0    1.5  1  CTP_transf_3     Cytidylyltransferase
       0.21    9.7   0.3       0.33    9.0   0.3    1.2  1  DUF4954          Domain of unknown function (DUF4954)
        2.1    8.2   5.3        3.2    7.6   0.3    3.0  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.0   5.8e-41   1.5e-37       1     241 [.       2     240 ..       2     246 .. 0.94
   2 ?   -0.4   0.0      0.27   6.9e+02     167     190 ..     251     274 ..     250     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 5.8e-41
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kav+LaGG GtRL+PLt+  +k+++p +gk +++++ +  l+++g+++ i++  ++  + v e++k    ++     
  gi|320100522|ref|YP_004176114.1|   2 KAVVLAGGLGTRLYPLTKVAPKPMIPLAGK-PILEYIVDGLVRHGFTD-IIIAARYLGTQVVEYFKGHPYAK----- 71 
                                       79****************************.*****************.99***************887544..... PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                        +   +k+tAdAv+l   +++d++     +v  gD l++ +y+e+ + +++++a   +t+++++ve++  yG++  d
  gi|320100522|ref|YP_004176114.1|  72 PVILDSKDTADAVRLLDGVFDDHF-----IVSMGDTLCNADYREIYDYHKSSNA--VATIALKQVENPLPYGIVYLD 141
                                       33346789*******999999777.....8999*********************..9******************** PP

                                       TTSBEEEEECS-SSHSH................CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTT CS
                   NTP_transferase 155 eegrverfvEKPkeaka................selassGiYvfnsevllflakdleelkrgedeitdilpkaleeg 215
                                       e+g++  f+EKP   ++                ++l+++GiYvfn+ +l++l    e+ +   d++  ++p+++e+g
  gi|320100522|ref|YP_004176114.1| 142 EHGDILLFIEKPLSIEVyllslayyrqkgasayENLINAGIYVFNPHILEIL----ERNPGLMDFGRHVFPYLVENG 214
                                       **************999**********************************9....78999**************** PP

                                       EEEEEECSTTEE-EEEXSSHHHHHHH CS
                   NTP_transferase 216 kvalaflfkdaeyWsDvGtldsllea 241
                                       ++   ++   + yW+D+G l+ +  +
  gi|320100522|ref|YP_004176114.1| 215 YRVRGHVLGHSVYWNDIGRLETYKSV 240
                                       *99998888878*******9988665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                                       SSHSHCSEECCSEEEEETTHHHHH CS
                   NTP_transferase 167 keakaselassGiYvfnsevllfl 190
                                         ++a+ +as+G+Y+ +s ++  +
  gi|320100522|ref|YP_004176114.1| 251 GLEPAAPMASKGVYIHDSAIVRGR 274
                                       5667788999*****999988765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   2.6e-13   6.6e-10       1     124 [.       3     128 ..       3     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.6e-13
                                       EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-..EEE-TTS CS
                      NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvr..vvededp 68 
                                       av+LAGG ++R+    +  +K+++pl+gkp+le+++d l ++g+ ++++++++   +v ++++++++   v+ d+  
  gi|320100522|ref|YP_004176114.1|   3 AVVLAGGLGTRLYpltKvaPKPMIPLAGKPILEYIVDGLVRHGFTDIIIAARYlgTQVVEYFKGHPYAkpVILDS-- 77 
                                       79**********5333257**********************************8888999999888432255554.. PP

                                       S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                      NTP_transf_3  69 gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                        k ++ +++        +d+++v ++D+ +   + ++++ + +++s+a ++++  +
  gi|320100522|ref|YP_004176114.1|  78 -KDTADAVRLLDGV--FDDHFIVSMGDTLC--NADYREIYDYHKSSNAVATIALKQ 128
                                       .4445554433222..35778888888865..567777777766555555544444 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.6   0.00088       2.3      16      35 ..     275     294 ..     261     294 .. 0.90
   2 !   22.4   0.3   2.8e-08   7.1e-05       1      31 [.     284     314 ..     284     314 .. 0.95
   3 !    6.7   0.1    0.0024       6.2       2      30 ..     320     347 ..     319     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00088
                                       EETTEEE-TTEEEETTEEEE CS
                           Hexapep  16 iggnVkIGdnvkIgagvvig 35 
                                       + ++V IG+ v++++g+ +g
  gi|320100522|ref|YP_004176114.1| 275 VNPPVYIGRSVVVEEGASVG 294
                                       6799************9875 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.8e-08
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETT CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgag 31 
                                       s+v+++++ +gp+av+ +n+++G++++I +g
  gi|320100522|ref|YP_004176114.1| 284 SVVVEEGASVGPYAVLEDNAVVGKGSVIQEG 314
                                       689*************************986 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0024
                                       EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       t IG+++ I   +++++ V++ +++++ +
  gi|320100522|ref|YP_004176114.1| 320 TLIGEGSRIY-DSILMNRVEVAPGSTLVS 347
                                       7799999999.999999999999887655 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 ?   13.6   0.0   1.6e-05     0.042       2      49 ..       2      52 ..       1      82 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                      EEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEE CS
                              IspD  2 vvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivv 49
                                       +v+ A G G+R+    +  pK  + l+g+++le  vd+l  ++  d i+ 
  gi|320100522|ref|YP_004176114.1|  2 KAVVLAGGLGTRLyplTKVAPKPMIPLAGKPILEYIVDGLVRHGFTDIIIA 52
                                      689*********73336789**********************988776654 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.7e-05      0.12      15      46 ..      22      52 ..      18      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.7e-05
                                      TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEE CS
                      CTP_transf_3 15 gKnlldlggkpliayvleaalkskafekviva 46
                                       K++++l+gkp+++y+++ ++  + f+++i+a
  gi|320100522|ref|YP_004176114.1| 22 PKPMIPLAGKPILEYIVDGLVRHG-FTDIIIA 52
                                      6********************955.5888888 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3   0.00013      0.33     174     254 ..     273     356 ..     261     363 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00013
                           DUF4954 174 GeigekvkilnaglikN.vkigdyatiegasklengtinSs..keapveiGegViledfiissGskikdgavisrcf 247
                                       G+++  v i ++ +++  + +g+ya++e    +  g+++ +      + iGeg  + d+i+++  +++ g++++ ++
  gi|320100522|ref|YP_004176114.1| 273 GRVNPPVYIGRSVVVEEgASVGPYAVLEDNAVVGKGSVIQEgiVWRDTLIGEGSRIYDSILMNRVEVAPGSTLVSTV 349
                                       56666666666665543256677777777666666666654223455667777777777777777777777777777 PP

                           DUF4954 248 vGqavkl 254
                                       vG + ++
  gi|320100522|ref|YP_004176114.1| 350 VGTGSRV 356
                                       7766665 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.2    0.0018       4.6       2      33 ..     279     312 ..     261     313 .. 0.82
   2 ?    7.6   0.3    0.0013       3.2      20      32 ..     299     311 ..     296     330 .. 0.70
   3 ?   -0.8   0.0      0.53   1.4e+03       7      31 ..     319     344 ..     315     347 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                                       EEE-TT-EE-TT-EES..EEE-TT-EE-TT-EE- CS
                         Hexapep_2   2 viIGdnCliGanagiG..vslGdncvvgaGvvit 33 
                                       v IG  +++   a +G    l+dn+vvg G+vi 
  gi|320100522|ref|YP_004176114.1| 279 VYIGRSVVVEEGASVGpyAVLEDNAVVGKGSVIQ 312
                                       666666666666667667789***********95 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0013
                                       E-TT-EE-TT-EE CS
                         Hexapep_2  20 lGdncvvgaGvvi 32 
                                       l+dn+vvg G+vi
  gi|320100522|ref|YP_004176114.1| 299 LEDNAVVGKGSVI 311
                                       5666666666666 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.53
                                       T-EE-TT-EE.SEEE-TT-EE-TT-E CS
                         Hexapep_2   7 nCliGanagi.GvslGdncvvgaGvv 31 
                                       ++liG  + i   +l +++ v++G++
  gi|320100522|ref|YP_004176114.1| 319 DTLIGEGSRIyDSILMNRVEVAPGST 344
                                       56777777766666777788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2839.69
//
Query:       gi|320100523|ref|YP_004176115.1|  [L=415]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-10   39.4   0.0    1.4e-09   37.7   0.0    1.8  2  PGM_PMM_I   Phosphoglucomutase/phosphomannomutase, alpha/beta
    0.00018   22.0   0.0     0.0005   20.6   0.0    1.7  1  PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   1.6e-13   1.4e-09      21     119 ..      20     115 ..       6     123 .. 0.91
   2 ?   -3.3   0.0      0.75   6.7e+03      53      70 ..     160     177 ..     153     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.6e-13
                                       CHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECEEEEE CS
                         PGM_PMM_I  21 elveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkadagimi 97 
                                       e v+ lg+ ++++l +   ++ vv GrDt   sr+l++al agl++ G++v++++ +   ++sf++++++a++g+ i
  gi|320100523|ref|YP_004176115.1|  20 EDVAMLGAVFGTVLGR---RALVVSGRDTAPVSRMLKRALTAGLMSVGCDVMDFHEAVSGEISFSMKRFGAKGGFNI 93 
                                       5577789999999998...599999**************************************************** PP

                                       --TTS-TTCCCEEEEETTTCE- CS
                         PGM_PMM_I  98 taSHnppeyngiKvylsnGgpi 119
                                             p+y  i++y + G+++
  gi|320100523|ref|YP_004176115.1|  94 HLNPRRPGYITIRLYKAPGYEL 115
                                       **99999999999999988765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.75
                                       HHHHHHHHHHHHHCCT-C CS
                         PGM_PMM_I  53 srelaealaaglaanGve 70 
                                       s+e+++a ++++a++G  
  gi|320100523|ref|YP_004176115.1| 160 SDEISAAKLNIVASHGHG 177
                                       666666666777766654 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 !   20.6   0.0   5.6e-08    0.0005       3      98 ..     150     240 ..     148     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.6e-08
                                       HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TT.SS----TT-TTTTHHHHG CS
                        PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfpt.kapnpeekealkllielv 78 
                                       Y  al++ v+s+ i+ ++l +v++ +hGa++e+l +++  l+++ +      ++  ++ ++p  +   ++ ++++  
  gi|320100523|ref|YP_004176115.1| 150 YASALVSFVKSDEISAAKLNIVASHGHGASDEVLRRIFTLLELEYTL---MSSGRISGeTYPFVK---EMGKVAAST 220
                                       9999******99****************************9995544...445555552444444...588999999 PP

                                       GGGG-SEEEEE-TTS-BEEE CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgv 98 
                                       ++ +adlg++f  Da  l+v
  gi|320100523|ref|YP_004176115.1| 221 RAMRADLGVVFNIDASALAV 240
                                       ************99988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3279.45
//
Query:       gi|320100524|ref|YP_004176116.1|  [L=428]
Description: pyridoxal-phosphate dependent TrpB-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-42  146.0   0.0    1.8e-42  145.7   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 !  145.7   0.0     1e-46   1.8e-42       4     294 .]      75     415 ..      72     415 .. 0.81

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 1e-46
                                       CSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   4 gigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaall 77 
                                         +pTPl+r++rl+++l+++  +++K+E+  ptgS+K+++a+   ++ ++eg   ++ +e+++G++g al++a++l+
  gi|320100524|ref|YP_004176116.1|  75 LGRPTPLIRARRLEEALKTNavILFKYEGVMPTGSHKVNTAVAQAYYnAAEG-VERVSTETGAGQWGSALSLAGSLF 150
                                       679***************************************8888889999.999********************* PP

                                       T-EEEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH......................STTCE CS
                              PALP  78 Glkvtivvpadas...pekvallrllGaevvevggdydeavaaaaelaae......................gegay 129
                                       Glkv++++ + +    p+++ l++++Gaev  +++d +++ +   +l+ae                      g++a 
  gi|320100524|ref|YP_004176116.1| 151 GLKVRVFMVRASYlqkPYRRILMESYGAEVYPSPSDRTNTGR---RLLAEnpdhpgslgiaiseaiedvvssGGKAK 224
                                       *******9998877889****************555333333...33333355555555444444555666544444 PP

                                       E--TTTSHHHHHHHHTHHHHHHHHTT....TTEEEEEEE-SSSHHHHHHHHHHHH...HSTT.-EEEEEEECTTCGG CS
                              PALP 130 lvsqfdnptviegygtiglEileqlg....gkpdavvvpvGgGgliaGiaaglke...rrpd.vrvigvepegsdal 198
                                       +   +   +v + ++ iglE l+ql     +++d++v +vGgG+++aG++ ++     +++d + +i+vepe+++++
  gi|320100524|ref|YP_004176116.1| 225 YSLGSVLNHVLLHQTVIGLEALKQLEmlgvDRVDYIVGCVGGGSNFAGLSYPFIGhryNDGDpPVFIAVEPETVPSM 301
                                       4444446668888*********7777777************************99544444467777********** PP

                                       TTCC...S..S.SS..B...................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHH CS
                              PALP 199 arsl...ragrrvtvpvs..................dtiadglavgspselafelldrlvdeivtvsdeealeamrl 254
                                       +r+    +       +++                  +  a gl+ + +++    l+++ + + v+  + e+lea  l
  gi|320100524|ref|YP_004176116.1| 302 TRGEyryD-----YGDTAgltpllkmhtlghdyippPIYAGGLRYHGVAPSLSILVKNGLVKPVAYGESEVLEAGLL 373
                                       ****4443.....44444556669999****9999999999999996666666677888888*************** PP

                                       HHHHHSB-B-HHHHHHHHHH...HHHHHHCCTTCEEEEEEE-B CS
                              PALP 255 larregivvepssaaalaal...klreagelkegdrvvviltg 294
                                       +ar++gi++ p s +a+ a+    l+++g+ ++  ++++ l+g
  gi|320100524|ref|YP_004176116.1| 374 FARTQGILPAPESSHAVKAVidiALKHRGSSRRP-VILFNLSG 415
                                       ***********88888888878888888888777.88888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 3525.88
//
Query:       gi|320100525|ref|YP_004176117.1|  [L=145]
Description: DNA-binding protein, Tfx family [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   49.4   0.0    4.8e-13   48.9   0.0    1.3  1  TFX_C         DNA_binding protein, TFX, C-term
    2.2e-09   36.7   1.2      4e-09   35.9   1.2    1.5  1  Sigma70_r4    Sigma-70, region 4
    3.5e-08   32.9   0.1    7.8e-08   31.8   0.1    1.5  1  GerE          Bacterial regulatory proteins, luxR family
    5.2e-06   26.4   0.2    1.1e-05   25.4   0.2    1.5  1  HTH_3         Helix-turn-helix
    3.7e-05   23.4   0.4    3.7e-05   23.4   0.4    1.9  2  HTH_23        Homeodomain-like domain
    0.00014   22.1   1.2    0.00026   21.3   1.2    1.5  1  HTH_31        Helix-turn-helix domain
    0.00037   20.1   0.7     0.0009   18.9   0.2    1.9  2  Sigma70_r4_2  Sigma-70, region 4
     0.0013   18.4   0.1     0.0043   16.8   0.0    1.8  2  HTH_38        Helix-turn-helix domain
     0.0014   18.5   0.0     0.0029   17.5   0.0    1.6  1  HTH_37        Helix-turn-helix domain
     0.0036   17.1   0.1     0.0067   16.3   0.1    1.5  1  HTH_25        Helix-turn-helix domain
      0.008   16.2   0.0      0.015   15.3   0.0    1.5  1  HTH_19        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.025   14.4   0.4       0.79    9.6   0.1    2.9  3  HTH_10        HTH DNA binding domain
      0.036   14.0   0.1       0.13   12.2   0.1    1.9  2  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.042   14.0   0.2       0.12   12.5   0.2    1.8  1  HTH_28        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   3.7e-16   4.8e-13       1      79 [.      60     136 ..      60     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 3.7e-16
                                       SS-HHHHHHHH---EEEEE--GGGHHHHHHHHHHHHHHHS-S----HHHHHHHHHHH-SSS-----SSS-EEEEESS CS
                             TFX_C   1 AreTlaflealdapvlvtieeGtdlfdipkiiyaeadkagikvkydtieLikllreeapeaikgrvvkedlevyite 77 
                                       A+eT++++++++a   + i++Gt+++dip ii+++ad+ g+k+k d+  ++ +lr   +   +++++ + ++ +i +
  gi|320100525|ref|YP_004176117.1|  60 AQETVSIYKMMHAAGYIDIPAGTHMVDIPGIIIRKADELGVKLKGDFNLVYGQLRLLIGS--RATRLPRTVRAVIYR 134
                                       89*********************************************9999999877775..555566666666666 PP

                                       SS CS
                             TFX_C  78 dG 79 
                                       dG
  gi|320100525|ref|YP_004176117.1| 135 DG 136
                                       65 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   1.2   3.1e-12     4e-09       9      49 ..      17      58 ..      15      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.1e-12
                                      HHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        Sigma70_r4  9 erevlelrf.geglTleEIgerlgiSrerVrqiekrAlrkLR 49
                                      er+ l+l +  +glT+eE++ +lg+ r++V  ie+ AlrkLR
  gi|320100525|ref|YP_004176117.1| 17 ERQYLVLKYrAQGLTQEEVAGILGVARSTVAAIERAALRKLR 58
                                      8999999999*******************************9 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   6.1e-11   7.8e-08       3      52 ..      15      64 ..      14      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.1e-11
                                      S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSHHH CS
                              GerE  3 LskRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksrve 52
                                      +++R+  vL++ a+G++ +e+A +l+++  TV +  + +++KL++   ++
  gi|320100525|ref|YP_004176117.1| 15 FTERQYLVLKYRAQGLTQEEVAGILGVARSTVAAIERAALRKLRLAQETV 64
                                      69*****************************************9887665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.2   8.5e-09   1.1e-05       7      32 ..      27      52 ..      22      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.5e-09
                                      HTTHHHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEnG 32
                                      ++gl+qee+A  lGv rst+++iE+ 
  gi|320100525|ref|YP_004176117.1| 27 AQGLTQEEVAGILGVARSTVAAIERA 52
                                      69**********************98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.4   2.9e-08   3.7e-05       7      40 ..      18      52 ..      15      62 .. 0.78
   2 ?   -3.7   0.1       9.2   1.2e+04      31      38 ..     125     132 ..     125     134 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.9e-08
                            HTH_23  7 Rlr.illllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      R+  +l+  a+Gl+++e+A +Lgv r+Tv  + ++
  gi|320100525|ref|YP_004176117.1| 18 RQYlVLKYRAQGLTQEEVAGILGVARSTVAAIERA 52
                                      55505555556******************988665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.2
                            HTH_23  31 rrTvyrwl 38 
                                       +rTv+ ++
  gi|320100525|ref|YP_004176117.1| 125 PRTVRAVI 132
                                       58888665 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.2     2e-07   0.00026      11      39 ..      26      54 ..       2      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2e-07
                            HTH_31 11 eraGLsqeevAerlgvsestlsrlEqGrr 39
                                      +++GL+qeevA+ lgv +st+  +E+++ 
  gi|320100525|ref|YP_004176117.1| 26 RAQGLTQEEVAGILGVARSTVAAIERAAL 54
                                      366***********************876 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 !   18.9   0.2     7e-07    0.0009      15      51 ..      18      54 ..      14      57 .. 0.81
   2 ?   -2.1   0.0       2.5   3.1e+03      10      19 ..     123     132 ..     116     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7e-07
                                      HHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHH CS
                      Sigma70_r4_2 15 qreifllryleglsykEIAellgisegtVksrlsRAr 51
                                      ++  +l ++ +gl+++E+A +lg+  +tV    + A+
  gi|320100525|ref|YP_004176117.1| 18 RQYLVLKYRAQGLTQEEVAGILGVARSTVAAIERAAL 54
                                      556788899********************86555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.5
                                       TS-HHHHHHH CS
                      Sigma70_r4_2  10 eLperqreif 19 
                                       +Lp   r+++
  gi|320100525|ref|YP_004176117.1| 123 RLPRTVRAVI 132
                                       6888888776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.3e-06    0.0043      14      37 ..      23      46 ..      15      47 .. 0.85
   2 ?   -2.0   0.0       2.5   3.1e+03      22      22 ..      63      63 ..      50      75 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.3e-06
                            HTH_38 14 erllaeGlslreIArrLgrspsTI 37
                                       + +a+Gl++ e+A +Lg+++sT+
  gi|320100525|ref|YP_004176117.1| 23 LKYRAQGLTQEEVAGILGVARSTV 46
                                      46789******************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                            HTH_38 22 s 22
                                      +
  gi|320100525|ref|YP_004176117.1| 63 T 63
                                      2 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.3e-06    0.0029      28      62 ..      26      60 ..      19      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                                      HHCT--HHHHHHHHT--HHHHHHHHTT--TT--HH CS
                            HTH_37 28 ekrelsqseaaqllgiaqPkvsrllrgklsrfsld 62
                                      ++++l+q+e+a +lg+a++ v +++r+ l++++l 
  gi|320100525|ref|YP_004176117.1| 26 RAQGLTQEEVAGILGVARSTVAAIERAALRKLRLA 60
                                      689************************99998875 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   5.2e-06    0.0067       8      39 ..      27      58 ..      26      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-06
                                      TTT--HHHHHHHSS--HHHHHHHHCT--TTSS CS
                            HTH_25  8 arglsleevaketkIrkdylealEeddfdalp 39
                                      a+gl+ eeva  + ++ +++ a+E+  + +l 
  gi|320100525|ref|YP_004176117.1| 27 AQGLTQEEVAGILGVARSTVAAIERAALRKLR 58
                                      89***********************9988875 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05     0.015      12      34 ..      29      51 ..      26      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                            HTH_19 12 gltqeelaerlgisrskisaiEn 34
                                      gltqee+a+ lg+ rs  +aiE 
  gi|320100525|ref|YP_004176117.1| 29 GLTQEEVAGILGVARSTVAAIER 51
                                      8*********************6 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.55     7e+02       1      10 [.      15      24 ..      15      25 .. 0.90
   2 ?    9.6   0.1   0.00062      0.79      25      51 ..      31      57 ..      26      58 .. 0.91
   3 ?    0.5   0.0      0.41   5.2e+02      13      29 ..      71      87 ..      62     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.55
                            HTH_10  1 LTdkqlevlk 10
                                      +T++q+ vlk
  gi|320100525|ref|YP_004176117.1| 15 FTERQYLVLK 24
                                      7*****9997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00062
                            HTH_10 25 tlkeLAkelGIskstlsehLrkaeskl 51
                                      t +e+A +lG+++st+  + r+a +kl
  gi|320100525|ref|YP_004176117.1| 31 TQEEVAGILGVARSTVAAIERAALRKL 57
                                      6789*****************999998 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.41
                            HTH_10 13 yemGYFdyPRrvtlkeL 29
                                      +++GY d P  +++ ++
  gi|320100525|ref|YP_004176117.1| 71 HAAGYIDIPAGTHMVDI 87
                                      56899999988776665 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   0.1    0.0001      0.13      22      40 ..      30      48 ..      16      61 .. 0.85
   2 ?   -1.0   0.0       1.4   1.8e+03      35      52 ..      61      77 ..      55      98 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHTTSSHHHHHH CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsr 40
                                      ltqee A +lG+ r+tv  
  gi|320100525|ref|YP_004176117.1| 30 LTQEEVAGILGVARSTVAA 48
                                      8***************975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 35 retvsrilseLkreglis 52
                                      +etvs i + +  +g+i+
  gi|320100525|ref|YP_004176117.1| 61 QETVS-IYKMMHAAGYID 77
                                      55554.555666666666 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   9.2e-05      0.12       5      32 ..      22      49 ..      18      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                            HTH_28  5 iikllaaGhsvreaArelgisrrtvyrW 32
                                      ++k+ a+G ++ e+A +lg+ r+tv   
  gi|320100525|ref|YP_004176117.1| 22 VLKYRAQGLTQEEVAGILGVARSTVAAI 49
                                      788889999****************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1018.92
//
Query:       gi|320100526|ref|YP_004176118.1|  [L=86]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit delta [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-11   45.0  32.0    2.1e-07   31.4  11.6    1.7  3  Fer4_7    4Fe-4S dicluster domain
    1.9e-10   40.1  15.1    2.7e-05   23.8   2.4    2.1  2  Fer4      4Fe-4S binding domain
    5.6e-09   35.7  14.5    0.00025   21.0   4.1    2.2  2  Fer4_6    4Fe-4S binding domain
    8.6e-09   35.4  19.4    8.3e-07   29.1   9.8    1.6  2  Fer4_9    4Fe-4S dicluster domain
    2.3e-08   34.0   6.2    0.00092   19.3   0.6    2.1  2  Fer4_21   4Fe-4S dicluster domain
    3.2e-08   33.5   9.3    4.9e-08   33.0   9.3    1.3  1  Fer4_10   4Fe-4S dicluster domain
    3.3e-08   33.1  13.5    0.00032   20.6   2.7    2.2  2  Fer4_2    4Fe-4S binding domain
      9e-08   32.5   4.7     0.0045   17.4   0.1    2.1  2  Fer4_8    4Fe-4S dicluster domain
    3.6e-07   30.2  12.1     0.0022   18.4   2.1    2.2  2  Fer4_4    4Fe-4S binding domain
    1.5e-05   25.4  12.0    0.00065   20.2  12.7    2.1  2  Fer4_17   4Fe-4S dicluster domain
    1.9e-05   25.5  11.6      0.048   14.6  13.1    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0049   17.4  11.3      0.081   13.5   1.1    2.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.015   16.2  15.1        0.2   12.7   2.6    2.2  2  Fer4_3    4Fe-4S binding domain
       0.08   13.7   7.2        2.4    8.9   0.5    2.2  2  Fer4_15   4Fe-4S single cluster domain
        0.4   10.9  10.9         18    5.5  10.9    2.1  1  Fer4_18   4Fe-4S dicluster domain
        1.2   10.1  12.6        2.2    9.2   1.3    2.1  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.5   1.4e-06    0.0015      27      51 ..      16      40 ..      10      41 .. 0.80
   2 !   31.4  11.6   1.9e-10   2.1e-07       1      49 [.      26      75 ..      26      79 .. 0.88
   3 !   17.3   2.5   4.9e-06    0.0055       1      19 [.      63      81 ..      63      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                            Fer4_7 27 gtekveidpekClgCgaCvavCPtg 51
                                      g+ +v+i  ++C  Cg C+avCP +
  gi|320100526|ref|YP_004176118.1| 16 GRYRVNIIVDRCKECGICIAVCPMK 40
                                      5567788899999999999999976 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.9e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekve.idpekClgCgaCvavCP 49
                                      rC +Cg C a+Cp+k++      n +g + +e  + ekC+gC+ C+  CP
  gi|320100526|ref|YP_004176118.1| 26 RCKECGICIAVCPMKVLAKSSILNRNGYRPPEpAHVEKCIGCRLCEYNCP 75
                                      8*****************999888888766652589************** PP

  == domain 3  score: 17.3 bits;  conditional E-value: 4.9e-06
                            Fer4_7  1 rCigCgaCvaaCpvkaiel 19
                                      +CigC+ C+ +Cp  ai++
  gi|320100526|ref|YP_004176118.1| 63 KCIGCRLCEYNCPDFAIYV 81
                                      7************999876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   5.0   7.5e-08   8.4e-05       2      22 ..      21      41 ..      20      43 .. 0.88
   2 !   23.8   2.4   2.4e-08   2.7e-05       6      24 .]      62      80 ..      59      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.5e-08
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                       i+ ++C  CG+C+ vCP  +
  gi|320100526|ref|YP_004176118.1| 21 NIIVDRCKECGICIAVCPMKV 41
                                      6899**************865 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2.4e-08
                                      TTSSS-THHHHHSTTTEEE CS
                              Fer4  6 ekCigCGaCvevCPvgAIt 24
                                      ekCigC +C+  CP  AI+
  gi|320100526|ref|YP_004176118.1| 62 EKCIGCRLCEYNCPDFAIY 80
                                      9*************99996 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   4.1   2.3e-07   0.00025       2      24 .]      20      42 ..      19      42 .. 0.88
   2 !   20.4   2.7   3.4e-07   0.00039       7      24 .]      62      79 ..      60      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      v i  d+C  Cg C++vCP++++
  gi|320100526|ref|YP_004176118.1| 20 VNIIVDRCKECGICIAVCPMKVL 42
                                      56788**************9875 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.4e-07
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                      +kCigC+ C+ +CP  ai
  gi|320100526|ref|YP_004176118.1| 62 EKCIGCRLCEYNCPDFAI 79
                                      79************8665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.0     3e-06    0.0033      34      49 ..      25      40 ..       7      42 .. 0.67
   2 !   29.1   9.8   7.4e-10   8.3e-07       1      50 [.      26      78 ..      26      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3e-06
                            Fer4_9 34 eaCigCgaCveaCpkg 49
                                      ++C +Cg C+++Cp +
  gi|320100526|ref|YP_004176118.1| 25 DRCKECGICIAVCPMK 40
                                      4799999999999987 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 7.4e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase...eaCigCgaCveaCpkga 50
                                      +C +Cg C+++Cp++v  +++  + + +r  +    e+CigC+ C+  Cp  a
  gi|320100526|ref|YP_004176118.1| 26 RCKECGICIAVCPMKVLAKSSILNRNGYRPPEPahvEKCIGCRLCEYNCPDFA 78
                                      5********************9999999988879****************855 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.6   8.2e-07   0.00092      31      53 ..      17      39 ..       7      44 .. 0.81
   2 !   18.1   0.6     2e-06    0.0022      38      52 ..      61      75 ..      49      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.2e-07
                           Fer4_21 31 ktvlkvvedeCvGCnlCssvCPv 53
                                      + +++++ d+C  C +C++vCP+
  gi|320100526|ref|YP_004176118.1| 17 RYRVNIIVDRCKECGICIAVCPM 39
                                      45667889**************8 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2e-06
                           Fer4_21 38 edeCvGCnlCssvCP 52
                                       ++C+GC lC   CP
  gi|320100526|ref|YP_004176118.1| 61 VEKCIGCRLCEYNCP 75
                                      478888888888888 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   9.3   4.4e-11   4.9e-08       2      56 .]      20      75 ..      19      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.4e-11
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      v i  d+C +Cg C ++CP+++ +++ +  +++  + +   vekC+gc  C   CP
  gi|320100526|ref|YP_004176118.1| 20 VNIIVDRCKECGICIAVCPMKVLAKSSILNRNGYRPPEPaHVEKCIGCRLCEYNCP 75
                                      567889**************9955555555555555555599*************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 !   20.6   2.7   2.8e-07   0.00032       7      21 ..      24      38 ..      19      39 .. 0.91
   2 !   18.1   3.2   1.8e-06     0.002       7      21 ..      61      75 ..      56      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.8e-07
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                       drC +Cg+C+ +CP
  gi|320100526|ref|YP_004176118.1| 24 VDRCKECGICIAVCP 38
                                      79************* PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.8e-06
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                       ++CigC+ C  +CP
  gi|320100526|ref|YP_004176118.1| 61 VEKCIGCRLCEYNCP 75
                                      589************ PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     4e-06    0.0045      47      65 .]      23      41 ..       7      55 .. 0.75
   2 !   17.0   1.1   5.3e-06     0.006       2      16 ..      61      75 ..      60      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4e-06
                            Fer4_8 47 alwsCttcgaCtevCpvgi 65
                                      ++++C +cg C  vCp+++
  gi|320100526|ref|YP_004176118.1| 23 IVDRCKECGICIAVCPMKV 41
                                      5677777777777777664 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.3e-06
                            Fer4_8  2 lekCieCgaCqsaCp 16
                                      +ekCi+C +C+ +Cp
  gi|320100526|ref|YP_004176118.1| 61 VEKCIGCRLCEYNCP 75
                                      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 !   17.0   2.6   5.4e-06     0.006       2      16 ..      25      39 ..      25      42 .. 0.94
   2 !   18.4   2.1     2e-06    0.0022       2      15 ..      62      75 ..      62      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.4e-06
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      +rC +Cg C+a+CP+
  gi|320100526|ref|YP_004176118.1| 25 DRCKECGICIAVCPM 39
                                      89************7 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2e-06
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e+CigC+ C++ CP
  gi|320100526|ref|YP_004176118.1| 62 EKCIGCRLCEYNCP 75
                                      79************ PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.3   6.1e-05     0.069      44      59 ..      25      40 ..      12      42 .. 0.73
   2 !   20.2  12.7   5.8e-07   0.00065       1      57 [.      26      75 ..      26      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C eCg C ++CP++
  gi|320100526|ref|YP_004176118.1| 25 DRCKECGICIAVCPMK 40
                                      6777777777777776 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.8e-07
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57
                                      rC +Cg C+++Cp+    ++   ++l++  +    +  +   +++Ci+C++Ce+ CP
  gi|320100526|ref|YP_004176118.1| 26 RCKECGICIAVCPMKVLAKS---SILNRNGY----RPPEPAHVEKCIGCRLCEYNCP 75
                                      7*************999777...78887222....22345799************** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6  13.1   4.3e-05     0.048       1      65 [.      26      75 ..      26      76 .. 0.80
   2 !   12.8   1.6   0.00016      0.18       1      20 [.      63      82 ..      63      86 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      rC++Cg C+ vCP +++ +    +i           +++++++ e ++   e+++gC+ C+  CP
  gi|320100526|ref|YP_004176118.1| 26 RCKECGICIAVCPMKVLAKS---SIL----------NRNGYRPPEPAHV--EKCIGCRLCEYNCP 75
                                      6****************999...332..........2355666666666..779**********9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00016
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++C+ C   CP  ai  +
  gi|320100526|ref|YP_004176118.1| 63 KCIGCRLCEYNCPDFAIYVE 82
                                      5************9999765 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   3.4    0.0022       2.5       4      17 ..      25      38 ..      24      40 .. 0.90
   2 !   13.5   1.1   7.2e-05     0.081       4      19 ..      62      77 ..      61      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0022
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d+C +cg+C +++P
  gi|320100526|ref|YP_004176118.1| 25 DRCKECGICIAVCP 38
                                      59************ PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.2e-05
                           Fer4_13  4 dtCiacgaCvelaPdv 19
                                      ++Ci+c +C   +Pd+
  gi|320100526|ref|YP_004176118.1| 62 EKCIGCRLCEYNCPDF 77
                                      69************96 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.9    0.0022       2.5       1      13 [.      27      39 ..      27      41 .. 0.91
   2 ?   12.7   2.6   0.00018       0.2       1      12 [.      64      75 ..      64      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C  Cg C  vCP 
  gi|320100526|ref|YP_004176118.1| 27 CKECGICIAVCPM 39
                                      99**********6 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00018
                            Fer4_3  1 CtgCgaCvevCP 12
                                      C+gC++C+  CP
  gi|320100526|ref|YP_004176118.1| 64 CIGCRLCEYNCP 75
                                      ***********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.5    0.0022       2.4       6      19 ..      25      38 ..      20      49 .. 0.87
   2 ?    8.4   1.2    0.0032       3.5       6      21 ..      62      77 ..      61      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                           Fer4_15  6 daCigcglCvaeap 19
                                      d+C  cg C+a++p
  gi|320100526|ref|YP_004176118.1| 25 DRCKECGICIAVCP 38
                                      89***********8 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0032
                           Fer4_15  6 daCigcglCvaeapev 21
                                      ++Cigc lC  ++p++
  gi|320100526|ref|YP_004176118.1| 62 EKCIGCRLCEYNCPDF 77
                                      68***********986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  10.9     0.016        18      59      95 ..      25      74 ..      13      77 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                           Fer4_18 59 gdcidcescvkvcPtgidi......rkGlq.......leciscllcidac 95
                                        c +c+ c++vcP+++        r+G +        +ci c lc   c
  gi|320100526|ref|YP_004176118.1| 25 DRCKECGICIAVCPMKVLAkssilnRNGYRppepahvEKCIGCRLCEYNC 74
                                      67************987431111236665422222223577777776655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.0     0.014        16       1      13 [.      26      38 ..      17      41 .. 0.76
   2 ?    6.6   3.8     0.012        14       1      14 [.      26      39 ..      26      51 .. 0.86
   3 ?    9.2   1.3     0.002       2.2      78      93 ..      60      75 ..      40      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                           Fer4_22  1 rClsCgaCtlvCp 13
                                      rC +Cg C +vCp
  gi|320100526|ref|YP_004176118.1| 26 RCKECGICIAVCP 38
                                      5777777777777 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      rC +Cg C +vCp 
  gi|320100526|ref|YP_004176118.1| 26 RCKECGICIAVCPM 39
                                      69999999999985 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.002
                           Fer4_22 78 gesgCvGCgRCieacp 93
                                      + ++C+GC  C+ +cp
  gi|320100526|ref|YP_004176118.1| 60 HVEKCIGCRLCEYNCP 75
                                      6678999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 636.42
//
Query:       gi|320100527|ref|YP_004176119.1|  [L=372]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-65  219.4   0.2    6.9e-65  219.0   0.2    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.9e-15   55.7   0.1      1e-14   54.7   0.1    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    9.3e-10   38.5   0.0    2.7e-09   37.0   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
    0.00021   21.0   0.3    0.00037   20.1   0.3    1.3  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
       0.13   11.2   0.0        0.2   10.6   0.0    1.2  1  Asparaginase_II  L-asparaginase II


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 !  219.0   0.2   1.9e-68   6.9e-65       1     219 [.      14     238 ..      14     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 1.9e-68
                                       .HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCC CS
                             POR_N   1 eaaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmie 77 
                                       eaai ag++++a+YPITPssei+e lae+l++++     v+qme+Ei++i+av+GA++a ++a+TaTSg+G++Lm e
  gi|320100527|ref|YP_004176119.1|  14 EAAITAGLKFYAGYPITPSSEIMEYLAEHLPRHGG---IVIQMEDEIASINAVVGASWANVKAMTATSGPGFSLMAE 87 
                                       589*******************************5...9************************************** PP

                                       CHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEE CS
                             POR_N  78 nlglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPv 149
                                        lgla+++e+P+v+v+v+Ra+pstg++++t q D+++ar     d+ +   a+ +vqea+dl+++Afn+Aek+r+Pv
  gi|320100527|ref|YP_004176119.1|  88 GLGLAVMTETPLVVVDVMRAGPSTGVPTKTTQADIFQARwlahgDYIIPSYAPWSVQEAYDLTIKAFNTAEKLRTPV 164
                                       ***************************************************************************** PP

                                       EEEEEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX......SXXXBXXTXXTSSXXEEESBXBXTTSXBXX CS
                             POR_N 150 ivlfDgfllshevekvelpdeedelklikekleeyerkey......aldpekpiargtaanpdtglehrekgneae 219
                                       i+l+D++++ h  e++ + ++  e+++i++++++ ++ ++      +l p +  + ++ ++ + +l+h+e+g+ a 
  gi|320100527|ref|YP_004176119.1| 165 ILLSDAVIA-HLWEPLVIRERG-EVEIIERRKPAGREGYKpympgdDLVPPMACFGEGFKVLVESLTHDERGFYAP 238
                                       *********.**********99.777777777666665556799999***********************998665 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 !   54.7   0.1   2.8e-18     1e-14       1      83 [.     272     348 ..     272     356 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.8e-18
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Aev++v +Gs+a+t+ + ++elR++g+k+Gllrl+tl+P  ee++ + + k+ +++v++ n+     G l+ +vk+ 
  gi|320100527|ref|YP_004176119.1| 272 AEVALVSYGSTARTVYALMRELRRKGVKAGLLRLKTLWPLDEEKIYRSV-KAGRIIVVENNM-----GKLYLDVKRI 342
                                       9**********************************************98.8999********.....*********9 PP

                                       TGGGTS CS
                           PFOR_II  78 lkkskv 83 
                                         +++v
  gi|320100527|ref|YP_004176119.1| 343 FRDREV 348
                                       998844 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   7.5e-13   2.7e-09       9      71 ..     271     332 ..     266     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 7.5e-13
                                       TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEE CS
                   Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeav 71 
                                         +v+lv+yGs+ +++ + + eL+++g++a ++ l t++plD+e i  svk  gr++vve+++
  gi|320100527|ref|YP_004176119.1| 271 DAEVALVSYGSTARTVYALMRELRRKGVKAGLLRLKTLWPLDEEKIYRSVK-AGRIIVVENNM 332
                                       579********************************************9987.57888888875 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 !   20.1   0.3     1e-07   0.00037       6     157 ..      11     166 ..       7     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-07
                                       HHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHC CS
                      TPP_enzyme_N   6 alvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatna 79 
                                       a+++a   +g + + g+p + + +++++l+e+    g  v+++ +E + ++a +g + a  ++ +  +tsgpG+  +
  gi|320100527|ref|YP_004176119.1|  11 AVAEAAITAGLKFYAGYPITPSSEIMEYLAEHLprhGGIVIQMEDEIASINAVVGASWA--NVKAMTATSGPGFSLM 85 
                                       56677777899999999999999999999999887444555555555555555555444..6999999********* PP

                                       HHHHHHHHHHT--EEEEEEE--CCCHH..S..TC--T-CCHHHC..CCSSEEEE-SSGGGHHHHHHHHHHHHHSSS- CS
                      TPP_enzyme_N  80 ltalaeAkvdriPllvlsgdrptslrg..qgvlqqeldqlalfr..pvtkyaervtspeelpealrrAirtalsgrp 152
                                         +l  A  + +Pl+v+   r+  ++g  ++++q  + q+  ++  ++   ++ + s++e+  +  +A+ ta ++ +
  gi|320100527|ref|YP_004176119.1|  86 AEGLGLAVMTETPLVVVDVMRAGPSTGvpTKTTQADIFQARWLAhgDYIIPSYAPWSVQEAYDLTIKAFNTA-EKLR 161
                                       *****************9999888888667777766666666555577777888888888888888999999.7777 PP

                                       -EEEE CS
                      TPP_enzyme_N 153 gPvyl 157
                                       +Pv l
  gi|320100527|ref|YP_004176119.1| 162 TPVIL 166
                                       78876 PP

>> Asparaginase_II  L-asparaginase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.7e-05       0.2      33     118 ..     242     323 ..     228     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.7e-05
                   Asparaginase_II  33 pervtfpRSaaKplqAlalleagaaekfglddeelAlacaSHsGeeehvaavrsiLakagldedaLrcgahlpldee 109
                                        +r t++R a+K l+ +  + +  a  + +dd+e+Al+  S+ ++++ v a+ + L++ g+++  Lr ++ +pldee
  gi|320100527|ref|YP_004176119.1| 242 YHRSTVVRLALKILKNIDYVFEYEA--YMMDDAEVALV--SYGSTARTVYALMRELRRKGVKAGLLRLKTLWPLDEE 314
                                       5778899999999999999887666..9*********9..89*********************************** PP

                   Asparaginase_II 110 areallrag 118
                                       +  + ++ag
  gi|320100527|ref|YP_004176119.1| 315 KIYRSVKAG 323
                                       999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 2485.99
//
Query:       gi|320100528|ref|YP_004176120.1|  [L=276]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-29  101.7   0.5    1.1e-28   99.9   0.1    1.8  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.032   5.8e+02      26      43 ..      22      44 ..       6      65 .. 0.66
   2 !   99.9   0.1   6.4e-33   1.1e-28       2     153 .]      61     208 ..      55     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.032
                                      TTS-TTTHHHHHHHHHH.....H CS
                      TPP_enzyme_C 26 glgtmGyglpaAiGakl.....a 43
                                      +l + G gl++++Ga l      
  gi|320100528|ref|YP_004176120.1| 22 TLYCPGCGLGIGLGAMLraldkR 44
                                      56788999******999643330 PP

  == domain 2  score: 99.9 bits;  conditional E-value: 6.4e-33
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+ +          +  y++ ++ ++ +G+++p+AiGakla+p+ + +++ GDG+++ i ++++ +a++rn++++
  gi|320100528|ref|YP_004176120.1|  61 IGCSAR----------MAFYVNyDSAHVLHGRAIPFAIGAKLANPELTLIVVGGDGDIAGIgGNHILHAAKRNIDLV 127
                                       555555..........3335555679*************************************************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       +v++ N +y+mtggq   ++p   k++++p+g+ ++p+++ k++++l a+ +ar + +++  +e+ + +al  kg+ 
  gi|320100528|ref|YP_004176120.1| 128 TVMFTNFVYAMTGGQvapTTPLRVKTTTTPHGNPEPPLNIIKVVASLNANyVARASITTPHYIEQFFYRALGMKGFR 204
                                       **************************************************9998888888***************** PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       ++ev
  gi|320100528|ref|YP_004176120.1| 205 FLEV 208
                                       *997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1999.88
//
Query:       gi|320100529|ref|YP_004176121.1|  [L=178]
Description: Pyruvate/ketoisovalerate oxidoreductase, catalytic domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-25   88.9   0.0    4.8e-25   88.6   0.0    1.1  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   2.7e-29   4.8e-25       1     176 [.      11     174 ..      11     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 2.7e-29
                                       CTSTHHHHHHHHHHHH.HHTT-EEEEEEEEESSSSSSCEEEEEEEES.S.-SSS--TTSEEEEEESSHHHHHHHGGG CS
                               POR   1 GGqGvvtagkilakaa.araGyyvqanreygseirGghsyshvrisd.epivpsievgeadllvaldaetlsehldg 75 
                                       GGqGv+++g++l+ aa  +aG+y++a+++y +e rGg s ++v i+   + +++++v+ +d+ v + +  ++++ + 
  gi|320100529|ref|YP_004176121.1|  11 GGQGVLLLGRLLGLAAsKYAGLYAVATETYAAETRGGESRADVVIGGsMSDIDYVKVQSPDIAVFMYPFNIEKYRQL 87 
                                       9***************999***************************954566************************* PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleale 151
                                       lkp++ +++++e +kpd +k +k+             y   ++ +a+   g++r+aN+v+ G +a+++g l+le+l+
  gi|320100529|ref|YP_004176121.1|  88 LKPESRVFIDEEYVKPDFFKGFKL-------------YSQRYSGLAESTVGSSRVANMVIAGHIARATGiLSLEDLK 151
                                       ****************99999886.............7889************************************ PP

                                       HHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 152 eaikkrfpkkkeviekNlkafragy 176
                                       + + +  p++    ++N+ka+++g+
  gi|320100529|ref|YP_004176121.1| 152 KTVIDLTPER--WHQANIKALELGF 174
                                       ********96..9**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1296.01
//
Query:       gi|320100530|ref|YP_004176122.1|  [L=216]
Description: alpha-glucosidase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        7.9    6.8   6.4         29    5.0   0.4    3.2  3  DUF2754   Protein of unknown function (DUF2754)


Domain annotation for each model (and alignments):
>> DUF2754  Protein of unknown function (DUF2754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.4    0.0016        29       7      27 ..     105     125 ..      98     156 .. 0.88
   2 ?   -0.6   0.1     0.088   1.6e+03      46      59 ..     165     178 ..     152     188 .. 0.69
   3 ?    3.6   0.1    0.0044        79      43      59 ..     198     214 ..     191     216 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0016
                           DUF2754   7 irrdwhyyavalGlifilnGv 27 
                                       +r+ + yy   + l fil G 
  gi|320100530|ref|YP_004176122.1| 105 VRKGYRYYLTGMILFFILAGT 125
                                       689999***********9996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.088
                           DUF2754  46 vtwvisfwiaGlii 59 
                                       +  vi  wi G+ +
  gi|320100530|ref|YP_004176122.1| 165 LPLVIFTWILGYAV 178
                                       55677777777655 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.0044
                           DUF2754  43 vGlvtwvisfwiaGlii 59 
                                        Glv +++++++aG +i
  gi|320100530|ref|YP_004176122.1| 198 AGLVYFILALYLAGSVI 214
                                       69************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1483.14
//
Query:       gi|320100531|ref|YP_004176123.1|  [L=36]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 262.13
//
Query:       gi|320100532|ref|YP_004176124.1|  [L=516]
Description: sodium:neurotransmitter symporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-49  166.6  39.7    2.9e-26   92.2  21.1    2.1  2  SNF       Sodium:neurotransmitter symporter family
  ------ inclusion threshold ------
       0.13   12.2   0.1       0.13   12.2   0.1    4.3  4  FixQ      Cbb3-type cytochrome oxidase component FixQ


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 !   80.4  11.5   1.2e-26   1.1e-22       1     114 [.       7     134 ..       7     138 .. 0.81
   2 !   92.2  21.1   3.3e-30   2.9e-26     157     494 ..     136     474 ..     131     500 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.2e-26
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytre...Gait..v 72 
                                       Retw +++  ils++G avgLgn WRFP l   nGGGaf+iPY+ +ll+ GiPl+++e a G+y  +   G+++   
  gi|320100532|ref|YP_004176124.1|   7 RETWATRIGLILSMAGNAVGLGNFWRFPRLLAGNGGGAFMIPYFAALLLLGIPLMWVEWATGRYGGKyghGTLGptF 83 
                                       9*************************************************************996432225543222 PP

                               SNF  73 w....rkicP....llkgi.GyasivvalyvglyYnvilawalfYlfssft 114
                                       +    + + P    ++  i G+ ++ v+++++ yY+ +++w++ Y + s t
  gi|320100532|ref|YP_004176124.1|  84 YlmarESVKPrtaiVFGIIgGMLAFAVTTLLNSYYIHVIGWTAAYAIYSAT 134
                                       22222456662222466664467788999****************998876 PP

  == domain 2  score: 92.2 bits;  conditional E-value: 3.3e-30
                               SNF 157 efwere.vlklsssieelGelrweltlcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlL....p 228
                                        ++  + v  +++ i ++G++ +  ++ +++ ++  y ++ kG++   k+++      y+  ++l v++v+     +
  gi|320100532|ref|YP_004176124.1| 136 AYYGVDtVQFFNNHIGNTGMVMATWAIPMILLFIAAYRGVSKGIELFNKIMMPLL---YLFAVILAVKSVTTgapvR 209
                                       55544404445699************************************99855...6777777778877522112 PP

                               SNF 229 ...GavkgikfyltpdlekllepkvWi...daatqiffslgigfGvlialasYnkfennvyrdallvslinsltsvl 299
                                           ++ g+++  +pd+  l++   W+   +aa qiff+l++g+G++  +asY k+++++   al ++ +n + +v+
  gi|320100532|ref|YP_004176124.1| 210 pdwSSWAGLEYSWKPDFGVLMQN-FWVislAAAGQIFFTLSLGMGIIQNYASYVKKDDDIALAALTTASLNEVAEVV 285
                                       2234689***********99875.45323389********************************************9 PP

                               SNF 300 aglvvFsvlGfmaeeqgekisevaeeGpgLaFiaypealtklp.lsplwsvlFFlmlillgldsqfgtvegiitavv 375
                                        g ++   + +     g   s v++   gL F+a p++ t l  ++ +++vl+Fl l ++g +s++++ + +++ + 
  gi|320100532|ref|YP_004176124.1| 286 LGGTIAIPIAYAY--LGP--SVVKQGSLGLSFMALPNVFTSLGeAGRVFGVLWFLLLFFAGWTSAIAMYNYLVALLE 358
                                       9887766666643..333..44888999*************963789****************************** PP

                               SNF 376 DefkvllrrrelltlivavlaflvglllvtegGiyvltlldkyaaslsllvvvlleaiavawvyglkkflddikeml 452
                                       +++ v   +r++  ++v+++++l+gl +  +  + ++  ld+++ s+ l+++ l+++i+ +++++  ++ +++++  
  gi|320100532|ref|YP_004176124.1| 359 EDLGV---KRKVAAVVVFIVYLLLGLPVALDPSLTYFGELDNWVGSYLLVLLGLFDVIVAVYLFKPGNLWRELHNGA 432
                                       ****9...9******************************************************************** PP

                               SNF 453 gfrpllflklcwkfvspllllvlliasivklkpltynayvyP 494
                                         r+   +k+++ +++p+ +l+ll+ + + + +++  a   P
  gi|320100532|ref|YP_004176124.1| 433 LIRVPEVFKYILMTLTPAYILILLVGTTIDYYKSGVFAQSDP 474
                                       *************************99999865555444444 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.1      0.96   8.6e+03       9      28 ..      99     118 ..      98     119 .. 0.74
   2 ?    1.5   2.2     0.032   2.9e+02      10      25 ..     327     342 ..     320     347 .. 0.64
   3 ?   -5.7   2.9         2   1.8e+04      17      26 ..     368     377 ..     367     378 .. 0.73
   4 ?   12.2   0.1   1.5e-05      0.13       9      38 ..     398     429 ..     393     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.96
                              FixQ   9 fadswgllflvllfygvviy 28 
                                       f+ + g+l+++++ +   +y
  gi|320100532|ref|YP_004176124.1|  99 FGIIGGMLAFAVTTLLNSYY 118
                                       56678999999988766665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.032
                              FixQ  10 adswgllflvllfygv 25 
                                       ++ +g l+++llf + 
  gi|320100532|ref|YP_004176124.1| 327 GRVFGVLWFLLLFFAG 342
                                       4556666666666655 PP

  == domain 3  score: -5.7 bits;  conditional E-value: 2
                              FixQ  17 flvllfygvv 26 
                                       + v++f+ ++
  gi|320100532|ref|YP_004176124.1| 368 AAVVVFIVYL 377
                                       5688998887 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 1.5e-05
                              FixQ   9 fadswgllflvllfygvviyafrpgn..rkdf 38 
                                       +  s++l++l l+ ++v +y+f+pgn  r+ +
  gi|320100532|ref|YP_004176124.1| 398 WVGSYLLVLLGLFDVIVAVYLFKPGNlwRELH 429
                                       7889**********************888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3739.46
//
Query:       gi|320100533|ref|YP_004176125.1|  [L=414]
Description: sodium:dicarboxylate symporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-100  334.4  33.9   9.9e-100  334.3  33.9    1.0  1  SDF       Sodium:dicarboxylate symporter family
  ------ inclusion threshold ------
       0.16   10.7   0.2       0.23   10.1   0.2    1.1  1  DUF3525   Protein of unknown function (DUF3525)


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.3  33.9  1.1e-103  9.9e-100       2     389 ..      13     403 ..      12     404 .. 0.97

  Alignments for each domain:
  == domain 1  score: 334.3 bits;  conditional E-value: 1.1e-103
                               SDF   2 llqiliglvlGlviGll.......elvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgklglkt 71 
                                       l+ il++++lGl++G+l       e+++++a++++ lgd+f++l++ +i  l++++i+ +++s+ +a+klg+++  +
  gi|320100533|ref|YP_004176125.1|  13 LAVILAAFLLGLLAGYLvssfapkETASATASWLKALGDVFVRLIRIVIPLLILFTIAAATSSIASARKLGRILAWM 89 
                                       56799****************************************9877667************************* PP

                               SDF  72 llyfllttliAaiiglilalllkpgselaleassakeaekketdslldlilslipsnifealaegnvlavivfailf 148
                                       l++++ t+++Aa+ g++ ++++kpg  +    +  k+ +  + +s  dl+ls++ +++ + l+ +  +++i+fail+
  gi|320100533|ref|YP_004176125.1|  90 LILYIGTSILAATWGVLGGVFFKPG--EGIGLQVPKDYKPPTPPSGVDLLLSFFQPDFSNLLTVSGSMTMIIFAILL 164
                                       *************************..455566777888888999******************************** PP

                               SDF 149 GialaalgekgepllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalsslakflltvylglaihlliv 225
                                       G+a++ +ge g+++ ++++ l+++++k+v++vm++aP++vf++ a+l++s+g  +l+ +a fl++ y   ++h++iv
  gi|320100533|ref|YP_004176125.1| 165 GVAAVLMGEPGRRVASGLSLLSSLMVKFVSVVMYYAPVAVFSYSAWLMISYGPAMLGAYARFLGVQYGFTLMHFFIV 241
                                       ***************************************************************************** PP

                               SDF 226 lpllllvltkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGatinmdGtalyeava 302
                                       ++++++ ++++nplk++k+ l ++l+Af+T+SSa tLP ++e+a+k +g+++++ +++lP+Gat+nmdGtaly+a+ 
  gi|320100533|ref|YP_004176125.1| 242 YSIIVY-VGGLNPLKYFKAQLTPFLVAFTTRSSAVTLPFNMEAARK-MGIPDEVFEITLPVGATVNMDGTALYQALS 316
                                       ****98.9**************************************.9***************************** PP

                               SDF 303 aifiaqlfgvelslgqllllvlvatlasiGaagvPgaglvalllvlsalglpvegialilaidrllDmfrTavNvtG 379
                                       a+fiaqlfg++l+ gql ++++ a++ s+++a++Pg+g+++l+ vls+lglp+eg++++l +d+l D +rTavN +G
  gi|320100533|ref|YP_004176125.1| 317 ALFIAQLFGISLTPGQLGMAIMAAVIGSVATAAIPGGGTIMLAYVLSVLGLPLEGVGIMLVVDPLADAVRTAVNASG 393
                                       ***************************************************************************** PP

                               SDF 380 davaalivak 389
                                       d ++++++++
  gi|320100533|ref|YP_004176125.1| 394 DNACTVLISR 403
                                       ******9987 PP

>> DUF3525  Protein of unknown function (DUF3525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   2.6e-05      0.23     368     444 ..      33     107 ..      28     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.6e-05
                           DUF3525 368 yaprvln.elvvwlkglaenlyrvaepilelllramraaisvsdraarsvyqclchwldvmyggsapkrvktvwglt 443
                                       +ap+      + wlk l++ + r+   ++ ll+    aa + s  +ar + + l  w+ ++y g++   + + wg+ 
  gi|320100533|ref|YP_004176125.1|  33 FAPKETAsATASWLKALGDVFVRLIRIVIPLLILFTIAAATSSIASARKLGRILA-WMLILYIGTS--ILAATWGVL 106
                                       566544304568*********************99999***********999875.8888888765..355667765 PP

                           DUF3525 444 g 444
                                       g
  gi|320100533|ref|YP_004176125.1| 107 G 107
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3052.02
//
Query:       gi|320100534|ref|YP_004176126.1|  [L=168]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-18   65.7   0.2    4.7e-18   65.2   0.2    1.2  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.2   2.6e-22   4.7e-18       2      75 ..      99     165 ..      98     166 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 2.6e-22
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtkaspgkivvknlaDiGeYlR 75 
                                       ++v+ek+ k FLYG+dvl esi++ +e+v+ + v vV++ +  ++G++k+      +p ++v++n++D+G YlR
  gi|320100534|ref|YP_004176126.1|  99 IIVREKGVKAFLYGNDVLPESIVEKREPVE-GLVTVVDSSDHGIVGFAKW------DPVRKVYRNIYDLGVYLR 165
                                       89****************************.*******************......99***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1325.17
//
Query:       gi|320100535|ref|YP_004176127.1|  [L=344]
Description: ribosomal RNA methyltransferase NOP2 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  135.9   0.0    1.7e-39  135.6   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    4.8e-11   43.0   0.0    7.4e-11   42.4   0.0    1.3  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer


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 !  135.6   0.0   1.9e-43   1.7e-39      11     195 ..     140     335 ..     130     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 1.9e-43
                                       EEEESS-TTSHHHHHHHHHTTTT..SEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEE CS
                   Methyltr_RsmB-F  11 tilDlcaaPGgKTthiaelmknk..gtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLl 85 
                                        +lD+caaPGgK t+ a+++k++  gtv+A+d    Rlk+++  + r+ + n+ v+ + a + +  +g   f riLl
  gi|320100535|ref|YP_004176127.1| 140 DVLDACAAPGGKATFTAQILKERggGTVYANDYVLYRLKSLIGHVLRMKLDNIVVTWGNAAELPGRVGR-RFKRILL 215
                                       58*****************99873369****************************************95.******* PP

                                       EE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEE CS
                   Methyltr_RsmB-F  86 DaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvel 162
                                       DaPCsg g i+ dp  k+r +  d+a ++k++ ell ++id+l ++Gv+ YsTCs+++eEne v++++L++r dve+
  gi|320100535|ref|YP_004176127.1| 216 DAPCSGEGRISVDPGRKTRTSILDLAIMVKREVELLGSLIDMLDEEGVIAYSTCSIAPEENEYVVAKILESRRDVEV 292
                                       ****************************************************************************9 PP

                                       ESSBSTTSTTSSECEEC..........TSEEE-TTTTSS-SEE CS
                   Methyltr_RsmB-F 163 vetelsepkglklgeea..........gtlrllPhtenkdgff 195
                                        +     +++++  + +          + +r++Ph++   gf 
  gi|320100535|ref|YP_004176127.1| 293 ADPGPLPFNHSRWLTSYrsmeypreleKCIRIWPHRHGLFGFT 335
                                       86543333333333333345778998889999**999887775 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 !   42.4   0.0   8.3e-15   7.4e-11       6      84 ..      35     119 ..      31     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 8.3e-15
                                       HHHHHHHHGG.GHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---......TTSHH CS
                   Methyltr_RsmF_N   6 iekmkellge.eaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerp...gkhpl 76 
                                       ++++ ++lg  ea ++l+a+e+p ++ +R Ntl +++ el++  e  +f+le++pw++  f++ e +r    g + +
  gi|320100535|ref|YP_004176127.1|  35 VQRYIDMLGPrEAVELLEAFEKPVRQVVRANTLLVEPGELKTRLEslGFRLEEIPWAPGSFWVAEAPRSpsiGSTHE 111
                                       67888889888*****************************99777799*****************9877788***** PP

                                       HHTTS-EE CS
                   Methyltr_RsmF_N  77 heaGlyYi 84 
                                       + +G yY+
  gi|320100535|ref|YP_004176127.1| 112 YLKGFYYV 119
                                       *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2622.88
//
Query:       gi|320100536|ref|YP_004176128.1|  [L=230]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-42  143.8   0.1    9.5e-42  143.6   0.1    1.0  1  DUF72     Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.1   5.3e-46   9.5e-42       9     216 ..      18     225 ..      13     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 5.3e-46
                                       CHHHHHCCT..-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS.G.-.SCHHHHHHHHHH.CHHHC CS
                             DUF72   9 erLeyYarh..fntVEinstFYalpspetvakwaaqtpedFrFavKapraithern.e.daeealerflesalepLg 81 
                                        +Le Ya++  +n+VE+n++FY++p +++va+w ++     r+++K++r+ith r+ + +a e + rf    ++p++
  gi|320100536|ref|YP_004176128.1|  18 ASLEWYAEEsgLNAVELNASFYRFPFRNQVASWSRKG-RRLRWSIKVHRSITHLRRlDeKALETWGRFHGV-FNPME 92 
                                       58********************************998.68*************753444799********6.***** PP

                                       T-EEEEEEE--TT--S.HHHHHHHHHH..TTTS-S.EEEE--BGGGH.H.HHHHHHHTT-EEEE.E--SSC------ CS
                             DUF72  82 eklgpllfQlppsfkfdeenlerLeaf..laalpl.lavEvRhrswf.e.llellrehgvavvl.depkkpklpled 152
                                       + +  +lfQ+pp f++  +nler+++f   + l + +avE+Rh+s f e + e+ r++g++vv  d+p      + +
  gi|320100536|ref|YP_004176128.1|  93 GLIDFYLFQMPPGFTCHSSNLERVDRFheASGLGPrMAVEFRHESCFnEeVAEWGRRKGIVVVSiDAP-----IASW 164
                                       ****************988********664455555***********955***********7766932.....2344 PP

                                       --SS.TEEEEEE--SHHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHHHHH CS
                             DUF72 153 vtta.dfvyvRlhgreeryayrYseeelaewaerikawaaegrevyvffnndaegqaplnaraLa 216
                                       ++ +  +vy+R+hgr  +y ++Y+eeel+ +ae+i +++    ++yvffnn+++  + +nar L 
  gi|320100536|ref|YP_004176128.1| 165 IVESgGVVYLRMHGRTTWYGHEYTEEELRGIAEKILSLNP--VKAYVFFNNNHW--MLENARSLL 225
                                       444449*********99********************998..79*******776..788888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1851.08
//
Query:       gi|320100537|ref|YP_004176129.1|  [L=394]
Description: phosphate transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-63  214.8  24.9    1.9e-63  214.5  24.9    1.0  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 !  214.5  24.9   1.1e-67   1.9e-63       2     335 ..      17     382 ..      16     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: 214.5 bits;  conditional E-value: 1.1e-67
                              PHO4   2 GanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwll 78 
                                       Gan +an+++t++g++al +r+A+++a++fe++G v+ G+ +++t+++ +vd++   p++ ++g+ +al+ +++ ++
  gi|320100537|ref|YP_004176129.1|  17 GANNAANSIGTVIGARALPVRRALLIASFFELAGGVVYGEYISSTLASRVVDTSNLPPRVAAVGFASALIVSFIIVF 93 
                                       9*****************************************************99********************* PP

                              PHO4  79 latvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalr 155
                                       +at  ++P S +  +vGa++G++laa g+e v+   + + ++ w+l Pl++++++++ + l  +l  ++++   a++
  gi|320100537|ref|YP_004176129.1|  94 AATRRRIPFSISIVMVGAVAGVGLAA-GVEHVNTVLISELFALWILIPLISILAGYTYYRLYSYL--RSRRSLYAKT 167
                                       *************************5.779****99*****************************..6667777889 PP

                              PHO4 156 alpvlvlvtiailalsilfk.ge...................................sk.kddeeteklfkflqvv 195
                                       +lp+l+l   ++++++ +   g+                                   ++ + d  + ++ + +++ 
  gi|320100537|ref|YP_004176129.1| 168 FLPLLLLYASFTVSAVYMAIpGHllsdplilgtitlllaaplaslllylyrvlhrevlEEsEVDAVVGRFNRRMLIA 244
                                       99988555544333333333322444444444455555555555555555555443332246677777778****** PP

                              PHO4 196 saalvsfahGanDvanaiGpllaalisiykask.evplwvlllgglaialGlllgGkrviktvGekitkkltpsrGf 271
                                       s+a+++f+hG+ Dvana +pl+++l + + +++  ++l +l++  l+i++G+l +G  v +t+Ge+it  l+p +++
  gi|320100537|ref|YP_004176129.1| 245 SSAILAFTHGGHDVANAAAPLMVIL-ESTGVNHtGSQLLILAYSSLGISTGVLSWGASVARTIGEEIT-VLNPESAL 319
                                       *********************7765.4333555477999*****************************.5******* PP

                              PHO4 272 aaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwklvrnivlaWvlTlpvsal 335
                                       +a++a+a t l++++lglP S   ++vg+++GvGla+ + s++n +l+++++  W   + v+al
  gi|320100537|ref|YP_004176129.1| 320 VANIAGAQTTLVVTRLGLPSSMVGIVVGSIIGVGLAR-GVSGINTRLFARMLSYWYAGFTVAAL 382
                                       *************************************.79******************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3114.73
//
Query:       gi|320100538|ref|YP_004176130.1|  [L=186]
Description: pyruvate/ketoisovalerate oxidoreductase subunit gamma [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-37  127.3   0.1    7.5e-37  127.1   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 !  127.1   0.1   4.2e-41   7.5e-37       1     177 []      11     181 ..      11     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 4.2e-41
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH.HHGGGE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls.ehldgl 76 
                                       GGqG+ ta++i a aaa +G++vq+++ +g+e++G++  s  risdepi  +  ++e+d+ v+ld ++ls   ++gl
  gi|320100538|ref|YP_004176130.1|  11 GGQGAWTASNIVAMAAALEGKHVQSFPAFGPERSGAPMLSFTRISDEPIEVHSMIYEPDVAVVLDYTLLSpSIVSGL 87 
                                       9**********************************************99999999***************9****** PP

                                       EEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHH CS
                               POR  77 kpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealee 152
                                       k+gg+i+ n   + +++l k   +     +  +++v+ v+a+k+a ei++ + ++Nt+m+G l++ +g ++ e++e+
  gi|320100538|ref|YP_004176130.1|  88 KKGGTIVTNYAGTVDQVLGKLGVR-----RGGDYKVILVPASKLALEILR-ANITNTAMIGGLLRHGGiVKWESVEK 158
                                       **********99999999997764.....23389****************.*****************9999***** PP

                                       HHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 153 aikkrfpkkkeviekNlkafragye 177
                                       a+k+rf++   v+ekN+  ++++ye
  gi|320100538|ref|YP_004176130.1| 159 AVKARFKGP--VAEKNISLIKRAYE 181
                                       *******95..*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1397.94
//
Query:       gi|320100539|ref|YP_004176131.1|  [L=93]
Description: pyruvate ferredoxin oxidoreductase subunit delta [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-13   49.0  13.6    1.4e-07   31.0   3.3    2.2  2  Fer4      4Fe-4S binding domain
      2e-09   37.4   9.5    2.5e-09   37.1   9.5    1.1  1  Fer4_21   4Fe-4S dicluster domain
    2.6e-08   33.6  12.5    0.00012   22.0   3.0    2.2  2  Fer4_6    4Fe-4S binding domain
    1.4e-07   31.5   9.6    2.1e-07   31.0   9.6    1.3  1  Fer4_9    4Fe-4S dicluster domain
    1.5e-07   32.3   7.7     0.0004   21.3   1.9    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    1.2e-06   29.0  10.0    4.5e-06   27.2  10.5    1.7  1  Fer4_7    4Fe-4S dicluster domain
    2.2e-06   27.4  10.4    0.00019   21.3   1.7    2.2  2  Fer4_2    4Fe-4S binding domain
    3.1e-06   27.2  21.4    0.00017   21.6  11.4    1.8  2  Fer4_10   4Fe-4S dicluster domain
    0.00013   22.5  11.4      0.003   18.1   1.6    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0025   18.2  10.9        3.3    8.2   1.7    2.1  2  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.016   16.0  13.1        1.3    9.8   1.5    3.1  3  Fer4_15   4Fe-4S single cluster domain
      0.018   15.5  10.6       0.76   10.4   0.9    2.2  2  Fer4_4    4Fe-4S binding domain
      0.078   13.5  11.6       0.25   11.9   2.5    2.1  3  Fer4_17   4Fe-4S dicluster domain
       0.24   11.6   6.7       0.55   10.5   6.7    1.6  1  Fer4_18   4Fe-4S dicluster domain
        3.3    8.6  12.5       0.35   11.7   2.0    2.1  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   2.7   2.1e-08   2.5e-05       1      23 [.      33      55 ..      33      56 .. 0.95
   2 !   31.0   3.3   1.2e-10   1.4e-07       1      24 []      62      85 ..      62      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.1e-08
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +v+d  kC++C++C   CP  AI
  gi|320100539|ref|YP_004176131.1| 33 PVVDHGKCTKCMICWLFCPDMAI 55
                                      69******************999 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.2e-10
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++++ + C gCG+C+  CPv AI+
  gi|320100539|ref|YP_004176131.1| 62 IQVNLDYCKGCGICAHECPVKAIS 85
                                      589*******************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 !   37.1   9.5   2.1e-12   2.5e-09       2      59 .]      34      86 ..      33      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.1e-12
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      ++d+ kC +C  C + C+d    ai  d++++ +v  d C GC +C++ CPv ++i+m
  gi|320100539|ref|YP_004176131.1| 34 VVDHGKCTKCMICWLFCPD---MAIVWDGEKI-QVNLDYCKGCGICAHECPV-KAISM 86
                                      68999*************9...8999998776.999***************9.99988 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.1   3.4e-06     0.004       1      24 []      32      55 ..      32      55 .. 0.95
   2 !   22.0   3.0   9.8e-08   0.00012       1      24 []      61      84 ..      61      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.4e-06
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++++d  kC+ C+ C   CP  ai
  gi|320100539|ref|YP_004176131.1| 32 KPVVDHGKCTKCMICWLFCPDMAI 55
                                      699*****************9998 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 9.8e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +++++ d C gCg C+  CP +ai
  gi|320100539|ref|YP_004176131.1| 61 KIQVNLDYCKGCGICAHECPVKAI 84
                                      6899*****************998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   9.6   1.7e-10   2.1e-07       1      51 []      39      84 ..      38      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kCt+C  C   Cp +++v d  +  ++l+      C gCg C++ Cp +ai
  gi|320100539|ref|YP_004176131.1| 39 KCTKCMICWLFCPDMAIVWDGEKIQVNLDY-----CKGCGICAHECPVKAI 84
                                      7*************************9964.....************9987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.4   3.7e-05     0.044       1      20 [.      39      58 ..      39      67 .. 0.84
   2 !   21.3   1.9   3.4e-07    0.0004       2      22 ..      69      89 ..      68      93 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++C  C   CP  ai  +
  gi|320100539|ref|YP_004176131.1| 39 KCTKCMICWLFCPDMAIVWD 58
                                      6****************866 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.4e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikekke 22
                                      C++Cg Ca  CP++ai++  e
  gi|320100539|ref|YP_004176131.1| 69 CKGCGICAHECPVKAISMVPE 89
                                      ****************98833 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2  10.5   3.7e-09   4.5e-06       1      52 []      39      83 ..      39      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.7e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C++C  C   Cp  ai +d e       k++++ ++C gCg C+ +CP++a
  gi|320100539|ref|YP_004176131.1| 39 KCTKCMICWLFCPDMAIVWDGE-------KIQVNLDYCKGCGICAHECPVKA 83
                                      7******************876.......79******************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 !   11.2   1.7   0.00026      0.31       2      21 ..      32      51 ..      31      52 .. 0.85
   2 !   21.3   1.7   1.6e-07   0.00019       2      21 ..      61      80 ..      60      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++vvd  +C+ C +C   CP
  gi|320100539|ref|YP_004176131.1| 32 KPVVDHGKCTKCMICWLFCP 51
                                      689999*********55599 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.6e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      +++v+ d C gCg+C + CP
  gi|320100539|ref|YP_004176131.1| 61 KIQVNLDYCKGCGICAHECP 80
                                      799***************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  11.4   1.4e-07   0.00017       2      56 .]      33      80 ..      32      80 .. 0.95
   2 !   17.0   2.3   3.9e-06    0.0047       2      23 ..      62      83 ..      61      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v+d  +C++C  C  +CP         ++ +++e+++++++ C gcg C+ +CP
  gi|320100539|ref|YP_004176131.1| 33 PVVDHGKCTKCMICWLFCPD-------MAIVWDGEKIQVNLDYCKGCGICAHECP 80
                                      688999*************9.......8999999********************9 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.9e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      ++++ d C +Cg C   CP+++
  gi|320100539|ref|YP_004176131.1| 62 IQVNLDYCKGCGICAHECPVKA 83
                                      67899**************954 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   1.6   2.5e-06     0.003       1      18 [.      35      52 ..      35      54 .. 0.95
   2 !    9.5   2.4    0.0011       1.4       1      17 [.      64      80 ..      64      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD  +C+ c++C+ ++Pd
  gi|320100539|ref|YP_004176131.1| 35 VDHGKCTKCMICWLFCPD 52
                                      8999*************9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      V+ d C +cg+C++ +P
  gi|320100539|ref|YP_004176131.1| 64 VNLDYCKGCGICAHECP 80
                                      78899***********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 !    8.2   1.7    0.0027       3.3      48      62 ..      37      51 ..       4      54 .. 0.80
   2 !    6.6  11.9    0.0087        10      45      64 ..      63      82 ..      36      83 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0027
                            Fer4_8 48 lwsCttcgaCtevCp 62
                                       ++Ct c+ C   Cp
  gi|320100539|ref|YP_004176131.1| 37 HGKCTKCMICWLFCP 51
                                      468999999999998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0087
                            Fer4_8 45 eealwsCttcgaCtevCpvg 64
                                      + +l++C +cg C+ +Cpv+
  gi|320100539|ref|YP_004176131.1| 63 QVNLDYCKGCGICAHECPVK 82
                                      44689999999999999987 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.5    0.0011       1.3       2      21 ..      34      53 ..      34      59 .. 0.92
   2 ?    9.6   3.3    0.0013       1.5       1      19 [.      62      80 ..      62      82 .. 0.90
   3 ?    7.6   0.1    0.0052       6.2      56      65 ..      76      85 ..      76      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                           Fer4_15  2 vvDrdaCigcglCvaeapev 21
                                      vvD+ +C+ c  C+  +p++
  gi|320100539|ref|YP_004176131.1| 34 VVDHGKCTKCMICWLFCPDM 53
                                      69***************985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      + v+ d C gcg C+ e+p
  gi|320100539|ref|YP_004176131.1| 62 IQVNLDYCKGCGICAHECP 80
                                      568899************8 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0052
                           Fer4_15 56 araCPvdAIr 65
                                      a++CPv+AI+
  gi|320100539|ref|YP_004176131.1| 76 AHECPVKAIS 85
                                      89*******8 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.9   0.00064      0.76       3      15 ..      39      51 ..      37      59 .. 0.92
   2 ?    9.8   2.9     0.001       1.2       2      16 ..      67      81 ..      66      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00064
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +C+ C+ C  +CP
  gi|320100539|ref|YP_004176131.1| 39 KCTKCMICWLFCP 51
                                      8************ PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.001
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C gCg C   CP+
  gi|320100539|ref|YP_004176131.1| 67 DYCKGCGICAHECPV 81
                                      89************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 ?    7.2   1.8    0.0063       7.5      45      57 ..      39      51 ..       9      55 .. 0.74
   2 ?    5.8   2.4     0.017        20       1      15 [.      39      53 ..      39      65 .. 0.74
   3 ?   11.9   2.5   0.00021      0.25      43      57 ..      66      80 ..      54      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0063
                           Fer4_17 45 lCieCgeCerkCP 57
                                      +C++C  C   CP
  gi|320100539|ref|YP_004176131.1| 39 KCTKCMICWLFCP 51
                                      6777777777776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      +C++C  C   Cp +
  gi|320100539|ref|YP_004176131.1| 39 KCTKCMICWLFCPDM 53
                                      588888887777765 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00021
                           Fer4_17 43 aslCieCgeCerkCP 57
                                       + C +Cg C+++CP
  gi|320100539|ref|YP_004176131.1| 66 LDYCKGCGICAHECP 80
                                      566777777777776 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   6.7   0.00046      0.55      52      95 ..      31      79 ..      12      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00046
                           Fer4_18 52 erkekgagdcidcescvkvcPtgidirkGlqle.....ciscllcidac 95
                                      ++   ++g+c++c  c   cP    + +G +++     c  c+ c   c
  gi|320100539|ref|YP_004176131.1| 31 LKPVVDHGKCTKCMICWLFCPDMAIVWDGEKIQvnldyCKGCGICAHEC 79
                                      55567899*************9999999976654466799999999988 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.8      0.17     2e+02       1      13 [.      39      51 ..      39      60 .. 0.90
   2 ?   11.7   2.0   0.00029      0.35      76      95 ..      63      82 ..      53      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                           Fer4_22  1 rClsCgaCtlvCp 13
                                      +C +C  C l Cp
  gi|320100539|ref|YP_004176131.1| 39 KCTKCMICWLFCP 51
                                      7***********9 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00029
                           Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                      +++   C GCg C + cpvk
  gi|320100539|ref|YP_004176131.1| 63 QVNLDYCKGCGICAHECPVK 82
                                      567889***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 740.05
//
Query:       gi|320100540|ref|YP_004176132.1|  [L=419]
Description: pyruvate ferredoxin oxidoreductase subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-76  256.5   0.8    3.3e-76  256.1   0.8    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.4e-29  102.3   0.1    2.8e-29  101.4   0.1    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    5.8e-05   23.0   0.0    0.00013   21.8   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.1   0.8   5.5e-80   3.3e-76       2     230 ..      29     265 ..      28     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 256.1 bits;  conditional E-value: 5.5e-80
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a+++  vdv+aaYPITP++ i+e+++e++++g v ++e+v +esE++a+sa++GAaaaGara+TaTS+qGl+Lm+e 
  gi|320100540|ref|YP_004176132.1|  29 AVKQSYVDVVAAYPITPQTIIVEKYSEFVNDGLV-HTEFVPVESEHSAMSACVGAAAAGARAFTATSSQGLALMVEI 104
                                       6778889**************************9.89**************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       +++a+ ++lP+v++vv+Ral+++ ++i++d+sD++ +rd+g+i+l++envqea+d++++Af++Ae+  v++Pv v +
  gi|320100540|ref|YP_004176132.1| 105 VYIASAMRLPIVMAVVNRALSAP-INIHNDHSDAYLMRDSGWIQLFVENVQEAYDTTIQAFKIAEDprVQLPVAVNL 180
                                       ***********************.***************************************************** PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXH CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkey........aldpekpiargtaanpdtglehrekgneaedaa 222
                                       Dgf+lsh+ e+v+++++++   +   +++  + k           l+p +pi  g  + +d+++eh+ ++ ea++a+
  gi|320100540|ref|YP_004176132.1| 181 DGFFLSHTLEEVYMLPDDEVYGFLGGPRKTVNVKVDyfeeevpfTLNPARPISLGSLDLYDYYFEHKVQQVEAMKAV 257
                                       ******************55444444333333222257888899********************************* PP

                                       HHHHHHHH CS
                             POR_N 223 ekvveeve 230
                                       ++vv+ev+
  gi|320100540|ref|YP_004176132.1| 258 PQVVREVN 265
                                       ****9986 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 !  101.4   0.1   4.7e-33   2.8e-29       1     100 [.     289     390 ..     289     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 4.7e-33
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A++v+vamGs agt++s+v++lRe+g+++Gll+lr++rPFP+ e++e l+++k vvv+d++i  g+ G+l+e+v+ +
  gi|320100540|ref|YP_004176132.1| 289 ADIVVVAMGSGAGTVRSVVRKLREKGERIGLLQLRMFRPFPYSEVAEKLSGAKLVVVMDKAIGPGAFGALYEDVAVS 365
                                       9*************************************************************99999********** PP

                                       TGGG..TSEEEEEE--GGG----HH CS
                           PFOR_II  78 lkks..kvkvvnfvaglgGrditve 100
                                       l++s  ++ +v++++glgGrd++++
  gi|320100540|ref|YP_004176132.1| 366 LYDSgeRPMLVDYIYGLGGRDLQPS 390
                                       *****99**************9986 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.2e-08   0.00013       9      78 ..     288     357 ..     282     396 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.2e-08
                                       TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHH CS
                   Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigs 78 
                                         d+++va+Gs   ++  ++ +L+++g ++ ++ lr ++p+    ++e +   + +vv++ a   g++g+
  gi|320100540|ref|YP_004176132.1| 288 DADIVVVAMGSGAGTVRSVVRKLREKGERIGLLQLRMFRPFPYSEVAEKLSGAKLVVVMDKAIGPGAFGA 357
                                       689********************************************99999999999999988888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3423.61
//
Query:       gi|320100541|ref|YP_004176133.1|  [L=352]
Description: thiamine pyrophosphate TPP-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   83.8   0.3    1.5e-23   83.3   0.3    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.3   8.1e-28   1.5e-23       2     153 .]      81     249 ..      80     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 8.1e-28
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH...........STTSEEEEEEEHHHHHHT.GGGHH CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla...........kpdrevvaivGDGgflmi.lqela 66 
                                       +Gcl+++        + +s+  + +++++ ++ ++A G++ a           + + +vv+++GDGg+++i +q+l+
  gi|320100541|ref|YP_004176133.1|  81 TGCLEVASTI----FPYTSWAVPWIHVAFENAAAVAGGVESAikalkktgrlpYDHVDVVVFAGDGGTFDIgFQALS 153
                                       7899983333....3456788899****************94445666776444468******************** PP

                                       HHHHTT-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHH CS
                      TPP_enzyme_C  67 tavrrnlpitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadvee 134
                                        +++r++++++++++Ne+y++tg q    +p+++ ++++pag+     +++++ +a ++ a+ ++ +a+ ++a++ +
  gi|320100541|ref|YP_004176133.1| 154 GMAERGHDVLYILYDNEAYMNTGIQrsgGTPQFAATTTSPAGEvvpgkTQPKKPIADIMVAHRIPyVATGTPAHWMD 230
                                       ***************************999*****************879999************999999****** PP

                                       HHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C 135 leealkealekkgpaliev 153
                                       + +++++ +e +gpa+i++
  gi|320100541|ref|YP_004176133.1| 231 FMKKVRRGIEVNGPAFIHA 249
                                       *****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2914.62
//
Query:       gi|320100542|ref|YP_004176134.1|  [L=182]
Description: hydrogenase maturation protease [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-14   53.4   0.0      3e-14   52.9   0.0    1.1  1  HycI      Hydrogenase maturation protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   1.7e-18     3e-14      28     128 ..      66     164 ..      63     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.7e-18
                                       GGHHHHCC..-SEEEEEEE--S.SS-TT-EEEEECCHHHHHHTTC.CGCCCHCHHHHHHHHHHCCS--SEEEEEEE- CS
                              HycI  28 elvgtlee..adkliivDavdf.glepGevkiikddevpkklkakkmsaHqlplaevlklleekgeipkevillgvq 101
                                       + ++ ++e  a +l++vDav++ g epGe+++  +d + +  k++  ++H+lp+  vl+ l e+g   +ev ++g+ 
  gi|320100542|ref|YP_004176134.1|  66 NCINEIREsgAVRLVVVDAVLYeGAEPGEIVVASGDALAE--KYSLATTHTLPVKTVLRILGETGV--REVYVVGIA 138
                                       567888888899***************************5..77778*****************96..999****** PP

                                       -S-BST.CCS--HHHHCCHHHHHHHCC CS
                              HycI 102 pesledvgielseevkkavekavelil 128
                                       p++l   g+e+s++v+++vek+ve+ +
  gi|320100542|ref|YP_004176134.1| 139 PKQLGY-GLEVSDKVAESVEKLVEAFT 164
                                       *****9.****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1390.56
//
Query:       gi|320100543|ref|YP_004176135.1|  [L=219]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.7   0.0        2.8    7.9   0.0    2.5  2  DUF4905   Domain of unknown function (DUF4905)


Domain annotation for each model (and alignments):
>> DUF4905  Domain of unknown function (DUF4905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00015       2.8      49      78 ..      36      65 ..      32      67 .. 0.84
   2 ?    3.1   0.0    0.0049        87      10      46 ..     112     148 ..     104     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00015
                           DUF4905 49 aiykgvlllhkyekpdsPehkgliaiDikt 78
                                      ++y    ++hky   + Peh+ l+ +  +t
  gi|320100543|ref|YP_004176135.1| 36 IFYCVDCFFHKYSATSAPEHRLLLSYSSRT 65
                                      5666778**************999887766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0049
                           DUF4905  10 iElRdkdlkealFsaldletgkllfedlvleekwwtg 46 
                                        E R+k+  +++F ++ l     +  d  +ee w+ g
  gi|320100543|ref|YP_004176135.1| 112 SEEREKNPGKLSFRSMLLGLILPRQRDALQEEGWYWG 148
                                       599*************999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1697.61
//
Query:       gi|320100544|ref|YP_004176136.1|  [L=366]
Description: cellulase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-105  352.7   0.2   1.4e-105  352.5   0.2    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    4.6e-11   42.8   0.0    7.9e-11   42.0   0.0    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
    5.3e-07   29.5   0.0    0.00012   21.8   0.0    2.2  2  Peptidase_M28  Peptidase family M28
      0.003   16.4   0.0     0.0065   15.3   0.0    1.4  1  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
  ------ inclusion threshold ------
      0.024   14.3   0.2      0.054   13.2   0.2    1.6  1  Tudor_2        Jumonji domain-containing protein 2A Tudor dom


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 !  352.5   0.2  3.9e-109  1.4e-105       1     290 [.      48     342 ..      48     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 352.5 bits;  conditional E-value: 3.9e-109
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTE.EEEEEEEE--CGG CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkg.kisGvigskppHl 76 
                                       Gn+++++kg++ + ++m+aAHmDeiG+ +++I++dGflr+ +vGGv +++l  qrv ++t++g  ++Gvig kppH+
  gi|320100544|ref|YP_004176136.1|  48 GNVVGYRKGSKGAGRIMLAAHMDEIGLFISHIEDDGFLRVIPVGGVLERTLLYQRVVVKTRDGrLYRGVIGLKPPHV 124
                                       9********99999*************************************************9************* PP

                                       CHHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS CS
                     Peptidase_M42  77 lkeeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeee 153
                                        k+ee +k +ei elfiD+ga+s+ee+e++Gi+vGdi+vfd++++el++++i++ka+Ddr+gvav+l++l++l e++
  gi|320100544|ref|YP_004176136.1| 125 IKPEEAQKVPEIRELFIDVGASSREEVEKMGIRVGDIAVFDRDVAELSGDRITGKAFDDRVGVAVMLKALESLGEHQ 201
                                       *************************************************************************9987 PP

                                       -SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT....CCSHHH CS
                     Peptidase_M42 154 leatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas....giyhpk 224
                                         ++vy+vatvqEEvGl+Ga+ts++ i+pd+a+a+Dvt+a+d pg+ + e    lg Gp+i+v+D +    +i+hpk
  gi|320100544|ref|YP_004176136.1| 202 --VDVYFVATVQEEVGLKGARTSSYGISPDVALAIDVTIASDVPGVAKSEWFtrLGYGPAIKVVDGRnasgLIAHPK 276
                                       ..********************************************99998788***********9989999***** PP

                                       HHHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHH CS
                     Peptidase_M42 225 lrkkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatv 290
                                       ++++l+ +A+k +ipyql+v+sgg+tDA+ i l++egv +++isip ryiHspvev++l+dl ++ 
  gi|320100544|ref|YP_004176136.1| 277 VVDFLVSVAEKRKIPYQLDVISGGTTDASIIALNKEGVAAGTISIPSRYIHSPVEVVDLKDLYNAS 342
                                       **************************************************************9986 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 !   42.0   0.0   2.2e-14   7.9e-11      29     206 ..     175     350 ..     165     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.2e-14
                                       EEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  29 klyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgil 105
                                       ++ G  a d+  gv+ +l+al++l ++    + ++ +++++ EE+g +Ga+    g+     +d ++   i   +i 
  gi|320100544|ref|YP_004176136.1| 175 RITGK-AFDDRVGVAVMLKALESLGEH----QVDVYFVATVQEEVGLKGARTSSYGIS----PDVAL--AID-VTIA 239
                                       55555.89****************999....68***********88899999988554....33333..222.2233 PP

                                       CHSTETEEEE............EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH... CS
                                       xxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx... RF
                     Peptidase_M20 106 eagklaigvv............kvevelleggapvtlndsplvkalaeaaeelfgekveli.vsgpggtdarff... 166
                                       +    ++gv             +++v   +++a+  + ++++v++l ++ae+  +  ++l  +sg g+tda+++   
  gi|320100544|ref|YP_004176136.1| 240 S---DVPGVAksewftrlgygpAIKVV-DGRNASGLIAHPKVVDFLVSVAEKR-KIPYQLDvISG-GTTDASIIaln 310
                                       3...12333344555666677668888.46666666667*************8.66644444899.********865 PP

                                       .TTTEEEEEEESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 167 .agiptvmifgpgsglaHspnEyvdledlekgikvlarlle 206
                                        +g+ +  i  p+   +Hsp E vdl+dl+++  + +++le
  gi|320100544|ref|YP_004176136.1| 311 kEGVAAGTISIPS-RYIHSPVEVVDLKDLYNASLLAKAFLE 350
                                       5555333434477.****************99877777765 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0029        11       1      25 [.      49      73 ..      49      85 .. 0.86
   2 !   21.8   0.0   3.5e-08   0.00012      35     175 ..     180     329 ..     166     350 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0029
                                      EEEEEESTTCESEEEEEEEE--B-T CS
                     Peptidase_M28  1 NviatlegkatdevlllgAHyDsvg 25
                                      Nv++  +g++ + +++l+AH+D +g
  gi|320100544|ref|YP_004176136.1| 49 NVVGYRKGSKGAGRIMLAAHMDEIG 73
                                      9999999999899*********987 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.5e-08
                                       TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH..HHCCCTTEEEEEEECS-SSSS--EEE CS
                     Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak..akpelkkiaavlnlDmvgsggkellf 109
                                       A D+ +gva++L+ ++ l +     + +v f+++  EE gl G++      + + + +i++ +  D  g  ++e ++
  gi|320100544|ref|YP_004176136.1| 180 AFDDRVGVAVMLKALESLGE----HQVDVYFVATVQEEVGLKGARTSSYgiSPDVALAIDVTIASDVPGVAKSEWFT 252
                                       8899***************7....589******************99987554488999999999999999999999 PP

                                       .........HHHHHHCHHHHHHHH..HHHHHTT-TTSCCEEEEES.STT-STTHHHH..TTT--EEEECTSSS-TTT CS
                     Peptidase_M28 110 .........esgdkssselekelk..alakpvgraaaedpfders.grgrsDhspfl..kagvpvldlaetgfpevy 172
                                                ++ ++++s+l +  k  +    v+++++  p + ++ + g++D+s+++  k+gv + ++     p++y
  gi|320100544|ref|YP_004176136.1| 253 rlgygpaikVVDGRNASGLIAHPKvvDFLVSVAEKRK-IPYQLDViSGGTTDASIIAlnKEGVAAGTI---SIPSRY 325
                                       8988888774444444444333331133333333322.344444436666888776644666777766...556666 PP

                                       .TST CS
                     Peptidase_M28 173 .Htp 175
                                        H+p
  gi|320100544|ref|YP_004176136.1| 326 iHSP 329
                                       6665 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 !   15.3   0.0   1.8e-06    0.0065     308     431 ..     221     348 ..     206     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-06
                                       HC-EEEEE--EE---TTSGG....GS-TTTS--TTSEEEEEEETTSS...STT-HHHHHHHHHHHHHHC-EEEEEEE CS
                     Peptidase_M18 308 akSlliSaDvahaihPnyss....kheenhapllnkGvvikvnanqr...yatnsagaallkevaqkanvklQelvv 377
                                       + S  iS Dva ai+   +s    + +++ +  l++G+ ikv  +       ++ + +  l +va+k +++ Q  v+
  gi|320100544|ref|YP_004176136.1| 221 TSSYGISPDVALAIDVTIASdvpgVAKSEWFTRLGYGPAIKVVDGRNasgLIAHPKVVDFLVSVAEKRKIPYQLDVI 297
                                       56778888888887765544222267899999*********97765544467777778888999*******998555 PP

                                       -TTS----HCHH..HHHHHHT-EEEEEE-EEBSTTSSSEEEECCHHHHHHHHHHHC CS
                     Peptidase_M18 378 rndspcGstigp..ilaaktGirtiDlGaaqlsmHSireltgskdveeavklfkaF 431
                                            +G+t+ +  i+  k G+    + ++   +HS+ e+++ kd+++a+ l kaF
  gi|320100544|ref|YP_004176136.1| 298 -----SGGTTDAsiIALNKEGVAAGTISIPSRYIHSPVEVVDLKDLYNASLLAKAF 348
                                       .....566655511345699***999****************************99 PP

>> Tudor_2  Jumonji domain-containing protein 2A Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.5e-05     0.054       2      18 ..     101     117 ..     101     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                           Tudor_2   2 qdVivrwtDgryYnakv 18 
                                       q+V+v+ +Dgr+Y++ +
  gi|320100544|ref|YP_004176136.1| 101 QRVVVKTRDGRLYRGVI 117
                                       89************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2505.31
//
Query:       gi|320100545|ref|YP_004176137.1|  [L=698]
Description: alpha amylase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-60  205.7   0.0    2.2e-60  205.0   0.0    1.3  1  Alpha-amylase   Alpha amylase, catalytic domain
    3.2e-07   30.5   0.0    6.4e-06   26.3   0.0    2.7  2  AMPK1_CBM       Glycogen recognition site of AMP-activated pr
     0.0002   21.1   0.2    0.00037   20.2   0.2    1.4  1  Bac_A_amyl_C    Bacterial Alpha amylase C-terminal domain
     0.0061   16.6   0.0      0.012   15.7   0.0    1.4  1  Malt_amylase_C  Maltogenic Amylase, C-terminal domain
  ------ inclusion threshold ------
      0.075   13.4   0.0        8.4    6.8   0.0    2.7  2  CBM_48          Carbohydrate-binding module 48 (Isoamylase N-


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.0   0.0   6.2e-64   2.2e-60       1     337 []     265     583 ..     265     583 .. 0.85

  Alignments for each domain:
  == domain 1  score: 205.0 bits;  conditional E-value: 6.2e-64
                                       --CHHHHCTCCCCCCCT-SCEEE-B-CE-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC- CS
                     Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifkspqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHt 77 
                                       GD++Gii +L+ + +LGv+a++l+Pif++   +h Ydi d+t++d   G ++d+k+L++++h++g+k++lD+   Ht
  gi|320100545|ref|YP_004176137.1| 265 GDIQGIIRRLNHIVGLGVDALYLTPIFQAA-TYHRYDIYDFTSVDRYLGSMDDFKRLVDELHKRGVKLVLDVTLHHT 340
                                       9****************************9.********************************************** PP

                                       -TTSCCCHCCHH.STTSGGGCCC-E...............ESS-STTC-TTTTCSCEECTTTTCEEESSS-TTS-BB CS
                     Alpha-amylase  78 sdehewfkeslk.kkgepkrdyyiwkegk.........eekeppnnwkslfdgsaweydekaqeyylhlflkklpdL 144
                                       s  ++ f ++l+  +g+p+ d+y +ke           +    + + +s + ++a++       y  + +l+++p+L
  gi|320100545|ref|YP_004176137.1| 341 SPCFHAFVKALReGPGSPYWDWYLFKEEPprgllhevlG--YLEGECRSRELEKAMRSRGLEPFYESFFNLWSMPKL 415
                                       **9888877765157889*****9987778888877432..334444455666666666666555567899****** PP

                                       -TTTCCCCCCCCCCCCCCCTTT-SEEEETTCCCTTTCCCCHCCHCCHHHHHHHHHHHTCCGTT-EEEEE-TT-SCCC CS
                     Alpha-amylase 145 nteneevrkelkdvvkfwlekgidGfRlDvvkhvskvealesngeflheftqalnetvasrkevmtvgEvssdased 221
                                       n+en+ev  +  +v ++w ekg+dGfR+Dv+  ++          +l  + + ++ +   r ++ ++gE ++     
  gi|320100545|ref|YP_004176137.1| 416 NHENPEVLDYFMEVTRYWAEKGVDGFRIDVALGIPY--------TWLMLYYKLVKDM---RSDFLLLGELNDYP--A 479
                                       ************************************........9999999999966...6********99833..3 PP

                                       HCCCC-CGG-SICECCITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-C.CCTTCEEES--TTS--HHHHTT CS
                     Alpha-amylase 222 lrvyttearlelemvldfphldvaqkakikeqlksisakklkellkkwlkalee.aaeeavtflgnHDqeRilsrlg 297
                                        ++  +++++++           ++ +++k  ++  s++++   l++ ++++++ +a +    lg HD++R+++++g
  gi|320100545|ref|YP_004176137.1| 480 YYTGYFDSVMDYY------W---RKIVFSKIIDEGLSMEDFIGELNREYSEIPHyKAISLYHSLGTHDTPRVMTYAG 547
                                       4555555555555......2...22333333446668*****************99999999*************** PP

                                       SSTTTTHHHHHHHHHCCCTSSSEEEEETTCCCT----STT CS
                     Alpha-amylase 298 ddsaeaekklklaaillltlrGvpviYyGeEigmtggkdp 337
                                        d      k+kl+ +ll+tl+G p+iYyG+E+gm gg dp
  gi|320100545|ref|YP_004176137.1| 548 GDTG----KVKLLFTLLFTLPGSPAIYYGDEVGMEGGGDP 583
                                       ***5....****************************9987 PP

>> AMPK1_CBM  Glycogen recognition site of AMP-activated protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.8e-09   6.4e-06       4      54 ..      23      74 ..      20      87 .. 0.91
   2 ?    0.5   0.0       0.2   7.2e+02      34      64 ..     132     162 ..     123     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.8e-09
                         AMPK1_CBM  4 vikWkggGkkVyvtGsfnnW.kkkipLkksekdfsvilkLpeGthqykFiVD 54
                                       + W+ g+++Vy+ G f++W   +++L++ +++  ++lkL +G+++y F V+
  gi|320100545|ref|YP_004176137.1| 23 SVPWPSGARRVYLIGVFSGWfPGHLRLRRVGDRGRIVLKLWPGEYHYGFSVN 74
                                      678*****************67899*************************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                         AMPK1_CBM  34 kdfsvilkLpeGthqykFiVDgewrvdpdlp 64 
                                       ++ +v +++p+G  + + iV+ge  ++p  +
  gi|320100545|ref|YP_004176137.1| 132 DTLVVRIRVPRGLDKPRLIVEGEGEYKPAVE 162
                                       56678899***************99998766 PP

>> Bac_A_amyl_C  Bacterial Alpha amylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2     1e-07   0.00037       6      58 ..     627     679 ..     622     686 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1e-07
                                       -GGG-EEEEEEETTEEEEEEE-TT--EEEEE--S-SEEEEETTTSEEEEEETT CS
                      Bac_A_amyl_C   6 deedivvvtYelkekklvGiFsLkgkegevkvdlpDGsYkNlidgseveVkdG 58 
                                        ++d+v +++  k+++++ + +L   e++v+  +p G+Y +l++g+ev V +G
  gi|320100545|ref|YP_004176137.1| 627 IDDDVVLIKRWIKGEEVYVLANLSRGEKTVEPGIPEGVYVDLVSGEEVYVGGG 679
                                       579***********************************************998 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.3e-06     0.012      17      74 ..     635     690 ..     627     691 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.3e-06
                                       EEEETTEEEEEEEESS-EEEEE--GGGTT-EEEETTTTEE-----SSEEEEE-TT-EE CS
                    Malt_amylase_C  17 lReyedetilvvaNrsaqaveldlselagrvpvelfggeefpaigelytltLppygfy 74 
                                        R  ++e ++v+aN s  + +++   + ++v v+l +gee+   g+  +ltL+ ygf+
  gi|320100545|ref|YP_004176137.1| 635 KRWIKGEEVYVLANLSRGEKTVEPG-IPEGVYVDLVSGEEVYVGGG-VKLTLGGYGFR 690
                                       577789********77777777766.77**************9998.5*********7 PP

>> CBM_48  Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0023       8.4      18      74 ..      26      76 ..      19      88 .. 0.79
   2 ?    3.4   0.0     0.027        98      39      74 ..     161     193 ..     148     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0023
                                      E-TTSSEEEEEECGTTTEEECCB-EEECGGCEEEEEEETTSTTTT.EEEEEEEETTS CS
                            CBM_48 18 wapnAekVslvldfnnwdaeeiplkrrrtggvWelflpgdlphgslrYkyrvkgpsg 74
                                      w + A++V l++ f +w    + l+r  + g   ++l+  +p g  +Y y + ++sg
  gi|320100545|ref|YP_004176137.1| 26 WPSGARRVYLIGVFSGWFPGHLRLRRVGDRG--RIVLK-LWP-G--EYHYGFSVNSG 76
                                      8899*********************855555..79999.999.5..56666666665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                                       CB-EEECGGCEEEEEEETTSTTTT.EEEEEEEETT.S CS
                            CBM_48  39 iplkrrrtggvWelflpgdlphgslrYkyrvkgps.g 74 
                                       +++   r+  v+e  l+  ++  s++Ykyr+  ++ g
  gi|320100545|ref|YP_004176137.1| 161 VEYV-FRDAAVYEYHLQ-YIG--SHVYKYRFLIRHqG 193
                                       5555.578999*****9.888..57999999777753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4859.35
//
Query:       gi|320100546|ref|YP_004176138.1|  [L=311]
Description: ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-64  213.3   0.1    1.5e-63  212.5   0.1    1.4  1  AAA_3            ATPase family associated with various cellul
    7.9e-21   73.7   0.0    1.8e-20   72.5   0.0    1.7  1  AAA_lid_2        AAA lid domain
    1.7e-16   60.5   0.0    4.3e-16   59.1   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-06   28.5   0.0    2.5e-06   27.3   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
      2e-06   28.3   0.0    5.6e-06   26.8   0.0    1.8  1  AAA              ATPase family associated with various cellul
    2.4e-05   23.8   0.2       0.11   11.9   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00012   21.3   0.0    0.00021   20.4   0.0    1.4  1  MCM              MCM P-loop domain
    0.00038   20.2   0.0       0.13   12.0   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.096   12.4   0.1       0.55    9.9   0.0    2.1  3  AAA_30           AAA domain
       0.11   12.9   0.0       0.22   12.0   0.0    1.5  1  MCM_lid          MCM AAA-lid domain
       0.15   12.2   0.0       0.29   11.2   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.18   10.9   0.0        0.3   10.2   0.0    1.2  1  Njmu-R1          Mjmu-R1-like protein family


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 !  212.5   0.1   9.9e-67   1.5e-63       1     131 []      36     166 ..      36     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 9.9e-67
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hv++egvPG+akt ++ka+a+ ldlefkr+q+tpdllPsdi+G ++f+ k+  f++++Gp+f+n+lladeinra+p+
  gi|320100546|ref|YP_004176138.1|  36 HVIMEGVPGVAKTYTAKAVARLLDLEFKRVQMTPDLLPSDIVGYSIFDPKTGGFTVRRGPIFTNILLADEINRASPR 112
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       tqsalleam+erqvt+egeth+lpepf+v+at nP+e+eG++plpeaqldrfl+
  gi|320100546|ref|YP_004176138.1| 113 TQSALLEAMQERQVTIEGETHRLPEPFMVIATMNPVEMEGVFPLPEAQLDRFLV 166
                                       ****************************************************95 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   1.2e-23   1.8e-20       2      64 ..     230     293 ..     229     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.2e-23
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaege 64 
                                       +tr h+a++lg s+r a +al+r+A+ lA++egr yV+p+Dvkea+++VL+HRl+  +e e +g 
  gi|320100546|ref|YP_004176138.1| 230 ETRRHPAVRLGGSPR-AGIALVRVAKSLAYMEGRGYVIPDDVKEACKPVLSHRLIlkPEYEVQGL 293
                                       89*************.***************************************6655555554 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 !   59.1   0.0   2.9e-19   4.3e-16       1     138 []      36     164 ..      36     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.9e-19
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +v++ G pG++K+  a+ +a++l  e+  vq+t d+ ++d++g   ++   g+   + +p+        il+ DE++
  gi|320100546|ref|YP_004176138.1|  36 HVIMEGVPGVAKTYTAKAVARLLDLEFKRVQMTPDLLPSDIVGYSIFDpkTGGFTVRRGPIF-----TNILLADEIN 107
                                       79*****************************************8887776788888888888.....79******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra++ ++++Ll  + er++   eg +    ++      f+viat+np++  ++ +l +a ++Rf
  gi|320100546|ref|YP_004176138.1| 108 RASPRTQSALLEAMQERQVT-IEGETHRLPEP------FMVIATMNPVEmEGVFPLPEAQLDRF 164
                                       ********************.55555555666......***********999******999999 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.7e-09   2.5e-06      13     142 ..      25     146 ..      18     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.7e-09
                                       HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHH CS
                   Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlf 89 
                                       + i +++  + +v+++G  G+ K++ a+a+ +  + + k  v++    +p++++  ++F  + G Ft     ++G +
  gi|320100546|ref|YP_004176138.1|  25 RVIVAAMLAKGHVIMEGVPGVAKTYTAKAVARLLDLEFK-RVQMTPDLLPSDIVGYSIFDPKTGGFT----VRRGPI 96 
                                       55667778889*******************998875443.455555677888888888888888887....466766 PP

                                       HHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  90 ekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                             +l+ Dei++ ++++Q+ Ll+++qe++v+  G+++  +  +++ia+ n
  gi|320100546|ref|YP_004176138.1|  97 F---TNILLADEINRASPRTQSALLEAMQERQVTIEGETHRLPEPFMVIATMN 146
                                       5...469***********************************99999998776 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 !   26.8   0.0   3.8e-09   5.6e-06       1     129 [.      37     169 ..      37     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.8e-09
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                       v++ G pG+ KT++akava+ l+ ef ++++ ++ll s++vg s  + +    ++++    + il+ DEi +  ++ 
  gi|320100546|ref|YP_004176138.1|  37 VIMEGVPGVAKTYTAKAVARLLDLEFKRVQMtPDLLpSDIVGYSIFDPKTGGFTVRRGPiFTNILLADEINRASPRT 113
                                       5789**********************9998736888889999887666655445555555459**********9998 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEE CS
                               AAA  75 sgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkie 129
                                                  +++Ll+++++ +           ++++vi++ n      +  l++a l +Rf +++e
  gi|320100546|ref|YP_004176138.1| 114 -----------QSALLEAMQERQVTiegethrlPEPFMVIATMNPvemegVFPLPEAQL-DRFLVRVE 169
                                       ...........***********99999999999777*****999844333334666777.77777766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00033       0.5      11      46 ..      23      58 ..      15      68 .. 0.81
   2 !   11.9   0.0   7.2e-05      0.11     108     159 ..      99     148 ..      86     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00033
                      Mg_chelatase 11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsll 46
                                        r++  a   + ++++ G pG  Kt  ak+++ ll
  gi|320100546|ref|YP_004176138.1| 23 ELRVIVAAMLAKGHVIMEGVPGVAKTYTAKAVARLL 58
                                      45566666778889*****************99998 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.2e-05
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                        +L+ DE+   + ++  +L e +++++vti+  ++  + p  f+++a+mNp 
  gi|320100546|ref|YP_004176138.1|  99 NILLADEINRASPRTQSALLEAMQERQVTIEGETH--RLPEPFMVIATMNPV 148
                                       58999*************************97766..56999*********7 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.4e-07   0.00021      56     174 ..      33     148 ..      19     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-07
                                       SS-EEEEEESSTSTHHHHHHHHHHHSSSEEEE..ESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESG CS
                               MCM  56 gdinvllvgdpgtaKsqlLkyveklapravyt..sgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDef 130
                                       ++ +v++ g pg+aK+   k+v++l++              ++++ +   d++tg f++  G + +    +++ De+
  gi|320100546|ref|YP_004176138.1|  33 AKGHVIMEGVPGVAKTYTAKAVARLLDLEFKRvqMTPDLLPSDIVGYSIFDPKTGGFTVRRGPIFTN---ILLADEI 106
                                       6779*******************998766543003344567899999999*************9865...9****** PP

                                       GGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                               MCM 131 dkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                       ++ + +++sal+Eam + +++i   G +  L+    v+a +np+
  gi|320100546|ref|YP_004176138.1| 107 NRASPRTQSALLEAMQERQVTIE--GETHRLPEPFMVIATMNPV 148
                                       **********************8..5569999999999999997 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   8.9e-05      0.13      32      63 ..      33      64 ..      18      80 .. 0.80
   2 !    6.0   0.0    0.0063       9.4      86     115 ..      99     128 ..      93     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-05
                            RuvB_N 32 aldhvllyGpPGlGkttlakiiakelgvklki 63
                                      a  hv++ G PG+ kt  ak +a+ l+ ++k 
  gi|320100546|ref|YP_004176138.1| 33 AKGHVIMEGVPGVAKTYTAKAVARLLDLEFKR 64
                                      456*********************99999875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0063
                            RuvB_N  86 dvlfideihrlsraveevlysamedfrldi 115
                                       ++l+ dei r s+ ++  l  am++ ++ i
  gi|320100546|ref|YP_004176138.1|  99 NILLADEINRASPRTQSALLEAMQERQVTI 128
                                       79999******************9998876 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   0.00037      0.55      10      48 ..      28      64 ..      22      69 .. 0.82
   2 ?   -0.9   0.0      0.78   1.2e+03      91     118 ..     100     127 ..      95     136 .. 0.80
   3 ?   -4.0   0.0       6.6   9.8e+03      96     114 ..     169     187 ..     161     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                            AAA_30 10 vealltsgdrvavltGpAGtGKttalkalreaweaaggr 48
                                      v+a+l++g+  ++++G++G  Kt++ ka++++++ + +r
  gi|320100546|ref|YP_004176138.1| 28 VAAMLAKGH--VIMEGVPGVAKTYTAKAVARLLDLEFKR 64
                                      667778885..9*****************9998766555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.78
                            AAA_30  91 llivDEagmvdtkqlaallkaaekagak 118
                                       +l+ DE+  ++ ++  all+a+++++++
  gi|320100546|ref|YP_004176138.1| 100 ILLADEINRASPRTQSALLEAMQERQVT 127
                                       6778999999999999999999986544 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 6.6
                            AAA_30  96 Eagmvdtkqlaallkaaek 114
                                       Eag ++ + l ++lk+ae+
  gi|320100546|ref|YP_004176138.1| 169 EAGYTSHEGLVKILKRAEE 187
                                       8888899999999998876 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.22      50      81 ..     244     275 ..     224     280 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                           MCM_lid  50 RqLesliRLseAlAklrlsevvteedveeair 81 
                                       R+  +l+R++++lA ++ + +v ++dv+ea++
  gi|320100546|ref|YP_004176138.1| 244 RAGIALVRVAKSLAYMEGRGYVIPDDVKEACK 275
                                       56669*************************86 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.29       3      84 ..      34     114 ..      32     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                       ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.....EEEE CS
                             AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.....ivll 74 
                                       ++ +++ g  gv kt++aka+a+ll++    ++ r+ ++  l     + +v   i  p+       +G     i+l 
  gi|320100546|ref|YP_004176138.1|  34 KGHVIMEGVPGVAKTYTAKAVARLLDL----EFKRVQMTPDLL---PSDIVGYSIFDPKTGGFTVRRGpiftnILLA 103
                                       567889999*****************8....********8877...577777777777777666777789999**** PP

                                       ETGGG----.- CS
                             AAA_2  75 DEidKihpk.e 84 
                                       DEi +++p+ +
  gi|320100546|ref|YP_004176138.1| 104 DEINRASPRtQ 114
                                       *****999542 PP

>> Njmu-R1  Mjmu-R1-like protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002       0.3      40      74 ..      11      46 ..       6      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                           Njmu-R1 40 lvdtnlPseaepelrsyiakrlskGal.leGlGnva 74
                                      lvd +l  e e elr ++a  l+kG + +eG+  va
  gi|320100546|ref|YP_004176138.1| 11 LVDGELLIERERELRVIVAAMLAKGHViMEGVPGVA 46
                                      9************************86268876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2225.89
//
Query:       gi|320100547|ref|YP_004176139.1|  [L=357]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   33.4   0.9    1.7e-07   31.4   0.7    2.2  2  DUF4129   Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
      0.027   14.4   0.0      0.047   13.7   0.0    1.4  1  NICE-3    NICE-3 protein


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.3   1.2e+04       3      17 ..     107     122 ..     106     145 .. 0.61
   2 !   31.4   0.7   1.9e-11   1.7e-07       6      67 ..     286     350 ..     281     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.3
                           DUF4129   3 rallraLaer.gldrr 17 
                                       rall+ L ++  l + 
  gi|320100547|ref|YP_004176139.1| 107 RALLQGLLDKgSLSPD 122
                                       7777777777444444 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.9e-11
                           DUF4129   6 lraLaer.gldrrpgeTprEyarrv..riapspaaalaalaelfeearYGgrpasaeeyrrlvea 67 
                                       +++   r    +  +eTprEy+ rv  + +p+ a  l++++ l+ee r+G+  ++ e     +e+
  gi|320100547|ref|YP_004176139.1| 286 VALVGWRyRAAKMLHETPREYLSRVkgALPPDVAGLLREVTVLYEECRFGHASVDKESIGKYREL 350
                                       555555545555567***********999999***********************9965554444 PP

>> NICE-3  NICE-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.2e-06     0.047     123     179 ..     299     354 ..     287     356 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-06
                            NICE-3 123 pgenlrsyLlrlrssplksvrkslidqlldlyehARhgpeeFgeeeylkyqelleeL 179
                                        +e  r+yL r++ ++l+     l+ ++  lye++R+g+ + ++e   ky+el+++L
  gi|320100547|ref|YP_004176139.1| 299 LHETPREYLSRVK-GALPPDVAGLLREVTVLYEECRFGHASVDKESIGKYRELVRRL 354
                                       478889******9.888888899******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2572.56
//
Query:       gi|320100548|ref|YP_004176140.1|  [L=379]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   15.0   0.4       0.02   15.0   0.4    3.7  4  Osw5      Outer spore wall 5


Domain annotation for each model (and alignments):
>> Osw5  Outer spore wall 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.8     0.091   1.6e+03      16      36 ..      46      64 ..      31      85 .. 0.72
   2 ?   -4.0   0.5      0.94   1.7e+04       8      21 ..     136     149 ..     128     151 .. 0.58
   3 ?    0.4   0.2      0.04   7.1e+02      11      37 ..     259     288 ..     251     297 .. 0.67
   4 ?   15.0   0.4   1.1e-06      0.02      18      38 ..     309     329 ..     306     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.091
                              Osw5 16 viaslfilPLLgiSfifatgv 36
                                      ++as  +l LL + +++atg 
  gi|320100548|ref|YP_004176140.1| 46 AAAS--LLTLLLAGLVLATGS 64
                                      4444..456888889999875 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 0.94
                              Osw5   8 lvlFliigviaslf 21 
                                       l++ l +++++ +f
  gi|320100548|ref|YP_004176140.1| 136 LTIALTLAFFSGAF 149
                                       44445555555555 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.04
                              Osw5  11 Fliigviasl...filPLLgiSfifatgvv 37 
                                       +l+ ++++s    +++ +L+ S+ fa+   
  gi|320100548|ref|YP_004176140.1| 259 WLSKATASSWymgLLVDFLTGSLAFAISAA 288
                                       555566666522246889*******98765 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 1.1e-06
                              Osw5  18 aslfilPLLgiSfifatgvvv 38 
                                       +sl+i PLL++ fi+at vv+
  gi|320100548|ref|YP_004176140.1| 309 SSLIIKPLLVLAFIYATSVVL 329
                                       8******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2748.72
//
Query:       gi|320100549|ref|YP_004176141.1|  [L=89]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.16   12.3   4.3        0.2   12.0   4.3    1.1  1  Papilloma_E5A  Papillomavirus E5A protein
        5.5    7.3   8.5         10    6.4   4.7    2.0  2  DUF423         Protein of unknown function (DUF423)


Domain annotation for each model (and alignments):
>> Papilloma_E5A  Papillomavirus E5A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.3   2.2e-05       0.2      18      70 ..      15      68 ..       8      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                     Papilloma_E5A 18 lplvialtvclvsivliili.seflvytsvlvltlllylllwlllttalqfyll 70
                                      +pl++al v ++s  ++ili s   + ++++ l+ll  l+ + ll+++l +  l
  gi|320100549|ref|YP_004176141.1| 15 FPLLLALGVAVLSASIVILIlSLGYMGSAMVGLSLLAALIGFSLLSASLYILRL 68
                                      7***********986666551555666777789999999999999998855444 PP

>> DUF423  Protein of unknown function (DUF423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.9    0.0046        41      56      75 ..      17      36 ..       5      42 .. 0.83
   2 ?    6.4   4.7    0.0012        10      34      75 ..      31      69 ..      28      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0046
                            DUF423 56 llflaGivlFSgslyllalt 75
                                      ll+++G+++ S s+++l l+
  gi|320100549|ref|YP_004176141.1| 17 LLLALGVAVLSASIVILILS 36
                                      68899***********9984 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0012
                            DUF423 34 allavallaskaaasrllklagllflaGivlFSgslyllalt 75
                                      ++l+++l     + s ++ l+ l+ l+G  l S sly+l l 
  gi|320100549|ref|YP_004176141.1| 31 VILILSL---GYMGSAMVGLSLLAALIGFSLLSASLYILRLA 69
                                      4444444...35678999999*****************9884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 681.71
//
Query:       gi|320100550|ref|YP_004176142.1|  [L=512]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0047   16.9   0.1      0.092   12.7   0.0    2.2  2  Mor       Mor transcription activator family


Domain annotation for each model (and alignments):
>> Mor  Mor transcription activator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.1e-06     0.092      21      73 ..     351     402 ..     341     409 .. 0.87
   2 ?    1.5   0.1     0.016   2.8e+02      75      92 ..     479     496 ..     476     508 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.1e-06
                                       TS.S-....TTSHHHHHHHHHHHH-SS------SHHHHHHHHHHHHHHH--SS CS
                               Mor  21 lgeidealaeqigeevadalaahwGGqqiyiPrgvklelelrdreifnefkGn 73 
                                       l  ++ a a+ ++  +a a+ +h+ G++++ P +   e+ +rd ++f++ +G+
  gi|320100550|ref|YP_004176142.1| 351 LL-LNPAAATAASLIAALAVYKHLSGREVFAPDEALREQVERDISVFESTRGK 402
                                       55.7788999999999********************************99986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.016
                                       HHHHHHHHT--HHHHHHH CS
                               Mor  75 vaeLarkYglseqwiyki 92 
                                       ++e++r Yg++e+ i   
  gi|320100550|ref|YP_004176142.1| 479 HRETSRAYGMTEKMITAL 496
                                       7899*********99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3406.27
//
Query:       gi|320100551|ref|YP_004176143.1|  [L=438]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-18   64.6   0.1    1.4e-17   63.7   0.1    1.5  1  DUF58     Protein of unknown function DUF58
  ------ inclusion threshold ------
       0.01   15.2   0.2      0.016   14.6   0.2    1.4  1  VWA_CoxE  VWA domain containing CoxE-like protein


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.1   1.6e-21   1.4e-17       1      85 [.     192     276 ..     192     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.6e-21
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarql 77 
                                       g++f+++R+Y pgD+++rI W+++A +++l v e e+e  ++v+++ld+++em +g  g++ +e++++++asl+ +l
  gi|320100551|ref|YP_004176143.1| 192 GVEFYDVRDYFPGDEMKRIVWRVYASRRTLAVWEPEREVYQPVVFILDATREMWSGPFGQSMVEHSARITASLIHYL 268
                                       689************************************************************************** PP

                             DUF58  78 ldegdrvg 85 
                                        ++g++v+
  gi|320100551|ref|YP_004176143.1| 269 TRRGYPVS 276
                                       ******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 ?   14.6   0.2   1.7e-06     0.016      53     189 ..     228     375 ..     212     423 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-06
                          VWA_CoxE  53 rerkprelvllvDv.....Sg....Smaays.aiflallhAllqqlprtevfaFdtrlvdlTral..rerDpaeaLa 117
                                       re+ + ++v+++D      Sg    Sm ++s +i+++l+h l+++ + +++++F+ ++++ +       r   e+L+
  gi|320100551|ref|YP_004176143.1| 228 REVYQ-PVVFILDAtremwSGpfgqSMVEHSaRITASLIHYLTRRGYPVSTVVFNESVTHASGRPihGYRGYMESLR 303
                                       55555.666666652222232444499999846999*************************977534569******* PP

                          VWA_CoxE 118 rvsaavedlgGgTrigaalaeflelvtrpaLsr.ravvvlvsDglergdreellaelarlvrrarrlvwlnpl 189
                                        +s+a+  ++G+ +  +a+ ++l+    + L r r++v l++ + +++    +++  +  ++r++ l ++ pl
  gi|320100551|ref|YP_004176143.1| 304 TISRARLSWEGTLQRRSAVSSVLSYTYERILPRdRSIVFLFTHL-DEDVLGDVASWNSIYSARGHVLYIVHPL 375
                                       ***99999****99999999999999988886537777777765.6666666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3297.37
//
Query:       gi|320100552|ref|YP_004176144.1|  [L=105]
Description: rubrerythrin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-10   40.6   0.2    3.7e-10   40.3   0.2    1.1  1  Rubrerythrin  Rubrerythrin
    0.00042   20.6   0.1    0.00049   20.4   0.1    1.2  1  DUF2383       Domain of unknown function (DUF2383)
     0.0025   17.8   0.0     0.0029   17.6   0.0    1.1  1  Ferritin      Ferritin-like domain
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.013   15.3   0.0    1.1  1  COQ7          Ubiquinone biosynthesis protein COQ7
      0.022   14.9   0.6       0.51   10.5   0.6    2.3  1  Sigma70_r3    Sigma-70 region 3
       0.03   14.3   0.2      0.035   14.1   0.2    1.1  1  DUF892        Domain of unknown function (DUF892)
      0.031   13.9   0.0       0.04   13.5   0.0    1.1  1  DUF3231       Protein of unknown function (DUF3231)
      0.041   13.7   0.0      0.049   13.5   0.0    1.2  1  DUF2202       Uncharacterized protein domain (DUF2202)
       0.22   11.2   3.3         10    5.9   0.0    3.0  3  NepR          Anti-sigma factor NepR


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 !   40.3   0.2   1.9e-13   3.7e-10       1      61 [.      22      80 ..      22     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.9e-13
                                      HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH CS
                      Rubrerythrin  1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele 61
                                      e L  +i++E +a +lY  la+ ++   ++++++Fe++A eE+ H + +  lle+l+pe+ 
  gi|320100552|ref|YP_004176144.1| 22 EALRLSIIAELDAVNLYLQLARSID--DENVRKVFEDVANEEKTHIGEFLALLEALDPEQS 80
                                      7899*********************..9999**************************9987 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.5e-07   0.00049       4      63 ..      22      81 ..      19      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.5e-07
                                      HHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----- CS
                           DUF2383  4 eaLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralggeped 63
                                      eaL   i ++ d+++ y + a+ ++d+++++++e++a+e + ++ e+ + ++al  e  +
  gi|320100552|ref|YP_004176144.1| 22 EALRLSIIAELDAVNLYLQLARSIDDENVRKVFEDVANEEKTHIGEFLALLEALDPEQSK 81
                                      55666677889************************************9999988766655 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06    0.0029       2      59 ..      22      76 ..      21      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                          Ferritin  2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalG 59
                                      +aL+  + +el+a ++yl++a+ +++++ +++   f++ a ee +h+ +++  + al+
  gi|320100552|ref|YP_004176144.1| 22 EALRLSIIAELDAVNLYLQLARSIDDENVRKV---FEDVANEEKTHIGEFLALLEALD 76
                                      567777889*****************998888...**************999988887 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   6.4e-06     0.013       2      59 ..      20      75 ..      19      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.4e-06
                              COQ7  2 ldrllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellker 59
                                      ++++lR     El Av +Y   +  +  +d+++++++++++++Ek H+  f +ll+  
  gi|320100552|ref|YP_004176144.1| 20 IAEALRLSIIAELDAVNLYLQLARSI--DDENVRKVFEDVANEEKTHIGEFLALLEAL 75
                                      6899***************9888875..888999**************9999998765 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   0.00026      0.51      18      76 ..      12      79 ..       7      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                      SSXXXHHHHHHHHTXX....HHHHHHHHHHHXX.....XEETTXBSSSSTTXBSTTTXBXSSSXXHHH CS
                        Sigma70_r3 18 grePtpeEiAeeLgls....eekVrevleaare.....pvSldlpvgeeedtelgdlleddeaespee 76
                                      gr  t eEiAe+L ls    ++ V  +l++ar+     ++ +  +v +ee t++g++l+  ea +pe+
  gi|320100552|ref|YP_004176144.1| 12 GRKLTREEIAEALRLSiiaeLDAVNLYLQLARSiddenVRKVFEDVANEEKTHIGEFLALLEALDPEQ 79
                                      6777999******9984333588888888887522222566666888899999999999888888886 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.8e-05     0.035       8      74 ..      22      88 ..      16     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHH CS
                            DUF892  8 deLrDlyaaEkqllkalpkmakaaespeLkaaleqHleeTegqierLeqvferlgesasekkcdame 74
                                      ++Lr    aE  ++++  ++a++++++++++ +e+  +e +++i +   ++e+l+ ++s++  ++++
  gi|320100552|ref|YP_004176144.1| 22 EALRLSIIAELDAVNLYLQLARSIDDENVRKVFEDVANEEKTHIGEFLALLEALDPEQSKRLGEGAS 88
                                      567777889*********************************************9998887655544 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     2e-05      0.04       7      70 ..       9      73 ..       5      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                           DUF3231  7 lgkkrpLtasEias.lwssyianslgialitgFlqvaedkeikelleralelsnkhikelkelLk 70
                                      l+  r+Lt  Eia+ l  s+ia+  +  l+ + + +++d+++++++e + +  + hi e+  lL+
  gi|320100552|ref|YP_004176144.1|  9 LQPGRKLTREEIAEaLRLSIIAELDAVNLYLQLARSIDDENVRKVFEDVANEEKTHIGEFLALLE 73
                                      567799******96477899*****************************9999999999988886 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.5e-05     0.049      88     142 ..      22      76 ..      13      95 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                           DUF2202  88 daLkvgatiedldiaDl.ekalketdnkdikevYenllkGsrnhlRsfvrkleerg 142
                                       +aL+ ++ i +ld  +l  ++ ++ d++++ +v+e + +  + h+  f+  le  +
  gi|320100552|ref|YP_004176144.1|  22 EALRLSI-IAELDAVNLyLQLARSIDDENVRKVFEDVANEEKTHIGEFLALLEALD 76 
                                       5555543.445666665445555666666666666666666666666665555443 PP

>> NepR  Anti-sigma factor NepR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.75   1.5e+03       2       9 ..      18      25 ..      17      27 .. 0.85
   2 ?    5.9   0.0     0.005        10       5      19 ..      47      61 ..      47      61 .. 0.92
   3 ?    4.5   0.3     0.013        26      23      32 ..      67      76 ..      67      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.75
                              NepR  2 aqIgrnLR 9 
                                      ++I++ LR
  gi|320100552|ref|YP_004176144.1| 18 EEIAEALR 25
                                      79***999 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.005
                              NepR  5 grnLRrlYddvvdEp 19
                                      ++n R +++dv++E+
  gi|320100552|ref|YP_004176144.1| 47 DENVRKVFEDVANEE 61
                                      7999*********96 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.013
                              NepR 23 rFldLLeqLd 32
                                      +Fl+LLe Ld
  gi|320100552|ref|YP_004176144.1| 67 EFLALLEALD 76
                                      5********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 763.22
//
Query:       gi|320100553|ref|YP_004176145.1|  [L=164]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-07   30.2   4.1    3.3e-06   27.5   4.1    1.9  1  Rubrerythrin     Rubrerythrin
  ------ inclusion threshold ------
      0.013   15.3   5.1       0.47   10.2   3.6    2.7  3  COQ7             Ubiquinone biosynthesis protein COQ7
      0.014   14.2   0.3        1.5    7.6   0.0    2.1  2  FA_desaturase_2  Fatty acid desaturase
      0.033   14.5   0.6       0.18   12.1   0.6    2.2  1  FCH              Fes/CIP4, and EFC/F-BAR homology domain
       0.05   13.8   0.2        0.1   12.8   0.2    1.5  1  Ferritin_2       Ferritin-like domain
      0.069   13.7   0.6        0.1   13.1   0.6    1.3  1  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.081   13.2   0.0        6.7    7.0   0.0    2.3  2  Coat_F           Coat F domain
       0.12   12.4   0.2       0.22   11.5   0.2    1.5  1  DUF1043          Protein of unknown function (DUF1043)


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 !   27.5   4.1   1.5e-09   3.3e-06       8     133 ..      21     130 ..      16     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHH CS
                      Rubrerythrin   8 agEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttakn 84 
                                       ++E++  r+  +l e +k   p +++lF+ +A++ ++Ha i  ++l +l  + +           + ++++l++ k 
  gi|320100553|ref|YP_004176145.1|  21 RIEEDYARRLSNLGESLK--HPVLRALFKSIARDSEKHAMIY-RALADLLTSPQ----------PFITEDELERVK- 83 
                                       6799999999********..******************9765.55556555555..........244444444333. PP

                                       HHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  85 LeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerl 133
                                         + +   ++ e+em r+ ee+++ ++++++k l++++ ++E +H  +l
  gi|320100553|ref|YP_004176145.1|  84 --AEVSHHIETEKEMLRTVEEMLKTVEDPRVKLLLAAIRDDEAEHHALL 130
                                       ..3346788899*********************************9876 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.055   1.2e+02      99     138 ..      21      58 ..      19      63 .. 0.86
   2 ?    6.8   0.3    0.0023       5.2      19      58 ..      67     106 ..      59     110 .. 0.82
   3 ?   10.2   3.6   0.00021      0.47      95     143 ..      81     133 ..      79     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.055
                              COQ7  99 vigeHYneqlreleeleeeedkelleiikqfrddEleHld 138
                                        i+e Y+++l +l e    +++ l+++ k++  d  +H+ 
  gi|320100553|ref|YP_004176145.1|  21 RIEEDYARRLSNLGES--LKHPVLRALFKSIARDSEKHAM 58 
                                       59999********964..7999999999999999999975 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0023
                              COQ7  19 iYkgqlavlakkdpelkpllkemleqEkeHlatfeellke 58 
                                       + + q ++ + + +++k+ ++++ e+Eke l+t+ee+lk+
  gi|320100553|ref|YP_004176145.1|  67 LTSPQPFITEDELERVKAEVSHHIETEKEMLRTVEEMLKT 106
                                       55566677777788899*******************9986 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00021
                              COQ7  95 avEtvigeHYneqlreleelee....eedkelleiikqfrddEleHldtAven 143
                                        v  ++++H +   + l+++ee     ed++++ +++ +rddE+eH+   v+ 
  gi|320100553|ref|YP_004176145.1|  81 RVKAEVSHHIETEKEMLRTVEEmlktVEDPRVKLLLAAIRDDEAEHHALLVSI 133
                                       567788899988777777666677788999****************9876655 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00067       1.5     173     207 ..      31      65 ..      27      72 .. 0.82
   2 ?    4.5   0.1    0.0056        13     174     211 ..     102     139 ..      94     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00067
                   FA_desaturase_2 173 aklakeagdellakicgaiaadEkrHeaaYtrvve 207
                                       ++l ++ + ++l  + + ia d ++H++ Y+++ +
  gi|320100553|ref|YP_004176145.1|  31 SNLGESLKHPVLRALFKSIARDSEKHAMIYRALAD 65 
                                       55666778899*******************98866 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0056
                   FA_desaturase_2 174 klakeagdellakicgaiaadEkrHeaaYtrvveklle 211
                                       ++ k+ +d+ ++ +++ai  dE+ H+a   ++ ek+  
  gi|320100553|ref|YP_004176145.1| 102 EMLKTVEDPRVKLLLAAIRDDEAEHHALLVSIREKIAS 139
                                       5668899*******************999999888765 PP

>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   8.2e-05      0.18      26      48 ..      19      51 ..      16     109 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                                      HHHHHHHHHHHHHHHCT----T..........T CS
                               FCH 26 RaeiEkeYakkLqkLakkylkr..........r 48
                                       + iE++Ya++L++L ++ ++           r
  gi|320100553|ref|YP_004176145.1| 19 YSRIEEDYARRLSNLGESLKHPvlralfksiaR 51
                                      578*************99999544333333332 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   4.6e-05       0.1      32     132 ..      35     132 ..      14     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                        Ferritin_2  32 kalldaevrevaeeiakheeaHveflkaaleGaaavakptfdfafdpfadeksflalaavlEdvgvsAYlgaaplls 108
                                       ++l  +  r+++++ia + e+H+ + +a      + ++p ++   d++++ k+ +      E+  ++      + ++
  gi|320100553|ref|YP_004176145.1|  35 ESLKHPVLRALFKSIARDSEKHAMIYRALAD-LLTSPQPFITE--DELERVKAEVSHHIETEKEMLRTVEEMLKTVE 108
                                       4566677799************988888763.33345666666..99**999999999999**************** PP

                        Ferritin_2 109 nkelltaaasIlsvEArHaavirt 132
                                       ++ ++ + a I  +EA+H a++ +
  gi|320100553|ref|YP_004176145.1| 109 DPRVKLLLAAIRDDEAEHHALLVS 132
                                       ********************9865 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 ?   13.1   0.6   4.6e-05       0.1      16      96 ..      55     138 ..      42     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                      Syntaxin-6_N  16 kaeslyrrwerlledtss.stseeldetrteLrkalrsiewdledLeetvriveknpsk..fkidekelsrrrafve 89 
                                       k + +yr   +ll++++   t++el++ + e+   +++ ++ l+  ee  ++ve  + k       ++ ++++a+++
  gi|320100553|ref|YP_004176145.1|  55 KHAMIYRALADLLTSPQPfITEDELERVKAEVSHHIETEKEMLRTVEEMLKTVEDPRVKllLAAIRDDEAEHHALLV 131
                                       556677888888888777658*********************************98877443333455667777888 PP

                      Syntaxin-6_N  90 evreevk 96 
                                       ++re++ 
  gi|320100553|ref|YP_004176145.1| 132 SIREKIA 138
                                       8888875 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.033        75      28      47 ..      38      57 ..      36      60 .. 0.90
   2 ?    7.0   0.0     0.003       6.7      11      48 ..      91     128 ..      86     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.033
                            Coat_F 28 snpelRqtlkqilneeiemq 47
                                       +p lR+ +k+i+ + ++++
  gi|320100553|ref|YP_004176145.1| 38 KHPVLRALFKSIARDSEKHA 57
                                      59***********9999876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.003
                            Coat_F  11 steKsaarnyataitEasnpelRqtlkqilneeiemqe 48 
                                        teK + r+   ++    +p ++  l +i+++e e++ 
  gi|320100553|ref|YP_004176145.1|  91 ETEKEMLRTVEEMLKTVEDPRVKLLLAAIRDDEAEHHA 128
                                       79**********************************95 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   9.8e-05      0.22      37      68 ..      76     107 ..      74     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.8e-05
                           DUF1043  37 kaeleeqkqeledHfaqsaelLetlaedyqkL 68 
                                       ++ele+ k+e+++H+++ +e+L+t +e  +++
  gi|320100553|ref|YP_004176145.1|  76 EDELERVKAEVSHHIETEKEMLRTVEEMLKTV 107
                                       689*********************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1345  (0.0750181); expected 358.6 (0.02)
Passed bias filter:                      909  (0.0507); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1173.08
//
Query:       gi|320100554|ref|YP_004176146.1|  [L=405]
Description: flavodoxin/nitric oxide synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-08   32.8   1.1    1.3e-07   31.9   1.1    1.4  1  Lactamase_B   Metallo-beta-lactamase superfamily
    0.00078   19.2   0.0      0.048   13.4   0.0    2.2  2  FMN_red       NADPH-dependent FMN reductase
      0.004   16.9   0.4       0.12   12.0   0.2    2.0  2  Peripla_BP_6  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   1.1   2.1e-11   1.3e-07       6     154 ..      44     177 ..      40     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.1e-11
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                        nsy+++g +g++++Dt + + ++  +le  +  ++p+dv+++++ H+ +DH G+l+ lv ++d  v  +++++ + 
  gi|320100554|ref|YP_004176146.1|  44 YNSYVLTGSEGAVVFDT-WKGKWSGVFLEALRGIVDPRDVKYLVVHHMEPDHSGALRQLVGEADPIVLGHPLTKGMI 119
                                       69***************.6777777777788999******************************************* PP

                                       HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTT.STSCCEEEEEETTCCEEEECTTTSS CS
                       Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggp.ghghghgvveygggkvlftGDalla 154
                                       + +++ + +                 +  +++  ++g+++l+++++p +h +  +  +  g++ l++ Da+ a
  gi|320100554|ref|YP_004176146.1| 120 ESFYGLTPRF---------------KPVGDGERVTLGDVDLVFHHTPwLHWPETIMTYVAGEGALLSCDAFGA 177
                                       *****66544...............788888889999999999999878889999999999999999999876 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0     0.009        54      38      86 ..      78     118 ..      65     121 .. 0.80
   2 !   13.4   0.0     8e-06     0.048      61     139 ..     306     382 ..     277     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.009
                                       ETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTC CS
                           FMN_red  38 dladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngs 86 
                                       d +d  +   l++ +      ++d+  +l++ + +ad ++++ P  +g+
  gi|320100554|ref|YP_004176146.1|  78 DPRDV-KY--LVVHHM-----EPDHSGALRQLVGEADPIVLGHPLTKGM 118
                                       44553.44..777566.....89*********************88876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8e-06
                                       HHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH. CS
                           FMN_red  61 ddvaellekiaaadaliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvla. 136
                                        d+ +++    +a+ ++++t +Y++ + +l+ ++  ++ r   k +   K ++++ +g g r g+++ee lr++   
  gi|320100554|ref|YP_004176146.1| 306 VDLSDVISEAYDAESIVFATATYEADVHPLMRHVASVIAR---KTPGGRKTAVIAIYGWGGRAGRVMEELLRNAGFn 379
                                       567788888899**************************85...999999***********************99884 PP

                                       HTT CS
                           FMN_red 137 elg 139
                                       ++g
  gi|320100554|ref|YP_004176146.1| 380 VVG 382
                                       444 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1   0.00087       5.2     134     211 ..     259     340 ..     247     342 .. 0.83
   2 !   12.0   0.2   2.1e-05      0.12     112     175 ..     322     389 ..     314     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00087
                                       T....SCEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHH CS
                      Peripla_BP_6 134 g....gkkvalvyadyafgregiaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaal 206
                                       g    gk++ + ++ y f   +++ ++++++++G  +v   +++ g  d+s ++ ++ +a   +  +a++ ad+  l
  gi|320100554|ref|YP_004176146.1| 259 GlpeqGKTLLVYTSMYGFVERIVEVVRDYFASKGRRLVVAGFTDGGRVDLSDVISEAYDAESIVFATATYEADVHPL 335
                                       344447888888888*********************66689999999***********9999999999999999998 PP

                                       HHHHH CS
                      Peripla_BP_6 207 lkaaa 211
                                       ++ +a
  gi|320100554|ref|YP_004176146.1| 336 MRHVA 340
                                       88766 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.1e-05
                                       EESS--HHHHHHHHHHHHHH.....HTTSCEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TT CS
                      Peripla_BP_6 112 fslgpsysaqasalveylak.....elggkkvalvyadyafgregiaalkaaakaaGgevvgeepvplg 175
                                       + ++++y a++  l++++a+     + gg+k a+++  y +g  + + ++++++ aG++vvg +++++g
  gi|320100554|ref|YP_004176146.1| 322 VFATATYEADVHPLMRHVASviarkTPGGRKTAVIA-IYGWGGRAGRVMEELLRNAGFNVVGVVEFKAG 389
                                       56789999*********8854443367899999886.5889999******************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2889.78
//
Query:       gi|320100555|ref|YP_004176147.1|  [L=235]
Description: 1-Cys peroxiredoxin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-32  112.2   0.0    1.9e-32  111.8   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
    1.6e-16   60.3   0.0    2.2e-16   59.9   0.0    1.1  1  Redoxin     Redoxin
      6e-11   42.0   0.0    1.3e-10   41.0   0.0    1.5  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
      0.023   14.8   0.0      0.029   14.5   0.0    1.3  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
       0.03   15.0   0.1      0.071   13.8   0.1    1.7  1  Sel1        Sel1 repeat
       0.19   12.0   0.0        0.4   11.0   0.0    1.5  1  DUF4368     Domain of unknown function (DUF4368)


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.0   6.4e-36   1.9e-32       1     123 [.       8     137 ..       8     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 6.4e-36
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       +g+++p++e+ +++g+++  +dykgk++vlf +p+d++pvCtte  a+a++ye+fk+++ e++g+svds +sh k++
  gi|320100555|ref|YP_004176147.1|   8 IGEPFPQMEVMTTHGKKKLPDDYKGKYLVLFSHPADFTPVCTTEFVAFARRYEDFKKLNTELLGLSVDSTFSHIKWV 84 
                                       799***********988888********************************************************* PP

                                       HH-H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekes......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                       e ++      ++fp+++D++g+v++++g l+ + ++ ++ra++++d +g++r+
  gi|320100555|ref|YP_004176147.1|  85 EWIQeklgveIPFPIIADPNGEVSRKLGFLHAQsATSTVRAVVIVDGNGIVRA 137
                                       ******************************9999999**************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   7.2e-20   2.2e-16       3     145 ..       9     151 ..       7     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 7.2e-20
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.... CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.... 75 
                                       g+++P  +   ++t+g++   +++kgk +v+++ p+ f+P+C++e ++++  +e +k+ + + +++++d+       
  gi|320100555|ref|YP_004176147.1|   9 GEPFPQMEV--MTTHGKKKLPDDYKGKYLVLFSHPADFTPVCTTEFVAFARRYEDFKKLNTELLGLSVDSTFShikw 83 
                                       889999997..679999999999************************888887888**********99998877775 PP

                                       HHHHHHH..TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                           Redoxin  76 vkefwgk..eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepeteesnaea 145
                                       v    +k   +++fp+++D++++++++lG  +  ++s++   ++++++d +g v+++ + p ++   +n+++
  gi|320100555|ref|YP_004176147.1|  84 VEWIQEKlgVEIPFPIIADPNGEVSRKLG--FLHAQSATSTVRAVVIVDGNGIVRAILYYPQET--GRNIDE 151
                                       4444444776669999*************..666667777899***********9998888774..466555 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 !   41.0   0.0   4.2e-14   1.3e-10       1      38 [.     158     199 ..     158     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 4.2e-14
                                       HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHHHHH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavkryl 38 
                                       ALQl dk++ a PA+W p     Gd  ivpP++t ++a++r++
  gi|320100555|ref|YP_004176147.1| 158 ALQLNDKYKRAVPAGW-PnnelvGDALIVPPASTIQEARERLK 199
                                       9***************.99**********************97 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.6e-06     0.029       4      55 ..      57     124 ..      54     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.6e-06
                        AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.s...akkFvkl...tgfpfelyvDpsaklyqalglk.........r 55 
                                       r+ +++++ +++l + ++++  s     +++++   +++pf++++Dp++++ ++lg+          r
  gi|320100555|ref|YP_004176147.1|  57 RRYEDFKKLNTELLGLSVDSTfShikWVEWIQEklgVEIPFPIIADPNGEVSRKLGFLhaqsatstvR 124
                                       678899999999999999999985334466666889999*****************974555555550 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.4e-05     0.071      11      34 ..     208     231 ..     202     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                              Sel1  11 ylylnGlgvpk.DpekAiewyekAA 34 
                                       ++y++G+ vp+  +++A+ w+e+A 
  gi|320100555|ref|YP_004176147.1| 208 MCYEEGR-VPPeEVREARAWLERAS 231
                                       688****.88868999********7 PP

>> DUF4368  Domain of unknown function (DUF4368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013       0.4      13      34 ..      50      71 ..      47      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                           DUF4368 13 ekFlalvrkytdieeLtpeiln 34
                                      ++F+a +r+y d+++L  e+l 
  gi|320100555|ref|YP_004176147.1| 50 TEFVAFARRYEDFKKLNTELLG 71
                                      68*****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1684.65
//
Query:       gi|320100556|ref|YP_004176148.1|  [L=70]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00037   20.7   0.2      0.039   14.2   0.0    2.2  2  zinc_ribbon_9    zinc-ribbon
    0.00062   19.1   0.9       0.21   11.1   0.0    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0012   18.2   1.5        0.6    9.6   0.4    2.3  2  Mu-like_Com      Mu-like prophage protein Com
      0.002   17.8   1.5        1.1    9.1   0.1    2.3  2  zinc_ribbon_2    zinc-ribbon domain
     0.0033   17.4   0.5        1.8    8.6   0.0    2.1  2  CpXC             CpXC protein
     0.0068   16.3   0.4          3    7.8   0.0    2.2  2  zinc_ribbon_4    zinc-ribbon domain
     0.0088   16.0   0.4        3.9    7.5   0.0    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.4   0.8        1.9    8.1   0.1    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.016   15.3   0.7        3.2    7.9   0.0    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.02   15.0   0.9        3.9    7.6   0.1    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
      0.026   13.9   0.3          2    7.8   0.0    2.2  2  zf-TFIIB         Transcription factor zinc-finger
      0.051   13.1   0.9        5.3    6.6   0.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.054   13.6   1.7        9.2    6.4   0.2    2.4  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.058   13.3   4.2        1.5    8.7   0.2    2.4  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
      0.058   13.1   2.6        2.3    8.0   0.0    2.2  2  zf-CCHC_5        GAG-polyprotein viral zinc-finger
       0.08   13.0   3.5        2.5    8.3   0.2    2.2  2  UPF0547          Uncharacterised protein family UPF0547
       0.11   12.5   0.4        1.9    8.5   0.0    1.9  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.36   11.2   2.1        1.1    9.6   2.1    1.7  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.69    9.9   2.3         14    5.6   0.2    2.2  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.035        33      22      28 ..       6      11 ..       1      15 [. 0.75
   2 !   14.2   0.0   4.1e-05     0.039      16      31 ..      38      54 ..      32      57 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.035
                     zinc_ribbon_9 22 vlCPhCg 28
                                      + CP+Cg
  gi|320100556|ref|YP_004176148.1|  6 K-CPRCG 11
                                      4.****7 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.1e-05
                     zinc_ribbon_9 16 pdedsd.vlCPhCgggF 31
                                      ++e ++ v+CP+Cg gF
  gi|320100556|ref|YP_004176148.1| 38 ERERPImVICPRCGEGF 54
                                      344444559*******9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0044       4.2       4       9 ..       6      11 ..       2      12 .. 0.63
   2 !   11.1   0.0   0.00022      0.21       2      10 ..      44      52 ..      43      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0044
                       zf-ribbon_3  4 rCPnCG 9 
                                      +CP+CG
  gi|320100556|ref|YP_004176148.1|  6 KCPRCG 11
                                      566666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
                       zf-ribbon_3  2 tvrCPnCGa 10
                                      +v CP+CG+
  gi|320100556|ref|YP_004176148.1| 44 MVICPRCGE 52
                                      899999998 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 !    9.6   0.4   0.00064       0.6      25      31 ..       5      11 ..       2      14 .. 0.88
   2 !    7.7   0.0    0.0024       2.3      23      31 ..      43      51 ..      34      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00064
                       Mu-like_Com 25 iKCPRCG 31
                                      +KCPRCG
  gi|320100556|ref|YP_004176148.1|  5 LKCPRCG 11
                                      7*****9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0024
                       Mu-like_Com 23 ltiKCPRCG 31
                                      + + CPRCG
  gi|320100556|ref|YP_004176148.1| 43 IMVICPRCG 51
                                      6678****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0024       2.2       1       6 [.       6      11 ..       3      18 .. 0.77
   2 !    9.1   0.1    0.0011       1.1      16      21 ..      47      52 ..      33      54 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +Cp+CG
  gi|320100556|ref|YP_004176148.1|  6 KCPRCG 11
                                      577777 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                     zinc_ribbon_2 16 CpyCGt 21
                                      Cp+CG+
  gi|320100556|ref|YP_004176148.1| 47 CPRCGE 52
                                      888887 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0033       3.1      38      56 ..       5      23 ..       3      44 .. 0.77
   2 !    8.6   0.0    0.0019       1.8      37      53 ..      44      60 ..      39      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0033
                              CpXC 38 atCpkCgatakleapllyh 56
                                       +Cp+Cg t+++e  + ++
  gi|320100556|ref|YP_004176148.1|  5 LKCPRCGFTGRPEEFTFMQ 23
                                      58******99998766554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
                              CpXC 37 eatCpkCgatakleapl 53
                                      ++ Cp+Cg+ ++le p+
  gi|320100556|ref|YP_004176148.1| 44 MVICPRCGEGFYLESPV 60
                                      578*********99987 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0075       7.1      26      32 ..       5      11 ..       2      14 .. 0.74
   2 !    7.8   0.0    0.0032         3      23      34 ..      42      53 ..      38      57 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0075
                     zinc_ribbon_4 26 vrCskCg 32
                                      ++C++Cg
  gi|320100556|ref|YP_004176148.1|  5 LKCPRCG 11
                                      6888887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0032
                     zinc_ribbon_4 23 gvkvrCskCghv 34
                                        +v C++Cg+ 
  gi|320100556|ref|YP_004176148.1| 42 PIMVICPRCGEG 53
                                      567777777764 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 !    7.5   0.0    0.0041       3.9      19      28 ..       5      15 ..       2      34 .. 0.73
   2 !    7.3   0.1    0.0048       4.6      19      26 ..      45      52 ..      35      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0041
                     Zn_Tnp_IS1595 19 fvCPhCgsr.k 28
                                        CP+Cg + +
  gi|320100556|ref|YP_004176148.1|  5 LKCPRCGFTgR 15
                                      57*****7763 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0048
                     Zn_Tnp_IS1595 19 fvCPhCgs 26
                                      ++CP+Cg 
  gi|320100556|ref|YP_004176148.1| 45 VICPRCGE 52
                                      67****94 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1      0.01       9.7       4      10 ..       6      12 ..       3      19 .. 0.83
   2 ?    8.1   0.1    0.0021       1.9       3      12 ..      45      54 ..      44      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.01
                            zf_UBZ  4 lCerCgk 10
                                       C+rCg 
  gi|320100556|ref|YP_004176148.1|  6 KCPRCGF 12
                                      7****96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                            zf_UBZ  3 ylCerCgkei 12
                                      ++C+rCg+ +
  gi|320100556|ref|YP_004176148.1| 45 VICPRCGEGF 54
                                      78*****865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.017        16      27      33 ..       5      11 ..       1      15 [. 0.72
   2 ?    7.9   0.0    0.0034       3.2      23      34 ..      40      52 ..      31      55 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                       Zn-ribbon_8 27 taCPeCg 33
                                       +CP+Cg
  gi|320100556|ref|YP_004176148.1|  5 LKCPRCG 11
                                      4599998 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0034
                       Zn-ribbon_8 23 daplta.CPeCgs 34
                                      ++p  + CP+Cg+
  gi|320100556|ref|YP_004176148.1| 40 ERPIMViCPRCGE 52
                                      5566666****96 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0042       3.9      16      35 ..       4      23 ..       1      32 [. 0.76
   2 ?    6.6   0.1    0.0089       8.4      11      27 ..      39      55 ..      32      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0042
                          zf-Mss51 16 dfeCpdCGiptycseehwed 35
                                      +++Cp+CG+     e  +++
  gi|320100556|ref|YP_004176148.1|  4 ALKCPRCGFTGRPEEFTFMQ 23
                                      679*****987666666665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0089
                          zf-Mss51 11 apkhvdfeCpdCGipty 27
                                       ++++ + Cp+CG   y
  gi|320100556|ref|YP_004176148.1| 39 RERPIMVICPRCGEGFY 55
                                      57889999*****7666 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0022         2       1      20 [.       6      28 ..       6      32 .. 0.66
   2 ?    4.4   0.1     0.026        24       2       6 ..      47      51 ..      46      58 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0022
                          zf-TFIIB  1 kCPkCq.d.eleeser.ggveid 20
                                      kCP+C+ +  +ee+ + ++ +i+
  gi|320100556|ref|YP_004176148.1|  6 KCPRCGfTgRPEEFTFmQEATIY 28
                                      8****944456666556666665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                          zf-TFIIB  2 CPkCq 6 
                                      CP+C+
  gi|320100556|ref|YP_004176148.1| 47 CPRCG 51
                                      77776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.013        12       2       7 ..       6      11 ..       5      23 .. 0.86
   2 ?    6.6   0.1    0.0057       5.3       2       8 ..      46      52 ..      37      62 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                                      EETTTT CS
                      TF_Zn_Ribbon  2 kCPnCg 7 
                                      kCP Cg
  gi|320100556|ref|YP_004176148.1|  6 KCPRCG 11
                                      899998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0057
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                      +CP Cg 
  gi|320100556|ref|YP_004176148.1| 46 ICPRCGE 52
                                      4555554 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0097       9.2       3       8 ..       6      11 ..       5      12 .. 0.92
   2 ?    6.3   0.1     0.011        10       4      10 ..      47      53 ..      45      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0097
                            zf-ACC  3 KCpsCg 8 
                                      KCp+Cg
  gi|320100556|ref|YP_004176148.1|  6 KCPRCG 11
                                      9****8 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                            zf-ACC  4 CpsCgem 10
                                      Cp+Cge 
  gi|320100556|ref|YP_004176148.1| 47 CPRCGEG 53
                                      *****96 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 ?    8.7   0.2    0.0016       1.5       3       8 ..       6      11 ..       4      19 .. 0.88
   2 ?    5.9   0.5     0.012        12      24      27 ..      47      50 ..      45      52 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                                      B-TTT- CS
                      zf-FPG_IleRS  3 pCpRCw 8 
                                      +CpRC+
  gi|320100556|ref|YP_004176148.1|  6 KCPRCG 11
                                      9****8 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                                      -TTT CS
                      zf-FPG_IleRS 24 CprC 27
                                      CprC
  gi|320100556|ref|YP_004176148.1| 47 CPRC 50
                                      5555 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.8     0.023        22       5       9 ..       7      11 ..       4      12 .. 0.90
   2 ?    8.0   0.0    0.0024       2.3       5      11 ..      47      53 ..      45      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.023
                                      -TTT- CS
                         zf-CCHC_5  5 CpRCk 9 
                                      CpRC+
  gi|320100556|ref|YP_004176148.1|  7 CPRCG 11
                                      ****8 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0024
                                      -TTT-SS CS
                         zf-CCHC_5  5 CpRCkkg 11
                                      CpRC+ g
  gi|320100556|ref|YP_004176148.1| 47 CPRCGEG 53
                                      *****88 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0026       2.5      14      22 ..       4      12 ..       3      13 .. 0.82
   2 ?    5.7   0.3     0.017        16      14      21 ..      44      51 ..      44      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                           UPF0547 14 aqfCphCGy 22
                                      a +Cp CG+
  gi|320100556|ref|YP_004176148.1|  4 ALKCPRCGF 12
                                      678999998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                           UPF0547 14 aqfCphCG 21
                                      +++Cp CG
  gi|320100556|ref|YP_004176148.1| 44 MVICPRCG 51
                                      56788887 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   0.2      0.21     2e+02      86      93 ..       4      11 ..       1      15 [. 0.69
   2 ?    8.5   0.0     0.002       1.9      48      83 ..      19      57 ..      16      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.21
                                      HHS-TTTS CS
                              HypA 86 alrCpkCg 93
                                      al+Cp+Cg
  gi|320100556|ref|YP_004176148.1|  4 ALKCPRCG 11
                                      46788887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.002
                                      HHHHHCC.T.TTT-EEEEE..EE--EEEETTTS-EEECH CS
                              HypA 48 fellaegtv.legaeLeie..evpvkvrCreCgkefele 83
                                      f++++e t+   g  Le e  e p+ v C +Cg+ f le
  gi|320100556|ref|YP_004176148.1| 19 FTFMQEATIyYTGRGLEHEerERPIMVICPRCGEGFYLE 57
                                      777888888777888887633678999*****9988765 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.1    0.0012       1.1       2      36 ..       3      52 ..       2      65 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                   Lar_restr_allev  2 eLkpCPfCg...gravlersqrvvaeigq...............cvyCadCga 36
                                      e + CP Cg    +++  ++q  +    +               +v+C  Cg 
  gi|320100556|ref|YP_004176148.1|  3 EALKCPRCGftgRPEEFTFMQEATI---YytgrgleheererpiMVICPRCGE 52
                                      6678999984423444444444443...23568999999************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 ?    5.6   0.2     0.015        14      30      39 ..       6      15 ..       4      32 .. 0.74
   2 ?    4.1   0.2     0.046        43      43      54 ..      41      52 ..      21      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                    OrfB_Zn_ribbon 30 tCseCgsknk 39
                                      +C++Cg +++
  gi|320100556|ref|YP_004176148.1|  6 KCPRCGFTGR 15
                                      4666666655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.046
                    OrfB_Zn_ribbon 43 sgrtfkCpnCgf 54
                                       +  + Cp+Cg 
  gi|320100556|ref|YP_004176148.1| 41 RPIMVICPRCGE 52
                                      555666777765 PP



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:                      396  (0.0220871); 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):              19  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 498.11
//
Query:       gi|320100557|ref|YP_004176149.1|  [L=539]
Description: metal dependent phosphohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-07   30.5   0.2    9.6e-07   29.1   0.2    1.8  1  HD        HD domain
  ------ inclusion threshold ------
       0.16   12.3   1.2        1.3    9.5   0.1    2.9  3  DUF3194   Protein of unknown function (DUF3194)


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 !   29.1   0.2   1.1e-10   9.6e-07       1      70 [.      71     163 ..      71     193 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHHHHHHHHHHHHHH................HHHHHHH...HHHHHHTTTTHHHHTS..HHH....HHH.. CS
                                HD   1 rleHsleVaklarrlaedlge................eedrell...llaaLlHDiGkgpfgdafekk....eee.. 52 
                                       r+ Hsl+V++ + r+   l +                e  rel+   +l +LlHDiG+gpf++af+++    + +  
  gi|320100557|ref|YP_004176149.1|  71 RFSHSLGVMYSSYRYMSFLMRsavvsgiqgerrrsvlEYQRELIyasRLLGLLHDIGHGPFSHAFDRYvyknK-Dfl 146
                                       67888888888888887776688888888888888885555554112689******************98651.156 PP

                                       ...CTCCHHHHHHHHHHHHHH CS
                                HD  53 ...fekflaHekvgaeilrev 70 
                                          +    +He+vg+  l ++
  gi|320100557|ref|YP_004176149.1| 147 gyrV---GNHEVVGYL-LYRS 163
                                       5423...469999993.3333 PP

>> DUF3194  Protein of unknown function (DUF3194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.25   2.2e+03      31      57 ..     163     189 ..     154     192 .. 0.80
   2 ?   -1.7   0.0      0.42   3.8e+03      13      30 ..     413     430 ..     411     448 .. 0.72
   3 ?    9.5   0.1   0.00014       1.3       4      24 ..     508     528 ..     505     531 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.25
                                       TTEEEEEEEEEEEESSSEEEEEEEEEE CS
                           DUF3194  31 kevldlditvevkeneeLdvdvevele 57 
                                       + v+d+  ++ + e e L+vd ev + 
  gi|320100557|ref|YP_004176149.1| 163 STVRDIIEKTLLRERERLQVDPEVLIS 189
                                       567777777888999*****9998775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHTTS-T CS
                           DUF3194  13 seflaeviekkifkkvsk 30 
                                       +e l++ ie+ ++++vs+
  gi|320100557|ref|YP_004176149.1| 413 GETLQKKIEEGVSSEVST 430
                                       566777777777777765 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00014
                                       -SHHHHHHHHHHHHHHHHHHH CS
                           DUF3194   4 Lteedldeiseflaeviekki 24 
                                       Lt+e+l +ise++++++e+ i
  gi|320100557|ref|YP_004176149.1| 508 LTSEELRKISEIATRIVEDAI 528
                                       9*****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3939.61
//
Query:       gi|320100558|ref|YP_004176150.1|  [L=251]
Description: dolichyl-phosphate beta-D-mannosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-31  109.7   0.0    1.6e-31  109.4   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    3.5e-15   56.5   0.1      4e-15   56.3   0.1    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0028   17.2   0.0     0.0036   16.8   0.0    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.025   14.2   0.0    1.5  2  Glyco_transf_7N  N-terminal region of glycosyl transferase gr
      0.025   14.1   0.0      0.037   13.5   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
      0.068   13.7   0.0        0.2   12.2   0.0    1.8  1  Glyco_tranf_2_4  Glycosyl transferase family 2
        0.2   11.6   0.1        0.3   11.0   0.1    1.2  1  CHAD             CHAD domain


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.0   6.4e-35   1.6e-31       1     130 [.       6     134 ..       6     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 6.4e-35
                                       EEEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnagl 75 
                                       s+v+ptyNe ++++ ++  + +   d+  d+eiivvDD+S+D+t+e +  l++   +v+v++r+ + G+++a+ +g+
  gi|320100558|ref|YP_004176150.1|   6 SIVVPTYNERENIRILIPMIHRAlrDTGVDYEIIVVDDNSPDGTAEEAVHLSS-AYPVKVVKRSGKLGLSSAIYEGV 81 
                                       8********77777666544444556*************************75.999******************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC- CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernk 130
                                       r+atgd+++++DaD++++p++++ l+++++    d+v+++r++ +g    ++  +
  gi|320100558|ref|YP_004176150.1|  82 RHATGDIVVVMDADLQHPPEYIPALLRRIDG--CDLVVASRYAPGGRVEGFPLVR 134
                                       *****************************99..779*****99988776666655 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 !   56.3   0.1   1.6e-18     4e-15       4     118 ..       5     114 ..       2     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.6e-18
                   Glyco_tranf_2_3   4 lavlVptfneed...vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                        +++Vpt+ne +    l  +++ +l+++  ++e++vv+d+s ++t+e+a +l  a+p    +vv ++    + g s 
  gi|320100558|ref|YP_004176150.1|   5 ASIVVPTYNEREnirILIPMIHRALRDTGVDYEIIVVDDNSPDGTAEEAVHLSSAYPV---KVVKRSG---KLGLSS 75 
                                       589*******999999999********99********************9*9999976...5775555...555677 PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqffltpkvg 118
                                       a++e++r++++d+v+++D+D    P+++++ll+ +  ++++
  gi|320100558|ref|YP_004176150.1|  76 AIYEGVRHATGDIVVVMDADLQHPPEYIPALLRRI--DGCD 114
                                       899***************************99887..5555 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 !   16.8   0.0   1.4e-06    0.0036       1      97 [.       6     101 ..       6     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                   Glyco_tranf_2_2   1 svviplraseerhyieerv..lqkakyy.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarN 74 
                                       s+v+p ++++e+  i+  +   ++a      + e+ivvdd S++ ++ee   +  +     +k       +l+ a  
  gi|320100558|ref|YP_004176150.1|   6 SIVVPTYNEREN--IRILIpmIHRALRDtGVDYEIIVVDDNSPDGTAEEAVHLSSAYPVKVVKRS--GKLGLSSAIY 78 
                                       789999999999..4444432222222113478****************9999888766665555..5788999999 PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissD 97 
                                        G+ +a +d+v+ +DaD    ++
  gi|320100558|ref|YP_004176150.1|  79 EGVRHATGDIVVVMDADLQHPPE 101
                                       *****************766555 PP

>> Glyco_transf_7N  N-terminal region of glycosyl transferase group 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.9e-06     0.025      48      89 ..       4      45 ..       2      67 .. 0.87
   2 ?   -3.0   0.0       2.1   5.3e+03      61      84 ..     214     237 ..     201     238 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.9e-06
                   Glyco_transf_7N 48 kvaiiipyrnreehLkillkrLhpllqrQqldykiyvieqag 89
                                      k  i++p  n +e+++il+  +h+ l+   +dy+i+v++ ++
  gi|320100558|ref|YP_004176150.1|  4 KASIVVPTYNERENIRILIPMIHRALRDTGVDYEIIVVDDNS 45
                                      6789***999999*************************8764 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.1
                   Glyco_transf_7N  61 hLkillkrLhpllqrQqldykiyv 84 
                                        ++++l+++  l +   +++++yv
  gi|320100558|ref|YP_004176150.1| 214 TVRVMLSYIRTLFKLNPVSFTLYV 237
                                       346677788777777777777777 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.4e-05     0.037      22      68 ..      77     121 ..      64     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                   Glyco_transf_21  22 llqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpv 68 
                                       +  +++ a  d++v+ D+d   +p+y+  ll+++   ++ lV++  +
  gi|320100558|ref|YP_004176150.1|  77 IYEGVRHATGDIVVVMDADLQHPPEYIPALLRRID--GCDLVVASRY 121
                                       567888999*************************9..5999998776 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.7e-05       0.2       6      81 ..      21      95 ..      16      96 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-05
                   Glyco_tranf_2_4  6 iLpeflahhlalgfd.rilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                                      ++p   +++++ g+d +i+v+d++s Dgt++    l  +  ++v+k   +     ++++ +   +a +d v+v+DaD
  gi|320100558|ref|YP_004176150.1| 21 LIPMIHRALRDTGVDyEIIVVDDNSPDGTAEEAVHLSSAYPVKVVKRSGKLGLSSAIYEGVR--HATGDIVVVMDAD 95
                                      6788889999****955************986655544333333332222334444555444..4567777777777 PP

>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00012       0.3      31      79 ..     151     202 ..     150     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHTTTSS-HHHHHHHH....HHHHHHHHHHHHHHHHHHHHHTHH CS
                              CHAD  31 alRRlRsalrlfapvldkeeaaale....kelrwlaraLGeaRDldVllerll 79 
                                       ++RR R a++ f  + ++e +a+++    +  + l ++LGe++D+ V +e + 
  gi|320100558|ref|YP_004176150.1| 151 GTRRARDAVSGF-FAAKREVVARWRmvepRGYKVLVEILGELHDIRVCEEPIV 202
                                       69**********.88899********999******************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1799.89
//
Query:       gi|320100559|ref|YP_004176151.1|  [L=1062]
Description: isoleucyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-172  575.4   0.0   1.4e-172  575.1   0.0    1.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    7.6e-37  126.6   0.0    1.6e-36  125.6   0.0    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    5.4e-18   64.9   0.0    3.1e-06   26.2   0.0    3.9  3  tRNA-synt_1g   tRNA synthetases class I (M)
    0.00012   21.7   0.0    0.00045   19.8   0.0    2.0  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.086   12.2   0.0       0.43    9.9   0.0    1.9  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
       0.58   10.3   2.2         27    5.0   0.1    2.5  2  UPF0547        Uncharacterised protein family UPF0547


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 !  575.1   0.0  4.8e-176  1.4e-172       2     601 ..      24     639 ..      23     640 .. 0.92

  Alignments for each domain:
  == domain 1  score: 575.1 bits;  conditional E-value: 4.8e-176
                       tRNA-synt_1   2 lyekWeeedvfkkelekeke.kkefilvdgPPyvtGsl.HiGhalaktlkdivirykrmkGkevlyvpGwDhaGlai 76 
                                       +++ W++ +v+   ++++++ + +f ++dgPPy  G + HiG a++k+lkd v rykrmkG++v  +pG+D++Gl+i
  gi|320100559|ref|YP_004176151.1|  24 VLDYWDAVGVYSLVKKADESkQLRFNFIDGPPYPSGDIpHIGTAWNKALKDAVLRYKRMKGYRVYDRPGYDCHGLPI 100
                                       7899*********99888885778************855************************************** PP

                       tRNA-synt_1  77 eakvekklgakekker.kklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrlad 152
                                       e kve+klg + kke  + +g+e+f+e++r  + + a+ i++ +k+lGv +D+d++ylTl +e+ ea ++ +++ ++
  gi|320100559|ref|YP_004176151.1| 101 EVKVEQKLGVSVKKEIeERIGVERFIEECRRLALTNANAITRWFKELGVFMDWDNPYLTLRDEYIEAEWWLIKKAHE 177
                                       *********99777651679********************************************************* PP

                       tRNA-synt_1 153 kgliyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv.. 227
                                        gl+ +  ++v+w+++++t+l+e E ey++ +d++i+v+ ++++k   +lvi+TTtP+Tl+++t v v+p++dyv  
  gi|320100559|ref|YP_004176151.1| 178 AGLLEEEYRVVHWCPRCSTTLAEYELEYRELEDPSIYVKLQVEGKPGEYLVIWTTTPWTLPANTFVMVHPDEDYVkv 254
                                       ***************************************************************************99 PP

                       tRNA-synt_1 228 .itkeklilaeallkslvkke..sekkiledergkeLegkevelpl..........vnrkipii..addyvdkeaGt 289
                                        + +ek+ila+++l++++k+   +++k++e+++g++L+g ++++pl             k   +  a ++v++ +Gt
  gi|320100559|ref|YP_004176151.1| 255 eVGGEKWILAKQRLEAVMKELgvEDYKVVEEFKGRSLIGVRYIHPLadviplqrelS--KYHAVypAPEFVTMYEGT 329
                                       999****************9985566********************99999887433..444441156********* PP

                       tRNA-synt_1 290 GvVkiaPahdedDyevgkkynl.evinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfc 365
                                       G+V+ aP+h+++D+ v+k++++   ++++d++g++t ea++++gl+v +a++ ++e+l+++++llka++i+h++p+c
  gi|320100559|ref|YP_004176151.1| 330 GLVHSAPGHGFEDFIVAKRNGIdAAASPVDDEGRFTSEAGKYTGLRVREANQLIIEDLRARNALLKASTIMHKYPVC 406
                                       **********************55689************************************************** PP

                       tRNA-synt_1 366 erskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeev 442
                                       +r k+p+++rat qW ++v++l++ + ++ ++v+++p+++++r+  ++ niqdW iSRqr+WG+++p++   +   +
  gi|320100559|ref|YP_004176151.1| 407 WRCKTPVVMRATRQWVIKVSRLRERLREEADRVKWIPEWARERIGFMIDNIQDWLISRQRYWGTPLPIWECPNGHRL 483
                                       *************************************************************************9988 PP

                       tRNA-synt_1 443 vvreelkelvagreeeeaekkalekeakdkl....kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkff 515
                                       vv  ++ el+       ++ ++l++  +d++     +   e+++++dv DvW +Sg  +++  g+p+e ++e    +
  gi|320100559|ref|YP_004176151.1| 484 VV-GSIRELES---YGGVRPRELHRPWIDSVvlkcPHCGLEMRRVPDVADVWLDSGVAFYAAKGHPDELSPED---V 553
                                       88.66666554...55666666666666666553234445789************************955543...5 PP

                       tRNA-synt_1 516 padmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlil 592
                                         d+++eG D++rgW+ +l+  ++  ++++P+++vlvhg+++de+Gr m KslgN++  ++ i+++g d lRl+l+ 
  gi|320100559|ref|YP_004176151.1| 554 ILDFIVEGHDQTRGWFFSLLRAGVLGFNRSPYRTVLVHGFMLDEKGREMHKSLGNYVGTDEAISRVGRDPLRLWLLG 630
                                       79**************************************************************************8 PP

                       tRNA-synt_1 593 sdvgrdinl 601
                                       +++ +d ++
  gi|320100559|ref|YP_004176151.1| 631 NTTWEDARF 639
                                       888888876 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 !  125.6   0.0   5.3e-40   1.6e-36       1     150 [.     688     838 ..     688     840 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 5.3e-40
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d+wils++n l+k+v+e +e+y+ ++a++ l eff++dl+ wy++l++pr + e+++ ++  a++vl++v++ + rl
  gi|320100559|ref|YP_004176151.1| 688 DKWILSRVNTLIKQVSELMESYQVYEAVRLLREFFVEDLSHWYIRLIRPRVWVEENTGDKLaAYTVLYYVIDRVARL 764
                                       9*****************************************************9999866699************* PP

                       Anticodon_1  77 laPfmPfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                       +aPf+Pfi+E+++q   + + ++ si+l ++pe ++ + +++l eee+ l++++ +a  ++r +++ik +++++ 
  gi|320100559|ref|YP_004176151.1| 765 IAPFTPFIAEYMYQALMKPVYGEPSIHLLPYPEpDEGFINGKL-EEEMRLIRQVYEASASARMKQGIKLRQPVRR 838
                                       *************99444467789********95554447777.99*************************9886 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0     1e-09   3.1e-06       8      68 ..      55     117 ..      52     206 .. 0.80
   2 !   16.1   0.0   1.2e-06    0.0035     166     238 ..     403     473 ..     388     484 .. 0.84
   3 !   17.3   0.0   5.3e-07    0.0016     310     375 ..     583     648 ..     565     652 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1e-09
                                       B--SS.---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HHHHHH CS
                      tRNA-synt_1g   8 pYang.klHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpeelve 68 
                                       pY++g  +H+G + +    D++ Rykr++g+ v+   g D hG pie+k e++ gv++++ +e
  gi|320100559|ref|YP_004176151.1|  55 PYPSGdIPHIGTAWNKALKDAVLRYKRMKGYRVYDRPGYDCHGLPIEVKVEQKlGVSVKKEIE 117
                                       67776258******99999******************************87543888776554 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-06
                                       ...........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 166 npksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                        p++  +++  +++ t+++  k+s+++++l+e    ++ ++  +  +    ++ ++++d+ isr+  wG p+P
  gi|320100559|ref|YP_004176151.1| 403 YPVCWRCKTPVVMRATRQWVIKVSRLRERLREEA--DRVKWIPEWARERIGFMIDNIQDWLISRQRYWGTPLP 473
                                       599*****************************88..44457777777777888888***************99 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 5.3e-07
                                       ---S-EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1g 310 klpkkvvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfverv 375
                                       +  ++v +h+++   +g+ + kS g+ v ++ea+ r+  d lR +l+ ++ + +D+ fsw+++ e v
  gi|320100559|ref|YP_004176151.1| 583 SPYRTVLVHGFMLdEKGREMHKSLGNYVGTDEAISRVGRDPLRLWLLGNT-TWEDARFSWKSLEEAV 648
                                       556799****986267999***************************9876.568******9987765 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 !   19.8   0.0   1.5e-07   0.00045      11     136 ..     214     353 ..     210     387 .. 0.80
   2 ?   -3.2   0.0       1.7   4.9e+03      18      36 ..     834     852 ..     827     860 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-07
                     tRNA-synt_1_2  11 eiefkvees.eeklevfttrpdtlfGvtfvalapehplvekl..aekkkelaafieevkkksesereletkekeGv. 83 
                                        ++++ve++  e l ++tt p tl   tfv++ p+ + v+     ek    ++ +e v k+   e  +  +e +G  
  gi|320100559|ref|YP_004176151.1| 214 YVKLQVEGKpGEYLVIWTTTPWTLPANTFVMVHPDEDYVKVEvgGEKWILAKQRLEAVMKELGVEDYKVVEEFKGRs 290
                                       6899999998899*************************998755444444455667777777777777777777876 PP

                     tRNA-synt_1_2  84 ftglkaihPitgek.........ipiwva.nyvlmeygtgavmavPahdqrDfeFakkynlpi 136
                                         g+  ihP+ +             ++ a ++v m  gtg v + P+h  +Df  ak+ +++ 
  gi|320100559|ref|YP_004176151.1| 291 LIGVRYIHPLADVIplqrelskyHAVYPApEFVTMYEGTGLVHSAPGHGFEDFIVAKRNGIDA 353
                                       8899999998765445556566667886658**************************999876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                     tRNA-synt_1_2  18 eseeklevfttrpdtlfGv 36 
                                       +  ++l v+t+r d+   v
  gi|320100559|ref|YP_004176151.1| 834 QPVRRLIVYTNREDVAAAV 852
                                       4445789******987766 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.26   7.8e+02      21      48 ..      60      87 ..      57      89 .. 0.93
   2 ?    9.9   0.0   0.00014      0.43     240     298 ..     588     646 ..     579     649 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.26
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdv 48
                                      d  h+G a +    D + r+ +++gY v
  gi|320100559|ref|YP_004176151.1| 60 DIPHIGTAWNKALKDAVLRYKRMKGYRV 87
                                      678***********************98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00014
                                       EEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1e 240 yflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeellee 298
                                         +h  +l  +g+ m ksL+n++   +++ ++    lRl ll +   +   f+ + lee
  gi|320100559|ref|YP_004176151.1| 588 VLVHGFMLDEKGREMHKSLGNYVGTDEAISRVGRDPLRLWLLGNTTWEDARFSWKSLEE 646
                                       56788899999***************************999987666666676666666 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0089        27       3      11 ..     191     199 ..     190     200 .. 0.90
   2 ?    4.5   0.3     0.013        38      15      21 ..     512     518 ..     511     520 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0089
                           UPF0547   3 CPeCeakvP 11 
                                       CP+C+++++
  gi|320100559|ref|YP_004176151.1| 191 CPRCSTTLA 199
                                       ******997 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                           UPF0547  15 qfCphCG 21 
                                        +CphCG
  gi|320100559|ref|YP_004176151.1| 512 LKCPHCG 518
                                       58****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1062 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 6899.44
//
Query:       gi|320100560|ref|YP_004176152.1|  [L=139]
Description: cytidine deaminase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-15   55.5   0.1    5.2e-15   55.2   0.1    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    4.4e-11   43.1   0.3    6.5e-11   42.6   0.3    1.3  1  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
    2.6e-05   23.9   1.0      0.011   15.3   0.1    2.1  2  LmjF365940-deam  A distinct subfamily of CDD/CDA-like deamina


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 !   55.2   0.1   8.7e-19   5.2e-15       6     100 ..       7     106 ..       3     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 8.7e-19
                                       HHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHT.SSCETTEEEEE... CS
                   dCMP_cyt_deam_1   6 kllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaakng.gsklegatlyv... 77 
                                        l++ a ++  +++ ++sn++V+a+++++  ++++g+n e+a++  ti+AE++Ai +++  g +  +  a+ +v   
  gi|320100560|ref|YP_004176152.1|   7 ALIKEASRVLGNSYaPYSNIHVAAAVLTSSGRVYLGVNVENASYGLTICAERSAISAMVAAGeRDPV--AVAIVtdl 81 
                                       567889999999999*************99*****************************99645555..66666788 PP

                                       ..EE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  78 ..tlePCsmCakaiiqsgikkvvvg 100
                                          + PC+ C+++i++++++ ++v+
  gi|320100560|ref|YP_004176152.1|  82 edPIPPCGACRQVIAEFNPRALIVM 106
                                       88899*************9999875 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.3   1.1e-14   6.5e-11      45     110 ..       6      71 ..       1      83 [. 0.89

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.1e-14
                                       -HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHHTT--G CS
                   dCMP_cyt_deam_2  45 delkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvlggkef 110
                                       d+l ++A +   +syapys+ + + a+ t++g+vy G  +E+a +  ++ + ++A+ a+v++g++ 
  gi|320100560|ref|YP_004176152.1|   6 DALIKEASRVLGNSYAPYSNIHVAAAVLTSSGRVYLGVNVENASYGLTICAERSAISAMVAAGERD 71 
                                       67999********************************************************87764 PP

>> LmjF365940-deam  A distinct subfamily of CDD/CDA-like deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2   0.00039       2.3      56      88 ..      35      67 ..      21      78 .. 0.83
   2 !   15.3   0.1   1.9e-06     0.011     152     188 ..      83     116 ..      68     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00039
                   LmjF365940-deam 56 greelvrgvNlEvSmPtGSlCsErnaigkalas 88
                                      +  +++ gvN+E        C+Er ai+  +a+
  gi|320100560|ref|YP_004176152.1| 35 SSGRVYLGVNVENASYGLTICAERSAISAMVAA 67
                                      566799*******99999*********986665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.9e-06
                   LmjF365940-deam 152 nPLkPCGaCeewLkkiaevnpdfkvltFddseckkvy 188
                                        P+ PCGaC++    iae np   ++++   + ++v+
  gi|320100560|ref|YP_004176152.1|  83 DPIPPCGACRQV---IAEFNPRALIVMHSTRSGRTVV 116
                                       8********986...9**********99887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1052.52
//
Query:       gi|320100561|ref|YP_004176153.1|  [L=826]
Description: SMC domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-19   70.8  13.9    2.1e-19   70.8  13.9    4.5  2  AAA_23         AAA domain
    1.8e-10   40.6   0.0    4.2e-10   39.5   0.0    1.6  1  SMC_N          RecF/RecN/SMC N terminal domain
    4.5e-09   36.5  11.5    5.2e-07   29.8   0.8    3.4  3  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
      7e-08   32.6   5.8       0.16   11.7   0.0    3.6  2  AAA_15         AAA ATPase domain
    9.6e-06   25.3   0.0    9.6e-06   25.3   0.0    4.2  5  AAA_27         AAA domain
    1.5e-05   25.0  23.0       0.13   12.3   0.0    5.2  5  DUF1664        Protein of unknown function (DUF1664)
    0.00013   20.8  38.2      0.039   12.6  13.3    4.9  5  AAA_13         AAA domain
    0.00066   19.5   0.9    0.00066   19.5   0.9    4.0  1  Rad50_zn_hook  Rad50 zinc hook motif
    0.00082   19.0   5.4    0.00082   19.0   5.4    3.8  3  PspA_IM30      PspA/IM30 family
     0.0009   18.9   0.0     0.0017   18.1   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
      0.006   16.2   4.3      0.045   13.3   0.0    4.0  3  AAA_25         AAA domain
     0.0074   16.3  29.8      0.049   13.6   1.2    4.7  4  Laminin_II     Laminin Domain II
     0.0083   16.5   2.8     0.0083   16.5   2.8    3.0  3  Gp-FAR-1       Nematode fatty acid retinoid binding protein (
  ------ inclusion threshold ------
      0.018   15.5   7.5        2.5    8.6   0.1    4.2  2  ABC_tran       ABC transporter
      0.033   14.4   5.2        0.6   10.4   0.0    3.9  3  AAA_22         AAA domain
      0.039   12.9  56.5       0.23   10.3   7.7    4.6  5  Spc7           Spc7 kinetochore protein
      0.042   13.9   0.3       0.22   11.5   0.0    2.3  2  ResIII         Type III restriction enzyme, res subunit
      0.083   12.2  41.7      0.087   12.1   2.8    4.8  4  DUF3450        Protein of unknown function (DUF3450)
       0.16   11.3   0.1       0.16   11.3   0.1    3.2  3  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.17   12.2   0.0       0.17   12.2   0.0    4.1  1  AAA_16         AAA ATPase domain
       0.18   12.2   0.0       0.77   10.1   0.0    2.1  1  AAA_19         AAA domain
       0.19   12.0   4.9         12    6.3   0.0    5.1  4  DUF948         Bacterial protein of unknown function (DUF948)
        0.2    9.9   5.8        1.5    7.1   0.0    2.6  3  Gp58           gp58-like protein
       0.25   10.6   0.0       0.25   10.6   0.0    2.5  3  DUF2075        Uncharacterized conserved protein (DUF2075)
       0.29   11.2  10.0        1.7    8.7   0.0    4.4  4  FlxA           FlxA-like protein
       0.31   11.1  48.0        0.2   11.7  10.2    4.1  4  UPF0242        Uncharacterised protein family (UPF0242) N-ter
       0.47    9.8  34.6      0.094   12.0   8.4    3.0  2  DUF4407        Domain of unknown function (DUF4407)
       0.48   10.1   4.2        9.6    5.9   0.1    3.2  2  DUF842         Eukaryotic protein of unknown function (DUF842
       0.48    9.9  35.4       0.87    9.1   8.2    3.8  3  MscS_porin     Mechanosensitive ion channel porin domain
        0.8   10.2  67.4       0.63   10.6   9.1    4.8  4  APG6_N         Apg6 coiled-coil region
        1.2    9.4  56.7       0.39   10.9  10.2    4.6  4  ATG16          Autophagy protein 16 (ATG16)
        1.3    7.3  50.5       0.51    8.6  19.8    2.5  2  MAD            Mitotic checkpoint protein
        2.2    7.0  32.9       0.93    8.3   0.2    4.2  4  Fmp27_WPPW     RNA pol II promoter Fmp27 protein domain
        3.6    6.6   8.8          2    7.4   0.0    3.2  3  Effector_1     Effector from type III secretion system
        3.8    7.0  24.2          7    6.1  10.7    2.6  2  Cas_DxTHG      CRISPR-associated (Cas) DxTHG family
        4.2    6.7  57.6       0.76    9.1   5.7    5.0  5  GAS            Growth-arrest specific micro-tubule binding
        4.9    7.0  15.6        3.3    7.6   0.0    4.5  5  Sec34          Sec34-like family
          6    5.8   8.1       0.25   10.3   0.6    2.3  2  DUF3818        Domain of unknown function in PX-proteins (DUF
        6.6    4.6  15.0       0.75    7.7   1.8    3.0  3  Prominin       Prominin
        7.6    6.2  27.9      0.055   13.3   3.5    3.9  1  AAA_11         AAA domain
        8.6    5.5  27.2       0.77    8.9   1.4    4.3  4  TMPIT          TMPIT-like protein
        9.5    6.4  24.8        4.9    7.3   1.4    4.9  4  Fib_alpha      Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8  13.9     5e-22   2.1e-19       2     175 ..       6     263 ..       5     303 .. 0.64
   2 ?   -0.2   8.0       2.8   1.2e+03     147     198 ..     340     396 ..     313     399 .. 0.59

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 5e-22
                            AAA_23   2 LkienfrsfrdqeidF.skgltlItGpNGaGKTTildAiklaLygetprlsrks.............grgfeksdve 64 
                                       L +en+rsfr++ + F +kg+t+I+G +G+GKT+il  +  aL+g  +r+sr+              + ++ ++ ++
  gi|320100561|ref|YP_004176153.1|   6 LMLENIRSFRKEYVVFpNKGVTVIHGATGSGKTSILMSVSAALFGL-QRESRDPfrafayptgrdlvRADASSARIR 81 
                                       679**********9999****************************5.555555558999999554444444455555 PP

                            AAA_23  65 iesegkvkay.veltfenkdgrytrsiererelsk..kkgkttkkaklelleideleqfisellgskki........ 130
                                       + +e+++k y ve++f+++++r  ++ e++r + +  +++ ++ +++  +l+++el+++++e+lg+k++        
  gi|320100561|ref|YP_004176153.1|  82 LLFEHNGKLYlVEREFRRDGERV-VNAEYNRLEEYvvDSSGRVVNTNQWILSPTELNKRVKEILGIKEKareqpllf 157
                                       66668888899999999988875.66666555444334555556778888899*********999999999999999 PP

                            AAA_23 131 ..........ilnlilflgqerfeefel.......kdkke..................................... 153
                                                 i +++++ +++r+e +e+       k   e                                     
  gi|320100561|ref|YP_004176153.1| 158 tsvlyapqfnIHEVLSLSDEDRTEIIERslglskyK---Eykknseeveniirsrvdelarnmerlktrlrerskes 231
                                       999999977677888888888855555544443331...12223345557777766666664444434333333333 PP

                            AAA_23 154 ..........rleelekeleeledekkllekl 175
                                                 ++e +ek+  e+  + +++e+ 
  gi|320100561|ref|YP_004176153.1| 232 lleekkrltaEVEGYEKARTEKLRRLEEVEAS 263
                                       33333334443333333322222222222222 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.8
                            AAA_23 147 elkdkkerleelekeleeledekkllekl.....eqekekekeleeleeeleeilke 198
                                       +++  +e++e +e+ lee+    ++l+++      ++ +  ++  ele++l+ +++ 
  gi|320100561|ref|YP_004176153.1| 340 KEALIEEEIEGFEQRLEEARRAYSELKAKiggleSDKRNILARRRELEDQLKRYKEL 396
                                       223344566666666666666666666666666545556666666666666666554 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 !   39.5   0.0   9.7e-13   4.2e-10       2     199 ..       3     732 ..       2     743 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 9.7e-13
                                       EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHH...HHHCTT.TTTTTTCHCC...CCCC--BTTCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                             SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAi...lFvLGersakklrsekl...sdlihkskeka 72 
                                       +  l++en +s++ k+ ++  +k++t+i G+ GSGK+++l ++   lF L  +s   +r+  +   +dl+ +     
  gi|320100561|ref|YP_004176153.1|   3 IYGLMLENIRSFR-KEYVVFPNKGVTVIHGATGSGKTSILMSVsaaLFGLQRESRDPFRAFAYptgRDLVRA----- 73 
                                       56799*******8.8888889999***************876622257777777777777544222788887..... PP

                                       STTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHHHCTT-STT........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                             SMC_N  73 svkkaeveitfdnedkklkiekeevsisrrvkrkge...seykingkevtkkevsellesagiske........... 135
                                        +++a++ ++f++++k   +e+e      rv++ +     ey ++ +    +  + +l+ ++++k            
  gi|320100561|ref|YP_004176153.1|  74 DASSARIRLLFEHNGKLYLVEREFRRDGERVVNAEYnrlEEYVVDSSGRVVNTNQWILSPTELNKRvkeilgikeka 150
                                       899********99999833333322222222222112335777777777777777788888888889999999999* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|320100561|ref|YP_004176153.1| 151 reqpllftsvlyapqfnihevlslsdedrteiierslglskykeykknseeveniirsrvdelarnmerlktrlrer 227
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|320100561|ref|YP_004176153.1| 228 skeslleekkrltaevegyekarteklrrleeveasiereqrllmeaerevaelksrieqarrlearlreiegeiag 304
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|320100561|ref|YP_004176153.1| 305 vaagiggveadpasilgeltrrideasgrlrelhekealieeeiegfeqrleearrayselkakigglesdkrnila 381
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|320100561|ref|YP_004176153.1| 382 rrreledqlkrykellergicplclqpiphehgvklidevskgirdleekareteekrtgiaaeisrveeeirrleg 458
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|320100561|ref|YP_004176153.1| 459 evrgrkaerdrvrgeykkleeevrrlqltaekirsmlreaervraelsgaagledklkealskrssieaalrelrea 535
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|320100561|ref|YP_004176153.1| 536 ekglqaeireldsriarskasieyvekmiheierdeeelrrleeekmfhewmlallaslnevvdevekrvslevvqe 612
                                       ***************************************************************************** PP

                                       ..........................................CS-HHHHHHHHHHHHHH....HHCCS-...-SEEE CS
                                       ..........................................xxxxxxxxxxxxxxxxx....xxxxxx...xxxxx RF
                             SMC_N 136 ..........................................lLSgGektLvalaLlfA....iqkvkp...aplyl 163
                                                                                 +LSgG+   ++la ++A    +++++p   + + +
  gi|320100561|ref|YP_004176153.1| 613 frrrfyailgtlmreqpvevvvrddftleskvkiggkayaisSLSGGQSIAISLAYRLAlnatVRAYSPflrNTVLI 689
                                       ***********************************************************666644444422257789 PP

                                       ECTTTTTS-HHHHHHHHHHHH.......HHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF
                             SMC_N 164 lDeidaaLDeknvkkvaellk.......eksknaQfivislre 199
                                       lDe      ++ v+++ e l+       + ++  Q+iv++++e
  gi|320100561|ref|YP_004176153.1| 690 LDEPTTGFSQELVRRLGEALRlmssargQGQEGGQIIVVTHDE 732
                                       ***9999999999999999985544333334558999999976 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 !    8.3   0.0    0.0043       1.8       1      36 [.      26      58 ..      26     155 .. 0.69
   2 ?    2.2   3.0      0.31   1.3e+02      59     215 ..     191     353 ..     184     400 .. 0.86
   3 !   29.8   0.8   1.2e-09   5.2e-07     219     301 ..     626     734 ..     511     736 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0043
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdel 36
                                      ++v+ G+ gsGK+++L   + +      ++++  ++
  gi|320100561|ref|YP_004176153.1| 26 VTVIHGATGSGKTSILMSVSAAL---FGLQRESRDP 58
                                      69**************9887663...3333333333 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.31
                            AAA_21  59 efeieeflsqgvryryglrlersqv..eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvs 133
                                       ++  ++++s++v+   + r+++ +   e+ +++++++ +  ll  k+ l  e++ + +ar+++  + ++++++++++
  gi|320100561|ref|YP_004176153.1| 191 KYKEYKKNSEEVENIIRSRVDELARnmERLKTRLRERSKESLLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIERE 267
                                       56677888899999999999999999*************************************************** PP

                            AAA_21 134 epndlqfgkaltditsrawsllllldglrke....rigllnifadyfgfakekrllqrlvrslklveielsdlgege 206
                                       +   ++ ++   +++sr+++++ l   lr+     +   + i + ++ +a++++ l+r++++ + +  el+  ++ +
  gi|320100561|ref|YP_004176153.1| 268 QRLLMEAEREVAELKSRIEQARRLEARLREIegeiAGVAAGIGGVEADPASILGELTRRIDEASGRLRELHEKEALI 344
                                       ************************99999999988777788888888888888888888888888888777777766 PP

                            AAA_21 207 eliasvder 215
                                       e+  + +e+
  gi|320100561|ref|YP_004176153.1| 345 EEEIEGFEQ 353
                                       666665555 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 1.2e-09
                            AAA_21 219 r............gvvflengdgqelparelSdGtkrllalltallralkkg........sllliDEpEngLHPkll 275
                                       r            ++   ++ +g+   +++lS G+  ++ l+  l+  +  +        ++l++DEp +g   +l+
  gi|320100561|ref|YP_004176153.1| 626 ReqpvevvvrddfTLESKVKIGGKAYAISSLSGGQSIAISLAYRLALNATVRayspflrnTVLILDEPTTGFSQELV 702
                                       04444445555556666666677778899999999999988888888888889999********************* PP

                            AAA_21 276 rrllellkelsr......ngaQviltTHSpll 301
                                       rrl e l++ s+      +g+Q+i++TH+ ll
  gi|320100561|ref|YP_004176153.1| 703 RRLGEALRLMSSargqgqEGGQIIVVTHDELL 734
                                       ****9997777778899************887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3  10.2   0.00094       0.4       1     258 [.       1     304 [.       1     381 [. 0.51
   2 !   11.7   0.0   0.00037      0.16     220     366 ..     514     732 ..     427     734 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00094
                            AAA_15   1 MkIkkikikNFRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn...................... 54 
                                       M+I  + ++N Rs+++ ++ + ++ +tv+ G+ +sGK+sil+     l   ++ +                      
  gi|320100561|ref|YP_004176153.1|   1 MRIYGLMLENIRSFRKEYVVFPNKgVTVIHGATGSGKTSILMSVSAALFGLQRESrdpfrafayptgrdlvradass 77 
                                       88888999**********************************98764444434445667777777775444444444 PP

                            AAA_15  55 .......kkvikiekedleifeniseskdikIdvef...............................aekekakeye 93 
                                              +                                                           +         
  gi|320100561|ref|YP_004176153.1|  78 arirllfE---------------------------HngklylverefrrdgervvnaeynrleeyvvD--------- 118
                                       44333220...........................222222222222444444333322322222221......... PP

                            AAA_15  94 ktlkskekkkadlllkkkesdlkktikdkklklkknelsdekis...vekkks............kkelpkekeekl 155
                                           s+++  ++++++  +++l k++k+     +k + +   ++   +  + +            + +++   ++  
  gi|320100561|ref|YP_004176153.1| 119 ----SSGRVVNTNQWILSPTELNKRVKEILGIKEKAREQPLLFTsvlYAPQFNihevlslsdedrTEIIE---RSLG 188
                                       ....333333344444444444444443322222222111111100011111100000011100011111...1111 PP

                            AAA_15 156 ekekeelkidkedlkklikkleeslkkee........elknvlksaiiklllisakRnvsd.edsekkssllgklke 223
                                        ++ +e+k+++e+++++i+       +          +lk  l + ++++ll ++kR   + e +ek ++ + + +e
  gi|320100561|ref|YP_004176153.1| 189 LSKYKEYKKNSEEVENIIR-------SRVdelarnmeRLKTRLRERSKESLLEEKKRLTAEvEGYEKARTEKLRRLE 258
                                       1222222222222222222.......221223333344444444555555555555544333334443333333333 PP

                            AAA_15 224 kileealqekl............eeelteklkeiqeklkeidkklae 258
                                       +   ++ +e +             ++ +e++ +++  l+ei++++a 
  gi|320100561|ref|YP_004176153.1| 259 EVEASIERE-QrllmeaerevaeLKSRIEQARRLEARLREIEGEIAG 304
                                       333332222.1355666666666666677777777777777777665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00037
                            AAA_15 220 klkekileealqekleeelteklkeiqeklkeidkklaeelk..kilkkkidkik.kfnykgkkneeieik...... 287
                                       klke +++ ++ e +  el+e+ k +q +++e+d+ +a +++  + ++k i +i+ +++  +  +ee+ ++      
  gi|320100561|ref|YP_004176153.1| 514 KLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKAsiEYVEKMIHEIErDEEELRRLEEEKMFHewmlal 590
                                       33333333333333377888888888888888888887777788667777777776666666666665555777777 PP

                            AAA_15 288 ........................................................ddeelplnknGsGvqrlllli 308
                                                                                                +    ++  + G++ +++l+
  gi|320100561|ref|YP_004176153.1| 591 laslnevvdevekrvslevvqefrrrfyailgtlmreqpvevvvrddftleskvkiGGKAYAISSLSGGQSIAISLA 667
                                       777777777777777788888888888999999999***************************************** PP

                            AAA_15 309 llileaekk..dekeeknvilliEEPEahLHpqaqkvlikllkelandnkt.....QviitTHSp 366
                                       + ++ +      +   +n +l+++EP +    ++ + l ++l+ +++   +     Q+i+ TH +
  gi|320100561|ref|YP_004176153.1| 668 YRLALNATVraYSPFLRNTVLILDEPTTGFSQELVRRLGEALRLMSSARGQgqeggQIIVVTHDE 732
                                       *99888777444445569****************************9998899**********86 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.3e-08   9.6e-06       1      62 [.       1      60 [.       1     129 [. 0.93
   2 ?   -2.1   1.2       5.8   2.5e+03     157     166 ..     256     265 ..     204     299 .. 0.56
   3 ?   -0.4   0.3       1.8   7.5e+02     142     191 ..     321     370 ..     314     391 .. 0.58
   4 ?   -1.3   2.2       3.1   1.3e+03     135     200 ..     482     546 ..     432     553 .. 0.72
   5 ?   -0.4   2.2       1.7   7.3e+02     168     201 ..     514     547 ..     469     604 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.3e-08
                            AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkdnfl 62
                                      Mr+  L Le   +f  + + f+  ++++++i+G+  +GK+++l ++s+ lfG++++++d f+
  gi|320100561|ref|YP_004176153.1|  1 MRIYGLMLENIRSFRKEYVVFP--NKGVTVIHGATGSGKTSILMSVSAALFGLQRESRDPFR 60
                                      9********************9..89********************************9886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.8
                            AAA_27 157 slrevleaLe 166
                                       +l+ev +++e
  gi|320100561|ref|YP_004176153.1| 256 RLEEVEASIE 265
                                       2222222222 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.8
                            AAA_27 142 gelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeele 191
                                       gel++ + eas+ l++l+e  + +e+e + + ++ ++++ra+ e ++++ 
  gi|320100561|ref|YP_004176153.1| 321 GELTRRIDEASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIG 370
                                       45555555666666666655555555555444444444455555555554 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.1
                            AAA_27 135 ealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                       ++l  + +++ ++L ea+   a+l+   + Le++ +e  ++r+s ++a++e +e+ + +++e+re 
  gi|320100561|ref|YP_004176153.1| 482 RRLQLTAEKIRSMLREAERVRAELSG-AAGLEDKLKEALSKRSSIEAALRELREAEKGLQAEIREL 546
                                       44444555555666666665555554.456777777777777777777777777777777777765 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.7
                            AAA_27 168 eadelfkprkskkrainealeeleeakkelreaq 201
                                       + +e  ++r+s ++a++e +e+ + +++e+re +
  gi|320100561|ref|YP_004176153.1| 514 KLKEALSKRSSIEAALRELREAEKGLQAEIRELD 547
                                       4444444444444444444444444444444332 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   4.1     0.019       8.3      43     122 ..     217     300 ..     206     302 .. 0.75
   2 !   12.3   0.0    0.0003      0.13      46     116 ..     305     375 ..     296     383 .. 0.86
   3 ?    5.3   1.2     0.045        19      45     111 ..     420     489 ..     413     501 .. 0.48
   4 !   10.1   1.6    0.0015      0.63      61     116 ..     516     570 ..     491     581 .. 0.58
   5 !   10.4   1.4    0.0012       0.5      49     100 ..     524     575 ..     510     605 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.019
                           DUF1664  43 vesvskql.eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg...les 115
                                       +e++ ++l e+ +esl + k++L+++++  +k   e  +  +e+++ +++ ++ l e +++v ++k+ +e+   le+
  gi|320100561|ref|YP_004176153.1| 217 MERLKTRLrERSKESLLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIEREQRLLMEAEREVAELKSRIEQarrLEA 293
                                       55555555234458899999999999999999888888888888888888888888888888888888764344888 PP

                           DUF1664 116 kleriee 122
                                       +l++ie+
  gi|320100561|ref|YP_004176153.1| 294 RLREIEG 300
                                       8888875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0003
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       v+  +  v ++ a+   +L++rid+   +l e  e  + i+ee++  ++ l+e ++  +++k+ + gles 
  gi|320100561|ref|YP_004176153.1| 305 VAAGIGGVEADPASILGELTRRIDEASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESD 375
                                       556666666666777789*************************************************9985 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.045
                           DUF1664  45 svskqleqvseslaat...krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       +vsk + ++ e+ ++t   +  ++++i rv++++   +   +  k+e ++vr++ ++++e+v+ ++ + e
  gi|320100561|ref|YP_004176153.1| 420 EVSKGIRDLEEKARETeekRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAE 489
                                       3444433333333322110334555555555555555555555555555555555555555555555555 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0015
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       k+ Ls+r  ++++ l e  e+ k +++e+ e+ + +++ +  +e v+++++++e  
  gi|320100561|ref|YP_004176153.1| 516 KEALSKR-SSIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERD 570
                                       4555554.455666666666666666666666666666666666666666665532 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.0012
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseig 100
                                       ++e    +l+++ + L+++i ++d+++  +k+ ++ +++ ++e+++d +e++
  gi|320100561|ref|YP_004176153.1| 524 SIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEELR 575
                                       5666677777777777778888887777777777777777777777766665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   6.6e+02      20      32 ..      28      40 ..      23      62 .. 0.77
   2 !   12.6  13.3   9.1e-05     0.039     271     470 ..     200     393 ..     184     399 .. 0.76
   3 !    8.6   3.1    0.0015      0.63     393     471 ..     433     510 ..     412     513 .. 0.68
   4 !    8.8   8.9    0.0013      0.55     386     485 ..     482     582 ..     476     585 .. 0.84
   5 ?   -0.4   0.0      0.78   3.4e+02     493     570 ..     649     731 ..     636     737 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                            AAA_13 20 liYGwNGaGKTtL 32
                                      +i G+ G+GKT++
  gi|320100561|ref|YP_004176153.1| 28 VIHGATGSGKTSI 40
                                      89*********86 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.1e-05
                            AAA_13 271 aaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaK 347
                                       ++ e+ + ++++e  +++e+l++++ ++++e l + k+  +++   + +e+++ e  +++e++e++++  qr l + 
  gi|320100561|ref|YP_004176153.1| 200 EEVENIIRSRVDELARNMERLKTRLRERSKESLLEEKKRLTAE--VEGYEKARTEKLRRLEEVEASIEREQRLLMEA 274
                                       4445555555555555566665555444443333333333322..23445555555556777777777777777766 PP

                            AAA_13 348 rkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykkleka 424
                                         e+++   l+s  +++ +++  + ei+  ia   + +  +e++ +++  +l + ++ e+   l e+++k + +e++
  gi|320100561|ref|YP_004176153.1| 275 EREVAE---LKSRIEQARRLEARLREIEGEIAGVAAGIGGVEADPASILGELTR-RIDEASGRLRELHEKEALIEEE 347
                                       655554...777777778999999999999999999999999999999999999.789999**************** PP

                            AAA_13 425 ieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       ie  e++l+e+ ++  +l+++i  Le   r++     e++++Lk++
  gi|320100561|ref|YP_004176153.1| 348 IEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRELEDQLKRY 393
                                       ********************************************99 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0015
                            AAA_13 393 eeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLe...kqlrdekpaaeeinke 466
                                        e ++k        + +e+++ ++++++le ++   ++e +    e kkleee++ L+   +++r+  + ae +  e
  gi|320100561|ref|YP_004176153.1| 433 RETEEK-----RTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQltaEKIRSMLREAERVRAE 504
                                       222222.....234667888888889999999999999999999999999999998885555677888888888888 PP

                            AAA_13 467 Lkaf.G 471
                                       L+   G
  gi|320100561|ref|YP_004176153.1| 505 LSGAaG 510
                                       776555 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0013
                            AAA_13 386 anleeekeeakkklelhlveeleseld...eykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpa 459
                                        +l+  +e++++ l+    e++++el+    +++k+k++  + ++ e++l+e  ++ k l++ei+eL  ++   k +
  gi|320100561|ref|YP_004176153.1| 482 RRLQLTAEKIRSMLREA--ERVRAELSgaaGLEDKLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKAS 556
                                       55566667777777774..44555655445899******************************************** PP

                            AAA_13 460 aeeinkeLkafGlgeleLkfeeekkg 485
                                       +e ++k ++++ + e eL+  ee+k 
  gi|320100561|ref|YP_004176153.1| 557 IEYVEKMIHEIERDEEELRRLEEEKM 582
                                       ***********999999999999876 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.78
                            AAA_13 493 gsqaaetLSeGEktaIaflYFlkslk..eddseigkdkivviDDPvSSLDsnslf...ivfsliksrll.kkkkakQ 563
                                       ++ a  +LS G   aI + Y l++    ++ s +  +++ ++D P   ++++ +     +  l+ s  + + ++  Q
  gi|320100561|ref|YP_004176153.1| 649 KAYAISSLSGGQSIAISLAYRLALNAtvRAYSPFLRNTVLILDEPTTGFSQELVRrlgEALRLMSSA-RgQGQEGGQ 724
                                       444558999***********998877788999999**********9999998755111566677666.668999999 PP

                            AAA_13 564 lfiLTHn 570
                                       +++ TH 
  gi|320100561|ref|YP_004176153.1| 725 IIVVTHD 731
                                       9999996 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 !   19.5   0.9   1.6e-06   0.00066       9      51 ..     390     431 ..     383     432 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHHHH.. CS
                     Rad50_zn_hook   9 nkkieelkeakgcCPlCgReldeehrseLikelqsklerlpee 51 
                                        k+++el e++  CPlC +++++eh  +Li+e ++ +++l+e+
  gi|320100561|ref|YP_004176153.1| 390 LKRYKELLERG-ICPLCLQPIPHEHGVKLIDEVSKGIRDLEEK 431
                                       57889999999.*****************************98 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  15.6     0.074        32      87     147 ..     230     290 ..     177     307 .. 0.57
   2 !   19.0   5.4   1.9e-06   0.00082      23     138 ..     339     470 ..     329     484 .. 0.88
   3 ?    0.3  12.6         1   4.4e+02      52     132 ..     493     575 ..     472     585 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.074
                         PspA_IM30  87 realaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaaka 147
                                       + +l+e+k+l+ ++e++e+  ++     e++++++e+  + + e+++++ +lk+r ++a+ 
  gi|320100561|ref|YP_004176153.1| 230 ESLLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIEREQRLLMEAEREVAELKSRIEQARR 290
                                       3445555555555555555555555555555555555555555555555555555555543 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.9e-06
                         PspA_IM30  23 DPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkA...kaALtkg.............ee 83 
                                       + e ++e++i+  ++ l++ar+a  +++a+   le + ++  ++ ++le++    k++L++g               
  gi|320100561|ref|YP_004176153.1| 339 EKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRELEDQLkryKELLERGicplclqpiphehGV 415
                                       557889999999999999999999999999999999999999999999976522269***************98888 PP

                         PspA_IM30  84 eLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkell 138
                                       +L+ e+ + i +le++a++ e++ +  ++ +  +++++++le  ++  ka+++ +
  gi|320100561|ref|YP_004176153.1| 416 KLIDEVSKGIRDLEEKARETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRV 470
                                       9*********************************************999999865 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1
                         PspA_IM30  52 rqkqlerkleeqkeqakklekkAkaALtkg..eeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealet 126
                                       +  + +++++++   a+ le+k k+AL+k    e++ re+ +  k l+ ++++l+   a++++++e ++k + + e+
  gi|320100561|ref|YP_004176153.1| 493 SMLREAERVRAELSGAAGLEDKLKEALSKRssIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIER 569
                                       34444567888889999999999999999866677778888888888888888888888888888888888877777 PP

                         PspA_IM30 127 kieelk 132
                                         eel+
  gi|320100561|ref|YP_004176153.1| 570 DEEELR 575
                                       666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.9e-06    0.0017       8      50 ..      10      52 ..       5      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.9e-06
                            AAA_29  8 NWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      N  +f+++ + +  kg+t++ G++GsGK+++l +++a L + +
  gi|320100561|ref|YP_004176153.1| 10 NIRSFRKEYVVFPNKGVTVIHGATGSGKTSILMSVSAALFGLQ 52
                                      667899999999999*****************99999988765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00011     0.045      30      59 ..      21      51 ..      16     124 .. 0.62
   2 ?   -0.6   1.9         2   8.5e+02     103     103 ..     270     270 ..     198     365 .. 0.58
   3 ?   -0.9   0.0       2.5   1.1e+03      77     106 ..     605     633 ..     603     643 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava.t 59
                                       p ++++++ Ga+g+GKt +++++++a+  +
  gi|320100561|ref|YP_004176153.1| 21 FPNKGVTVIHGATGSGKTSILMSVSAALFgL 51
                                      6899**********************99853 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2
                            AAA_25 103 l 103
                                       l
  gi|320100561|ref|YP_004176153.1| 270 L 270
                                       2 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.5
                            AAA_25  77 vsaEdsedelrrRlravgealrddarllvl 106
                                       vs+E  + e+rrR++a++ +l + + + v+
  gi|320100561|ref|YP_004176153.1| 605 VSLEVVQ-EFRRRFYAILGTLMREQPVEVV 633
                                       5677777.9*******99988444444333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   4.3     0.084        36      14      79 ..     231     299 ..     226     312 .. 0.78
   2 !   10.0   0.4    0.0016      0.67      18     100 ..     319     398 ..     305     400 .. 0.92
   3 !   13.6   1.2   0.00012     0.049       5      85 ..     425     505 ..     421     517 .. 0.87
   4 ?    4.5   0.8     0.076        33      11      70 ..     514     573 ..     506     601 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.084
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-...-TTTTTGGGHHHHH CS
                        Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLe...klapqLldklkelk 79 
                                       + le ++ l +++e  ++   e  r +ee+++ ++  ++ + +A+r+v +L+   ++a +L+++l+e++
  gi|320100561|ref|YP_004176153.1| 231 SLLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIEREQRLLMEAEREVAELKsriEQARRLEARLREIE 299
                                       567888889999998766655555667999999999999999999999999844456777999999997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHH CS
                        Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnise 94 
                                       +l +l  ++++ +  l e++++ + ++e+++ + + +++Arr+ ++L+ ++  L++  +++  ++ +   l d++++
  gi|320100561|ref|YP_004176153.1| 319 ILGELTRRIDEASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRE---LEDQLKR 392
                                       56789999**********************************************9887999999998...9999999 PP

                                       HHHHHH CS
                        Laminin_II  95 ikelIa 100
                                        kel +
  gi|320100561|ref|YP_004176153.1| 393 YKELLE 398
                                       999987 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       +++ +e+a e++e+ +++++++++++e++ +++++v+  +++ +      +  +++v+ L+ +a+++ + l+e +  
  gi|320100561|ref|YP_004176153.1| 425 IRDLEEKARETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKIRSMLREAERV 501
                                       78999******************************999999999999999999999999999999999999988876 PP

                                       HHH. CS
                        Laminin_II  82 eeas 85 
                                       + + 
  gi|320100561|ref|YP_004176153.1| 502 RAEL 505
                                       6654 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.076
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70 
                                       ++ke l++   +++ l +++e  ++++++++e +  +  ++  i+ +++ + ++e+  ++
  gi|320100561|ref|YP_004176153.1| 514 KLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEE 573
                                       455555555555555555555555555555555555555555555555555554444333 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 !   16.5   2.8     2e-05    0.0083      17     123 ..     173     289 ..     164     306 .. 0.72
   2 ?    2.5   0.1      0.39   1.7e+02      55      93 ..     356     390 ..     341     402 .. 0.87
   3 ?   -1.7   0.1       8.1   3.5e+03      62      62 ..     537     537 ..     469     621 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2e-05
                          Gp-FAR-1  17 nltdeekaqlkevvkn...ykg.yknedellaalKkkspaLyekaeklqaklkekv.dkLspeakeFvkkli....a 84 
                                       +l+de++++++e       yk+  kn +e+ +++ ++ ++L+ ++e+l++ l+e+  ++L +e k ++ ++     a
  gi|320100561|ref|YP_004176153.1| 173 SLSDEDRTEIIERSLGlskYKEyKKNSEEVENIIRSRVDELARNMERLKTRLRERSkESLLEEKKRLTAEVEgyekA 249
                                       79********9976542125556789**************************9986368999999999998877664 PP

                          Gp-FAR-1  85 kgrkleaqvlagekpdlselkkv.aktifnkykslseeak 123
                                          kl+     +++++++++  + a+  +++ ks +e+a+
  gi|320100561|ref|YP_004176153.1| 250 RTEKLRRLEEVEASIEREQRLLMeAEREVAELKSRIEQAR 289
                                       4445555555555555554433215555666666655555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.39
                          Gp-FAR-1  55 ekaeklqaklkekvdkLspeakeFvkkliakgrkleaqv 93 
                                       e+a + +++lk+k+ +L+ + +    +++a  r+le+q 
  gi|320100561|ref|YP_004176153.1| 356 EEARRAYSELKAKIGGLESDKR----NILARRRELEDQL 390
                                       6788999***********9999....999999**99996 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 8.1
                          Gp-FAR-1  62 a 62 
                                       +
  gi|320100561|ref|YP_004176153.1| 537 K 537
                                       2 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0058       2.5      12      32 ..      25      45 ..      19      54 .. 0.85
   2 ?    8.1   0.3    0.0083       3.5      79     136 ..     595     694 ..     419     695 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0058
                                      SEEEEEESTTSSHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlklla 32
                                       +++i G +G+GK+++l+ ++
  gi|320100561|ref|YP_004176153.1| 25 GVTVIHGATGSGKTSILMSVS 45
                                      5789************98765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0083
                                       H................HHHTCHHHHHHHSTTGG............TTCBGESTTS.....GGS-HHHHHHHHHHHH CS
                                       x................xxxxxxxxxxxxxxxxx............xxxxxxxxxx.....xxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n................esdeeiekalsklglke............lkdtvvkssp.....ssLSgGqkqrvalara 122
                                       n                e +++++++l +l  ++               ++vk ++     ssLSgGq   ++la  
  gi|320100561|ref|YP_004176153.1| 595 NevvdevekrvslevvqEFRRRFYAILGTLMREQpvevvvrddftlE--SKVKIGGkayaiSSLSGGQSIAISLAYR 669
                                       04444444444444444333334444444443335555555555331..2222222335569********9999988 PP

                                       HHHTS...........SEEEEESTT CS
                                       xxxxx...........xxxxxxxxx RF
                          ABC_tran 123 llkkp...........kllllDEpt 136
                                       l+ ++           ++l+lDEpt
  gi|320100561|ref|YP_004176153.1| 670 LALNAtvrayspflrnTVLILDEPT 694
                                       8776511111222222578888887 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    0.0014       0.6       5      25 ..      24      44 ..      22      84 .. 0.85
   2 ?    3.3   0.5      0.21        91      54     116 ..     557     617 ..     513     635 .. 0.77
   3 ?   -1.1   0.0       5.1   2.2e+03      86     130 ..     676     730 ..     665     735 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                            AAA_22  5 agilvvtGesGtGKTtllrrl 25
                                      +g++v++G +G+GKT  l  +
  gi|320100561|ref|YP_004176153.1| 24 KGVTVIHGATGSGKTSILMSV 44
                                      899************987655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.21
                            AAA_22  54 kdllrellralglelka.erlsseell.ealeqalraravielliiDEaqh.lrseealeeLrsll 116
                                        +  +++ ++++++ ++ +rl++e ++ e +   l +       ++DE+++ + s e+++e+r+++
  gi|320100561|ref|YP_004176153.1| 557 IEYVEKMIHEIERDEEElRRLEEEKMFhEWMLALLASLNE----VVDEVEKrV-SLEVVQEFRRRF 617
                                       4556777777777777798999999998889999999999....*******99.999999997664 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5.1
                            AAA_22  86 lrarav...ielliiDEaqh.lrseealeeL....rsllnl...srkgvqliLvGt 130
                                       +ra++      +li+DE    + s+e+++ L    r ++     ++ g q+i+v +
  gi|320100561|ref|YP_004176153.1| 676 VRAYSPflrNTVLILDEPTTgF-SQELVRRLgealRLMSSArgqGQEGGQIIVVTH 730
                                       4444445555788888877766.655555543331333333665666666666655 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  14.0    0.0088       3.8     156     244 ..     204     293 ..     188     305 .. 0.50
   2 ?    9.3   1.6    0.0011      0.46     198     263 ..     331     396 ..     317     407 .. 0.75
   3 ?   10.3   7.7   0.00054      0.23     177     261 ..     419     506 ..     411     512 .. 0.87
   4 ?    5.5   8.2     0.016       6.8     199     266 ..     513     580 ..     508     584 .. 0.89
   5 ?    0.5   0.1      0.51   2.2e+02     122     146 ..     576     600 ..     573     610 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0088
                              Spc7 156 elLekqeeeldellpeleeekaeleee..leklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqle 230
                                       + + ++ +el + +++l+++  e ++e  le+ ++  +e+e ++k++ e+lr +l+e++a ie+ ++ l e +++++
  gi|320100561|ref|YP_004176153.1| 204 NIIRSRVDELARNMERLKTRLRERSKEslLEEKKRLTAEVEGYEKARTEKLR-RLEEVEASIEREQRLLMEAEREVA 279
                                       3333333333333333333333322221122222244456666666666666.467777777777777777777777 PP

                              Spc7 231 eleekieelkeqks 244
                                       el+++ie+++   +
  gi|320100561|ref|YP_004176153.1| 280 ELKSRIEQARRLEA 293
                                       77777766544333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgw 263
                                       + +L+el+e+ a +++eie ++++l+e ++   el++ki  l++ k+++ ++ +e e+ l++ k+ 
  gi|320100561|ref|YP_004176153.1| 331 SGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRELEDQLKRYKEL 396
                                       456778888888888888888888888888888888888888888888888888888777776655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00054
                              Spc7 177 aeleeeleklqeaaeelesid...keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeei 250
                                       +e+++ +++l+e+a+e e+      +e+  + ee+++l+ e++ +k+e ++++ + ++lee++  l+   +++++ +
  gi|320100561|ref|YP_004176153.1| 419 DEVSKGIRDLEEKARETEEKRtgiAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKIRSML 495
                                       56777788888877777773323589*************************************************** PP

                              Spc7 251 aeaervleeck 261
                                       +eaerv+ e  
  gi|320100561|ref|YP_004176153.1| 496 REAERVRAELS 506
                                       ******99865 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.016
                              Spc7 199 eeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwses 266
                                       ++L+e+ ++ ++++a ++e+++  + lq+++ el+++i+  k++++ +e+ i e er  ee ++ +e+
  gi|320100561|ref|YP_004176153.1| 513 DKLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEELRRLEEE 580
                                       78888889999999999999999999999999999999999999999999999999999999988765 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.51
                              Spc7 122 rlqakkdWYeWRmqllegLkeglee 146
                                       rl+ +k+  eW++ ll +L e+++e
  gi|320100561|ref|YP_004176153.1| 576 RLEEEKMFHEWMLALLASLNEVVDE 600
                                       88999***************99987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00052      0.22      23      54 ..      23      54 ..       7      63 .. 0.74
   2 ?   -1.8   0.4       6.5   2.8e+03      63     128 ..     179     253 ..     166     272 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00052
                                      TTSEEEEEESTTSTHHHHHHHHHHHH-S.... CS
                            ResIII 23 rdkrglikmaTGtGKTlvaaklierllkkgke 54
                                      ++   +i+ aTG+GKT +++++ ++l+  ++e
  gi|320100561|ref|YP_004176153.1| 23 NKGVTVIHGATGSGKTSILMSVSAALFGLQRE 54
                                      4445679**************99999876655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.5
                                       SHHHHHHHH..HHGGGGTGG...........GEEEESSS-B--...............-SEEEEEHHHHHHTH.... CS
                            ResIII  63 rkslleqtl..eefkkflseayke.......igkkvsgdkkka........kekdstnkkilvttiqsldadseeee 122
                                       r++++e+ l  +++k+++++  +        +    ++             ++ ++ +k+ l+++ ++l+a+ e  e
  gi|320100561|ref|YP_004176153.1| 179 RTEIIERSLglSKYKEYKKNSEEVeniirsrV----DE----LarnmerlkTRLRERSKESLLEEKKRLTAEVEGYE 247
                                       55566666555444444444432222222221....11....12223444445566667777777777777775554 PP

                                       ....HH CS
                            ResIII 123 eeseel 128
                                       ++++e+
  gi|320100561|ref|YP_004176153.1| 248 KARTEK 253
                                       444444 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   8.9       0.2        84      34      98 ..     231     295 ..     208     298 .. 0.85
   2 ?    5.8   0.4     0.017       7.2      37     109 ..     325     397 ..     317     402 .. 0.73
   3 ?   12.1   2.8    0.0002     0.087      19      97 ..     426     497 ..     414     507 .. 0.49
   4 ?    9.7   5.2    0.0012      0.49      20      87 ..     510     577 ..     504     632 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                           DUF3450  34 qsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98 
                                       +  +++++l+ e + +++  ++  ++le+ e+  e+ +rl+ ++e+e+a+l+ +ie+++++e++l
  gi|320100561|ref|YP_004176153.1| 231 SLLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIEREQRLLMEAEREVAELKSRIEQARRLEARL 295
                                       445677788888888888888899999*******************************9999887 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                           DUF3450  37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrL 109
                                       ++id+ +   +el ++   ++ee+e  e   e+ +r  ++++++i  le ++ +i + +rel+  l++  + L
  gi|320100561|ref|YP_004176153.1| 325 RRIDEASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRELEDQLKRYKELL 397
                                       5666666666777777777788888888888888888888888888888888888888888888777765555 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.0002
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                       ++++       ++a+++++k + ++ e + +++e+r+l+ e+   ++++++++   +++e+e+ +l+   e+i+ + 
  gi|320100561|ref|YP_004176153.1| 426 RDLE-------EKARETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKIRSML 495
                                       3444.......444555555555555555555555555555555555555555555555555555555555444443 PP

                           DUF3450  96 re 97 
                                       re
  gi|320100561|ref|YP_004176153.1| 496 RE 497
                                       33 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0012
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeq 87 
                                        ++++ ++a ++++++++   +l +  + l+ae+r+l +++++ ++  e++e+++ + e++ ++l++ 
  gi|320100561|ref|YP_004176153.1| 510 GLEDKLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEELRRL 577
                                       56777888888888888888888888888888888888888888888888888888877777776653 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00037      0.16      41      58 ..      26      43 ..       5      50 .. 0.76
   2 ?   -1.1   0.1       2.3   9.8e+02      87     132 ..     406     451 ..     405     497 .. 0.70
   3 ?   -1.2   0.0       2.4     1e+03     106     155 ..     591     637 ..     581     675 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                                      SEEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE 41 hllvaGatgsGKStalnt 58
                                       ++++GatgsGK+  l++
  gi|320100561|ref|YP_004176153.1| 26 VTVIHGATGSGKTSILMS 43
                                      379*************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                                       GTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHH CS
                      FtsK_SpoIIIE  87 lediphllsvavatdperalraleeLvkemeeryalfreagvrsia 132
                                       l+ iph   v+ ++++ + +r lee   e ee    ++++  r  +
  gi|320100561|ref|YP_004176153.1| 406 LQPIPHEHGVKLIDEVSKGIRDLEEKARETEEKRTGIAAEISRVEE 451
                                       6789999999999999999999999999988887766665444433 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHHH..HHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-.. CS
                      FtsK_SpoIIIE 106 lraleeLvkemeery..alfreagvrsiaaydgeiaedpldifgdvflvlDn 155
                                       l+ l+e+v+e+e+r   ++ +e++ r  a     + e+p++     ++v+D+
  gi|320100561|ref|YP_004176153.1| 591 LASLNEVVDEVEKRVslEVVQEFRRRFYAILGTLMREQPVE-----VVVRDD 637
                                       56789999999999977778888777777766666666666.....456655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00041      0.17      25      49 ..      25      49 ..      14     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00041
                            AAA_16 25 elvllsGesGvGKsslvrellrale 49
                                      ++++++G+ G+GK+s++ ++  al 
  gi|320100561|ref|YP_004176153.1| 25 GVTVIHGATGSGKTSILMSVSAALF 49
                                      6789*************99987654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0018      0.77       9      49 ..      23      63 ..      16      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0018
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillva 49
                                      +++v ++ +  G+GKT +l+ + a l  l++++ +++ + a
  gi|320100561|ref|YP_004176153.1| 23 NKGVTVIHGATGSGKTSILMSVSAALFGLQRESRDPFRAFA 63
                                      57889999**************9999888877777766655 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 ?    1.9   0.3      0.65   2.8e+02      46      55 ..     257     266 ..     202     300 .. 0.48
   2 ?   -0.3   0.0         3   1.3e+03      23      51 ..     322     350 ..     317     397 .. 0.62
   3 ?    6.3   0.0     0.027        12      19      87 ..     416     484 ..     413     486 .. 0.78
   4 ?    0.1   0.1       2.4     1e+03      51      51 ..     589     589 ..     491     612 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.65
                            DUF948  46 lkevedllak 55 
                                       l+eve+ ++ 
  gi|320100561|ref|YP_004176153.1| 257 LEEVEASIER 266
                                       3444444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3
                            DUF948  23 klkktldeaaatieelekqvdpilkeved 51 
                                       +l++ +dea+ +++el ++   i +e+e+
  gi|320100561|ref|YP_004176153.1| 322 ELTRRIDEASGRLRELHEKEALIEEEIEG 350
                                       56666666666666666555555444443 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.027
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +++ +++k ++ +++  +e+e++ ++i  e+ ++ +++++l  +v+++ ++ d++  + ++l e v+ l
  gi|320100561|ref|YP_004176153.1| 416 KLIDEVSKGIRDLEEKARETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRL 484
                                       445566777777777777777888888888888888888899999999999999999999999988877 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.4
                            DUF948  51 d 51 
                                       +
  gi|320100561|ref|YP_004176153.1| 589 A 589
                                       2 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.5   6.6e+02     179     279 ..     204     305 ..     189     315 .. 0.51
   2 ?    7.1   0.0    0.0034       1.5     278     330 ..     343     398 ..     327     403 .. 0.77
   3 ?    3.9   1.0     0.031        13     226     349 ..     436     557 ..     418     566 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                              Gp58 179 atlasdklglkaeiqasaqgLsqkyddeirkLsakitttssGtteayesk...LddlraeftrsnqGmrveleskis 252
                                       + ++s   +l  +++  ++ L ++  + + + + ++t   +G  +a  +k   L+++ a   r +q + +e e +++
  gi|320100561|ref|YP_004176153.1| 204 NIIRSRVDELARNMERLKTRLRERSKESLLEEKKRLTAEVEGYEKARTEKlrrLEEVEASIER-EQRLLMEAEREVA 279
                                       444444444555555555555555555554444444444444444444440003444444444.3446666667777 PP

                              Gp58 253 Glqstqqstakqisqeiknregavsrv 279
                                        l+s     a++++ ++++ eg+++ v
  gi|320100561|ref|YP_004176153.1| 280 ELKSRI-EQARRLEARLREIEGEIAGV 305
                                       777643.34666677777776666655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0034
                              Gp58 278 rvqqdldsyqrrlqdaeknyssLtqtvkGlqst...vsdpnsklesrvtqLadlie 330
                                        ++ +++++ +rl++a + ys L+  + Gl+s+   + +  ++le ++++ ++l+e
  gi|320100561|ref|YP_004176153.1| 343 LIEEEIEGFEQRLEEARRAYSELKAKIGGLESDkrnILARRRELEDQLKRYKELLE 398
                                       5788999***********************98622255677778777777777766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.031
                              Gp58 226 eskLddlraeftrsnqGmrveleskisGlqstqqstakqisqeiknregavsrvqqdldsyqrrlqdaeknyssLtq 302
                                       e+k  ++ ae +r +  +r  le ++ G    +++   ++  e k+ e++v r+q +++  ++ l++ae+  + L+ 
  gi|320100561|ref|YP_004176153.1| 436 EEKRTGIAAEISRVEEEIR-RLEGEVRG----RKAERDRVRGEYKKLEEEVRRLQLTAEKIRSMLREAERVRAELSG 507
                                       6677888899999999877.68999999....666777899999999999999999999999999999999999986 PP

                              Gp58 303 tvkGlqstvsdpnsklesrvtqLadlieq....kvtrgdvesiirqsgdsi 349
                                         +Gl+ ++++  sk +s  + L++l e     +    +++s i++s  si
  gi|320100561|ref|YP_004176153.1| 508 -AAGLEDKLKEALSKRSSIEAALRELREAekglQAEIRELDSRIARSKASI 557
                                       .57999998887776666655665555431011222334556666666665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00058      0.25       2      39 ..      25      65 ..      24      95 .. 0.85
   2 ?   -3.3   0.2       9.3     4e+03     204     230 ..     213     242 ..     192     265 .. 0.67
   3 ?   -0.2   0.2       1.1   4.7e+02     167     197 ..     547     583 ..     498     615 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00058
                           DUF2075  2 avvlVtGvaGtGKtvvllnllael...eddeeertavylsv 39
                                       v +++G++G+GKt +l+++ a+l   ++++++  +++++ 
  gi|320100561|ref|YP_004176153.1| 25 GVTVIHGATGSGKTSILMSVSAALfglQRESRDPFRAFAYP 65
                                      5899****************999988777777777776665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.3
                           DUF2075 204 vfddleelkkalkeknkesg...rsrlvat 230
                                       +++++e lk+ l+e++kes    + rl a 
  gi|320100561|ref|YP_004176153.1| 213 LARNMERLKTRLRERSKESLleeKKRLTAE 242
                                       677788888888888776543224555554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.1
                           DUF2075 167 qfRvaaseaviewvdalldgkkekakplss......q 197
                                         R+a+s+a ie+v++++ + +  +++l +       
  gi|320100561|ref|YP_004176153.1| 547 DSRIARSKASIEYVEKMIHEIERDEEELRRleeekmF 583
                                       3588999999999999987766666665445554444 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6       4.4   1.9e+03      18      48 ..     209     237 ..     193     301 .. 0.59
   2 ?    1.8   0.0      0.56   2.4e+02      13      54 ..     314     355 ..     302     379 .. 0.75
   3 ?    8.7   0.0    0.0039       1.7      26      80 ..     418     468 ..     416     487 .. 0.75
   4 ?    3.7   0.4      0.14        60      29      69 ..     515     554 ..     509     580 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.4
                              FlxA  18 qiasLqkQiknlqkqLkelsesdeltkeekk 48 
                                       ++ +L + +++l+  L+e s++     eekk
  gi|320100561|ref|YP_004176153.1| 209 RVDELARNMERLKTRLRERSKE--SLLEEKK 237
                                       4444555555555555544443..2222222 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.56
                              FlxA  13 sgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqli 54 
                                        + as + +L++ i++++  L+el e+++l +ee +  +q +
  gi|320100561|ref|YP_004176153.1| 314 ADPASILGELTRRIDEASGRLRELHEKEALIEEEIEGFEQRL 355
                                       555666778999999999999999999888888877555554 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0039
                              FlxA  26 iknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekq 80 
                                       i++++k +++l e+  +t+    +++  i a+I+ ++ +I++l+ + +  ++e +
  gi|320100561|ref|YP_004176153.1| 418 IDEVSKGIRDLEEKARETE----EKRTGIAAEISRVEEEIRRLEGEVRGRKAERD 468
                                       5566777777777733333....69******************999776666655 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.14
                              FlxA  29 lqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlq 69 
                                       l++ L++ s+  e    e ++ ++ +qa+I  l + Ia+ +
  gi|320100561|ref|YP_004176153.1| 515 LKEALSKRSSI-EAALRELREAEKGLQAEIRELDSRIARSK 554
                                       45555555555.56666788999999999999999999865 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 ?    7.8  12.0    0.0078       3.3      81     186 ..     186     302 ..     155     304 .. 0.57
   2 ?    7.8   2.9    0.0074       3.2      79     152 ..     322     398 ..     313     401 .. 0.82
   3 ?   11.7  10.2   0.00047       0.2      72     179 ..     430     550 ..     411     554 .. 0.82
   4 ?    5.4   4.8      0.04        17      58     128 ..     512     579 ..     506     612 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0078
                           UPF0242  81 d......eglktkeealeel.qeeeeeLkeeldakeeelerlk.....eenqqLqekleaiae...dfeelklelee 142
                                       +      +++k++ e++e+  +++ +eL+++++  ++ l+++      ee++ L  + e   +   +  + + e+e+
  gi|320100561|ref|YP_004176153.1| 186 SlglskyKEYKKNSEEVENIiRSRVDELARNMERLKTRLRERSkesllEEKKRLTAEVEGYEKartEKLRRLEEVEA 262
                                       23333333445555555553245555555555555555554440000034444444443322244466666778888 PP

                           UPF0242 143 qLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEi 186
                                        ++++q ll e ++++ e++s +    +q  +Le++ r +  Ei
  gi|320100561|ref|YP_004176153.1| 263 SIEREQRLLMEAEREVAELKSRI----EQARRLEARLREIEGEI 302
                                       89999999999888888877655....67788888888777666 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0074
                           UPF0242  79 eldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqek...leaiaedfeelkleleeqLaekqellq 152
                                       el   +++    l+el e+e   +ee++  e+ le+ ++   +L+ k   le  ++++ + ++ele+qL++ +ell+
  gi|320100561|ref|YP_004176153.1| 322 ELTRRIDEASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKiggLESDKRNILARRRELEDQLKRYKELLE 398
                                       555566777779999***********999999999999999999998444566677999999********9999986 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00047
                           UPF0242  72 ekeaklteld...........eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelk 137
                                       ek +   e++           e+++  e +++ +++e ++ + e+++ eee++rl+   +++++ l ++ +  +el+
  gi|320100561|ref|YP_004176153.1| 430 EKARETEEKRtgiaaeisrveEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKIRSMLREAERVRAELS 506
                                       33333333334444444566699999999***************************************999888887 PP

                           UPF0242 138 le..leeqLaekqellqeyqetieeqrsvlekrqdqieqLeskV 179
                                        +  le++L+e   + +  ++ + e+r+  +  q++i +L+s++
  gi|320100561|ref|YP_004176153.1| 507 GAagLEDKLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRI 550
                                       54238*************************************98 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.04
                           UPF0242  58 ekalkekl.ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqeklea 128
                                       e++lke l + s +e+  + l e +   k  + +++el ++  + k  +++ e+ +++ ++++++L+ +le+
  gi|320100561|ref|YP_004176153.1| 512 EDKLKEALsKRSSIEAALRELREAE---KGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEELR-RLEE 579
                                       4455554433344444444444444...666666666666666666667777777777777777776.4443 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7  18.3      0.61   2.6e+02     109     251 ..     221     387 ..     180     401 .. 0.51
   2 ?   12.0   8.4   0.00022     0.094     117     228 ..     432     559 ..     415     594 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.61
                           DUF4407 109 daelaeeqqeeakelkeqlaaa.................ltaelaeleaqiaalqaeidaaearldalraeaqk..e 166
                                       +++l+e+ +e+  e k++l+a+                  +a ++++++ + ++++e++++++r++++r+  ++  e
  gi|320100561|ref|YP_004176153.1| 221 KTRLRERSKESLLEEKKRLTAEvegyekarteklrrleeVEASIEREQRLLMEAEREVAELKSRIEQARRLEARlrE 297
                                       34444444444444444444445555555555555555555555555555557777777777777766665443113 PP

                           DUF4407 167 ldgtk...gtgttgvaGkgpaakekkaqldaaqaelaelkakld........atarlaalraelaeleaerakeraa 232
                                       ++g+           aG g +     + l +++++++e++++l+         +++++  +++l+e+++++++ +a+
  gi|320100561|ref|YP_004176153.1| 298 IEGEIagvA------AGIGGVEADPASILGELTRRIDEASGRLRelhekealIEEEIEGFEQRLEEARRAYSELKAK 368
                                       333322221......44444444444444444444444444444555555684444444444444444444444444 PP

                           DUF4407 233 sqaaaaaddGllarleald 251
                                           +++++ +lar + l+
  gi|320100561|ref|YP_004176153.1| 369 IGGLESDKRNILARRRELE 387
                                       4444444444444444433 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
                           DUF4407 117 qeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...................gtg 174
                                       ++e++e ++       ae+++ e++i++l++e++  +a++d+ r e++k  +  +                    ++
  gi|320100561|ref|YP_004176153.1| 432 ARETEEKRTG----IAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRrlqltaekirsmlreaervRAE 504
                                       2233333333....334444444444433333333333333333333333222222223223344455566777444 PP

                           DUF4407 175 ttgvaGkgpaake...kkaqldaaqaelaelkakldatarlaalraelaeleaerak 228
                                        +g aG ++  ke   k++ ++aa +el e+++    +a++ +l++++a+ +a ++ 
  gi|320100561|ref|YP_004176153.1| 505 LSGAAGLEDKLKEalsKRSSIEAALRELREAEKG--LQAEIRELDSRIARSKASIEY 559
                                       4444444444444222666666666666666666..666666666666665554443 PP

>> DUF842  Eukaryotic protein of unknown function (DUF842)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.062        26      57      99 ..     337     379 ..     327     401 .. 0.74
   2 ?    5.9   0.1     0.022       9.6      47      81 ..     522     556 ..     471     603 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.062
                            DUF842  57 lqkaqkvvqqEleqfqerLqrcvmvCqdkakdklgp.nssekqt 99 
                                       l++ ++++++E+e f++rL++ + +++ ++k k+g  +s +++ 
  gi|320100561|ref|YP_004176153.1| 337 LHEKEALIEEEIEGFEQRLEE-ARRAYSELKAKIGGlESDKRNI 379
                                       5677889************98.5789999999996643333333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.022
                            DUF842  47 eqCvekCseplqkaqkvvqqEleqfqerLqrcvmv 81 
                                        + +e + ++l++a+k +q E+ ++ +r+ r+  +
  gi|320100561|ref|YP_004176153.1| 522 RSSIEAALRELREAEKGLQAEIRELDSRIARSKAS 556
                                       678999999*********************98654 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 ?    9.1   8.2     0.002      0.87      41     139 ..     194     288 ..     189     305 .. 0.56
   2 ?    7.2   0.7    0.0077       3.3      80     130 ..     320     370 ..     312     397 .. 0.81
   3 ?    3.4  11.8      0.11        47      46     206 ..     418     577 ..     415     585 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                        MscS_porin  41 elqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrper 117
                                       e++k+ ++  + +r+   el++      e  k++l++ s e L  + +   ++++  ++++++   +l e + ++er
  gi|320100561|ref|YP_004176153.1| 194 EYKKNSEEVENIIRSRVDELARN----MERLKTRLRERSKESLLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIER 266
                                       55555555555555555555555....55555555555555555555555555555555555555555555555555 PP

                        MscS_porin 118 aqqqltearqrlqeirnrLnst 139
                                        q  l ea ++ +e+ +r+++ 
  gi|320100561|ref|YP_004176153.1| 267 EQRLLMEAEREVAELKSRIEQA 288
                                       5555555555555555555444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0077
                        MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlq 130
                                       l eL +r++++s +l el e+ a +++++   ++r+e+a+ + +e + ++ 
  gi|320100561|ref|YP_004176153.1| 320 LGELTRRIDEASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIG 370
                                       668999999999999999999999999999999999999999999887765 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.11
                        MscS_porin  46 iddaPkelrelqqelealqkkkeeaskeila.klsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqq 121
                                       id+  k +r+l+++  + ++k +   +ei + +  ++ Le ++  ++++  +++ + ++l+++++ lq   e++++ 
  gi|320100561|ref|YP_004176153.1| 418 IDEVSKGIRDLEEKARETEEKRTGIAAEISRvEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKIRSM 494
                                       56666666666666666633333333333322456789999999999999999999999999999999999999999 PP

                        MscS_porin 122 ltearqrlqeirnrLnstaaage.alsqaqrtalqaelaaleaqiee..leqellsnnnrqeLlklqrdllklriqq 195
                                       l ea +  +e++       a+ e +l +a+     +e a++e++ +e  l+ e    + r++ +k+  ++ ++ i +
  gi|320100561|ref|YP_004176153.1| 495 LREAERVRAELSG----A-AGLEdKLKEALSKRSSIEAALRELREAEkgLQAEIRELDSRIARSKASIEYVEKMIHE 566
                                       9999887777766....2.2222366666666666666666665544338999999999999999999999999988 PP

                        MscS_porin 196 leqelqaLqel 206
                                       +e+  + L+ l
  gi|320100561|ref|YP_004176153.1| 567 IERDEEELRRL 577
                                       88877777655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1  16.1       1.2   5.2e+02      18     100 ..     210     287 ..     187     304 .. 0.56
   2 ?    9.7   7.0    0.0028       1.2      20      99 ..     322     398 ..     318     401 .. 0.86
   3 ?   10.6   9.1    0.0015      0.63      34     101 ..     427     491 ..     415     505 .. 0.67
   4 ?    3.7  14.9       0.2        85      13     103 ..     493     576 ..     487     604 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.2
                            APG6_N  18 leqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleal 94 
                                       ++++ + ++ +++ l++  ke+       ee ++l  e+e  ek++ e+l+ L+e+e+  e+ ++ l ++e+e ++l
  gi|320100561|ref|YP_004176153.1| 210 VDELARNMERLKTRLRERSKES-----LLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIEREQRLLMEAEREVAEL 281
                                       3333333333333333333332.....23455666666666666666666666666666666666666666666665 PP

                            APG6_N  95 eeeeer 100
                                       +   e+
  gi|320100561|ref|YP_004176153.1| 282 KSRIEQ 287
                                       554333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0028
                            APG6_N  20 qaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96 
                                       ++++ +d+ +  l++l++++   e   ee+e  e++le+ +++ +el +++  le+ ++++ a +++le +l++ +e
  gi|320100561|ref|YP_004176153.1| 322 ELTRRIDEASGRLRELHEKEALIE---EEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRELEDQLKRYKE 395
                                       566777777888888888866655...8********************************************99988 PP

                            APG6_N  97 eee 99 
                                         e
  gi|320100561|ref|YP_004176153.1| 396 LLE 398
                                       766 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0015
                            APG6_N  34 klkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                                        l+++++e+   +e++  +  e++++e+e ++l+ e +  ++er++++ e ++leee ++l+   e+ 
  gi|320100561|ref|YP_004176153.1| 427 DLEEKARET---EEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKI 491
                                       444444443...46777777778888888888888888888888888888888888877777666554 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.2
                            APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaalee 89 
                                        + ++ e++++e       ++klk+         +++ ++e  l++l+++e+ l++e++el++  ++ +a ++  e+
  gi|320100561|ref|YP_004176153.1| 493 SMLREAERVRAELSGAAGLEDKLKEA-------LSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEK 562
                                       45666666666666666677777766.......34677888899999999999999999999999998888888888 PP

                            APG6_N  90 elealeeeeerfwr 103
                                          ++e++ee+  r
  gi|320100561|ref|YP_004176153.1| 563 MIHEIERDEEELRR 576
                                       88877776666543 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  10.2   0.00092      0.39      68     148 ..     221     304 ..     178     313 .. 0.73
   2 ?    4.1   6.3      0.12        49     122     184 ..     324     386 ..     317     399 .. 0.56
   3 ?    8.2   8.0    0.0062       2.7     102     170 ..     423     491 ..     416     505 .. 0.57
   4 ?    1.4  11.5      0.77   3.3e+02      78     153 ..     503     578 ..     487     604 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00092
                             ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraa...letklkd 141
                                       ++  ++ + +sl ++ ++l +e++   k+r+e   rl e+++++++ ++ l+e e+++ael++++++   le +l++
  gi|320100561|ref|YP_004176153.1| 221 KTRLRERSKESLLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIEREQRLLMEAEREVAELKSRIEQarrLEARLRE 297
                                       44456777899999************************************************988762225556665 PP

                             ATG16 142 reeelre 148
                                        e e+++
  gi|320100561|ref|YP_004176153.1| 298 IEGEIAG 304
                                       5555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.12
                             ATG16 122 eerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENkeL 184
                                       ++r++e++ + ++l +k +  eee+++ e+ +++ + ++s L+ +   +E+ +r++ +  +eL
  gi|320100561|ref|YP_004176153.1| 324 TRRIDEASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRREL 386
                                       556666666666666666666666666666666666666666666666666555443333333 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0062
                             ATG16 102 qrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqa 170
                                       + +++l+e+ ++ eek +  ++++ ++e+e+++le +++ r++e    +   ++l +E+  Lql+++++
  gi|320100561|ref|YP_004176153.1| 423 KGIRDLEEKARETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKI 491
                                       345555555555555555555555555555555555555555555555555556666666666555554 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.77
                             ATG16  78 sleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklv 153
                                       +  +  a l + l+e++ +r+  +  l+el e+ + l+++++e ++r+a+ +a+++ +e+ + + e   +e+++l 
  gi|320100561|ref|YP_004176153.1| 503 AELSGAAGLEDKLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEELRRLE 578
                                       4444445566667777777777777777777777777777777777777777777777766666655555555554 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  19.8    0.0012      0.51      98     240 ..     195     358 ..     176     365 .. 0.73
   2 ?    3.8  24.4     0.036        15      24     235 ..     357     579 ..     356     604 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                               MAD  98 klaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqli...........qqlekkqk 163
                                        +++ +ev++ ++ ++ el+r++e+ +  l+e+++e   l e+++ l ++++++e+ +           ++ e +q+
  gi|320100561|ref|YP_004176153.1| 195 YKKNSEEVENIIRSRVDELARNMERLKTRLRERSKES--LLEEKKRLTAEVEGYEKARteklrrleeveASIEREQR 269
                                       3456788999999999999999999999998877652..3333333333333333333333344445559999**** PP

                               MAD 164 elaeaeqrikeLefeiqsqeddslivknskselaripe............lekelerlreenkklnelkenkelLkE 228
                                        l eae  + eL+ +i++    ++ +++++ e+a ++             l ++ +r  e   +l+el+e   l++E
  gi|320100561|ref|YP_004176153.1| 270 LLMEAEREVAELKSRIEQARRLEARLREIEGEIAGVAAgiggveadpasiLGELTRRIDEASGRLRELHEKEALIEE 346
                                       ******************999999999999998877533333333333336677888999999************** PP

                               MAD 229 evedlkkkLere 240
                                       e+e+++++Le  
  gi|320100561|ref|YP_004176153.1| 347 EIEGFEQRLEEA 358
                                       *********965 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.036
                               MAD  24 ehkrarielekkasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekeskla 100
                                       e +ra  el++k   l+ +  +  +r +el++++k++++  e     l  q   +    k  ++++k  ++ e+k  
  gi|320100561|ref|YP_004176153.1| 357 EARRAYSELKAKIGGLESDKRNILARRRELEDQLKRYKELLERGICPLCLQPIPHEHGVKLIDEVSKGIRDLEEKAR 433
                                       6789999999999999999999999**********999999888777777766777789999999999999999999 PP

                               MAD 101 earevisalknelaelkrqiekqelelsekeseleelq...erldllkkklseleqli.......qqlekkqkelae 167
                                       e +e  + +  e+++ +++i++ e e++ ++ e  +++   ++l+++ ++l+ + ++i       +   ++ +  a 
  gi|320100561|ref|YP_004176153.1| 434 ETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRgeyKKLEEEVRRLQLTAEKIrsmlreaERVRAELSGAAG 510
                                       99999999999999999999999999999999988887333344555556665556656666666888888888899 PP

                               MAD 168 aeqrikeLefeiqsqeddslivknsksel.aripelekelerlreenkklnelkenkelLkEevedlkk 235
                                        e+++ke   + +s e    +++++++ l a i el++ ++r ++ +++ +++++++e  +Ee+  l++
  gi|320100561|ref|YP_004176153.1| 511 LEDKLKEALSKRSSIEAALRELREAEKGLqAEIRELDSRIARSKASIEYVEKMIHEIERDEEELRRLEE 579
                                       9******9999999999999***9999999**************************9999999988876 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 ?    2.1   7.7      0.16        69     167     240 ..     197     271 ..     139     284 .. 0.72
   2 ?    8.3   0.2    0.0022      0.93     169     245 ..     284     368 ..     278     399 .. 0.78
   3 ?    3.8   3.9     0.051        22     179     243 ..     438     505 ..     428     528 .. 0.76
   4 ?    6.4   3.2    0.0078       3.3     185     245 ..     520     581 ..     508     624 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.16
                        Fmp27_WPPW 167 dpervqkelleeRleeleeqiekleekleelelkseke.deelkeeieelekeikelkeklefletlledlkese 240
                                       +  +  ++++++R++el +++e+l+++l+e +++s  e +++l++e+e +ek   e  ++le +e+ +e+ ++  
  gi|320100561|ref|YP_004176153.1| 197 KNSEEVENIIRSRVDELARNMERLKTRLRERSKESLLEeKKRLTAEVEGYEKARTEKLRRLEEVEASIEREQRLL 271
                                       444555789********************9999988876888999999999888888888888888777655554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0022
                        Fmp27_WPPW 169 ervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse. 244
                                       +  q++ le Rl+e+e +i+ +   ++ +e +  +   el+++i+e +  ++el+ek  ++e+ +e ++++ e+++ 
  gi|320100561|ref|YP_004176153.1| 284 RIEQARRLEARLREIEGEIAGVAAGIGGVEADPASILGELTRRIDEASGRLRELHEKEALIEEEIEGFEQRLEEARr 360
                                       556889999********************9999999999******************************99987664 PP

                        Fmp27_WPPW 245 .......e 245
                                              +
  gi|320100561|ref|YP_004176153.1| 361 ayselkaK 368
                                       44433330 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.051
                        Fmp27_WPPW 179 Rleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlkeseess 243
                                         + + ++i+++ee++++le + + +   +++++ e+++le+e+++l+   e ++++l++ ++ +++ 
  gi|320100561|ref|YP_004176153.1| 438 KRTGIAAEISRVEEEIRRLEGEVRGRkaeRDRVRGEYKKLEEEVRRLQLTAEKIRSMLREAERVRAEL 505
                                       45668889999999999999887776677788999************************998877643 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0078
                        Fmp27_WPPW 185 eqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse.....e 245
                                       ++++++e +l+el +     ++ l++ei+el + i++ k ++e +e+++++++++ee+ +     +
  gi|320100561|ref|YP_004176153.1| 520 SKRSSIEAALRELREA----EKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEELRrleeeK 581
                                       3334444444444444....556******************************9998544554321 PP

>> 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 ?    0.9   0.9      0.44   1.9e+02     186     261 ..     227     298 ..     206     308 .. 0.79
   2 ?    7.4   0.0    0.0047         2     187     245 ..     340     398 ..     331     405 .. 0.92
   3 ?    1.0   0.5      0.42   1.8e+02     185     225 ..     533     574 ..     526     611 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.44
                        Effector_1 186 eakdklakEkeqvrkdlksaekAkekvkellkrveadkkltteqkaklkdelngYadeleaiveqLaelkvllrkl 261
                                       + k+ l +Ek+++ + ++  ekA++     l++vea  ++  eq+  +  e++  + el+  +eq   l+  lr++
  gi|320100561|ref|YP_004176153.1| 227 RSKESLLEEKKRLTAEVEGYEKARTEKLRRLEEVEA--SIEREQRLLM--EAEREVAELKSRIEQARRLEARLREI 298
                                       66788999***************9999999999998..4666776555..55566777777777777777777766 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0047
                        Effector_1 187 akdklakEkeqvrkdlksaekAkekvkellkrveadkkltteqkaklkdelngYadele 245
                                        ++ +++E+e  ++ l++a++A   +k+ +   e dk+   +++ +l d+l+ Y + le
  gi|320100561|ref|YP_004176153.1| 340 KEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRELEDQLKRYKELLE 398
                                       5667899******************************9999*************99886 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.42
                        Effector_1 185 eeakdklakEkeqvrkdlksaekAkekvkellkrveadk.kl 225
                                        ea++ l+ E+  ++  +  +++ +e v+++++++e d+ +l
  gi|320100561|ref|YP_004176153.1| 533 REAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEeEL 574
                                       678889999999999999999999999999999999987433 PP

>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  10.7     0.016         7     158     348 ..     163     381 ..     137     485 .. 0.59
   2 ?    4.3   7.2      0.06        26     184     296 ..     487     585 ..     467     647 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                         Cas_DxTHG 158 dPildlteflels........dwltaverflktg.daeklaellrekkekkkeklkklkklkeklkkeleefskale 225
                                       +P +++ e+l+ls        + + +++++ +++ + e                     ++++ +++ ++e+++++e
  gi|320100561|ref|YP_004176153.1| 163 APQFNIHEVLSLSdedrteiiERSLGLSKYKEYKkNSE---------------------EVENIIRSRVDELARNME 218
                                       56667777777775522222222222333333333333.....................666666666666666666 PP

                         Cas_DxTHG 226 lirplell.ekaekleke..............iveklk..eeleeiesleeeesakplel..........lldeikk 275
                                        ++  +l   ++e+l +e                   +  ++le               +          ll+e ++
  gi|320100561|ref|YP_004176153.1| 219 RLK-TRLReRSKESLLEEkkrltaevegyekaRT---EklRRLE---------------EveasiereqrLLMEAER 276
                                       666.222211222222221222222332211111...1112222...............122222222223444444 PP

                         Cas_DxTHG 276 klekf.........................................lkkqikwclekgliqqaltllreliisllle 311
                                       +++++                                         l          ++i +a   lrel  + +l 
  gi|320100561|ref|YP_004176153.1| 277 EVAELksrieqarrlearlreiegeiagvaagiggveadpasilgeL---------TRRIDEASGRLRELHEKEALI 344
                                       33333444444466666666666665555777777666655554432.........455666666777777222222 PP

                         Cas_DxTHG 312 gedilnkkkrreeieeelknlskvekksseekeekls 348
                                       +e+i   ++r ee+++++++l+ ++   +++k++ l+
  gi|320100561|ref|YP_004176153.1| 345 EEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILA 381
                                       5566666666666666665555555444443333333 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.06
                         Cas_DxTHG 184 daeklaellre.kkekkkeklkklkklkeklkkeleefskalelirplellekaeklekeiveklkeeleeieslee 259
                                        aek++++lre ++  ++++l+ ++ l++klk++l++ s +  ++r  el e+++ l+ e +++l    ++  ++++
  gi|320100561|ref|YP_004176153.1| 487 TAEKIRSMLREaER--VRAELSGAAGLEDKLKEALSKRSSIEAALR--ELREAEKGLQAE-IREL---DSR--IARS 553
                                       78999999966422..333355666888888888888888888888..333333344444.2222...222..2333 PP

                         Cas_DxTHG 260 eesakplellldeikkklekf..lkkqikwclekgliqq 296
                                       ++s+++ e++++ei++  e++  l        e +++++
  gi|320100561|ref|YP_004176153.1| 554 KASIEYVEKMIHEIERDEEELrrL-------EEEKMFHE 585
                                       445555555555555555555221.......22222211 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 ?   -0.7   0.9       1.8   7.6e+02      32      65 ..     193     226 ..     180     231 .. 0.45
   2 ?    8.6   9.5    0.0024         1      24      93 ..     232     301 ..     227     309 .. 0.93
   3 ?    6.3   3.5     0.013       5.5      38     104 ..     330     396 ..     318     399 .. 0.79
   4 ?    9.1   5.7    0.0018      0.76      28     105 ..     425     502 ..     414     508 .. 0.60
   5 ?    3.9  15.4     0.069        29      39     164 ..     481     604 ..     475     612 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.8
                               GAS  32 KeeieelkkkeernekelseisqenkrlkepLkk 65 
                                       Ke  ++ ++ e+  + +++e++ + +rlk  L++
  gi|320100561|ref|YP_004176153.1| 193 KEYKKNSEEVENIIRSRVDELARNMERLKTRLRE 226
                                       2222223333333333333333333333333333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0024
                               GAS  24 NLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkar 93 
                                        Le  k+l  e+e  +k  +++ ++l+e+++  +r +  L +ae+ev+eL+ ++++ ++  ++l++++ +
  gi|320100561|ref|YP_004176153.1| 232 LLEEKKRLTAEVEGYEKARTEKLRRLEEVEASIEREQRLLMEAEREVAELKSRIEQARRLEARLREIEGE 301
                                       688899********************************************************99998765 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.013
                               GAS  38 lkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                          + ++   + + i++e +  ++ L++a++   eL++++   e+dk  + + +++l+++ k +k+l
  gi|320100561|ref|YP_004176153.1| 330 ASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRELEDQLKRYKEL 396
                                       5555555566666788999999999999999999999999999999998888888888888888876 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0018
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                       I+ l e+  e ++k +    e+s +++e +rl+ +++  ++e+++ r + k+ e++  +l+ + ++++++ +e +++
  gi|320100561|ref|YP_004176153.1| 425 IRDLEEKARETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKIRSMLREAERV 501
                                       55666666666666666666666666666666666666666666666666666666666666666666665555544 PP

                               GAS 105 k 105
                                       +
  gi|320100561|ref|YP_004176153.1| 502 R 502
                                       4 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.069
                               GAS  39 kkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrf 115
                                        ++ + +  ++  +  e +r + +L  a    ++L+++l + ++  ++l++l++  k l+ e+++l       +  +
  gi|320100561|ref|YP_004176153.1| 481 VRRLQLTAEKIRSMLREAERVRAELSGAAGLEDKLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKASI 557
                                       3444455556777888999********************************************************** PP

                               GAS 116 ekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaq 164
                                       e vek + e+++  e+ ++ + ++  +++ +L   l++l+e +++ e++
  gi|320100561|ref|YP_004176153.1| 558 EYVEKMIHEIERDEEE-LRRLEEEKMFHEWMLAL-LASLNEVVDEVEKR 604
                                       **********988777.67777777777777753.66666666666655 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3       3.9   1.7e+03       7      55 ..     197     237 ..     191     259 .. 0.56
   2 ?   -1.6   0.6       5.3   2.3e+03      29      60 ..     257     281 ..     225     303 .. 0.47
   3 ?    5.1   0.1     0.046        20      18      59 ..     326     367 ..     317     398 .. 0.48
   4 ?    7.6   0.0    0.0076       3.3       6      69 ..     433     496 ..     428     509 .. 0.91
   5 ?    2.5   0.6      0.28   1.2e+02      22      63 ..     511     552 ..     496     621 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.9
                             Sec34   7 skeeecdell.eqtdealeqLeeleekfksvsektsslheaceqlleeqk 55 
                                       +++ee+++++ +++de+ +++e l+++ ++ s+         e+llee+k
  gi|320100561|ref|YP_004176153.1| 197 KNSEEVENIIrSRVDELARNMERLKTRLRERSK---------ESLLEEKK 237
                                       555555555534566666666666655554433.........33333333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.3
                             Sec34  29 leekfksvsektsslheaceqlleeqkrleel 60 
                                       lee   s++ + +        l+e ++++ el
  gi|320100561|ref|YP_004176153.1| 257 LEEVEASIEREQRL-------LMEAEREVAEL 281
                                       22222222222222.......22222222222 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.046
                             Sec34  18 qtdealeqLeeleekfksvsektsslheaceqlleeqkrlee 59 
                                       ++dea   L+el+ek   ++e+ + ++++ e+  +  ++l+ 
  gi|320100561|ref|YP_004176153.1| 326 RIDEASGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKA 367
                                       455555555555555555555555555444444333333332 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0076
                             Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       +++ee+ + + +++++++e+++ le +++  +++  +++ + ++l ee +rl+ +ae+i++ L+
  gi|320100561|ref|YP_004176153.1| 433 RETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQLTAEKIRSMLR 496
                                       56788889999*************************************************9885 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.28
                             Sec34  22 aleqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                       ++++L+e  +k +s+++  ++l+ea + l +e ++l++    
  gi|320100561|ref|YP_004176153.1| 511 LEDKLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIAR 552
                                       455666666666666666666666666665555555433322 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 ?   -2.2   1.6       3.7   1.6e+03     188     227 ..     191     232 ..     135     291 .. 0.60
   2 ?   10.3   0.6    0.0006      0.25     106     181 ..     533     612 ..     529     640 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.7
                           DUF3818 188 eakkeeksasekeenedae..lfedlkellklylrerDkell 227
                                       ++k+ +k+++e e+  +++    ++ +e lk  lrer ke l
  gi|320100561|ref|YP_004176153.1| 191 KYKEYKKNSEEVENIIRSRvdELARNMERLKTRLRERSKESL 232
                                       333333333333332222211122333333444444444433 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0006
                           DUF3818 106 nedlkelekeikelekkidkseelieklkkfveaseeeqeeireeseeekl.dllvvilrseel..pklske.qlee 178
                                       +e  k l+ ei+el+++i +s+  ie ++k++++ e+++ee+r+  ee+   + ++++l s ++   +++k+ +le 
  gi|320100561|ref|YP_004176153.1| 533 REAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEELRRLEEEKMFhEWMLALLASLNEvvDEVEKRvSLEV 609
                                       556678999**************************999999999988888889999999887776877777734444 PP

                           DUF3818 179 vie 181
                                       v+e
  gi|320100561|ref|YP_004176153.1| 610 VQE 612
                                       443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.3     0.035        15     581     685 ..     166     266 ..     139     303 .. 0.54
   2 ?   -0.0   0.0      0.37   1.6e+02     667     711 ..     419     463 ..     406     484 .. 0.70
   3 ?    7.7   1.8    0.0018      0.75     201     352 ..     472     623 ..     439     636 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.035
                          Prominin 581 vdlsnlelLteeerkdLeklresglskihsslyleqlckkltkvnletlaekleelanelsngkknlkqslkneaqd 657
                                        +++++  L++e+r ++ + r+ glsk++  +  ++  ++++   +++la+++e l+++l ++    k+sl +e++ 
  gi|320100561|ref|YP_004176153.1| 166 FNIHEVLSLSDEDRTEIIE-RSLGLSKYKEYKKNSEEVENIIRSRVDELARNMERLKTRLRER---SKESLLEEKKR 238
                                       5666666666666666655.3446666654443333344456667777777777777777555...34444444444 PP

                          Prominin 658 lraiqqelvlplessvkklkksvkklde 685
                                       l a  + + +  +++++ l++   ++++
  gi|320100561|ref|YP_004176153.1| 239 LTAEVEGYEKARTEKLRRLEEVEASIER 266
                                       3333333333333333333333333333 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.37
                          Prominin 667 lplessvkklkksvkkldeensdlqesikkllaaveraenflkkn 711
                                       +++++ +++l+++ ++ +e+ ++++++i+++ ++++r+e +++ +
  gi|320100561|ref|YP_004176153.1| 419 DEVSKGIRDLEEKARETEEKRTGIAAEISRVEEEIRRLEGEVRGR 463
                                       455666677777777777777777777777777777777777654 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0018
                          Prominin 201 vqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglr 277
                                        + y++le++v   L+ + +++ + l+++ +      L+  + l ++lkea  + +++++ + eLr+  + L++ +r
  gi|320100561|ref|YP_004176153.1| 472 GE-YKKLEEEV-RRLQLTAEKIRSMLREAERVR--AELSGAAGLEDKLKEALSKRSSIEAALRELREAEKGLQAEIR 544
                                       44.77887655.567777888888887766655..778888888888888888888888888888888888888888 PP

                          Prominin 278 gvkrdlnqalsn.lCqseeCskilssl.eiekldtskcl..dqlpnvdevlealeevletnlssivkeglarlneip 350
                                       +   ++ ++ ++ +  ++  ++i++++ e  +l+ +k +    l  + ++ e ++ev +    ++v+e   r+ +i 
  gi|320100561|ref|YP_004176153.1| 545 ELDSRIARSKASiEYVEKMIHEIERDEeELRRLEEEKMFheWMLALLASLNEVVDEVEKRVSLEVVQEFRRRFYAIL 621
                                       88888888877755445777777655414567888888876445555555566666666666677777777887775 PP

                          Prominin 351 ek 352
                                        +
  gi|320100561|ref|YP_004176153.1| 622 GT 623
                                       54 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.5   0.00013     0.055      16     191 ..      23     267 ..      10     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                            AAA_11  16 eseitliqGPPGtgKTktivellsqll.................................................. 42 
                                       ++++t+i+G  G+gKT+ ++++ ++l                                                   
  gi|320100561|ref|YP_004176153.1|  23 NKGVTVIHGATGSGKTSILMSVSAALFglqresrdpfrafayptgrdlvradassarirllfehngklylverefrr 99 
                                       45689********************99*****99***9999999999999999999998888888888877777766 PP

                            AAA_11  43 ........sr........rkseeeksakpriLvCapSNaAvDellerllrglldsegekykpkivRvgneeerisea 103
                                               ++         +s +  ++++ iL  ++ N+ v e+l    +    +  e+  + +  +++++ +i ++
  gi|320100561|ref|YP_004176153.1| 100 dgervvnaEYnrleeyvvDSSGRVVNTNQWILSPTELNKRVKEILGI-KE----KAREQPLLFTSVLYAPQFNI-HE 170
                                       6665555511566656654589999******************9975.33....34444445555567777444.45 PP

                            AAA_11 104 vksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeek..........eklkkskekskskleqerrkl 170
                                       v s+s e ++e     +   ++ ke +k++e++++ +r++ +e ++          e++k+s  ++k++l++e +  
  gi|320100561|ref|YP_004176153.1| 171 VLSLSDEDRTEIIE-RSLGLSKYKEYKKNSEEVENIIRSRVDELARnmerlktrlrERSKESLLEEKKRLTAEVEGY 246
                                       66677444444433.445677777788888888888877777777777788888889999999999999******** PP

                            AAA_11 171 kkerkelskeleeaeesleee 191
                                       +k+r+e  ++lee+e+s+e+e
  gi|320100561|ref|YP_004176153.1| 247 EKARTEKLRRLEEVEASIERE 267
                                       ***************999843 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   4.1       0.1        44      41      84 ..     212     273 ..     178     307 .. 0.44
   2 ?    2.8   0.1      0.13        57      15      81 ..     331     396 ..     318     403 .. 0.48
   3 ?    8.9   1.4    0.0018      0.77       4      88 ..     418     501 ..     415     509 .. 0.81
   4 ?    4.0   2.5     0.058        25       5      73 ..     523     579 ..     506     613 .. 0.49

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                             TMPIT  41 kqkkrlkelksslkklkksvk..................eeeeeeveelkeelkerkkvlke 84 
                                       +  +++++lk++l++ +k++                   +e+ +++ee++++++++++ l e
  gi|320100561|ref|YP_004176153.1| 212 ELARNMERLKTRLRERSKESLleekkrltaevegyekarTEKLRRLEEVEASIEREQRLLME 273
                                       22233333333333222221111111111111122222223333333333333333333333 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                             TMPIT  15 eetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                       + + +e+++k + +++ ++ + +++++ ++ ++elk+++  l++++ ++   + +el+++lk+ k+ 
  gi|320100561|ref|YP_004176153.1| 331 SGRLRELHEKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDK-RNILARRRELEDQLKRYKEL 396
                                       3333344444444444445555555555555555555555555442.33344445555555555444 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0018
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       ++e++k +++lee+a+e ++k   +++ +s++ +ei++ + +++  k++ ++++ +  ++ eeev++l+ + +++++
  gi|320100561|ref|YP_004176153.1| 418 IDEVSKGIRDLEEKARETEEKRTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEY-KKLEEEVRRLQLTAEKIRS 493
                                       578888889999999999999999999999999999999999999888888888875.5778888899999999998 PP

                             TMPIT  81 vlkevesl 88 
                                       +l+e e +
  gi|320100561|ref|YP_004176153.1| 494 MLREAERV 501
                                       88887765 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.058
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelke 73 
                                       +++e  ++el+e++k ++++++el + + + + +i+  +k+++e++++ ++l++             +e
  gi|320100561|ref|YP_004176153.1| 523 SSIEAALRELREAEKGLQAEIRELDSRIARSKASIEYVEKMIHEIERDEEELRRL------------EE 579
                                       3344444444444444444444444444444444444444444444433333332............22 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 ?   -0.8   7.2       3.6   1.6e+03      34     113 ..     207     287 ..     189     303 .. 0.36
   2 ?    4.3   0.1       0.1        43      26      88 ..     337     399 ..     333     412 .. 0.81
   3 ?    4.2   0.6       0.1        44      52     122 ..     416     485 ..     384     494 .. 0.70
   4 ?    7.3   1.4     0.011       4.9      39     108 ..     510     578 ..     492     585 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.6
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHH......HHHHHCCCHHHHHHHCCHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikkss......keleeeilrlketidaqesn 103
                                       + ++++l +++e+++ + +e      + k+sl e++k  + + + + k  +      +e+e  i+r ++ + + e++
  gi|320100561|ref|YP_004176153.1| 207 RSRVDELARNMERLKTRLRE------RSKESLLEEKKRLTAEvEGYEKARTeklrrlEEVEASIEREQRLLMEAERE 277
                                       33333333333333322221......122222222222222212222222200000123333333333333333334 PP

                                       HHHHHHHHHH CS
                         Fib_alpha 104 irvLqnvles 113
                                       + +L++ +e+
  gi|320100561|ref|YP_004176153.1| 278 VAELKSRIEQ 287
                                       4444443333 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee 88 
                                       l ++e  +++++e  e++lee+++ ++e +  +  +++  r+  +  ++ +  +k++++ le+
  gi|320100561|ref|YP_004176153.1| 337 LHEKEALIEEEIEGFEQRLEEARRAYSELKAKIGGLESDKRNILARRRELEDQLKRYKELLER 399
                                       566677788888888999999999999988888888888888888888888888888888886 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  52 keaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLe 122
                                       k ++e++k i+d  +++ +++++  + i    +++eeei rl+ ++     +    ++ ++++e+++ +L+
  gi|320100561|ref|YP_004176153.1| 416 KLIDEVSKGIRDLEEKARETEEK-RTGIAAEISRVEEEIRRLEGEVRGRKAERDRVRGEYKKLEEEVRRLQ 485
                                       56677788888877777666664.55555555667778888888888888888888888888888888886 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.011
                                       CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHH CS
                         Fib_alpha  39 kleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLq 108
                                        le++l+e+ ++ +++e   +e+++  +  q++ ++ d+ i +s+ ++e  ++++ ++i + e+++r L 
  gi|320100561|ref|YP_004176153.1| 510 GLEDKLKEALSKRSSIEAALRELREAEKGLQAEIRELDSRIARSKASIE-YVEKMIHEIERDEEELRRLE 578
                                       5899999999999999999999999999999999999999999999999.99999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (826 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2068  (0.115344); expected 358.6 (0.02)
Passed bias filter:                      932  (0.0519828); expected 358.6 (0.02)
Passed Vit filter:                       204  (0.0113782); expected 17.9 (0.001)
Passed Fwd filter:                       123  (0.00686039); 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: 2.09u 0.39s 00:00:02.48 Elapsed: 00:00:00.59
# Mc/sec: 4230.89
//
Query:       gi|320100562|ref|YP_004176154.1|  [L=657]
Description: DNA double-strand break repair protein mre11 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-12   48.2   0.1    1.1e-09   38.7   0.0    2.3  2  DUF87          Helicase HerA, central domain
    7.9e-05   22.1   1.4     0.0054   16.1   0.1    2.8  3  FtsK_SpoIIIE   FtsK/SpoIIIE family
    0.00025   20.1   0.0    0.00046   19.2   0.0    1.3  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
     0.0018   17.3   0.2       0.68    8.8   0.1    2.5  2  AAA_10         AAA-like domain
  ------ inclusion threshold ------
      0.047   13.6   0.5       0.15   11.9   0.1    2.0  2  NACHT          NACHT domain
      0.048   13.4   0.0      0.093   12.5   0.0    1.4  1  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
        0.1   12.1   0.2       0.18   11.3   0.2    1.3  1  AAA_7          P-loop containing dynein motor region
       0.11   12.5   0.0        0.3   11.1   0.0    1.6  2  ResIII         Type III restriction enzyme, res subunit
       0.14   12.6   0.1       0.34   11.3   0.1    1.7  1  AAA_16         AAA ATPase domain
       0.18   12.3   0.0       0.56   10.7   0.0    1.8  2  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   6.4e-13   1.1e-09      20      69 ..     165     232 ..     151     321 .. 0.67
   2 !    7.4   0.0    0.0024       4.3     182     226 ..     467     505 ..     382     506 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 6.4e-13
                             DUF87  20 klvtrHlAilgsTGsGKSntvavLleelle..kkgatililDpHGEYgkal................e 69 
                                       +++++H++i+g+TGsGK+   + ++ + ++  + ++  l++D+HGEY+                   +
  gi|320100562|ref|YP_004176154.1| 165 SILSKHVLIVGQTGSGKTSGLKGIMVRYAResSEKTGWLVIDRHGEYAEDCsqerftwrlyeafsgnK 232
                                       789**************************9999999***********986655555555555555440 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0024
                             DUF87 182 fsnsstdliallleklekegkitiidlsgvdelaqqlvvsvilrr 226
                                          s ++++ ++     + g+++i+d+s +++++++lvv  ++rr
  gi|320100562|ref|YP_004176154.1| 467 A-GSIDEIVGDV-----DAGNVVILDVSRLSNEQADLVVLTVVRR 505
                                       3.6667777777.....99******************99988887 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     3e-06    0.0054      40      61 ..     169     190 ..     148     199 .. 0.82
   2 ?   -2.1   0.0       1.1   1.9e+03     190     208 ..     284     302 ..     280     314 .. 0.83
   3 ?    3.9   0.0     0.016        30     108     239 ..     425     566 ..     408     587 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3e-06
                                       .SEEEE--TTSSHHHHHHHHHH CS
                      FtsK_SpoIIIE  40 shllvaGatgsGKStalntLil 61 
                                        h+l++G tgsGK+ +l+ +++
  gi|320100562|ref|YP_004176154.1| 169 KHVLIVGQTGSGKTSGLKGIMV 190
                                       7*****************9997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                       ---EEEEEEC-HHHHHHHH CS
                      FtsK_SpoIIIE 190 krpslvvivderieLrlaa 208
                                        +p lv+ + e++e +l+a
  gi|320100562|ref|YP_004176154.1| 284 VKPELVSEIEEFAEIILQA 302
                                       6799999999999999987 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHTT-SSHHH...........HHHHHHHHHHTT---B...-TT-................. CS
                      FtsK_SpoIIIE 108 aleeLvkemeeryalfreagvrsiaa...........ydgeiaedpldifgdv...flvlDnyddlaaeneritsLs 170
                                       +l +L++e+ +  +++++ag  +              +++  a ++++i gdv   ++v+ + + l +e++  ++L 
  gi|320100562|ref|YP_004176154.1| 425 TLSWLLNELAKQLNKMEKAGLGEYPWrkvetgsqqieFRSIEAGSIDEIVGDVdagNVVILDVSRLSNEQADLVVLT 501
                                       45555555555555555554433222222225556664444455555555555222467778999999999777777 PP

                                       .....-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES CS
                      FtsK_SpoIIIE 171 nqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatq 239
                                        ++  + + +  t+g e +k ++ v iv e + L l+  k       ++++R+ar gr+ ++ l+  tq
  gi|320100562|ref|YP_004176154.1| 502 VVRRLFEQRM--TMGVEEAKGRPAVTIVSEEAPLYLSPDKV--NSPFNPFARIAREGRKFRVGLIAVTQ 566
                                       7666666554..55577778888899999999999998888..44568999999999977777776665 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.6e-07   0.00046      15      61 ..     168     217 ..     158     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.6e-07
                     TrwB_AAD_bind  15 tqhilivGttGsGKtqalekll.rairarg..draivlDltGafvsrfyd 61 
                                        +h+livG tGsGKt  l++++ r +r+       +v+D +G++ ++  +
  gi|320100562|ref|YP_004176154.1| 168 SKHVLIVGQTGSGKTSGLKGIMvRYARESSekTGWLVIDRHGEYAEDCSQ 217
                                       58*****************9773677876632567*********998655 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00038      0.68      21      63 ..     168     213 ..     160     322 .. 0.80
   2 !    5.8   0.0     0.003       5.4     265     319 ..     550     602 ..     547     606 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00038
                            AAA_10  21 asasliiGdlGnGKSvlak.llvlyisllggk..aliiDpkkerek 63 
                                       + ++li+G++G GK    k ++v y++   +k   l+iD+  e  +
  gi|320100562|ref|YP_004176154.1| 168 SKHVLIVGQTGSGKTSGLKgIMVRYARESSEKtgWLVIDRHGEYAE 213
                                       5799**********888873678888877655226*****999333 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.003
                            AAA_10 265 lvRiGRsynaavylvtqsadDvlkeelknniglklaFretdkeeikkvLeflgld 319
                                       + R GR++   ++ vtq a+ ++k+ + +n+ +++a r + +++  + L+ +g++
  gi|320100562|ref|YP_004176154.1| 550 IAREGRKFRVGLIAVTQLASMIEKQ-ILGNFNTVIALRTKSRSD-IELLKDIGVP 602
                                       68****************9988776.6689********666665.4556655555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   8.6e-05      0.15       3      31 ..     171     199 ..     169     207 .. 0.88
   2 ?   -1.6   0.0       1.2   2.2e+03     108     136 ..     566     594 ..     563     598 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.6e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpq 31 
                                       v++ G+ GsGKT  l+++++  a++  ++
  gi|320100562|ref|YP_004176154.1| 171 VLIVGQTGSGKTSGLKGIMVRYARESSEK 199
                                       89******************999987665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                       .HHHHHCTTTTT--EEEEEEECCCHHHHC CS
                             NACHT 108 lLselirkkllpeasllltvrpralrdle 136
                                        L+++i+k++l +   ++++r+++++d+e
  gi|320100562|ref|YP_004176154.1| 566 QLASMIEKQILGNFNTVIALRTKSRSDIE 594
                                       68999*****************9998875 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.2e-05     0.093       2      50 ..     169     214 ..     168     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkYkktqaiefsdeviDtPGeylen 50 
                                       k++l++G++gsGKt+    lkg  ++Y +  + +    viD  Gey+e 
  gi|320100562|ref|YP_004176154.1| 169 KHVLIVGQTGSGKTS---GLKGIMVRYARESSEKTGWLVIDRHGEYAED 214
                                       89************8...689999******99999999********996 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2    0.0001      0.18      33      58 ..     168     193 ..     166     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkld 58 
                                       +k+vl+vG+tG+GKt+ +k ++ ++ 
  gi|320100562|ref|YP_004176154.1| 168 SKHVLIVGQTGSGKTSGLKGIMVRYA 193
                                       589*************9999776655 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 ?   11.1   0.0   0.00017       0.3      25      63 ..     169     207 ..     160     246 .. 0.88
   2 ?   -2.9   0.0       3.4   6.1e+03      66      96 ..     298     328 ..     294     342 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                       SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESS CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvpr 63 
                                       k++li+  TG+GKT  +  ++ r++++ +e+   ++++r
  gi|320100562|ref|YP_004176154.1| 169 KHVLIVGQTGSGKTSGLKGIMVRYARESSEKTGWLVIDR 207
                                       899***********************9999877777776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.4
                                       HHHHHHHHGGGGTGG....GEEEESSS-B-- CS
                            ResIII  66 lleqtleefkkflseaykeigkkvsgdkkka 96 
                                       ++ q+l ++++  +++++ +g++++gd+ ++
  gi|320100562|ref|YP_004176154.1| 298 IILQALLNIREEDEKHRSIVGEFLTGDSGDE 328
                                       5556666666666666666788888877776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00019      0.34      24      63 ..     166     212 ..     155     317 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            AAA_16  24 p..elvllsGesGvGKsslvrellralekd.....ggiflrgkcdql 63 
                                            vl++G+ G+GK+s ++ ++ ++ ++     g++++  + +  
  gi|320100562|ref|YP_004176154.1| 166 IlsKHVLIVGQTGSGKTSGLKGIMVRYAREssektGWLVIDRHGEYA 212
                                       45579*************88666654444445554777765554443 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       9.4   1.7e+04     104     124 ..      63      83 ..      55      85 .. 0.80
   2 ?   10.7   0.0   0.00031      0.56      11      37 ..     168     194 ..     158     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9.4
                                       TTSGGS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 104 sspssLSgGqkqrvalarall 124
                                       s+p  LS   k+ va+a ++l
  gi|320100562|ref|YP_004176154.1|  63 SKPDVLSDVSKEIVAIASLFL 83 
                                       566889999999999999886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00031
                                       TSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkp 37 
                                       ++ v ivG++G+GK++ lk ++  +  
  gi|320100562|ref|YP_004176154.1| 168 SKHVLIVGQTGSGKTSGLKGIMVRYAR 194
                                       56799***********99999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4458.77
//
Query:       gi|320100563|ref|YP_004176155.1|  [L=434]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3291.29
//
Query:       gi|320100564|ref|YP_004176156.1|  [L=426]
Description: metallophosphoesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-10   39.4   0.0    1.7e-09   38.5   0.0    1.5  1  Metallophos     Calcineurin-like phosphoesterase
    0.00039   20.6   0.1      0.005   17.1   0.1    2.3  1  Metallophos_2   Calcineurin-like phosphoesterase superfamily 
  ------ inclusion threshold ------
      0.034   14.7   0.2        4.6    7.8   0.1    2.7  2  MerR-DNA-bind   MerR, DNA binding
      0.094   13.2   0.0       0.26   11.7   0.0    1.7  1  Acetyltransf_7  Acetyltransferase (GNAT) 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 !   38.5   0.0   3.8e-13   1.7e-09       1     204 []       1     211 [.       1     211 [. 0.69

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 3.8e-13
                                       EEEEEEESBTB....TTCCTHHHHHHHHHHHHHHH..TTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....TSEE CS
                       Metallophos   1 lrilvigDlHl....algggqlddllkllddllre..ekpdlvllaGDlvdrgdlekellellaalvky....pipv 67 
                                       + ++++gDlHl    +++ +    ++++ld++l++  e +  +l+ GD++d+  +++ l+  +a+ +++    ++ v
  gi|320100564|ref|YP_004176156.1|   1 MVFIHTGDLHLgcnlSEESALSKLYMDVLDEILENalEHRAPLLISGDFFDHYAVSYTLMIEVARRLRRlreaGVEV 77 
                                       5699*********997777777777888888866666777888889*******99998888888888878999**** PP

                                       EEEC-TTS.....CHHHHHHHHHHHHHHHHHHHEHH.HCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHH CS
                       Metallophos  68 ylllGNHe.....gfeeellnkygylgifsepwrsd.aevfnnlplaslgsgslkvlllhGgspellvsldklgsln 138
                                       +++ GNH+         ++l +y + g+ + + + +  +++   pl +        ++ +G  p++           
  gi|320100564|ref|YP_004176156.1|  78 VAVQGNHDnarggR---GVLDLYSETGLIKLTRYEErEGYLVLHPLKA------GGYVFYGV-PGF----------- 133
                                       ********755321...5555555555554444333233334444444......45555554.333........... PP

                                       HSCHHHHCCHHHHHH......HHHHTTCSEEEEEESSESS.......CSSSCSCCHHHHH..HH.HHHTTESEEEEE CS
                       Metallophos 139 leleapepgdewlkd......lekrekadwvivlgHsply.......rgsgylfgdeale..dl.lkkygvdlvisG 199
                                         ++++e     +k+       + ++++ ++ivl+H+ ++        +s+ + + ++le   +    +g  +v  G
  gi|320100564|ref|YP_004176156.1| 134 --RNQAE--SRYIKErrvrftGVGEAGGAPIIVLAHVSVEfagfkpsAYSEIYGDMDVLEneLWsILPGGTRYVALG 206
                                       ..22222..3444444455678999***************9999997444444444444455555888889999*** PP

                                       SSSSE CS
                       Metallophos 200 HtHvy 204
                                       H+H +
  gi|320100564|ref|YP_004176156.1| 207 HVHIP 211
                                       ***75 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 !   17.1   0.1   1.1e-06     0.005       1     130 [.       1     211 [.       1     242 [. 0.53

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                     Metallophos_2   1 MklaiiSDlH.............snldaleavlealkevgvdaiihaGDl...eeeep....evleellela....p 53 
                                       M +++  DlH               +d l+++le + e+    ++ +GD+   ++++     ev ++l++l+    +
  gi|320100564|ref|YP_004176156.1|   1 MVFIHTGDLHlgcnlseesalskLYMDVLDEILENALEH-RAPLLISGDFfdhYAVSYtlmiEVARRLRRLReagvE 76 
                                       788999999999777777666554455666667777777.4557889**87777777733333444444444999** PP

                     Metallophos_2  54 vlaVrGNnD......................................eevveedvlreaaelgtdl........... 81 
                                       v+aV+GN+D                                      +                 +           
  gi|320100564|ref|YP_004176156.1|  77 VVAVQGNHDnarggrgvldlysetglikltryeeregylvlhplkagG-----------------Yvfygvpgfrnq 136
                                       *********777766666666555555544444444333333333321.................012222222111 PP

                     Metallophos_2  82 .....peeaelel..agek.......vlliHgdpl.............gvkdalaellkeaeegsd.vvvcGHtHvp 130
                                             +e+++ +             + l H +               g++d l++ l +   g + +v++GH H+p
  gi|320100564|ref|YP_004176156.1| 137 aesryIKERRVRFtgV--GeaggapiIVLAHVSVEfagfkpsayseiyGDMDVLENELWSILPGGTrYVALGHVHIP 211
                                       1111112222222120..11222233444444422566555555655555555555554444444447777777766 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.012        54      11      27 ..     356     371 ..     356     376 .. 0.81
   2 ?    7.8   0.1     0.001       4.6      12      30 ..     376     395 ..     372     416 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                                       HHTT--HHHHHHHHHHH CS
                     MerR-DNA-bind  11 rrlGFsLdeIrelLaly 27 
                                       +++G++L++I ++  l+
  gi|320100564|ref|YP_004176156.1| 356 QATGLTLEDIEDMV-LR 371
                                       89*********998.54 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.001
                                       HTT--HHHHHHHHHH.HHST CS
                     MerR-DNA-bind  12 rlGFsLdeIrelLal.yddr 30 
                                       rlG++++ Ire+L l y++r
  gi|320100564|ref|YP_004176156.1| 376 RLGLPVEKIREILRLlYEER 395
                                       8************5536664 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.9e-05      0.26      37      74 ..     243     281 ..     240     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.9e-05
                                       TTSSHHHHHHHHTT.SE.EEEE.EEEETHHHHHH.HHHHTTE CS
                    Acetyltransf_7  37 rgkGiGraLleaae.kg.iile.qlelnaekaik.fYeklGF 74 
                                        gkG+Gr++l +   +g i  +  lel++  a + fYek GF
  gi|320100564|ref|YP_004176156.1| 243 SGKGVGRRILLV-DvEGdIPSVeALELES--APRvFYEKTGF 281
                                       59*******975.2245333333455643..4446******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3283.57
//
Query:       gi|320100565|ref|YP_004176157.1|  [L=422]
Description: L-threonine synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-72  241.8   0.0    1.1e-71  241.6   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.6   0.0   6.4e-76   1.1e-71       2     294 .]      74     384 ..      73     384 .. 0.93

  Alignments for each domain:
  == domain 1  score: 241.6 bits;  conditional E-value: 6.4e-76
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       +lg+g+TPl++++rl ++lg + l+lK+E  nptgSfKdR+++  ++ +    g k+ v assGN++++lAa++a++
  gi|320100565|ref|YP_004176157.1|  74 SLGEGGTPLLKAKRLGERLGLRnLYLKDETRNPTGSFKDRAMSVSVSMAVYF-GFKRAVIASSGNAAASLAAYGARA 149
                                       789*************************************************.************************ PP

                                       T-EEEEEEETTS-HHHHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTT..SHHHHHHHHTHHHHH CS
                              PALP  78 GlkvtivvpadaspekvallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfd..nptviegygtiglEi 150
                                       G++v+ +vp+ a  +k+a+l  +Ga+v +v   ++ d +v++++ l ++ +g+y  ++f+  np+ +eg +ti +E+
  gi|320100565|ref|YP_004176157.1| 150 GIEVYAFVPDFAGYGKIAQLLYYGAKVFKVrwVESEDPTVKMMRILYEK-HGFYPSPSFGvfNPYQVEGPKTISMEV 225
                                       *************************999997755567777776677777.9999999999***************** PP

                                       HHHTT.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCC.S..S.SS..B....... CS
                              PALP 151 leqlg.gkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarsl.ragrrvtvpvs...... 213
                                        eqlg ++p  v+vp+G ++l++G+  g+++    ++ d  +r+++v+peg++++ r++ ++ +++++  +      
  gi|320100565|ref|YP_004176157.1| 226 SEQLGwTVPSQVFVPTGAASLLTGVFNGFRDlnmvGWVDgyPRLVAVQPEGNHPFVRAWmERADPLRI--Kpwekpp 300
                                       *******************************8887666699******************544444444..3458999 PP

                                       SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEE CS
                              PALP 214 dtiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdr 287
                                       +tia+gl+     +++  +++l ++ +++v vsd +++eamr la  eg+++eps+aa+la+l k++e ge++++++
  gi|320100565|ref|YP_004176157.1| 301 ETIATGLEDTypWDGDAGLRALYKTDGYGVVVSDRDIVEAMRMLAGLEGVFAEPSGAAGLAGLvKAVENGEVDRDEV 377
                                       ***************************************************************************** PP

                                       EEEEE-B CS
                              PALP 288 vvviltg 294
                                       vvv++tg
  gi|320100565|ref|YP_004176157.1| 378 VVVLVTG 384
                                       ****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3068.34
//
Query:       gi|320100566|ref|YP_004176158.1|  [L=307]
Description: 6-phosphofructokinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-54  185.3   0.2    1.9e-54  185.0   0.2    1.0  1  PfkB          pfkB family carbohydrate kinase
    3.9e-05   23.1   0.0    6.6e-05   22.4   0.0    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.0   0.2   2.1e-58   1.9e-54       3     295 ..       6     288 ..       4     294 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 2.1e-58
                                       EEEEEEEEEEEEEEECSSH.TTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   3 kvvviGealidliavsekl.egelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       +vv +G+al+d+  v++++   +l  +v + + +aGG++ NvA +++rlg +++ i +vG D fG+ + + l  egv
  gi|320100566|ref|YP_004176158.1|   6 DVVTVGHALVDIRIVVNEFpSVDLEsKVLNQSWGAGGSAVNVAIGVSRLGMKSSIIARVGFDSFGRIIVDDLLREGV 82 
                                       699*****************999999*************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaea 154
                                       d+++++  + t+tg +++ ++++ge  ++ + gaa++l++e+   +e +++ a++ +i++     l+ ++  +++e+
  gi|320100566|ref|YP_004176158.1|  83 DISGLR-IGFTQTGFTIVAINNKGEIMMYGYKGAAEELQPED--ISEYAISRAKWMHIAS-----LRLDTTMKAIEV 151
                                       ******.8888**********999888888888888888875..5**************9.....999999999999 PP

                                       HHHTTE...EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEG CS
                              PfkB 155 aknggt...fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlG 228
                                       a+++g     dp  + ++    +e+l+++++ +d++ +ne+E++ +tg +  d  ea++ +        + ++ ++G
  gi|320100566|ref|YP_004176158.1| 152 ARKHGLtisWDPGRVLASQG--LEKLRDVVSAVDYVMLNEKEAKLMTGVE--DYREAAKTIAG---DTSASILLKRG 221
                                       99999878877766666664..9***************************..55555555555...67799****** PP

                                       GGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSS CS
                              PfkB 229 keGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkga 295
                                       ++G++v +k+ +  +pa   ++v+DttGAGD+f++gf+ ++l+g sl++a++++navAal + k g+
  gi|320100566|ref|YP_004176158.1| 222 SKGVYVLSKEYTGDIPAYSVENVIDTTGAGDAFASGFITGILRGYSLRKAVQYGNAVAALKIGKLGS 288
                                       ***************************************************************9987 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.3e-09   6.6e-05     102     226 ..     165     277 ..     157     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.3e-09
                                       SBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEE CS
                      Phos_pyr_kin 102 elleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvly 178
                                       ++l+++ +e+l++ ++  ++ +  N +Ea+ ++g     +ed +eaak+++  ++ ++l+k g     + v  +vl 
  gi|320100566|ref|YP_004176158.1| 165 RVLASQGLEKLRD-VVSAVDYVMLNEKEAKLMTG-----VEDYREAAKTIAGDTSASILLKRGS----KGV--YVLS 229
                                       5677788899998.9999***************9.....9*********************997....344..6676 PP

                                       TSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHH CS
                      Phos_pyr_kin 179 dgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAke 226
                                       ++ +  +   +  +  +t G+G++++s   + + +g+sl++Av+ +++
  gi|320100566|ref|YP_004176158.1| 230 KEYTGDIPAYSVENVIDTTGAGDAFASGFITGILRGYSLRKAVQYGNA 277
                                       44433333333334448**************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2238.01
//
Query:       gi|320100567|ref|YP_004176159.1|  [L=272]
Description: fructose-bisphosphate aldolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-35  121.3   0.0    5.8e-35  121.0   0.0    1.1  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.0   0.0   3.2e-39   5.8e-35       2     235 .]      22     243 ..      21     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 3.2e-39
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       v++a+D++v+++++++      + d+++++ +++++g +av++ pg + + ++  a +++l+vk+ ++t l ++ +r
  gi|320100567|ref|YP_004176159.1|  22 VVFAFDHGVEHGPGDFP---REYLDPRVIIGKVVEAGVDAVMMLPGAAFITRDLWAGRASLIVKVTSKTNLRPEDGR 95 
                                       679*************9...79******************************************************* PP

                                       EEE.TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHH CS
                              DeoC  79 dvd.evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlva 154
                                       ++  ++  ve a+alGA+av ++vy+   gs++e  +l++  +vk +++ +g p +   y+r++aik+ + d ++v+
  gi|320100567|ref|YP_004176159.1|  96 LLQsVFGHVEDAVALGAEAVAATVYW---GSQYEDAMLRQWFEVKRQAERYGYPCLQLSYPRGPAIKNMY-DVEVVK 168
                                       999899********************...*****************************************.****** PP

                                       HHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHC.HSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEE CS
                              DeoC 155 eAarvsaelGaDiiKvevpkevvnateedaevfkdvika.apvpgvvlsGGv...seedfletvedAvkeagasGvl 227
                                        + r+++e GaD+iK+ ++        ++ e+f++v++a a +p v++sGG+      dfl+ ve  v +ag+ Gv+
  gi|320100567|ref|YP_004176159.1| 169 YGVRAAIESGADLIKTYYT--------GSLESFREVVEAaAGIP-VLMSGGAvreRFIDFLRDVENVV-KAGGRGVV 235
                                       *******************........9******9987526899.*******6444447777777777.******** PP

                                       ESHHHHTT CS
                              DeoC 228 sGRaifqk 235
                                       +GR++f +
  gi|320100567|ref|YP_004176159.1| 236 VGRNVFRH 243
                                       *****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2043.62
//
Query:       gi|320100568|ref|YP_004176160.1|  [L=164]
Description: small multi-drug export protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-26   91.9   2.5    6.2e-26   91.4   2.5    1.2  1  Sm_multidrug_ex  Putative small multi-drug export protein
  ------ inclusion threshold ------
       0.34   11.3   2.8       0.16   12.3   0.4    1.6  3  DUF1440          Protein of unknown function (DUF1440)
       0.37   11.0  10.8       0.59   10.3  10.8    1.5  1  EI24             Etoposide-induced protein 2.4 (EI24)


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 !   91.4   2.5     1e-29   6.2e-26       1     121 []      19     146 ..      19     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 1e-29
                   Sm_multidrug_ex   1 Elrgaiplgill....gldpllallvsvlgnllpvplillflrklle.llkkkkl....lkklfekleekaekksek 68 
                                       E+rgaip+ +++     +  +  ll+sv++n+  vp+  + +  +l+ l++k ++    +k+l+ +l+  +e+k+ +
  gi|320100568|ref|YP_004176160.1|  19 EVRGAIPYLLIAtsgdAVGAVYGLLLSVAANMA-VPFAAFPILDVLDaLAAK-PWmpsvVKRLYGFLRGLGERKALG 93 
                                       99******9977677677889999*******64.455554444444423333.222345****************** PP

                   Sm_multidrug_ex  69 iekygflGLllFvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                       +++ ++++L++Fva+PLp TGawtGsl+a++lgl+++k++lai +Gv+ a+lI
  gi|320100568|ref|YP_004176160.1|  94 VRRGSYIALMVFVAVPLPATGAWTGSLVAYVLGLDRRKSILAIDAGVAAASLI 146
                                       **************************************************998 PP

>> DUF1440  Protein of unknown function (DUF1440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   2.6e-05      0.16      54     116 ..       8      71 ..       3      77 .. 0.84
   2 ?   -3.3   0.0       1.8   1.1e+04      73      90 ..     105     122 ..      99     134 .. 0.65
   3 ?   -3.0   0.0       1.4   8.6e+03      65      70 ..     146     151 ..     117     156 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                           DUF1440  54 wvsvlvhilfsivf.avlYvvvaevfpkiklwqGalfGllvtiavHlivlPllglvpalkelpl 116
                                       w+ +l    +s v  a+ Y ++a   +++  ++G+l ++++ +av   ++P+l + +al+  p+
  gi|320100568|ref|YP_004176160.1|   8 WAMILAFAPISEVRgAIPYLLIATSGDAVGAVYGLLLSVAANMAVPFAAFPILDVLDALAAKPW 71 
                                       555556666665541677**************************************99998887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.8
                           DUF1440  73 vvaevfpkiklwqGalfG 90 
                                       +va  +p+   w G l++
  gi|320100568|ref|YP_004176160.1| 105 FVAVPLPATGAWTGSLVA 122
                                       455556666666666554 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.4
                           DUF1440  65 ivfavl 70 
                                       ivfa++
  gi|320100568|ref|YP_004176160.1| 146 IVFAAA 151
                                       344444 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  10.8   9.9e-05      0.59      33     123 ..      10     127 ..       3     164 .] 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.9e-05
                                       HHHHHH.............-............TTHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHH.H CS
                              EI24  33 llvlll.............w............vllasllvllllllplwlfp...lvalllaapfygllaekvekrh 81 
                                       +++++              +                +l v + +++p+  fp   ++  l a p+++ +++++    
  gi|320100568|ref|YP_004176160.1|  10 MILAFApisevrgaipyllIatsgdavgavygL---LLSVAANMAVPFAAFPildVLDALAAKPWMPSVVKRLY--- 80 
                                       333333555555554444303444444443323...5556666666677777777******************6... PP

                                       HCCTTSHH....HHHHHHHHHHHHHHHHHHH...HHTTHHH....HHHH CS
                              EI24  82 lglvksla....eslkslllllllllvllpl...liPvvglilspllls 123
                                        g++++l+     ++++  ++ l++ v+ pl   +  + g +++++l++
  gi|320100568|ref|YP_004176160.1|  81 -GFLRGLGerkaLGVRRGSYIALMVFVAVPLpatG-AWTGSLVAYVLGL 127
                                       .6777777777799*****************7533.8888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1374.33
//
Query:       gi|320100569|ref|YP_004176161.1|  [L=461]
Description: nucleoside-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-35  120.1   0.5    2.1e-34  118.9   0.4    1.5  2  Bmp           ABC transporter substrate-binding protein PnrA-
     0.0044   16.7   1.4     0.0068   16.1   0.4    1.8  2  Peripla_BP_6  Periplasmic binding protein
  ------ inclusion threshold ------
       0.12   11.2   0.0       0.17   10.7   0.0    1.1  1  RAI16-like    Retinoic acid induced 16-like protein


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 !  118.9   0.4   3.5e-38   2.1e-34       2     244 ..      43     284 ..      42     296 .. 0.91
   2 ?   -2.5   0.0      0.33     2e+03     109     131 ..     433     455 ..     431     456 .. 0.87

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 3.5e-38
                                       EEEEEECSS-TTTSCHHHHHHHHHHHHHHHC..TTEEEEEEEEC.GGGHHHHHHHHHHCTT-SEEEEESCCHHHHHH CS
                               Bmp   2 vkvavlvegtidDksfnessyeGirrlkkeq..nieliskesslltdedyiadlknlkeegsdlivatgfalqdalq 76 
                                       vk+a +++g+i D++++++++ G+++++k +   +++ + es++  + + + +++ l ++g+++i++t+f+++d ++
  gi|320100569|ref|YP_004176161.1|  43 VKAAWIYVGPIGDAGWTYMHDIGRKYVEKLYgeWLQTTYVESVS--EDQLLGTIDRLVSQGYNVIFTTSFEFMDKTI 117
                                       68899**************************8889999999999..7999*************************** PP

                                       HHHHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEECSS-SCCCHHCHHHHHHHHHHH CS
                               Bmp  77 evssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvgGveipvvksfingFeaGikyv 153
                                       e ++++p+v F ++++++ +   nv +++   ++  +L G++a++++kt++ig+v++  ip+v + in+F+ G+k v
  gi|320100569|ref|YP_004176161.1| 118 EAGKKYPNVMFFHCSGYKRAP--NVGTYFADLYQVYYLNGLMAGALTKTGQIGYVAAYLIPEVVRHINAFAIGAKEV 192
                                       *********************..****************************************************88 PP

                                       -....TT-EEEEEE-SSSS-HHHHHHHHHHHHH.CT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--CGCSTT CS
                               Bmp 154 n....pdievvvkvagtfsDakkgkslAsslyk.egvdvifpaagkagkgvieaakelglsnyvIgvdkdqsylape 225
                                       +    ++i v+v  +g ++D++k+ ++A+ l    +vdv +     +++ ++e  + +g++  v      +   +p+
  gi|320100569|ref|YP_004176161.1| 193 GdalgKNITVHVIEIGAWYDPTKAGQAADTLKTqYKVDVLAF--TEDSTKIVEYGEANGVY--VFSHYGPMLRYGPN 265
                                       5333389*************************989*****99..77778888888888888..77777777778888 PP

                                       CCEEEEEEEHHHHHHHHHH CS
                               Bmp 226 nvitsiiknvedlvvsiie 244
                                       +v+   i+ +e +++ i+ 
  gi|320100569|ref|YP_004176161.1| 266 YVVSGQIVRWEIIYADILA 284
                                       8888888877777766665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHHHHCTTTTEE CS
                               Bmp 109 eegaFLaGvaaAlmsktnkigfv 131
                                        + +F aG++a++    n+++fv
  gi|320100569|ref|YP_004176161.1| 433 TQVSFPAGYMAGHDDLWNMDYFV 455
                                       578999*******9999999998 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.21   1.3e+03     261     295 ..     144     181 ..      82     186 .. 0.61
   2 !   16.1   0.4   1.1e-06    0.0068      23      99 ..     183     255 ..     171     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.21
                                       HHHHHHHHH.....TTGGC--HHHHHHHHHHHHHHHHHHC CS
                      Peripla_BP_6 261 fvaayeaay.....ggapppsqfaaggyiaadlllealka 295
                                       f++ y+ +y         + ++ ++ gy+aa l+ e++++
  gi|320100569|ref|YP_004176161.1| 144 FADLYQVYYlnglmA--GALTKTGQIGYVAAYLIPEVVRH 181
                                       444444444443221..23677778888888888777776 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHTTEETTEEEEEEEEE..-TTSHHHHHHHHHHHHHCT--SEEEE-BSHHHHHHHHHHHHHHT-EEE CS
                      Peripla_BP_6  23 agaqaafeeiNaaGGinGrkielverD..daydpdraaeaarrlvdqdgvdalvgplssavaaavaevlakdgvpvi 97 
                                       +++   ++e+   G  +G+ i++ + +    ydp++a +aa  l++q +vd+l     + + + ++e+ +++gv v+
  gi|320100569|ref|YP_004176161.1| 183 NAFAIGAKEV---GDALGKNITVHVIEigAWYDPTKAGQAADTLKTQYKVDVLAF---TEDSTKIVEYGEANGVYVF 253
                                       5566666666...7788997776666621568*******************9977...58899*************9 PP

                                       ES CS
                      Peripla_BP_6  98 gp 99 
                                       + 
  gi|320100569|ref|YP_004176161.1| 254 SH 255
                                       93 PP

>> RAI16-like  Retinoic acid induced 16-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.8e-05      0.17     224     276 ..     105     173 ..      82     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.8e-05
                        RAI16-like 224 sFlslleFcqslikeahs................eiaeallklieesFLadvLePsLletsegssltvl 276
                                        F +++eF++++i+  ++                +++ + ++l +  +L++++  +L +t + + +++ 
  gi|320100569|ref|YP_004176161.1| 105 IFTTSFEFMDKTIEAGKKypnvmffhcsgykrapNVGTYFADLYQVYYLNGLMAGALTKTGQIGYVAAY 173
                                       5999********************************************************998888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.36
# Mc/sec: 3818.16
//
Query:       gi|320100570|ref|YP_004176162.1|  [L=309]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-30  106.5   0.1    1.3e-29  103.4   0.0    2.1  2  ABC_tran     ABC transporter
    0.00027   20.9   0.0    0.00045   20.1   0.0    1.4  1  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0021   17.7   0.0     0.0045   16.7   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0036   17.7   0.0     0.0057   17.0   0.0    1.4  1  AAA_16       AAA ATPase domain
     0.0069   16.9   0.0      0.015   15.9   0.0    1.5  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.019   14.8   0.0       0.42   10.4   0.0    2.1  2  MukB         MukB N-terminal
      0.039   13.7   0.0       0.06   13.1   0.0    1.2  1  AAA_15       AAA ATPase domain
      0.046   13.6   0.0      0.088   12.7   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.081   12.1   0.0      0.085   12.0   0.0    1.1  1  G-alpha      G-protein alpha subunit
        0.1   12.3   0.2        3.4    7.3   0.1    2.8  2  AAA_30       AAA domain
       0.11   11.4   0.0       0.18   10.7   0.0    1.3  1  AAA_10       AAA-like domain
       0.13   11.7   0.0        1.3    8.4   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 !  103.4   0.0   8.8e-33   1.3e-29       1     136 [.      24     173 ..      24     174 .. 0.92
   2 ?    0.7   0.1      0.46   6.9e+02       3      21 ..     283     301 ..     281     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 8.8e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltv 76 
                                       l++vs+++++ge+va++GenGaGKSt++k+l+g + p+eGe+ +d  k + +++l   r+ i +++q pql ++ltv
  gi|320100570|ref|YP_004176162.1|  24 LDKVSFDVYRGEIVALLGENGAGKSTIVKILYGIYFPDEGEVYVDsRKAVFYNPLDAIRSGIVMVSQIPQLIDRLTV 100
                                       789******************************************7777778************************* PP

                                       HHH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ren                   de++ k+ +++g+  + + +       L + qkq+v++ ra+l ++kl++lDE+ 
  gi|320100570|ref|YP_004176162.1| 101 RENlaiglrllglsglsstsRIDEKARKVSEEIGMRIDLNAKT----WRLTYTQKQMVEILRAFLLNAKLVMLDEAL 173
                                       ****************777777777777777777777666665....9***************************96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.46
                                       EEEEEEETTSEEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenG 21 
                                          +++++ge+v+i G  G
  gi|320100570|ref|YP_004176162.1| 283 GARISVRKGEVVGIAGVAG 301
                                       567899**********877 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 !   20.1   0.0     3e-07   0.00045       1      83 [.      36     129 ..      36     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarl...........drdvegltdelsggggirkipslldlydpeipfefeieefl 66 
                                       + +l G Ng+GKS++ ++l+++ +            +   ++l  ++sg+++ + ip l+d+   ++  ++++++++
  gi|320100570|ref|YP_004176162.1|  36 IVALLGENGAGKSTIVKILYGIYFPdegevyvdsrkAVFYNPLDAIRSGIVMVSQIPQLIDRLTVRENLAIGLRLLG 112
                                       5789******************8889999999998888888888899999999999999998888888888888888 PP

                            AAA_21  67 sqgvryryglrlersqv 83 
                                       ++g   + +++ + + v
  gi|320100570|ref|YP_004176162.1| 113 LSGLSSTSRIDEKARKV 129
                                       88877777777777777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0045      13      39 ..      25      51 ..      22      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      d+ ++++ + +++ l G++G+GKST++
  gi|320100570|ref|YP_004176162.1| 25 DKVSFDVYRGEIVALLGENGAGKSTIV 51
                                      556677775669*************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.8e-06    0.0057      23     107 ..      33     133 ..      24     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.8e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd.g.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                       r+e+v l Ge G GKs++v+ l+  +  d g +++ + k++ +    p++a+ + +   + + ql d+++ +e  a 
  gi|320100570|ref|YP_004176162.1|  33 RGEIVALLGENGAGKSTIVKILYGIYFPDeGeVYVDSRKAVFY---NPLDAIRSGIVMVSQIPQLIDRLTVRENLAI 106
                                       4589*******************87777753477755555555...6888899999888999999998777777777 PP

                            AAA_16  98 rekleeala.................a 107
                                         +l++  +                 +
  gi|320100570|ref|YP_004176162.1| 107 GLRLLGLSGlsstsridekarkvseeI 133
                                       777777666655555444333333330 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.7e-06     0.015      11      37 ..      25      52 ..      10      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTild 37
                                      +++++d     ++++ G+NGaGK+Ti+ 
  gi|320100570|ref|YP_004176162.1| 25 DKVSFDVyRGEIVALLGENGAGKSTIVK 52
                                      55566664457999************86 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00028      0.42      28      54 ..      36      62 ..      25      69 .. 0.85
   2 ?    2.2   0.0     0.091   1.4e+02     191     218 ..     179     207 ..     120     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                                      HHHHHS--SHHHHHHHHHHHHHHS--T CS
                              MukB 28 vttlsGgnGaGksttmaafvtaliPdl 54
                                      + +l G nGaGkst++  ++ +  Pd 
  gi|320100570|ref|YP_004176162.1| 36 IVALLGENGAGKSTIVKILYGIYFPDE 62
                                      67999****************999996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.091
                                       HHHHHHHHHHHHHH.SSS-HHHHHHHHHH CS
                              MukB 191 edrskfyrlieasl.yGGissaitrslrd 218
                                       e+r +fy ++ea    GG s +it+++ +
  gi|320100570|ref|YP_004176162.1| 179 EERRRFYVILEAFKkNGGSSLVITHKITE 207
                                       799********965268888899988766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     4e-05      0.06      25      44 ..      36      55 ..      23      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                            AAA_15 25 ltvliGkNnsGKSsileald 44
                                      +  l G+N++GKS+i+++l+
  gi|320100570|ref|YP_004176162.1| 36 IVALLGENGAGKSTIVKILY 55
                                      8899**************97 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   5.9e-05     0.088      96     120 ..      31      55 ..      19      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                                       HCTTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinall 120
                                       + ++++++l+G+ G+GKSt+++ l 
  gi|320100570|ref|YP_004176162.1|  31 VYRGEIVALLGENGAGKSTIVKILY 55 
                                       45679****************9886 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.7e-05     0.085      26      83 ..      37      93 ..      26     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                                      EEEEESTTSSHHHHHHHHHHHCS----HHHH.HCCHHHHHHHHHHHHHHHHHHHHHTT. CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkgfseeel.atwraviqlnivrsiktilealesles 83
                                      + llG+++ GKsTi+k l  +y +     e+    r+ ++ n +++i++ +  +++  +
  gi|320100570|ref|YP_004176162.1| 37 VALLGENGAGKSTIVKILYGIYFPDEG--EVyVDSRKAVFYNPLDAIRSGIVMVSQIPQ 93
                                      679************999988855432..332557888999999999988888877433 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0023       3.4      20      49 ..      36      65 ..      31     176 .. 0.81
   2 ?    1.5   0.0      0.14   2.1e+02      81      98 ..     253     277 ..     185     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0023
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrv 49
                                      +++l G  G+GK+t++k l  ++  ++g+v
  gi|320100570|ref|YP_004176162.1| 36 IVALLGENGAGKSTIVKILYGIYFPDEGEV 65
                                      78899***********99987776665555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                            AAA_30  81 k.......grarlepgtllivDEag 98 
                                       +       +++ ++ ++l++vDE g
  gi|320100570|ref|YP_004176162.1| 253 RlpsspplDQQCITVEDLVVVDEYG 277
                                       04555566556677889******88 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012      0.18      22      60 ..      35      72 ..      22     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                            AAA_10 22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkke 60
                                        ++++G+ G+GKS ++k+l + i + ++  +++D +k 
  gi|320100570|ref|YP_004176162.1| 35 EIVALLGENGAGKSTIVKIL-YGIYFPDEGEVYVDSRKA 72
                                      55799*************76.67889999999***9886 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00089       1.3      25      42 ..      35      52 ..      24      71 .. 0.87
   2 ?    0.9   0.0      0.17   2.6e+02     160     209 ..     165     216 ..     157     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00089
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                      ++ a++G+NG+GKs ++ 
  gi|320100570|ref|YP_004176162.1| 35 EIVALLGENGAGKSTIVK 52
                                      57899*********9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.17
                                       SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS.HHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkekskn.aQfivislr.eemlekadklv 209
                                        l++lDe    L  ++++++  +l++ +kn    +vi+++ +e le ad+++
  gi|320100570|ref|YP_004176162.1| 165 KLVMLDEALTYLPLEERRRFYVILEAFKKNgGSSLVITHKiTEALEIADRII 216
                                       5789999999999999999999999998887788999998456777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2224.39
//
Query:       gi|320100571|ref|YP_004176163.1|  [L=167]
Description: ribose ABC transporter ATP-binding protein, partial [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1252.36
//
Query:       gi|320100572|ref|YP_004176164.1|  [L=373]
Description: nucleoside ABC transporter membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   72.8  36.6    2.8e-20   72.6  28.7    2.3  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 !    4.9   0.9    0.0007        13      59      94 ..      16      51 ..       3      55 .. 0.86
   2 !   72.6  28.7   1.6e-24   2.8e-20       6     266 ..      59     356 ..      56     360 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0007
                      BPD_transp_2 59 llvallvgaavglllgllvlrlkvdeliitllllsv 94
                                       ++ +l+++avg+ll++l+l l+ ++++ +l ++++
  gi|320100572|ref|YP_004176164.1| 16 TILIILLSLAVGVLLYTLILSLQGRSPVEVLYTITA 51
                                      67899***********************99998875 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 1.6e-24
                      BPD_transp_2   6 ltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl..........lllallvallvgaavgll 72 
                                       +  ++il++++ +l ++f ++ ++n+g++g++ ++ + + +l  ++ ++          +l+++++a ++ga+++ +
  gi|320100572|ref|YP_004176164.1|  59 VKDFIILTMLGYALLVSF-KGSLWNIGAEGQLFISTIPVIVLTLYVAPNpstpletiavILASIVIATATGALWASA 134
                                       56799*************.****************988888888888888*************************** PP

                      BPD_transp_2  73 lgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.............. 135
                                        g++ ++l vde+ +tl+l++v+++ +++l+ g+ +g+  + + +++ +++ a++ ++ +                 
  gi|320100572|ref|YP_004176164.1| 135 AGFIRAYLEVDEVPVTLILNYVAYYTVNILVIGPLKGTR-VYGYNRTDEIPAAYRLYITGLQRtpagnpvadtvmgf 210
                                       ****************************99999999987.788889999999999999888889999********** PP

                      BPD_transp_2 136 ...........llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallall. 200
                                                  + ++l++++ ++ll++t++G+++r +g+n++  +  G+n++ + +++ ++sga+ g+  a+++l+ 
  gi|320100572|ref|YP_004176164.1| 211 vyealyylpwlIAMVLIMVFTWFLLNKTQIGLRVRILGSNPDYLKSIGVNTRLTLVTALALSGAIVGFTSAFYTLSd 287
                                       **********9999999999*****************************************************9973 PP

                      BPD_transp_2 201 .lgsipp..nigvglgfnaiaavvlGgagsllgtviGaliigvvksllltllgi.ptelarvllgallil 266
                                        l  ++p      g+g+ ai+++ l ++     + + a+ii+ + + +++l       l+++ll + lil
  gi|320100572|ref|YP_004176164.1| 288 lLRLSYPveGQTAGYGYLAILVAWLSML-DYKLIPVSAYIIASLRTAGINLQVGgLGGLEQMLLLIGLIL 356
                                       35556666888888**************.88888888888888888666664334355555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2584.65
//
Query:       gi|320100573|ref|YP_004176165.1|  [L=311]
Description: inner-membrane translocator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-19   70.4  29.5    1.7e-19   70.0  29.5    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 !   70.0  29.5   9.6e-24   1.7e-19       5     267 ..      11     281 ..       8     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 9.6e-24
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalG.ayvaalllalllsl..........lllallvallvgaavg 70 
                                       l++ +++ ++aAlG +++  ++G++nl++ g++ ++ ++++ l++al++ l            la+l+  l+ a++g
  gi|320100573|ref|YP_004176165.1|  11 LIAAFSTMYLAALGHSVME-KSGILNLAIDGAFFFStGVSIYLAVALYGLLtplgltypatTVLAVLLTGLFTAVIG 86 
                                       57889**************.****************99999999999998899899988887888888888888888 PP

                      BPD_transp_2  71 lllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv...llalllvla 144
                                       +++++  + l + + + +l l ++ +gl           ++g +  + +  +++++l++   v+    +  ++  +a
  gi|320100573|ref|YP_004176165.1|  87 VFMAWVLTSLPISHGALGLSLQFLGYGLGI---------MAGYPVRQSVGSIEPYSLPRDPVVYGallASSIITGVA 154
                                       888888888888887777777777777777.........666666666666666666666666665547889999** PP

                      BPD_transp_2 145 vllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp..nigvglgfnaiaa 219
                                       v++l+ +t++G  ++a+gen++aa alG+nv +++l++ +++  + g+ + l+ l  +  +   +  +g+g+ a+++
  gi|320100573|ref|YP_004176165.1| 155 VHFLMEKTPLGASIKACGENPHAASALGVNVLKTRLIAGALGFYILGVGASLYPLAWQRYWDikSYTLGYGWFAFTI 231
                                       *****************************************************999988877799************ PP

                      BPD_transp_2 220 vvlGgagsllgtviGaliigvvksllltllgi...ptelarvllgallilv 267
                                       ++ Gg  +++  +  +l++g + ++ + ++ +   + ++a+++ ++  + v
  gi|320100573|ref|YP_004176165.1| 232 ALAGGR-NPIYLIPLSLVFGGLLEFNIRIMTMlkiSADVAKLIPFLATLGV 281
                                       ******.*************9998766665555558999999999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2369.33
//
Query:       gi|320100574|ref|YP_004176166.1|  [L=545]
Description: lysyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-90  303.4   0.0    2.3e-90  303.1   0.0    1.1  1  tRNA-synt_1f    tRNA synthetases class I (K)
  ------ inclusion threshold ------
       0.03   13.8   3.0      0.082   12.4   3.0    1.7  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.24   11.4   0.8       0.51   10.3   0.8    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.5   10.3   3.3        1.4    8.8   3.3    1.7  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.1   0.0   5.2e-94   2.3e-90       1     357 [.       3     368 ..       3     371 .. 0.94

  Alignments for each domain:
  == domain 1  score: 303.1 bits;  conditional E-value: 5.2e-94
                      tRNA-synt_1f   1 kaWadklaeklieerkkkkaekdevvvesGispSGliHiGnlr.evltadlvaralrkrgeevrlilisDdmDglRk 76 
                                       k+W+d+la+ l +  +k+  +k+ +v++ G+s+SGl+H+G+lr e++ a+ ++r l++rg +v++ l+ ++ D ++ 
  gi|320100574|ref|YP_004176166.1|   3 KHWIDELADSLYDALTKR--GKEVYVFNGGLSVSGLQHVGRLRgEIIIAETLRRLLSERGLRVKQYLTLYTQDAWKG 77 
                                       69**********888776..89********************99********************************9 PP

                      tRNA-synt_1f  77 vpe...nlpek.llekylgkpltsiPdpkgkhesyaehfnaelvesLdelgi.evefisatelYksglydeaikeal 148
                                        ++   ++ +   +++y g+pl ++Pdpkg+h +++eh+++++  ++ e++   +e++++t++Yk g+ ++ +k  l
  gi|320100574|ref|YP_004176166.1|  78 KDSqlkQFQNPaEASRYKGNPLIRVPDPKGCHGNWVEHYWSDFGPFIGEFTDgAIEVVTTTDMYK-GRMRDFVKLTL 153
                                       99856555667779************************************9989**********8.778999***** PP

                      tRNA-synt_1f 149 enrekikeilekyrgee.reetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkv 224
                                        +re+++++++kyrg++ + e+++p++pvce+cgr+dtte+  +  +e+++eY+ce+cG+++ +di++  gKL W++
  gi|320100574|ref|YP_004176166.1| 154 GKREEVRRVVNKYRGRKpYPEDWIPVEPVCERCGRIDTTEALRLV-DEDHVEYVCEHCGYRGVADISD--GKLMWRI 227
                                       ***************9999*************************8.9********************9..7****** PP

                      tRNA-synt_1f 225 dwamrWaalgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkgge....kmssSkGnvltledwl 296
                                       +w   W+ lgVdfEp+GkDha +GgS d   ++a +++g ++Pe+++Ye++  +  +    +m sS + ++t++dwl
  gi|320100574|ref|YP_004176166.1| 228 EWVGVWWTLGVDFEPYGKDHAMPGGSRDSCVDLAvNVYGLKPPEGLPYEWVEWRRPDgqvaDMGSSDFIGFTPRDWL 304
                                       ***************************************************9876555567**************** PP

                      tRNA-synt_1f 297 evaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf....aeqeeeeekekrvyels 357
                                       eva+p + rf++l++ P k+ ++ l+ e+++++ +Y+++er+y+     ++eeee   kr yels
  gi|320100574|ref|YP_004176166.1| 305 EVAHPHIYRFIVLKTPPMKKYSVGLH-EVPQYYSQYYRAERIYYglekPKDEEEEVLLKRSYELS 368
                                       **************************.*****************987666777777888888887 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.0   1.8e-05     0.082       2      27 ..     182     212 ..     181     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                                       EETTTTCEE.C....HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstn.l....veDpergelvCtdCGl 27 
                                       +C  Cg  + +    ++D+++ e+vC+ CG+
  gi|320100574|ref|YP_004176166.1| 182 VCERCGRIDtTealrLVDEDHVEYVCEHCGY 212
                                       799999955259999***************6 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.8   0.00011      0.51      31      60 ..     183     218 ..     181     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                    OrfB_Zn_ribbon  31 CseCgsknke......alsgrtfkCpnCgfeadrDv 60 
                                       C +Cg+++++      + ++ +++C++Cg++  +D+
  gi|320100574|ref|YP_004176166.1| 183 CERCGRIDTTealrlvDEDHVEYVCEHCGYRGVADI 218
                                       *********99**99999999*********999997 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 ?    8.8   3.3   0.00032       1.4       3      27 ..     182     210 ..     181     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00032
                                       B-TTT--BBEEEEC....TTEEEEE-TTT CS
                      zf-FPG_IleRS   3 pCpRCwryiervgq....agrstyfCprC 27 
                                       +C+RC+r+++++ +      +  y+C++C
  gi|320100574|ref|YP_004176166.1| 182 VCERCGRIDTTEALrlvdEDHVEYVCEHC 210
                                       7************9999888889999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3807.71
//
Query:       gi|320100575|ref|YP_004176167.1|  [L=541]
Description: carbohydrate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-45  154.0   0.1    2.1e-44  151.8   0.0    1.9  2  Carb_kinase   Carbohydrate kinase
    3.1e-40  137.8   0.5      7e-40  136.7   0.4    1.6  2  YjeF_N        YjeF-related protein N-terminus
  ------ inclusion threshold ------
      0.034   13.9   0.2       0.39   10.5   0.0    2.6  3  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
      0.038   14.5   0.0      0.085   13.3   0.0    1.5  1  Tex_YqgF      Tex protein YqgF-like domain


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 ?   -0.5   0.0      0.15   6.9e+02      60      98 ..     132     175 ..      77     179 .. 0.77
   2 !  151.8   0.0   4.7e-48   2.1e-44       3     243 ..     264     519 ..     262     520 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                                       ...--SSS-SEEE...E-TT-SSSHCHHH..HCHHHCCCCS-EE CS
                       Carb_kinase  60 kileklerldavv...iGpGLgrdekikk..lleevlekdeplv 98 
                                          ++l+++d+vv   iG GL  + ++ +  ++e v +  +p+v
  gi|320100575|ref|YP_004176167.1| 132 ALEKSLRWADIVVsglIGVGLRGEVSGLHrrVIELVNSSGKPVV 175
                                       44567888898876669999998888777779999999888876 PP

  == domain 2  score: 151.8 bits;  conditional E-value: 4.7e-48
                                       EEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT..........HTTTS...--SSS-S CS
                       Carb_kinase   3 vigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll..........edeqakileklerld 69 
                                        ++Gs  y+GA++  a++ l+ g g  + a+ +  i  + s  p+v+  pl+          + e+   l +++ +d
  gi|320100575|ref|YP_004176167.1| 264 AVAGSRYYYGAPYYVASSFLKTGGGYARLAAPKGVIPFIASRAPQVVYVPLEetaegsiaygNLEKILSLIEEHGID 340
                                       689************************************************999999999876666644555668** PP

                                       EEEE-TT-SSSHCHHHHCHH.HCCCCS-EEEEGGGGGSGGGG....TTTTSSEEEE--HHHHHHHCTTTCH.HCCSH CS
                       Carb_kinase  70 avviGpGLgrdekikkllee.vlekdeplviDAdgLnllaqkne.lserkaeviLTPhkkEfkrLlkaivk.keddr 143
                                       +vv+GpG   + ++++ll+  v++ d+p++iD+dgL+ ++++   l +rka++iLTPh+ Ef+rL++ +++  + + 
  gi|320100575|ref|YP_004176167.1| 341 IVVLGPGTSLNRETQELLRSlVEALDKPVIIDGDGLTAVSENPGlLRKRKAPTILTPHPAEFARLTGKPLAeVQGNP 417
                                       *********9999999877526778999**************9999***********************998999** PP

                                       HHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTS.SHHHHHHHHHHHHH CS
                       Carb_kinase 144 lelarelaqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqne.asyeaaiaaawlhg 219
                                       +e +r++  +l++ ++ k ++ +i +p+g ++ n tg++++ak+GsGDvLaG+i++l  +   ++  a   ++ +hg
  gi|320100575|ref|YP_004176167.1| 418 VEHVRKACVELGSYIVYKTAHSLICYPNGYIYVNMTGNPGMAKAGSGDVLAGVIAGLYGVGLrDPGAALRMGVLVHG 494
                                       ************************************************************9889999999******* PP

                                       HHHHHHCCCT-T.S-HCHHHHHHHC CS
                       Carb_kinase 220 aasdeaaekkgv.gmlatelskiip 243
                                        a+d+aae+ g  g++++ l++ +p
  gi|320100575|ref|YP_004176167.1| 495 LAGDLAAEEIGEdGVTPDTLMEHLP 519
                                       ********************99987 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 !  136.7   0.4   1.6e-43     7e-40       3     171 .]      41     209 ..      39     209 .. 0.96
   2 ?   -3.3   0.0       1.5   6.9e+03      82     100 ..     338     365 ..     326     374 .. 0.48

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 1.6e-43
                            YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellk 79 
                                        Lme a++av  v+ + +g  +++++++v++G gnnGgd+la+Ar L+++g  V+++++ ++  +++ a  + + l 
  gi|320100575|ref|YP_004176167.1|  41 PLMEEAASAVYTVILREYG--VEGRRFTVVAGTGNNGGDALAVARRLHSAGGIVEAFVIGDPGRMSDAAGFNHRVLS 115
                                       69**********9999994..******************************************************** PP

                            YjeF_N  80 kaggkvveekpeedleekls..apvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsg 154
                                       ++g+ v + ++ee l+   +  + +d+v+ +l G+glrge+++   ++ie +nss++pv+++DiPSG+d+dtG v+g
  gi|320100575|ref|YP_004176167.1| 116 AMGVPVATVSSEEGLTALEKslRWADIVVSGLIGVGLRGEVSGLHRRVIELVNSSGKPVVSIDIPSGVDGDTGLVKG 192
                                       ********99999987666699******************************************************* PP

                            YjeF_N 155 tavkadvtvtfgapkrg 171
                                       +avk++vtv++g++k g
  gi|320100575|ref|YP_004176167.1| 193 VAVKSSVTVALGLLKYG 209
                                       *************9965 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                            YjeF_N  82 ggkvveekpeedleekls.........a 100
                                       g+++v   p  +l+++++          
  gi|320100575|ref|YP_004176167.1| 338 GIDIVVLGPGTSLNRETQellrslveaL 365
                                       4444444444444444443333333322 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.28   1.3e+03      15      50 ..      94     129 ..      80     138 .. 0.82
   2 ?   -1.0   0.0      0.31   1.4e+03      16      44 ..     148     176 ..     145     178 .. 0.75
   3 ?   10.5   0.0   8.6e-05      0.39       2      55 ..     328     382 ..     327     391 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.28
                                       EEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTT CS
                      TPP_enzyme_M  15 vilvGggvarsgaseelrelaeklgiPvvttlmgkg 50 
                                       ++++G   + s+a+   ++++ ++g+Pv+t     g
  gi|320100575|ref|YP_004176167.1|  94 AFVIGDPGRMSDAAGFNHRVLSAMGVPVATVSSEEG 129
                                       5789999999999999999*********99776665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.31
                                       EEE-CHHCHTTGHHHHHHHHHHHT-EEEE CS
                      TPP_enzyme_M  16 ilvGggvarsgaseelrelaeklgiPvvt 44 
                                       i vG +   sg ++ + el+++ g Pvv+
  gi|320100575|ref|YP_004176167.1| 148 IGVGLRGEVSGLHRRVIELVNSSGKPVVS 176
                                       55666666778888888888888888875 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 8.6e-05
                                       HHHHHHHHH-SSEEEEE-CHHCHT.TGHHHHHHHHHHHT-EEEEEGGGTTSS-TT CS
                      TPP_enzyme_M   2 ekaaellkaakrpvilvGggvars.gaseelrelaeklgiPvvttlmgkgviped 55 
                                       ek+++l++++   ++++G g++ + +++e lr+l+e+l+ Pv+    g  +++e+
  gi|320100575|ref|YP_004176167.1| 328 EKILSLIEEHGIDIVVLGPGTSLNrETQELLRSLVEALDKPVIIDGDGLTAVSEN 382
                                       78899999999999********99899****************999999999875 PP

>> Tex_YqgF  Tex protein YqgF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05     0.085      42      83 ..     325     367 ..     304     381 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHHTT--EEEEESSTT.HHHHHHHHHHHHHHGGG CS
                          Tex_YqgF  42 eakkklkklvkkykveliaiGnGta.sreteklvaelikeeel 83 
                                          +k+ +l++++ ++++ +G Gt+  ret++l+++l++  ++
  gi|320100575|ref|YP_004176167.1| 325 GNLEKILSLIEEHGIDIVVLGPGTSlNRETQELLRSLVEALDK 367
                                       45678999****************857*********9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3822.35
//
Query:       gi|320100576|ref|YP_004176168.1|  [L=131]
Description: transcriptional regulator NikR [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-21   75.9   2.4    2.8e-21   75.5   2.4    1.2  1  NikR_C    NikR C terminal nickel binding domain
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.027   15.1   0.0    1.6  2  RHH_6     Ribbon-helix-helix domain
      0.017   15.0   0.2      0.046   13.7   0.0    1.9  2  RHH_1     Ribbon-helix-helix protein, copG family
      0.039   13.8   0.0      0.071   13.0   0.0    1.4  1  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


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 !   75.5   2.4   6.2e-25   2.8e-21       1      74 [.      53     126 ..      53     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 6.2e-25
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkl 74 
                                       vG i+++y h + +++++lt++qh+y  + +   h+h+d+++cL +i+++G+++ei++l++++r+lkgV  vk 
  gi|320100576|ref|YP_004176168.1|  53 VGYIMVLYQHGVGDVDRELTEVQHKYIGVALFENHIHVDEERCLLTIAVRGRYSEIQKLIDEVRGLKGVLLVKH 126
                                       79*******************************************************************99985 PP

>> RHH_6  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   5.9e-06     0.027       7      50 ..       8      48 ..       4      52 .. 0.85
   2 ?   -3.0   0.0       2.7   1.2e+04      63      70 ..     107     114 ..     104     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.9e-06
                             RHH_6  7 vavspetdqavrafLAsqGggrkGdLSrfieeAVrayllelave 50
                                      v ++ ++++ +  +LA++ ggr    S+ i+eA r+yll +++ 
  gi|320100576|ref|YP_004176168.1|  8 VYIPGDIEDLLEDYLARH-GGRS--VSSVIQEALRSYLLGEKIP 48
                                      6788899999********.7886..5************987765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.7
                             RHH_6  63 elsdlide 70 
                                       e+++lide
  gi|320100576|ref|YP_004176168.1| 107 EIQKLIDE 114
                                       89999998 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 ?   13.7   0.0     1e-05     0.046      16      37 ..      21      42 ..       6      43 .. 0.85
   2 ?   -3.3   0.1       2.3     1e+04       4       9 ..      88      93 ..      88      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                                      HHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1 16 elarrrgrSrSelIReAlreyl 37
                                       lar +grS+S +I eAlr yl
  gi|320100576|ref|YP_004176168.1| 21 YLARHGGRSVSSVIQEALRSYL 42
                                      599999**************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                                      EEEEHH CS
                             RHH_1  4 irldee 9 
                                      i++dee
  gi|320100576|ref|YP_004176168.1| 88 IHVDEE 93
                                      899997 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 ?   13.0   0.0   1.6e-05     0.071       3      32 ..       5      35 ..       3      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                             RHH_5  3 RvnvtLPeelleeLee.wAdeegRsvSnlaa 32
                                      ++ v+ P ++ + Le  +A + gRsvS++++
  gi|320100576|ref|YP_004176168.1|  5 KIGVYIPGDIEDLLEDyLARHGGRSVSSVIQ 35
                                      7889**********9736**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 967.60
//
Query:       gi|320100577|ref|YP_004176169.1|  [L=126]
Description: DtxR family iron (metal) dependent repressor [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-19   67.4   3.1    1.1e-18   67.1   1.8    1.7  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    2.4e-16   59.7   0.1    9.1e-16   57.8   0.1    1.9  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      6e-07   29.3   0.3    1.7e-06   27.8   0.0    1.8  3  MarR_2          MarR family
    1.2e-06   28.3   0.0    2.5e-06   27.3   0.0    1.4  1  MarR            MarR family
    0.00017   22.0   0.0    0.00032   21.1   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain
     0.0002   21.1   0.0    0.00052   19.8   0.0    1.7  2  HTH_IclR        IclR helix-turn-helix domain
    0.00025   20.7   0.0     0.0008   19.1   0.0    1.9  2  LexA_DNA_bind   LexA DNA binding domain
     0.0004   20.3   0.0     0.0025   17.8   0.0    2.3  1  HTH_29          Winged helix-turn helix
    0.00074   19.1   0.0     0.0019   17.8   0.0    1.7  1  GntR            Bacterial regulatory proteins, gntR family
    0.00099   18.9   0.1     0.0022   17.8   0.1    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0013   19.0   0.0     0.0023   18.2   0.0    1.5  1  Rrf2            Transcriptional regulator
     0.0014   18.4   0.0     0.0024   17.7   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0015   18.5   0.0     0.0037   17.2   0.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0016   18.1   0.0     0.0048   16.6   0.0    1.8  1  HTH_38          Helix-turn-helix domain
     0.0024   17.9   0.0      0.004   17.2   0.0    1.2  1  DUF2250         Uncharacterized protein conserved in archaea 
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.024   14.3   0.0    1.4  2  DUF4423         Domain of unknown function (DUF4423)
      0.019   14.5   0.0      0.045   13.3   0.0    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.022   14.7   0.1      0.063   13.2   0.1    1.7  2  LcrG            LcrG protein
      0.035   13.9   0.0       0.22   11.4   0.0    2.3  3  IF2_N           Translation initiation factor IF-2, N-termina
      0.041   13.9   0.0       0.08   12.9   0.0    1.6  1  HTH_45          Winged helix-turn-helix
      0.057   13.6   0.1       0.47   10.6   0.0    2.2  2  Mrr_N           Mrr N-terminal domain
       0.12   12.0   0.0       0.23   11.0   0.0    1.5  1  HTH_CodY        CodY helix-turn-helix domain
       0.13   11.2   0.0       0.18   10.7   0.0    1.1  1  Topoisom_bac    DNA topoisomerase
       0.16   12.2   0.0       0.29   11.3   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.6   2.7e+03       5      26 ..      25      45 ..      23      60 .. 0.62
   2 !   67.1   1.8   1.4e-21   1.1e-18       1      64 [.      62     124 ..      62     126 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.6
                                      HHHHHHHHHHHHHHHHHHHHHC CS
                     Fe_dep_repr_C  5 relAkrlvrrhrllerfLvdvl 26
                                      re+A+rl  +   + +fL ++l
  gi|320100577|ref|YP_004176169.1| 25 REIARRLCVKPSSVVEFL-RKL 45
                                      566777666666666666.445 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 1.4e-21
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TT CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPh 64 
                                       TekG  +A+++ +rhrll +fL + +gv+ e+a+e+A+r+Eh+l++e++ +++e+l+ +    h
  gi|320100577|ref|YP_004176169.1|  62 TEKGLAVARDVHQRHRLLAEFL-ESIGVPREIAEEDACRMEHVLHPETVAKIREFLESIHAARH 124
                                       9*********************.88*******************************98877666 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 !   57.8   0.1   1.2e-18   9.1e-16       3      56 ..       3      55 ..       1      58 [. 0.96
   2 ?   -1.3   0.0       3.6   2.7e+03       2      16 ..     108     122 ..     107     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.2e-18
                                      -HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress  3 vestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                      +++ E+YLe+IY ls +++ +++ ++a+rL v+pssV e l+kL+++Gy++yek
  gi|320100577|ref|YP_004176169.1|  3 SQRVEEYLEVIYVLS-SQGRPRVREIARRLCVKPSSVVEFLRKLSSEGYIIYEK 55
                                      5789***********.************************************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.6
                                       --HHHHHHHHHHHHH CS
                    Fe_dep_repress   2 LvestEdYLetIYtl 16 
                                       +v+++ ++Le I  +
  gi|320100577|ref|YP_004176169.1| 108 TVAKIREFLESIHAA 122
                                       678899999999765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.3e-09   1.7e-06      10      56 ..      12      56 ..       8      59 .. 0.88
   2 ?   -2.4   0.0         6   4.5e+03      45      56 ..      61      72 ..      60      77 .. 0.69
   3 ?   -2.6   0.0         7   5.2e+03       8      29 ..      76      94 ..      73      95 .. 0.56

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.3e-09
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      v+++L   ++   +v+e+arrl +++s+v   l++L++ G++ +++g
  gi|320100577|ref|YP_004176169.1| 12 VIYVLSSQGR--PRVREIARRLCVKPSSVVEFLRKLSSEGYIIYEKG 56
                                      6777777776..7*****************************99987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6
                                      HHHTTSEEEEES CS
                            MarR_2 45 LvaaGLverrpg 56
                                      L ++GL + r+ 
  gi|320100577|ref|YP_004176169.1| 61 LTEKGLAVARDV 72
                                      788999877754 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7
                                      HHHHHHHHCTTTSEEEHHHHHH CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelar 29
                                      +r+La+   + g    ++e+a+
  gi|320100577|ref|YP_004176169.1| 76 HRLLAEFLESIG---VPREIAE 94
                                      566666555544...4556665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   3.3e-09   2.5e-06       7      47 ..      11      51 ..       8      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.3e-09
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      ++++ l++qg ++v e+a++l+v++s+v ++l++L  +G+i
  gi|320100577|ref|YP_004176169.1| 11 EVIYVLSSQGRPRVREIARRLCVKPSSVVEFLRKLSSEGYI 51
                                      68899**********************************99 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.3e-07   0.00032       9      68 .]      10      65 ..       7      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.3e-07
                            HTH_27  9 Lhlir..hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      L++i+    ++r + +++++rl v  s++++ l+kL   G++         +  r++lT+kG
  gi|320100577|ref|YP_004176169.1| 10 LEVIYvlSSQGRPRVREIARRLCVKPSSVVEFLRKLSSEGYI------IYEKGGRIELTEKG 65
                                      666666668999******************************......66699********9 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     7e-07   0.00052       6      48 ..      10      51 ..       6      54 .. 0.91
   2 ?   -2.8   0.1       7.5   5.6e+03      36      42 ..      76      82 ..      76      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7e-07
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      l+++  l++++++ +++e+Arr+ + +S+v  +L+ L  +Gy+
  gi|320100577|ref|YP_004176169.1| 10 LEVIYVLSSQGRP-RVREIARRLCVKPSSVVEFLRKLSSEGYI 51
                                      6677789999998.****************************7 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.5
                                      HHHHHHH CS
                          HTH_IclR 36 hRlLqtL 42
                                      hRlL+ +
  gi|320100577|ref|YP_004176169.1| 76 HRLLAEF 82
                                      9999866 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 !   19.1   0.0   1.1e-06    0.0008      18      58 ..      14      53 ..       3      58 .. 0.82
   2 ?   -2.9   0.0       8.2   6.1e+03      15      32 ..      79      93 ..      76      95 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                                      HHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 18 sieetgypPsireiaralglkSpsaveehLkaLerKGyier 58
                                      ++ + +  P +reiar+l +k ps+v e L++L+  Gyi  
  gi|320100577|ref|YP_004176169.1| 14 YVLSSQGRPRVREIARRLCVK-PSSVVEFLRKLSSEGYIIY 53
                                      455666779************.****************965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.2
                                      HHHHHHHHSS---HHHHH CS
                     LexA_DNA_bind 15 ikasieetgypPsireia 32
                                      + +++e+ g p   reia
  gi|320100577|ref|YP_004176169.1| 79 LAEFLESIGVP---REIA 93
                                      55666666666...4444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.4e-06    0.0025       6      40 ..      15      49 ..      12      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-06
                            HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwlkrfeegG 40
                                       l+++G ++v++iA++l++ +++v  +l+    +G
  gi|320100577|ref|YP_004176169.1| 15 VLSSQGRPRVREIARRLCVKPSSVVEFLRKLSSEG 49
                                      5889**********************999999988 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.5e-06    0.0019      25      61 ..      22      58 ..      21      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                                      --HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                              GntR 25 PsereLaaefgVsrttvReALrrLeaeglverrqgrG 61
                                      P++re+a ++ V+ ++v e Lr+L++eg+++ ++g+ 
  gi|320100577|ref|YP_004176169.1| 22 PRVREIARRLCVKPSSVVEFLRKLSSEGYIIYEKGGR 58
                                      99*****************************999976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.9e-06    0.0022      17      58 ..      16      57 ..       7      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      L ++g+ +++eia++l v  s+v e Lr+L++ G++  ekg 
  gi|320100577|ref|YP_004176169.1| 16 LSSQGRPRVREIARRLCVKPSSVVEFLRKLSSEGYIIYEKGG 57
                                      4489999*****************************999975 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.1e-06    0.0023       5      60 ..       4      56 ..       1      74 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-06
                                      HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2  5 skteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrG 60
                                      +++e  l ++++L+++ +    +++eia+r  ++ps +   l+kL+ +g++  ++G
  gi|320100577|ref|YP_004176169.1|  4 QRVEEYLEVIYVLSSQGR---PRVREIARRLCVKPSSVVEFLRKLSSEGYIIYEKG 56
                                      566666677777777766...56****************************99988 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 !   17.7   0.0   3.3e-06    0.0024       5      46 ..      10      52 ..       8      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      l++++ L++ g   v e+a+ l + +s v + L+kL  +G++ 
  gi|320100577|ref|YP_004176169.1| 10 LEVIYVLSSqGRPRVREIARRLCVKPSSVVEFLRKLSSEGYII 52
                                      7899999998889****************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.9e-06    0.0037      25      60 ..      25      62 ..      14      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.9e-06
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE..ETEEEEES CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis..rgrriril 60
                                      +e+A++l + +++v   l++L+ eg+i   +g+ri+++
  gi|320100577|ref|YP_004176169.1| 25 REIARRLCVKPSSVVEFLRKLSSEGYIIyeKGGRIELT 62
                                      79*************************97545449876 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   6.5e-06    0.0048      11      37 ..      11      38 ..      11      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.5e-06
                            HTH_38 11 eeIerllaeG.lslreIArrLgrspsTI 37
                                      e+I+ l ++G   +reIArrL+++ps++
  gi|320100577|ref|YP_004176169.1| 11 EVIYVLSSQGrPRVREIARRLCVKPSSV 38
                                      6899999999889*************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 !   17.2   0.0   5.3e-06     0.004       7      78 ..       6      77 ..       2      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.3e-06
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHt 78
                                       e++l+v++ l   +    + ia++l ++ + v e l+kL + G + + +g  i  te+ l  +  vh++H 
  gi|320100577|ref|YP_004176169.1|  6 VEEYLEVIYVLSSQGRPRVREIARRLCVKPSSVVEFLRKLSSEGYIIYEKGGRIELTEKGLAVARDVHQRHR 77
                                      567899*****************************************************************5 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.3e-05     0.024      34      90 ..      19      73 ..       7      82 .. 0.88
   2 ?   -2.7   0.0       5.5   4.1e+03     135     142 ..     109     116 ..      91     123 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-05
                           DUF4423 34 dfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevk 90
                                      ++++ ++e+a+rl+  ++ + v + l+ L + g +  ++ g+++ tek l++  +v 
  gi|320100577|ref|YP_004176169.1| 19 QGRPRVREIARRLC--VKPSSVVEFLRKLSSEGYIIYEKGGRIELTEKGLAVARDVH 73
                                      45689*********..**********************************9988775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.5
                           DUF4423 135 kkeirefr 142
                                       + +iref 
  gi|320100577|ref|YP_004176169.1| 109 VAKIREFL 116
                                       22233333 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 ?   13.3   0.0     6e-05     0.045       8      47 ..      12      51 ..      10      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                            HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++ +L  ++r   re+A+rl + ps v + l++L +eG+I
  gi|320100577|ref|YP_004176169.1| 12 VIYVLSSQGRPRVREIARRLCVKPSSVVEFLRKLSSEGYI 51
                                      6778899999999**************************9 PP

>> LcrG  LcrG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.7     2e+03      27      49 ..      25      47 ..      15      55 .. 0.75
   2 ?   13.2   0.1   8.5e-05     0.063      15      42 ..      67      95 ..      58     126 .] 0.69

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.7
                              LcrG 27 qelleglGlapeageklfgglea 49
                                       e+ + l ++p  + +++ +l+ 
  gi|320100577|ref|YP_004176169.1| 25 REIARRLCVKPSSVVEFLRKLSS 47
                                      67788888888888887776665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.5e-05
                              LcrG 15 ai.rdsdeRakllqelleglGlapeagek 42
                                      a+ rd  +R +ll+e+le++G+  e++e+
  gi|320100577|ref|YP_004176169.1| 67 AVaRDVHQRHRLLAEFLESIGVPREIAEE 95
                                      442899****************9998876 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.22       5      28 ..      23      45 ..      21      52 .. 0.91
   2 ?   -2.0   0.0       4.6   3.4e+03      21      31 ..      79      89 ..      76      94 .. 0.67
   3 ?   -1.9   0.0         4     3e+03      37      49 ..     102     114 ..      99     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                             IF2_N  5 rVyeLAkeLgvkskevikkLfkel 28
                                      rV+e+A++L vk+  v+++L k l
  gi|320100577|ref|YP_004176169.1| 23 RVREIARRLCVKPSSVVEFLRK-L 45
                                      9*******************77.6 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.6
                             IF2_N 21 ikkLfkelGie 31
                                      ++++ ++ G++
  gi|320100577|ref|YP_004176169.1| 79 LAEFLESIGVP 89
                                      44444778887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4
                             IF2_N  37 ssLDeetaeliae 49 
                                       + L  et+++i+e
  gi|320100577|ref|YP_004176169.1| 102 HVLHPETVAKIRE 114
                                       6777899999986 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   0.00011      0.08      35      75 ..      37      78 ..      10      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            HTH_45 35 llnkYLdmLvekgli.kkskekYvlTekGlelleklkeleel 75
                                       + ++L +L ++g+i  ++++  +lTekGl + +++++ ++l
  gi|320100577|ref|YP_004176169.1| 37 SVVEFLRKLSSEGYIiYEKGGRIELTEKGLAVARDVHQRHRL 78
                                      56789*********857899************9999888776 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.1   8.5e+02       6      28 ..      10      32 ..       7      35 .. 0.71
   2 ?   10.6   0.0   0.00063      0.47      60      86 ..      44      70 ..      39      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                             Mrr_N  6 lplLealad.gsehrlkeirerva 28
                                      l+++ +l++ g+ + ++ei +r+ 
  gi|320100577|ref|YP_004176169.1| 10 LEVIYVLSSqGRPR-VREIARRLC 32
                                      67778888845555.599999875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00063
                             Mrr_N 60 yLkkagllespkrgvwkiTekGrevlk 86
                                      +L+ +g++ ++k g +++TekG +v +
  gi|320100577|ref|YP_004176169.1| 44 KLSSEGYIIYEKGGRIELTEKGLAVAR 70
                                      68999******************9975 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00031      0.23       4      34 ..      21      51 ..      18      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                          HTH_CodY  4 rLtaskiaDriGitrsvivnaLrkLesaGii 34
                                      r    +ia r+ +  s +v  LrkL s G i
  gi|320100577|ref|YP_004176169.1| 21 RPRVREIARRLCVKPSSVVEFLRKLSSEGYI 51
                                      5556789********************9976 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.18     343     382 ..      35      75 ..      34      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                      Topoisom_bac 343 paTraeiieklvergYverkk.kslvptelGkalvellekf 382
                                       p++  e ++kl ++gY+  +k +++  te+G a+++ +++ 
  gi|320100577|ref|YP_004176169.1|  35 PSSVVEFLRKLSSEGYIIYEKgGRIELTEKGLAVARDVHQR 75 
                                       899999**************99************9988544 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 ?   11.3   0.0   0.00039      0.29       3      49 ..      10      56 ..       9      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                            HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                      l+v+ +L+s+ +   +e+   l +  +     l+kL + gYi ++k+
  gi|320100577|ref|YP_004176169.1| 10 LEVIYVLSSQGRPRVREIARRLCVKPSSVVEFLRKLSSEGYIIYEKG 56
                                      78999***************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 972.46
//
Query:       gi|320100578|ref|YP_004176170.1|  [L=246]
Description: glutaredoxin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-11   44.3   0.0    2.6e-07   30.6   0.0    2.5  2  Thioredoxin_3  Thioredoxin domain
    1.1e-06   28.8   0.7    8.9e-05   22.6   0.4    2.7  2  Glutaredoxin   Glutaredoxin
     0.0052   17.4   0.3       0.11   13.2   0.2    2.2  2  DUF2946        Protein of unknown function (DUF2946)
  ------ inclusion threshold ------
      0.012   15.6   0.0       0.29   11.1   0.0    2.2  2  Thioredoxin    Thioredoxin
      0.014   15.8   3.5        2.7    8.5   1.7    3.6  3  Thioredoxin_2  Thioredoxin-like domain
      0.016   15.0   0.0      0.032   14.0   0.0    1.5  1  Thioredoxin_9  Thioredoxin
      0.018   15.2   0.1        6.5    6.9   0.0    2.4  2  Thioredoxin_4  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00012       0.3       9      72 ..      55     119 ..      52     122 .. 0.81
   2 !   30.6   0.0     1e-10   2.6e-07       2      55 ..     150     206 ..     149     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                       SSTTCHHHHHHHHHHCHCCT..CECEEECCTTHHHH.HHCT-SSSSEEECT...TCEEEESS---CCHHH CS
                     Thioredoxin_3   9 gCakCpklekavkeaaaekg..ikaevekvtdfeei.ekygVmsvPalvid...gkvvvsGkvpseeeir 72 
                                       gC++C +++++++e++  +g  + ++v +++d e +  +      Pa ++d    +v++ G +ps++e++
  gi|320100578|ref|YP_004176170.1|  55 GCPTCGEAKMLAEEIVRISGgrVRFTVLDAKDAEALkPR----YLPAFIYDtpkRNVRYYG-LPSGQEFA 119
                                       8******************62677799999999988444....589999988777888999.88888865 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 1e-10
                                       EEEE.ESSSSTTCHHHHHHHHHHCHCC.TCECEEECC.TTHHHHHHCT-SSSSEEEC CS
                     Thioredoxin_3   2 eikv.lgpgCakCpklekavkeaaaek.gikaevekv.tdfeeiekygVmsvPalvi 55 
                                       ++k+ ++p C++Cp ++ ++++a   + gi +e +++ +++ e + ygV+ vP ++i
  gi|320100578|ref|YP_004176170.1| 150 HVKIfVTPECPYCPLVVDFFNQAGLVNqGIVVETIEAfEHPVEADAYGVQYVPYVAI 206
                                       79**99********999999999766648999888887888899*********9987 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.032        81       8      32 ..      55      85 ..      53      97 .. 0.72
   2 !   22.6   0.4   3.5e-08   8.9e-05       1      55 [.     151     206 ..     151     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.032
                                      SSHHHHHHHHHHHHTT......GGEEEEEGC CS
                      Glutaredoxin  8 tCpyCkkakrlLkelg......vkfeeidvd 32
                                      +Cp C  ak l++e        v+f++ d  
  gi|320100578|ref|YP_004176170.1| 55 GCPTCGEAKMLAEEIVrisggrVRFTVLDAK 85
                                      7**********98764444444556666655 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.5e-08
                                       EEEEESTSSHHHHHHHHHHHHTT.....GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEE CS
                      Glutaredoxin   1 vvlftkptCpyCkkakrlLkelg.....vkfeeidvdkdeeireelkelsgvrtvPqvfi 55 
                                       v +f++p CpyC+ +++++++ g     + +e+i+  +++ + ++     gv+ vP v i
  gi|320100578|ref|YP_004176170.1| 151 VKIFVTPECPYCPLVVDFFNQAGlvnqgIVVETIEAFEHPVEADAY----GVQYVPYVAI 206
                                       78*****************999975555669999999999999888....8888887766 PP

>> DUF2946  Protein of unknown function (DUF2946)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   4.3e-05      0.11      41      67 ..      34      60 ..       9      71 .. 0.85
   2 ?    2.1   0.0      0.11   2.9e+02      61      69 ..     157     165 ..     133     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                           DUF2946 41 aysaaytaagagspasamdseaCgyCs 67
                                      ++s+ ++ +++ +++++++++ C+ C+
  gi|320100578|ref|YP_004176170.1| 34 EESHVHGEDEDEHHHHHHHHGGCPTCG 60
                                      568999********************6 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                           DUF2946  61 eaCgyCsll 69 
                                        +C+yC l+
  gi|320100578|ref|YP_004176170.1| 157 PECPYCPLV 165
                                       58****987 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.069   1.8e+02      28      60 ..      57      86 ..      55     115 .. 0.75
   2 ?   11.1   0.0   0.00011      0.29      22      83 ..     151     211 ..     134     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.069
                                      TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTT CS
                       Thioredoxin 28 pwCghCkalaPeleklaeelkdkvklakvdvde 60
                                      p Cg  k+la e+ +++    ++v++  +d+++
  gi|320100578|ref|YP_004176170.1| 57 PTCGEAKMLAEEIVRISG---GRVRFTVLDAKD 86
                                      789999999988877654...345555555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                                       EEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                       Thioredoxin  22 lveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk 83 
                                       +  F  p C+ C  +  +++++    +  +++  +++ e++  a+ y+v+++P + +++ ++
  gi|320100578|ref|YP_004176170.1| 151 VKIFVTPECPYCPLVVDFFNQAGLVNQ-GIVVETIEAFEHPVEADAYGVQYVPYVAITRLSD 211
                                       44589999*****99999999887666.9************************999988766 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   7.8e+02      15      36 ..      57      78 ..      45     107 .. 0.73
   2 ?    0.1   0.0      0.41     1e+03      76     106 ..      90     119 ..      84     122 .. 0.78
   3 ?    8.5   1.7     0.001       2.7      69     108 ..     189     235 ..     149     236 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                     Thioredoxin_2 15 pdCpyCkklkkelkelddvtvr 36
                                      p+C+  k l +e+  +++ +vr
  gi|320100578|ref|YP_004176170.1| 57 PTCGEAKMLAEEIVRISGGRVR 78
                                      6788889999999999776666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.41
                     Thioredoxin_2  76 ygvrgtPtivfldgk.eivarlpGyvpaeele 106
                                       ++ r +P++++  +k ++  r+ G+ + +e++
  gi|320100578|ref|YP_004176170.1|  90 LKPRYLPAFIYDTPKrNV--RYYGLPSGQEFA 119
                                       566889******999444..999998888886 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.001
                     Thioredoxin_2  69 nvelarkygvrgtPtiv...fldgk....eivarlpGyvpaeeleal 108
                                       + + a++ygv+ +P++    + d +    ++++++pGy+p+ee  ++
  gi|320100578|ref|YP_004176170.1| 189 HPVEADAYGVQYVPYVAitrLSDYDkygaKPIEVIPGYLPPEENVKI 235
                                       3356789********5523444444889999**********986665 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.032      24      90 ..     130     196 ..     126     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                       HHHHHH---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTT CS
                     Thioredoxin_9  24 kkvelseeteekiksiekklkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqy 90 
                                       + v+ls+ + e+++si+ +l++ ++ ++ C+ +  +v +++++   n++i v+ +   e++   d y
  gi|320100578|ref|YP_004176170.1| 130 NGVKLSKSVVEELESIDAPLHVKIFVTPECPYCPLVVDFFNQAGLVNQGIVVETIEAFEHPVEADAY 196
                                       6799**********************************************99998877777666666 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0025       6.5       3      55 ..      34      84 ..      32      98 .. 0.86
   2 ?    6.2   0.1     0.004        10      12      28 ..     146     162 ..     144     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0025
                                      SSSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE- CS
                     Thioredoxin_4  3 etdiviGnpdApvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdf 55
                                      e+++v G+ +  ++ +  +   Cp+C + +   e++++   + G+v+f++ d 
  gi|320100578|ref|YP_004176170.1| 34 EESHVHGEDEDEHHHHHHHHGGCPTCGEAKMLAEEIVRI--SGGRVRFTVLDA 84
                                      67889999999*************************986..599****98776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.004
                                       T-SEEEEEEE-TT-HHH CS
                     Thioredoxin_4  12 dApvtvieyedlrCphC 28 
                                       dAp +v +++  +Cp+C
  gi|320100578|ref|YP_004176170.1| 146 DAPLHVKIFVTPECPYC 162
                                       8**************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1908.72
//
Query:       gi|320100579|ref|YP_004176171.1|  [L=254]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-05   23.5   0.1    8.5e-05   22.4   0.1    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    4.7e-05   23.2   0.4    0.00092   19.1   0.1    2.7  2  MarR_2          MarR family
    0.00014   21.4   0.3    0.00033   20.1   0.0    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00042   20.0   0.3     0.0015   18.3   0.1    2.1  2  HTH_IclR        IclR helix-turn-helix domain
     0.0013   18.7   0.0     0.0066   16.5   0.0    2.2  2  HemN_C          HemN C-terminal domain
     0.0037   17.4   0.0     0.0076   16.4   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0043   17.0   0.0     0.0096   15.9   0.0    1.5  1  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
      0.014   15.2   1.1      0.064   13.1   0.9    2.2  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.016   15.2   0.0       0.03   14.3   0.0    1.4  1  Prefoldin_2     Prefoldin subunit
      0.021   15.1   0.1      0.043   14.1   0.1    1.5  1  Rx_N            Rx N-terminal domain
      0.071   13.5   0.1       0.23   11.8   0.0    1.9  1  FaeA            FaeA-like protein
      0.076   13.5   0.1         23    5.5   0.0    2.4  2  HSCB_C          HSCB C-terminal oligomerisation domain
      0.096   12.6   0.0       0.21   11.5   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
        0.1   12.4   0.1       0.62    9.9   0.0    2.3  3  LexA_DNA_bind   LexA DNA binding domain
        0.1   13.1   0.1       0.24   11.9   0.1    1.7  1  HTH_27          Winged helix DNA-binding domain
       0.11   12.9   0.0       0.23   11.9   0.0    1.5  1  DUF4140         N-terminal domain of unknown function (DUF414
       0.12   12.7   0.4       0.32   11.3   0.4    1.8  1  ABC_tran_CTD    ABC transporter C-terminal domain
       0.12   12.2   0.2       0.49   10.2   0.0    2.0  2  IF2_N           Translation initiation factor IF-2, N-termina
       0.17   11.9   0.0       0.38   10.8   0.0    1.6  1  Replic_Relax    Replication-relaxation
       0.18   11.9   0.0       0.18   11.9   0.0    2.1  3  DUF2161         Putative PD-(D/E)XK phosphodiesterase (DUF216


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   9.4e-08   8.5e-05      17      55 ..      13      52 ..       4      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.4e-08
                                      HH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 17 Ll.klgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      Ll +  +++++++ae+lgv+ +++ e+L++L   G+Ve+ 
  gi|320100579|ref|YP_004176171.1| 13 LLnSAPSLSVRDVAEALGVDVARAKEILERLRYGGYVEKA 52
                                      45377889******************************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1     1e-06   0.00092      11      53 ..      11      51 ..       8      56 .. 0.87
   2 ?    0.8   0.0      0.52   4.7e+02       3      17 ..     223     237 ..     222     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      L  L  +p   l+v+++a++lg++ +++  il+rL   G+ve+
  gi|320100579|ref|YP_004176171.1| 11 LELLNSAPS--LSVRDVAEALGVDVARAKEILERLRYGGYVEK 51
                                      555556666..******************************97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.52
                                       --HHHHHHHHHHHCT CS
                            MarR_2   3 ltpaqarvLaaLgrr 17 
                                       l+pa++++L + +r+
  gi|320100579|ref|YP_004176171.1| 223 LSPAERMLLEEMRRE 237
                                       79*********9985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.7e-07   0.00033       5      47 ..       7      49 ..       4      50 .. 0.92
   2 ?   -3.3   0.1       7.7   6.9e+03      35      42 ..     123     130 ..     122     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.7e-07
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++k LelL   p++s r++Ae+lg+ ++  ++ l+rL   G++
  gi|320100579|ref|YP_004176171.1|  7 TLKALELLNSAPSLSVRDVAEALGVDVARAKEILERLRYGGYV 49
                                      6899*********************************988887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.7
                            HTH_24  35 nrrlkrLe 42 
                                       + rl++Le
  gi|320100579|ref|YP_004176171.1| 123 SNRLRELE 130
                                       56999998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.6e-06    0.0015       6      50 ..       8      51 ..       7      53 .. 0.94
   2 ?   -3.4   0.0       9.8   8.8e+03      10      20 ..     113     125 ..     113     129 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      l  L++l++ap  l+++++A+++g+  + +  +L  L   Gyve+
  gi|320100579|ref|YP_004176171.1|  8 LKALELLNSAPS-LSVRDVAEALGVDVARAKEILERLRYGGYVEK 51
                                      5679********.9*****************************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.8
                                       CT-CTTBSS-..B CS
                          HTH_IclR  10 dalaeapqel..t 20 
                                       dala++ +el  +
  gi|320100579|ref|YP_004176171.1| 113 DALAKRVEELsnR 125
                                       6778877777334 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.4e-06    0.0066      21      65 ..      20      63 ..      19      64 .. 0.94
   2 ?   -2.6   0.0       6.6   5.9e+03       5       8 ..     232     235 ..     209     240 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.4e-06
                            HemN_C 21 ldlaafeqrfgldleellaaaleklqeqGLLeldggrlrltprGr 65
                                      l+ ++++++ g+d++ + + +le+l+  G++e +g+++  t++Gr
  gi|320100579|ref|YP_004176171.1| 20 LSVRDVAEALGVDVARA-KEILERLRYGGYVEKAGHGYAITEKGR 63
                                      67899********8888.**************************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                            HemN_C   5 drle 8  
                                       + ++
  gi|320100579|ref|YP_004176171.1| 232 EEMR 235
                                       2333 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   0.0   8.4e-06    0.0076      23      55 ..      20      52 ..       8      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.4e-06
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyveye 55
                                       ++ d+ae+L+v  + + e l++L+  Gyve +
  gi|320100579|ref|YP_004176171.1| 20 LSVRDVAEALGVDVARAKEILERLRYGGYVEKA 52
                                      6789**************************976 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05    0.0096      32      68 ..      32      68 ..      24      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                            HTH_45 32 sykllnkYLdmLvekglikkskekYvlTekGlellek 68
                                      +  ++++ L+ L   g+++k ++ Y +TekG+ ll +
  gi|320100579|ref|YP_004176171.1| 32 DVARAKEILERLRYGGYVEKAGHGYAITEKGRALLAD 68
                                      56788999**************************986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9   7.1e-05     0.064       9      41 ..      11      43 ..       8      44 .. 0.87
   2 ?   -1.7   0.0       3.1   2.8e+03      27      41 ..     108     122 ..     107     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.1e-05
                     HTH_AsnC-type  9 LeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      Le+L   +++s++++Ae++G++ +++ + ++rL
  gi|320100579|ref|YP_004176171.1| 11 LELLNSAPSLSVRDVAEALGVDVARAKEILERL 43
                                      99*******************999888777776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                     HTH_AsnC-type  27 vGlSestvlrRvrrL 41 
                                       vG ++++ ++Rv+ L
  gi|320100579|ref|YP_004176171.1| 108 VGEAPDALAKRVEEL 122
                                       677788999999877 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.3e-05      0.03      58      96 ..     106     144 ..     105     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-05
                                       E-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  58 qdkeevkeeLeerketlekeiktlekqleklekeleelk 96 
                                       q++ e+ + L +r e+l+ ++++le++l+++e +l+ l+
  gi|320100579|ref|YP_004176171.1| 106 QPVGEAPDALAKRVEELSNRLRELESRLRDIESRLASLE 144
                                       67889999***************************9987 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.8e-05     0.043       7      48 ..     113     154 ..     108     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-05
                              Rx_N   7 qkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerq 48 
                                       + La+ ++e  ++l+++++ l+ ++++L s++++++da +r 
  gi|320100579|ref|YP_004176171.1| 113 DALAKRVEELSNRLRELESRLRDIESRLASLEGFVRDAARRS 154
                                       56777788888****************************996 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00026      0.23       6      48 ..      11      52 ..       7      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                                      HHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE CS
                              FaeA  6 leylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrs 48
                                      le lns   +   r++A+alg+    a+  Le L+  g ++++
  gi|320100579|ref|YP_004176171.1| 11 LELLNS-APSLSVRDVAEALGVDVARAKEILERLRYGGYVEKA 52
                                      666777.667789**************************9996 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.026        23      45      67 ..      24      45 ..      18      49 .. 0.87
   2 ?    5.4   0.2      0.03        27      24      49 ..     118     143 ..     108     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                                      HHHHHHHTT-HHHHHHHHHHHHH CS
                            HSCB_C 45 eleeafekkdleaaadllrrlrY 67
                                       ++ea+   d+++a+++l rlrY
  gi|320100579|ref|YP_004176171.1| 24 DVAEAL-GVDVARAKEILERLRY 45
                                      677888.67************** PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.03
                                       SHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HSCB_C  24 dkeeleelkaeveerieeleaeleea 49 
                                         eel++  +e+e+r++++e++l+++
  gi|320100579|ref|YP_004176171.1| 118 RVEELSNRLRELESRLRDIESRLASL 143
                                       34888888888899998888888876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.21       5      47 .]       8      51 ..       7      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                      HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  5 lkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      lk L lL++ + l+v + ae+lg+  +   + L +Lr  G+Vek
  gi|320100579|ref|YP_004176171.1|  8 LKALELLNSAPsLSVRDVAEALGVDVARAKEILERLRYGGYVEK 51
                                      68899****888*****************************987 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 ?    9.9   0.0   0.00069      0.62      27      58 ..      21      51 ..      11      55 .. 0.89
   2 ?   -2.8   0.0       6.3   5.7e+03      41      50 ..     134     143 ..     119     149 .. 0.62
   3 ?   -1.8   0.0       3.2   2.8e+03      39      56 ..     172     189 ..     166     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00069
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyier 58
                                      s+r++a+alg+   + ++e L++L+  Gy+e 
  gi|320100579|ref|YP_004176171.1| 21 SVRDVAEALGVD-VARAKEILERLRYGGYVEK 51
                                      79**********.77789************96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.3
                                       HHHHHHHHHH CS
                     LexA_DNA_bind  41 saveehLkaL 50 
                                       + +e++L+ L
  gi|320100579|ref|YP_004176171.1| 134 RDIESRLASL 143
                                       3456666666 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.2
                                       .HHHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind  39 SpsaveehLkaLerKGyi 56 
                                       S + ++++L +L  K ++
  gi|320100579|ref|YP_004176171.1| 172 SIAEAQSRLGTLLEKYLV 189
                                       667788999988887655 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00027      0.24      18      68 .]      19      62 ..       7      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                        + +d++++l v+ + + ++l++L   G+ve+ g         +++T+kG
  gi|320100579|ref|YP_004176171.1| 19 SLSVRDVAEALGVDVARAKEILERLRYGGYVEKAGHG-------YAITEKG 62
                                      45669**************************888877.......9999998 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00026      0.23      56      91 ..     101     143 ..      83     145 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                           DUF4140  56 rvpnreaeee.......elkalraeleeledelaaledelaaa 91 
                                       r++ ++++ e       ++++l ++l+ele +l+++e++la++
  gi|320100579|ref|YP_004176171.1| 101 RQTPPQPVGEapdalakRVEELSNRLRELESRLRDIESRLASL 143
                                       3333333333333355345555556666666655555555554 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 ?   11.3   0.4   0.00036      0.32       8      39 ..     117     149 ..     114     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                      ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpely.sd 39 
                                       ++ eel +++ +LE ++ ++e +la+ e +  d
  gi|320100579|ref|YP_004176171.1| 117 KRVEELSNRLRELESRLRDIESRLASLEGFvRD 149
                                       78999999**************99998888444 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 ?   10.2   0.0   0.00055      0.49       4      36 ..      20      55 ..      18      71 .. 0.70
   2 ?   -1.6   0.1       2.8   2.5e+03       4      13 ..     117     126 ..     116     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00055
                             IF2_N  4 irVyeLAkeLg...vkskevikkLfkelGie.vkshs 36
                                      ++V+++A+ Lg    ++ke++++L  + G+  ++ h 
  gi|320100579|ref|YP_004176171.1| 20 LSVRDVAEALGvdvARAKEILERL-RYGGYVeKAGHG 55
                                      69*********5555679999999.844554355555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                             IF2_N   4 irVyeLAkeL 13 
                                       +rV eL ++L
  gi|320100579|ref|YP_004176171.1| 117 KRVEELSNRL 126
                                       79***99887 PP

>> Replic_Relax  Replication-relaxation
   #    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       1      78 [.      11      75 ..      11      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                      Replic_Relax  1 LrlLaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqra.epep 78
                                      L+lL+    l+ r +a++l  ++ + a  +L rLr++g++++             ++ Ya+t+kG++ll a++a + +p
  gi|320100579|ref|YP_004176171.1| 11 LELLNSAPSLSVRDVAEALGVDVAR-AKEILERLRYGGYVEKA------------GHGYAITEKGRALL-ADHAeQGSP 75
                                      5667777779999999999999999.**************993............3459**********.555544444 PP

>> DUF2161  Putative PD-(D/E)XK phosphodiesterase (DUF2161)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.18      60     115 ..       7      64 ..       3      65 .. 0.82
   2 ?   -3.1   0.1       9.3   8.3e+03      32      47 ..      78      93 ..      72      97 .. 0.76
   3 ?   -2.8   0.1       7.3   6.5e+03      32      47 ..     147     162 ..     141     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                           DUF2161  60 alriaalLaeegelspaelkkatgee..kaakiLrknyYg.WFerverGvYrlteaGrk 115
                                        l+  +lL+++ +ls++++++a g++  +a++iL++  Yg + e+  +G Y++te+Gr+
  gi|320100579|ref|YP_004176171.1|   7 TLKALELLNSAPSLSVRDVAEALGVDvaRAKEILERLRYGgYVEKAGHG-YAITEKGRA 64 
                                       67888999*************988654499******9987255777777.*******85 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.3
                           DUF2161 32 lkEferregdpnvGGs 47
                                       + +++++g++++GG 
  gi|320100579|ref|YP_004176171.1| 78 TSFIQGKQGSTEAGGG 93
                                      5567889999999985 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.3
                           DUF2161  32 lkEferregdpnvGGs 47 
                                       +++ +rr+g ++ GG+
  gi|320100579|ref|YP_004176171.1| 147 VRDAARRSGAEARGGE 162
                                       6788999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      888  (0.0495287); expected 358.6 (0.02)
Passed Vit filter:                       195  (0.0108762); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 1840.05
//
Query:       gi|320100580|ref|YP_004176172.1|  [L=168]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1239.09
//
Query:       gi|320100581|ref|YP_004176173.1|  [L=284]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  103.2   0.0    1.8e-29  102.8   0.0    1.2  1  XdhC_C           XdhC Rossmann domain
    1.5e-20   73.2   0.5    2.9e-20   72.2   0.5    1.5  1  XdhC_CoxI        XdhC and CoxI family
    3.5e-05   24.0   0.0    5.3e-05   23.4   0.0    1.3  1  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.011   15.1   0.0       0.13   11.7   0.0    2.0  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.016   15.8   0.0      0.029   15.0   0.0    1.5  1  PglD_N           PglD N-terminal domain
      0.023   14.0   0.0      0.034   13.5   0.0    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.051   13.8   0.0      0.088   13.1   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.0   6.9e-33   1.8e-29       1     125 []     114     258 ..     114     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 6.9e-33
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE..................-EEEE--S-HHHHHH CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade..................tavvvlthdhklDae 59 
                                       lv++Gaghv++++a++++ lg+r++v+d+++++a++er+p a++                  ++vvv+  + + D++
  gi|320100581|ref|YP_004176173.1| 114 LVLIGAGHVGKPIADIGSILGYRIVVLDKDPSLASRERYPYAEAvrsgditrelaslelsdtDIVVVAFGEVEADYQ 190
                                       799*************************************9998********************************* PP

                                       HHHHHSSS--S.EEEESS-HHHHHHHCTTS.--.......T.TEESS-S--S---SHHHHHHHHHHHH CS
                            XdhC_C  60 aleaalrkkaa.yigllGSrkkaarrlerlraaglseeela.rlhaPiGldigaktpeeIAvsilAei 125
                                       +l++++++ ++    +l Sr++a+ +lerlr++g++ e l  r+h+P+Gldi+a+tp eIAvsi +ei
  gi|320100581|ref|YP_004176173.1| 191 VLRHLVERGFKgHAWILCSRNRARWMLERLRSEGFDTEGLTgRIHMPAGLDIEAETPGEIAVSIWSEI 258
                                       ******877666***********************9888766************************98 PP

>> XdhC_CoxI  XdhC and CoxI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.5   1.1e-23   2.9e-20       3      67 ..      15      79 ..      13      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.1e-23
                                      HCT..EEEEEEEEEECSSSSGTT-EEEEETTS-EEE-SSSSCHHHHHHHHHHHHHHCT--EEEEE CS
                         XdhC_CoxI  3 aagrpvalaTVvdteGsaprplGakmlvrpdgrviGsvgggclEaavideArallaagrtalvry 67
                                      ++grpvala +v +eGs+pr lG++++v++dg+ +G++ggg  Ea vi+eA+++l++g+++l+++
  gi|320100581|ref|YP_004176173.1| 15 DKGRPVALAVIVGKEGSGPRGLGSMLAVTADGSKYGTIGGGEFEAFVIKEALTALREGKPRLLKV 79
                                      68******************************77***************************9876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.1e-08   5.3e-05       2      85 ..     115     197 ..     114     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.1e-08
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEE.S-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvv.gdatdeevLeeagiekadaviaatgddean 76 
                                       ++iG+G vG+ +a+  s  g+ ++vv dkd++ + + r   +e+v  gd t+e  L+++++++ d+v++a g+ ea 
  gi|320100581|ref|YP_004176173.1| 115 VLIGAGHVGKPIADIGSIlGY-RIVVLDKDPSLASRERYPYAEAVRsGDITRE--LASLELSDTDIVVVAFGEVEAD 188
                                       79****************999.5******************997777****76..99***************99998 PP

                                       HHHHHHHHH CS
                            TrkA_N  77 ilavllake 85 
                                         ++ ++ e
  gi|320100581|ref|YP_004176173.1| 189 YQVLRHLVE 197
                                       888777644 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 ?   11.7   0.0   4.9e-05      0.13      38      73 ..     113     148 ..     105     163 .. 0.83
   2 ?    2.5   0.0     0.032        83       8      47 ..     148     185 ..     145     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                                       ++ +iG+G++G+ +a++ + +g ++++ d+ ++  +
  gi|320100581|ref|YP_004176173.1| 113 RLVLIGAGHVGKPIADIGSILGYRIVVLDKDPSLAS 148
                                       6789*************************9987544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.032
                                       HTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHH CS
                      2-Hacid_dh_C   8 lrrlaeadeevregewksekallgkelsgktvGiiGlGrI 47 
                                       +r+   + e+vr+g+    ++l + els+  + ++ +G++
  gi|320100581|ref|YP_004176173.1| 148 SRERYPYAEAVRSGDI--TRELASLELSDTDIVVVAFGEV 185
                                       5777889999****99..8999****************97 PP

>> PglD_N  PglD N-terminal 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     0.029       1      68 [.     113     185 ..     113     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                            PglD_N   1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk.tevegypvlgk.....aiellkslseeeye.vviAIGnn 68 
                                       ++v+iGaG  gk +adi    g y+i+ +lD++++  + e yp+ +      +  +l+sl+  +++ vv+A G+ 
  gi|320100581|ref|YP_004176173.1| 113 RLVLIGAGHVGKPIADIGSILG-YRIV-VLDKDPSlASRERYPYAEAvrsgdITRELASLELSDTDiVVVAFGEV 185
                                       589*******************.7665.56666653677888887642211145567888767788356799975 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.3e-05     0.034      29      98 ..     112     181 ..      95     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE- CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigt 98 
                                        + + iG+G +G   + + + lg +++vlD++p+ + + +   a+ v+    ++el + +++++d+v+ +
  gi|320100581|ref|YP_004176173.1| 112 PRLVLIGAGHVGKPIADIGSILGYRIVVLDKDPSLASRERYPYAEAVRSGDITRELASLELSDTDIVVVA 181
                                       57899*****************************999999966777*********************976 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 ?   13.1   0.0   3.5e-05     0.088       2      93 ..     115     199 ..     114     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-S CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnls 77 
                                       ++iGaG vG+++a+  +  + +  +i+v d++ + + ++      +   a+a+   +++  La+l l+++d+vv + 
  gi|320100581|ref|YP_004176173.1| 115 VLIGAGHVGKPIADIGSILG-Y--RIVVLDKDPSLASRERY----P--YAEAVRSGDITRELASLeLSDTDIVVVAF 182
                                       89**********99877765.6..9*********9777753....2..477888888888899999********999 PP

                                       SGG.GHHHHHHHHHHHT CS
                   Sacchrp_dh_NADP  78 ppi.ssldvlkaCietg 93 
                                       + +  + +vl+  +e+g
  gi|320100581|ref|YP_004176173.1| 183 GEVeADYQVLRHLVERG 199
                                       99987888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2175.63
//
Query:       gi|320100582|ref|YP_004176174.1|  [L=89]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 716.85
//
Query:       gi|320100583|ref|YP_004176175.1|  [L=174]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00042   20.4   0.1    0.00073   19.6   0.1    1.4  1  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   4.1e-08   0.00073      26     131 ..      42     144 ..      22     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.1e-08
                                       EECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS....S CS
                             THUMP  26 velkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhf....e 98 
                                       ++   e+p++   +l e+   + ++ rvipv +v+   +e + e+a+e+ ++++     t++V+   r   +     
  gi|320100583|ref|YP_004176175.1|  42 LR--VEDPYGFTSRLREIAGEIQVVYRVIPVDSVVDPYVEVVAEKARELAEERIPRDR-TYRVTLHGRLYWLetrlP 115
                                       44..4688899999999999999********99999999*************997765.*****9998877677889 PP

                                       SHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEE CS
                             THUMP  99 ftsreinrevGkaivektglkVdlenPdivvrv 131
                                          ++  r++++ i +     V+l+nPd++v v
  gi|320100583|ref|YP_004176175.1| 116 AHTMDAVRIIAEKIDR----PVSLTNPDYLVYV 144
                                       9999999999999999....9**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1391.96
//
Query:       gi|320100584|ref|YP_004176176.1|  [L=221]
Description: PhoU family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-13   47.9   2.8    2.8e-12   46.4   3.2    1.5  1  PhoU_div  Protein of unknown function DUF47
    1.6e-07   31.6   3.3     0.0075   16.7   0.5    2.3  2  PhoU      PhoU domain
  ------ inclusion threshold ------
       0.23   11.7   3.5          3    8.2   0.2    3.6  4  TPR_2     Tetratricopeptide repeat


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 !   46.4   3.2   4.7e-16   2.8e-12       9     213 ..      16     217 ..      13     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4.7e-16
                          PhoU_div   9 pekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedllelve 85 
                                       ++++ +  + +v++   k++ell+ +  gd   + ++  e ++lE ++ +++ e +  + +  +     ++ll +v+
  gi|320100584|ref|YP_004176176.1|  16 KLREYVSISSEVVRKFKKAVELLNKYQVGD---ARAVFAELVKLEDKGEKLRGELEYSISSLRLEASFMSELLSFVS 89 
                                       5677788889999999************88...78899*********************99555556689******* PP

                          PhoU_div  86 slDeildvlediamlvtlrkv.efpeelkdeflallkktveaiealaevieeleklletalskk.diveeieslEde 160
                                       s+D i d ++++ + +++  + e+p+el++++l+l +++ ea+e ++e++e++     ++++k  ++v +  +lE++
  gi|320100584|ref|YP_004176176.1|  90 SVDRISDHVKEVSKELRILPFlEIPQELRNGLLELCETVAEAVETYNEAFEAVV---SGDYNKAlELVGKTLELEEK 163
                                       **************998876549***************************9987...566665568*********** PP

                          PhoU_div 161 iDqlqrklikklfsredasnplevlllv.eiieklenvsdraedvadrisiill 213
                                       +D+l+ + +   ++  d+  pl + ++v ++ + le  +d  +  a+ ++i+++
  gi|320100584|ref|YP_004176176.1| 164 ADDLEVRNRGLILEAGDRFKPLTMAIIVhNLNRALEDTADICAVSANNLRILIM 217
                                       ******999999999999998887665516778899999999999999888875 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.8e-06     0.016       9      87 ..      28     103 ..      20     105 .. 0.73
   2 !   16.7   0.5   1.2e-06    0.0075      10      83 ..     133     206 ..     121     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHHHHHCT-HHHHHHHHHH....HHHHHHHHHHHHHHHHHHH.HHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   9 eemlddalealeekdtelarevier....ddeidrlekeierslleal.akrqplaedlrellsllriardlERigD 80 
                                          +++a+e+l ++ +  ar+v ++    +d+ ++l+ e+e s +  l  + +       ++++ll+ +++  Ri+D
  gi|320100584|ref|YP_004176176.1|  28 VRKFKKAVELLNKYQVGDARAVFAElvklEDKGEKLRGELEYS-ISSLrLEAS-------FMSELLSFVSSVDRISD 96 
                                       5568899999999998888887655444488888888888777.444414444.......55559************ PP

                                       HHHHHHH CS
                              PhoU  81 havniae 87 
                                       h++++++
  gi|320100584|ref|YP_004176176.1|  97 HVKEVSK 103
                                       ***9998 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHH....HCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  10 emlddaleal....eekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82 
                                       e  ++a ea+    ++k  el+ + +e+++++d+le +++  +lea  + +pl++    ++ + ++ r lE  +D +
  gi|320100584|ref|YP_004176176.1| 133 ETYNEAFEAVvsgdYNKALELVGKTLELEEKADDLEVRNRGLILEAGDRFKPLTM----AIIVHNLNRALEDTADIC 205
                                       33344444443333444469999999*************9998888888998766....88899***********99 PP

                                       H CS
                              PhoU  83 v 83 
                                       +
  gi|320100584|ref|YP_004176176.1| 206 A 206
                                       6 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17     1e+03      23      31 ..      30      38 ..      26      41 .. 0.60
   2 ?    1.4   0.2     0.076   4.5e+02       8      31 ..      34      57 ..      30      59 .. 0.66
   3 ?    1.1   0.1     0.096   5.7e+02      18      29 ..     129     140 ..     121     142 .. 0.85
   4 ?    8.2   0.2    0.0005         3       5      32 ..     135     162 ..     131     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                             TPR_2 23 afekAleld 31
                                       f+kA+el 
  gi|320100584|ref|YP_004176176.1| 30 KFKKAVELL 38
                                      566666653 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.076
                             TPR_2  8 GlayyklgdyeeAleafekAleld 31
                                      +  ++++ +  +A++ f + ++l+
  gi|320100584|ref|YP_004176176.1| 34 AVELLNKYQVGDARAVFAELVKLE 57
                                      555566666777888888888775 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.096
                             TPR_2  18 eeAleafekAle 29 
                                       +eA+e +++A e
  gi|320100584|ref|YP_004176176.1| 129 AEAVETYNEAFE 140
                                       79*******976 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0005
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldP 32 
                                       yn +  +  +gdy++Ale+  k lel++
  gi|320100584|ref|YP_004176176.1| 135 YNEAFEAVVSGDYNKALELVGKTLELEE 162
                                       6777778889*************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1765.02
//
Query:       gi|320100585|ref|YP_004176177.1|  [L=411]
Description: GntR family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  142.8   0.0    1.8e-41  142.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    4.7e-06   25.7   0.0    9.1e-06   24.7   0.0    1.6  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
     0.0053   16.1   0.0     0.0074   15.6   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.049   12.6   0.0      0.072   12.0   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
       0.13   11.5   0.0       0.24   10.7   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5   0.0   5.2e-45   1.8e-41       2     356 ..      36     389 ..      35     396 .. 0.89

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 5.2e-45
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGa 77 
                                       +vi ++++e++ d     + e   + ++  ++  ++   y+p dglp+l+ ++a f+++ e++++++e ++vv+ G 
  gi|320100585|ref|YP_004176177.1|  36 KVISFAAGEPDPD---VIPRELYGELAReVFAREKKSVAYSPADGLPDLKAEIAGFMKEYEGVATTPE-NIVVTLGG 108
                                       5777888888777...55555555555577888888889*******************999*******.99999999 PP

                                       HHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE CS
                     Aminotran_1_2  78 galiealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilv 154
                                       +++i+++ +l+ l+pgd ++v +p+y + + ++r++g+  + +p++   d ++  e leea+k    +  k k++++
  gi|320100585|ref|YP_004176177.1| 109 SQAIDIVGRLM-LDPGDIVFVENPSYVNTILVWRHYGVRTIGIPVD---DEGMVTERLEEAVKAMRGEGRKLKLVYT 181
                                       99*********.9*******************************66...779999********99999999999985 PP

                                       .ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 155 .esphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRv 230
                                         + +NP+G+ ++ e  + ll++a ++ ll++ D aY ++v+++ +  + +  ++ e  +l  gs+sK fG +G+R+
  gi|320100585|ref|YP_004176177.1| 182 iPTGQNPSGVTMSMERRKHLLEIASRHDLLIVEDAAYNHLVYEPAGIKP-LRAMDGEGRVLYIGSFSKIFG-TGLRI 256
                                       3789***************************************766555.4444444559***********.8**** PP

                                       EEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCS CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasq 303
                                       G++ +  ++v+ +r ++ p+    + + q++v+++l+++l ++   e++++++  +r+ + +++++   gl ++ + 
  gi|320100585|ref|YP_004176177.1| 257 GWLEAPGEIVEKARAAKGPMDMcaPVPSQYIVLNILRNKL-YRTIREKAVSEYRVKRDLMISAIEKHlpGLRHTRPV 332
                                       *****************99877669*************88.6678999****************998********** PP

                                       CSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS....TTEEEEECTTS-HHHH CS
                     Aminotran_1_2 304 sgmflltdlsae.takelskkLleevgvyvtpgtsftv....pgrlRitvAglteeel 356
                                       +gmf l  l+   +   ++++Lle+++v+v+p   f++    ++ +R+++ +++e++l
  gi|320100585|ref|YP_004176177.1| 333 AGMFILLWLPGMlDGRVFADQLLEKHNVAVIPAAAFYTddsgRNVVRLNF-SMSEKDL 389
                                       *******99999788889999*******************99999*****.8888765 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.5e-09   9.1e-06     127     220 ..     126     220 ..      71     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.5e-09
                                       EEEEES--HHHHHHHHHHT-EEEEEEEETTEE-HH....HHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHH CS
                    Aminotran_MocR 127 llvtvpGydrhfllleelGielltvdlqddGpdvd....aveklvaedasvkGilavpkysnptGetiseevarrla 199
                                       ++v  p y    l+ +++G++ + ++++d+G   +    av+ + +e   +k ++++p+  np+G t+s e+ ++l 
  gi|320100585|ref|YP_004176177.1| 126 VFVENPSYVNTILVWRHYGVRTIGIPVDDEGMVTErleeAVKAMRGEGRKLKLVYTIPTGQNPSGVTMSMERRKHLL 202
                                       56889**************************987611125666778999***********************99999 PP

                                       T---SSTT-EEEEE-TTSS-B CS
                    Aminotran_MocR 200 alkaaapdfrifaddayavhd 220
                                        + a+  d+ i  d ay+  +
  gi|320100585|ref|YP_004176177.1| 203 EI-ASRHDLLIVEDAAYN--H 220
                                       87.456899999999996..3 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.1e-06    0.0074      52     169 ..     104     217 ..      71     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-06
                                       EES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EE CS
                   Beta_elim_lyase  52 fvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheeki 128
                                        +  G +A  i  +++l +g+ v+v++p+ + +     +    gv+ + ++ ++   m  e+le+a+k+      k 
  gi|320100585|ref|YP_004176177.1| 104 VTLGGSQAIDIVGRLMLDPGDIVFVENPSYVNTILVWRH---YGVRTIGIPVDD-EGMVTERLEEAVKAMRGEGRKL 176
                                       455666666677777777777777777776665554333...577777788887.66899*****9999766789** PP

                                       EEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 129 klisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       kl+++  T +   G  +s+e  + + +ia ++++ ++ D+A
  gi|320100585|ref|YP_004176177.1| 177 KLVYTIPTGQNPSGVTMSMERRKHLLEIASRHDLLIVEDAA 217
                                       ***************************************98 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05     0.072      59     178 ..      97     218 ..      82     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                                       STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE..GGGHH CS
                       Aminotran_5  59 eseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld..ldele 133
                                       ++ e+i++t G+++ai +v + +   l+pgd + v +  +  +++ w++     g++   ip+d+eg ++  l+e+ 
  gi|320100585|ref|YP_004176177.1|  97 TTPENIVVTLGGSQAIDIVGRLM---LDPGDIVFVENPSYVNTILVWRHY----GVRTIGIPVDDEGMVTerLEEAV 166
                                       45699*****************9...*********999999999999887....5777799********97767776 PP

                                       HH-...-TTEEEEE.EESBETTTTEB--H...HHHHHHHHHTT-EEEEE-TT CS
                       Aminotran_5 134 kll...nektklva.ithvsnvtGtiqpv...eeigklakkkgalvlvDaaq 178
                                       k++     k klv+ i   +n +G+   +   +++ ++a +++ l++ Daa 
  gi|320100585|ref|YP_004176177.1| 167 KAMrgeGRKLKLVYtIPTGQNPSGVTMSMerrKHLLEIASRHDLLIVEDAAY 218
                                       77755548899997366789****96655122689999999******99986 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.6e-05      0.24      47     147 ..     108     218 ..      83     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE......EEEEE CS
                   DegT_DnrJ_EryC1  47 GtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitert......kaIlp 117
                                       G++A+ ++ r l ++pgd V v   ++v t+ + ++ g +++ + vd +   +  +++e+a+   +      k + +
  gi|320100585|ref|YP_004176177.1| 108 GSQAIDIVGR-LMLDPGDIVFVENPSYVNTILVWRHYGVRTIGIPVDDEG--MVTERLEEAVKAMRgegrklKLVYT 181
                                       5555555433.457789999999999999999999999999988888443..4457788888887778888877766 PP

                                       B-GG....GB---HH...HHHHHHHHCT-EEEEE-TT CS
                   DegT_DnrJ_EryC1 118 Vhly....Gqvadmd...alkaiaakhglkvieDaAh 147
                                       + +     G  + m+   +l +ia++h+l ++eDaA 
  gi|320100585|ref|YP_004176177.1| 182 IPTGqnpsGVTMSMErrkHLLEIASRHDLLIVEDAAY 218
                                       655411115555665333799**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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 0.26s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3078.80
//
Query:       gi|320100586|ref|YP_004176178.1|  [L=421]
Description: von Willebrand factor type A [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-06   27.9   0.0    2.4e-06   27.1   0.0    1.5  1  VWA_CoxE  VWA domain containing CoxE-like protein
    1.8e-05   25.3   0.0    7.1e-05   23.4   0.0    2.0  2  VWA_2     von Willebrand factor type A domain
    2.8e-05   24.4   0.0    4.7e-05   23.7   0.0    1.3  1  VWA       von Willebrand factor type A domain
     0.0038   17.2   0.0     0.0077   16.2   0.0    1.6  1  VWA_3     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> 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 !   27.1   0.0   5.4e-10   2.4e-06      46     173 ..     244     377 ..     192     406 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.4e-10
                          VWA_CoxE  46 elvrrkprerkprelvllvDvSgSmaaysaif.......lallhAllqqlp.rtevfaFdtrlvdlTralrerDpae 114
                                        l + k+ e++  ++ +l+D SgSm+  ++i+       + +l+A++ +++    +  Fd++   l r  r   p e
  gi|320100586|ref|YP_004176178.1| 244 LLLYEKAVEESMGPVYVLLDKSGSMDG-TKITwgkavavSLYLKAVRTGREfY--IRFFDSQPYPLLRVRRRPRPGE 317
                                       5666777788888999**********9.7665111111144455555555443..44578887777777777779** PP

                          VWA_CoxE 115 aLarvsaaved.lgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreellael 173
                                       aL+ +   v     GgT+i++a+ ++   ++  + +r++ +vl++Dg +r + + +  +l
  gi|320100586|ref|YP_004176178.1| 318 ALRLIDHVVRVkGAGGTDISRAIITACTDIRTGSAGRESDIVLITDGVDRIAESMVRLNL 377
                                       *****888887789********9988888888888************9997766655555 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3     6e+03      43      70 ..     164     193 ..     140     196 .. 0.69
   2 !   23.4   0.0   1.6e-08   7.1e-05       2     106 ..     259     364 ..     258     365 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                             VWA_2  43 vtfsdgpevliplt..kdkakilnalrnle 70 
                                       ++f++++  ++ l    d ++il+ lr+l+
  gi|320100586|ref|YP_004176178.1| 164 LSFEEDAVEVLRLArdVDARRILEVLRGLK 193
                                       467777777777742245777777777776 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.6e-08
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakd.aveallkslp.gdrvglvtfsdgpevliplt..kdkakilnalrnleak.. 72 
                                        ++lD SgSm ++     ++   k+ av+ +lk+ + g  + +  f+++p+ l+ +     +++ l+ ++ +     
  gi|320100586|ref|YP_004176178.1| 259 YVLLDKSGSMDGT-----KITWGKAvAVSLYLKAVRtGREFYIRFFDSQPYPLLRVRrrPRPGEALRLIDHVVRVkg 330
                                       689*********8.....444444438888999887699***********999999733569999999999998899 PP

                             VWA_2  73 gggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       +ggt++  a+ +a   ++ +++g+++ ivlitDg
  gi|320100586|ref|YP_004176178.1| 331 AGGTDISRAIITACTDIRTGSAGRESDIVLITDG 364
                                       9**************9999999***********9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.1e-08   4.7e-05       2     139 ..     258     392 ..     258     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.1e-08
                                       EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTG.SGGGGS CS
                               VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnl.kysggg 77 
                                       ++++lD Sgsm++ +++  k  + +l  k    ++g  + +  f s++++  ++++     e+l+ ++++ +++g g
  gi|320100586|ref|YP_004176178.1| 258 VYVLLDKSGSMDGTKITWGKAVAVSLYLKAV--RTGREFYIRFFDSQPYPLLRVRRRPRPGEALRLIDHVvRVKGAG 332
                                       79***************88888888877777..78999******************8899*********99999999 PP

                                       SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS..HTHHHHHHHHGCTEEEEEEEE CS
                               VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksndg..dpkeaaneakeqgikvfavGv 139
                                        t++  a+  a + + ++sag     ++ i+l+tdG +      ++ ++++a ++ i+v + G 
  gi|320100586|ref|YP_004176178.1| 333 GTDISRAIITACTDIRTGSAG----RESDIVLITDGVDRIAesMVRLNLKKADARLITVMVMGD 392
                                       999******************....5699*******9955223455555555555555555443 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.7e-06    0.0077       4     122 ..     259     380 ..     256     402 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                             VWA_3   4 vivvDvsssmsaen..klvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelelslgas 78 
                                        +++D s sm + +     + a s+ l++  t+ +++++ f+++p pl +  r   + e  ++ + +   +   g++
  gi|320100586|ref|YP_004176178.1| 259 YVLLDKSGSMDGTKitWGKAVAVSLYLKAVRTGREFYIRFFDSQPYPLLRVRRRPRPGEALRLIDHVVRVKG-AGGT 334
                                       5688999999998875445668999**************************999999999999999999999.**** PP

                             VWA_3  79 nlegaLkealrqp..akpgevrsvilltDgssaqgeervsdlisra 122
                                       +  +a+ +a +     + g+ + ++l+tDg +   e+ v  ++++a
  gi|320100586|ref|YP_004176178.1| 335 DISRAIITACTDIrtGSAGRESDIVLITDGVDRIAESMVRLNLKKA 380
                                       *********97444578899***********655555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3026.47
//
Query:       gi|320100587|ref|YP_004176179.1|  [L=383]
Description: ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-26   91.9   0.6    3.8e-25   88.5   0.0    2.8  4  AAA_5         AAA domain (dynein-related subfamily)
    2.8e-06   27.2   0.0    4.4e-06   26.6   0.0    1.3  1  AAA_3         ATPase family associated with various cellular 
    1.9e-05   25.1   0.5    0.00034   21.0   0.0    3.1  4  AAA           ATPase family associated with various cellular 
    2.6e-05   24.0   0.0     0.0001   22.1   0.0    2.1  1  AAA_lid_8     AAA lid domain
      6e-05   23.5   0.5    0.00074   19.9   0.0    2.3  2  AAA_16        AAA ATPase domain
    0.00046   19.6   0.0     0.0036   16.7   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0006   20.1   0.3     0.0067   16.7   0.0    2.8  2  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.013   15.3   0.1       0.21   11.3   0.1    2.4  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.023   13.8   0.0       0.22   10.6   0.0    2.3  2  MCM           MCM P-loop domain
      0.028   14.8   0.1      0.081   13.3   0.1    1.8  1  HEAT_2        HEAT repeats
       0.19   12.0   2.9        1.8    8.8   0.1    3.7  4  SelB-wing_2   Elongation factor SelB, winged helix


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 !   88.5   0.0   2.3e-28   3.8e-25       2     138 .]      45     171 ..      44     171 .. 0.95
   2 ?   -1.5   0.0       1.4   2.3e+03      65      84 ..     203     222 ..     192     269 .. 0.76
   3 ?   -1.0   0.0      0.99   1.6e+03      62      85 ..     287     309 ..     255     318 .. 0.79
   4 ?   -1.5   0.0       1.4   2.3e+03      72      94 ..     356     379 ..     350     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 2.3e-28
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------....G-SEEEEESG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilvlDEv 74 
                                        +L+G+pGt+Ks la+rla +++++++ ++ltr+t++++l+g+++i     +l+++ +vr  r    e++i+++DE+
  gi|320100587|ref|YP_004176179.1|  45 AILIGEPGTAKSALARRLADLVKARFFKYLLTRFTEPDELFGPLDI----GALREGRYVRVTRgklpEADIAFIDEI 117
                                       69*******************************************9....78888888887778899********** PP

                                       GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                       ++a+s+vln Ll+l++er ++  +g  ++k +       +++i ++n+++ ++ e  +a+++Rf
  gi|320100587|ref|YP_004176179.1| 118 FNANSAVLNMLLTLMNERVVY--DGYSEIKIPL------LTLISASNNVP-DEPE-LQAVYDRF 171
                                       *********************..*********9......9**********.7777.899****9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                       G-SEEEEESGGG--HHHHHH CS
                             AAA_5  65 egeilvlDEveraesevlns 84 
                                        + ++ +DEv+ a s v+++
  gi|320100587|ref|YP_004176179.1| 203 AKPVVSIDEVKAAGSLVFKV 222
                                       56688899999888888776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.99
                                       ---G-SEEEEESGGG--HHHHHHH CS
                             AAA_5  62 aaregeilvlDEveraesevlnsL 85 
                                       +a+++  ++lDEve a+ + l +L
  gi|320100587|ref|YP_004176179.1| 287 EAEKAFSILLDEVE-AREKHLREL 309
                                       45578889999999.655555555 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.4
                                       ESGGG--.HHHHHHHHHHHHSSEE CS
                             AAA_5  72 DEverae.sevlnsLlslleerrl 94 
                                       DEv r +  +vl++L+  +++ ++
  gi|320100587|ref|YP_004176179.1| 356 DEVVRRRaVDVLGELNDAIDTVKR 379
                                       788877778999999999987665 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 !   26.6   0.0   2.7e-09   4.4e-06       1     112 [.      44     158 ..      44     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.7e-09
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGt.evfeeke.kefefkkGpvf.anllladeinra 74 
                                       h +l g PG+ak  l++ la+ ++++f +  +t    P ++ G  ++   +e + +++++G +  a++ + dei  a
  gi|320100587|ref|YP_004176179.1|  44 HAILIGEPGTAKSALARRLADLVKARFFKYLLTRFTEPDELFGPlDIGALREgRYVRVTRGKLPeADIAFIDEIFNA 120
                                       899****************************************635655555477899***995379********** PP

                             AAA_3  75 ppktqsalleameerqvtvegethklpepflvlatqnP 112
                                       ++ +   ll  m+er v  + +  k+p   l+ a +n 
  gi|320100587|ref|YP_004176179.1| 121 NSAVLNMLLTLMNERVVYDGYSEIKIPLLTLISASNNV 158
                                       ***************99999999999988777777663 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 !   21.0   0.0   2.1e-07   0.00034       2     124 ..      46     171 ..      45     178 .. 0.74
   2 ?   -0.3   0.0      0.82   1.3e+03      59      74 ..     204     219 ..     192     261 .. 0.66
   3 ?   -1.7   0.0       2.3   3.7e+03      80      98 ..     286     304 ..     271     320 .. 0.65
   4 ?   -2.6   0.1       4.3     7e+03      67      93 ..     347     371 ..     344     382 .. 0.47

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-07
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk........yvgesekkirelfkeakekakpsilfiDEidal 70 
                                       +l+G pGt K++la+ +a  ++++f++  ++++++         +   +e +   +  + k   +  i fiDEi + 
  gi|320100587|ref|YP_004176179.1|  46 ILIGEPGTAKSALARRLADLVKARFFKYLLTRFTEPdelfgpldIGALREGRYVRVT-RGKLP-EADIAFIDEIFNA 120
                                       79********************************66788877742222223322222.22333.469******9998 PP

                                       HHHHTTCCCHHHHHHHHHHHHHHHHTTTS.......SSTEEEEEEESS.GGGSTHHHHSTTS CS
                               AAA  71 aksrsgseseeeervvnqLlteldgvkkk.......eskvivigatnr.pdkldpallrgRf 124
                                       +++            +n Llt +++   +          +++i a+n+ pd+++ + + +Rf
  gi|320100587|ref|YP_004176179.1| 121 NSAV-----------LNMLLTLMNERVVYdgyseikIPLLTLISASNNvPDEPELQAVYDRF 171
                                       7666...........9*****99999888888888745578888888877766654444665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.82
                                       SEEEEEETGGGHHHHH CS
                               AAA  59 psilfiDEidalaksr 74 
                                       + ++ iDE+ a ++  
  gi|320100587|ref|YP_004176179.1| 204 KPVVSIDEVKAAGSLV 219
                                       5899999999987666 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHHHTTT CS
                               AAA  80 eeeervvnqLlteldgvkk 98 
                                       +e+e++ + Ll e++  +k
  gi|320100587|ref|YP_004176179.1| 286 DEAEKAFSILLDEVEAREK 304
                                       4444555555555554444 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 4.3
                                       GGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  67 idalaksrsgseseeeervvnqLltel 93 
                                       +++la++   s++ +++r+v++L +  
  gi|320100587|ref|YP_004176179.1| 347 LEKLAREA--SDEVVRRRAVDVLGELN 371
                                       56666666..44444555444443333 PP

>> AAA_lid_8  AAA lid domain
   #    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       8      64 ..     233     287 ..     224     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.4e-08
                         AAA_lid_8   8 eiknkleeeeeaiyvSDRRwkkivkllkasAylngrdevnlsDllllkhclWnepeq 64 
                                       ++      e+++i + DRR  k +k   a+A+lngr +  ++Dl++lk++  ++ ++
  gi|320100587|ref|YP_004176179.1| 233 KLYAVF--EDQGIHLTDRRKGKTLKAVAANALLNGRLKAVEDDLFVLKYTAPRDRDE 287
                                       333333..6899************************************987666555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.5e-07   0.00074       1      61 [.      24      79 ..      24     155 .. 0.77
   2 ?    1.5   0.2      0.21   3.4e+02     106     129 ..     300     353 ..     231     379 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.5e-07
                            AAA_16  1 rlvGReeeleqL.lsalervrsgrpelvllsGesGvGKsslvrellralekd...ggiflrgkcd 61
                                      ++vGR ee + L ls    + sg  e  +l+Ge+G+ Ks+l+r+l++ ++++   +   l ++++
  gi|320100587|ref|YP_004176179.1| 24 PFVGRSEEARLLvLS----LISG--EHAILIGEPGTAKSALARRLADLVKARffkY---LLTRFT 79
                                      69******8666444....4456..7899*****************6555553330...444444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                            AAA_16 106 a........................avpelagaea......srllellkrllal 129
                                       +                         +pel++ +       + l+++l +l++ 
  gi|320100587|ref|YP_004176179.1| 300 EarekhlrelseieanireakayiaRSPELDPRLLdylrsfETLRDKLEKLARE 353
                                       123332222223333344444444466666666667744444444444444443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.2e-06    0.0036       6      46 ..      26      66 ..      23      75 .. 0.84
   2 ?   -0.1   0.0      0.31     5e+02     109     135 ..     111     137 ..      96     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.2e-06
                      Mg_chelatase  6 kGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsll 46
                                      +G++e  r l ++ + g + +l+G pG+ K+ la+rl+ l+
  gi|320100587|ref|YP_004176179.1| 26 VGRSEEARLLVLSLISGEHAILIGEPGTAKSALARRLADLV 66
                                      57888888888887777777889**************9986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.31
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgev 135
                                       + f+DE+ + ++ vl++L + ++++ v
  gi|320100587|ref|YP_004176179.1| 111 IAFIDEIFNANSAVLNMLLTLMNERVV 137
                                       78***************9887776655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.1e-06    0.0067       6      60 ..      43      88 ..      40     149 .. 0.91
   2 ?   -0.3   0.1      0.72   1.2e+03     109     113 ..     306     310 ..     250     381 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrel 60
                                       + +++Ge+Gt K+ l+rrl++           +++++++ l+  t++++l+  l
  gi|320100587|ref|YP_004176179.1| 43 EHAILIGEPGTAKSALARRLADLV---------KARFFKYLLTRFTEPDELFGPL 88
                                      5789*******************9.........9*********999999998765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.72
                            AAA_22 109 leeLr 113
                                       l+eL+
  gi|320100587|ref|YP_004176179.1| 306 LRELS 310
                                       22222 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 ?   11.3   0.1   0.00013      0.21      34     111 ..      43     135 ..      39     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl......kitsgPvlekagdlaallt.........nleekdvlfideihr 95 
                                       +h +l+G PG  k++la+ +a+ +++++      + t    l  + d+ al           +l e d+ fidei  
  gi|320100587|ref|YP_004176179.1|  43 EHAILIGEPGTAKSALARRLADLVKARFfkylltRFTEPDELFGPLDIGALREgryvrvtrgKLPEADIAFIDEIFN 119
                                       689999999999999999888888776432223355655566666666665322222222237999*********** PP

                            RuvB_N  96 lsraveevlysamedf 111
                                        ++av ++l + m++ 
  gi|320100587|ref|YP_004176179.1| 120 ANSAVLNMLLTLMNER 135
                                       *********9999875 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.22      55      85 ..      40      70 ..      20     138 .. 0.76
   2 ?    0.6   0.0      0.16   2.6e+02     108     131 ..     191     213 ..     188     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                      CSS-EEEEEESSTSTHHHHHHHHHHHSSSEE CS
                               MCM 55 rgdinvllvgdpgtaKsqlLkyveklaprav 85
                                      ++  + +l+g+pgtaKs+l +++++l++   
  gi|320100587|ref|YP_004176179.1| 40 ISGEHAILIGEPGTAKSALARRLADLVKARF 70
                                      5666999*************99998877654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                                       SSEEEEETHHHHTTTSEEEEESGG CS
                               MCM 108 gefvleaGalvladkGvcciDefd 131
                                         + +e+Ga + a k v+ iDe+ 
  gi|320100587|ref|YP_004176179.1| 191 ASWLIESGAYMEA-KPVVSIDEVK 213
                                       57999****9988.5699999986 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     5e-05     0.081      31      60 ..     342     372 ..     326     382 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                            HEAT_2  31 ealpaLvell.ededpavRraaaeaLgaigd 60 
                                       ++++ L +l+ e +d+ vRr a++ Lg++ d
  gi|320100587|ref|YP_004176179.1| 342 TLRDKLEKLArEASDEVVRRRAVDVLGELND 372
                                       5567777777555677777777777777765 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 ?    8.8   0.1    0.0011       1.8      14      43 ..      50      79 ..      49      84 .. 0.91
   2 ?   -0.9   0.0       1.2     2e+03      22      41 ..     173     191 ..     168     194 .. 0.80
   3 ?   -2.6   0.0       4.1   6.8e+03      27      40 ..     251     264 ..     248     272 .. 0.68
   4 ?    0.1   0.0      0.57   9.2e+02      31      46 ..     288     303 ..     276     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                                      S--EEHHHHHHHCSSSS-HCCHHHHHHHHH CS
                       SelB-wing_2 14 rpGmskeeLrsrlaprlpaklfqallealv 43
                                      +pG  k +L +rla  ++a++f  ll ++ 
  gi|320100587|ref|YP_004176179.1| 50 EPGTAKSALARRLADLVKARFFKYLLTRFT 79
                                      79************************8875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                                       HHHHCSSSS-HCCHHHHHHH CS
                       SelB-wing_2  22 Lrsrlaprlpaklfqallea 41 
                                       Lr+ l+  ++++l+  llea
  gi|320100587|ref|YP_004176179.1| 173 LRHFLK-PVSENLWGRLLEA 191
                                       666665.699999*999997 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.1
                                       SSSS-HCCHHHHHH CS
                       SelB-wing_2  27 aprlpaklfqalle 40 
                                        ++l+a +++all+
  gi|320100587|ref|YP_004176179.1| 251 GKTLKAVAANALLN 264
                                       45677777788876 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.57
                                       -HCCHHHHHHHHHHTT CS
                       SelB-wing_2  31 paklfqallealvarg 46 
                                        +k+f  ll++ +ar 
  gi|320100587|ref|YP_004176179.1| 288 AEKAFSILLDEVEARE 303
                                       489********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2632.11
//
Query:       gi|320100588|ref|YP_004176180.1|  [L=133]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   59.4   1.9    4.3e-16   59.2   1.9    1.1  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   1.9   2.4e-20   4.3e-16       3     104 ..       4     116 ..       2     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.4e-20
                                       EEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT......EE-....S-EEEEEEEEEEEE.. CS
                            DUF296   3 hvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee......kll....grfeilslsGtilp.. 66 
                                       + lr+ +G  ++++ie+++  +g +++++ ++iG +s++  ++++  +      + l    + +e+ sl+G++l   
  gi|320100588|ref|YP_004176180.1|   4 VPLRIGEGGVVHAEIERAVASNGLKGGFI-TGIGGLSEADiGFYNPATreyareH-LeaggEVIEVASLQGNYLIta 78 
                                       679**************************.**************99999776642.168878*************77 PP

                                       TT...EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE CS
                            DUF296  67 dg...lHlhvslagedgqvvgGhlaegplvaattvevvvae 104
                                       dg   +Hlh++++ + g+vv+Ghl++g  v+   +ev++ e
  gi|320100588|ref|YP_004176180.1|  79 DGsvsVHLHIVAGLK-GRVVAGHLLHG--VVKPFLEVFLVE 116
                                       44799*******996.*********99..559999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1040.28
//
Query:       gi|320100589|ref|YP_004176181.1|  [L=171]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-18   65.3   0.0    6.6e-18   65.0   0.0    1.1  1  DUF123    Domain of unknown function DUF123


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   3.7e-22   6.6e-18       3      93 ..      46     136 ..      44     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3.7e-22
                            DUF123   3 lkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvv.a.seerlEcalaeale.aea 76 
                                       l + vy+Y+Gsa g+ g+  Rv rH++      k  +Wh+D L++++ +  + +++ + +  ++E+a+++ l+   +
  gi|320100589|ref|YP_004176181.1|  46 LGPAVYFYIGSARGPCGVPCRVARHLAAV----KAVRWHVDALTTNPVVVKHGFFMvRdTGGDCEAAVSRLLRgVLE 118
                                       66789********************5555....57************999999998646999**********42444 PP

                            DUF123  77 pvagfGasDck.cesHLl 93 
                                       pv+gfG+sD+  + sHL+
  gi|320100589|ref|YP_004176181.1| 119 PVKGFGCSDKPgDVSHLY 136
                                       **********9899**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1255.64
//
Query:       gi|320100590|ref|YP_004176182.1|  [L=155]
Description: nucleic acid-binding OB-fold tRNA/helicase-type [Desulfurococcus mucosus DSM 2162]
Scores for 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   0.2    2.9e-09   36.8   0.2    1.2  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0023   17.8   0.0     0.0033   17.3   0.0    1.2  1  REPA_OB_2        Replication protein A OB domain
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.17   11.6   0.0    1.1  1  CDC24_OB3        Cell division control protein 24, OB domain 


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.2   4.9e-13   2.9e-09       1      70 [.      25      97 ..      25     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 4.9e-13
                                      EEEEEEEEEEE.......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsis.......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkv 70
                                      V+v++rv++ +       + + + +++++l D+tgr++++l+     + a +lkeGd v+v G +++  +g+++l++
  gi|320100590|ref|YP_004176182.1| 25 VSVKARVIKAEaprvirtRNGPRTISNAVLGDETGRVEATLWG----EKAGTLKEGDAVEVHGAWTTEFRGKVQLNI 97
                                      89999**99999999995555599*******************....***************999999888799976 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.5e-07    0.0033      28      95 ..      40     103 ..      21     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.5e-07
                         REPA_OB_2  28 itskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFgg.rslsllssstl 95 
                                       i ++++ +++   +  l De+g+ ve tlWg++a +++  e + v + g+  ++F g  +l++ +ss++
  gi|320100590|ref|YP_004176182.1|  40 IRTRNGPRTI--SNAVLGDETGR-VEATLWGEKAGTLK--EGDAVEVHGAWTTEFRGkVQLNIGRSSEV 103
                                       5555555443..46678999986.9**********976..8899*************457888888876 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 ?   11.6   0.0   2.9e-05      0.17       1      65 [.      17      79 ..      17     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                         CDC24_OB3  1 DLrekmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeagklhfkrlrvGhlv 65
                                      DL++ m +v++ +rv++      +r +n+     ++++  + D+tG ++atlw e +   +     G+ v
  gi|320100590|ref|YP_004176182.1| 17 DLKPGMEKVSVKARVIKAeaprvIRTRNGPR---TISNAVLGDETGRVEATLWGEKAGTLKE----GDAV 79
                                      99***************98776444555544...4458999************885544333....5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1157.20
//
Query:       gi|320100591|ref|YP_004176183.1|  [L=119]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   45.8   0.4    8.1e-12   45.3   0.4    1.2  1  PqqD       Coenzyme PQQ synthesis protein D (PqqD)
     0.0058   16.5   0.1        3.6    7.5   0.0    2.6  3  HTH_5      Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.098   12.7   0.1       0.16   12.0   0.1    1.3  1  DUF2603    Protein of unknown function (DUF2603)
       0.12   11.0   0.0       0.12   11.0   0.0    1.0  1  Ecm29      Proteasome stabiliser
       0.14   11.3   0.0       0.16   11.1   0.0    1.1  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.4   2.2e-15   8.1e-12       2      67 .]      54     117 ..      53     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.2e-15
                                       EEEE-SS-..EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD   2 yvlldpetgkyisLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67 
                                       yv l++e   +++L+  ++++W ++dge++v e+++a+++e +vd + + + +   ldqL+e+gl+
  gi|320100591|ref|YP_004176183.1|  54 YVALSEEE--VYELSALAYYVWVMCDGEHTVGELAEAISKEAQVDFNDVVEPLVVALDQLHEAGLV 117
                                       78999999..***********************************999999*************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 ?   -2.4   0.0       1.2   4.5e+03      14      23 ..      58      67 ..      54      69 .. 0.65
   2 !    7.5   0.0     0.001       3.6      11      26 ..      75      90 ..      73      92 .. 0.88
   3 !    6.0   0.0    0.0029        11      36      47 .]     108     119 .]     108     119 .] 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                      SSEEHHHHHH CS
                             HTH_5 14 gelcvcelae 23
                                      +e  v el++
  gi|320100591|ref|YP_004176183.1| 58 SEEEVYELSA 67
                                      5667777775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.001
                                      HTTSSEEHHHHHHHHT CS
                             HTH_5 11 Laegelcvcelaeelg 26
                                      +++ge++v+elae++ 
  gi|320100591|ref|YP_004176183.1| 75 MCDGEHTVGELAEAIS 90
                                      799**********975 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0029
                                       HHHHHHTTSEEE CS
                             HTH_5  36 LkkLreaGLVek 47 
                                       L +L+eaGLV++
  gi|320100591|ref|YP_004176183.1| 108 LDQLHEAGLVNY 119
                                       789*******96 PP

>> DUF2603  Protein of unknown function (DUF2603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.5e-05      0.16      43     103 ..      45     112 ..      34     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                           DUF2603  43 fvideedkkyvllpeellsklvell....kkakeerlelkLEkdilqqiPiDFeDvwe...Valdeik 103
                                       f+ +e++k yv l+ee + +l  l+         e+   +L  +i +++ +DF+Dv+e   Vald+++
  gi|320100591|ref|YP_004176183.1|  45 FLGEEKEKFYVALSEEEVYELSALAyyvwVMCDGEHTVGELAEAISKEAQVDFNDVVEplvVALDQLH 112
                                       6677888888888887655554433111145677888899****************754438888876 PP

>> Ecm29  Proteasome stabiliser
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.4e-05      0.12     205     275 ..      42     112 ..       7     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                             Ecm29 205 kkeeleetKlailkflasgaftdeerevlpallvasadsdssvsdraeelLKrlsvdled..ealvdkLfslf 275
                                       ++e l e K +    l+++ +  e  ++l +++ + +d +++v ++ae + K  +vd++d  e lv  L +l+
  gi|320100591|ref|YP_004176183.1|  42 QGEFLGEEKEKFYVALSEEEV-YEL-SALAYYVWVMCDGEHTVGELAEAISKEAQVDFNDvvEPLVVALDQLH 112
                                       466677777777777777777.343.5889999999*********************9997777777777766 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.4e-05      0.16       4      34 ..      53      83 ..      50     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                                      EEEESTSHHHHHHHCTC--SEEEEESSTSSS CS
                         HpcH_HpaI  4 lflpganaalaekaaiagaDsvliDlEdava 34
                                      ++++++++++ e  a+a + +v+ D+E+ v 
  gi|320100591|ref|YP_004176183.1| 53 FYVALSEEEVYELSALAYYVWVMCDGEHTVG 83
                                      79****************************2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 923.55
//
Query:       gi|320100592|ref|YP_004176184.1|  [L=391]
Description: propanoyl-CoA C-acyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-17   62.7   0.4    4.4e-16   59.0   0.0    2.5  2  Thiolase_N       Thiolase, N-terminal domain
    5.3e-12   45.5   0.1    1.2e-11   44.3   0.1    1.6  1  Thiolase_C       Thiolase, C-terminal domain
    0.00015   21.4   3.0    0.00015   21.4   3.0    3.1  3  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
     0.0007   19.6   1.4       0.12   12.4   0.2    2.7  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
  ------ inclusion threshold ------
      0.023   14.5   7.8       0.64    9.9   0.1    3.4  4  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth


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 !   59.0   0.0   1.2e-19   4.4e-16       1     258 [.       4     220 ..       4     222 .. 0.86
   2 ?   -1.2   0.1      0.29   1.1e+03      19      47 ..     256     284 ..     226     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.2e-19
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-T CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekag.vdpeevdevivGnvlqa.gegqn.iarqaalkagipe 74 
                                       v+iv+  +t+ig+    + + s +eL ++al++++e+ag v+p +   ++vGn++++   +q  +   +a  ag+ +
  gi|320100592|ref|YP_004176184.1|   4 VFIVGVGMTKIGR----FYEQSGRELFSQALWKAIEDAGgVKPRA---LVVGNMMSStLMNQDsLGALLADYAGL-R 72 
                                       79***********....99*******************99***86...6999999997556655888889999**.* PP

                                       TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT.TGGSSSSEEEEEHHHHHHTEETT CS
                        Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr.sglklgdekakdllipdgladaf 150
                                        +pa  v+ +c+Sg +a++++   +++g advv +gG E+ ++a+t + t++  + +  + e   +++ +       
  gi|320100592|ref|YP_004176184.1|  73 GIPAFKVEAACGSGGAALYAGYALVKSGVADVVAVGGLEKQTEATTPYVTRALaQAADADFEVFYGVTFTG------ 143
                                       *******************************************9998776555145555556666666555...... PP

                                       TTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHH CS
                        Thiolase_N 151 neehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLa 227
                                            ++ a+ + + ++ s e++  + +k h+ a+ ++ a+ +     P k          +  e ++s+v a++++
  gi|320100592|ref|YP_004176184.1| 144 ---LNAMIARLYMQLFGYSDEDLSYWPLKMHEYASYNPYAQ-L-----PRK---------TSMKEILDSPVIADPIR 202
                                       ...66899********************************9.3.....322.........36678999999999999 PP

                                       TS-BSSSTTSS-BTTSB--BEEEEEEEEEEE CS
                        Thiolase_N 228 klkpaFkkeGtvtAgnasqisDGaaavllms 258
                                                       a +i DGaaav+l++
  gi|320100592|ref|YP_004176184.1| 203 LF-------------HAAPIGDGAAAVILVR 220
                                       99.............8999999999999986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.29
                                       TTS-HHHHHHHHHHHHHHHHTS-GGGCCE CS
                        Thiolase_N  19 kdlsaeeLlaealkallekagvdpeevde 47 
                                       ++l + e  a+a++++l  ag+  ++vd+
  gi|320100592|ref|YP_004176184.1| 256 NNLVVMEATAKAAQEALRMAGIGVKDVDY 284
                                       55566677788889999999988888886 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   3.4e-15   1.2e-11      19      98 ..     259     356 ..     244     366 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.4e-15
                                       GGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHH CS
                        Thiolase_C  19 ilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaia 77 
                                        +  + a a++++l  ag+ v+d+d+ E+++AF +   a+++++++++                    vN  GG  a
  gi|320100592|ref|YP_004176184.1| 259 VVMEATAKAAQEALRMAGIGVKDVDYAEVHDAFHVTGYAALEDIGFAPkgeaprlfkegrfqkgdkPEVNFSGGLKA 335
                                       455577899*******************************************************9888********* PP

                                       H-B-TTTHHHHHHHHHHHHHH CS
                        Thiolase_C  78 lGHPlGasGaRivvtllselk 98 
                                        GHP+Ga+G+ +v+ ++ +l+
  gi|320100592|ref|YP_004176184.1| 336 RGHPVGATGVYQVAEAVMQLR 356
                                       ***************999987 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 !   21.4   3.0   4.3e-08   0.00015     146     216 ..      47     124 ..       4     135 .. 0.75
   2 ?   -1.8   0.1      0.52   1.8e+03     238     252 ..     209     223 ..     208     224 .. 0.87
   3 ?   -0.5   0.0      0.22   7.7e+02      94     114 ..     266     286 ..     259     311 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.3e-08
                                       HHH......HSTTHHHHHHHHHHT--S.SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHH CS
                     ketoacyl-synt 146 vga......vlanviagrisyalglrG.psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfs 215
                                       vg+      +++  + + ++   glrG p++ v++AC S+ +a+ a +  ++sg adv+ +GG e  +++ + ++  
  gi|320100592|ref|YP_004176184.1|  47 VGNmmsstlMNQDSLGALLADYAGLRGiPAFKVEAACGSGGAALYAGYALVKSGVADVVAVGGLEKQTEATTPYVTR 123
                                       3333333457778888999999*****899***********************************988776655554 PP

                                       H CS
                     ketoacyl-synt 216 a 216
                                       a
  gi|320100592|ref|YP_004176184.1| 124 A 124
                                       4 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.52
                                       BB-EEEEEEEEECHH CS
                     ketoacyl-synt 238 lGEGvGavvLkrled 252
                                       +G+G++av+L r e+
  gi|320100592|ref|YP_004176184.1| 209 IGDGAAAVILVRGEE 223
                                       69********99875 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHTS-HHTCTTGG CS
                     ketoacyl-synt  94 eaawealedagltpeeldgsr 114
                                       +aa+eal+ ag+  +++d  +
  gi|320100592|ref|YP_004176184.1| 266 KAAQEALRMAGIGVKDVDYAE 286
                                       678899999998887776554 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 !   12.4   0.2   3.3e-05      0.12      23      51 ..     261     289 ..     237     292 .. 0.74
   2 !    5.3   0.1    0.0054        19      88     107 ..     337     356 ..     331     359 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHHHHHHHT--GGGEEEEE-SS CS
                   Ketoacyl-synt_C  23 geaqaraiekalaeagvdpedvdyveahg 51 
                                        ea a+a ++al++ag+  +dvdy e h+
  gi|320100592|ref|YP_004176184.1| 261 MEATAKAAQEALRMAGIGVKDVDYAEVHD 289
                                       5788999*********************8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0054
                                       -B-GGGHHHHHHHHHHHHHH CS
                   Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalk 107
                                       GH  +A Gv +++ +v++l+
  gi|320100592|ref|YP_004176184.1| 337 GHPVGATGVYQVAEAVMQLR 356
                                       9*****************98 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 ?    1.3   0.0     0.087   3.1e+02      26      54 ..      41      67 ..      32      70 .. 0.74
   2 ?    6.4   0.1    0.0023       8.2       1      33 [.      77     109 ..      77     126 .. 0.83
   3 ?    9.9   0.1   0.00018      0.64      52      73 ..     209     230 ..     197     236 .. 0.83
   4 ?   -3.4   0.2       2.6   9.2e+03      34      58 ..     243     267 ..     240     268 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.087
                                      -SEEEEEEEEEGGGCS-TTTHHHHTTB-E CS
                       ACP_syn_III 26 akrvLvigaetlskilDwkdrstavlfGD 54
                                        r+Lv+g    s +++++  s   l++D
  gi|320100592|ref|YP_004176184.1| 41 KPRALVVGNMMSSTLMNQD--SLGALLAD 67
                                      4589******9999*9994..44445555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0023
                                       EEEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEE CS
                       ACP_syn_III   1 fDlnaaCsgfvyalsvAdaliesgaakrvLvig 33 
                                       f ++aaC +  +al    al++sg a  v v g
  gi|320100592|ref|YP_004176184.1|  77 FKVEAACGSGGAALYAGYALVKSGVADVVAVGG 109
                                       6689********************777666555 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00018
                                       B-EEEEEEEEEEESSSSCEEEE CS
                       ACP_syn_III  52 fGDGAgAvvleaseeegarild 73 
                                        GDGA+Av+l ++ee+  +i +
  gi|320100592|ref|YP_004176184.1| 209 IGDGAAAVILVRGEEKAREIAK 230
                                       7***********9888777765 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 2.6
                                       EEEGGGCS-TTTHHHHTTB-EEEEE CS
                       ACP_syn_III  34 aetlskilDwkdrstavlfGDGAgA 58 
                                           ++ +D + r++ v++   A A
  gi|320100592|ref|YP_004176184.1| 243 VGMATDSVDIASRNNLVVMEATAKA 267
                                       5555667788888888777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2998.68
//
Query:       gi|320100593|ref|YP_004176185.1|  [L=518]
Description: acetyl-CoA carboxylase carboxyltransferase subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-184  614.1   0.1   1.9e-184  614.0   0.1    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    6.3e-06   25.8   0.0    1.2e-05   24.9   0.0    1.5  1  MdcE            Malonate decarboxylase gamma subunit (MdcE)
     0.0057   17.3   0.0      0.012   16.3   0.0    1.5  1  PMC2NT          PMC2NT (NUC016) domain
  ------ inclusion threshold ------
      0.073   12.6   0.1       0.12   11.9   0.1    1.2  1  DUF417          Protein of unknown function, DUF417


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 !  614.0   0.1  4.2e-188  1.9e-184       1     487 [.      28     506 ..      28     516 .. 0.98

  Alignments for each domain:
  == domain 1  score: 614.0 bits;  conditional E-value: 4.2e-188
                                       SSCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSG CS
                    Carboxyl_trans   1 kehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgp 76 
                                       +++++Gkl +r+ri+ lldp+sF+el+    hr+t +g+ k k+++dgvv+g+G+++ r v+++aqd+tvlggs+g+
  gi|320100593|ref|YP_004176185.1|  28 QQRQKGKLWVRDRINRLLDPDSFVELQWVRTHRSTYFGLdKVKYYGDGVVAGYGTIDRRLVYIYAQDFTVLGGSIGE 104
                                       589************************************999*********************************** PP

                                       GGCEEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHH CS
                    Carboxyl_trans  77 akgekllkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpal 153
                                       a+gek+ +  e+a+++g+p+ig++dsgGa  riqegv sl+g G+if+ n+kasg++pqi++v+g+caG +aY+pal
  gi|320100593|ref|YP_004176185.1| 105 AHGEKIARLIELAVETGAPVIGLYDSGGA--RIQEGVASLHGCGRIFYSNVKASGVVPQIAVVMGPCAGAAAYSPAL 179
                                       *****************************..********************************************** PP

                                       TSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGG CS
                    Carboxyl_trans 154 gdrvimveetskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnr 230
                                        d+vimv+  s++f+tGp+v+k++lg  +vt e+lgGa++h+++sGvah++ ed+e al+l+rkllsylP   snn+
  gi|320100593|ref|YP_004176185.1| 180 MDFVIMVKS-SYMFITGPEVVKAALG-VDVTFEQLGGANIHASTSGVAHFITEDEESALSLVRKLLSYLP---SNNM 251
                                       *********.****************.*******************************************...999* PP

                                       SS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--S CS
                    Carboxyl_trans 231 esaPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetr 304
                                       e++P+v++ d++dr+   ++e+vP+++ kp+Dv++vi  +vdeg+FlE++e+y+++ VvGf+r+gG++vG+vAn+++
  gi|320100593|ref|YP_004176185.1| 252 EEPPRVPSEDPVDRRmdeIYEVVPTDPVKPFDVKKVISMIVDEGDFLEVHEHYGRSAVVGFGRIGGYTVGIVANQPA 328
                                       ***************88777********************************************************* PP

                                       EEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEH CS
                    Carboxyl_trans 305 veaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayG 381
                                       v+aG v++id++ K arf+r+cd +n+P+v+l+d++Gf++G +qe+ggi++hGak+++a+aea+vPkit+++rkayG
  gi|320100593|ref|YP_004176185.1| 329 VNAG-VIDIDASNKIARFVRFCDSFNIPIVTLVDTPGFMPGVDQEHGGIIRHGAKVLYAYAEATVPKITLVMRKAYG 404
                                       ****.************************************************************************ PP

                                       HHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Carboxyl_trans 382 GayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargf 458
                                       Gay++m+s  +g+d+++awpta+iaV+gpega+ il+rke+a+a     d+++ +++kl+ey+e ++np++aa++g+
  gi|320100593|ref|YP_004176185.1| 405 GAYIAMGSLSLGSDVNLAWPTAEIAVMGPEGAIRILYRKELAQAP----DPEELARRKLAEYREVFANPFRAAELGY 477
                                       ********************************************9....9*************************** PP

                                       HHTTSSHHHHHHTTSSSEEEHGGGHHHHH CS
                    Carboxyl_trans 459 aDavidpsetraklvialelewkkarklp 487
                                       +D+vidp+ tr ++ + le++++k++++ 
  gi|320100593|ref|YP_004176185.1| 478 IDDVIDPALTRLRIYQVLEALKSKREEFL 506
                                       ************************99653 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.8e-09   1.2e-05      19     151 ..     310     440 ..     297     479 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.8e-09
                                       EEEEEETTEEEEEEEE---TTSS-B-HHHHHHHHHHHHHHHTSSS--EEEEEEEE--B--SHHHHHHTHHHHHHHHH CS
                              MdcE  19 vldgsltlesvrfvaVigdankgevGvdealaLaaaVleaieraekrpilvlvDvasQrlgrrdEllGihealahla 95 
                                       v  g+++++ v+ va  +  n g + +d + ++a  V      + + pi+ lvD+++   g  +E  Gi    a + 
  gi|320100593|ref|YP_004176185.1| 310 VGFGRIGGYTVGIVANQPAVNAGVIDIDASNKIARFVRFC--DSFNIPIVTLVDTPGFMPGVDQEHGGIIRHGAKVL 384
                                       4558888899999999999999999999999999988754..36689**********************99999988 PP

                                       HHHHHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET-EEESS-HHHHHHHH CS
                              MdcE  96 kalarArlaGhpvigllvGkavsGaflahg...lqanrlialpgvqvavmdkasaArvT 151
                                        a+a A +   p i+l++ ka  Ga++a+g   l +++ +a p +++avm+   a r+ 
  gi|320100593|ref|YP_004176185.1| 385 YAYAEATV---PKITLVMRKAYGGAYIAMGslsLGSDVNLAWPTAEIAVMGPEGAIRIL 440
                                       88888875...9****************985446789999999********99999985 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.7e-06     0.012      16      76 ..     216     274 ..     212     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.7e-06
                            PMC2NT  16 dfyrsldpefaksldeqserllslinsllklaaskseisassklededdveekfksvvdvv 76 
                                       + + s  +++a++++e++e  lsl+ +ll++++s++  +  ++  +ed v+++++++ +vv
  gi|320100593|ref|YP_004176185.1| 216 NIHAST-SGVAHFITEDEESALSLVRKLLSYLPSNNMEEP-PRVPSEDPVDRRMDEIYEVV 274
                                       578999.9***************************99977.6999999999******9997 PP

>> DUF417  Protein of unknown function, DUF417
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.7e-05      0.12      95     150 ..     158     216 ..     150     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                            DUF417  95 vivgilvliglrnakvgllggllvlviaivtlSfLittPeawvpslG...gfPylsgag 150
                                       v+  i v++g+    +++  +l+ +vi++    + it Pe+ +++lG    f +l ga+
  gi|320100593|ref|YP_004176185.1| 158 VVPQIAVVMGPCAGAAAYSPALMDFVIMVKSSYMFITGPEVVKAALGvdvTFEQLGGAN 216
                                       566799***********************999999************999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 4065.74
//
Query:       gi|320100594|ref|YP_004176186.1|  [L=326]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2618.86
//
Query:       gi|320100595|ref|YP_004176187.1|  [L=749]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   14.8   0.0      0.044   13.9   0.0    1.4  1  DUF2780   Protein of unknown function VcgC/VcgE (DUF2780)
      0.034   14.5   0.0        0.1   13.0   0.0    1.8  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> DUF2780  Protein of unknown function VcgC/VcgE (DUF2780)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.9e-06     0.044      90     166 ..     549     629 ..     547     638 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-06
                           DUF2780  90 qLsksvPGldsLlgavpklsl..ssglsglLska.....gellgslksladvnkaFeaLGlssemisqfvpvilqYL 159
                                       +L   +PGl++L  a  +l l  ++g ++ L+ka      + +++++ l++  kaFe+LG +   +s + + +l+YL
  gi|320100595|ref|YP_004176187.1| 549 SLVARLPGLTQLHRAFVALALfgKQGFNNELEKAnvtlsPDETKDIEALEKTIKAFEKLGGDHVWLSLLTNYALAYL 625
                                       578899******9999988889*999999999976777766788999999999************************ PP

                           DUF2780 160 dtsggqg 166
                                          + q+
  gi|320100595|ref|YP_004176187.1| 626 ---STQK 629
                                       ...4444 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 ?   13.0   0.0   1.1e-05       0.1      86     110 ..      62      86 ..      58      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                          PDDEXK_3  86 eaqllnYlkltklklGlliNFnkkk 110
                                       + qllnY+klt+++ Glli   ++k
  gi|320100595|ref|YP_004176187.1|  62 RSQLLNYMKLTGYRFGLLIDIPTEK 86 
                                       68*****************998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (749 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.40
# Mc/sec: 5656.34
//
Query:       gi|320100596|ref|YP_004176188.1|  [L=175]
Description: biotin/lipoyl attachment domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-14   53.3   7.3    4.5e-14   52.0   7.3    1.7  1  Biotin_lipoyl    Biotin-requiring enzyme
    3.5e-10   39.5   2.7    3.9e-05   23.4   0.1    2.6  2  Biotin_lipoyl_2  Biotin-lipoyl like
    1.5e-06   27.6   2.6     0.0062   15.8   0.1    2.3  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    2.5e-06   28.2   4.4      0.022   15.4   0.1    2.8  3  HlyD_3           HlyD family secretion protein
     0.0023   17.9   8.5      0.011   15.7   5.5    2.2  2  DUF2118          Uncharacterized protein conserved in archaea
     0.0084   16.0   2.1     0.0084   16.0   2.1    2.2  2  GCV_H            Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.014   15.2   7.9       0.51   10.2   0.4    2.4  2  PASTA            PASTA domain
      0.033   14.0   3.2        2.6    7.8   0.1    2.4  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
      0.098   12.7   1.3       0.21   11.6   0.7    1.9  1  Hjc              Archaeal holliday junction resolvase (hjc)
       0.13   11.7   6.5        2.2    7.6   0.5    2.1  2  NQRA             Na(+)-translocating NADH-quinone reductase s
       0.26   11.4   1.9        9.6    6.3   0.1    3.0  3  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
       0.83    9.7   6.3       0.54   10.3   0.9    3.0  3  Peptidase_S24    Peptidase S24-like


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   7.3     3e-17   4.5e-14       8      72 ..     111     170 ..     100     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 3e-17
                                       SEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEE CS
                     Biotin_lipoyl   8 iGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllak 72 
                                              g vvev+v++G+++ +++v+a+ve+mKm +e++ p +Gvv+ ++vk G+tv+ gd l+k
  gi|320100596|ref|YP_004176188.1| 111 S------GrVVEVKVAEGQSIGENDVVAVVESMKMLIEVKTPFKGVVEAVYVKPGSTVNKGDKLVK 170
                                       3......45777****************************************************98 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   3.9e-06    0.0058       5      37 ..     106     138 ..     105     144 .. 0.84
   2 !   23.4   0.1   2.6e-08   3.9e-05       3      34 ..     141     172 ..     135     175 .] 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-06
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37 
                                       ++ p+sGrV+++ V +Gq + + dv a+ +s +
  gi|320100596|ref|YP_004176188.1| 106 VSTPISGRVVEVKVAEGQSIGENDVVAVVESMK 138
                                       789***************998888888877766 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 2.6e-08
                   Biotin_lipoyl_2   3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelD 34 
                                       ++++ p+ G+V++++Vk G  V++Gd L+   
  gi|320100596|ref|YP_004176188.1| 141 IEVKTPFKGVVEAVYVKPGSTVNKGDKLVKVK 172
                                       578999*********************99776 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 !   11.9   0.6   6.3e-05     0.094     101     142 ..      96     137 ..      77     140 .. 0.80
   2 !   15.8   0.1   4.1e-06    0.0062      20      52 ..     141     172 ..     137     175 .] 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 101 ktgkvqktvtvkapisGvVteknvreGqyvqpgdtlftiadl 142
                                       +t  + ++  v++pisG V+e +v+eGq + ++d+++ + ++
  gi|320100596|ref|YP_004176188.1|  96 QTPAAMEEGVVSTPISGRVVEVKVAEGQSIGENDVVAVVESM 137
                                       444455667799********************9999998876 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 4.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23  20 arvsarveGwveklyvnatgdkVkkGqpLaely 52 
                                        +v++ ++G ve +yv+  g++V+kG++L++++
  gi|320100596|ref|YP_004176188.1| 141 IEVKTPFKGVVEAVYVK-PGSTVNKGDKLVKVK 172
                                       56777777777777777.777777777777765 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         5   7.5e+03      18      33 ..      17      32 ..       7      47 .. 0.48
   2 !   14.0   0.7   4.3e-05     0.064       2      32 ..     106     136 ..     105     144 .. 0.85
   3 !   15.4   0.1   1.5e-05     0.022       2      30 ..     143     171 ..     142     175 .] 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5
                            HlyD_3 18 gevvqagdelleiipp 33
                                       ev+++   ++ + +p
  gi|320100596|ref|YP_004176188.1| 17 IEVLARERDVVVLKDP 32
                                      3344444444444433 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.3e-05
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdelleiip 32 
                                       +  p++G+vve++v eg+ + ++d+++ +  
  gi|320100596|ref|YP_004176188.1| 106 VSTPISGRVVEVKVAEGQSIGENDVVAVVES 136
                                       778***********************99874 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.5e-05
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                       ++ p+ Gvv ++ v++g+ v++gd+l+++
  gi|320100596|ref|YP_004176188.1| 143 VKTPFKGVVEAVYVKPGSTVNKGDKLVKV 171
                                       899***********************998 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 !   15.7   5.5   7.3e-06     0.011      27     135 ..      50     156 ..      37     158 .. 0.85
   2 !    8.1   0.1    0.0016       2.4      87     116 ..     146     175 .]     141     175 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.3e-06
                           DUF2118  27 vekfadkveekklkgkvvYeelldeivdvleekvtrdviivlp.derklillkkGdklklipvegvkvtlivdvGdr 102
                                       v ++ d++  + + g  vY +l   +v +++e+v +   ++ + ++++   +++G  +   p++g +v + v +G+ 
  gi|320100596|ref|YP_004176188.1|  50 VLYIDDRMVSAGVIGDKVYVNLEPLLVKKVKETVAAAKAVERKeEKQTPAAMEEG--VVSTPISGRVVEVKVAEGQS 124
                                       4566777778888899999999999999******999999998677777888888..8999**************** PP

                           DUF2118 103 veegdtlaavttrkgevrylrapvegvVvfike 135
                                       + e d++a v + k  +  +++p +gvV  ++ 
  gi|320100596|ref|YP_004176188.1| 125 IGENDVVAVVESMKMLI-EVKTPFKGVVEAVYV 156
                                       **************977.69*******977765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                           DUF2118  87 pvegvkvtlivdvGdrveegdtlaavttrk 116
                                       p +gv+  ++v+ G  v++gd+l  v+tr+
  gi|320100596|ref|YP_004176188.1| 146 PFKGVVEAVYVKPGSTVNKGDKLVKVKTRS 175
                                       7899************************96 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4     0.053        80      60      74 ..     103     117 ..      40     120 .. 0.68
   2 !   16.0   2.1   5.6e-06    0.0084      30      74 ..     111     154 ..     104     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.053
                                       EEEEE-SSSEEEEEE CS
                             GCV_H  60 asevyapvsGevvev 74 
                                        + v +p+sG vvev
  gi|320100596|ref|YP_004176188.1| 103 EGVVSTPISGRVVEV 117
                                       355889999999998 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 5.6e-06
                                       H-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                             GCV_H  30 lgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                                        g+vv v++  +g+++ +++ +a+vEs K+  ev +p++G v  v
  gi|320100596|ref|YP_004176188.1| 111 SGRVVEVKVA-EGQSIGENDVVAVVESMKMLIEVKTPFKGVVEAV 154
                                       6899999996.59***************************99766 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.5    0.0018       2.6      10      59 ..      78     133 ..      70     137 .. 0.80
   2 ?   10.2   0.4   0.00034      0.51      32      57 ..     143     168 ..     133     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                                       BHHHHHHHHHHTT--CCCEEE......ECTCCGTTBEEEECS-TTSEECTTS-EEE CS
                             PASTA  10 svdeAkatLkalGlkiktvee......tsddvpeGtVisQsPeaGtevskgskvtl 59 
                                       +v+e +a++ka++ k   +++      ++++  +G+V+++ +++G+++ +++ v +
  gi|320100596|ref|YP_004176188.1|  78 KVKETVAAAKAVERKEEKQTPaameegVVSTPISGRVVEVKVAEGQSIGENDVVAV 133
                                       5667777777777755555557777789********************99999877 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00034
                                       CTCCGTTBEEEECS-TTSEECTTS-E CS
                             PASTA  32 sddvpeGtVisQsPeaGtevskgskv 57 
                                       +++  +G V ++++++G++v+kg+k+
  gi|320100596|ref|YP_004176188.1| 143 VKTPFKGVVEAVYVKPGSTVNKGDKL 168
                                       56777999****************96 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 ?    6.1   0.7    0.0059       8.8      17     105 ..      53     136 ..      42     146 .. 0.79
   2 ?    7.8   0.1    0.0017       2.6      85     104 ..     153     172 ..     143     175 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0059
                                       SSSHHHHT-TTSEEEEEEE-SSEEEES--EEEEE--SSSSEEEEESSSS-EEEEE-SSSTTTTTTTTEEES----SE CS
                        PTS_EIIA_1  17 vpDevfaekmlGdGvaiepsegkvvapvdGkvekvfptkHaigiktddgvevlihiGidtvklkgegFellvkegdk 93 
                                       + D + + +++Gd v ++  e  +v     kv+ ++    a+  k+++++   +  G+    + g++ e++v+eg++
  gi|320100596|ref|YP_004176188.1|  53 IDDRMVSAGVIGDKVYVNL-EPLLVK----KVKETVAAAKAVERKEEKQTPAAMEEGVVSTPISGRVVEVKVAEGQS 124
                                       6788888888888888888.334444....45555555668999999999999999999999*************** PP

                                       E-SEEEEEEE-H CS
                        PTS_EIIA_1  94 Vkagdklvevdl 105
                                       + ++d ++ v+ 
  gi|320100596|ref|YP_004176188.1| 125 IGENDVVAVVES 136
                                       *99999887765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0017
                                       EES----SEE-SEEEEEEE- CS
                        PTS_EIIA_1  85 ellvkegdkVkagdklvevd 104
                                        ++vk g++V++gdklv+v+
  gi|320100596|ref|YP_004176188.1| 153 AVYVKPGSTVNKGDKLVKVK 172
                                       689**************997 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   0.00014      0.21      30      57 ..     127     157 ..     111     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                       S-SEEEEETTEEEEEEEEEESSS...EEEEE CS
                               Hjc  30 lpDviAirgdvvlviEvKsskke...riylk 57 
                                         Dv+A+ + + ++iEvK+  k     +y+k
  gi|320100596|ref|YP_004176188.1| 127 ENDVVAVVESMKMLIEVKTPFKGvveAVYVK 157
                                       47****************9765333366665 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 ?    7.2   1.3     0.002       2.9      33      81 ..      65     119 ..      45     133 .. 0.78
   2 ?    7.6   0.5    0.0015       2.2      31      63 ..     142     174 ..     121     175 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                              NQRA  33 gedyvglkpklkvkegdkVkkGqvlf..edKknpgv....lftspasGevveinr 81 
                                        + yv+l+p l+ k+ ++V + +++   e+K++p      ++ +p+sG+vve++ 
  gi|320100596|ref|YP_004176188.1|  65 DKVYVNLEPLLVKKVKETVAAAKAVErkEEKQTPAAmeegVVSTPISGRVVEVKV 119
                                       3569******************9995336788775422226899********986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                              NQRA  31 llgedyvglkpklkvkegdkVkkGqvlfedKkn 63 
                                        + ++++g+   + vk g +V+kG+ l++ K++
  gi|320100596|ref|YP_004176188.1| 142 EVKTPFKGVVEAVYVKPGSTVNKGDKLVKVKTR 174
                                       45679***********************99975 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 ?   -1.0   0.0       1.3   1.9e+03      11      30 ..       8      27 ..       5      28 .. 0.80
   2 ?    5.2   0.2     0.014        21      46      68 ..     113     135 ..      82     142 .. 0.87
   3 ?    6.3   0.1    0.0065       9.6      29      68 ..     130     172 ..     127     175 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                                      HGCTTSEEEEEEEESSSEEE CS
                         QRPTase_N 11 lipeekkakaeiiakeegvv 30
                                      ++ +++ +++e++a+e  vv
  gi|320100596|ref|YP_004176188.1|  8 VFFNDEAVEIEVLARERDVV 27
                                      67789999999999997665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                                       TEEEESS-TT-EEETTEEEEEEE CS
                         QRPTase_N  46 levellvkDGervekgdvlleie 68 
                                         ve++v++G+++ ++dv++ +e
  gi|320100596|ref|YP_004176188.1| 113 RVVEVKVAEGQSIGENDVVAVVE 135
                                       568999*************9987 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0065
                                       EE-SHHHHHHHHHHH...TTTEEEESS-TT-EEETTEEEEEEE CS
                         QRPTase_N  29 vvaGlevaeevfell...pglevellvkDGervekgdvlleie 68 
                                       vva +e +++++e+    +g+   ++vk G++v+kgd+l++++
  gi|320100596|ref|YP_004176188.1| 130 VVAVVESMKMLIEVKtpfKGVVEAVYVKPGSTVNKGDKLVKVK 172
                                       6777777777777778777777789***************997 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00036      0.54      25      57 ..      21      53 ..       4      72 .. 0.78
   2 ?   -0.2   0.1      0.65   9.7e+02      43      47 ..      76      80 ..      62     134 .. 0.57
   3 ?    0.7   0.1      0.34   5.1e+02      16      30 ..     153     167 ..     151     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00036
                                      --TTSEEEEEETTCE-EEEEEEEEETTEEEEE. CS
                     Peptidase_S24 25 pkrGdivvfrlpgeeeayiKrviglpgdrvlla 57
                                      ++  d+vv ++pg++++ ++ +++ +g+ vl+ 
  gi|320100596|ref|YP_004176188.1| 21 ARERDVVVLKDPGGRIYRVRVLKEGDGRYVLYI 53
                                      6778***********999999998888888854 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.65
                                      EEEEE CS
                     Peptidase_S24 43 iKrvi 47
                                      +K+v+
  gi|320100596|ref|YP_004176188.1| 76 VKKVK 80
                                      33333 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.34
                                       EEEEECTS---TTSE CS
                     Peptidase_S24  16 lilVdkfsepkrGdi 30 
                                        + V+++s++++Gd 
  gi|320100596|ref|YP_004176188.1| 153 AVYVKPGSTVNKGDK 167
                                       58899********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1217.13
//
Query:       gi|320100597|ref|YP_004176189.1|  [L=362]
Description: Wyosine base formation domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-19   69.2   0.0    5.3e-19   68.3   0.0    1.5  1  Wyosine_form  Wyosine base formation
    2.9e-16   60.3   0.0    1.2e-15   58.3   0.0    1.9  1  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.075   13.4   0.0       0.19   12.1   0.0    1.6  1  HAD           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 !   68.3   0.0   8.9e-23   5.3e-19       1      63 []     267     328 ..     267     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 8.9e-23
                                       HHT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   1 kaepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       ka+p ++EvKay+++G sr rL ++n+P+h ev+  a rl++ ++ Y++l+e+ +Sr+vll+r
  gi|320100597|ref|YP_004176189.1| 267 KAQPSYIEVKAYMHIGGSRGRLFKNNMPSHGEVRNVAARLAELTG-YQVLSESIPSRIVLLSR 328
                                       69*******************************************.**************986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   1.9e-19   1.2e-15       2     164 ..      77     259 ..      76     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.9e-19
                                       EEESEESS--TTTSCCTT............................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEE CS
                                       xxxxxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet............................vrregrgrslsveeileevkelkaekgvkev 50 
                                       +v  +C +rC +C+r +                             +r    g    ++   ++v+e+  ++ ++  
  gi|320100597|ref|YP_004176189.1|  77 PVAAWCWNRCLHCWRLQPedigmhwddtrppvvddpevlveesirvHREIMAGFKGNPRADQRLVEEA-LNP-KHAA 151
                                       67889***********99******55555555555555555555554444444444444444444444.344.6666 PP

                                       EEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...HHHHHHTCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                       Radical_SAM  51 ilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde...kvlklmnrg 124
                                       i++ gepllyp++ el+e+++++   gi+++++t gt+p    +   le ++ ++++++ea+d++    + +++  +
  gi|320100597|ref|YP_004176189.1| 152 ISLTGEPLLYPRLGELIEEYHRR---GITTFLVTHGTRP---DVLGSLEVEPSQLYISIEAWDKDsyeHFNRPL-VP 221
                                       666*******************9...************9...4444455559*************777777777.88 PP

                                       SHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 125 htfeevlealeklreagikrvvdrivglpGendeeleell 164
                                         +e + e+l ++ +   + +v+r ++++G+nd++ ++l+
  gi|320100597|ref|YP_004176189.1| 222 RAWELFNETLGLIPSFKSP-TVFRFTIVKGFNDHD-VALR 259
                                       9999999999999999888.**************9.5555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.1e-05      0.19      62     113 ..     130     187 ..     113     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                               HAD  62 laglseelaaelerfvaevirpk..........lldpgalellaahraaGdrvvvvSgglrp 113
                                       ++g + ++ + +e+++     pk          ll+p + el+++ +++G+++ +v+ g rp
  gi|320100597|ref|YP_004176189.1| 130 FKGNPRADQRLVEEAL----NPKhaaisltgepLLYPRLGELIEEYHRRGITTFLVTHGTRP 187
                                       4444455555555555....3333444667788888**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2971.21
//
Query:       gi|320100598|ref|YP_004176190.1|  [L=292]
Description: 6-phosphogluconate dehydrogenase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-19   69.4   0.2      7e-19   68.5   0.2    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    2.4e-07   30.9   0.0    4.6e-07   30.0   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00014   22.4   0.0    0.00031   21.3   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0032   17.7   0.0     0.0058   16.9   0.0    1.4  1  NAD_binding_11   NAD-binding of NADP-dependent 3-hydroxyisobu
     0.0059   15.9   0.1     0.0091   15.3   0.1    1.2  1  FAD_binding_3    FAD binding domain
     0.0059   16.5   0.0     0.0098   15.8   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.023   14.3   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.066   12.6   0.0       0.11   11.9   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.16   12.2   0.0       0.29   11.4   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.2   3.5e-22     7e-19       2     158 .]       5     162 ..       4     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 3.5e-22
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglle 78 
                                       i + G G MGs++a+ l  +g  v+vynrt ek+++l +e    + +  + + + d+ ++++ +++av  +ie l++
  gi|320100598|ref|YP_004176190.1|   5 ILVAGAGLMGSSLAKCLSTRGVVVYVYNRTVEKARALCSEAGCRVLENLDSMPGFDATVVFLFDDQAVSGFIEALVD 81 
                                       5688**********************************99755555556689999*******************875 PP

                                       C-..-TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEE CS
                     NAD_binding_2  79 al..kkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakv 153
                                       +   ++  +l+ +st+spe++++l+  ++++g  +++aPV G++ +A++ +L  m++G++ a +r++++ + +++++
  gi|320100598|ref|YP_004176190.1|  82 KGltAEAGVLMVSSTISPETSIRLHGLVTRAGGVYVEAPVYGSTGEASSCSLVSMLAGDQVARSRAEEAASLYSRRM 158
                                       4323566788999******************************************************9999999888 PP

                                       EEE-E CS
                     NAD_binding_2 154 thviG 158
                                       + ++G
  gi|320100598|ref|YP_004176190.1| 159 Y-WVG 162
                                       7.766 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.3e-10   4.6e-07      14      59 ..       4      48 ..       2      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.3e-10
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge 59
                                      ++l+ GaG m++ +ak L+++gv  v v NRt+e+a++l++e +  
  gi|320100598|ref|YP_004176190.1|  4 RILVAGAGLMGSSLAKCLSTRGVV-VYVYNRTVEKARALCSEAGCR 48
                                      79*********************9.***************998554 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 !   21.3   0.0   1.6e-07   0.00031       3      81 ..       6      79 ..       4      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
                                      EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae..eadvvvlavkpedveevls 79
                                       + GaG mg++la+ l+++g     ++ + +r+ eka++l +e+g +v +  n + +   +a+vv+l +  ++v+ +++
  gi|320100598|ref|YP_004176190.1|  6 LVAGAGLMGSSLAKCLSTRG---VVVY-VYNRTVEKARALCSEAGCRVLE--NLDSMPgfDATVVFL-FDDQAVSGFIE 77
                                      455*****************...7777.66***************88888..777776545555554.55555555555 PP

                                      HC CS
                     F420_oxidored 80 el 81
                                      +l
  gi|320100598|ref|YP_004176190.1| 78 AL 79
                                      55 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0058       5     120 ..     169     281 ..     166     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                    NAD_binding_11   5 avKlvnnlllainlaaasEalvlaekaGldpekvlevinassgrsnalenklpqrvlsrdfdpgFaldlmlKDlgla 81 
                                       a Kl+ n +  +    ++E l+l+e++G+  +++  v  + +    ++e++++ r ++ + +p+F+++  +KD +++
  gi|320100598|ref|YP_004176190.1| 169 ALKLALNNIGLALPGLLAESLALLEAYGVGSDVFRMV-AGDLWFGSMVERYME-RAMAAAGRPRFTVSGAAKDYRVI 243
                                       667776666666677899***********98766555.555555558899998.677789999************** PP

                    NAD_binding_11  82 lelareagaplpllalaeqlyaaaaaegggdaDhsaivr 120
                                         +    g+p  + +  + +y  a a++ +++D+ ++v+
  gi|320100598|ref|YP_004176190.1| 244 ACTLAGKGYPPLVSQGLAGFYTLA-ASVMPGEDYPRAVN 281
                                       *********988888888877766.55566667766665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   4.6e-06    0.0091       4      41 ..       5      39 ..       3      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-06
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr 41
                                      +l+ GaG+ G +la+ Ls++Gv v + ++  +++   r
  gi|320100598|ref|YP_004176190.1|  5 ILVAGAGLMGSSLAKCLSTRGVVVYVYNRTVEKA---R 39
                                      699*******************988766654443...3 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 !   15.8   0.0   4.9e-06    0.0098       2      37 ..       5      40 ..       4      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.9e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealek 37
                                      + v GaG+mG+++a+ +  +g+ V +++++ e++++
  gi|320100598|ref|YP_004176190.1|  5 ILVAGAGLMGSSLAKCLSTRGVVVYVYNRTVEKARA 40
                                      6699***********************998777665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.023       1      43 [.       5      49 ..       5      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrl 43
                                      i+++GaG +Gs la +L+  g  v++++r+  ++ a  +++G+r+
  gi|320100598|ref|YP_004176190.1|  5 ILVAGAGLMGSSLAKCLSTRGVVVYVYNRTVeKARAlCSEAGCRV 49
                                      89****************************999999888899887 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.3e-05      0.11      39      81 ..       5      48 ..       2      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                                      EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCE CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgve 81
                                      + + G+G +G+++ak+l+  g+ v++y+r+ +k +  ++e g++
  gi|320100598|ref|YP_004176190.1|  5 ILVAGAGLMGSSLAKCLSTRGVVVYVYNRTVEKARaLCSEAGCR 48
                                      7799**************************98776555555664 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.29       1      46 [.       5      46 ..       5      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTT CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalg 46
                                      +l+ GaG +G+++a+ l+ ++ v   + v  r+ ek++al+++a g
  gi|320100598|ref|YP_004176190.1|  5 ILVAGAGLMGSSLAKCLSTRGVV---VYVYNRTVEKARALCSEA-G 46
                                      7999*****************99...***********9999764.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); 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:                         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 0.21s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2442.53
//
Query:       gi|320100599|ref|YP_004176191.1|  [L=241]
Description: ERCC4 domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   57.2   0.0    3.3e-15   56.6   0.0    1.2  1  ERCC4          ERCC4 domain
    1.6e-11   44.1   0.0      3e-11   43.3   0.0    1.4  1  HHH_2          Helix-hairpin-helix motif
    1.2e-10   41.8   0.1    5.5e-10   39.7   0.0    2.0  2  HHH_5          Helix-hairpin-helix domain
    1.1e-06   28.2   0.0    1.7e-05   24.5   0.0    2.6  2  HHH            Helix-hairpin-helix motif
     0.0082   15.9   0.0       0.02   14.6   0.0    1.6  1  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin
  ------ inclusion threshold ------
       0.08   13.2   0.1       0.25   11.6   0.1    1.9  1  HHH_3          Helix-hairpin-helix motif
      0.096   12.3   0.0       0.15   11.6   0.0    1.3  1  Pex2_Pex12     Pex2 / Pex12 amino terminal region


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   1.3e-18   3.3e-15       1     153 [.      13     143 ..      13     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.3e-18
                                       EEGGG.CT.SHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSH CS
                             ERCC4   1 iDsre.lk.sgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgr 75 
                                       iDsre  k ++ +e  + ++g++++++ lp gd+ l+   ++ e   +          +lverks+ddl++si+d+r
  gi|320100599|ref|YP_004176191.1|  13 IDSREdSKhPEFREA-FTREGLKTAVRELPAGDF-LL---MAPEGRRS----------ILVERKSVDDLANSIRDNR 74 
                                       899993333334444.9*****************.55...55544444..........******************* PP

                                       HHHHHHHHHH.H-SE....EEEEEES.-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHH CS
                             ERCC4  76 leeqvsrlkrngykk....pillveg.ldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesan 147
                                       ++eq s l + + ++    p++lveg l+ + ++               ++ +++  +L +l ld g+++l t  + 
  gi|320100599|ref|YP_004176191.1|  75 IWEQSSMLLE-EARRdghqPLILVEGcLSILEKQR------G-------WRIQSVLRVLDTLILDMGIPVLNTPGKD 137
                                       ********66.33333566*******877776653......2.......77778*********************** PP

                                       HHHHHH CS
                             ERCC4 148 etaewl 153
                                        t+ w+
  gi|320100599|ref|YP_004176191.1| 138 ATIAWI 143
                                       ***998 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.2e-14     3e-11      11      59 ..     182     230 ..     180     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.2e-14
                             HHH_2  11 VGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFenek 59 
                                       +G   A++L +rFk+l +L++as  +Ll+v++iGe+ A++i+  F++++
  gi|320100599|ref|YP_004176191.1| 182 IGPVLARKLLERFKTLRNLANASKHDLLSVEGIGEKRAEEIYLLFNTPW 230
                                       899*******************************************998 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   3.8e+03      19      32 ..      58      69 ..      54      73 .. 0.73
   2 !   39.7   0.0   2.1e-13   5.5e-10      10      53 ..     182     224 ..     181     225 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                                      HTTT--SHHHHHHS CS
                             HHH_5 19 lsaGiesvedlaaa 32
                                      ++   +sv+dla+ 
  gi|320100599|ref|YP_004176191.1| 58 VER--KSVDDLANS 69
                                      455..799999985 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 2.1e-13
                                       --HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5  10 iGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                       iGp++A++ll+  ++++  la+a++++L ++ GiG+k+Ae i l
  gi|320100599|ref|YP_004176191.1| 182 IGPVLARKLLER-FKTLRNLANASKHDLLSVEGIGEKRAEEIYL 224
                                       9***********.***************************9975 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.33   8.4e+02      19      29 ..     182     192 ..     182     192 .. 0.90
   2 !   24.5   0.0   6.5e-09   1.7e-05       2      28 ..     197     223 ..     196     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.33
                                       -SHHHHHHHHH CS
                               HHH  19 VGpktAeaIls 29 
                                       +Gp  A++ l+
  gi|320100599|ref|YP_004176191.1| 182 IGPVLARKLLE 192
                                       8******9985 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6.5e-09
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIl 28 
                                       l +l +as  +Ll+++G+G+k+Ae I+
  gi|320100599|ref|YP_004176191.1| 197 LRNLANASKHDLLSVEGIGEKRAEEIY 223
                                       789**********************96 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   7.9e-06      0.02      33      61 ..     194     222 ..     191     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-06
                                       --BHHHHHHS-HHHHTTSSS-SSHHHHHH CS
                     RNA_pol_A_CTD  33 iktvgeLvklseeeLlkikNlGkKSleEI 61 
                                        kt+++L++ s+++Ll+++ +G+K  eEI
  gi|320100599|ref|YP_004176191.1| 194 FKTLRNLANASKHDLLSVEGIGEKRAEEI 222
                                       69**************************9 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   9.7e-05      0.25       7      60 ..     199     222 ..     171     224 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.7e-05
                             HHH_3   7 diNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgpktfeql 60 
                                       ++  A                              s  +Ll+v+g+g+k  e++
  gi|320100599|ref|YP_004176191.1| 199 NLANA------------------------------SKHDLLSVEGIGEKRAEEI 222
                                       33334..............................4556666666666665544 PP

>> Pex2_Pex12  Pex2 / Pex12 amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.9e-05      0.15      67     112 ..     161     206 ..     149     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                        Pex2_Pex12  67 elkkrrllskrqrllsllllvlipYlkekldelysarerysaeals 112
                                       ++++r++     r+l+++  v++p l +kl e++++ +++ + +++
  gi|320100599|ref|YP_004176191.1| 161 MRTERKPMDINERILYVAEGVIGPVLARKLLERFKTLRNLANASKH 206
                                       5788999999************************444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1730.12
//
Query:       gi|320100600|ref|YP_004176192.1|  [L=338]
Description: family 4 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-29  101.5  11.5    4.3e-29  101.5  11.5    1.6  2  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1      0.76   1.4e+04      93     108 ..      57      72 ..      53      77 .. 0.59
   2 !  101.5  11.5   2.4e-33   4.3e-29       6     159 ..      92     247 ..      87     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.76
                   Glycos_transf_4  93 gvsiiialalvvlaav 108
                                       gv ++ ++a+++l++v
  gi|320100600|ref|YP_004176192.1|  57 GVWVLLGAAFGILSYV 72 
                                       4555555555555554 PP

  == domain 2  score: 101.5 bits;  conditional E-value: 2.4e-33
                   Glycos_transf_4   6 ltillilllGflDDv....lglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvt 78 
                                        +++l++llG++DD+    +gl+++ +++l++ ++++l+++   ++t+++l+l+ ++++lg+++ +l++ + ++g++
  gi|320100600|ref|YP_004176192.1|  92 QVLVLAGLLGLMDDIlgwkKGLSQVKRVLLTLPISFPLVVVKA-GYTSVELPLI-GVLDLGPLYPLLVVPVGVMGAS 166
                                       567899********988889*****************988766.**********.********************** PP

                   Glycos_transf_4  79 NavNliDGldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavl 155
                                       Na+N+i+G++Gl+a ++++i+ + +++a+ +g  +++ l+l++++a+l fl++N+ pA+vF G+++++  G+++a +
  gi|320100600|ref|YP_004176192.1| 167 NAFNMIAGYNGLEALQALVITGFTLLFALKKGIVDVIPLLLVMAAAILVFLRYNWCPARVFPGNTFTYGFGAFYASI 243
                                       ****************************999*******9999999******************************** PP

                   Glycos_transf_4 156 ailg 159
                                       +i+g
  gi|320100600|ref|YP_004176192.1| 244 VIYG 247
                                       *987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2321.31
//
Query:       gi|320100601|ref|YP_004176193.1|  [L=104]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   15.5   0.1      0.011   15.3   0.1    1.0  1  HTH_42    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_42  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   6.3e-07     0.011      53     143 ..      12      96 ..       7     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-07
                            HTH_42  53 vpaedlpllrpamapalaaelara.kgldareaaalaaavlerlaaegpltarelgealarrgwwgwkkpgkaskra 128
                                       v++ed+ +lr+++++ +a+  +++  +   r ++++++ +++rl +e    +++l ++l+        k ++ + r+
  gi|320100601|ref|YP_004176193.1|  12 VSREDAEWLRALKKEFQASS-SSElFQVLRRILDEYVDGAARRLCTEYSSAKAALPAWLSIF------KRERIPLRL 81 
                                       89**************9998.44469********************************9999......899****** PP

                            HTH_42 129 lellrlegelvvarr 143
                                       l+ lr eg ++v+  
  gi|320100601|ref|YP_004176193.1|  82 LYMLRPEGGVMVVDS 96 
                                       ***********9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 807.39
//
Query:       gi|320100602|ref|YP_004176194.1|  [L=109]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.049   13.6   0.2       0.12   12.4   0.1    1.7  2  zf-C2HC5     Putative zinc finger motif, C2HC5-type
       0.21   11.0   2.1       0.41   10.1   0.1    2.4  3  zf-ribbon_3  zinc-ribbon domain


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 ?   12.4   0.1   1.4e-05      0.12      21      41 ..      38      64 ..      33      68 .. 0.90
   2 ?   -3.4   0.0       1.1     1e+04      15      20 ..      90      95 ..      86      98 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                          zf-C2HC5 21 lnCGkiiCakegls......kpCsfCg 41
                                      ++CG+i+ + ++l        +C+fCg
  gi|320100602|ref|YP_004176194.1| 38 MSCGNIMGEIKELArlideqRKCPFCG 64
                                      68********99999999999*****8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                          zf-C2HC5 15 eaapnC 20
                                      e+a  C
  gi|320100602|ref|YP_004176194.1| 90 EIASAC 95
                                      445555 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   0.0      0.26   2.3e+03       7      10 ..      39      42 ..      39      44 .. 0.66
   2 ?   10.1   0.1   4.5e-05      0.41      14      24 ..      55      65 ..      53      66 .. 0.86
   3 ?   -1.6   0.0      0.22     2e+03       7      10 ..      94      97 ..      93     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.26
                       zf-ribbon_3  7 nCGa 10
                                      +CG+
  gi|320100602|ref|YP_004176194.1| 39 SCGN 42
                                      4776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 4.5e-05
                       zf-ribbon_3 14 sddnvCpyCGt 24
                                      +++++Cp CG+
  gi|320100602|ref|YP_004176194.1| 55 DEQRKCPFCGY 65
                                      57899****97 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.22
                       zf-ribbon_3  7 nCGa 10
                                      +CG+
  gi|320100602|ref|YP_004176194.1| 94 ACGS 97
                                      6775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 805.91
//
Query:       gi|320100603|ref|YP_004176195.1|  [L=54]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 402.73
//
Query:       gi|320100604|ref|YP_004176196.1|  [L=359]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-25   88.0  13.1      1e-24   87.6  13.1    1.2  1  VIT1          VIT family
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.033   14.6   0.0    1.8  1  Rubrerythrin  Rubrerythrin
      0.058   13.7   0.0       0.16   12.3   0.0    1.8  1  Rrf2          Transcriptional regulator


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 !   87.6  13.1   1.7e-28     1e-24       1     214 [.     145     348 ..     145     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.7e-28
                              VIT1   1 lrdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkreeeeleed 77 
                                       l+dav+G+ D Lv + a  +G++aa+  ++ +  +aGl   +AG+iSM +G+Yls+kse++  ++e+ + +     d
  gi|320100604|ref|YP_004176196.1| 145 LKDAVYGMIDALVEIEAGLIGVAAAT--QPIIAGVAGLISSIAGSISMSVGAYLSTKSENEAASSEELADSVLSTVD 219
                                       69*********************666..7899999999999*********************999877755555444 PP

                              VIT1  78 peegeaeelaeilearglseelaqevaaellknpdallelmlreelgpsaseelasplkaAlssalsfliGgliPll 154
                                       +  +  e+  + l++ gl+ e+a + + el++  +all+l+  ++++        sp+kaA   +l++++G++ P++
  gi|320100604|ref|YP_004176196.1| 220 K-TRFLEKAWRRLREAGLTSEEASA-IVELASGSQALLKLLSLHGEKA------SSPVKAARNAGLFYVLGAIGPVA 288
                                       4.34467788889999*******88.5567777777788665555443......49********************* PP

                              VIT1 155 pylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaaylig 214
                                       p+l        +++s+++tll+ll++ ++ +l++g+++l+   + +l++++A+aa++ +g
  gi|320100604|ref|YP_004176196.1| 289 PFLANLPLYHSVMLSLLLTLLVLLALSVFISLVSGARVLRVFAEYALLTLAATAATFTVG 348
                                       **985569999**********************************************997 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.5e-06     0.033      10      57 ..      15      56 ..      11     134 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                                      HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCS CS
                      Rubrerythrin 10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnkllekle 57
                                      E    rlY++la  +       +++FeelA +E++Ha+i++ l+  + 
  gi|320100604|ref|YP_004176196.1| 15 EVVSARLYRFLAAATG------RRVFEELALMEEKHAGIIAGLMIGRG 56
                                      5566789999999999......9*****************98885443 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   2.7e-05      0.16       8      55 ..     187     237 ..     179     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHSSTCC-B-HHHHHHHH..TS.-HHHHHHHHHHHHHTTSE CS
                              Rrf2   8 eyalhallyLakeeeeepvsseeiaerq..ni.spsylekilakLrkaglv 55 
                                       ++++ + +yL++++e+e +ssee+a+++   + + ++lek  ++Lr+agl 
  gi|320100604|ref|YP_004176196.1| 187 SISMSVGAYLSTKSENEAASSEELADSVlsTVdKTRFLEKAWRRLREAGLT 237
                                       56667778******************8843332468*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2761.08
//
Query:       gi|320100605|ref|YP_004176197.1|  [L=426]
Description: citrate transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-33  115.4  30.0    2.8e-33  115.4  30.0    2.1  2  CitMHS         Citrate transporter
    1.1e-13   51.1  30.8    5.1e-07   29.1  10.3    2.1  2  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    0.00014   20.8   6.2    0.00014   20.8   6.2    2.2  2  DctM           Tripartite ATP-independent periplasmic transpo


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 !  115.4  30.0   4.7e-37   2.8e-33       3     300 .]      15     366 ..       4     366 .. 0.85
   2 !   11.5   5.5   2.1e-05      0.13      99     166 ..     342     421 ..     342     424 .. 0.71

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 4.7e-37
                                       xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                            CitMHS   3 llileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.l 74 
                                       l+ ++ + + v    vl+ll     l++ e+++++ ++++ +++g+ ++ + l ++G+ + +++++++++++ ++ l
  gi|320100605|ref|YP_004176197.1|  15 LVSMDLVEKHVLGAAVLALLlftgALSPVELYEAVEWDVLGVVAGMSLLTGFLRDSGFGEAVSKRIVSRVRS-PRlL 90 
                                       444555555555444444445689***********************************************6.777* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                            CitMHS  75 lvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraa......... 141
                                       ++ l+ll++++s f++n+ +v +m+ +v+ +ak+ ++l+p+ l+i +alaa++ g++t++G+p+++ +         
  gi|320100605|ref|YP_004176197.1|  91 FFTLILLSGFISLFLDNVSTVSLMGLVVFYVAKE-AGLNPVdLFIGVALAAGMSGSATMVGDPPAMIVagyfnlsfl 166
                                       *********************************9.6666666*********************99999********* PP

                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                            CitMHS 142 ....arpglslpnllllalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpvatillla....... 207
                                            r ++s++++ + a+l+  l++ ++    +++   p + +++ ++  + ea a+  l+v ++ll++       
  gi|320100605|ref|YP_004176197.1| 167 dfffYRGRPSMFFITVAAMLASTLVYTLFHSGRSRVQGSPSAGGEGFDKVYLAEASAS--LTVTVALLSVrnvlglp 241
                                       ****999*********999999999999998777777777776655555555555555..55555555557777777 PP

                                       ..............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxx. RF
                            CitMHS 208 ..............................ykkveWsvlllfaGvfllvgaleqtGilealadll.ga.ggplval. 251
                                                                     + + eW + +++a vf l+++l + G ++ +++++ +a gg ++a+ 
  gi|320100605|ref|YP_004176197.1| 242 ltlcvsaglalilaarllvhrdykgvlevaRGSLEWRLPVFIASVFALSAGLLKYGWIDRFVAAVlSAtGGGFTAVs 318
                                       8888888888888899999**********9**************************888888777566655567775 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 252 alvlgliallsafisnvavaalmapialgmapalgllspsplalalavg 300
                                       ++++g+++l safi+n+++ +  +p+  ++a a+g  +p++la+al++g
  gi|320100605|ref|YP_004176197.1| 319 SVLIGVSVLASAFIDNTPYIVASLPLTSKLATAIG-ADPVALAWALLLG 366
                                       888999999***********************999.9999999999987 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.1e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                            CitMHS  99 ipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnllllal................... 156
                                       +p++ +la  ++ +p++l+ +l l+  +gg++tpiG +             n++++++                   
  gi|320100605|ref|YP_004176197.1| 342 LPLTSKLATAIGADPVALAWALLLGTTLGGCITPIGAS------------SNMVAVGIlemaghrvsftgfvkkala 406
                                       599999********************************............999996665555555544444444444 PP

                                       .....xxxxxxxxxx RF
                            CitMHS 157 .....llvgllplvl 166
                                            +l+g l+ +l
  gi|320100605|ref|YP_004176197.1| 407 fnmvnVLTGWLIYLL 421
                                       443334444444444 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1  10.3   8.5e-11   5.1e-07     286     445 ..      17     170 ..       1     197 [. 0.82
   2 !   28.3  12.5   1.5e-10   9.1e-07     315     464 ..     270     416 ..     219     423 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 8.5e-11
                     Na_sulph_symp 286 geslnidattvaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspav 362
                                       + +l +++ + +  vl++ll +  l+    + +   W++l + +g+  l  +l  sg+ e +++ +++ +   sp +
  gi|320100605|ref|YP_004176197.1|  17 SMDL-VEKHVLGAAVLALLLFTGALSPV-ELYEAVEWDVLGVVAGMSLLTGFLRDSGFGEAVSKRIVSRVR--SPRL 89 
                                       3344.88888888899999999988877.5778899***********************************..**** PP

                     Na_sulph_symp 363 aiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylk 439
                                       +++ +++l+ ++  lf  ++ t++ +  ++  va+ + g +p+ + + +ala ++ g+ + ++ +p++iv g   l+
  gi|320100605|ref|YP_004176197.1|  90 LFFTLILLSGFIS-LFLDNVSTVSLMGLVVFYVAKEA-GLNPVDLFIGVALAAGMSGSATMVGDPPAMIVAGYFNLS 164
                                       *****99997775.57789*****************9.99*******************************999999 PP

                     Na_sulph_symp 440 vkdywr 445
                                         d+  
  gi|320100605|ref|YP_004176197.1| 165 FLDFFF 170
                                       988764 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.5e-10
                     Na_sulph_symp 315 ivkqktaWntllllgglialakllersgliewlgnklttsls.glsp.avaiiiilslfvlvhylfaSatAttaall 389
                                       + +    W   ++ +++ al+ +l + g i     +++  ls    + +++  +++ ++vl+   f  +t +++a l
  gi|320100605|ref|YP_004176197.1| 270 VARGSLEWRLPVFIASVFALSAGLLKYGWI---DRFVAAVLSaTGGGfTAVSSVLIGVSVLA-SAFIDNTPYIVASL 342
                                       45666789999*****************55...55555544432233033344566666554.57889********* PP

                     Na_sulph_symp 390 pillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiigllillllgal 464
                                       p+   +a+ai ga+p+ +a +l l t l+g+++p++++ n+++ g+  +  +    +Gf+ + + + ++ +l  +
  gi|320100605|ref|YP_004176197.1| 343 PLTSKLATAI-GADPVALAWALLLGTTLGGCITPIGASSNMVAVGILEMAGHRVSFTGFVKKALAFNMVNVLTGW 416
                                       **********.************************************************9988888777666544 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 !   20.8   6.2   2.4e-08   0.00014     244     365 ..      10     140 ..       5     147 .. 0.79
   2 ?    2.0  14.6     0.012        74     185     406 ..     189     414 ..     152     423 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.4e-08
                              DctM 244 avvyalviallvyrrltleevaaallstaktt.........aavlfilaaagifaglltltgvplklselllslsgg 311
                                       a+v alv + lv++ +  + v+a ll t+ ++          +vl ++a++++++g+l  +g++ ++s+ ++s   +
  gi|320100605|ref|YP_004176197.1|  10 AAVVALVSMDLVEKHVLGAAVLALLLFTGALSpvelyeaveWDVLGVVAGMSLLTGFLRDSGFGEAVSKRIVSRVRS 86 
                                       4444444444447777777777777777777777777777789*****************************99999 PP

                              DctM 312 kllfLilvnllvlvlGmfldttaaiiilvpilaPaaaklgidpihfgvvivlnl 365
                                       + l++   +ll+ ++ +fld ++++ +++ +++ +a+++g++p+ + + + l++
  gi|320100605|ref|YP_004176197.1|  87 PRLLFFTLILLSGFISLFLDNVSTVSLMGLVVFYVAKEAGLNPVDLFIGVALAA 140
                                       975666666667799****************************97655555444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.012
                              DctM 185 lllavaiaakkenlrsktkaelkrlgqalkeaipalllpliiligillgiftpteagavavvyalviallvyrrltl 261
                                        l+++ +++ +  +++++ a  + + ++ + ++ a l++ + l  +   +  p     v++ +al++a+ +    + 
  gi|320100605|ref|YP_004176197.1| 189 TLVYTLFHSGRSRVQGSPSAGGEGFDKVYLAEASASLTVTVALLSVRNVLGLPLT-LCVSAGLALILAARLLVHRDY 264
                                       3445555666677777777777777777777775555555555555555555543.344444555555544455555 PP

                              DctM 262 eevaaallstakttaavlfilaaagifaglltltgvplklselllslsggkllfLilvnllvlvlGmfldttaaiii 338
                                       + v+++   +++    v++      + agll    +   ++++l++++gg   +  + + ++ +   f+d t+ i+ 
  gi|320100605|ref|YP_004176197.1| 265 KGVLEVARGSLEWRLPVFI-ASVFALSAGLLKYGWIDRFVAAVLSATGGGFTAVSSVLIGVSVLASAFIDNTPYIVA 340
                                       6666666666666666543.334445666777777788888888888777755555555566677899********* PP

                              DctM 339 lvpilaPaaaklgidpihfgvvivlnlsiglitPPvGlalfvas.sia.....kvsveeivkalvPflvvlvva 406
                                         p+   +a ++g dp+++   ++l + +g +  P+G+   + + +i      +vs+++ vk+++ f +v v+ 
  gi|320100605|ref|YP_004176197.1| 341 SLPLTSKLATAIGADPVALAWALLLGTTLGGCITPIGASSNMVAvGILemaghRVSFTGFVKKALAFNMVNVLT 414
                                       *************************************9886544155588897799999999999998887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2923.27
//
Query:       gi|320100606|ref|YP_004176198.1|  [L=306]
Description: transcription factor TFIIB cyclin-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-05   25.5   3.1    0.00016   21.6   0.2    2.3  2  TFIIB     Transcription factor TFIIB repeat
     0.0016   18.5   0.0       0.46   10.6   0.0    2.3  2  Cyclin_C  Cyclin, C-terminal domain
  ------ inclusion threshold ------
      0.086   12.6   0.0        4.4    7.0   0.0    2.2  2  TRAPP     Transport protein particle (TRAPP) component
       0.12   12.4   0.5        1.6    8.8   0.1    2.6  2  HTH_29    Winged helix-turn helix
       0.13   12.2   0.3         13    5.8   0.0    2.7  2  TrmB      Sugar-specific transcriptional regulator TrmB
       0.15   11.9   0.2       0.53   10.1   0.2    2.0  1  HTH_23    Homeodomain-like 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 ?    4.2   0.2     0.015        44      39      67 ..      52      80 ..      49      84 .. 0.85
   2 !   21.6   0.2   5.4e-08   0.00016      31      70 ..     130     169 ..     106     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.015
                                      HHTTHHHHHHTTTTSS--HHHHHHHSS-- CS
                             TFIIB 39 iaAAclyiAcrkeevkrtqkeissvlqVs 67
                                       aAA++y A r  +v  +++ + + + Vs
  gi|320100606|ref|YP_004176198.1| 52 KAAAAVYAALRSMGVCVSPRCVEEYAGVS 80
                                      59*********999998888888888877 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5.4e-08
                                       TTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
                             TFIIB  31 lkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70 
                                       + G s+ ++aAA+ly+A+r   +++t + i  v++Vs+  
  gi|320100606|ref|YP_004176198.1| 130 MGGLSNSTVAAASLYLAARGRLTQKTVSSILCVSEVSVRN 169
                                       56899***************************99999876 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.006        18      46      86 ..      51      91 ..      42      93 .. 0.88
   2 !   10.6   0.0   0.00015      0.46      41      90 ..     132     178 ..     124     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.006
                                      HHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHH CS
                          Cyclin_C 46 liAaaalllarstlnspewtetlehytgyskedlkpcveli 86
                                        Aaaa+++a++ ++ +   + +e+y g+s  ++ ++ + +
  gi|320100606|ref|YP_004176198.1| 51 FKAAAAVYAALRSMGVCVSPRCVEEYAGVSRTRFTEVLRSM 91
                                      569***********999999*********999999988766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00015
                                       CS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                          Cyclin_C  41 syppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                       + + S++Aaa+l+la +       ++t+ +++ +s+  ++++++ ++ ll
  gi|320100606|ref|YP_004176198.1| 132 GLSNSTVAAASLYLAARG---RLTQKTVSSILCVSEVSVRNIARRMEGLL 178
                                       5678*************9...78889999999999999999999999877 PP

>> TRAPP  Transport protein particle (TRAPP) component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0015       4.4       4      54 ..      39      89 ..      37      93 .. 0.90
   2 ?    3.6   0.0     0.016        48      20      39 ..     241     260 ..     162     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                             TRAPP  4 llgelvsylqrdskdveevekrLekmGyrvGlrllelllarerpretdile 54
                                      +++el +y+ ++ k +++v + L++mG+ v  r++e++   +r+r+t++l 
  gi|320100606|ref|YP_004176198.1| 39 VFTELTKYFDKRFKAAAAVYAALRSMGVCVSPRCVEEYAGVSRTRFTEVLR 89
                                      589*********************************888888899998876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.016
                             TRAPP  20 eevekrLekmGyrvGlrlle 39 
                                       +e   rLe mG  vG  l  
  gi|320100606|ref|YP_004176198.1| 241 AEATGRLEHMGIAVGRALSY 260
                                       67779**********98865 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.16   4.8e+02       8      32 ..      96     119 ..      89     133 .. 0.81
   2 ?    8.8   0.1   0.00054       1.6       7      55 ..     145     197 ..     140     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                            HTH_29   8 laeGvstvsqiAkllglsrrtvyrw 32 
                                       ++ +++ vs + ++lgl+ +t  ++
  gi|320100606|ref|YP_004176198.1|  96 CSLAGY-VSYASRVLGLDDSTAADA 119
                                       566667.88999******9998776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00054
                            HTH_29   7 llaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaa......lldrrrsgrprn 55 
                                       l+a+G  t + +  +l++s+ +v+++ +r  ++Gl +      l++  ++grpr 
  gi|320100606|ref|YP_004176198.1| 145 LAARGRLTQKTVSSILCVSEVSVRNIARR--MEGLLGdalsfsLREADAPGRPRG 197
                                       6788999**********************..777766666664444666777775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0044        13      12      46 ..      56      91 ..      52      93 .. 0.79
   2 ?    3.5   0.1     0.022        65      15      47 ..     143     175 ..     136     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0044
                                      CHCHHHHHHCC.CHHCHHCCCTTSSCHCHHHHHHHH CS
                              TrmB 12 kvYlaLlklgp.atadeiaeelgvprskvYevLrsL 46
                                       vY+aL + g   + + + e +gv+r++  evLrs+
  gi|320100606|ref|YP_004176198.1| 56 AVYAALRSMGVcVSPRCVEEYAGVSRTRFTEVLRSM 91
                                      5677777555425678899***************98 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.022
                                       HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHH CS
                              TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLe 47 
                                       l+L ++g++t ++++++l v++ +v ++ r++e
  gi|320100606|ref|YP_004176198.1| 143 LYLAARGRLTQKTVSSILCVSEVSVRNIARRME 175
                                       57899*****************99999988886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00018      0.53      11      44 ..     143     175 ..     138     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                            HTH_23  11 llllae.GlsvreIAreLgvsrrTvyrwlkryree 44 
                                       l+l+a+ +l++++++ +L vs+  v+++ +r   e
  gi|320100606|ref|YP_004176198.1| 143 LYLAARgRLTQKTVSSILCVSEVSVRNIARRM--E 175
                                       5666779*********************9995..4 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:                      324  (0.0180713); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2240.69
//
Query:       gi|320100607|ref|YP_004176199.1|  [L=144]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-05   24.1   6.1    5.3e-05   24.1   6.1    1.8  2  Pilin_N         Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.038   13.8   0.0    1.8  2  A2M             Alpha-2-macroglobulin family
      0.026   14.8   2.6      0.037   14.3   2.6    1.3  1  CARDB           CARDB
      0.096   13.0   1.7       0.31   11.3   0.9    2.0  2  DUF4352         Domain of unknown function (DUF4352)
       0.43   11.1   6.8          1    9.9   6.8    1.7  1  DUF4179         Domain of unknown function (DUF4179)
       0.49   10.6  17.2        4.7    7.4  17.2    2.2  1  Arch_flagellin  Archaebacterial flagellin
        7.5    7.6   6.2         20    6.2   0.1    2.2  2  Pap_E4          E4 protein


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 !   24.1   6.1   2.1e-08   5.3e-05       1      75 [.       3      84 ..       3      90 .. 0.74
   2 ?   -0.3   0.0      0.81   2.1e+03      57      64 ..     111     118 ..      86     140 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.1e-08
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidss.astgkna......vslehkgGdsidtkdl 72
                                      +A+SpVi  +++va+t+ +a  +a  ++gl +  +++ + +i + + ++ ++t++n+      +++++ g  +++ +++
  gi|320100607|ref|YP_004176199.1|  3 KAISPVIATVIIVAVTIAIAIAVALWMTGLVGSFTATENLQIITAYAEQfTNTTTNTtywtitLQVKNVGTTDVTIDNI 81
                                      69****************************7777777788885553333033333335566668888888888888888 PP

                           Pilin_N 73 kiv 75
                                       i+
  gi|320100607|ref|YP_004176199.1| 82 FIN 84
                                      876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.81
                           Pilin_N  57 vslehkgG 64 
                                       ++++ ++G
  gi|320100607|ref|YP_004176199.1| 111 LTITISSG 118
                                       44444444 PP

>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.8   4.6e+03       3      10 ..      61      68 ..      52      79 .. 0.53
   2 ?   13.8   0.0   1.5e-05     0.038      57      92 .]      94     129 ..      90     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                                      CEEEEEEC CS
                               A2M  3 lWedvlvt 10
                                      +W+ +l+ 
  gi|320100607|ref|YP_004176199.1| 61 YWTITLQV 68
                                      34443333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                                       EEEEE--SEEETTSEEEEEEEEEE-SSS-EEEEEEE CS
                               A2M  57 fvdlnlPysvrrgeqveikavvfNyldkeikvrvel 92 
                                        ++++lPys++ ge+  ++++++   ++ + v+v+l
  gi|320100607|ref|YP_004176199.1|  94 TLNITLPYSIKTGETKGLTITISSGFSSGQMVEVKL 129
                                       5789*****************************986 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.6   1.4e-05     0.037      12      83 ..      53     130 ..      39     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                       -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE.......SEE-CTEEEEEEEEEE-S-S-CEEE.E CS
                             CARDB  12 pseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv.......psLaagesttvsftwtteategevt.l 80 
                                        +++++ +  tit++vkN Gt +   t  +++++g+  g+v v        s++ ge++  ++t+    ++g++  +
  gi|320100607|ref|YP_004176199.1|  53 TNTTTNTTYWTITLQVKNVGTTDV--TIDNIFINGKPYGSVGVtlnitlpYSIKTGETKGLTITISSGFSSGQMVeV 127
                                       4456667778**********9875..799*********9999999999999************99999666665446 PP

                                       EEE CS
                             CARDB  81 tvv 83 
                                       +++
  gi|320100607|ref|YP_004176199.1| 128 KLH 130
                                       665 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9   0.00012      0.31      24      59 ..      46      81 ..      34      84 .. 0.83
   2 ?   -0.0   0.0      0.39     1e+03      99     121 ..      99     121 ..      91     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                      EETTS-CEETT-.SEEEEEEEEEEE-SSS-EEEEGG CS
                           DUF4352 24 svgkneylqpdaggeflivdvtvkNkgkealtvnss 59
                                      + ++++++++ +  ++ +++++vkN g  ++t++ +
  gi|320100607|ref|YP_004176199.1| 46 TAYAEQFTNTTTNTTYWTITLQVKNVGTTDVTIDNI 81
                                      55568899999999*******************987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.39
                                       EEEEESTT-CG.EEEEE.HBB-TT CS
                           DUF4352  99 lvFdvpkgkkk.leLeyqtslsfs 121
                                       l + +++g++k l++++++++ +s
  gi|320100607|ref|YP_004176199.1|  99 LPYSIKTGETKgLTITISSGF-SS 121
                                       668888888877888885555.33 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.8    0.0004         1       6      73 ..      14     117 ..       8     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0004
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.--SS-HHHHT--SS-...........HHHHSEEE............. CS
                           DUF4179   6 ikkvaaaaaalvllllssrllspalAsalnpvigslfeklsdskg...........eqeyvkpv............. 58 
                                       i  v++a+a++v+l  ++ ++s +  ++l ++i ++ e++ ++++           ++  +++v             
  gi|320100607|ref|YP_004176199.1|  14 IVAVTIAIAIAVALWMTGLVGSFTATENL-QIITAYAEQFTNTTTnttywtitlqvKNVGTTDVtidnifingkpyg 89 
                                       67799999999999666666676777777.78888887777776667778876664333333336677777777777 PP

                                       .............EEEEEETTEEEEEEE CS
                           DUF4179  59 .............nksaednGitvtvne 73 
                                                     k+ e +G+t+t++ 
  gi|320100607|ref|YP_004176199.1|  90 svgvtlnitlpysIKTGETKGLTITISS 117
                                       7777777777777777799999999986 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  17.2    0.0018       4.7      17     160 ..       8     137 ..       6     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSE....EEEEEE--TTS--EEGGG-EE CS
                    Arch_flagellin  17 VAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtine....itiyvklnaGsspidlnktti 89 
                                       V A+++ v+++ a  ++ +   tg  ++  ++++l+i+ ++ ++ tn+t+n+    it++vk n G +++ +++  i
  gi|320100607|ref|YP_004176199.1|   8 VIATVIIVAVTIAIAIAVALWMTGLVGSFTATENLQIITAYAEQFTNTTTNTtywtITLQVK-NVGTTDVTIDNIFI 83 
                                       5688889999999999999999********************88888888888899******.*****999888777 PP

                                       EEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--E CS
                    Arch_flagellin  90 svtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGast 160
                                       +    g                + +  +t     ++ ge+  l+++ +  +g+  g+ v+v++ + +G+++
  gi|320100607|ref|YP_004176199.1|  84 NGKPYG--------------SVGVTLNITLP-YSIKTGETKGLTITIS--SGFSSGQMVEVKLHTASGKEY 137
                                       755555..............22222222222.3477777777777774..777777777777777777665 PP

>> Pap_E4  E4 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.2      0.07   1.8e+02      64      92 ..      50      78 ..      35      79 .. 0.75
   2 ?    6.2   0.1    0.0078        20      70      95 ..     105     130 ..      98     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.07
                            Pap_E4 64 eeespwtvtttgssvtltaqtkdGttVtv 92
                                      e+ ++ t++tt  ++tl+++    t Vt+
  gi|320100607|ref|YP_004176199.1| 50 EQFTNTTTNTTYWTITLQVKNVGTTDVTI 78
                                      467788899999999***99888888886 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0078
                            Pap_E4  70 tvtttgssvtltaqtkdGttVtvtlh 95 
                                       t +t+g ++t++   ++G+ V+v+lh
  gi|320100607|ref|YP_004176199.1| 105 TGETKGLTITISSGFSSGQMVEVKLH 130
                                       5679999******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1329  (0.0741257); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1008.69
//
Query:       gi|320100608|ref|YP_004176200.1|  [L=425]
Description: transposase, IS605 OrfB family [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-22   78.2   0.6    6.5e-22   77.2   0.6    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0046   17.6   1.8        0.2   12.3   1.7    2.7  2  DUF2285         Uncharacterized conserved protein (DUF2285)
     0.0085   16.3   0.9      0.013   15.7   0.3    1.7  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.013   15.2   3.5          2    8.3   0.0    3.0  3  zinc_ribbon_2   zinc-ribbon domain
      0.017   15.1   3.1        2.7    8.1   0.1    3.3  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.021   14.8   3.7      0.021   14.8   3.7    2.2  2  DZR             Double zinc ribbon
      0.035   14.2   1.3      0.035   14.2   1.3    2.1  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.058   12.9   3.2       0.18   11.3   0.6    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.16   12.1   0.5       0.39   10.9   0.5    1.6  1  Ribosomal_L37e  Ribosomal protein L37e
       0.22   10.3   0.6       0.33    9.7   0.6    1.2  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.92    9.7   5.8        2.6    8.2   0.3    2.7  3  Zn-ribbon_8     Zinc ribbon domain
       0.92    9.8   4.9       0.78   10.1   1.0    2.4  2  zinc_ribbon_9   zinc-ribbon
          1    9.1   4.2        1.1    9.0   2.5    2.0  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        1.6    8.2   9.3        1.6    8.2   0.2    2.8  3  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.6     5e-25   6.5e-22       1      69 []     300     367 ..     300     367 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 5e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +r+++ +l ++++++G++ + vnp  TS+tC++Cgs++ e +  r++kCp+CgfeadrD++A++Ni ++
  gi|320100608|ref|YP_004176200.1| 300 YRRFEYWLDWQCEKHGVPCIAVNPKDTSSTCPRCGSRLIE-NGYRRLKCPSCGFEADRDTVAVLNIRRK 367
                                       799*************************************.*************************985 PP

>> DUF2285  Uncharacterized conserved protein (DUF2285)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   1.7   0.00015       0.2      55      99 ..     205     251 ..     199     252 .. 0.80
   2 ?    2.3   0.0      0.21   2.7e+02      92     105 ..     332     345 ..     324     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                           DUF2285  55 lagaslreiAevl...fgaervaaedW.kdsalrsrvrrlvrrgralmr 99 
                                       ++   +re Ae l   + +  +  + W ++ ++r+rvrr  +++r+ ++
  gi|320100608|ref|YP_004176200.1| 205 EKAVRYRELAERLqrkYSNGSY--RAWlRRRGIRDRVRRFHEKARSIIE 251
                                       55678********744444443..47******************99875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.21
                           DUF2285  92 rrgralmrGGYrkL 105
                                       r g +l++ GYr+L
  gi|320100608|ref|YP_004176200.1| 332 RCGSRLIENGYRRL 345
                                       6699*********8 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3     1e-05     0.013      48     104 ..     205     266 ..     168     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                        OrfB_IS605  48 sdykylakeiaelqsklkkskn.....ykkasrklarlhrkrsrrrkhllhklathliktlk 104
                                       ++  ++++   +lq+k++         ++  + +++r h+k + ++ + ++k++++++    
  gi|320100608|ref|YP_004176200.1| 205 EKAVRYRELAERLQRKYSNGSYrawlrRRGIRDRVRRFHEKARSIIEDWARKTSHEIVVVAR 266
                                       5667888888899999877765788889999**************************96555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0015         2      10      23 .]     324     337 ..     320     339 .. 0.82
   2 ?    5.9   0.1    0.0083        11       1       8 [.     346     353 ..     346     359 .. 0.79
   3 ?   -0.4   0.1      0.81     1e+03      18      22 ..     391     395 ..     390     397 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                     zinc_ribbon_2  10 qdnakFCpyCGtpl 23 
                                       +d++  Cp+CG+ l
  gi|320100608|ref|YP_004176200.1| 324 KDTSSTCPRCGSRL 337
                                       488999****9865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0083
                     zinc_ribbon_2   1 fCpnCGae 8  
                                       +Cp+CG e
  gi|320100608|ref|YP_004176200.1| 346 KCPSCGFE 353
                                       79999976 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.81
                     zinc_ribbon_2  18 yCGtp 22 
                                       +CG+p
  gi|320100608|ref|YP_004176200.1| 391 KCGEP 395
                                       56665 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0021       2.7       1      10 [.     329     338 ..     329     341 .. 0.87
   2 ?    5.5   0.1     0.014        18       1      11 [.     346     356 ..     346     361 .. 0.82
   3 ?   -0.5   0.0         1   1.3e+03       5      14 ..     392     401 ..     391     409 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                    DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                       +CP CGs ++
  gi|320100608|ref|YP_004176200.1| 329 TCPRCGSRLI 338
                                       7******997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.014
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP+CG ++ R
  gi|320100608|ref|YP_004176200.1| 346 KCPSCGFEADR 356
                                       6*****87755 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1
                    DNA_ligase_ZBD   5 CGsavvReeg 14 
                                       CG +v R+ g
  gi|320100608|ref|YP_004176200.1| 392 CGEPVNRPKG 401
                                       *****99865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.7   1.6e-05     0.021       4      41 ..     318     357 ..     310     359 .. 0.77
   2 ?    0.6   0.5      0.45   5.8e+02      17      34 ..     391     423 ..     389     425 .] 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                               DZR   4 Cgeelppdar.fCseCgtklkavaa.edrCpsCgekvdpe 41 
                                       C + +p+d   +C++Cg++l +      +CpsCg ++d +
  gi|320100608|ref|YP_004176200.1| 318 CIAVNPKDTSsTCPRCGSRLIENGYrRLKCPSCGFEADRD 357
                                       55556655444*********96655899******988765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.45
                               DZR  17 eCgtklkavaa...............edrCpsC 34 
                                       +Cg+++++++                 ++C+ C
  gi|320100608|ref|YP_004176200.1| 391 KCGEPVNRPKGnpllgrgggqglvkpVEACVVC 423
                                       799999876668889999999999888889888 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.3   2.8e-05     0.035      15      40 .]     327     351 ..     326     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                     Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCvaCd 40 
                                       ++tCp+Cg+ L ++ +  ++ C++C+
  gi|320100608|ref|YP_004176200.1| 327 SSTCPRCGSRLIEN-GYRRLKCPSCG 351
                                       789**********9.56899*****6 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00014      0.18       2      27 ..     310     335 ..     309     342 .. 0.89
   2 ?    1.5   0.1      0.17   2.2e+02       2       7 ..     346     351 ..     345     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                       +C ++g + + ++p+ +  +C++CG+
  gi|320100608|ref|YP_004176200.1| 310 QCEKHGVPCIAVNPKDTSSTCPRCGS 335
                                       699999999***************98 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                       EETTTT CS
                      TF_Zn_Ribbon   2 kCPnCg 7  
                                       kCP Cg
  gi|320100608|ref|YP_004176200.1| 346 KCPSCG 351
                                       788888 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5    0.0003      0.39      15      43 ..     326     356 ..     315     358 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                    Ribosomal_L37e  15 tHilCrrCgkrsyh..vqkktCascGypsak 43 
                                       t  +C rCg+r     +++ +C scG+ + +
  gi|320100608|ref|YP_004176200.1| 326 TSSTCPRCGSRLIEngYRRLKCPSCGFEADR 356
                                       6678******98753389999******8876 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   0.00026      0.33     493     529 ..     311     354 ..     302     366 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00026
                                       HHHTT--EEEEE--..EEEETT.--....EESS.SB-TTT--BE CS
                              NRDD 493 akktgigYfsinpk..idvCnecgy....kgei.ekCpkCgsee 529
                                       ++k+g++ +++npk  +++C++cg     +g++  kCp+Cg e 
  gi|320100608|ref|YP_004176200.1| 311 CEKHGVPCIAVNPKdtSSTCPRCGSrlieNGYRrLKCPSCGFEA 354
                                       6789999999*9953389*******65544444977*****554 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3     0.002       2.6       8      35 ..     311     336 ..     303     339 .. 0.65
   2 ?    3.7   0.1     0.052        67      28      38 ..     346     356 ..     342     358 .. 0.69
   3 ?   -3.5   0.1       9.7   1.2e+04      31      38 ..     391     398 ..     390     398 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.002
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgse 35 
                                       Ce++g    ++ +  ++   +CP+Cgs+
  gi|320100608|ref|YP_004176200.1| 311 CEKHGVPCIAVNP--KDTSSTCPRCGSR 336
                                       6665644444443..445678*****95 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.052
                       Zn-ribbon_8  28 aCPeCgsevrr 38 
                                       +CP+Cg e+ r
  gi|320100608|ref|YP_004176200.1| 346 KCPSCGFEADR 356
                                       48888766555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.7
                       Zn-ribbon_8  31 eCgsevrr 38 
                                       +Cg++v r
  gi|320100608|ref|YP_004176200.1| 391 KCGEPVNR 398
                                       57777665 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.0   0.00061      0.78      14      33 ..     321     339 ..     310     340 .. 0.73
   2 ?    0.4   0.2      0.66   8.4e+02      22      28 ..     346     351 ..     343     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00061
                     zinc_ribbon_9  14 vspdedsdvlCPhCgggFVE 33 
                                       v p+++s  +CP+Cg+  +E
  gi|320100608|ref|YP_004176200.1| 321 VNPKDTSS-TCPRCGSRLIE 339
                                       55554444.6******9887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.66
                     zinc_ribbon_9  22 vlCPhCg 28 
                                       + CP+Cg
  gi|320100608|ref|YP_004176200.1| 346 K-CPSCG 351
                                       4.****7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.5   0.00086       1.1       6      28 ..     330     351 ..     325     353 .. 0.88
   2 ?   -3.7   0.0       7.7   9.8e+03       8      12 ..     391     395 ..     391     397 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00086
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCg 28 
                                       C+rCG++ + + g + + Cp+Cg
  gi|320100608|ref|YP_004176200.1| 330 CPRCGSRLIEN-GYRRLKCPSCG 351
                                       *******8755.89999*****8 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.7
                     zf-NADH-PPase   8 rCGap 12 
                                       +CG p
  gi|320100608|ref|YP_004176200.1| 391 KCGEP 395
                                       69988 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   0.2    0.0013       1.6      12      26 .]     323     337 ..     318     337 .. 0.79
   2 ?    8.0   4.6    0.0015       1.9       4      24 ..     329     352 ..     327     354 .. 0.84
   3 ?   -1.8   0.1       1.8   2.3e+03       7      11 ..     391     395 ..     390     397 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                       zf-ribbon_3  12 lssddnvCpyCGtkl 26 
                                       +++  ++Cp CG++l
  gi|320100608|ref|YP_004176200.1| 323 PKDTSSTCPRCGSRL 337
                                       588889999999886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0015
                       zf-ribbon_3   4 rCPnCGa.plssddn..vCpyCGt 24 
                                       +CP+CG+ +++ + +  +Cp+CG 
  gi|320100608|ref|YP_004176200.1| 329 TCPRCGSrLIENGYRrlKCPSCGF 352
                                       6*********99854449****96 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.8
                       zf-ribbon_3   7 nCGap 11 
                                       +CG+p
  gi|320100608|ref|YP_004176200.1| 391 KCGEP 395
                                       78886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2932.56
//
Query:       gi|320100609|ref|YP_004176201.1|  [L=200]
Description: Pyruvate/ketoisovalerate oxidoreductase, catalytic domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-33  114.1   0.4    8.8e-33  113.8   0.4    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 !  113.8   0.4   4.9e-37   8.8e-33       1     175 [.      12     187 ..      12     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 4.9e-37
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG +t+++ila aa+++G+ v + ++ g+++r g+++s+vri+ ++++p  ++gead lv+l+  ++ ++ ++lk
  gi|320100609|ref|YP_004176201.1|  12 GGQGGLTLSRILAGAAVKTGLSVRTGETLGMAQRYGSVVSYVRIGVSVHSPVFSRGEADALVGLELVEAVRNTAYLK 88 
                                       9*****************************************************************8888******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH...T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl...gvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleal 150
                                       p g++++  e ++p+     +  +++    +   ++  + v+a++ia e+g+ +raaN+vmlGal a l+ lp  ++
  gi|320100609|ref|YP_004176201.1|  89 PRGVLLVADEYKPPSLASITRRTQDRSIYMEqvvKAGGVIVPARRIASEAGN-PRAANIVMLGALNASLKlLPHSTV 164
                                       *********999999888888776666555599*999************877.************999999****** PP

                                       HHHHHCCS-CH.HHHHHHHHHHHHH CS
                               POR 151 eeaikkrfpkkkeviekNlkafrag 175
                                       eeai +++p+  e+    + a  ag
  gi|320100609|ref|YP_004176201.1| 165 EEAILEAIPG--EAGSTSITAYHAG 187
                                       *********8..5666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.46
# Mc/sec: 1299.07
//
Query:       gi|320100610|ref|YP_004176202.1|  [L=625]
Description: thiamine pyrophosphate TPP-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   86.6   0.0    2.7e-24   85.7   0.0    1.5  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    5.6e-17   62.2   0.0    8.1e-17   61.7   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    5.5e-10   38.6  12.1    4.3e-05   23.1   3.7    2.6  2  Fer4             4Fe-4S binding domain
    3.5e-06   26.7   2.5    1.5e-05   24.7   0.4    2.4  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
    9.2e-06   26.2   9.0      0.013   16.1   1.6    2.5  2  Fer4_7           4Fe-4S dicluster domain
    1.7e-05   24.7  17.9    0.00043   20.2   1.3    3.0  3  Fer4_6           4Fe-4S binding domain
    0.00017   21.6   9.4    0.00043   20.3   9.4    1.7  1  Fer4_10          4Fe-4S dicluster domain
    0.00027   21.0   7.6    0.00062   19.8   7.6    1.6  1  Fer4_21          4Fe-4S dicluster domain
     0.0008   19.5   9.8     0.0017   18.4   9.8    1.6  1  Fer4_9           4Fe-4S dicluster domain
     0.0012   18.9   4.5     0.0012   18.9   4.5    2.8  2  Fer4_2           4Fe-4S binding domain
     0.0034   17.8  12.5       0.14   12.8   1.8    2.6  2  Fer4_4           4Fe-4S binding domain
     0.0065   16.4   0.0      0.023   14.6   0.0    1.9  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.16   11.1   0.0       0.26   10.5   0.0    1.2  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
       0.24   12.2  10.1       0.33   11.7   0.7    2.6  2  Fer4_15          4Fe-4S single cluster domain
       0.83   10.6  11.5       0.86   10.6   1.6    2.4  4  Fer4_16          4Fe-4S double cluster binding domain
        2.6    9.2  14.4        5.7    8.1   4.1    2.8  2  Fer4_3           4Fe-4S binding domain
          3    8.5  13.3          1   10.0   2.6    2.5  2  Fer4_17          4Fe-4S dicluster domain
        3.6    8.1  13.3    3.9e+03   -1.6  13.3    2.5  1  Fer4_8           4Fe-4S dicluster domain
        8.3    7.3   9.0         20    6.1   1.6    2.4  2  Fer4_22          4Fe-4S dicluster domain
        9.4    6.9  11.3       0.85   10.2   1.1    2.5  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 !   85.7   0.0     3e-27   2.7e-24       1     152 [.     406     548 ..     406     549 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 3e-27
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc+ l      +v++p   +   +  +mG ++++A+G+ l   + ++va++GD++f++  ++ l+ av +++ ++
  gi|320100610|ref|YP_004176202.1| 406 DIGCYAL------SVNPPLGSIW--TEHSMGASISMAMGLRLSGFKGPIVAVIGDSTFFHAgIPSLIEAVHKKVSLL 474
                                       89****9......99**999999..899**************54456****************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                       v++l+N + +mtg+q++p+ +++++g a    ++++++ +++a+G++ +a+v+++ ++e  ea++  le +g+ +++
  gi|320100610|ref|YP_004176202.1| 475 VLILDNDVVAMTGHQSTPAWSRTETGRA---ARSISIVDVVKAIGVDkVAVVDPYRLDEAVEAIAGLLEGEGVRVLV 548
                                       ***********************99988...9************************************999998875 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 !   61.7   0.0   9.1e-20   8.1e-17       2     176 ..      26     194 ..      25     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 9.1e-20
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++agv v+++YP TPsse++e+l+++    +    +   + +E  a++ ++GAa+aGara+ +  ++Gl  + + 
  gi|320100610|ref|YP_004176202.1|  26 GAVEAGVYVATGYPGTPSSEVVETLQRYGGGLG---FYAEWAVNERVAFEIALGAAIAGARALATMKAPGLNVALDP 99 
                                       8999***********************985555...4888899********************************** PP

                                       HHHHH..HTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEE CS
                             POR_N  79 lglaa..geelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlf 153
                                       ++ aa  g e  +v+ v+   +p t   ++t+q     a   +l ++++++ qea d +++Af ++e++++Pvi+ +
  gi|320100610|ref|YP_004176202.1| 100 VVSAAysGVEGGLVVLVADDPGPHT---TQTEQDSRWLAKLAKLPAISPSSPQEAKDYTVAAFDISEELKLPVILRT 173
                                       *999833668899**********99...99**9999**************************************998 PP

                                       EHHHH.HEEEEEEC-SGG.GS-- CS
                             POR_N 154 Dgfllshevekvelpdeedelkl 176
                                          +  h+v +v l  +  e k 
  gi|320100610|ref|YP_004176202.1| 174 TTRVN-HAVGEVVLGGVR-EPKG 194
                                       77776.999988877666.4444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.3   4.4e-07   0.00039       1      17 [.     567     583 ..     567     583 .. 0.90
   2 !   23.1   3.7   4.8e-08   4.3e-05       2      24 .]     597     619 ..     596     619 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.4e-07
                                       EEEETTTSSS-THHHHH CS
                              Fer4   1 vvideekCigCGaCvev 17 
                                       +++d+ kC+gCGaC+ +
  gi|320100610|ref|YP_004176202.1| 567 YTVDPGKCTGCGACIAA 583
                                       589***********975 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 4.8e-08
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       vi  e+C+gCG+C+  C ++AI+
  gi|320100610|ref|YP_004176202.1| 597 VIAVEDCTGCGLCARYCGFNAIK 619
                                       56679*****************6 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.4   1.7e-08   1.5e-05       3     157 ..      19     171 ..      17     179 .. 0.78
   2 ?    1.2   0.1      0.28   2.5e+02      52     105 ..     431     485 ..     421     540 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-08
                                       HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE..-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq.girvvl..arhEqgaafaAdgyaratgkpgvvlvtsgpGa 76 
                                       + ea++r   ++gv ++ g+pG+ + ++++ l++   g+ ++   a++E++a  +A g a a     ++++   pG+
  gi|320100610|ref|YP_004176202.1|  19 GNEAIARGAVEAGVYVATGYPGTPSSEVVETLQRYGgGLGFYAewAVNERVAFEIALGAAIAGA--RALATMKAPGL 93 
                                       67999********************************666665449*************99964..45555568*** PP

                                       HHCHHHHHHHHHHT--..EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSE.EEE-SSGGGHHHHHHHHHHHHHSS CS
                      TPP_enzyme_N  77 tnaltalaeAkvdriP..llvlsgdrptslrgqgvlqqeldqlalfrpvtky.aervtspeelpealrrAirtalsg 150
                                         al  +++A+++++   l+vl++d p  ++     q + + +  +++++k  a  ++sp+e++ +   A++++ ++
  gi|320100610|ref|YP_004176202.1|  94 NVALDPVVSAAYSGVEggLVVLVADDPGPHTT----Q-TEQDSRWLAKLAKLpAISPSSPQEAKDYTVAAFDIS-EE 164
                                       *************9965599999999988877....4.332333333344433677777777777777777777.66 PP

                                       S--EEEE CS
                      TPP_enzyme_N 151 rpgPvyl 157
                                        + Pv l
  gi|320100610|ref|YP_004176202.1| 165 LKLPVIL 171
                                       6666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHH.TS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCH CS
                      TPP_enzyme_N  52 afaAdgyarat.gkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslr 105
                                       + +A g+  +  + p v++    + +  ++++l+eA + ++ llvl  d+++   
  gi|320100610|ref|YP_004176202.1| 431 ISMAMGLRLSGfKGPIVAVIGDSTFFHAGIPSLIEAVHKKVSLLVLILDNDVVAM 485
                                       5677777665543333333333445667899999999999999999988876544 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.6   1.4e-05     0.013      19      49 ..     555     587 ..     547     589 .. 0.83
   2 !   13.7   1.0   8.1e-05     0.072       2      17 ..     603     618 ..     593     623 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                            Fer4_7  19 ldeeenekgtekveidpekClgCgaCva..vCP 49 
                                       l+e+ ++++t+ +++dp kC+gCgaC+a   CP
  gi|320100610|ref|YP_004176202.1| 555 LQERRRARRTAPYTVDPGKCTGCGACIAatGCP 587
                                       5677788899999*************8733577 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.1e-05
                            Fer4_7   2 CigCgaCvaaCpvkai 17 
                                       C+gCg C+++C  +ai
  gi|320100610|ref|YP_004176202.1| 603 CTGCGLCARYCGFNAI 618
                                       7777777777777776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.5       5.6     5e+03       6      12 ..     372     378 ..     372     378 .. 0.86
   2 !   20.2   1.3   4.8e-07   0.00043       3      21 ..     568     588 ..     568     592 .. 0.93
   3 !   14.7   2.7   2.7e-05     0.024       3      24 .]     597     618 ..     595     618 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.6
                            Fer4_6   6 pdkCigC 12 
                                       p +C gC
  gi|320100610|ref|YP_004176202.1| 372 PPLCPGC 378
                                       579**** PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.8e-07
                            Fer4_6   3 eidpdkCigCgdCvrv..CPe 21 
                                       ++dp kC+gCg+C+++  CP+
  gi|320100610|ref|YP_004176202.1| 568 TVDPGKCTGCGACIAAtgCPA 588
                                       69***********99999*97 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.7e-05
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       +i  + C+gCg C+r C ++ai
  gi|320100610|ref|YP_004176202.1| 597 VIAVEDCTGCGLCARYCGFNAI 618
                                       556677**************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 !   20.3   9.4   4.8e-07   0.00043       4      55 ..     569     613 ..     567     614 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.8e-07
                           Fer4_10   4 idddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       +d+ +C++Cg+C +a  CPa         +   e++  ++ve+Ctgcg C++ C
  gi|320100610|ref|YP_004176202.1| 569 VDPGKCTGCGACIAAtgCPA---------IFLSEGKAVIAVEDCTGCGLCARYC 613
                                       6899**********888***.........77777777889***********999 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   7.6   6.9e-07   0.00062       3      57 ..     569     618 ..     567     619 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.9e-07
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +d+ kC gCg C+ a    +  ai +++ +   +  ++C+GC lC+  C   ++i
  gi|320100610|ref|YP_004176202.1| 569 VDPGKCTGCGACIAAT---GCPAIFLSEGKA-VIAVEDCTGCGLCARYCGF-NAI 618
                                       7999********9984...467997765444.566799***********75.555 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   9.8   1.9e-06    0.0017       1      51 []     573     618 ..     573     618 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                            Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgCgaC++a  Cpa   +e +a   ++        C+gCg C+  C  +ai
  gi|320100610|ref|YP_004176202.1| 573 KCTGCGACIAAtgCPAIFLSEGKAVIAVED-------CTGCGLCARYCGFNAI 618
                                       7*******88777******99999999885.......***********87765 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   4.5   1.3e-06    0.0012       1      22 []     565     588 ..     565     588 .. 0.88
   2 !    9.4   3.4    0.0014       1.2       7      20 ..     600     613 ..     594     613 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                            Fer4_2   1 apvvvdtdrCigCgaCvsa..CPa 22 
                                       ap+ vd+ +C+gCgaC+ a  CPa
  gi|320100610|ref|YP_004176202.1| 565 APYTVDPGKCTGCGACIAAtgCPA 588
                                       5789************96667**8 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                            Fer4_2   7 tdrCigCgaCvsaC 20 
                                        + C+gCg C   C
  gi|320100610|ref|YP_004176202.1| 600 VEDCTGCGLCARYC 613
                                       455********999 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   1.8   0.00015      0.14       3      15 ..     573     587 ..     571     593 .. 0.90
   2 !    9.5   3.4    0.0016       1.5       3      15 ..     602     614 ..     601     616 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                            Fer4_4   3 rCigCgsCvaa..CP 15 
                                       +C+gCg+C+aa  CP
  gi|320100610|ref|YP_004176202.1| 573 KCTGCGACIAAtgCP 587
                                       8**********9999 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                        C+gCg C ++C 
  gi|320100610|ref|YP_004176202.1| 602 DCTGCGLCARYCG 614
                                       5***********5 PP

>> Transketolase_C  Transketolase, 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     0.023       6      69 ..     239     301 ..     235     315 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                                       EETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEE CS
                   Transketolase_C   6 lregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvvee 69 
                                       +  g d ++v+ G+  + ++eA+e L   g ++++v l  + pl    i+ s++  +r++vvee
  gi|320100610|ref|YP_004176202.1| 239 VEGGGDTCVVTEGAAYNYVVEAVESLGLTG-DVRIVKLGLIHPLPSGFIAGSIEGCRRILVVEE 301
                                       55699*********************9885.9*******************************9 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 ?   10.5   0.0   0.00029      0.26     113     174 ..     426     483 ..     417     498 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                    DXP_synthase_N 113 s.stsisaalGlavardlkgekkkvvaviGDgal.tgGmafealnnigelkkkllvilNdNems 174
                                       s ++sis+a+Gl    +l+g k  +vaviGD+++  +G+   +l ++ ++k +llv++ dN+ +
  gi|320100610|ref|YP_004176202.1| 426 SmGASISMAMGL----RLSGFKGPIVAVIGDSTFfHAGI--PSLIEAVHKKVSLLVLILDNDVV 483
                                       323455555555....67788899*******99626776..589999999999***99999876 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00036      0.33       2      34 ..     568     600 ..     568     602 .. 0.78
   2 ?    4.7   3.3     0.057        51       6      18 ..     601     613 ..     597     623 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                           Fer4_15   2 vvDrdaCigcglCvaea..pevfeldedglasvll 34 
                                       +vD  +C+gcg+C+a+   p +f  +  g+a++ +
  gi|320100610|ref|YP_004176202.1| 568 TVDPGKCTGCGACIAATgcPAIFLSE--GKAVIAV 600
                                       68999********9986558888776..7876665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.057
                           Fer4_15   6 daCigcglCvaea 18 
                                       + C+gcglC++ +
  gi|320100610|ref|YP_004176202.1| 601 EDCTGCGLCARYC 613
                                       68********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 ?    2.2   3.8       0.4   3.6e+02       1      11 [.     573     583 ..     553     589 .. 0.63
   2 ?    1.9   5.5       0.5   4.5e+02       1      20 [.     573     594 ..     573     603 .. 0.74
   3 ?    9.1   1.5    0.0028       2.6      52      67 .]     601     616 ..     592     616 .. 0.84
   4 ?   10.6   1.6   0.00096      0.86       2      19 ..     603     620 ..     602     624 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.4
                           Fer4_16   1 rCgtCgkCaev 11 
                                       +C++Cg+C+ +
  gi|320100610|ref|YP_004176202.1| 573 KCTGCGACIAA 583
                                       35555555543 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.5
                           Fer4_16   1 rCgtCgkCaev..CPtnaikek 20 
                                       +C++Cg+C+ +  CP+  ++e 
  gi|320100610|ref|YP_004176202.1| 573 KCTGCGACIAAtgCPAIFLSEG 594
                                       5*******98767998888777 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0028
                           Fer4_16  52 eaitgCdiCqdvCPan 67 
                                       e++tgC+ C++ C +n
  gi|320100610|ref|YP_004176202.1| 601 EDCTGCGLCARYCGFN 616
                                       7899*********998 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00096
                           Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                       C++Cg Ca  C  naik 
  gi|320100610|ref|YP_004176202.1| 603 CTGCGLCARYCGFNAIKP 620
                                       999999999999999986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.6     0.032        29       1       9 [.     574     582 ..     574     583 .. 0.89
   2 ?    8.1   4.1    0.0064       5.7       1      15 []     603     617 ..     603     617 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.032
                            Fer4_3   1 CtgCgaCve 9  
                                       CtgCgaC  
  gi|320100610|ref|YP_004176202.1| 574 CTGCGACIA 582
                                       *******86 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0064
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       CtgCg+C + C  +A
  gi|320100610|ref|YP_004176202.1| 603 CTGCGLCARYCGFNA 617
                                       ***********6665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.0      0.13   1.1e+02       1      13 [.     573     587 ..     556     591 .. 0.75
   2 ?   10.0   2.6    0.0011         1      42      56 ..     599     613 ..     591     617 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                           Fer4_17   1 rCiqCgyClp..eCp 13 
                                       +C++Cg+C++   Cp
  gi|320100610|ref|YP_004176202.1| 573 KCTGCGACIAatGCP 587
                                       466777766533444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                           Fer4_17  42 kaslCieCgeCerkC 56 
                                       ++++C++Cg+C+r+C
  gi|320100610|ref|YP_004176202.1| 599 AVEDCTGCGLCARYC 613
                                       6799*********** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6  13.3       4.4   3.9e+03       4      61 ..     573     613 ..     570     617 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.4
                            Fer4_8   4 kCieCgaCqsa..CpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevC 61 
                                       kC++CgaC +a  Cp++  +       +g+a              a++ Ct+cg C++ C
  gi|320100610|ref|YP_004176202.1| 573 KCTGCGACIAAtgCPAIFLS-------EGKAVI------------AVEDCTGCGLCARYC 613
                                       57777777644446644332.......233222............256677777777777 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.0     0.045        40      77      91 ..     569     583 ..     554     589 .. 0.76
   2 ?    6.1   1.6     0.023        20      78      93 ..     599     614 ..     591     617 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.045
                           Fer4_22  77 fgesgCvGCgRCiea 91 
                                       ++  +C+GCg Ci+a
  gi|320100610|ref|YP_004176202.1| 569 VDPGKCTGCGACIAA 583
                                       46678*******875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.023
                           Fer4_22  78 gesgCvGCgRCieacp 93 
                                         + C+GCg C + c 
  gi|320100610|ref|YP_004176202.1| 599 AVEDCTGCGLCARYCG 614
                                       5678*********995 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 ?   10.2   1.1   0.00095      0.85       1      23 [.     569     593 ..     569     602 .. 0.82
   2 ?    1.0   3.5      0.72   6.4e+02       4      16 ..     601     613 ..     598     614 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00095
                           Fer4_13   1 VDrdtCiacgaCvel..aPdvFeed 23 
                                       VD  +C++cgaC ++  +P +F  +
  gi|320100610|ref|YP_004176202.1| 569 VDPGKCTGCGACIAAtgCPAIFLSE 593
                                       8999********9987799999665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.72
                           Fer4_13   4 dtCiacgaCvela 16 
                                       + C++cg+C+  +
  gi|320100610|ref|YP_004176202.1| 601 EDCTGCGLCARYC 613
                                       57*******9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4396.26
//
Query:       gi|320100611|ref|YP_004176203.1|  [L=234]
Description: acetyl-CoA synthetase (ADP-forming) subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-74  250.4   0.1    1.6e-74  250.1   0.1    1.0  1  ATP-grasp_5  ATP-grasp domain
    0.00034   20.2   0.0    0.00043   19.9   0.0    1.3  1  ATP-grasp_2  ATP-grasp domain
  ------ inclusion threshold ------
      0.064   12.8   0.0       0.12   11.9   0.0    1.3  1  ATP-grasp    ATP-grasp 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 !  250.1   0.1   2.7e-78   1.6e-74       6     220 ..      16     229 ..      12     231 .. 0.99

  Alignments for each domain:
  == domain 1  score: 250.1 bits;  conditional E-value: 2.7e-78
                       ATP-grasp_5   6 grtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaae 82 
                                       gr+ L  + + +lle ygip+++  +as+++ea+++ae++g+pvv+Kivspdi+hK+dvgGv+l+l++ +ev++aa+
  gi|320100611|ref|YP_004176203.1|  16 GRGKLPDHLVFQLLESYGIPLAPYGFASTPMEAAAVAEKLGFPVVVKIVSPDIVHKSDVGGVALGLSSGREVAEAAS 92 
                                       789999*********************************************************************** PP

                       ATP-grasp_5  83 eilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlarelie 159
                                       ++le+v+ek+ +ari+g+lVq+m + +g+E+ivg  +D vFG v+++GlGG+ +ev++dv+++++p++ ++a e++ 
  gi|320100611|ref|YP_004176203.1|  93 RMLEAVSEKARGARIQGFLVQKMMP-KGVEVIVGGLNDRVFGGVVMLGLGGVFTEVFRDVSFRVAPVSLEDALEMMG 168
                                       ***********************99.9************************************************** PP

                       ATP-grasp_5 160 rtkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDari 220
                                       ++kas++ +g+rg +++d aal++++v+ s+L+ + p+++++d+nP++++ +++v++Dari
  gi|320100611|ref|YP_004176203.1| 169 ELKASRVFEGYRGMPPVDKAALADIVVKASRLIAENPWVDSMDLNPVIAYTDKAVVVDARI 229
                                       ************************************************************9 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   7.3e-08   0.00043       5     123 ..      23     138 ..      19     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.3e-08
                                       HHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE.--SSSTCCCTTCEEE.ESSHHHHHHHHHCCTTSE CS
                       ATP-grasp_2   5 yqakeilakygvkvpegevaesaeeaeeaakklgekelvvKa.QvlaGGRGKagGvkl.vkskeeakeaakellgke 79 
                                       +   ++l++yg++ +    a+++ ea+++a+klg  + vvK     +  +   gGv l  +s  e++eaa+++l + 
  gi|320100611|ref|YP_004176203.1|  23 HLVFQLLESYGIPLAPYGFASTPMEAAAVAEKLGFPV-VVKIvSPDIVHKSDVGGVALgLSSGREVAEAASRMLEAV 98 
                                       556699*****************************99.888513345556666***98457789**********987 PP

                                       EE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEE CS
                       ATP-grasp_2  80 lvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvvi 123
                                             +++G +++  lv+++++   E+ ++ + Dr   +vv++
  gi|320100611|ref|YP_004176203.1|  99 SE----KARGARIQGFLVQKMMPKGVEVIVGGLNDRVFGGVVML 138
                                       66....789************************99998887765 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.12       2      34 ..      30      62 ..      29      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                                      HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEE CS
                         ATP-grasp  2 eklglpvprflaveskeeleeaaeelglpvvvK 34
                                      e+ g+p++++ ++++  e+ ++ae+lg+pvvvK
  gi|320100611|ref|YP_004176203.1| 30 ESYGIPLAPYGFASTPMEAAAVAEKLGFPVVVK 62
                                      6789***************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1679.39
//
Query:       gi|320100612|ref|YP_004176204.1|  [L=320]
Description: PP-loop domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   63.7   0.0    4.8e-17   62.3   0.0    1.6  1  ATP_bind_3     PP-loop family
    0.00034   20.2   0.1       0.82    9.1   0.1    2.2  2  QueC           Queuosine biosynthesis protein QueC
     0.0027   16.6   0.0     0.0045   15.8   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase
     0.0039   16.7   2.6     0.0039   16.7   2.6    3.0  3  RecR           RecR protein
  ------ inclusion threshold ------
      0.023   15.0   1.8       0.79   10.1   0.1    3.2  3  C1_2           C1 domain
      0.037   13.7   0.1      0.051   13.2   0.1    1.1  1  Asn_synthase   Asparagine synthase
       0.13   11.8   0.1       0.55    9.8   0.1    1.9  1  ThiI           Thiamine biosynthesis protein (ThiI)
       0.16   11.1   0.1       0.26   10.4   0.1    1.3  1  NAD_synthase   NAD synthase
       0.76    9.2   2.5        6.6    6.2   0.0    2.7  3  Vps36-NZF-N    Vacuolar protein sorting 36 NZF-N zinc-finger 


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 !   62.3   0.0   2.4e-20   4.8e-17       2     165 ..      51     224 ..      50     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.4e-20
                                       EEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv......... 68 
                                       v+vAvSgG+DSm Ll ++ak + ++g+ k+v +hv+ g+   s+  +++v+e+c +l++++++ +++          
  gi|320100612|ref|YP_004176204.1|  51 VVVAVSGGVDSMSLLAITAKRRVEMGVeKIVGVHVNLGIEGYSDLAEAAVREYCGSLGVECTVLRLRDilgvglpel 127
                                       89*******************99999989999**********************************98787766665 PP

                                       .HHCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT.CCEE-C CS
                        ATP_bind_3  69 .akkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias.irlvRP 143
                                        ++            +RY +++ ++ + g++ + ++hh dD a  +l  l  g   ++lag+k+a +  +      P
  gi|320100612|ref|YP_004176204.1| 128 aSRAGRPPCSVCGLVKRY-LITAYAVATGASAVFTGHHLDDAARYMLKDLYVGDF-KSLAGLKPAVREPGlPVKAKP 202
                                       333223334444445677.6777778889**********************9988.59****99887777355589* PP

                                       CCT--HHHHHHHHHHTT---B- CS
                        ATP_bind_3 144 lLkvskeeleeylkekkikwve 165
                                       l+++ k+++e+y++  ++++ e
  gi|320100612|ref|YP_004176204.1| 203 LITLGKKDIEAYAELAGVPHLE 224
                                       *************999988765 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00041      0.82       2      36 ..      51      90 ..      50     124 .. 0.63
   2 !    8.9   0.0   0.00049      0.98     106     176 ..     148     221 ..     143     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00041
                                      EEEE--SSHHHHHHHHHHHHH-.....SEEEEEEEESS-T CS
                              QueC  2 avvllSGGlDSttvlalakkeg.....kevealtfdYgqr 36
                                      +vv +SGG+DS  +la+  k+      +++  ++++ g  
  gi|320100612|ref|YP_004176204.1| 51 VVVAVSGGVDSMSLLAITAKRRvemgvEKIVGVHVNLGIE 90
                                      799********99998876653122335566666666655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00049
                                       HHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH...HTS--EEE-.TTTT--HHHHHHHHHHTTHH CS
                              QueC 106 asyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg...edkkieiea.PlidlsKaeivklgkelgvp 176
                                       ++ya a+ga+a+++G +  d++ Y   +d +v  +++++ l    ++  + ++a Pli+l K++i + ++  gvp
  gi|320100612|ref|YP_004176204.1| 148 TAYAVATGASAVFTGHHLDDAARYM-LKDLYVGDFKSLAGLKpavREPGLPVKAkPLITLGKKDIEAYAELAGVP 221
                                       68**********************6.68889999988887777678888999755**********9999888876 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.3e-06    0.0045       2     125 ..      50     164 ..      49     178 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.3e-06
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78 
                                       +vvva+SgGVDS   +a+ +++    +gv  k++  + + g e  ++   + +++ +  lg++++v+ +++     +
  gi|320100612|ref|YP_004176204.1|  50 RVVVAVSGGVDSMSLLAITAKRRV-EMGV-EKIVGVHVNLGIEGYSDLAEAAVREYCGSLGVECTVLRLRD-----I 119
                                       79*********9543333333222.2222.2333333444444466666677899************9975.....6 PP

                     tRNA_Me_trans  79 feefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHY 125
                                       +   l e+++     P+ +C   +K  +++ +a++ +ga+a+ tGH 
  gi|320100612|ref|YP_004176204.1| 120 LGVGLPELASRAGRPPCSVCG-LVKRYLITAYAVA-TGASAVFTGHH 164
                                       777777777766677999996.7999999999998.9********97 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4      0.64   1.3e+03      18      23 ..       3       8 ..       1       9 [. 0.83
   2 ?    1.3   0.1      0.13   2.6e+02      18      23 ..     135     140 ..     130     144 .. 0.73
   3 !   16.7   2.6     2e-06    0.0039      13      39 ..     274     300 ..     273     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.64
                                      E-TTT- CS
                              RecR 18 hCsrCg 23
                                       C+rCg
  gi|320100612|ref|YP_004176204.1|  3 KCRRCG 8 
                                      7****8 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.13
                                       E-TTT- CS
                              RecR  18 hCsrCg 23 
                                       +Cs+Cg
  gi|320100612|ref|YP_004176204.1| 135 PCSVCG 140
                                       577777 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 2e-06
                                       HHH-EE-TTT--EESSSS-CCCCSTTS CS
                              RecR  13 kekvrhCsrCgnlteedlCaICsdprR 39 
                                       ke+ r+Cs+Cg  + + +C++C+ ++R
  gi|320100612|ref|YP_004176204.1| 274 KETYRRCSVCGMPSRSSVCSFCRLTER 300
                                       67889*****************98887 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.37   7.3e+02      20      31 ..       3      13 ..       1      18 [. 0.71
   2 ?    1.4   0.0       0.2     4e+02      17      26 ..     132     141 ..     119     150 .. 0.82
   3 ?   10.1   0.1    0.0004      0.79       3      39 ..     250     296 ..     248     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.37
                              C1_2 20 nCsaCgrkidgf 31
                                      +C+ Cgr+  g+
  gi|320100612|ref|YP_004176204.1|  3 KCRRCGREA-GY 13
                                      8*****994.43 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.2
                              C1_2  17 esfnCsaCgr 26 
                                       ++ +Cs+Cg 
  gi|320100612|ref|YP_004176204.1| 132 GRPPCSVCGL 141
                                       5678****97 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0004
                              C1_2   3 Hp.HpLtls...........kgedssesfnCsaCgrkidgffYsCseCd 39 
                                       Hp  +L+l            ++ +++  ++Cs+Cg ++ ++   Cs C+
  gi|320100612|ref|YP_004176204.1| 250 HPgARLILLssmlkliegyiEPVEKETYRRCSVCGMPSRSS--VCSFCR 296
                                       56566666667777778876666777779********8666..888886 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.6e-05     0.051      17     125 ..      48     162 ..      31     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                      Asn_synthase  17 dvpvGalLSGGlDSSliaalaarqsk....splktFsigfeekgsdeakya..kevaehlgtehtelvlteeellda 87 
                                         +v +  SGG+DS ++ a+ a+ +     +++  +++ +  +g+++++ a  +e +  lg+e t l+l  +++l +
  gi|320100612|ref|YP_004176204.1|  48 GGRVVVAVSGGVDSMSLLAITAKRRVemgvEKIVGVHVNLGIEGYSDLAEAavREYCGSLGVECTVLRL--RDILGV 122
                                       4678899*******9999999998878999999999999966999999765236778888888654444..444444 PP

                      Asn_synthase  88 .lpdviyhlee.pfadrsaiplyllsrlakrkgvkvvLsG 125
                                        lp++++   + p      +  yl+  +a ++g   v++G
  gi|320100612|ref|YP_004176204.1| 123 gLPELASRAGRpPCSVCGLVKRYLITAYAVATGASAVFTG 162
                                       4666666555545555555555666666666666666666 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00028      0.55       3     156 ..      48     215 ..      46     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00028
                              ThiI   3 qgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklae.llaeyqtslevklvvvdfkevlk. 77 
                                        g+v++ +SgG+DS     +  kR +++ +  +    ++ +  ie   +lae  + ey +sl v+ +v+ ++++l  
  gi|320100612|ref|YP_004176204.1|  48 GGRVVVAVSGGVDSMSLLAITAKRRVEMGVEKIV--GVHVNLGIEGYSDLAEaAVREYCGSLGVECTVLRLRDILGv 122
                                       6899**********87777777777666665553..555556666666666526899***************99763 PP

                              ThiI  78 ...eilekv..kekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavv....n.......l 138
                                          e+ +++  ++ + + l+kr ++     +a  +ga+a+ tG  L   a   l+ l v +  +    +       l
  gi|320100612|ref|YP_004176204.1| 123 glpELASRAgrPPCSVCGLVKRYLIT---AYAVATGASAVFTGHHLDDAARYMLKDLYVGDFKSlaglKpavrepgL 196
                                       33367766666777788888988764...3678899***************99999998653321111211111112 PP

                              ThiI 139 li.lrPLigldKeeiiklA 156
                                       ++  +PLi+l K++i + A
  gi|320100612|ref|YP_004176204.1| 197 PVkAKPLITLGKKDIEAYA 215
                                       2323577777777777766 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00013      0.26      18      84 ..      48     119 ..      28     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                       TSEEEEEE-SSHHH.HHHHHHHHHHH..TCGEEEEEE--SSSTTHHHHHHH..HHHHHHHTSEEEE---HHH CS
                      NAD_synthase  18 akgvvlGlSGGvDS.slvaalavkal..gkenvlalllPssvsseedveda..lalaenlgievktidikpi 84 
                                          vv+ +SGGvDS sl a  a++ +  g e+++++ +    +  +d+ +a  ++ + +lg+e +++ +++i
  gi|320100612|ref|YP_004176204.1|  48 GGRVVVAVSGGVDSmSLLAITAKRRVemGVEKIVGVHVNLGIEGYSDLAEAavREYCGSLGVECTVLRLRDI 119
                                       4579**********6788888888776689999999988555555554444124677788887777777666 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 ?   -2.6   0.1       1.9   3.8e+03      35      40 ..       3       8 ..       1      15 [. 0.76
   2 ?    6.2   0.0    0.0033       6.6      32      55 ..     132     155 ..     125     164 .. 0.78
   3 ?    2.0   0.3     0.066   1.3e+02      25      44 ..     269     288 ..     262     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                       Vps36-NZF-N 35 pClaCG 40
                                      +C  CG
  gi|320100612|ref|YP_004176204.1|  3 KCRRCG 8 
                                      7****9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0033
                       Vps36-NZF-N  32 plPpClaCGvkpdlelikksikas 55 
                                         PpC  CG    + ++  ++ + 
  gi|320100612|ref|YP_004176204.1| 132 GRPPCSVCGLVKRYLITAYAVATG 155
                                       56*******999998888777665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.066
                       Vps36-NZF-N  25 fdpnastplPpClaCGvkpd 44 
                                       ++p ++++   C  CG ++ 
  gi|320100612|ref|YP_004176204.1| 269 IEPVEKETYRRCSVCGMPSR 288
                                       56667778889*****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2213.64
//
Query:       gi|320100613|ref|YP_004176205.1|  [L=178]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-36  125.9   7.5    2.4e-36  125.6   7.5    1.1  1  DUF1616        Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
       0.24   11.3   9.0       0.45   10.4   9.0    1.4  1  7TMR-DISM_7TM  7TM diverse intracellular signalling
       0.76   10.1   9.2        2.9    8.2   9.2    1.7  1  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 !  125.6   7.5     4e-40   2.4e-36       4     113 ..      68     177 ..      64     178 .] 0.94

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 4e-40
                           DUF1616   4 lalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtpwg 80 
                                        +++++l+  ++  +  plR +lg +  Lf+PGY+l+ aL+P++rd+  +eRlaLS+glS+a++pligl+ln+tpwg
  gi|320100613|ref|YP_004176205.1|  68 TIITVVLTSWINAAWLMPLRYILGALYTLFIPGYTLVEALYPGERDLAPLERLALSIGLSLAVIPLIGLFLNYTPWG 144
                                       45666677788899999************************************************************ PP

                           DUF1616  81 irlepilvslslftlllalvAivrRsrlpeeer 113
                                       irlep+l+s+++ft+++a +A++r++r+ +e r
  gi|320100613|ref|YP_004176205.1| 145 IRLEPVLASITVFTVATATIALYRKHRVLQESR 177
                                       ***************************999876 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 ?   10.4   9.0   7.6e-05      0.45      26     149 ..      50     171 ..      47     174 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.6e-05
                     7TMR-DISM_7TM  26 lrdksylyYalyllsfllyllslngllfqylwpnappalnnkllyltlllllilfll...Farsflelkkkp..... 94 
                                       lr  + l+Y + + + +l+++  +  l  ++  na   +   l y++ +l + lf+     +  +   +  +     
  gi|320100613|ref|YP_004176205.1|  50 LRPEYSLWYWATCTAAALTII--TVVLTSWI--NAA--WLMPLRYILGALYT-LFIPgytLVEALYPGE--Rdlapl 117
                                       566778888888888888888..67777777..444..44444444444444.2222202334444433..145745 PP

                     7TMR-DISM_7TM  95 rllklllllavllsllllllpll.pyteslslaqllallvillllligikawrkgn 149
                                         l l ++l+++  ++ l+  +l ++++ ++l  +la +++++++++ i+++rk++
  gi|320100613|ref|YP_004176205.1| 118 ERLALSIGLSLA--VIPLIGLFLnYTPWGIRLEPVLASITVFTVATATIALYRKHR 171
                                       555555555555..44444445559999999999*****************99986 PP

>> DUF4395  Domain of unknown function (DUF4395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   9.2   0.00048       2.9       9     110 ..      64     162 ..      58     167 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00048
                           DUF4395   9 naalvvvllvlalltgapwllallavvfalralagprlsplgllarrlvaprlgpkpeledaapkrFAqliGlvfll 85 
                                       +aal+++ +vl+  ++a+wl+ l  +  al  l+ p        ++++ a     + e++ a+ +r A  iGl +++
  gi|320100613|ref|YP_004176205.1|  64 AAALTIITVVLTSWINAAWLMPLRYILGALYTLFIP-------GYTLVEA---LYPGERDLAPLERLALSIGLSLAV 130
                                       344444444444444444444444444444444332.......2222222...255689999*************** PP

                           DUF4395  86 valvlfllgapv.......lglvltalllvaa 110
                                       + l++++l++++       +   +t++ ++ a
  gi|320100613|ref|YP_004176205.1| 131 IPLIGLFLNYTPwgirlepVLASITVFTVATA 162
                                       **********9977776653333344333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1373.80
//
Query:       gi|320100614|ref|YP_004176206.1|  [L=162]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-08   34.9   0.0    1.1e-08   34.8   0.0    1.0  1  DUF1616   Protein of unknown function (DUF1616)


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   6.1e-13   1.1e-08     140     268 ..       7     133 ..       3     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 6.1e-13
                           DUF1616 140 alnvlLvvsivlavaalgyavvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvv 216
                                       +  v+L+vs+v++++ ++ +v  P  +e+fT++ ll+++      ++yp + + g++  + + i Nh +e   Y+v 
  gi|320100614|ref|YP_004176206.1|   7 VFAVVLAVSVVASAVGIA-LVLGPGGSEAFTAIGLLNSEC---RIGEYPVKAYNGSTLHLCLFIYNHMGEAIYYRVA 79 
                                       677889999887765544.45569*************998...*********************************9 PP

                           DUF1616 217 vllqev..tdeeevevlerteldrrevtladnetweqelevepeatgenlrlef 268
                                         +  +     ++++   r ++ + +  l d++ +++++ev ++a+ ++ r+++
  gi|320100614|ref|YP_004176206.1|  80 YKIAASqgDMPTNTTPSPRPVIAEWKGVLGDGWNETTRVEVPVAAPSGSSRVAL 133
                                       988877665666677778999************999999999999877777643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1236.29
//
Query:       gi|320100615|ref|YP_004176207.1|  [L=140]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1100.16
//
Query:       gi|320100616|ref|YP_004176208.1|  [L=535]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-09   37.3   0.0    1.1e-08   35.3   0.0    2.1  2  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1      0.76   1.4e+04      64      83 ..     119     138 ..     113     144 .. 0.68
   2 !   35.3   0.0   5.9e-13   1.1e-08       2      70 ..     322     394 ..     321     409 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.76
                             DUF58  64 etavsaaaslarqlldegdr 83 
                                        ta++a+  la++ l+e+ r
  gi|320100616|ref|YP_004176208.1| 119 STALTALGVLAASSLREQLR 138
                                       56666666677777777665 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 5.9e-13
                             DUF58   2 ldfaglReYvpgDplrrIdWkat.ARtge..lyvrefeaera.......rtvllvldlspemslgstgdekletavs 68 
                                       +++ g+ReY+pgDplr I+Wk+t +R g    yv+++  e +       +++++v dl++ +         l+ +++
  gi|320100616|ref|YP_004176208.1| 322 GEYTGVREYQPGDPLRLIHWKKTlSREGGegIYVKQYAVEGEgagmgggGDLVVVADLTSVNP------VELDLLLH 392
                                       6899****************99846754457******77766557777778888888777753......45555555 PP

                             DUF58  69 aa 70 
                                       a+
  gi|320100616|ref|YP_004176208.1| 393 AV 394
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 4175.90
//
Query:       gi|320100617|ref|YP_004176209.1|  [L=280]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2242.52
//
Query:       gi|320100618|ref|YP_004176210.1|  [L=577]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 4545.53
//
Query:       gi|320100619|ref|YP_004176211.1|  [L=84]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 650.79
//
Query:       gi|320100620|ref|YP_004176212.1|  [L=232]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1717.05
//
Query:       gi|320100621|ref|YP_004176213.1|  [L=315]
Description: ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-43  146.9   0.0    4.1e-43  146.4   0.0    1.2  1  AAA_3            ATPase family associated with various cellul
    5.1e-20   71.1   0.5    5.1e-20   71.1   0.5    2.0  2  AAA_lid_2        AAA lid domain
    4.2e-12   46.2   0.0    6.7e-12   45.6   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-08   34.8   0.0    5.8e-08   33.2   0.0    1.8  1  AAA              ATPase family associated with various cellul
    1.5e-07   31.3   0.4      0.011   15.4   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
    1.1e-05   25.8   0.6    0.00048   20.6   0.1    2.2  2  AAA_16           AAA ATPase domain
    4.6e-05   23.2   0.1     0.0003   20.6   0.1    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00023   20.6   0.3     0.0039   16.6   0.1    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00034   20.4   1.3     0.0038   17.0   0.5    2.2  2  AAA_30           AAA domain
    0.00073   20.1   0.0     0.0018   18.9   0.0    1.7  1  AAA_18           AAA domain
     0.0017   17.5   0.0       0.02   14.0   0.0    2.1  1  MCM              MCM P-loop domain
  ------ inclusion threshold ------
      0.011   16.0   0.4       0.04   14.2   0.4    2.0  1  AAA_22           AAA domain
      0.011   15.0   0.3      0.026   13.8   0.1    1.6  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.011   15.9   0.1      0.026   14.7   0.1    1.7  1  AAA_33           AAA domain
      0.016   14.5   0.3      0.027   13.7   0.3    1.3  1  TIP49            TIP49 P-loop domain
      0.021   14.8   0.3       0.16   11.9   0.2    2.3  3  NACHT            NACHT domain
      0.022   15.0   0.2        5.8    7.1   0.2    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.029   14.7   0.0      0.068   13.6   0.0    1.7  1  RNA_helicase     RNA helicase
      0.061   13.3   0.1       0.13   12.3   0.1    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.084   12.6   0.1       0.17   11.6   0.1    1.5  1  IstB_IS21        IstB-like ATP binding protein
       0.11   11.9   0.2       0.23   10.8   0.2    1.5  1  ATPase           KaiC
       0.15   12.2   0.0       0.33   11.1   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.17   12.1   0.0       0.34   11.1   0.0    1.5  1  AAA_28           AAA domain
       0.18   10.6   0.0        0.3    9.9   0.0    1.3  1  Phage_stabilise  Phage stabilisation protein
       0.18   11.6   0.0       0.29   10.9   0.0    1.2  1  AAA_11           AAA domain
       0.18   10.9   0.1       0.29   10.2   0.1    1.2  1  PIF1             PIF1-like helicase
       0.19   10.8   0.0       0.32   10.1   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1


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 !  146.4   0.0   6.2e-46   4.1e-43       1     130 [.      42     171 ..      42     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 6.2e-46
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvl+eg PG++ktll+kalaka++  +kr+q  pd+lPsdilG ++++   +++ + +Gpvf+n+ll de+nrap++
  gi|320100621|ref|YP_004176213.1|  42 HVLIEGYPGTGKTLLAKALAKAIGGAYKRVQGHPDILPSDILGFHMYRLGGERI-LVQGPVFTNVLLFDEVNRAPTR 117
                                       9**********************************************9988776.668******************* PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieq.eGtyplpeaqldrfl 130
                                       +q+alleam+e qvt++g t++lp+p++v+atq P  +  G+y++ e+  drf 
  gi|320100621|ref|YP_004176213.1| 118 SQAALLEAMQELQVTIDGVTYQLPRPLIVIATQVPYRHaVGAYQVMETLADRFA 171
                                       ***********************************97527*************6 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       5.6   3.7e+03      35      51 ..      21      37 ..      20      37 .. 0.85
   2 !   71.1   0.5   7.7e-23   5.1e-20       4      72 ..     237     306 ..     235     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.6
                         AAA_lid_2 35 rdyVtpeDvkeaaplVL 51
                                      r yV + Dv ++a  +L
  gi|320100621|ref|YP_004176213.1| 21 RVYVGKRDVVKLAVAAL 37
                                      78999999999998876 PP

  == domain 2  score: 71.1 bits;  conditional E-value: 7.7e-23
                         AAA_lid_2   4 rahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeivee 72 
                                       r+h+a+++g s r a+++l+r++rAlA ++grdyV+p+Dvk+++p V aHR++  +e eaeg+t+e+iv+e
  gi|320100621|ref|YP_004176213.1| 237 RSHPAVAYGPSHR-ATIHLMRVSRALAVMDGRDYVIPDDVKQLFPHVVAHRVKlrEEYEAEGVTAESIVKE 306
                                       8999*****9877.****************************************99999999*****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 !   45.6   0.0     1e-14   6.7e-12       1     124 [.      42     154 ..      42     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1e-14
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEver 76 
                                       +vl+ G pGtgK+ la+ la+a++  +  vq++ d+ ++d++g   ++ +g++ lv++p+        +l++DEv+r
  gi|320100621|ref|YP_004176213.1|  42 HVLIEGYPGTGKTLLAKALAKAIGGAYKRVQGHPDILPSDILGFHMYRlGGERILVQGPVF-----TNVLLFDEVNR 113
                                       79***********************************************************.....789******** PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                       a++  +++Ll  + e ++   +g +++  ++      + viat  p +
  gi|320100621|ref|YP_004176213.1| 114 APTRSQAALLEAMQELQVT-IDGVTYQLPRP------LIVIATQVPYR 154
                                       *************999998.67777776666......67777665555 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   8.8e-11   5.8e-08       1     110 [.      43     150 ..      43     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 8.8e-11
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakekakpsilfiDEidalaksrs 75 
                                       vl+ G pGtGKTllaka+ak +g  + +++g +++l s+++g  + ++ +    ++    + +l++DE+ +  ++r 
  gi|320100621|ref|YP_004176213.1|  43 VLIEGYPGTGKTLLAKALAKAIGGAYKRVQGhPDILpSDILGFHMYRLGGERILVQGPVFTNVLLFDEVNRA-PTR- 117
                                       6899*******************999999984577777777766666644332222222348*********9.566. PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatn 110
                                         ++    +++++L   +dgv+ +  + ++++at+
  gi|320100621|ref|YP_004176213.1| 118 --SQAALLEAMQELQVTIDGVTYQLPRPLIVIATQ 150
                                       ..577888999999999999999877666666665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   4.8e-05     0.032      11      44 ..      29      62 ..      24      75 .. 0.82
   2 !   15.4   0.0   1.7e-05     0.011      96     163 ..     105     171 ..     101     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                                      HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraihe 44
                                      +++ + ++  t  +vli+G  GtGK+lla+a+ +
  gi|320100621|ref|YP_004176213.1| 29 VVKLAVAALFTGGHVLIEGYPGTGKTLLAKALAK 62
                                      6666777777889*****************9976 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.7e-05
                                       EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HHHHHHTTSS-HHHHHHHT CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedleeaveegkfredLyyrln 163
                                       +l++De+++ p++ Q+ Ll+++qe +v+  G + + +    i+ at+   ++av + ++ e L  r +
  gi|320100621|ref|YP_004176213.1| 105 VLLFDEVNRAPTRSQAALLEAMQELQVTIDGVTYQLPRP-LIVIATQVPYRHAVGAYQVMETLADRFA 171
                                       7999************************99999888765.5778999999999999888888877765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   7.2e-07   0.00048      19      63 ..      37      78 ..      24      93 .. 0.78
   2 ?    3.3   0.1      0.15        98     138     163 ..     105     130 ..      95     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.2e-07
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      + +g  + vl+ G++G+GK+ l+++l++a+ ++  +  ++g+ d l
  gi|320100621|ref|YP_004176213.1| 37 LFTG--GHVLIEGYPGTGKTLLAKALAKAIGGA--YKrVQGHPDIL 78
                                      4555..79********************99977..22377776665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                            AAA_16 138 vlvlDdlqwadeaslqllaaLlrlle 163
                                       vl++D++ +a + s+++l + +++l+
  gi|320100621|ref|YP_004176213.1| 105 VLLFDEVNRAPTRSQAALLEAMQELQ 130
                                       89***************666555554 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 !   20.6   0.1   4.5e-07    0.0003      34     115 ..      41     133 ..      29     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.5e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsg.Pvlekagdlaal.ltnlee..........kdvlfideihrlsr 98 
                                        hvl+ G PG Gkt lak +ak +g   k   g P +  ++d+ ++ + +l            ++vl+ de+ r  +
  gi|320100621|ref|YP_004176213.1|  41 GHVLIEGYPGTGKTLLAKALAKAIGGAYKRVQGhPDIL-PSDILGFhMYRLGGerilvqgpvfTNVLLFDEVNRAPT 116
                                       6************************9998877635554.55555431333322011111122268899999999999 PP

                            RuvB_N  99 aveevlysamedfrldi 115
                                         +  l  am++ ++ i
  gi|320100621|ref|YP_004176213.1| 117 RSQAALLEAMQELQVTI 133
                                       99999999999888765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.8e-06    0.0039      15      44 ..      32      62 ..      20      70 .. 0.72
   2 ?    1.8   0.0       0.2   1.3e+02     108     144 ..     104     140 ..      90     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                      Mg_chelatase 15 leiaa..aGgHnlllvGppGsGKtmlakrlps 44
                                      l +aa  +GgH +l+ G pG+GKt+lak+l++
  gi|320100621|ref|YP_004176213.1| 32 LAVAAlfTGGH-VLIEGYPGTGKTLLAKALAK 62
                                      33333224665.889*************9976 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgevtisrakakv 144
                                        vL++DE+    ++   +L e +++ +vti   ++++
  gi|320100621|ref|YP_004176213.1| 104 NVLLFDEVNRAPTRSQAALLEAMQELQVTIDGVTYQL 140
                                       599**************************98776654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   5.7e-06    0.0038       9      50 ..      33      72 ..      31      75 .. 0.85
   2 ?    1.7   0.0      0.28   1.8e+02      90     128 ..     104     140 ..      96     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.7e-06
                            AAA_30  9 avealltsgdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      av+al t+g+  ++++G++GtGKt + kal++a+  a +rv 
  gi|320100621|ref|YP_004176213.1| 33 AVAALFTGGH--VLIEGYPGTGKTLLAKALAKAIGGAYKRVQ 72
                                      7888888886..9*******************9987766765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.28
                            AAA_30  90 tllivDEagmvdtkqlaallkaaekagakvilvGDerQl 128
                                       ++l+ DE+  + t++ aall+a+++   +v + G + Ql
  gi|320100621|ref|YP_004176213.1| 104 NVLLFDEVNRAPTRSQAALLEAMQE--LQVTIDGVTYQL 140
                                       68999*****************988..666666666666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.6e-06    0.0018       1      25 [.      43      84 ..      43     147 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.6e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf................g 25
                                      +l+ G+pG+GKt lak+L+k   g                 g
  gi|320100621|ref|YP_004176213.1| 43 VLIEGYPGTGKTLLAKALAKAIgGAykrvqghpdilpsdilG 84
                                      79******************9743356666666555544443 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.9e-05      0.02      59     187 ..      42     169 ..      17     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                                       EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHS..SSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGS CS
                               MCM  59 nvllvgdpgtaKsqlLkyveklapravytsgkgssaagL..taavvrdeetgefvleaGalvladkGvcciDefdkm 133
                                       +vl+ g pgt+K+ l k+++k a  + y   +g            +  +  ge +l  G + +    v++ De+++ 
  gi|320100621|ref|YP_004176213.1|  42 HVLIEGYPGTGKTLLAKALAK-AIGGAYKRVQGHPDILPsdILGFHMYRLGGERILVQGPVFT---NVLLFDEVNRA 114
                                       677777777777766666663.44455555555433211001112223344555555555543...4899******* PP

                                       TCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S...SSSCCTTS-HHHH CS
                               MCM 134 keedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk...agrydkkksvaen 187
                                        ++ + al+Eam + +++i   G++++L+    v+a   p     g y+  +++a+ 
  gi|320100621|ref|YP_004176213.1| 115 PTRSQAALLEAMQELQVTI--DGVTYQLPRPLIVIATQVPYrhaVGAYQVMETLADR 169
                                       ************7666666..69******9999999999975556788877777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4     6e-05      0.04       4      28 ..      39      63 ..      35     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      t g++++ G +GtGKT+l++ l++ 
  gi|320100621|ref|YP_004176213.1| 39 TGGHVLIEGYPGTGKTLLAKALAKA 63
                                      6899*****************9986 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.9e-05     0.026       4      25 ..      43      64 ..      41      80 .. 0.85
   2 ?   -2.2   0.0       2.7   1.8e+03      90     106 ..     104     120 ..     101     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                           DUF2075  4 vlVtGvaGtGKtvvllnllael 25
                                      vl++G +GtGKt+++ +l+ ++
  gi|320100621|ref|YP_004176213.1| 43 VLIEGYPGTGKTLLAKALAKAI 64
                                      79*************9999887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                           DUF2075  90 dvvivDEAhrlltksdq 106
                                       +v+++DE  r+ t+s++
  gi|320100621|ref|YP_004176213.1| 104 NVLLFDEVNRAPTRSQA 120
                                       6999******9997665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.9e-05     0.026       2      28 ..      43      71 ..      43     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg..avll 28
                                      vl+ G pG+GK+ la+ l+k+ g  + ++
  gi|320100621|ref|YP_004176213.1| 43 VLIEGYPGTGKTLLAKALAKAIGgaYKRV 71
                                      6899***************9998775555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3     4e-05     0.027      40      76 ..      30      66 ..      25      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 40 velikekklaGravLlaGpsgtGktalaiaiskelge 76
                                      v+l  +  ++G  vL+ G +gtGkt la a++k++g 
  gi|320100621|ref|YP_004176213.1| 30 VKLAVAALFTGGHVLIEGYPGTGKTLLAKALAKAIGG 66
                                      5555666788999*********************984 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00024      0.16       3      25 ..      43      65 ..      42      73 .. 0.89
   2 ?   -2.6   0.0       6.7   4.5e+03      85      99 ..     106     120 ..      93     148 .. 0.58
   3 ?   -0.3   0.0       1.4   9.2e+02      73      96 ..     250     273 ..     192     312 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                      EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                      v+++G +G GKT L++ la a+ 
  gi|320100621|ref|YP_004176213.1| 43 VLIEGYPGTGKTLLAKALAKAIG 65
                                      79****************99875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.7
                                       EEEE-STT-SS-TCH CS
                             NACHT  85 lilDglDelvtdlgq 99 
                                       l++D +++++t  ++
  gi|320100621|ref|YP_004176213.1| 106 LLFDEVNRAPTRSQA 120
                                       555555555554444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                                       HHHHCCSCCCEEEEEE-STT-SS- CS
                             NACHT  73 wavllelperlLlilDglDelvtd 96 
                                        ++ l +  r+L ++Dg D++  d
  gi|320100621|ref|YP_004176213.1| 250 ATIHLMRVSRALAVMDGRDYVIPD 273
                                       333344567888899998886554 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 ?    7.1   0.2    0.0088       5.8       2      27 ..      43      68 ..      42      73 .. 0.89
   2 ?    5.7   0.0     0.024        16      17      40 ..     287     310 ..     283     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0088
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAl 27
                                      +++ G P +GKt  a +Lak+ + A+
  gi|320100621|ref|YP_004176213.1| 43 VLIEGYPGTGKTLLAKALAKAIGGAY 68
                                      689*****************998886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
                         Hydin_ADK  17 vtLakkYeaAlltiDsvvleAisd 40 
                                       v+L  +Yea  +t +s+v+eA+s+
  gi|320100621|ref|YP_004176213.1| 287 VKLREEYEAEGVTAESIVKEALSN 310
                                       78999******************8 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    0.0001     0.068       1      27 [.      43      80 ..      43     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl...........k 27
                                      +++ G +g+GK++lak Laka+ +++            
  gi|320100621|ref|YP_004176213.1| 43 VLIEGYPGTGKTLLAKALAKAIGGAYkrvqghpdilpS 80
                                      5789******************9888555555555544 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00019      0.13      18      46 ..      37      67 ..      24      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                      H..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglakalgve 46
                                      l  g  +l+eG  G+GKT l+++laka+g +
  gi|320100621|ref|YP_004176213.1| 37 LftGGHVLIEGYPGTGKTLLAKALAKAIGGA 67
                                      1345679********************9864 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   0.1   0.00026      0.17      48      70 ..      41      63 ..      19      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                         IstB_IS21 48 enivllGpsGvGKshlaialgve 70
                                        +++ G +G+GK+ la al+++
  gi|320100621|ref|YP_004176213.1| 41 GHVLIEGYPGTGKTLLAKALAKA 63
                                      458999**************976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00034      0.23      19      37 ..      40      58 ..      31      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                            ATPase 19 grvvlitGepGtGKtifal 37
                                      g  vli G pGtGKt++a+
  gi|320100621|ref|YP_004176213.1| 40 GGHVLIEGYPGTGKTLLAK 58
                                      6679*************97 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00049      0.33      23      96 ..      42     129 ..      30     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                                       -EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-HHHHHHH...............TTTSEEEEEE-TT--HH CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwleifvverlaklpldlleq...............akggtLylkdiadlska 84 
                                        v++ G +G+gk+l A++L+k  g+  + ++  ++  lp+d+l +               +   +L++ +++  +  
  gi|320100621|ref|YP_004176213.1|  42 HVLIEGYPGTGKTLLAKALAKAIGGAYKRVQG-HPDILPSDILGFhmyrlggerilvqgpVFTNVLLFDEVNRAPTR 117
                                       59*******************99995555333.44457766666655555555554445557778899999999999 PP

                                       HHHHHHHHHHHH CS
                   Sigma54_activ_2  85 eqkeLlellaka 96 
                                        q+ Lle++++ 
  gi|320100621|ref|YP_004176213.1| 118 SQAALLEAMQEL 129
                                       999999988875 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   0.00052      0.34       2      22 ..      43      63 ..      42      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                      + i G ++tGKT l++aLa+ 
  gi|320100621|ref|YP_004176213.1| 43 VLIEGYPGTGKTLLAKALAKA 63
                                      7899***************76 PP

>> Phage_stabilise  Phage stabilisation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00045       0.3      15      66 ..     190     240 ..     185     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00045
                   Phage_stabilise  15 tadyidalpvnllatpkevlnasgylrsfpgiekkkdvkgvsrgvefntakn 66 
                                       ++d + +lpv+ +atp+ev + sg l+ +  +e +  ++ + + v++  ++ 
  gi|320100621|ref|YP_004176213.1| 190 KSDTVLTLPVEQVATPREVEEVSGMLQGLVHVENHV-ADYIVKLVNYVRSHP 240
                                       578999*********************999998764.456666666666555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00044      0.29      10      59 ..      34      97 ..      28     105 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                            AAA_11 10 iksalseseitliqGPPGtgKT...ktivellsqllsr............rkseeeksakpriLv 59
                                      ++   +  + +li+G PGtgKT   k++++ +  +++r               ++ + +++riLv
  gi|320100621|ref|YP_004176213.1| 34 VAALFTGGH-VLIEGYPGTGKTllaKALAKAIGGAYKRvqghpdilpsdiLGFHMYRLGGERILV 97
                                      555556666.8***********5554444444433322333444444333225556666666666 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00044      0.29      21      51 ..      39      69 ..      25      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00044
                                      CTS-EEEEESTTSSCHHHHHHHHHHCHCTCC CS
                              PIF1 21 kgklfFvtGsgGtgKtflwkallkklrsegk 51
                                       g+ + ++G+ GtgKt l kal k++ +  k
  gi|320100621|ref|YP_004176213.1| 39 TGGHVLIEGYPGTGKTLLAKALAKAIGGAYK 69
                                      5788899*****************9977655 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 ?   10.1   0.0   0.00048      0.32     111     138 ..      24      64 ..       9      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                         Parvo_NS1 111 lgkrntvwfy.............GpantGktnlaeaIakav 138
                                        gkr+ v +              G + tGkt la+a+aka+
  gi|320100621|ref|YP_004176213.1|  24 VGKRDVVKLAvaalftgghvlieGYPGTGKTLLAKALAKAI 64 
                                       67777777777777778888888****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2280.14
//
Query:       gi|320100622|ref|YP_004176214.1|  [L=148]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1087.11
//
Query:       gi|320100623|ref|YP_004176215.1|  [L=303]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-20   72.7   0.0    3.9e-20   72.3   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    3.8e-10   40.1   0.0    5.3e-10   39.6   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.4e-05   24.3   0.3    7.2e-05   23.2   0.1    1.6  2  NTP_transf_3     MobA-like NTP transferase domain
     0.0094   16.5   0.0      0.027   15.0   0.0    1.8  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.013   15.9   0.9      0.037   14.4   0.9    1.7  1  DUF3624          Protein of unknown function (DUF3624)


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 !   72.3   0.0   1.1e-23   3.9e-20       1     128 [.      10     129 ..      10     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 1.1e-23
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       +vvip++Ne++ +  +l+ +la    p+ +i+vvD gStD+tve + +      +vrv+++e + Gka a+ +++r 
  gi|320100623|ref|YP_004176215.1|  10 TVVIPVFNEAEAIGLVLDEVLAA-GVPRERILVVDGGSTDGTVEAASSR-----GVRVVQQEGR-GKADAVKTAARL 79 
                                       69*********************.*************************.....9*******55.************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCH CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeier 128
                                       + + + l++D D +++ ++++ l+ ++ + g+d+v+g r+  +g+     r
  gi|320100623|ref|YP_004176215.1|  80 VETGFTLIMDGDYTYPAGFIQALYVKARE-GYDLVVGWRRWGEGSQPLVYR 129
                                       *****************************.********9988877666555 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.5e-13   5.3e-10       3     108 ..       8     102 ..       6     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.5e-13
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       dl+v++p+fne++ +g vl+++la   pr ++ vv+ +s+++t+e a      +++ +vrvv+++   g +gk++a+
  gi|320100623|ref|YP_004176215.1|   8 DLTVVIPVFNEAEAIGLVLDEVLAAGVPRERILVVDGGSTDGTVEAA------SSR-GVRVVQQE---G-RGKADAV 73 
                                       699*********************999***************99955......456.89*98554...4.6****** PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrl 108
                                       + a r v++ ++l++D+D     +++++l
  gi|320100623|ref|YP_004176215.1|  74 KTAARLVETGFTLIMDGDYTYPAGFIQAL 102
                                       ******************98887777764 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 !   23.2   0.1     2e-08   7.2e-05      27     134 ..      22     129 ..      12     152 .. 0.82
   2 ?   -2.4   0.0       1.5   5.4e+03      10      24 ..     198     212 ..     175     220 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-08
                                       HHHHHHHHCTT.-..CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT- CS
                      NTP_transf_3  27 lervldalraagv..devvvvggd..eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPll 99 
                                       +  vld + aagv  ++++vv g   +   +a+ ++gvrvv++e  g+g + ++++a+r + ++   l++ +D  + 
  gi|320100623|ref|YP_004176215.1|  22 IGLVLDEVLAAGVprERILVVDGGstDGTVEAASSRGVRVVQQE--GRGKADAVKTAARLV-ETGFTLIMDGDYTY- 94 
                                       566788888887644688888444356667788999*******9..9************88.9***********77. PP

                                       -HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEE CS
                      NTP_transf_3 100 tpelverllaaaaasgadvvvptyegerghpllfr 134
                                       ++ ++++l  +a++  + vv +++ ge  +pl++r
  gi|320100623|ref|YP_004176215.1|  95 PAGFIQALYVKAREGYDLVVGWRRWGEGSQPLVYR 129
                                       9**********987777777788889999***995 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                                       TTTTTTHHHHCCCCC CS
                      NTP_transf_3  10 sRmggdKallplggk 24 
                                       +R+g+ K+ ++ g +
  gi|320100623|ref|YP_004176215.1| 198 RRLGRKKLGVRHGLR 212
                                       455666665555555 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.6e-06     0.027       2      45 ..      17      61 ..      16      95 .. 0.78
   2 ?   -2.6   0.0       2.2     8e+03       6      15 ..     243     252 ..     242     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.6e-06
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgf..drilvydndstDgtrailkelpevkl 45
                                      nea++++ +l+  la+g+  +rilv+d +stDgt +  ++   v++
  gi|320100623|ref|YP_004176215.1| 17 NEAEAIGLVLDEVLAAGVprERILVVDGGSTDGTVEAASSR-GVRV 61
                                      9****************76589*************988763.4444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                   Glyco_tranf_2_4   6 iLpeflahhl 15 
                                       +L++++a+h+
  gi|320100623|ref|YP_004176215.1| 243 ALGSWVAYHY 252
                                       5899***996 PP

>> DUF3624  Protein of unknown function (DUF3624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.9     1e-05     0.037      28      73 ..     242     287 ..     236     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                           DUF3624  28 lsvlswlvWwllfkdtpksvesialllaafafsgLLllHlvvlayr 73 
                                       l+++sw+++ ++f+ t+++v+ ++ ++ ++a    Lll +++l ++
  gi|320100623|ref|YP_004176215.1| 242 LALGSWVAYHYFFTGTVYHVKGLTAVILTAAGLQSLLLAVIALYMK 287
                                       7899******************987666655554445555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2288.82
//
Query:       gi|320100624|ref|YP_004176216.1|  [L=369]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-24   87.0   0.0    1.9e-24   86.4   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    7.1e-24   85.0   0.0    2.4e-23   83.2   0.0    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.2e-13   50.6   0.2    3.3e-13   50.0   0.2    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    4.4e-09   36.1   0.0    9.2e-09   35.0   0.0    1.5  1  Glyco_transf_21  Glycosyl transferase family 21
    0.00031   21.2   0.2    0.00096   19.6   0.1    1.8  2  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 !   86.4   0.0   5.2e-28   1.9e-24       2     169 ..      46     215 ..      45     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 5.2e-28
                                       EEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnagl 75 
                                       vviptyNe+ ++++ le + +q +p++++++++vD +S+D+tv  + ++a+  +d  vr++   e++Gk++aln++l
  gi|320100624|ref|YP_004176216.1|  46 VVIPTYNEAGNIERKLEDIYSQdYPRDRITVYIVDSASSDGTVGKALDWASrhKDIEVRIVEEGERRGKGRALNTAL 122
                                       9**************************************************************************** PP

                                       HH--SS..EEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCC CS
                   Glycos_transf_2  76 raatgd..yilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkg 149
                                          +g   +i++ DaD  ++    l+  + ++ ++ + +++ ++   +g+ ++    ++  ++  ++  +   s  +
  gi|320100624|ref|YP_004176216.1| 123 NTIDGGfdFIVVTDADAFWANRdALRNALSYFSDESV-GAVSCVKTPGGG-GFTGVESG--YRDFYNVVRLGESSAY 195
                                       *****999*********998877***********554.444444444444.44444444..678999999999999* PP

                                       CSTTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 150 nlsfeigsaallrrealeel 169
                                       ++++++g  +++rr++le+l
  gi|320100624|ref|YP_004176216.1| 196 STPVFHGELSAYRRRLLEDL 215
                                       *****************997 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.0   6.7e-27   2.4e-23       1     214 [.      42     253 ..      42     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 6.7e-27
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       pr +av++pt+ne+  +++ le++ +q+ypr  + v++v+  s+++t+  a   a +++d++vr+v   ++++++gk
  gi|320100624|ref|YP_004176216.1|  42 PR-VAVVIPTYNEAGNIERKLEDIYSQDYPRdrITVYIVDSASSDGTVGKALDWASRHKDIEVRIV---EEGERRGK 114
                                       67.**************************7765888888899*******999************99...67899*** PP

                   Glyco_tranf_2_3  76 sralnealravk..sdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrfl 149
                                        raln al++++  +d++++ D+D+ +   d+l+ +l +f +++vgav + +    +  +   +g+    +++ ++ 
  gi|320100624|ref|YP_004176216.1| 115 GRALNTALNTIDggFDFIVVTDADAFWaNRDALRNALSYFSDESVGAVSCVKTPGGGGFTGVESGY----RDFYNVV 187
                                       ***************************88999********999*****998877665544443433....4444444 PP

                   Glyco_tranf_2_3 150 aarral..gvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfp 214
                                       ++ ++   +++ ++G++s++rr++l++l+g+    +  dD +++  +   g+r  ++p++ ++e  p
  gi|320100624|ref|YP_004176216.1| 188 RLGESSaySTPVFHGELSAYRRRLLEDLGGFPT-DIGSDDSHTATLIAVKGYRAIVAPDVYCYEPVP 253
                                       4443332257889*****************999.999999999999999***********9988644 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.2   9.2e-17   3.3e-13       2     182 ..     132     321 ..     131     353 .. 0.69

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 9.2e-17
                   Glyco_trans_2_3   2 illlDaDtv.lppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsvGsg 76 
                                       i++ DaD    ++d lr +++ +++  v++v++  ++  ++ + +e  + +f++  + +++ +++++     ++G  
  gi|320100624|ref|YP_004176216.1| 132 IVVTDADAFwANRDALRNALSYFSDESVGAVSCVKTPGgGGFTGVESGYRDFYN--VVRLGESSAYST--PVFHGEL 204
                                       9999****989*************99***********84556777888888886..455566655553..3599*** PP

                   Glyco_trans_2_3  77 aflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspl.tlraalrQrkRwayGceleklill 152
                                       ++ rr++l+++gg++  ++  s+D + +  ++ kGyr + +p++ ++e +p+  +  ++ +r+ ++      k i+l
  gi|320100624|ref|YP_004176216.1| 205 SAYRRRLLEDLGGFP--TDIGSDDSHTATLIAVKGYRAIVAPDVYCYEPVPRrKYFHWRVRRAQHLIQH-FAKSIRL 278
                                       ***************..9**********************************55666666666666652.2334444 PP

                   Glyco_trans_2_3 153 vrll.gylgsllwsalplhla..llllfslla..........l 182
                                       + ++ + ++++l++ ++lhla  +lll s++           l
  gi|320100624|ref|YP_004176216.1| 279 LPRSpKAFRKILAAEIFLHLAnpILLLISIALlaysaykgspL 321
                                       4333344555555555555542233333333322222233332 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 !   35.0   0.0   2.6e-12   9.2e-09      13     162 ..     112     259 ..     100     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.6e-12
                   Glyco_transf_21  13 vgvnpKvnnllqaleaakydllvisDsdvr.vkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl..nt 86 
                                       +g  + +n  l++++    d++v+ D+d++ +++d+L++ l +++d+ vg V+++    +  g  + +e+ +   + 
  gi|320100624|ref|YP_004176216.1| 112 RGKGRALNTALNTID-GGFDFIVVTDADAFwANRDALRNALSYFSDESVGAVSCVKTPGG--GGFTGVESGYRdfYN 185
                                       444444444444433.5789********984689*******************9765443..333445555542267 PP

                   Glyco_transf_21  87 lagvlqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslr 162
                                       + ++  +++  +    G   a+rr+ Le++GGf    d   +D  +++l++ +G++ +++p++ + + vprr+++ 
  gi|320100624|ref|YP_004176216.1| 186 VVRLGESSAYSTPVFHGELSAYRRRLLEDLGGFPT--DIGSDDSHTATLIAVKGYRAIVAPDVYCYEPVPRRKYFH 259
                                       777777767788999*******************9..7778**********************9999999866554 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.7e-07   0.00096       2      94 ..      52     149 ..      51     154 .. 0.70
   2 ?   -1.6   0.0       1.1   3.9e+03      28      60 ..     223     261 ..     220     277 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-07
                   Glyco_tranf_2_4   2 neadiLpeflahhlalgf..dr..ilvydndstDgt....railkelpevkllhvdksyederrqvellkallarya 70 
                                       nea  +++ l+ +++ ++  dr  ++++d  s+Dgt     ++ ++++++++  v++   ++r + ++l+++l+ + 
  gi|320100624|ref|YP_004176216.1|  52 NEAGNIERKLEDIYSQDYprDRitVYIVDSASSDGTvgkaLDWASRHKDIEVRIVEEG--ERRGKGRALNTALNTID 126
                                       7777788888876666643355558999********5444455566666666655553..23455789999999986 PP

                   Glyco_tranf_2_4  71 ea.dwvlvvDaDEflvvpdsrslra 94 
                                        + d+++v DaD f +++d+  lr 
  gi|320100624|ref|YP_004176216.1| 127 GGfDFIVVTDADAFWANRDA--LRN 149
                                       544***************95..443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                   Glyco_tranf_2_4  28 dstDgtrailkelpevkllhvdksy......ederrqve 60 
                                       +s+D  +a l + + ++ +  ++ y      ++++++ +
  gi|320100624|ref|YP_004176216.1| 223 GSDDSHTATLIAVKGYRAIVAPDVYcyepvpRRKYFHWR 261
                                       677888888887777776666655544444433344422 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2539.97
//
Query:       gi|320100625|ref|YP_004176217.1|  [L=300]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-07   32.1   0.0    1.3e-07   31.8   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.6e-06   28.0   0.0    3.3e-06   27.0   0.0    1.6  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.03   13.8   0.1      0.069   12.6   0.0    1.6  2  Glyco_transf_21  Glycosyl transferase family 21


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 !   31.8   0.0   2.2e-11   1.3e-07       2     208 ..       3     222 ..       2     248 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.2e-11
                   Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvn..arnlgstgks 76 
                                       + +avl+p+f++++ l  +l   la+  +   v+v ++ s+ae+l++ + + + l++ + +++ +  + + gs  ++
  gi|320100625|ref|YP_004176217.1|   3 G-VAVLIPSFDRARMLKIILPRWLAS-AHVCSVIVLAEASSAEVLDEYRRVLQGLDASG-KLIYRimPGRMGSVEAR 76 
                                       5.9***********999999999995.7899**********999985554444444322.33333113334543333 PP

                   Glyco_tranf_2_3  77 ral.nealravksdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfllnrstl............vsalgal 139
                                       ++l + al+++++++ ll DdD +  + dtl ++l  ++++kvgavg++v +l+ +++             +al++ 
  gi|320100625|ref|YP_004176217.1|  77 NMLlEMALKHTTCEYFLLTDDDYLPiDEDTLGVMLKHMRDDKVGAVGGRVVVLRKRRVdpdfflntpfliADALTR- 152
                                       333134566799************99**************************999888888888867665333333. PP

                   Glyco_tranf_2_3 140 efaerhlrflaarralgvltlnGsgslirrevlkelegldplfllt....dDyelglrlrragfrtayvpgaa 208
                                        ++  +l++    r+  +l+   s++++rrev ++  +  ++f++     +  +l+  +++ g+r +  p+a 
  gi|320100625|ref|YP_004176217.1| 153 LIGYVFLDVEHGPRYAEFLP---SFFMVRREVIENGVRYSKAFSTPtgfrEESDLQQQIKNLGYRLVLEPRAR 222
                                       23445555555577888887...99999999999877544434433123344466666666666666655555 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 !   27.0   0.0   5.5e-10   3.3e-06       2     119 ..       6     128 ..       5     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.5e-10
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH......C-TTEEEEEESSS-HHHHHHH CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak......edprvrvirreenvGkagaln 72 
                                       v ip++ ++ +l+  l + la   +    +iv+  +S   ++e+l+e+++       ++++++  ++ + G   a+n
  gi|320100625|ref|YP_004176217.1|   6 VLIPSFDRARMLKIILPRWLAS--AHVCSVIVLAEAS---SAEVLDEYRRvlqgldASGKLIYRIMPGRMGSVEARN 77 
                                       7888888888888888888887..8888999999999...78888888888889999**********999******* PP

                                       H....HHHH--SSEEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEE CS
                   Glycos_transf_2  73 a....glraatgdyilflDaDdepdpd.wleklvealekdgadvvlgqrpri 119
                                            +l+++t +y+l+ D+D  p ++ +l  +++++ +d +++v g ++  
  gi|320100625|ref|YP_004176217.1|  78 MllemALKHTTCEYFLLTDDDYLPIDEdTLGVMLKHMRDDKVGAVGGRVV-V 128
                                       6333478899999**********98887***********66655555544.3 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 ?   12.6   0.0   1.2e-05     0.069      24      75 ..      82     134 ..      65     154 .. 0.83
   2 ?   -3.1   0.0      0.76   4.5e+03     134     157 ..     206     229 ..     204     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                   Glyco_transf_21  24 qaleaakydllvisDsdvr.vkpdyLeellaaledpkvglVtslpvgsdakgl 75 
                                        al+    +++++ D+d + +++d+L  +l++++d+kvg V + +v+ +++ +
  gi|320100625|ref|YP_004176217.1|  82 MALKHTTCEYFLLTDDDYLpIDEDTLGVMLKHMRDDKVGAVGGRVVVLRKRRV 134
                                       4556678899999999987479*******************999988887765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.76
                   Glyco_transf_21 134 kllraaGlkvvlspapiaqtsvpr 157
                                       ++++  G+++vl p++ + + vp+
  gi|320100625|ref|YP_004176217.1| 206 QQIKNLGYRLVLEPRARVVNLVPE 229
                                       567888999999988866666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2290.96
//
Query:       gi|320100626|ref|YP_004176218.1|  [L=383]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-34  118.0   0.1    9.8e-34  116.4   0.0    1.8  2  Glycos_transf_1  Glycosyl transferases group 1
    1.9e-23   83.4   0.1    4.3e-23   82.2   0.1    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.7e-20   73.7   0.4      4e-20   72.5   0.4    1.6  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.8e-13   51.3   0.0    3.3e-13   50.4   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.4e-05   23.9   0.0    7.5e-05   22.8   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    5.1e-05   23.1   0.1    6.9e-05   22.7   0.1    1.3  1  Glyco_transf_5   Starch synthase catalytic domain
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.033   14.6   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.7   1.8e+03      15      75 ..     111     173 ..     102     177 .. 0.61
   2 !  116.4   0.0   3.8e-37   9.8e-34       6     166 ..     193     354 ..     188     360 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.7
                                       -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGG CS
                   Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnv 75 
                                       + ++ ++g    +  ++lli+ f  + +++ ++ ++ +a     ++e+e + l e+++++++v
  gi|320100626|ref|YP_004176218.1| 111 PVVVYFLGVSYLRHHYNLLIRIFGYFYQRMVERGVVELADmaLATNEYEAELLREKYGVKATV 173
                                       455555555556666666666666666666665555555566556667777777777777665 PP

  == domain 2  score: 116.4 bits;  conditional E-value: 3.8e-37
                                       HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEEC CS
                   Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflge 80 
                                       r+k+++  + +ii +vgr+ ++Kg+dll+kafa++ kq  ++++lviaG  +++++++  +lae+l++s +vi++g+
  gi|320100626|ref|YP_004176218.1| 193 REKYRI--NNRIIAYVGRIHYTKGLDLLLKAFAQIAKQ-VDDTVLVIAGkgDKKYFDKCMHLAEKLGVSSRVIYVGF 266
                                       444444..699************************998.***********99************************* PP

                                       CHSSSHHHHHHCESEEEEEESS..BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHH CS
                   Glycos_transf_1  81 vsredleellknadifvlpsis..EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkl 155
                                       + +ed++ l+ ++d++vlps+   E+f++ ++E ++   p++++nag++   v++ge+G++v+  + + l++ai  +
  gi|320100626|ref|YP_004176218.1| 267 LTEEDKIGLIDASDVVVLPSRHagESFPLLVYEVISRLRPIVVTNAGMLGYHVRNGEDGFVVAVDDLQGLSNAILAI 343
                                       ***************************************************************************** PP

                                       HHSHHHHHHHH CS
                   Glycos_transf_1 156 ledeelrerlg 166
                                       l+d++lre ++
  gi|320100626|ref|YP_004176218.1| 344 LKDRDLREYIK 354
                                       ******99876 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       6.1   1.6e+04      91     104 ..      31      44 ..      29      57 .. 0.74
   2 !   82.2   0.1   1.7e-26   4.3e-23       2     134 .]     201     346 ..     200     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.1
                                       HHTT-EEEE-TGGG CS
                   Glyco_trans_1_4  91 maaglpvVatdvgg 104
                                       m +++ v++++ g+
  gi|320100626|ref|YP_004176218.1|  31 MGHEVHVITSNYGA 44 
                                       78889999999843 PP

  == domain 2  score: 82.2 bits;  conditional E-value: 1.7e-26
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---....HHHHHHHT..T-T.TEEEE---..THHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgprp..eeleelaa..gleerveftGfv..edlaell 70 
                                       ++i +vGr+ +  kg+dlll+a+++++k+ d   lvi+G+g+++  +++ +la+  g+++rv+++Gf+  ed+  l+
  gi|320100626|ref|YP_004176218.1| 201 RIIAYVGRI-HYTKGLDLLLKAFAQIAKQvDdTVLVIAGKGDKKyfDKCMHLAEklGVSSRVIYVGFLteEDKIGLI 276
                                       5799*****.566**************998569******99744454444455468999*********9889***** PP

                                       HH-SEEEE--....---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  71 aaadvfvaPs....egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +a+dv+v+Ps    e+f+l ++E  +  +p+V+t++g +   v  ge+g++v+ +d + l +ail++l+d
  gi|320100626|ref|YP_004176218.1| 277 DASDVVVLPSrhagESFPLLVYEVISRLRPIVVTNAGMLGYHVrnGEDGFVVAVDDLQGLSNAILAILKD 346
                                       **********99888*********************655666679**********************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 !   72.5   0.4   1.5e-23     4e-20       1     167 [.      14     179 ..      14     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.5e-23
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvH 77 
                                       vGG e  v  +a++  ++GheV+v+t++++   + + e v ++++v ++ ++rl++    ++    +   ek+DvvH
  gi|320100626|ref|YP_004176218.1|  14 VGGLEKAVQKVAEEQTKMGHEVHVITSNYGANGRPK-EEVLNGVYVHRVRSWRLGFADLTIPLEYPVDLFEKVDVVH 89 
                                       7**************************998666666.33444444444444444443333332222223359***** PP

                    Glyco_transf_4  78 ahspaalgaallalrr.rlgiplVltvHglye..krllkarlkplsrllralerrllrradrviavSeatadelrer 151
                                       ++s  +l+  l   ++ rl++p+V+++ g  +  +++    + +++ + r++er ++  ad  +a+ e++a+ lre+
  gi|320100626|ref|YP_004176218.1|  90 SWSQNSLFTYLMSKKAkRLRKPVVVYFLGVSYlrHHYNLLIRIFGYFYQRMVERGVVELADMALATNEYEAELLREK 166
                                       ***99987655555557**************8644444445556778888899999********************* PP

                    Glyco_transf_4 152 ygvppekitVipnGvD 167
                                       ygv++   tV+p+G+D
  gi|320100626|ref|YP_004176218.1| 167 YGVKA---TVVPHGID 179
                                       **997...*******9 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 !   50.4   0.0   1.3e-16   3.3e-13       1     160 []      15     177 ..      15     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.3e-16
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgape..leedgvrvhrlpvprrpspladlaalral.rrllrqrrerp 74 
                                       gG ++ v+ +a+++ + GheV+v+t+++ ++ ++  ++ +gv vhr++  r   ++adl  +     +l+    e++
  gi|320100626|ref|YP_004176218.1|  15 GGLEKAVQKVAEEQTKMGHEVHVITSNYGANGRPkeEVLNGVYVHRVRSWRL--GFADLTIPLEYpVDLF----EKV 85 
                                       89***********************998888776335567999999887766..5999998765526676....9** PP

                   Glyco_trans_4_4  75 dvvh..ahspt.aglaarlarrrrgiplvvtlhg..lllrrgsgavrrly.....ralerrllrradavlvvseaea 141
                                       dvvh  +++++ + l  + a+ r + p+vv + g    lr++   + r++     r++er ++  ad  l++ e+ea
  gi|320100626|ref|YP_004176218.1|  86 DVVHswSQNSLfTYLMSKKAK-RLRKPVVVYFLGvsY-LRHHYNLLIRIFgyfyqRMVERGVVELADMALATNEYEA 160
                                       ****44344443566677888.889999999998432.33333333443333446999******************* PP

                   Glyco_trans_4_4 142 eelra.lgvpadrvvvvpng 160
                                       e+lr+ +gv     +vvp g
  gi|320100626|ref|YP_004176218.1| 161 ELLREkYGVK---ATVVPHG 177
                                       *****77776...5677765 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 !   22.8   0.0   2.9e-08   7.5e-05      14     114 ..      22     124 ..      14     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                   Glyco_trans_4_2  14 lrlakeLakrgyeVhvitpkkga...kdeleaegihvhrlkvdrkgpleylka.fkl.kklikkikPDvvhahyakp 85 
                                        ++a+e  k g+eVhvit++ ga    +e++ +g++vhr++ +++  + +l++ +++ ++l++k   Dvvh    ++
  gi|320100626|ref|YP_004176218.1|  22 QKVAEEQTKMGHEVHVITSNYGAngrPKEEVLNGVYVHRVR-SWRLGFADLTIpLEYpVDLFEK--VDVVHSWSQNS 95 
                                       5677788889*********87665557888899*******9.8888999999625998999986..6*********9 PP

                   Glyco_trans_4_2  86 y.gllgslaarlsgvipvvlsvwGldvlkf 114
                                       +  +l s  a++++ +pvv+ + G ++l++
  gi|320100626|ref|YP_004176218.1|  96 LfTYLMSKKAKRLR-KPVVVYFLGVSYLRH 124
                                       96666777788898.9****9999888766 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 !   22.7   0.1   2.7e-08   6.9e-05       2      93 ..       3     105 ..       2     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.7e-08
                    Glyco_transf_5   2 ilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeek......keleevaelskaaed.eveve. 70 
                                       i+++   ++p   +GGL ++v++ +++  k+gh+v+vi+ +yga  + k        +++v +++  ++d ++++e 
  gi|320100626|ref|YP_004176218.1|   3 IVHIFHNYCP--VVGGLEKAVQKVAEEQTKMGHEVHVITSNYGANGRPKeevlngVYVHRVRSWRLGFADlTIPLEy 77 
                                       6777777788..89****************************65555445688775677888888888888888885 PP

                    Glyco_transf_5  71 .v...ekvkvaklkkd.gvdvyfldnpe 93 
                                        v   ekv+v ++ ++  + +y++++++
  gi|320100626|ref|YP_004176218.1|  78 pVdlfEKVDVVHSWSQnSLFTYLMSKKA 105
                                       4267899999998885366666665554 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-05     0.033       2      90 ..     282     374 ..     281     376 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                   Glyco_trans_1_2   2 vLnpsrs..espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaar 74 
                                       v+ psr+  es+ l ++E+    ++++++ a  l++++++g+++++++  dl+ l  +i + l+++++r+ i  + +
  gi|320100626|ref|YP_004176218.1| 282 VVLPSRHagESFPLLVYEVISRLRPIVVTNAGMLGYHVRNGEDGFVVAvdDLQGLSNAILAILKDRDLREYIKLNLI 358
                                       56677887788999999************9****************************************9999998 PP

                   Glyco_trans_1_2  75 ervlaehtydhraeql 90 
                                       er +    ++  a ++
  gi|320100626|ref|YP_004176218.1| 359 ERRRVLWLWRDVASKF 374
                                       8866556666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2719.10
//
Query:       gi|320100627|ref|YP_004176219.1|  [L=613]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4257.59
//
Query:       gi|320100628|ref|YP_004176220.1|  [L=273]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  106.2   0.0    1.7e-30  105.8   0.0    1.1  1  Glycos_transf_1  Glycosyl transferases group 1
    4.2e-22   79.0   0.0    5.9e-22   78.5   0.0    1.2  1  Glyco_trans_1_4  Glycosyl transferases group 1
      2e-07   31.3   0.2    4.2e-07   30.3   0.2    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.0   2.9e-34   1.7e-30      12     169 ..      90     246 ..      81     249 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 2.9e-34
                                       TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHH CS
                   Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredlee 88 
                                       +++   +++v+rl ++Kg  +l+kaf ++ ++  ++++l+++G+g+e   l++l+ +l+l+++vif+g + r +   
  gi|320100628|ref|YP_004176220.1|  90 DSNSASVVFVSRLMEYKGGFRLVKAFVHVVEE-VKDTVLHVIGEGPEGPLLRELVRKLGLEKHVIFHGWLGRRETLR 165
                                       5667789***********************97.******************************************** PP

                                       HHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHH CS
                   Glycos_transf_1  89 llknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerl 165
                                       ++ ++ i+ +ps +E+fG v+ EA a+g+pv+a+ a+  +e+v++   Gl+v + + + +aea+  ll+d++l++rl
  gi|320100628|ref|YP_004176220.1| 166 VIASSRILTHPSLYESFGYVIAEAYALGKPVVAHRASYSLELVENFGAGLVVNTFDEKRYAEALMTLLTDDNLYRRL 242
                                       ***************************************************************************** PP

                                       HHHH CS
                   Glycos_transf_1 166 gena 169
                                       +++a
  gi|320100628|ref|YP_004176220.1| 243 SQRA 246
                                       9987 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   9.9e-26   5.9e-22       3     134 .]      95     235 ..      93     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 9.9e-26
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaa 72 
                                        ++fv+rl  ++kg   l++a+ ++ ++  d  l+++G+gp   + l+el++  gle++v+f+G++   +  +++a+
  gi|320100628|ref|YP_004176220.1|  95 SVVFVSRL-MEYKGGFRLVKAFVHVVEEvkDTVLHVIGEGPeG-PLLRELVRklGLEKHVIFHGWLgrRETLRVIAS 169
                                       68******.566**********77776654599*******954.5788877668************9888******* PP

                                       -SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--...TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs..egfglkllEamaaglpvVatdvggiaevv...gengllvppgdpealaeailrLled 134
                                       ++++  Ps  e+fg+++ Ea a+g+pvVa +++   e+v   g +gl+v+  d++ +aea+ +Ll+d
  gi|320100628|ref|YP_004176220.1| 170 SRILTHPSlyESFGYVIAEAYALGKPVVAHRASYSLELVenfG-AGLVVNTFDEKRYAEALMTLLTD 235
                                       ********************************86699997533.79****9**************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 !   30.3   0.2     7e-11   4.2e-07       4      91 ..     175     264 ..     169     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7e-11
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervl 78 
                                       +ps +es+ +++ Ea+a G ++++ +a+   el+++   ++++   d++  ae++  ll+++ ++r+++++a + ++
  gi|320100628|ref|YP_004176220.1| 175 HPSLYESFGYVIAEAYALGKPVVAHRASYSLELVENFGAGLVVNtfDEKRYAEALMTLLTDDNLYRRLSQRALATAE 251
                                       58899**********************9999999998899999989******************************* PP

                   Glyco_trans_1_2  79 aehtydhraeqll 91 
                                       + ++ ++ ae++l
  gi|320100628|ref|YP_004176220.1| 252 EYFDIRRTAEEYL 264
                                       **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1993.53
//
Query:       gi|320100629|ref|YP_004176221.1|  [L=204]
Description: polysaccharide deacetylase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   99.5   0.0    5.1e-28   97.5   0.0    1.8  2  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
      0.091   12.5   0.2       0.67    9.7   0.1    2.1  2  HTH_39           Helix-turn-helix domain
       0.17   11.7   0.0       0.23   11.2   0.0    1.1  1  DUF4675          Domain of unknown function (DUF4675)


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.0   8.6e-32   5.1e-28       7     118 ..       2     120 ..       1     123 [. 0.95
   2 ?   -0.6   0.0      0.19   1.1e+03       8      36 ..     165     193 ..     161     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 8.6e-32
                                       TEEEEEEEESSCSCHHHHHHHHHHCT--EEEEE-HHHHCH-........HHHHHHHHHTTEEEEE--SS--EGGGSH CS
                   Polysacc_deac_1   7 ksvalTfDdgprdntteilpvLkkykvkatffvigglvedy........pdevremaasGveignHtinhsnlkrls 75 
                                       ++++lTfDdg+ + + ei ++L + +v+atff+i+gl+e +        p+++rem + G+ei++Ht++h +l+r  
  gi|320100629|ref|YP_004176221.1|   2 RCAVLTFDDGYLSHY-EIAKMLYRMDVPATFFIITGLMEYNgrrllatrPELIREMRDMGHEIASHTVSHRDLTRIP 77 
                                       689********7766.799******************888888888888**************************** PP

                                       HHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHH CS
                   Polysacc_deac_1  76 eeevrreierakdalrkalgreprlfryPygsasatvlevare 118
                                         ev+re +++k++l++ + +e++ ++yPygs++++v+ev+r+
  gi|320100629|ref|YP_004176221.1|  78 VWEVEREAAESKKMLEETVRDEVKGLAYPYGSFNDRVVEVVRR 120
                                       ***************************************9986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.19
                                       EEEEEEEESSCSCHHHHHHHHHHCT--EE CS
                   Polysacc_deac_1   8 svalTfDdgprdntteilpvLkkykvkat 36 
                                        v+lT  d  +  +++++++L++ +++ t
  gi|320100629|ref|YP_004176221.1| 165 LVVLTMHDERQLIVRAVVELLRALGFRLT 193
                                       57888888888888888888888887766 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00011      0.67      34      51 ..      53      70 ..      46      75 .. 0.86
   2 ?   -0.1   0.0      0.13   7.8e+02      34      49 ..     182     197 ..     178     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                            HTH_39 34 IkeLrekGyeIktervte 51
                                      I+e+r++G+eI  ++v  
  gi|320100629|ref|YP_004176221.1| 53 IREMRDMGHEIASHTVSH 70
                                      99***********99765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.13
                            HTH_39  34 IkeLrekGyeIkterv 49 
                                       +  Lr+ G++ +t  +
  gi|320100629|ref|YP_004176221.1| 182 VELLRALGFRLTTLSE 197
                                       5668999999998764 PP

>> DUF4675  Domain of unknown function (DUF4675)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.9e-05      0.23      48     101 ..      46     101 ..      41     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.9e-05
                           DUF4675  48 istsPtL.RRLRgsGcg.tlhslpqqdalevptWgswkepagspcyLskslpgspk 101
                                       ++t P L R +R  G   ++h+++++d   +p+W+  +e a+s + L + + ++ k
  gi|320100629|ref|YP_004176221.1|  46 LATRPELiREMRDMGHEiASHTVSHRDLTRIPVWEVEREAAESKKMLEETVRDEVK 101
                                       67888774779****8646799*************************998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1472.58
//
Query:       gi|320100630|ref|YP_004176222.1|  [L=405]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-09   36.2   0.0    1.4e-08   35.3   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.4e-08   33.7   0.0    4.1e-08   32.9   0.0    1.4  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 !   35.3   0.0   1.5e-12   1.4e-08      13     118 ..     238     349 ..     224     377 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.5e-12
                                       G.GTHHHHHHHHHHHH.HH...EEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE--.... CS
                   Glyco_trans_1_4  13 nvkgvdllleavpllrkkd...vrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfvaPs.... 80 
                                         kg++++   ++ lrk+    + +v+ G    + + ++++++   ++++ Gf+  ++  ++l+ +d++ +P     
  gi|320100630|ref|YP_004176222.1| 238 FLKGLHYIPVIWKMLRKEYggrIVIVLTG---VSGRWRDMLRE--MGIRVYGFLphQEFLRFLSTSDIYFFPAtggy 309
                                       56899998889999998844456666666...33356656653..58*******9888***************7655 PP

                                       .---SHHHHHHHHTT-EEEE-TGG.GTTT--TTSSEE--T CS
                   Glyco_trans_1_4  81 .egfglkllEamaaglpvVatdvg.giaevvgengllvpp 118
                                         g g++++Eama+g+pvV+ +    ++e++ ++g +v p
  gi|320100630|ref|YP_004176222.1| 310 yGGPGVAVMEAMALGKPVVSPTFLeMPREAIPRTGAVVTP 349
                                       4488****************99852568888777877654 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 !   32.9   0.0   4.6e-12   4.1e-08      74     151 ..     279     363 ..     226     384 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.6e-12
                                       GGGEEECCHSSSHHHHHHCESEEEEEESS...BSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTT...SEEEE-TT CS
                   Glycos_transf_1  74 nviflgevsredleellknadifvlpsis...EgfGivllEAmaaglpviasn.aggpaevvkdge...tGllvkpn 143
                                        ++++g++++++   +l+ +di+++p++     g G++++EAma+g+pv++    ++p+e +       t ++  ++
  gi|320100630|ref|YP_004176222.1| 279 GIRVYGFLPHQEFLRFLSTSDIYFFPATGgyyGGPGVAVMEAMALGKPVVSPTfLEMPREAIPRTGavvTPFVGNAK 355
                                       579***********************987888*******************99899999988765534444444444 PP

                                       -HHHHHHH CS
                   Glycos_transf_1 144 naealaea 151
                                       +   ++++
  gi|320100630|ref|YP_004176222.1| 356 DLNVFIKR 363
                                       44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 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:                        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: 00:00:00.42
# Mc/sec: 2882.48
//
Query:       gi|320100631|ref|YP_004176223.1|  [L=331]
Description: oxidoreductase domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-29  102.9   0.4    2.7e-29  102.4   0.4    1.2  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00032   21.2   0.1    0.00058   20.4   0.1    1.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00066   19.7   0.0     0.0011   18.9   0.0    1.3  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.023   15.2   0.2      0.043   14.3   0.2    1.4  1  CoA_binding_2   CoA binding domain
      0.041   14.5   0.2      0.074   13.7   0.2    1.4  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
      0.047   13.7   0.2      0.097   12.7   0.0    1.6  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.071   13.7   0.1       0.16   12.6   0.1    1.5  1  Biotin_carb_N   Biotin carboxylase, N-terminal domain
       0.15   12.8   0.1       0.27   11.9   0.1    1.4  1  CoA_binding     CoA binding domain
       0.19   12.2   0.5       0.38   11.2   0.1    1.6  2  NAD_binding_7   Putative NAD(P)-binding


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 !  102.4   0.4   1.4e-32   2.7e-29       1     118 [.       4     120 ..       4     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.4e-32
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngthe 76 
                                       lrv+i+G+G+++ +h++ ++++  +++vva+ d+  era+ +aes g++  +s+lee+l+d e d+v+++tp++th+
  gi|320100631|ref|YP_004176223.1|   4 LRVGIVGGGFAAGHHVKGWRAN--KAKVVAVSDIAVERARVFAESHGIPrYFSSLEEMLKDVELDVVSICTPPQTHR 78 
                                       69******************99..9************************999************************* PP

                                       HHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEE CS
                      GFO_IDH_MocA  77 elakaaleagkhvllEKPlattveeakelvelaekkgklvsv 118
                                       e+a ++++a+ + ++EKPlat++++a e+++ a++kg++v+v
  gi|320100631|ref|YP_004176223.1|  79 EVAVKVAQANANMFVEKPLATSYSDAAEILNVARSKGVKVGV 120
                                       ***************************************988 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.9e-07   0.00058       1      84 [.       5      86 ..       5      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.9e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S-HHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae..eadvvvlavkpedveev 77
                                      ++gi+G+G  +   ++g+ a+     ++v +++   e+a+ +ae+ g+    ++ ee+++  e dvv ++ +p+ + ev
  gi|320100631|ref|YP_004176223.1|  5 RVGIVGGGFAAGHHVKGWRANK---AKVVAVSDIAVERARVFAESHGIPRYFSSLEEMLKdvELDVVSICTPPQTHREV 80
                                      69*******************9...999999999*************5555559*****98999*************** PP

                                      HHHCGHH CS
                     F420_oxidored 78 lselakd 84
                                      + ++ ++
  gi|320100631|ref|YP_004176223.1| 81 AVKV-AQ 86
                                      9888.33 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 !   18.9   0.0   5.6e-07    0.0011       1      99 [.     134     228 ..     134     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.6e-07
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCT CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaea 77 
                                       + l+++g++G+v  vd+ ++  r+   a+++++ +   +g v+g+ + H i++lq + G+  +v+++  r+++ + +
  gi|320100631|ref|YP_004176223.1| 134 RRLVREGVIGPVCRVDIAVYAPREVVLARSGGWLES-LPGHVFGEVLPHAIYILQDIIGKLDVVSVDFSRLSEGGWT 209
                                       5799*****************************986.999****************************998888888 PP

                                       CCSCSEEEEEEEEEEETTEEEE CS
                    GFO_IDH_MocA_C  78 aededaavmsvlnlekgsgevi 99 
                                         de +a   vl++e g+g+++
  gi|320100631|ref|YP_004176223.1| 210 LYDELYA---VLRGERGVGRLT 228
                                       8888888...899999999865 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   2.2e-05     0.043      39     105 ..      45     118 ..      13     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                       EETTEES-.---T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHTT-EE CS
                     CoA_binding_2  39 eilgekvy.aslaed..pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeeagirv 105
                                       e +g + y  sl+e   + ++d+v+++tpp++  e++ ++++++a+ ++  p     s  +e++++a+++g++v
  gi|320100631|ref|YP_004176223.1|  45 ESHGIPRYfSSLEEMlkDVELDVVSICTPPQTHREVAVKVAQANANMFVEKPLatsySDAAEILNVARSKGVKV 118
                                       55666644155555246899*********************999998888877887788899999999999987 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   3.7e-05     0.074      13     114 ..      19     118 ..       6     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                                       HHH---SSEEEEEEEEESSEEE-TT.HHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE- CS
                     NAD_binding_3  13 lkrqqseielelvavadrdsllskd.rkallasealtldlddliahldpdvvVEcasseavaelvlkaLkagkdvvt 88 
                                       +k  +++ ++++vav d    ++++  ++  +  +  ++l++++++++ dvv  c++++  +e+++k+ +a+ ++ +
  gi|320100631|ref|YP_004176223.1|  19 VKGWRAN-KAKVVAVSDIA-VERARvFAESHGIPRYFSSLEEMLKDVELDVVSICTPPQTHREVAVKVAQANANMFV 93 
                                       4444444.55555555555.44444588889999999*************************************999 PP

                                       S--CGGG-HHHHHHHTSSSTTS--.E CS
                     NAD_binding_3  89 ankgaladealyeeLreaaeangaki 114
                                           a +     +e+++ a+++g+k+
  gi|320100631|ref|YP_004176223.1|  94 EKPLATS-YSDAAEILNVARSKGVKV 118
                                       8888888.888999999999999987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05     0.097      14      89 ..       5      78 ..       1      97 [. 0.76
   2 ?   -3.3   0.0       4.2   8.4e+03     104     117 ..     143     158 ..     132     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHH..T-SEEEE-SSSSS-S CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkella..eadvvisataseepi 89
                                      +v ++G G  a   +k   a+++k v+v    +era+ +ae++ g     + +++l+e+l+  e dvv ++t  +++ 
  gi|320100631|ref|YP_004176223.1|  5 RVGIVGGGFAAGHHVKGWRANKAKVVAVSDIAVERARVFAESH-GI---PRYFSSLEEMLKdvELDVVSICTPPQTHR 78
                                      899***************************************9.55...46667777777611456666666555544 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
                                       ..EEEEE--S..S-SB CS
                      Shikimate_DH 104 kplllvDiav..PRdv 117
                                        p+  vDiav  PR+v
  gi|320100631|ref|YP_004176223.1| 143 GPVCRVDIAVyaPREV 158
                                       5667899998668776 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 ?   12.6   0.1   7.9e-05      0.16      21      76 ..      60     117 ..      40     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.9e-05
                                       HHHTT-EEEEEEEGGGTTSH...HHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-S CS
                     Biotin_carb_N  21 vrelgietvavyseedansl...hvreadeavelgpasasesYlniekivkaakesgad 76 
                                       ++++++++v ++++++++ +    v +a++ + ++ ++ ++sY ++++i+++a+++g++
  gi|320100631|ref|YP_004176223.1|  60 LKDVELDVVSICTPPQTHREvavKVAQANANMFVE-KPLATSYSDAAEILNVARSKGVK 117
                                       34559999999999955543222566677777775.88899*************99986 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00014      0.27       5      88 ..       5      90 ..       3      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                      EEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TT..TTTCEETTEEEE.SCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding  5 kviviGagglgiagl.yhfkeklkygikavfgvnpr..kvgtevlglpvy.ksvdeleektevdvavitvPaesaqeav 79
                                      +v+++G g    ag  +++++ +k +++av ++  +   v  e +g+p y  s++e+ +++e dv  i++P++  +e++
  gi|320100631|ref|YP_004176223.1|  5 RVGIVGGGFA--AGHhVKGWRANKAKVVAVSDIAVEraRVFAESHGIPRYfSSLEEMLKDVELDVVSICTPPQTHREVA 81
                                      6889998888..99999999********99887765337779999999763678888888889999999********** PP

                                      HHHHHTT-S CS
                       CoA_binding 80 delveagik 88
                                      +++++a+ +
  gi|320100631|ref|YP_004176223.1| 82 VKVAQANAN 90
                                      ****99866 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 ?   11.2   0.1   0.00019      0.38       8      84 ..       4      87 ..       1      97 [. 0.67
   2 ?   -2.5   0.0       3.5   6.9e+03      28      56 ..     113     142 ..     104     160 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                     NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee.....l...ekdlegad..lviaatddrelne 76
                                       +v +vGgG  A + v+   +++akv+ v+     ++e+   +ae++     +   e+ l++++  +v ++t+ +  +e
  gi|320100631|ref|YP_004176223.1|  4 LRVGIVGGGFAAGHHVKGWRANKAKVVAVSDI---AVERARVFAESHgipryFsslEEMLKDVEldVVSICTPPQTHRE 79
                                      5899**************************99...55543333322222222444477777755438888887666666 PP

                     NAD_binding_7 77 riaeaaka 84
                                        ++ a+a
  gi|320100631|ref|YP_004176223.1| 80 VAVKVAQA 87
                                      55555543 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.5
                     NAD_binding_7  28 eagakvtvvapevkeele.elvklaeeele 56 
                                       ++g kv vv++ +   ++ +  +l +e + 
  gi|320100631|ref|YP_004176223.1| 113 SKGVKVGVVSNYLYTPVSiKARRLVREGVI 142
                                       456677777766533333344445555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2534.99
//
Query:       gi|320100632|ref|YP_004176224.1|  [L=310]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-11   44.2   0.1    2.9e-11   43.7   0.1    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.8e-10   39.8   0.0    6.1e-10   39.2   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.2e-05   25.4   0.2    4.7e-05   23.4   0.1    1.8  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.3e-05   24.8   0.0    2.9e-05   23.6   0.0    1.6  1  Glyco_transf_21  Glycosyl transferase family 21
     0.0035   16.9   0.0      0.028   13.9   0.0    1.9  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0088   15.7   0.0      0.033   13.9   0.0    1.7  2  Glyco_tranf_2_5  Glycosyltransferase like family
  ------ inclusion threshold ------
       0.15   11.6   0.0       0.25   10.9   0.0    1.2  1  Gal-bind_lectin  Galactoside-binding lectin


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 !   43.7   0.1   1.1e-14   2.9e-11      15     223 ..      11     227 ..       3     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.1e-14
                   Glyco_tranf_2_3  15 dvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlv 91 
                                        +l+ +l+sl++q+  ++e++v  + sd+e le+++    +++d+   + v a   g   k r  n+a+   ++d+v
  gi|320100632|ref|YP_004176224.1|  11 GYLRLLLRSLSRQTMRPSEIIVASEVSDRELLETVKR---ECGDT---CMVLAT--GLWNKCRTANRAILESRGDIV 79 
                                       5777899******9999****************9975...9***6...777766..666899999999999****** PP

                   Glyco_tranf_2_3  92 llvDdDtvvePdtlkrllqff.ltpkvgavg.tpvflln.rstl........vsalgalefaerhlrflaar..ral 155
                                        l++dD v+  d+++ ++ +f ++ ++g+v+  +v++ + + +         ++ l +l + e  l + +++  r l
  gi|320100632|ref|YP_004176224.1|  80 FLLEDDLVLREDFIEEVVKTFdRDGSIGCVYsRCVWVFReGARSrggplglaTRLLSKLSVHESLLPRQVRTidRHL 156
                                       *********************9888******8888884413333556677778888999988888877777643333 PP

                   Glyco_tranf_2_3 156 gvltlnGsgslirrevlkelegldp...lflltdDyelglrlrragfrtayvpgaavrevfpsslkayikq 223
                                         +++ +  ++ rre l + ++ d+     + ++D++l++r+r+ag+r++   +a+ ++ +++  k++ ++
  gi|320100632|ref|YP_004176224.1| 157 AEIPVFTMSVACRREALLRAGLYDEsveEPIQGEDFDLAMRVRAAGYRIVANGKAVSYHFTRQVSKRVERL 227
                                       3366667779***********666666789999****************9777776666666444444443 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 !   39.2   0.0   2.4e-13   6.1e-10       6     115 ..       6     111 ..       4     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.4e-13
                                       ESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSE CS
                   Glycos_transf_2   6 tyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdy 82 
                                       t+ +  +l+ +l+sl +q +    eiiv+   S  e+ e +++ +    + + +  +  + k +  n+++ +++gd+
  gi|320100632|ref|YP_004176224.1|   6 THERLGYLRLLLRSLSRQ-TMRPSEIIVASEVSDRELLETVKRECG---DTCMVLATGLWNKCRTANRAILESRGDI 78 
                                       5667889***********.**************99********994...555555555567**************** PP

                                       EEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEE CS
                   Glycos_transf_2  83 ilflDaDdepdpdwleklvealekdgadvvlgq 115
                                       +++l +D++  +d++e++v+ +++dg  + +++
  gi|320100632|ref|YP_004176224.1|  79 VFLLEDDLVLREDFIEEVVKTFDRDGSIGCVYS 111
                                       ************************777444444 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 ?   -0.3   0.0      0.34   8.8e+02       1      27 [.      78     105 ..      78     124 .. 0.78
   2 !   23.4   0.1   1.9e-08   4.7e-05      71     160 ..     160     253 ..     151     292 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.34
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelas.pe 27 
                                       i+ ll +D vl +d+++e++  +++ + 
  gi|320100632|ref|YP_004176224.1|  78 IVFLLEDDLVLREDFIEEVVKTFDRdGS 105
                                       6789999999*********999985244 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.9e-08
                   Glyco_trans_2_3  71 psvGsgaflrrsalqevggwdgdes....svsEDfdmglrlqrkGyrvrfv....peslvkekspltlraalrQrkR 139
                                       p+++  ++ rr+al ++g +d  es      +EDfd+++r +++Gyr++      ++++++++s +    +lr+  R
  gi|320100632|ref|YP_004176224.1| 160 PVFTMSVACRREALLRAGLYD--ESveepIQGEDFDLAMRVRAAGYRIVANgkavSYHFTRQVSKR--VERLRRDPR 232
                                       556667889*********777..3333459******************776222255555555555..778999*** PP

                   Glyco_trans_2_3 140 wayGc..eleklillvrllgylg 160
                                       ++ G+  +  ++++l +++g+ g
  gi|320100632|ref|YP_004176224.1| 233 HIEGVyrS--EVYFLAKNRGLVG 253
                                       ****7431..2222333333333 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 !   23.6   0.0   1.1e-08   2.9e-05      18     149 ..      63     211 ..      57     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.1e-08
                   Glyco_transf_21  18 KvnnllqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakg.........laaaleaafl 84 
                                       K    ++a+ + + d++ ++ +d ++++d++ee+++++ +   +g+V s  v + ++g         la++l + + 
  gi|320100632|ref|YP_004176224.1|  63 KCRTANRAILESRGDIVFLLEDDLVLREDFIEEVVKTFDRdGSIGCVYSRCVWVFREGarsrggplgLATRLLSKLS 139
                                       5555667778899*************************765899***998887766665556667766666644443 PP

                   Glyco_transf_21  85 ...ntlagvlqa...klsglgfavGksmalrreaLeaiGGfealade.L.AeDyalgkllraaGlkvvlspap 149
                                          + l++ +     +l++   ++ +s+a rreaL ++G + +  +e +  eD+ l++++raaG+++v   ++
  gi|320100632|ref|YP_004176224.1| 140 vheSLLPRQVRTidrHLAE-IPVFTMSVACRREALLRAGLYDESVEEpIqGEDFDLAMRVRAAGYRIVANGKA 211
                                       3544445555555324444.56788****************8766663459***************9987765 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 !   13.9   0.0   1.1e-05     0.028      67     215 ..      61     214 ..       3     264 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                   Glyco_tranf_2_2  67 yslaaarNrGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltas 143
                                       + + ++ Nr + ++ +d+v+ l+ D     D +e ++k      + +      v++   ++  +     +++ l   
  gi|320100632|ref|YP_004176224.1|  61 WNKCRTANRAILESRGDIVFLLEDDLVLREDFIEEVVK-----TFDRDGSIGCVYSRCVWVFREGA-RSRGGPLGLA 131
                                       66666666666666677666666666666666666666.....44444444444443333222221.2344555555 PP

                   Glyco_tranf_2_2 144 srvledllaakstlvk..........ffapssssilinrraflevGGyDErfrGh.gaEDfdlllRlakaikslekm 209
                                       +r+l +l +  s l +           +   + s+  +r+a+l+ G yDE++  +   EDfdl +R+ +a   +   
  gi|320100632|ref|YP_004176224.1| 132 TRLLSKLSVHESLLPRqvrtidrhlaEIPVFTMSVACRREALLRAGLYDESVEEPiQGEDFDLAMRVRAAGYRIVAN 208
                                       5555555554444443445555533333334567889***************988346********98876555455 PP

                   Glyco_tranf_2_2 210 pvelly 215
                                          ++y
  gi|320100632|ref|YP_004176224.1| 209 GKAVSY 214
                                       555555 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.3e-05     0.033      42      88 ..      64     109 ..      59     109 .. 0.87
   2 ?   -1.3   0.0      0.58   1.5e+03     161     179 ..     189     207 ..     168     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                   Glyco_tranf_2_5  42 aeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkkiGmi 88 
                                       ++  n+a+ +s+  + v+l +D l++++dfi+++++ F+ d +iG +
  gi|320100632|ref|YP_004176224.1|  64 CRTANRAILESRGDI-VFLLEDDLVLREDFIEEVVKTFDRDGSIGCV 109
                                       678899999999987.677777788899****************975 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.58
                   Glyco_tranf_2_5 161 fYdvsqslefekagykvvV 179
                                         d + +++++ agy++v 
  gi|320100632|ref|YP_004176224.1| 189 GEDFDLAMRVRAAGYRIVA 207
                                       568899999******9986 PP

>> Gal-bind_lectin  Galactoside-binding lectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.7e-05      0.25      82     121 ..     188     227 ..     181     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.7e-05
                                       TTSEEEEEEEEESSEEEEEETTEEEEEEE-SSSG.GGEEEE CS
                   Gal-bind_lectin  82 egklFeltirageegfhiavngrhvtsFpyrlpf.edvtgl 121
                                       +g+ F+l++r++  g++i  ng+ v+ +++  +  ++v++l
  gi|320100632|ref|YP_004176224.1| 188 QGEDFDLAMRVRAAGYRIVANGKAVS-YHFTRQVsKRVERL 227
                                       7999******************9865.55544444777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2334.61
//
Query:       gi|320100633|ref|YP_004176225.1|  [L=328]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-20   71.9   0.0    8.9e-20   71.2   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    3.8e-11   43.3   0.0      4e-10   40.0   0.0    2.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.9e-10   40.7   0.0      8e-10   38.6   0.0    1.8  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
       0.02   15.3   0.0         11    6.5   0.0    2.6  2  Toprim_3         Toprim domain
       0.11   12.1   0.0       0.23   11.1   0.0    1.5  2  CAP59_mtransfer  Cryptococcal mannosyltransferase 1
       0.62   10.2   4.8         21    5.3   0.0    2.4  2  Na_H_antiport_2  Na+-H+ antiporter 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 !   71.2   0.0     3e-23   8.9e-20       1     147 [.       7     152 ..       7     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 3e-23
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH....C-TTEEEEEESSS-H....HHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak....edprvrvirreenvG....kag 69 
                                       s+vip+ Ne  ++++++ s+  q +y  +e++vvD gStD+t e l+el +     +  ++v++ e  +G    +a+
  gi|320100633|ref|YP_004176225.1|   7 SIVIPVKNERGNVEQLIMSIYGQ-TYRPIEVVVVDGGSTDGTLEALQELKAklkgAGFAIKVLKEE-DFGslrsPAN 81 
                                       8**********************.*************************99**7644455555444.3354444799 PP

                                       HHHHHHHH--SSEEEEEESSEEE..-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCH CS
                   Glycos_transf_2  70 alnaglraatgdyilflDaDdep..dpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerk 144
                                       a+n g+ +++g++i+f+DaD     dp+ +ek+v+ l ++++ ++ +++  + + +++              +  + 
  gi|320100633|ref|YP_004176225.1|  82 ARNIGVLNSSGEVIVFFDADFDLsgDPEAIEKIVAGLGEGEHVAITYAPNGHTWVERHL---------ALDDIVYYF 149
                                       *******************865511677***********88833333333332222222.........233444444 PP

                                       CCC CS
                   Glycos_transf_2 145 rsl 147
                                       r  
  gi|320100633|ref|YP_004176225.1| 150 RGG 152
                                       444 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 !   40.0   0.0   1.3e-13     4e-10       4     119 ..       6     126 ..       5     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.3e-13
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalp..dvrvrvvvnarnlgstgksra 78 
                                       +++++p+ ne   ++ +++s+  q+y ++evvvv+ +s+++tle ++el a+l+  +  ++v+  ++ ++ ++ ++a
  gi|320100633|ref|YP_004176225.1|   6 VSIVIPVKNERGNVEQLIMSIYGQTYRPIEVVVVDGGSTDGTLEALQELKAKLKgaGFAIKVLKEEDFGSLRSPANA 82 
                                       79****************************************************66556898888888899****** PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvv..ePdtlkrllqff.ltpkvga 119
                                        n ++ + ++++++++D+D  +  +P++++++++ + + + v++
  gi|320100633|ref|YP_004176225.1|  83 RNIGVLNSSGEVIVFFDADFDLsgDPEAIEKIVAGLgEGEHVAI 126
                                       *******************888799******9998866666655 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 !   38.6   0.0   2.7e-13     8e-10       1      98 [.       7     108 ..       7     120 .. 0.81
   2 ?   -0.7   0.0      0.26   7.7e+02     181     244 ..     171     245 ..     159     253 .. 0.55

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 2.7e-13
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnl....lv.ylkdeddk.ayslaa 71 
                                       s+vip+++++++  +e+ ++ +  +    ie++vvd+gS++ +le ++ ++++ +     +  lk+ed     s+a 
  gi|320100633|ref|YP_004176225.1|   7 SIVIPVKNERGN--VEQLIMSIYGQTYRPIEVVVVDGGSTDGTLEALQELKAKLKgagfAIkVLKEEDFGsLRSPAN 81 
                                       79**********..*****9998888899****************99999875431111454567776555679*** PP

                   Glyco_tranf_2_2  72 arNrGaskaesdlvlFlDaDcfissDk 98 
                                       arN G+ ++ +++++F DaD   s D 
  gi|320100633|ref|YP_004176225.1|  82 ARNIGVLNSSGEVIVFFDADFDLSGDP 108
                                       ********************8777663 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.26
                   Glyco_tranf_2_2 181 yDErfrGhgaEDfdlllRlakaikslekmpvellykaraksls..............nykGfrrflealakeaaalg 243
                                       +D ++ G g ED ++l+R     + +    v   y   +++l+                 G  r+  ++a+ +a lg
  gi|320100633|ref|YP_004176225.1| 171 FDASL-GFG-EDLEFLARAKTMWRVV-GTGVRRCYPHTLGQLMkqqlwygrtalryfRKVGAMRWPIDVARSNAVLG 244
                                       55555.443.7777777765555554.44444445544444444444444443332234455566666666666666 PP

                   Glyco_tranf_2_2 244 l 244
                                       +
  gi|320100633|ref|YP_004176225.1| 245 I 245
                                       5 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0036        11      39      79 ..      29      70 ..      10      77 .. 0.81
   2 ?    6.2   0.0    0.0044        13      26      69 ..      76     120 ..      69     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0036
                          Toprim_3 39 ergkrv.viaaDnDaandGreaaeklaerleaagieavllep 79
                                      ++++ + v++ D+++++   ea ++l ++l++ag+++ +l  
  gi|320100633|ref|YP_004176225.1| 29 QTYRPIeVVVVDGGSTDGTLEALQELKAKLKGAGFAIKVLKE 70
                                      577777799*******99*****************9998876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                          Toprim_3  26 llsaanlkaiawpergkrvviaaDnDaand.Greaaeklaerlea 69 
                                       l+s an ++i + + + +v++++D+D   +  +ea+ek+++ l +
  gi|320100633|ref|YP_004176225.1|  76 LRSPANARNIGVLNSSGEVIVFFDADFDLSgDPEAIEKIVAGLGE 120
                                       67778999999999************9876889999999876654 PP

>> CAP59_mtransfer  Cryptococcal mannosyltransferase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.8e-05      0.23      34      67 ..      34      67 ..      18      88 .. 0.83
   2 ?   -3.4   0.0       2.2   6.4e+03     190     209 ..     151     169 ..     136     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.8e-05
                   CAP59_mtransfer 34 vfvSiyesgskdgtkeaLraleaelealgversi 67
                                      + v ++++gs+dgt eaL++l+a+l+ +g   ++
  gi|320100633|ref|YP_004176225.1| 34 IEVVVVDGGSTDGTLEALQELKAKLKGAGFAIKV 67
                                      56889*********************99988777 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.2
                   CAP59_mtransfer 190 agldpvpVksCWnGmvalda 209
                                        g +p++V +C+   v  +a
  gi|320100633|ref|YP_004176225.1| 151 GG-RPLHVVCCFRRSVFSRA 169
                                       44.49999999876655444 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 ?    5.3   0.0     0.007        21      42      64 ..     110     132 ..     102     136 .. 0.88
   2 ?    2.2   5.1     0.068     2e+02       1      36 [.     240     275 ..     240     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.007
                   Na_H_antiport_2  42 tieafasGlgggaevAlsyallG 64 
                                        ie + +Glg+g +vA++ya  G
  gi|320100633|ref|YP_004176225.1| 110 AIEKIVAGLGEGEHVAITYAPNG 132
                                       689999*************9766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.068
                   Na_H_antiport_2   1 NavviavlvmlvLsllrvnvvlallisalvgGlvgg 36 
                                       Nav+  v++ ++ s++ +nv+l+l+++al+  +v++
  gi|320100633|ref|YP_004176225.1| 240 NAVLGIVALDVIVSAASMNVLLTLAVTALLLAFVAH 275
                                       89999999********************98777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2517.08
//
Query:       gi|320100634|ref|YP_004176226.1|  [L=96]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 799.10
//
Query:       gi|320100635|ref|YP_004176227.1|  [L=374]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-20   72.2   0.0    1.3e-19   70.7   0.0    1.8  1  Glycos_transf_2  Glycosyl transferase family 2
    2.9e-19   69.9   0.0    3.9e-19   69.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    9.1e-09   35.5   0.2    1.9e-08   34.4   0.2    1.6  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0029   17.1   0.1     0.0074   15.8   0.0    1.7  2  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
       0.02   14.4   0.0        6.1    6.2   0.0    2.1  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
       0.11   12.1   0.0       0.22   11.2   0.0    1.3  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   4.2e-23   1.3e-19       2     168 ..      20     196 ..      19     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 4.2e-23
                                       EEEEESS-....TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHH CS
                   Glycos_transf_2   2 vviptyNe....ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnag 74 
                                       +vi  yN      ++l ++++s+l q  y ++++i++D+gS D+++e + +    +++vrv+r+ +n G+  + n +
  gi|320100635|ref|YP_004176227.1|  20 IVILGYNArkslGPLLDRAIDSALGQ-SYGNVKVIFADNGSADDSAEYVSSKY--GDKVRVVRLGRNYGFCLGNNLA 93 
                                       7788899988889999**********.**************999999999885..8********************* PP

                                       HHH--SS..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.......EEEECCHCCC CS
                   Glycos_transf_2  75 lraatgd..yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv.......generlyfke 142
                                       +r+ + d  yilf++ D + ++ ++eklv+ +e+d+  +++++  r+ g+++     +            + l ++ 
  gi|320100635|ref|YP_004176227.1|  94 VRHLSPDikYILFMNPDAVLEERYVEKLVGIMERDESVGIAQGLQRSLGGSFSSLGGYVDsygraveVDVSGLEGRL 170
                                       **********************************9999988888888877776666554466654432233333333 PP

                                       CHCCCCCCSTTCSTCCCEEEEHHHHH CS
                   Glycos_transf_2 143 rkrslkgnlsfeigsaallrrealee 168
                                              +++  +gsa+++rre++e+
  gi|320100635|ref|YP_004176227.1| 171 SGLDAVFEVAWASGSAMMVRRELFER 196
                                       33333335555566666666666665 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 !   69.5   0.0   1.3e-22   3.9e-19       1     225 [.      15     256 ..      15     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.3e-22
                   Glyco_tranf_2_3   1 prdlavlVptfneed....vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgst 73 
                                       p+++a+++  +n+ +     l + ++s+l q+y++v+v++ +++s ++ +e +     +++d +vrvv   r ++ +
  gi|320100635|ref|YP_004176227.1|  15 PSKVAIVILGYNARKslgpLLDRAIDSALGQSYGNVKVIFADNGSADDSAEYVSS---KYGD-KVRVV---RLGRNY 84 
                                       56788999999998855556667999999999*************9998887765...9***.9***9...666678 PP

                   Glyco_tranf_2_3  74 gksralnealravksd..lvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs..tl...vsal.galef 141
                                       g+  + n a+r+ ++d  ++l+++ D+v+e +++++l+ ++ ++++vg++++ +++l +s  +l   v+ +  a+e+
  gi|320100635|ref|YP_004176227.1|  85 GFCLGNNLAVRHLSPDikYILFMNPDAVLEERYVEKLVGIMeRDESVGIAQGLQRSLGGSfsSLggyVDSYgRAVEV 161
                                       899999********7777*********************************99999754443334447777455588 PP

                   Glyco_tranf_2_3 142 aerhl..rflaarralgvltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrevfps 215
                                       +   l  r + ++  + v+  +Gs +++rre++++l+g+ p lf   d ++l+ r+ + g+rt+++p+a+ ++ +++
  gi|320100635|ref|YP_004176227.1| 162 DVSGLegRLSGLDAVFEVAWASGSAMMVRRELFERLGGFSPeLFMYHDEIDLCARALSLGYRTVVYPRAVYYHRRGT 238
                                       88888557777778889*999*************************************************9998665 PP

                   Glyco_tranf_2_3 216 s........lkayikqrn 225
                                       +        l+ y  +rn
  gi|320100635|ref|YP_004176227.1| 239 EgapkrinwLSWYLANRN 256
                                       544444444455555555 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 !   34.4   0.2   6.5e-12   1.9e-08       1     176 [.     103     287 ..     103     312 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 6.5e-12
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvmnvanwleelaalf......faedhgkdilvrealgrvv 70 
                                       +il++  D vl + ++++++  ++ +  v+i+qg     +++      +++        + + +  +l++       
  gi|320100635|ref|YP_004176227.1| 103 YILFMNPDAVLEERYVEKLVGIMErDESVGIAQGLQRSLGGSFSSLGGYVDSygraveVDVSGLEGRLSGLDAV--- 176
                                       79**********************559*******9998844322223333332432224444454445543222... PP

                   Glyco_trans_2_3  71 p...sv.GsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkeksplt.........lraal 134
                                       +   ++ Gs +++rr++++++gg++   +   +  d++ r++++Gyr++ +p + v+ + + t         l  +l
  gi|320100635|ref|YP_004176227.1| 177 FevaWAsGSAMMVRRELFERLGGFSPELFMYHDEIDLCARALSLGYRTVVYPRA-VYYHRRGTegapkrinwLSWYL 252
                                       2444557*********************************************99.4444444434444455444445 PP

                   Glyco_trans_2_3 135 rQrkRwayGceleklillvrllgylgsllwsalplhlallll 176
                                       + r +w+        ++++ +l+   + l+ +lp+ +++ +l
  gi|320100635|ref|YP_004176227.1| 253 ANRNKWLTT------VRYF-PLKHVLRALLLYLPVEVLINVL 287
                                       555555555......3333.4555555566666665555554 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.5e-06    0.0074      33     121 ..     103     202 ..      90     241 .. 0.72
   2 ?   -2.7   0.0       1.2   3.6e+03      11      35 ..     236     260 ..     228     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-06
                   Glyco_transf_21  33 llvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdak..g......laaaleaaflntlagvlqa..klsgl 98 
                                       ++++   d+++++ y+e+l++ +e+ + vg+ ++l +  + +  +       +++ + + ++ l g+l+   ++ ++
  gi|320100635|ref|YP_004176227.1| 103 YILFMNPDAVLEERYVEKLVGIMERdESVGIAQGLQRSLGGSfsSlggyvdSYGRAVEVDVSGLEGRLSGldAVFEV 179
                                       66777778999999999999999865889999999986666643433332222222333346777777776556699 PP

                   Glyco_transf_21  99 gfavGksmalrreaLeaiGGfea 121
                                         a G++m++rre +e++GGf +
  gi|320100635|ref|YP_004176227.1| 180 AWASGSAMMVRRELFERLGGFSP 202
                                       99*******************87 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                   Glyco_transf_21  11 dpvgvnpKvnnllqaleaakydllv 35 
                                         ++  pK  n l ++ a+++++l+
  gi|320100635|ref|YP_004176227.1| 236 RGTEGAPKRINWLSWYLANRNKWLT 260
                                       4556678999999999999999985 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 ?    6.1   0.0    0.0022       6.6      28     105 ..      48     124 ..      33     139 .. 0.80
   2 ?    6.2   0.0    0.0021       6.1     163     215 ..     182     233 ..     144     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0022
                   Glyco_tranf_2_2  28 eeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesd..lvlFlDaDcfissDkfeki 102
                                        ++++i+ d+gS+++ +e vss    + +v       + y+     N+ + +   d  ++lF++ D       +ek+
  gi|320100635|ref|YP_004176227.1|  48 GNVKVIFADNGSADDSAEYVSSKYGDKVRVVR---LGRNYGFCLGNNLAVRHLSPDikYILFMNPDAVLEERYVEKL 121
                                       5899*****************99888888852...234688888899999988765447999999988887777777 PP

                   Glyco_tranf_2_2 103 lkl 105
                                       + +
  gi|320100635|ref|YP_004176227.1| 122 VGI 124
                                       765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0021
                   Glyco_tranf_2_2 163 pssssilinrraflevGGyDErfrGhgaEDfdlllR.lakaikslekmpvelly 215
                                        s+s ++++r+ f ++GG+  ++     ++ dl +R l + ++ + + p  + y
  gi|320100635|ref|YP_004176227.1| 182 ASGSAMMVRRELFERLGGFSPELF-MYHDEIDLCARaLSLGYRTV-VYPRAVYY 233
                                       46699**************86652.33455788888344455555.56655555 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.2e-05      0.22      21      64 ..     184     226 ..     178     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-05
                   Glyco_transf_7C  21 gGvlalrkedfekiNGfsntfwgWGgEDdelyaRlakkgleier 64 
                                       g  +++r+e fe+++Gfs +++ +  +  +l+aR ++ g++   
  gi|320100635|ref|YP_004176227.1| 184 GSAMMVRRELFERLGGFSPELFMYH-DEIDLCARALSLGYRTVV 226
                                       5679**************9999995.559999999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2736.84
//
Query:       gi|320100636|ref|YP_004176228.1|  [L=528]
Description: polysaccharide biosynthesis protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   85.4  43.5    6.9e-23   81.4  22.8    2.6  3  Polysacc_synt    Polysaccharide biosynthesis protein
    2.1e-22   79.7  11.7    2.1e-22   79.7  11.7    1.7  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    8.8e-13   48.5  40.1      6e-12   45.8  19.2    4.4  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.2e-06   28.3  39.7    2.5e-05   24.0   7.9    4.1  3  MatE             MatE


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4  22.8   1.5e-26   6.9e-23       3     271 ..      15     294 ..      13     296 .. 0.90
   2 !   14.2   7.2   4.8e-06     0.022      76     186 ..     313     424 ..     300     449 .. 0.80
   3 ?   -1.4   0.5      0.28   1.2e+03      80      94 ..     466     480 ..     424     514 .. 0.60

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.5e-26
                     Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.......ke 72 
                                       +g ++l++++ ++  l+++  +++ar+lgpeg+G+++l+l++  +   l++lG+++a++r++a   ++        +
  gi|320100636|ref|YP_004176228.1|  15 RGGAYLFAGNALSLALSALASILIARLLGPEGYGIYSLVLTVPAIVGPLIGLGIGQAVTRYVAMLGSEgkgcdasMY 91 
                                       7899************************************************************9999999999855 PP

                     Polysacc_synt  73 lvslillnvllvllvlvllfllllliaa.flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvve 148
                                       +   ++ ++ l+l+ +vl+fl+++l+a+  lg+p   +l+ + +  + l  +++    g f ++ + ky a+  +++
  gi|320100636|ref|YP_004176228.1|  92 IRVALIFEASLGLVAMVLVFLCSDLVAMyMLGRPGIGSLVGLVSPLV-LTGSIIGICDGVFLAFLKTKYSALVKSLQ 167
                                       555556667778888899********776677777777666655555.5**************************** PP

                     Polysacc_synt 149 qlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr......prfvilslklvrellsfsapltissl 219
                                        l+ ++l+ ++ +  + +++a++g v++++v+ i+sla+l  + r      + +++   +  r ++s++ pl + +l
  gi|320100636|ref|YP_004176228.1| 168 ALVKLALSPLLALSLG-VMGALGGNVASYIVATIASLALLASACRtlgsnnKATSVGYVEALRSMISYAYPLYLPTL 243
                                       ****************.************************999778887655555558999*************** PP

                     Polysacc_synt 220 aillytyidsillglllgaeavGiYnaayqllvaisgllapivtaalfPvfs 271
                                       ++ l+ ++  +l + + +++++G+Y++a++l++ is+  ++i + +lf vfs
  gi|320100636|ref|YP_004176228.1| 244 LGFLIGRVIFVLTAHFVSDYELGNYSVAQNLYSPISMATSAIGS-SLFAVFS 294
                                       *************************************9999999.9998887 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.8e-06
                     Polysacc_synt  76 lillnvllvllvlvllfllllliaaflglp.elavlylilalmll.llvgvasfrrglfqglermkyaavsqvveql 150
                                       + ++ vl+v  +++++ +  +l+  ++gl  e+a lyl+l+++++  +  +a + +glf g  + + ++ s++v+ l
  gi|320100636|ref|YP_004176228.1| 313 VKYSTVLMVPAIAMAILFSRDLVVLVYGLDyEAAPLYLALTATGAlGVGLGAYVLGGLFAGIGKTQEVFRSWIVNTL 389
                                       455667777788888888888886688876368899********9889999999*********************** PP

                     Polysacc_synt 151 srvilvliavflfldivaavlgavlaalvggivsla 186
                                       + + l+li++   + +v+a+++ +++  ++ +++l+
  gi|320100636|ref|YP_004176228.1| 390 VSLPLTLILLPRLG-MVGAIVAGLIGGYASTVYLLM 424
                                       **************.777777666666666666554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.28
                     Polysacc_synt  80 nvllvllvlvllfll 94 
                                        v+l++++ v+ +++
  gi|320100636|ref|YP_004176228.1| 466 RVILASIIYVASYAI 480
                                       222222222222222 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7  11.7   4.8e-26   2.1e-22       2     289 ..      38     344 ..      37     347 .. 0.85
   2 ?   -3.3   0.9       0.9     4e+03     126     134 ..     435     443 ..     381     484 .. 0.57

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 4.8e-26
                   Polysacc_synt_3   2 LARLLspedFGvvaialvvislanlfvdmGlssaliqke.dltee........dlstvftfnlvlgllialvlflla 69 
                                       +ARLL pe +G+++++l+v +++  ++ +G+++a+ +    l +e        +++++  f+  lgl++++++fl++
  gi|320100636|ref|YP_004176228.1|  38 IARLLGPEGYGIYSLVLTVPAIVGPLIGLGIGQAVTRYVaMLGSEgkgcdasmYIRVALIFEASLGLVAMVLVFLCS 114
                                       7**********************************997634444456676677999********************* PP

                   Polysacc_synt_3  70 plias.fynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwAL... 142
                                       +l+a  +++ p +  ++ +++  ++  +++ +    +   lk k  + ++ +  +v ++++ +lAl +  + AL   
  gi|320100636|ref|YP_004176228.1| 115 DLVAMyMLGRPGIGSLVGLVSPLVLTGSIIGICDGVFLAFLKTKYSALVKSLQALVKLALSPLLALSLGVMGALggn 191
                                       ****9779**************************9999999999999999999999888888888754433333333 PP

                   Polysacc_synt_3 143 ....vigtllssll.slvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlY 214
                                           ++ t++s +l  +++ +l s+ +      +++l++++s+   l l +ll +l+ ++  +l + ++s+++LG Y
  gi|320100636|ref|YP_004176228.1| 192 vasyIVATIASLALlASACRTLGSNNKATSVGYVEALRSMISYAYPLYLPTLLGFLIGRVIFVLTAHFVSDYELGNY 268
                                       000055555443330233344455566777778999***************************************** PP

                   Polysacc_synt_3 215 svakrlaslpvaeitsviakVlfPalSrlq..ddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWl 289
                                       sva++l  +p+++ ts+i + lf ++S l   +++++++e+++ +++ ++++++P++++ +++++ lv +++G  ++
  gi|320100636|ref|YP_004176228.1| 269 SVAQNLY-SPISMATSAIGSSLFAVFSGLDpgRESREVAEVFRASVKYSTVLMVPAIAMAILFSRDLVVLVYGLDYE 344
                                       *****97.6999***************997447999*************************************8886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.9
                   Polysacc_synt_3 126 vivaivlAl 134
                                       ++  i+ ++
  gi|320100636|ref|YP_004176228.1| 435 GAKEIARVY 443
                                       222222233 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  10.2         4   1.8e+04      55     104 ..      59     107 ..      23     139 .. 0.43
   2 !   16.9  12.9   1.2e-06    0.0052       5      83 ..     134     212 ..     130     261 .. 0.79
   3 ?   -2.4   2.1      0.97   4.4e+03      64     112 ..     244     296 ..     236     341 .. 0.50
   4 ?    1.3   2.9     0.075   3.4e+02      88     137 ..     316     368 ..     300     371 .. 0.55
   5 !   45.8  19.2   1.3e-15     6e-12       2     142 ..     350     486 ..     349     487 .. 0.90

  Alignments for each domain:
  == domain 1  score: -7.5 bits;  conditional E-value: 4
                   Polysacc_synt_C  55 ivGaaiatvlallvvavlnlyalrrllgikl.ellrrllkpllaalvmgiv 104
                                       ivG++i+  ++++v+ ++ +     + g +  + + r+  ++ a+l+++++
  gi|320100636|ref|YP_004176228.1|  59 IVGPLIGLGIGQAVTRYVAMLGSEGK-GCDAsM-YIRVALIFEASLGLVAM 107
                                       25555555555555555543333322.222212.22222333333333333 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.2e-06
                   Polysacc_synt_C   5 lalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrll 81 
                                       +++ ++  s++ ++ +++ +  ++k+ +++  + alvkl+l+ ll  ++g++Ga+ + v++++v+++  l +l    
  gi|320100636|ref|YP_004176228.1| 134 VSPLVLTGSIIGICDGVFLAFLKTKYSALVKSLQALVKLALSPLLALSLGVMGALGGNVASYIVATIASLALLASAC 210
                                       6788889999*********************************************************9988887665 PP

                   Polysacc_synt_C  82 gi 83 
                                       + 
  gi|320100636|ref|YP_004176228.1| 211 RT 212
                                       54 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.97
                   Polysacc_synt_C  64 lallvvavlnlyalrrllgikl...ellrrll.kpllaalvmgivvyllllll 112
                                       l++l++ v+ +  ++    + l   ++ ++l+  + +a+ ++g  ++++++ l
  gi|320100636|ref|YP_004176228.1| 244 LGFLIGRVIFVLTAHFVSDYELgnySVAQNLYsPISMATSAIGSSLFAVFSGL 296
                                       55555555544444444444444443455554233333344444444444433 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.075
                   Polysacc_synt_C  88 lrrllkpllaalvmgiv..vylllllllglllla.alalllavlvgalvYlll 137
                                        + l++p++a+++++    v+l++ l  ++ +l  al+   a++vg  +Y+l 
  gi|320100636|ref|YP_004176228.1| 316 STVLMVPAIAMAILFSRdlVVLVYGLDYEAAPLYlALTATGALGVGLGAYVLG 368
                                       44455555555555554764444444444444333446666666888888775 PP

  == domain 5  score: 45.8 bits;  conditional E-value: 1.3e-15
                   Polysacc_synt_C   2 Lailalsiiflsls.tvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       La+ a +++  +l   vl++++ g+g++++++++ ++  lv l l+l+l+p++g+vGa++a +++  +++v++l+++
  gi|320100636|ref|YP_004176228.1| 350 LALTATGALGVGLGaYVLGGLFAGIGKTQEVFRSWIVNTLVSLPLTLILLPRLGMVGAIVAGLIGGYASTVYLLMRA 426
                                       788899999999999************************************************************** PP

                   Polysacc_synt_C  78 rrllgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       + + g+++   + + +++++a++ +++++ +l++ +       l ++la ++ ++ Y+++l ll+
  gi|320100636|ref|YP_004176228.1| 427 KIEAGVSI-GAKEIARVYVSAAISALATLPVLYVEIHE----VLRVILASIIYVASYAIILPLLG 486
                                       ********.699***************55444444443....347888888********998876 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  11.5   5.9e-07    0.0026       5     136 ..      23     156 ..      20     177 .. 0.90
   2 !   24.0   7.9   5.5e-09   2.5e-05       4     159 ..     240     395 ..     237     400 .. 0.80
   3 ?    0.4   1.1       0.1   4.5e+02      80     123 ..     467     512 ..     426     520 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.9e-07
                              MatE   5 enllesllslidtllvgrl.gskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglill 79 
                                        n+l   ls++ ++l++rl g++  + +s++l++  +++  ++lg++ a+t  v+    +++  +a+ ++r++li+ 
  gi|320100636|ref|YP_004176228.1|  23 GNALSLALSALASILIARLlGPEGYGIYSLVLTVPAIVGPlIGLGIGQAVTRYVAMLGSEGKGCDASMYIRVALIFE 99 
                                       56777778888888888888*******************99************************************ PP

                              MatE  80 lllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilr 136
                                       + l+l++++lv+l+s+  + ++   + + +l+    ++++ g ++ ++  v+ ++l+
  gi|320100636|ref|YP_004176228.1| 100 ASLGLVAMVLVFLCSDLVAMYMLGRPGIGSLVGLVSPLVLTGSIIGICDGVFLAFLK 156
                                       ****************************99999999999999999988888777776 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 5.5e-09
                              MatE   4 lenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglill 79 
                                       l  ll +l++ ++ +l++++ ++ +l+ +s+a+++ s++ +   +++++l ++ +     +  ++++e++r +++ +
  gi|320100636|ref|YP_004176228.1| 240 LPTLLGFLIGRVIFVLTAHFvSDYELGNYSVAQNLYSPISMATSAIGSSLFAVFSGLDPGRESREVAEVFRASVKYS 316
                                       556667778888899999999*****************************9999999999999************** PP

                              MatE  80 lllsliiallvllfseqilslftqdeevlelakrylrililgipalal.qlvlsgilrgagktkvplyislisllln 155
                                       ++l+++++++++lfs++++ l+   +   e+a  yl +++ g+++ +l   vl g + g+gkt  ++   ++ +l+ 
  gi|320100636|ref|YP_004176228.1| 317 TVLMVPAIAMAILFSRDLVVLVYGLD--YEAAPLYLALTATGALGVGLgAYVLGGLFAGIGKTQEVFRSWIVNTLVS 391
                                       ****************9988764444..4555555555555555554413477778888888888887777777777 PP

                              MatE 156 ipln 159
                                       +pl+
  gi|320100636|ref|YP_004176228.1| 392 LPLT 395
                                       7775 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.1
                              MatE  80 lllsliiallvllfseqilslftqdee..vlelakrylrililgip 123
                                       ++l+ ii ++ ++ + ++l  ++ de   ++++a+r  ++l++ ++
  gi|320100636|ref|YP_004176228.1| 467 VILASIIYVASYAIILPLLGALKEDEVsiLVNVARRSGPVLLPLTL 512
                                       4445555555577777777777777777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3490.12
//
Query:       gi|320100637|ref|YP_004176229.1|  [L=398]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   49.8   0.0    9.2e-13   48.1   0.0    1.8  2  Glycos_transf_1  Glycosyl transferases group 1
    8.7e-11   42.4   0.0    3.7e-10   40.4   0.0    2.1  3  Glyco_trans_1_4  Glycosyl transferases group 1
      5e-06   26.6   4.4    5.2e-06   26.6   2.0    2.1  2  Glyco_transf_4   Glycosyltransferase Family 4
    0.00011   22.6   0.5    0.00011   22.6   0.5    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.069   13.5   0.0       0.24   11.8   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.98   3.5e+03      80     101 ..      76      97 ..      73     105 .. 0.83
   2 !   48.1   0.0   2.6e-16   9.2e-13      11     159 ..     218     363 ..     212     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.98
                                       CCHSSSHHHHHHCESEEEEEES CS
                   Glycos_transf_1  80 evsredleellknadifvlpsi 101
                                       +++ e l +l ++ad + +ps+
  gi|320100637|ref|YP_004176229.1|  76 FSNTETLRKLVEKADTIYIPSH 97 
                                       6677889999999999999998 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 2.6e-16
                                       TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
                   Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredle 87 
                                       k+ +++++l+ g  ++ Kg++l++ a+ +l ++   ++ +++      +     l++++ l+  ++ +g+v++e+l 
  gi|320100637|ref|YP_004176229.1| 218 KRLGRPLLLFTGGDSYLKGFHLVLGAALELTRR-GLDAEVLVTR----RLGEIGLSAARRLGRVLKPIGHVDYERLL 289
                                       667889999999999999999999999999887.7777776644....555789999******************** PP

                                       HHHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT.SEEEE-TT-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  88 ellknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdge.tGllvkpnnaealaeairkllede 159
                                       el++ + ++++psi+ E+++ +++E+m +g++ ias +gg++e+v       + + p+++  lae+i++++  +
  gi|320100637|ref|YP_004176229.1| 290 ELYSTSYALLHPSIWeEPLPYAVIESMLSGTIPIASRVGGVPEIVDGTPaERFMFIPGDPLILAEKIEEVIAMG 363
                                       ********************************************98777889*****************99877 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 ?   -1.8   0.0       1.1   3.9e+03      63      85 ..      79     102 ..      23     107 .. 0.72
   2 ?   -3.5   0.0       3.5   1.3e+04      66      92 ..     144     174 ..     130     184 .. 0.57
   3 !   40.4   0.0     1e-13   3.7e-10       2     132 ..     223     360 ..     222     362 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                                       -THHHHHHHH-SEEEE--.---SH CS
                   Glyco_trans_1_4  63 vedlaellaaadvfvaPs.egfgl 85 
                                        e l++l+++ad   +Ps   ++l
  gi|320100637|ref|YP_004176229.1|  79 TETLRKLVEKADTIYIPShTLLPL 102
                                       356888888888888888544455 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.5
                                       HHHHHHH-SEEEE--....---SHHHHHHHH CS
                   Glyco_trans_1_4  66 laellaaadvfvaPs....egfglkllEama 92 
                                       + el+++ dv+ a       ++g+  + a+a
  gi|320100637|ref|YP_004176229.1| 144 IVELYEHGDVARAIAtgllDTLGVNRVSALA 174
                                       5566666666533332333344555555555 PP

  == domain 3  score: 40.4 bits;  conditional E-value: 1e-13
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaad 74 
                                       p +lf+G      kg++l+l a+ +l ++  d+++++  +   +  l   a++l    +  G+v  e l el++ + 
  gi|320100637|ref|YP_004176229.1| 223 PLLLFTGGD-SYLKGFHLVLGAALELTRRglDAEVLVTRRL-GEIGLS-AARRLGRVLKPIGHVdyERLLELYSTSY 296
                                       788999987.6789999999999555546455666665521.112333.3335545689999998778********* PP

                                       EEEE--...---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSS..EE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  75 vfvaPs...egfglkllEamaaglpvVatdvggiaevv.geng..llvppgdpealaeailrLl 132
                                        ++ Ps   e ++++++E+m +g+  +a++vgg++e+v g+ +  +++ pgdp  lae+i++++
  gi|320100637|ref|YP_004176229.1| 297 ALLHPSiweEPLPYAVIESMLSGTIPIASRVGGVPEIVdGTPAerFMFIPGDPLILAEKIEEVI 360
                                       ********88****************************985434499999**********9987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   2.0   1.4e-09   5.2e-06       2     150 ..      18     194 ..      17     209 .. 0.69
   2 ?   -1.4   0.0      0.59   2.1e+03      12      36 ..     244     268 ..     239     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.4e-09
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvv..tpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvv 76 
                                       GG e  ++ ++++   r +eV vv  t+++ g+     ++++ ++ + + ++  +l+ +++   lr+l++  k D +
  gi|320100637|ref|YP_004176229.1|  18 GGGELATHLITKHILSRHFEVIVVsgTRHPTGEVMGYCRYLYWPVLREPYKPLEWLKLFSNTETLRKLVE--KADTI 92 
                                       9***********************4444444444433244444444444555555556666666666666..99999 PP

                    Glyco_transf_4  77 Hahspaalgaallalrr.rlgiplVltvHglye..............................krllkarlk.plsr 121
                                        + s+  l +a +a      ++++++++H+  +                              +       + + + 
  gi|320100637|ref|YP_004176229.1|  93 YIPSHTLLPLAIAAK-NiNPRARVIVHLHNYQPltytsvilhdvntrslgdvivelyehgdvaR---AIATGlLDTL 165
                                       777755554454444.458********************************9999877765321...2222213344 PP

                    Glyco_transf_4 122 llralerrllrradrviavSeatadelre 150
                                        ++++ + +l  adrv++vS+     +++
  gi|320100637|ref|YP_004176229.1| 166 GVNRVSALALGYADRVVCVSRRQCGIIAS 194
                                       567777777***********987776666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.59
                    Glyco_transf_4  12 araLarrGheVtvvtpgddgpleee 36 
                                       a +L rrG + +v++ ++ g+++  
  gi|320100637|ref|YP_004176229.1| 244 ALELTRRGLDAEVLVTRRLGEIGLS 268
                                       6689999999999977776666655 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 !   22.6   0.5   3.2e-08   0.00011       1     141 [.      18     189 ..      18     209 .. 0.69
   2 ?   -2.0   0.1       1.2   4.4e+03      13      27 ..     246     260 ..     237     291 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.2e-08
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrps.pladla...alralrrllrqrrer 73 
                                       gG++  ++ + ++   r  eV v+  + +p  +  + + +r+   pv r+p  pl +l+    +  lr l+    e+
  gi|320100637|ref|YP_004176229.1|  18 GGGELATHLITKHILSRHFEVIVVSGTRHPTGE--VMGYCRYLYWPVLREPYkPLEWLKlfsNTETLRKLV----EK 88 
                                       7888888889999999989*****987777766..7789***********953555544222456667776....** PP

                   Glyco_trans_4_4  74 pdvvhahsptaglaarlar.rrrgiplvvtlh............................glllrrgsgavrrly.. 119
                                        d +++ s t+ ++a +a+    +++++v+lh                            +       g v+r++  
  gi|320100637|ref|YP_004176229.1|  89 ADTIYIPSHTLLPLAIAAKnINPRARVIVHLHnyqpltytsvilhdvntrslgdvivelyE------HGDVARAIat 159
                                       *******9776666666664788*********99999998888887777666443332221......2233332222 PP

                   Glyco_trans_4_4 120 ........ralerrllrradavlvvseaea 141
                                                ++  ++l  ad+v++vs+   
  gi|320100637|ref|YP_004176229.1| 160 glldtlgvNRVSALALGYADRVVCVSRRQC 189
                                       222221245556688888********9865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                   Glyco_trans_4_4  13 aLaarGheVtvltpa 27 
                                       +L +rG + +vl+++
  gi|320100637|ref|YP_004176229.1| 246 ELTRRGLDAEVLVTR 260
                                       556666666665532 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.2   7.9e+03      41      70 ..     128     158 ..     123     160 .. 0.81
   2 ?   11.8   0.0   6.6e-05      0.24      11      83 ..     308     384 ..     296     392 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.2
                   Glyco_trans_1_2  41 kevilfe.dleelaekiryllanpeerraia 70 
                                       ++vil + ++ +l + i +l ++ + +raia
  gi|320100637|ref|YP_004176229.1| 128 TSVILHDvNTRSLGDVIVELYEHGDVARAIA 158
                                       5677777888888899999999999999998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.6e-05
                   Glyco_trans_1_2  11 pnlrlfEaaacGafaltddaegleelf..tpgkevilfe.dleelaekirylla.npeerraiaeaarervlaehty 83 
                                       + + + E + +G++ ++++  g++e++  tp + ++++  d+  laeki++++a  +ee  +i+ + re +l+++  
  gi|320100637|ref|YP_004176229.1| 308 LPYAVIESMLSGTIPIASRVGGVPEIVdgTPAERFMFIPgDPLILAEKIEEVIAmGREELLSIGGQLREATLRKFEA 384
                                       556789*******************97224666888888***************999**************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2696.32
//
Query:       gi|320100638|ref|YP_004176230.1|  [L=221]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-05   24.5   0.0    0.00055   19.7   0.0    2.0  2  Thymidylate_kin  Thymidylate kinase
     0.0012   18.5   0.2      0.002   17.8   0.2    1.3  1  SRP54            SRP54-type protein, GTPase domain
     0.0034   17.6   0.0      0.024   14.8   0.0    2.0  2  AAA_33           AAA domain
     0.0036   17.8   0.1      0.051   14.1   0.1    2.2  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.013   15.4   0.9      0.021   14.7   0.3    1.7  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.035   14.5   0.2      0.054   13.9   0.2    1.4  1  AAA_16           AAA ATPase domain
      0.082   11.9   0.2       0.12   11.4   0.2    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.12   12.2   0.0       0.18   11.7   0.0    1.2  1  APS_kinase       Adenylylsulphate kinase
       0.14   12.1   0.0       0.22   11.4   0.0    1.3  1  NTPase_1         NTPase
       0.21   11.8   0.1       0.32   11.2   0.1    1.2  1  AAA_28           AAA domain
       0.24   11.5   0.2       0.45   10.6   0.2    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


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 !   19.7   0.0   3.4e-07   0.00055       2      29 ..       8      35 ..       7      53 .. 0.89
   2 ?    3.0   0.0     0.045        73     105     180 ..     128     205 ..      97     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.4e-07
                                      EESTTSSHHHHHHHHHHHHHHTTE.EEE CS
                   Thymidylate_kin  2 EGlDGaGKttqaellkerlkeegikvvl 29
                                       Gl+GaGKtt+++ll+ rlk++g++v +
  gi|320100638|ref|YP_004176230.1|  8 AGLEGAGKTTHIRLLAIRLKKRGLRVRT 35
                                      59*********************98655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.045
                                       HHHHHHGGGTTS.E-SEEEEEESSHHHHHTSCCTTSS...TTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS- CS
                   Thymidylate_kin 105 dlvlslnedvll.kPdltflldvdpevalkRlakrde...ldeeeeeqldflrkvrerylelakederiliidasks 177
                                       +lv+ l++ + + +P++ +l   +p+   +R +kr++   l+  ++ q+ +l++  +r   l++ +e  +ii++sk+
  gi|320100638|ref|YP_004176230.1| 128 KLVRILSRLMWGrSPEVLVLWA-PPSSLPERWRKRGTppeLKTYVFTQILVLKTWVKREGCLIN-TEGRKIINTSKE 202
                                       4455555555569999999999.*************9998889999999999999999999996.666667778888 PP

                                       HHH CS
                   Thymidylate_kin 178 iee 180
                                       +e+
  gi|320100638|ref|YP_004176230.1| 203 LEC 205
                                       876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   1.2e-06     0.002       3      32 ..       4      33 ..       2      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkv 32
                                      vi+++Gl+GaGKTt +  La +lkk+g +v
  gi|320100638|ref|YP_004176230.1|  4 VIVFAGLEGAGKTTHIRLLAIRLKKRGLRV 33
                                      89***********************98776 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   1.5e-05     0.024       1      34 [.       4      39 ..       4      78 .. 0.87
   2 ?    0.5   0.0      0.37     6e+02      96     121 ..     139     164 ..     122     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg..avllssdtlr 34
                                      ++++ Gl G+GK+t ++ l+ +l+  + ++++ +l+
  gi|320100638|ref|YP_004176230.1|  4 VIVFAGLEGAGKTTHIRLLAIRLKkrGLRVRTTYLK 39
                                      89*****************99998888888887654 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.37
                            AAA_33  96 gvpvrivvvetdeetlkeRlakRaan 121
                                       g   +++v+ ++++ l eR +kR  +
  gi|320100638|ref|YP_004176230.1| 139 GRSPEVLVLWAPPSSLPERWRKRGTP 164
                                       5556899999*************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   3.2e-05     0.051       1      25 [.       5      41 ..       5     175 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf...........g 25
                                      I+ +G  G+GKtt  + L+ rl +            +
  gi|320100638|ref|YP_004176230.1|  5 IVFAGLEGAGKTTHIRLLAIRLkKRglrvrttylktV 41
                                      899***************8777444444454333331 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   1.3e-05     0.021       1      32 [.       4      35 ..       4      40 .. 0.93
   2 ?   -3.2   0.0       4.4   7.1e+03      86      97 ..      91     102 ..      84     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvgt 32
                                      v+ ++g +g+GKTt +  l   lk+rglrv t
  gi|320100638|ref|YP_004176230.1|  4 VIVFAGLEGAGKTTHIRLLAIRLKKRGLRVRT 35
                                      6889*************************976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                              MobB  86 arlsevDlvlvE 97 
                                       a +++ D++lvE
  gi|320100638|ref|YP_004176230.1|  91 AITRRNDFILVE 102
                                       445668999998 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   3.3e-05     0.054      25     106 ..       3      72 ..       1     148 [. 0.58

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekl 101
                                       +++++ G  G GK++ +r l+ +l+k+g   lr +++ l    +  ++a+      ll  l +++   ++e ++++ 
  gi|320100638|ref|YP_004176230.1|   3 RVIVFAGLEGAGKTTHIRLLAIRLKKRG---LRVRTTYL---KTVFIFAR------LLPRLFSRLGLGKREIYAAHR 67 
                                       67999****************9999997...33333333...11122444......444444444443555555555 PP

                            AAA_16 102 eeala 106
                                       +++l 
  gi|320100638|ref|YP_004176230.1|  68 CGVLL 72 
                                       55544 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   7.2e-05      0.12      31      60 ..       4      33 ..       1      37 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--E CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrv 60
                                      v+ + G+ GaGk t +  l+++l++rG rv
  gi|320100638|ref|YP_004176230.1|  4 VIVFAGLEGAGKTTHIRLLAIRLKKRGLRV 33
                                      78899************************9 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.18       2      34 ..       2      34 ..       1      46 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EE CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvy 34
                                      g v+ ++Gl g+GK+t  + l+ +L+++g +v 
  gi|320100638|ref|YP_004176230.1|  2 GRVIVFAGLEGAGKTTHIRLLAIRLKKRGLRVR 34
                                      779************************997664 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.22       2      37 ..       5      40 ..       4      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfytee 37
                                      ++  G  G GKtT ++ ++  lk++g++v+  y + 
  gi|320100638|ref|YP_004176230.1|  5 IVFAGLEGAGKTTHIRLLAIRLKKRGLRVRTTYLKT 40
                                      5678999**********************9887665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0002      0.32       2      27 ..       5      34 ..       4      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                            AAA_28  2 ivitGgestGKTtlleaLa....argypvv 27
                                      iv+ G e++GKTt ++ La    +rg +v 
  gi|320100638|ref|YP_004176230.1|  5 IVFAGLEGAGKTTHIRLLAirlkKRGLRVR 34
                                      99****************965544577665 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 ?   10.6   0.2   0.00028      0.45       2      30 ..       5      33 ..       4      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  2 aiastkGGvGKTtlaanLaralarrglrV 30
                                      ++ ++  G+GKTt    La+ l++rglrV
  gi|320100638|ref|YP_004176230.1|  5 IVFAGLEGAGKTTHIRLLAIRLKKRGLRV 33
                                      56667779********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1618.16
//
Query:       gi|320100639|ref|YP_004176231.1|  [L=381]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-05   24.3   0.0      5e-05   23.4   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    4.3e-05   24.0   0.0    0.00011   22.7   0.0    1.7  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00039   20.9   0.0     0.0007   20.1   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   8.4e-09     5e-05      65     165 ..      60     162 ..      15     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.4e-09
                    Glyco_transf_4  65 rrllkre.kpDvvHahspaalgaallalrr.rlgiplVltvHglye.krllkarlkplsrllralerrl.lrradrv 137
                                        + l    k D+v + +  +++ a   l+r   +  +V+ vHg +   ++  +  +   r++  l ++l +++a+ +
  gi|320100639|ref|YP_004176231.1|  60 PKTLSSLlKSDIVIVSGTNPWISAFMVLARkIFRRTTVVDVHGVAWlESISTGQPGIIGRFILFLSEYLtYKHAHYI 136
                                       23333334899999999888877766666657999**********9877778888888888888877778******* PP

                    Glyco_transf_4 138 iavSeatadelrerygvppekitVipnG 165
                                       ia S +t + + + y  p +k +Vi n+
  gi|320100639|ref|YP_004176231.1| 137 IAASTYTSEAIYR-YFTP-RKARVIENA 162
                                       *************.7756.8******97 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.8e-08   0.00011      32     104 ..     230     310 ..     207     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.8e-08
                                       EEEEEES---...HHHHHHHT.T-T.TEEEE---..THHHHHHHH-SEEEE--...-...--SHHHHHHHHTT-EEE CS
                   Glyco_trans_1_4  32 vrlvivGdgp.rpeeleelaa.gleerveftGfv..edlaellaaadvfvaPs...e...gfglkllEamaaglpvV 98 
                                       v +++ G +  ++++l+++ + + + +v+ +Gf+  +  a+ll ++   ++P        g ++k+lEa   g+p+V
  gi|320100639|ref|YP_004176231.1| 230 VLIIVTG-HRiKRPSLRAKNEeNSRYKVIQVGFLtyPAYAALLLSSEAIILPYpknAicgGARNKVLEAGYIGKPIV 305
                                       4344555.4465569987775565567*******8878***************97615559**************** PP

                                       E-TGGG CS
                   Glyco_trans_1_4  99 atdvgg 104
                                       +t++ g
  gi|320100639|ref|YP_004176231.1| 306 STPA-G 310
                                       **99.5 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 !   20.1   0.0   1.2e-07    0.0007      60     159 ..      49     161 ..      18     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                   Glyco_trans_4_4  60 l..ralrrll....rqrrerpdvvhahs..ptaglaarlarrrrgiplvvtlhglllrrg.sgavrrly.ral.... 122
                                       l   +l++l+         + d+v++ +  p ++++++lar   +   vv++hg ++ +  s+ ++ ++ r +    
  gi|320100639|ref|YP_004176231.1|  49 LpiSRLAQLFmpktLSSLLKSDIVIVSGtnPWISAFMVLARKIFRRTTVVDVHGVAWLESiSTGQPGIIgR-Filfl 124
                                       23346666655555456778899998874455888899999889*********955433345555555532.22445 PP

                   Glyco_trans_4_4 123 .errllrradavlvvseaeaeelralgvpadrvvvvpn 159
                                        e++++++a  +++ s++  e++ ++  p+ + +v+ n
  gi|320100639|ref|YP_004176231.1| 125 sEYLTYKHAHYIIAASTYTSEAIYRYFTPR-KARVIEN 161
                                       8************************98885.8899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2913.23
//
Query:       gi|320100640|ref|YP_004176232.1|  [L=371]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for 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   61.1   0.0    1.4e-16   60.5   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
      2e-13   50.9   0.0      4e-13   49.9   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00068   20.0   0.0     0.0015   18.9   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00095   19.2   0.0     0.0017   18.4   0.0    1.4  1  DUF3880          DUF based on E. rectale Gene description (DU
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.041   13.8   0.0    1.4  1  UNC45-central    Myosin-binding striated muscle assembly cent


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 !   60.5   0.0     4e-20   1.4e-16      11     157 ..     171     323 ..     165     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 4e-20
                                       TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEE.ES....STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklvi.aG...ngeeekelkklaeelelsdnviflgevsr 83 
                                       k++++ +i++vg+    Kg d +  ++ +l  +  p+++  i  G     +  + l++la++  ++ +++ l     
  gi|320100640|ref|YP_004176232.1| 171 KQSDRFTIVFVGARY-GKGADIAYSVISSLLPR-FPDIHAKIfLGhgtLPALVQHLQNLADKFPNRVDIFHLLSRR- 244
                                       556777788888755.59***********9998.999999772576677778899*******99988888887776. PP

                                       SSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTT.....SEEEE-TT-HHHHHHHHHH CS
                   Glycos_transf_1  84 edleellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdge.....tGllvkpnnaealaeairk 154
                                        d  + l +a+++++ps +E fG+v+lEA+a+g+pv+a +  g p++++k+++      G + k+ + ++l +++ k
  gi|320100640|ref|YP_004176232.1| 245 -DFLKELLQAHLLLFPSKYETFGLVVLEALACGTPVVAFDiPGAPRDLLKPAVsrgelCGHIAKNFDLKSLTRGVLK 320
                                       .777777788******************************9999*********988888888888888888888887 PP

                                       HHH CS
                   Glycos_transf_1 155 lle 157
                                       +  
  gi|320100640|ref|YP_004176232.1| 321 YYL 323
                                       765 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 !   49.9   0.0   1.1e-16     4e-13       2     109 ..     176     292 ..     175     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.1e-16
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEE.EEEES---.....HHHHHHHTT-T.TEEEE---..THHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvr.lvivGdgprp...eeleelaagleerveftGfv..edlaell 70 
                                       ++i+fvG+     kg+d+    +  l+ +  d++  ++ G g+ p   ++l++la+++ +rv +   +   d  + l
  gi|320100640|ref|YP_004176232.1| 176 FTIVFVGAR--YGKGADIAYSVISSLLPRfpDIHaKIFLGHGTLPalvQHLQNLADKFPNRVDIFHLLsrRDFLKEL 250
                                       689****87..349999999999777766654542566788874435677776666666665555544445877778 PP

                                       HH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGT.TT-- CS
                   Glyco_trans_1_4  71 aaadvfvaPs..egfglkllEamaaglpvVatdvggi.aevv 109
                                        +a+++++Ps  e+fgl++lEa+a+g+pvVa+d++g+ ++++
  gi|320100640|ref|YP_004176232.1| 251 LQAHLLLFPSkyETFGLVVLEALACGTPVVAFDIPGApRDLL 292
                                       8899*******99*********************98525544 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 !   18.9   0.0   4.1e-07    0.0015       3      33 ..     257     287 ..     255     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.1e-07
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegl 33 
                                       L+ps +e++ l+++Ea+acG+++++ d++g 
  gi|320100640|ref|YP_004176232.1| 257 LFPSKYETFGLVVLEALACGTPVVAFDIPGA 287
                                       89***********************999543 PP

>> DUF3880  DUF based on E. rectale Gene description (DUF3880)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.8e-07    0.0017      13      77 ..     121     185 ..     115     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                           DUF3880  13 ksiandcnyiftfDkeqyeelkelGvknvyylPLAanverldpleaeaekeekyrsdisFvGslY 77 
                                       + i n+ + i +  +  ++ +++l +++v y+P +   ++l++ +++++++++ r  i+FvG  Y
  gi|320100640|ref|YP_004176232.1| 121 TFINNQICSIHVLNSFDLQVFRALRFRRVAYIPWGIPNTILENCQPSPDEKQSDRFTIVFVGARY 185
                                       567899999*****************************************************988 PP

>> UNC45-central  Myosin-binding striated muscle assembly central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.041      59      94 ..     191     226 ..     163     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHSSHHHHHHHHTSTTHHHHHHHHHHS CS
                     UNC45-central  59 nalsvltalFpvvpdvasalflsegflesllelves 94 
                                       +a+sv+++l+p  pd+ +++fl  g+l+ l++++++
  gi|320100640|ref|YP_004176232.1| 191 IAYSVISSLLPRFPDIHAKIFLGHGTLPALVQHLQN 226
                                       699****************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2629.09
//
Query:       gi|320100641|ref|YP_004176233.1|  [L=212]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   20.5   0.6      0.005   17.4   0.6    2.1  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.032   14.5   0.2       0.13   12.5   0.1    2.0  2  AAA_28           AAA domain
      0.039   13.1   0.1      0.056   12.6   0.1    1.2  1  NB-ARC           NB-ARC domain
       0.07   13.0   0.0       0.12   12.3   0.0    1.3  1  APS_kinase       Adenylylsulphate kinase
       0.11   12.2   0.0       0.28   10.8   0.0    1.6  2  SRP54            SRP54-type protein, GTPase domain
       0.18   12.4   0.0       0.28   11.7   0.0    1.2  1  ABC_tran         ABC transporter
       0.24   11.1   0.0       0.39   10.4   0.0    1.3  1  Thymidylate_kin  Thymidylate kinase


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 !   17.4   0.6   1.9e-06     0.005       1      25 [.       6      42 ..       6     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf...........g 25
                                      ++  G+ G+GK+tla  Ls+ l  +           g
  gi|320100641|ref|YP_004176233.1|  6 VCFFGCDGSGKSTLAGLLSRYLsDCtgkqsvvvwvrG 42
                                      7899***************998777654444444331 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.1e-05      0.13       2      22 ..       6      26 ..       5      50 .. 0.82
   2 ?   -0.9   0.0      0.66   1.7e+03      73      92 ..     103     122 ..     100     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                      ++++G+ ++GK+tl+  L++ 
  gi|320100641|ref|YP_004176233.1|  6 VCFFGCDGSGKSTLAGLLSRY 26
                                      89*************999975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.66
                            AAA_28  73 nkvlfcDrglldtlaYaray 92 
                                       ++v++ +r+++d l+++ + 
  gi|320100641|ref|YP_004176233.1| 103 GRVVVAERCPVDFLVWLAVT 122
                                       57899999999999998665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.2e-05     0.056      21      64 ..       4      47 ..       1      60 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                      EEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdk 64
                                      +vv + G  G+GK+tla    + ++  +g+  +v+wv  ++t++
  gi|320100641|ref|YP_004176233.1|  4 VVVCFFGCDGSGKSTLAGLLSRYLSDCTGKQSVVVWVRGTHTFS 47
                                      68999********************************8777775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.5e-05      0.12       2      29 ..       3      30 ..       2      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHT CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvek 29
                                       vvv + G  gsGKst+a  l+++L + 
  gi|320100641|ref|YP_004176233.1|  3 CVVVCFFGCDGSGKSTLAGLLSRYLSDC 30
                                      57999*******************9874 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.28       3      33 ..       5      36 ..       3      43 .. 0.82
   2 ?   -1.9   0.0      0.85   2.2e+03      88      98 ..     188     198 ..     178     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                      EEEEEESTTSSHHHHHHHHHHHHHHT.TS-EE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkke.gkkvl 33
                                      v+ ++G  G+GK t ++ L+++l++  gk+ +
  gi|320100641|ref|YP_004176233.1|  5 VVCFFGCDGSGKSTLAGLLSRYLSDCtGKQSV 36
                                      889*******************9987644443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.85
                                       EEEE--SSTTH CS
                             SRP54  88 lvDTaGrlqnd 98 
                                       +vDT+G++ ++
  gi|320100641|ref|YP_004176233.1| 188 VVDTSGKSVEE 198
                                       79999997654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.28      14      40 ..       6      32 ..       3      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      EEEEESTTSSHHHHHHHHTTSS--SEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkpteG 40
                                      v ++G  G+GKStL+ ll++ l++  G
  gi|320100641|ref|YP_004176233.1|  6 VCFFGCDGSGKSTLAGLLSRYLSDCTG 32
                                      7789**************998887666 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.39       3      22 ..      10      29 ..       8      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                      ESTTSSHHHHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlke 22
                                      G DG+GK+t a ll ++l++
  gi|320100641|ref|YP_004176233.1| 10 GCDGSGKSTLAGLLSRYLSD 29
                                      99**************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1520.49
//
Query:       gi|320100642|ref|YP_004176234.1|  [L=294]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   28.4   0.0    2.3e-06   27.4   0.0    1.5  1  NTP_transf_5  Uncharacterised nucleotidyltransferase


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 !   27.4   0.0   1.3e-10   2.3e-06      67     208 ..      69     200 ..      45     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.3e-10
                      NTP_transf_5  67 leeegipvllLKGpalaq.lYpdpalRemgDiDllvkredldraeelLeelGyelesdgsekhevyyrekkgveiel 142
                                       l+e +    +LKG+  a   + +p     +DiDll ++  l+ a + L++lGy    + + +  ++ r  k   ++l
  gi|320100642|ref|YP_004176234.1|  69 LRELESVSRALKGVEHAFiKLRKPVAYVPSDIDLLLSPSSLRSAVSRLRDLGYSIIVK-EPYCVTLVR--KTSIVDL 142
                                       55555556678899989888899999999************************99999.99**9****..99***** PP

                      NTP_transf_5 143 hwrllppesprlepdfddlleerarpveiggksilvlspedlllylalHl.akhfwnrglgLrwlvD 208
                                         + +      ++ + + ll+  ++++ ++g +++vl+   + +++++H+ +k++++       l D
  gi|320100642|ref|YP_004176234.1| 143 YVHPTIA--GVIYAEGSRLLSY-TETAGFNGVEVKVLERDAEAVLAVAHAlYKERVYT------LND 200
                                       9999987..578889999**97.999***********************758999863......333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2239.08
//
Query:       gi|320100643|ref|YP_004176235.1|  [L=236]
Description: O-methyltransferase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-14   55.0   0.0    2.4e-14   54.2   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
    6.9e-12   45.5   0.0    7.8e-11   42.0   0.0    2.0  1  CmcI             Cephalosporin hydroxylase
    2.7e-06   26.7   0.0    3.8e-06   26.2   0.0    1.2  1  Methyltransf_3   O-methyltransferase
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.017   15.2   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   5.4e-18   2.4e-14       1     106 []      95     211 ..      95     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 5.4e-18
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.........aeeaaalare..aglddrvrlikads......ee 60 
                                       +EiG+  G + +++ r + + +   +++vd   g         +     ++ +  a  ++ + l+++ds      ++
  gi|320100643|ref|YP_004176235.1|  95 LEIGTARGGTLFLFSRIASDDAL--IISVDLPGGlfgggypylK----TFLYRcfARTKQKIVLLREDShseetlSK 165
                                       7****************999997..******9988877754431....33333455568888888888877433344 PP

                   Methyltransf_24  61 alaslaagsiDllfiDgghaaeavledleallprlapggvvlfdDi 106
                                       ++++l+ + +D lfiDg+h++e v++d+e+  p++++gg++ f+Di
  gi|320100643|ref|YP_004176235.1| 166 VRKHLNGRGVDSLFIDGDHSYEGVKRDFEMYSPLVKKGGIIAFHDI 211
                                       444666999************************************7 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.8e-14   7.8e-11      15     147 ..      73     210 ..      62     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.8e-14
                              CmcI  15 iklpqDlvayQeliwelkPdliietGiahGGsalfsasllallkskrkvlaidid.......ireknrq.aieahpl 83 
                                       +++ + ++a+  l+ ++kP++i+e+G+a GG + +++ + +    ++ ++++d+            +    +   ++
  gi|320100643|ref|YP_004176235.1|  73 MQVREEITALLSLLESVKPRTILEIGTARGGTLFLFSRIASD---DALIISVDLPgglfgggYPYLKTFlYRCFART 146
                                       68889999****************************999764...58899999852222111222222203334578 PP

                              CmcI  84 asrieliegssvdpeiveqvkslakekekvlvilDsdHthehvlaeLeayaplvsaGsYivveD 147
                                       +++i l++ +s + e++++v+++ +      + +D dH++e v +++e+y+plv++G  i+  D
  gi|320100643|ref|YP_004176235.1| 147 KQKIVLLREDSHSEETLSKVRKHLNGRGVDSLFIDGDHSYEGVKRDFEMYSPLVKKGGIIAFHD 210
                                       99************************99999999***********************9776655 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   8.4e-10   3.8e-06      16     157 ..      61     210 ..      48     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.4e-10
                                       HHHHTTTST.TGGGS--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHH CS
                    Methyltransf_3  16 LreatakktdlsemevsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfi 92 
                                       L e+t+ k+ + +m+v  + + +LslL + v  + +leiG+ +G +l+  +    +D  i+++d        + +++
  gi|320100643|ref|YP_004176235.1|  61 LSEKTVAKM-IRPMQVREEITALLSLL-ESVKPRTILEIGTARGGTLFLFSRIASDDALIISVDLPGGLFGGGYPYL 135
                                       788999999.9*****99999999876.566789*******************************998877776666 PP

                                       HH......TT-GGGEEEEE..S-HHHHHHHHHTSSS---EEEEEE-S-GG..GHHHHHHHHHHTEEEEEEEEEE- CS
                    Methyltransf_3  93 qk......agvaekielie..gdalkvLeelvkdkklpefDfifvDaDks..syvnyyeklleLvkvGgliaiDn 157
                                       +       a  ++ki l +  +++ ++L ++ k+ +    D +f+D D s    ++ +e    Lvk+Gg+ia+ +
  gi|320100643|ref|YP_004176235.1| 136 KTflyrcfARTKQKIVLLRedSHSEETLSKVRKHLNGRGVDSLFIDGDHSyeGVKRDFEMYSPLVKKGGIIAFHD 210
                                       543333567889999997612556789****99999999*********862245788999************975 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   3.8e-06     0.017      21     110 ..      90     197 ..      47     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.8e-06
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.................HHH.TTEEEECS-CCCSSHHHHH CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.................apl.pgvttiqgditdpetieki 79 
                                       + +t++++g a Gg     ++    ++ +++vDl  +                 a   +++ +++ d  ++et  k+
  gi|320100643|ref|YP_004176235.1|  90 KPRTILEIGTARGGTLFLFSRIASDDALIISVDLPGGlfgggypylktflyrcfARTkQKIVLLREDSHSEETLSKV 166
                                       3478999999999966555555444799******666799999999999887753335888888************* PP

                                       CHCHHHSSEEEEEE--S-SS-CHHHHHHHHH CS
                              FtsJ  80 kealserkvdlvvsDgapdvsgvhdldeylq 110
                                       +++l++r+vd    Dg  + +gv+   e+ +
  gi|320100643|ref|YP_004176235.1| 167 RKHLNGRGVDSLFIDGDHSYEGVKRDFEMYS 197
                                       ******************9999976666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1923.49
//
Query:       gi|320100644|ref|YP_004176236.1|  [L=418]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.22s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3036.55
//
Query:       gi|320100645|ref|YP_004176237.1|  [L=362]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   12.5   1.8       0.14   11.9   1.8    1.2  1  Phage_GP20  Phage minor structural protein GP20


Domain annotation for each model (and alignments):
>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.8   8.1e-06      0.14      58     133 ..     130     202 ..     118     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-06
                        Phage_GP20  58 ieelqaknkkakaeyeakiadlkldnaielaLkeakaknekavkalldkdklklkedgelkgLdeqikkLkesdky 133
                                       ++el+ k++     +e+k ++   d+a e+a kea+   ek++ +l  k+++++   g++++L+e +++ ++ d+y
  gi|320100645|ref|YP_004176237.1| 130 LKELKDKIESFCGAHENKEYKNIADKAREEACKEAEKAREKILEGL-SKNTVQV--YGNIIDLEELLTEDRNRDSY 202
                                       799***************************************9996.6699999..778********998888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2643.94
//
Query:       gi|320100646|ref|YP_004176238.1|  [L=285]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   99.0   0.0    3.9e-28   98.5   0.0    1.2  1  AAA_31       AAA domain
    1.1e-17   64.3   0.0    1.6e-17   63.7   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    2.1e-12   46.9   0.0      4e-12   46.0   0.0    1.4  1  ArsA_ATPase  Anion-transporting ATPase
    2.1e-07   30.5   0.0    1.2e-05   24.8   0.0    2.4  2  MipZ         ATPase MipZ
    3.2e-07   30.1   0.1    2.2e-06   27.4   0.1    1.9  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    4.6e-06   26.3   3.0    2.1e-05   24.1   3.0    2.2  1  ParA         NUBPL iron-transfer P-loop NTPase
      0.004   16.5   0.0      0.052   12.8   0.0    2.1  2  VirC1        VirC1 protein
     0.0049   16.4   0.0      0.008   15.6   0.0    1.3  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0088   15.9   0.2      0.023   14.5   0.0    1.7  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
  ------ inclusion threshold ------
      0.033   13.8   0.0        1.7    8.3   0.1    2.2  2  SRP54        SRP54-type protein, GTPase domain
      0.069   12.1   0.1      0.096   11.6   0.1    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   2.4e-31   3.9e-28       3     164 ..       4     170 ..       2     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 2.4e-31
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgi.ekneiektlyevli.eeknikeaiikt 76 
                                       vI+++nqKGG GKTT s  l+  la++g+ vLl+DlDpQa +++  ++i + ++++   +e+    + ni+ + i t
  gi|320100646|ref|YP_004176238.1|   4 VITVTNQKGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAHLSSlFVKItNLENVSDGAIEMAQdLRFNIRPINIGT 80 
                                       9****************************************998344553455565666666554788999999955 PP

                            AAA_31  77 kvenldlipssid.Laeaeielvelekkeeilkellek..vkdeYDyiiiDcpPsLglltenaLvasdsviipvqae 150
                                          +l li s ++ ++++   ++  ++   i+k++ ++  +  +YDy+i D+pP+L   t+ +L+a+d++iip + e
  gi|320100646|ref|YP_004176238.1|  81 -RGRLGLIASGLNyIIKVYRGMIPSTDPYAIYKRIEREpaITRNYDYVICDTPPELFPPTIWGLFAADYIIIPSNLE 156
                                       .4889******9978999999**9999999998887533399*********************************** PP

                            AAA_31 151 ayaleGleqllkti 164
                                       ++++ G + l+k +
  gi|320100646|ref|YP_004176238.1| 157 ELSILGTKLLIKEV 170
                                       *******9999876 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 !   63.7   0.0     1e-20   1.6e-17       1     116 [.       5     237 ..       5     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1e-20
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+++++kGG+GKTtl+a L++ la +g++Vll+D+Dpqa +++ l+ +  ++e+                       
  gi|320100646|ref|YP_004176238.1|   5 ITVTNQKGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAHLSS-LFVKITNLENvsdgaiemaqdlrfnirpinigt 80 
                                       79*****************************************.66666666666888999**************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|320100646|ref|YP_004176238.1|  81 rgrlgliasglnyiikvyrgmipstdpyaiykrierepaitrnydyvicdtppelfpptiwglfaadyiiipsnlee 157
                                       ***************************************************************************** PP

                                       .....CCHCCCHHH.HHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHC.........TS-EEE.EE CS
                                       .....xxxxxxxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxx.xx RF
                              CbiA  55 .....dlkrllell.ealgkkkall...lkiagvvlnrvdgeneetllkealeelkqry.........gvpvlg.vi 112
                                            +   ++e+l e++  +k+ +   l +a + + +  g++++++l++al++ ++ +         ++p+++  i
  gi|320100646|ref|YP_004176238.1| 158 lsilgTKLLIKEVLpEVIMYSKK-NvrvLGMALINISKKYGQDTFNKLNDALTRFIRNLpvpvrerfyARPLFQaRI 233
                                       *9996455566677655554443.4478788888889999999***********99988444444444444444555 PP

                                       E--C CS
                                       xxxx RF
                              CbiA 113 prde 116
                                       +r e
  gi|320100646|ref|YP_004176238.1| 234 HRHE 237
                                       5555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   2.4e-15     4e-12       8     134 ..      10     133 ..       3     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.4e-15
                                       ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHH..HCCHHG CS
                       ArsA_ATPase   8 GKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleea..kqevqk 82 
                                        KGG GKtt+sa +++ l+ kg++vlli +DP   ls  f + +++      eN s   i++ ++l+ +    +  +
  gi|320100646|ref|YP_004176238.1|  10 QKGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAHLSSLFVK-ITN-L----ENVSDGAIEMAQDLRFNirPINIGT 80 
                                       59***********************************99976.333.3....4554444444444443300444445 PP

                                       GGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHH.CSSSSEEEEESBS CS
                       ArsA_ATPase  83 eeeallgleeledvlaeelaslPGideilsfeellkyvk.eeeydvvvlDtaP 134
                                         +  l +++l+ +++     +P +d  ++++++ ++   +++yd+v+ Dt+P
  gi|320100646|ref|YP_004176238.1|  81 RGRLGLIASGLNYIIKVYRGMIPSTDPYAIYKRIEREPAiTRNYDYVICDTPP 133
                                       555567889***************************98879***********9 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   7.3e-09   1.2e-05       2      44 ..       4      46 ..       3      75 .. 0.86
   2 ?    3.3   0.0     0.026        42      95     130 ..     119     154 ..      97     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.3e-09
                                      EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HH CS
                              MipZ  2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtl 44
                                      vi ++n+kGG+Gk+t +  + + L++kG +v  idld + + +
  gi|320100646|ref|YP_004176238.1|  4 VITVTNQKGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAHLS 46
                                      799**********************************866554 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                                       HHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEE CS
                              MipZ  95 dleaeldfividtPGsdsalsrlahsladtlvtPln 130
                                       ++++++d+++ dtP +  + +  +   ad ++ P n
  gi|320100646|ref|YP_004176238.1| 119 AITRNYDYVICDTPPELFPPTIWGLFAADYIIIPSN 154
                                       57899*********9999999999999999999977 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.3e-09   2.2e-06       3      48 ..       4      49 ..       1      90 [. 0.91
   2 ?    0.5   0.0      0.21   3.5e+02     110     132 ..     118     140 ..      95     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.3e-09
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhF 48
                                      v++++  +GG+G+t+l+a L++ l + g++vl+iDl p+  L   F
  gi|320100646|ref|YP_004176238.1|  4 VITVTNQKGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAHLSSLF 49
                                      7889999*******************************99998777 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.21
                          CBP_BcsQ 110 kelkeqyrwillDlpagasaltr 132
                                        +++++y++++ D p +  + t 
  gi|320100646|ref|YP_004176238.1| 118 PAITRNYDYVICDTPPELFPPTI 140
                                       57889**********98766555 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   3.0   1.3e-08   2.1e-05       4      45 ..       3      44 ..       1     194 [. 0.79

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.3e-08
                              ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGp 45
                                      +vi+v+  KGG GK+t+++ l + La+kg++v l+D+D   +
  gi|320100646|ref|YP_004176238.1|  3 NVITVTNQKGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAH 44
                                      79***********************************96555 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.2e-05     0.052       2      44 ..       3      45 ..       2      67 .. 0.86
   2 ?    1.5   0.0      0.09   1.5e+02      79     121 ..     119     161 ..     104     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                             VirC1  2 klitfcslkGGaGkttalmglcsalasdgkrvalfeadenrPl 44
                                      ++it++  kGG+Gktt    l   las+g  v l + d    l
  gi|320100646|ref|YP_004176238.1|  3 NVITVTNQKGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAHL 45
                                      689************966666668**********999977665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.09
                             VirC1  79 aegeGfdyaladtrgGsselnnti..iassdllliPtmltpldid 121
                                       a ++ +dy++ dt         ti  + ++d+++iP+ l  l i 
  gi|320100646|ref|YP_004176238.1| 119 AITRNYDYVICDTPPELF--PPTIwgLFAADYIIIPSNLEELSIL 161
                                       557778888888875543..344422568999*****99999773 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.9e-06     0.008       7      58 ..      10      61 ..       5      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldt 58
                                       kGG Gk+t s+ l + la++g  vl++  DP+a   +l ++  + e v d 
  gi|320100646|ref|YP_004176238.1| 10 QKGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAHLSSLFVKITNLENVSDG 61
                                      59*********************************99999888777776554 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 !   14.5   0.0   1.4e-05     0.023       4      33 ..      13      42 ..      11      48 .. 0.92
   2 ?   -2.0   0.0       1.6   2.6e+03     140     181 ..     198     238 ..     178     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                       +GK+Tl++lL   +++kg++++++DlD+ 
  gi|320100646|ref|YP_004176238.1| 13 GTGKTTLSALLGIGLASKGYNVLLIDLDPQ 42
                                      59**************************95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                            CLP1_P 140 eellnelkrdlplskvkvvklpkspgvvqrsreerrelreer 181
                                       ++ +n+l+++l+ ++++ + +p+ ++ + r   ++r  r+e 
  gi|320100646|ref|YP_004176238.1| 198 QDTFNKLNDALT-RFIRNLPVPVRERFYARPLFQARIHRHEE 238
                                       456788888888.88888888888888877777776666665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1     0.001       1.7      11      38 ..      13      40 ..       2      43 .. 0.88
   2 ?    3.3   0.0     0.034        56      65      91 ..     104     131 ..      86     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.001
                                      TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54 11 GaGKTttlaKLaallkkegkkvllvaaD 38
                                      G+GKTt  a L   l ++g++vll+ +D
  gi|320100646|ref|YP_004176238.1| 13 GTGKTTLSALLGIGLASKGYNVLLIDLD 40
                                      8***********************9888 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
                                       TSCHHHHHHH.HHHHHHHTTSSEEEEEE CS
                             SRP54  65 eadpaavake.avekakeekidvvlvDT 91 
                                        +dp a+ k+ + e a  +++d+v++DT
  gi|320100646|ref|YP_004176238.1| 104 STDPYAIYKRiEREPAITRNYDYVICDT 131
                                       4567766665245678999********9 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   5.9e-05     0.096      32     106 ..       5      87 ..       2     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                                       EEEEE-.TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCC.......TSTTEEEEEE-.. CS
                              MeaB  32 vGltGv.PGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleela.......vdegvfiRslp.. 98 
                                       + +t    G+Gk tl   lg+ l+++G+ v ++ +DP +  +  s++   + le+++       +d    iR++   
  gi|320100646|ref|YP_004176238.1|   5 ITVTNQkGGTGKTTLSALLGIGLASKGYNVLLIDLDPQAHLS--SLFVKITNLENVSdgaiemaQDLRFNIRPINig 79 
                                       5556541589***************************88765..555555555555545555434444446654222 PP

                                       ----HHHH CS
                              MeaB  99 srGalGGl 106
                                       +rG+lG +
  gi|320100646|ref|YP_004176238.1|  80 TRGRLGLI 87 
                                       56666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2027.42
//
Query:       gi|320100647|ref|YP_004176239.1|  [L=158]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-05   24.0   0.0    0.00011   22.5   0.0    1.7  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    9.6e-05   22.6   0.0    0.00051   20.3   0.0    2.1  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.024   15.0   0.0    1.7  2  Phage_int_SAM_5  Phage integrase SAM-like domain
      0.064   13.0   0.0       0.13   12.0   0.0    1.4  2  FANCI_S3         FANCI solenoid 3


Domain annotation for each model (and alignments):
>> 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 ?   -2.6   0.0       1.7   7.7e+03      25      40 ..      28      42 ..      26      54 .. 0.58
   2 !   22.5   0.0   2.6e-08   0.00011      26      80 ..      97     153 ..      93     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                   Phage_int_SAM_4 25 aikrflrflkkkapee 40
                                      +++ f r +   +p++
  gi|320100647|ref|YP_004176239.1| 28 WLESFSREIA-MRPSQ 42
                                      5555655555.44444 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.6e-08
                   Phage_int_SAM_4  26 ikrflrflkkk..apeeltkedieaYlnyLanerklsastqknalnalsffykkvle 80 
                                       ++ f+ +++++   + ++++e ++a+ln +++ r ++++t+++++ +l+ f++ ++ 
  gi|320100647|ref|YP_004176239.1|  97 LRKFVSWIQQRglGVGSIDEEAVNAFLNAYLEGRAVKKNTVDRYRGILRRFVEYLAT 153
                                       799*****9778899****************8888*****************99875 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 !   20.3   0.0   1.1e-07   0.00051      26      81 ..      97     152 ..      96     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHH.TS--TTT--HHHHHHHHHS-----.-----HHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  26 Lrrflkflaergkesleqlttedvraflaeleeeg.lsatslarrlsalrsFfqflv 81 
                                       Lr+f+ + ++ ++  + ++++e v afl++++e + ++ +++ r++  lr+F  +l 
  gi|320100647|ref|YP_004176239.1|  97 LRKFVSWIQQ-RGLGVGSIDEEAVNAFLNAYLEGRaVKKNTVDRYRGILRRFVEYLA 152
                                       8999999999.999999***********99999889999***********9999986 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 ?   -2.3   0.0       1.3   5.8e+03      52      64 ..      23      32 ..       8      59 .. 0.56
   2 ?   15.0   0.0   5.3e-06     0.024      30      82 ..      95     150 ..      46     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                      HHHHHHHHHTS-- CS
                   Phage_int_SAM_5 52 eeFedYLkkkkgl 64
                                      ++  d+L   +  
  gi|320100647|ref|YP_004176239.1| 23 KHLADWL---ESF 32
                                      4455555...222 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.3e-06
                                       HHTTTS-.....S---TTT--HHHHHHH.HHHHHHTS---HHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5  30 khlkkFl...kkkditfeeidkefleeF.edYLkkkkglsentiskyfkklkavlnk 82 
                                         l+kF    ++  + +  id+e +++F  +YL +++ +++nt+ +y  +l++++ +
  gi|320100647|ref|YP_004176239.1|  95 FILRKFVswiQQRGLGVGSIDEEAVNAFlNAYL-EGRAVKKNTVDRYRGILRRFVEY 150
                                       45667776668889**************457**.9*****************99875 PP

>> FANCI_S3  FANCI solenoid 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.9e-05      0.13     107     193 ..      13     105 ..      11     108 .. 0.90
   2 ?   -2.7   0.0      0.89     4e+03     119     145 ..     119     149 ..     113     156 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                          FANCI_S3 107 ilntvqelyesklseFLkaigeeedlteklkelikqlqrvlvnflsedeedesi......sKlallLveilelLskk 177
                                        ++++q   +++l+++L+++  +++++ + +++i ++ + + +  + + e+  +      +K  + L ei+e +s++
  gi|320100647|ref|YP_004176239.1|  13 KFRIIQLELPKHLADWLESF--SREIAMRPSQFIATILTYFYEAWKVGRESAFAatrepyKKKEQSLDEIVERFSRE 87 
                                       5899999*************..999*****************99998877766669999****************** PP

                          FANCI_S3 178 lepssrqlv..qvltwlv 193
                                       ++ + + +   ++++w++
  gi|320100647|ref|YP_004176239.1|  88 VKLGRNIFIlrKFVSWIQ 105
                                       ***999887668999987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.89
                          FANCI_S3 119 lseFLkai....geeedlteklkelikqlqr 145
                                       +++FL+a     + +++   +   +++++ +
  gi|320100647|ref|YP_004176239.1| 119 VNAFLNAYlegrAVKKNTVDRYRGILRRFVE 149
                                       5666666632212344444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1151.77
//
Query:       gi|320100648|ref|YP_004176240.1|  [L=65]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       662  (0.0369234); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 489.85
//
Query:       gi|320100649|ref|YP_004176241.1|  [L=563]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   29.7  20.9      3e-07   29.2  20.9    1.2  1  PTPS_related  6-pyruvoyl-tetrahydropterin synthase related do


Domain annotation for each model (and alignments):
>> PTPS_related  6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2  20.9   1.7e-11     3e-07       1     231 [.      73     312 ..      73     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.7e-11
                      PTPS_related   1 lrYyaPlpYyilAllaalvgdlivafklvvllivfvgalgwylllrr.egrrlvavvaavLwllfpenlrvafseGn 76 
                                       lr+y+Pl+  ++ l+  + gd   a +   +l++ v alg  +l+r  +g+rl +++ a+ +l +   +  + +   
  gi|320100649|ref|YP_004176241.1|  73 LRFYPPLGLTLIYLIGRAAGDFPYAAQTSFFLAIYVFALGAWALGRSlTGSRLAGLATALTALSITGYVSTISVYWE 149
                                       79**************************************66676652778***99999999999999999888888 PP

                      PTPS_related  77 iprvlaiaLvpllllallvfvdkrekrslvalallmslialshamvalivglaifvf...lLllevlrk...rflen 147
                                       + r+l  +L +l l  l +f++ +ek+s++   ++ +l +l+h++ +l++ ++++v     +++ + ++   + l++
  gi|320100649|ref|YP_004176241.1| 150 YTRILGEGLAMLALSELNEFMRHGEKKSALLFGVFTGLTVLTHLIASLLLATLSAVTaayWVMRHMKKGagvSALTY 226
                                       *************************************************9999998833333333322222256778 PP

                      PTPS_related 148 lvalvaialgia..lssfWlvPll.kgglts.ldsgsvsevlksltvpltvaLdPllrlsnggfyfGlaivllilag 220
                                       +  l+a+a+++a  +s++Wl+P+l   g+ + +  +  ++++   +++ +v+L+P l ++ g+    l+++++ +a 
  gi|320100649|ref|YP_004176241.1| 227 IARLLAVAVALAlaISGWWLIPALiPFGISHyMRVQPQPGLVAGVFTN-SVSLFPPL-YEPGIQAPLLLLGFTGIAL 301
                                       877766555444339*********644665514444455555555555.66666654.2333334444556666666 PP

                      PTPS_related 221 vllakkrktpg 231
                                        ++ ++ ++p 
  gi|320100649|ref|YP_004176241.1| 302 QVFKGRERLPL 312
                                       66666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); 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:                         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 0.23s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4147.79
//
Query:       gi|320100650|ref|YP_004176242.1|  [L=188]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-06   25.4  15.3    1.2e-05   25.0  15.3    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 !   25.0  15.3   6.8e-10   1.2e-05     101     254 ..      16     166 ..       9     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.8e-10
                   Exosortase_EpsH 101 rlllfpllll.llalPlpavlvaqlslpLqllvaavagfllsllgip.vereGnviqlptg....qveVaeaCsGlr 171
                                         +l  +++  +la      +++++sl L+    ++ +f+  ++gi+ v ++  ++ l ++    +v   + C+G  
  gi|320100650|ref|YP_004176242.1|  16 YTFLTGVVVAtVLA---YILTLDPISLLLIGGELSILEFIAGYIGIHtVRVSPDTLILHRMshavTVIMTPDCTG-- 87 
                                       44444444442222...235666677777777777778888888877533333444444443344677899****.. PP

                   Exosortase_EpsH 172 sllallalglllallfrrrlwkrklllllaavpiaflaNlvRilllvllayhygpeaaegllHeiaGwllfgvalll 248
                                        ++a ++lgll++    +rl+ + +++l + +++ +++N+vRi + ++++  +gp a+   +H+++G +++++  +l
  gi|320100650|ref|YP_004176242.1|  88 -VFAPVVLGLLVLSTPGVRLRVK-ARVLPVHLLVMLVVNMVRIEASAVAGVFFGPIAF-RIIHDTIGGAIMLAL-AL 160
                                       .9*******************99.**********************************.8********998777.66 PP

                   Exosortase_EpsH 249 llgllp 254
                                       +l+l +
  gi|320100650|ref|YP_004176242.1| 161 VLWLDW 166
                                       666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1412.44
//
Query:       gi|320100651|ref|YP_004176243.1|  [L=438]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-22   78.4   0.0    9.9e-22   78.0   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.4e-17   64.0   0.1      2e-17   63.5   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    8.9e-11   42.1   2.1    8.9e-11   42.1   2.1    1.8  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.9e-08   34.0   0.2    1.9e-07   30.7   0.0    2.1  2  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.016   13.7   1.3      0.081   11.4   0.3    2.2  3  Cellulose_synt   Cellulose synthase
      0.072   13.1   0.1       0.23   11.5   0.0    1.8  2  Rad10            Binding domain of DNA repair protein Ercc1 (
        2.9    7.8   4.2        2.3    8.1   1.8    2.0  2  LapA_dom         Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   3.9e-25   9.9e-22       1     230 []      71     300 ..      71     300 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 3.9e-25
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       p  + +l+p++n   ++++ + sl  ++yp++ vvvv+d +d++ l ++    a l   rv++v+  r+++++ k+ 
  gi|320100651|ref|YP_004176243.1|  71 PK-VGILIPVYND-YEVLASIKSLQGIDYPNTVVVVVDDSDDEDLLHELSN--ASLRS-RVKLVHYRRKGRKGLKAG 142
                                       45.899****999.778899************************9998876..45544.9********9******** PP

                   Glyco_tranf_2_3  78 alnealra...vk.sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrs.tlvsalgalefaerhlrfl 149
                                       aln+a++    v+  d+vl++D+D  +eP+ + +l+ +++++++++v++ ++ + +s t++  l++  +a     +l
  gi|320100651|ref|YP_004176243.1| 143 ALNDAIEYllsVEhVDYVLILDADFEIEPGMVWKLVSLAFDHDAHVVQGYQRHRKGSdTVIGTLYRASTAGSIV-NL 218
                                       *******755544599********************************9999998654889999**9*999999.66 PP

                   Glyco_tranf_2_3 150 aarralgv.ltlnGsgslirrevlkelegldplflltdDyelglrlrr..agfrtayvpgaavrevfpsslkayikq 223
                                       + r++ g  ++++Gs+ li r+v+++  +++p ++l++D++l+    +   gf++    +aa   + p++  a+++q
  gi|320100651|ref|YP_004176243.1| 219 VGRYRDGLyPIFTGSCGLISRRVFERV-RFRP-GSLAEDWRLTIDSSMeiPGFKILATHEAAASGAVPKTHRALWRQ 293
                                       667777754******************.9999.********9998887779************************** PP

                   Glyco_tranf_2_3 224 rnRwvyg 230
                                         Rw+ g
  gi|320100651|ref|YP_004176243.1| 294 QVRWAAG 300
                                       ****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 !   63.5   0.1   7.8e-21     2e-17       2     169 ..      75     245 ..      74     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 7.8e-21
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnaglr 76 
                                       + ip+yN + ++l++++sl  + +yp+  ++vvDD++ +++   l +++   + + v++ r+ ++  kagaln +++
  gi|320100651|ref|YP_004176243.1|  75 ILIPVYNDY-EVLASIKSLQGI-DYPNTVVVVVDDSDDEDLLHELSNASLrsRVKLVHYRRKGRKGLKAGALNDAIE 149
                                       78******5.566799******.*************955555555555445788888999999888*********** PP

                                       H--SS....EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCC CS
                   Glycos_transf_2  77 aatgd....yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkg 149
                                       +  +     y+l+lDaD e++p+ + klv  + +++a vv g  ++++g+++ i   +r             r ++g
  gi|320100651|ref|YP_004176243.1| 150 YLLSVehvdYVLILDADFEIEPGMVWKLVSLAFDHDAHVVQGYQRHRKGSDTVIGTLYRA-STAGSIVNLVGRYRDG 225
                                       *99888999***********************************************9995.3333333344455667 PP

                                       CSTTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 150 nlsfeigsaallrrealeel 169
                                         ++++gs+ l++r+++e++
  gi|320100651|ref|YP_004176243.1| 226 LYPIFTGSCGLISRRVFERV 245
                                       899**************986 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 ?   -4.1   1.4         5   1.3e+04     167     187 ..      22      42 ..       5      52 .. 0.41
   2 !   42.1   2.1   3.5e-14   8.9e-11       1     182 [.     159     362 ..     159     409 .. 0.68

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 5
                   Glyco_trans_2_3 167 lplhlallllfsllalalvll 187
                                       + ++++l++++s +  +++++
  gi|320100651|ref|YP_004176243.1|  22 VNASIVLYIVSSAVLGVYAAW 42 
                                       333344444444333222222 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 3.5e-14
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsv.Gs 75 
                                       ++l+lDaD  + p  + +++++  ++++++vqg    + ++ +++ +l+ + +a ++ +  lv+ +  +  p++ Gs
  gi|320100651|ref|YP_004176243.1| 159 YVLILDADFEIEPGMVWKLVSLAFDHDAHVVQGYQRHRkGSDTVIGTLYRASTAGSIVN--LVGRYRDGLYPIFtGS 233
                                       79*******************99988**********997889***********999887..58888888888666** PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrl..qrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.....e 145
                                       + +++r+++++v +++  ++s++ED+ + +       G+++   +e++    +p t ra +rQ  Rwa G      +
  gi|320100651|ref|YP_004176243.1| 234 CGLISRRVFERV-RFR--PGSLAEDWRLTIDSsmEIPGFKILATHEAAASGAVPKTHRALWRQQVRWAAGTlsefaS 307
                                       ************.777..8*******9999873257799999999999**********************7543331 PP

                   Glyco_trans_2_3 146 leklil..........................................lvrllgylgsllwsalplhlallllfsll 180
                                                                                       l                            
  gi|320100651|ref|YP_004176243.1| 308 -----TfleilackglsrtaklgyvlqglyftngvwvyvntlaplahyL---------------------------- 351
                                       .....02344456666655555544444444444333222222211110............................ PP

                   Glyco_trans_2_3 181 a.........l 182
                                                  
  gi|320100651|ref|YP_004176243.1| 352 VtgshlrmpwP 362
                                       12222222220 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.12   3.1e+02      22      64 ..      91     130 ..      88     141 .. 0.86
   2 !   30.7   0.0   7.3e-11   1.9e-07      29     172 ..     155     298 ..     132     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                   Glyco_transf_21  22 llqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVt 64 
                                        lq++++ ++ ++v+ Dsd   ++d L+el +a  +++v+lV+
  gi|320100651|ref|YP_004176243.1|  91 SLQGIDYPNTVVVVVDDSD---DEDLLHELSNASLRSRVKLVH 130
                                       5677888888899999999...99********99999***998 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 7.3e-11
                   Glyco_transf_21  29 akydllvisDsdvrvkpdyLeellaaledpkvglVtslpv.gsdakglaaaleaafl.ntlagvlqa.klsglgfav 102
                                          d+++i+D+d  ++p  + +l+    d ++ +V+++ +   + +++ ++l +a   +   +++ + + +   + +
  gi|320100651|ref|YP_004176243.1| 155 EHVDYVLILDADFEIEPGMVWKLVSLAFDHDAHVVQGYQRhRKGSDTVIGTLYRASTaGSIVNLVGRyRDGLYPIFT 231
                                       5679***********************9**********994555568999997777756667777774557789*** PP

                   Glyco_transf_21 103 GksmalrreaLeaiGGfealadeLAeDyalg..kllraaGlkvvlspapiaqtsvprrsslrallaRqlrWa 172
                                       G++ +++r+++e++  f++    LAeD  l+    +   G+k+   ++++a+ +vp+  + ral+++q+rWa
  gi|320100651|ref|YP_004176243.1| 232 GSCGLISRRVFERV-RFRP--GSLAEDWRLTidSSMEIPGFKILATHEAAASGAVPK--THRALWRQQVRWA 298
                                       *************9.9999..9*********75666666************999995..99**********8 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.06   1.5e+02     143     215 ..      96     171 ..      67     194 .. 0.74
   2 ?   -2.2   0.0       0.4     1e+03     425     463 ..     187     224 ..     179     241 .. 0.81
   3 ?   11.4   0.3   3.2e-05     0.081     434     554 ..     266     383 ..     233     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.06
                    Cellulose_synt 143 dhagiiqvllkksgaedveGnelprlvyvsrekrpGydhn....kkaGamnalvrvsavlsnapfilnldcdhyinn 215
                                       d++  + v+++ s++ed+  +el      sr k   y  +     kaGa+n  +     +    ++l ld d  i+ 
  gi|320100651|ref|YP_004176243.1|  96 DYPNTVVVVVDDSDDEDLL-HELSNASLRSRVKLVHYRRKgrkgLKAGALNDAIEYLLSVEHVDYVLILDADFEIEP 171
                                       7777788888888888775.344444444444444443321111589****9999999999999******9998865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.4
                    Cellulose_synt 425 dvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhq 463
                                        v+ G++ h +G  +v     r++  Gs  +nl  r ++
  gi|320100651|ref|YP_004176243.1| 187 HVVQGYQRHRKGSDTVIGTLYRASTAGSI-VNLVGRYRD 224
                                       5899*********9999999999988875.788887765 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 3.2e-05
                    Cellulose_synt 434 arGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalfagykkklkllerlaylnviiypftsif 510
                                         G++ +   t+ +a  G+ p       +q +rwa G++  f s    ++a+  k l    +l y+  ++y    + 
  gi|320100651|ref|YP_004176243.1| 266 IPGFKIL--ATHEAAASGAVPKTHRALWRQQVRWAAGTLSEFASTFLEILAC--KGLSRTAKLGYVLQGLYFTNGVW 338
                                       5555543..46778888999999888899**********************9..999999***********999999 PP

                    Cellulose_synt 511 llvycilp.alsllsgkfivkelsnlasiyllllflslivlavle 554
                                       + v  + p a  l++g  +     + + ++ll +   li+ a+le
  gi|320100651|ref|YP_004176243.1| 339 VYVNTLAPlAHYLVTGSHLRMPWPIGVYLWLLGIETLLIAGAMLE 383
                                       98888888566799****9999999999*****999999999998 PP

>> Rad10  Binding domain of DNA repair protein Ercc1 (rad10/Swi10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.9e-05      0.23      56      98 ..      87     129 ..      78     132 .. 0.78
   2 ?   -3.1   0.0       2.9   7.6e+03      68      99 ..     159     190 ..     150     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.9e-05
                             Rad10  56 erlkklk.kkyklrvlLvlvDvedseevlkeLnkicilndltll 98 
                                         +k+l+  +y  + ++v+vD +d e++l+eL++ +++++++l+
  gi|320100651|ref|YP_004176243.1|  87 ASIKSLQgIDYP-NTVVVVVDDSDDEDLLHELSNASLRSRVKLV 129
                                       557777743444.5566889999****************99997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                             Rad10  68 rvlLvlvDvedseevlkeLnkicilndltlll 99 
                                        vl++  D e +  ++ +L ++++ +d  ++ 
  gi|320100651|ref|YP_004176243.1| 159 YVLILDADFEIEPGMVWKLVSLAFDHDAHVVQ 190
                                       47777777777777777787777777777665 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 ?    8.1   1.8    0.0009       2.3      11      40 ..      17      47 ..      15      54 .. 0.82
   2 ?   -2.2   0.0       1.5   3.7e+03      16      46 ..     397     429 ..     392     435 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0009
                          LapA_dom 11 l.faqvelpLsllllvafgiGallgwllslw 40
                                      l  ++v+++++l ++ ++++G+ ++w +s +
  gi|320100651|ref|YP_004176243.1| 17 LlDFTVNASIVLYIVSSAVLGVYAAWYISSF 47
                                      435566********************99985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                          LapA_dom  16 elpLsllllvafgiGallgwllslwsyl..rlr 46 
                                        +p +  l+++ ++G + g+l + ++++   +r
  gi|320100651|ref|YP_004176243.1| 397 AIPMIYYLALMHVAGTVKGILPGGVKWVvtSKR 429
                                       578888999999999999999998665533444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3268.76
//
Query:       gi|320100652|ref|YP_004176244.1|  [L=384]
Description: regulatory protein ArsR [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   47.8   1.1      3e-12   46.4   1.1    1.6  1  HTH_20           Helix-turn-helix domain
    2.1e-07   30.7   0.0    5.8e-07   29.3   0.0    1.8  1  HTH_5            Bacterial regulatory protein, arsR family
    2.5e-05   23.7   0.5    9.1e-05   21.9   0.0    2.1  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00014   21.7   0.2     0.0036   17.2   0.1    2.4  2  MarR_2           MarR family
     0.0015   18.5   0.2      0.025   14.5   0.0    2.6  3  MarR             MarR family
     0.0034   17.1   1.1     0.0066   16.2   0.2    2.0  2  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.037   14.4   0.0      0.079   13.3   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
        0.1   12.8   0.0       0.32   11.2   0.0    1.8  2  HTH_34           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 !   46.4   1.1   1.3e-15     3e-12       5      55 ..     256     306 ..     252     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.3e-15
                                       HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20   5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                       eALahP Rr+i+raL  ++++t sel ++l ++k+tls HL vLe+ g++ 
  gi|320100652|ref|YP_004176244.1| 256 EALAHPARREIMRALEARGAVTMSELLRLLNMPKATLSWHLYVLESRGIIS 306
                                       79**********************************************995 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   2.6e-10   5.8e-07       1      47 []     260     307 ..     260     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.6e-10
                                       SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       +p+R++I+++L+  g  + +el + l+++++t+S HL +L+  G++++
  gi|320100652|ref|YP_004176244.1| 260 HPARREIMRALEArGAVTMSELLRLLNMPKATLSWHLYVLESRGIISS 307
                                       599*********9999*****************************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 !   21.9   0.0   4.1e-08   9.1e-05       5      47 ..     263     305 ..     261     306 .. 0.97
   2 ?   -1.4   0.1      0.78   1.8e+03      23      44 ..     354     375 ..     352     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.1e-08
                            HTH_24   5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +r+I+++L++ +  +++eL + l+++++t++++l  Le+ G+I
  gi|320100652|ref|YP_004176244.1| 263 RREIMRALEARGAVTMSELLRLLNMPKATLSWHLYVLESRGII 305
                                       699***************************************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.78
                            HTH_24  23 LAerlglSpstvnrrlkrLeee 44 
                                       ++e+l+l+   ++r  k Le+e
  gi|320100652|ref|YP_004176244.1| 354 VSEALNLPTESITRLAKLLEKE 375
                                       5899999999999888888875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.6e-06    0.0036       5      51 ..     261     305 ..     257     313 .. 0.93
   2 ?    2.0   0.0     0.087     2e+02      23      47 ..     350     374 ..     327     378 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2   5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51 
                                       pa + ++ aL +r+   +t++el r l+++k+++s +l  L+++G +
  gi|320100652|ref|YP_004176244.1| 261 PARREIMRALEARGA--VTMSELLRLLNMPKATLSWHLYVLESRGII 305
                                       88999*********9..***************************988 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.087
                                       EHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  23 tvgelarrlglsksavsrilkrLva 47 
                                        +  + ++l+l+  +++r+ k L++
  gi|320100652|ref|YP_004176244.1| 350 DPVRVSEALNLPTESITRLAKLLEK 374
                                       566678999************9997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.1e-05     0.025       7      49 ..     265     307 ..     261     310 .. 0.94
   2 ?   -2.3   0.0       1.9   4.3e+03      15      30 ..     319     334 ..     318     338 .. 0.82
   3 ?    0.3   0.1       0.3   6.8e+02      25      44 ..     356     375 ..     354     375 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49 
                                       +i+r l+ +g+ ++seL + l++ k+t++  l  Le +G i++
  gi|320100652|ref|YP_004176244.1| 265 EIMRALEARGAVTMSELLRLLNMPKATLSWHLYVLESRGIISS 307
                                       58999************************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                                       STTEEHHHHHHHHTS- CS
                              MarR  15 qgplsvseLakklgvs 30 
                                       +gp  v  La++l+ +
  gi|320100652|ref|YP_004176244.1| 319 SGPTGVESLASRLSRE 334
                                       58899999***99876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.3
                                       HHHTS-HHHHHHHHHHHHHT CS
                              MarR  25 kklgvskstvtrvldrLekk 44 
                                       ++l++ + ++tr+++ Lek+
  gi|320100652|ref|YP_004176244.1| 356 EALNLPTESITRLAKLLEKE 375
                                       678888889********995 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 !   16.2   0.2   2.9e-06    0.0066       8      48 ..     266     305 ..     265     307 .. 0.87
   2 ?   -2.6   0.0       2.2   4.8e+03      25      43 ..     355     373 ..     352     376 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.9e-06
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                       i++al++++  +t sel r + +pk+t + +L  L+ +G++
  gi|320100652|ref|YP_004176244.1| 266 IMRALEARGA-VTMSELLRLLNMPKATLSWHLYVLESRGII 305
                                       6777766655.8**************************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                                       HHHHTS-HHHHHHHHHHHH CS
                          HTH_IclR  25 ArrtglpkStvhRlLqtLv 43 
                                       ++++ lp  +  Rl + L+
  gi|320100652|ref|YP_004176244.1| 355 SEALNLPTESITRLAKLLE 373
                                       6666777666666666655 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.5e-05     0.079       5      64 ..     263     318 ..     261     322 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                                       -SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE- CS
                   Penicillinase_R   5 EaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsp 64 
                                        +e+m++l ++g +t++e+   l+ +    ++T    l  L+ +g++s+ k  ++  Y +
  gi|320100652|ref|YP_004176244.1| 263 RREIMRALEARGAVTMSELLRLLNMP----KATLSWHLYVLESRGIISSFKWRKSLFYFA 318
                                       589***********************....9***********************999988 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.32       2      46 ..     263     307 ..     262     317 .. 0.91
   2 ?   -3.0   0.0       3.8   8.6e+03      16      40 ..     350     374 ..     347     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                            HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46 
                                       R +++  L +   ++++el   l++ ++ Ls hl +Le+ g i+ 
  gi|320100652|ref|YP_004176244.1| 263 RREIMRALEARGAVTMSELLRLLNMPKATLSWHLYVLESRGIISS 307
                                       5689************************************99875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.8
                            HTH_34  16 dfvelkealeatdgnLsvhlkkLek 40 
                                       d+v+++eal++ +  +   +k Lek
  gi|320100652|ref|YP_004176244.1| 350 DPVRVSEALNLPTESITRLAKLLEK 374
                                       5678889999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2822.25
//
Query:       gi|320100653|ref|YP_004176245.1|  [L=230]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1749.71
//
Query:       gi|320100654|ref|YP_004176246.1|  [L=716]
Description: type I phosphodiesterase/nucleotide pyrophosphatase [Desulfurococcus mucosus DSM 2162]
Scores for 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  145.5   0.2    7.8e-22   78.3   0.0    2.2  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
    7.9e-06   25.5   0.2      0.025   14.0   0.1    2.5  2  Sulfatase      Sulfatase
  ------ inclusion threshold ------
      0.061   12.7   0.0       0.12   11.7   0.0    1.4  1  Metalloenzyme  Metalloenzyme superfamily


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.3   1.5e-21   8.8e-18       1     178 [.      33     243 ..      33     249 .. 0.67
   2 !   78.3   0.0   1.3e-25   7.8e-22     170     339 ..     363     560 ..     265     576 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.5e-21
                                       EEEEEETT-B....TTHHHHHG.S..TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEE CS
                      Phosphodiest   1 vlvislDGlr....adlldrla.e..llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfyd 70 
                                       v+++s+D lr    ++ll++   +   lp+++++a++g+ a+ ++ +fP+ T+ +ha + TG+ P+ +Gi+gN +  
  gi|320100654|ref|YP_004176246.1|  33 VVLLSIDALRadmvWQLLSNQTpGapQLPGFRYIAEHGYIAKGMIVSFPSSTAVSHAVISTGAPPAVTGITGNAMHL 109
                                       89********8888888888665599*************************************************** PP

                                       TTTTEEEEEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSE...BTTCT.SC.................. CS
                      Phosphodiest  71 rktgeyvvfvtededaprwwqgepiwdtaakarglkaaalfwpgsevd...ystyyylvs................. 127
                                       ++t      +  +     ++  ep+w ta ++ gl+a ++ +p s++      +++ +v                  
  gi|320100654|ref|YP_004176246.1| 110 PGTPLTSLVSGFNG---SLLLAEPLWMTADRQ-GLTAVVAAFPQSNPSaweGKMRRSMVFnpydssmgpptystlyt 182
                                       ***99644444444...58999**********.***88777765555500055554444488888655544444433 PP

                                       ..TBHHSBTCT.....CSTTSCHHHHHH.HHHHHHH..............HHCHTHSHHHHHCTSSESEEEE CS
                      Phosphodiest 128 ..etppryled....dfnakvpledkvd.kavlqtw..............ldaafakvvlekelekpdlllv 178
                                          + p         d++ ++ + + +   +v ++w              +++   +       e+pd+++v
  gi|320100654|ref|YP_004176246.1| 183 snRSVP----AatyvDVSPALNWTGSLPgVSVVKAWeasfsygdeawflyIADTNGD-------ERPDVVAV 243
                                       332222....12222444444444433322233333444444433333333333333.......67777766 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 1.3e-25
                                       T......SSESEEEEEECCCHHHHHHH.-TTSHH...............HHHHHHHHHHHHHHHHHHHHHTTGTTTE CS
                      Phosphodiest 170 l......ekpdlllvyleetDtvgHkf.Gpdspe...............vedalrrvDkaigdLlealderglsaet 224
                                               ++dll++y + +D v H+f G  +p                ++ +++ +D++++ +l+++d +    +t
  gi|320100654|ref|YP_004176246.1| 363 TrwlirnTNWDLLMTYTPIVDNVYHEFlGMTDPRmpyydpvkapkywgyILRTIQWADQFVQMILSEVDLT----NT 435
                                       033344478*****************9666677777788889999**************************....** PP

                                       EEEEEES---EEEHTTSEEEGGGTSTGGH.....GEEEEECBHHS.SSE...EEEEESTEE.E.CCCTTHHHHHHHH CS
                      Phosphodiest 225 niilvSDHGmadvsddkvielndlleekg.....llhlkdegkggakal...iainpkare.lnrvaeaeaeevyae 292
                                       ++++vSDHG+ +v   k++++n++le++g      +++  +++ +++     + in+k+re  + v++a++++v+++
  gi|320100654|ref|YP_004176246.1| 436 AVVVVSDHGQWPV--AKLVYVNNILEQAGllkrsGSTILLNETLAYYTGynqVFINLKGREaGGIVDPADYDRVVNN 510
                                       *************..**************9999966666666666666678899999******************** PP

                                       HHTCHHCCHST.HTT.TEEEEEGGGS-GGGCH.STTS-SEEEEE-TTEEE CS
                      Phosphodiest 293 lkakleelrkk.ege.alavylkeaipkrlhy.kkrapdlvlvadpgwsi 339
                                       + + l++ r++ +ge  + v +k    + l + ++r++d+v+ ++pg+ +
  gi|320100654|ref|YP_004176246.1| 511 VMSVLASTRDPdTGEpVFSVVMKKSEAASLGLwGDRVGDIVISCKPGYAP 560
                                       *********9999**9777777773333333357**************86 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00014      0.82       2      73 ..      32     108 ..      31     121 .. 0.88
   2 !   14.0   0.1   4.2e-06     0.025     212     251 ..     410     445 ..     333     460 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00014
                                       EEEEEEESSE-TT.GSGGGTTTSCSSHHH...HHHHHTSEEESSEE-SSS.SHHHHHHHHHHSS-HHHHTHSSCCST CS
                         Sulfatase   2 nvvliladdlgag.dlglyggktattpnl...drlaeeglrftnfysaap.lcspsraalltgryphnsgvasntev 73 
                                        vvl+ +d l+a+  ++l ++ t+  p+l    ++ae+g++ + ++++ p +++ s a + tg +p+ +g++ n ++
  gi|320100654|ref|YP_004176246.1|  32 KVVLLSIDALRADmVWQLLSNQTPGAPQLpgfRYIAEHGYIAKGMIVSFPsSTAVSHAVISTGAPPAVTGITGNAMH 108
                                       69***********999*********999999999************876526899***************9999864 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.2e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSS CS
                         Sulfatase 212 eaylnsveyvDdligrvlaaLeenglldntlvvftSDhga 251
                                       +  l+++ ++D++++ +l ++     l nt vv++SDhg+
  gi|320100654|ref|YP_004176246.1| 410 GYILRTIQWADQFVQMILSEV----DLTNTAVVVVSDHGQ 445
                                       56789****************....**************7 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.1e-05      0.12     156     187 ..     414     445 ..     408     451 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 156 aaieaaDeavkeildaieqvdgilvvtADHgn 187
                                       + i+ aD+ v++il++++ +++ +vv++DHg 
  gi|320100654|ref|YP_004176246.1| 414 RTIQWADQFVQMILSEVDLTNTAVVVVSDHGQ 445
                                       67999**************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 5004.80
//
Query:       gi|320100655|ref|YP_004176247.1|  [L=96]
Description: acylphosphatase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-29  101.2   0.1    3.5e-29  101.1   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 !  101.1   0.1   1.9e-33   3.5e-29       2      85 .]      10      93 ..       9      93 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 1.9e-33
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      r++v+G VQgv+FR+++++ A++lg++G+vrNl+dgsVe+v+ege++ ve+++++ ++gpp+arv+ veve++++++ef
  gi|320100655|ref|YP_004176247.1| 10 RIRVRGLVQGVFFRATMKEVADQLGVSGWVRNLPDGSVEAVVEGERQRVEELIKWAHRGPPAARVEAVEVEWEPYKGEF 88
                                      799**************************************************************************** PP

                   Acylphosphatase 81 kdFei 85
                                      k+F+i
  gi|320100655|ref|YP_004176247.1| 89 KGFKI 93
                                      ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 711.49
//
Query:       gi|320100656|ref|YP_004176248.1|  [L=432]
Description: transposase, IS605 OrfB family [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   78.8   0.2      4e-22   77.9   0.2    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0026   17.2   1.2       0.12   11.9   0.1    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.011   15.8   1.0       0.63   10.2   0.1    2.4  2  Zn-ribbon_8     Zinc ribbon domain
      0.011   15.9   0.9      0.024   14.9   0.9    1.5  1  OrfB_IS605      Probable transposase
      0.014   15.0   0.7        2.3    8.1   0.0    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.016   14.6   2.4      0.048   13.1   2.3    1.8  1  zf-ribbon_3     zinc-ribbon domain
      0.017   15.1   1.3      0.028   14.4   1.3    1.3  1  DZR             Double zinc ribbon
      0.033   14.3   2.1      0.059   13.5   2.1    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.039   13.6   2.3      0.088   12.5   2.3    1.6  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.044   13.8   2.7        1.5    8.9   0.5    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.068   13.1   0.1       0.13   12.2   0.1    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.077   13.3   3.5      0.096   13.0   0.4    2.3  2  zinc_ribbon_9   zinc-ribbon
       0.12   11.2   0.2       0.18   10.5   0.2    1.2  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.14   12.2   0.3       0.27   11.3   0.3    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.14   12.0   0.0       0.28   11.0   0.0    1.4  1  VasL            Type VI secretion system, EvfB, or VasL
       0.18   12.0   0.4       0.34   11.1   0.4    1.4  1  DUF678          Protein of unknown function (DUF678)
        2.3    8.4   4.0        3.5    7.8   2.3    2.1  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 !   77.9   0.2   3.8e-25     4e-22       1      69 []     300     367 ..     300     367 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 3.8e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +r+++ +l ++++++G++ + vnp  TS+tC++Cgs++ e    r++kCp+CgfeadrD++A++Ni ++
  gi|320100656|ref|YP_004176248.1| 300 YRRFEYWLDWQCEKHGVPHIAVNPKDTSSTCPRCGSRLVE-SGYRRMKCPDCGFEADRDTVAVLNIRRK 367
                                       799*************************************.9************************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 !   11.9   0.1   0.00012      0.12       2      27 ..     310     335 ..     309     340 .. 0.92
   2 ?    4.0   0.2     0.034        35       1       7 [.     345     351 ..     345     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                       +C ++g +++ ++p+ +  +C++CG+
  gi|320100656|ref|YP_004176248.1| 310 QCEKHGVPHIAVNPKDTSSTCPRCGS 335
                                       69999********************7 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.034
                                       EEETTTT CS
                      TF_Zn_Ribbon   1 ykCPnCg 7  
                                       +kCP+Cg
  gi|320100656|ref|YP_004176248.1| 345 MKCPDCG 351
                                       79****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0006      0.63       7      36 ..     310     337 ..     303     340 .. 0.68
   2 ?    3.8   0.1     0.059        62      28      37 ..     346     355 ..     342     358 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0006
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgsev 36 
                                       +Ce++g  + ++ +  ++   +CP+Cgs++
  gi|320100656|ref|YP_004176248.1| 310 QCEKHGVPHIAVNP--KDTSSTCPRCGSRL 337
                                       58887755555544..445678******65 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.059
                       Zn-ribbon_8  28 aCPeCgsevr 37 
                                       +CP+Cg e+ 
  gi|320100656|ref|YP_004176248.1| 346 KCPDCGFEAD 355
                                       4888876655 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9   2.3e-05     0.024      48     102 ..     205     264 ..     165     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                        OrfB_IS605  48 sdykylakeiaelqsklkkskn.....ykkasrklarlhrkrsrrrkhllhklathlikt 102
                                       ++  ++++   +lq+k++         ++  + +++r h+k + ++ + ++k++++++ t
  gi|320100656|ref|YP_004176248.1| 205 ERAVRYRELAERLQRKYSNGSYrawlrRRGIRDRVRRFHEKARSIIEDWARKVSREIALT 264
                                       5556677777777777766655899989999*************************9866 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0021       2.3      11      23 .]     325     337 ..     321     338 .. 0.81
   2 ?    5.0   0.1      0.02        21       1       8 [.     346     353 ..     346     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                     zinc_ribbon_2  11 dnakFCpyCGtpl 23 
                                       d++  Cp+CG+ l
  gi|320100656|ref|YP_004176248.1| 325 DTSSTCPRCGSRL 337
                                       8889999999865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                     zinc_ribbon_2   1 fCpnCGae 8  
                                       +Cp CG e
  gi|320100656|ref|YP_004176248.1| 346 KCPDCGFE 353
                                       79999976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.3   4.5e-05     0.048       4      24 ..     329     352 ..     327     353 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                       zf-ribbon_3   4 rCPnCGa.plssd..dnvCpyCGt 24 
                                       +CP+CG+ +++s+   ++Cp CG 
  gi|320100656|ref|YP_004176248.1| 329 TCPRCGSrLVESGyrRMKCPDCGF 352
                                       6***********84468******6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.3   2.6e-05     0.028       9      41 ..     324     357 ..     309     359 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                               DZR   9 ppdarfCseCgtklkavaa.edrCpsCgekvdpe 41 
                                       ++ + +C++Cg++l +      +Cp Cg ++d +
  gi|320100656|ref|YP_004176248.1| 324 KDTSSTCPRCGSRLVESGYrRMKCPDCGFEADRD 357
                                       345679*******9754448999*****988765 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.1   5.6e-05     0.059      15      40 .]     327     351 ..     326     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                     Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCvaCd 40 
                                       ++tCp+Cg+ L+++ +  ++ C+ C+
  gi|320100656|ref|YP_004176248.1| 327 SSTCPRCGSRLVES-GYRRMKCPDCG 351
                                       789**********9.56899*****6 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 ?   12.5   2.3   8.4e-05     0.088       6      28 ..     330     351 ..     325     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCg 28 
                                       C+rCG++ + ++g + + Cp+Cg
  gi|320100656|ref|YP_004176248.1| 330 CPRCGSRLV-ESGYRRMKCPDCG 351
                                       *******85.78**********9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.5    0.0015       1.5       1      10 [.     329     338 ..     329     341 .. 0.89
   2 ?    4.4   0.1     0.036        38       1      11 [.     346     356 ..     346     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                    DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                       +CP CGs +v
  gi|320100656|ref|YP_004176248.1| 329 TCPRCGSRLV 338
                                       7*******99 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.036
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP CG ++ R
  gi|320100656|ref|YP_004176248.1| 346 KCPDCGFEADR 356
                                       6*****87755 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012      0.13       9      38 ..     325     354 ..     318     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       SS--B-TTT-SB--SSSS-EEEETTT--EE CS
                              C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllv 38 
                                       + +++C  Cg+ l + +++ +kC +C++ +
  gi|320100656|ref|YP_004176248.1| 325 DTSSTCPRCGSRLVESGYRRMKCPDCGFEA 354
                                       56789********99***********9875 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   9.1e-05     0.096      11      33 ..     318     339 ..     310     340 .. 0.79
   2 ?    0.2   0.2       0.9   9.5e+02      22      28 ..     346     351 ..     343     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.1e-05
                     zinc_ribbon_9  11 fVsvspdedsdvlCPhCgggFVE 33 
                                       ++ v p+++s + CP+Cg+  VE
  gi|320100656|ref|YP_004176248.1| 318 HIAVNPKDTSST-CPRCGSRLVE 339
                                       567777666666.******9999 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.9
                     zinc_ribbon_9  22 vlCPhCg 28 
                                       + CP+Cg
  gi|320100656|ref|YP_004176248.1| 346 K-CPDCG 351
                                       4.****7 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00017      0.18     493     529 ..     311     354 ..     302     366 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                       HHHTT--EEEEE--..EEEETT.--....EESS.SB-TTT--BE CS
                              NRDD 493 akktgigYfsinpk..idvCnecgy....kgei.ekCpkCgsee 529
                                       ++k+g++ +++npk  +++C++cg     +g++  kCp Cg e 
  gi|320100656|ref|YP_004176248.1| 311 CEKHGVPHIAVNPKdtSSTCPRCGSrlveSGYRrMKCPDCGFEA 354
                                       688999******954389*******65544444988*****554 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   0.3   0.00025      0.27      62      94 ..     319     352 ..     300     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                       EEEEEE--EEEETTTS-EEECHHH.HHS-TTTSS CS
                              HypA  62 LeieevpvkvrCreCgkefeleek.alrCpkCgs 94 
                                       ++++ ++ + +C +Cg++  ++ + +++Cp+Cg 
  gi|320100656|ref|YP_004176248.1| 319 IAVNPKDTSSTCPRCGSRLVESGYrRMKCPDCGF 352
                                       6677888999******99997775599*****95 PP

>> VasL  Type VI secretion system, EvfB, or VasL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.28      36      84 ..     245     293 ..     240     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                              VasL  36 avkaltrqWqqqlearalpaeslsgweqartqlqqLsdkLlelerqrgk 84 
                                       +++ + + W++++++++   +  +g+  ar+ l+ L + L +l rq ++
  gi|320100656|ref|YP_004176248.1| 245 KARSIIEDWARKVSREIALTARRDGYAVAREDLTYLVESLRRLPRQHRT 293
                                       67788899************************************99887 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00032      0.34      15      37 ..     317     339 ..     310     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                            DUF678  15 pkttvededdctTCSlCqSkLvk 37 
                                       p+++v+++d + TC  C S+Lv 
  gi|320100656|ref|YP_004176248.1| 317 PHIAVNPKDTSSTCPRCGSRLVE 339
                                       7889*****************96 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.4      0.05        53      11      24 ..     322     335 ..     305     341 .. 0.79
   2 ?    7.8   2.3    0.0033       3.5       2      24 ..     330     352 ..     329     356 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.05
                          zf-Mss51  11 apkhvdfeCpdCGi 24 
                                       +pk+ + +Cp+CG 
  gi|320100656|ref|YP_004176248.1| 322 NPKDTSSTCPRCGS 335
                                       7899999*****95 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0033
                          zf-Mss51   2 CPvpkhkqtapkhvdfeCpdCGi 24 
                                       CP + ++  ++   +++CpdCG+
  gi|320100656|ref|YP_004176248.1| 330 CPRCGSRLVESGYRRMKCPDCGF 352
                                       **********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3170.15
//
Query:       gi|320100657|ref|YP_004176249.1|  [L=271]
Description: nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-33  116.7   0.0    1.4e-33  116.4   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 !  116.4   0.0   7.7e-38   1.4e-33      17     261 .]      20     253 ..      11     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 7.7e-38
                                       HHHHHHHHHHHHHHT..TESEEEEETTTTTBS...SSHHHHHHHHB.HSSSHHHHHHHHHHHHHTEEEEEEEEEEEC CS
                      CN_hydrolase  17 nlqklleliaeAark..gadLivlPElfitgy...keeahfleaAe.aglgetlallaalarkngiavviglierel 87 
                                       n +k+++++++       adLivlPE++        ++ +++ +Ae  + ++ l  l++la++ g  + +++ie+ +
  gi|320100657|ref|YP_004176249.1|  20 NAGKAVDMVRK---GfrEADLIVLPEYSMLNPfkiGDPVKVYGYAEtPVTSKYLSELSRLAEELGAFILAHFIEKTD 93 
                                       55555555555...2459*********98755688899999999999999*************************76 PP

                                       CTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEEEEGGGGGSHHHHH CS
                      CN_hydrolase  88 tngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGaaiCyeigfpellr 163
                                       t++    y t vl+ ++g+ +  y+K+hLf    +  +++e++ f+pg+g   v++++++kiG+ iCy+ +fpel+r
  gi|320100657|ref|YP_004176249.1|  94 TPPLT--YSTSVLITDKGEAIPVYSKTHLF----DAYGFRESSFFKPGKGpGRVVSVKGVKIGFTICYDLRFPELYR 164
                                       77777..**********************9....479**************99************************ PP

                                       HHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEECC CS
                      CN_hydrolase 164 alalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilaglg 240
                                        +al g ++++   + ++v +   ++ ++ l+  ra en ++++ a +vg        +vg S +++p+G    +lg
  gi|320100657|ref|YP_004176249.1| 165 LYALSGSDLILV--QAGWVKGPYKEEALDKLASVRAHENTVYIALADHVGE------AFVGRSGVFNPWGLRELDLG 233
                                       ************..88***********************************......******************** PP

                                       SSSTEEEEEEEEHHHHHHHHH CS
                      CN_hydrolase 241 eeeegvliaeidladvratrr 261
                                       + e + +  e+d ++v+++r+
  gi|320100657|ref|YP_004176249.1| 234 WRE-TYMEHEVDASLVAEARK 253
                                       ***.7***********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2171.49
//
Query:       gi|320100658|ref|YP_004176250.1|  [L=149]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       343  (0.019131); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1209.96
//
Query:       gi|320100659|ref|YP_004176251.1|  [L=654]
Description: molybdopterin molybdochelatase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-53  181.1   0.0      2e-53  180.4   0.0    1.3  1  PBP_like       PBP superfamily domain
    2.7e-42  144.2   1.0      6e-42  143.1   1.0    1.6  1  MoeA_N         MoeA N-terminal region (domain I and II)
    3.4e-25   88.4   0.0    7.3e-25   87.3   0.0    1.6  1  MoCF_biosynth  Probable molybdopterin binding domain
    5.7e-10   39.2   0.1    1.9e-09   37.6   0.1    2.0  1  MoeA_C         MoeA C-terminal region (domain IV)
     0.0021   17.9   0.0      0.011   15.5   0.0    2.1  2  SBP_bac_11     Bacterial extracellular solute-binding 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 !  180.4   0.0   5.6e-57     2e-53      13     193 .]     440     627 ..     433     627 .. 0.94

  Alignments for each domain:
  == domain 1  score: 180.4 bits;  conditional E-value: 5.6e-57
                                       EEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC CS
                          PBP_like  13 vavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdl 89 
                                        +v n+Gs++G +a ++gead+a +hlld+e+ +yn p+l++     ++vlv+++ r +g+vvakgnpk+i+++ d 
  gi|320100659|ref|YP_004176251.1| 440 SRVLNTGSLAGWHAAARGEADVAPTHLLDEESMTYNRPFLKRFNLVDKAVLVRGFDRLIGIVVAKGNPKNIRSVGDF 516
                                       6899**************************************977779***************************** PP

                                       -S-B-EEEEE-TTSHHHHHHHHHHC-CEECT........E-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCC CS
                          PBP_like  90 adaplrlvnRetGSGtrdlfdellkkegisk........ssikgyaqearshlavaaaVaagradvgvgieavaeel 158
                                        + ++r+vnR +GSG r+++d+llkk   ++          ++gy+ e+++h ava aV++grad+g++   vae +
  gi|320100659|ref|YP_004176251.1| 517 LRGDVRIVNRVKGSGVRVYMDHLLKKILEAEgkpfkqvgRLVNGYTYEVKTHTAVALAVKQGRADAGIASGYVAEMF 593
                                       ************************886333357899999***********************************866 PP

                                       CCCECTTCE-EEEEEEEECTCCCSHHHHHHHHHHC CS
                          PBP_like 159 kgldfvplaeerydlvvrkealddpevqafleflk 193
                                        +ldf+pl++e+yd++v++e+l +p v++fle+lk
  gi|320100659|ref|YP_004176251.1| 594 -DLDFIPLTWEEYDFLVPREKLAKPLVASFLEALK 627
                                       .*******************************985 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 !  143.1   1.0   1.7e-45     6e-42       2     157 .]      11     176 ..      10     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 143.1 bits;  conditional E-value: 1.7e-45
                                       -HHHHHHHHHHH-HH..-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............ CS
                            MoeA_N   2 sveealaiilaalel..eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep....... 68 
                                       s++eal++++a++++  +  e v l +ealgrvlaedv+Ap+d Ppfd+S +DGYAvr+ + + a+e +p       
  gi|320100659|ref|YP_004176251.1|  11 SISEALEAVKARIPVspKGVEeVGL-SEALGRVLAEDVYAPIDHPPFDRSEVDGYAVRSMDVEWADELSPvelkitg 86 
                                       899*********9778855555***.99***************************************999******* PP

                                       .......-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-T CS
                            MoeA_N  69 .saageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllra 141
                                        +  ge+p+++ ++g av+++TGa++P g+d Vv+ E++e +     tv++ ++v+pgenv +aG+d++aG+++l +
  gi|320100659|ref|YP_004176251.1|  87 vVGVGEAPATPCRPGeAVEVATGAVVPGGCDSVVMEEYAEaS---GGTVRIyRSVSPGENVSTAGSDVSAGDLVLLK 160
                                       *888888888888888**********************9532...33344469************************ PP

                                       TBB--CCCHHHHHHCT CS
                            MoeA_N 142 gtrltpaeigllasvG 157
                                       gtrl+  +i++l  +G
  gi|320100659|ref|YP_004176251.1| 161 GTRLSHEHIAVLSGLG 176
                                       ************9877 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.0     2e-28   7.3e-25       1     141 [.     189     323 ..     189     325 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 2e-28
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       av ++G+e++        g+++D ng l a++l+elgv++   +++pDd+ e+k+al++al+++d+++t+GGt+++ 
  gi|320100659|ref|YP_004176251.1| 189 AVYSTGNEVVepgaplpLGRVYDVNGRLTASYLRELGVDAVFKGLLPDDYGELKKALEDALSQYDLVVTSGGTSAGV 265
                                       6899*****************************************************9999999************* PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGG CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpa 141
                                        D+++++ ++l+e       ++++++++kpgkp+++a      r+  + +igLPG+p ++ ++l+ +++p+
  gi|320100659|ref|YP_004176251.1| 266 GDLVYRVFEDLGE-------IVVHGLRAKPGKPTVIAVS----RG--RLLIGLPGFPLSCYMILRGLVKPI 323
                                       *************.......9***********9998887....43..3699****************9886 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 !   37.6   0.1   5.2e-13   1.9e-09       2      72 .]     339     408 ..     338     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 5.2e-13
                                       EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       a+l  +l++  g++ +l+v+l e   ++ a+p+ + +Sg +++l  ++g++++pe+t+ +eaG  V v l+
  gi|320100659|ref|YP_004176251.1| 339 AVLPVKLRKQVGKAWLLPVSLVEGRQGVSAYPV-SLSSGSIAALIYSDGYVELPEDTDTVEAGSRVRVRLF 408
                                       7899999***************99999******.*********************************9876 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.38   1.4e+03      66     128 ..     174     277 ..     119     340 .. 0.53
   2 !   15.5   0.0   3.1e-06     0.011      81     165 ..     498     586 ..     483     633 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.38
                                       GGGGGGG-EEEEEEEEEEEESTT-.......T.............................T---SHHHHHHS.... CS
                        SBP_bac_11  66 glvqaesavplassplviavpkgn.......p.............................kkikgwadLlkp.... 102
                                       gl++  s+v ++  p + ++ +gn       p                               +++  +L+k+    
  gi|320100659|ref|YP_004176251.1| 174 GLGV--SRVRVYVKPKAAVYSTGNevvepgaPlplgrvydvngrltasylrelgvdavfkgLLPDDYGELKKAleda 248
                                       5555..66666666666666666644443331334444444444444444444333333331222222222223333 PP

                                       ..S--EEEE--T-.TTTTHH.HHHHGGG- CS
                        SBP_bac_11 103 ..glklavadPtt.spsGlaalalleaag 128
                                         +  l+v++  t +++G+ ++ ++e +g
  gi|320100659|ref|YP_004176251.1| 249 lsQYDLVVTSGGTsAGVGDLVYRVFEDLG 277
                                       33334444444442555666666666555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.1e-06
                                       EEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTH......H.HHHHGGG--.HHHHHHHHHTEEEEESSHHHH CS
                        SBP_bac_11  81 lviavpkgnpkkikgwadLlkpglklavadPttspsGl......aalalleaaga.qellkalekkvvklgessrql 150
                                       + i+v kgnpk+i+++ d l+ +++++      ++sG         +++lea g+  + + +l ++ + ++++ + +
  gi|320100659|ref|YP_004176251.1| 498 IGIVVAKGNPKNIRSVGDFLRGDVRIVNR---VKGSGVrvymdhLLKKILEAEGKpFKQVGRLVNGYTYEVKTHTAV 571
                                       679*******************9986533...2344444555666677777878785566788889999999***** PP

                                       HHHHHTTT-SEEEEE CS
                        SBP_bac_11 151 ltaveageadagivy 165
                                       + av++g+adagi+ 
  gi|320100659|ref|YP_004176251.1| 572 ALAVKQGRADAGIAS 586
                                       ************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4720.99
//
Query:       gi|320100660|ref|YP_004176252.1|  [L=714]
Description: DEAD/DEAH box helicase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-23   82.8   0.0    5.3e-23   81.7   0.0    1.6  1  DEAD           DEAD/DEAH box helicase
    3.2e-08   33.9   0.0    1.4e-07   31.9   0.0    2.0  1  Helicase_C     Helicase conserved C-terminal domain
    6.6e-08   33.0   0.1    2.3e-07   31.3   0.1    2.0  1  HHH_5          Helix-hairpin-helix domain
    2.3e-05   24.5   0.0    3.6e-05   23.9   0.0    1.3  1  ResIII         Type III restriction enzyme, res subunit
    6.3e-05   23.0   0.0    0.00031   20.8   0.0    2.2  1  HHH_2          Helix-hairpin-helix motif
     0.0022   17.7   0.0     0.0082   15.9   0.0    2.0  1  AAA_30         AAA domain
  ------ inclusion threshold ------
      0.048   13.7   0.1       0.41   10.7   0.0    2.8  4  HemN_C         HemN C-terminal domain
       0.15   11.8   0.0        0.3   10.9   0.0    1.5  1  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin


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 !   81.7   0.0   2.4e-26   5.3e-23       2     170 ..      29     183 ..      28     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 2.4e-26
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       ++Q+ea++  l g+g+++v+a+T+sGKTl++ ++++++ +     +g + ++++P+r+La + + ++k++ + i+++
  gi|320100660|ref|YP_004176252.1|  29 PVQSEAVEKGLlGEGNMVVSAPTASGKTLIAELALVDAWL-----KGGMGVYLTPLRALASEKYWEFKTLES-IGVK 99 
                                       89*****99886778*********************9995.....57799*******************999.7777 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       v   ++  ++++  ++l  g+di+v+t +r+d++l+ +   l +v+++V+DE++++ d ++++ i+ i+++l     
  gi|320100660|ref|YP_004176252.1| 100 VG--VSTGDYDQPADHL-GGYDILVATYERFDSILRLKPWWLPRVSVVVVDEVHMVGDPERGPIIEVIAARL----- 168
                                       76..4444666777888.99***************878888*******************************..... PP

                                       TSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlp 170
                                         k   +vi lSAT+ 
  gi|320100660|ref|YP_004176252.1| 169 -LKRGVRVIGLSATVG 183
                                       .344567*******85 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   6.1e-11   1.4e-07      17     109 ..     250     384 ..     236     386 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6.1e-11
                                       SEEEEEESSHHHHHH..................HHHH.....HHHT............TSTEEEESTTSTHHHHHHH CS
                        Helicase_C  17 gkilifvntidrlek..................vkll.....lekk............gikvavlhgelpqnereei 58 
                                        ++l+f+++++r+e+                  +kll                     +  va +h+ l+   r  +
  gi|320100660|ref|YP_004176252.1| 250 VQTLVFTHNRRRVEEyaekaaqrlpmapvgdalAKLLreleeA--PtsverdglselmKRGVAFHHAGLSGVARSIV 324
                                       5666666666666433333322222222222222222443330..0333333444455889999************* PP

                                       HHHHHTTSSSEEEESGGGTSSSTSTTESEEE...ESSSS......SSHHHHHHHHTTSSS CS
                        Helicase_C  59 leqfnkgesdvLiatdvaerGidipkvnlVi...nfdlp......rnvtsyiqriGRtgR 109
                                        ++f++  +++L at  ++ G+++p  ++++   ++d+        +v++y+q++GR+gR
  gi|320100660|ref|YP_004176252.1| 325 EKAFRERLIRILYATPTLAAGVNLPARRVLVsvkRYDPArgrkvsISVSEYKQMAGRAGR 384
                                       *************************99998877788888554444447************ PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1     1e-10   2.3e-07       3      56 ..     654     707 ..     652     708 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1e-10
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       eL s+  iG+++A+ l+++G++++ dla+a v  +a++p +G++ Ae +  +l+
  gi|320100660|ref|YP_004176252.1| 654 ELASLRLIGRVRARILIEHGFKTLRDLAEAPVSSIASLPRFGQRVAEEVERQLR 707
                                       8999999***************************************98766666 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.6e-08   3.6e-05       4     169 ..      27     182 ..      24     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.6e-08
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       l++ Q ea+e+ l      ++ ++++ ++T +GKTl+a ++l+++ lk  +    + l p ++l +  + efk + s
  gi|320100660|ref|YP_004176252.1|  27 LNPVQSEAVEKGL-----LGEGNMVVSAPTASGKTLIAeLALVDAWLKG-G--MGVYLTPLRALASEKYWEFKTLES 95 
                                       6778888888777.....5788999*************89999888885.4..589********************* PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilek 156
                                         +  + ++ +gd +++ + +    +ilv+t++++d+++       +     r  v+++DE+H +g+  +   i+e 
  gi|320100660|ref|YP_004176252.1|  96 IGV--KVGVSTGDYDQP-ADHLGGYDILVATYERFDSIL-----RLKPWWLPRVSVVVVDEVHMVGDP-ERGPIIEV 163
                                       998..688889998888.9999*****************.....67788888899************5.44444444 PP

                                       ---......SEEEEEESS- CS
                            ResIII 157 fke......avllglTATp 169
                                       + +        ++gl+AT 
  gi|320100660|ref|YP_004176252.1| 164 IAArllkrgVRVIGLSATV 182
                                       4433444468999999996 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.4e-07   0.00031       8      53 ..     658     704 ..     654     712 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                             HHH_2   8 IrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53 
                                       +r +G   A++L ++ Fk+l  L++a +  +++++  G+++A+++ +
  gi|320100660|ref|YP_004176252.1| 658 LRLIGRVRARILIEHgFKTLRDLAEAPVSSIASLPRFGQRVAEEVER 704
                                       799**********998****************************976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.7e-06    0.0082       1     115 [.      26     167 ..      26     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.7e-06
                            AAA_30   1 elnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaaggrviglAptgkaAkvLae.........elg 67 
                                       eln+ Q++ave+ l ++   +v+ +p  +GKt + + + ++aw + g+ v +    + a+++  e         ++g
  gi|320100660|ref|YP_004176252.1|  26 ELNPVQSEAVEKGLLGEG-NMVVSAPTASGKTLIAELAlVDAWLKGGMGVYLTPLRALASEKYWEfktlesigvKVG 101
                                       58999*****99877775.799999999******99877******99777766666666666553333333333222 PP

                            AAA_30  68 ieastiakllkrlk....................grarlepg.tllivDEagmvdtkqlaallkaaeka 115
                                       + +   ++  + l+                    +   + p+ ++++vDE+ mv+  +   +++ ++++
  gi|320100660|ref|YP_004176252.1| 102 VSTGDYDQPADHLGgydilvatyerfdsilrlkpW---WLPRvSVVVVDEVHMVGDPERGPIIEVIAAR 167
                                       32222222222222444555566666666668543...44555***********999988888877664 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         4   8.9e+03      48      65 ..     208     225 ..     208     226 .. 0.90
   2 ?   10.7   0.0   0.00018      0.41      37      65 ..     466     494 ..     450     495 .. 0.87
   3 ?   -3.2   0.0       4.2   9.4e+03      18      30 ..     566     578 ..     566     581 .. 0.85
   4 ?   -3.9   0.0       6.6   1.5e+04      29      45 ..     693     709 ..     693     709 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4
                            HemN_C  48 qGLLeldggrlrltprGr 65 
                                       +G+Le ++ r++   +Gr
  gi|320100660|ref|YP_004176252.1| 208 EGYLEKHEWRIVFPSEGR 225
                                       699***********9998 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                            HemN_C  37 llaaaleklqeqGLLeldggrlrltprGr 65 
                                        ++aa++ l+e G++e +gg+lr++  Gr
  gi|320100660|ref|YP_004176252.1| 466 KVEAAVKLLTELGMIEEAGGSLRASALGR 494
                                       56889*********************998 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.2
                            HemN_C  18 reGldlaafeqrf 30 
                                       r+G+d +++ ++f
  gi|320100660|ref|YP_004176252.1| 566 RAGVDYDDWLEAF 578
                                       689*****99887 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 6.6
                            HemN_C  29 rfgldleellaaalekl 45 
                                       rfg+ ++e+++ +l++l
  gi|320100660|ref|YP_004176252.1| 693 RFGQRVAEEVERQLREL 709
                                       79999999998889886 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014       0.3      28      67 .]     669     708 ..     651     708 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                       HHHTT--BHHHHHHS-HHHHTTSSS-SSHHHHHHHHHHHH CS
                     RNA_pol_A_CTD  28 LkragiktvgeLvklseeeLlkikNlGkKSleEIkekLee 67 
                                       L + g kt+++L++   + + +++ +G++  eE+ ++L e
  gi|320100660|ref|YP_004176252.1| 669 LIEHGFKTLRDLAEAPVSSIASLPRFGQRVAEEVERQLRE 708
                                       557899*****************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4728.96
//
Query:       gi|320100661|ref|YP_004176253.1|  [L=239]
Description: uracil phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-34  117.9   0.0    4.8e-34  117.6   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    1.2e-10   41.1   0.0    3.6e-10   39.6   0.0    1.7  2  Pribosyltran  Phosphoribosyl transferase domain


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 !  117.6   0.0   5.4e-38   4.8e-34       2     204 ..      17     216 ..      16     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 5.4e-38
                           UPRTase   2 sshpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysgelldeekialVpilRaG 78 
                                       +++pl+k  l+ilR+ +t++  fre+++++++++++e+ ++ l+ + v +++ +g+ + g++ +++ + +V +l a 
  gi|320100661|ref|YP_004176253.1|  17 VDNPLAKYYLSILRKPATTPGLFREYMRKLGFIIGYEVSRH-LEWRRVFIESGMGRAE-GVY-PSRPLYIVGVLGAS 90 
                                       5899************************************9.**********999987.444.4459********** PP

                           UPRTase  79 egmeealrellpearvghlglqr..eeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeek 153
                                        ++++++ +++p a +g +   r   e   e+++yy+++P+++++ t l++Dp++a+G+++  +++ +  rg+  ++
  gi|320100661|ref|YP_004176253.1|  91 IPLVHGIWDAMPWAGLGLVAARRivGEGRVEAELYYERMPSDLSAYTTLVVDPTLASGRTMTRVVEEVEARGC--RS 165
                                       ***************999998885556679999*************************************998..69 PP

                           UPRTase 154 IlvlsvlaseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRl 204
                                       I+ ++v+as+ gv+ ++++f ++ +++++vD+ +d+  +ivpG+GD+GDR 
  gi|320100661|ref|YP_004176253.1| 166 IIAATVVASRYGVEVFHSRFSSIPLIAVEVDPVVDKGFFIVPGIGDAGDRS 216
                                       **************************************************5 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.14   1.3e+03      39      59 ..      46      66 ..      44      74 .. 0.86
   2 !   39.6   0.0   4.1e-14   3.6e-10      26     130 ..      76     178 ..      65     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.14
                                      TTHHHHHHHHHHSTT-EE-EE CS
                      Pribosyltran 39 gGvpfakiladeLevplayvr 59
                                       G++++++++++Le + ++++
  gi|320100661|ref|YP_004176253.1| 46 LGFIIGYEVSRHLEWRRVFIE 66
                                      5999*********99998886 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 4.1e-14
                                       --GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSH CS
                      Pribosyltran  26 yngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGg 101
                                       y+ +p ++vg++  ++p+++ + d++  + l  v +++  ++g  ea    +   r+++d+   + l+VD  l++G+
  gi|320100661|ref|YP_004176253.1|  76 YPSRPLYIVGVLGASIPLVHGIWDAMpWAGLGLVAARRIVGEGRVEAELYYE---RMPSDLSAYTTLVVDPTLASGR 149
                                       778899********************74557777777766666666654332...7********************* PP

                                       HHHHHHHHHHCC-BSEEEEEEEEE-HHHH CS
                      Pribosyltran 102 TllaalelLkekgpeevriavlvdkpate 130
                                       T+++++e ++++g+ ++++a++v+ + ++
  gi|320100661|ref|YP_004176253.1| 150 TMTRVVEEVEARGCRSIIAATVVASRYGV 178
                                       ***********************877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1757.71
//
Query:       gi|320100662|ref|YP_004176254.1|  [L=241]
Description: ParA/MinD-like ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-41  142.1   0.0    2.8e-41  141.6   0.0    1.2  1  ParA         NUBPL iron-transfer P-loop NTPase
    9.6e-10   38.6   0.0    1.4e-09   38.1   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.2e-06   28.5   0.3    0.00015   21.8   0.3    2.1  1  AAA_31       AAA domain
     0.0025   17.1   0.1      0.012   14.8   0.1    1.9  2  ArsA_ATPase  Anion-transporting ATPase
  ------ inclusion threshold ------
      0.014   15.8   0.1      0.025   15.0   0.1    1.5  1  AAA_16       AAA ATPase domain
      0.098   12.2   0.1       0.18   11.3   0.1    1.4  1  AAA_25       AAA domain
       0.16   11.7   0.1        5.9    6.6   0.0    2.2  2  RuvB_N       Holliday junction DNA helicase RuvB P-loop domai


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 !  141.6   0.0   1.1e-44   2.8e-41       4     176 ..      19     190 ..      16     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1.1e-44
                              ParA   4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs.ekkliPveakgikvmSig 79 
                                       +v++vlS+KGGVGK+tvav lAl+  ++ lk gl+DaD++ ps   llg++ + ++ + ek++ P + +g++ + ++
  gi|320100662|ref|YP_004176254.1|  19 RVYVVLSTKGGVGKTTVAVLLALHA-SRRLKAGLMDADLTNPSTHILLGIDPSAVKYReEKGIEPYRINGLRYVTMA 94 
                                       689*******************985.6789*********************9988877577899************* PP

                              ParA  80 fllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkk 155
                                         +   ++++  rG  + +a+++ll+ v+wg lD+L+iD+PPG gDe+l ++ +l ++   ++V+tp  +++  v +
  gi|320100662|ref|YP_004176254.1|  95 AYTG--EKPLPLRGREAGEALRELLAIVKWGPLDILLIDTPPGVGDEHLDLLYSLkNIVRPLVVATPSVLSVRSVAR 169
                                       9998..99**********************************************9788999**************** PP

                              ParA 156 aiemfkkvkvkvlGvveNmsg 176
                                        i++++++    +G+veNm  
  gi|320100662|ref|YP_004176254.1| 170 LIQLLREAGYGWIGLVENMGS 190
                                       *******************65 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   5.5e-13   1.4e-09       2      83 ..      22     188 ..      21     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.5e-13
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       ++ stkGGvGKTt+a+ La   +r +l+  l DaD   ++++il g  +   +                        
  gi|320100662|ref|YP_004176254.1|  22 VVLSTKGGVGKTTVAVLLALHASR-RLKAGLMDADLTNPSTHILLGIDPSAVKyreekgiepyringlryvtmaayt 97 
                                       799****************99998.*****************97777766666677778888888899999999999 PP

                                       ....................................................................CCHCCCHHH CS
                                       ....................................................................xxxxxxxxx RF
                              CbiA  55 ....................................................................dlkrllell 63 
                                                                                                           ++ rl++ll
  gi|320100662|ref|YP_004176254.1|  98 gekplplrgreagealrellaivkwgpldillidtppgvgdehldllyslknivrplvvatpsvlsvrSVARLIQLL 174
                                       99999999999888888888888888888888888888888888888888888888888888777666666666666 PP

                                       HHHCHCHHHH..EEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              CbiA  64 ealgkkkalllkiagvvlnr 83 
                                       ++ g +      ++g+v n+
  gi|320100662|ref|YP_004176254.1| 175 REAGYG------WIGLVENM 188
                                       555543......66666665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   5.7e-08   0.00015       2      47 ..      19      63 ..      18     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.7e-08
                            AAA_31  2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattg 47
                                      +v ++   KGGvGKTT +v la    ++  k  l+D+D  + +t  
  gi|320100662|ref|YP_004176254.1| 19 RVYVVLSTKGGVGKTTVAVLLALHA-SRRLKAGLMDADLTNPSTHI 63
                                      6778999**************9875.55677778899987666653 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   4.6e-06     0.012       3      29 ..      21      47 ..      19      55 .. 0.86
   2 ?   -0.1   0.0      0.16   4.2e+02     112     135 ..     112     135 ..      67     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.6e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTT CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekg 29
                                      +++++ KGGVGKttv+  +a++ s+  
  gi|320100662|ref|YP_004176254.1| 21 YVVLSTKGGVGKTTVAVLLALHASRRL 47
                                      68999**************99988765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHCSSSSEEEEESBSC CS
                       ArsA_ATPase 112 sfeellkyvkeeeydvvvlDtaPT 135
                                       ++ ell  vk    d++++Dt+P 
  gi|320100662|ref|YP_004176254.1| 112 ALRELLAIVKWGPLDILLIDTPPG 135
                                       556666666666677777777773 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   9.7e-06     0.025      11      63 ..       6      54 ..       5     164 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                            AAA_16 11 qLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      +L++al+++++ +  +v+ls   GvGK++++  l+ +++++    l++   + 
  gi|320100662|ref|YP_004176254.1|  6 RLHNALRNLSQAGRVYVVLSTKGGVGKTTVAVLLALHASRR----LKAGLMDA 54
                                      799****9999999*****************9998888888....44444444 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   7.1e-05      0.18      32      59 ..      17      45 ..       2      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.1e-05
                            AAA_25 32 agel.allaGapgtGKttlaldlalavat 59
                                      ag + ++l   +g+GKtt+a+ lal+ ++
  gi|320100662|ref|YP_004176254.1| 17 AGRVyVVLSTKGGVGKTTVAVLLALHASR 45
                                      55442678889**************9874 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 ?    6.6   0.0    0.0023       5.9      35      62 ..      21      48 ..       9      64 .. 0.85
   2 ?    3.0   0.0     0.029        75      32      83 ..     124     175 ..     115     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0023
                            RuvB_N 35 hvllyGpPGlGkttlakiiakelgvklk 62
                                      +v+l+   G+Gktt+a ++a     +lk
  gi|320100662|ref|YP_004176254.1| 21 YVVLSTKGGVGKTTVAVLLALHASRRLK 48
                                      6899999***********9987666555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.029
                            RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnle 83 
                                       +ld +l+  pPG+G   l  + + +  v+  + ++P +   + +a l++ l+
  gi|320100662|ref|YP_004176254.1| 124 PLDILLIDTPPGVGDEHLDLLYSLKNIVRPLVVATPSVLSVRSVARLIQLLR 175
                                       68999**********9999888877777777777787777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1802.53
//
Query:       gi|320100663|ref|YP_004176255.1|  [L=129]
Description: hydrogenase nickel incorporation protein HypA [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-18   64.5   0.0      1e-17   64.2   0.0    1.0  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0015   18.8   0.2        1.7    9.0   0.0    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0029   17.1   0.0     0.0034   16.9   0.0    1.0  1  Mcm10            Mcm10 replication factor
     0.0039   17.1   0.2      0.084   12.9   0.1    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.7   2.2        2.4    8.1   0.2    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.024   14.3   1.5        5.9    6.7   0.3    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.031   14.2   0.6        5.4    7.0   0.0    2.4  2  zinc_ribbon_4    zinc-ribbon domain
      0.033   14.9   0.6       0.12   13.0   0.1    2.1  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
      0.043   14.0   0.7        3.2    8.0   0.0    2.2  2  DUF2387          Probable metal-binding protein (DUF2387)
      0.047   13.9   0.8       0.46   10.7   0.1    2.1  2  Ribosomal_L37e   Ribosomal protein L37e
       0.09   13.5   0.0       0.13   13.0   0.0    1.3  1  zinc_ribbon_15   zinc-ribbon family
        0.1   12.3   1.6        5.7    6.7   0.1    2.2  3  zf-CSL           CSL zinc finger
       0.13   12.4   0.0       0.17   12.0   0.0    1.2  1  Mut7-C           Mut7-C RNAse domain
       0.14   12.3   4.1        1.5    9.0   0.0    2.5  2  UPF0547          Uncharacterised protein family UPF0547
       0.18   11.2   1.8        1.2    8.7   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.22   11.7   3.5        1.8    8.8   2.9    2.1  2  Zn-ribbon_8      Zinc ribbon domain
       0.29   11.1   1.2         19    5.2   0.1    2.3  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.32   10.9   3.1       0.85    9.6   0.4    2.5  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !   64.2   0.0     1e-20     1e-17       2     108 ..       3     124 ..       2     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1e-20
                                       CHHHHHHHHHHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS- CS
                              HypA   2 HElsiaesivevveeeakeaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCgk 78 
                                       HE+++aesiv+ + ++      r+++ +++++G l+gv++e+L f ++ +a+ + +e  e+++e+++ +++C++Cg+
  gi|320100663|ref|YP_004176255.1|   3 HEWALAESIVNYLVDQG----LRRIRVLRLRLGLLQGVDKEVLLFSLREVASMQGVEIGEVAVEDEEPVLKCNTCGY 75 
                                       ***********999988....78****************************************************** PP

                                       EEECHHHHH...................S-TTTSSS-EEEEESSSEEEE CS
                              HypA  79 efeleekal...................rCpkCgsadveivsGeellvk 108
                                       ++++ ++al                   rCp+Cgs+d+++v+G+++ + 
  gi|320100663|ref|YP_004176255.1|  76 TWSMPASALsdeereavhfvpeaihaftRCPRCGSRDFTVVKGRGVSLV 124
                                       ***775433566899*****************************99875 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0035       3.5      27      56 ..      60      93 ..      37      94 .. 0.75
   2 !    9.0   0.0    0.0018       1.7       5      23 ..     104     122 ..     100     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0035
                   Lar_restr_allev 27 q......cvyCadCgastpwfkiaedeaeaekeaie 56
                                             +  C  Cg+  +w   a++  ++e ea++
  gi|320100663|ref|YP_004176255.1| 60 AvedeepVLKCNTCGY--TWSMPASALSDEEREAVH 93
                                      044444599*******..888888888888888876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                   Lar_restr_allev   5 pCPfCggravlersqrvva 23 
                                        CP Cg+r+  +  +r+v+
  gi|320100663|ref|YP_004176255.1| 104 RCPRCGSRDFTVVKGRGVS 122
                                       6********9999988876 PP

>> Mcm10  Mcm10 replication factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.5e-06    0.0034     259     302 ..      67     112 ..      53     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.5e-06
                             Mcm10 259 vVtCktCkYtafkasdrCveenHe.lkwh.davKrFFkCakCgkRt 302
                                       v +C+tC Yt+  +++   +e+ e ++ + +a+  F +C+ Cg R 
  gi|320100663|ref|YP_004176255.1|  67 VLKCNTCGYTWSMPASALSDEEREaVHFVpEAIHAFTRCPRCGSRD 112
                                       789**********999877665541565449************996 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 ?    2.3   0.0      0.17   1.7e+02      37      46 .]      67      76 ..      52      76 .. 0.86
   2 !   12.9   0.1   8.4e-05     0.084      20      36 ..     103     120 ..      87     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.17
                     Zn_Tnp_IS1595 37 lfqCkeCrkq 46
                                      +++C+ C+++
  gi|320100663|ref|YP_004176255.1| 67 VLKCNTCGYT 76
                                      5799999985 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.4e-05
                     Zn_Tnp_IS1595  20 v.CPhCgsrkayriktrg 36 
                                       + CP+Cgsr ++ +k+rg
  gi|320100663|ref|YP_004176255.1| 103 TrCPRCGSRDFTVVKGRG 120
                                       33*******999999987 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 ?    8.1   0.2    0.0025       2.4      29      38 ..      68      77 ..      62      78 .. 0.84
   2 ?    7.3   0.1    0.0044       4.3       2      13 ..     104     115 ..     103     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                           TFIIS_C 29 ykCtkCghrW 38
                                       kC++Cg++W
  gi|320100663|ref|YP_004176255.1| 68 LKCNTCGYTW 77
                                      69******** PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0044
                           TFIIS_C   2 kCpkCgsreayf 13 
                                       +Cp+Cgsr+ + 
  gi|320100663|ref|YP_004176255.1| 104 RCPRCGSRDFTV 115
                                       7******98775 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0067       6.7      12      25 ..      61      75 ..      57      76 .. 0.71
   2 ?    6.7   0.3     0.006       5.9      19      26 ..     104     111 ..      99     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0067
                                      --SSS--.--SSS-- CS
                    DNA_RNApol_7kD 12 lkkgdpi.RCkeCGh 25
                                      ++ ++p+ +C +CG+
  gi|320100663|ref|YP_004176255.1| 61 VEDEEPVlKCNTCGY 75
                                      555565449*****8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.006
                                       --SSS--- CS
                    DNA_RNApol_7kD  19 RCkeCGhR 26 
                                       RC  CG+R
  gi|320100663|ref|YP_004176255.1| 104 RCPRCGSR 111
                                       9*****99 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0054       5.4      24      35 ..      66      77 ..      55      78 .. 0.79
   2 ?    5.1   0.3     0.022        22       4      10 ..     104     110 ..     102     111 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0054
                     zinc_ribbon_4 24 vkvrCskCghvF 35
                                        ++C  Cg ++
  gi|320100663|ref|YP_004176255.1| 66 PVLKCNTCGYTW 77
                                      579********9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.022
                     zinc_ribbon_4   4 tCpsCka 10 
                                       +Cp+C++
  gi|320100663|ref|YP_004176255.1| 104 RCPRCGS 110
                                       6777765 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 ?   -0.7   0.1       2.3   2.3e+03       4       9 ..      69      74 ..      66      79 .. 0.71
   2 ?   13.0   0.1   0.00012      0.12       3      22 ..     103     123 ..     101     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.3
                           zf-ISL3  4 rCPnCg 9 
                                      +C +Cg
  gi|320100663|ref|YP_004176255.1| 69 KCNTCG 74
                                      577777 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                           zf-ISL3   3 hrCPnCgsk..tvvkhgkkerr 22 
                                       +rCP+Cgs+  t v++g+  + 
  gi|320100663|ref|YP_004176255.1| 103 TRCPRCGSRdfT-VVKGRGVSL 123
                                       69*******744.777776665 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0032       3.2      25      55 ..      62      90 ..      58      98 .. 0.79
   2 ?    4.6   0.1     0.035        35      10      20 ..     104     114 ..      98     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0032
                           DUF2387 25 edeveyrECvsCgftdelsekgqsvakelkt 55
                                      ede+++  C  Cg+t +++++  + + e+++
  gi|320100663|ref|YP_004176255.1| 62 EDEEPVLKCNTCGYTWSMPAS--ALSDEERE 90
                                      7899***********999988..44444444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.035
                           DUF2387  10 vCPrCsemDki 20 
                                        CPrC + D +
  gi|320100663|ref|YP_004176255.1| 104 RCPRCGSRDFT 114
                                       5******9943 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.33   3.3e+02      33      39 ..      69      75 ..      67      79 .. 0.79
   2 ?   10.7   0.1   0.00046      0.46      15      32 ..     101     118 ..      97     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.33
                    Ribosomal_L37e 33 tCascGy 39
                                      +C  cGy
  gi|320100663|ref|YP_004176255.1| 69 KCNTCGY 75
                                      6999999 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00046
                    Ribosomal_L37e  15 tHilCrrCgkrsyhvqkk 32 
                                        +++C rCg+r + v k 
  gi|320100663|ref|YP_004176255.1| 101 AFTRCPRCGSRDFTVVKG 118
                                       579**********99886 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013      0.13      30      73 ..      60     110 ..      44     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                    zinc_ribbon_15  30 kwkkkkpylacskCkslleaskelgkeiekkesse........kkeCknCgk 73 
                                        ++ ++p+l+c++C+++ ++  +  ++ e +e+++         ++C++Cg+
  gi|320100663|ref|YP_004176255.1|  60 AVEDEEPVLKCNTCGYTWSMPASALSDEE-REAVHfvpeaihaFTRCPRCGS 110
                                       567889**********9999984444443.333336899999999*****86 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2      0.03        30      30      50 ..      57      73 ..      42      78 .. 0.76
   2 ?    5.6   1.8     0.013        13       6      50 ..      57     108 ..      52     109 .. 0.67
   3 ?    6.7   0.1    0.0057       5.7       5      29 ..      89     115 ..      85     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.03
                                      EHHHHHTT....--EEEETTS CS
                            zf-CSL 30 teedleegaegaevvvqCssC 50
                                       e  +e++    e v++C++C
  gi|320100663|ref|YP_004176255.1| 57 GEVAVEDE----EPVLKCNTC 73
                                      44455666....99******* PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.013
                                       GGSEEETTTTEEEEEE.TTSSEEEEEHHHHHTT............--EEEETTS CS
                            zf-CSL   6 edfefdeeeesyyypC.RCgdeFelteedleegae........gaevvvqCssC 50 
                                        ++ +++e  + + +C  Cg + +++ + l ++++             ++C+ C
  gi|320100663|ref|YP_004176255.1|  57 GEVAVEDE--EPVLKCnTCGYTWSMPASALSDEEReavhfvpeAIHAFTRCPRC 108
                                       45444333..34678888888888888888887667777777767777777777 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0057
                                       GGGSEEETTTTEEEEEE.TTSSE.EEE CS
                            zf-CSL   5 ledfefdeeeesyyypC.RCgde.Fel 29 
                                        e+++f +e+ + +  C RCg++ F +
  gi|320100663|ref|YP_004176255.1|  89 REAVHFVPEAIHAFTRCpRCGSRdFTV 115
                                       5677777777778899******99976 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.17      62     130 ..      40     109 ..      15     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                            Mut7-C  62 vlltsrdveeqlreviarlglklslkpelsrCvaCng..eleevekeevkervpekvyeeadeftrCekCr 130
                                       vll s +  + ++ v +  +++++ ++ + +C +C     +     ++ ++++ + v+e  ++ftrC++C+
  gi|320100663|ref|YP_004176255.1|  40 VLLFSLREVASMQGV-EIGEVAVEDEEPVLKCNTCGYtwSMPASALSDEEREAVHFVPEAIHAFTRCPRCG 109
                                       555555555556666.556667777777999999998442223333334446888999************7 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0015       1.5      15      26 .]      68      79 ..      66      79 .. 0.87
   2 ?    3.2   1.7     0.094        94      16      21 ..     104     109 ..      93     111 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                           UPF0547 15 qfCphCGyvFqa 26
                                       +C  CGy +++
  gi|320100663|ref|YP_004176255.1| 68 LKCNTCGYTWSM 79
                                      58********85 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.094
                           UPF0547  16 fCphCG 21 
                                       +Cp CG
  gi|320100663|ref|YP_004176255.1| 104 RCPRCG 109
                                       566665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.19   1.9e+02       4       9 ..      69      74 ..      67      75 .. 0.76
   2 ?    8.7   0.1    0.0012       1.2       3      10 ..     103     110 ..     101     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
                       zf-ribbon_3  4 rCPnCG 9 
                                      +C+ CG
  gi|320100663|ref|YP_004176255.1| 69 KCNTCG 74
                                      688887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                       zf-ribbon_3   3 vrCPnCGa 10 
                                       +rCP+CG+
  gi|320100663|ref|YP_004176255.1| 103 TRCPRCGS 110
                                       79*****7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2       0.1     1e+02      26      33 ..      67      74 ..      57      78 .. 0.62
   2 ?    8.8   2.9    0.0018       1.8       7      35 ..      69     112 ..      67     116 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                       Zn-ribbon_8 26 ltaCPeCg 33
                                        +C +Cg
  gi|320100663|ref|YP_004176255.1| 67 VLKCNTCG 74
                                      44477776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0018
                       Zn-ribbon_8   7 rCeeCghefe.........vlqsisdap............ltaCPeCgs.e 35 
                                       +C+ Cg +           +                     t CP+Cgs +
  gi|320100663|ref|YP_004176255.1|  69 KCNTCGYTWSmpasalsdeE-------ReavhfvpeaihaFTRCPRCGSrD 112
                                       68888877777544444440.......1344444445554888*****955 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.032        32      39      56 ..      61      77 ..      46      83 .. 0.77
   2 ?    5.2   0.1     0.019        19      29      39 ..     103     113 ..      85     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.032
                    OrfB_Zn_ribbon 39 kealsgrtfkCpnCgfea 56
                                       e +++ ++kC+ Cg+++
  gi|320100663|ref|YP_004176255.1| 61 VE-DEEPVLKCNTCGYTW 77
                                      44.677889999999986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.019
                    OrfB_Zn_ribbon  29 ktCseCgsknk 39 
                                       ++C++Cgs++ 
  gi|320100663|ref|YP_004176255.1| 103 TRCPRCGSRDF 113
                                       68****99875 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 ?    0.8   0.1      0.46   4.6e+02      13      18 ..      69      74 ..      67      83 .. 0.85
   2 ?   -3.0   0.0       7.2   7.2e+03      19      26 ..      91      98 ..      90      99 .. 0.79
   3 ?    9.6   0.4   0.00085      0.85      27      36 ..     104     113 ..     101     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.46
                           DUF35_N 13 rCpdCG 18
                                      +C  CG
  gi|320100663|ref|YP_004176255.1| 69 KCNTCG 74
                                      8999*9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.2
                           DUF35_N 19 tvqfPPra 26
                                      +v+f P+a
  gi|320100663|ref|YP_004176255.1| 91 AVHFVPEA 98
                                      69999986 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00085
                           DUF35_N  27 vCphCgsddl 36 
                                        Cp+Cgs+d+
  gi|320100663|ref|YP_004176255.1| 104 RCPRCGSRDF 113
                                       5888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 932.88
//
Query:       gi|320100664|ref|YP_004176256.1|  [L=426]
Description: hydroxymethylglutaryl-CoA reductase, degradative [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-106  356.5   6.4   1.7e-106  356.3   6.4    1.0  1  HMG-CoA_red   Hydroxymethylglutaryl-coenzyme A reductase
  ------ inclusion threshold ------
      0.048   13.9   0.1       0.15   12.4   0.1    1.8  1  Phasin_2      Phasin protein
      0.098   12.9   0.1       0.21   11.8   0.1    1.5  1  Peptidase_A8  Signal peptidase (SPase) II


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 !  356.3   6.4  2.9e-110  1.7e-106       2     367 .]      14     380 ..      13     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: 356.3 bits;  conditional E-value: 2.9e-110
                                       HHHHHHHHHH...S-HHHHHHH.TT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHH CS
                       HMG-CoA_red   2 veeRrkllee...lteeeleel.keesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsas 74 
                                       ++eRr+++ e   lt+eele+l + ++l+e++ad+miEnv+G +  P++va+++ling+e l+Pm++eE s+vA+as
  gi|320100664|ref|YP_004176256.1|  14 IHERRRIVGEwagLTGEELETLgNLGNLPEKIADSMIENVVGGMTYPFAVATNFLINGRERLIPMVIEETSVVAAAS 90 
                                       789*****88899*********55699************************************************** PP

                                       HHHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-.. CS
                       HMG-CoA_red  75 rgakainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaest..srggglkdiev.vla.. 146
                                       ++a+++++++G+  + ++++ +++q++l++  +   ++ + ie+k+e+ e a++ ++t  + ggg +d+ev vl+  
  gi|320100664|ref|YP_004176256.1|  91 NAARMLRHGEGI-GANAERQEMISQIHLVKVDSPWFKAMRVIERKKEILEHAAQQDPTllKYGGGPRDLEVrVLEhp 166
                                       ************.6667777899******5556666778888*****************************888888 PP

                                       ..SSEEEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHH CS
                       HMG-CoA_red 147 ..grlvvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatige 221
                                         g ++v++l vd++DAmGaN+vn+++ea+a+++e+++g+e+ l+i sN + ++ a+a++a +++++        g 
  gi|320100664|ref|YP_004176256.1| 167 alGGVIVVHLVVDVRDAMGANTVNTMAEAVAPILEKITGGEARLRIVSNHAVYRVARAWAATPVDEV-------GGM 236
                                       8888**************************************************************9.......9** PP

                                       HHHHHHHHHHHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT.......SEEE... CS
                       HMG-CoA_red 222 evvekilkasaealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa.......leev... 288
                                       +v++ki++as  a++d++ra  +t+nkGi       +Ng+ Av+lAtGqD +a+e+++ha+aa       l+++   
  gi|320100664|ref|YP_004176256.1| 237 DVARKIMEASILAEIDPYRA--VTHNKGI-------MNGVIAVALATGQDHRAIEAGAHAYAArtgvyrpLSRWevt 304
                                       ********************..*******.......**********************************9999876 PP

                                       TTTEEEEEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHH CS
                       HMG-CoA_red 289 edgdlygsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmk 364
                                       +dg l gs+++P l+VG+vGG++k++p a+++ k+lgv++a+   eLae++aavgLAq+l+alrAL++eg+qkgHm+
  gi|320100664|ref|YP_004176256.1| 305 QDGLLAGSLEIP-LQVGVVGGAVKVHPVARIAlKILGVSTAR---ELAEVMAAVGLAQNLAALRALVTEGIQKGHMR 377
                                       7777********.*****************************...******************************** PP

                                       HHH CS
                       HMG-CoA_red 365 lhr 367
                                       lh+
  gi|320100664|ref|YP_004176256.1| 378 LHA 380
                                       *96 PP

>> Phasin_2  Phasin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.5e-05      0.15      30      93 ..     357     420 ..     341     422 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                          Phasin_2  30 elqleaarasleeslaaakallsakdpqellelqselaqpalekavayarklaelaaktqeeaa 93 
                                       +++l+a+ra++ e+++     l+a++++ ++ +  +l+ +++ek+v++ r  ++ a ++ e+aa
  gi|320100664|ref|YP_004176256.1| 357 AQNLAALRALVTEGIQKGHMRLHARNLAIMAGATGDLIDRVAEKMVKDGRIRYDYAKELVEKAA 420
                                       79********************************************************999987 PP

>> Peptidase_A8  Signal peptidase (SPase) II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.6e-05      0.21      74     107 ..     370     404 ..     334     407 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                      Peptidase_A8  74 k.kkkskllrialalilgGalGNliDrllygkVvD 107
                                         +k +  l      i++Ga G liDr+  + V D
  gi|320100664|ref|YP_004176256.1| 370 GiQKGHMRLHARNLAIMAGATGDLIDRVAEKMVKD 404
                                       244445556666788**************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3158.24
//
Query:       gi|320100665|ref|YP_004176257.1|  [L=121]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 900.46
//
Query:       gi|320100666|ref|YP_004176258.1|  [L=239]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1699.83
//
Query:       gi|320100667|ref|YP_004176259.1|  [L=285]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-20   72.0   0.0    9.3e-20   71.5   0.0    1.2  1  ABC_tran     ABC transporter
    1.5e-13   51.3   0.1    1.2e-05   25.2   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00011   21.8   0.0       0.14   11.6   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0037   17.0   0.0     0.0063   16.2   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
     0.0051   16.4   0.0     0.0083   15.7   0.0    1.4  1  AAA_25       AAA domain
     0.0068   16.7   0.0      0.012   15.8   0.0    1.5  1  AAA_28       AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.015   15.8   0.0    1.2  1  AAA_23       AAA domain
      0.027   14.2   0.0       0.11   12.2   0.0    2.0  2  AAA_30       AAA domain
      0.038   12.8   0.0      0.067   12.0   0.0    1.3  1  DLIC         Dynein light intermediate chain (DLIC)
      0.038   13.7   0.0        0.1   12.3   0.0    1.7  2  AAA_24       AAA domain
      0.066   13.5   0.1       0.53   10.6   0.1    2.3  1  AAA_22       AAA domain
      0.087   12.7   0.1       0.18   11.7   0.1    1.5  1  NACHT        NACHT domain
       0.11   13.1   0.2       0.26   11.8   0.1    1.7  1  AAA_18       AAA domain
       0.12   12.8   0.1       0.16   12.3   0.1    1.5  1  AAA_16       AAA ATPase domain
       0.18   11.6   0.0       0.45   10.2   0.0    1.6  2  IstB_IS21    IstB-like ATP binding protein
       0.18   11.5   0.0        2.6    7.7   0.0    2.0  2  AAA_15       AAA ATPase domain
       0.22   11.1   0.0         34    4.0   0.0    2.8  3  Terminase_6  Terminase-like family
       0.24   11.0   0.1       0.42   10.2   0.1    1.3  1  SRP54        SRP54-type protein, GTPase domain
       0.33    9.5   0.0       0.58    8.7   0.0    1.3  1  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 !   71.5   0.0   9.8e-23   9.3e-20       9     137 .]      25     156 ..      18     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 9.8e-23
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...... 79 
                                       +eg ++a++G+nG+GK+tLl +lagl  pt G+ l++g +    e+e++ + i++++++p+++ ++++r+       
  gi|320100667|ref|YP_004176259.1|  25 YEGARIAVLGPNGSGKTTLLTILAGLRYPTTGRALVNGIEPYV-ERERAVRAISFMFEKPRFNLGIRIRDIvkilse 100
                                       689**********************************999888.899999********************9**9877 PP

                                       ..HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ..esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                            +e+e +++ lgl+e+ d ++    + LS Gq q v + ++l++   ++++DEp+a
  gi|320100667|ref|YP_004176259.1| 101 drGCGDEAESLARLLGLTEFYDVKL----AGLSSGQAQLVGIWASLACWDGVVIIDEPFA 156
                                       7666777***************999....*****************************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 !   23.9   0.0   3.4e-08   3.2e-05       3      78 ..      31      91 ..      30      97 .. 0.73
   2 !   25.2   0.0   1.3e-08   1.2e-05     230     300 ..     121     184 ..     106     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.4e-08
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78
                                      ++ GpNgsGK++LL +l +l+                 + r   + + +y ++++++ +i+ f  +++r++ g+r+
  gi|320100667|ref|YP_004176259.1| 31 AVLGPNGSGKTTLLTILAGLR--------------YPTTGRALVNGIEPYVERERAVRAIS-FMFEKPRFNLGIRI 91
                                      689****************95..............45566666666666666666666666.66666666666665 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.3e-08
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       +++ ++ lS+G+ +l ++ ++l+  +   ++++iDEp ++L+ ++   l+ l+++     + +i+tTH p+
  gi|320100667|ref|YP_004176259.1| 121 YDVKLAGLSSGQAQLVGIWASLACWD---GVVIIDEPFAHLDIRRAGVLANLISRR----SDIIFTTHTPE 184
                                       56777889*********999999999...*********************999555....55******885 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00015      0.14      12      41 ..      15      44 ..       5      50 .. 0.80
   2 !    8.2   0.0    0.0016       1.5     137     205 ..     128     189 ..      93     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                      TEECEEEEEETTSSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 12 syagktvilpfsksftaivGpNGSGKsnll 41
                                      ++a ++v+  ++    a++GpNGSGK+ ll
  gi|320100667|ref|YP_004176259.1| 15 TWALSEVSFAYEGARIAVLGPNGSGKTTLL 44
                                      55556677777788899**********987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0016
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                       LS G+ +Lv +   +A        ++++De  a+LD ++   +a+l+ ++s    +i ++++ e  e  
  gi|320100667|ref|YP_004176259.1| 128 LSSGQAQLVGIWASLACW----DGVVIIDEPFAHLDIRRAGVLANLISRRS---DIIFTTHTPEEAEAL 189
                                       666666666655555543....35789********************9998...899999988877665 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   0.0   6.7e-06    0.0063      17      48 ..      21      53 ..      14      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.7e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalLvp 48
                                      +++  +g  + + Gp+GsGK+Tll  ++ l +p
  gi|320100667|ref|YP_004176259.1| 21 VSFAYEGaRIAVLGPNGSGKTTLLTILAGLRYP 53
                                      66777788899************9555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.8e-06    0.0083      31      98 ..      25     106 ..      13     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.8e-06
                            AAA_25  31 pagelallaGapgtGKttlaldlalava..tGkpwlg...pvap..eqgkVlyvsaEdsedelrrRlravgeal... 97 
                                        +g+ +++ G+ g+GKttl++ la      tG+ +     p++   + ++ +   +E ++ +l  R+r + + l   
  gi|320100667|ref|YP_004176259.1|  25 YEGARIAVLGPNGSGKTTLLTILAGLRYptTGRALVNgiePYVEreRAVRAISFMFEKPRFNLGIRIRDIVKILsed 101
                                       58999**************9999977766899999889*97777234555556668999999999999998777655 PP

                            AAA_25  98 ....r 98 
                                           +
  gi|320100667|ref|YP_004176259.1| 102 rgcgD 106
                                       56663 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-05     0.012       1      29 [.      29      57 ..      29      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                            AAA_28  1 kivitGgestGKTtlleaLaargypvvpE 29
                                      +i+++G+ ++GKTtll  La   yp+  +
  gi|320100667|ref|YP_004176259.1| 29 RIAVLGPNGSGKTTLLTILAGLRYPTTGR 57
                                      79******************877776544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   1.6e-05     0.015      24      41 ..      32      49 ..      20     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                            AAA_23 24 ItGpNGaGKTTildAikl 41
                                      + GpNG+GKTT+l  +  
  gi|320100667|ref|YP_004176259.1| 32 VLGPNGSGKTTLLTILAG 49
                                      68*********9976654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.11      21     114 ..      30     172 ..      17     180 .. 0.68
   2 ?   -3.5   0.0       7.6   7.2e+03     115     128 ..     197     210 ..     185     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                            AAA_30  21 avltGpAGtGKttalkalreaweaa.g....grviglAptgkaAkvLa........................eelgi 68 
                                        ++ Gp G+GKtt+l+ l+ +     g      +  +   ++a ++++                        +++g 
  gi|320100667|ref|YP_004176259.1|  30 IAVLGPNGSGKTTLLTILAGLRYPTtGralvNGIEPYVERERAVRAISfmfekprfnlgirirdivkilsedRGCGD 106
                                       4578*************988765554744444444555566666666677777776666666666666665446777 PP

                            AAA_30  69 eastiakllkrlk...................grarlepg.tllivDE.agmvdtkqlaallkaaek 114
                                       ea+++a+ll  ++                   + a+l+    ++i+DE  + +d++ +  l++ +++
  gi|320100667|ref|YP_004176259.1| 107 EAESLARLLGLTEfydvklaglssgqaqlvgiW-ASLACWdGVVIIDEpFAHLDIRRAGVLANLISR 172
                                       888888888777799999999999999888874.333333378899984466677777666666655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.6
                            AAA_30 115 agakvilvGDerQl 128
                                       ++ +v+ +G ++Ql
  gi|320100667|ref|YP_004176259.1| 197 NNGRVVWAGTRDQL 210
                                       46899999999998 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.1e-05     0.067      26      57 ..      28      59 ..      18      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                              DLIC 26 ksvlvlGedgsGkttliaklqGveeekkGrGl 57
                                        + vlG +gsGkttl++ l G+  +  Gr l
  gi|320100667|ref|YP_004176259.1| 28 ARIAVLGPNGSGKTTLLTILAGLRYPTTGRAL 59
                                      5789********************99999976 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011       0.1       2      22 ..      27      47 ..      26      69 .. 0.84
   2 ?   -2.0   0.0       2.7   2.5e+03     119     134 ..     170     185 ..     163     214 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      +++i++ Gp+g+GKTtl++ l
  gi|320100667|ref|YP_004176259.1| 27 GARIAVLGPNGSGKTTLLTIL 47
                                      689**************9876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                            AAA_24 119 qelrknvifiahektr 134
                                        + r ++if+ h+ ++
  gi|320100667|ref|YP_004176259.1| 170 ISRRSDIIFTTHTPEE 185
                                       4444566666666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00056      0.53       8      28 ..      30      50 ..      25     183 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                            AAA_22  8 lvvtGesGtGKTtllrrlleq 28
                                      ++v G+ G+GKTtll  l+  
  gi|320100667|ref|YP_004176259.1| 30 IAVLGPNGSGKTTLLTILAGL 50
                                      7899**********9877765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00019      0.18       3      21 ..      30      48 ..      28      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      +++ G++GsGKTtLl  la
  gi|320100667|ref|YP_004176259.1| 30 IAVLGPNGSGKTTLLTILA 48
                                      799***********98665 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   0.00028      0.26       1      21 [.      30      50 ..      30      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      I++ G+ G+GKttl   L+ +
  gi|320100667|ref|YP_004176259.1| 30 IAVLGPNGSGKTTLLTILAGL 50
                                      89*************999754 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00017      0.16      26      51 ..      29      53 ..      12     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                            AAA_16 26 lvllsGesGvGKsslvrellralekd 51
                                       + + G+ G+GK++l++ l+  l+  
  gi|320100667|ref|YP_004176259.1| 29 RIAVLGPNGSGKTTLLTILA-GLRYP 53
                                      578*************8776.34444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00048      0.45      35      67 ..      15      47 ..       5      56 .. 0.85
   2 ?   -3.4   0.0       7.5     7e+03     111     137 ..     148     173 ..     140     184 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00048
                         IstB_IS21 35 vkeLatlsfiekkenivllGpsGvGKshlaial 67
                                      + +L + sf  + + i++lGp G GK+ l + l
  gi|320100667|ref|YP_004176259.1| 15 TWALSEVSFAYEGARIAVLGPNGSGKTTLLTIL 47
                                      5579999********************986655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.5
                         IstB_IS21 111 llilDdlgllpldqaeaellfeviekr 137
                                       ++i+D+  + +ld   a +l ++i++r
  gi|320100667|ref|YP_004176259.1| 148 VVIIDE-PFAHLDIRRAGVLANLISRR 173
                                       566666.35556666666666666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0028       2.6      28      43 ..      32      47 ..      22      51 .. 0.90
   2 ?    1.7   0.0      0.18   1.7e+02     326     366 ..     148     183 ..      89     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0028
                            AAA_15 28 liGkNnsGKSsileal 43
                                      + G+N+sGK+++l +l
  gi|320100667|ref|YP_004176259.1| 32 VLGPNGSGKTTLLTIL 47
                                      67***********998 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                       +++i+EP ahL +    vl++l+   ++ +   +i+tTH+p
  gi|320100667|ref|YP_004176259.1| 148 VVIIDEPFAHLDIRRAGVLANLI---SRRS--DIIFTTHTP 183
                                       56778888877777777776654...3344..599****98 PP

>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.81   7.6e+02       5      16 ..       9      20 ..       8      25 .. 0.82
   2 ?    4.0   0.0     0.036        34       3      18 ..      33      48 ..      31      69 .. 0.87
   3 ?    3.5   0.0     0.052        49      92     146 ..     145     193 ..     125     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.81
                                      -SSS-HHHHHHH CS
                       Terminase_6  5 grqsGKTfagar 16
                                      + + GKT+a+++
  gi|320100667|ref|YP_004176259.1|  9 SKRFGKTWALSE 20
                                      6789*****986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.036
                                      EE-SSS-HHHHHHHHH CS
                       Terminase_6  3 lggrqsGKTfagarel 18
                                      lg+++sGKT+++++ +
  gi|320100667|ref|YP_004176259.1| 33 LGPNGSGKTTLLTILA 48
                                      89********998765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.052
                                       HHTS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT--EEEEEE---SSSHHHHHH CS
                       Terminase_6  92 iqGaqidliyfDElteipksqelekvtrlratkgtdtktfattpptpdhgvydfv 146
                                       + G    ++++DE++ + + +    ++ l++++++ +  f t +p+++  ++d +
  gi|320100667|ref|YP_004176259.1| 145 WDG----VVIIDEPFAHLDIRRAGVLANLISRRSDII--FTTHTPEEAEALADYI 193
                                       677....99*************************999..9999999998888766 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00044      0.42       4      23 ..      30      49 ..      28      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00044
                                      EEEEESTTSSHHHHHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaa 23
                                      i+++G++G+GKTt l+ La 
  gi|320100667|ref|YP_004176259.1| 30 IAVLGPNGSGKTTLLTILAG 49
                                      7899***********99985 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00061      0.58      22      40 ..      33      51 ..      29      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00061
                            AAA_13 22 YGwNGaGKTtLSrllrsle 40
                                       G NG+GKTtL ++l+ l 
  gi|320100667|ref|YP_004176259.1| 33 LGPNGSGKTTLLTILAGLR 51
                                      59*************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1922.32
//
Query:       gi|320100668|ref|YP_004176260.1|  [L=308]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2379.17
//
Query:       gi|320100669|ref|YP_004176261.1|  [L=42]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 362.68
//
Query:       gi|320100670|ref|YP_004176262.1|  [L=681]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 4804.26
//
Query:       gi|320100671|ref|YP_004176263.1|  [L=530]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.64    9.9   4.8        1.5    8.7   4.8    1.6  1  PKD       PKD 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 ?    8.7   4.8   8.2e-05       1.5       3      63 ..     138     201 ..     136     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 8.2e-05
                                       ---S--BSSEEEEEEEES..-SS-SEEEEE--SS..--EEEEETTEEEEEE-SSEEEEEEEEEE CS
                               PKD   3 asptvlvpgatvaftaav.pdganvtysWdfgdg..svvqvlseptvthtYlspGeYeVtvtas 63 
                                        s++   +g+ v+ + av p+ + v y    gdg     + +   + +h+Y+s G Y+V  +as
  gi|320100671|ref|YP_004176263.1| 138 SSRQGYFTGEAVNISVAVsPPVDTVEYVVSWGDGvvEHYTGGAAVNLSHVYASSGAYTVVINAS 201
                                       5667778999999999999999999999999**98877788888899************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 4091.86
//
Query:       gi|320100672|ref|YP_004176264.1|  [L=191]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-33  114.0  23.8      6e-33  114.0  23.8    1.7  2  DUF996           Protein of unknown function (DUF996)
     0.0054   15.8  29.6      0.026   13.6  11.4    2.2  2  DUF973           Protein of unknown function (DUF973)
  ------ inclusion threshold ------
      0.094   12.7   0.5      0.094   12.7   0.5    2.6  4  DUF1201          Protein of unknown function (DUF1201)
       0.28   10.5  19.3       0.42    9.9  19.3    1.3  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
       0.47   10.7   0.0       0.47   10.7   0.0    2.9  3  Adeno_E3B        Adenovirus E3B protein
       0.62   10.5   6.8       0.11   13.0   2.5    1.8  2  DUF805           Protein of unknown function (DUF805)
        2.7    6.0   4.9        3.4    5.7   4.9    1.1  1  UPF0182          Uncharacterised protein family (UPF0182)
        3.1    7.7  30.5      0.041   13.8  16.6    2.4  3  Colicin_V        Colicin V production protein
        6.2    6.7  23.4        1.1    9.2  10.9    2.3  2  DUF2975          Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.9       2.3   4.5e+03     123     133 ..       9      20 ..       6      21 .. 0.71
   2 !  114.0  23.8     3e-36     6e-33       1     135 []      26     164 ..      26     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                            DUF996 123 vl.vGliillia 133
                                       v+ vG+i+l i+
  gi|320100672|ref|YP_004176264.1|   9 VAgVGAILLAIG 20 
                                       444888888886 PP

  == domain 2  score: 114.0 bits;  conditional E-value: 3e-36
                            DUF996   1 lsivGliLvlvalkeiskavndekifsnaliafilsiialvvailalllvlgalatalelpg.leeaas...lilll 73 
                                       l+++GliL+l++lk +s+a++d++if+nal+a+i+++i+lvv+i++++++++++  +l+l+g l+e+ +   ++++l
  gi|320100672|ref|YP_004176264.1|  26 LALIGLILLLIGLKGLSEAYRDDTIFTNALYAVIIEFIGLVVFIVLIGASMFSMGLGLGLGGgLHEMGAglgFLAGL 102
                                       579******************************************************99975267777688888888 PP

                            DUF996  74 llvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGliilliaei 135
                                       ++ l++++++l+++avf++ks+++l++++g+klF tagll++iGa+Lti+lvG+iill+a+i
  gi|320100672|ref|YP_004176264.1| 103 FIGLVVLFIFLVVAAVFFRKSFDTLAAKSGEKLFGTAGLLILIGAVLTIILVGAIILLVAWI 164
                                       8889*********************************************************9 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6  11.4   1.3e-05     0.026     127     192 ..       7      70 ..       1      82 [. 0.68
   2 !    6.5  19.3    0.0018       3.6      12     121 ..      54     162 ..      52     179 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                            DUF973 127 lslillgviilligi...ilaliGqillglsfyklGevYnnglikigGiliiipvidilsfIGyilsyi 192
                                        + + +g+i+l+ig+   ilaliG+ill ++ + l e Y +++i +  +  +i      +fIG+++ ++
  gi|320100672|ref|YP_004176264.1|   7 KIVAGVGAILLAIGGftpILALIGLILLLIGLKGLSEAYRDDTIFTNALYAVII-----EFIGLVVFIV 70 
                                       3334455555666659***************************98887765544.....4444443333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                            DUF973  12 slfliiasllaliliilvlvvlftaissglsqliqssasilssvlllliaaiiliiiasvllilgllkirsgfsiLs 88 
                                       +l+ +i++++ l++ i+ +   + ++  gl       ++ + + l+ l +  i  ++  ++l+++ + +r+ f +L+
  gi|320100672|ref|YP_004176264.1|  54 ALYAVIIEFIGLVVFIVLIGASMFSMGLGL--GLGGGLHEMGAGLGFLAGLFIGLVVLFIFLVVAAVFFRKSFDTLA 128
                                       577888888888887777765555444444..334445556667777777777777788899999999********9 PP

                            DUF973  89 stgrdvgiGitgltliligai..iiiigvilaivs 121
                                       +++ +   G++gl+ iliga+  ii++g+i+++v 
  gi|320100672|ref|YP_004176264.1| 129 AKSGEKLFGTAGLL-ILIGAVltIILVGAIILLVA 162
                                       99888888888864.45555511344555544432 PP

>> DUF1201  Protein of unknown function (DUF1201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.9       6.6   1.3e+04      10      25 ..      16      32 ..      14      36 .. 0.52
   2 ?   -0.9   0.3      0.87   1.7e+03      22      30 ..      63      71 ..      54      76 .. 0.74
   3 ?   12.7   0.5   4.7e-05     0.094      13      40 ..      96     123 ..      92     133 .. 0.88
   4 ?   -3.4   1.0       5.3   1.1e+04      22      22 ..     154     154 ..     139     171 .. 0.49

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.6
                           DUF1201 10 llaf.Gfliclflfclv 25
                                      lla  Gf   l l  l+
  gi|320100672|ref|YP_004176264.1| 16 LLAIgGFTPILALIGLI 32
                                      55551455555555554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.87
                           DUF1201 22 fclvvfiwf 30
                                        lvvfi +
  gi|320100672|ref|YP_004176264.1| 63 IGLVVFIVL 71
                                      468999965 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 4.7e-05
                           DUF1201  13 fGfliclflfclvvfiwfvykqilfrtt 40 
                                       +Gfl  lf+  +v+fi++v   ++fr +
  gi|320100672|ref|YP_004176264.1|  96 LGFLAGLFIGLVVLFIFLVVAAVFFRKS 123
                                       79***********************975 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 5.3
                           DUF1201  22 f 22 
                                        
  gi|320100672|ref|YP_004176264.1| 154 V 154
                                       2 PP

>> Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  19.3   0.00021      0.42      81     227 ..      26     171 ..       7     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00021
                   Cyt_bd_oxida_II  81 ylpllliLlglilRgvafefrskaeskrwrklwdlaf.figSllaalllGvalgnllqGvpfdad..eygflsdlln 154
                                       + ++ liLl++ l+g++ ++r        ++l+ +++ fig ++  +l+G+ + ++  G+ +     e+g  + l  
  gi|320100672|ref|YP_004176264.1|  26 LALIGLILLLIGLKGLSEAYRDDTI--FTNALYAVIIeFIGLVVFIVLIGASMFSMGLGLGLGGGlhEMG--AGLGF 98 
                                       5566789999999********9875..5677777766377778888999998888888888742232443..22445 PP

                   Cyt_bd_oxida_II 155 pfallvglllvalflllGalylalktegelqerarrlalvlalvllvllvvvllwtlllvllllavlalllav 227
                                       +  l++gl+++++fl+ +a+++    +  +++  ++l   ++l++l+++v++++++ +++ll++ ++a+++++
  gi|320100672|ref|YP_004176264.1|  99 LAGLFIGLVVLFIFLVVAAVFFRKSFDTLAAKSGEKLFGTAGLLILIGAVLTIILVGAIILLVAWIIAAIAFF 171
                                       689*******************999976677777777777777777777777776555555433333333332 PP

>> Adeno_E3B  Adenovirus E3B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.9      0.71   1.4e+03      26      43 ..      52      69 ..      47      76 .. 0.71
   2 ?   -1.7   0.3       1.8   3.5e+03      19      30 ..     105     114 ..      97     130 .. 0.51
   3 ?   10.7   0.0   0.00024      0.47      22      55 ..     141     176 ..     131     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.71
                         Adeno_E3B 26 icslvtvviafiqfidwv 43
                                        +l +v+i fi ++ ++
  gi|320100672|ref|YP_004176264.1| 52 TNALYAVIIEFIGLVVFI 69
                                      556788888888777655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
                         Adeno_E3B  19 gfvtlilicslv 30 
                                       g+v l +   lv
  gi|320100672|ref|YP_004176264.1| 105 GLVVLFI--FLV 114
                                       3333222..222 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00024
                         Adeno_E3B  22 tlilicslvtvvi..afiqfidwvcvriaylrhhpq 55 
                                        lili +++t+++  a+i ++ w+   ia++  +p 
  gi|320100672|ref|YP_004176264.1| 141 LLILIGAVLTIILvgAIILLVAWIIAAIAFFSAKPP 176
                                       47999999998654499*************988875 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.0      0.55   1.1e+03      36      36 ..      47      47 ..       8      73 .. 0.44
   2 ?   13.0   2.5   5.3e-05      0.11      22      88 ..      63     161 ..      46     180 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.55
                            DUF805 36 a 36
                                      +
  gi|320100672|ref|YP_004176264.1| 47 D 47
                                      1 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.3e-05
                            DUF805  22 llvivlallaavlaa.......................aavasalsvvlallllvpslavtvRRlHD.......... 65 
                                       +  +v+ +l     +                         +a+ ++ +++l+++++ +av++R   D          
  gi|320100672|ref|YP_004176264.1|  63 IGLVVFIVLI----GasmfsmglglglggglhemgaglGFLAGLFIGLVVLFIFLVVAAVFFRKSFDtlaaksgekl 135
                                       2222222222....1222244677899999*99999988888899999999999999**********8877777777 PP

                            DUF805  66 tgrsgwllllllvpli...alllllv 88 
                                        g  g+l+l+++v  i   ++++llv
  gi|320100672|ref|YP_004176264.1| 136 FGTAGLLILIGAVLTIilvGAIILLV 161
                                       77777788888875442222222222 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.9    0.0017       3.4     136     254 ..      50     171 ..      45     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0017
                           UPF0182 136 vFklPflelllslllalvllaliavllvyllsgesl..girl..kfaelskaarrhlsvllallllllalsywLdry 208
                                       +F+  ++ ++ +++  +v+++li + ++ +  g  l  g  l  + a+l   a   + +++ +++l++a+ ++ + +
  gi|320100672|ref|YP_004176264.1|  50 IFTNALYAVIIEFIGLVVFIVLIGASMFSMGLGLGLggG--LheMGAGLGFLAGLFIGLVVLFIFLVVAAVFFRKSF 124
                                       677777777777777777777777777777777444433..24466788888888888899999999999999999* PP

                           UPF0182 209 ellyskrg.vvtGagYtdvnavlpaktilavialvvavlllvaivlk 254
                                       + l +k+g  ++G     + +  ++++il+ + +++ +++++ai++ 
  gi|320100672|ref|YP_004176264.1| 125 DTLAAKSGeKLFGTAGLLILIGAVLTIILVGAIILLVAWIIAAIAFF 171
                                       *9999877688888877777777777777666666666666666333 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8  16.6   2.1e-05     0.041      25     125 ..       5     123 ..       3     132 .. 0.82
   2 ?   -1.7   9.6       1.3   2.6e+03      36      84 ..     115     167 ..     114     173 .. 0.58
   3 ?   -1.0   6.1      0.79   1.6e+03      22      41 ..     154     173 ..     135     186 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                         Colicin_V  25 vlsllgwvvafvvasllypslaellae..................lilspalaaiiaf.lllfllvllivsllgall 82 
                                          +++ v+a+++a+    ++ +l++                   +++++ +a ii f  l++++vl+ +s++++ l
  gi|320100672|ref|YP_004176264.1|   5 TSKIVAGVGAILLAIGGFTPILALIGLillliglkglseayrddtIFTNALYAVIIEFiGLVVFIVLIGASMFSMGL 81 
                                       5678888888888888888888888889999999999999888*9999**********6667777777788888888 PP

                         Colicin_V  83 sklvsktglglldrllGaifGllkglllvvllllllalvplpk 125
                                       +      gl+ +   lG++ Gl+ gl++++++l+++a++  ++
  gi|320100672|ref|YP_004176264.1|  82 GL-GLGGGLHEMGAGLGFLAGLFIGLVVLFIFLVVAAVFFRKS 123
                                       77.77899999*******************9998888886555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                         Colicin_V  36 vvasllypslaellae....lilspalaaiiaflllfllvllivsllgallsk 84 
                                       v+a+++ +s+  l a+    l++++ l  +i+ +l+ +lv +i+ l++ ++  
  gi|320100672|ref|YP_004176264.1| 115 VAAVFFRKSFDTLAAKsgekLFGTAGLLILIGAVLTIILVGAIILLVAWIIAA 167
                                       56666666666666665557555666666666666666666666666655544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.79
                         Colicin_V  22 vrevlsllgwvvafvvasll 41 
                                       v  ++ l++w++a+++ +  
  gi|320100672|ref|YP_004176264.1| 154 VGAIILLVAWIIAAIAFFSA 173
                                       33344555555555555544 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  10.9   0.00053       1.1      25     116 ..      25     118 ..       3     123 .. 0.59
   2 ?    0.7   8.4      0.23   4.6e+02      78     118 ..     124     166 ..     111     169 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00053
                           DUF2975  25 vlallafvvalvqlwkLlrsirkgevFspanvrrLrriglaliaaalllaagivalallaelelap.....gvvlll 96 
                                       +lal+ +++ l+ l  L  ++r++++F+ a +  +   ++++++++l+ a   ++ ++l+   l +     g  l++
  gi|320100672|ref|YP_004176264.1|  25 ILALIGLILLLIGLKGLSEAYRDDTIFTNALYAVIIEFIGLVVFIVLIGAS--MFSMGLGL-GLGGglhemGAGLGF 98 
                                       4555555666666666************99998887777777776333333..33333333.233311113444444 PP

                           DUF2975  97 lgvafaslvigllvlvlael 116
                                       l   f++lv+ ++ lv+a++
  gi|320100672|ref|YP_004176264.1|  99 LAGLFIGLVVLFIFLVVAAV 118
                                       44455555555555566655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.23
                           DUF2975  78 valallaelelap....gvvllllgvafaslvigllvlvlaella 118
                                       +++  +++   +       +l+l+g++++ +++g+++l++a+++a
  gi|320100672|ref|YP_004176264.1| 124 FDTLAAKS--GEKlfgtAGLLILIGAVLTIILVGAIILLVAWIIA 166
                                       33333333..22234445677777888999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1341  (0.074795); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        56  (0.00312343); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.41
# Mc/sec: 1405.56
//
Query:       gi|320100673|ref|YP_004176265.1|  [L=633]
Description: sigma 54 interacting domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-14   53.5   0.0    1.6e-06   27.3   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    7.2e-14   52.4   0.0      1e-13   51.9   0.0    1.2  1  DUF87            Helicase HerA, central domain
    1.7e-07   31.3   0.0    2.8e-07   30.5   0.0    1.3  1  TraG-D_C         TraM recognition site of TraD and TraG
    6.8e-07   29.6   0.0     0.0006   20.1   0.0    2.8  2  AAA_22           AAA domain
    0.00014   22.3   0.3      0.034   14.5   0.1    2.7  2  AAA_16           AAA ATPase domain
    0.00031   19.5   0.1    0.00047   18.9   0.1    1.2  1  DUF853           Bacterial protein of unknown function (DUF85
    0.00039   20.2   0.1      0.046   13.5   0.0    2.4  2  AAA_30           AAA domain
      0.001   18.0   0.0      0.012   14.5   0.0    2.0  2  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
     0.0035   17.8   0.0      0.007   16.9   0.0    1.4  1  ABC_tran         ABC transporter
     0.0079   15.1   0.0      0.016   14.2   0.0    1.4  1  AAA_10           AAA-like domain
     0.0086   15.4   0.0       0.08   12.3   0.0    2.1  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
       0.06   12.6   0.0        0.1   11.9   0.0    1.3  1  Zeta_toxin       Zeta toxin
      0.062   13.6   0.1        2.9    8.2   0.0    2.7  2  AAA_19           AAA domain
       0.08   12.9   0.2       0.19   11.7   0.2    1.6  1  NACHT            NACHT domain
       0.12   12.3   0.0        0.6   10.0   0.0    2.0  2  ATPase_2         ATPase domain predominantly from Archaea
       0.15   11.6   0.1        0.3   10.6   0.1    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.19   11.7   0.0       0.33   11.0   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> 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 !   23.8   0.0   1.8e-08   1.9e-05      10      73 ..     271     336 ..     266     337 .. 0.86
   2 !   27.3   0.0   1.5e-09   1.6e-06     222     313 ..     498     582 ..     471     593 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.8e-08
                     TrwB_AAD_bind  10 pkeretqhilivGttGsGKtqalekllrairargdraiv.lDltGafvsrfydegk.dillnPlDa 73 
                                         ++ ++h+ +vG tGsGKt  l+ l++ +   g  ai+ +D++G++ ++ + e    + l+P+Da
  gi|320100673|ref|YP_004176265.1| 271 GIRDLERHVYVVGQTGSGKTSLLKLLVHRLHGLGGAAIIlVDPHGDMSRELAGEIPgAVFLDPVDA 336
                                       5667789************************9988777637**********997655999***997 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.5e-09
                     TrwB_AAD_bind 222 llsawldlaikallslpesrerrlWfflDElpaLgrleelksllaegRkfGgavvlglqsiaqlrevYGedaaqsil 298
                                       +l +w ++ ++a l    + +  +++++DE++ +  l+ ++++l e+Rk+G  +v++ q++ ql    G+   qsil
  gi|320100673|ref|YP_004176265.1| 498 VLKIWSEVLARARLG---EPRTHVFLVIDEFQFVADLPVVDTMLSEARKYGLHLVIAHQHTGQLP---GS-LLQSIL 567
                                       333333444444333...344569****************************************8...44.788999 PP

                     TrwB_AAD_bind 299 slvntklilrvsdae 313
                                        +++ kl+++v+ ++
  gi|320100673|ref|YP_004176265.1| 568 TNTGVKLVFQVAGGD 582
                                       999999999998655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   9.8e-17     1e-13       8     188 ..     262     465 ..     257     500 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 9.8e-17
                             DUF87   8 sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal...........eklls 73 
                                       ++s+ +v+l + + ++rH+ ++g+TGsGK+ + ++L+++l    ga i+++DpHG+ ++ l           +    
  gi|320100673|ref|YP_004176265.1| 262 TESGREVRLGI-RDLERHVYVVGQTGSGKTSLLKLLVHRLHGLGGAAIILVDPHGDMSRELageipgavfldPVDA- 336
                                       57777899***.556**************************99999***************666666666654444. PP

                             DUF87  74 ekvkvitpspsa...............kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeeke 135
                                                  +                +  + i++ +  ++e+l+l+ +     a + r +l+ +l+ +    e  
  gi|320100673|ref|YP_004176265.1| 337 -----------PygvnpldlprhrdreYAVSVAIDVLLTVFQEVLKLMST-----AVNVRYLLRVILRALY--AESD 395
                                       ...........344444444444588899*********************.....8889999999999999..8999 PP

                             DUF87 136 klssdepveklleelk..............kekeelrklknqaiarlldkledllrkggsf...snsstd 188
                                       + + ++  e +l  +               ++ e lr++++q+  + l++le   r+g ++   s ++ d
  gi|320100673|ref|YP_004176265.1| 396 SPTMADVYEAILGLYSgrlvlgdpgdpewrRQLEVLRSMQRQTLISALSRLEPYARDGFLRrltSRTTID 465
                                       9999999999998888999999998885433333444444444444444444444444444444444444 PP

>> TraG-D_C  TraM recognition site of TraD and TraG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   2.7e-10   2.8e-07       1      73 [.     517     587 ..     517     603 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.7e-10
                          TraG-D_C   1 pvlfllDEfanlgkipdleellstgrsrgislvlilQsiaqleelYgkegaetilgncdvklflg..vndeetae 73 
                                       +v +++DEf+ ++ +p ++++ls++r++g++lv++ Q   ql         ++il n+ vkl+++  + d+e + 
  gi|320100673|ref|YP_004176265.1| 517 HVFLVIDEFQFVADLPVVDTMLSEARKYGLHLVIAHQHTGQLPGSL----LQSILTNTGVKLVFQvaGGDVEKLS 587
                                       6899***************************************877....59**********9995444666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.6e-07    0.0006       5      67 ..     276     332 ..     272     443 .. 0.85
   2 !    6.4   0.0    0.0096        10      89     113 ..     508     542 ..     477     558 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.6e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralgle 67 
                                       +++++v+G++G+GKT ll+ l+++l+        ++ +++v++ +++ s++l+ e+  a+ l+
  gi|320100673|ref|YP_004176265.1| 276 ERHVYVVGQTGSGKTSLLKLLVHRLHGL-----GGAAIILVDPHGDM-SRELAGEIPGAVFLD 332
                                       6899********************9643.....46677777777777.777777777666655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0096
                            AAA_22  89 rav......ielliiDEaqhlr..s..eealeeLr 113
                                       ra+      +++l+iDE+q++   +  +++l+e r
  gi|320100673|ref|YP_004176265.1| 508 RARlgeprtHVFLVIDEFQFVAdlPvvDTMLSEAR 542
                                       44446666789*********964425677777764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.2e-05     0.034      25      51 ..     277     303 ..     267     330 .. 0.85
   2 ?    4.7   0.0     0.035        37     106     156 ..     459     535 ..     371     551 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekd 51 
                                       + v+++G+ G+GK+sl++ l ++l + 
  gi|320100673|ref|YP_004176265.1| 277 RHVYVVGQTGSGKTSLLKLLVHRLHGL 303
                                       899***************999988765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.035
                            AAA_16 106 a.....................avpelagaea.....srllellkrllallsrderp..lvlvlDdlqwadeaslql 154
                                       +                     + + l  ++a     + +l  +++ la+++ +e+   + lv+D++q    a+l +
  gi|320100673|ref|YP_004176265.1| 459 TsrttidvggmlspgsltlfstPKAVLGEDLArlvasTVVLKIWSEVLARARLGEPRthVFLVIDEFQF--VADLPV 533
                                       14444555555555555555442222222222445555555566666655555333344*********3..333444 PP

                            AAA_16 155 la 156
                                        +
  gi|320100673|ref|YP_004176265.1| 534 VD 535
                                       44 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 !   18.9   0.1   4.4e-07   0.00047       5      62 ..     260     318 ..     256     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.4e-07
                            DUF853   5 iakeaeqelalalklanrhGliaGatGtGktvtLqvlaeslsea.GvpvfladvkGdLs 62 
                                         +e+ +e++l ++   rh  + G tG Gkt  L++l + l    G +++l+d  Gd+s
  gi|320100673|ref|YP_004176265.1| 260 GVTESGREVRLGIRDLERHVYVVGQTGSGKTSLLKLLVHRLHGLgGAAIILVDPHGDMS 318
                                       5677889999999***************************9876268899*******98 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   4.3e-05     0.046      19      65 ..     277     324 ..     268     330 .. 0.87
   2 ?    4.3   0.1     0.028        30      87     122 ..     515     551 ..     479     606 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaee 65 
                                       r + ++G  G+GKt +lk l++ ++   g  +i++ p g ++++La e
  gi|320100673|ref|YP_004176265.1| 277 RHVYVVGQTGSGKTSLLKLLVHRLHGLgGAAIILVDPHGDMSRELAGE 324
                                       56789***************88888886899**********9999866 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.028
                            AAA_30  87 epgtllivDEagmv.dtkqlaallkaaekagakvilv 122
                                       +++  l++DE   v d   ++++l++a+k+g +++++
  gi|320100673|ref|YP_004176265.1| 515 RTHVFLVIDEFQFVaDLPVVDTMLSEARKYGLHLVIA 551
                                       233679*****99879**************9877764 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 ?    1.2   0.0      0.12   1.2e+02      45      59 ..     277     291 ..     251     325 .. 0.72
   2 !   14.5   0.0   1.1e-05     0.012     299     369 ..     513     578 ..     440     589 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                   T4SS-DNA_transf  45 ehvlvvAptrsgKgv 59 
                                        hv vv+ t+sgK+ 
  gi|320100673|ref|YP_004176265.1| 277 RHVYVVGQTGSGKTS 291
                                       7************96 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.1e-05
                   T4SS-DNA_transf 299 derpkevlflLDEfpslGkleileealatiagYgirltlIiQsisqlketYgkegaksilsnsavvivfaa 369
                                       ++r  +v + +DEf+ +  l+   + l   ++Yg+ l++  Q ++ql +       +sil+n  v++vf++
  gi|320100673|ref|YP_004176265.1| 513 EPR-THVFLVIDEFQFVADLPVVDTMLSEARKYGLHLVIAHQHTGQLPGS----LLQSILTNTGVKLVFQV 578
                                       344.5799***************************************864....45667777666666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.6e-06     0.007      12      41 ..     277     306 ..     267     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-06
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGe 41 
                                       + v +vG++G+GK++Llkll + l+   G 
  gi|320100673|ref|YP_004176265.1| 277 RHVYVVGQTGSGKTSLLKLLVHRLHGLGGA 306
                                       56899***************9998876665 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.5e-05     0.016      21      63 ..     276     319 ..     265     381 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                            AAA_10  21 asasliiGdlGnGKSvlakllvlyisllggka.liiDpkkerek 63 
                                         ++ ++G++G GK  l kllv+ +  lgg a +++Dp  ++ +
  gi|320100673|ref|YP_004176265.1| 276 ERHVYVVGQTGSGKTSLLKLLVHRLHGLGGAAiILVDPHGDMSR 319
                                       56889*******************998887651669**999543 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   7.5e-05      0.08      27      60 ..     264     297 ..     249     300 .. 0.81
   2 ?    0.3   0.0      0.35   3.6e+02     168     240 ..     536     554 ..     509     568 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-05
                                       TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE  27 sgnplvldlkkmashllvaGatgsGKStalntLi 60 
                                       sg+ + l ++  + h+ v+G tgsGK+  l+ L+
  gi|320100673|ref|YP_004176265.1| 264 SGREVRLGIRDLERHVYVVGQTGSGKTSLLKLLV 297
                                       56677777788889***************99886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.35
                                       ........-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES- CS
                      FtsK_SpoIIIE 168 sLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqr 240
                                        + ++                                                      +r+ glHl++a q 
  gi|320100673|ref|YP_004176265.1| 536 TMLSE------------------------------------------------------ARKYGLHLVIAHQH 554
                                       33344......................................................45555555555543 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.7e-05       0.1      19      44 ..     279     304 ..     276     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.7e-05
                        Zeta_toxin  19 illgGqpGAGKselaellkdele.rqg 44 
                                       + ++Gq+G+GK++l++ll  +l+   g
  gi|320100673|ref|YP_004176265.1| 279 VYVVGQTGSGKTSLLKLLVHRLHgL-G 304
                                       6789**************9999742.3 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0028       2.9      10      46 ..     276     309 ..     272     327 .. 0.81
   2 ?    2.2   0.0       0.2   2.1e+02     102     126 ..     516     542 ..     438     551 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeil 46 
                                       e+++ v++  G+GKT +lk  v+ l  lgg     i+
  gi|320100673|ref|YP_004176265.1| 276 ERHVYVVGQTGSGKTSLLKLLVHRLHGLGGA---AII 309
                                       57899*****************999888765...454 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
                            AAA_19 102 eeellivDEfqdvd..elqyrLlkall 126
                                        +  l++DEfq v   ++  ++l++  
  gi|320100673|ref|YP_004176265.1| 516 THVFLVIDEFQFVAdlPVVDTMLSEAR 542
                                       44489******9874666666666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00018      0.19       2      24 ..     278     300 ..     277     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                       CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalaw 24 
                                        v + G+ GsGKT Ll+ l++ +
  gi|320100673|ref|YP_004176265.1| 278 HVYVVGQTGSGKTSLLKLLVHRL 300
                                       6899*************999876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00056       0.6      22      49 ..     278     305 ..     271     326 .. 0.81
   2 ?   -1.3   0.0       1.6   1.7e+03     112     133 ..     510     531 ..     480     579 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                          ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdk 49 
                                        +++ G  gsGKt+Llk ++ +l+ ++ 
  gi|320100673|ref|YP_004176265.1| 278 HVYVVGQTGSGKTSLLKLLVHRLHGLGG 305
                                       57888****************9977665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                          ATPase_2 112 kikkkgkkiiiiiDelqklidl 133
                                        + + ++ + ++iDe+q + dl
  gi|320100673|ref|YP_004176265.1| 510 RLGEPRTHVFLVIDEFQFVADL 531
                                       34455667999****9988765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00029       0.3       4      32 ..     280     308 ..     278     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                                       EEEESTTCCHHHHHHHHHCT--SS-EEEE CS
                              cobW   4 vltGflGsGKTtLlnhllenraglklavi 32 
                                        ++G  GsGKT+Ll+ l+++ +gl  a i
  gi|320100673|ref|YP_004176265.1| 280 YVVGQTGSGKTSLLKLLVHRLHGLGGAAI 308
                                       689***************98888876655 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00031      0.33      22      61 ..     274     311 ..     257     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEE CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflv 61 
                                       + +++++++  TG+GKT ++  l+ rl+  g+   +++lv
  gi|320100673|ref|YP_004176265.1| 274 DLERHVYVVGQTGSGKTSLLKLLVHRLHGLGG--AAIILV 311
                                       568899*********************99877..444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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 0.29s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 4450.06
//
Query:       gi|320100674|ref|YP_004176266.1|  [L=87]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0054   16.5   5.2      0.006   16.4   5.2    1.0  1  CbtA      Probable cobalt transporter subunit (CbtA)
  ------ inclusion threshold ------
      0.016   15.1   2.5      0.021   14.7   2.5    1.1  1  CbiM      Cobalt uptake substrate-specific transmembrane regi


Domain annotation for each model (and alignments):
>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   5.2   6.7e-07     0.006     117     197 ..       5      84 ..       2      87 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-07
                              CbtA 117 flavvlvPflklPpepPgvgaadtieaRqalylatvalsavalalavflarrlaar.g.wnavlaaavaflvlvava 191
                                        +a++ +P  + P  pPg+g+a    +R + +l  +a  ava a+++ + + +    +  ++++++ava +vl+a +
  gi|320100674|ref|YP_004176266.1|   5 HVALYSIPVTVTPEPPPGIGEAV---SRILSWLYWLAWMAVAGAGVYGVLKTVMGDtEeGRRLILGAVAGAVLLAFL 78 
                                       58999*****************9...9*999999888777766666666666656667799************9999 PP

                              CbtA 192 llalPh 197
                                       ++++  
  gi|320100674|ref|YP_004176266.1|  79 WVIISA 84 
                                       998765 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 ?   14.7   2.5   2.4e-06     0.021       6      56 ..      30      80 ..      27      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-06
                              CbiM  6 iLspavllaayavalallalalrrlrkeldearvpllallaafifaaqmin 56
                                      iLs+  +la++ava+a+++ +l+ +  +++e r   l+++a ++++a+++ 
  gi|320100674|ref|YP_004176266.1| 30 ILSWLYWLAWMAVAGAGVYGVLKTVMGDTEEGRRLILGAVAGAVLLAFLWV 80
                                      89999***********************88777555555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 664.72
//
Query:       gi|320100675|ref|YP_004176267.1|  [L=594]
Description: putative TrbE protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-11   44.4   0.0    1.1e-06   27.9   0.0    2.1  2  AAA_10         AAA-like domain
      4e-08   33.6   0.0    7.2e-08   32.8   0.0    1.4  1  DUF87          Helicase HerA, central domain
    2.1e-05   23.6   0.0      0.031   13.2   0.0    2.1  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00077   18.5   0.0     0.0014   17.7   0.0    1.3  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
    0.00088   18.8   0.0     0.0013   18.2   0.0    1.2  1  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
      0.001   19.3   0.0       0.44   10.8   0.0    2.9  3  AAA_22         AAA domain
     0.0039   16.6   0.0     0.0092   15.4   0.0    1.6  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
  ------ inclusion threshold ------
       0.03   14.7   0.1       0.18   12.2   0.0    2.3  2  AAA_16         AAA ATPase domain
      0.043   14.3   0.0      0.087   13.3   0.0    1.4  1  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   7.1e-06     0.014      21      98 ..     286     358 ..     282     379 .. 0.76
   2 !   27.9   0.0   5.3e-10   1.1e-06     237     289 ..     466     518 ..     441     542 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.1e-06
                            AAA_10  21 asasliiGdlGnGKSvlakllvlyisllggkali..iDpkkerekfketlpeiakkinvvtLdseeenegvLdPlvl 95 
                                       +++ +i+G  G+GKS+ +k+    ++ +++++ +  +Dp  e  +    l +       v++ +++e    LdP++l
  gi|320100675|ref|YP_004176267.1| 286 NLNFVILGVSGAGKSMAVKVFLKRLREMDKRITYvgVDPESEYTRIAGLLGA-----SPVEIVEGQEL--GLDPVRL 355
                                       77889************************99988335898885554444433.....55667644444..6788777 PP

                            AAA_10  96 lke 98 
                                       l+e
  gi|320100675|ref|YP_004176267.1| 356 LSE 358
                                       765 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 5.3e-10
                            AAA_10 237 dkkefkvvifDEawiftssaeGkkllkelvRiGRsynaavylvtqsadDvlke 289
                                       +++   v ++DEaw f +++    ll+++ R GR++  a + vtq a+D+   
  gi|320100675|ref|YP_004176267.1| 466 SRTRRSVFFIDEAWLFLETPSIMGLLENIARRGRKHGSAFIYVTQRAEDLART 518
                                       67788999*****************************************9765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   3.6e-11   7.2e-08       8     105 ..     271     363 ..     263     410 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.6e-11
                             DUF87   8 sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkalekllsekvkvitpsp 83 
                                       s+s+ pv ldl +  +  + ilg +G+GKS  v+v l++l e +k++t + +Dp +EY ++   l+++ v++++ + 
  gi|320100675|ref|YP_004176267.1| 271 SASGSPVVLDLWSKPNLNFVILGVSGAGKSMAVKVFLKRLREmDKRITYVGVDPESEYTRIAGLLGASPVEIVEGQ- 346
                                       78999******777799*************************99******************88888888888886. PP

                             DUF87  84 sakdkelkinpwsldpeelldl 105
                                            el ++p +l  e +l+l
  gi|320100675|ref|YP_004176267.1| 347 -----ELGLDPVRLLSEGVLEL 363
                                       .....88888888777766665 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 !    8.3   0.0   0.00049      0.98      15      55 ..     286     328 ..     278     331 .. 0.80
   2 !   13.2   0.0   1.6e-05     0.031     217     311 ..     446     538 ..     439     549 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00049
                     TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdra..ivlDltGaf 55 
                                       +  ++i+G  G+GK+ a++ +l+ +r+  +r+  + +D++ ++
  gi|320100675|ref|YP_004176267.1| 286 NLNFVILGVSGAGKSMAVKVFLKRLREMDKRItyVGVDPESEY 328
                                       56799**********************9998622445666665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.6e-05
                     TrwB_AAD_bind 217 allrpllsawldl.aikallslpesrerrlWfflDE...lpaLgrlee.lksllaegRkfGgavvlglqsiaqlrev 288
                                       + l++l+s+++++ a ++ll    sr rr  ff+DE   + + + ++  l++++ +gRk+G a++   q  + l  +
  gi|320100675|ref|YP_004176267.1| 446 KRLKALISSLISVyAYNKLL----SRTRRSVFFIDEawlFLETPSIMGlLENIARRGRKHGSAFIYVTQRAEDLART 518
                                       55677777777763455555....578999999999444233344443256777889*****************986 PP

                     TrwB_AAD_bind 289 YGedaaqsilslvntklilrvsd 311
                                           + +sil+  +t lilr ++
  gi|320100675|ref|YP_004176267.1| 519 ---PQGRSILEQSATALILRQEP 538
                                       ...5779************9775 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.9e-07    0.0014      34      72 ..     291     329 ..     286     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.9e-07
                                       EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------- CS
                              MeaB  34 ltGvPGaGkstlvealglelrrrGkrvavlavDPsspft 72 
                                       + Gv GaGks +v+ +  +lr+  kr++ + vDP s++t
  gi|320100675|ref|YP_004176267.1| 291 ILGVSGAGKSMAVKVFLKRLREMDKRITYVGVDPESEYT 329
                                       679*********************************998 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   6.6e-07    0.0013       3      45 ..     289     331 ..     287     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.6e-07
                         Fer4_NifH   3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrl 45 
                                       + i G  G Gks++++  ++ l em k++  vG DP ++ tr+
  gi|320100675|ref|YP_004176267.1| 289 FVILGVSGAGKSMAVKVFLKRLREMDKRITYVGVDPESEYTRI 331
                                       578999***********************************97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3   2.5e+03      44      70 ..     191     220 ..     169     264 .. 0.76
   2 !   10.8   0.0   0.00022      0.44       8      49 ..     289     326 ..     284     345 .. 0.76
   3 ?    4.9   0.0     0.015        30      82     130 ..     461     510 ..     403     516 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                            AAA_22  44 fvtlpsst...sskdllrellralglelka 70 
                                       +vt+ps+    +s+ +l++ll+ +gle++a
  gi|320100675|ref|YP_004176267.1| 191 TVTAPSLRgleESAGVLKNLLKSYGLEADA 220
                                       788888887888999999999999999888 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00022
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49 
                                        v+ G sG+GK++ ++ +l++l e      +r ++v v++ s
  gi|320100675|ref|YP_004176267.1| 289 FVILGVSGAGKSMAVKVFLKRLREMD----KRITYVGVDPES 326
                                       5899*****************95432....344444555544 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.015
                            AAA_22  82 leqalraravielliiDEaqh.lr..s.eealeeLrsllnlsrkgvqliLvGt 130
                                        ++ l+++++ +++ iDEa   l   s + +le++ ++    ++g ++i+v +
  gi|320100675|ref|YP_004176267.1| 461 YNKLLSRTRR-SVFFIDEAWLfLEtpSiMGLLENIARRGR--KHGSAFIYVTQ 510
                                       3445555555.********995546438999999998888..88888888765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.6e-06    0.0092      21      60 ..     267     307 ..     259     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-06
                                       EEEEETTS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE  21 algkeisgnplvldlkkma.shllvaGatgsGKStalntLi 60 
                                        lg+  sg+p+vldl + +  + +++G +g GKS a+++++
  gi|320100675|ref|YP_004176267.1| 267 FLGVSASGSPVVLDLWSKPnLNFVILGVSGAGKSMAVKVFL 307
                                       5778889************889***************9987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.8e-05      0.18      25     107 ..     287     390 ..     278     485 .. 0.63
   2 ?   -1.4   0.0       1.3   2.7e+03      48     106 ..     498     549 ..     487     582 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.8e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekl 101
                                        + ++ G sG GKs  v+ +l++l++ +   ++   d      +y  +a +l + + ++ ++ +  +  l++ r   
  gi|320100675|ref|YP_004176267.1| 287 LNFVILGVSGAGKSMAVKVFLKRLREMDKRITYVGVDPE---SEYTRIAGLLGA-SPVEIVEGQ--ELGLDPVRLLS 357
                                       5788********************998533333333333...345556666644.666666655..22344444444 PP

                            AAA_16 102 eeala...........................a 107
                                       e++l+                            
  gi|320100675|ref|YP_004176267.1| 358 EGVLElgqvadlladlyavpprlhgalrrelfV 390
                                       444444433334443333333333333344442 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                            AAA_16  48 lekdggif..lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala 106
                                        +k+g  f  +++++++l         a++   +++l+q ++++  ++ ++ r++ +++++
  gi|320100675|ref|YP_004176267.1| 498 GRKHGSAFiyVTQRAEDL---------ARTPQGRSILEQSATALILRQEPEGRDTVKAVYR 549
                                       444444442344444444.........6777777888888888777777777777776666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.4e-05     0.087      13      49 ..     288     324 ..     279     339 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdl 49 
                                         +i+G +GaGKS  +k++++ l+    +i++ g d 
  gi|320100675|ref|YP_004176267.1| 288 NFVILGVSGAGKSMAVKVFLKRLREMDKRITYVGVDP 324
                                       678******************9999888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4170.74
//
Query:       gi|320100676|ref|YP_004176268.1|  [L=84]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 662.26
//
Query:       gi|320100677|ref|YP_004176269.1|  [L=301]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00015   22.2   0.6    0.00015   22.2   0.6    2.7  3  FtsX       FtsX-like permease family
    0.00046   19.7   0.0     0.0011   18.5   0.0    1.5  1  Trimer_CC  Trimerisation motif


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.2     0.053   4.8e+02      25      47 ..      29      48 ..      26     147 .. 0.68
   2 ?   -3.1   0.1       1.3   1.1e+04      73      76 ..     188     191 ..     170     205 .. 0.50
   3 !   22.2   0.6   1.6e-08   0.00015       2      85 ..     209     286 ..     208     297 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.053
                              FtsX 25 illitlvalviGlglgllaaqll 47
                                      ++li +v+++i+l++   a++ +
  gi|320100677|ref|YP_004176269.1| 29 AWLILAVSTPIALAV---ALETV 48
                                      689999999999666...22223 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                              FtsX  73 ivll 76 
                                       +vl+
  gi|320100677|ref|YP_004176269.1| 188 LVLA 191
                                       1111 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 1.6e-08
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                        e+  lra G++++++ l  lt ++ ++l+a+v G+  g+laa ++ + ++s       +i+i++ ++ + +++   
  gi|320100677|ref|YP_004176269.1| 209 EEYRALRATGVSSASLTLACLTSLFSLSLPAAVTGVSMGVLAAHASLTAMGSL------SIYIPYRPLGTQAAVTPY 279
                                       58999****************************************88887655......444444444444444444 PP

                              FtsX  79 lallagl 85 
                                       l+++a+l
  gi|320100677|ref|YP_004176269.1| 280 LVTVASL 286
                                       4444433 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-07    0.0011      10      34 ..     194     217 ..     192     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-07
                                       XXXXXXXXXXX--HHHHHHHHHHHH CS
                         Trimer_CC  10 peasgtpssdavSRLEEelrkLqat 34 
                                       p as + s +++SRLEEe r L+at
  gi|320100677|ref|YP_004176269.1| 194 PVAS-VASYNVLSRLEEEYRALRAT 217
                                       6666.8999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.38
# Mc/sec: 2381.59
//
Query:       gi|320100678|ref|YP_004176270.1|  [L=353]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2610.30
//
Query:       gi|320100679|ref|YP_004176271.1|  [L=500]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3541.04
//
Query:       gi|320100680|ref|YP_004176272.1|  [L=220]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-29  100.9   0.0    9.7e-29  100.6   0.0    1.1  1  ABC_tran  ABC transporter
    2.8e-06   26.3   0.0      0.025   13.3   0.0    2.1  2  AAA_13    AAA domain
    1.2e-05   25.3   0.0      0.072   12.9   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0013   18.3   0.0       0.52    9.7   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
     0.0018   18.5   0.0     0.0036   17.5   0.0    1.5  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.019   14.7   0.0       0.04   13.6   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
      0.028   14.3   0.0       0.11   12.4   0.0    1.8  2  NACHT     NACHT domain
      0.072   13.4   0.4       0.54   10.5   0.4    2.1  1  AAA_22    AAA domain
      0.077   10.5   0.5        0.1   10.1   0.5    1.0  1  DUF3584   Protein of unknown function (DUF3584)
       0.11   11.6   0.1       0.57    9.3   0.0    2.0  2  NB-ARC    NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   5.4e-32   9.7e-29       1     136 [.      19     167 ..      19     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 5.4e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ v+l+++ege v + G+nG+GK+tL+++ + ++kp++G+++l g+d          +     ig++ q+ +l p 
  gi|320100680|ref|YP_004176272.1|  19 LSGVNLEVEEGEAVTVKGRNGSGKTTLCRIASLMEKPDAGSVRLHGRDAGFsseaSMARLRLLYIGYVDQQYTLIPW 95 
                                       6789*******************************************998876644445555689************ PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ltv +n             e++++++++l+ l+lk+   +      + LS Gq+qrva+aral+kkp+ll++DEp+
  gi|320100680|ref|YP_004176272.1|  96 LTVWRNielplvilgwgreERRRRVAELLDALELKGRGGDYP----YRLSAGQRQRVAIARALAKKPRLLVMDEPF 167
                                       ****************99888888999999999999666665....*****************************7 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.4e-05     0.025      23      41 ..      36      54 ..      33     127 .. 0.89
   2 !   11.4   0.0     5e-05     0.089     525     559 ..     156     191 ..     145     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                            AAA_13 23 GwNGaGKTtLSrllrslel 41
                                      G+NG+GKTtL+r+ + +e+
  gi|320100680|ref|YP_004176272.1| 36 GRNGSGKTTLCRIASLMEK 54
                                      9***********9877754 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5e-05
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrll.kkk 559
                                       +k +  v+D P SSLD+ s+ +v+ l+k++++ +k+
  gi|320100680|ref|YP_004176272.1| 156 KKPRLLVMDEPFSSLDDHSSGLVVDLLKNYVAaEKA 191
                                       58999************************9954554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0     4e-05     0.072       4      24 ..      34      54 ..      32      84 .. 0.74
   2 !   11.0   0.0   0.00015      0.27     225     296 ..     128     197 ..      65     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                            AAA_21  4 liGpNgsGKSnLLdaldllar 24
                                      + G+NgsGK++L ++ +l+  
  gi|320100680|ref|YP_004176272.1| 34 VKGRNGSGKTTLCRIASLMEK 54
                                      56*************999844 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                            AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltT 296
                                       e ++++   ++ lS G+++  a++ al+   kk++ll+ DEp ++L+ +    +++ll ++ ++++a +++tT
  gi|320100680|ref|YP_004176272.1| 128 ELKGRGGDYPYRLSAGQRQRVAIARALA---KKPRLLVMDEPFSSLDDHSSGLVVDLLkNYVAAEKASILATT 197
                                       5556666677778888888855555555...555*************99999999999544444788888888 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0     0.002       3.6      26      41 ..      31      46 ..       5      53 .. 0.81
   2 !    9.7   0.0   0.00029      0.52     122     187 ..     119     186 ..      65     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.002
                                      EEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnll 41
                                         + G+NGSGK+ l+
  gi|320100680|ref|YP_004176272.1| 31 AVTVKGRNGSGKTTLC 46
                                      45689*******9875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00029
                                       HHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 122 evsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks 187
                                        v+ell   +++         LS G+++ va+a  +A    k+  l ++De  + LD++    v++llk+  
  gi|320100680|ref|YP_004176272.1| 119 RVAELLDALELKGRggdypyRLSAGQRQRVAIARALA----KKPRLLVMDEPFSSLDDHSSGLVVDLLKNYV 186
                                       5555555555554455555589******999998876....444599*********************9754 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 !   17.5   0.0     2e-06    0.0036      60      89 ..     154     183 ..     138     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                           SbcCD_C  60 repalrlvfLDEAFsklDeesiatllelle 89 
                                         +++rl+++DE Fs+lD++s+  +++ll+
  gi|320100680|ref|YP_004176272.1| 154 LAKKPRLLVMDEPFSSLDDHSSGLVVDLLK 183
                                       4678*********************99997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05      0.04      14      38 ..      21      45 ..       3      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTl 38
                                      g  +e+++ +a+ + G++GsGK+Tl
  gi|320100680|ref|YP_004176272.1| 21 GVNLEVEEGEAVTVKGRNGSGKTTL 45
                                      4456677555999***********9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.3e-05      0.11       3      28 ..      32      56 ..      30      63 .. 0.81
   2 ?   -0.8   0.0       0.7   1.2e+03      79     129 ..     155     199 ..     136     209 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                      v ++G++GsGKTtL +++a+++ +++
  gi|320100680|ref|YP_004176272.1| 32 VTVKGRNGSGKTTL-CRIASLMEKPD 56
                                      789**********7.78888887765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.7
                                       SCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEEC CS
                             NACHT  79 lperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrp 129
                                        ++  Ll++D   e  + l+ +    v +lL++ + +    +as+l+t++ 
  gi|320100680|ref|YP_004176272.1| 155 AKKPRLLVMD---EPFSSLDDHSSGLVVDLLKNYVAA---EKASILATTTG 199
                                       4455555554...333334442334445555555555...55555555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4    0.0003      0.54       6      26 ..      30      50 ..      25     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                            AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                        ++v G  G+GKTtl+r   
  gi|320100680|ref|YP_004176272.1| 30 EAVTVKGRNGSGKTTLCRIAS 50
                                      567899***********9654 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   5.6e-05       0.1       8      36 ..      20      48 ..      15      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.6e-05
                           DUF3584  8 kGrvaeldldghtnieGtNaaGKTtLlrL 36
                                       G+  e++  + + ++G N++GKTtL r+
  gi|320100680|ref|YP_004176272.1| 20 SGVNLEVEEGEAVTVKGRNGSGKTTLCRI 48
                                      566668888899**************996 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00032      0.57      19      38 ..      30      47 ..      19      64 .. 0.85
   2 ?   -0.3   0.0      0.28     5e+02      92     111 ..     146     165 ..     122     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00032
                                      CSEEEEEEESTTSSHHHHHH CS
                            NB-ARC 19 qslvvalvGmgGvGKttlak 38
                                      +   v++ G+ G+GKttl +
  gi|320100680|ref|YP_004176272.1| 30 E--AVTVKGRNGSGKTTLCR 47
                                      4..79*************86 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.28
                                       HHHHHHHHCCCTTEEEEEEE CS
                            NB-ARC  92 lkrklvrlLltkrfllvlDD 111
                                           + r+L +k  llv+D 
  gi|320100680|ref|YP_004176272.1| 146 QRVAIARALAKKPRLLVMDE 165
                                       456899******99999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1607.88
//
Query:       gi|320100681|ref|YP_004176273.1|  [L=140]
Description: flagellar protein G [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1113.73
//
Query:       gi|320100682|ref|YP_004176274.1|  [L=419]
Description: type II secretion system protein E [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-34  119.8   0.0    1.6e-34  119.2   0.0    1.1  1  T2SSE            Type II/IV secretion system protein
    0.00019   21.0   0.0    0.00055   19.6   0.0    1.7  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00032   21.1   0.0    0.00057   20.3   0.0    1.4  1  AAA_16           AAA ATPase domain
    0.00056   20.4   0.0    0.00096   19.7   0.0    1.4  1  ABC_tran         ABC transporter
     0.0015   18.8   0.0     0.0046   17.2   0.0    1.8  1  AAA_22           AAA domain
     0.0046   16.7   0.0     0.0095   15.7   0.0    1.5  1  AAA_30           AAA domain
     0.0064   16.1   0.0      0.019   14.6   0.0    1.7  2  AAA_25           AAA domain
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.019   14.9   0.0    1.4  1  NACHT            NACHT domain
      0.012   16.0   0.0      0.028   14.8   0.0    1.8  1  AAA              ATPase family associated with various cellul
      0.012   15.9   0.0      0.034   14.5   0.0    1.7  2  AAA_19           AAA domain
      0.015   14.7   0.0      0.032   13.6   0.0    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.017   14.9   0.0      0.036   13.8   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.019   14.5   0.0      0.032   13.8   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
      0.021   14.8   0.0      0.052   13.6   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
      0.036   13.9   0.0      0.046   13.5   0.0    1.2  1  AAA_11           AAA domain
      0.039   13.7   0.0      0.062   13.0   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.043   14.0   0.0      0.073   13.2   0.0    1.5  1  AAA_33           AAA domain
      0.043   14.4   0.0      0.084   13.4   0.0    1.5  1  AAA_18           AAA domain
       0.06   13.1   0.0      0.093   12.4   0.0    1.2  1  AAA_24           AAA domain
      0.062   13.2   0.0       0.13   12.2   0.0    1.5  1  NTPase_1         NTPase
      0.086   13.3   0.0       0.13   12.8   0.0    1.2  1  AAA_23           AAA domain
      0.093   12.0   0.0       0.16   11.2   0.0    1.3  1  Zeta_toxin       Zeta toxin
       0.11   11.7   0.0       0.19   10.9   0.0    1.3  1  NB-ARC           NB-ARC 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 !  119.2   0.0     2e-37   1.6e-34       5     245 ..      90     343 ..      87     361 .. 0.87

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 2e-37
                             T2SSE   5 leallddekvsdihvekpervkvrervdg......ielreveelekaalerlisriaalakldiseerplqdarlp. 74 
                                       l+ lldd+ v di v  p+ ++vr r+            +++  + ++++ l + ia   +  +s +rp++da+lp 
  gi|320100682|ref|YP_004176274.1|  90 LQVLLDDPFVEDISVTGPGPIWVRHRLAAsdprvdFIETNLKVGSLEEVAELQQLIALKCGTYVSASRPIVDAQLPl 166
                                       6889*********************9987444433333445555668899999************************ PP

                             T2SSE  75 .ekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyal 149
                                        ++g+r+++v + ++ + +++++Rkk  +  ++  l+ e+ l + +ae  r  v++ ++++++G+ gsGKttll ++
  gi|320100682|ref|YP_004176274.1| 167 eDGGHRVHIVSALTAPHrPEIAVRKKPRSPPSMTRLIEEGVLPASVAEYFRMLVEKGMSLIIAGPPGSGKTTLLRSI 243
                                       9999****99988888889*****9999999*******************************************777 PP

                             T2SSE 150 lkeinksderivtvEDpvEiqleganqvqlnak....kakvtfadllraaLRlrPDr.imvGEiRdketleilkAvn 221
                                       l      + +iv++ED+ E+++    + +  ++    ++kv++ dl +aaLR    r i+vGE R++e+  +++A+ 
  gi|320100682|ref|YP_004176274.1| 244 LYSYIPLNWKIVIIEDTGEVDPPMGSAWARYTSaelgAVKVDLFDLAKAALRSSATRlIVVGETRGAEARVLVQAML 320
                                       76555555*************96655555555557889**************998764889**************** PP

                             T2SSE 222 TGHlgslsTlHansaagalerLeq 245
                                       +G  g l+T H +s+ +++ rL  
  gi|320100682|ref|YP_004176274.1| 321 SGMGG-LTTFHGGSPEEVVARLTS 343
                                       **766.***************986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     7e-07   0.00055       3      39 ..     226     263 ..     224     265 .. 0.75
   2 ?    0.8   0.0      0.42   3.3e+02      84     100 ..     253     269 ..     250     299 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7e-07
                                       EEEEESTTCCHHHHHHHHHCT--SS-EE.EEESS-SSC CS
                              cobW   3 tvltGflGsGKTtLlnhllenraglkla.vivNefgev 39 
                                       ++++G++GsGKTtLl+++l     l++  vi+ + gev
  gi|320100682|ref|YP_004176274.1| 226 LIIAGPPGSGKTTLLRSILYSYIPLNWKiVIIEDTGEV 263
                                       699****************6555555542566777765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.42
                                       SEEEEEECTTTTHHHHH CS
                              cobW  84 dviliEttGlaePapva 100
                                        +++iE tG ++P +  
  gi|320100682|ref|YP_004176274.1| 253 KIVIIEDTGEVDPPMGS 269
                                       679******99987762 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   7.3e-07   0.00057      13      76 ..     213     275 ..     210     328 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.3e-07
                            AAA_16  13 lsalervrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipy.salaqal 76 
                                       +++++++ + +  ++++ G++G+GK++l+r++l ++     +++ ++ + +      p+ sa+a++ 
  gi|320100682|ref|YP_004176274.1| 213 AEYFRMLVEKG-MSLIIAGPPGSGKTTLLRSILYSYIPLnwKIVIIEDTGEVD---PPMgSAWARYT 275
                                       56677666665.7999****************976665522333366666666...56633355555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.2e-06   0.00096       8      42 ..     220     254 ..     215     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-06
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGei 42 
                                       +++g  + i G+ G+GK+tLl+ ++  + p + +i
  gi|320100682|ref|YP_004176274.1| 220 VEKGMSLIIAGPPGSGKTTLLRSILYSYIPLNWKI 254
                                       789999*******************9999966555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.9e-06    0.0046       5      29 ..     223     247 ..     219     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.9e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleql 29 
                                         +l++ G++G+GKTtllr +l+++
  gi|320100682|ref|YP_004176274.1| 223 GMSLIIAGPPGSGKTTLLRSILYSY 247
                                       6689***************999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05    0.0095      12      63 ..     218     268 ..     213     319 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                            AAA_30  12 alltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa 63 
                                        l+++g +  ++ Gp+G+GKtt+l+++   +   + +++++  tg++   ++
  gi|320100682|ref|YP_004176274.1| 218 MLVEKG-MSLIIAGPPGSGKTTLLRSILYSYIPLNWKIVIIEDTGEVDPPMG 268
                                       444455.5889**************998877777777777766666655555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.4e-05     0.019      19      57 ..     209     247 ..     192     260 .. 0.83
   2 ?   -3.4   0.0       7.9   6.1e+03      73      97 ..     299     323 ..     293     340 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                            AAA_25  19 ppprrwlvkgllpagelallaGapgtGKttlaldlalav 57 
                                       p+++  +++ l+ +g   ++aG+pg+GKttl+ ++ +++
  gi|320100682|ref|YP_004176274.1| 209 PASVAEYFRMLVEKGMSLIIAGPPGSGKTTLLRSILYSY 247
                                       56666777788999999**************98887765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.9
                            AAA_25  73 kVlyvsaEdsedelrrRlravgeal 97 
                                       + l+v++E + +e r  ++a++  +
  gi|320100682|ref|YP_004176274.1| 299 TRLIVVGETRGAEARVLVQAMLSGM 323
                                       5678888888888777777777666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.4e-05     0.019       3      21 ..     226     244 ..     224     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                                       EEEEC-TTTCHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                       +i+ G++GsGKTtLl+++ 
  gi|320100682|ref|YP_004176274.1| 226 LIIAGPPGSGKTTLLRSIL 244
                                       699*************996 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.6e-05     0.028       2      21 ..     227     246 ..     226     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-05
                                       EEESSTTSSHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavake 21 
                                       ++ GppG GKT+l +++  +
  gi|320100682|ref|YP_004176274.1| 227 IIAGPPGSGKTTLLRSILYS 246
                                       789*************9877 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.3e-05     0.034      10      35 ..     222     248 ..     215     271 .. 0.79
   2 ?   -2.4   0.0       7.1   5.5e+03     124     137 ..     292     306 ..     277     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-05
                            AAA_19  10 ekvllvtaG.pGtGKTrvlkhivallv 35 
                                       +++ l++aG pG+GKT++l+ i+  ++
  gi|320100682|ref|YP_004176274.1| 222 KGMSLIIAGpPGSGKTTLLRSILYSYI 248
                                       55666665527*********9987776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.1
                            AAA_19 124 allgek.kklllvGD 137
                                       a l ++ ++l++vG 
  gi|320100682|ref|YP_004176274.1| 292 AALRSSaTRLIVVGE 306
                                       444333355555553 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.1e-05     0.032      42      64 ..     226     248 ..     209     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                                       EEEE--TTSSHHHHHHHHHHHHH CS
                      FtsK_SpoIIIE  42 llvaGatgsGKStalntLilSla 64 
                                       l++aG +gsGK+t l++++ S +
  gi|320100682|ref|YP_004176274.1| 226 LIIAGPPGSGKTTLLRSILYSYI 248
                                       89****************99966 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.7e-05     0.036      22      43 ..     222     244 ..     214     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                            AAA_29  22 kg.atlltGpsGsGKSTllDAiq 43 
                                       kg + +++Gp GsGK+Tll +i 
  gi|320100682|ref|YP_004176274.1| 222 KGmSLIIAGPPGSGKTTLLRSIL 244
                                       67678899**********96665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.1e-05     0.032      25      66 ..     215     256 ..     208     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekylslt 66 
                                        +++l+++++++++ Gp G+GKt++++++l ++ + ++++++
  gi|320100682|ref|YP_004176274.1| 215 YFRMLVEKGMSLIIAGPPGSGKTTLLRSILYSYIPLNWKIVI 256
                                       5789************************88776666666655 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   6.6e-05     0.052       2      29 ..     226     256 ..     225     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-05
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEE CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nrevey 29 
                                       +++ GppG+gK++l ++++  +   n+++++
  gi|320100682|ref|YP_004176274.1| 226 LIIAGPPGSGKTTLLRSILYSYiplNWKIVI 256
                                       899**************99988866666554 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.9e-05     0.046      11      42 ..     217     248 ..     208     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-05
                            AAA_11  11 ksalseseitliqGPPGtgKTktivellsqll 42 
                                       +  +++    +i GPPG+gKT+ + ++l + +
  gi|320100682|ref|YP_004176274.1| 217 RMLVEKGMSLIIAGPPGSGKTTLLRSILYSYI 248
                                       5666677777899**********999987765 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 ?   13.0   0.0   7.9e-05     0.062       2      21 ..     227     246 ..     226     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrt 21 
                                       +++G pG+GK+tl+r++l +
  gi|320100682|ref|YP_004176274.1| 227 IIAGPPGSGKTTLLRSILYS 246
                                       899*************9966 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   9.3e-05     0.073       3      20 ..     227     244 ..     226     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.3e-05
                            AAA_33   3 llvGlpGsGKstlaerll 20 
                                       ++ G+pGsGK+tl++++l
  gi|320100682|ref|YP_004176274.1| 227 IIAGPPGSGKTTLLRSIL 244
                                       789***********9876 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     0.084       2      17 ..     227     242 ..     226     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            AAA_18   2 lltGtpGvGKttlake 17 
                                       +++G+pG+GKttl + 
  gi|320100682|ref|YP_004176274.1| 227 IIAGPPGSGKTTLLRS 242
                                       79***********886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.093       2      22 ..     223     243 ..     222     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_24   2 klkiliyGpsgiGKTtlakel 22 
                                       +++++i Gp+g+GKTtl++++
  gi|320100682|ref|YP_004176274.1| 223 GMSLIIAGPPGSGKTTLLRSI 243
                                       67899************9987 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.13       2      20 ..     226     244 ..     225     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                       EEEE--TTSSHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvl 20 
                                       ++i GppG+GKtTl++ +l
  gi|320100682|ref|YP_004176274.1| 226 LIIAGPPGSGKTTLLRSIL 244
                                       79*************9886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00016      0.13      23      41 ..     227     245 ..     216     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                            AAA_23  23 lItGpNGaGKTTildAikl 41 
                                       +I Gp G+GKTT+l+ i +
  gi|320100682|ref|YP_004176274.1| 227 IIAGPPGSGKTTLLRSILY 245
                                       789************9987 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    0.0002      0.16      17      40 ..     224     247 ..     214     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                        Zeta_toxin  17 klillgGqpGAGKselaellkdel 40 
                                        +++++G pG+GK++l++ +  + 
  gi|320100682|ref|YP_004176274.1| 224 MSLIIAGPPGSGKTTLLRSILYSY 247
                                       5789*************9887665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00024      0.19      21      43 ..     224     246 ..     211     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                       EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnk 43 
                                       + + + G +G+GKttl+++il +
  gi|320100682|ref|YP_004176274.1| 224 MSLIIAGPPGSGKTTLLRSILYS 246
                                       347899*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3240.36
//
Query:       gi|320100683|ref|YP_004176275.1|  [L=473]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3441.86
//
Query:       gi|320100684|ref|YP_004176276.1|  [L=121]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 863.83
//
Query:       gi|320100685|ref|YP_004176277.1|  [L=250]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1721.78
//
Query:       gi|320100686|ref|YP_004176278.1|  [L=548]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 4134.08
//
Query:       gi|320100687|ref|YP_004176279.1|  [L=89]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.8   0.5       0.02   15.1   0.5    1.4  1  DUF5388   Family of unknown function (DUF5388)
       0.14   12.9   0.1        0.2   12.4   0.1    1.3  1  GST_N_4   Glutathione S-transferase N-terminal domain


Domain annotation for each model (and alignments):
>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.5   2.2e-06      0.02      41      67 ..      31      59 ..      25      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-06
                           DUF5388 41 lveslids..LsesdkkrfkkqleiLEek 67
                                      +ves +ds  Lse+dk+r+k +leiLEek
  gi|320100687|ref|YP_004176279.1| 31 VVESRVDSsdLSEEDKARLKAILEILEEK 59
                                      6777777545*****************98 PP

>> GST_N_4  Glutathione S-transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.3e-05       0.2      60      87 ..      34      62 ..      21      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                           GST_N_4 60 vdld.aelseeqkadaralkalveeklyn 87
                                        +d ++lsee+ka+ +a+   +eek++n
  gi|320100687|ref|YP_004176279.1| 34 SRVDsSDLSEEDKARLKAILEILEEKVFN 62
                                      345679********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 644.14
//
Query:       gi|320100688|ref|YP_004176280.1|  [L=601]
Description: arginine decarboxylase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   72.9   0.0    4.1e-20   72.2   0.0    1.3  1  Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal b
  ------ inclusion threshold ------
      0.026   14.7   0.1         32    4.7   0.0    3.2  3  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos
       0.11   12.9   0.2       0.28   11.6   0.2    1.6  1  ThiD2          ThiD2 family


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 !   72.2   0.0   6.8e-24   4.1e-20      17     247 .]     102     341 ..      85     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 6.8e-24
                                       CCEEEEEGGG---HHHHHHHHHTT....EEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHH...HHHHHHCTHT. CS
                     Orn_Arg_deC_N  17 rikvfYavKansdlavlellaelG....lgldcaSkaElelvlaagvsperiifanpckqree...lryalekgvk. 85 
                                         ++++++K+n+   v+  + + G     g++ +S +Elel  + +++  ri + +++ + +    l+   ekg + 
  gi|320100688|ref|YP_004176280.1| 102 GLQPVFPMKVNPIDIVIDAIWRYGekygWGFNTGSIGELELLSKYAGKGPRILVYDGVLSDNVariLEGFREKGWRv 178
                                       5689*********9999988665555449***************999988887777665544301155556666664 PP

                                       EEEESSHHHHHHHHHHHCCEEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHH..HTTEEEEEEE-- CS
                     Orn_Arg_deC_N  86 vvtvdnveeleklaklapeakvllRiktdvsaatcelistggessKFGaaleeavealleaak..eenlqlvGvsfH 160
                                       vv v++++ l++l+k +pe +v lRik+ ++    ++  ++g + KFG ++++ v+  +e  k  ee   l  +++H
  gi|320100688|ref|YP_004176280.1| 179 VVDVESEHDLDILSK-HPELEVGLRIKPLFK-PGGKWAHSAGLEGKFGLTVNTLVKLREE-YKwiEERARL--LHVH 250
                                       556788888887765.89**********655.5566777777889******655544444.4323566777..9*** PP

                                       -BSSC-SCHHHHHHHHHHHHHHHHHHHHT-.--SEEE--S-BS-HCSTTSSSST...HHHHHHHHHHHHHHHHHTSS CS
                     Orn_Arg_deC_N 161 vGSgvsdleafvkavekalklfdelaelGv.klkiLdvGGGfgveyeeeeeplk...leeiaekirealeeafpgdk 233
                                        GS++   ++  + ++++++++++l+  G+  l+++d GGG++  y ++++ +       ++   ++ l  + + dk
  gi|320100688|ref|YP_004176280.1| 251 AGSQIYKWSDVEAFINEVYNIYVQLTANGFsRLELVDPGGGLAYPYLDTRSGSIespDYTVVDYFNHMLRVFSRLDK 327
                                       ******************************889*************9988755433333455566666655555899 PP

                                       S-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 234 evtiiaEpGRalva 247
                                       ++ ++ E GR++va
  gi|320100688|ref|YP_004176280.1| 328 HPVLVYEGGRYIVA 341
                                       ************98 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 ?    1.9   0.0     0.038   2.3e+02      87     108 ..      81     102 ..      75     107 .. 0.87
   2 ?    3.8   0.1    0.0098        59      29      60 ..     240     272 ..     225     282 .. 0.75
   3 ?    4.7   0.0    0.0053        32      28      86 ..     378     436 ..     358     440 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.038
                                       HHHHHHHHHTT--EEEEEEEEE CS
                       HTH_Tnp_1_2  87 kAieLylkrrgeltdkkkveak 108
                                       kA++L+++ + el   + +++ 
  gi|320100688|ref|YP_004176280.1|  81 KAMRLVYETFTELARIHGFKGG 102
                                       8************999888775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0098
                                       HHHHHHHHTS-H.HHHHHHHH-HHHHHHHHHHH CS
                       HTH_Tnp_1_2  29 ldeiaeevgvsr.sTlykWkkkkeFieyvnela 60 
                                       ++e a+ + v   s +ykW + ++Fi++v ++ 
  gi|320100688|ref|YP_004176280.1| 240 IEERARLLHVHAgSQIYKWSDVEAFINEVYNIY 272
                                       5667777777542779**********9987665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0053
                                       -HHHHHHHHTS-HHHHHHHHH-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHSSS--H CS
                       HTH_Tnp_1_2  28 tldeiaeevgvsrsTlykWkkkkeFieyvnelaeefleeeraevykaLlrkilkgrssv 86 
                                       t++++ + +   r+ +++  + ++++ +  elae+++++ r+ev  +L ++ + + ssv
  gi|320100688|ref|YP_004176280.1| 378 TIRDLKAVLKEYRRLIHRGSQGQQYTLEERELAEDLVSKIREEVVLKLSELLRAEPSSV 436
                                       66666666777788889999999*************************99999887776 PP

>> ThiD2  ThiD2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   4.8e-05      0.28      13      71 ..     365     421 ..     361     440 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                             ThiD2  13 GlRvlediarfvlddeelteelkelRhelaelekeleeaellaaRdtegDvgkelstee 71 
                                       G  v+ed++r v   ++l + lke+R  +++ ++   ++  l++R+ ++D  +++++e 
  gi|320100688|ref|YP_004176280.1| 365 GTSVVEDVLRGVRTIRDLKAVLKEYRRLIHRGSQG--QQYTLEERELAEDLVSKIREEV 421
                                       6679*************************999998..7899*********999987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4161.98
//
Query:       gi|320100689|ref|YP_004176281.1|  [L=527]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-16   59.4   0.0    1.6e-15   57.9   0.0    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 ?   -1.8   0.0       0.2   3.7e+03      95      95 ..     127     127 ..      45     182 .. 0.51
   2 !   57.9   0.0   8.9e-20   1.6e-15       2     164 ..     194     389 ..     193     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.2
                                       H CS
                                       x RF
                       Radical_SAM  95 e 95 
                                       +
  gi|320100689|ref|YP_004176281.1| 127 K 127
                                       2 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 8.9e-20
                                       EEESEESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.............SSTGGGST CS
                                       xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlr....CsfCarpetvrregrgrslsveeileevkelkaekgvkevilg.............ggepllyp 61 
                                       +++rgC++     CsfC+ p    r+gr+ ++ +  i+ee+++l ++ gv+++ lg             g e + +p
  gi|320100689|ref|YP_004176281.1| 194 ETYRGCSRWltggCSFCIEP----RYGRPIMRGLKGIVEEAEAL-YSLGVRHIRLGrqpdilaymsedtGREEFPRP 265
                                       5667776655555*******....69******************.8**********999999998888855555555 PP

                                       THHHHHHHHHHTC.....CCTEEEEEEECSSCHG.....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSH CS
                                       xxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx.....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  62 dfvellerlakla.....vpgiritvetngtlpd.....eeklerllelg..vdrvslgleaaddekvlklmnrght 126
                                       + + l +  + ++        ++i  + +gt ++      + l+++++++   d+ +lg+e++d++ v k +n + +
  gi|320100689|ref|YP_004176281.1| 266 NPEALEKLFHGIRsvapgLVTLHIDNVNPGTIVShvdesVKALKTIVKYHtpGDVAALGIESFDEK-VVKANNLKVG 341
                                       5555555555555669**6666666666666666666669**************************.99999999** PP

                                       HHHHHHHHHHHHHTTSET..........EEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikr..........vvdrivglpGendeeleell 164
                                       +ee lea+++ +++g+ r           v+ i+glpGe++e+++  l
  gi|320100689|ref|YP_004176281.1| 342 PEEALEAIRIVNRVGGLRgwngmphllpGVNLIYGLPGESRETYRVNL 389
                                       ***************8888888888888*************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3866.13
//
Query:       gi|320100690|ref|YP_004176282.1|  [L=390]
Description: hydrogenase expression/formation protein HypD [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.6e-127  425.5   0.0   1.9e-127  425.2   0.0    1.0  1  HypD       Hydrogenase formation hypA family
  ------ inclusion threshold ------
       0.06   13.2   0.2       0.13   12.1   0.2    1.5  1  zf-RING_6  zf-RING of BARD1-type protein


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 !  425.2   0.0  2.2e-131  1.9e-127       5     349 ..      13     367 ..      10     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 425.2 bits;  conditional E-value: 2.2e-131
                                       HHHHHHHHHHHT......SS-EEEEE--HHHHHHHHHTTHHHHS-TTEEEEE-S--TTTTS-HHHHHHHHHHHHH-- CS
                              HypD   5 kllekikkeakk......erelkimevCGghthaivryglrslLpenielisGPGCpVCvtpeeeidkaielaekee 75 
                                       kl+e+i++e+k+       +e++im++CG+h+++i++yglrsl+p+ i+li+GPGCpVC+tp  +id +++++ +++
  gi|320100690|ref|YP_004176282.1|  13 KLAERIREESKRvlsehgGDEIRIMNFCGTHEWTITHYGLRSLMPPWINLIAGPGCPVCITPGYYIDVLVDVSFEKD 89 
                                       66777777776666667789********************************************************* PP

                                       EEEEE-CCHHG---T....T--HHHHHHTT-EEEE-SSHHHHHHHHHH-TTSEEEEEEEE-HHHHHHHHHHHHHHHH CS
                              HypD  76 vilatfgDmlrvpgs....kksLleakaegadvrivyspldalkiakenpdkevvflavGFEttapatalalleakk 148
                                       ++++t+gD++++pgs     +sL++aka g++v++vys+ da++ a+++p ++ vflavGFEtt+p+ta+ l++   
  gi|320100690|ref|YP_004176282.1|  90 TVVLTYGDAFKLPGSrgkqPRSLFHAKAMGGNVKVVYSFRDAITEAAREPGRRHVFLAVGFETTMPSTAIPLAA--G 164
                                       ***************887669*************************************************9988..9 PP

                                       HT-SSEEEEEEEE-HHHHHHHHHHT.T.---SEEEEEHHHHHHHTTHHHHHHHHHH---EEEE-SSHHHHHHHHHHH CS
                              HypD 149 eglknfsvlsshklvppalealles.eelkidgfiapghvstviGlkayeelaeeykvpvvvaGFepldilqailml 224
                                       e + n++vls+ +l+pp++++l+e+ +e+++dg+iapghvstviG++a++++a+ey++pvvv+GFepld+l +i+m+
  gi|320100690|ref|YP_004176282.1| 165 EVPGNLYVLSAYRLTPPIMRFLAEAhPEVRLDGVIAPGHVSTVIGAEAWRFIADEYGIPVVVSGFEPLDVLLSIYMI 241
                                       9*********************986257************************************************* PP

                                       HHHHHTT---EEETTTTT--TT--HHHHHHHHHHEEEEEEEETTTEEEEEEEEEE-GGGGGGBGGGT---.-S---S CS
                              HypD 225 vkqleegeaeveneYkrvvkeegnkkaqklieevfevrdaewRglgvipksglklreeyaefdaekkfel.ekeeek 300
                                       +++l+eg++++ neY+rvv +egnk a +++ ev+e+rd+ wRg+gv+p sg   r++y+ +d  ++  l e+ +++
  gi|320100690|ref|YP_004176282.1| 242 IRNLAEGKPRLMNEYSRVVAPEGNKYALNAMWEVYEARDSYWRGIGVVPLSGAVHRPRYSGHDFFESTGLrETVTDD 318
                                       ********************************************************************997778889 PP

                                       S-TT--HHHHHTTS--GGGSTTBTTTB-SSS-SSHHHHSTT-HHHHHHH CS
                              HypD 301 ekkackcgevlkGkakPedCklFgkaCtpenpvGacmvSsEGaCaayyk 349
                                       ++++c+c++v+ G akP++C+lF+kaCtp np+G+cmvSsEG+C+++ +
  gi|320100690|ref|YP_004176282.1| 319 KHPGCICDKVVLGLAKPTQCPLFMKACTPGNPYGPCMVSSEGTCRIWAE 367
                                       99********************************************986 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.5e-05      0.13      39      58 ..      64      83 ..      58      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                         zf-RING_6 39 fgsgcpvcytpawiqdvkin 58
                                       g gcpvc tp +  dv ++
  gi|320100690|ref|YP_004176282.1| 64 AGPGCPVCITPGYYIDVLVD 83
                                      599**********9999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        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 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3051.42
//
Query:       gi|320100691|ref|YP_004176283.1|  [L=207]
Description: molybdenum cofactor cytidylyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-25   88.5   0.0    7.4e-25   88.2   0.0    1.0  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00011   22.0   0.0    0.00018   21.4   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0018   18.2   0.0     0.0037   17.2   0.0    1.5  1  CTP_transf_3     Cytidylyltransferase
  ------ inclusion threshold ------
      0.044   13.4   0.0      0.059   12.9   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.0   1.7e-28   7.4e-25       2     158 ..       5     176 ..       4     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 1.7e-28
                                       EEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHC.........HHHHHHTTCTS-EEE-TTS CS
                      NTP_transf_3   2 viLAGGrSsRmggdKallplggkpllervldalraag.vdevvvvggde.........evlaalarlgvrvvededp 68 
                                       ++ A+G S+R+  +K l+ l+ kpl+ ++l++++a++ v++v++v+g+e         e ++   + ++rvv+++d+
  gi|320100691|ref|YP_004176283.1|   5 IVPAAGFSTRFPWNKMLYTLD-KPLVVQTLENISASTyVSRVILVTGHEssrvsrvveEHASSRLKERLRVVYNPDY 80 
                                       677****************97.89999******999769*********85545443322222224558********* PP

                                       S-SHHHHHHHHHHHH.....SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHH CS
                      NTP_transf_3  69 gkgplaslaaalraaa....dadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsal 141
                                        +g+++s++ +l++++    + ++++v ++D +++ p ++++++ ++ +sg++++v++y+g+rghp++f+++l ++l
  gi|320100691|ref|YP_004176283.1|  81 AAGMSSSVRKGLESIRdearSLKGIMVNPGDAAWIHPGVYDYVALRFLESGKKIAVASYRGRRGHPIIFSSDLYAEL 157
                                       ************885433337788***************************************************** PP

                                       HHH.CTHTTHHHCHHHH.H CS
                      NTP_transf_3 142 aal.lgdqgarrllrrl.d 158
                                        a+ ++ qg+++++rr+ d
  gi|320100691|ref|YP_004176283.1| 158 TAIdEETQGLKAVVRRHlD 176
                                       ***666799******9954 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   3.9e-08   0.00018       1      93 [.       2     103 ..       2     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.9e-08
                                       EEEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.......CCEEE CS
                              IspD   1 vvvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.......ksiql 70 
                                       ++ ++pAAG+ +R     +K++++l+ ++l+ +t++ + as+ v+++++v  ++  ++++ +  +       +++ +
  gi|320100691|ref|YP_004176283.1|   2 IACIVPAAGFSTRFP--WNKMLYTLD-KPLVVQTLENISASTYVSRVILVTGHES-SRVSRVVEEhassrlkERLRV 74 
                                       5789*********86..699999986.8********************9998877.555555444477777766778 PP

                                       EE--SS...HHHHHHHHHHTTSSTT...S CS
                              IspD  71 vaGGde...RaesVlnglkalegea...k 93 
                                       v   d     + sV +gl+ +++ea   k
  gi|320100691|ref|YP_004176283.1|  75 VYNPDYaagMSSSVRKGLESIRDEArslK 103
                                       87665411156788888888888875444 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.3e-07    0.0037       1      51 [.       3      53 ..       3      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.3e-07
                                      EEEEEE-SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HH CS
                      CTP_transf_3  1 iaIipARsgSkRlpgKnlldlggkpliayvleaalkskafekvivaTDsee 51
                                      ++I+pA   S+R+p   +l  ++kpl+  +le++  s  +++vi+ T +e+
  gi|320100691|ref|YP_004176283.1|  3 ACIVPAAGFSTRFPWNKMLYTLDKPLVVQTLENISASTYVSRVILVTGHES 53
                                      79************87788888*************************9886 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05     0.059      22     117 ..      18     116 ..      13     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                       GGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--...BGGHHHHHTHH CS
                   NTP_transferase  22 kklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegk...gtAdAvalaae 95 
                                        k++  l+k +l+ +tl+++++s + + ++ +t ++s +v + ++e +  ++++   +  +++   g+  +v++++e
  gi|320100691|ref|YP_004176283.1|  18 NKMLYTLDK-PLVVQTLENISASTYVSRVILVTGHESSRVSRVVEEHASSRLKERLRVVYNPDyaaGMSSSVRKGLE 93 
                                       588999999.************9999989999999999******9999999888888888888889*********** PP

                                       HHTTSSE...EEEEETTEEEEST CS
                   NTP_transferase  96 lledeks.delvlvLggDhlikd 117
                                        ++de++  + ++v +gD    +
  gi|320100691|ref|YP_004176283.1|  94 SIRDEARsLKGIMVNPGDAAWIH 116
                                       *****998888999999976544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1726.68
//
Query:       gi|320100692|ref|YP_004176284.1|  [L=217]
Description: putative phosphate transport regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  104.5   4.0    5.8e-30  104.2   4.0    1.0  1  PhoU_div      Protein of unknown function DUF47
    9.9e-05   22.7   5.1    0.00074   19.9   1.8    2.3  2  PhoU          PhoU domain
  ------ inclusion threshold ------
      0.014   15.2   0.1      0.029   14.2   0.1    1.8  1  DrrA_P4M      DrrA phosphatidylinositol 4-phosphate binding d
      0.027   14.9   0.2          8    7.0   0.0    3.3  2  NPV_P10       Nucleopolyhedrovirus P10 protein
       0.03   14.8   1.4       0.86   10.1   0.0    2.6  3  ZapB          Cell division protein ZapB
      0.064   12.6   0.0      0.074   12.3   0.0    1.2  1  Amidohydro_1  Amidohydrolase family
      0.077   13.3   0.1         14    6.1   0.0    2.6  2  DUF2999       Protein of unknown function (DUF2999)
       0.12   12.3   0.1       0.49   10.3   0.0    2.2  2  OST-HTH       OST-HTH/LOTUS domain
        0.2   12.1   5.1         36    4.8   0.4    4.3  5  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 !  104.2   4.0   2.9e-33   5.8e-30       7     210 ..      10     212 ..       6     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 2.9e-33
                          PhoU_div   7 sspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedllel 83 
                                       +s + s+++h++ v   v kl el +++  g+ e v+ l  e   +E+++De+kr i  +l+   + P dRe+ll++
  gi|320100692|ref|YP_004176284.1|  10 ESMFSSIREHARTVEIGVSKLSELVSSIQ-GGVETVSRLYGELNRVEEHGDELKRSIMEELKATYLHPDDRENLLRF 85 
                                       5789999*****************99875.688******************************************** PP

                          PhoU_div  84 veslDeildvlediamlvtlrkve...fpeelkdeflallkktveaiealaevieeleklletalskkdiveeiesl 157
                                       v slD++l +++++++++ +  ++   ++e+++  + ++ +k++ a +++ e +e+++++ + als   i +e+e+l
  gi|320100692|ref|YP_004176284.1|  86 VLSLDDALGYAKSAGKRILIAVESgivIDEKIQALMKEMTEKSLTASRKIIELFESMSRDPARALS---ISHEVEEL 159
                                       ***************9998765433349**************************************...9******* PP

                          PhoU_div 158 EdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisi 210
                                       E++iD+l+ + i + +s  +++   e l+l +i++ +e +sd +ed+ad  ++
  gi|320100692|ref|YP_004176284.1| 160 EEKIDELRLEAIAMIYSACSREVKPECLVLPQIVDDIEGISDVFEDIADIYRL 212
                                       ************************************************97665 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.033        65      25      71 ..      42      92 ..      16     108 .. 0.64
   2 !   19.9   1.8   3.7e-07   0.00074       2      88 ..     122     209 ..     119     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.033
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HH..HGG-SH..HHHHHHHHHHH CS
                              PhoU 25 elarevierddeidrlekeierslleal.ak..rqplae..dlrellsllri 71
                                      e++ +++ + +++++  +e++rs++e+l a+  + p ++   lr++lsl ++
  gi|320100692|ref|YP_004176284.1| 42 ETVSRLYGELNRVEEHGDELKRSIMEELkATylH-PDDRenLLRFVLSLDDA 92
                                      5555555556667777788888888888666742.33333558888776555 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.7e-07
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HH.HGG-SH.HHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeierslleal.ak.rqplae.dlrellsllriardl 75 
                                       ++m e ++++ ++ +e++e+  ++ ar++ +   e+++le++i++  lea+ ++ + + +e +  e l l +i+ d+
  gi|320100692|ref|YP_004176284.1| 122 KEMTEKSLTASRKIIELFESMSRDPARAL-SISHEVEELEEKIDELRLEAIaMIySACSREvK-PECLVLPQIVDDI 196
                                       57888888888999999999998888887.788999999999988888888555433333332.2457899****** PP

                                       HHHHHHHHHHHHH CS
                              PhoU  76 ERigDhavniaer 88 
                                       E i+D  ++ia++
  gi|320100692|ref|YP_004176284.1| 197 EGISDVFEDIADI 209
                                       ***********86 PP

>> 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 ?   14.2   0.1   1.4e-05     0.029      26      61 ..      57      92 ..      15     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                      -HHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHTS CS
                          DrrA_P4M 26 kGDaLKtkILkdfKdkleeistkeeLeklvkefkks 61
                                      +GD LK++I++++K    + +++e+L ++v ++++ 
  gi|320100692|ref|YP_004176284.1| 57 HGDELKRSIMEELKATYLHPDDRENLLRFVLSLDDA 92
                                      7*************************9999988775 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.004         8       7      56 ..      14      63 ..      10      73 .. 0.85
   2 ?    3.3   0.6     0.059   1.2e+02       9      23 ..     152     166 ..     101     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.004
                           NPV_P10  7 lvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56
                                        Ir+  + v+  V+ l++ v ++q  +++v+ l  +L++  +  +el+ 
  gi|320100692|ref|YP_004176284.1| 14 SSIREHARTVEIGVSKLSELVSSIQGGVETVSRLYGELNRVEEHGDELKR 63
                                      679999999999999***************99999999998887777765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.059
                           NPV_P10   9 IradikavddkVdal 23 
                                       I ++++++++k+d l
  gi|320100692|ref|YP_004176284.1| 152 ISHEVEELEEKIDEL 166
                                       344444444444443 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   0.0   0.00043      0.86       6      43 ..      30      67 ..      27      88 .. 0.86
   2 ?   -1.7   0.0       2.1   4.2e+03      60      69 ..     115     124 ..     106     138 .. 0.68
   3 ?    2.9   0.1     0.077   1.5e+02      33      44 ..     155     166 ..     148     181 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                              ZapB  6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenre 43
                                      L++L s+iq  ++t+++L  e+ +++e   elk+ + e
  gi|320100692|ref|YP_004176284.1| 30 LSELVSSIQGGVETVSRLYGELNRVEEHGDELKRSIME 67
                                      89999***************************997644 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                              ZapB  60 erlkkLLgkl 69 
                                       e++++L++++
  gi|320100692|ref|YP_004176284.1| 115 EKIQALMKEM 124
                                       3333333333 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.077
                              ZapB  33 eneelkeenrel 44 
                                       e+eel+e+++el
  gi|320100692|ref|YP_004176284.1| 155 EVEELEEKIDEL 166
                                       444444444444 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.7e-05     0.074     235     308 ..      96     161 ..      33     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                       HHHHTSCEEEEEECTTSSCCGGHHHH.....HHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS CS
                      Amidohydro_1 235 aldeGvkvglgtDgaasgnslnllee.....lrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsi 306
                                       a ++G+++ +++    sg ++   +e     ++ +++++        ++  ++ e+++ ++ ++A+al+++++v ++
  gi|320100692|ref|YP_004176284.1|  96 AKSAGKRILIAVE---SGIVI---DEkiqalMKEMTEKSL-------TASRKIIELFESMSRDPARALSISHEVEEL 159
                                       3344777888888...77777...3333345777777777.......88899***********************99 PP

                                       -T CS
                      Amidohydro_1 307 ev 308
                                       e+
  gi|320100692|ref|YP_004176284.1| 160 EE 161
                                       97 PP

>> DUF2999  Protein of unknown function (DUF2999)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.013        26      12      32 ..     111     131 ..     102     135 .. 0.80
   2 ?    6.1   0.0    0.0069        14      16      49 ..     133     166 ..     130     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                           DUF2999  12 nvsdekiaelfealtenPlaa 32 
                                        v deki+ l++ +te  l a
  gi|320100692|ref|YP_004176284.1| 111 IVIDEKIQALMKEMTEKSLTA 131
                                       57899*********9999988 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0069
                           DUF2999  16 ekiaelfealtenPlaamaliqqlGipqeklqal 49 
                                        ki elfe++ ++P  a+++ +++   +ek+ +l
  gi|320100692|ref|YP_004176284.1| 133 RKIIELFESMSRDPARALSISHEVEELEEKIDEL 166
                                       69****************9988887777777665 PP

>> OST-HTH  OST-HTH/LOTUS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00025      0.49      43      65 ..      24      46 ..       6      52 .. 0.79
   2 ?   -2.4   0.0       2.2   4.3e+03       8      17 ..     133     145 ..     130     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                                      CCTSSSHHHHHHTSTTTEEEEEE CS
                           OST-HTH 43 kyGfskLseLlkalpdvveveer 65
                                      ++G skLseL+++++  ve+ +r
  gi|320100692|ref|YP_004176284.1| 24 EIGVSKLSELVSSIQGGVETVSR 46
                                      79*************99999876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                                       HHHHHHHHH...T CS
                           OST-HTH   8 keirelLrs...d 17 
                                       ++i+el+ s   d
  gi|320100692|ref|YP_004176284.1| 133 RKIIELFESmsrD 145
                                       6777887776332 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.042        83       6      44 ..      10      48 ..       7      49 .. 0.82
   2 ?    2.4   0.1      0.11   2.1e+02       8      30 ..      43      65 ..      24      72 .. 0.68
   3 ?   -0.6   0.0       0.9   1.8e+03      37      49 ..     129     144 ..     112     146 .. 0.54
   4 ?    4.8   0.4     0.018        36      26      40 ..     152     166 ..     134     184 .. 0.69
   5 ?    1.2   0.0      0.24   4.8e+02      25      44 ..     191     210 ..     188     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.042
                         FlaC_arch  6 EnklsklsteletvkkeneelsksveelkenVkdllsLY 44
                                      E+ +s++     tv+   ++ls+ v  ++  V+ +  LY
  gi|320100692|ref|YP_004176284.1| 10 ESMFSSIREHARTVEIGVSKLSELVSSIQGGVETVSRLY 48
                                      667777788888999999999999999999998888888 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                         FlaC_arch  8 klsklsteletvkkeneelsksv 30
                                       +s+l  el+ v++  +el+ s+
  gi|320100692|ref|YP_004176284.1| 43 TVSRLYGELNRVEEHGDELKRSI 65
                                      35566667777777777777666 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.9
                         FlaC_arch  37 V...kdllsLYEvVsn 49 
                                           +++++L+E  s+
  gi|320100692|ref|YP_004176284.1| 129 LtasRKIIELFESMSR 144
                                       2445677777776665 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.018
                         FlaC_arch  26 lsksveelkenVkdl 40 
                                       +s +veel+e++ +l
  gi|320100692|ref|YP_004176284.1| 152 ISHEVEELEEKIDEL 166
                                       677777777777433 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.24
                         FlaC_arch  25 elsksveelkenVkdllsLY 44 
                                       ++ +++e + + ++d+ ++Y
  gi|320100692|ref|YP_004176284.1| 191 QIVDDIEGISDVFEDIADIY 210
                                       78999******999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 1785.83
//
Query:       gi|320100693|ref|YP_004176285.1|  [L=139]
Description: transcriptional regulator TrmB [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-05   24.6   1.0      5e-05   23.1   0.6    1.9  2  TrmB       Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.056   13.4   0.1      0.076   13.0   0.1    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain
       0.12   12.2   0.0       0.14   12.0   0.0    1.3  1  DUF742     Protein of unknown function (DUF742)
       0.12   12.6   0.1       0.26   11.5   0.1    1.5  1  PaaX       PaaX-like protein


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.57   2.6e+03      37      52 ..       7      21 ..       3      24 .. 0.74
   2 !   23.1   0.6   1.1e-08     5e-05      16      66 ..      32      82 ..      27      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.57
                                      HCHHHHHHHHHHCTSE CS
                              TrmB 37 skvYevLrsLedkGlV 52
                                       ++Y++ r L+++G+V
  gi|320100693|ref|YP_004176285.1|  7 ESIYDI-RFLMKRGIV 21
                                      566664.779999988 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.1e-08
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                      a+++l++ tad++a+ +g+ r+   ++L++L + G+V ++k+ +++Y   +
  gi|320100693|ref|YP_004176285.1| 32 AVITLKKVTADDVAKYTGRARTIESRYLSRLNKIGIVAKVKEGRRVYYIEP 82
                                      6778999************************************99998655 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   0.1   1.7e-05     0.076      17      60 ..      33      81 ..      12      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                      EEEE.EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TEE.EEES CS
                         HTH_Crp_2 17 eiel.pltqeelAsmlGltretvsrilseLkreglis..r.grr.iril 60
                                       i+l ++t ++ A + G  r   sr ls+L + g++   + grr   i 
  gi|320100693|ref|YP_004176285.1| 33 VITLkKVTADDVAKYTGRARTIESRYLSRLNKIGIVAkvKeGRRvYYIE 81
                                      5666469******************************753346655555 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     3e-05      0.14      53      94 ..      94     134 ..      48     139 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                            DUF742  53 replsVaelaAelklPvgvvrvLlsdLldaglltvrapvtdr 94 
                                        + + V  la +++lP  +v+ L+ dL+++g++  ++p+  +
  gi|320100693|ref|YP_004176285.1|  94 GDNMMVEQLAHQISLPADIVK-LIIDLMKSGKIPPPQPAGGQ 134
                                       45778999************9.677********999998774 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.7e-05      0.26      44      64 ..      59      79 ..      51      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.7e-05
                              PaaX 44 lsRlakaGwlvrekegrrsfY 64
                                      lsRl+k G +++ kegrr++Y
  gi|320100693|ref|YP_004176285.1| 59 LSRLNKIGIVAKVKEGRRVYY 79
                                      89******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1061.82
//
Query:       gi|320100694|ref|YP_004176286.1|  [L=100]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00024   20.9   0.2    0.00061   19.6   0.2    1.8  2  RHH_1           Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.055   14.0   0.0      0.079   13.5   0.0    1.3  1  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys
       0.11   13.4   0.1       0.15   13.0   0.1    1.2  1  DUF4065         Protein of unknown function (DUF4065)


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 !   19.6   0.2     1e-07   0.00061       2      29 ..      32      60 ..      31      73 .. 0.95
   2 ?   -1.4   0.0      0.42   2.5e+03      11      16 ..      64      69 ..      59      80 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-07
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelI 29
                                      +s+r++e++le +d+ a+r g +Sr +l+
  gi|320100694|ref|YP_004176286.1| 32 ISLRVSEDDLEIIDKFAARNGsVSRTYLL 60
                                      89***********************9985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.42
                                      HHHHHH CS
                             RHH_1 11 lerLde 16
                                      +e++ e
  gi|320100694|ref|YP_004176286.1| 64 VEAVAE 69
                                      333333 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.3e-05     0.079      36      65 ..      23      52 ..       3      66 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                    CopG_antitoxin 36 peLkkktksislrlpedlLealkekAnkrd 65
                                        Lk++++ islr++ed Le + + A + +
  gi|320100694|ref|YP_004176286.1| 23 ISLKPRKRMISLRVSEDDLEIIDKFAARNG 52
                                      479*******************88776655 PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.5e-05      0.15      52     103 ..       6      59 ..       2      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                           DUF4065  52 keeeisdeklekkekkeveeleddkeae..lseeekevidkvikkykdlsaseL 103
                                        ++++sd+ + +++ +e++ +  ++      se+++e+idk+ ++++++s + L
  gi|320100694|ref|YP_004176286.1|   6 ARSDFSDSIIVNDNIIEISLKPRKRMISlrVSEDDLEIIDKFAARNGSVSRTYL 59 
                                       567788888888888888887777666699******************998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 793.00
//
Query:       gi|320100695|ref|YP_004176287.1|  [L=94]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-32  109.3   6.0    8.2e-32  109.2   6.0    1.0  1  DUF211     Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
      0.036   14.5   1.5       0.53   10.8   1.4    2.1  1  HMA        Heavy-metal-associated domain
       0.23   11.7   1.0       0.28   11.4   1.0    1.1  1  Fasciclin  Fasciclin domain


Domain annotation for each model (and alignments):
>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   6.0   1.4e-35   8.2e-32       2      87 ..       2      88 ..       1      90 [. 0.98

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 1.4e-35
                                      EEEEEEEEEEE.SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEE CS
                            DUF211  2 irrlvLDvlkp.hepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevv 79
                                      ++r++LDvl p +++siv+lak++ e++gv++v+itvkevD++t+n+ +++eG++i++e++++aie+ ggvihSiD+vv
  gi|320100695|ref|YP_004176287.1|  2 LKRIILDVLYPvRGTSIVDLAKSIVEITGVSSVSITVKEVDVDTQNILVMVEGSDISFEDVRDAIEKEGGVIHSIDQVV 80
                                      79***************************************************************************** PP

                                      EESS---- CS
                            DUF211 80 aGkkivee 87
                                      aG++i+e 
  gi|320100695|ref|YP_004176287.1| 81 AGERIIEP 88
                                      ******95 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.4   8.9e-05      0.53      18      60 ..      23      70 ..      20      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.9e-05
                               HMA 18 kvLselpgVesvk.....vdlatktvtVegdaestklrkiieaiekag 60
                                      k++ e++gV+sv+     vd++t+   V+++ +++++++++ aiek g
  gi|320100695|ref|YP_004176287.1| 23 KSIVEITGVSSVSitvkeVDVDTQNILVMVEGSDISFEDVRDAIEKEG 70
                                      566677888777422223799999999999999999*********965 PP

>> Fasciclin  Fasciclin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   4.6e-05      0.28      87     125 ..      40      79 ..      15      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.6e-05
                                       EEEEEEEGGTTEEEETT...EEEEEEEEEEESSEEEEEESS- CS
                         Fasciclin  87 klrvniekgngtvtvng...karvvrsdieatngvihvidkv 125
                                       ++ v+++  n  v+v+g   + + vr  ie + gvih id+v
  gi|320100695|ref|YP_004176287.1|  40 EVDVDTQ--NILVMVEGsdiSFEDVRDAIEKEGGVIHSIDQV 79 
                                       3333333..66788888766555578999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 749.93
//
Query:       gi|320100696|ref|YP_004176288.1|  [L=256]
Description: Mn2+-dependent serine/threonine protein kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2070.20
//
Query:       gi|320100697|ref|YP_004176289.1|  [L=359]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-34  117.1   0.0    1.2e-33  116.5   0.0    1.3  1  ABC_tran      ABC transporter
    5.8e-10   39.2   0.2      4e-08   33.3   0.1    2.9  3  TOBE_2        TOBE domain
    2.8e-06   27.4   0.5      0.029   14.2   0.2    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00025   21.3   1.7     0.0039   17.5   1.7    2.1  1  AAA_22        AAA domain
     0.0013   19.1   0.0     0.0023   18.3   0.0    1.4  1  RNA_helicase  RNA helicase
     0.0026   18.3   0.3     0.0052   17.3   0.3    1.7  1  AAA_23        AAA domain
     0.0028   18.1   0.3      0.043   14.2   0.3    2.4  1  AAA           ATPase family associated with various cellular 
     0.0051   16.6   0.0      0.095   12.4   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0065   16.4   0.2      0.018   14.9   0.1    1.6  2  Rad17         Rad17 P-loop domain
  ------ inclusion threshold ------
      0.039   13.9   0.0      0.064   13.2   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
       0.05   14.0   0.1      0.088   13.2   0.1    1.6  1  AAA_16        AAA ATPase domain
      0.052   13.0   0.0      0.084   12.3   0.0    1.3  1  HSM3_N        DNA mismatch repair protein HSM3, N terminal do
       0.17   11.8   0.1       0.31   11.0   0.1    1.3  1  Rop           Rop 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 !  116.5   0.0   8.7e-37   1.2e-33       2     136 ..      20     165 ..      19     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 8.7e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++v+++++ ge   ++G++G+GK+t l+++ag ++p++G++ +d++d++    + ++++ ++++q+  l+p++tv+e
  gi|320100697|ref|YP_004176289.1|  20 EDVNIEIQSGEFFTLLGPSGCGKTTTLRIIAGFETPDKGRVYFDDEDVTF--VKPYKRNTSMVFQNYALWPHMTVYE 94 
                                       689***********************************************..************************* PP

                                       H.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n                 + ++ +++al+ ++l++++++       +LSgGq+qrvalaral+ kp++lllDEp 
  gi|320100697|ref|YP_004176289.1|  95 NvayglklrkkelgltdeDIRKMVKEALELVKLSGMENRYP----LQLSGGQQQRVALARALVVKPRVLLLDEPL 165
                                       ******999999988754444449999********999998....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.13   1.8e+02      28      51 ..     127     150 ..     121     157 .. 0.84
   2 ?   -1.5   0.0       2.1   2.8e+03      50      75 ..     212     234 ..     198     234 .. 0.72
   3 !   33.3   0.1   2.9e-11     4e-08       1      75 [.     282     355 ..     282     356 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.13
                            TOBE_2  28 ylGsstryvvelaggqlvvvrqpn 51 
                                         G + ry ++l ggq+++v+ + 
  gi|320100697|ref|YP_004176289.1| 127 LSGMENRYPLQLSGGQQQRVALAR 150
                                       569999************998765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                            TOBE_2  50 pnadrdsalapGdtVelswdpddavv 75 
                                       + ++    +++G+  el ++p++++v
  gi|320100697|ref|YP_004176289.1| 212 NKGR---VVQVGSPKELYFKPRSLFV 234
                                       4444...7889999999999998876 PP

  == domain 3  score: 33.3 bits;  conditional E-value: 2.9e-11
                            TOBE_2   1 laiRPEklrla...aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddav 74 
                                       ++iRPE +rl    a++g++ ++G+V+   +lG+ ++ +v++++ +l +v+ pn+    ++  G +Vel+++ + ++
  gi|320100697|ref|YP_004176289.1| 282 VVIRPEIIRLGggrAEEGDTVVKGVVDFAMFLGEKVEARVKIGNLPL-LVYLPNTV---DVSTGNEVELTLPWRNII 354
                                       78********987666666799***********************99.99*****9...9*********99877776 PP

                            TOBE_2  75 v 75 
                                       +
  gi|320100697|ref|YP_004176289.1| 355 I 355
                                       5 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00013      0.19       2      22 ..      32      52 ..      31      86 .. 0.76
   2 !   14.2   0.2   2.1e-05     0.029     226     287 ..     127     185 ..      81     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                        l Gp g+GK++ L+++ ++
  gi|320100697|ref|YP_004176289.1| 32 FTLLGPSGCGKTTTLRIIAGF 52
                                      6799**************776 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.1e-05
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                        ++  ++ + +lS G+++  al+ al   +   ++ll+DEp ++L+ kl  +  e l++l+r
  gi|320100697|ref|YP_004176289.1| 127 LSGMENRYPLQLSGGQQQRVALARALVVKP---RVLLLDEPLSNLDAKLRIEMREELRKLQR 185
                                       555566778899999999989999999877...*****************999999988887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.7   2.9e-06    0.0039       4     132 ..      28     198 ..      24     202 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.9e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..................................erpevv... 43 
                                       +  + ++ G+sG+GKTt+lr ++   + +    +                                       +   
  gi|320100697|ref|YP_004176289.1|  28 SGEFFTLLGPSGCGKTTTLRIIAGFETPD----KgrvyfddedvtfvkpykrntsmvfqnyalwphmtV----Yenv 96 
                                       5678899****************998544....244569998888888887666666666666644430....2222 PP

                            AAA_22  44 ....fvtlpsst.sskdllrellralglelka.....erlsseellealeqalrarav...ielliiDEaqh.lr.. 104
                                           +   ++++ + +d+++++ +al+l + +     +   ++    + ++ + ara    +++l++DE    l+  
  gi|320100697|ref|YP_004176289.1|  97 ayglKLRKKELGlTDEDIRKMVKEALELVKLSgmenrY--PLQLSGGQQQRVALARALvvkPRVLLLDEPLSnLDak 171
                                       33223333333366666666666666666655887442..33333344444444444456888*****965558876 PP

                            AAA_22 105 .seealeeLrsllnlsrkgvqliLvGtpe 132
                                        + e+ eeLr+l+   + +++ i+v++ +
  gi|320100697|ref|YP_004176289.1| 172 lRIEMREELRKLQR--SLNLTTIYVIHDQ 198
                                       56999999999999..8888888887665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.6e-06    0.0023       3      58 ..      34      84 ..      32      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDf 58
                                      l Gpsg+GK+t+ +         ++++ k++vy+   + +f++ Y++++ +v++  
  gi|320100697|ref|YP_004176289.1| 34 LLGPSGCGKTTTLRI-----IAGFETPDKGRVYFDDEDVTFVKPYKRNTSMVFQNY 84
                                      78***********99.....445679*************************99876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   3.8e-06    0.0052       1      40 [.       3      50 ..       3     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.8e-06
                            AAA_23  1 kLkienfrsf.......rdqeidF.skgltlItGpNGaGKTTildAik 40
                                      ++++e++ ++       +d++i+  s  ++ + Gp G+GKTT l+ i 
  gi|320100697|ref|YP_004176289.1|  3 RVRLEGVSKYygavvaaEDVNIEIqSGEFFTLLGPSGCGKTTTLRIIA 50
                                      689999999999999999999***6668***************99886 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 !   14.2   0.3   3.1e-05     0.043       3      21 ..      34      52 ..      32     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      l Gp G+GKT++ + +a  
  gi|320100697|ref|YP_004176289.1| 34 LLGPSGCGKTTTLRIIAGF 52
                                      89**************975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   6.9e-05     0.095      15      74 ..      20      76 ..      18      85 .. 0.82
   2 ?    2.5   0.0     0.068        94     145     184 ..      90     129 ..      68     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenises 74
                                      +dv i++++  + +l G+ ++GK++ l+++  F + +    k  +++++ed+   + ++++
  gi|320100697|ref|YP_004176289.1| 20 EDVNIEIQSGeFFTLLGPSGCGKTTTLRIIAGFETPD----KGRVYFDDEDVTFVKPYKRN 76
                                      57888888888999****************9999988....77888888887776666655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.068
                            AAA_15 145 kelpkekeeklekekeelkidkedlkklikkleeslkkee 184
                                       +  +++  + l+++k+el +++ed++k  k+  e +k + 
  gi|320100697|ref|YP_004176289.1|  90 MTVYENVAYGLKLRKKELGLTDEDIRKMVKEALELVKLSG 129
                                       56788999999*****************998777776655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.3e-05     0.018      46      66 ..      30      50 ..      17      60 .. 0.83
   2 ?   -2.0   0.0       2.2     3e+03      90     163 ..     112     187 ..      76     203 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                             Rad17 46 riLLisGPsGCgkstvvkvLs 66
                                      +   + GPsGCgk+t++++++
  gi|320100697|ref|YP_004176289.1| 30 EFFTLLGPSGCGKTTTLRIIA 50
                                      566788************997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                             Rad17  90 sdfkgltekesrf..lsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrds.dalrevirkylrss 163
                                       +d++ +++   ++  ls +e    l+L + + +++  l   l  + +++l+++  ++    +   +re +rk  rs 
  gi|320100697|ref|YP_004176289.1| 112 EDIRKMVKEALELvkLSGMENRYPLQLSGGQQQRVA-LARALVVKPRVLLLDEPLSNLDAKLrIEMREELRKLQRSL 187
                                       455555544444444556666555666666666655.5666666666666666445555555345666666655544 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   4.7e-05     0.064      20      68 ..      29      76 ..      23     135 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                                       e+  + Gp g+GKt+ l+ ii   e  dk ++y+++    + + +++ 
  gi|320100697|ref|YP_004176289.1| 29 GEFFTLLGPSGCGKTTTLR-IIAGFETPDKGRVYFDDEDVTFVKPYKRN 76
                                      5667788*********997.6777788899******9999999988887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.4e-05     0.088      23      51 ..      28      56 ..      20     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                      ++e   l G+sG+GK++ +r ++   + d
  gi|320100697|ref|YP_004176289.1| 28 SGEFFTLLGPSGCGKTTTLRIIAGFETPD 56
                                      4578889************9988544444 PP

>> HSM3_N  DNA mismatch repair protein HSM3, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.1e-05     0.084      27     121 ..     133     227 ..     112     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-05
                            HSM3_N  27 kcslnlstvaklkedakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalkseidsl 103
                                       +  l+ls  ++ +    r l+   r+l+ +++ ++ld +l +e+ ++l k+    ++ ++y ++d v+a+  +    
  gi|320100697|ref|YP_004176289.1| 133 RYPLQLSGGQQQRVALARALVVKPRVLLLDEPLSNLDAKLRIEMREELRKLQRSLNLTTIYVIHDQVEAMSLSDRIA 209
                                       567889999999999999999999**********************************************9999999 PP

                            HSM3_N 104 vvaackvieksyPkglfa 121
                                       v+   +v++   Pk l+ 
  gi|320100697|ref|YP_004176289.1| 210 VMNKGRVVQVGSPKELYF 227
                                       99999*********9974 PP

>> Rop  Rop protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00022      0.31       3      44 ..     142     183 ..     141     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                               Rop   3 KQektALnmAkFIksQsLlLLeKLneLdlDeqAdlCErLHed 44 
                                        Q++ AL  A  +k   LlL e L +Ld+  + ++ E+L  +
  gi|320100697|ref|YP_004176289.1| 142 QQQRVALARALVVKPRVLLLDEPLSNLDAKLRIEMREELRKL 183
                                       599********************************9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2381.87
//
Query:       gi|320100698|ref|YP_004176290.1|  [L=746]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-19   69.8  48.3      5e-12   45.9  23.7    5.2  5  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.056   13.8   0.0    1.9  1  Sterol_MT_C   Sterol methyltransferase C-terminal


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   5.7      0.84   7.6e+03     143     171 ..      55      82 ..       3      90 .. 0.45
   2 ?    1.1   1.9     0.032   2.9e+02     137     177 ..     128     165 ..     119     171 .. 0.53
   3 !   38.5  16.6     1e-13   9.4e-10       2     175 ..     239     426 ..     238     442 .. 0.74
   4 ?   -1.8   1.0      0.25   2.3e+03      52      52 ..     486     486 ..     436     543 .. 0.47
   5 !   45.9  23.7   5.6e-16     5e-12       9     182 ..     538     740 ..     530     742 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.84
                      BPD_transp_1 143 eailgydyseisnggvlalviavlllnlv 171
                                         +++  ys+++   ++ + ++++ ++l+
  gi|320100698|ref|YP_004176290.1|  55 YNYESVKYSFTM-SFLALVFLIYIFVILL 82 
                                       222223333333.2222222222333332 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.032
                      BPD_transp_1 137 lgtllleailgydyseisnggvlalviavlllnlvadilqr 177
                                       l++++ ++ ++ d +++    + ++++a+l l  v+ i+  
  gi|320100698|ref|YP_004176290.1| 128 LTRRIRNTVSQLDATMWF---FTVFGLAYLTLFMVVPIVLV 165
                                       566666666666666444...44444444444444444433 PP

  == domain 3  score: 38.5 bits;  conditional E-value: 1e-13
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivll.slPsfv.........laillvlvf..........vilsilghlilp 55 
                                       +llGi++a    ++++++  llr+l iv+l  +P++                             + ++    +i +
  gi|320100698|ref|YP_004176290.1| 239 TLLGIIVAfvlARYRFPGHTLLRILAIVPLfNTPFINsyvvkliwgQ-------DgpvsslfntfFGFKLRVEGIVG 308
                                       57888888887799999**********99853444434433333330.......14444444554566666689*** PP

                      BPD_transp_1  56 viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflg 132
                                       v+++ +++++p+v+l+ ++ + +++ + +e a+ lGa+ +++fr+v+lP+alp i++g il+f+++l +  ++  + 
  gi|320100698|ref|YP_004176290.1| 309 VMLAQIVTFFPIVYLNAYNSFINIDPSTEEQAENLGAKGFRLFRTVTLPLALPGIAAGSILVFVFSLEDLGAPIVFN 385
                                       *************************************************************************9999 PP

                      BPD_transp_1 133 swpGlgtllleailgydyseis..nggvlalviavlllnlvadil 175
                                           +++l+   i +   + +      v+al++++lll+lv+++ 
  gi|320100698|ref|YP_004176290.1| 386 ----VQSLMSYKIYMGIRTTTGliSPEVAALGVVLLLLTLVSFLA 426
                                       ....55555444333333322245344555555555555554443 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.25
                      BPD_transp_1  52 l 52 
                                       l
  gi|320100698|ref|YP_004176290.1| 486 L 486
                                       0 PP

  == domain 5  score: 45.9 bits;  conditional E-value: 5.6e-16
                      BPD_transp_1   9 a........lnrnkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilp.viil 59 
                                       a        + + k+l ++l+ l+  +l++P +vla+  +++f                  + ++l ++ +   ii+
  gi|320100698|ref|YP_004176290.1| 538 AtavgysvsRLKIKWLANILDSLSTSPLAIPGLVLALGYYYFFyilanalsqlvpgavtyLLPGSLSFATWLvFIIA 614
                                       33333444477889********************999999988999*************966666666666659*** PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                       + +  +pyv++ + a+++++ ++l+eaa  lGasr ++++ v+lP ++ +i++g++l f+++ ++ +   ++g   G
  gi|320100698|ref|YP_004176290.1| 615 FSVRRLPYVVRSVFAGFQQVHENLEEAAMNLGASRMRVVFGVILPFIIGYILSGALLGFIYMATEVSTSITFG---G 688
                                       *****************************************************************99999999...4 PP

                      BPD_transp_1 137 lgtllleailgydyseis.......nggvlalviavlllnlvadilqrlldpr 182
                                       ++     ++ +y+ ++i+       + ++++++i++l+ ++v+ i++ ++ +r
  gi|320100698|ref|YP_004176290.1| 689 MN-DAYAPLTYYMAQNIAgaagqgpMLVAAMGTILILIQLVVVVIVVYVFKQR 740
                                       33.44445555555555556698876666666666666666666666666665 PP

>> Sterol_MT_C  Sterol methyltransferase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.2e-06     0.056      18      58 ..     617     658 ..     602     662 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-06
                       Sterol_MT_C  18 vkvl.eflglapkGtqkvaefLekAadsLvaGGkegiFTPmy 58 
                                       v+ l  +++ + +G q+v+e Le+Aa++L a++++ +F  + 
  gi|320100698|ref|YP_004176290.1| 617 VRRLpYVVRSVFAGFQQVHENLEEAAMNLGASRMRVVFGVIL 658
                                       444546789999*************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 5149.06
//
Query:       gi|320100699|ref|YP_004176291.1|  [L=540]
Description: family 1 extracellular solute-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-17   63.6   0.7    2.5e-17   63.6   0.7    1.7  1  SBP_bac_8       Bacterial extracellular solute-binding protei
      1e-16   61.1   0.2    1.8e-16   60.3   0.2    1.4  1  SBP_bac_6       Bacterial extracellular solute-binding protei
    4.3e-09   36.8   3.1    1.9e-08   34.6   3.1    2.0  1  SBP_bac_1       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
       0.11   10.7  15.4       0.16   10.1  15.4    1.2  1  SSP160          Special lobe-specific silk protein SSP160


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.7   5.5e-21   2.5e-17      14     273 ..     122     392 ..     114     402 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 5.5e-21
                                       EEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHH.HHHHHHTTSB--GGGS.TTHHH.......-HH...HHHTT CS
                         SBP_bac_8  14 vnvvtaasndleqklkaalaagtapdidvvwaneda.latlaeeglladlsdl.dnldd.......ltd...alaav 78 
                                       +++v a+ ++l++ +   +a+  +p idv+w+ +   + +l+++g+l +++ + ++ +        +++    ++++
  gi|320100699|ref|YP_004176291.1| 122 IQFVAAP-AELWTSYIDNAAKAGTP-IDVAWGGGPTlFNNLDAAGYLLPVDPSkPEFNAvmyelnkIPKtigGAETF 196
                                       6676554.79999999987655444.9****997766999999******9944455555445544477755566666 PP

                                       --TS...----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHHHHH-SEGG--.-GGGGGGTHHETTEE-- CS
                         SBP_bac_8  79 gydgk..lygvPyasetpyvliynkdlleka..edpktwdellaaakklkgkfglpdpa.sgwlqaallakdgksld 150
                                       ++dg+  + ++   +++  ++ +n   l +     p+ w++l +  +++  ++ lpd + + ++  ++   ++    
  gi|320100699|ref|YP_004176291.1| 197 KVDGNglIHWIGASVSS-FGFTVNLVRLNQYglPMPQKWEDLAS--PQY--ARYLPDIPqIATADPTMST-SNTRIF 267
                                       66666659999988886.9*****99999857779*********..999..4555664424666666666.555655 PP

                                       -H...HHH.HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEE CS
                         SBP_bac_8 151 ddg.gkdglkealellkklkdngktydtgadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkgl 226
                                       + + + +g++e +++l+ l +n ++y+ ++da +++  G+va +++ +     aq+ +++ ++i+p+  ++++++++
  gi|320100699|ref|YP_004176291.1| 268 EIIlQAKGWEEGWRILTLLAANAVIYQGSSDARDAVIRGDVAVGTTIDFYGYMAQQVNPNCKYIAPQGETIVNSDPI 344
                                       55667789**********************************************************999******** PP

                                       EEBTTS-HHHHHHHHHHHHHTTSH.HHHHHHH.HH---BS-S-TTTHHH CS
                         SBP_bac_8 227 avpknaknedlaAldFlkwltspe.nqaalae.ktgyipvnksaalspe 273
                                       a  k +k+    A++F+ w++++  +q+ +   +++ +pvn+++ ++ +
  gi|320100699|ref|YP_004176291.1| 345 ALVKTTKHLVH-AVAFMAWVLNEYgGQQIWLLqDINRLPVNPKVFETQA 392
                                       **********7.************888888888*********9987655 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.2     4e-20   1.8e-16       4     220 ..     146     390 ..     143     409 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 4e-20
                         SBP_bac_6   4 pdlilsfdkdflekfieeglfqpld.........panlpnvnkdfa.eeglkdp.dg..kyypygvgplvlavnkdr 67 
                                       +d+ ++ ++ ++ ++ ++g++ p+d         +  l++++k +  +e++k + +g  ++++ +v+ +++ vn  r
  gi|320100699|ref|YP_004176291.1| 146 IDVAWGGGPTLFNNLDAAGYLLPVDpskpefnavMYELNKIPKTIGgAETFKVDgNGliHWIGASVSSFGFTVNLVR 222
                                       68888889999999999999999998888886665555555555556666665546633566999************ PP

                         SBP_bac_6  68 lkgrpv..PksWaDLldPeykg......kvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaq.mvka 135
                                       l++  +  P++W+DL +P+y+       ++a  ++  s++++ ++ ++ + +g+++++++l  l+an   +q + +a
  gi|320100699|ref|YP_004176291.1| 223 LNQYGLpmPQKWEDLASPQYARylpdipQIATADPTMSTSNTRIFEIILQAKGWEEGWRILTLLAANAVIYQgSSDA 299
                                       *97655449*************999999999999999**************************************** PP

                         SBP_bac_6 136 agslesgepavsvvpyffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspe.vqaila 210
                                        ++++ g+ av  +++f++ ++++ +   n k + P+  ++v+ + ++++k  k+   a af+ + l +  +q+i+ 
  gi|320100699|ref|YP_004176291.1| 300 RDAVIRGDVAVGTTIDFYGYMAQQVN--PNCKYIAPQGETIVNSDPIALVKTtKHLVHAVAFMAWVLNEYgGQQIWL 374
                                       **********************9998..6****************999999999****************6666665 PP

                         SBP_bac_6 211 kagg.vfPvv.....t 220
                                        +    +Pv+     t
  gi|320100699|ref|YP_004176291.1| 375 LQDInRLPVNpkvfeT 390
                                       5444568875443332 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 !   34.6   3.1   4.3e-12   1.9e-08      34     311 ..     132     366 ..     103     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 4.3e-12
                                       HHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHHHTHHHHCE.EE.. CS
                         SBP_bac_1  34 sgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkdaadklsssvlpkilds.kv.. 106
                                       + s+++    a  aG+ p+Dv+++ +++ +  l  ag+llp+dp   + +a  +   +++ ++++     ++ ++  
  gi|320100699|ref|YP_004176291.1| 132 WTSYID---NAAKAGT-PIDVAWGgGPTLFNNLDAAGYLLPVDPSKPEFNAVMY---ELNKIPKTI---GGAeTFkv 198
                                       444444...7889999.*******9999999*************9988886664...455444444...44434344 PP

                                       .....ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHH CS
                         SBP_bac_1 107 .....ly.vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgtayyfalalaksl 176
                                            +  +     + g+ +N   + ++gl++p  W++l+ +      ++    +  +  + s+ +   ++ +++  
  gi|320100699|ref|YP_004176291.1| 199 dgnglIHwIGASVsSFGFTVNLVRLNQYGLPMPQKWEDLASPQYARYLPDIPQ-IATADPTMSTSNTRIFEIILQAK 274
                                       88888666777744889999888888**************8888777777777.33333333333333334444444 PP

                                       TGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEE CS
                         SBP_bac_1 177 ggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvap 253
                                       g                  + + ++ l         l+ + +  +++++a++++ +G++a++    ++ + a +v+p
  gi|320100699|ref|YP_004176291.1| 275 G------------------WEEGWRILT-------LLAANAVIYQGSSDARDAVIRGDVAVGTTIDFYGYMAQQVNP 326
                                       4..................888888888.......9********************************99999999* PP

                                       EECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSH CS
                         SBP_bac_1 254 kvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllsp 311
                                       + +++a++ +                     +++++a++k++k+ + A +F++++l++
  gi|320100699|ref|YP_004176291.1| 327 NCKYIAPQGETIV------------------NSDPIALVKTTKHLVHAVAFMAWVLNE 366
                                       ****999999976..................************************986 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  15.4   3.6e-05      0.16     674     707 ..      34      68 ..       9      88 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.6e-05
                            SSP160 674 pdeatttts.sttttttttttaaptttttkaanap 707
                                       p+ +tttt  +tttttttttt+ p+tttt ++  p
  gi|320100699|ref|YP_004176291.1|  34 PQTTTTTTQpATTTTTTTTTTTQPATTTTTTTGKP 68 
                                       44444444335677777777778877777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      771  (0.043003); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 3665.02
//
Query:       gi|320100700|ref|YP_004176292.1|  [L=649]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-74  248.1   0.2    1.8e-73  246.7   0.2    1.7  1  Glucodextran_C  C-terminal binding-module, SLH-like, of gluco
    0.00068   19.2   0.0     0.0012   18.4   0.0    1.4  1  ABC_transp_aux  ABC-type uncharacterized transport system
  ------ inclusion threshold ------
       0.32   11.3   3.2        1.9    8.9   1.0    2.8  2  DUF2929         Protein of unknown function (DUF2929)


Domain annotation for each model (and alignments):
>> Glucodextran_C  C-terminal binding-module, SLH-like, of glucodextranase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.7   0.2   3.1e-77   1.8e-73       1     227 [.     325     566 ..     325     567 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.7 bits;  conditional E-value: 3.1e-77
                    Glucodextran_C   1 ifelkDPvgDDkGpGeytYPtdevfkpgvfDlvkfkvlekgdkvvfevkfaelgenpwngpngFslqlvqiYiddtk 77 
                                       ++e++DP gDDkG+G++ YPt++vfkpgvfD++kf+vl++++++++++++++lg+npw+gpngF+lq++q+Yi++t+
  gi|320100700|ref|YP_004176292.1| 325 VLEVNDPSGDDKGQGTLRYPTNPVFKPGVFDMLKFTVLQDKEYIYLQIQVKDLGGNPWGGPNGFCLQHIQVYIKTTD 401
                                       6799************************************************************************* PP

                    Glucodextran_C  78 eggstrtdtpGlnvtlaeespWdkavlis.gwesa..............gklvvqeeaketedsvkveadqvkntiv 139
                                       ++++++t+t Gl v+la+  +W++a+ +  gw+++              g+l+++e+++ t   ++v+a +  n i 
  gi|320100700|ref|YP_004176292.1| 402 NTLPVNTSTMGLYVNLAP--GWNYALAAVpGWGNTpfpdgevsalfkadGSLIADEYNNGT--LFDVYAFTNANIIE 474
                                       ******************..*******999***99*************9999999999888..9****9999***** PP

                    Glucodextran_C 140 vevpkslL.dgeniakwgyvvlvgsqdgygpdkiRkvse.eagewrfgggs..aidagvaPkviDllapegetQeev 212
                                       v++ kslL d++ni +w ++v+++s+dg+g++kiR +++ ++gew +ggg+  a  a+v+Pkv+Dllap++++Q+++
  gi|320100700|ref|YP_004176292.1| 475 VKIAKSLLgDTGNIGNWIWYVFLTSYDGFGEKKIRGIQAgDPGEWALGGGDpqALLANVQPKVVDLLAPSEQEQYTM 551
                                       **************************************99***********999*********************** PP

                    Glucodextran_C 213 LssydvsakklAtlv 227
                                       Lssyd++a+k+At++
  gi|320100700|ref|YP_004176292.1| 552 LSSYDTAAGKPATVY 566
                                       *************97 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 !   18.4   0.0     2e-07    0.0012     187     259 ..      71     136 ..      27     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-07
                    ABC_transp_aux 187 edilpedidvlviakptkdlseeelykldqflmnGgkllvfldpvaeeqdslsepsaaprtsnLedllaeyGv 259
                                       ++++ +d+d+l+i +pt +++++el++++++l+ G k+l ++   +        +    +  n ++ll+  G 
  gi|320100700|ref|YP_004176292.1|  71 NSDVLKDVDILLIGQPTVAFTPDELDAISKWLDTGRKALYVAGDSDY-------GGGPTTIDNVNKLLEYIGA 136
                                       333448********************************987766552.......2223345666666666665 PP

>> DUF2929  Protein of unknown function (DUF2929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.092   5.5e+02      17      31 ..      49      63 ..      47      72 .. 0.83
   2 ?    8.9   1.0   0.00031       1.9      27      54 ..     621     648 ..     617     649 .] 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.092
                           DUF2929 17 vgYIgsaLtgvtydf 31
                                      ++YI+++Lt v++++
  gi|320100700|ref|YP_004176292.1| 49 LNYIMGNLTFVNWKI 63
                                      68*******999984 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00031
                           DUF2929  27 vtydfttalilavvfgvlviliialisk 54 
                                       ++ d+tt++i+av++ v+ i+++ l++k
  gi|320100700|ref|YP_004176292.1| 621 TQLDVTTTGIIAVITLVIGIAVGMLFKK 648
                                       6899*****************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
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: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 4460.36
//
Query:       gi|320100701|ref|YP_004176293.1|  [L=746]
Description: metallophosphoesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   48.5   0.4    2.7e-12   47.6   0.4    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    4.1e-05   23.6   6.6    5.7e-05   23.2   6.6    1.1  1  RIFIN          Rifin
  ------ inclusion threshold ------
      0.044   14.0   0.0       0.35   11.0   0.0    2.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
       0.16   12.5   0.0       0.16   12.5   0.0    3.4  3  MG2            MG2 domain
       0.75    9.2  16.4        1.5    8.2  16.4    1.5  1  DUF5305        Family of unknown function (DUF5305)
        4.4    6.8   7.7        6.9    6.1   7.7    1.2  1  Stevor         Subtelomeric Variable Open Reading frame
        8.2    5.7  12.1         12    5.1  12.1    1.2  1  DUF908         Domain of Unknown Function (DUF908)


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 !   47.6   0.4     1e-15   2.7e-12       7     203 ..     152     353 ..     146     354 .. 0.68

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1e-15
                                       ESBTB......TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TTSC CS
                       Metallophos   7 gDlHl......algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllGNHeg 76 
                                       +D+H+        +g   + +  ++d+ll    p ++l++GD  d+ + +++++   +++ + y+ipv  ++GNH+ 
  gi|320100701|ref|YP_004176293.1| 152 TDIHFitgqpdVFTGDTCRFAGFTIDNLL---SPHFILWLGDTADTASSNEYVMASaYRYAYLYNIPVLGIAGNHD- 224
                                       67777766666555555555555666664...56************866666777768888888************. PP

                                       HHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH CS
                       Metallophos  77 feeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkd 153
                                               y + g +  ++  ++++f  l    l+ g   ++    g+p +                 e  d+ +++
  gi|320100701|ref|YP_004176293.1| 225 --------YSSGGSYYTNYLGPTKWFRVLAGKLLIIG---IWSPEQGYPSW-----------------E--DLAFAE 271
                                       ........44444444445555777766666665555...66666664444.................1..334444 PP

                                       ..HHHHTTCSEEEEEESSESS.........................CSSSCSCCHHHHH................HH CS
                       Metallophos 154 ..lekrekadwvivlgHsply.........................rgsgylfgdeale................dl 187
                                         l++ +  +++++l H+p+                          +                            + 
  gi|320100701|ref|YP_004176293.1| 272 evLKNYSSIPYKMILVHHPPFyyqgelytryddetvlkpyvpggpsT-----------PlssywstnmtafryflKM 337
                                       68888****************88665555555555555555555552...........05555555555577999** PP

                                       HHHTTESEEEEESSSS CS
                       Metallophos 188 lkkygvdlvisGHtHv 203
                                        ++y+v +v+sGHtH+
  gi|320100701|ref|YP_004176293.1| 338 VEDYNVTMVLSGHTHR 353
                                       ***************7 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   6.6   2.2e-08   5.7e-05     205     302 ..     619     741 ..     581     745 .. 0.50

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.2e-08
                             RIFIN 205 l.........................klkkskaaltsakekekkeasskekikkkvekivekaekkaaaaaaeaaae 256
                                       l                         +++++ a++t++++++++ a++++++++ v++++++ ++++++++++++++
  gi|320100701|ref|YP_004176293.1| 619 LpltiqvadnagntgsyvfnitfqaaTTTTQPATTTTTTTTTTQPATTTTTTTQPVTTTTTQQTTTTTTTTTTTTTT 695
                                       14444444444444444554443322222222222222333333333333333333333333333333333344444 PP

                             RIFIN 257 ataeaekaetaaveattaslqtaiiasivaivvIvLimvIIYLiLR 302
                                       +t+++++++  a++++t   q +    ++a+v +v++ v+ +L+LR
  gi|320100701|ref|YP_004176293.1| 696 TTTTTTTTTSPATTTETGVAQASGSTLVIAVVAVVVVAVVAFLLLR 741
                                       44444444444444555555666667799****************9 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.35      30     138 ..     184     366 ..     163     384 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                     Metallophos_2  30 aiihaGDl..eeeepe.vleellela.....pvlaVrGNnD.......................eevveedvlreaa 75 
                                        i+ +GD    +++ e v++ + + a     pvl + GN+D                       +            
  gi|320100701|ref|YP_004176293.1| 184 FILWLGDTadTASSNEyVMASAYRYAylyniPVLGIAGNHDyssggsyytnylgptkwfrvlagK------------ 248
                                       688899975433333335555555547889999999*****877776666666555444444430............ PP

                     Metallophos_2  76 elgtdl............peeaelelagek..........vlliHgdpl............................ 102
                                            l            p+ ++l +a+e           + l+H+ p                             
  gi|320100701|ref|YP_004176293.1| 249 -----LliigiwspeqgyPSWEDLAFAEEVlknyssipykMILVHHPPFyyqgelytryddetvlkpyvpggpstpl 320
                                       .....133333443334433333332221122333455558888888778999999999999999999999888998 PP

                     Metallophos_2 103 .....gvkdalaellke.aeegsdvvvcGHtHvp....evekeggv 138
                                              + a+++ lk  +++++++v++GHtH+     + ++++g+
  gi|320100701|ref|YP_004176293.1| 321 ssywsTNMTAFRYFLKMvEDYNVTMVLSGHTHRDffvkYTSTRTGT 366
                                       875543333333333334456666********99655533333444 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.1e-05      0.16      46      85 ..      89     128 ..      54     134 .. 0.80
   2 ?   -1.6   0.1       1.5   3.8e+03      26      47 ..     612     632 ..     602     660 .. 0.59
   3 ?   -5.3   8.4         7   1.8e+04      34      56 ..     672     694 ..     637     720 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.1e-05
                                       SEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECST CS
                               MG2  46 kevkelplatdetggaesefalpeaaklGeysvelsadsa 85 
                                        +v++ +l+ +++g+  +++ +p++a+ G y ++l+a s+
  gi|320100701|ref|YP_004176293.1|  89 LVVFNYTLTLTTQGSGRYSLSIPSTAEEGLYDLVLKAGST 128
                                       37889999***************************44433 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                                       TTCSB---EEEEEEEE-TTSSE CS
                               MG2  26 etlqglaklplkltirdpdgke 47 
                                       e++++++  pl++++ d  g++
  gi|320100701|ref|YP_004176293.1| 612 ESATTVTL-PLTIQVADNAGNT 632
                                       44444444.7777777776664 PP

  == domain 3  score: -5.3 bits;  conditional E-value: 7
                                       EEEEEEEE-TTSSEEEEEEEEE- CS
                               MG2  34 lplkltirdpdgkevkelplatd 56 
                                       +p++ t +++   ++ +++ +t+
  gi|320100701|ref|YP_004176293.1| 672 QPVTTTTTQQTTTTTTTTTTTTT 694
                                       22222222222222222222222 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  16.4   0.00058       1.5      56     135 ..     651     735 ..     593     744 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00058
                           DUF5305  56 vlevnvegeidg.esieesktsrlpiplteqtyeikkdetdeengeitetvtvkespslae......gilliilgll 125
                                        ++++ ++++++  ++++++t+ ++ + t+qt++ ++++t ++++++t+t+t++ + +++e         ++ l+++
  gi|320100701|ref|YP_004176293.1| 651 ATTTTTTTTTTQpATTTTTTTQPVTTTTTQQTTTTTTTTTTTTTTTTTTTTTTTSPATTTEtgvaqaS--GSTLVIA 725
                                       33344444444437777888888888889999999998888888888888888888888888877541..3333333 PP

                           DUF5305 126 aliglvvlir 135
                                        ++++vv+++
  gi|320100701|ref|YP_004176293.1| 726 VVAVVVVAVV 735
                                       3333333332 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.7    0.0027       6.9     172     257 ..     652     738 ..     631     744 .. 0.38

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0027
                            Stevor 172 kaaavaakvalsaealkklasslsilnlfsesslesalkaavsaaaasdlagta.asaassafepygiaalvllila 247
                                       +++++++++++ a++++++++ ++++   ++++ +++ ++++++++++ +++t  a+++ + +   + + lv+ ++a
  gi|320100701|ref|YP_004176293.1| 652 TTTTTTTTTTQPATTTTTTTQPVTTTTTQQTTTTTTTTTTTTTTTTTTTTTTTSpATTTETGVAQASGSTLVIAVVA 728
                                       22222222333333333333444443333333333333322222222222222224444444444444555555555 PP

                            Stevor 248 vvliiLYiwl 257
                                       vv++ +  +l
  gi|320100701|ref|YP_004176293.1| 729 VVVVAVVAFL 738
                                       5554443333 PP

>> DUF908  Domain of Unknown Function (DUF908)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  12.1    0.0049        12     100     213 ..     583     709 ..     565     730 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0049
                            DUF908 100 vsdssakaasekkastteyaldlvslakedskv..............lpsewgdvkvtYYkkssseeqkaesksske 162
                                       +++ +  ++++++ +++ + ++lv +++ +s++                  +  +++t+   +++++++++++++++
  gi|320100701|ref|YP_004176293.1| 583 IPGDNTFTMTPSTYTEQFNRMSLVITVRVESATtvtlpltiqvadnaGNTGSYVFNITFQAATTTTQPATTTTTTTT 659
                                       45555555555566666777777777777777777777777777666667777888899888888887777776666 PP

                            DUF908 163 easesli...ssspstPtplrrssklgktssspsspaktstpskaaksqeglkt 213
                                       ++++ ++   +++p t t+++++++ +     ++++++t+t ++++++++ ++t
  gi|320100701|ref|YP_004176293.1| 660 TTQPATTtttTTQPVTTTTTQQTTTTTT----TTTTTTTTTTTTTTTTTSPATT 709
                                       6555544445333333333333332222....1111122222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2074  (0.115679); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                       173  (0.00964917); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.01u 0.34s 00:00:01.35 Elapsed: 00:00:00.48
# Mc/sec: 4714.77
//
Query:       gi|320100702|ref|YP_004176294.1|  [L=144]
Description: Holliday junction-type resolvase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   96.6   0.1    7.8e-28   96.3   0.1    1.1  1  Hjc        Archaeal holliday junction resolvase (hjc)
    7.8e-05   22.7   0.0     0.0001   22.4   0.0    1.1  1  RecU       Recombination protein U
  ------ inclusion threshold ------
       0.15   11.6   0.0       0.22   11.1   0.0    1.3  1  AHJR-like  REase_AHJR-like


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.1   1.3e-31   7.8e-28       2      90 ..      10     102 ..       9     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 1.3e-31
                                       HHHHHHHHHHHTT-EEEEBSCSSSSSS..SS-SEEEEETTEEEEEEEEEESSS.EEEEEHHHHHHHHHHHHHHTCEE CS
                               Hjc   2 yERelvkiLrergfavvRsagSggatk..plpDviAirgdvvlviEvKsskke.riylkkeqvekllefarkaggel 75 
                                        ER+l++ L+e+gfavvR+++Sg+  +    pD++Ai  + v+++EvK+ ++e ++y+++eqvekl+ef+r+ag+ +
  gi|320100702|ref|YP_004176294.1|  10 HERDLARRLWEHGFAVVRAPASGSRARvlRYPDIVAIYRGRVIALEVKTLREEkPVYVRREQVEKLAEFSRRAGAMP 86 
                                       6***********************9998899*****************98877699********************* PP

                                       EEEEEE.TTTEEEEEE CS
                               Hjc  76 llavkl.qgkewkllv 90 
                                       ++avk+  + ew l++
  gi|320100702|ref|YP_004176294.1|  87 FIAVKYvGEGEWFLVP 102
                                       ******6666676554 PP

>> RecU  Recombination protein U
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.7e-08    0.0001      55     145 ..      42     127 ..      38     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.7e-08
                                       SEEEEETTEEEEEEEEE---SSEEGGGS-HHHHHHHHHHHHTT-.EEEEEE..EETTEEEEEEHHHHHHHHHHHSS- CS
                              RecU  55 DYiGvykgkyidfeaKetkkktfplknihehQiehlkkvekqgG.iaFlliyfskkdefylleakkllkllekkgkr 130
                                       D + +y+g+ i++e+K  ++++     ++++Q+e+l ++++  G + F+ +++  + e +l+++++l ++ e   ++
  gi|320100702|ref|YP_004176294.1|  42 DIVAIYRGRVIALEVKTLREEK--PVYVRREQVEKLAEFSRRAGaMPFIAVKYVGEGEWFLVPLDRLVEAGE---GN 113
                                       56679*************9987..345899*********98755278*******************999855...66 PP

                                       SEEEHHHHHHHSEE- CS
                              RecU 131 ksipleelkekgiei 145
                                        +ip+e + ++g+++
  gi|320100702|ref|YP_004176294.1| 114 YKIPVEAV-REGLRL 127
                                       88888888.555555 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.8e-05      0.22      15      73 ..      13      73 ..       4      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                         AHJR-like 15 slaeqyrekGyevllhPnredlPdfLksYrpDliarkdeeaviiEvksrrs....saseqyLq 73
                                      +la+ + e+G+ v+ +P +      L+   pD++a+     +++Evk+ r      + +++ +
  gi|320100702|ref|YP_004176294.1| 13 DLARRLWEHGFAVVRAPASGSRARVLR--YPDIVAIYRGRVIALEVKTLREekpvYVRREQVE 73
                                      68889999*************999998..4*****************9776443334445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1071.89
//
Query:       gi|320100703|ref|YP_004176295.1|  [L=522]
Description: PilT family ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-11   41.3   0.0    4.5e-10   39.0   0.0    1.9  2  T2SSE            Type II/IV secretion system protein
    6.1e-05   23.1   0.0      0.025   14.6   0.0    2.4  2  AAA_14           AAA domain
    0.00031   21.3   0.1     0.0018   18.8   0.0    2.3  2  AAA_18           AAA domain
     0.0011   19.4   0.1      0.016   15.6   0.0    2.5  2  AAA              ATPase family associated with various cellul
     0.0025   18.2   0.0      0.005   17.2   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0035   17.1   0.0     0.0063   16.3   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0038   17.0   0.0     0.0094   15.7   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0038   16.6   0.0     0.0089   15.4   0.0    1.5  1  DnaB_C           DnaB-like helicase C terminal domain
     0.0043   16.6   0.0       0.01   15.4   0.0    1.7  1  AAA_25           AAA domain
     0.0062   16.8   0.0      0.016   15.5   0.0    1.7  1  AAA_28           AAA domain
     0.0071   16.3   0.3       0.18   11.7   0.0    2.8  2  NTPase_1         NTPase
     0.0094   16.0   0.0      0.021   14.8   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0098   15.9   0.0      0.022   14.7   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.029   14.0   0.0    1.6  1  SRP54            SRP54-type protein, GTPase domain
      0.022   14.7   0.0      0.039   13.9   0.0    1.4  1  NACHT            NACHT domain
      0.032   14.1   0.0      0.067   13.1   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
      0.043   14.0   0.0       0.11   12.7   0.0    1.7  1  AAA_33           AAA domain
      0.047   13.4   0.0       0.13   11.9   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
      0.049   12.9   0.0       0.13   11.5   0.0    1.7  1  Zeta_toxin       Zeta toxin
      0.055   13.2   0.1       0.11   12.2   0.1    1.5  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.06   13.3   0.0       0.12   12.4   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
      0.061   13.0   0.3       0.18   11.5   0.0    1.9  2  AAA_24           AAA domain
      0.093   13.1   0.0       0.23   11.8   0.0    1.6  1  AAA_19           AAA domain
      0.093   13.0   0.0       0.29   11.4   0.0    1.8  1  AAA_22           AAA domain
      0.096   13.1   0.1       0.97    9.9   0.0    2.5  2  AAA_17           AAA domain
       0.11   12.9   0.0       0.25   11.8   0.0    1.6  1  RNA_helicase     RNA helicase
       0.14   11.5   0.0        0.3   10.4   0.0    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.15   12.1   0.0        0.4   10.8   0.0    1.6  1  Sigma54_activ_2  Sigma-54 interaction 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 ?   -0.6   0.0      0.88   5.6e+02      53     119 ..      94     159 ..      92     170 .. 0.84
   2 !   39.0   0.0     7e-13   4.5e-10      52     243 ..     187     377 ..     172     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.88
                             T2SSE  53 riaalakldiseerplqdarlpekgvrlrvvllPvvagealviRkksakeltlddlgaeealkekia 119
                                       ++   +++ + e    +++ l  +g +l++ ++ ++  + + +R++++ +l ++ +  e++++ +++
  gi|320100703|ref|YP_004176295.1|  94 QVVNEVNAVVREYAYSVNGVLI-TGSELQYQVAKAMGVQVILVRDREQGRLGFERFFTENTMSIHLK 159
                                       5666777888888999999999.9999999999999999999**99999999999988888876655 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 7e-13
                             T2SSE  52 sriaalakldiseerplqdarlp..........ekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkek 117
                                       ++i  +a++ i+  r   da ++           +++r+ +  +P++ g e  ++R    k+l+l+d+   e+l ++
  gi|320100703|ref|YP_004176295.1| 187 QEIEEMANEIIEATRSRSDAFIEidragstivqLGSYRIVITRPPLSDGwEITAVR--PLKKLRLEDYNLPEELVKR 261
                                       6788899999999999999999888999988888899************999****..6788999**9988776555 PP

                             T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfadllra 194
                                       ++e   +       il++G+ g GKtt++ al ++    ++ + tvE p+ + l   + +q  ++    ++ +l   
  gi|320100703|ref|YP_004176295.1| 262 LNE---R----AEGILIAGAPGMGKTTFAQALAEYYMRMNKVVKTVESPRDMMLPP-DITQYSKH--YADIGELHDI 328
                                       443...3....4789************************999**********9953.33444433..5688899999 PP

                             T2SSE 195 aLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerL 243
                                       +L  rPD  +  E+R  e +++   +     g ++ +Ha s+++a++r 
  gi|320100703|ref|YP_004176295.1| 329 LLLSRPDYTVFDEMRTDEDFKLFADLRLAGIGMIGVVHATSPIDAVQRF 377
                                       99********************66665555666**************97 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.02        13      11     103 ..      31     121 ..      26     129 .. 0.69
   2 !   14.6   0.0     4e-05     0.025       5      81 ..     269     350 ..     266     356 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                            AAA_14  11 RrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewekalk 84 
                                       R vGK ++ + li+ l     k + i y  l++ +  ++   ++  ++ le  ++e+ +  + DE q v+e+  +++
  gi|320100703|ref|YP_004176295.1|  31 RVVGKVVIHRSLIQILEyhaSKGRVIGYTGLEEVKRLREH--SDSGTIGLEI-TGERLKGPITDEEQVVNEVNAVVR 104
                                       6788888888887665566444555556667765554333..2234455553.4445555799************** PP

                            AAA_14  85 slvdegknldvivtGSnsk 103
                                       ++  +  n  v++tGS ++
  gi|320100703|ref|YP_004176295.1| 105 EYAYSV-N-GVLITGSELQ 121
                                       **9988.6.7******875 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke..........ekktylflD 71 
                                       ++i Ga  +GKTt+++ l++ ++  + + +  +++++rd +l  p+ + + + +++ +          ++  y ++D
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYYM--RMNKVVKTVESPRDMMLP-PD-I-TQYSKHYADigelhdilllSRPDYTVFD 340
                                       6899***********99997777..777788889999995544.32.1.22222211122344466777999***** PP

                            AAA_14  72 Eiqevpewek 81 
                                       E+   ++++ 
  gi|320100703|ref|YP_004176295.1| 341 EMRTDEDFKL 350
                                       *999888865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       5.1   3.3e+03     103     114 ..     255     266 ..     254     268 .. 0.88
   2 !   18.8   0.0   2.9e-06    0.0018       1      34 [.     269     325 ..     269     358 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.1
                            AAA_18 103 peelleRlekRg 114
                                       peel +Rl++R 
  gi|320100703|ref|YP_004176295.1| 255 PEELVKRLNERA 266
                                       79********97 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.9e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........................gvnlrdvake 34 
                                       Il++G+pG GKtt+a++L++   +                        + ++ d+   
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYY-MrmnkvvktvesprdmmlppditqySKHYADIGEL 325
                                       99****************8863.13344455544444445555555544444444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.5e-05     0.016       1      22 [.     269     290 ..     269     317 .. 0.84
   2 ?    0.7   0.0         1   6.6e+02      78     130 ..     459     514 ..     448     516 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-05
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       +l+ G pG+GKT++a+a+a+  
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYY 290
                                       6899***************984 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                                       CCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESS.GGGSTHHHHS.TTSSEEEET CS
                               AAA  78 eseeeervvnqLlteldgvkkk.eskvivigatnr.pdkldpallr.gRfdrkiei 130
                                       ++  +e+v+++L + + + + + e++ iv+ +t +  +k+++++ r +++++k+++
  gi|320100703|ref|YP_004176295.1| 459 KHPTHEKVIEELGKLMPEADIRfENDAIVVSITRSdLRKYNKKIKRlRKIEEKYNL 514
                                       55667788888888887777766777899999988899999999999999988776 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   7.9e-06     0.005      15      51 ..     258     293 ..     252     382 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.9e-06
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       +++r+++   e +l+ G++G+GK++ +++l++++ + 
  gi|320100703|ref|YP_004176295.1| 258 LVKRLNERA-EGILIAGAPGMGKTTFAQALAEYYMRM 293
                                       566666555.89******************9876555 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   9.9e-06    0.0063      45      79 ..     264     298 ..     253     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.9e-06
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsvl 79 
                                       e++e+i++ G +G+GK+ +a al+   +r ++ v 
  gi|320100703|ref|YP_004176295.1| 264 ERAEGILIAGAPGMGKTTFAQALAEYYMRMNKVVK 298
                                       6899********************99999887775 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-05    0.0094      28      56 ..     261     289 ..     251     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                            RuvB_N  28 kreealdhvllyGpPGlGkttlakiiake 56 
                                       + +e  + +l++G+PG+Gktt+a+ +a+ 
  gi|320100703|ref|YP_004176295.1| 261 RLNERAEGILIAGAPGMGKTTFAQALAEY 289
                                       55788899******************974 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   1.4e-05    0.0089      20      48 ..     267     295 ..     257     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                       XEEEEEEXTTSSHHHHHHHHHHHHHHCST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  20 dliiiAarpsmGktalalniaenaavkek 48 
                                       + i+iA+ p+mGkt++a  +ae  +  +k
  gi|320100703|ref|YP_004176295.1| 267 EGILIAGAPGMGKTTFAQALAEYYMRMNK 295
                                       5589*****************98774333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.6e-05      0.01      23      58 ..     256     291 ..     252     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava 58 
                                       + lvk+l  + e +l+aGapg GKtt+a  la  ++
  gi|320100703|ref|YP_004176295.1| 256 EELVKRLNERAEGILIAGAPGMGKTTFAQALAEYYM 291
                                       6799999999999****************9996655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.5e-05     0.016       2      25 ..     269     292 ..     268     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                            AAA_28   2 ivitGgestGKTtlleaLaargyp 25 
                                       i i G+++ GKTt ++aLa+  ++
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYYMR 292
                                       789****************97433 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.42   2.7e+02      31     103 ..     128     212 ..      94     227 .. 0.60
   2 !   11.7   0.0   0.00029      0.18       2      30 ..     269     297 ..     268     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.42
                                       EEEEEEEE-.------EEEEEET.T--EEEEEETT...........---SSEETTEEE-HHHHHHHHHHHHHHHHHH CS
                          NTPase_1  31 gGfyteevr.eggrrigFkivdlasgeegiLarve...........akreprvgkyvvdvesfeelalealrkalse 95 
                                        G+ +  vr +++ r gF+     +++  i  +++           + r  r+g   ++ +++ee+a e+++ + s+
  gi|320100703|ref|YP_004176295.1| 128 MGVQVILVRdREQGRLGFERFFT-ENTMSIHLKEGvapvakvgrpgEWRFTRLGDKPLTRQEIEEMANEIIEATRSR 203
                                       44444455544444555543333.12211111111233333335555566677777777788888888888888888 PP

                                       H-.EEEE-- CS
                          NTPase_1  96 ad.viviDE 103
                                       +d  i iD 
  gi|320100703|ref|YP_004176295.1| 204 SDaFIEIDR 212
                                       875555775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00029
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       ++i G pG+GKtT+ + ++e   + +  v
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYYMRMNKVV 297
                                       789***************99988877666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.3e-05     0.021       2      36 ..     269     306 ..     268     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-05
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdt 36 
                                       +l+ G+pG gK+++a+ la+ +   n+ v +v  +rd+
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYYmrmNKVVKTVESPRDM 306
                                       7999*****************99999999999888887 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.5e-05     0.022       9      51 ..     257     303 ..     249     308 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT.T--....----T CS
                              TsaE   9 algkklakalgdvilLeGdLGaGKTtlvrglakal.gve....evkSP 51 
                                       +l k+l +  ++ il+ G  G+GKTt++++la+ +  ++    +v+SP
  gi|320100703|ref|YP_004176295.1| 257 ELVKRLNE-RAEGILIAGAPGMGKTTFAQALAEYYmRMNkvvkTVESP 303
                                       33344433.2456*******************9763222334567777 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.6e-05     0.029       4      32 ..     269     297 ..     266     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkkv 32 
                                       il++G  G+GKTt +  La+++++++k v
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYYMRMNKVV 297
                                       89*********************998866 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.1e-05     0.039       3      22 ..     269     288 ..     267     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       +++ G++G+GKTt++q la+
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAE 288
                                       789*************9986 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.067       2      43 ..     269     314 ..     268     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                             AAA_3   2 vllegvPGlaktllvkalaka...ldlefkriqftpdl.lPsdilG 43 
                                       +l+ g+PG++kt++++ala+    ++  +k +    d+ lP di+ 
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYymrMNKVVKTVESPRDMmLPPDITQ 314
                                       799****************962224555666777777526999985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.11       2      21 ..     269     288 ..     269     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                            AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                       +l+ G+pG+GK+t+a+ l++
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAE 288
                                       5789************9974 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.13      14      53 ..     258     297 ..     250     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                       HHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                   Sigma54_activat  14 qikkvaktdlsvlitGesGtGKellaraiheaskrkekpf 53 
                                        +k++ +    +li G  G GK+++a+a+ e   r +k +
  gi|320100703|ref|YP_004176295.1| 258 LVKRLNERAEGILIAGAPGMGKTTFAQALAEYYMRMNKVV 297
                                       57777888889******************99888877754 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.13      15      47 ..     265     297 ..     256     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvv 47 
                                       r   il++G+pG GK++ a++l+++  r ++vv
  gi|320100703|ref|YP_004176295.1| 265 RAEGILIAGAPGMGKTTFAQALAEYYMRMNKVV 297
                                       55669*****************99986666655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00018      0.11       1      30 [.     271     300 ..     271     301 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavv 30 
                                       ++G +G GKttf +al+e+++  ++ v++v
  gi|320100703|ref|YP_004176295.1| 271 IAGAPGMGKTTFAQALAEYYMRMNKVVKTV 300
                                       68******************9998888777 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018      0.12      13      53 ..     256     295 ..     237     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                       HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII  13 enlleklkskrdkrglikmaTGtGKTlvaaklierllkkgk 53 
                                       e+l++ l+ +r + +li+ a G+GKT  a +l+e++++ +k
  gi|320100703|ref|YP_004176295.1| 256 EELVKRLN-ERAEGILIAGAPGMGKTTFAQALAEYYMRMNK 295
                                       55666776.99999*********************998755 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         8   5.1e+03     156     176 ..     185     205 ..     178     228 .. 0.74
   2 ?   11.5   0.0   0.00028      0.18       5      22 ..     269     286 ..     265     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8
                            AAA_24 156 tanelkeevDlvlranlkred 176
                                       t +e++e++ ++++a+ +r+d
  gi|320100703|ref|YP_004176295.1| 185 TRQEIEEMANEIIEATRSRSD 205
                                       678899999999999887776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00028
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       ili G +g+GKTt+a  l
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQAL 286
                                       89*************977 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00035      0.23      10      40 ..     266     296 ..     256     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggv 40 
                                       ++ +l+ + pG+GKT+  ++  +++ ++++v
  gi|320100703|ref|YP_004176295.1| 266 AEGILIAGAPGMGKTTFAQALAEYYMRMNKV 296
                                       456899999*************999999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00045      0.29       5      29 ..     266     290 ..     261     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                            AAA_22   5 agilvvtGesGtGKTtllrrlleql 29 
                                       a  +++ G +G+GKTt ++ l+e +
  gi|320100703|ref|YP_004176295.1| 266 AEGILIAGAPGMGKTTFAQALAEYY 290
                                       56689***************99865 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.4   1.5e+03      30      78 ..      67     117 ..      53     131 .. 0.75
   2 ?    9.9   0.0    0.0015      0.97       2      19 ..     273     290 ..     272     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.4
                                       HHHHHHTT..TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEEEE CS
                            AAA_17  30 lreeakrg..glakardemrklpleekkelqkeaaekiaeea.kkkgvlvdg 78 
                                       lre   +g  gl +  +e  k+p+ +++++  e+ + ++e a + +gvl++g
  gi|320100703|ref|YP_004176295.1|  67 LREHSDSGtiGL-EITGERLKGPITDEEQVVNEVNAVVREYAySVNGVLITG 117
                                       666665663334.555666699999999999999999999886667888887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                                       E-TTSSHHHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklveky 19 
                                       G PG+GK+t ++ l+e y
  gi|320100703|ref|YP_004176295.1| 273 GAPGMGKTTFAQALAEYY 290
                                       9************99976 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   0.00038      0.25       1      26 [.     269     294 ..     269     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i++ G++g GK+t+a+ La+  ++  
  gi|320100703|ref|YP_004176295.1| 269 ILIAGAPGMGKTTFAQALAEYYMRMN 294
                                       6899**************99887544 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00047       0.3      35      59 ..     262     286 ..     241     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                                       GGGS-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  35 lkkmashllvaGatgsGKStalntL 59 
                                       l++ a  +l+aGa+g GK+t+ ++L
  gi|320100703|ref|YP_004176295.1| 262 LNERAEGILIAGAPGMGKTTFAQAL 286
                                       55556689*************9998 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00062       0.4      15      52 ..     260     297 ..     255     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00062
                                       HHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--S CS
                   Sigma54_activ_2  15 eqaaqsklpvfltGekGsgkelvArlLhknsgpwleif 52 
                                       + + ++   ++++G++G gk+++A++L++   +  +++
  gi|320100703|ref|YP_004176295.1| 260 KRLNERAEGILIAGAPGMGKTTFAQALAEYYMRMNKVV 297
                                       5667777889*****************99887766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      786  (0.0438396); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 3490.40
//
Query:       gi|320100704|ref|YP_004176296.1|  [L=504]
Description: calcineurin superfamily metallophosphoesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0036   17.8   0.9      0.012   16.1   0.9    1.8  1  Metallophos  Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
       0.17   11.9  14.4       0.29   11.1  14.4    1.3  1  Mucin        Mucin-like glycoprotein
       0.84   10.1   5.3        1.5    9.3   5.3    1.4  1  MGC-24       Multi-glycosylated core protein 24 (MGC-24), sia


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.9     2e-06     0.012      34     202 ..      83     228 ..      70     230 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-06
                                       ESEEEEESTSSSSSHHHHHHHHHHHHHHHH.TSEEEEEC-TTS....CHHHHHHHHHHHHHHHHHHHEHHHCEEETS CS
                       Metallophos  34 pdlvllaGDlvdrgdlekellellaalvky.pipvylllGNHe....gfeeellnkygylgifsepwrsdaevfnnl 105
                                       p +++ +GD v  g l++ +++l++ l k    ++++++GNH+    g        ++++  f +p  + ++   ++
  gi|320100704|ref|YP_004176296.1|  83 PLAFIGLGDHVGLGTLDQ-YVKLYEILNKTrLENIWMTPGNHDvaysG---VNGTGFDFWRQFIGPDSMVVDDIPGW 155
                                       5677878*******9999.6666555555443667********75552...44444555555555555556666666 PP

                                       EEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESS...CSSSCSC CS
                       Metallophos 106 plaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkdlekrekadwvivlgHsply...rgsgylf 179
                                        +a + s   + +  +G    +                    +  +    + ++++ +++ +H+ply   +++ ++ 
  gi|320100704|ref|YP_004176296.1| 156 RIALIDSE--TDISTWGQ--QI--------------------QAAY----NSTGGRMLLLGFHRPLYpnvNHNLKQG 204
                                       66666666..55555554..11....................2222....224444444444666665544444444 PP

                                       CHHHHHHHHHHTT.ESEEEEESSS CS
                       Metallophos 180 gdealedllkkyg.vdlvisGHtH 202
                                        d +l  + + +g + lv+ +H H
  gi|320100704|ref|YP_004176296.1| 205 YDTVLLGYMNSNGwPALVLQAHFH 228
                                       444444444444455555555555 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  14.4   4.8e-05      0.29      54     140 ..     403     495 ..     369     498 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                             Mucin  54 ppttttttt......tasttittkttkatt.ttttttttttateaPsdavttaeaPtttttrapsrlrevdGslsss 123
                                          + t+t+      t ++t+t ++t +tt t t+ tt t + + P +++t  +  t+t t +   + e   ++++ 
  gi|320100704|ref|YP_004176296.1| 403 VVKAETVTStsiayiTRTATKTITSTYSTTlTETSVTTVTETQQLPPTTITVQRNVTSTYTTTVPLIVE-HEAPGGD 478
                                       333333333224555444444444444444133444555667778888999998888887764444444.4567888 PP

                             Mucin 124 aWvcaPLllavsalayt 140
                                       a+  +  +l v+a+a  
  gi|320100704|ref|YP_004176296.1| 479 AYLYIAAVLGVIAVAEL 495
                                       88888888888887765 PP

>> MGC-24  Multi-glycosylated core protein 24 (MGC-24), sialomucin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.3   0.00024       1.5      39     127 ..     408     502 ..     391     504 .] 0.52

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                            MGC-24  39 tvedCsvvnvtelcsaaskst....pkptnstaktttkpsstttstsvatsgttnttvtptsqparkstFDaAsFiG 111
                                       tv++ s++  t++++ + +st     + t+ t+ t+t++  +tt t     ++t tt +p    +  ++ Da  +i 
  gi|320100704|ref|YP_004176296.1| 408 TVTSTSIAYITRTATKTITSTysttLTETSVTTVTETQQLPPTTITVQRNVTSTYTTTVPLIVEHEAPGGDAYLYIA 484
                                       443333333333332222222211123333333444444444444444444444445555555678999***99999 PP

                            MGC-24 112 GivLvLgvq..AviFFly 127
                                        +  v++v   Avi F+ 
  gi|320100704|ref|YP_004176296.1| 485 AVLGVIAVAelAVIIFVK 502
                                       887777774447777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3737.30
//
Query:       gi|320100705|ref|YP_004176297.1|  [L=443]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   21.5   0.0    0.00027   20.5   0.0    1.5  1  ParA        NUBPL iron-transfer P-loop NTPase
    0.00038   20.1   0.0     0.0037   16.9   0.0    2.0  2  cobW        CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.08   11.9   1.8       0.15   11.0   0.3    1.9  2  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.088   12.9   1.1       0.16   12.0   0.5    1.8  2  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
        0.1   12.4   0.0       0.29   10.9   0.0    1.7  2  AAA_26      AAA domain
       0.13   11.5   0.0       0.24   10.6   0.0    1.4  1  Zeta_toxin  Zeta toxin


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 !   20.5   0.0   8.9e-08   0.00027       2      38 ..     118     154 ..     117     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.9e-08
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgll 38 
                                       ++ viav+  K G GKS v+ ++Al+L+++glk+g++
  gi|320100705|ref|YP_004176297.1| 118 IRPVIAVTGVKTGAGKSMVSREVALELRRRGLKTGVV 154
                                       7789*******************************97 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 ?    0.7   0.0      0.12   3.5e+02       1      32 [.     120     154 ..     120     170 .. 0.81
   2 !   16.9   0.0   1.2e-06    0.0037     111     175 ..     233     294 ..     222     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                                       EEEEEEES.TTCCHHHHHHHHH..CT--SS-EEEE CS
                              cobW   1 pvtvltGf.lGsGKTtLlnhll..enraglklavi 32 
                                       pv+ +tG   G+GK+++ +++    +r+glk+ v+
  gi|320100705|ref|YP_004176297.1| 120 PVIAVTGVkTGAGKSMVSREVAleLRRRGLKTGVV 154
                                       5777888647******9999988878889998887 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.2e-06
                                       CECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-E CS
                              cobW 111 tldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakv 175
                                       + d++++v Da +     e ++  +e  l ++d +++nK+D+++  a  ++++e + + np+a+v
  gi|320100705|ref|YP_004176297.1| 233 KPDFMITVADAMR--PGIEASSFPGEVNLRMCDAVIINKVDQAKPGAV-DRIKESILARNPDAHV 294
                                       6699*******55..5677777788999****************9965.9**9999999998876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   5.1e-05      0.15      31      63 ..     121     154 ..     111     156 .. 0.91
   2 ?   -0.6   0.1      0.17   5.1e+02     167     193 ..     260     286 ..     257     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.1e-05
                                       EEEEEE-.TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB  31 vvGltGv.PGaGkstlvealglelrrrGkrvavl 63 
                                       v+ +tGv  GaGks +  +++lelrrrG + +v+
  gi|320100705|ref|YP_004176297.1| 121 VIAVTGVkTGAGKSMVSREVALELRRRGLKTGVV 154
                                       7899**956*********************9997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.17
                                       HH-SEEEEE---HHHHHHHHHHHHHHH CS
                              MeaB 167 eiaDiivvnkaDkkeaekaarelraal 193
                                        + D +++nk D+++   + r  +++l
  gi|320100705|ref|YP_004176297.1| 260 RMCDAVIINKVDQAKPGAVDRIKESIL 286
                                       57899*******887777766666655 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   5.5e-05      0.16       1      30 [.     122     151 ..     122     155 .. 0.93
   2 ?   -3.4   0.0       3.2   9.6e+03      79      87 ..     265     273 ..     257     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.5e-05
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrV 30 
                                       ia+++ k G+GK++++   a  l rrgl++
  gi|320100705|ref|YP_004176297.1| 122 IAVTGVKTGAGKSMVSREVALELRRRGLKT 151
                                       89*************************997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.2
                                       EEEEEESS. CS
                                       xxxxxxxxx RF
                              CbiA  79 vvlnrvdge 87 
                                       v++n+vd  
  gi|320100705|ref|YP_004176297.1| 265 VIINKVDQA 273
                                       899999976 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.9e-05      0.29       3      36 ..     122     155 ..     121     192 .. 0.89
   2 ?   -2.5   0.0       1.2   3.7e+03     161     178 ..     264     283 ..     258     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.9e-05
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36 
                                       i vtg+ tg+GK++vs  ++  l+r+g k+g+++
  gi|320100705|ref|YP_004176297.1| 122 IAVTGVKTGAGKSMVSREVALELRRRGLKTGVVR 155
                                       779****************************987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                            AAA_26 161 GvilNkvrnpe..nvetlek 178
                                       +vi+Nkv +++  +v+ +++
  gi|320100705|ref|YP_004176297.1| 264 AVIINKVDQAKpgAVDRIKE 283
                                       59999986653335555554 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   8.1e-05      0.24      11      43 ..     115     147 ..     109     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.1e-05
                        Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdelerq 43 
                                        ++ rP++ + g  +GAGKs ++++++ el+r+
  gi|320100705|ref|YP_004176297.1| 115 LESIRPVIAVTGVKTGAGKSMVSREVALELRRR 147
                                       56789**********************999754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3365.60
//
Query:       gi|320100706|ref|YP_004176298.1|  [L=837]
Description: phosphoenolpyruvate synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-121  404.3   0.0   6.1e-121  403.7   0.0    1.3  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    2.8e-91  305.7   0.0    4.4e-91  305.0   0.0    1.3  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    4.3e-29  100.1   1.1    9.5e-29   98.9   1.1    1.6  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.061   13.7   0.0    2.1  1  Radical_SAM      Radical SAM superfamily
       0.18   10.6   0.0       0.38    9.6   0.0    1.5  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase


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 !  403.7   0.0  1.7e-124  6.1e-121       2     324 ..      20     364 ..      19     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 403.7 bits;  conditional E-value: 1.7e-124
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelP 78 
                                       +lvGGK+anL+e++n agipvPpgfa+ta+af++fle++gl eki  +l++ldv++++el++++++ire+i+++++P
  gi|320100706|ref|YP_004176298.1|  20 PLVGGKNANLGEMIN-AGIPVPPGFAVTAYAFKYFLEKTGLGEKIYGMLRKLDVNNTKELEETTARIREMIMNQPMP 95 
                                       69***********77.************************************************************* PP

                            PPDK_N  79 eeleeaikeayeelgkkfgde..elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAil 153
                                       +e+e++ik++y el+ k+g +  +l+vaVRSSataEDlp+asfaGqqdtyLnv g+++v+  +k+++aSlf++rA++
  gi|320100706|ref|YP_004176298.1|  96 KEVEDEIKKYYLELAGKLGLDpgKLRVAVRSSATAEDLPEASFAGQQDTYLNVYGADNVVYYVKRCWASLFTARATF 172
                                       *********************999***************************************************** PP

                            PPDK_N 154 YrkekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkil 230
                                       Yr ++g++he + ++v+vqkmvns+  ++GV+f+l+p tG++++v+i+ s+GlGe+VV+G+vtpdef+v+k+t +i+
  gi|320100706|ref|YP_004176298.1| 173 YRVAQGIPHERTFMSVTVQKMVNSK--SAGVMFTLHPVTGDENVVVIEGSWGLGESVVGGKVTPDEFIVDKKTLSIV 247
                                       *************************..************************************************** PP

                            PPDK_N 231 ekkigekeikivydekeegtkevevpeeerekl.....................aLsdeeveeLaeiakkiekhygt 286
                                       e+++++k  +i++d++  ++++ +++e ++ ++                     aLsd+ev++Lae+a  i+khyg+
  gi|320100706|ref|YP_004176298.1| 248 ERHLNKKTFMITFDPALGRNVHLKWDE-QKGRWvseegegvnppltqiahpdkpALSDDEVKRLAELALLIQKHYGK 323
                                       ****************97777777655.44455788899999999999999999*********************** PP

                            PPDK_N 287 pmdiEfaid...eeegklyllQaRpetrtsekkekkaaetl 324
                                        mdiE+aid   +   +++++QaRpet++s+kk+k+a+++ 
  gi|320100706|ref|YP_004176298.1| 324 HMDIEWAIDsdlPFPSNVFIVQARPETVWSTKKAKEAEKKP 364
                                       *********99999********************9998875 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 !  305.0   0.0   1.2e-94   4.4e-91       4     293 ..     507     812 ..     504     813 .. 0.95

  Alignments for each domain:
  == domain 1  score: 305.0 bits;  conditional E-value: 1.2e-94
                                       STSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTS.CC.HHHHHH..........HHHHH CS
                   PEP-utilizers_C   4 sgklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmar.ee.lpteee..........qaeay 68 
                                       +g + ++l ++++++++k+++N+++p+++ek+++ +++GiGL+R+Ef+f+++ ++ + +++e          +ae +
  gi|320100706|ref|YP_004176298.1| 507 VGISPEQLLPLYPVTATKIYMNLGEPDAIEKYKDLPFDGIGLMRIEFIFTDWvQYhPLYLIEigkpeivvnkLAEGI 583
                                       56678899999*****************************************65568889999************** PP

                                       HHHHHHTTTSEEEEEXXXSSCC..GGSGGC.HHHH.XSXGGGSSXTHHHHCCS..HHHHHHHHHHHHHHCCCC...E CS
                   PEP-utilizers_C  69 kkvleamngrpvvvRtlDiggd..kelpel.keepeevNPmlGfRgirlglse..pelfetqlrAllrasaag...k 137
                                       +kv++a+++rpvvvR+ D++++  + l+ + k+ep e+NPm+G+Rg++++++   +  f+ ++rA+ ++++++   +
  gi|320100706|ref|YP_004176298.1| 584 AKVAQAIYPRPVVVRFSDFKTNeyRGLKGGeKYEPDERNPMIGWRGVSRYIHPkyEPAFRLEVRAIRKVREEMgltN 660
                                       *********************98899**9856799****************976699**************66677* PP

                                       EEEEESSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHT CS
                   PEP-utilizers_C 138 leimlPmvasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytla 214
                                       +++m+P+v++++ele+a ki+ee+       g+k++k++kv++M Evps+allad++ak+vd+fSiG+NDLtQ++l+
  gi|320100706|ref|YP_004176298.1| 661 VWVMFPFVRTTWELEKAIKIMEEE-------GLKRSKDFKVWAMAEVPSIALLADEFAKYVDGFSIGSNDLTQLVLG 730
                                       **********************99.......89999***************************************** PP

                                       XXCCCHCHHHH..SXTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCC.SCCCHHHHHHCTXSEEEEXGGGHHHHHHH CS
                   PEP-utilizers_C 215 vdRdneevakl..ydplepavlrlikevikaaeekglkvgiCGelag.dpsavellvglGldelSmsaasvpaaraa 288
                                       +dRd++ +a++  +d+ +pavl++i+++i++a+++g++v+iCG++++ +p++ve+lv+ G+d++S+++++v+ +r++
  gi|320100706|ref|YP_004176298.1| 731 ADRDSNILAEMgyFDERDPAVLQAIRMIIEKAHSRGATVSICGQAPSvYPEIVEFLVKYGIDSISVNPDAVISTRRL 807
                                       ************9**********************************9***************************** PP

                                       HHCTT CS
                   PEP-utilizers_C 289 laqve 293
                                       +a++e
  gi|320100706|ref|YP_004176298.1| 808 VASIE 812
                                       *9986 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   1.1   2.6e-32   9.5e-29       2      73 .]     409     480 ..     408     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 2.6e-32
                                       --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       ++eg+ILv+++t+p++++ ++ka++ivt++GGmtSHaAiv+relgiPaVvg+g+at+++k+g ++tvDg +G
  gi|320100706|ref|YP_004176298.1| 409 FKEGDILVTKMTDPDWVPLMKKARAIVTDEGGMTSHAAIVSRELGIPAVVGTGSATQVIKTGIEVTVDGGRG 480
                                       799******************************************************************998 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.7e-05     0.061      32     138 ..     701     824 ..     646     832 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHTTSEEEEEE..............SSTGGGS...........TTHHHHHHHHHHTCCCTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx..............xxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  32 eeileevkelkaekgvkevilg..............ggeplly...........pdfvellerlaklavpgiritve 83 
                                        +i+ +++e+ a+  v+++ +g              +     +           ++ v  + r++ ++   +  tv+
  gi|320100706|ref|YP_004176298.1| 701 PSIALLADEF-AKY-VDGFSIGsndltqlvlgadrdS-----NilaemgyfderDPAVLQAIRMIIEKAHSRGATVS 770
                                       5555555555.333.5555555333333333333330.....13333434433355555555555555588888999 PP

                                       ECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHH CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  84 tngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklr 138
                                       ++g  p+  +e++e l+++g+d +s++ +a+ +  +++l+    +++  l+a++++r
  gi|320100706|ref|YP_004176298.1| 771 ICGQAPSvyPEIVEFLVKYGIDSISVNPDAVIS--TRRLV-ASIERKIMLDAVRNAR 824
                                       999999999*********************988..57777.6677788888887777 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 ?    9.6   0.0   0.00011      0.38     241     315 ..     412     488 ..     370     505 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00011
                                       TEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHH....CT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHH CS
                       Epimerase_2 241 nvtlieplgyldflsllknaklvltdSgGiqeEaps....lgvpvvnlReeteRpegveagtnvlvgtdkeeIvaal 313
                                         +l++ +   d + l+k+a++++td gG+   a++    lg+p+v+   +++  + ++ g  v v+  +  I++ +
  gi|320100706|ref|YP_004176298.1| 412 GDILVTKMTDPDWVPLMKKARAIVTDEGGMTSHAAIvsreLGIPAVVG--TGSATQVIKTGIEVTVDGGRGVIYEGI 486
                                       55688889999********************99998777789999998..899999999999999999988888876 PP

                                       HH CS
                       Epimerase_2 314 ek 315
                                        +
  gi|320100706|ref|YP_004176298.1| 487 VE 488
                                       54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (837 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 5762.38
//
Query:       gi|320100707|ref|YP_004176299.1|  [L=502]
Description: carbamoyl-phosphate synthase L chain ATP-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  131.3   0.0    6.3e-38  130.4   0.0    1.4  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.5e-23   83.5   0.0    4.1e-23   82.0   0.0    1.8  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    8.4e-21   74.1   0.0    1.6e-20   73.2   0.0    1.5  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    8.6e-10   38.5   0.0    1.7e-09   37.5   0.0    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    7.8e-09   35.3   0.0    1.5e-08   34.4   0.0    1.4  1  ATP-grasp        ATP-grasp domain
    2.8e-05   24.0   0.0    5.7e-05   23.0   0.0    1.5  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00047   19.5   0.0    0.00085   18.6   0.0    1.3  1  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    0.00062   19.4   0.0     0.0014   18.3   0.0    1.6  1  ATP-grasp_4      ATP-grasp domain
     0.0022   18.1   0.0     0.0091   16.1   0.0    1.9  2  ATP-grasp_3      ATP-grasp domain
  ------ inclusion threshold ------
       0.14   11.4   0.0       0.26   10.5   0.0    1.3  1  ATPgrasp_YheCD   YheC/D like ATP-grasp
       0.31   11.4   1.5         21    5.5   0.0    2.6  2  NUC130_3NT       NUC130/3NT 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 ?   -3.6   0.0       3.8   6.2e+03     139     183 ..      44      88 ..      40      90 .. 0.66
   2 !  130.4   0.0   3.8e-41   6.3e-38       1     209 [.     109     313 ..     109     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CC CS
                       CPSase_L_D2 139 qalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsve 183
                                        +l+ea v    +v+ + ++ +e   ++ +  y ++E N+   +e
  gi|320100707|ref|YP_004176299.1|  44 YMLEEAKVSSYMDVKEIVEAALELGAEAVHPCYGFLENNPEFHRE 88 
                                       566666666666666667777777777777777788877777666 PP

  == domain 2  score: 130.4 bits;  conditional E-value: 3.8e-41
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       Dk + k++++k++vp+ p s++  ++  +  ++a+ +gyP ++k+a g  G+G rv ++e++ +  +k+a++ea+  
  gi|320100707|ref|YP_004176299.1| 109 DKPAVKTLAEKLDVPTLPWSIV--DDDADLEEFARAHGYPLVLKPARGAWGRGIRVLWSEKDAE-QLKTAVKEAEKL 182
                                       889999*************999..9999******************************998865.5789******** PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT- CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgv 154
                                       +g+++++ve ++   k +Ev+v+ D +  vi++ ere slq    k + +APs+t+++e r++l   av+v +++ +
  gi|320100707|ref|YP_004176299.1| 183 YGDRRIYVEPYMGSAKLLEVQVIGDGE-KVIHLYEREASLQDDYLKTVIEAPSKTVSKELRDKLVGYAVAVGEALRL 258
                                       *************************85.79*********************************************** PP

                                       EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 155 vgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       ++ +tvefl+d +s+  ++ EvN+ ls e+  +e++TG+d+v++++  al   L+
  gi|320100707|ref|YP_004176299.1| 259 RNTATVEFLYDVRSRTLFLNEVNPGLSPEHVATEAVTGVDIVEKQVEAALYSALD 313
                                       *********************************************9999877665 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 !   82.0   0.0   2.5e-26   4.1e-23       2     109 ..       2     103 ..       1     104 [. 0.95

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2.5e-26
                                       --EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEE CS
                     Biotin_carb_N   2 ikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadav 78 
                                        +++++a rGe+Avri+r++ e g++ + +y+e+d++s+h r+  e  ++      +sY+++++iv+aa e ga+av
  gi|320100707|ref|YP_004176299.1|   2 PRRIMVAGRGEAAVRIARTLVEKGYHPLGIYTEKDEASPHRRYMLEEAKV------SSYMDVKEIVEAALELGAEAV 72 
                                       589*************************************9988776666......6******************** PP

                                       E--SSTTTT-HHHHHHHHHTT-EESSS-HHH CS
                     Biotin_carb_N  79 hpGyGflsEnaefaeaveeagivfiGPsaea 109
                                       hp yGfl +n+ef ++v+++g+v iGP+++ 
  gi|320100707|ref|YP_004176299.1|  73 HPCYGFLENNPEFHREVARRGLVPIGPPPSL 103
                                       ***************************9976 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 !   73.2   0.0   9.7e-24   1.6e-20      13     108 .]     338     432 ..     327     432 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 9.7e-24
                                       TEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS-BSHHHHHH CS
                     Biotin_carb_C  13 flpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGvktnieflra 89 
                                         pssG v+++++p+g gv vdsgv++g + s++y  llaK+ ++g +r++al rlrraL+e+ i+Gv+tni++lr+
  gi|320100707|ref|YP_004176299.1| 338 GEPSSGVVKSYNEPAGLGVAVDSGVAAGLKLSEEY-VLLAKVLAWGGSRATALGRLRRALSEMSIDGVQTNIPVLRE 413
                                       57*********************************.8**************************************** PP

                                       HHH-HHHHHT---TTTCCC CS
                     Biotin_carb_C  90 iledeefakgeldtkflee 108
                                       +l+ +e+++g +++++lee
  gi|320100707|ref|YP_004176299.1| 414 LLALREIEEGVYTVRLLEE 432
                                       ***************9985 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 !   37.5   0.0   1.1e-12   1.7e-09       5     174 ..     120     282 ..     116     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.1e-12
                                       TT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEE...SSGGGHHHHHHHHHTT..-SCEE CS
                   Dala_Dala_lig_C   5 aGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskv...eseeelkeaieeafky..dekvl 76 
                                       +++p+ p+ +++ ++        le+   + gyp++ Kpar     G+      + +e+lk a++ea k   d+++ 
  gi|320100707|ref|YP_004176299.1| 120 LDVPTLPWSIVDDDAD-------LEEFARAHGYPLVLKPARGAWGRGIRVLwseKDAEQLKTAVKEAEKLygDRRIY 189
                                       5566666666554443.......44568999**********999999987722245689********88555***** PP

                                       EEE--.ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS-.---HHHHHHHHHHHHHHHHHTT- CS
                   Dala_Dala_lig_C  77 vEeai.egreievavlgneklevsevgeivvkkgfydyeakysddkaqlevpa.klekeveekiqelalkaykaldl 151
                                       vE ++ +++ +ev v+g+++  ++ + e+ ++      +  y   k+ +e p  +++ke ++k+  +a+ + +al l
  gi|320100707|ref|YP_004176299.1| 190 VEPYMgSAKLLEVQVIGDGEKVIH-LYEREAS-----LQDDYL--KTVIEAPSkTVSKELRDKLVGYAVAVGEALRL 258
                                       *****99**********7665555.4444433.....455665..4445555415899******************* PP

                                       -SEEEEEEEE.ETTTEEEEEEEES CS
                   Dala_Dala_lig_C 152 rGlaRvDffl.teegeivlnEvNt 174
                                       r +a v f++  ++ +++lnEvN+
  gi|320100707|ref|YP_004176299.1| 259 RNTATVEFLYdVRSRTLFLNEVNP 282
                                       **********5567899******4 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   9.4e-12   1.5e-08       2     158 ..     118     282 ..     117     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 9.4e-12
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC.......GTTCEEEEE- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal.......keekvivEef 71 
                                       ekl +p+ ++ +v+++++lee+a++ g+p+v+K +  g  G+G  v+ se+d+eq+ +a+       ++++++vE +
  gi|320100707|ref|YP_004176299.1| 118 EKLDVPTLPWSIVDDDADLEEFARAHGYPLVLK-PARGAWGRGIRVLWSEKDAEQLKTAVkeaeklyGDRRIYVEPY 193
                                       6899*****************************.888888*******9999998887777777999999******99 PP

                                       ---SEEEEEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE.-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  72 vpfekElsvlvvrsaeGetafypvvetvqedgilrlsvapae.vsekaqkkaeeiakkiveeLggvGvfavElFvle 147
                                       +   k l v v+ + e  ++ y+    +q+d    +  ap++ vs++   k   +a  + e+L      +vE+ +  
  gi|320100707|ref|YP_004176299.1| 194 MGSAKLLEVQVIGDGEKVIHLYEREASLQDDYLKTVIEAPSKtVSKELRDKLVGYAVAVGEALRLRNTATVEFLYDV 270
                                       999999999999888888999***9999999998888899762566788999********************97764 PP

                                       TCT.EEEEEEES CS
                         ATP-grasp 148 dge.llvnElap 158
                                        ++ l++nE+ p
  gi|320100707|ref|YP_004176299.1| 271 RSRtLFLNEVNP 282
                                       4445*****988 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.5e-08   5.7e-05       3     108 ..     110     214 ..     108     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.5e-08
                                       HHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCT.S-TTCC CS
                            GARS_A   3 KsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeile.kkkfGe 78 
                                       K   k+l +k ++pt  ++ ++d ++++e+ ++++ +  V+K+++ a g+g+ v  se++a +  + + e +k +G 
  gi|320100707|ref|YP_004176299.1| 110 KPAVKTLAEKLDVPTLPWSIVDDDADLEEFARAHGYPL-VLKPARGAWGRGIRVLWSEKDAEQLKTAVKEaEKLYG- 184
                                       5567999*******************************.****************888888776666555135677. PP

                                       CCSSEEEEE---SEE.EEEEEEECTTEEEE- CS
                            GARS_A  79 agekvviEelleGeE.vsllalvdgktvkpl 108
                                         +++ +E ++     + ++++ dg++v++l
  gi|320100707|ref|YP_004176299.1| 185 -DRRIYVEPYMGSAKlLEVQVIGDGEKVIHL 214
                                       .99*******976652678999999999877 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 !   18.6   0.0   5.2e-07   0.00085      16      91 ..     104     175 ..      98     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.2e-07
                       ATPgrasp_ST  16 fplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkss 91 
                                       ++   dK  +k+l  ++ l+vp+l  +    ++ ++le+f + +   +v+Kpa+g +G+Gi+v+ +++d++ lk  
  gi|320100707|ref|YP_004176299.1| 104 IEFTRDKPAVKTL--AEKLDVPTLPWS--IVDDDADLEEFARAHGYPLVLKPARGAWGRGIRVLWSEKDAEQLKTA 175
                                       5666789999999..677888885444..445667788888888545*****************998888877654 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.5e-07    0.0014       2     150 ..     144     282 ..     143     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.5e-07
                       ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdeeGep 78 
                                        +P+v+KP+ g+  +G++++ +e++ ++    +++ +++a++ y      ++++ vE y+ G    +++ +  +Ge+
  gi|320100707|ref|YP_004176299.1| 144 GYPLVLKPARGAWGRGIRVLWSEKDAEQ----LKTAVKEAEKLYG-----DRRIYVEPYM-GSAKLLEVQVIGDGEK 210
                                       59*********************99887....5555555666666.....57889***98.566669999999**** PP

                       ATP-grasp_4  79 vilnilkkefaseedvsdrlyvtsakvieetlealeellkevnallglknfpvHiElrvsedg.kiipiEvnp 150
                                       vi    +   +++++++ ++   s+ v++e  ++l  +  +v+++l+l+n ++ +E+  + ++ ++++ Evnp
  gi|320100707|ref|YP_004176299.1| 211 VIHLYEREASLQDDYLKTVIEAPSKTVSKELRDKLVGYAVAVGEALRLRNTAT-VEFLYDVRSrTLFLNEVNP 282
                                       **999988899999999999******************************876.8888877664677778888 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.6e-06    0.0091      13     156 ..     118     282 ..     109     285 .. 0.79
   2 ?   -1.7   0.0       1.7   2.7e+03      26      53 ..     323     350 ..     309     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.6e-06
                                       TT.S---............-EESS--.SSSEEEEESS-------B--SS--TTE..................EEEE- CS
                       ATP-grasp_3  13 eagvkvP........tkleaeeleee.ekklvvKprdGaggesvrvveekeeaeaaieeve...........lvqef 69 
                                       e+ + vP        + +  ee++++  ++lv+Kp++Ga g ++rv   +++ae+    v+            v  +
  gi|320100707|ref|YP_004176299.1| 118 EK-LDVPtlpwsivdDDADLEEFARAhGYPLVLKPARGAWGRGIRVLWSEKDAEQLKTAVKeaeklygdrriYVEPY 193
                                       44.5555555666665555555544449*****************99877666655444446779*****9756666 PP

                                       --S.EEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEES CS
                       ATP-grasp_3  70 ieG.kplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlk 145
                                       + + k l v++++dgekv  l   ++ ++   ++ v    +  + +el++++v  a  v e+l  l+  + v++++ 
  gi|320100707|ref|YP_004176299.1| 194 MGSaKLLEVQVIGDGEKVIHLYEREASLQDDYLKTVIEAPSKTVSKELRDKLVGYAVAVGEAL-RLRNTATVEFLYD 269
                                       65416689**********************9999999999999999*****************.**********965 PP

                                       S...SEEEEEEES CS
                       ATP-grasp_3 146 d..eepyviEvNP 156
                                            + + EvNP
  gi|320100707|ref|YP_004176299.1| 270 VrsRTLFLNEVNP 282
                                       4437777789999 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                                       ESS--SSSEEEEESS-------B--SS- CS
                       ATP-grasp_3  26 eleeeekklvvKprdGaggesvrvveek 53 
                                        +++e+k +  Kp++G  +++v++  ++
  gi|320100707|ref|YP_004176299.1| 323 GWAFEAKVFNKKPFKGEPSSGVVKSYNE 350
                                       56677888889********999998776 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00016      0.26      27      78 ..     123     174 ..     113     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                    ATPgrasp_YheCD  27 pyLPetellesledleemlekyks.vylKpanGskGkgilriekeekelllls 78 
                                       p LP+++  ++  dlee+ + ++  ++lKpa+G  G+gi  + +e+++ +l++
  gi|320100707|ref|YP_004176299.1| 123 PTLPWSIV-DDDADLEEFARAHGYpLVLKPARGAWGRGIRVLWSEKDAEQLKT 174
                                       56777776.58999********9889*************99999555444443 PP

>> NUC130_3NT  NUC130/3NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.013        21       5      41 ..     211     247 ..     210     248 .. 0.92
   2 ?    3.9   0.5     0.042        69      22      39 ..     428     445 ..     427     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                        NUC130_3NT   5 vahcYpketkefpqeLselLlehhsvLhpdlRkklvq 41 
                                       v+h Y  e++   + L+++++  +++++ +lR+klv+
  gi|320100707|ref|YP_004176299.1| 211 VIHLYEREASLQDDYLKTVIEAPSKTVSKELRDKLVG 247
                                       889999999999999********************96 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.042
                        NUC130_3NT  22 elLlehhsvLhpdlRkkl 39 
                                       +lL+e+  +L+++lR+k+
  gi|320100707|ref|YP_004176299.1| 428 RLLEEKRGELESKLREKM 445
                                       79**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3580.18
//
Query:       gi|320100708|ref|YP_004176300.1|  [L=221]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0027   17.5   0.0     0.0042   16.8   0.0    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.4e-07    0.0042      67      97 ..     136     166 ..     122     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-07
                          Prok-JAB  67 glevvgiwHSHpggsarPSetDrrdaaalar 97 
                                       +l+ v  +H+Hp+ +a PS  D+++  +++ 
  gi|320100708|ref|YP_004176300.1| 136 RLRHVFAAHTHPEEHANPSPRDLSTILEELS 166
                                       5678889****************99988644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1602.68
//
Query:       gi|320100709|ref|YP_004176301.1|  [L=410]
Description: acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-39  133.3   0.1    1.2e-38  132.9   0.1    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    3.7e-19   68.7   0.0      7e-19   67.8   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.1   1.3e-42   1.2e-38       2     206 ..      86     400 ..      85     401 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 1.3e-42
                                       EEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.T CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.g 76 
                                       +++H+DvV ++e   w+t pf++ ++ + +yGrGa+dmkgg++a+l a+ +l++   +p   ++ +++pdEE+g+  
  gi|320100709|ref|YP_004176301.1|  86 FNGHYDVVAPGEG--WETpPFKPVIRGDLVYGRGATDMKGGIAAVLTAMISLAEGR-EPGVVVEAALVPDEEIGGrT 159
                                       79*******6655..***********99*********************9987764.5555***********6555* PP

                                       HHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                     Peptidase_M20  77 Gakallegleerekvdavfelhieepgileagklaigvv...................................... 115
                                       G+++l+ +l  + k+d+v+   i ep++l+     i ++                                      
  gi|320100709|ref|YP_004176301.1| 160 GTGYLVSEL--GSKPDYVV---IAEPSGLD----NIYIGhrgnvwgivktygrqahgsapwlgdnafekmivfaqvf 227
                                       *******54..57999966...********....466668899********************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|320100709|ref|YP_004176301.1| 228 lkkyrelislrkssymyederaaqptitpggalyapgsinivpgeagfsidrrliveekvedvareikdmvekvaae 304
                                       ***************************************************************************** PP

                                       ...EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSG.GCTTST CS
                                       ...xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxx RF
                     Peptidase_M20 116 ...kvevelleggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgs.glaHsp 185
                                          +++++l+e+++p+ ++ +++ + +l++++e+++g++++ +++  gg d r++  +gip+v  +gpg+ glaH+p
  gi|320100709|ref|YP_004176301.1| 305 lgvQASFTLVESSPPAFTPpSHEYTVLLSKVVEKTTGVEPRKTICV-GGLDLRYYtlKGIPAV-SYGPGEvGLAHKP 379
                                       **88999988999998888***************99*999999888.*************988.7****88****** PP

                                       TTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 186 nEyvdledlekgikvlarlle 206
                                       nEy++l+d++k+++++a++++
  gi|320100709|ref|YP_004176301.1| 380 NEYIRLSDVVKAAAIYAEYVR 400
                                       ******************997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   7.8e-23     7e-19       1     107 [.     188     304 ..     188     306 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 7.8e-23
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC..............TCCTCCCCCEECCE-C. CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.........eerslprttlnvtgiegGs. 67 
                                       igh+G ++g +++ g+++H++ap  g+NA+ek++ + + + +++++           e+++++++t++++g      
  gi|320100709|ref|YP_004176301.1| 188 IGHRGNVWGIVKTYGRQAHGSAPWLGDNAFEKMIVFAQVFLKKYRELIslrkssymyEDERAAQPTITPGGALYAPg 264
                                       69*****************************************99999**********************9877778 PP

                                       CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCST CS
                         M20_dimer  68 aknvipdeaeakidiRllpgedpeevleeieeilekeape 107
                                       ++n++p+ea ++id+Rl  +e++e+v  ei++++ek+a+e
  gi|320100709|ref|YP_004176301.1| 265 SINIVPGEAGFSIDRRLIVEEKVEDVAREIKDMVEKVAAE 304
                                       ************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2997.83
//
Query:       gi|320100710|ref|YP_004176302.1|  [L=77]
Description: ferredoxin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-20   73.0   2.7    2.6e-20   72.7   2.7    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.4e-15   57.8   2.5    1.6e-15   57.6   2.5    1.1  1  Fer4_15   4Fe-4S single cluster domain
     0.0058   16.4   5.5      0.051   13.4   1.3    2.4  2  Fer4      4Fe-4S binding domain
     0.0092   16.6   2.0      0.028   15.0   2.1    1.7  2  Fer4_7    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.016   15.3   6.6      0.019   15.0   0.9    2.3  2  Fer4_6    4Fe-4S binding domain
      0.044   14.3   3.5      0.051   14.1   0.2    2.3  2  Fer4_4    4Fe-4S binding domain
       0.14   12.3   3.3       0.72   10.0   3.3    2.0  1  Fer4_10   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   2.7     1e-23   2.6e-20       3      58 .]       9      74 ..       6      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 1e-23
                           Fer4_13  3 rdtCiacgaCvelaPdvFeeddeggasvvaeqpts..........eeekadaeeAadaCPvesIgv 58
                                      r++Ci++++Cv+++PdvFe+++++++s+++ + +           +++ ++a++Aa+aCPv++I+v
  gi|320100710|ref|YP_004176302.1|  9 RENCISDMVCVSICPDVFEMNPDDNKSQIVGKYREggniavgvipDDLAQCAQDAANACPVQIIHV 74
                                      79***************************9754433778888998********************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 !   57.6   2.5   6.1e-19   1.6e-15       1      66 []       4      74 ..       4      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 6.1e-19
                           Fer4_15  1 VvvD.rdaCigcglCvaeapevfelded.glasvl...lddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      V+++ r++Ci++ +Cv  +p+vfe++ d  +++++    ++g+ia g +pdd+ ++aq+Aa aCPv+ I+v
  gi|320100710|ref|YP_004176302.1|  4 VKIEpRENCISDMVCVSICPDVFEMNPDdNKSQIVgkyREGGNIAVGVIPDDLAQCAQDAANACPVQIIHV 74
                                      677779********************961566666666456677788**********************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   1.3     2e-05     0.051       6      19 ..      10      23 ..       8      25 .. 0.93
   2 ?    4.8   0.2      0.01        27      15      23 ..      64      72 ..      64      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                      TTSSS-THHHHHST CS
                              Fer4  6 ekCigCGaCvevCP 19
                                      e Ci  + Cv++CP
  gi|320100710|ref|YP_004176302.1| 10 ENCISDMVCVSICP 23
                                      89************ PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.01
                                      HHHSTTTEE CS
                              Fer4 15 vevCPvgAI 23
                                      +++CPv  I
  gi|320100710|ref|YP_004176302.1| 64 ANACPVQII 72
                                      589***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 !    9.8   0.4   0.00048       1.2      32      49 ..       5      23 ..       2      26 .. 0.80
   2 !   15.0   2.1   1.1e-05     0.028       2      52 .]      12      71 ..      11      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00048
                            Fer4_7 32 eidp.ekClgCgaCvavCP 49
                                      +i+p e+C++  +Cv+ CP
  gi|320100710|ref|YP_004176302.1|  5 KIEPrENCISDMVCVSICP 23
                                      5554279***********9 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.1e-05
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenek.........gtekveidpekClgCga.CvavCPtga 52
                                      Ci    Cv+ Cp +++e+++++n++         g+  v + p++  +C +  +++CP+++
  gi|320100710|ref|YP_004176302.1| 12 CISDMVCVSICP-DVFEMNPDDNKSqivgkyregGNIAVGVIPDDLAQCAQdAANACPVQI 71
                                      888899******.9*****998888666655554445567779999999988******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 ?   15.0   0.9   7.5e-06     0.019       6      20 ..       9      23 ..       3      30 .. 0.86
   2 ?    3.4   0.5     0.034        87      17      24 .]      65      72 ..      58      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.5e-06
                            Fer4_6  6 pdkCigCgdCvrvCP 20
                                      +++Ci+ + Cv++CP
  gi|320100710|ref|YP_004176302.1|  9 RENCISDMVCVSICP 23
                                      89************* PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.034
                            Fer4_6 17 rvCPegai 24
                                      ++CP ++i
  gi|320100710|ref|YP_004176302.1| 65 NACPVQII 72
                                      69***997 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2     2e-05     0.051       2      16 ..      10      24 ..       9      39 .. 0.88
   2 ?    0.9   0.1      0.35   8.9e+02      12      17 .]      65      70 ..      64      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e+Ci  ++Cv++CP+
  gi|320100710|ref|YP_004176302.1| 10 ENCISDMVCVSICPD 24
                                      789999********4 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
                            Fer4_4 12 aaCPqg 17
                                      +aCP++
  gi|320100710|ref|YP_004176302.1| 65 NACPVQ 70
                                      689975 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.3   0.00028      0.72       5      30 ..       8      42 ..       3      77 .] 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                           Fer4_10  5 dddtCirCgkCvkaCPadl.........tsvgakg 30
                                      +++ Ci    Cv+ CP  +         + vg++ 
  gi|320100710|ref|YP_004176302.1|  8 PRENCISDMVCVSICPDVFemnpddnksQIVGKYR 42
                                      5678************9778877777542222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 548.44
//
Query:       gi|320100711|ref|YP_004176303.1|  [L=269]
Description: cation diffusion facilitator family transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-14   52.6   7.2    6.3e-14   52.2   7.2    1.2  1  Cation_efflux  Cation efflux family
  ------ inclusion threshold ------
       0.01   15.6   0.9       0.31   10.8   0.0    2.4  2  L27            L27 domain
      0.029   14.2   7.7      0.041   13.7   7.7    1.1  1  Bax1-I         Inhibitor of apoptosis-promoting Bax1


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   7.2   1.1e-17   6.3e-14       6     190 ..      15     185 ..       9     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.1e-17
                     Cation_efflux   6 lanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllgla 82 
                                       +  ++ +++++ +g+l +S +l++da+ s+++++sl+ +l   +l+  ppd ++ fG++r+e++g l     l+  +
  gi|320100711|ref|YP_004176303.1|  15 ATGIAGSVMKILGGVLYGSNTLFVDALTSVANMASLISILWFRRLAYTPPDSDHHFGHERFEYIGVLPM---LITYG 88 
                                       44455789*********************************************************8864...44444 PP

                     Cation_efflux  83 vfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalv 159
                                       + + l ++ +l+   +re   +l ++++++++ +++ ++ +  r       ++l+a    + + +l  l+ +v++l+
  gi|320100711|ref|YP_004176303.1|  89 FVAGL-SVARLY--YVREYRVELNAFYLALAAMLMYGVAVASSRR----APPSLRAYGAFTVSELLEGLVGVVASLG 158
                                       44444.445666..3666666777776666666667666666665....69***************99999999999 PP

                     Cation_efflux 160 illfnlksgplaDpvaslligliilysalkl 190
                                         l+     +l+D  +++l+  +i+y  ++ 
  gi|320100711|ref|YP_004176303.1| 159 GALY----SYLVDYGGAVLLTSYIFYEIYEE 185
                                       9998....588***************99876 PP

>> L27  L27 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.017        99      37      46 ..     200     209 ..     200     212 .. 0.89
   2 ?   10.8   0.0   5.2e-05      0.31      11      29 ..     236     254 ..     235     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.017
                               L27  37 levHDrVaet 46 
                                       lev++rV et
  gi|320100711|ref|YP_004176303.1| 200 LEVYERVVET 209
                                       89*****998 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.2e-05
                               L27  11 LqslsdvnedlaeLqkvLq 29 
                                       Lq+ s ++ dl+eL++vLq
  gi|320100711|ref|YP_004176303.1| 236 LQPKSTAPSDLRELRRVLQ 254
                                       9*****************9 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   7.7   6.8e-06     0.041      30     169 ..      25     181 ..       4     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.8e-06
                            Bax1-I  30 a.........qlflslhivlflvvilaplalvflslsaarlk.............kkssalalallllftlleGlsl 84 
                                                 +lf+     l  v+ +a+l+ +   l+++rl              ++ +   l++l+++ +++Gls+
  gi|320100711|ref|YP_004176303.1|  25 IlggvlygsnTLFVDA---LTSVANMASLISI---LWFRRLAytppdsdhhfgheRFEYIGVLPMLITYGFVAGLSV 95 
                                       2444222211122222...3333444444444...344344444466666666555555577*************** PP

                            Bax1-I  85 spillvytgaiilqaflltaaifgglslyalttkr...dlsglggflfagli...gliiaslvnlFlpssalelais 155
                                       + + +v    + l+af l++a++    +++++ +r   +l  +g f ++ l+   + ++asl+  +      + ++ 
  gi|320100711|ref|YP_004176303.1|  96 ARLYYVREYRVELNAFYLALAAMLMYGVAVASSRRappSLRAYGAFTVSELLeglVGVVASLGGAL-----YSYLVD 167
                                       ***********************9999999999996667777788888777753233556666654.....344456 PP

                            Bax1-I 156 ylgvllfsglilyD 169
                                       y+g++l + +i+y+
  gi|320100711|ref|YP_004176303.1| 168 YGGAVLLTSYIFYE 181
                                       ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2004.18
//
Query:       gi|320100712|ref|YP_004176304.1|  [L=203]
Description: multiple antibiotic resistance (MarC)-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-44  151.2  17.1    2.9e-44  150.9  17.1    1.1  1  MarC      MarC family integral membrane protein


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 !  150.9  17.1   1.6e-48   2.9e-44       4     201 ..       7     195 ..       4     197 .. 0.95

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 1.6e-48
                              MarC   4 iikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgill 80 
                                       +++ f+ L+ai+np++++p f+sl+e  ++++r +i++ka + +l++++vf l+G++il+ f+is+ +l+++Ggi+l
  gi|320100712|ref|YP_004176304.1|   7 LLSYFTQLIAIMNPFSAIPTFMSLTEGLDHRRRIAIVKKAYLAGLILVTVFTLVGRYILEAFNISVASLRVGGGIIL 83 
                                       67899************************************************************************ PP

                              MarC  81 fliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalit 157
                                       ++ia+dml  + ++    k+ +       +iavvP+A+Pli GPg+itt+l+l+s+ + + e ++++la + a++ t
  gi|320100712|ref|YP_004176304.1|  84 MTIALDMLGDDVRT----KRMH-----PGDIAVVPIATPLIIGPGTITTILLLTSSSTGVAEVALILLAGVTACSAT 151
                                       ********999983....2223.....368*********************************************** PP

                              MarC 158 llilllsslilrllgktginaleRlmGllLvalavqlivdGike 201
                                       +lil ls++++rll  + ++a+ R m+l+++ +av++iv+Gi+ 
  gi|320100712|ref|YP_004176304.1| 152 FLILGLSDVLTRLLSMSTVRAIGRFMALIIAGVAVEMIVHGIHS 195
                                       ******************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1453.12
//
Query:       gi|320100713|ref|YP_004176305.1|  [L=444]
Description: amidohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   92.3   0.0    4.5e-26   92.0   0.0    1.1  1  Amidohydro_1  Amidohydrolase family
    2.5e-14   53.6   0.1    4.4e-06   26.4   0.0    2.3  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.0     5e-30   4.5e-26       2     343 ..      51     419 ..      50     420 .. 0.80

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 5e-30
                                       EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH....HHHHHHHHHHT.S CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst....giealleaaee.l 73 
                                        +PG+ID+H H++             ++     e  e+g  +a  +G ttv dm+  t+      +e  le+a++  
  gi|320100713|ref|YP_004176305.1|  51 TVPGGIDIHAHIY-------------DQAYAGNEDWETGSLAAAFGGLTTVVDMPLRTIVdnerVLEEKLEEARRnS 114
                                       58**********8.............889999************************888877776666666666688 PP

                                       SSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEE CS
                      Amidohydro_1  74 plglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpva 149
                                        l+++++gg      + +e   +++ +l+++            v   ++    ++ +sd++l ea++ ++ ++   +
  gi|320100713|ref|YP_004176305.1| 115 YLNYGVIGG------FINEKNYTVIPELARRG-----------VRlFKFFTCRPFKISDDALPEAFEHVAIANGVAV 174
                                       89*******......66777777777776664...........33345556789*************9999999999 PP

                                       EEETSSCHHHHHHHHHHTTTEEEETTTTSTCC..........HHTTTHCCEEEHCTCEEE.HHHHHHHHHHHHHHCE CS
                      Amidohydro_1 150 iHaletkgevedaeaafgetiehgthlevaes..........lglldeiklilahgvhlt.pteaellkerlkeagv 215
                                       +Ha ++  +  + ++     ++ ++h ++ +s          +  ld+   +++h+ hl+  + +e ++  +k++++
  gi|320100713|ref|YP_004176305.1| 175 VHAEDEALIGYWERKLSTQNTITAYHSSRTGSteasaiyrvgYIGLDV--GARVHIAHLSsREGVEAVANLKKKTSI 249
                                       ***776666667666666677777888888888888888855334444..78********76677788888888999 PP

                                       E.....................HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECT...TSSCCGGHHHH......HH CS
                      Amidohydro_1 216 a.....................hcpfsnsilrsgrealrkaldeGvkvglgtDga...asgnslnllee......lr 262
                                       +                     +  ++ +++ ++r+al++ l++Gv+ ++++D+a    s++ +n++e       l 
  gi|320100713|ref|YP_004176305.1| 250 TsevtphhlfftredsarfgayLKVAPTLKSIEDRDALWRGLEAGVIDAYVSDNApapRSMKEVNVWEAwggvpnLE 326
                                       988888865555555555555544555555***********************999998888889999999888855 PP

                                       HHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC....CT..........CGGG CS
                      Amidohydro_1 263 lalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl....di..........laaf 325
                                       +++   ++  y++ +  lsl+++++++  n+A++lg++  +G+++vG  AD+vv+++    +i           +++
  gi|320100713|ref|YP_004176305.1| 327 VMM--PFLFTYGVLQRRLSLARFIEVTARNPARILGVYPLKGELAVGSHADIVVLETgsprKItasthhhkvdWTPW 401
                                       555..333455555666****************************************865533888999999***** PP

                                       TTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 326 vglkkdgnvkkvivkGkl 343
                                       +g++  g + ++iv+G +
  gi|320100713|ref|YP_004176305.1| 402 EGMELYGHPYHLIVNGSV 419
                                       ****************76 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   4.9e-10   4.4e-06       1      49 [.      42      90 ..      42     112 .. 0.93
   2 !   25.3   0.0   1.1e-09   9.7e-06     405     471 ..     339     419 ..     233     421 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.9e-10
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavr 49
                                      ev Da Gr+ +PG++D+H+H++   ++ ++ +  ++ + ++ g++t+v+
  gi|320100713|ref|YP_004176305.1| 42 EVLDAGGRITVPGGIDIHAHIYDQAYAGNEDWETGSLAAAFGGLTTVVD 90
                                      799*********************9999*99999999999999999986 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.1e-09
                      Amidohydro_3 405 deelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear.............vrltvv 467
                                        ++lsl   +  + r+pA++lg    kG L+vG +AD+vvl+   p ++++++ ++++             + + +v
  gi|320100713|ref|YP_004176305.1| 339 QRRLSLARFIEVTARNPARILGVYPLKGELAVGSHADIVVLEtGSPRKITASTHHHKVdwtpwegmelyghPYHLIV 415
                                       689***************************************98999999998888777777777777776666666 PP

                      Amidohydro_3 468 dGrv 471
                                       +G v
  gi|320100713|ref|YP_004176305.1| 416 NGSV 419
                                       6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3222.67
//
Query:       gi|320100714|ref|YP_004176306.1|  [L=966]
Description: leucyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  181.5   0.0    3.1e-52  177.7   0.0    2.5  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    5.5e-21   74.8   1.2    1.1e-09   37.5   0.1    4.0  4  tRNA-synt_1g  tRNA synthetases class I (M)
    5.2e-16   59.0   0.0    1.1e-15   58.0   0.0    1.5  1  Anticodon_1   Anticodon-binding domain of tRNA
      1e-07   31.6   0.1      0.002   17.6   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
     0.0027   16.7   0.0     0.0096   14.9   0.0    1.9  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.7   0.0   8.7e-56   3.1e-52       1     593 [.      16     678 ..      16     687 .. 0.83

  Alignments for each domain:
  == domain 1  score: 177.7 bits;  conditional E-value: 8.7e-56
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       k++++W e+ vf++       k+++ ++++ Py +  lHiGh  + t+ div rykr+kG++vly + +   G ++ 
  gi|320100714|ref|YP_004176306.1|  16 KWQARWRESRVFQAD--PVPGKPKYFITVPYPYSNAPLHIGHGRTYTMGDIVARYKRLKGFNVLYPMAFHITGTPVL 90 
                                       58899********99..6777*****************************************************995 PP

                       tRNA-synt_1  78 akvekklgakekkerkkl..greef......rekv.re......wkaeyaeeirkqvkrlGvsvDfdreylTldkel 139
                                        +v +++++ e++ ++ +    + +      ++++  +       +  +ae+i++++  lG s+D+ r   T ++ +
  gi|320100714|ref|YP_004176306.1|  91 -AVSEMIARGEERVVNMYksYIKYYvddesrVNEIlESfknplnLAVFFAERIQSDFDALGYSIDWRRRFHTGEPIY 166
                                       .56666666555443322111222211111122221221111113445899************************** PP

                       tRNA-synt_1 140 eeavkevfvrladkgliyrgkklvnwstklktalselEveykdkk....dalihvafpladkeevklviaTTtPeTl 212
                                       +  v++ f++l +kgli  g ++v ++   k +  e +++  d++       + v+f+  + ++ +l +aT +PeT+
  gi|320100714|ref|YP_004176306.1| 167 NRFVTWQFMKLREKGLITTGDHVVTYCLLHKQPEGEDDIQDADVNpvevLEYTAVKFHDRERNA-YLAAATLRPETI 242
                                       ***************************9999999888888888884422234456666555555.************ PP

                       tRNA-synt_1 213 lgdtavavnpeldyv...itkeklilaeallkslvkke.sek.kiledergkeLegkevelplvnrkipiiaddyvd 284
                                        g   + vnp  +y     ++e++i+ e+   +l++++ +++ +i+ +++g+eL+g++v  pl +r++ ++  ++vd
  gi|320100714|ref|YP_004176306.1| 243 YGAINIWVNPAAKYLellWRGERIIVSEKAYVKLLHQHpEDEiRIVAEMQGRELVGRRVVSPL-GRELIVLPAEFVD 318
                                       **************99999999999998766666555546666*******************8.79999******** PP

                       tRNA-synt_1 285 keaGtGvVkiaPahdedDyevgkkynl..................evinildedgtlteea................ 327
                                        ++ tG+V   P   + Dy + ++ +                   e++ i++  g  +++a                
  gi|320100714|ref|YP_004176306.1| 319 PDNATGIVYSEPSDAPYDYVALQELKArremlkeygvdpgvvdalEPVRIIEVPGLSDHHAkvavekagitsqldar 395
                                       *******************998877666655777777888888877777777777777777999************* PP

                       tRNA-synt_1 328 ......................aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfv 382
                                                             +  +g+ v++ar++v + l e g+ ++  + + +   c  ++++i+ +++ qWf 
  gi|320100714|ref|YP_004176306.1| 396 leevtrevyreqyysgvmivddPVLKGVPVKEAREIVRRRLLEAGQAFTFYELNRK-ARCRAGGEIIVAKIKGQWFL 471
                                       *********************999**********************9999998877.579999*************9 PP

                       tRNA-synt_1 383 r..vkeladaalkave.kvqfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelva 453
                                          vke+++++ + +e + + +p++++k + + le        R+r  G+++p    ++ ++  + ++      +v+
  gi|320100714|ref|YP_004176306.1| 472 DygVKEVKEKVREYIErELTVIPEKYRKAFLDTLEWLDKRPCARKRGIGTPLPWspeWIIESLSDSTIYMAFYTVVH 548
                                       744799*********99******************999999**********98533478777777777667777777 PP

                       tRNA-synt_1 454 greeeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgW 530
                                       ++ e+ ++ ++l+ e+ d +      +    d + v    g +p  +l+   e ++e++  +p d   + +  i   
  gi|320100714|ref|YP_004176306.1| 549 KIRENGVKPEQLTPEVFDYV------FLGLGDPVEVSARTG-IPLRVLE---EMRSEFTYWYPVDHRHTSIPHISNH 615
                                       77777777777777777776......555566666655544.3555665...55999******************** PP

                       tRNA-synt_1 531 varlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlils 593
                                       ++  i+    ++ +e + ++++   ++  eG KmSKs+gNvi   d+++ y+ad  Rl++  +
  gi|320100714|ref|YP_004176306.1| 616 LSFYIIHHAVIFPREHWPRMITLNETVIREGAKMSKSKGNVIPLRDIARLYSADLFRLYISWA 678
                                       ******99999999999999998889999******************************9844 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 !   37.5   0.1   3.2e-13   1.1e-09       1      71 [.      38     108 ..      38     119 .. 0.84
   2 !    3.2   0.0    0.0083        30      62     127 ..     130     197 ..     123     206 .. 0.82
   3 !    3.4   0.0    0.0071        26     166     241 ..     451     527 ..     400     560 .. 0.80
   4 !   26.2   0.0   8.6e-10   3.1e-06     292     371 ..     619     692 ..     576     703 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.2e-13
                                       EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHH CS
                      tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvh 71 
                                       +++t++ pY+n++lH+Gh +++  +Di+aRykrl+g +vl+  +    Gtp+    e      e +v+ ++
  gi|320100714|ref|YP_004176306.1|  38 YFITVPYPYSNAPLHIGHGRTYTMGDIVARYKRLKGFNVLYPMAFHITGTPVLAVSEMIARGEERVVNMYK 108
                                       58********************************************99**998766655555555555555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0083
                                       -HHHHHHHHHHHHHHHHHHTT---SEEE..ETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTT CS
                      tRNA-synt_1g  62 tpeelvekvheeikelfkklnisfdkyg..rttseehkelvqeifkklkekgliyekeieqlycpkde 127
                                       +p +l+  + e+i+++f+ l+ s d     +t +   +++v   f kl ekgli++++  ++yc  ++
  gi|320100714|ref|YP_004176306.1| 130 NPLNLAVFFAERIQSDFDALGYSIDWRRrfHTGEPIYNRFVTWQFMKLREKGLITTGDHVVTYCLLHK 197
                                       57777777889999999998877775541157788899999999********************8665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0071
                                       ...........EEE.EEEEEE-..GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EETTE CS
                      tRNA-synt_1g 166 npksaisgskpevketehlffk..lskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvPga 240
                                       ++++   g+  + k + ++f++  ++++++k++e+ie+e +  +e+ +k  +++l+  L ++  +r+   G p+P +
  gi|320100714|ref|YP_004176306.1| 451 KARCRAGGEIIVAKIKGQWFLDygVKEVKEKVREYIERELTVIPEKYRKAFLDTLEW-LDKRPCARKRGIGTPLPWS 526
                                       5788888888899999999987446899********999988999999999999988.8888888888888888844 PP

                                       C CS
                      tRNA-synt_1g 241 e 241
                                       +
  gi|320100714|ref|YP_004176306.1| 527 P 527
                                       4 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 8.6e-10
                                       GHHHHHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-H CS
                      tRNA-synt_1g 292 iikFHtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfsw 368
                                        i +H++++P        + p+ ++ +e +  eg+K+SkS+g+v+  ++++  ++adl+R y++ +a+ ++ ld+++
  gi|320100714|ref|YP_004176306.1| 619 YIIHHAVIFPR------EHWPRMITLNETVIREGAKMSKSKGNVIPLRDIARLYSADLFRLYISWAASLDSVLDWRE 689
                                       36688888885......5679999999999*********************************99998888777777 PP

                                       HHH CS
                      tRNA-synt_1g 369 edf 371
                                       +d+
  gi|320100714|ref|YP_004176306.1| 690 RDV 692
                                       665 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0     3e-19   1.1e-15       2     152 .]     725     855 ..     724     855 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 3e-19
                       Anticodon_1   2 rwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrlla 78 
                                        w++ ++n+lvk ++e++e++++++ +++     + +l d y +++ ++               ++ vl+ ++ +l+
  gi|320100714|ref|YP_004176306.1| 725 TWFIDRFNQLVKAASESIEHMEIREYVQNSLFN-VLSLVDKYRDIAGEKYI-----------CGVKQVLRDWITVLN 789
                                       5***************************99986.55688******977653...........5689*********** PP

                       Anticodon_1  79 PfmPfitEelwqreeeelgkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpsselkvvi 152
                                       P++P+itEe+     e++g+k +++l++wp+  e+ ++e  +++v+    ++++ +++r+   + ++++ +++i
  gi|320100714|ref|YP_004176306.1| 790 PVIPHITEEIH----ELMGGKGFLSLSSWPSPREPVNPEV-DAAVDN---AIMLQEDIREVVSLLKKTPSRIYI 855
                                       ***********....9**************7555555555.445555...999999999999999999998886 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 !   11.7   0.0   3.4e-05      0.12      23      50 ..      51      78 ..      40     125 .. 0.85
   2 !   17.6   0.0   5.5e-07     0.002     236     299 ..     631     695 ..     608     697 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                                      -BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 23 shlGhaRslvafDilrrilqalgYdvqf 50
                                       h+Gh+R++ + Di++r+ + +g++v +
  gi|320100714|ref|YP_004176306.1| 51 LHIGHGRTYTMGDIVARYKRLKGFNVLY 78
                                      7*************************98 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.5e-07
                                       --EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHH.SS-TTS-EEE-HHHHHHH CS
                      tRNA-synt_1e 236 qlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllll.sahyrsqldfkeelleea 299
                                       ++ +    n+ +  eg kmsks +n+i ++d+ + +++  +Rl++   a   s ld++e +++ +
  gi|320100714|ref|YP_004176306.1| 631 HWPRMITLNETVIREGAKMSKSKGNVIPLRDIARLYSADLFRLYISwAASLDSVLDWRERDVAVV 695
                                       555666667788889***************************9997256789999*999988765 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         1   3.8e+03     138     162 ..     105     129 ..     103     131 .. 0.89
   2 !   14.9   0.0   2.7e-06    0.0096     275     308 ..     642     675 ..     624     699 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1
                      tRNA-synt_1f 138 glydeaikealenrekikeilekyr 162
                                       ++y++ ik  ++++++++eile+++
  gi|320100714|ref|YP_004176306.1| 105 NMYKSYIKYYVDDESRVNEILESFK 129
                                       68999****************9885 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.7e-06
                      tRNA-synt_1f 275 llkggekmssSkGnvltledwlevaepevlrfli 308
                                        +++g+kms+SkGnv+ l+d+ ++++ ++ r++i
  gi|320100714|ref|YP_004176306.1| 642 VIREGAKMSKSKGNVIPLRDIARLYSADLFRLYI 675
                                       577888************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (966 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.25s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 6368.05
//
Query:       gi|320100715|ref|YP_004176307.1|  [L=381]
Description: major facilitator superfamily protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-24   86.0  48.9    1.6e-12   47.0  21.6    2.4  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.013   14.1  11.0      0.017   13.8   0.2    3.4  3  ATG22     Vacuole effluxer Atg22 like


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0  24.8   2.5e-14   2.2e-10      32     207 ..      42     212 ..       5     236 .. 0.73
   2 !   47.0  21.6   1.8e-16   1.6e-12      22     169 ..     234     378 ..     214     381 .] 0.87

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.5e-14
                             MFS_1  32 seigllltlyal.gaavaslplGrlsdrfGrrrvlllglllfalglllll..fa.sslw.lllvlrvlqGlgagalf 103
                                        ++gl  +++++ ++  + ++ G++sd f r rvl+l +++  +  ++++  +a +  w l+++l v+  lg g+ +
  gi|320100715|ref|YP_004176307.1|  42 IAAGL--AGVGWlASYGSRFLSGVVSDYFRRPRVLWLLVFTGYFVNVIAIplLAfTRRWeLVIALIVFERLGKGLRA 116
                                       33333..344441455667778*******6655776666665555344444445699999***************** PP

                             MFS_1 104 pagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfyilaivsllafv.lfllllpeepp 177
                                       pa  +++a+++ ++ +g+++g+  a+ ++Ga+lgpl+++l+++s +  ++ vf +l++ +++a++ +++++++ + p
  gi|320100715|ref|YP_004176307.1| 117 PARDVILAEVSEGMGKGLGFGIHEAMDQAGAVLGPLIASLILASSSqdYSRVFTALGVPGAVAVIlVAAAWFLYPSP 193
                                       ****************************************997777899999***********88788899999999 PP

                             MFS_1 178 erkrkspkeeekgtgpaplvpawkallkdp 207
                                       ++ + +++             ++k l +  
  gi|320100715|ref|YP_004176307.1| 194 KSITARGVGV-----------GFKGLTRGY 212
                                       8888888777...........344444444 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 1.8e-16
                             MFS_1  22 alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlg 98 
                                       ++a++ g++++ i ll+t+ +l+ +v+++p G l dr+G r+ +l+ l++ ++g+ll+l+  +    ++  v  Gl+
  gi|320100715|ref|YP_004176307.1| 234 YYARSTGFTGDYIALLYTVAMLVDGVLAIPSGILYDRVGVRSAVLAPLAAAVAGVLLPLLQVN---PFIPVVAWGLA 307
                                       6788999***********************************************888886433...25667778888 PP

                             MFS_1  99 agalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfl 169
                                       +ga+ +++ +++ad++p+e+r++a+gl++++ +l++  g ++ + ++ s+g +a+ + +a+v ll++ +f 
  gi|320100715|ref|YP_004176307.1| 308 MGAYETNVRVAVADLVPREKRAFAYGLYGLAEGLAVFTGGIIQAGILGSAGIQALAIYIAVVELLGAAVFT 378
                                       89999************************************************************988544 PP

>> ATG22  Vacuole effluxer Atg22 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.1   0.00096       8.6     419     451 ..     136     169 ..      32     190 .. 0.72
   2 ?    1.0   0.2     0.014   1.3e+02      73     124 ..     246     297 ..     231     299 .. 0.87
   3 ?   13.8   0.2   1.8e-06     0.017     386     453 ..     299     366 ..     294     381 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.00096
                             ATG22 419 FsLyaitdkgssvigplivglItDrt.gnirsaf 451
                                       F++ + +d++++v+gpli +lI     ++++  f
  gi|320100715|ref|YP_004176307.1| 136 FGIHEAMDQAGAVLGPLIASLILASSsQDYSRVF 169
                                       99*******************9765424445555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.014
                             ATG22  73 vlytfslsvllqavvvislsglADygnyrknlLlafaligslstilfllvtp 124
                                       + ++  +++l+ +v++i  + l D+   r  +L+ +a + + + +++l v+p
  gi|320100715|ref|YP_004176307.1| 246 IALLYTVAMLVDGVLAIPSGILYDRVGVRSAVLAPLAAAVAGVLLPLLQVNP 297
                                       566778999*************************999999999999988875 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 1.8e-06
                             ATG22 386 vlavvyglvlgglssysRslfseLiPrGkEaaFFsLyaitdkgssvigplivglItDrtgnirsafvf 453
                                       +  v+ gl++g++++  R++ + L+Pr k a  ++Ly + +  + + g +i + I    g +  a+++
  gi|320100715|ref|YP_004176307.1| 299 IPVVAWGLAMGAYETNVRVAVADLVPREKRAFAYGLYGLAEGLAVFTGGIIQAGILGSAGIQALAIYI 366
                                       556889*********************************************99998877766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2725.19
//
Query:       gi|320100716|ref|YP_004176308.1|  [L=408]
Description: oxidoreductase domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   60.5   0.0    4.6e-16   59.7   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
  ------ inclusion threshold ------
      0.062   13.3   0.0       0.14   12.2   0.0    1.6  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   5.1e-20   4.6e-16       1     114 [.       2     124 ..       2     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 5.1e-20
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.HHHTTHE...EESSHHHHHTCTTESEEEE-S-GG CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav.aesfgve...aysdleelladpeidavivatpng 73 
                                       lrv+++G+G++++ hlr++    +++ v  +++p   r   + a++ g +   +ysdl+e+l++++ida+++ tpn+
  gi|320100716|ref|YP_004176308.1|   2 LRVGFVGSGFVARFHLRAFASV-PNAIVSSVYSPTGRRDLVAlAREIGYPepsVYSDLREMLRKEKIDALWILTPNH 77 
                                       69**************777777.*************9999888******99************************** PP

                                       GHHHHHHHHHHTT-......EEEEESSS-SSHHHHHHHHHHHHHHTS CS
                      GFO_IDH_MocA  74 theelakaaleagk......hvllEKPlattveeakelvelaekkgk 114
                                       t  ++++ ++e         +v  EKPla ++eea  ++el++k+g 
  gi|320100716|ref|YP_004176308.1|  78 TRLDVTRTIVEEVTqgssvkAVAYEKPLARNLEEAAGILELVRKAGL 124
                                       *9999999999877777789************************986 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 ?   12.2   0.0   1.5e-05      0.14      28      68 ..     170     209 ..     156     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                                       HHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEE CS
                    GFO_IDH_MocA_C  28 akkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaal 68 
                                       + + w+ +   +gGvl d+g+H i   ++L+ +p  ++ +l
  gi|320100716|ref|YP_004176308.1| 170 SHWFWNPA-YSGGGVLLDMGCHSIEAGRYLLSEPGKNYKDL 209
                                       44555555.59*******************99998777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2894.55
//
Query:       gi|320100717|ref|YP_004176309.1|  [L=466]
Description: family 1 extracellular solute-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.6e-36  124.6   4.4    2.8e-35  122.8   4.4    1.8  1  SBP_bac_1  Bacterial extracellular solute-binding protein
    1.2e-22   81.1   2.9    1.5e-22   80.7   2.9    1.1  1  SBP_bac_8  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.092   12.9   0.0        0.3   11.3   0.0    1.9  1  VF530      DNA-binding protein VF530
        0.2   11.6   0.0       0.44   10.5   0.0    1.5  1  DUF1310    Protein of unknown function (DUF1310)


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   4.4   6.3e-39   2.8e-35      13     313 ..      54     378 ..      40     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 6.3e-39
                                       HHHHH.HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCC CS
                         SBP_bac_1  13 lvaka.fekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkd 88 
                                        ++ + +ek+++ +kV+++++++g+++q +t  + a + +aD+i++d+ w+++l ++g  ++l++ ++++       
  gi|320100717|ref|YP_004176309.1|  54 NFTSYaQEKLGYPVKVVFDFTPWGTYYQRVTSIVTARSSEADIIFSDSQWLGELFEGGHIIDLTDWINNDPD----- 125
                                       34334579*************************************************************943..... PP

                                       TEEEEHHHHTHHHHC.E.EE......ES.EEEE.E.EEEEEEETTTHH..........CTTGGGSHBHHHHHHHHHH CS
                         SBP_bac_1  89 aadklsssvlpkild.s.kv......ly.vPly.a.argliYNkdlfe..........kagldppwtWdelveaakk 144
                                        ++ ++++++++    + ++      ++ vP y   +++l+Y+kdlf           k+g d+p t +++ +++  
  gi|320100717|ref|YP_004176309.1| 126 -MKAATQDTYENLVKfYmTYpqgsnrYVgVPGYaDaVMLLYYRKDLFNdpveranfkaKYGYDLPSTLEDFKRLDW- 200
                                       .444444455544443334455599********99*********************99999999********9999. PP

                                       HHHHCTCT..HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT...............................HH CS
                         SBP_bac_1 145 lkekgkkp..iggarggsasgtayyfalalakslggkvfdkdgg...............................gl 188
                                       l  k+ ++    +a+   a++t+  +++               g                               ++
  gi|320100717|ref|YP_004176309.1| 201 LQLKDIAEffTRRAGETLAGQTLTEDFY---------------GitlvlsrdydyiscsflsmfwswgaelwnpsTM 262
                                       7777777745222333333333333332...............1444444444567777777777777777888888 PP

                                       CSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTT CS
                         SBP_bac_1 189 dnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpk 265
                                       d + + ++++ +++l++  nlt+ ++ ++++++d + + + f++G+aam++ ++++a         + f+++++ + 
  gi|320100717|ref|YP_004176309.1| 263 DPRSYINSTQGVEALQFLHNLTRYMP-PSPATYDYDKVITTFAQGKAAMTVLWPSMA--------PALFDPATSRVS 330
                                       88888888888888888888666665.5****************************6........************ PP

                                       STEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHH CS
                         SBP_bac_1 266 eelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspea 313
                                       +++gva+lP   g  +  lg+++l+i++ s ++e+Ak F++++++ ++
  gi|320100717|ref|YP_004176309.1| 331 DKIGVAILPQHNGVRYITLGGQPLVISSYSNHKEEAKLFIKWFYTVAY 378
                                       *********988888888*************************98765 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 !   80.7   2.9   3.5e-26   1.5e-22       6     274 ..      58     400 ..      53     408 .. 0.67

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 3.5e-26
                                       HHHH-.TEEEEEEE-..-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH......... CS
                         SBP_bac_8   6 fekkt.gvkvnvvta..asndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnldd......... 70 
                                       + +++ g+ v+vv    +++++ q +++ + a +  ++d+++ ++ +l++l+e g + dl+d  n d+         
  gi|320100717|ref|YP_004176309.1|  58 YAQEKlGYPVKVVFDftPWGTYYQRVTSIVTARSS-EADIIFSDSQWLGELFEGGHIIDLTDWINNDPdmkaatqdt 133
                                       67777796666444335***********9999987.6799*********************5444444444454444 PP

                                       ...-HHHHHTT.--TS.----EEEEEEE-EEEEEHHHHHH....S.........---BHHHHH..HH..HHHH.... CS
                         SBP_bac_8  71 ...ltdalaav.gydgklygvPyasetpyvliynkdllek....a........edpktwdell..aa..akkl.... 123
                                          l +++ ++ ++   + gvP  +   ++l+y+kdl+ +    a        + p t+++++  ++  +k++    
  gi|320100717|ref|YP_004176309.1| 134 yenLVKFYMTYpQGSNRYVGVPGYADAVMLLYYRKDLFNDpverAnfkakygyDLPSTLEDFKrlDWlqLKDIaeff 210
                                       33344455555644444*********************88776635666999*99*******622443333332224 PP

                                       .HHH-...................SEGG---G...GGGGGTHHETTEE---H..........HHH.HHHHHHHHHHH CS
                         SBP_bac_8 124 .kgkf...................glpdpasg...wlqaallakdgksldddg........gkdglkealellkklk 169
                                           +                    l+++ +    +++ +++  +g++l +          ++ + +eal++l +l 
  gi|320100717|ref|YP_004176309.1| 211 tR--RagetlagqtltedfygitlVLSRDYDYiscSFLSMFWS-WGAELWNPStmdprsyiNSTQGVEALQFLHNLT 284
                                       30..134435544355555544332233322233444445555.4444422212334455455566*********** PP

                                       HTT-....EE-S..--SSTTTTTSBSEEEE-TTHHHHHH.....-TTTSEEEE.--.S--...EEEEEEEEEEBTTS CS
                         SBP_bac_8 170 dngk....tydtgadavsefanGevaftingswdiaaaq.....kagkklgai.vp.kqg...sfaggkglavpkna 232
                                        ++     ty ++++++  fa+G++a+t+ +++ + a+        ++k+g++ +p  +g     +gg++l++++ +
  gi|320100717|ref|YP_004176309.1| 285 RYMPpspaTY-DYDKVITTFAQGKAAMTVLWPSMAPALFdpatsRVSDKIGVAiLPqHNGvryITLGGQPLVISSYS 360
                                       **98766455.558999****************999776454433368*****4443234787999999******** PP

                                       -HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTT.HHHH CS
                         SBP_bac_8 233 knedlaAldFlkwltspenqaalaektgyipvnksaal.spev 274
                                       +++++ A+ F+kw+++ ++    +     ++++ks a+ s++v
  gi|320100717|ref|YP_004176309.1| 361 NHKEE-AKLFIKWFYTVAYKD--YSLRVGFTARKSIAQsSDFV 400
                                       ****7.*********998766..33356677777777744444 PP

>> VF530  DNA-binding protein VF530
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.8e-05       0.3      35      61 ..     387     413 ..     377     415 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.8e-05
                                       TTSS--HHHHHHHHHHSHHHHHHHHHH CS
                             VF530  35 FksnpsikSslkFLrktpWArekvEel 61 
                                       F+   si+ s  F+  +pWAr+ vE+l
  gi|320100717|ref|YP_004176309.1| 387 FTARKSIAQSSDFVNSKPWARAFVESL 413
                                       88999********************87 PP

>> DUF1310  Protein of unknown function (DUF1310)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.9e-05      0.44       3      39 ..       6      42 ..       4      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.9e-05
                           DUF1310  3 ivlvilvivilavGvkfyldeeklneEmvnvvkSdea 39
                                      ++ ++++ ++++ Gv  yl  ++ ++E+  vv S e 
  gi|320100717|ref|YP_004176309.1|  6 LIAIVVLAIVVIGGVAYYLSTQQPRKEVTIVVLSPEW 42
                                      56777788888889999***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 3026.36
//
Query:       gi|320100718|ref|YP_004176310.1|  [L=299]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for 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  32.1    5.7e-11   42.5  32.1    2.2  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 !   42.5  32.1   3.2e-15   5.7e-11      19     174 ..     105     292 ..       9     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3.2e-15
                      BPD_transp_1  19 llrpliivllslPsfvlaillvlvf.........................vilsilghlilpviillllsaapyvrl 70 
                                       ++ +   ++l++ +++ a+++ ++f                             ++ +++l+vi++ ++ ++p+v++
  gi|320100718|ref|YP_004176310.1| 105 VVITALTIPLMIAPVASALIFRYLFdemfgpvnqflrshlgvsplwfsneLSPIGVPYAMLMVILVETWIWTPFVMF 181
                                       4444444444444444666666677999999999999999999999996655556669******************* PP

                      BPD_transp_1  71 irraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleail 146
                                       ++ a+++++p+dlve +r++G++ + +fr v+lP ++p+++  li++f+ +l+ +  ++ l+++++  +t l+++ +
  gi|320100718|ref|YP_004176310.1| 182 LIMAGISAIPQDLVEQSRVDGLRFRYVFRFVILPYVKPMLAIALIFRFMDSLKTFDTVYVLTAGGPgTTTELISVHI 258
                                       **********************************************************9988665536666666666 PP

                      BPD_transp_1 147 gydyseis......nggvlalviavlllnlvadi 174
                                       ++   e        + ++l+lvi++++ nl++  
  gi|320100718|ref|YP_004176310.1| 259 YKLAFERWdfgsatALSYLVLVIVIFATNLFMHY 292
                                       6666666687666666666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2176.54
//
Query:       gi|320100719|ref|YP_004176311.1|  [L=278]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-23   82.0  17.8    4.4e-23   82.0  17.8    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   2.9    0.0019        33       8      75 ..       8      73 ..       7      81 .. 0.76
   2 !   82.0  17.8   2.5e-27   4.4e-23       2     183 ..      88     271 ..      87     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0019
                      BPD_transp_1  8 aalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraa 75
                                      ++++ +k+l++ll+ +   ++ lP+++++ + +     ++  g+l++p++i+l  +  +y++  ++a+
  gi|320100719|ref|YP_004176311.1|  8 TGYRVKKVLRYLLLLILTSIWLLPVYAMFSIAF--RPRWDMYGNLFIPAAITLENFVEAYNYGAFSAI 73
                                      5688999********************777766..367788888888888776555555555555555 PP

  == domain 2  score: 82.0 bits;  conditional E-value: 2.5e-27
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraa 75 
                                       +ll++laa    ++n ++++ll+++i  ++++P + l+i+++++ ++l +l+ + l++i+++ ++++p+ +++++++
  gi|320100719|ref|YP_004176311.1|  88 LLLAVLAAyafSRFNMRGKNLLMFYILSTRMMPGITLVIPIFVMYYNL-GLKGTYLGLILVYSMMTLPLSLWMIKSF 163
                                       7899999999999***********************999999886666.9999************************ PP

                      BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydy 150
                                       ++ +p+d  eaa ++G s+w i++k++lP++ p +++++++a+++++++++++++l s      + ll ++  ++ +
  gi|320100719|ref|YP_004176311.1| 164 IDDVPRDIDEAAILDGHSTWYILFKITLPSITPGLAASAAFAAIAVWNEFLFALLLSSIETkpTSVLLSSIRGERGF 240
                                       ********************************************************98877779999999999999* PP

                      BPD_transp_1 151 seisnggvlalviavlllnlvadilqrlldprv 183
                                       +++   ++ + v+++l+++l++++lqr++ + +
  gi|320100719|ref|YP_004176311.1| 241 NWGR--VASIEVVYILPIVLLVFWLQRYILRGL 271
                                       *999..99********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2137.40
//
Query:       gi|320100720|ref|YP_004176312.1|  [L=373]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-33  115.9   0.0    2.9e-33  115.3   0.0    1.3  1  ABC_tran     ABC transporter
    1.5e-10   41.4   0.0    5.3e-05   23.2   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      1e-06   28.4   0.0    3.2e-06   26.7   0.0    1.7  1  SMC_N        RecF/RecN/SMC N terminal domain
    6.1e-06   26.7   0.1    2.3e-05   24.8   0.1    1.9  1  AAA_16       AAA ATPase domain
    0.00039   20.2   0.0    0.00081   19.2   0.0    1.4  1  AAA_30       AAA domain
    0.00073   20.0   1.0      0.012   16.0   1.0    2.6  1  AAA          ATPase family associated with various cellular a
     0.0027   17.4   0.0     0.0058   16.3   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
     0.0033   17.3   0.0     0.0073   16.2   0.0    1.5  1  NACHT        NACHT domain
      0.006   16.9   0.0      0.011   16.0   0.0    1.5  1  AAA_22       AAA domain
     0.0078   16.5   0.1      0.011   16.0   0.1    1.4  1  AAA_19       AAA domain
  ------ inclusion threshold ------
      0.012   15.8   0.1       0.12   12.6   0.1    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.015   14.9   0.0      0.027   14.1   0.0    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.016   14.8   0.0      0.045   13.3   0.0    1.7  2  AAA_25       AAA domain
      0.017   15.6   0.0      0.074   13.6   0.0    1.9  2  AAA_18       AAA domain
      0.019   15.4   0.0      0.043   14.3   0.0    1.5  1  AAA_23       AAA domain
      0.021   14.7   0.0      0.044   13.7   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.023   14.7   0.2       0.14   12.2   0.0    2.3  3  AAA_5        AAA domain (dynein-related subfamily)
      0.027   13.5   0.0      0.043   12.9   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
       0.03   14.1   0.0      0.041   13.7   0.0    1.4  1  AAA_11       AAA domain
      0.032   14.5   0.1      0.069   13.4   0.1    1.5  1  AAA_28       AAA domain
      0.033   14.3   0.0      0.074   13.2   0.0    1.7  1  AAA_33       AAA domain
      0.063   13.0   0.0       0.13   12.0   0.0    1.5  1  RuvB_N       Holliday junction DNA helicase RuvB P-loop domai
      0.064   13.2   0.1       0.19   11.6   0.0    1.7  2  ATPase_2     ATPase domain predominantly from Archaea
      0.078   13.0   0.0       0.18   11.8   0.0    1.7  1  AAA_14       AAA domain
      0.092   12.5   0.0       0.19   11.4   0.0    1.5  1  IstB_IS21    IstB-like ATP binding protein
       0.11   12.5   0.1       0.23   11.4   0.1    1.5  1  NTPase_1     NTPase
       0.11   12.2   0.0       0.21   11.3   0.0    1.4  1  AAA_24       AAA domain
       0.11   11.8   0.0        0.5    9.7   0.0    1.8  2  DnaB_C       DnaB-like helicase C terminal domain
       0.13   12.5   0.0       0.37   11.0   0.0    1.8  1  TOBE_2       TOBE domain
       0.16   12.4   0.3       0.45   10.9   0.1    1.9  2  AAA_17       AAA domain
       0.16   11.9   0.0       0.27   11.1   0.0    1.3  1  Rad17        Rad17 P-loop domain
       0.17   10.4   0.0        1.1    7.6   0.1    1.8  2  T6SS_TssF    Type VI secretion system, TssF
       0.21   11.3   0.0       0.45   10.2   0.0    1.4  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 !  115.3   0.0   5.3e-36   2.9e-33       1     137 []      19     162 ..      19     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 5.3e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vs+++ +ge+ +i+G+ G+GK+tLlk++agl++++eG+ill+g+++++  ++ +++ +++++++  l ++ltv+
  gi|320100720|ref|YP_004176312.1|  19 LDDVSFHIDQGELCVILGPPGSGKTTLLKIIAGLVRQDEGSILLNGESIDD--KPPSQRPVSMMFETLALYSHLTVY 93 
                                       79************************************************9..9999******************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en             e d+++ +++  l++++l ++++     +LSgG++qrva+aral+k+++++llDEp+a
  gi|320100720|ref|YP_004176312.1|  94 ENiaspliaakktpeEIDRRVRELAGVLKIEHLLERKA----DKLSGGERQRVAMARALAKDASIYLLDEPFA 162
                                       **********9998888888999999999999999998....*****************************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 !   16.2   0.0   1.3e-05    0.0072       3      24 ..      33      54 ..      31      81 .. 0.70
   2 !   23.2   0.0   9.8e-08   5.3e-05     203     299 ..     101     194 ..      85     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      v+ Gp gsGK++LL+++ +l r
  gi|320100720|ref|YP_004176312.1| 33 VILGPPGSGKTTLLKIIAGLVR 54
                                      89***************99944 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 9.8e-08
                            AAA_21 203 gegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll 279
                                        ++++ ++++d+r re     l+ ++  e+ a++lS G ++  a++ al+ ++   s++l+DEp ++L+ k+ + l 
  gi|320100720|ref|YP_004176312.1| 101 IAAKKTPEEIDRRVRE-LAGVLKIEHLLERKADKLSGGERQRVAMARALAKDA---SIYLLDEPFANLDAKIRHALR 173
                                       4555666677777777.9999999******************99999999999...********************* PP

                            AAA_21 280 ellkelsr.ngaQviltTHSp 299
                                       + +k+l++  g  ++l+T +p
  gi|320100720|ref|YP_004176312.1| 174 TEFKKLKQaLGKTIVLATSDP 194
                                       ***777776888888888655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   5.9e-09   3.2e-06      24     194 ..      29     188 ..       8     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 5.9e-09
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsi 99 
                                        ++ +i+Gp GSGK+ ll  i    G      +r+++ s l++  s + +  ++  v+++f+     ++ +  e +i
  gi|320100720|ref|YP_004176312.1|  29 GELCVILGPPGSGKTTLLKII---AG-----LVRQDEGSILLNGeSIDDKPPSQRPVSMMFETLALYSHLTVYE-NI 96 
                                       35689**************99...44.....5899*******99888889999999*****9999885555555.55 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                          ++  +++  +i+++  + + v ++ +  + + + LSgGe++ va+a  +A    k a++yllDe  a+LD+k +
  gi|320100720|ref|YP_004176312.1|  97 ASPLIAAKKTPEEIDRRVRELAGVLKIEHLLERKADKLSGGERQRVAMARALA----KDASIYLLDEPFANLDAKIR 169
                                       666666666788999999999888887777777899********999988776....899***************** PP

                                       HHHHHHHHHHCTT.SEEEE CS
                                       xxxxxxxxxxxxx.xxxxx RF
                             SMC_N 177 kkvaellkekskn.aQfiv 194
                                       +++ + +k+ ++     iv
  gi|320100720|ref|YP_004176312.1| 170 HALRTEFKKLKQAlGKTIV 188
                                       *999999988766344555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   4.2e-08   2.3e-05      22     107 ..      27     140 ..      16     207 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.2e-08
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdg.giflrgkcdql..esaipysalaqal.areellrqlldeaesael 94 
                                       +++el+++ G++G+GK++l++ ++  +++d+  i+l+g+  +   +s++p s+  ++l   ++l   ++ +    ++
  gi|320100720|ref|YP_004176312.1|  27 DQGELCVILGPPGSGKTTLLKIIAGLVRQDEgSILLNGESIDDkpPSQRPVSMMFETLaLYSHLTVYENIA----SP 99 
                                       45699*******************98888864888999999998888888888666550222222222222....22 PP

                            AAA_16  95 eawrekleeala............................a 107
                                         +++k +e++                             +
  gi|320100720|ref|YP_004176312.1| 100 LIAAKKTPEEIDrrvrelagvlkiehllerkadklsggerQ 140
                                       22222222222232223333444555554433333333330 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.5e-06   0.00081      17      50 ..      28      61 ..      22      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-06
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      +  ++v+ Gp+G+GKtt+lk ++ ++++++g+++
  gi|320100720|ref|YP_004176312.1| 28 QGELCVILGPPGSGKTTLLKIIAGLVRQDEGSIL 61
                                      45699*********************99976665 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 !   16.0   1.0   2.2e-05     0.012       2      37 ..      33      70 ..      32     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-05
                                      EEESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS CS
                               AAA  2 llyGppGtGKTllakavakelgve..fleisgsellsk 37
                                      ++ GppG GKT+l k +a  + ++   + ++g ++ +k
  gi|320100720|ref|YP_004176312.1| 33 VILGPPGSGKTTLLKIIAGLVRQDegSILLNGESIDDK 70
                                      578***************98753322444555555444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-05    0.0058      12      39 ..      19      46 ..      11      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      +d+ +++id+ + +++ Gp GsGK+Tll
  gi|320100720|ref|YP_004176312.1| 19 LDDVSFHIDQGELCVILGPPGSGKTTLL 46
                                      466889999777***************8 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05    0.0073       2      27 ..      31      56 ..      30      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                      l+++ G++GsGKTtLl+ +a + +++
  gi|320100720|ref|YP_004176312.1| 31 LCVILGPPGSGKTTLLKIIAGLVRQD 56
                                      789**************999877765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-05     0.011       4      68 ..      28     104 ..      25     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsstsskdllrellralglel 68 
                                       +  ++v+ G++G+GKTtll+ ++    +++                +rp  + ++  ++ s  ++++++++ l   +
  gi|320100720|ref|YP_004176312.1|  28 QGELCVILGPPGSGKTTLLKIIAGLVRQDEGSILlngesiddkppsQRPVSMMFETLALYSHLTVYENIASPLIAAK 104
                                       567899*************9888776555444446666666655433333333344444455555555555555544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.1e-05     0.011      10      38 ..      29      57 ..      24     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                       ++++++++pG+GKT++lk i  l+ + +
  gi|320100720|ref|YP_004176312.1| 29 GELCVILGPPGSGKTTLLKIIAGLVRQDE 57
                                      57899***********9998776665544 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 ?   12.6   0.1   0.00022      0.12      26      83 ..     127     171 ..     109     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiat 83 
                                       l+r++ +lSGGe+q    +a+a     ++ +      + ++ +LDE F++lD++ +++
  gi|320100720|ref|YP_004176312.1| 127 LERKADKLSGGERQR---VAMA----RALAK------DASIYLLDEPFANLDAKIRHA 171
                                       7899999******54...3444....44444......246789*********997765 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 ?   14.1   0.0     5e-05     0.027       3      22 ..      32      52 ..      30      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                                      EEEEESTTCCHHHHHHHHH.C CS
                              cobW  3 tvltGflGsGKTtLlnhll.e 22
                                       v+ G++GsGKTtLl+ +   
  gi|320100720|ref|YP_004176312.1| 32 CVILGPPGSGKTTLLKIIAgL 52
                                      6899***********988752 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.4e-05     0.045      29      50 ..      25      46 ..       9      77 .. 0.89
   2 ?   -2.1   0.1       4.6   2.5e+03      83     138 ..     107     169 ..      94     174 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-05
                            AAA_25 29 llpagelallaGapgtGKttla 50
                                      ++  gel+++ G+pg+GKttl+
  gi|320100720|ref|YP_004176312.1| 25 HIDQGELCVILGPPGSGKTTLL 46
                                      7999****************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.6
                            AAA_25  83 edelrrRlravgeal.......rddarllvldlagv.eslpLfakdrggtl..ltadvdaleaaie 138
                                        +e+ rR+r++   l       r  ++l    +++v + + L++ d   ++  l++ +++l+a+i+
  gi|320100720|ref|YP_004176312.1| 107 PEEIDRRVRELAGVLkiehlleRKADKLSGGERQRVaMARALAK-D--ASIylLDEPFANLDAKIR 169
                                       45677777776644444555665566666666666655554433.2..222335666666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00014     0.074       2      20 ..      33      51 ..      33      88 .. 0.80
   2 ?   -1.5   0.0       6.4   3.5e+03      31      76 ..     148     186 ..     123     202 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00014
                            AAA_18  2 lltGtpGvGKttlakeLsk 20
                                      ++ G+pG+GKttl k ++ 
  gi|320100720|ref|YP_004176312.1| 33 VILGPPGSGKTTLLKIIAG 51
                                      589***********99865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.4
                            AAA_18  31 vakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                       +ak+  ++l ++p+       ld + +++l +++++  +  + gk+
  gi|320100720|ref|YP_004176312.1| 148 LAKDASIYLLDEPF-----ANLDAKIRHALRTEFKKLKQ--ALGKT 186
                                       44444444444444.....56666666666666666643..44444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.8e-05     0.043      11      39 ..      20      49 ..      11      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-05
                            AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAi 39
                                      +d++++ ++  l +I Gp G+GKTT+l  i
  gi|320100720|ref|YP_004176312.1| 20 DDVSFHIDQgELCVILGPPGSGKTTLLKII 49
                                      4455555552699**************877 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     8e-05     0.044      83     127 ..      12      57 ..       4      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8e-05
                                       -TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  83 saktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       s ++++ l++++ ++++ +++v++G+ G GK+tL++ +++  ++  
  gi|320100720|ref|YP_004176312.1|  12 SYNDRKILDDVSFHIDQgELCVILGPPGSGKTTLLKIIAGLVRQDE 57 
                                       566778899999999998******************9998766655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025      0.14       3      24 ..      33      55 ..      32      68 .. 0.82
   2 ?   -1.6   0.0       4.4   2.4e+03      99     113 ..     136     151 ..     108     200 .. 0.51
   3 ?   -2.2   0.0         7   3.8e+03      65      89 ..     247     271 ..     235     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                      EEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.n 24
                                      +++GppG+gK++l + +a ++ +
  gi|320100720|ref|YP_004176312.1| 33 VILGPPGSGKTTLLKIIAGLVrQ 55
                                      689**************999844 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.4
                                       SSSEEE---....... CS
                             AAA_5  99 ggelvkakndd.ller 113
                                       gge+++++    l+++
  gi|320100720|ref|YP_004176312.1| 136 GGERQRVAMARaLAKD 151
                                       4444444444333333 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7
                                       G-SEEEEESGGG--HHHHHHHHHHH CS
                             AAA_5  65 egeilvlDEveraesevlnsLlsll 89 
                                       +g  lv+++++r++ +   +Ll l+
  gi|320100720|ref|YP_004176312.1| 247 RGGELVVEGINRMRLSLPRELLELI 271
                                       5566789999999988888888776 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     8e-05     0.043     126     162 ..      26      62 ..       9      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8e-05
                             T2SSE 126 vrerglilvsGgTgsGKttllyallkeinksderivt 162
                                       + +  l ++ G+ gsGKttll ++   + +++  i++
  gi|320100720|ref|YP_004176312.1|  26 IDQGELCVILGPPGSGKTTLLKIIAGLVRQDEGSILL 62 
                                       5556678899******************999888875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.6e-05     0.041      10      40 ..      22      55 ..      13     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.6e-05
                            AAA_11 10 iksalseseitliqGPPGtgKT...ktivellsq 40
                                      +++ + + e+++i GPPG+gKT   k i++l++q
  gi|320100720|ref|YP_004176312.1| 22 VSFHIDQGELCVILGPPGSGKTtllKIIAGLVRQ 55
                                      5667888999************444444444443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00013     0.069       2      20 ..      32      50 ..      31      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                       vi+G++++GKTtll+ +a
  gi|320100720|ref|YP_004176312.1| 32 CVILGPPGSGKTTLLKIIA 50
                                      69*************9887 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   0.00014     0.074       2      20 ..      32      50 ..      31     195 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                       ++ G+pGsGK+tl++ ++
  gi|320100720|ref|YP_004176312.1| 32 CVILGPPGSGKTTLLKIIA 50
                                      6789**********98654 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   0.00024      0.13      36      55 ..      32      51 ..      23      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            RuvB_N 36 vllyGpPGlGkttlakiiak 55
                                      +++ GpPG Gkttl kiia 
  gi|320100720|ref|YP_004176312.1| 32 CVILGPPGSGKTTLLKIIAG 51
                                      5789**************95 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 ?   11.6   0.0   0.00034      0.19      20      43 ..      29      52 ..      21      63 .. 0.83
   2 ?   -1.9   0.0       4.8   2.6e+03      78     121 ..     144     187 ..     114     193 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiien 43
                                       e  +i Gp gsGKt+Llk i+  
  gi|320100720|ref|YP_004176312.1| 29 GELCVILGPPGSGKTTLLKIIAGL 52
                                      56789*************988755 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.8
                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkkii 121
                                       +++al+++     l+e + +  +++  a+   ++k+k+   k i
  gi|320100720|ref|YP_004176312.1| 144 MARALAKDASIYLLDEPFANLDAKIRHALRTEFKKLKQALGKTI 187
                                       33333344444444444445555555666666666666655544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00034      0.18       3      45 ..      30      71 ..      28      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45
                                      +++vi G+  +GKTtllk ++  l  ++e  + +n ++ +dk 
  gi|320100720|ref|YP_004176312.1| 30 ELCVILGPPGSGKTTLLKIIA-GLVRQDEGSILLNGESIDDKP 71
                                      6789************97666.555588999999999988865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.19      43      64 ..      25      46 ..       7      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                         IstB_IS21 43 fiekkenivllGpsGvGKshla 64
                                      +i++ e +v+lGp+G GK+ l 
  gi|320100720|ref|YP_004176312.1| 25 HIDQGELCVILGPPGSGKTTLL 46
                                      4999***************885 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00041      0.23       3      26 ..      33      56 ..      32      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                                      EEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkss 26
                                      +i GppG+GKtTl+k ++ l++++
  gi|320100720|ref|YP_004176312.1| 33 VILGPPGSGKTTLLKIIAGLVRQD 56
                                      577***********9999988765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00039      0.21       5      22 ..      32      49 ..      29      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i Gp+g+GKTtl+k +
  gi|320100720|ref|YP_004176312.1| 32 CVILGPPGSGKTTLLKII 49
                                      699***********9976 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00092       0.5       9      44 ..      19      54 ..       8      68 .. 0.81
   2 ?   -0.5   0.0       1.1   6.1e+02      81     126 ..     131     181 ..      87     198 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00092
                                      HHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  9 LDkltsGlqkgdliiiAarpsmGktalalniaenaa 44
                                      LD++   + +g+l++i + p+ Gkt+l   ia  + 
  gi|320100720|ref|YP_004176312.1| 19 LDDVSFHIDQGELCVILGPPGSGKTTLLKIIAGLVR 54
                                      899999999******************988886554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                                       HTTSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHH.HH....HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx....xxxxxxxxx RF
                            DnaB_C  81 tgklkeedweklteaieelseaklfiddtpaltvs.ei....rskarrlkk 126
                                         kl+  + ++++ a +  ++a++++ d+p  ++  +i    r++ ++lk+
  gi|320100720|ref|YP_004176312.1| 131 ADKLSGGERQRVAMARALAKDASIYLLDEPFANLDaKIrhalRTEFKKLKQ 181
                                       346777788888888888888999999998665431331111444444444 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00067      0.37      26      76 .]     309     359 ..     284     359 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00067
                            TOBE_2  26 veylGsstryvvelaggqlvvvrqpnadr.dsalapGdtVelswdpddavvl 76 
                                        ey+Gs++ ++ + a+  ++++ +++a+    +l+ Gd+Ve+++d   ++v+
  gi|320100720|ref|YP_004176312.1| 309 AEYRGSEYIVYASEADR-IFKCLMHPAEFtLMDLKYGDEVEVCIDLSNTIVF 359
                                       79*******99665555.66999999998779*************9999887 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00082      0.45       1      16 [.      35      50 ..      35      62 .. 0.87
   2 ?   -2.0   0.0       8.1   4.4e+03      58      58 ..     140     140 ..     101     193 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00082
                                      EE-TTSSHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklv 16
                                      lG+PGsGK+t+++ ++
  gi|320100720|ref|YP_004176312.1| 35 LGPPGSGKTTLLKIIA 50
                                      7***********6654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.1
                                       H CS
                            AAA_17  58 q 58 
                                       q
  gi|320100720|ref|YP_004176312.1| 140 Q 140
                                       2 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0005      0.27      45      68 ..      29      52 ..      12     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                             Rad17 45 kriLLisGPsGCgkstvvkvLske 68
                                       ++ +i GP+G gk+t +k+++  
  gi|320100720|ref|YP_004176312.1| 29 GELCVILGPPGSGKTTLLKIIAGL 52
                                      568899**************9864 PP

>> T6SS_TssF  Type VI secretion system, TssF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0021       1.1      33      80 ..     141     188 ..     137     200 .. 0.86
   2 ?    0.2   0.0      0.39   2.1e+02     532     587 ..     288     343 ..     274     354 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0021
                         T6SS_TssF  33 rlgldgeeveDPhVeRLlegfAflaaRiqqklddefpelteaLlevly 80 
                                       r ++ +  ++D  +  L e fA l a+i++ l  ef++l +aL ++++
  gi|320100720|ref|YP_004176312.1| 141 RVAMARALAKDASIYLLDEPFANLDAKIRHALRTEFKKLKQALGKTIV 188
                                       6778888899999999**************************987775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                         T6SS_TssF 532 vpgkgglvfarGveitltldesafegesvylfgavLerffaryasinsftqlvlrs 587
                                          ++ +  ++G+ i+ +   ++++g+++++ ++  +r f++     +ft + l+ 
  gi|320100720|ref|YP_004176312.1| 288 CSISRSSRGCKGLGIKAKYIGAEYRGSEYIVYASEADRIFKCLMHPAEFTLMDLKY 343
                                       5555666779***********************************99999988875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00084      0.45      17      50 ..      24      56 ..      16      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00084
                            AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFlnnk 50
                                      ++id  e l v+ G+ +sGK+++l+++  +  ++
  gi|320100720|ref|YP_004176312.1| 24 FHIDQGE-LCVILGPPGSGKTTLLKIIAGLVRQD 56
                                      4566555.*******************8777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 2889.10
//
Query:       gi|320100721|ref|YP_004176313.1|  [L=376]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-29  101.4   0.0    8.4e-29  100.8   0.0    1.3  1  ABC_tran     ABC transporter
    7.9e-07   29.3   0.0    2.2e-06   27.9   0.0    1.8  1  TOBE         TOBE domain
    1.2e-06   28.5   0.0    0.00076   19.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.9e-06   28.0   0.2    1.4e-05   25.8   0.1    2.3  2  OB_MalK      MalK OB fold domain
    2.7e-05   24.2   0.0    7.8e-05   22.8   0.0    1.8  1  TOBE_2       TOBE domain
    0.00068   20.2   0.3     0.0014   19.2   0.3    1.4  1  AAA_23       AAA domain
      0.002   18.6   0.0     0.0029   18.0   0.0    1.3  1  AAA_16       AAA ATPase domain
      0.004   16.6   0.1          1    8.8   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0079   16.1   0.0     0.0098   15.8   0.0    1.4  1  ATPase_2     ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.028   14.3   0.0    1.6  1  RsgA_GTPase  RsgA GTPase
      0.017   15.1   0.0      0.027   14.4   0.0    1.3  1  Rad17        Rad17 P-loop domain
      0.017   15.1   0.0      0.045   13.7   0.0    1.7  1  TOBE_3       TOBE-like domain
      0.026   14.1   0.1       0.25   10.9   0.0    2.3  2  AAA_25       AAA domain
      0.027   14.7   0.1      0.048   13.9   0.1    1.5  1  AAA_22       AAA domain
      0.037   14.5   0.0      0.093   13.2   0.0    1.7  1  AAA          ATPase family associated with various cellular a
      0.049   13.5   0.0      0.094   12.6   0.0    1.4  1  NACHT        NACHT domain
       0.05   13.4   0.0       0.11   12.2   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.052   13.8   0.1       0.11   12.7   0.1    1.6  1  AAA_28       AAA domain
      0.062   13.0   0.0       0.12   12.1   0.0    1.4  1  IstB_IS21    IstB-like ATP binding protein
      0.081   12.6   0.0       0.26   11.0   0.0    1.7  2  AAA_30       AAA domain
       0.18   10.9   0.0       0.33   10.1   0.0    1.5  1  NB-ARC       NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.0   9.9e-32   8.4e-29       1     136 [.      27     168 ..      27     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 9.9e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk ++l ++ ge  ai+G++G+GK+tLl+++agl+kp  G++ +dg d++    +   +++++++q   l p++ v+
  gi|320100721|ref|YP_004176313.1|  27 LKGIDLFIRSGEFFAILGPSGCGKTTLLRIIAGLEKPSTGRVFFDGVDVTG--YPAEYRNVAMVFQFYALYPTT-VY 100
                                       6889999********************************************..999999*************99.** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e  e++ k+ + +gl+++ + +v    ++LS   kqrvalara++++p+l+llDEp 
  gi|320100721|ref|YP_004176313.1| 101 ENialplksrkykgkEIYERVRKISEVVGLSDKLNLHV----NKLSVADKQRVALARAMAREPNLYLLDEPL 168
                                       *******9999655555555777777777777666666....*****************************6 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.5e-09   2.2e-06       7      58 ..     305     355 ..     303     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.5e-09
                              TOBE   7 lpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalik 58 
                                       +  +V+v+e+lg ++ +++++gg++   ++++++++eeL  ++GeeV+++i 
  gi|320100721|ref|YP_004176313.1| 305 FASRVSVIEFLGTRYIITLEAGGQE-FKVVMDTKRFEELSPKVGEEVYVRIR 355
                                       788**********************.***********************996 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   8.9e-07   0.00076       1      72 [.      39     112 ..      39     126 .. 0.75
   2 !    7.0   0.0    0.0051       4.4     251     299 ..     155     201 ..     146     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.9e-07
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarl..drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvry 72 
                                       + ++ Gp g+GK++LL+++ +l      r ++++ d+ +   ++r ++  + +y+  + +++e + +++++ +y
  gi|320100721|ref|YP_004176313.1|  39 FFAILGPSGCGKTTLLRIIAGLEKPstGRVFFDGVDVTGYPAEYRNVAMVFQFYALYPTTVYENIALPLKSRKY 112
                                       679****************9996667767777777777777777777777777777776666666666666555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0051
                            AAA_21 251 llralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQv.iltTHSp 299
                                       ++r +    l+l+DEp + L+P + r ++   lk+ +r+++Q  i +TH+ 
  gi|320100721|ref|YP_004176313.1| 155 MAREP---NLYLLDEPLTILDP-VSRIIMrSELKRVQRELGQTvIYVTHDQ 201
                                       33333...89************.666666989999999777777*****96 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   1.7e-08   1.4e-05       1      52 [.     242     291 ..     242     292 .. 0.86
   2 ?   -2.3   0.0       9.6   8.2e+03      22      46 ..     328     352 ..     318     355 .. 0.60

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.7e-08
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                       G P MNf++++v+++g  ++ gg ++ +++++++ l+++  ++v+lG+R E+
  gi|320100721|ref|YP_004176313.1| 242 GEPGMNFIDVQVSGEG--LAIGGSAIYVNRDMAAVLRKKGFDRVLLGFRGEN 291
                                       99*************9..55555699999999778888888********996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.6
                           OB_MalK  22 ggvtlplpeeqkl.alklyagkevil 46 
                                       +++++ +++++ + +l++++g+ev +
  gi|320100721|ref|YP_004176313.1| 328 QEFKVVMDTKR-FeELSPKVGEEVYV 352
                                       33444444443.35888888888876 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   9.1e-08   7.8e-05       4      70 ..     288     356 ..     285     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.1e-08
                            TOBE_2   4 RPEklrla.aaggan.glsGtVedveylGsstryvvelaggqlvvvrqpnadr.dsalapGdtVelswdp 70 
                                       R E+  ++ + gg++ +++ +V+ +e+lG+ + +++e +g+++ +v+++  +  +  +++G++V ++++ 
  gi|320100721|ref|YP_004176313.1| 288 RGENAIVSrHSGGGGvSFASRVSVIEFLGTRYIITLEAGGQEF-KVVMDTKRFeELSPKVGEEVYVRIRD 356
                                       555555665556667799****************999887766.888888888789**********9875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   1.6e-06    0.0014       7      39 ..      21      57 ..      12      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                            AAA_23  7 frsfrdqe.idF...skgltlItGpNGaGKTTildAi 39
                                      f++ +  + id+   s  +++I Gp G+GKTT+l+ i
  gi|320100721|ref|YP_004176313.1| 21 FGKVEALKgIDLfirSGEFFAILGPSGCGKTTLLRII 57
                                      555566667899998889****************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.4e-06    0.0029      23     117 ..      36     141 ..      25     197 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.4e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd...ggif....lrgkcdqlesaipy.salaqalareellrqlldeaes 91 
                                       ++e   + G+sG+GK++l+r ++  lek    +++f    ++g   ++ +++++  ++  +  + ++++ ++ +++s
  gi|320100721|ref|YP_004176313.1|  36 SGEFFAILGPSGCGKTTLLRIIA-GLEKPstgRVFFdgvdVTGYPAEY-RNVAMvFQFYALYPT-TVYENIALPLKS 109
                                       447889**************999.566665643444666677777777.555552336666644.777777766444 PP

                            AAA_16  92 aeleawrekleealaavpelagaea........s 117
                                         + +  +++ e+++ ++e+ g +          
  gi|320100721|ref|YP_004176313.1| 110 --RKYKGKEIYERVRKISEVVGLSDklnlhvnkL 141
                                       ..66666666666664444444333344555443 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0097       8.3      25      42 ..      38      55 ..      27      65 .. 0.87
   2 !    8.8   0.0    0.0012         1     116     203 ..     120     203 ..      79     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0097
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                      +f ai+Gp G+GK+ ll 
  gi|320100721|ref|YP_004176313.1| 38 EFFAILGPSGCGKTTLLR 55
                                      6899**********9986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                                       EEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                             SMC_N 116 kevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQ 191
                                       +  + +ev  l  + +++ + LS  +k+ vala      +++   lyllDe    LD   + ++ + lk+ + +  Q
  gi|320100721|ref|YP_004176313.1| 120 RVRKISEVVGLSDKLNLHVNKLSVADKQRVALARA----MAREPNLYLLDEPLTILDPVSRIIMRSELKRVQRElGQ 192
                                       44445888888888899999999999998887655....567788***********************987777344 PP

                                       .EEEE-SSHHHCC CS
                                       .xxxxxxxxxxxx RF
                             SMC_N 192 .fivislreemle 203
                                        +i +++++  +e
  gi|320100721|ref|YP_004176313.1| 193 tVIYVTHDQ--VE 203
                                       133445543..33 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05    0.0098       9      54 ..      28      70 ..      21     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                          ATPase_2  9 keleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                                      k +   +++   e+  i Gp g+GKt+Ll+ i+    + +  ++++
  gi|320100721|ref|YP_004176313.1| 28 KGIDLFIRS--GEFFAILGPSGCGKTTLLRIIAGLE-KPSTGRVFF 70
                                      555555555..5778899***********9666555.445556665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.2e-05     0.028      91     130 ..      28      68 ..       6      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       + +   +++ ++ +++G+SG GK+tL+  +++ ++ +tg v
  gi|320100721|ref|YP_004176313.1|  28 KGIDLFIRSgEFFAILGPSGCGKTTLLRIIAGLEKPSTGRV 68 
                                       55555565558999***************999878777765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.1e-05     0.027      43      67 ..      35      59 ..      17      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                             Rad17 43 rkkriLLisGPsGCgkstvvkvLsk 67
                                      r  +   i GPsGCgk+t +++++ 
  gi|320100721|ref|YP_004176313.1| 35 RSGEFFAILGPSGCGKTTLLRIIAG 59
                                      555677899************9985 PP

>> TOBE_3  TOBE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.3e-05     0.045      10      60 .]     308     355 ..     299     355 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-05
                            TOBE_3  10 tvrrirpvGpivRlELerlgdtgeliEvelprdrfeelglaeGetvylrPr 60 
                                       +v+ i  +G    + Le   + g+ + v +   rfeel +++Ge+vy+r r
  gi|320100721|ref|YP_004176313.1| 308 RVSVIEFLGTRYIITLE---AGGQEFKVVMDTKRFEELSPKVGEEVYVRIR 355
                                       56666667777777773...66999***********************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00029      0.25      27      50 ..      31      54 ..       6      88 .. 0.83
   2 ?    0.6   0.0      0.41   3.5e+02     170     188 ..     181     199 ..     168     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                            AAA_25 27 kgllpagelallaGapgtGKttla 50
                                      + +++ ge+ ++ G++g+GKttl+
  gi|320100721|ref|YP_004176313.1| 31 DLFIRSGEFFAILGPSGCGKTTLL 54
                                      558999****************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.41
                            AAA_25 170 ealeriarrtgaavllvhH 188
                                       + l+r++r++g +v+ v H
  gi|320100721|ref|YP_004176313.1| 181 SELKRVQRELGQTVIYVTH 199
                                       5689999********9999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.6e-05     0.048       4      27 ..      36      59 ..      34     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                      +  + ++ G+sG+GKTtllr ++ 
  gi|320100721|ref|YP_004176313.1| 36 SGEFFAILGPSGCGKTTLLRIIAG 59
                                      567899*************97765 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   0.00011     0.093       3      20 ..      42      59 ..      40      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      + Gp G+GKT+l + +a 
  gi|320100721|ref|YP_004176313.1| 42 ILGPSGCGKTTLLRIIAG 59
                                      67**************97 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.094       4      21 ..      41      58 ..      38      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      EEEC-TTTCHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqkla 21
                                      ++ G++G+GKTtLl+ +a
  gi|320100721|ref|YP_004176313.1| 41 AILGPSGCGKTTLLRIIA 58
                                      799***********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 ?   12.2   0.0   0.00013      0.11      22      39 ..      36      54 ..      26      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_29 22 kg.atlltGpsGsGKSTll 39
                                      +g ++ + GpsG GK+Tll
  gi|320100721|ref|YP_004176313.1| 36 SGeFFAILGPSGCGKTTLL 54
                                      455899************8 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00013      0.11       2      20 ..      40      58 ..      39      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      ++i+G++++GKTtll+ +a
  gi|320100721|ref|YP_004176313.1| 40 FAILGPSGCGKTTLLRIIA 58
                                      68*************9887 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   0.00014      0.12      34      64 ..      23      54 ..      11      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                         IstB_IS21 34 kvkeLatls.fiekkenivllGpsGvGKshla 64
                                      kv++L + + fi++ e +++lGpsG GK+ l 
  gi|320100721|ref|YP_004176313.1| 23 KVEALKGIDlFIRSGEFFAILGPSGCGKTTLL 54
                                      56777776559******************875 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   0.00031      0.26      13      46 ..      33      65 ..      27      78 .. 0.81
   2 ?   -2.0   0.0       2.9   2.4e+03      38      67 ..     183     212 ..     178     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                            AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaweaag 46
                                      ++ sg+ + ++ Gp G GKtt+l+ ++ + + + 
  gi|320100721|ref|YP_004176313.1| 33 FIRSGE-FFAILGPSGCGKTTLLRIIAGLEKPST 65
                                      566775.8999*************9988766664 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.9
                            AAA_30  38 lreaweaaggrviglAptgkaAkvLaeelg 67 
                                       l+++ ++ g++vi +++ +  A +La+ + 
  gi|320100721|ref|YP_004176313.1| 183 LKRVQRELGQTVIYVTHDQVEALTLADRIA 212
                                       566666669999999999999988887765 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   0.0   0.00038      0.33      22      41 ..      39      58 ..      24     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00038
                                      EEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 22 vvalvGmgGvGKttlakqil 41
                                      + a+ G  G+GKttl++ i 
  gi|320100721|ref|YP_004176313.1| 39 FFAILGPSGCGKTTLLRIIA 58
                                      789************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 2993.27
//
Query:       gi|320100722|ref|YP_004176314.1|  [L=92]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   13.0   3.4      0.085   13.2   0.8    2.0  2  DUF2929   Protein of unknown function (DUF2929)
       0.17   12.1   0.2       0.17   12.1   0.2    2.0  2  DUF3784   Domain of unknown function (DUF3784)
       0.52   10.5   2.3       0.94    9.7   2.3    1.4  1  DUF3270   Protein of unknown function (DUF3270)


Domain annotation for each model (and alignments):
>> DUF2929  Protein of unknown function (DUF2929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.2   1.2e+03      33      44 ..      11      22 ..       3      27 .. 0.61
   2 ?   13.2   0.8   1.4e-05     0.085       9      52 ..      36      87 ..      32      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                           DUF2929 33 talilavvfgvl 44
                                      t+li++++   l
  gi|320100722|ref|YP_004176314.1| 11 TLLIVGLIGLAL 22
                                      556666654443 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                           DUF2929  9 WsfiLgevvgYIgsaLtgvtyd........fttalilavvfgvlviliiali 52
                                      W ++    + Y++s+Lt ++y+         +t++i+ +v++ +++l i+l+
  gi|320100722|ref|YP_004176314.1| 36 WYVLMAATTLYVASTLTPTSYHgtrfllryALTLTIVLLVVASFILLSIKLA 87
                                      8889999999************988888887778888888888777777665 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.8e-05      0.17      45      86 ..       7      47 ..       2      53 .. 0.88
   2 ?    1.6   0.5     0.055   3.3e+02       4      18 ..      71      85 ..      60      92 .] 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                           DUF3784 45 fmgivllligilflllgllsaiesealliialiviiiiviyl 86
                                      f+ + ll++g l+ l+ +++++ ++a++++ ++++ ++++y+
  gi|320100722|ref|YP_004176314.1|  7 FIEKTLLIVG-LIGLALIIQPFSRDAYTWGWYVLMAATTLYV 47
                                      6778899999.888888889*****************99997 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.055
                           DUF3784  4 allflilGilflkgk 18
                                      ++l++++++++l+ k
  gi|320100722|ref|YP_004176314.1| 71 IVLLVVASFILLSIK 85
                                      455555555555444 PP

>> DUF3270  Protein of unknown function (DUF3270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.3   0.00016      0.94      50      68 ..      72      90 ..      61      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                           DUF3270 50 vitvlvsfillalklatll 68
                                      v++v++sfill++kla+ll
  gi|320100722|ref|YP_004176314.1| 72 VLLVVASFILLSIKLAPLL 90
                                      789*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 692.20
//
Query:       gi|320100723|ref|YP_004176315.1|  [L=515]
Description: ABC transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-16   58.0   8.5    1.6e-15   57.2   8.5    1.6  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.7e-05   24.1   8.3    1.7e-05   24.1   8.3    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
          2    7.9  15.6       0.19   11.2  10.5    1.8  2  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   8.5   2.6e-19   1.6e-15      76     288 .]     233     513 ..      10     513 .. 0.75

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.6e-19
                   ABC2_membrane_2  76 v...................................................................vstimavli 85 
                                                                                                           +++++++++
  gi|320100723|ref|YP_004176315.1| 233 SylgtirealktyvyeaavdpkllessrpveirlallsregeilggleismgltnpaveaitefvagtGVGLFSGFF 309
                                       04444444444444444455555666666666677777788888888888888888888888888888999****** PP

                   ABC2_membrane_2  86 pviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledll 162
                                       p++ + +g+ +ia+ k++g l++ L++P++R++++l    +g++++    +a+ a++ +al   +++   +al  l 
  gi|320100723|ref|YP_004176315.1| 310 PIVVLYLGYVLIAKPKTQGALEFILARPITRRDLYLTRYAAGVLVA----LAAPAVFTIALYTGVYSTLRVALNPLD 382
                                       ********************************************94....444444445555555555555555444 PP

                   ABC2_membrane_2 163 llvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp..qeindflslls 237
                                        l++   l + l  f +l + +++ ar  ++ +a+ + l+++ +i ++i+++  ++   g+++    +++ +l +ls
  gi|320100723|ref|YP_004176315.1| 383 ALLIYLGLAASLAGFYTLCYYIAVEAR-GASYLAITITLYLLYLIGFQILGFM-IAFTVGHSIEdyLKLTYKLYYLS 457
                                       333333333332346889999999999.6677777777777777777777743.33444444448889999****** PP

                   ABC2_membrane_2 238 ptsayntllneilagsdlna....lgstatnl.lilllllavllvlgyvlFkrkDl 288
                                       p +  +++++ +l + +         ++++++ +++ ++++v++  g+v+Fkrk l
  gi|320100723|ref|YP_004176315.1| 458 PMRLADLVTALVLYRHGYLGaavlEVVKPEYIaVATAAWIIVPFTAGLVRFKRKNL 513
                                       ***************97555899988888886257889***************975 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.9      0.66     4e+03     243     259 ..      19      35 ..      15      41 .. 0.62
   2 !   24.1   8.3   2.8e-09   1.7e-05      98     289 ..     220     435 ..     195     477 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.66
                   ABC2_membrane_3 243 llfllfglayialgyll 259
                                         ++lf++a + l+y++
  gi|320100723|ref|YP_004176315.1|  19 TALILFIMAGVGLTYMV 35 
                                       45566666666666654 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.8e-09
                   ABC2_membrane_3  98 satvtvlinssnlnsskailnalns.llqqlnasalvlqseatstsaninvestql..............eeel.sn 158
                                       ++    ++n s+ +   +i++al++ ++++    +  ++    s + +i + ++++              ++++ + 
  gi|320100723|ref|YP_004176315.1| 220 ESRGPMVSNISGMSYLGTIREALKTyVYEAAV--D--PKLLESSRPVEIRLALLSRegeilggleismglTNPAvEA 292
                                       44445555555555556666666665554322..1..1222222222222222222444444444444443333344 PP

                   ABC2_membrane_3 159 vasflvg.....liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllq.lllilllaf 229
                                       ++ f++g     +  +++i + ++  +  i++ k+++++e++l  ++++  ++l ++ + +lv+l   ++++++l+ 
  gi|320100723|ref|YP_004176315.1| 293 ITEFVAGtgvglFSGFFPIVVLYLGYV-LIAKPKTQGALEFILARPITRRDLYLTRYAAGVLVALAApAVFTIALYT 368
                                       444433343337777888888888777.59***********************************761556677988 PP

                   ABC2_membrane_3 230 glgipfg...nlglllllfllfglayialgyllsslfkns.etaqilifivil...llsgffgglfp 289
                                       g+  +     n + +ll +l  + +++ +++l+ ++   + ++ +++i+i++    l+++ ++g+++
  gi|320100723|ref|YP_004176315.1| 369 GVYSTLRvalNPLDALLIYLGLAASLAGFYTLCYYIAVEArGASYLAITITLYllyLIGFQILGFMI 435
                                       8634444557888899999999999999*99999995555244455544444444334444444443 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 ?   -2.0   0.2      0.36   2.2e+03     154     161 ..      21      28 ..       3      46 .. 0.44
   2 ?   11.2  10.5   3.2e-05      0.19      34     167 ..     300     433 ..     290     470 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.36
                   ABC2_membrane_5 154 ifgiifll 161
                                        +++i+ +
  gi|320100723|ref|YP_004176315.1|  21 LILFIMAG 28 
                                       11111111 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.2e-05
                   ABC2_membrane_5  34 dsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn 110
                                       ++v l+ +++++v++++    ++++ + ++   ++l  P+tr+++   +Y  ++++ l+a  +++++l+ +v+ + +
  gi|320100723|ref|YP_004176315.1| 300 TGVGLFSGFFPIVVLYL-GYVLIAKPKTQGALEFILARPITRRDLYLTRYAAGVLVALAAPAVFTIALYTGVYSTLR 375
                                       55667888888888887.5569999*******************************************999999999 PP

                   ABC2_membrane_5 111 vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiif.llvaifsl 167
                                       v ++++   ++   + a++++  +l  y+  +++ + +++i+i + + + ++++i+ +
  gi|320100723|ref|YP_004176315.1| 376 VALNPLDALLIYLGLAASLAGFYTLCYYIAVEARGASYLAITITLYLLYlIGFQILGF 433
                                       9987775555555555566666666666666666666655554444333255555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3628.10
//
Query:       gi|320100724|ref|YP_004176316.1|  [L=327]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-22   80.3   0.0    2.9e-22   79.6   0.0    1.4  1  ABC_tran  ABC transporter
    8.2e-09   35.7   0.1    6.7e-05   22.8   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.038   13.0   0.2      0.068   12.1   0.2    1.4  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.049   13.4   0.1       0.14   11.8   0.1    1.7  1  Cupin_2   Cupin domain
      0.068   13.7   0.0       0.13   12.8   0.0    1.4  1  AAA_23    AAA domain
      0.083   12.6   0.1       0.19   11.4   0.1    1.5  1  AAA_30    AAA domain
       0.14   11.8   0.1       0.25   11.0   0.1    1.3  1  SRP54     SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   1.1e-25   2.9e-22       1     136 [.      43     186 ..      43     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.1e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vs+k+  ge+v+ vG nGaGK+t +++++g l+p++Ge+l+dg ++ + e+++++++ig++p+ p +  e ++ 
  gi|320100724|ref|YP_004176316.1|  43 LSDVSFKVGDGEVVGYVGLNGAGKTTTIRIITGVLNPDKGEVLVDGYSVLR-EKRKASERIGWVPELPIFETEFKAL 118
                                       689***********************************************9.8888999********9999999888 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +              e+ +   ++l+k+gl +   +++    s++S+G+k+r ala +l+ +p+ +++DE  
  gi|320100724|ref|YP_004176316.1| 119 DYfvylagyhglsrgEAVRLGRELLEKVGLGDAVYKRL----SEYSQGMKKRFALAVSLIGNPQNFVFDEVL 186
                                       889******99987555555889999999999888888....****************************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 !   10.6   0.2   0.00014      0.36       5      24 ..      59      78 ..      59     146 .. 0.78
   2 !   22.8   0.0   2.6e-08   6.7e-05     234     297 ..     156     216 ..     132     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                            AAA_21  5 iGpNgsGKSnLLdaldllar 24
                                      +G Ng+GK++ ++++ ++  
  gi|320100724|ref|YP_004176316.1| 59 VGLNGAGKTTTIRIITGVLN 78
                                      799************88853 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 2.6e-08
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++e S+G+k+ +al+++l+  ++    +++DE+ ngL+P+ ++ + el +  +++g  v++++H
  gi|320100724|ref|YP_004176316.1| 156 LSEYSQGMKKRFALAVSLIGNPQN---FVFDEVLNGLDPQGIAFFRELTRGFKKEGRAVLFSSH 216
                                       5678******************88...************7777777777555557889****** PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.7e-05     0.068      16      53 ..      40      77 ..      27      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHH CS
                              MeaB 16 kellerllakaGraqvvGltGvPGaGkstlvealglel 53
                                      +++l+ ++ k G  +vvG  G+ GaGk t++  ++  l
  gi|320100724|ref|YP_004176316.1| 40 RRVLSDVSFKVGDGEVVGYVGLNGAGKTTTIRIITGVL 77
                                      6799999***********************98877655 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.6e-05      0.14      19      44 ..     262     286 ..     256     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                                       EEEEEEEEESEEEEEECTEEEEEETT CS
                           Cupin_2  19 edeffyVleGegeltvdgeeveleaG 44 
                                         e + VleG+ge++v+g ev+++++
  gi|320100724|ref|YP_004176316.1| 262 G-EALRVLEGYGEIRVEGSEVVVKTD 286
                                       4.999******************987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     5e-05      0.13      24      44 ..      58      78 ..      34     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                            AAA_23 24 ItGpNGaGKTTildAiklaLy 44
                                       +G NGaGKTT ++ i+ +L 
  gi|320100724|ref|YP_004176316.1| 58 YVGLNGAGKTTTIRIITGVLN 78
                                      589*************99886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   7.5e-05      0.19      19      50 ..      54      85 ..      47     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       v+  +G  G+GKtt+++ ++ +++ ++g+v+
  gi|320100724|ref|YP_004176316.1| 54 EVVGYVGLNGAGKTTTIRIITGVLNPDKGEVL 85
                                      488899***************99998877775 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.6e-05      0.25       6      31 ..      58      83 ..      54      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.6e-05
                                      EEESTTSSHHHHHHHHHHHHHHTTS- CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkk 31
                                       vGl+GaGKTtt+  +  +l+ ++ +
  gi|320100724|ref|YP_004176316.1| 58 YVGLNGAGKTTTIRIITGVLNPDKGE 83
                                      69**********98777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2442.84
//
Query:       gi|320100725|ref|YP_004176317.1|  [L=177]
Description: Appr-1-p processing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-28   97.2   0.1    8.6e-28   96.7   0.1    1.2  1  Macro     Macro domain
    8.6e-06   25.3   1.1    0.00051   19.5   1.1    2.6  1  Macro_2   Macro-like domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.1   9.6e-32   8.6e-28       1     118 []      26     137 ..      26     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 9.6e-32
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeel 77 
                                       Vn+aN+++ +gggva ai +++g  ++ee+ +     +++++G avvt++++l +k vih+  p++ + ++ +++ +
  gi|320100725|ref|YP_004176317.1|  26 VNPANTYGYMGGGVALAIRKKGGDVIEEEAVKQ----APIPIGGAVVTTGGSLGVKAVIHA--PTVVEPGGASSPVN 96 
                                       9****************************9988....99**********************..****99******** PP

                                       HHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  78 lakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       + ka+  al+++ e+g++++afP +++G++gvp+ e+ar++
  gi|320100725|ref|YP_004176317.1|  97 VYKATAAALSKVLENGFRKIAFPLMGAGVGGVPPAESARAM 137
                                       *************************************9976 PP

>> Macro_2  Macro-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.1   5.7e-08   0.00051      71     218 ..      24     149 ..       4     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.7e-08
                           Macro_2  71 aivspGnsfGylGGGfdlalfeyfGGkpfetwfrkklgnryytvGsatvidltrcllediielrdgiryiihvptvv 147
                                       a+v p n++Gy+GGG  la+ +  GG  +e    + + +   ++G a v              + g++ +ih ptvv
  gi|320100725|ref|YP_004176317.1|  24 ALVNPANTYGYMGGGVALAIRK-KGGDVIEE---EAVKQAPIPIGGAVVTT----------GGSLGVKAVIHAPTVV 86 
                                       79*****************976.58888886...56667789999997743..........4566899********* PP

                           Macro_2 148 apsksifqkaeklktGyepvfnamwnslmsap.kdvdgliisGlctGyaGvpaeiscksmafalslymlqdk 218
                                        p  ++     ++      v+ a+  +l ++  +    + ++ + +G  Gvp+  s ++ma al+ + ++  
  gi|320100725|ref|YP_004176317.1|  87 EPGGAS----SPV-----NVYKATAAALSKVLeNGFRKIAFPLMGAGVGGVPPAESARAMARALREHGAGAA 149
                                       **9765....333.....366666666665541456678889999999*************99987766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1478.35
//
Query:       gi|320100726|ref|YP_004176318.1|  [L=513]
Description: amidohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-110  368.4   0.2     1e-109  368.2   0.2    1.0  1  Amidohydro_3  Amidohydrolase family
    4.2e-15   55.9   0.0    1.1e-08   34.8   0.0    3.2  3  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.2   0.2  1.1e-113    1e-109       1     472 [.      51     507 ..      51     508 .. 0.95

  Alignments for each domain:
  == domain 1  score: 368.2 bits;  conditional E-value: 1.1e-113
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfp 77 
                                       e +D++G++ lPGF+DsH+Hl+g+g+ l+ l+l++  v s+e+++++vr++a+  + g  +vg+Gwd+  f e+r+p
  gi|320100726|ref|YP_004176318.1|  51 EAVDLEGKTILPGFIDSHMHLDGVGLQLSTLDLRG--VGSIEELKEKVREYAAS-HSGGPVVGRGWDQEFFREKRWP 124
                                       679********************************..****************9.9********************* PP

                      Amidohydro_3  78 yalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllreg.afhlvldlapl 153
                                        ++++lde++ d+pv+l ++++Haav+n++a++lag+ +         ++rd+ ge atg++ eg   ++++ l+ +
  gi|320100726|ref|YP_004176318.1| 125 -TRWDLDEAVVDRPVILVRVCGHAAVLNTKAMELAGLIHVESPW----VVRDESGE-ATGVILEGaVGEALRVLQGS 195
                                       .*********************************9987766665....9*******.********666666666655 PP

                      Amidohydro_3 154 .areaeaaavaaalaalasyGitsveagggnvsslddleplfeltaeeklplrvi...ikelldaaerlglplspgs 226
                                        ++ + a  +++al+ +as G+t+    g +++s d l +l  l+ e ++p rv    + +ll   ++lg + ++gs
  gi|320100726|ref|YP_004176318.1| 196 mDTREKALLMRRALEYAASLGVTTL---GFMSCSGDSLRALMLLHSEWRYP-RVRvyvEPGLLRELSKLGFTGGFGS 268
                                       599999999****************...********************999.55556*999**************** PP

                      Amidohydro_3 227 eeltigavklfadgvlgsrtalltepyf.....tgwpdfedealaelvaaadergldvaihaigdaavddvldafea 298
                                       e l++++vk+fadg+lg rta+l++py+     tg + +++ +l+ lv++a  +g++va+haigdaavd vld +++
  gi|320100726|ref|YP_004176318.1| 269 EYLRVKGVKAFADGSLGARTAWLSKPYSddplnTGRQLISRSELEGLVEEASRAGFQVAVHAIGDAAVDLVLDVYRS 345
                                       ***************************************************************************88 PP

                      Amidohydro_3 299 aaekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD 375
                                       a+    ++   r+eha++++++q++++ +l++a +vqp+f+  d+++ +rlg+er ++++p+k++   gv + +++D
  gi|320100726|ref|YP_004176318.1| 346 ARGSGVRH---RIEHASVIRPEQVAEASSLGIAVSVQPRFAVSDWWAGQRLGDERLKWLYPFKTMAGRGVALGFSTD 419
                                       86665555...****************************************************************** PP

                      Amidohydro_3 376 apvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldv 452
                                       apv+p++pw +i+aav r+          +e l+leeal+ yT g+A++lg+e + GtL +G+ ADl+v d+dp++ 
  gi|320100726|ref|YP_004176318.1| 420 APVEPLNPWETIYAAVAREG---------GEALTLEEALHYYTYGSAYVLGEEGELGTLTEGKLADLIVVDRDPFKT 487
                                       ****************7555.........699********************************************* PP

                      Amidohydro_3 453 dppelaearvrltvvdGrvv 472
                                       +  el+ +rv++t+v+G+ v
  gi|320100726|ref|YP_004176318.1| 488 PLGELRGIRVVETYVGGERV 507
                                       *****************988 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   1.4e-05      0.13       1      24 [.      59      81 ..      59     107 .. 0.66
   2 !    5.7   0.0   0.00088       7.9     129     156 ..     307     334 ..     301     362 .. 0.89
   3 !   34.8   0.0   1.2e-12   1.1e-08     236     343 ..     408     506 ..     400     507 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                                      EEEE-EEEEEEECETTECSSSGHH CS
                      Amidohydro_1  1 ivlPGlIDaHvHleqsllrgatle 24
                                      ++lPG+ID+H Hl +++++   ++
  gi|320100726|ref|YP_004176318.1| 59 TILPGFIDSHMHL-DGVGLQLSTL 81
                                      69***********.4544333444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.00088
                                       SHHHHHHHHHHHHHHHTTEEEEEETSSC CS
                      Amidohydro_1 129 fsdeelkealkeakkrdlpvaiHaletk 156
                                       +s++el+ +++ea++++ +va+Ha ++ 
  gi|320100726|ref|YP_004176318.1| 307 ISRSELEGLVEEASRAGFQVAVHAIGDA 334
                                       5889********************6654 PP

  == domain 3  score: 34.8 bits;  conditional E-value: 1.2e-12
                                       HHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB- CS
                      Amidohydro_1 236 ldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdA 312
                                         +Gv  g++tD  a    ln +e++  a+      ++e+    l+l+eal  +T++ A +lg + ++G++++Gk A
  gi|320100726|ref|YP_004176318.1| 408 AGRGVALGFSTD--APVEPLNPWETIYAAV------AREG-GEALTLEEALHYYTYGSAYVLGEEGELGTLTEGKLA 475
                                       556999999999..3333344455544444......3444.555********************************* PP

                                       -EEEECCCTCGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 313 DlvvvdldilaafvglkkdgnvkkvivkGkl 343
                                       Dl+vvd d+ ++  g  +   v+ ++v+G+ 
  gi|320100726|ref|YP_004176318.1| 476 DLIVVDRDPFKTPLGELRGIRVVETYVGGER 506
                                       ******9884444444466677888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3655.08
//
Query:       gi|320100727|ref|YP_004176319.1|  [L=87]
Description: sulfur carrier protein ThiS [Desulfurococcus mucosus DSM 2162]
Scores for complete 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    9.3e-13   48.6   0.0    1.0  1  ThiS      ThiS family
    4.4e-05   23.2   0.4    0.00015   21.5   0.4    2.0  1  Ub-Mut7C  Mut7-C ubiquitin
      0.004   17.2   0.4       0.01   15.9   0.1    1.7  2  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 !   48.6   0.0   1.6e-16   9.3e-13       1      74 [.       7      83 ..       7      87 .] 0.96

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.6e-16
                                      EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG....TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEES CS
                              ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypela....lerrvavavNgeivprlwldtelkdgDevailpp 73
                                      vll + l ++ag   ee+ l++gs v+el+ea+ +r+++l+      ++++++vNg++v+    +++l dgDev+i pp
  gi|320100727|ref|YP_004176319.1|  7 VLLLGVLADAAGthMEEHALKDGSRVSELIEAVVKRHSGLKalveTLPVLNIYVNGRHVDL---NHALGDGDEVVIAPP 82
                                      789999*******999*****************************77**************...************999 PP

                                      T CS
                              ThiS 74 V 74
                                      +
  gi|320100727|ref|YP_004176319.1| 83 F 83
                                      7 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.4   2.5e-08   0.00015      24      77 ..      35      83 ..       1      85 [. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-08
                          Ub-Mut7C 24 alavafdeaatvkhviEalGVPhtEVelilvnGesvgfshiledGdrvavypvf 77
                                       +++ +++++ +k ++E+l      V  i vnG++v+++h l dGd v ++p f
  gi|320100727|ref|YP_004176319.1| 35 LIEAVVKRHSGLKALVETLP-----VLNIYVNGRHVDLNHALGDGDEVVIAPPF 83
                                      56677889999999999995.....5689********************99976 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.54   3.2e+03      48      56 ..      24      32 ..      22      41 .. 0.70
   2 !   15.9   0.1   1.7e-06      0.01      38      58 ..      59      79 ..      57      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.54
                                      SBB-SSEEE CS
                               TGS 48 hvLedgdvv 56
                                      h L+dg  v
  gi|320100727|ref|YP_004176319.1| 24 HALKDGSRV 32
                                      667766544 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.7e-06
                                      EECSEEEETTSBB-SSEEEEE CS
                               TGS 38 lVnGqrvgldhvLedgdvveI 58
                                      +VnG++v+l+h L dgd v I
  gi|320100727|ref|YP_004176319.1| 59 YVNGRHVDLNHALGDGDEVVI 79
                                      59****************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 687.98
//
Query:       gi|320100728|ref|YP_004176320.1|  [L=162]
Description: (2Fe-2S)-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-28   98.2   0.1      2e-28   98.2   0.1    1.5  2  Fer2_2           [2Fe-2S] binding domain
    1.6e-07   31.2   7.1    6.3e-07   29.3   7.1    2.3  1  Fer2             2Fe-2S iron-sulfur cluster binding domain
    1.1e-05   25.4   0.3    2.1e-05   24.5   0.3    1.6  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
     0.0081   16.2   1.4       0.28   11.2   1.4    2.9  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   1.8         4   1.8e+04      26      31 ..      43      48 ..      39      49 .. 0.77
   2 !   98.2   0.1   4.4e-32     2e-28       1      75 [.      73     145 ..      73     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 4
                            Fer2_2 26 qCGyCt 31
                                       CG Ct
  gi|320100728|ref|YP_004176320.1| 43 ECGACT 48
                                      699998 PP

  == domain 2  score: 98.2 bits;  conditional E-value: 4.4e-32
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       Tvegl +e +e +pvq+af+eega+qCGyCtpGf++ a  + +++  +p++e+ire l+gnlCRCtgY +i++Av
  gi|320100728|ref|YP_004176320.1|  73 TVEGLTSE-REPSPVQKAFMEEGAVQCGYCTPGFIVMAEYMRRRR-VEPSDENIREYLKGNLCRCTGYVNIYKAV 145
                                       9****987.6799***********************999998777.88888***********************9 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 !   29.3   7.1   1.4e-10   6.3e-07       2      73 ..       6      59 ..       5     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.4e-10
                                      ETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGG CS
                              Fer2  2 tidgkevevevadgettlldaaee.nggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaC 73
                                       ++gk+ve++v+++e  l   +++  g ++++y+Cg g Cg+C+v ++            ge+      +l+C
  gi|320100728|ref|YP_004176320.1|  6 RVNGKPVELDVEPNEL-LINTLRNrLGLTGVKYGCGIGECGACTVLID------------GEP------ALSC 59
                                      69*********99999.66666665********************866............444......2444 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 !   24.5   0.3   4.7e-09   2.1e-05      49      88 ..      36      74 ..      21     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.7e-09
                            Fer2_3 49 rasCregiCGscavainGkptlaCtatikdlakqkseiel 88
                                      ++ C+ g CG+c+v i+G+p+l C   + d++ ++   ++
  gi|320100728|ref|YP_004176320.1| 36 KYGCGIGECGACTVLIDGEPALSCLVLTVDVNGREV-ETV 74
                                      689**********************99999887753.344 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 !   11.2   1.4   6.3e-05      0.28       4      70 ..       3      62 ..       1      76 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                            Fer2_4  4 vtltfDGkevt..vpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstp 70
                                      v+++++Gk+v+  v++++ +++ l +    + +  ky       c +geC  C V ++gep   +c + 
  gi|320100728|ref|YP_004176320.1|  3 VSFRVNGKPVEldVEPNELLINTLRN-RLGL-TGVKY------GCGIGECGACTVLIDGEP-ALSCLVL 62
                                      77888888765447777777777653.2222.55555......49****************.5677654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1302.01
//
Query:       gi|320100729|ref|YP_004176321.1|  [L=302]
Description: molybdopterin dehydrogenase FAD-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for 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  183.9   0.0    3.2e-54  183.2   0.0    1.2  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    3.2e-21   75.4   0.2    6.7e-21   74.4   0.2    1.5  1  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai


Domain annotation for each model (and alignments):
>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.0   3.6e-58   3.2e-54       2     168 ..      19     186 ..      18     187 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 3.6e-58
                                       EEEEEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHH CS
                     FAD_binding_5   2 kfeylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlsel 77 
                                       +f+y+ pasl eal++l++ + +a+++aGgtdl+v mk+++++p+++++i++i elk+i+ ++g ++i A++tl e+
  gi|320100729|ref|YP_004176321.1|  19 SFNYYEPASLREALEILSElGGSARILAGGTDLLVKMKTRQVEPKAVVNIKRIRELKGITVEDGRVRIKALTTLREI 95 
                                       699****************9********************************************************* PP

                                       HHHHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTE CS
                     FAD_binding_5  78 aaealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgk 154
                                        ++++v++ +pal++a++++As q+R++aTiGGNl++asp++D+ap+Ll+ +A+v++ + ++er+vpl++f+kgpg+
  gi|320100729|ref|YP_004176321.1|  96 EESPIVAKYIPALRDAVKQMASIQVRSMATIGGNLCNASPAADTAPPLLVHNASVKIVGLNRERTVPLASFFKGPGS 172
                                       ***************************************************************************** PP

                                       ESS-TT-EEEEEEE CS
                     FAD_binding_5 155 talepgelitavei 168
                                       t+lepge++ +v++
  gi|320100729|ref|YP_004176321.1| 173 TVLEPGEILAEVIV 186
                                       ***********986 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.2   7.5e-25   6.7e-21       2     100 ..     194     290 ..     193     293 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 7.5e-25
                                       EE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHH CS
                     CO_deh_flav_C   2 ay.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelsp 77 
                                       a+ k+ r +  d+a+++aA+ vel++d ++e+aria g+vaptp+r++ ae aL+G++lse  l +++k +e e++p
  gi|320100729|ref|YP_004176321.1| 194 AFmKIGRVAV-DLAVASAAVYVELNGD-IVEEARIAAGAVAPTPIRCPVAEGALKGRRLSEVGL-NVFKPIEGEVKP 267
                                       7878888887.**************99.********************************8776.58999******* PP

                                       HTCTTC-HHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  78 asdprasaeYRrslavsllfrfl 100
                                       +sd rasaeYRr+l++ l+  ++
  gi|320100729|ref|YP_004176321.1| 268 ISDARASAEYRRHLVRILAHDAF 290
                                       ***************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2428.73
//
Query:       gi|320100730|ref|YP_004176322.1|  [L=781]
Description: aldehyde oxidase and xanthine dehydrogenase molybdopterin-binding subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-137  458.1   0.0   5.2e-137  457.6   0.0    1.2  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    3.5e-18   66.0   0.0    7.9e-18   64.8   0.0    1.6  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.6   0.0  5.8e-141  5.2e-137       7     550 .]     161     711 ..     157     711 .. 0.92

  Alignments for each domain:
  == domain 1  score: 457.6 bits;  conditional E-value: 5.8e-141
                                       TTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT- CS
                     Ald_Xan_dh_C2   7 dnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlgl 81 
                                        n++a  ++ +Gdv++af+e+d+v+e++f+tg+ +h+ lE++a+l+vp + +g+lt+ys+tq +h +r lv++++++
  gi|320100730|ref|YP_004176322.1| 161 GNIAAslNYVEGDVDKAFQESDVVLERRFKTGKRYHMQLEPKAVLCVP-EPGGKLTIYSTTQSIHNTRILVSQIFDI 236
                                       67777566678*************************************.77************************** PP

                                       -GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEE CS
                     Ald_Xan_dh_C2  82 penkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitald 158
                                       p ++v+v++  +GG+FG+ +q+  l ++a+++++k g+pVk+ ++Reed+l + +   f++++kvga+++G +t+ +
  gi|320100730|ref|YP_004176322.1| 237 PLSRVNVVKIPIGGSFGSSIQVNYLVPIAVALCLKSGKPVKIAYTREEDIL-DHSNFVFHFRIKVGAKRNGVLTGAE 312
                                       *************************************************99.677899******************* PP

                                       EEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT-- CS
                     Ald_Xan_dh_C2 159 vdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgld 235
                                       ++ + d+Ga +    ++l + l+ + ++Yk++n+r+ gr+vytN++p+ a RG+G+p++ +a+E++mdelAeelg+d
  gi|320100730|ref|YP_004176322.1| 313 FENTLDVGAHQVQPYPLLGTSLGWFVSMYKWRNIRYIGRAVYTNKTPACALRGYGAPEVQWAVETIMDELAEELGVD 389
                                       **********99999999*********************************************************** PP

                                       HHHHHHHHBCECGCC.SEEET.....EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS-- CS
                     Ald_Xan_dh_C2 236 plelRrrNlikpgeltpygqp.....vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglg 307
                                       p+elR +N++  ge+   gq      +  s ++pell+k+ke +++++r   + ++   + +rGig+a +++ +g+g
  gi|320100730|ref|YP_004176322.1| 390 PVELRLKNYVGRGEI-FWGQGptvksIIRSDGVPELLEKGKELIGWDKRGDPRGKKG--RFRRGIGVARGFHTSGAG 463
                                       ***************.77885566678899*****************9977777655..569************988 PP

                                       S...EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HH CS
                     Ald_Xan_dh_C2 308 f..takflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrst 382
                                            +  +  g+ +++n+dG+    t+++++G G+  ++++i++e+Lgvp+e v++ +++t+++p+++ t aSr+t
  gi|320100730|ref|YP_004176322.1| 464 GpiSGEVIDYTGCILKLNEDGTLDYITALQDHGGGTLDAHVKIISEVLGVPPELVNLASASTENTPYDVCTHASRGT 540
                                       88866788899****************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCT..S-CCCEEE......ETTEEEET..EEEECHHHHHHHHHH.TTSSEEEE CS
                     Ald_Xan_dh_C2 383 dlngnAvkkAaeklrerllkiaaelle..vspedlel......edgkvvvk..eksvslaelaaaayl.ervslsat 448
                                       +++g+A+++Aae ++ ++ ++aa+l++  v+pe+ ++      ++  v+++  + +++l+e+a+aa++ +  ++ a 
  gi|320100730|ref|YP_004176322.1| 541 YVGGEAARRAAEIVKSKIFEYAARLVGkaVNPEAFKIrydeglKQAVVYIEgtDVRIPLSEIARAAWQrNWGTIGAF 617
                                       ***********************7765225666666677776666677777888888*******9976333466666 PP

                                       EEE...EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT--- CS
                     Ald_Xan_dh_C2 449 gfyktldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEel 525
                                        +y     + ++ pp    ++ ++++eVevDt tg+vk  rvv+  DvG+ +Np +vegQ++GGf+++ G+a +E++
  gi|320100730|ref|YP_004176322.1| 618 VSY-----RATSAPP----SFTVYFVEVEVDTWTGRVKPIRVVAGADVGTPVNPDMVEGQLHGGFAMAWGMAFTEDM 685
                                       667.....3444555....789******************************************************* PP

                                       EEETTTEESS-ST.TTS----GGGS- CS
                     Ald_Xan_dh_C2 526 vydedGqlltasl.adYkiPtaadiP 550
                                       vy+e+G+l  ++l +dYkiPt+ad+P
  gi|320100730|ref|YP_004176322.1| 686 VYEENGELAGRGLiTDYKIPTIADVP 711
                                       **********997479*********9 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   8.8e-22   7.9e-18       2     108 ..      20     127 ..      19     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 8.8e-22
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT.....TSSS-EE..EES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig.....siledee..dal 71 
                                       G  ++v+D++apg+l ++++rS++a A+i++idvs+a+++  V   +t +++p++  +       ++    +  d+ 
  gi|320100730|ref|YP_004176322.1|  20 GTLRFVNDLEAPGMLIGRILRSPYAFADIKRIDVSEAERIGAV--TLTPDEVPQKPFNPRlvsvhEV----TfkDTY 90 
                                       8899************************************955..699*******999986543222....134678 PP

                                       S-SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE CS
                      Ald_Xan_dh_C  72 laedkvrsvgqavaavvAedeetArkAaklvkveYee 108
                                        +++k r+ g+avaav+A +ee A++A++ ++veYe+
  gi|320100730|ref|YP_004176322.1|  91 VLTKKPRYIGDAVAAVAAPSEELAQRALESIRVEYER 127
                                       9999*******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (781 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5786.08
//
Query:       gi|320100731|ref|YP_004176323.1|  [L=158]
Description: (2Fe-2S)-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-21   76.5   0.0    1.2e-21   76.5   0.0    1.6  2  Fer2_2    [2Fe-2S] binding domain
    1.9e-06   27.7   2.4    2.3e-06   27.5   0.1    2.1  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
    4.8e-06   26.6   0.0    7.6e-06   25.9   0.0    1.4  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.016   15.2   1.9      0.093   12.8   1.9    2.2  1  Fer2_4    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   1.1       3.8   1.7e+04      26      31 ..      43      48 ..      39      49 .. 0.81
   2 !   76.5   0.0   2.7e-25   1.2e-21       1      75 [.      73     144 ..      73     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3.8
                            Fer2_2 26 qCGyCt 31
                                       CG Ct
  gi|320100731|ref|YP_004176323.1| 43 ECGSCT 48
                                      599998 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 2.7e-25
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       Tvegl+ ++  l ++ e+f e+ga+qCG+CtpG++++a a ++e  + +++++i+e + gnlCRCtgY +i++Av
  gi|320100731|ref|YP_004176323.1|  73 TVEGLQGDPL-LGKLVESFTEKGAVQCGFCTPGILLTAWAAIREG-RIRERKDIAEYI-GNLCRCTGYVKIAEAV 144
                                       9****98855.88*******************************9.77788*****99.8**************8 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 !   27.5   0.1   5.1e-10   2.3e-06       2      53 ..       6      57 ..       5      73 .. 0.77
   2 ?   -0.0   0.2      0.19   8.6e+02      39      48 ..      96     106 ..      91     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 5.1e-10
                                      ETTTEEEEEEEETTTHBHHHHHH.HTTTTTSTTSSSSSSSSTTEEEEEESCE.C CS
                              Fer2  2 tidgkevevevadgettlldaae.enggidipysCggggCgtClvevlegev.q 53
                                      +++g  vev++++ e  lld ++ + +   ++ +C+ g Cg+C+v ++ g+   
  gi|320100731|ref|YP_004176323.1|  6 KLNGVAVEVDAPPSEI-LLDTLRlRLKVRSVKRGCERGECGSCTVLLD-GKPvA 57
                                      689*******977777.8888884699*****************9644.55433 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                                       S.SSTTEEEEE CS
                              Fer2  39 g.CgtClvevl 48 
                                         Cg C+  +l
  gi|320100731|ref|YP_004176323.1|  96 VqCGFCTPGIL 106
                                       25999986555 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 !   25.9   0.0   1.7e-09   7.6e-06      49     101 ..      36      87 ..      12      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.7e-09
                            Fer2_3  49 rasCregiCGscavainGkptlaCtatikdlakqkseieleplpkfpvirDLv 101
                                       ++ C+ g CGsc+v ++Gkp   C   + +++ ++  +++e l++ p++  Lv
  gi|320100731|ref|YP_004176323.1|  36 KRGCERGECGSCTVLLDGKPVASCMLLTPQVEGRS-VVTVEGLQGDPLLGKLV 87 
                                       689***************************99876.7******9999876666 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 ?   12.8   1.9   2.1e-05     0.093      43      77 ..      36      71 ..       2      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                            Fer2_4 43 gelcaggeCrnClVevegepnvracs..tpvedGlkv 77
                                      +  c +geC  C V ++g+p v++c+  tp  +G +v
  gi|320100731|ref|YP_004176323.1| 36 KRGCERGECGSCTVLLDGKP-VASCMllTPQVEGRSV 71
                                      3459****************.****844556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1191.70
//
Query:       gi|320100732|ref|YP_004176324.1|  [L=292]
Description: molybdopterin dehydrogenase FAD-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-55  185.6   0.0    8.5e-55  185.1   0.0    1.1  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
      9e-27   93.3   0.0    1.5e-26   92.5   0.0    1.4  1  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai


Domain annotation for each model (and alignments):
>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.1   0.0   9.5e-59   8.5e-55       2     170 ..       7     176 ..       6     177 .. 0.99

  Alignments for each domain:
  == domain 1  score: 185.1 bits;  conditional E-value: 9.5e-59
                                       EEEEEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHH CS
                     FAD_binding_5   2 kfeylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlsel 77 
                                       +++y+rpasleeal+ll + + +a+++aGgtdl++ +k k+ ++++lid++g++elk+i+ ++g l+iGA++t++e+
  gi|320100732|ref|YP_004176324.1|   7 EVKYHRPASLEEALELLGKlSGKARILAGGTDLVLDLKIKRYDVSDLIDVSGLKELKYITDEGGVLRIGALTTIQEI 83 
                                       578****************9********************************************************* PP

                                       HHHHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTE CS
                     FAD_binding_5  78 aaealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgk 154
                                       a++ +v+e+ p l++a+e++A  q+Rn aTiGGNl++asp++D+ap+L++ +A v   s +ger++pl+ef+kgp++
  gi|320100732|ref|YP_004176324.1|  84 ADSTIVAEKTPLLKKAAEEFAYWQVRNIATIGGNLCNASPAADTAPPLMVHEAWVRAVSMDGERRIPLKEFFKGPRT 160
                                       ***************************************************************************** PP

                                       ESS-TT-EEEEEEEE- CS
                     FAD_binding_5 155 talepgelitaveiPa 170
                                       tal+p+e++ +v+iP 
  gi|320100732|ref|YP_004176324.1| 161 TALKPNEILAEVSIPY 176
                                       ***************6 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   1.7e-30   1.5e-26       2     100 ..     185     283 ..     184     286 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.7e-30
                                       EE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHH CS
                     CO_deh_flav_C   2 ay.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelsp 77 
                                       ay kl rrr++di++v++A++v++ee+ + +d+ria+g+vaptpvra  +e+ L+G++ s e +++a++ ++ +++p
  gi|320100732|ref|YP_004176324.1| 185 AYhKLGRRRGHDISVVSIAVAVRVEEG-VFRDVRIALGSVAPTPVRAWSVEEELKGREASVENINRAVEKITGDIKP 260
                                       899*********************999.************************************************* PP

                                       HTCTTC-HHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  78 asdprasaeYRrslavsllfrfl 100
                                       +sd rasaeYR ++ ++ll+ +l
  gi|320100732|ref|YP_004176324.1| 261 ISDARASAEYRLHVSKELLRDML 283
                                       *******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2169.85
//
Query:       gi|320100733|ref|YP_004176325.1|  [L=780]
Description: aldehyde oxidase and xanthine dehydrogenase molybdopterin-binding subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-176  587.3   1.1   3.3e-176  587.0   1.1    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.8e-19   70.1   0.0    3.9e-19   69.0   0.0    1.6  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.0   1.1  3.6e-180  3.3e-176       1     550 []     159     717 ..     159     717 .. 0.97

  Alignments for each domain:
  == domain 1  score: 587.0 bits;  conditional E-value: 3.6e-180
                                       STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlv 75 
                                       vheea++n+++  ++++G ve++f++a++vve+e+r++ qeh+ylEt+aala+p   ++ +tv    q ph  +r+v
  gi|320100733|ref|YP_004176325.1| 159 VHEEAGSNIAFrtRVRRGSVEEGFSRAHVVVENEYRLHHQEHAYLETEAALAIP-SMENGVTVIGGLQYPHLGQRIV 234
                                       6999*******999999*************************************.78999***************** PP

                                       HHHHT--GGGEEEE-SB-S--TTTT.SS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TT CS
                     Ald_Xan_dh_C2  76 aevlglpenkvrvivprvGGGFGgK.tqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkd 151
                                       a+vlglp+++v++i+p+vGGGFGgK  +  ++ + aal+A+ tg+p  lv++Ree+m ++ kr++ +i+yk gad++
  gi|320100733|ref|YP_004176325.1| 235 ARVLGLPSSRVKIIAPYVGGGFGGKdDEGPLTCAKAALVAYLTGKPALLVYSREESMRIHPKREAAIIRYKSGADSE 311
                                       *************************8888888889****************************************** PP

                                       S-EEEEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 152 GkitaldvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdel 228
                                       G++ta++v++++d+Gaya+ +p++l+ra++h+ gpY +pn++v+g++vytN++ ++ fRGfG+    fa+Er+md+l
  gi|320100733|ref|YP_004176325.1| 312 GRLTAIEVTIIHDTGAYANRGPFILWRATMHASGPYIVPNAKVDGYAVYTNKVYQGSFRGFGNLSIQFAVERQMDQL 388
                                       ***************************************************************************** PP

                                       HHHHT--HHHHHHHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCT..ECEEEEEEEEEEEE CS
                     Ald_Xan_dh_C2 229 AeelgldplelRrrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnag..wkkrGiglapvveg 303
                                       Ae+lgldp+e+R rN++++g+ t +gq + +s +++e+l++++e+s+++err+e++e+n++  + krGig+a++++g
  gi|320100733|ref|YP_004176325.1| 389 AEKLGLDPVEFRLRNIVREGSHTITGQLLDHSVGVAEALKRVAEASRWRERRREIEEYNKSggRFKRGIGVAVAWHG 465
                                       **********************99****999****************************7668999*********** PP

                                       BS--S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-H.HHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT CS
                     Ald_Xan_dh_C2 304 iglgftakflnqegalvrvntdGsvtvstggtemGqGl.etklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaS 379
                                       i+++  +  ++ ++a v++++dGsvt++tg +e+GqG+   +++qi++e Lgv++++vrvv+g+td  p++++t aS
  gi|320100733|ref|YP_004176325.1| 466 ISTS--RGVPDWSNAYVKIEQDGSVTLYTGIVEIGQGSpSSAHVQIVSELLGVTPDRVRVVHGSTDA-PDAGATHAS 539
                                       *555..467999*************************9446789**********************9.77777**** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHHTTSSEEEEEEE.. CS
                     Ald_Xan_dh_C2 380 rstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaaylervslsatgfykt 453
                                       r++ ++g  v+ Aa  lrerl+ +a+++++v+ edl ++ +kv+ +   +k+++l++l+++a+ ++v+lsatg++  
  gi|320100733|ref|YP_004176325.1| 540 RGSSIGGIGVYMAAAVLRERLAGLASRIMGVPVEDLVFAGNKVYSRnnpDKQLQLRDLVKEAVARGVELSATGYFFL 616
                                       **********************************************9999999*********************866 PP

                                       .....EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---E CS
                     Ald_Xan_dh_C2 454 ....ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelv 526
                                           +d++tg+g ++ +++y ++v+eVevDt+tg vkv rv+    +G++iNp  vegQieG+++qGiG++lmE+lv
  gi|320100733|ref|YP_004176325.1| 617 pkgrFDDSTGQGFAYPAYSYMVVVSEVEVDTLTGVVKVTRVYPGLAAGRVINPVQVEGQIEGAIAQGIGYTLMERLV 693
                                       8**************************************************************************** PP

                                       EETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 527 ydedGqlltasladYkiPtaadiP 550
                                       +de+G l++ +l+dY +P+++d+P
  gi|320100733|ref|YP_004176325.1| 694 FDEKGALINVNLTDYVVPSMRDMP 717
                                       ***********************9 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   4.3e-23   3.9e-19       6     110 .]      43     143 ..      35     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 4.3e-23
                                       CGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEESSTT- CS
                      Ald_Xan_dh_C   6 YvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvrsvgq 82 
                                       Y  D+ + +aly++ v+St++hA+++ i   +al+ +GV   ita d+p+en+ + s l d+   llae kvr++g+
  gi|320100733|ref|YP_004176325.1|  43 YFIDYFMGNALYVKQVLSTHPHARLKGISLPDALKGKGV-RLITARDIPGENQVGYS-LPDQ--PLLAEGKVRYHGE 115
                                       77788888888***************************8.689********998864.4444..4************ PP

                                       EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  83 avaavvAedeetArkAaklvkveYeelp 110
                                       +va+v+ ++   A +A++ v+v+Ye+lp
  gi|320100733|ref|YP_004176325.1| 116 VVALVASTSLDDALRAVEEVRVDYEPLP 143
                                       *************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (780 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 5268.19
//
Query:       gi|320100734|ref|YP_004176326.1|  [L=451]
Description: dihydroorotase, multifunctional complex type [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-22   80.4   0.0    2.3e-22   79.8   0.0    1.3  1  Amidohydro_1  Amidohydrolase family
    8.2e-12   45.3   1.2      3e-05   23.7   0.3    2.6  2  Amidohydro_3  Amidohydrolase family
     0.0031   17.8   0.9     0.0049   17.2   0.1    1.8  2  Urease_alpha  Urease alpha-subunit, N-terminal domain


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   3.9e-26   2.3e-22       1     343 [.      50     425 ..      50     426 .. 0.79

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 3.9e-26
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee 72 
                                       +v+PG ID HvH +             +p+ +++  + +g ++alk+G+ttv ++++t ++      + a ++ +e+
  gi|320100734|ref|YP_004176326.1|  50 LVFPGVIDEHVHMR-------------EPGLEYKDDFTHGSRAALKGGVTTVVEHPNTLPPvdepgKLVAKARLLEQ 113
                                       59***********9.............******************************98889995544444444555 PP

                                       .SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTE CS
                      Amidohydro_1  73 .lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlp 147
                                        +   + + + +v  d g+++ +++   + +ag+         +v++ ++++  ++p+ +   l+e+l+e  ++++ 
  gi|320100734|ref|YP_004176326.1| 114 kA--YVDFALLGVLHD-GNTHLFEDMLAEGAAGF---------KVFMgPTTGNIPPPSEP--SLYEVLRESGRMGVT 176
                                       43..345555556666.99999999999999998.........34555888888888777..999************ PP

                                       EEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC..........HHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHC CS
                      Amidohydro_1 148 vaiHaletkgevedaeaafgetiehgthlevaes..........lglldeiklilahgvhltpteaellkerlkeag 214
                                       va+Ha ++      +e+a   + +++ + ++a            ++++ + +  +  +vh++ + a     ++k+ag
  gi|320100734|ref|YP_004176326.1| 177 VAFHAEDHALVTYFTEKARSTGGMDPALHDDARPplveeysvvkIAAIAKHTGGRPLIVHISSAQALEAVSQAKRAG 253
                                       *****665555555566666666777777777768988866655333333244488899999776677777789999 PP

                                       EE.........HHHHHHHH...................SEHHHHHHHHHHHHTSCEEEEEECT.............. CS
                      Amidohydro_1 215 va.........hcpfsnsi...................lrsgrealrkaldeGvkvglgtDga.............. 249
                                       v          +     +                     + +r++l +a+ +G   ++g+D+a              
  gi|320100734|ref|YP_004176326.1| 254 VEiygetcphyL-----LLdkpdyarygslikvnppirGGVHRARLVEAVAKGGVDTVGSDHAphapeekrrdiwsa 325
                                       999999555441.....445555578888899999999**************999*******************998 PP

                                       ..TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC...CT CS
                      Amidohydro_1 250 ..asgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl...di 321
                                         ++  + +ll ++ ++++          +  ++l ++  +   n+Ak  gl  ++G i+vG+d Dlv+vd+   ++
  gi|320100734|ref|YP_004176326.1| 326 asGMPGVQTLLPSMLDLAL----------RNIIPLTRIPLLLAENPAKLWGLWPRKGFIDVGFDGDLVIVDPgseTL 392
                                       6655555577777555552..........555****************************************76522 PP

                                       ...........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 322 ...........laafvglkkdgnvkkvivkGkl 343
                                                  l++f+g+  +g v++v+++G++
  gi|320100734|ref|YP_004176326.1| 393 vteewleykykLTPFTGWRFKGRVRHVVIRGRV 425
                                       67788899999********************86 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3     5e-09     3e-05       1      49 [.      42      90 ..      42     110 .. 0.82
   2 !   20.4   0.0     5e-08    0.0003     367     471 ..     301     425 ..     104     427 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5e-09
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavr 49
                                      eviDa+G+lv+PG +D H H+ + g+++   +  +  r+    gv+t+v+
  gi|320100734|ref|YP_004176326.1| 42 EVIDASGMLVFPGVIDEHVHMREPGLEYkDDFTHGS-RAALKGGVTTVVE 90
                                      79************************9988888887.5555566666554 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5e-08
                      Amidohydro_3 367 gvkvalgsD.apvgpfdpwprigaavmrktrrgg.....evlrpdeelsleealalyTrgpAkalgledrkGtLevG 437
                                       g   + gsD ap +p  +   i++a  + ++ +        l  ++ ++l+ +  l+ ++pAk+ gl  rkG + vG
  gi|320100734|ref|YP_004176326.1| 301 GGVDTVGSDhAPHAPEEKRRDIWSAASGMPGVQTllpsmLDLALRNIIPLTRIPLLLAENPAKLWGLWPRKGFIDVG 377
                                       44445566666666666666666666555544435555544455556777778888899****************** PP

                      Amidohydro_3 438 adADlvvldadpldvdppelaear..............vrltvvdGrv 471
                                       +d+Dlv+ d    ++ ++e  e +              vr++v++Grv
  gi|320100734|ref|YP_004176326.1| 378 FDGDLVIVDPGSETLVTEEWLEYKykltpftgwrfkgrVRHVVIRGRV 425
                                       *********888888888888877899*******************98 PP

>> Urease_alpha  Urease alpha-subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   8.1e-07    0.0049      68     108 ..       3      43 ..       1      54 [. 0.85
   2 ?   -3.2   0.1       1.7     1e+04      81      95 ..     420     434 ..     418     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.1e-07
                      Urease_alpha  68 lvitnavilDatgivkadigikdgrivaiGkagnpdvmdgv 108
                                       l++ n +++  +g+++ad+ i+dg i+++G+  + + +d+v
  gi|320100734|ref|YP_004176326.1|   3 LLVRNGLVVTSKGVLRADVRIQDGVITSVGRHLDSSGVDEV 43 
                                       6789**************************98776666655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                      Urease_alpha  81 ivkadigikdgriva 95 
                                       +++  ++++dg i++
  gi|320100734|ref|YP_004176326.1| 420 VIRGRVALRDGVITG 434
                                       677889999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3355.35
//
Query:       gi|320100735|ref|YP_004176327.1|  [L=307]
Description: aspartate carbamoyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-40  136.0   0.0    1.4e-39  135.4   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
      6e-25   88.2   0.0    9.4e-25   87.5   0.0    1.3  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 !  135.4   0.0   1.6e-43   1.4e-39       3     147 ..       7     147 ..       5     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 1.6e-43
                                       BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCT CS
                          OTCace_N   3 llsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediql 79 
                                       ++s  +++++++e+l++ a+el+++ ++ ++ + +kg++l++ F+epStRTr+Sf+ A+ rlGg+v+ l+ +e+   
  gi|320100735|ref|YP_004176327.1|   7 VISALQFTRSDVERLITIAEELRRRLEAGERIEAAKGRILFTAFFEPSTRTRLSFQFAMVRLGGSVVDLG-PEE--V 80 
                                       78999*****************************************************************.544..3 PP

                                       TTGGSTTSSCHHHHHHHHHHHT.SEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  80 ssvskgrkEsleDtarvlsryv.daiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       +s +kg  Es eDt+r++++y  d+iv+Rh+  g   +++ a+ ++ pv+Nagdg +eHPtQaL+D++ti+
  gi|320100735|ref|YP_004176327.1|  81 TSRAKG--ESPEDTLRTVDSYNpDVIVVRHRepG--FASKAAEICRAPVVNAGDGYNEHPTQALLDVYTIW 147
                                       445788..***********************554..5999*****************************97 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   1.1e-28   9.4e-25       1     155 [.     154     302 ..     154     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1.1e-28
                                       CC.EEEEESS.TTSHHHHHHHHHHHHC.T-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEE CS
                            OTCace   1 kglkiafvGd.kknnvanslikllarl.gmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvv 75 
                                       +g+ i ++Gd k++++++sl ++l+ + ++++++++P++l+p +evl+ +    ++   ++++ e+l e+v+ +Dv+
  gi|320100735|ref|YP_004176327.1| 154 DGVSIGLMGDlKYGRTVSSLSYILSNFrDVTIYFISPPALRPREEVLRIL----DQRRTRYEFAESLDEVVSRVDVL 226
                                       5899*****************9888853799***********99999555....55689****************** PP

                                       EE--SSETTCCGGHH..HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHH CS
                            OTCace  76 ytdvwvsmgeekere..erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlht 149
                                       y ++++     ker+  e+++ lk+ y+v  e l++     +++H+LP  r  E+t +V+  p++++feqa+N+l++
  gi|320100735|ref|YP_004176327.1| 227 YVTRLQ-----KERMspEEYERLKGsYTVSYESLRKYGRIPLIMHPLP--RVWELTPDVDVLPQAIYFEQARNGLYM 296
                                       ******.....566556*******************************..*************************** PP

                                       HHHHHH CS
                            OTCace 150 ikAllv 155
                                       ++All 
  gi|320100735|ref|YP_004176327.1| 297 RMALLK 302
                                       ****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 2056.37
//
Query:       gi|320100736|ref|YP_004176328.1|  [L=112]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.018   14.7   0.6      0.018   14.7   0.6    1.8  2  DUF716           Family of unknown function (DUF716)
          4    6.6  13.5        9.2    5.4  13.5    1.6  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> DUF716  Family of unknown function (DUF716)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6     2e-06     0.018      41      80 ..       8      47 ..       4      52 .. 0.91
   2 ?   -0.6   0.1      0.11   9.5e+02      31      40 ..      92     101 ..      66     110 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-06
                            DUF716 41 valsllsalleallpksfllelvrsvllilqGtWflqmGf 80
                                      v++++l+ +l ++l  + ++e++ s+ll+l G W+ ++G+
  gi|320100736|ref|YP_004176328.1|  8 VVAAALILILTVALTYRYPVEIAVSALLVLLGAWIAVTGL 47
                                      7788999999999************************997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.11
                            DUF716  31 grvhlLLvlv 40 
                                         v  LL l+
  gi|320100736|ref|YP_004176328.1|  92 IAVITLLSLT 101
                                       2222233333 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 ?    5.4  13.5     0.001       9.2     134     209 ..      34     105 ..       7     111 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.001
                   ABC2_membrane_2 134 iavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailv 209
                                       ++v+l+a   ++ ++ + +  + +++  +  v++  l+++    l+++l++S+v++++r a+ +++ l+ ++  + 
  gi|320100736|ref|YP_004176328.1|  34 LLVLLGAWIAVTGLLAKPGRHEASVKTPTSRVAFGGLTAT----LGAALMVSAVTKDARAALIAVITLLSLTITAA 105
                                       3333444433455555555555555555555555555555....9***********88888888887776665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 853.75
//
Query:       gi|320100737|ref|YP_004176329.1|  [L=496]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   18.3   0.1      0.013   15.5   0.1    2.2  2  YfdX           YfdX protein
  ------ inclusion threshold ------
       0.15   12.6   0.8        6.6    7.3   0.1    3.3  3  TPR_19         Tetratricopeptide repeat
       0.17   11.9   1.0       0.32   11.0   1.0    1.3  1  DZR            Double zinc ribbon
       0.19   11.5   3.6       0.77    9.6   3.6    1.9  1  zinc_ribbon_2  zinc-ribbon domain
       0.19   11.8   0.1       0.58   10.3   0.0    1.8  2  TEA            TEA/ATTS domain
       0.24   10.9   1.9        7.7    6.1   0.3    2.3  2  zf-ribbon_3    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.29   8.8e+02      51      99 ..     136     184 ..     105     189 .. 0.68
   2 !   15.5   0.1   4.2e-06     0.013       4      79 ..     204     275 ..     201     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.29
                                       -EEEEEEEEEEE------HHHHHHHHHHHHHHHTT-HHHHHHHHHHTT- CS
                              YfdX  51 alvPvdaevividdladtpekkaaikkanellkkgdtqaArelLkllgs 99 
                                       ++v vd++ +    + +t   +a++ +  e   +gd +aA + L+ l++
  gi|320100737|ref|YP_004176329.1| 136 QMVVVDEDREFYSGVYATYVLNAHLSNYVETALSGDIDAAVRNLEKLAE 184
                                       5566666666666666777777777777777777888888888877765 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.2e-06
                                       HHHHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-S--SSSS-EEEEEEEEEEE------HHHHHHHHHHH CS
                              YfdX   4 diqkArlaldqgdtkeAkkllekAqgkleaaladdpklvkkapasadalvPvdaevividdladtpekkaaikkan 79 
                                       + +kA + l++gd  +A +lle A+ +l++a++  +      p  a  l Pvd+e+++++ + ++ e ++a+ +a 
  gi|320100737|ref|YP_004176329.1| 204 NAMKAWSSLEKGDYTSAMPLLETASLELSKARSLASGS----PQLAMMLPPVDVELKLVEAMRNIAECEKALFEAG 275
                                       5679999***********************99988777....666779*****************99999987765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.1   3.3e+03      59      68 .]      89      98 ..      82      98 .. 0.87
   2 ?    1.4   0.0      0.15   4.6e+02       4      22 ..     169     187 ..     167     196 .. 0.73
   3 ?    7.3   0.1    0.0022       6.6       2      22 ..     212     233 ..     211     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                            TPR_19 59 aryasLlAkl 68
                                      ++yasL+Ak+
  gi|320100737|ref|YP_004176329.1| 89 PEYASLKAKV 98
                                      89******95 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.15
                            TPR_19   4 egdyaeAlalleqalqedp 22 
                                       +gd ++A++ le++ +  p
  gi|320100737|ref|YP_004176329.1| 169 SGDIDAAVRNLEKLAESLP 187
                                       5788888888887655444 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0022
                            TPR_19   2 laegdyaeAlalleqa.lqedp 22 
                                       l+ gdy++A++lle a l+ + 
  gi|320100737|ref|YP_004176329.1| 212 LEKGDYTSAMPLLETAsLELSK 233
                                       789************9454443 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   0.00011      0.32      15      37 ..      10      35 ..       8      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                               DZR 15 CseCgtklkavaa...edrCpsCgek 37
                                      C +Cg++l+++++     rC  Cg+ 
  gi|320100737|ref|YP_004176329.1| 10 CVKCGAPLPQPEKgseYVRCEYCGTV 35
                                      99999999877779999999999986 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   3.6   0.00026      0.77       1      21 [.       9      34 ..       9      35 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00026
                     zinc_ribbon_2  1 fCpnCGael.q.d.nakF..CpyCGt 21
                                      +C +CGa+l q + ++ +  C+yCGt
  gi|320100737|ref|YP_004176329.1|  9 RCVKCGAPLpQpEkGSEYvrCEYCGT 34
                                      6********654356666*******8 PP

>> TEA  TEA/ATTS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.58       7      48 ..     251     292 ..     249     306 .. 0.82
   2 ?   -3.0   0.0       2.7   8.2e+03      58      63 ..     441     446 ..     440     447 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                               TEA   7 peledafleallliPpmgrrklklegklhgRnelIseyIlkk 48 
                                        ++e  ++ea+++i ++++  +  + ++ + + +I+ yI+  
  gi|320100737|ref|YP_004176329.1| 251 VDVELKLVEAMRNIAECEKALFEAGRQPQEAAAFIARYIRTV 292
                                       58999*****************999999***********532 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.7
                               TEA  58 vsShiQ 63 
                                       vsS++Q
  gi|320100737|ref|YP_004176329.1| 441 VSSRLQ 446
                                       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 ?    6.1   0.3    0.0026       7.7       4      12 ..       9      17 ..       7      22 .. 0.78
   2 ?    3.9   0.1     0.012        37       3      10 ..      27      34 ..      25      38 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0026
                       zf-ribbon_3  4 rCPnCGapl 12
                                      rC +CGapl
  gi|320100737|ref|YP_004176329.1|  9 RCVKCGAPL 17
                                      8******63 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.012
                       zf-ribbon_3  3 vrCPnCGa 10
                                      vrC +CG+
  gi|320100737|ref|YP_004176329.1| 27 VRCEYCGT 34
                                      66666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3154.83
//
Query:       gi|320100738|ref|YP_004176330.1|  [L=335]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   16.0   7.3      0.074   13.2   0.3    4.7  4  TPR_2         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.013   15.7   0.4      0.013   15.7   0.4    4.0  4  TPR_12        Tetratricopeptide repeat
      0.044   13.9   7.6       0.22   11.6   0.1    3.7  4  MIT           MIT (microtubule interacting and transport) dom
      0.058   13.6   4.1        1.1    9.6   0.1    4.4  4  TPR_8         Tetratricopeptide repeat
      0.067   12.9   0.4       0.73    9.6   0.0    3.1  3  TPR_11        TPR repeat
       0.14   11.8   0.0       0.26   11.0   0.0    1.3  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
       0.21   11.5   0.2       0.21   11.5   0.2    3.4  5  TPR_1         Tetratricopeptide repeat
       0.22   11.5   2.1       0.91    9.5   0.0    2.6  3  TetR_C_14     MftR C-terminal domain


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.3   3.3e-05     0.074       5      31 ..      17      43 ..      14      45 .. 0.88
   2 ?   -0.5   0.0      0.82   1.8e+03      13      21 ..     137     145 ..     132     149 .. 0.79
   3 ?    1.7   0.0      0.16   3.6e+02      11      28 ..     185     202 ..     183     203 .. 0.86
   4 ?    0.1   0.3      0.52   1.2e+03      14      28 ..     295     309 ..     284     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                             TPR_2  5 ynlGlayyklgdyeeAleafekAleld 31
                                      y  +l  +++g+++ A+e+f+kA e++
  gi|320100738|ref|YP_004176330.1| 17 YGKALNERNKGNLDGAVEHFNKAAEIA 43
                                      566788899***************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.82
                             TPR_2  13 klgdyeeAl 21 
                                        +++yeeA+
  gi|320100738|ref|YP_004176330.1| 137 LSKRYEEAA 145
                                       6799***96 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.16
                             TPR_2  11 yyklgdyeeAleafekAl 28 
                                       ++++ d+ +A+e++ +A+
  gi|320100738|ref|YP_004176330.1| 185 LAEREDPGRAVELYTEAV 202
                                       67889999********95 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.52
                             TPR_2  14 lgdyeeAleafekAl 28 
                                       +  ye A +a+e A+
  gi|320100738|ref|YP_004176330.1| 295 RHYYELAMKALEDAV 309
                                       456788888888776 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.4   5.9e-06     0.013       9      64 ..      19      74 ..      16      85 .. 0.74
   2 ?   -1.9   0.1       1.8   4.1e+03      56      66 ..     136     146 ..     132     151 .. 0.58
   3 ?    3.4   0.1     0.041        91      44      72 ..     174     202 ..     157     205 .. 0.79
   4 ?    0.1   0.3      0.45     1e+03      46      75 ..     284     312 ..     282     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.9e-06
                            TPR_12  9 laavlrrlgrydeAlellekaleiarrllGpdh.pltattlrnLgrlyralgryeeA 64
                                       a+ +r  g++d A e+++ka eia+++ G++   +  +   +++ +y++ + + eA
  gi|320100738|ref|YP_004176330.1| 19 KALNERNKGNLDGAVEHFNKAAEIASAS-GDQGlKAKGALAAAMASIYSLVKSPSEA 74
                                      5778899******************998.4444256666666666666666555554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                            TPR_12  56 ralgryeeAle 66 
                                       ++++ryeeA  
  gi|320100738|ref|YP_004176330.1| 136 ELSKRYEEAAG 146
                                       45567777654 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.041
                            TPR_12  44 tattlrnLgrlyralgryeeAlelleeal 72 
                                       +++  r +  ++ +++++  A+el++ea+
  gi|320100738|ref|YP_004176330.1| 174 LLALSRLMKAVLAEREDPGRAVELYTEAV 202
                                       55556666678889999999999999985 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.45
                            TPR_12  46 ttlrnLgrlyralgryeeAlelleealaia 75 
                                       t+++nLg++ ++   ye A ++le+a++++
  gi|320100738|ref|YP_004176330.1| 284 TAMYNLGDAISRH-YYELAMKALEDAVRRL 312
                                       5788888886555.8899999999988876 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.028        62      10      32 ..      19      41 ..      15      46 .. 0.90
   2 ?   -1.7   0.0       1.4   3.1e+03      25      36 ..     139     150 ..     132     155 .. 0.74
   3 ?   11.6   0.1   9.6e-05      0.22       9      40 ..     181     211 ..     175     228 .. 0.74
   4 ?    0.0   0.1      0.41   9.3e+02      25      52 ..     296     322 ..     291     327 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.028
                               MIT 10 kAveeDnagnyeeAlelYkeale 32
                                      kA +e n+gn + A+e + +a e
  gi|320100738|ref|YP_004176330.1| 19 KALNERNKGNLDGAVEHFNKAAE 41
                                      799999*************9987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                               MIT  25 elYkealelLlq 36 
                                       + Y+ea ++Llq
  gi|320100738|ref|YP_004176330.1| 139 KRYEEAAGILLQ 150
                                       568888888876 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 9.6e-05
                               MIT   9 kkAveeDnagnyeeAlelYkealelLlqalke 40 
                                        kAv +++ ++   A+elY+ea+++L+ +  +
  gi|320100738|ref|YP_004176330.1| 181 MKAVLAER-EDPGRAVELYTEAVGYLSSIADQ 211
                                       56666665.78889************999873 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.41
                               MIT  25 elYkealelLlqalke.kneerrellrek 52 
                                       ++Y+ a++ L  a+++ +     ++lr++
  gi|320100738|ref|YP_004176330.1| 296 HYYELAMKALEDAVRRlQ--MEIDALRNE 322
                                       688888888888887433..344444444 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0005       1.1      12      32 ..      24      44 ..      16      46 .. 0.86
   2 ?   -3.9   0.0         8   1.8e+04       6      14 ..     101     109 ..      98     110 .. 0.73
   3 ?   -1.6   0.0         2   4.5e+03      16      28 ..     190     202 ..     185     204 .. 0.80
   4 ?    1.9   0.2      0.14   3.2e+02      16      29 ..     297     310 ..     283     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0005
                                      HHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8 12 lklgdyeeAkeyyekaleldp 32
                                      +++g+++ A+e ++ka e++ 
  gi|320100738|ref|YP_004176330.1| 24 RNKGNLDGAVEHFNKAAEIAS 44
                                      79****************986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8
                                       HHHHHHHHT CS
                             TPR_8   6 nlgsiylkl 14 
                                       + g +y++l
  gi|320100738|ref|YP_004176330.1| 101 KAGELYREL 109
                                       568889877 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                                       -HHHHHHHHHHHH CS
                             TPR_8  16 dyeeAkeyyekal 28 
                                       d   A+e y +a+
  gi|320100738|ref|YP_004176330.1| 190 DPGRAVELYTEAV 202
                                       6678999999998 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.14
                                       -HHHHHHHHHHHHH CS
                             TPR_8  16 dyeeAkeyyekale 29 
                                        ye A++++e a++
  gi|320100738|ref|YP_004176330.1| 297 YYELAMKALEDAVR 310
                                       58999999999985 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00033      0.73       5      23 ..      24      42 ..      18      46 .. 0.88
   2 ?   -3.3   0.1       3.4   7.5e+03       9      13 ..     140     144 ..     132     145 .. 0.60
   3 ?   -1.9   0.0       1.2   2.7e+03      30      37 ..     285     292 ..     284     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00033
                            TPR_11  5 yeqGkyeeAieaYkkAlkl 23
                                      + +G++++A+e+++kA ++
  gi|320100738|ref|YP_004176330.1| 24 RNKGNLDGAVEHFNKAAEI 42
                                      569*************998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.4
                            TPR_11   9 kyeeA 13 
                                       +yeeA
  gi|320100738|ref|YP_004176330.1| 140 RYEEA 144
                                       55555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                            TPR_11  30 ayynLGla 37 
                                       a ynLG+a
  gi|320100738|ref|YP_004176330.1| 285 AMYNLGDA 292
                                       569**988 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 ?   11.0   0.0   0.00012      0.26     147     198 ..     261     314 ..     256     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                          Fe-ADH_2 147 aeAPrrllasGvGDllgkytaladwk..lanevseplaklsaamvqeaaeklve 198
                                       +eAP+ l+ sG G  ++ +ta ++ +  l++++s+++ +l+++ +++a+++l  
  gi|320100738|ref|YP_004176330.1| 261 EEAPNMLVESGGGQYIAVCTACYTAMynLGDAISRHYYELAMKALEDAVRRLQM 314
                                       58*******************996552266699999999999999998888753 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   9.3e-05      0.21       5      30 ..      17      42 ..      14      44 .. 0.84
   2 ?   -3.1   0.1       3.8   8.6e+03      15      20 ..     139     144 ..     138     145 .. 0.84
   3 ?    0.0   0.0      0.39   8.8e+02      12      28 ..     186     202 ..     183     203 .. 0.81
   4 ?   -2.9   0.0       3.2   7.3e+03       3       9 ..     285     291 ..     284     292 .. 0.79
   5 ?   -2.8   0.1         3   6.7e+03      17      27 ..     298     308 ..     298     310 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
                                      HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  5 ynlGnayfklgkydeAleyyekALel 30
                                      y++++  +++g++d A+e+++kA e+
  gi|320100738|ref|YP_004176330.1| 17 YGKALNERNKGNLDGAVEHFNKAAEI 42
                                      5566666899*************998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
                                       T-HHHH CS
                             TPR_1  15 gkydeA 20 
                                       ++y+eA
  gi|320100738|ref|YP_004176330.1| 139 KRYEEA 144
                                       799999 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.39
                                       HHTT-HHHHHHHHHHHH CS
                             TPR_1  12 fklgkydeAleyyekAL 28 
                                        + +++  A+e y +A+
  gi|320100738|ref|YP_004176330.1| 186 AEREDPGRAVELYTEAV 202
                                       56778889*****9995 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.2
                                       HHHHHHH CS
                             TPR_1   3 alynlGn 9  
                                       a ynlG 
  gi|320100738|ref|YP_004176330.1| 285 AMYNLGD 291
                                       679**96 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 3
                                       HHHHHHHHHHH CS
                             TPR_1  17 ydeAleyyekA 27 
                                       y+ A ++ e A
  gi|320100738|ref|YP_004176330.1| 298 YELAMKALEDA 308
                                       67777777655 PP

>> TetR_C_14  MftR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.28   6.3e+02      76     106 ..      55      82 ..      51      90 .. 0.64
   2 ?   -2.2   0.0       1.8     4e+03      44      76 ..     172     205 ..     169     226 .. 0.69
   3 ?    9.5   0.0   0.00041      0.91      52      94 ..     250     292 ..     242     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHH-TT.S-HHHHHHHHHHH CS
                         TetR_C_14  76 avlaaalaayeqwladed.adlaelLdealdl 106
                                        +laaa+a +   +++++ a l++    a+++
  gi|320100738|ref|YP_004176330.1|  55 GALAAAMASIYSLVKSPSeAALKQ----AMAS 82 
                                       578888888888888886344444....3333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHTS-TT.SHHHHHHHHH CS
                         TetR_C_14  44 lryaawrevvAefvAeRtgtdad.dlvprtvaaa 76 
                                       lr+ a  ++  +++AeR +     +l+  +v+++
  gi|320100738|ref|YP_004176330.1| 172 LRLLALSRLMKAVLAEREDPGRAvELYTEAVGYL 205
                                       5666667777777788777655447777777765 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHHHHHHH-TTS CS
                         TetR_C_14  52 vvAefvAeRtgtdaddlvprtvaaavlaaalaayeqwladeda 94 
                                        ++ ++A+R g++a  +++   ++  +a+++a y    +  da
  gi|320100738|ref|YP_004176330.1| 250 TITPYIAKRYGEEAPNMLVESGGGQYIAVCTACYTAMYNLGDA 292
                                       6899*****************************9987666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2482.63
//
Query:       gi|320100739|ref|YP_004176331.1|  [L=331]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-34  118.5   0.0      5e-34  117.9   0.0    1.3  1  Band_7_1      SPFH domain-Band 7 family
    9.9e-13   48.5   1.1      1e-12   48.5   0.1    1.5  2  Band_7        SPFH domain / Band 7 family
    7.6e-08   31.8   7.5    7.6e-08   31.8   7.5    1.9  2  SHOCT         Short C-terminal domain
      0.009   16.0   2.5       0.02   14.9   1.6    2.0  2  GvpG          Gas vesicle protein G
  ------ inclusion threshold ------
      0.012   16.4   4.6      0.012   16.4   4.6    1.5  1  DMAP_binding  DMAP1-binding Domain
       0.14   12.6   0.1        1.5    9.4   0.1    2.2  2  SecD-TM1      SecD export protein N-terminal TM region


Domain annotation for each model (and alignments):
>> 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 !  117.9   0.0   1.7e-37     5e-34       2     197 ..      20     212 ..      19     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 1.7e-37
                          Band_7_1   2 wrfprydneiknGakLivregqeavfvneGqiaDvfapGtytLttenlPvlstLkgwkyGf.esPfkaevYfvntrq 77 
                                       w +p y++ i+ G+ ++v+e  +avf+++G+i Dv  pG++t+tt+n+P+l++  ++  G+ e+Pfka + f++ +q
  gi|320100739|ref|YP_004176331.1|  20 WVYP-YED-IRWGSVVVVHEYEAAVFMRDGKIYDVLPPGRHTITTQNIPLLTRAYNLVMGYgETPFKARIVFISLKQ 94 
                                       7888.777.*************************************************99648************** PP

                          Band_7_1  78 ftdlkwGtknpvilrDpefglvrvrafGtyslrvvdpakllreivGtdgefdteeiseqlkslivtrlsdvlaeski 154
                                       f+  ++Gt   v l  +   +++++a+G+y +rv dp  +l+++ G+ +e++t  ++e l+ l ++++ + la+   
  gi|320100739|ref|YP_004176331.1|  95 FKG-RFGTSTRVKLGPRTLYMTELQAYGEYWFRVADPVLFLTQVAGAVPELSTPAVTEFLRGLFTEQFIQELAN--Y 168
                                       *86.9***************************************************************999976..5 PP

                          Band_7_1 155 pvldlaakseelaeklke.alkeelaeyGlelekleienislpe 197
                                       +++d+ ++ +e++ ++k  ++ e+l++ G+el +++i  +slp+
  gi|320100739|ref|YP_004176331.1| 169 TAIDVYTRLTEVTTRIKTgTIYEALKQRGIELIDVKIGGVSLPQ 212
                                       789999*****999997538999********************7 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.1   3.4e-16     1e-12       2     151 ..      34     212 ..      33     218 .. 0.81
   2 ?   -3.8   0.1       3.7   1.1e+04     122     137 ..     273     288 ..     257     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.4e-16
                            Band_7   2 iieegevgvvvrfGklsrvlepG...................lhfilP.....fgrsvtvvsvrvqtldvsv..slt 52 
                                       +++e e++v +r Gk+++vl+pG                              f  +++++s+++++ ++    +++
  gi|320100739|ref|YP_004176331.1|  34 VVHEYEAAVFMRDGKIYDVLPPGrhtittqniplltraynlvM----GygetpFKARIVFISLKQFKGRFGTstRVK 106
                                       799********************55555555555555555552....055555*****************9977555 PP

                            Band_7  53 vptkDg..lpvtidvtviyrvpddapklvaav.....eresanldnlirrvlesalrevisemtleellsnreelae 122
                                       +  +     +++  + +++rv  d+  + ++v     e +   + +++r ++ ++  + ++++t+++++    e++ 
  gi|320100739|ref|YP_004176331.1| 107 LGPRTLymTELQAYGEYWFRV-ADPVLFLTQVagavpELSTPAVTEFLRGLFTEQFIQELANYTAIDVYTRLTEVTT 182
                                       5555552245555555677**.**********8877777777788888888888888888***********9***** PP

                            Band_7 123 elkn.elneqlrkyGvevldvritdidppp 151
                                       ++k+  + e+l++ G+e++dv+i+ +++p+
  gi|320100739|ref|YP_004176331.1| 183 RIKTgTIYEALKQRGIELIDVKIGGVSLPQ 212
                                       **974799*******************996 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.7
                            Band_7 122 eelknelneqlrkyGv 137
                                       + ++ ++++q ++  v
  gi|320100739|ref|YP_004176331.1| 273 QTMAPQVQQQPQQPQV 288
                                       5556666666666655 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2   6.5e+03      20      26 ..     190     196 ..     190     198 .. 0.55
   2 !   31.8   7.5   2.6e-11   7.6e-08       1      28 []     298     325 ..     298     325 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                             SHOCT  20 FeakKak 26 
                                       +ea K++
  gi|320100739|ref|YP_004176331.1| 190 YEALKQR 196
                                       5555554 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 2.6e-11
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       d+L++Lk+++++G+It+EE+e+ K+++L
  gi|320100739|ref|YP_004176331.1| 298 DKLRELKKMLDEGLITREEYEQLKKEIL 325
                                       79*************************8 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.2   3.5e+03      32      51 ..     172     191 ..     162     196 .. 0.82
   2 !   14.9   1.6   6.6e-06      0.02      26      65 ..     289     328 ..     275     331 .] 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                              GvpG  32 nlrkeLaaLqqeLdaGeIde 51 
                                       ++ ++L++   +++ G I e
  gi|320100739|ref|YP_004176331.1| 172 DVYTRLTEVTTRIKTGTIYE 191
                                       57789999999999999977 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.6e-06
                              GvpG  26 qlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrL 65 
                                       q  +q+    +L +L++ Ld+G I+ ee+++   e+L+  
  gi|320100739|ref|YP_004176331.1| 289 QQPQQKSPTDKLRELKKMLDEGLITREEYEQLKKEILEEF 328
                                       33445566789*************************9875 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   4.6     4e-06     0.012      11      42 ..     298     329 ..     291     331 .] 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4e-06
                      DMAP_binding  11 erLaeLeldlseGdiTeKgyekkklkLLreFl 42 
                                       ++L+eL + l+eG iT+++ye+ k+++L+eF 
  gi|320100739|ref|YP_004176331.1| 298 DKLRELKKMLDEGLITREEYEQLKKEILEEFK 329
                                       59****************************95 PP

>> SecD-TM1  SecD export protein N-terminal TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.27   8.1e+02      44      68 ..     181     204 ..     166     211 .. 0.67
   2 ?    9.4   0.1   0.00049       1.5      17      59 ..     260     302 ..     257     331 .] 0.72

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.27
                          SecD-TM1  44 kvdeatlskveqaLkeagievksie 68 
                                       ++  +t  ++++aLk++gie  +++
  gi|320100739|ref|YP_004176331.1| 181 TTRIKT-GTIYEALKQRGIELIDVK 204
                                       333333.4799********987665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00049
                          SecD-TM1  17 ligllyalPnlygedpavqisaakatlkvdeatlskveqaLke 59 
                                       ++g+l alP++ +++ a q++++ ++ +v++  +++ +++L+e
  gi|320100739|ref|YP_004176331.1| 260 VLGALVALPQMLPQTMAPQVQQQPQQPQVQQPQQKSPTDKLRE 302
                                       899*****************99988888877666555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1067  (0.0595125); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2371.97
//
Query:       gi|320100740|ref|YP_004176332.1|  [L=179]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1390.94
//
Query:       gi|320100741|ref|YP_004176333.1|  [L=442]
Description: 4-aminobutyrate aminotransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-95  318.3   0.0      7e-95  318.1   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 !  318.1   0.0   3.9e-99     7e-95      11     404 ..      19     421 ..      13     423 .. 0.93

  Alignments for each domain:
  == domain 1  score: 318.1 bits;  conditional E-value: 3.9e-99
                                       EEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-.. CS
                       Aminotran_3  11 lvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgl 87 
                                       + + +++G+++ d++g++++D+vs+ av n+G + ++vv+av +qa  l       +  e+ ++la+kl++++p+ +
  gi|320100741|ref|YP_004176333.1|  19 FKAVEGRGARVLDAEGREFIDFVSGAAVYNVGINREEVVNAVVDQARRLLNYTSLYFYMEEPVRLARKLVEVTPGRF 95 
                                       66789******************************************998888799999****************** PP

                                       S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TT CS
                       Aminotran_3  88 d.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkyp 163
                                       d +v++  +Gs+A e Al  +++      +t k+ +++f+g+fHG ++++ls++g     +    ++   v +++yp
  gi|320100741|ref|YP_004176333.1|  96 DkRVVYGFTGSDAAEIALTSSMN------YTGKPWLLSFTGSFHGTLYLSLSASGI-FAGRGRGAAVYRRVLYAEYP 165
                                       *999**************99999......9*************************9.444444455688999***** PP

                                       BGGGTB-HH.......HHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE- CS
                       Aminotran_3 164 deevlkene.......eeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDE 233
                                        +++ k          e +a +l e+e+ ++++k +vaAvi+Ep+ g++Gvvv++++fl++lre++++h+v+li DE
  gi|320100741|ref|YP_004176333.1| 166 NPYRNKWGVdgyekpgELTALALSEVEEKIREAKGDVAAVIFEPVEGDAGVVVPPAGFLKGLREVADRHGVVLIGDE 242
                                       9998776545676565666677777777779********************************************** PP

                                       TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHH CS
                       Aminotran_3 234 vqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiiee 310
                                       vqtG+GrTG ++A+eh+ v+pDl++ +Kal+gG+p+sav+++ae+ +     + g T +G  + +++ala++e++e+
  gi|320100741|ref|YP_004176333.1| 243 VQTGIGRTGSMWAVEHFSVEPDLLLAGKALGGGMPISAVIGRAEILESQPLLGLGFTNMGHAVCARAALATIEVVEK 319
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETT.. CS
                       Aminotran_3 311 ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGd.. 379
                                       e+l+e+a+ lg+  +++L+e++++ e +++vRg+Glmi++e++ ++  ++       + + +a ekG+l+ ++G+  
  gi|320100741|ref|YP_004176333.1| 320 EHLAERARVLGEHASKRLREIAERVEAVGDVRGLGLMIGVEVVRDKASRRpdrataLKTCWRAWEKGLLVTTLGShg 396
                                       *******************************************9999777899999889**************9999 PP

                                       TEEEE---TT--HHHHHHHHHHHHH CS
                       Aminotran_3 380 nvirllppliitdeeidelleilkk 404
                                       nv+r++ppl+i+ ee+d++++ l++
  gi|320100741|ref|YP_004176333.1| 397 NVLRIMPPLTISMEELDKGIDVLEE 421
                                       *********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3215.96
//
Query:       gi|320100742|ref|YP_004176334.1|  [L=428]
Description: hydroxymethylpyrimidine transporter CytX [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-31  107.8  32.0    8.4e-31  107.2  32.0    1.3  1  Transp_cyt_pur  Permease for cytosine/purines, uracil, thiami


Domain annotation for each model (and alignments):
>> Transp_cyt_pur  Permease for cytosine/purines, uracil, thiamine, allantoin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2  32.0   4.7e-35   8.4e-31       1     419 [.      10     392 ..      10     415 .. 0.84

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 4.7e-35
                    Transp_cyt_pur   1 pvpeeeRtwktlnlfsiWlganlnintwvigalg.lalgLnwwqsvlviivgnligaifvallglaGakyGlpfpil 76 
                                       pvp  eR  +  ++fsiW+ga ++i+ +  ga++  +lgLn+ +++l+ i+g l+g  ++a  +l+G   G+p+++l
  gi|320100742|ref|YP_004176334.1|  10 PVPRGERSLGFPEVFSIWFGAGISIAEFWAGAMLvGVLGLNLPSAILATILGHLLGNTILAAVSLMGYYSGVPTMVL 86 
                                       899**********************998888888689**************************************** PP

                    Transp_cyt_pur  77 sRasfGirgsllplllrvviaivwfgvqawiGsealllmlgkifgkwleigg.ailgtsltelvtffifwvvslviv 152
                                       sR s G rgs+  ++   +  ++w++v  ++++ a  ++l ++ g    ++g  ++ +s++ +  ++++w+++ v  
  gi|320100742|ref|YP_004176334.1|  87 SRISLGSRGSIAASIANYLQLVGWTAVMLVVAARASETVLAEASG----LKGwMVYSSSIMLIGLAVVAWALTGVKG 159
                                       *******************************************99....6664556666666666677888888777 PP

                    Transp_cyt_pur 153 llgvskirkffviaallvpvaafgfliwalvkaegGpvldkavklgkselflsavagvlagfatlilnapDFtryak 229
                                       +  v+       + a++++v++  +   +++  ++  +l ++  +   e f+ +v +++a ++++++ a+D++r+ +
  gi|320100742|ref|YP_004176334.1| 160 WRRVE------LASAAALAVLSAWLTAVVASSRDLPRLLAEPLVID--ERFWLGVDLAAAMPVSWAPVAADYSRFSR 228
                                       76554......33333333333344555666667766666664444..58*************************** PP

                    Transp_cyt_pur 230 tkkssvkiqlvavpllftlllligilvaaaakaayganawspldilakfdetagvllililvalaqlgvnisanlls 306
                                       +  ++ ++  v+++  ++l+++ig+l   +    + + + +++          g+ ++++l+ +    ++ ++ ++s
  gi|320100742|ref|YP_004176334.1| 229 SGLAAFWGTYVGYFASSSLFYIIGALSNLLVNQPDPVGVIAVY----------GLGVPAMLLVVLSTTTTTFLDVYS 295
                                       ***********99999999999998877766555555555555..........566788888888889999****** PP

                    Transp_cyt_pur 307 agldlaallPkkinikrgsliaavialvivpwkllssssklftaflsllavflspvagviiadyfvvrrgylklaal 383
                                       a+  l++ lP +i i+  +++a v+++ + ++    +s +  + fl l+++++++  gv++ad++++r +y++  + 
  gi|320100742|ref|YP_004176334.1| 296 AAISLKNTLP-RIDIRKHIVVAGVLGIGVGLV-FPVESYE--W-FLLLIGGVFTSLSGVMVADFLRNRLAYVEWRDP 367
                                       **********.*************99988888.4444444..3.9****************************9999 PP

                    Transp_cyt_pur 384 ytrrrgsaYwyrkgvNwravaayivGiaaglvgvag 419
                                       +             v  r ++a+++G+++ +++ a+
  gi|320100742|ref|YP_004176334.1| 368 VV-----------HVETRGLVAWVAGTVLYILLSAS 392
                                       99...........78889999999999988887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2828.74
//
Query:       gi|320100743|ref|YP_004176335.1|  [L=357]
Description: AIR synthase-like protein domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-19   68.8   0.9    8.5e-19   68.2   0.9    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.1e-10   42.0   0.1    3.2e-10   40.5   0.1    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 !   68.2   0.9   9.5e-23   8.5e-19       1     154 [.     159     326 ..     159     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 9.5e-23
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT..TSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds..avqlgdvlleptliyvkralaal..kglvkaahDvTgGGLl 73 
                                       +pGd++++t++  + +ag++++      e++  s  a++    + ++t++  ++ala +  k  v+a+hD T+ G++
  gi|320100743|ref|YP_004176335.1| 159 RPGDLVLMTKGPAVEAAGILSVMFPSVLEAEYGSgfAREAQGIFWLQTVVPDALALAGAglKTVVTAMHDATEYGVW 235
                                       79*********88888887777766666665444777888889********************************** PP

                                       HHHHHHHHTTTEEEEEECG..........THHHHHHHH....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTC CS
                            AIRS_C  74 galaemapasgvgaeidld..........kvpifdele....splemllsensGrllvavppeeadavlaileeegl 136
                                       gal+ + + s+vg++++ d           +++f   e     +++++ + ++G l+ +v++ +  ++l++l+++g+
  gi|320100743|ref|YP_004176335.1| 236 GALHDVSESSRVGIRVYRDrlfirgdvakVLKAF---EkytgMEIDPFAAISEGTLIATVKRSRVSEALEALRRAGV 309
                                       *******************666666544333333...1455777888888*************************** PP

                                       CCEEEEEEEEESSSEEEE CS
                            AIRS_C 137 peaavIGevtakeelsvi 154
                                        eaavIGev+++ +++++
  gi|320100743|ref|YP_004176335.1| 310 -EAAVIGEVVEGSGVELV 326
                                       .8**********988775 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 !   40.5   0.1   3.6e-14   3.2e-10       5      90 ..      49     143 ..      27     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 3.6e-14
                                       EEEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvp 72 
                                       +++++d    pv+v p  +    G+ av+  +sD+a+ G  P++l+  l+lp      +l+ +   +++ +e+lg++
  gi|320100743|ref|YP_004176335.1|  49 LIFEVD----PVFVVPQYGwerSGWFAVHILASDVAVSGVPPRYLFIDLNLPlsmrdeELKTLWMAIHRECEKLGIA 121
                                       467777....677766666899******************************************************* PP

                                       EEEEEEEEESS....EEEEEEE CS
                              AIRS  73 lvgGdtsfsne....ptisvta 90 
                                       +vgG+t ++ +    ++  +++
  gi|320100743|ref|YP_004176335.1| 122 IVGGHTGRYGGvdypMLGGAVM 143
                                       *******998777743333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2544.88
//
Query:       gi|320100744|ref|YP_004176336.1|  [L=454]
Description: phosphomethylpyrimidine kinase [Desulfurococcus mucosus DSM 2162]
Scores for 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  326.4   0.3    1.3e-97  326.0   0.3    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    1.5e-55  187.3   2.0    2.5e-55  186.6   0.1    2.2  2  ThiP_synth    Thiamine-phosphate synthase
    2.9e-11   43.2   0.1    6.8e-11   42.0   0.1    1.5  1  PfkB          pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.022   14.3   1.3      0.036   13.5   1.3    1.4  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.0   0.3  2.9e-101   1.3e-97       1     246 []      14     257 ..      14     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: 326.0 bits;  conditional E-value: 2.9e-101
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAG+qADlktf+a+gv+g+s+it++taqnt++v+++h++p+e+v+aq+eav+ed++vda+K+Gml+++ ii+v
  gi|320100744|ref|YP_004176336.1|  14 DSGGGAGVQADLKTFAAMGVHGASAITSITAQNTREVRAIHDVPPEIVKAQIEAVVEDIGVDAAKTGMLSNSGIIRV 90 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH. CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk. 153
                                       vae++++y++p+V+DPVm+aksg++ll+e+ave lk+ Ll+la+v+tPN+pEae+Llge+ik   d+++aa+++++ 
  gi|320100744|ref|YP_004176336.1|  91 VAEAVERYGFPLVVDPVMIAKSGARLLREDAVEELKR-LLRLAKVVTPNIPEAEVLLGEEIKGIGDAERAAREIAEr 166
                                       ************************************8.**************************************9 PP

                                       TT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 154 lgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvte 230
                                       +g++aV++kGgh+  + + v+dvly+ ++++e++++rie +++hGtGC++s+aiaa lakg+s+eeAv+ A+e v++
  gi|320100744|ref|YP_004176336.1| 167 YGCEAVVVKGGHM--KGDLVIDVLYHAGRITEFKGRRIERRTKHGTGCSFSAAIAAGLAKGRSIEEAVRVARELVET 241
                                       ************8..667889******************************************************** PP

                                       HHHCG-BSTSSS-B-- CS
                      Phos_pyr_kin 231 aikealelgkgagpvn 246
                                       ai+++le+g g+gpvn
  gi|320100744|ref|YP_004176336.1| 242 AIEYGLEVGGGHGPVN 257
                                       **************97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.21   9.5e+02      38      53 ..     186     201 ..     180     249 .. 0.63
   2 !  186.6   0.1   5.5e-59   2.5e-55       1     164 [.     274     446 ..     274     447 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                                       GEEEETT-EEE-TSSE CS
                        ThiP_synth  38 DvaavpGRIvrvkgrv 53 
                                       Dv+   GRI+++kgr 
  gi|320100744|ref|YP_004176336.1| 186 DVLYHAGRITEFKGRR 201
                                       6777789999999653 PP

  == domain 2  score: 186.6 bits;  conditional E-value: 5.5e-59
                                       HHHHHHHHHHCC--..GCC--TT-B-EEEE-S..T--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHH CS
                        ThiP_synth   1 eleralelleeeee.fakliPevgsNiayalp..dAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaa 74 
                                       ++e+a+++l+++e+ +++l+Pevg Ni++a++  +A+++ DvaavpGRI+r++++++v+g+pefg+s+h+a+++l+a
  gi|320100744|ref|YP_004176336.1| 274 NVEEAVRMLKDNEKlVNALVPEVGINIGMAIEhpYARTPMDVAAVPGRITRYRDGLMVPGKPEFGVSRHIANAVLTA 350
                                       599***********9****************988******************************************* PP

                                       HCC-TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC..S-ECEEEE--BCTB CS
                        ThiP_synth  75 mkfdpevraainirydekilealeelglkvvefdreeepeev....gstmewgvaeaieel..evpdviydeGgvGk 145
                                       m+ +p++raa++i++ +  +ea++ lg+k+++fdr+ ep+ev    g+t +wgv+ a++++   +pd+i d G+ Gk
  gi|320100744|ref|YP_004176336.1| 351 MRINPSIRAAADIAMPDGWEEAARGLGFKTSYFDRRLEPPEVkrveGGTTRWGVEWAVRRTggVIPDIIADYGEHGK 427
                                       *****************************************99******************977************* PP

                                       --EEEEEESSHHHHHHHHH CS
                        ThiP_synth 146 Epmiyvlgkdaeevvekvl 164
                                       Ep + vlg++a++v+ k++
  gi|320100744|ref|YP_004176336.1| 428 EPLLLVLGETATDVAGKIV 446
                                       ***************9986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1   1.5e-14   6.8e-11     161     285 ..     104     238 ..      85     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.5e-14
                                       EEEEECESSSHH.....HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SEEEEEEGG.G CS
                              PfkB 161 fdpnlldplgaq.....fkeallellaladllkpneeElealtgekledieealaalhklkakga.ktvvvtlGk.e 230
                                       +dp++ +++ga      ++e+l++ll+la +++pn  E+e l+ge+++ i +a +a+ ++ +++  + vvv+ G  +
  gi|320100744|ref|YP_004176336.1| 104 VDPVMIAKSGARllredAVEELKRLLRLAKVVTPNIPEAEVLLGEEIKGIGDAERAAREIAERYGcEAVVVKGGHmK 180
                                       6888888888888888999********************************************99*********758 PP

                                       EEEEEE....TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHH CS
                              PfkB 231 Galvve....kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanav 285
                                       G lv +     +   +++  + ++     G+G sf ++++a+l++g s+eea+r a ++
  gi|320100744|ref|YP_004176336.1| 181 GDLVIDvlyhAGRITEFKG-RRIERRTKHGTGCSFSAAIAAGLAKGRSIEEAVRVAREL 238
                                       8888889887666666777.778888899*************************99765 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   8.1e-06     0.036      90     218 ..      95     239 ..       7     245 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.1e-06
                                       HCCCCS-EEEE.....GGGGGSGGGG......TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTT.E CS
                       Carb_kinase  90 vlekdeplviD.....AdgLnllaqkne...lserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklna.v 157
                                       v+    plv+D      +g  ll ++     +   + + + TP++ E + Ll+  +k   d   +are+a+++++  
  gi|320100744|ref|YP_004176336.1|  95 VERYGFPLVVDpvmiaKSGARLLREDAVeelKRLLRLAKVVTPNIPEAEVLLGEEIKGIGDAERAAREIAERYGCeA 171
                                       444445566652222112222333322235677778899*****************9999999**********9856 PP

                                       EEEESTT...SE...EEECTTEEEEE----GG.G-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHH CS
                       Carb_kinase 158 vllkgek...dv...ivspegevlinstgssa.lakGGsGDvLaGligalLaqneasyeaaiaaawlh 218
                                       v++kg +   d+   + +++g ++  +      ++k G+G   + +i+a La  ++  ea+ +a +l+
  gi|320100744|ref|YP_004176336.1| 172 VVVKGGHmkgDLvidVLYHAGRITEFKGRRIErRTKHGTGCSFSAAIAAGLAKGRSIEEAVRVARELV 239
                                       77888652224422234567777776655543145677777777777777777777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3307.31
//
Query:       gi|320100745|ref|YP_004176337.1|  [L=217]
Description: BioY protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   99.9  21.9    1.2e-28   99.9  21.9    1.9  2  BioY      BioY family


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 ?    0.7   0.1     0.027   4.9e+02      79     101 ..      26      48 ..       8      56 .. 0.75
   2 !   99.9  21.9   6.6e-33   1.2e-28       1     132 [.      57     203 ..      57     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.027
                              BioY  79 lllallagllviyalGvlwlalv 101
                                       ++l +l+  ++i +lGv++lal 
  gi|320100745|ref|YP_004176337.1|  26 IALKALMREALIIVLGVAGLALS 48 
                                       46667778899999999999884 PP

  == domain 2  score: 99.9 bits;  conditional E-value: 6.6e-33
                              BioY   1 lgpvpitlqtlavllaglllgprrgalavllYlllGalglPvfagggGlavllgptgGYllGFlvaalvvgll.... 73 
                                       ++pvp+tlqtl+++   l+lg+ r+   +++Y+llG++glPvfa ggG++++ +pt+GYllGF vaa+v g++    
  gi|320100745|ref|YP_004176337.1|  57 FTPVPFTLQTLVLFYEILALGR-RAWRITATYVLLGLAGLPVFAYGGGPGYVSSPTFGYLLGFTVAAAVGGWIiggg 132
                                       68******************96.599999********************************************9987 PP

                              BioY  74 ...kklaelllallagllviyalGvlwlalv..........lslaaalaagvlpfipgdlvkavlaallaka 132
                                          +  ++ll+al+a ++++yalG+++la++          + la a+a g++pfi  d+vka++aa  ++a
  gi|320100745|ref|YP_004176337.1| 133 llvT-PRRLLTALAASITAVYALGAAYLAAWvtilsnaplhVALAMAVAQGIAPFIALDVVKALIAAGALYA 203
                                       7542.578899999999*************43445555555558888999****************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1737.29
//
Query:       gi|320100746|ref|YP_004176338.1|  [L=174]
Description: flavin reductase domain-containing FMN-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-22   79.7   0.0    2.6e-22   79.5   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 !   79.5   0.0   1.5e-26   2.6e-22       7     140 ..      12     143 ..       6     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 1.5e-26
                                       E-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCC CS
                     Flavin_Reduct   7 pvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprtd 83 
                                         ++vt+ v p++ + +t+ +++ ls +P +v++s+ ++++t++ lk+ gefv+ +   s    ++  ++ sgp+++
  gi|320100746|ref|YP_004176338.1|  12 RTFLVTSGVYPEHFDVMTADWVVVLSGEPFMVGVSVSPRRYTHRLLKKHGEFVVAVPTLSMLRGVWLAGTESGPSKV 88 
                                       5689****************************************************999999988888888888888 PP

                                       CCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTEC CS
                     Flavin_Reduct  84 dksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddad 140
                                        ++ f  l  +e  ++ap++++a+a+leC+vv+s+ +gdhe f geVv+ +   +a 
  gi|320100746|ref|YP_004176338.1|  89 PRLGFK-LRRGE-VVKAPLVEDAVANLECRVVDSRVYGDHEFFAGEVVKEHYAPEAY 143
                                       884443.44444.799********************************998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1521.23
//
Query:       gi|320100747|ref|YP_004176339.1|  [L=539]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  48.9    3.3e-21   75.6  48.9    1.3  1  AA_permease_2  Amino acid permease
    1.2e-13   50.6  39.0    1.9e-13   49.9  39.0    1.3  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6  48.9   3.7e-25   3.3e-21       1     404 [.      18     491 ..      18     517 .. 0.75

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 3.7e-25
                     AA_permease_2   1 lsllsafalvigsv..igsgifvknlaas...ggpalilwvwiavligslavllvy.aElssalprsgGiyvytkaa 71 
                                       ls+++ ++ +i ++   g++++++ ++++    g  ++l +++a +i+ l++ +++ + ++s +prs  +yv+++++
  gi|320100747|ref|YP_004176339.1|  18 LSWIDIALWSIATPaaSGMTYYAVKALGYpdtYGGNIALAFIVAGIIF-LPLTIAFyLIVAS-FPRSNSMYVVVSRT 92 
                                       678888888888873344445555544443335555778888888888.56666651666**.************** PP

                     AA_permease_2  72 fgkkvaflsawfnwfayvpvlasil..svaasyllnalgpdlqgn..............twltyliaiaililvali 132
                                        ++++++l  w++ ++   ++++++  +++++++ + l   +  +              +++++++a++++ +++l+
  gi|320100747|ref|YP_004176339.1|  93 LHPVLGYLPFWYYIVGGGGAMCAGFimYIGLKAFSGPLTVAGIATgskglldaanamvdPVIQLIVAVVLVFILWLL 169
                                       **************99999888875335578888666554333335678888889999999**************** PP

                     AA_permease_2 133 nirgikesakiqnilgilkillpliiliilglitvdgggfssl..................stetdt........ff 183
                                       n+ g+k +++   i++++ ++++l++li+l+ +  ++g+  +                        t         +
  gi|320100747|ref|YP_004176339.1| 170 NLGGMKVIKWTMRIGTVIPLVVTLATLIALASLGPGAGTKAFDavygegasskiisaaldeK----TagsygisaLT 242
                                       *********************99999998888888777776668998888877776654332....24555666666 PP

                     AA_permease_2 184 pn.gwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddei....... 250
                                       pn   +g+ ++l+ +lw+ +G e+ + v +evk   + + +++ ig + v++ly++ ++++ +v + d +       
  gi|320100747|ref|YP_004176339.1| 243 PNsLFTGTYGMLFWTLWAWTGLEVTTFVGSEVKDpsRSYLRGLLIGYIAVMLLYVFNAMVLPYVFGYDFLaayaylk 319
                                       66677778999999*****************8877689******************777777777777776666555 PP

                     AA_permease_2 251 ........anlsnlgsv..........aalffeavg.gkvvaiivvilialsllgaintavigssrvlealardgvl 308
                                               +       +          +  ++  ++ +++++i+v ++ +l  l  ++ +++++ r +++++ d++l
  gi|320100747|ref|YP_004176339.1| 320 sehpevleS-------IlpgkplpdpsVPFYVSIAFpNPWLSIVVGLAYFLWYLNTAIPVWVAAVRGFFSMSFDRAL 389
                                       544443441.......13344455554344444444458************************************** PP

                     AA_permease_2 309 Prffakvn.kfgspiraiiltaivslillllfllas..saaynfllsvsslgliisylll.iigalilrkkrphlkr 381
                                       P+ +a+v+ +f +p+ a  +ta++ ++ ++++++ s  s+  ++l s+  ++l+i++  + +++al+ ++++ +++r
  gi|320100747|ref|YP_004176339.1| 390 PEKMASVSpRFAAPTWANHVTALIGVLGAVVTYYESlgSELATALISWLDFSLFIFVWPVgLALALMPWWRPDIFER 466
                                       ********9****************999988887668888888888888888888777776899***********99 PP

                     AA_permease_2 382 ...pgkilvaiigalfllfllvalff 404
                                          + ki+++ ig++++ +   +l++
  gi|320100747|ref|YP_004176339.1| 467 tvfKSKIVTSVIGIIVFAIG-WWLML 491
                                       88433455555554444443.33333 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9  39.0   2.1e-17   1.9e-13      29     424 ..      52     493 ..      37     525 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.1e-17
                       AA_permease  29 lgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitvlaleltaasiliqfwe 105
                                       +++ la+++ag++++  +++++ i+  +p+s + y+ +sr+l+p lG+     ++++ + + ++ +++ +++i++  
  gi|320100747|ref|YP_004176339.1|  52 GNIALAFIVAGIIFLPLTIAFYLIVASFPRSNSMYVVVSRTLHPVLGYLP---FWYYIVGGGGAMCAGFIMYIGLKA 125
                                       3678*******************************************966...555666666666666667776664 PP

                       AA_permease 106 lvtdlpkawvt.......................gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgii 159
                                       +   l    ++                       ++v++++l ++nl g+kv   +  i ++i ++  +a++i +++
  gi|320100747|ref|YP_004176339.1| 126 FSGPLT-VAGIatgskglldaanamvdpviqlivAVVLVFILWLLNLGGMKVIKWTMRIGTVIPLVVTLATLIALAS 201
                                       444443.333346777777777777888888888999999************9988888777777777777777755 PP

                       AA_permease 160 llaggkpnkga.....gfrflgdngsifknnlppgfa.kee..egafknfisvfvivvfaftGielvaiiagEvkdP 228
                                       l  g++++++      g+++   +++ +++   +++  +     + f++ ++++   + a tG e ++ +++EvkdP
  gi|320100747|ref|YP_004176339.1| 202 LGPGAGTKAFDavygeGASSKIISAA-LDEKTAGSYGiSALtpNSLFTGTYGMLFWTLWAWTGLEVTTFVGSEVKDP 277
                                       55555544444446753333222222.2222222222222211367******************************* PP

                       AA_permease 229 eksiPkailqvviritifYvlsllligllvprndlgllndsasa.................aspfvifikesgvsvl 288
                                       ++s  ++ l   i ++++Yv+ ++++  +++++ l   +   s                  + pf + i +  ++ l
  gi|320100747|ref|YP_004176339.1| 278 SRSYLRGLLIGYIAVMLLYVFNAMVLPYVFGYDFLAAYAYLKSEhpevlesilpgkplpdpSVPFYVSIAF-PNPWL 353
                                       ********************99999888888888777775555588889999999***9976666666655.47899 PP

                       AA_permease 289 aplinaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaap.i 363
                                       + ++ ++ ++  l++a+   ++a R ++s++ d+++P k+++++ +   P  a  ++++i++l+ +++++ +     
  gi|320100747|ref|YP_004176339.1| 354 SIVVGLAYFLWYLNTAIPVWVAAVRGFFSMSFDRALPeKMASVSPRFAAPTWANHVTALIGVLGAVVTYYESLGSeL 430
                                       99999************************************************************999887654405 PP

                       AA_permease 364 vfnfllaisaliglivwlliilsyl..rfRkalkyqgrsieelgfkaallplgvilvlaalii 424
                                       +++ ++ +    +++vw++ ++  l   +R+ +++++   +++     +++ ++i ++++l +
  gi|320100747|ref|YP_004176339.1| 431 ATALISWLDFSLFIFVWPVGLALALmpWWRPDIFERTVFKSKIVTSVIGIIVFAIGWWLMLYT 493
                                       55555555556677899877666554599***9999885555555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.41
# Mc/sec: 3958.39
//
Query:       gi|320100748|ref|YP_004176340.1|  [L=316]
Description: Icc family phosphoesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-08   34.5   2.7    9.5e-05   21.8   0.7    3.3  3  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    3.1e-07   30.7   0.1    6.4e-05   23.2   0.1    3.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    7.8e-05   23.3   0.0    0.00045   20.8   0.0    2.0  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.039   2.3e+02      12      43 ..       8      39 ..       2      42 .. 0.85
   2 !    9.3   0.0    0.0001      0.63      63     123 ..     103     165 ..      85     174 .. 0.73
   3 !   21.8   0.7   1.6e-08   9.5e-05     194     239 ..     245     293 ..     191     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.039
                                      E--TT-GGGHHHHHHHHHHH--SEEEEES--- CS
                     Metallophos_3 12 sdlkgevellerlveviedkdpDllvlvGdlv 43
                                       d++g++ +  + +++ e+  +++l+l Gdl 
  gi|320100748|ref|YP_004176340.1|  8 VDVHGSTLVWRKWIKASEEYRVNALILAGDLT 39
                                      5788888889999999**************96 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0001
                                       -THHHHHHHHHHHHH.HHHHHHHHHTT-SEEEEE--TTS--HHHHHHHHH.HTTTT-TTEEE- CS
                     Metallophos_3  63 dkkeileekneiikl.ldklfrelgeldvpafvvPGkrDaPlevflreay.eaevvfpnlkvv 123
                                        +k+++e+  e ++  ld l   +++ +v ++v+PG+ D P    + +ay +  v++p  +vv
  gi|320100748|ref|YP_004176340.1| 103 VNKVMFEKMAERFRSwLDFLTSRVDTGKVAVIVMPGNDDEPFIDDIIKAYaDKGVIYPLERVV 165
                                       46888899999998725666678******************7555555551455777766665 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 1.6e-08
                                       S---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEEEE--B.GGG CS
                     Metallophos_3 194 lkekgsevvaelvktlnPevvvvghavkeh..eelgktlvvnPGa.lee 239
                                       +++ gs+ v +++  ++P + + gh + +   +++g+t+vvnPG+ ++e
  gi|320100748|ref|YP_004176340.1| 245 YEHVGSKAVRKVIERHQPLIGLHGHIHESGgqDTVGRTIVVNPGSeYSE 293
                                       5899*********************9986555************62555 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 !   23.2   0.1   1.1e-08   6.4e-05       8     145 ..       9     289 ..       1     294 [. 0.76

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.1e-08
                     Metallophos_2   8 DlHsnldaleavlealkevgvdaiihaGD................................................ 36 
                                       D+H++    +++++a +e +v+a+i+aGD                                                
  gi|320100748|ref|YP_004176340.1|   9 DVHGSTLVWRKWIKASEEYRVNALILAGDltgkvlvpivshpdgtwtaryfgsrwvmkseaevrsfeerlegagayy 85 
                                       9****************************999999999999999999999999999888888888888888888888 PP

                     Metallophos_2  37 ................leeeep.............evleellela............pvlaVrGNnD.......... 62 
                                                       +                  +    +   +             v++ +GN D          
  gi|320100748|ref|YP_004176340.1|  86 vrvdergleelkanpdA----VnkvmfekmaerfrS----W---LdfltsrvdtgkvAVIVMPGNDDepfiddiika 151
                                       77777776665555551....044444433322221....1...133355567788999********9999999999 PP

                     Metallophos_2  63 ............................eevveedvlreaaelgtdlpeeaelel..agekvlliHgdpl....... 102
                                                                   ++ ++  +  e++el+++l e+++  l  + + v+ +H  p+       
  gi|320100748|ref|YP_004176340.1| 152 yadkgviyplervvelqgveivsspfvnPTPWKTPRELEEKELEKHL-EKQVSRLrdPSKAVFNFHAPPYntmldla 227
                                       99999999999999999999999888755558888899999998888.44444442244448888988779999999 PP

                     Metallophos_2 103 ................gvkdalaellkeaeegsd..vvvcGHtHvp.evekeggvlvvnPGs 145
                                                       ++++  ++++++  e+++  + ++GH+H+  + ++ g ++vvnPGs
  gi|320100748|ref|YP_004176340.1| 228 pkltrdlrvvtvagvpQYEHVGSKAVRKVIERHQplIGLHGHIHESgGQDTVGRTIVVNPGS 289
                                       999999999999888844444444444455555567**********556666999999***9 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   7.6e-08   0.00045       8     203 ..       9     272 ..       2     273 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.6e-08
                                       SBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS..................................... CS
                       Metallophos   8 DlHlalgggqlddllkllddllreekpdlvllaGDlvdrg..................................... 47 
                                       D+H     g+    +k+++   +e ++++++laGDl+                                        
  gi|320100748|ref|YP_004176340.1|   9 DVH-----GSTLVWRKWIKAS-EEYRVNALILAGDLTGKVlvpivshpdgtwtaryfgsrwvmkseaevrsfeerle 79 
                                       888.....8888888888665.7779999999999444444444444455677788888888888888888888888 PP

                                       ..................................HHHHHHHHHHHHHHHH.TSEEEEEC-TTSCHHHHHHHHHHHHH CS
                       Metallophos  48 ..................................dlekellellaalvky.pipvylllGNHegfeeellnkygylg 89 
                                                                          + + +l++l+  v+  ++ v++++GN +    e +       
  gi|320100748|ref|YP_004176340.1|  80 gagayyvrvdergleelkanpdavnkvmfekmaeRFRS-WLDFLTSRVDTgKVAVIVMPGNDD----EPFID----- 146
                                       88888888888888888877776666666655533333.5555444444499***********....33333..... PP

                                       HHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE...CEEETHHHHHHHHHHHSCHHHHCC.......HHHHHHHHH CS
                       Metallophos  90 ifsepwrsdaevfnnlplaslgsgslkvlllhGg...spellvsldklgslnleleapepg.......dewlkdlek 156
                                          ++++ +a+++ ++pl         v+ l G    s            ++ ++++++p+       ++ l++++ 
  gi|320100748|ref|YP_004176340.1| 147 ---DIIKAYADKGVIYPLER-------VVELQGVeivS----------SPFVNPTPWKTPReleekelEKHLEKQVS 203
                                       ...45566667777777766.......44444442221..........11222233333333343335555555666 PP

                                       HTTCSEEEEEE.SSESS.....................CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 157 rekadwvivlg.Hsply.....................rgsgylfgdealedllkkygvdlvisGHtHv 203
                                       r +++ + v++ H p+y                        + + g++a++++ +++++ + ++GH+H+
  gi|320100748|ref|YP_004176340.1| 204 RLRDPSKAVFNfHAPPYntmldlapkltrdlrvvtvagVPQYEHVGSKAVRKVIERHQPLIGLHGHIHE 272
                                       6666666666658888899999999999999999999999999***************9999******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2382.28
//
Query:       gi|320100749|ref|YP_004176341.1|  [L=279]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.098   12.6   0.0       0.28   11.1   0.0    1.7  2  Clat_adaptor_s  Clathrin adaptor complex small chain


Domain annotation for each model (and alignments):
>> Clat_adaptor_s  Clathrin adaptor complex small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.18   3.3e+03      50      68 ..      99     117 ..      75     125 .. 0.73
   2 ?   11.1   0.0   1.6e-05      0.28     102     136 ..     209     243 ..     207     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.18
                                       EEETTEEEEEEEETTEEEE CS
                    Clat_adaptor_s  50 veledlkviYkryasLYFv 68 
                                       + + + ++iY++  +LY v
  gi|320100749|ref|YP_004176341.1|  99 ALFAGKRLIYHHPGGLYHV 117
                                       5566778999999999976 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 1.6e-05
                                       HHHHCHHHHHHHHHCCEETTEES---HHHHHHCHH CS
                    Clat_adaptor_s 102 dlvfnfekvylildEivsgGeiletskkevlkrve 136
                                       d v n+ kv +il+E v+ G+i+e++ + +  r++
  gi|320100749|ref|YP_004176341.1| 209 DAVVNIGKVKDILAEAVKQGKIQEADATLITGRLD 243
                                       7799**********************998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2026.32
//
Query:       gi|320100750|ref|YP_004176342.1|  [L=523]
Description: family 5 extracellular solute-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-97  325.5   0.7      5e-97  325.2   0.7    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.056   13.0   0.1        3.2    7.2   0.1    2.4  2  OpuAC      Substrate binding domain of ABC-type glycine betai


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 !  325.2   0.7  5.6e-101     5e-97       2     376 ..      85     444 ..      84     445 .. 0.95

  Alignments for each domain:
  == domain 1  score: 325.2 bits;  conditional E-value: 5.6e-101
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       +vp+LAes w++s+D  t+tfkLR g+kFsDGtpltA Dvv s+er+++ ++ + +  + +    +++v+a+dd+tv
  gi|320100750|ref|YP_004176342.1|  85 IVPGLAES-WSTSQDQMTWTFKLRSGLKFSDGTPLTARDVVRSIERVMRINGDPAWLVTDF----VENVTAPDDVTV 156
                                       89******.799********************************************99995....************ PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEE CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldri 155
                                       +f+l kp+++fl+ll+ +p+ ++    +k+++++ d+++   g GPY++++f+++ +i+le np+Y+ g+kpk   i
  gi|320100750|ref|YP_004176342.1| 157 VFKLRKPTPYFLSLLTTPPYFPV---NPKYAQDKVDSDQTAGGAGPYRIASFQRDVEIRLEPNPYYY-GEKPKAPII 229
                                       ***********************...46666666677777777***********************9.9***99888 PP

                                       EEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS CS
                         SBP_bac_5 156 efkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAi 231
                                       + k+  +s+a ++al+sGeid++   ++psdi +lk  +++kv +e pg+ + y+ +Nt+ +p ++k vRqAl+ Ai
  gi|320100750|ref|YP_004176342.1| 230 IKKYG-SSSALRLALESGEIDVAwRTLNPSDIIALKSRSDVKV-IEVPGTFIRYICLNTRLDPTSNKLVRQALAAAI 304
                                       88887.999999999*****99878999***************.********************************* PP

                                       -HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSH CS
                         SBP_bac_5 232 DreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasgsp 308
                                       +r ei++++l+g ++p +s++p +++++   +k++y ++++e A+ lL +aG+  +++  +     +l ++ + ++ 
  gi|320100750|ref|YP_004176342.1| 305 NRSEIIEVALKGAGQPLYSMIPVGMWSYVSVFKEKYGDGNLELARSLLRQAGFSESKKLTI-----ELWYTPTHYGD 376
                                       ********************************************************99887.....899999999** PP

                                       HHHHHHHHHHHHHHHTT.EEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTCTT CS
                         SBP_bac_5 309 aekaiaeliqqqlkkiG.ikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsssgag 376
                                       +ek++a+++++ql+k G i+v+vk+ +w +ty +++++g++ m+llgw++dy dpd+++ pfl+s++++
  gi|320100750|ref|YP_004176342.1| 377 TEKDVAAILKEQLEKTGlITVTVKSAEW-STYVDYARKGNMMMYLLGWYPDYLDPDDYTTPFLKSTANS 444
                                       ****************************.***********************************99876 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0    0.0063        56      37      57 ..     234     254 ..     230     312 .. 0.84
   2 ?    7.2   0.1   0.00036       3.2      16      78 ..     381     445 ..     375     482 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0063
                                       ESHHHHHHHHHTTSSSEEEEE CS
                             OpuAC  37 gstavlfaalasGdiDvypee 57 
                                       gs+ +l+ al+sG+iDv++  
  gi|320100750|ref|YP_004176342.1| 234 GSSSALRLALESGEIDVAWRT 254
                                       556899***********9955 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH..HHHHHHHHHHHHEEEE CS
                             OpuAC  16 laeilkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgta..yeaykkaveekkglev 78 
                                       +a+ilk+ lek G+ +v++ +++   +++   ++G++ +y+ +w +     ++y + + + +   +
  gi|320100750|ref|YP_004176342.1| 381 VAAILKEQLEKTGLiTVTVKSAEW-STYVDYARKGNMMMYLLGWYPDYldPDDYTTPFLKSTANSW 445
                                       689***********7777777776.*******************9976664444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3778.68
//
Query:       gi|320100751|ref|YP_004176343.1|  [L=338]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-41  141.7  12.6    2.1e-41  141.7  12.6    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.9   0.1    0.0091   1.6e+02      23      44 ..       9      37 ..       6      86 .. 0.75
   2 !  141.7  12.6   1.2e-45   2.1e-41       1     185 []     119     338 .]      99     338 .] 0.98

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.0091
                      BPD_transp_1 23 liivllslPsfvlaillvlvf.......v 44
                                      +i +l+ +P+++++  lv+++        
  gi|320100751|ref|YP_004176343.1|  9 VIRALMIVPTVLILYTLVFIVlrvlpgdP 37
                                      67889999999988888865444444441 PP

  == domain 2  score: 141.7 bits;  conditional E-value: 1.2e-45
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       g+ +G+ aa++ +++ d ++r+++iv +sl + +l+i l++vf                                  
  gi|320100751|ref|YP_004176343.1| 119 GLSTGLAAAVKNRSRMDAAMRVYSIVSYSLFIPILGITLQYVFgvllkilptggrlsaryyvepvtgfmlidtliag 195
                                       567899999******************************************************************** PP

                      BPD_transp_1  44 ...vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglila 117
                                          ++ +++ hl+lp ++l+++ ++ y+rl+r++++++l +d+++ +ra+G ++ +++ +++++n+l+p++t ++l+
  gi|320100751|ref|YP_004176343.1| 196 dpgAFADAVAHLVLPSLTLGIVLSGSYTRLVRNNMVEVLRSDFIRSYRARGIPEGRVL-RYAFKNVLIPVVTYMGLQ 271
                                       ********************************************************55.5***************** PP

                      BPD_transp_1 118 fggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                       ++ llggavl+e+++swpG+g++++e i+++dy++i+ g+v++++++v l++lv+d++++l+dprvr+
  gi|320100751|ref|YP_004176343.1| 272 VAMLLGGAVLTETTFSWPGIGRFIVERIEYRDYTSIQ-GVVVVYALIVGLVSLVVDAVYALIDPRVRY 338
                                       *************************************.****************************95 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:                      421  (0.0234815); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2651.99
//
Query:       gi|320100752|ref|YP_004176344.1|  [L=284]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   79.2   9.8    3.1e-22   79.2   9.8    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
    1.2e-05   25.2   3.5    1.2e-05   25.2   3.5    3.5  4  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.12   1.1e+03     109     125 ..      22      38 ..       3      53 .. 0.58
   2 !   79.2   9.8   3.4e-26   3.1e-22       1     183 [.     100     282 ..     100     284 .] 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.12
                      BPD_transp_1 109 piitglilafggllgga 125
                                       ++++gl+++++++l + 
  gi|320100752|ref|YP_004176344.1|  22 MAAAGLAIVSTIALMAV 38 
                                       33333333333333332 PP

  == domain 2  score: 79.2 bits;  conditional E-value: 3.4e-26
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g++lG++++ ++++ ld++l+++++ ++++Ps+vlai +        +lg + l  +i l++++ + y+r++r++al
  gi|320100752|ref|YP_004176344.1| 100 GVPLGVVSG-YYGGLLDRALSTVMDSIYAFPSLVLAIAVA------AVLGPSPLNvAISLAVVYVPTYFRMVRSEAL 169
                                       89*******.******************************......9********99******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       r  ++ ++ea+r+lG +  +i+   +l+n++ +i+  + l+ + ++   ++l +lg    l+ ++ ++ +g d+ ++
  gi|320100752|ref|YP_004176344.1| 170 RLKNMLFIEAMRLLGYPGHHIMM-SILRNSAQTILVIFTLSTADAVLTEAALGYLG----LSITWPQPDWGLDLRSG 241
                                       ********************777.99******************************....***************** PP

                      BPD_transp_1 154 s...........nggvlalviavlllnlvadilqrlldprv 183
                                       +           +++ +++v++ l + l+  +l ++++ ++
  gi|320100752|ref|YP_004176344.1| 242 QgeiingywwisMFPGFFIVLLSLGFALIGEALSDYFSVKT 282
                                       ********999999999999999999999999999987665 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 !   25.2   3.5   1.3e-09   1.2e-05      15      51 .]      22      59 ..      19      59 .. 0.86
   2 ?   -3.4   0.2       1.1   9.8e+03      23      32 ..      86      95 ..      83     102 .. 0.56
   3 ?   -1.0   0.6       0.2   1.8e+03      23      34 ..     132     143 ..     130     158 .. 0.82
   4 !    4.4   0.4    0.0041        37      19      39 ..     257     277 ..     254     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.3e-09
                            OppC_N 15 lAvvglvilllllliaifaPliaPydp....qdliqnllpP 51
                                      +A +gl+i+ +++l+a++aPli+Pydp      +   ++pP
  gi|320100752|ref|YP_004176344.1| 22 MAAAGLAIVSTIALMAVLAPLISPYDPvarvAPP---YQPP 59
                                      7899**********************98774333...7887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                            OppC_N 23 lllllliaif 32
                                      l +++l a++
  gi|320100752|ref|YP_004176344.1| 86 LYIVVLSAVL 95
                                      4444554544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.2
                            OppC_N  23 lllllliaifaP 34 
                                       +l+++++a+++P
  gi|320100752|ref|YP_004176344.1| 132 VLAIAVAAVLGP 143
                                       577888899987 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0041
                            OppC_N  19 glvilllllliaifaPliaPy 39 
                                       g++i+ll l +a++++ ++ y
  gi|320100752|ref|YP_004176344.1| 257 GFFIVLLSLGFALIGEALSDY 277
                                       7899999999*****999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2094.59
//
Query:       gi|320100753|ref|YP_004176345.1|  [L=313]
Description: oligopeptide/dipeptide ABC transporter ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  105.6   0.0    3.8e-30  105.2   0.0    1.2  1  ABC_tran      ABC transporter
    8.7e-21   74.2   0.1    1.4e-20   73.5   0.1    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    7.7e-06   25.5   0.3    5.6e-05   22.7   0.3    1.9  1  SMC_N         RecF/RecN/SMC N terminal domain
    8.3e-06   25.8   1.6    0.00045   20.1   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.1e-05   23.6   0.0    0.00026   20.7   0.0    2.1  2  AAA_29        P-loop containing region of AAA domain
    0.00071   19.4   0.3       0.19   11.4   0.1    2.1  2  AAA_30        AAA domain
     0.0045   16.2   0.0     0.0093   15.2   0.0    1.4  1  NB-ARC        NB-ARC domain
  ------ inclusion threshold ------
      0.018   13.9   0.3       0.63    8.8   0.1    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.018   15.4   0.1      0.027   14.9   0.1    1.5  1  AAA_16        AAA ATPase domain
      0.034   13.2   0.1       0.29   10.2   0.0    2.0  2  T2SSE         Type II/IV secretion system protein
      0.051   13.5   0.0      0.099   12.6   0.0    1.4  1  NACHT         NACHT domain
      0.077   12.4   0.0       0.68    9.3   0.0    2.0  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
        0.1   12.5   0.0       0.29   11.1   0.0    1.7  2  NTPase_1      NTPase
        0.1   12.8   0.0       0.31   11.3   0.0    1.7  2  AAA_22        AAA domain
       0.11   11.8   0.1        1.7    7.9   0.1    2.0  2  DUF4941       Domain of unknown function (DUF4941)
       0.12   12.0   0.1        2.6    7.7   0.0    2.0  2  AAA_15        AAA ATPase domain
       0.15   11.9   0.1       0.27   11.1   0.1    1.3  1  RsgA_GTPase   RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.0   3.6e-33   3.8e-30       2     136 ..      22     177 ..      21     178 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 3.6e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..x RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe..p 68 
                                       + vs+++kege v ivGe+G+GKStL+  + +l+ p      G+i ++g+dl +    + +++   +ig+++q+  +
  gi|320100753|ref|YP_004176345.1|  22 DGVSIEVKEGEWVSIVGESGSGKSTLAYSIVNLVPPpgriVGGSIVFKGRDLLKlpesEMRSIRGGRIGFVFQDplT 98 
                                       789********************************999999999**********999888999999********999 PP

                                       -S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       +l+p  tv+++           + +e +eka++ l+ +++++++vks p++LSgGq+qr+a+a+a++ kp+l+++DE
  gi|320100753|ref|YP_004176345.1|  99 SLDPLRTVGDQlseviethqglNHKEALEKAARLLEEVGIPASRVKSYPHQLSGGQRQRIAIAMAIALKPDLVIADE 175
                                       9**************999999988888999999999999999*********************************** PP

                                       TT CS
                                       xx RF
                          ABC_tran 135 pt 136
                                       pt
  gi|320100753|ref|YP_004176345.1| 176 PT 177
                                       *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 !   73.5   0.1   1.3e-23   1.4e-20       1      65 []     228     291 ..     228     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 1.3e-23
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+g s++++++p HPYT++L++svp+l + k+ +++i+g++p+l++ ++GC+F+pRCp+a+eeC
  gi|320100753|ref|YP_004176345.1| 228 VEYGASRDIVERPGHPYTAGLIESVPDLWSDKQ-VKSIPGNPPDLRDPPKGCRFHPRCPYASEEC 291
                                       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 !   22.7   0.3   5.3e-08   5.6e-05      26     208 ..      33     219 ..      20     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.3e-08
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH...CCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrse...klsdlihk.skekasvkkaeveitfdnedkklkiekeevs 98 
                                         +ivG+ GSGKs l  +i  +      + +  +   k +dl++  ++e +s+  +++  +f+++  +    ++  +
  gi|320100753|ref|YP_004176345.1|  33 WVSIVGESGSGKSTLAYSIVNLVP-PPGRIVGGSivfKGRDLLKLpESEMRSIRGGRIGFVFQDPLTS---LDPLRT 105
                                       678****************76654.55655555422245778877677899999********999888...566677 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                       +  ++++  e++  +n ke+ + + ++lle++gi  +       +LSgG+++ +a+a+ +A++      l++ De  
  gi|320100753|ref|YP_004176345.1| 106 VGDQLSEVIETHQGLNHKEALE-KAARLLEEVGIPASrvksyphQLSGGQRQRIAIAMAIALKP----DLVIADEPT 177
                                       7777777777788888877654.456788888887777777777**************999853....49999**** PP

                                       TTS-HHHHHHHHHHHH.HHCTTSEEEEE-SSHHHCCC-.SCE CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxx RF
                             SMC_N 169 aaLDeknvkkvaellk.eksknaQfivislreemleka.dkl 208
                                        aLD     ++ +l+   k + + +i i+++  + ++  d++
  gi|320100753|ref|YP_004176345.1| 178 TALDVIVQDQIMDLFTgIKASGSSIILITHDIALASERsDRI 219
                                       *****9999999999843444599999999877765542444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.017        18       4      19 ..      36      51 ..      34      89 .. 0.84
   2 !   20.1   0.1   4.3e-07   0.00045     184     301 ..     125     211 ..     108     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                            AAA_21  4 liGpNgsGKSnLLdal 19
                                      ++G  gsGKS+L + +
  gi|320100753|ref|YP_004176345.1| 36 IVGESGSGKSTLAYSI 51
                                      8***********8776 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4.3e-07
                            AAA_21 184 llqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsl 260
                                        l++  r l +v+i++s  +                              +++lS G+++ +a++ a++  +   +l
  gi|320100753|ref|YP_004176345.1| 125 ALEKAARLLEEVGIPASRVKS----------------------------YPHQLSGGQRQRIAIAMAIALKP---DL 170
                                       555555555555555555543............................46899*******99999999877...9* PP

                            AAA_21 261 lliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                       ++ DEp + L+  ++  +++l+  ++++ g+ +il TH+  l
  gi|320100753|ref|YP_004176345.1| 171 VIADEPTTALDVIVQDQIMDLFtGIKAS-GSSIILITHDIAL 211
                                       **********************744444.8********9776 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      13      49 ..      22      58 ..      19      62 .. 0.81
   2 ?    0.3   0.0      0.57     6e+02      24      39 ..     189     204 ..     178     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      dg +ie+++ + + ++G+sGsGKSTl  +i  l  p+
  gi|320100753|ref|YP_004176345.1| 22 DGVSIEVKEGEWVSIVGESGSGKSTLAYSIVNLVPPP 58
                                      778899997779**************88777776665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.57
                            AAA_29  24 atlltGpsGsGKSTll 39 
                                       + l+tG   sG S +l
  gi|320100753|ref|YP_004176345.1| 189 MDLFTGIKASGSSIIL 204
                                       679********99887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0079       8.4      19      42 ..      32      55 ..      24      65 .. 0.79
   2 !   11.4   0.1   0.00018      0.19      58     122 ..     128     205 ..     111     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0079
                            AAA_30 19 rvavltGpAGtGKttalkalreaw 42
                                       ++ ++G  G+GK+t+  ++++++
  gi|320100753|ref|YP_004176345.1| 32 EWVSIVGESGSGKSTLAYSIVNLV 55
                                      477899*********998887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00018
                            AAA_30  58 aAkvLaeelgieastiakllkrlk.........grarlepg.tllivDEagmv....dtkqlaallkaaekagakvi 120
                                        A++L ee+gi+as+++++ ++l          + ++++ + +l+i DE   +     ++q+ +l++ ++++g ++i
  gi|320100753|ref|YP_004176345.1| 128 KAARLLEEVGIPASRVKSYPHQLSggqrqriaiA-MAIALKpDLVIADEPTTAldviVQDQIMDLFTGIKASGSSII 203
                                       5778888****************9******9964.5677777*******9887766678888999999999999998 PP

                            AAA_30 121 lv 122
                                       l+
  gi|320100753|ref|YP_004176345.1| 204 LI 205
                                       87 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.8e-06    0.0093      17      42 ..      30      53 ..      17      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.8e-06
                                      TSCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqiln 42
                                      e +  +v++vG  G+GK+tla +i+n
  gi|320100753|ref|YP_004176345.1| 30 EGE--WVSIVGESGSGKSTLAYSIVN 53
                                      555..9*****************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 ?    3.1   0.0     0.032        33     237     264 ..      21      51 ..      12      60 .. 0.79
   2 ?    8.8   0.1    0.0006      0.63     322     366 ..     149     193 ..     140     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.032
                                       EEEEEE..-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 237 vsGmgi..pkG.vtlIvGggfhGKsTLLeAl 264
                                       v G+ i  ++G  + IvG    GKsTL  ++
  gi|320100753|ref|YP_004176345.1|  21 VDGVSIevKEGeWVSIVGESGSGKSTLAYSI 51 
                                       666554227788889************8777 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0006
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelv 366
                                       + SG   q  +i+ a+ ++ +l++ DE t+A   +++D+ m+  +
  gi|320100753|ref|YP_004176345.1| 149 QLSGGQRQRIAIAMAIALKPDLVIADEPTTALDVIVQDQIMDLFT 193
                                       56999999*********************************8664 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   2.6e-05     0.027      23      56 ..      30      66 ..      14     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif...l 56
                                      ++e v ++GesG+GKs+l+ ++ + +   g i+   +
  gi|320100753|ref|YP_004176345.1| 30 EGEWVSIVGESGSGKSTLAYSIVNLVPPPGRIVggsI 66
                                      34899*************9888876666644444444 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 ?   10.2   0.0   0.00027      0.29     132     161 ..      34      62 ..      22      63 .. 0.83
   2 ?    0.6   0.0      0.22   2.3e+02     120     162 ..     178     221 ..     154     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                             T2SSE 132 ilvsGgTgsGKttllyallkeinksderiv 161
                                       + + G  gsGK+tl+y++++ ++    riv
  gi|320100753|ref|YP_004176345.1|  34 VSIVGESGSGKSTLAYSIVNLVPPP-GRIV 62 
                                       557899***************9988.7765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                             T2SSE 120 evlrkavrerglilvsGgTgsGKttllyal.lkeinksderivt 162
                                        +l   v+ + + l++G   sG +++l +  ++   ++++riv+
  gi|320100753|ref|YP_004176345.1| 178 TALDVIVQDQIMDLFTGIKASGSSIILITHdIALASERSDRIVV 221
                                       5677788899999***********99965515555566888875 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   9.4e-05     0.099       3      22 ..      34      53 ..      32      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.4e-05
                                      EEEEC-TTTCHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklal 22
                                      v + Ge+GsGK+tL+ +++ 
  gi|320100753|ref|YP_004176345.1| 34 VSIVGESGSGKSTLAYSIVN 53
                                      6799************9986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00064      0.68      17      48 ..      26      57 ..      11      61 .. 0.79
   2 ?    0.7   0.0      0.28     3e+02     174     199 ..     139     164 ..     128     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00064
                      Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsllpp 48
                                      i +  g  + +vG +GsGK+ la  + +l+pp
  gi|320100753|ref|YP_004176345.1| 26 IEVKEGEWVSIVGESGSGKSTLAYSIVNLVPP 57
                                      555555667799******************98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.28
                      Mg_chelatase 174 sekeierYlsklsgplldRidlqvev 199
                                        ++++++Y ++lsg    Ri + +++
  gi|320100753|ref|YP_004176345.1| 139 PASRVKSYPHQLSGGQRQRIAIAMAI 164
                                       5678999*************999987 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00027      0.29       2      39 ..      34      71 ..      33      94 .. 0.89
   2 ?   -2.3   0.0       3.4   3.6e+03      66     103 ..     138     175 ..     119     176 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                      v i G++G+GK+Tl   +++l+   g  vgG ++ + r
  gi|320100753|ref|YP_004176345.1| 34 VSIVGESGSGKSTLAYSIVNLVPPPGRIVGGSIVFKGR 71
                                      5689**************************98876655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                                       --SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE-- CS
                          NTPase_1  66 kreprvgkyvvdvesfeelalealrkalseadviviDE 103
                                           rv++y  ++   ++  +++      ++d+++ DE
  gi|320100753|ref|YP_004176345.1| 138 IPASRVKSYPHQLSGGQRQRIAIAMAIALKPDLVIADE 175
                                       44556666666665544443333333336777777777 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    0.0003      0.31       8      27 ..      34      53 ..      27      61 .. 0.84
   2 ?   -1.7   0.0       3.1   3.3e+03      60      99 ..     132     175 ..     105     203 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                            AAA_22  8 lvvtGesGtGKTtllrrlle 27
                                      + ++GesG+GK+tl+  +++
  gi|320100753|ref|YP_004176345.1| 34 VSIVGESGSGKSTLAYSIVN 53
                                      579***********976665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                            AAA_22  60 llralglelka...erlsseell.ealeqalraravielliiDE 99 
                                       ll+++g ++++   ++++++    ++++ a+  + ++ l+i DE
  gi|320100753|ref|YP_004176345.1| 132 LLEEVGIPASRvksYPHQLSGGQrQRIAIAMAIALKPDLVIADE 175
                                       34444444444544344444333333333333333356666665 PP

>> DUF4941  Domain of unknown function (DUF4941)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.12   1.3e+02      80     112 ..      46      80 ..       9     112 .. 0.79
   2 ?    7.9   0.1    0.0016       1.7      43     103 ..     167     226 ..     160     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                           DUF4941  80 klaemivediseigeii..evvyeGenklevseee 112
                                       +la  iv+ +   g+i+   +v++G++ l++ e e
  gi|320100753|ref|YP_004176345.1|  46 TLAYSIVNLVPPPGRIVggSIVFKGRDLLKLPESE 80 
                                       67778888888888888556*********998876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                           DUF4941  43 senllvlDgvkkksekvplddvlklF.gidyikegntlklaemivediseigeiievvyeGe 103
                                       + +l++ D+ + + + +  d++++lF gi+    g +++l++  +   se  + i+v+y G+
  gi|320100753|ref|YP_004176345.1| 167 KPDLVIADEPTTALDVIVQDQIMDLFtGIK--ASGSSIILITHDIALASERSDRIVVMYGGK 226
                                       568999********************5676..589************************997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0025       2.6      14      43 ..      21      51 ..      19      55 .. 0.83
   2 ?    2.4   0.0     0.097     1e+02     287     365 ..     133     208 ..      98     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0025
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileal 43
                                       + v+i+++e     ++G+ +sGKS++++ +
  gi|320100753|ref|YP_004176345.1| 21 VDGVSIEVKEGeWVSIVGESGSGKSTLAYSI 51
                                      556788888887899************9988 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.097
                            AAA_15 287 k.......ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                               + ++++ ++ + G+++ + +++ i+ + +          ++ +EP + L    q ++++l+  +  +++
  gi|320100753|ref|YP_004176345.1| 133 LeevgipaSRVKSYPHQLSGGQRQRIAIAMAIALKPDL---------VIADEPTTALDVIVQDQIMDLFTGIKASGS 200
                                       14444666888999999999*******99999876555.........888999999999999999999999888888 PP

                            AAA_15 357 tQviitTHS 365
                                         +i+ TH 
  gi|320100753|ref|YP_004176345.1| 201 -SIILITHD 208
                                       .88888885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00026      0.27      97     119 ..      28      51 ..       6      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                                       CTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinal 119
                                       +k+ + + +vG+SG GKStL  ++
  gi|320100753|ref|YP_004176345.1|  28 VKEgEWVSIVGESGSGKSTLAYSI 51 
                                       45448899************8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2195.25
//
Query:       gi|320100754|ref|YP_004176346.1|  [L=327]
Description: oligopeptide/dipeptide ABC transporter ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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
    1.7e-20   73.3   0.1    2.9e-20   72.6   0.1    1.4  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
      1e-05   25.5   0.5     0.0066   16.3   0.0    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
     0.0026   18.1   1.2       0.05   13.9   1.2    2.2  1  AAA_22     AAA domain
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.029   14.1   0.1    1.3  1  AAA_29     P-loop containing region of AAA domain
      0.053   13.9   0.7       0.11   12.9   0.7    1.4  1  AAA_16     AAA ATPase domain
       0.15   10.9   0.0        0.2   10.4   0.0    1.1  1  DLIC       Dynein light intermediate chain (DLIC)
       0.18   11.1   0.7       0.56    9.5   0.1    1.9  2  ATPase     KaiC
       0.19   12.0   0.0       0.34   11.2   0.0    1.4  1  IFT81_CH   Intraflagellar transport 81 calponin homology doma


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   1.8e-35   3.5e-32       2     136 ..      35     186 ..      34     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 1.8e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpel 74 
                                       + v+l++++ge++ ivGe+G+GK+tL ++++gl++p +G++l+ gk+l+e  ++++++r + +++ q+  ++l+p++
  gi|320100754|ref|YP_004176346.1|  35 DGVTLDVYRGEVLSIVGESGSGKTTLGRIMIGLEEPSKGTVLFHGKPLHEllEREKHVRLKAQMIYQDpySSLDPRV 111
                                       789*****************************************************************999****** PP

                                       BHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +++++              e++ ++ ++l+ +gl+  +++v ++ p++LSgGq+qr+a+ara+l +p++l++DEp 
  gi|320100754|ref|YP_004176346.1| 112 KIGDQlakplvihrlanpeEARIRVMEMLKDVGLTP-PEEVFERYPHQLSGGQRQRIAIARAMLVEPEFLVADEPV 186
                                       ***************998878888999******999.99999*********************************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 !   72.6   0.1   1.4e-23   2.9e-20       1      65 []     238     302 ..     238     302 .. 0.99

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.4e-23
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE g+s++++++plHPYT+aLl++vp+++ +k +  ki ge p++ ++++GC+F+pRCp+a+eeC
  gi|320100754|ref|YP_004176346.1| 238 VEVGDSRRVLENPLHPYTRALLSAVPSIHGRKIARLKITGEIPDPFNIPSGCRFHPRCPYASEEC 302
                                       8**************************************************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0012       2.3       4      22 ..      49      67 ..      46      94 .. 0.83
   2 !   16.3   0.0   3.3e-06    0.0066     209     301 ..     123     221 ..      82     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                            AAA_21  4 liGpNgsGKSnLLdaldll 22
                                      ++G  gsGK++L +++ +l
  gi|320100754|ref|YP_004176346.1| 49 IVGESGSGKTTLGRIMIGL 67
                                      9*************99555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.3e-06
                            AAA_21 209 iasvderlrer........gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrr 277
                                       i + ++++  r        +v +  ++   e+ +++lS G+++ +a++ a+l  +    +l+ DEp + ++ +l + 
  gi|320100754|ref|YP_004176346.1| 123 IHRLANPEEARirvmemlkDVGLTPPEEVFERYPHQLSGGQRQRIAIARAMLVEP---EFLVADEPVSMIDVSLRAG 196
                                       33333333333555577779999999999***************99999999988...9****************** PP

                            AAA_21 278 llell.kelsrngaQviltTHSpll 301
                                       +lell + ++r g   ++ TH+ ++
  gi|320100754|ref|YP_004176346.1| 197 ILELLmRFKERYGLTMVFITHDLSV 221
                                       **999888888**********9865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.2   2.5e-05      0.05       6     128 ..      45     215 ..      41     225 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee............................................e 38 
                                        +l ++GesG+GKTtl r +    +      +                                             
  gi|320100754|ref|YP_004176346.1|  45 EVLSIVGESGSGKTTLGRIMIGLEEPS----KgtvlfhgkplhellerekhvrlkaqmiyqdpyssldprvkigdqL 117
                                       5789************99888775321....1234565555555555444333333333333333333333333332 PP

                            AAA_22  39 rpevvfvtlpsstsskdllrellralglelka...............................erlsseellealeq 84 
                                                                   +l                                 ++++++      ++
  gi|320100754|ref|YP_004176346.1| 118 --------------------------AKPLVIhrlanpeearirvmemlkdvgltppeevferYPHQLSGGQ--RQR 166
                                       ..........................2222224444444444444444444433333355433333332222..222 PP

                            AAA_22  85 alrarav...ielliiDEaqhlr....seealeeLrsllnlsrkgvqliLv 128
                                        + ara+   +e+l+ DE   ++    ++ +le L ++ +  r+g++++++
  gi|320100754|ref|YP_004176346.1| 167 IAIARAMlvePEFLVADEPVSMIdvslRAGILELLMRFKE--RYGLTMVFI 215
                                       2222222446777777776665546333777777766666..777777766 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   1.5e-05     0.029      13      38 ..      35      60 ..      32      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                      dg t+++ + ++  ++G+sGsGK+Tl
  gi|320100754|ref|YP_004176346.1| 35 DGVTLDVYRGEVLSIVGESGSGKTTL 60
                                      67888888666999***********8 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   0.7   5.5e-05      0.11       3      41 ..      25      61 ..      24      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslv 41
                                       GR++ ++++  +  +v +g  e++ ++GesG+GK++l 
  gi|320100754|ref|YP_004176346.1| 25 RGRRRVVKAVDGVTLDVYRG--EVLSIVGESGSGKTTLG 61
                                      68888888888877778777..79*************95 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0001       0.2      29      57 ..      48      76 ..      41     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                              DLIC 29 lvlGedgsGkttliaklqGveeekkGrGl 57
                                       ++Ge+gsGkttl   + G+ee+ kG  l
  gi|320100754|ref|YP_004176346.1| 48 SIVGESGSGKTTLGRIMIGLEEPSKGTVL 76
                                      589***********************876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00028      0.56      17      36 ..      42      61 ..      31      73 .. 0.90
   2 ?   -0.7   0.1      0.37   7.4e+02     140     163 ..     193     217 ..     187     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00028
                            ATPase 17 pegrvvlitGepGtGKtifa 36
                                      ++g+v  i+Ge+G+GKt+++
  gi|320100754|ref|YP_004176346.1| 42 YRGEVLSIVGESGSGKTTLG 61
                                      6899**************98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.37
                            ATPase 140 aReilrqlvrvl.kklgvTailvse 163
                                       +R+ + +l++++ + +g+T ++++ 
  gi|320100754|ref|YP_004176346.1| 193 LRAGILELLMRFkERYGLTMVFITH 217
                                       5676777777775667888888876 PP

>> IFT81_CH  Intraflagellar transport 81 calponin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.34      52      95 ..     125     167 ..     114     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                          IFT81_CH  52 reespeetalrilelLrilkykppedleleefrqglvegekevi 95 
                                       r ++pee+ +r++e+L+ +  +ppe++  e++ ++l  g+++ i
  gi|320100754|ref|YP_004176346.1| 125 RLANPEEARIRVMEMLKDVGLTPPEEV-FERYPHQLSGGQRQRI 167
                                       5589**********************9.9**********99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 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:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2408.59
//
Query:       gi|320100755|ref|YP_004176347.1|  [L=245]
Description: phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-11   44.2   0.0    2.4e-11   43.4   0.0    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0036   16.8   0.0     0.0058   16.1   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.069   12.6   0.0       0.11   12.0   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase
       0.36   11.0   1.9         18    5.6   0.0    3.6  4  AbiEi_4       Transcriptional regulator, AbiEi antitoxin


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 !   43.4   0.0   5.4e-15   2.4e-11      31     128 ..     115     220 ..      97     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 5.4e-15
                                       EEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE................EE----TTSEEEEE-SEESS CS
                      Pribosyltran  31 dvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes........rlledpagkkVliVDDildt 99 
                                        +v+++++ G+p+a+++a  ++++l++  ++   + ++  +a  +s  +         + ++ +  +VliVDD+l t
  gi|320100755|ref|YP_004176347.1| 115 NTVATVESDGIPLATRIAEVMNAKLVVAKHRPEIGAKGYHQASYISRDPpaytilftPADALSRRDRVLIVDDLLNT 191
                                       589***********************************999999998889******9999999************** PP

                                       SHHHHHHHHHHHCC-BSEEEEEEEEE-HH CS
                      Pribosyltran 100 GgTllaalelLkekgpeevriavlvdkpa 128
                                       G+T +a l+l+k++g++ v++  ++  ++
  gi|320100755|ref|YP_004176347.1| 192 GKTSRALLQLVKAAGAKPVGLFSIISIGD 220
                                       *****************999988876555 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-06    0.0058     119     180 ..     175     237 ..     156     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                           UPRTase 119 i..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefp.kvkvvt 180
                                          ++++vl++D +++TG++  a +ql+k +g   + + + s+++     +r++++   k+ vv+
  gi|320100755|ref|YP_004176347.1| 175 AlsRRDRVLIVDDLLNTGKTSRALLQLVKAAG--AKPVGLFSIISIGDSWHRILSRELeKIYVVL 237
                                       4446788***********************55..6789999999998888887765443676665 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.11     111     160 ..     169     220 ..     163     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                          PRTase_2 111 yaedeellaaakelvLvDDEistGktalnliralqeklpr..kryvvvslvd 160
                                       + + +++l++++++++vDD + tGkt  +l++ ++++  +    + ++s+ d
  gi|320100755|ref|YP_004176347.1| 169 LFTPADALSRRDRVLIVDDLLNTGKTSRALLQLVKAAGAKpvGLFSIISIGD 220
                                       55667899999****************9999988877443224555555554 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0039        18       5      36 ..      17      49 ..      15      50 .. 0.90
   2 ?   -0.2   0.1      0.26   1.2e+03      36      47 ..      76      87 ..      74      89 .. 0.85
   3 ?   -2.6   0.0       1.5   6.6e+03      27      36 ..     104     113 ..     101     118 .. 0.60
   4 ?    1.8   0.1      0.06   2.7e+02       5      34 ..     174     203 ..     171     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0039
                           AbiEi_4  5 elasrqvGlfttrelea.aGispsalrrLvrkG 36
                                      +l+  ++ l  +r le+  G+++++l r+vr+G
  gi|320100755|ref|YP_004176347.1| 17 DLLKAYKELMDYRMLEEiTGLDTQSLWRYVRRG 49
                                      6778888999999*******************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                           AbiEi_4 36 GwLvrlrrGvYa 47
                                       +Lv ++ G+Y 
  gi|320100755|ref|YP_004176347.1| 76 RELVEVGNGIYG 87
                                      689********5 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.5
                           AbiEi_4  27 salrrLvrkG 36 
                                        a r+++++G
  gi|320100755|ref|YP_004176347.1| 104 VAFREFRDCG 113
                                       4556666655 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.06
                           AbiEi_4   5 elasrqvGlfttreleaaGispsalrrLvr 34 
                                       + +sr+  ++ +++l   G++ +al  Lv+
  gi|320100755|ref|YP_004176347.1| 174 DALSRRDRVLIVDDLLNTGKTSRALLQLVK 203
                                       567888899999*************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1904.09
//
Query:       gi|320100756|ref|YP_004176348.1|  [L=138]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 963.86
//
Query:       gi|320100757|ref|YP_004176349.1|  [L=82]
Description: ferredoxin [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-13   49.8   1.3    4.9e-13   49.6   1.3    1.1  1  Fer4_15   4Fe-4S single cluster domain
    7.7e-12   45.6   1.1      1e-11   45.2   1.1    1.2  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
       0.74    9.7   6.2        6.3    6.8   0.2    2.5  3  Fer4      4Fe-4S binding domain
       0.87    9.8   6.1        1.1    9.4   0.7    2.4  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   1.3   1.1e-16   4.9e-13       1      66 []       6      77 ..       6      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.1e-16
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfelded.glasvl.....lddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      V v+r+ C  cg+ va+++evfel +d g+++v+      +++e++ g +p ++ e+a+ Aa+ CPv AI++
  gi|320100757|ref|YP_004176349.1|  6 VIVNRSICLACGAAVAACSEVFELGDDnGKNRVVakysvETTSEVSVGVIPGELYECAKSAAEICPVSAISI 77
                                      789*********************9965***99999998667899999**********************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 !   45.2   1.1   2.3e-15     1e-11       1      57 [.       8      76 ..       8      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.3e-15
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqpts............eeekadaeeAadaCPvesIg 57
                                      V+r+ C acga v+++ +vFe  d+ g+ +v+++ +              e++++a++Aa+ CPv++I 
  gi|320100757|ref|YP_004176349.1|  8 VNRSICLACGAAVAACSEVFELGDDNGKNRVVAKYSVettsevsvgvipGELYECAKSAAEICPVSAIS 76
                                      8999***************************995333344566677887889****************7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0019       8.6       1      13 [.       6      18 ..       6      18 .. 0.90
   2 ?   -3.0   0.1       1.7   7.8e+03      13      16 ..      22      25 ..      20      26 .. 0.58
   3 ?    6.8   0.2    0.0014       6.3      15      24 .]      67      76 ..      67      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0019
                                      EEEETTTSSS-TH CS
                              Fer4  1 vvideekCigCGa 13
                                      v+++ + C +CGa
  gi|320100757|ref|YP_004176349.1|  6 VIVNRSICLACGA 18
                                      689*********7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                                      HHHH CS
                              Fer4 13 aCve 16
                                      aC e
  gi|320100757|ref|YP_004176349.1| 22 ACSE 25
                                      4655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0014
                                      HHHSTTTEEE CS
                              Fer4 15 vevCPvgAIt 24
                                      +e+CPv AI+
  gi|320100757|ref|YP_004176349.1| 67 AEICPVSAIS 76
                                      689*****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 ?    9.4   0.7   0.00026       1.1       1      19 [.       5      23 ..       5      26 .. 0.79
   2 ?    3.1   0.5     0.026   1.2e+02      17      24 .]      68      75 ..      60      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00026
                            Fer4_6  1 vveidpdkCigCgdCvrvC 19
                                      +v ++++ C+ Cg+ v++C
  gi|320100757|ref|YP_004176349.1|  5 KVIVNRSICLACGAAVAAC 23
                                      5889*********955555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.026
                            Fer4_6 17 rvCPegai 24
                                       +CP  ai
  gi|320100757|ref|YP_004176349.1| 68 EICPVSAI 75
                                      68**9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); 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:                         4  (0.000223102); expected 0.2 (1e-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: 596.14
//
Query:       gi|320100758|ref|YP_004176350.1|  [L=90]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   13.0   5.6       0.36   11.3   5.6    1.8  1  DUF202       Domain of unknown function (DUF202)
       0.98    9.1   6.2        2.5    7.8   6.2    1.7  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.6     4e-05      0.36      28      60 ..      14      86 ..       2      89 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                            DUF202 28 lrffl........................................tgepsalgkilglilivlgiltllvglv 60
                                      ++ ++                                        ++e  alg++l +++ivl++ltl++g +
  gi|320100758|ref|YP_004176350.1| 14 TAAWRvykgayslhvlaltlwasvlmftvdkayaylvegeafvdaSPESMALGAVLVATAIVLWLLTLAYGKM 86
                                      4444444455555555555555666999999999999999988554444445677777788888888877755 PP

>> 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 ?    7.8   6.2   0.00028       2.5      40      91 ..      36      85 ..       1      90 [] 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00028
                                      HHHHHHHHC.....................TTSCGGHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Oxidored_q2 40 llvlagvftegtlvi........tnpatefadplpqalvLtaivigaaetavgLallvrl 91
                                       +++          +         ++ + f+d  p+ ++L a+ ++ a++  +L+l++  
  gi|320100758|ref|YP_004176350.1| 36 SVLM----------FtvdkayayLVEGEAFVDASPESMALGAVLVATAIVLWLLTLAYGK 85
                                      2222..........14444555589999****************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 686.77
//
Query:       gi|320100759|ref|YP_004176351.1|  [L=123]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0016   18.5   0.5     0.0047   17.1   0.2    1.9  2  MHYT      Bacterial signalling protein N terminal repeat
  ------ inclusion threshold ------
      0.082   12.8   0.6       0.11   12.4   0.6    1.2  1  DUF4013   Protein of unknown function (DUF4013)
       0.21    9.9   0.0       0.22    9.9   0.0    1.1  1  BcsB      Bacterial cellulose synthase subunit


Domain annotation for each model (and alignments):
>> MHYT  Bacterial signalling protein N terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.52   3.1e+03      23      36 ..      33      46 ..      27      51 .. 0.70
   2 !   17.1   0.2   7.9e-07    0.0047      20      55 ..      72     107 ..      61     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.52
                              MHYT 23 ydpaltalSlliai 36
                                      +++ l + Sl++a+
  gi|320100759|ref|YP_004176351.1| 33 WSTMLLGGSLVLAV 46
                                      55556666777776 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.9e-07
                              MHYT  20 pigydpaltalSlliaivasvlAlalavrrrdtrlr 55 
                                        + +++++++ S+ +a++a++l++++ +r++ t++r
  gi|320100759|ref|YP_004176351.1|  72 VMFHEMLYVGGSMSAAVTAAWLGILAYTRSKLTAQR 107
                                       678999********************9999998876 PP

>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   1.8e-05      0.11      10      64 ..       3      59 ..       1     103 [. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                           DUF4013 10 ivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlkafvvslvYl..liplii 64
                                       ++++++lG +v+ lr+ + g+ +    d w+++l+ G  +++v  v+   ++p+  
  gi|320100759|ref|YP_004176351.1|  3 CFITPLVLGVIVEALRRLASGVGRKLRMDIWSTMLLGGSLVLAVEHVWHgeVVPWPP 59
                                      5677888*****************889999*****************9866555444 PP

>> BcsB  Bacterial cellulose synthase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   3.6e-05      0.22     144     193 ..      54     102 ..      15     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.6e-05
                              BcsB 144 llpapffdkrdserlelpivfpaapdpatlqaAgivAswfGaladyrgad 193
                                        +p p f   +++++ +p++f +    +   +A++ A+w+G+la  r  +
  gi|320100759|ref|YP_004176351.1|  54 VVPWPPFLTAMENPADIPVMFHEMLYVGGSMSAAVTAAWLGILAYTR-SK 102
                                       578888888899********************************544.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 900.81
//
Query:       gi|320100760|ref|YP_004176352.1|  [L=227]
Description: SagB-type dehydrogenase domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-23   83.6   0.0    1.9e-23   83.4   0.0    1.1  1  Nitroreductase  Nitroreductase family
  ------ inclusion threshold ------
       0.18   11.4   0.0        6.1    6.4   0.0    2.1  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0   2.1e-27   1.9e-23       2     169 ..      23     205 ..      22     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 2.1e-27
                                       HH--B---B-S----HHHHHHHHHHH..........HTS--GGG---EEEEEE.-CCCH...........HHHHHHH CS
                    Nitroreductase   2 rkRrSiRkFddepvpkeelekileaa..........rraPsagnlqpwrfvvvqdkelr...........yklaeaa 57 
                                       ++RrSiR+F+ e v + +l+ il+a+           + Psag ++p+r+++v  ++             y++++  
  gi|320100760|ref|YP_004176352.1|  23 LSRRSIREFKGEAVRLVDLALILWATygvndpaeglLTTPSAGATYPLRVYLVAGEKGVvdgeayleagvYRYEPRR 99 
                                       69*********************************999***************555555678777777774444444 PP

                                       HHHHHHHHTT-SS-GGGGGGHHHHHHHHHHHHSSEEEEE---TTS---HHHH.HHHHHHHHHHHHHHHHHHHHHHHT CS
                    Nitroreductase  58 lelllkaeaqaelaqryrkeelklkaqkalagapvlivivatldkserkaae.rayryalldagaaaqnllLaAtal 133
                                       + l+ ++  + +   ++      ++ q+ +agapv iv++a +d+  + +++ +++ry  ++ag+a++n +L+Atal
  gi|320100760|ref|YP_004176352.1| 100 HVLVHVRSGDVRGELSR-----AALMQEYVAGAPVSIVLTAVYDETVKVYGRrGRERYVPMEAGHACENTYLMATAL 171
                                       44444444444444443.....49***************88887766666650567999****************** PP

                                       T-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEEEE CS
                    Nitroreductase 134 GlgscpiggfdeaaeevrkllglpdeeeivvliavG 169
                                       G+g++ +g+f +++  v k +g  ++e +++++++G
  gi|320100760|ref|YP_004176352.1| 172 GYGAVAVGAFRDED--VLKAIGAGKGETPLYVVPIG 205
                                       **************..*******************9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0    0.0067        60       3      22 ..      19      38 ..      17      59 .. 0.81
   2 ?    6.4   0.0   0.00068       6.1      80     134 ..     153     208 ..     137     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0067
                                      HHHHHH--B---B--S---H CS
                    TM1586_NiRdase  3 yeaiekRhsvRkYkdealee 22
                                       ea+  R+s+R++k ea++ 
  gi|320100760|ref|YP_004176352.1| 19 EEALLSRRSIREFKGEAVRL 38
                                      689999********999875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS CS
                    TM1586_NiRdase  80 leekaGYygeqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyak 134
                                       + ++aG   e+  L +talG g   vg+  ++ + +++ + kge+ ++v+ +G + 
  gi|320100760|ref|YP_004176352.1| 153 VPMEAGHACENTYLMATALGYGAVAVGAFRDEdVLKAIGAGKGETPLYVVPIGVPV 208
                                       5689***********************99888666778999999999**9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1662.31
//
Query:       gi|320100761|ref|YP_004176353.1|  [L=299]
Description: dihydroorotate oxidase B, catalytic subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-52  176.6   0.0    7.1e-52  176.4   0.0    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
      3e-07   29.9   0.1    1.1e-06   27.9   0.1    1.7  1  Dus           Dihydrouridine synthase (Dus)
     0.0018   17.8   2.7     0.0026   17.3   0.1    2.3  3  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
       0.24   10.3   0.0       0.32    9.8   0.0    1.1  1  DOCK_N        DOCK N-terminus
       0.55    9.2   3.0        1.4    7.8   0.2    2.5  3  IMPDH         IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0     2e-55   7.1e-52       1     293 [.       1     280 [.       1     282 [. 0.89

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 2e-55
                                       GG-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTT.SSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS- CS
                            DHO_dh   1 slatkvlglkfknpiglAaGfdkegeeilkllklg.fgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneG 76 
                                       +l+++v+gl+++ p+++A+G+ +   e l++l+   f+a+  +++t+kp+eG p P +++l +   +lN++Gl n+G
  gi|320100761|ref|YP_004176353.1|   1 MLEVSVAGLRLEHPVMNASGILGSEPEHLEILAGYgFSALVSKTITLKPREGYPPPIIVELRNK-GLLNAVGLANPG 76 
                                       799*********************999999998655*************************988.9*********** PP

                                       HHHHHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHG.GGESEEEEES-SCTCC.TSCCCGCHHHHHH CS
                            DHO_dh  77 ldavlekllkrrkeqeekkelginlskakktenavddyvevvrkig.pfadilelNvSsPntp.glrdlqekeelka 151
                                       ++a+    ++ r+        + +ls+ +     +d++v++++  +   +d++elN+S+P+++ ++ +l+ +++l +
  gi|320100761|ref|YP_004176353.1|  77 VEAIGGLAKAARRL-G----KPLVLSIGGGG---IDEFVKLAEAASeAGVDAVELNLSCPHARgYGLELGGDPALVY 145
                                       ***98765555543.3....37899999998...9********999688**************8899********** PP

                                       HHHHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHH CS
                            DHO_dh 152 illkvvkevskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkd 228
                                        ++k    vs+ pv++Kl      +e + +a +  +  l+ i+    tv+ +aid+ s+k+v  nk GGlsG+++ +
  gi|320100761|ref|YP_004176353.1| 146 TIVKNTVSVSSAPVVAKLGLSDRIMESAGKALEGGAKALTLIN----TVKAMAIDVYSRKPVLSNKHGGLSGPPIHP 218
                                       ******************8743444444445555577777777....889999************************ PP

                                       HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHH CS
                            DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkelee 293
                                       ia++v++++y++ +    +IgvGG++s  Da e i aGA ++qv+ta+ f++ k++++i k+l e
  gi|320100761|ref|YP_004176353.1| 219 IAVRVVYDVYREYR--AEVIGVGGVSSWIDAAELILAGARAIQVGTAVLFNE-KVVEEINKGLRE 280
                                       ************99..889*****************************9976.688999999976 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   3.2e-10   1.1e-06      54     157 ..      92     186 ..      82     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.2e-10
                                       SCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEE CS
                               Dus  54 tplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkir 130
                                       +pl++ +gg   ++ ++ A+ + + g+d+++lN+ CP      +g+G  L  +p+lv+ ivk++v+  + Pv +k  
  gi|320100761|ref|YP_004176353.1|  92 KPLVLSIGGGGIDEFVKLAEAASEAGVDAVELNLSCPHA----RGYGLELGGDPALVYTIVKNTVSVSSAPVVAKLG 164
                                       689999*******************************85....69999999***********************988 PP

                                       SESSTTTC.HHHHHHHHHHCT-SEEEE CS
                               Dus 131 igiddeeenalelakiveaaGaqaltv 157
                                       +  +     ++e a ++ + Ga+alt+
  gi|320100761|ref|YP_004176353.1| 165 LSDR-----IMESAGKALEGGAKALTL 186
                                       8766.....667777777777777775 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.17   6.2e+02      79      99 ..     100     121 ..      77     126 .. 0.52
   2 ?   -3.1   0.0       1.2   4.4e+03      65      99 ..     148     184 ..     144     198 .. 0.54
   3 !   17.3   0.1   7.2e-07    0.0026      61     117 ..     220     276 ..     216     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.17
                                       ESSSSSHHH.HHHHHHCT-SEE CS
                      His_biosynth  79 GGGIrsled.veelleagadkv 99 
                                       GGGI ++ + +e++ eag+d v
  gi|320100761|ref|YP_004176353.1| 100 GGGIDEFVKlAEAASEAGVDAV 121
                                       3344444331223333444444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                                       HHHHHHH-SSEEEEESSS..SSHHHHHHHHHCT-SEE CS
                      His_biosynth  65 veeiaeevfipvqvGGGI..rsledveelleagadkv 99 
                                       v+++++  ++pv    G   r +e++ ++le ga+ +
  gi|320100761|ref|YP_004176353.1| 148 VKNTVSVSSAPVVAKLGLsdRIMESAGKALEGGAKAL 184
                                       5555555555555555541134566666666666643 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 7.2e-07
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHH CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelae 117
                                          +v  + +e +++v   GG++s  d++el+ aga+ + +gta++ n ++++e+ +
  gi|320100761|ref|YP_004176353.1| 220 AVRVVYDVYREYRAEVIGVGGVSSWIDAAELILAGARAIQVGTAVLFNEKVVEEINK 276
                                       5678999999999999999**********************************9976 PP

>> DOCK_N  DOCK N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0     9e-05      0.32       5      32 ..     258     285 ..     255     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9e-05
                            DOCK_N   5 igdetvvsaeeplvdEiascLREWhsll 32 
                                       i+  t+v  +e +v+Ei   LREW s+l
  gi|320100761|ref|YP_004176353.1| 258 IQVGTAVLFNEKVVEEINKGLREWVSTL 285
                                       7788999*****************9996 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.12   4.4e+02     187     232 ..      71     120 ..      68     125 .. 0.71
   2 ?    7.8   0.2    0.0004       1.4     195     237 ..     220     262 ..     212     268 .. 0.84
   3 ?   -0.7   0.0      0.15   5.4e+02     300     325 ..     268     293 ..     266     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.12
                                       SB---HHHHHHHHHHHHCTCT...-EEEEES---SHHHHHHHHH.TT-SE CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx.xxxxx RF
                             IMPDH 187 gvGvpqltAvaevaeaakkag...vpviaDGGikysgdivkAla.aGada 232
                                       g+  p + A+   a+aa++ g   v  i  GGi +  +++ A + aG da
  gi|320100761|ref|YP_004176353.1|  71 GLANPGVEAIGGLAKAARRLGkplVLSIGGGGIDEFVKLAEAASeAGVDA 120
                                       66678888999999999988844455578899988888877654355555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGs 237
                                       Av  v+++ +++  +vi  GG+++  d +  + aGa a+ +G 
  gi|320100761|ref|YP_004176353.1| 220 AVRVVYDVYREYRAEVIGVGGVSSWIDAAELILAGARAIQVGT 262
                                       7778888889999999999999999999999999999998886 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHT-SSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 300 kevveqlvgglrsgmgylGaktieel 325
                                       ++vve++ +glr+ ++ lG + +eel
  gi|320100761|ref|YP_004176353.1| 268 EKVVEEINKGLREWVSTLGYRRLEEL 293
                                       58999*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2079.85
//
Query:       gi|320100762|ref|YP_004176354.1|  [L=255]
Description: dihydroorotate dehydrogenase electron transfer subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   4.2    1.2e-09   37.8   4.2    1.8  2  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0013   19.3   0.0     0.0024   18.5   0.0    1.4  1  NAD_binding_1    Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
       0.11   12.7   0.0        0.2   11.8   0.0    1.4  1  NAD_binding_6    Ferric reductase 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 ?   -2.9   0.5         1   6.3e+03       6      12 ..     158     164 ..     157     165 .. 0.82
   2 !   37.8   4.2     2e-13   1.2e-09       1      41 [.     211     245 ..     211     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                                       SSSSSS- CS
                   DHODB_Fe-S_bind   6 CGvGaCl 12 
                                       C vG C+
  gi|320100762|ref|YP_004176354.1| 158 CRVGYCG 164
                                       7799997 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 2e-13
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e++ +CGvGaC++Cv+k +g        +C+ GPvF+ +ev
  gi|320100762|ref|YP_004176354.1| 211 EAYVKCGVGACGSCVLKPHG------LLLCRHGPVFKCSEV 245
                                       7899**************65......89*********9998 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 !   18.5   0.0     4e-07    0.0024       1      40 [.     101     137 ..     101     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4e-07
                                       EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGS CS
                     NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedl 40 
                                       ++agG+GiaP++ + +++ e+   +  v +v+G+r+  +l
  gi|320100762|ref|YP_004176354.1| 101 FVAGGSGIAPFFHLAEKAWEK---DIVVDVVWGVREAGEL 137
                                       79******************7...489********97665 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 ?   11.8   0.0   3.3e-05       0.2       1      27 [.      96     122 ..      96     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6   1 yenvllvagGiGitpfisilkdllkks 27 
                                       y+ +l+vagG+Gi+pf  ++ + ++k 
  gi|320100762|ref|YP_004176354.1|  96 YRRILFVAGGSGIAPFFHLAEKAWEKD 122
                                       6789**************999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1934.89
//
Query:       gi|320100763|ref|YP_004176355.1|  [L=199]
Description: orotate phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-18   65.2   0.4    6.5e-18   64.8   0.4    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.024   14.1   0.0    1.2  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 !   64.8   0.4   7.2e-22   6.5e-18      30     130 ..      59     149 ..      37     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 7.2e-22
                                       GEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHH CS
                      Pribosyltran  30 pdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaa 106
                                        d+vvg+a+ G+p+a  ++   + p+ayvr++++++++++ +          ++d+ g +Vl+VDD+ +tG+++l+a
  gi|320100763|ref|YP_004176355.1|  59 VDAVVGVATAGIPLAAYVSCLTGKPMAYVRSERKNHGTNSLI----------EGDVSGLRVLVVDDVSTTGSSILRA 125
                                       699************************************999..........58*********************** PP

                                       HHHHHCC-BSEEEEEEEEE-HHHH CS
                      Pribosyltran 107 lelLkekgpeevriavlvdkpate 130
                                       +e+++e+g + +++ v+vd+ +++
  gi|320100763|ref|YP_004176355.1| 126 IEAVREAGGTPMKAGVIVDREQGA 149
                                       ******************998875 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.6e-06     0.024     117     173 ..     102     156 ..      61     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-06
                           UPRTase 117 kkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeef 173
                                        +++  +vl++D v  TG+s+  ai+ ++e+g +   +    ++  e+g++ +++++
  gi|320100763|ref|YP_004176355.1| 102 GDVSGLRVLVVDDVSTTGSSILRAIEAVREAGGTP--MKAGVIVDREQGARGALARH 156
                                       4556677***********************87654..44444556666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1420.89
//
Query:       gi|320100764|ref|YP_004176356.1|  [L=224]
Description: orotidine 5'-phosphate decarboxylase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-29  101.3   0.0    6.9e-29  101.0   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   3.9e-33   6.9e-29       3     225 .]       2     211 ..       1     211 [. 0.88

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 3.9e-33
                                       EEEEE-SSSH....HHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT.SEEEEEEEE-S-HHHHHH CS
                         OMPdecase   3 LclalDvata....relleladkvgpsivvlKthydlvegwgfegtgaklaalarkhg.flifeDrKfaDIGntvek 74 
                                       L++alD++ +    r+   l++++++++  +K++++++ ++g      + ++++rk   ++i++D+K+aDIG+++++
  gi|320100764|ref|YP_004176356.1|   2 LVVALDPPVRekgrRKTSLLVEELDKYVSGYKIGLPFLIKHG-----RRGIRELRKSTeKPIIVDLKLADIGDVMAE 73 
                                       89*****99989999999************************.....**********99****************** PP

                                       HHHSTCHHHHTTESEEEEEGTGH.HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHT CS
                         OMPdecase  75 qatagsarikewadivtvhavaG.kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaed 150
                                         +   + + +++d+v++ha+ G +++++ l +a  ++g  gl+i++ ms+ g+++  + +  ++ +e a++  a+ 
  gi|320100764|ref|YP_004176356.1|  74 VLR---HLARLGVDAVIAHAFTGyTGALEDLSKASMATG-VGLIIVVSMSHRGSEEYID-RHVDEFLELAARIRAK- 144
                                       **9...789**************999************7.9*************99999.7888888888888877. PP

                                       TESEEECCCHTH....HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHH CS
                         OMPdecase 151 fvmGfvaqetln....ateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveea 222
                                          G+va +t++    + +e  +d++ +  pgig         +q  +p  +   aga++ ivGR I+++g+p e+a
  gi|320100764|ref|YP_004176356.1| 145 ---GVVAPATRPrvirHVREVlGDTVEIYSPGIG---------IQGAEPGSALC-AGANYEIVGRLITRSGNPGETA 208
                                       ...********96543333335566666666665.........56666666666.89******************** PP

                                       HHH CS
                         OMPdecase 223 ery 225
                                       +++
  gi|320100764|ref|YP_004176356.1| 209 RAI 211
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 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:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1626.17
//
Query:       gi|320100765|ref|YP_004176357.1|  [L=197]
Description: phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-23   82.7   0.0      3e-23   82.1   0.0    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.033   14.2   0.0       0.05   13.6   0.0    1.2  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
      0.034   13.6   0.2      0.046   13.1   0.2    1.4  1  UPRTase         Uracil phosphoribosyltransferase
      0.092   12.9   0.0       0.23   11.6   0.0    1.6  1  TAFII28         hTAFII28-like protein conserved region


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 !   82.1   0.0   6.8e-27     3e-23       7     150 ..       7     146 ..       4     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 6.8e-27
                                       T---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-.EE-EEEE.EE-TTT--EE........EE CS
                      Pribosyltran   7 enpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevp.layvrkv.kyrpdgseeaargssdesrl 81 
                                        + ++++ + rla+ il++ +++ d+vv+i rgG+ +a i++d ++v  + ++r++ +  +++  e ++++++    
  gi|320100765|ref|YP_004176357.1|   7 PWSKAIELCYRLASMILDN-GRHYDTVVAISRGGLLPARIISDVIGVDdFIVLRSRfWGIGGRIREEPEVAMH---E 79 
                                       55667788999********.*************************9884444444313344445566666665...8 PP

                                       ----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEE CS
                      Pribosyltran  82 ledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfva 150
                                       + +++gk V++VD ++dtG Tl ++++l+k+ g+ +v++avl++k+++ +++d++a +v++    ++  
  gi|320100765|ref|YP_004176357.1|  80 AVNVRGKDVIVVDEVVDTGATLAKITRLVKDMGARSVETAVLHYKSSSSFKPDYYAEKVDEWA--WIFY 146
                                       9**********************************************************9444..4444 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05      0.05      79     126 ..      81     128 ..      68     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                       S--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TT CS
                    Pribosyl_synth  79 GdvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssd 126
                                        +v G+  i+vd+++d   ++ + ++++k+ Ga  +   + h   ss+
  gi|320100765|ref|YP_004176357.1|  81 VNVRGKDVIVVDEVVDTGATLAKITRLVKDMGARSVETAVLHYKSSSS 128
                                       4799*****************************999988888766665 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2     1e-05     0.046     120     152 ..      84     116 ..      31     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                           UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgee 152
                                       + + v+++D v+ TG+++a++ +l+k+ g+++ 
  gi|320100765|ref|YP_004176357.1|  84 RGKDVIVVDEVVDTGATLAKITRLVKDMGARSV 116
                                       5678***********************988754 PP

>> TAFII28  hTAFII28-like protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.1e-05      0.23      46      86 .]     153     194 ..     147     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.1e-05
                           TAFII28  46 vvaglaKvFvgeiveeArevqeeweesg.plqpehlreayrr 86 
                                        + glaK   g+i eeA +v +e + ++  l p+ +re  +r
  gi|320100765|ref|YP_004176357.1| 153 TLYGLAKTRGGDIYEEAFRVLREVNATElYLDPHRIRESLKR 194
                                       5789***********************99*********8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1446.96
//
Query:       gi|320100766|ref|YP_004176358.1|  [L=523]
Description: GMP synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-33  112.6   0.1    2.1e-32  111.0   0.0    1.9  2  GMP_synt_C     GMP synthase C terminal domain
    8.4e-28   97.4   0.0    1.3e-27   96.8   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    2.6e-10   39.8   0.0    6.4e-05   22.2   0.0    2.4  2  NAD_synthase   NAD synthase
    3.7e-10   39.9   0.1    1.2e-09   38.2   0.1    1.9  1  Peptidase_C26  Peptidase C26
     0.0028   17.4   0.0     0.0095   15.7   0.0    1.8  1  ATP_bind_3     PP-loop family
  ------ inclusion threshold ------
      0.023   14.2   0.0       0.15   11.5   0.0    2.0  2  QueC           Queuosine biosynthesis protein QueC
       0.18   11.2   0.2        9.9    5.7   0.0    2.8  3  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       6.1   1.6e+04      57      78 ..     367     388 ..     362     389 .. 0.75
   2 !  111.0   0.0   8.2e-36   2.1e-32       3      91 ..     433     521 ..     431     522 .. 0.98

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6.1
                                       -HHHHHHHHHHHHHHSTT---E CS
                        GMP_synt_C  57 pyevLekissrivnevkgvnrv 78 
                                        ++vLe i     +ev++++r+
  gi|320100766|ref|YP_004176358.1| 367 RVKVLEPIRYLYKDEVREIARL 388
                                       5678888888888999999986 PP

  == domain 2  score: 111.0 bits;  conditional E-value: 8.2e-36
                                       CCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EE CS
                        GMP_synt_C   3 lkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvv 79 
                                       l+++g+y k+wQafav+ + k vGv+gd+R+++y+v++R+ves D+mtad+++lpy+vL++is+ri+n++++v+ v+
  gi|320100766|ref|YP_004176358.1| 433 LREHGFYGKVWQAFAVVGDDKWVGVKGDARSHGYIVTIRVVESVDGMTADYSRLPYDVLDEISRRITNSIPDVSMVT 509
                                       7899************************************************************************* PP

                                       EE---TTTS-S- CS
                        GMP_synt_C  80 yditskPpatiE 91 
                                       y +tskPp+tiE
  gi|320100766|ref|YP_004176358.1| 510 YAVTSKPPSTIE 521
                                       ***********9 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   5.1e-31   1.3e-27       2     188 ..      16     197 ..      15     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 5.1e-31
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHC.TSTS-EE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikear.enkiPiL 75 
                                       ++D++ ++t+ ++++++elgv+ e+v +    +      +++d++++sg   s+     g +e++++++ +  +P+L
  gi|320100766|ref|YP_004176358.1|  16 IVDYGGQYTHLIARRIRELGVYSEIVFHRDAGSLD---VEGYDAVILSGSHLSVRslSRGDLEVAEKILfNGSKPLL 89 
                                       89************************988544444...68*************999*78888887776515789*** PP

                                       EETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTE CS
                            GATase  76 GICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksedde 152
                                       GIC+G+Ql+++ +g++v +    e+      ++  + +l++g ++e +++++H+ +v++    p  l+++a+se+  
  gi|320100766|ref|YP_004176358.1|  90 GICFGHQLIGYLLGADVASGC-GEYGRTRVSITG-GDELFNGWSSEETVWMSHGECVEN---PPGSLRILAVSENR- 160
                                       ******************888.555555555555.77*********************9...8999*******998. PP

                                       EEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHH CS
                            GATase 153 elmeiiekkn.p.fvgvQFHPEststpegpellfnfli 188
                                        ++++    n + ++gvQFHPE+++t +g  l+ nf +
  gi|320100766|ref|YP_004176358.1| 161 VIAAFKAVVNnRaVYGVQFHPEVHHTGKGRLLFDNF-L 197
                                       8999888877778*************9966555555.4 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.5e-08   6.4e-05       5      80 ..     215     287 ..     209     311 .. 0.79
   2 !   15.0   0.0   3.8e-06    0.0097     146     177 ..     369     400 ..     356     403 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.5e-08
                                       HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                      NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktid 80 
                                       l d l+ +v + g   +v+G+SGG+DS+++a + +k++  e+ + + + +    e + e  +   e+lg++  ++d
  gi|320100766|ref|YP_004176358.1| 215 LLDELRREVVDDGV--AVVGVSGGIDSTVTALIGRKVF-GEKLIPVFVDHGLLREGERESVVSSLEKLGLNPLVVD 287
                                       45555555555554..69********************.5788888888888888888888888888888777666 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.8e-06
                                       -SBETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 146 adlapiaellKtevkeLakelnvPervlkkpP 177
                                         l+pi  l+K ev+e+a+ lnvP ++++++P
  gi|320100766|ref|YP_004176358.1| 369 KVLEPIRYLYKDEVREIARLLNVPWELVERHP 400
                                       5689**************************99 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.1   4.8e-13   1.2e-09     104     216 .]      84     182 ..      67     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4.8e-13
                     Peptidase_C26 104 rgvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike 180
                                        ++P+lgiC G+ql+   lG     d+ +          + +  + +v+++ g  l + ++ +e  v   H  ++++
  gi|320100766|ref|YP_004176358.1|  84 GSKPLLGICFGHQLIGYLLG----ADVAS---------GCGEYGRTRVSITGGDELFNGWS-SEETVWMSHGECVEN 146
                                       579************55444....45553.........333456899****9999999888.78889999******* PP

                     Peptidase_C26 181 laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                          +lr+ Av+e  vi a+++  ++  v+gvQ+HPE
  gi|320100766|ref|YP_004176358.1| 147 PPGSLRILAVSENRVIAAFKAVVNNRAVYGVQFHPE 182
                                       ***********************9***********9 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.7e-06    0.0095       3     163 ..     230     393 ..     228     395 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.7e-06
                                       EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT.-EEEEEE--H...HHCTTST CS
                        ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckkln.ikleiekvdv...akkkgkn 75 
                                       +v+vSgG+DS++  l+  k    +g kl+ + vdhgl  e ++e+ +v++l +kl+  +l+++  +      +    
  gi|320100766|ref|YP_004176358.1| 230 VVGVSGGIDSTVTALIGRKV---FGEKLIPVFVDHGLLREGERES-VVSSL-EKLGlNPLVVDAGERfisRLEGVVD 301
                                       89*********988887777...6679**********98877654.44444.4444144444444445533333455 PP

                                       CCCHHHHHH...HHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--C..CHHH-S-SEEEETTCCEE-CCCT- CS
                        ATP_bind_3  76 leeaARelR...YevlkealkkegievlllAhhadDqaEtfllrlargsgl..aglagikeaseiasirlvRPlLkv 147
                                        ee+ R +     ++++e+++keg++++l + +  D +E   +r a +  +  +++ g++e   ++ ++++ P+  +
  gi|320100766|ref|YP_004176358.1| 302 CEERRRVIGeefAKIFAEIVEKEGARYFLQGTTYPDIIESGGIRGAASVIKshHNVGGLPE-WFRDRVKVLEPIRYL 377
                                       6666665541213568888888888888888888888888877766654332144555554.446778888888888 PP

                                       -HHHHHHHHHHTT--- CS
                        ATP_bind_3 148 skeeleeylkekkikw 163
                                       +k+e++e+++  +++w
  gi|320100766|ref|YP_004176358.1| 378 YKDEVREIARLLNVPW 393
                                       8888888888777777 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.9e-05      0.15       2      58 ..     229     285 ..     228     320 .. 0.84
   2 ?    0.2   0.0      0.17   4.3e+02     148     178 ..     364     394 ..     328     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                                       EEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEE CS
                              QueC   2 avvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehki 58 
                                       avv +SGG+DSt+ +++ +k + ++++ + +d g  ++ e e++ +  ++lg+ +  +
  gi|320100766|ref|YP_004176358.1| 229 AVVGVSGGIDSTVTALIGRKVFgEKLIPVFVDHGLLREGERESVVSSLEKLGL-NPLV 285
                                       89**********99999888764889999999999999999988888888887.4444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.17
                                       HTS--EEE-TTTT--HHHHHHHHHHTTHHHH CS
                              QueC 148 edkkieieaPlidlsKaeivklgkelgvple 178
                                         +++++  P+  l K e+ +++  l+vp+e
  gi|320100766|ref|YP_004176358.1| 364 FRDRVKVLEPIRYLYKDEVREIARLLNVPWE 394
                                       45789*******************9999987 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 ?   -3.1   0.0       2.1   5.4e+03       6      22 ..      17      33 ..      16      34 .. 0.77
   2 ?    2.6   0.0     0.035        89      35      52 .]     152     169 ..     152     169 .. 0.90
   3 ?    5.7   0.0    0.0039       9.9      30      46 ..     382     398 ..     382     398 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                      HTH_Tnp_ISL3  6 arrrsriTlrleayile 22
                                      ++ + ++T++ ++ i e
  gi|320100766|ref|YP_004176358.1| 17 VDYGGQYTHLIARRIRE 33
                                      77889999998888866 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.035
                      HTH_Tnp_ISL3  35 rqlgvSwtTVwrildryv 52 
                                       r+l vS+++V+ +++++v
  gi|320100766|ref|YP_004176358.1| 152 RILAVSENRVIAAFKAVV 169
                                       7899**********9876 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0039
                      HTH_Tnp_ISL3  30 vkavArqlgvSwtTVwr 46 
                                       v+++Ar+l+v w  V+r
  gi|320100766|ref|YP_004176358.1| 382 VREIARLLNVPWELVER 398
                                       689************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); 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:                         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 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3459.39
//
Query:       gi|320100767|ref|YP_004176359.1|  [L=381]
Description: pyridoxal-5'-phosphate-dependent protein subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-13   50.0   0.1    4.9e-06   26.2   0.1    3.1  2  PALP      Pyridoxal-phosphate dependent enzyme
     0.0083   16.0   0.1      0.029   14.3   0.1    1.9  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.023   14.6   0.1      0.057   13.4   0.1    1.7  1  PadR      Transcriptional regulator PadR-like family
        0.1   12.6   0.1       0.31   11.0   0.0    1.9  2  HTH_11    HTH domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.3e-07    0.0028       2      75 ..      65     130 ..      64     155 .. 0.79
   2 !   26.2   0.1   1.1e-09   4.9e-06     133     274 ..     171     285 ..     137     296 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.3e-07
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBS.SHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveass.GNhgralAaaaa 75 
                                       ++g+g TPl+++++        + +K+E  nptgS+ dR+ + + ++++ + g ++v+      + + +lA++ +
  gi|320100767|ref|YP_004176359.1|  65 SMGEGLTPLRTVDG--------VIVKNERKNPTGSYSDRASSVIASYIAST-GWRGVLRVEYvEDFAYSLAYYTR 130
                                       688999***99999........9*******************999997777.66666666666788888888776 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.1e-09
                                       TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT...-EEEEEEECTTCGGTTCCS..S CS
                              PALP 133 qfdnptviegygtiglEileqlggkpdavvvpvGgGgliaGiaaglkerrpd...vrvigvepegsdalarslragr 206
                                       ++ np+ ieg +ti lEi+e+   +++ +vvpv +G l+  ++++l+e +     +  i+v        +++l    
  gi|320100767|ref|YP_004176359.1| 171 PYINPLTIEGLKTILLEIHERR-LNVENIVVPVETGTLAFSLCKALRELGEMgmhPGYIVV--------GATL---- 234
                                       445***************8555.67***********************4432222444444........3333.... PP

                                       .SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH CS
                              PALP 207 rvtvpvsdtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal 274
                                                  +g + +      + ++++++  + +v  +ea+e + +l  r+g+ +   sa a+a++
  gi|320100767|ref|YP_004176359.1| 235 -----------KGWGKP----WLLNHCKDSIR-VEEVEPAEAVESLLKLS-RMGLRTKLVSALAYAVA 285
                                       ...........233333....55555555555.66666666666666666.66666666666666666 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   6.4e-06     0.029      18      55 ..     319     358 ..     313     373 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
                                       H.HHCCCHHCHHCCCTTS.SCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  18 l.klgpatadeiaeelgv.prskvYevLrsLedkGlVere 55 
                                       l k+g +ta+e+ ++lg  +   vY++LrsLe+ Gl+ ++
  gi|320100767|ref|YP_004176359.1| 319 LeKHGDLTAYEVWRMLGKySLRGVYKALRSLEELGLICVK 358
                                       4489************9626677*************9766 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.3e-05     0.057       8      67 ..     323     375 ..     315     377 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                       S-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESH CS
                              PadR   8 qpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTd 67 
                                       +++  ye+ + l ++s          +Y+aL++Le+ gl+  + + +g+g++ k+Y + +
  gi|320100767|ref|YP_004176359.1| 323 GDLTAYEVWRMLGKYS-------LRGVYKALRSLEELGLICVKHVVKGVGRKVKTYSVCE 375
                                       5555555555555552.......2249**************999999*********9865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       2.7   1.2e+04      27      35 ..      45      53 ..      44      53 .. 0.85
   2 ?   11.0   0.0     7e-05      0.31       4      44 ..     314     354 ..     313     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.7
                            HTH_11 27 vSrrtvrrd 35
                                      +S++ ++r+
  gi|320100767|ref|YP_004176359.1| 45 RSEASIWRY 53
                                      7999***97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7e-05
                            HTH_11   4 qilelLleargpisgeeLAeeLnv.SrrtvrrdIkaLeelgv 44 
                                        il +L e++g++++ e  + L+  S r v++ +++Leelg+
  gi|320100767|ref|YP_004176359.1| 314 EILGIL-EKHGDLTAYEVWRMLGKySLRGVYKALRSLEELGL 354
                                       588899.9999************99****************3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2742.13
//
Query:       gi|320100768|ref|YP_004176360.1|  [L=199]
Description: pyridoxal phosphate synthase yaaE subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-49  167.0   0.0    4.6e-49  166.8   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    1.6e-11   44.2   0.0    2.2e-11   43.8   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    5.4e-07   29.6   0.0    7.5e-07   29.1   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
    0.00023   20.9   0.0    0.00029   20.5   0.0    1.1  1  Peptidase_S51  Peptidase family S51
    0.00028   20.7   0.1     0.0023   17.7   0.1    1.9  1  GATase         Glutamine amidotransferase class-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 !  166.8   0.0   1.3e-52   4.6e-49       1     185 [.       6     196 ..       6     199 .] 0.90

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 1.3e-52
                                       EESSSSSHHHHHHHHHH.TTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETH CS
                               SNO   1 vlalqGaveehveaikk.claenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCa 76 
                                       vlalqG++ eh + ++  +++e+  vk++ +l++vdal+iPGGest++++l+ + gl e+l++f+ ++ k++l tCa
  gi|320100768|ref|YP_004176360.1|   6 VLALQGDYLEHYQLLRSlSGVEAVPVKHPRELEGVDALVIPGGESTTIGLLVRKKGLEEPLKQFAGEG-KPILATCA 81 
                                       8**************87479***********************************************9.******** PP

                                       HHHHHCCEETTB.....SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.T.TTCEEE CS
                               SNO  77 Glillskelene.....lvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeildd.eavkvl 147
                                       G ill++e+           tl+l+++ v rna+Grq dsf +++++k+++ +++a firaP+i ++    e +  l
  gi|320100768|ref|YP_004176360.1|  82 GAILLAREVVDRtvgetGQYTLGLMDIAVVRNAYGRQRDSFIASVTLKDIG-EVKAAFIRAPIIARAYGSaEIIGFL 157
                                       *******98776444445679*****************************9.9************997540445555 PP

                                       EECT.T.EEEEEEETTEEEESS-GGGSTTHCHHHHHHHHH CS
                               SNO 148 yeld.g.eivvakqkkilatsfhPelaeddirvhdyfvee 185
                                        +   g + v+a+q+++ a++fhPe++ d i+++++ +++
  gi|320100768|ref|YP_004176360.1| 158 DDPTlGrHGVAARQGNMYAVTFHPEITGD-IKLYKHIIQQ 196
                                       5555886778888**************99.*****99987 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 !   43.8   0.0     6e-15   2.2e-11      18     119 ..      19     114 ..       6     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 6e-15
                          GATase_3  18 pLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeied 94 
                                       +L+  + v+   v+ + ++l+  +d++++pGg++t+  l + ++ gl+e +k++a +g+p+l+ C+G ++L +e++d
  gi|320100768|ref|YP_004176360.1|  19 LLRSLSGVEAVPVK-HPRELE-GVDALVIPGGESTTIGLLVRKK-GLEEPLKQFAGEGKPILATCAGAILLAREVVD 92 
                                       56666666666677.778895.5************999988776.*******************************9 PP

                          GATase_3  95 pegvegeageveglglLdietefek 119
                                             e+g    lgl+di ++ + 
  gi|320100768|ref|YP_004176360.1|  93 RTVG--ETG-QYTLGLMDIAVVRNA 114
                                       8654..343.456899999887665 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 !   29.1   0.0   2.1e-10   7.5e-07      60     111 ..      38      90 ..      13     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.1e-10
                                       CG-SEEEE--BHHHH.HHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTT CS
                         DJ-1_PfpI  60 aeyDalvlpGGragp.erlrenekvvelvkefaekgklvaaICagpqlLaaag 111
                                       +  Dalv+pGG++     l++++ + e +k+fa +gk++ a Cag++lLa++ 
  gi|320100768|ref|YP_004176360.1|  38 EGVDALVIPGGESTTiGLLVRKKGLEEPLKQFAGEGKPILATCAGAILLAREV 90 
                                       567********995425688899**********************99999865 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.1e-08   0.00029      74     163 ..      35     114 ..      13     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.1e-08
                                       HHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGTTTS-GGG-S---B CS
                     Peptidase_S51  74 eeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiettsysdspikapesfe 150
                                       +e    l+  d++++ GG+   +  l++++gl ++l++   +g+++  + AGai  ++++  +   +++ ++     
  gi|320100768|ref|YP_004176360.1|  35 RE----LEGVDALVIPGGESTTIGLLVRKKGLEEPLKQFAGEGKPILATCAGAILLAREVVDRT-VGETGQY----- 101
                                       33....5559************************************************999888.4444333..... PP

                                       ----SSSEEETTT CS
                     Peptidase_S51 151 aLgLvkfqivPHy 163
                                       +LgL++  +v  +
  gi|320100768|ref|YP_004176360.1| 102 TLGLMDIAVVRNA 114
                                       4777776666555 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   6.4e-07    0.0023      27     175 ..      29     185 ..      13     195 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.4e-07
                                       EETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECE CS
                            GATase  27 vpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekek 98 
                                       vp++++      +l+++d+++++gG  +        +g  e +k+++++++PiL  C G  lla e+   +v e+  
  gi|320100768|ref|YP_004176360.1|  29 VPVKHPR-----ELEGVDALVIPGGESTTIgllvrKKGLEEPLKQFAGEGKPILATCAGAILLAREVVDRTVGET-G 99 
                                       4444332.....3679*********988878998878889999999999*****************999888666.4 PP

                                       EEEEEEEEEEETTT............CGGTTTTSEEEEEEEEEEEEESG.......CHHHTTEEEEEEEETTE.EEE CS
                            GATase  99 ehhggtmrlgddet............allyglknevierhrHryevnpk.......elepaglevtaksedde.elm 155
                                       ++  g m +   ++              l++ +++             +       +      e+++  +d    ++
  gi|320100768|ref|YP_004176360.1| 100 QYTLGLMDIAVVRNaygrqrdsfiasVTLKDIGEVKA-----------AfirapiiARAYGSAEIIGFLDDPTlGRH 165
                                       5555555555533334555544444333333322222...........12222233223333444444433323699 PP

                                       EEEEETTTEEEESSBTTSTT CS
                            GATase 156 eiiekknpfvgvQFHPEsts 175
                                       ++  ++ ++++v FHPE t 
  gi|320100768|ref|YP_004176360.1| 166 GVAARQGNMYAVTFHPEITG 185
                                       99999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1426.31
//
Query:       gi|320100769|ref|YP_004176361.1|  [L=334]
Description: pyridoxal phosphate synthase yaaD subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-92  306.6   0.3    1.2e-91  306.1   0.1    1.3  2  SOR_SNZ       SOR/SNZ family
    2.9e-06   26.8   1.9    9.2e-06   25.1   0.1    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
      0.002   17.3   0.0       0.49    9.4   0.0    2.3  2  Dus           Dihydrouridine synthase (Dus)
      0.002   17.6   0.2        2.1    7.7   0.0    2.9  3  His_biosynth  Histidine biosynthesis protein
     0.0029   17.0   0.2     0.0059   16.0   0.0    1.6  2  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.026   14.1   0.0        1.4    8.5   0.0    2.2  2  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
      0.028   13.6   0.3        1.3    8.2   0.0    2.8  4  NanE          Putative N-acetylmannosamine-6-phosphate epimer
      0.086   12.0   0.0        1.3    8.2   0.0    2.4  2  IGPS          Indole-3-glycerol phosphate synthase
        0.1   12.6   0.0       0.22   11.6   0.0    1.5  1  TetR_C_27     Tetracyclin repressor-like, C-terminal domain
       0.11   11.3   0.0       0.23   10.3   0.0    1.4  1  Trp_syntA     Tryptophan synthase alpha chain


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 !  306.1   0.1   6.8e-95   1.2e-91       4     207 .]      43     250 ..      40     250 .. 0.97
   2 ?   -4.0   0.0       5.9   1.1e+04     128     141 ..     303     316 ..     300     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 306.1 bits;  conditional E-value: 6.8e-95
                                       HHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT CS
                           SOR_SNZ   4 vkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriG 80 
                                       vk g+ +mlkgGvimdv+n+eqa iae+aGav vm+l+++p d+r +ggvar++d+k+i+e++++++ipv ak+riG
  gi|320100769|ref|YP_004176361.1|  43 VKYGFVSMLKGGVIMDVTNPEQAGIAEDAGAVGVMVLDKLPYDVRMAGGVARTADVKVIEEVMNTITIPVSAKCRIG 119
                                       899************************************************************************** PP

                                       -HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHH CS
                           SOR_SNZ  81 hfveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavr 157
                                       h  ea+ile++gvd+iDesevltp+de+ahidk+ fk+pfv+Gar+l ealrri+eGa+mirtkGe+gtG+v+eavr
  gi|320100769|ref|YP_004176361.1| 120 HEWEARILEEIGVDLIDESEVLTPVDEKAHIDKWLFKTPFVNGARSLPEALRRIHEGASMIRTKGEPGTGNVAEAVR 196
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHTTS....-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 158 hvrkikeeirklksl....seeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                       h++ ++++i  l+      + e +  +++e k+p+el   +a+lgrlpvvnfaa
  gi|320100769|ref|YP_004176361.1| 197 HMKLVNRDIYVLNGYyrngDLEAIRIYSRENKVPYELALLTARLGRLPVVNFAA 250
                                       ***********9988655566778999*************************98 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.9
                                       HHHHHHHHHT-SEE CS
                           SOR_SNZ 128 gealrriaeGaami 141
                                        ea r ++e a+m+
  gi|320100769|ref|YP_004176361.1| 303 LEAQRMVSEKASML 316
                                       58999999999996 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4      0.16   2.8e+02     141     199 ..      69     133 ..      38     142 .. 0.64
   2 !   25.1   0.1   5.1e-09   9.2e-06     164     224 ..     230     293 ..     224     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.16
                                       HHTT-SEBEEB...SSSTTS----S-H...HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-S CS
                              ThiG 141 eevGcaavmPl...aapiGsglGllnk...ealkiiieeakvPvivDAGigspsdaaqamelGad 199
                                       e++G+  vm l      +  + G++ +   ++++ +++++++Pv     ig+  +a    e+G+d
  gi|320100769|ref|YP_004176361.1|  69 EDAGAVGVMVLdklPYDVRMAGGVARTadvKVIEEVMNTITIPVSAKCRIGHEWEARILEEIGVD 133
                                       45555555543111223444444444400045556667778999999999999999888888887 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 5.1e-09
                                       HHHHHHHHHH-.SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
                              ThiG 164 kealkiiieea.kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                                       ++ l ++++++ ++Pv+  A  G+ +p daa  m lGad+v++ + + +++dp a A+a+ la+
  gi|320100769|ref|YP_004176361.1| 230 PYELALLTARLgRLPVVNFAagGVATPADAALMMWLGADGVFVGSGIFKSSDPEARAHAIVLAT 293
                                       67888999999999*99654459************************************99986 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0043       7.8     112     134 ..      99     121 ..      86     136 .. 0.83
   2 !    9.4   0.0   0.00027      0.49     182     254 ..     243     316 ..     236     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0043
                                       HHHHHHHCCSSS-EEEEEESESS CS
                               Dus 112 qivkavvkaveiPvtvkirigid 134
                                       +++++v + + iPv++k rig +
  gi|320100769|ref|YP_004176361.1|  99 KVIEEVMNTITIPVSAKCRIGHE 121
                                       67999999999*********976 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00027
                                       -SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC..CSTTHHHHHHHHHHSC------HHHHHHHHHHHHHHC CS
                               Dus 182 vsipviaNGdIkdaedaqaileetGadgvmigrgal..gnPwlfaestavktgeaepapplaeeaeiveehlkkl 254
                                       ++++ +a G++ ++ da  +++  Gadgv +g g    ++P   a+   + t + +   ++ e  ++v+e++++l
  gi|320100769|ref|YP_004176361.1| 243 LPVVNFAAGGVATPADAALMMWL-GADGVFVGSGIFksSDPEARAHAIVLATAYWDDPETVLEAQRMVSEKASML 316
                                       56777899**************9.*********976114677766433333433333333677777777776665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.24   4.2e+02     196     210 ..      88     102 ..      74     133 .. 0.66
   2 !    5.6   0.0    0.0055       9.8     195     225 ..     248     278 ..     230     282 .. 0.67
   3 !    7.7   0.0    0.0012       2.1      94     132 ..     284     322 ..     282     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.24
                                       EESS--SHHHHHHHH CS
                      His_biosynth 196 asGGvgsledlkelk 210
                                       ++GGv++ +d+k ++
  gi|320100769|ref|YP_004176361.1|  88 MAGGVARTADVKVIE 102
                                       455555555554333 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0055
                                       EEESS--SHHHHHHHHHTTCSEEEESHHHHT CS
                      His_biosynth 195 iasGGvgsledlkelksegvdavivgsalye 225
                                        a+GGv++++d + +   g+d+v vgs +++
  gi|320100769|ref|YP_004176361.1| 248 FAAGGVATPADAALMMWLGADGVFVGSGIFK 278
                                       5777777777777777777777777776655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0012
                                       CT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE CS
                      His_biosynth  94 agadkviigtaavknpelikelaekfgsqkivvaiDarr 132
                                       a a+ ++++ta+ ++pe + e+ + + +++ ++++D+r+
  gi|320100769|ref|YP_004176361.1| 284 ARAHAIVLATAYWDDPETVLEAQRMVSEKASMLGLDVRQ 322
                                       66899********************************98 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.99   1.8e+03     176     176 ..      92      92 ..      54     133 .. 0.59
   2 !   16.0   0.0   3.3e-06    0.0059     147     235 ..     193     286 ..     148     312 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.99
                               NMO 176 v 176
                                       v
  gi|320100769|ref|YP_004176361.1|  92 V 92 
                                       1 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.3e-06
                               NMO 147 kearkvearGaDalivqGpeaGGhqG...tpevgdkglfaLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsg 218
                                       +++r +     D+ +++G+   G        + ++k   +L    +    +Pv+  AaGG+ +  + a ++ lGA g
  gi|320100769|ref|YP_004176361.1| 193 EAVRHMKLVNRDIYVLNGYYRNGDLEairIYSRENKVPYELALLTARLGRLPVVnfAAGGVATPADAALMMWLGADG 269
                                       44555666667888888876666555333122222333333333334445899777********************* PP

                               NMO 219 vqigtrfLltkesdakd 235
                                       v +g+     ++ +a++
  gi|320100769|ref|YP_004176361.1| 270 VFVGSGIFKSSDPEARA 286
                                       *****999998876654 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.024        43      81     130 ..     171     219 ..     164     259 .. 0.81
   2 ?    8.5   0.0   0.00077       1.4     198     224 ..     262     288 ..     245     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.024
                                       HHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHH CS
                         OMPdecase  81 arikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlml 130
                                        ri+e+a ++   + +G++ v+++++ ++  + r +++l  +   g l+ 
  gi|320100769|ref|YP_004176361.1| 171 RRIHEGASMIRTKGEPGTGNVAEAVRHMKLVN-RDIYVLNGYYRNGDLEA 219
                                       69************************998775.89888876666665555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00077
                                       HHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 198 igiagadiiivGRgIlkagdpveeaer 224
                                       +   gad + vG gI+k++dp++ a++
  gi|320100769|ref|YP_004176361.1| 262 MMWLGADGVFVGSGIFKSSDPEARAHA 288
                                       55569******************9987 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.86   1.5e+03     135     176 ..      15      56 ..      11      64 .. 0.85
   2 ?   -1.4   0.0      0.63   1.1e+03     154     172 ..      60      78 ..      30      82 .. 0.76
   3 ?    1.9   0.2     0.062   1.1e+02     130     171 ..      94     136 ..      55     156 .. 0.66
   4 ?    8.2   0.0    0.0007       1.3     147     178 ..     247     278 ..     224     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.86
                                       HHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
                              NanE 135 alvkalseaglkviaeGrintPekakkaieiGvdavvvGsai 176
                                       +l+ +l+e   +v+ eG       a   ++ G +++  G+ i
  gi|320100769|ref|YP_004176361.1|  15 NLLYKLLEYRDRVLEEGSAPGRTVATPLVKYGFVSMLKGGVI 56 
                                       688889999999999999999999999999999999999987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.63
                                       -SHHHHHHHHTT--SEEEE CS
                              NanE 154 ntPekakkaieiGvdavvv 172
                                         Pe+a  a + G++ v+v
  gi|320100769|ref|YP_004176361.1|  60 TNPEQAGIAEDAGAVGVMV 78 
                                       5688888888888888776 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.062
                                       SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEE CS
                              NanE 130 aepDfalvkalsea.glkviaeGrintPekakkaieiGvdavv 171
                                          D++++++++++  + v a  ri    +a+   eiGvd++ 
  gi|320100769|ref|YP_004176361.1|  94 RTADVKVIEEVMNTiTIPVSAKCRIGHEWEARILEEIGVDLID 136
                                       5678888887666525678888888888888888888888775 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0007
                                       EEEES---SHHHHHHHHTT--SEEEE-HHHH- CS
                              NanE 147 viaeGrintPekakkaieiGvdavvvGsaitr 178
                                         a G + tP+ a+ ++ +G+d v vGs i +
  gi|320100769|ref|YP_004176361.1| 247 NFAAGGVATPADAALMMWLGADGVFVGSGIFK 278
                                       568999**********************9865 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.12   2.1e+02      61      89 ..      52      80 ..      45     111 .. 0.90
   2 ?    8.2   0.0   0.00071       1.3     210     252 ..     245     287 ..     233     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                                      TEESBSS--HHHHHHHHTTT.-SEEEEE- CS
                              IGPS 61 kgliredfdpaeiAkkyeeagAsaiSVLt 89
                                      kg + +d+  +e+A   e+agA  + VL 
  gi|320100769|ref|YP_004176361.1| 52 KGGVIMDVTNPEQAGIAEDAGAVGVMVLD 80
                                      788999999**************999985 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00071
                                       SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHH CS
                              IGPS 210 vllvaeSGiktredveklkeegvnafLvGeslmrqedvekair 252
                                       v+  a  G++t++d+  +   g++++ vG+ + +++d e+  +
  gi|320100769|ref|YP_004176361.1| 245 VVNFAAGGVATPADAALMMWLGADGVFVGSGIFKSSDPEARAH 287
                                       5567889******************************998776 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.22      61      95 ..     273     307 ..     267     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                       HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGG CS
                         TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaewsd 95 
                                        +G Fk++dpea a+a++ ata   +P ++ e ++
  gi|320100769|ref|YP_004176361.1| 273 GSGIFKSSDPEARAHAIVLATAYWDDPETVLEAQR 307
                                       689**********************9999988776 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00013      0.23     179     241 ..     226     288 ..     221     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                                       TSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHCTTTSHH CS
                         Trp_syntA 179 enavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkieeeaeeke 241
                                       en+v  e+  l +rl +l  v  a G G++t+++++ ++  +adGv vGS + k  + ea+ ++
  gi|320100769|ref|YP_004176361.1| 226 ENKVPYELALLTARLGRLPVVNFAAG-GVATPADAALMMwLGADGVFVGSGIFKSSDPEARAHA 288
                                       56666677777777777777777777.*********99989***********998776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2478.82
//
Query:       gi|320100770|ref|YP_004176362.1|  [L=228]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1822.06
//
Query:       gi|320100771|ref|YP_004176363.1|  [L=293]
Description: mechanosensitive ion channel protein MscS [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-48  164.4   0.9    2.4e-48  164.4   0.9    1.8  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.051   13.6   3.0        0.6   10.1   2.5    2.8  2  TM_helix    Conserved TM helix


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 ?   -2.5   2.6      0.34     3e+03      11      48 ..       9      47 ..       1      54 [. 0.74
   2 !  164.4   0.9   2.7e-52   2.4e-48       3     206 .]      68     264 ..      66     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.34
                                      HHHHHHHHTTT--.SCCHHHHHHHHHHHHHHHHCHHHHH CS
                        MS_channel 11 vgilivlsllgvn.vsallavlGalglalglalkdlisn 48
                                       +++ +l ++g     al +  G+l la+g+ l +++  
  gi|320100771|ref|YP_004176363.1|  9 QAVIDALASIGLGrELALRVFTGLLVLAIGFLLVKVLTR 47
                                      5566667777766567899999999*****998777765 PP

  == domain 2  score: 164.4 bits;  conditional E-value: 2.7e-52
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedi 79 
                                       ++++++++++++++l +lgv+vs l+ + G++gl++g al+ ++sn++aG+ +++ek+++ GD veig+++G+V+ +
  gi|320100771|ref|YP_004176363.1|  68 LIYYTLLFIVVVTFLGVLGVDVSGLVIAGGFAGLVVGVALQPVLSNVFAGLYIIAEKAVQPGDAVEIGGVSGEVIAL 144
                                       799************************************************************************** PP

                                       -SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-E CS
                        MS_channel  80 glrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkel 156
                                       ++ +t+irt+dg +vt Pn++l++s+++N+sr + ++r++vsi ++ys d   +e ++++++eal +  +vl ++++
  gi|320100771|ref|YP_004176363.1| 145 SIMFTRIRTWDGVVVTLPNNMLLSSSFKNYSR-TVAKRVEVSIPIAYSGD---AEMAYSVVREALGKLTYVLVEPAP 217
                                       ********************************.*****************...************************ PP

                                       EEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 157 lvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       + ++  + d +ln++vr++v +   + y+   +e+   i k+l++ giei
  gi|320100771|ref|YP_004176363.1| 218 DIFVSSIVDGGLNLTVRAWVLD---KYYYTAIKELPWAITKALKASGIEI 264
                                       **********************...99*********************97 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.5   6.7e-05       0.6      17      42 ..      28      53 ..      25      56 .. 0.89
   2 ?    0.1   0.0     0.094   8.4e+02      37      48 ..     252     263 ..     245     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.7e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix 17 LvgAilILlvGwiiAkfvsrlvtkll 42
                                      ++  +l+L++G+++ k+++r   k+l
  gi|320100771|ref|YP_004176363.1| 28 VFTGLLVLAIGFLLVKVLTRFSAKVL 53
                                      78899***************999987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.094
                                       HHHHHHHHHTS- CS
                          TM_helix  37 lvtkllaktgid 48 
                                       ++tk l+++gi+
  gi|320100771|ref|YP_004176363.1| 252 AITKALKASGIE 263
                                       689*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2365.60
//
Query:       gi|320100772|ref|YP_004176364.1|  [L=243]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-28   96.9   0.0    1.2e-27   96.5   0.0    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 !   96.5   0.0   6.7e-32   1.2e-27       3     123 .]      56     181 ..      51     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 6.7e-32
                            DUF432   3 nlpkeitkyllveleeplvvepkseveiyvkvpveigvfikskkeveliDvfsl.skkkYaLYGs.....pesGvia 73 
                                       ++p+ it+ +l+el ++ +++p+s++ ++vk+pv++gvf+  ++ ++liDv++l +++kY+LYG+     + +G i+
  gi|320100772|ref|YP_004176364.1|  56 YVPEFITRHILIELADKSLIPPSSSIAFTVKIPVDLGVFVVGDDYYRLIDVIPLgKYYKYTLYGPhatleEITGLIC 132
                                       589***************************************************8999*******88877779**** PP

                            DUF432  74 ryvksevyseppeldpleeavveleikNetdevvevskivfdalglklyy 123
                                       r+++s+++ e+p  ++ +e+++e+e +Ne++e   +ski++da+ + l+y
  gi|320100772|ref|YP_004176364.1| 133 RHWRSQLHYEKPV-TEPGECILEVEAVNEAEEPLFISKILVDASFTPLFY 181
                                       **********997.5559******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1958.92
//
Query:       gi|320100773|ref|YP_004176365.1|  [L=484]
Description: thiamine biosynthesis/tRNA modification protein ThiI [Desulfurococcus mucosus DSM 2162]
Scores for 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-50  172.1   0.0      1e-49  168.8   0.0    2.0  2  ThiI             Thiamine biosynthesis protein (ThiI)
    2.2e-22   79.7   2.0    4.3e-22   78.8   0.8    1.9  2  THUMP            THUMP domain
    2.8e-08   34.2   0.0    2.8e-07   31.0   0.0    2.6  2  Rhodanese        Rhodanese-like domain
    5.1e-06   26.1   0.0    0.00049   19.7   0.0    2.4  2  QueC             Queuosine biosynthesis protein QueC
      0.009   15.5   0.0      0.019   14.5   0.0    1.5  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.034   12.9   0.0      0.052   12.3   0.0    1.2  1  tRNA_Me_trans    tRNA methyl transferase
        1.9    9.5   4.0        5.1    8.1   0.1    3.2  4  LytR_C           LytR cell envelope-related transcriptional a


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 ?    0.8   0.1      0.12   3.2e+02      24      89 ..      36      98 ..      32     111 .. 0.68
   2 !  168.8   0.0     4e-53     1e-49       1     191 [.     170     360 ..     170     365 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                              ThiI 24 lkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkeklti 89
                                       ++G+ v +v ++++ +  e+  + ++ l +++  +  s    +   +++e+++e+ ++       
  gi|320100773|ref|YP_004176365.1| 36 ARKGITVSAVRFTDAKILVEAGGDALQALSRVFGVHRVSEVQAIEFTSLEELVREVASR---SIEH 98
                                      589**********9999999999999999999888886444444444455555555444...3333 PP

  == domain 2  score: 168.8 bits;  conditional E-value: 4e-53
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaella.eyqtslevklvvvdfkevl 76 
                                       g+ g++l+L SgG+DSpVaa+l+ kRG++v+++h     + s e+  +   +a++la e+ +s + +++++df++++
  gi|320100773|ref|YP_004176365.1| 170 GSGGRALVLFSGGFDSPVAAWLMAKRGLEVDFLHYM---MGSSEVSRQAFAVAKKLAdEWLSSYDPRFITIDFTPLI 243
                                       6789*****************************994...555555555555555554268888999*********** PP

                              ThiI  77 keilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavv..nllilrPLigldKee 151
                                        ei  k++  ++ v+l+  m+ +A +vae+ g++alvtGe+Lgq +Sqtl Nlr+ + +     ++lrPLig+dKee
  gi|320100773|ref|YP_004176365.1| 244 AEIEGKIEWSYRQVVLRALMYMVAGRVAERLGYDALVTGEALGQASSQTLANLRAAEYAAspGCIVLRPLIGFDKEE 320
                                       ******************************************************9987664689************* PP

                              ThiI 152 iiklAkeigtyeisiekedkCsvlakhPttkakleeveka 191
                                       i+   ++ig ye s +  + C++ + h  t+  +e++++ 
  gi|320100773|ref|YP_004176365.1| 321 IVGYSRRIGLYEYSSRVAEACAIAPTHVATRVSPEKLREL 360
                                       **********************************999875 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.8   1.7e-25   4.3e-22       2     140 ..      30     156 ..      29     159 .. 0.87
   2 ?   -0.9   0.0      0.61   1.6e+03      20      56 ..     317     355 ..     313     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.7e-25
                                       HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHH CS
                             THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkk 78 
                                       +i+  l +++++v+ v++ + +i+ve +g         + +al++++g++rv+ v ++ +++le++ + + +   ++
  gi|320100773|ref|YP_004176365.1|  30 NIKRTLARKGITVSAVRFTDAKILVEAGGD--------ALQALSRVFGVHRVSEVQAIEFTSLEELVREVASRSIEH 98 
                                       8999999*******************9977........7899***********996666666655555555555555 PP

                                       HHHCT-.EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEE CS
                             THUMP  79 feeeke.tFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayi 140
                                        +     +FaVrvkr g h  fts +++re+G+a++  +++ VdlenP++ v ve+++++ay+
  gi|320100773|ref|YP_004176365.1|  99 VK---GkRFAVRVKRSGRH-GFTSLDVAREIGAALKP-FSAGVDLENPEVEVVVEVRGSTAYL 156
                                       54...44************.***************99.999********************98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.61
                                       ETTEEEEECTEEEEEETHHHHHHHHHTST..TECEEEEE CS
                             THUMP  20 gkgrivvelkgekpeedeellkealekar..giqrvipv 56 
                                        k++iv ++ +  ++e   ++ ea+ +a+  ++ rv+p+
  gi|320100773|ref|YP_004176365.1| 317 DKEEIVGYSRRIGLYEYSSRVAEACAIAPthVATRVSPE 355
                                       577888888888899999999999999999999999998 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.5   3.7e+03      13      30 ..     142     160 ..     137     163 .. 0.77
   2 !   31.0   0.0   1.1e-10   2.8e-07      14     105 ..     404     475 ..     394     477 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                         Rhodanese  13 kva.llDvRppeeYekghI 30 
                                       +v  ++ vR + +Y +g+I
  gi|320100773|ref|YP_004176365.1| 142 EVEvVVEVRGSTAYLHGRI 160
                                       4445999*********998 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.1e-10
                         Rhodanese  14 vallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkklG 90 
                                        +++D+R+ eeY +  +pgA+++              +  ++e+l +     +k+vv+yc++gg +  +a+ l+  G
  gi|320100773|ref|YP_004176365.1| 404 SIVIDARSYEEYRRDALPGALHL--------------SMVDFERLPR-----DKPVVLYCSTGGISLLLARELRGKG 461
                                       349********************..............4444455554.....7************9999*****9** PP

                         Rhodanese  91 yknvsvldGGfkawk 105
                                         + + l+GG+ a+ 
  gi|320100773|ref|YP_004176365.1| 462 -FKAYSLKGGIAAYR 475
                                       .79********9996 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.9e-07   0.00049       1      50 [.     174     225 ..     174     245 .. 0.87
   2 ?    4.1   0.0     0.011        29     136     175 ..     292     330 ..     256     342 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.9e-07
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T..TSHHHHHHHHHHHH CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr..hkkeleaakkiake 50 
                                       +a+vl+SGG DS ++++l+ k+g ev  l+   g+    ++   +akk+a+e
  gi|320100773|ref|YP_004176365.1| 174 RALVLFSGGFDSPVAAWLMAKRGLEVDFLHYMMGSSevSRQAFAVAKKLADE 225
                                       69****************************9999886567777888888765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHTS--EEE-TTTT--HHHHHHHHHHTTH CS
                              QueC 136 fvkalnkalnlgedkkieieaPlidlsKaeivklgkelgv 175
                                       ++++l  a++++ +    +  Pli ++K+eiv  + ++g+
  gi|320100773|ref|YP_004176365.1| 292 TLANLR-AAEYAASPGCIVLRPLIGFDKEEIVGYSRRIGL 330
                                       444444.34555557778999************9999995 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.4e-06     0.019       2      47 ..     174     220 ..     173     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.4e-06
                   Diphthami_syn_2   2 kvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnv 47 
                                       ++ vl+sGG Ds +a +  +k+  ev++L  ++   + s ++ +v  
  gi|320100773|ref|YP_004176365.1| 174 RALVLFSGGFDSPVAAWLMAKRgLEVDFLHYMMGSSEVSRQAFAVAK 220
                                       789**************999998**********99999888777655 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     2e-05     0.052       4      40 ..     176     212 ..     173     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                     tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqgyevigvflklweeede 40 
                                       +v++SgG DS vaa l++++g ev  +++ + ++e +
  gi|320100773|ref|YP_004176365.1| 176 LVLFSGGFDSPVAAWLMAKRGLEVDFLHYMMGSSEVS 212
                                       799*********************9887766665444 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 ?    8.1   0.1     0.002       5.1      15      69 ..      27      75 ..      24      92 .. 0.80
   2 ?   -3.1   0.0       6.4   1.6e+04      53      66 ..     120     133 ..     101     147 .. 0.56
   3 ?   -2.8   0.1         5   1.3e+04      16      39 ..     267     288 ..     266     304 .. 0.49
   4 ?    0.6   0.0      0.44   1.1e+03      18      32 ..     452     466 ..     444     476 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.002
                            LytR_C 15 lAarvadaLeerGftvgevgnagnadeettivyreaaaaaakalaaalglgelqe 69
                                      lA+++++ L+++G tv++v  ++++     i+  ea+++a +al++ +g+ +++e
  gi|320100773|ref|YP_004176365.1| 27 LAENIKRTLARKGITVSAVRFTDAK-----ILV-EAGGDALQALSRVFGVHRVSE 75
                                      9****************96666555.....777.55556999*****99988554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.4
                            LytR_C  53 aaakalaaalglge 66 
                                       + a+++ aal++  
  gi|320100773|ref|YP_004176365.1| 120 DVAREIGAALKPFS 133
                                       45667777776544 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5
                            LytR_C  16 AarvadaLeerGftvgevg.nagna 39 
                                       A+rva+ L   G+++  +g + g+a
  gi|320100773|ref|YP_004176365.1| 267 AGRVAERL---GYDALVTGeALGQA 288
                                       56666666...55444433123333 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.44
                            LytR_C  18 rvadaLeerGftvge 32 
                                        +a++L+++Gf++++
  gi|320100773|ref|YP_004176365.1| 452 LLARELRGKGFKAYS 466
                                       5799*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 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:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3451.54
//
Query:       gi|320100774|ref|YP_004176366.1|  [L=425]
Description: replication factor C large subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   57.8   0.0    2.9e-15   56.8   0.0    1.5  1  AAA              ATPase family associated with various cellul
    4.6e-08   33.0   0.0    8.9e-08   32.0   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.8e-07   30.2   0.1    5.7e-06   26.4   0.0    2.5  3  Rad17            Rad17 P-loop domain
    2.1e-06   28.0   0.0    4.2e-06   27.0   0.0    1.5  1  RFC1             Replication factor RFC1 C terminal domain
    3.5e-06   27.5   0.3    1.7e-05   25.2   0.1    2.4  1  AAA_16           AAA ATPase domain
      7e-06   26.1   0.0    2.3e-05   24.4   0.0    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
    5.6e-05   23.2   0.0    0.00011   22.3   0.0    1.5  1  AAA_14           AAA domain
      8e-05   21.9   0.0    0.00016   21.0   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
    0.00023   21.0   0.0    0.00043   20.1   0.0    1.3  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    0.00024   21.4   0.4      0.012   15.9   0.1    2.8  2  AAA_22           AAA domain
    0.00041   20.6   0.0     0.0012   19.1   0.0    1.8  1  AAA_assoc_2      AAA C-terminal domain
      0.001   18.8   0.0      0.002   17.9   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0018   18.5   0.0     0.0044   17.2   0.0    1.8  1  AAA_33           AAA domain
     0.0035   17.1   0.0     0.0056   16.5   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0042   17.2   0.0     0.0085   16.2   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.006   16.8   0.0      0.017   15.3   0.0    1.8  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.036   13.9   0.0    1.6  2  AAA_11           AAA domain
      0.015   14.9   0.3      0.055   13.0   0.2    2.0  2  AAA_25           AAA domain
      0.018   15.6   0.0      0.061   13.9   0.0    1.9  1  AAA_18           AAA domain
      0.023   13.9   0.1      0.066   12.4   0.0    1.8  2  NB-ARC           NB-ARC domain
      0.038   13.5   0.0      0.066   12.7   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.039   13.9   0.1       0.44   10.5   0.0    2.7  4  NACHT            NACHT domain
       0.06   13.8   0.0       0.18   12.2   0.0    1.9  1  AAA_17           AAA domain
      0.061   13.1   0.0       0.24   11.2   0.0    1.9  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.067   13.2   0.0       0.12   12.3   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.071   13.6   0.0       0.33   11.5   0.0    2.0  2  ABC_tran         ABC transporter
        0.1   12.5   0.0        4.8    7.1   0.0    2.3  2  NTPase_1         NTPase
       0.12   12.5   0.3       0.22   11.7   0.3    1.4  1  Peptidase_S48    Peptidase family S48
       0.12   12.8   0.0       0.35   11.3   0.0    1.8  1  AAA_23           AAA domain
       0.16   11.4   0.0       0.26   10.7   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.17   11.0   0.0       0.36   10.0   0.0    1.5  1  TIP49            TIP49 P-loop domain
       0.19   12.1   0.0       0.43   11.0   0.0    1.6  1  RNA_helicase     RNA helicase
        0.2   11.5   0.0        1.2    9.0   0.0    2.2  1  AAA_3            ATPase family associated with various cellul
       0.23   10.4   0.0       0.39    9.6   0.0    1.3  1  AAA_6            Hydrolytic ATP binding site of dynein motor 


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 !   56.8   0.0   5.5e-18   2.9e-15       2     113 ..      48     145 ..      47     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 5.5e-18
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaksr 74 
                                       ll+GppG+GKT+l++ava++ g +++e+++s+ +      ++++i  ++k a+++     + +i+++DE+d + ++ 
  gi|320100774|ref|YP_004176366.1|  48 LLHGPPGCGKTSLVEAVARSKGYQLFEMNASDAR------RKEDIDRIVKLASRSGaltgSRKIILLDEVDGMDPRA 118
                                       9*********************************......6666666666665444577666***********9988 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGG CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpd 113
                                              +   +++L+++++   +      +i+++n+p 
  gi|320100774|ref|YP_004176366.1| 119 -------DAGGIEALVEVIKATAN-----PIIMTANNPY 145
                                       .......7888999**99999988.....6889998852 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   1.7e-10   8.9e-08       2      81 ..      13      92 ..      12     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.7e-10
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaallt 80
                                      rP++lee+  qe+ kekl   +e+ +k        ll+GpPG Gkt+l + +a+  g +l    +    ++ d+  +++
  gi|320100774|ref|YP_004176366.1| 13 RPRTLEEFEDQEEAKEKLIAWLESWEKGVPGKKAALLHGPPGCGKTSLVEAVARSKGYQLFEMNASDARRKEDIDRIVK 91
                                      9**************************9999***************************999888888888888877654 PP

                            RuvB_N 81 n 81
                                       
  gi|320100774|ref|YP_004176366.1| 92 L 92
                                      3 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.1e-08   5.7e-06       7      76 ..       6      75 ..       2      88 .. 0.88
   2 ?    0.1   0.0       1.2   6.5e+02     121     142 ..      91     112 ..      85     141 .. 0.73
   3 ?   -1.9   0.0       5.2   2.8e+03      57      72 ..     165     180 ..     158     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.1e-08
                             Rad17  7 elWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew 76
                                       +W+ ky+P ++ee     +  e++  wl++       k+  L+ GP+GCgk+  v+ +++  g++l e 
  gi|320100774|ref|YP_004176366.1|  6 VPWVIKYRPRTLEEFEDQEEAKEKLIAWLESWEKGVPGKKAALLHGPPGCGKTSLVEAVARSKGYQLFEM 75
                                      58*************999999999999*99988888888999************************9885 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                             Rad17 121 klqklGddlrtdkklilvedlP 142
                                       kl  +   l + +k+il++++ 
  gi|320100774|ref|YP_004176366.1|  91 KLASRSGALTGSRKIILLDEVD 112
                                       67778888999********985 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.2
                             Rad17  57 gkstvvkvLskelgik 72 
                                       + s vvkvL k+ g +
  gi|320100774|ref|YP_004176366.1| 165 SESVVVKVLKKICGAE 180
                                       5678888888888765 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 !   27.0   0.0     8e-09   4.2e-06       1      90 [.     290     381 ..     290     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8e-09
                                       HHHHHHHHHHHTTSS-GGGHHHHHHHHTHHHHHTT-EE-SS....-----SHHHHHHHHHHHHHHHHHHHTTTTT-- CS
                              RFC1   1 isdgDlvdkkirseqnWsLlpthavlssvlPaslvrgsleg....risFpswLGknSktnKnkRllqelqshlrlkt 73 
                                       +s++D+   +i ++qnW+Ll +  vl ++ P+ + + ++ +     ++ p+ L  +S++++++ + + l+ +l+ ++
  gi|320100774|ref|YP_004176366.1| 290 LSRADVYMGRIVRTQNWDLLSY--VLEMMGPGVAFARKTYRyrwkPFKSPERLKLMSEAKRSREIRESLAEQLSRRL 364
                                       599*******************..9******6555544333455588899*************************** PP

                                       ----HHHHHTTTHHHHH CS
                              RFC1  74 saskselrldylpllkk 90 
                                        +sk+ +r d++p+l+ 
  gi|320100774|ref|YP_004176366.1| 365 LTSKTVVRSDVIPFLRV 381
                                       *************9985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   3.3e-08   1.7e-05      11      49 ..      29      69 ..      23     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.3e-08
                            AAA_16 11 qLlsalervrsgrp..elvllsGesGvGKsslvrellrale 49
                                      +L + le++ +g p   + ll+G++G+GK+slv++++r+  
  gi|320100774|ref|YP_004176366.1| 29 KLIAWLESWEKGVPgkKAALLHGPPGCGKTSLVEAVARSKG 69
                                      56667888888888889*******************98533 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 !   24.4   0.0   4.4e-08   2.3e-05       3      78 ..      48     115 ..      46     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.4e-08
                                       EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       lL GppG+gK++l+e +a+  + ++++++ ++  ++ed+   +++     + + ++l+    + +i++lDEv+ ++
  gi|320100774|ref|YP_004176366.1|  48 LLHGPPGCGKTSLVEAVARSKGYQLFEMNASDARRKEDIDRIVKL-----ASRSGALT---GSRKIILLDEVDGMD 115
                                       89****************************************998.....66677777...788899999998665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.1e-07   0.00011       2      76 ..      44     114 ..      43     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.1e-07
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek..lkeekktylflDEiqev 76 
                                       +k+ ++ G+  +GKT l++ +++++     + +++n  d r k+  d   + +l  ++  l++  +++++lDE+  +
  gi|320100774|ref|YP_004176366.1|  44 KKAALLHGPPGCGKTSLVEAVARSKG---YQLFEMNASDARRKEDIDR--IVKLASRSgaLTG-SRKIILLDEVDGM 114
                                       57899*****************9999...99*******9999765544..6777777664555.8999*****9765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     3e-07   0.00016      21     100 ..      11      91 ..       2     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-07
                            DUF815  21 evdevklddLvgidkqkealventeqfleglpann.vLLwGarGtGKSslvkallneyaeegLrlievekedlkelp 96 
                                       ++++ +l+++ + ++ ke+l++  e + +g p ++ +LL G  G+GK slv a+ ++   +   +   + ++ ++++
  gi|320100774|ref|YP_004176366.1|  11 KYRPRTLEEFEDQEEAKEKLIAWLESWEKGVPGKKaALLHGPPGCGKTSLVEAVARSKGYQLFEMNASDARRKEDID 87 
                                       6677789999**********************97637****************987655544444333333333444 PP

                            DUF815  97 klve 100
                                       ++v+
  gi|320100774|ref|YP_004176366.1|  88 RIVK 91 
                                       4443 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 !   20.1   0.0   8.1e-07   0.00043      49     173 ..      94     211 ..      66     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.1e-07
                                       STTTTSSSSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE-- CS
                    DNA_pol3_delta  49 cetlpffsdkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveakt 125
                                         +  + ++++i++l+    +      ++  +++L e+++   + + +i++a++  +++ + + +L +   v+ +k+
  gi|320100774|ref|YP_004176366.1|  94 SRSGALTGSRKIILLDEVDGM--DPRADAGGIEALVEVIKA--TANPIIMTANNPYSQALRPLRELSE---VIGFKR 163
                                       5566788999*****999444..555556666666666666..5677888999999999998888886...9***** PP

                                       --TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                    DNA_pol3_delta 126 lkeeelkkwiqkraqelglkiekealelLlelvennlsaikqelekLa 173
                                       l+e+ + k ++k++ +++l  e+eal +++ ++e++l+ + + le La
  gi|320100774|ref|YP_004176366.1| 164 LSESVVVKVLKKICGAEKLFCEDEALREIARRSEGDLRSAINDLEALA 211
                                       ********************************************9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.2e-05     0.012       5      48 ..      44      78 ..      42     146 .. 0.82
   2 ?   -2.4   0.0       9.8   5.2e+03      52      70 ..     348     366 ..     335     380 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48
                                      ++  +++G++G+GKT l++ +++++         + ++++++++
  gi|320100774|ref|YP_004176366.1| 44 KKAALLHGPPGCGKTSLVEAVARSK---------GYQLFEMNAS 78
                                      67899****************9997.........4444444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.8
                            AAA_22  52 sskdllrellralglelka 70 
                                        s+++++ l+++l ++l +
  gi|320100774|ref|YP_004176366.1| 348 RSREIRESLAEQLSRRLLT 366
                                       4555566666665555444 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.3e-06    0.0012       3      37 ..     180     214 ..     178     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.3e-06
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaa 37 
                                       +kl +ed+al+ +a+ ++GD R+a+n LE++a  +
  gi|320100774|ref|YP_004176366.1| 180 EKLFCEDEALREIARRSEGDLRSAINDLEALAGLS 214
                                       567789***********************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 !   17.9   0.0   3.8e-06     0.002      23     153 ..      19     147 ..      11     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.8e-06
                         IstB_IS21  23 dfraarsldkrkvkeLatl.sfiekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgk 98 
                                       +f+ +++++++ ++ L +  + +  k++ +l Gp+G GK+ l  a++++   +g++ + + ++d  ++  ++r   k
  gi|320100774|ref|YP_004176366.1|  19 EFEDQEEAKEKLIAWLESWeKGVPGKKAALLHGPPGCGKTSLVEAVARS---KGYQLFEMNASDARRKEDIDRI-VK 91 
                                       57777888899999886641568899999****************9875...7999988999988777665554.55 PP

                         IstB_IS21  99 laralkrllkv.dllilDdl.gllpldqa.eaellfeviekryerrsiiitsnlpfae 153
                                       la++  +l+ + ++++lD++ g+ p  +a   e l evi++    ++ii+t+n p ++
  gi|320100774|ref|YP_004176366.1|  92 LASRSGALTGSrKIILLDEVdGMDPRADAgGIEALVEVIKAT--ANPIIMTANNPYSQ 147
                                       55555555544399999**95666654441568999999886..6799****999875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.4e-06    0.0044       3      30 ..      48      75 ..      47     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.4e-06
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllss 30
                                      ll+G+pG+GK+ l+e +++  g++l + 
  gi|320100774|ref|YP_004176366.1| 48 LLHGPPGCGKTSLVEAVARSKGYQLFEM 75
                                      79******************99877544 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 !   16.5   0.0   1.1e-05    0.0056       2      71 ..      48     111 ..      47     127 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       + hG pGcGK++l+  ++r+     ++ + +e+ +++  + + +  r v+ +  +   + + ki++lDE 
  gi|320100774|ref|YP_004176366.1|  48 LLHGPPGCGKTSLVEAVARS-----KGYQLFEM-NASDARRKEDIDRIVKLASRSGALTGSRKIILLDEV 111
                                       57******************.....44442333.333334444444444433333333356899999996 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-05    0.0085       6      83 ..      47     117 ..      44     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                        ll gp g+Gkt l +a+a+        +l  ++as+   +e+++++v+     + + +g   + i+llDE+d   p
  gi|320100774|ref|YP_004176366.1|  47 ALLHGPPGCGKTSLVEAVARSKGY----QLFEMNASDARRKEDIDRIVKL-ASRSGALTG--SRKIILLDEVDGMDP 116
                                       5789****************9996....9999999999999999998864.444444443..455********9988 PP

                                       - CS
                             AAA_2  83 k 83 
                                       +
  gi|320100774|ref|YP_004176366.1| 117 R 117
                                       4 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.3e-05     0.017       4      28 ..      49      74 ..      46      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-05
                            AAA_28  4 itGgestGKTtlleaLaar.gypvvp 28
                                      + G++++GKT+l+ea a+  gy+ ++
  gi|320100774|ref|YP_004176366.1| 49 LHGPPGCGKTSLVEAVARSkGYQLFE 74
                                      78***************866999876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.8e-05     0.036      10      40 ..      37      67 ..      29      96 .. 0.75
   2 ?   -2.7   0.1       7.6     4e+03     164     199 ..     336     371 ..     325     374 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-05
                            AAA_11 10 iksalseseitliqGPPGtgKTktivellsq 40
                                      +++ +  ++ +l++GPPG+gKT+ + ++ ++
  gi|320100774|ref|YP_004176366.1| 37 WEKGVPGKKAALLHGPPGCGKTSLVEAVARS 67
                                      55666677789***********988776655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.6
                            AAA_11 164 eqerrklkkerkelskeleeaeesleeevldeaeiv 199
                                       ++er kl +e+k+ ++  e+  e+l++ +l+++ +v
  gi|320100774|ref|YP_004176366.1| 336 SPERLKLMSEAKRSREIRESLAEQLSRRLLTSKTVV 371
                                       556667777777777777777777777777777776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2    0.0001     0.055      19      54 ..      31      65 ..      13      78 .. 0.76
   2 ?   -2.1   0.0       4.5   2.4e+03     114     138 ..      70      94 ..      61     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                            AAA_25 19 ppprrwlvkgllpagelallaGapgtGKttlaldla 54
                                      ++ ++ + kg+ p ++ all G+pg+GKt l+  +a
  gi|320100774|ref|YP_004176366.1| 31 IAWLESWEKGV-PGKKAALLHGPPGCGKTSLVEAVA 65
                                      55566677888.9****************9975544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.5
                            AAA_25 114 lpLfakdrggtlltadvdaleaaie 138
                                        +Lf++ + ++++++d+d++ + + 
  gi|320100774|ref|YP_004176366.1|  70 YQLFEMNASDARRKEDIDRIVKLAS 94 
                                       5789999999999999999887665 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   0.00012     0.061       3      30 ..      49      79 ..      48     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf...gvnlrd 30
                                      l G+pG+GKt+l ++++++ g+     n +d
  gi|320100774|ref|YP_004176366.1| 49 LHGPPGCGKTSLVEAVARSKGYqlfEMNASD 79
                                      78**************999866666444444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.066       2      43 ..      24      67 ..      23      75 .. 0.85
   2 ?   -3.0   0.1       6.4   3.4e+03      80     105 ..     344     369 ..     335     374 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHHC..TTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  2 eksvekviekLle..kdelqslvvalvGmgGvGKttlakqilnk 43
                                      e+ +ek+i +L    k+ +++    l+G +G+GKt l++ + ++
  gi|320100774|ref|YP_004176366.1| 24 EEAKEKLIAWLESweKGVPGKKAALLHGPPGCGKTSLVEAVARS 67
                                      778999999998554788999999**************999876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.4
                                       CTTSSSS-STTSHHHHHHHHCCCTTE CS
                            NB-ARC  80 eddleekeeveslkrklvrlLltkrf 105
                                       ++   + e +esl+++l r Llt ++
  gi|320100774|ref|YP_004176366.1| 344 SEAKRSREIRESLAEQLSRRLLTSKT 369
                                       33333344444455555555555555 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   0.00013     0.066      31      82 ..      42      90 ..      36     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                                        kk  ll Gp G+GKt++++ + ++     y+   +n s     +++ +i+
  gi|320100774|ref|YP_004176366.1| 42 PGKKAALLHGPPGCGKTSLVEAVARSKG---YQLFEMNASDARRKEDIDRIV 90
                                      568999****************998766...888889988888888877776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       7.6     4e+03     120     141 ..       5      26 ..       3      35 .. 0.75
   2 ?   10.5   0.0   0.00083      0.44       4      22 ..      48      66 ..      45      68 .. 0.88
   3 ?   -1.3   0.0       3.5   1.8e+03      85     157 ..     106     171 ..      67     179 .. 0.63
   4 ?   -2.5   0.0       8.3   4.4e+03      49      61 ..     350     363 ..     338     379 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.6
                                       --EEEEEEECCCHHHHCTTSSC CS
                             NACHT 120 easllltvrpralrdleeqlee 141
                                       ++++++  rpr+l++ e q e 
  gi|320100774|ref|YP_004176366.1|   5 RVPWVIKYRPRTLEEFEDQEEA 26 
                                       6899999999999997666554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00083
                                      EEEC-TTTCHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklal 22
                                      +l+G++G+GKT L++ +a+
  gi|320100774|ref|YP_004176366.1| 48 LLHGPPGCGKTSLVEAVAR 66
                                      79************99875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.5
                                       EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHHHH CS
                             NACHT  85 lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegfsesrrkq 157
                                       ++lD +D +    ++       + L e i++   + +++++t+ +  ++ l+ + e ++v+  + +ses +++
  gi|320100774|ref|YP_004176366.1| 106 ILLDEVDGMDPRADA----GGIEALVEVIKA---TANPIIMTANNPYSQALRPLRELSEVIGFKRLSESVVVK 171
                                       777777777775555....333444455555...777777777777776666666666555555555555555 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 8.3
                                       -....-HCHHHCCC CS
                             NACHT  49 gna.rsladllfsq 61 
                                        ++  sla++l + 
  gi|320100774|ref|YP_004176366.1| 350 REIrESLAEQLSRR 363
                                       22222333333333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00034      0.18       2      26 ..      51      75 ..      50     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                                      E-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17  2 GgPGsGKgtqceklvekygfthlsa 26
                                      G+PG+GK+ ++e +++  g++ +++
  gi|320100774|ref|YP_004176366.1| 51 GPPGCGKTSLVEAVARSKGYQLFEM 75
                                      9****************99999865 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 ?   -0.9   0.0       2.3   1.2e+03      19      41 ..      44      66 ..      27      71 .. 0.85
   2 ?   11.2   0.0   0.00046      0.24      83     120 ..      81     119 ..      54     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.3
                   DNA_pol3_delta2 19 ahayLfeGdegigkkelalnlak 41
                                      ++a L++G+ g+gk +l  ++a+
  gi|320100774|ref|YP_004176366.1| 44 KKAALLHGPPGCGKTSLVEAVAR 66
                                      5799**********999887775 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00046
                   DNA_pol3_delta2  83 ikldqirelieelsrkpre.skkkiiiiedaekmtksAa 120
                                        ++++i ++ + +sr++   +++kii++++++ m+++A 
  gi|320100774|ref|YP_004176366.1|  81 RRKEDIDRIVKLASRSGALtGSRKIILLDEVDGMDPRAD 119
                                       4799***********98766****************996 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00023      0.12       7      46 ..      27      71 ..      18      78 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHCH......TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  7 tealgkklakal......gdvilLeGdLGaGKTtlvrglakalgve 46
                                       e+l + l +        +++ lL+G+ G+GKT lv ++a++ g++
  gi|320100774|ref|YP_004176366.1| 27 KEKLIAWLES-WekgvpgKKAALLHGPPGCGKTSLVEAVARSKGYQ 71
                                      3444444433.13445656679******************998876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00063      0.33      12      34 ..      45      67 ..      37      94 .. 0.81
   2 ?   -1.6   0.0       6.7   3.5e+03     122     134 ..      98     110 ..      87     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00063
                                      SEEEEEESTTSSHHHHHHHHTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagl 34
                                      +   + G+ G+GK++L++++a+ 
  gi|320100774|ref|YP_004176366.1| 45 KAALLHGPPGCGKTSLVEAVARS 67
                                      344577************99886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.7
                                       HHHHTSSEEEEES CS
                                       xxxxxxxxxxxxx RF
                          ABC_tran 122 allkkpkllllDE 134
                                       al   +k++llDE
  gi|320100774|ref|YP_004176366.1|  98 ALTGSRKIILLDE 110
                                       678899******9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.009       4.8       4      21 ..      49      66 ..      46      85 .. 0.85
   2 ?    3.2   0.0      0.14        72      95     152 ..     102     160 ..      82     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.009
                                      EE--TTSSHHHHHHHHHH CS
                          NTPase_1  4 iTGppGvGKtTlvkkvle 21
                                      + GppG GKt lv+ v++
  gi|320100774|ref|YP_004176366.1| 49 LHGPPGCGKTSLVEAVAR 66
                                      78************9986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                                       HH-EEEE---STTGGG-H.HHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EE CS
                          NTPase_1  95 eadviviDEiGkmElksk.kfkeaveevLk.sekpvlavihrrkdlalveeirerkdvkv 152
                                       +  +i++DE+  m   +    +ea+ ev+k + +p++++  ++  ++ ++ +re ++v  
  gi|320100774|ref|YP_004176366.1| 102 SRKIILLDEVDGMDPRADaGGIEALVEVIKaTANPIIMTANNP-YSQALRPLRELSEVIG 160
                                       456999****99*98775156899999999899*******999.6778888888766544 PP

>> Peptidase_S48  Peptidase family S48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00042      0.22     119     147 ..     346     374 ..     338     376 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00042
                     Peptidase_S48 119 adrrlplsealaehikrrllyaetvmrld 147
                                       a+r   + e+lae + rrll ++tv+r d
  gi|320100774|ref|YP_004176366.1| 346 AKRSREIRESLAEQLSRRLLTSKTVVRSD 374
                                       56777899*******************87 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00066      0.35      19      40 ..      44      65 ..      16      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00066
                            AAA_23 19 kgltlItGpNGaGKTTildAik 40
                                      k+  l++Gp G+GKT++++A+ 
  gi|320100774|ref|YP_004176366.1| 44 KKAALLHGPPGCGKTSLVEAVA 65
                                      56679***************75 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00049      0.26      19      42 ..      41      64 ..      17     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00049
                      Mg_chelatase 19 aaGgHnlllvGppGsGKtmlakrl 42
                                      + G+   ll GppG+GKt l +++
  gi|320100774|ref|YP_004176366.1| 41 VPGKKAALLHGPPGCGKTSLVEAV 64
                                      5689999***********998876 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00068      0.36      44      86 ..      38      78 ..      17      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00068
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 44 kekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgs 86
                                      +++  + +a Ll Gp+g Gkt+l  a++++ g       +++s
  gi|320100774|ref|YP_004176366.1| 38 EKGVPGKKAALLHGPPGCGKTSLVEAVARSKG--YQLFEMNAS 78
                                      4444456899*****************99877..444556665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00082      0.43       2      21 ..      48      67 ..      47      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00082
                      RNA_helicase  2 wlyGpsgeGKStlakeLaka 21
                                      +l+Gp+g+GK++l++ +a++
  gi|320100774|ref|YP_004176366.1| 48 LLHGPPGCGKTSLVEAVARS 67
                                      689***********998775 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0022       1.2       3      88 ..      48     128 ..      46     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                             AAA_3   3 llegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktq 79 
                                       ll+g PG +kt lv+a+a++ + ++  +         di  +  + +++  ++        +++l de++   p+++
  gi|320100774|ref|YP_004176366.1|  48 LLHGPPGCGKTSLVEAVARSKGYQLFEMNASDARRKEDIDRIVKLASRSGALTG-----SRKIILLDEVDGMDPRAD 119
                                       899****************99888777666555555555433333333333322.....246677777777777776 PP

                             AAA_3  80 salleamee 88 
                                       +  +ea+ e
  gi|320100774|ref|YP_004176366.1| 120 AGGIEALVE 128
                                       666666555 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00074      0.39      35      86 ..      47      98 ..      39     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00074
                             AAA_6 35 gapaGpagtGKtEtvkdLakalakqvvvfncsdqldykslgkifkGlaqsGa 86
                                      + ++Gp g GKt  v  +a++ + q++ +n sd+   + + +i k  ++sGa
  gi|320100774|ref|YP_004176366.1| 47 ALLHGPPGCGKTSLVEAVARSKGYQLFEMNASDARRKEDIDRIVKLASRSGA 98
                                      6689**************************************9998777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 2858.53
//
Query:       gi|320100775|ref|YP_004176367.1|  [L=347]
Description: replication factor C small subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-26   91.0   0.2    1.3e-25   89.6   0.0    1.8  1  Rep_fac_C        Replication factor C C-terminal domain
    2.3e-15   57.2   0.0    4.5e-15   56.2   0.0    1.5  1  AAA              ATPase family associated with various cellul
    4.7e-15   55.8   0.0    7.4e-11   42.1   0.1    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    3.9e-08   33.2   0.0    9.8e-08   31.9   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    4.6e-08   33.0   0.1    1.9e-06   27.8   0.0    2.4  2  DNA_pol3_delta   DNA polymerase III, delta subunit
      7e-07   29.3   0.0    1.4e-06   28.4   0.0    1.5  1  Rad17            Rad17 P-loop domain
    4.2e-06   27.3   0.3     0.0017   18.8   0.0    2.7  3  AAA_16           AAA ATPase domain
    6.1e-06   26.3   0.0    3.7e-05   23.7   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    6.1e-06   26.3   0.1    7.2e-05   22.8   0.0    2.2  2  AAA_14           AAA domain
    7.1e-06   26.3   0.1      3e-05   24.3   0.1    2.2  1  AAA_assoc_2      AAA C-terminal domain
      2e-05   24.9   1.2       0.23   11.7   0.0    3.0  3  AAA_22           AAA domain
    8.2e-05   22.5   0.0    0.00018   21.4   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
    0.00013   21.5   0.1     0.0062   15.9   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00015   21.5   0.0    0.00029   20.6   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
    0.00053   19.5   0.2      0.063   12.7   0.0    2.4  2  PhoH             PhoH-like protein
    0.00073   20.1   0.1     0.0025   18.3   0.0    1.9  1  AAA_18           AAA domain
     0.0019   18.2   0.0       0.14   12.2   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
      0.002   17.7   0.0     0.0031   17.0   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
     0.0021   17.8   1.0       0.29   10.8   0.1    2.8  2  AAA_30           AAA domain
     0.0029   17.7   0.0     0.0054   16.9   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0041   16.9   0.0      0.012   15.4   0.0    1.7  2  AAA_11           AAA domain
     0.0064   15.7   0.0     0.0097   15.1   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.011   15.7   0.0       0.43   10.5   0.0    2.4  2  NTPase_1         NTPase
      0.011   15.4   0.0        0.4   10.4   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
      0.012   14.9   0.0      0.036   13.3   0.0    1.8  2  TIP49            TIP49 P-loop domain
      0.015   15.5   0.1       0.03   14.5   0.1    1.7  1  AAA_33           AAA domain
      0.015   15.2   0.2        1.1    9.1   0.0    3.1  3  DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau do
      0.016   14.6   0.1        1.7    8.0   0.0    2.6  2  TniB             Bacterial TniB protein
      0.016   15.6   0.0      0.031   14.7   0.0    1.6  1  RNA_helicase     RNA helicase
      0.016   15.1   0.0        0.2   11.6   0.0    2.5  1  NACHT            NACHT domain
      0.017   14.7   0.2      0.048   13.2   0.1    1.9  1  AAA_25           AAA domain
      0.023   14.4   0.0      0.049   13.4   0.0    1.5  1  AAA_24           AAA domain
      0.029   13.7   0.1       0.24   10.7   0.0    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.035   14.0   0.0      0.065   13.1   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
      0.085   12.3   0.0       0.14   11.6   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
      0.095   13.0   0.4       0.63   10.4   0.1    2.2  2  AAA_19           AAA domain
       0.11   12.2   0.0       0.21   11.3   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   12.3   0.0        0.3   11.0   0.0    1.6  1  APS_kinase       Adenylylsulphate kinase
       0.12   13.2   0.6        1.5    9.6   0.0    2.8  2  DUF4373          Domain of unknown function (DUF4373)
       0.15   12.2   0.0       0.46   10.6   0.0    1.7  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.21   11.7   0.0       0.41   10.7   0.0    1.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


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 !   89.6   0.0   2.9e-28   1.3e-25       2      88 .]     249     336 ..     248     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 2.9e-28
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS...S-HHHHHHHHHHHHHHHHHHHCTH- CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq.eelpeaqkleilellgeiekrlveGas 77 
                                       hp e++e+l+ +l+g+f+ea++klr+l++e+G+s+ di++q+h+ +++q  ++p+++++ i +l+gei++rlveGa+
  gi|320100775|ref|YP_004176367.1| 249 HPREVREMLNEALSGNFTEARNKLRTLMIEYGLSGVDIIRQIHKEIFSQeVKIPDEMRVLIADLAGEIQFRLVEGAD 325
                                       9***********************************************9977************************* PP

                                       HHHHHHHHHHH CS
                         Rep_fac_C  78 ehlqlsallar 88 
                                       +++ql+a+lar
  gi|320100775|ref|YP_004176367.1| 326 DEIQLNAFLAR 336
                                       *********97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0     1e-17   4.5e-15       1     128 [.      64     180 ..      64     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1e-17
                                       EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TS.EEEEEETGGGH CS
                               AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka.kp.silfiDEidal 70 
                                       +l+ GppGtGKT++a+ +a++l     + ++le+++s+ +   ++    k++e+ ++       p +i+++DE+d++
  gi|320100775|ref|YP_004176367.1|  64 MLFAGPPGTGKTTMAHCLAHDLygddyKKYMLELNASDER--KIEVIRGKVKEFARSRVV-GeVPfKIVLLDEADNM 137
                                       89*******************966655699**********..567777777777765333.25688*********** PP

                                       HHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                               AAA  71 aksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrki 128
                                       + +            +++L + ++ ++    ++ +i+++n+p+k+ +++  +R  +  
  gi|320100775|ref|YP_004176367.1| 138 TADA-----------QQALRRLMELYSA---TTRFILTANYPSKIIEPIQ-SRTAIFR 180
                                       9888...........***********99...589****************.8987655 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 !   11.7   0.0   0.00037      0.16       2      47 ..      45      89 ..      44     101 .. 0.89
   2 !   42.1   0.1   1.7e-13   7.4e-11      83     162 ..     103     184 ..      88     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                   DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                                      q+e++  l+k ++++ + h +Lf+G+ g+gk ++a +la+ l  ++
  gi|320100775|ref|YP_004176367.1| 45 QKEIVVRLKKFVEEKSIPH-MLFAGPPGTGKTTMAHCLAHDLYGDD 89
                                      78899999999**999999.79*****************9998665 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 1.7e-13
                   DNA_pol3_delta2  83 ikldqirelieelsrkpresk..kkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqel 157
                                        k++ ir   +e+ r+ + ++   ki+++++a++mt+ A+ al +++E  s+ + fiL+++ ++k++++i+SR+ ++
  gi|320100775|ref|YP_004176367.1| 103 RKIEVIRGKVKEFARSRVVGEvpFKIVLLDEADNMTADAQQALRRLMELYSATTRFILTANYPSKIIEPIQSRTAIF 179
                                       489999988888888888765227***************************************************** PP

                   DNA_pol3_delta2 158 kfspl 162
                                       +fspl
  gi|320100775|ref|YP_004176367.1| 180 RFSPL 184
                                       ***97 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.3e-10   9.8e-08       2      57 ..      35      85 ..      34      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.3e-10
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                                      rP++l+e + q+++  +lk f+e     e+++ h+l++GpPG Gktt+a+ +a++l
  gi|320100775|ref|YP_004176367.1| 35 RPRTLDEVVNQKEIVVRLKKFVE-----EKSIPHMLFAGPPGTGKTTMAHCLAHDL 85
                                      9******************9997.....6899*********************998 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 !   27.8   0.0   4.4e-09   1.9e-06      59     170 ..     127     228 ..     122     231 .. 0.92
   2 ?    2.5   0.0      0.25   1.1e+02     143     173 ..     246     276 ..     238     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.4e-09
                                       EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHH CS
                    DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwi 135
                                       +iv+l+ +      ++ +++ +++L ++++ ++++t +il+a+       k++  +++++ ++++++l++e++ + +
  gi|320100775|ref|YP_004176367.1| 127 KIVLLDEA------DNMTADAQQALRRLMELYSATTRFILTAN-Y---PSKIIEPIQSRTAIFRFSPLRKEDVVERL 193
                                       56666666......679**************************.4...458999*********************** PP

                                       HHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 136 qkraqelglkiekealelLlelvennlsaikqele 170
                                        ++++++++k ++ ale+++el+e++++++ + l+
  gi|320100775|ref|YP_004176367.1| 194 RYICNAEKVKCDERALETIYELSEGDMRRAINILQ 228
                                       ******************************99987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.25
                                       T-EE-HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                    DNA_pol3_delta 143 glkiekealelLlelvennlsaikqelekLa 173
                                       gl   +e+ e+L e++++n++ + ++l  L+
  gi|320100775|ref|YP_004176367.1| 246 GLAHPREVREMLNEALSGNFTEARNKLRTLM 276
                                       566678999******************9986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   3.1e-09   1.4e-06       8     119 ..      29     136 ..      23     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.1e-09
                             Rad17   8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel.giklrewlnpvslk 83 
                                       lW eky+P +++e+   k+ +  +k++++ +++++      L +GP+G gk+t+ + L+  l g ++++++  ++  
  gi|320100775|ref|YP_004176367.1|  29 LWAEKYRPRTLDEVVNQKEIVVRLKKFVEEKSIPHM-----LFAGPPGTGKTTMAHCLAHDLyGDDYKKYMLELN-A 99 
                                       7***************************99999988.....9*****************9753888999987777.4 PP

                             Rad17  84 epdnqksdfkgltekesrflsqies.fkeleLkdaky 119
                                       + + + + ++g+++ + r     e+ fk ++L +a +
  gi|320100775|ref|YP_004176367.1| 100 SDERKIEVIRGKVKEFARSRVVGEVpFKIVLLDEADN 136
                                       4455666678888877765444443355555555544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.9e-06    0.0017      18      61 ..      55     113 ..      44     126 .. 0.73
   2 ?    6.0   0.1     0.033        15     119     164 ..     108     154 ..      96     161 .. 0.73
   3 ?   -1.2   0.0       5.1   2.2e+03      49      89 ..     258     294 ..     247     342 .. 0.43

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.9e-06
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd...............ggiflrgkcd 61 
                                        v + + + +l+ G++G+GK++++ +l++ l +d               ++ ++rgk +
  gi|320100775|ref|YP_004176367.1|  55 FVEEKSIPHMLFAGPPGTGKTTMAHCLAHDLYGDdykkymlelnasderKIEVIRGKVK 113
                                       455666799*******************9998886666555555555543555555555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.033
                            AAA_16 119 llellkrllallsrderp.lvlvlDdlqwadeaslqllaaLlrlles 164
                                       ++ ++k++++    +e p  +++lD+++   ++ +q+l+ L++l ++
  gi|320100775|ref|YP_004176367.1| 108 IRGKVKEFARSRVVGEVPfKIVLLDEADNMTADAQQALRRLMELYSA 154
                                       55566666644444566656999******************998665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.1
                            AAA_16  49 ekdggiflrgkcdqlesaipysalaqalareellrqlldea 89 
                                       +++    l+g++++ + +++ +++   l+  +++rq++ e 
  gi|320100775|ref|YP_004176367.1| 258 NEA----LSGNFTEARNKLRTLMIEYGLSGVDIIRQIHKEI 294
                                       444....4455555433322233333333334444444331 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   8.4e-08   3.7e-05       1      90 [.      63     150 ..      63     167 .. 0.84
   2 ?   -2.0   0.0       7.6   3.3e+03     113     124 ..     238     252 ..     198     264 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.4e-08
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                       ++l  GppGtgK+++a  la+ l ++ +  ++l  + + e  +  ++  ++ +++  s +v ++   +i++lDE ++
  gi|320100775|ref|YP_004176367.1|  63 HMLFAGPPGTGKTTMAHCLAHDLyGDDYKKYMLELNASDERKIEVIR--GKVKEFARSRVVGEV-PFKIVLLDEADN 136
                                       68999*****************9988887777777666665544444..688999999999333.789********* PP

                                       --HHHHHHHHHHHH CS
                             AAA_5  77 aesevlnsLlslle 90 
                                       +  +++++L +l+e
  gi|320100775|ref|YP_004176367.1| 137 MTADAQQALRRLME 150
                                       *********99987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.6
                                       ....-EEEEEESS-- CS
                             AAA_5 113 r...frviatanpld 124
                                       +     vi++a+p++
  gi|320100775|ref|YP_004176367.1| 238 EeavYKVIGLAHPRE 252
                                       023356777777777 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.58   2.5e+02      68      91 ..      37      60 ..      21      68 .. 0.79
   2 !   22.8   0.0   1.6e-07   7.2e-05       6      99 ..      65     162 ..      61     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.58
                            AAA_14 68 lflDEiqevpewekalkslvdegk 91
                                        lDE+ + +e+   lk++v+e++
  gi|320100775|ref|YP_004176367.1| 37 RTLDEVVNQKEIVVRLKKFVEEKS 60
                                      579*****************9984 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.6e-07
                            AAA_14   6 vitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev.pe 78 
                                       +  G+  +GKTt+++ l+++l+    k+ +l++n  der+ +     k+ e+ +++ + e   ++++lDE+ ++  +
  gi|320100775|ref|YP_004176367.1|  65 LFAGPPGTGKTTMAHCLAHDLYgdDYKKYMLELNASDERKIEVIRG-KVKEFARSRvVGEVPFKIVLLDEADNMtAD 140
                                       5679999***********9999876678888888888888765543.577777777444445678******987368 PP

                            AAA_14  79 wekalkslvdeg.knldvivtG 99 
                                       +++al++l++ +    ++i+t 
  gi|320100775|ref|YP_004176367.1| 141 AQQALRRLMELYsATTRFILTA 162
                                       **********665678999885 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 !   24.3   0.1   6.8e-08     3e-05       3      37 ..     200     234 ..     198     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.8e-08
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaa 37 
                                       +k+k+++ ale++ el++GD+R+a+n+L++ a+  
  gi|320100775|ref|YP_004176367.1| 200 EKVKCDERALETIYELSEGDMRRAINILQTTAALG 234
                                       689**************************655443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00094      0.41       7      29 ..      63      85 ..      57      96 .. 0.86
   2 !   11.7   0.0   0.00053      0.23      72     128 ..     102     161 ..      82     166 .. 0.71
   3 ?   -0.8   0.0         4   1.7e+03      57      57 ..     254     254 ..     187     338 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00094
                            AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                      +++  G++GtGKTt +  l++ l
  gi|320100775|ref|YP_004176367.1| 63 HMLFAGPPGTGKTTMAHCLAHDL 85
                                      67889***********9998765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00053
                            AAA_22  72 rlsseellealeqalrarav....ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                       + + e ++ ++ + +r+r v     +++++DEa+++ +++a + Lr+l++l +  +++iL 
  gi|320100775|ref|YP_004176367.1| 102 ERKIEVIRGKVKEFARSRVVgevpFKIVLLDEADNM-TADAQQALRRLMELYSATTRFILT 161
                                       33444455788888888888998889**********.888888888888876677777765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 4
                            AAA_22  57 l 57 
                                       +
  gi|320100775|ref|YP_004176367.1| 254 R 254
                                       2 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.1e-07   0.00018       1      90 [.      63     153 ..      63     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.1e-07
                             AAA_3   1 hvllegvPGlaktllvkalakaldle.fkriqftpdllPsdilGtevfeekekefefkk..Gpvfanllladeinra 74 
                                       h+l+ g PG++kt++++ la+ l  + +k  ++  +l  sd   +ev++ k kef  ++  G v  +++l de +  
  gi|320100775|ref|YP_004176367.1|  63 HMLFAGPPGTGKTTMAHCLAHDLYGDdYK--KYMLELNASDERKIEVIRGKVKEFARSRvvGEVPFKIVLLDEADNM 137
                                       99******************998765155..5677999****************98764449*************** PP

                             AAA_3  75 ppktqsalleameerq 90 
                                       ++ +q al   me   
  gi|320100775|ref|YP_004176367.1| 138 TADAQQALRRLMELYS 153
                                       ********99998655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.4e-05    0.0062      24      56 ..      63      96 ..      58     116 .. 0.79
   2 ?    2.9   0.0      0.14        62     109     149 ..     128     167 ..     126     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlps.llpplseeeale 56
                                      ++l++GppG+GKt +a++l+  l  +  ++ +le
  gi|320100775|ref|YP_004176367.1| 63 HMLFAGPPGTGKTTMAHCLAHdLYGDDYKKYMLE 96
                                      79****************9751445555555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefpar 149
                                       +++LDE+ ++++++ ++LR+ +e  + t +r   ++++p++
  gi|320100775|ref|YP_004176367.1| 128 IVLLDEADNMTADAQQALRRLMELYSAT-TRFILTANYPSK 167
                                       678*****************99987654.566667777765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   6.7e-07   0.00029      41     150 ..      53     165 ..      18     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.7e-07
                         IstB_IS21  41 lsfiekke..nivllGpsGvGKshlaialgveavraglsvlfvrvedL.veelkrarrdgklaralkrllkv..dll 112
                                        +f+e+k    +++ Gp+G+GK+ +a  l+++   ++++ + + +++   +++++ r++ k   + + + +v  +++
  gi|320100775|ref|YP_004176367.1|  53 KKFVEEKSipHMLFAGPPGTGKTTMAHCLAHDLYGDDYKKYMLELNASdERKIEVIRGKVKEFARSRVVGEVpfKIV 129
                                       567777753368999************************9988887651346666666655444444444444499* PP

                         IstB_IS21 113 ilDdlgllpldqaeaellfeviekryerrsiiitsnlp 150
                                       +lD+    + d ++   l +++e    ++  i+t+n p
  gi|320100775|ref|YP_004176367.1| 130 LLDEADNMTADAQQ--ALRRLMELYSATTRFILTANYP 165
                                       ****9887777554..4556666656677788888876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00014     0.063       8      46 ..      44      88 ..      40     114 .. 0.73
   2 ?    4.3   0.2     0.053        23     121     141 ..     127     146 ..      98     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHH....H-S..EEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH  8 eQkeylealk....knd..ivfaiGpaGtGKtylavalavealkk 46
                                      +Qke++  lk    +++   +  +Gp GtGKt +a +la +++ +
  gi|320100775|ref|YP_004176367.1| 44 NQKEIVVRLKkfveEKSipHMLFAGPPGTGKTTMAHCLAHDLYGD 88
                                      667766666655543333356789**************9887754 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.053
                                       EEEEE-SGGG--HHHHHHHHT CS
                              PhoH 121 afvilDEAQnttkeqmkmflt 141
                                       ++v+lDEA n+t    +  l 
  gi|320100775|ref|YP_004176367.1| 127 KIVLLDEADNMTADAQQ-ALR 146
                                       589********986544.344 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.8e-06    0.0025       3      45 ..      66     111 ..      64     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.8e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe....a 45 
                                        +G+pG+GKtt+a+ L+  l +g+ ++++  e + ++e+  e    +
  gi|320100775|ref|YP_004176367.1|  66 FAGPPGTGKTTMAHCLAHDL-YGDDYKKYMLELNASDERKIEvirgK 111
                                       79**************8887.79999999999888888877755552 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00031      0.14       8      53 ..      45      90 ..      39     102 .. 0.84
   2 ?    3.6   0.0      0.13        59     133     167 ..     126     162 ..      96     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgk 53
                                      Q+e++ +l++ +++k   ++l++ + GtGKT +a  l+  l+   +
  gi|320100775|ref|YP_004176367.1| 45 QKEIVVRLKKFVEEKSIPHMLFAGPPGTGKTTMAHCLAHDLYGDDY 90
                                      899999999888877778****************888888776655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.13
                                       -SEEEEETGGGTTS...TTTHHHHHT---SEEEEEES CS
                            ResIII 133 fdviiiDEaHrlgak..kswreilekfkeavllglTA 167
                                       f++++ DEa +++a+  ++ r+++e +++ +++ lTA
  gi|320100775|ref|YP_004176367.1| 126 FKIVLLDEADNMTADaqQALRRLMELYSATTRFILTA 162
                                       679***********854599999*************9 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 !   17.0   0.0   7.1e-06    0.0031      34      72 ..      62     100 ..      42     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.1e-06
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72 
                                        ++l+ Gp GtGKt++++ l + l  ++y+  +++++a+
  gi|320100775|ref|YP_004176367.1|  62 PHMLFAGPPGTGKTTMAHCLAHDLYGDDYKKYMLELNAS 100
                                       489****************************99999986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00067      0.29      21      63 ..      64     109 ..      52     161 .. 0.61
   2 ?    4.7   0.1     0.049        21      36      98 ..     231     314 ..     206     341 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00067
                            AAA_30  21 avltGpAGtGKttalkal.reaweaa..ggrviglAptgkaAkvLa 63 
                                       ++  Gp+GtGKtt+   l  +++ ++  ++ + + A+ ++  +v++
  gi|320100775|ref|YP_004176367.1|  64 MLFAGPPGTGKTTMAHCLaHDLYGDDykKYMLELNASDERKIEVIR 109
                                       5678**********98883444444432255555555555555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.049
                            AAA_30  36 kalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk....................grarlepg.tl 91 
                                       +al e++e+a ++viglA+  ++ + L+e+l  +     + l++l                     +++++ ++ ++
  gi|320100775|ref|YP_004176367.1| 231 AALGEVVEEAVYKVIGLAHPREVREMLNEALSGNFTEARNKLRTLMieyglsgvdiirqihkeifsQEVKIPDEmRV 307
                                       67789999999*****************9988633333333333333455777777777655555533444444455 PP

                            AAA_30  92 livDEag 98 
                                       li D ag
  gi|320100775|ref|YP_004176367.1| 308 LIADLAG 314
                                       5555444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-05    0.0054       5     104 ..      63     150 ..      59     166 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...EEEEETGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...ivllDEid 78 
                                        +l++gp g+Gkt +a  la  l  +++ k  +++ ++  e    +  v r ++++ +  ++  +    ivllDE d
  gi|320100775|ref|YP_004176367.1|  63 HMLFAGPPGTGKTTMAHCLAHDLY-GDDYKKYMLELNASDE---RKIEVIRGKVKEFARSRVVGEVpfkIVLLDEAD 135
                                       689******************999.5554444444444333...3444444444444444443333677******** PP

                                       G-------------HHHHHHHHHHHH CS
                             AAA_2  79 KihpkessgadvSregVqrdLLqile 104
                                         ++           + q++L +++e
  gi|320100775|ref|YP_004176367.1| 136 NMTA-----------DAQQALRRLME 150
                                       ***9...........88888888877 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.7e-05     0.012      11      43 ..      53      91 ..      42     119 .. 0.72
   2 ?   -2.2   0.0       6.4   2.8e+03     208     226 ..     118     134 ..     103     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-05
                            AAA_11 11 ksalsese..itliqGPPGtgKTktivellsqll....s 43
                                      k++++e++    l+ GPPGtgKT++   l + l+    +
  gi|320100775|ref|YP_004176367.1| 53 KKFVEEKSipHMLFAGPPGTGKTTMAHCLAHDLYgddyK 91
                                      6666666666689**************999999644331 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.4
                            AAA_11 208 sklleklakkfdvviIDEA 226
                                       s++  ++   f++v+ DEA
  gi|320100775|ref|YP_004176367.1| 118 SRVVGEV--PFKIVLLDEA 134
                                       4455555..89*******9 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.2e-05    0.0097      27     107 ..      36     117 ..      13     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                            DUF815  27 lddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvel 101
                                        ++L ++ +qke +v+  ++f+e ++  ++L+ G  GtGK ++ + l +++  +     ++e++ +d ++++ +  +
  gi|320100775|ref|YP_004176367.1|  36 PRTLDEVVNQKEIVVR-LKKFVEEKSIPHMLFAGPPGTGKTTMAHCLAHDLYGDDykKYMLELNASDERKIEVIRGK 111
                                       5567777777776665.899***************************999988774455788888888888888777 PP

                            DUF815 102 lrerpe 107
                                       ++e ++
  gi|320100775|ref|YP_004176367.1| 112 VKEFAR 117
                                       776655 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   0.00097      0.43       2      27 ..      64      89 ..      63      92 .. 0.83
   2 ?    3.3   0.0      0.16        70      73     156 ..      92     182 ..      87     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00097
                                      EEEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg 27
                                      ++  GppG+GKtT+ + +++ l  ++
  gi|320100775|ref|YP_004176367.1| 64 MLFAGPPGTGKTTMAHCLAHDLYGDD 89
                                      6778************9999887665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.16
                                       TEEE-HHHHHHHHHHHHHHHHHHH-...........EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--S CS
                          NTPase_1  73 kyvvdvesfeelalealrkalsead...........viviDEiGkmElkskkfkeaveevLksekpvlavihrrkdl 138
                                       ky++++++ +e  +e++r +++e             ++++DE  +m   +++  + + e+ +  + ++ +   +  +
  gi|320100775|ref|YP_004176367.1|  92 KYMLELNASDERKIEVIRGKVKEFArsrvvgevpfkIVLLDEADNMTADAQQALRRLMELYSATTRFILTANYP--S 166
                                       677777777777777777666443334556666677999*************9999999999999999999999..6 PP

                                       HHHHHHHT-TT-EEEE-- CS
                          NTPase_1 139 alveeirerkdvkvfevt 156
                                       +++e i++r    +f+ +
  gi|320100775|ref|YP_004176367.1| 167 KIIEPIQSR--TAIFRFS 182
                                       899999999..5666554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00092       0.4      10      58 ..      47      99 ..      40     110 .. 0.71
   2 ?    2.3   0.0      0.28   1.2e+02      96     118 ..     128     150 ..     120     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00092
                                      HHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHH.HH.HSTTTTS-EEEEET CS
                   Sigma54_activat 10 elleqikkvaktd..lsvlitGesGtGKellarai.he.askrkekpfvavnc 58
                                      e++ ++kk+++ +   ++l  G  GtGK+++a+++ h+   +  +k ++++n 
  gi|320100775|ref|YP_004176367.1| 47 EIVVRLKKFVEEKsiPHMLFAGPPGTGKTTMAHCLaHDlYGDDYKKYMLELNA 99
                                      5555666766666556899**************98354434445555666665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.28
                                       EEEEETGGGS-HHHHHHHHHHHH CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlq 118
                                       +++LDe  ++++++Q+ L r+++
  gi|320100775|ref|YP_004176367.1| 128 IVLLDEADNMTADAQQALRRLME 150
                                       679**************999887 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   8.3e-05     0.036      39      77 ..      52      89 ..      32     168 .. 0.82
   2 ?   -1.3   0.0       2.2   9.6e+02     207     260 ..     213     274 ..     186     282 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.3e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
                             TIP49 39 ivelikekklaGravLlaGpsgtGktalaiaiskelg.ed 77
                                      + ++++ek +    +L+aGp+gtGkt +a  ++++l  +d
  gi|320100775|ref|YP_004176367.1| 52 LKKFVEEKSIP--HMLFAGPPGTGKTTMAHCLAHDLYgDD 89
                                      45678888887..89******************9995233 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                                       ----S---S----XXXXX.XXXXXXXXXXXX.......XXXXXXX....XXXXXXXXXXXXX CS
                             TIP49 207 velPkGevekkkevvqev.tLhdlDvanarp.......qdllslllqllkskkteiteklre 260
                                        el +G++++  +++q+  +L ++   ++ +       +++  +l++ l+++ te ++klr+
  gi|320100775|ref|YP_004176367.1| 213 YELSEGDMRRAINILQTTaALGEVVEEAVYKviglahpREVREMLNEALSGNFTEARNKLRT 274
                                       55666666666666665313444322222112222233777777777888888888888775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.8e-05      0.03       3      24 ..      65      86 ..      64     207 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.8e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklg 24
                                      l+ G+pG+GK+t a+ l+  l 
  gi|320100775|ref|YP_004176367.1| 65 LFAGPPGTGKTTMAHCLAHDLY 86
                                      799************9986543 PP

>> DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.98   4.3e+02      42      66 ..     136     160 ..     122     181 .. 0.80
   2 ?    1.2   0.0      0.72   3.2e+02      15      44 ..     205     234 ..     202     235 .. 0.89
   3 ?    9.1   0.0    0.0026       1.1       1      42 [.     236     277 ..     236     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.98
                   DNA_pol3_gamma3  42 aaGadpvvvlrdLlellhqltllkv 66 
                                       +  ad++  lr L+el  + t++ +
  gi|320100775|ref|YP_004176367.1| 136 NMTADAQQALRRLMELYSATTRFIL 160
                                       5668999999999999999888755 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.72
                   DNA_pol3_gamma3  15 rarlldlleallegdaaaalaelreqyaaG 44 
                                        +r l+++ +l egd+++a++ l++ +a G
  gi|320100775|ref|YP_004176367.1| 205 DERALETIYELSEGDMRRAINILQTTAALG 234
                                       67889999***************9999887 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0026
                   DNA_pol3_gamma3   1 vsaaqVrdmLGladrarlldlleallegdaaaalaelreqya 42 
                                       v +++V +++Gla  +++ ++l++ l+g+ ++a ++lr+++ 
  gi|320100775|ref|YP_004176367.1| 236 VVEEAVYKVIGLAHPREVREMLNEALSGNFTEARNKLRTLMI 277
                                       56899********************************99764 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0039       1.7      26      53 ..      52      79 ..      41     109 .. 0.83
   2 ?    4.0   0.1     0.065        28     111     143 ..     117     149 ..      90     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0039
                              TniB 26 LleypkrkrmpnlllvGdsnnGKtmive 53
                                      L ++ ++k +p++l++G++ +GKt++++
  gi|320100775|ref|YP_004176367.1| 52 LKKFVEEKSIPHMLFAGPPGTGKTTMAH 79
                                      5566778999**************9876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.065
                              TniB 111 vlrllrelkvrvLiiDEihnllagsarkqrefl 143
                                         r+  e+  +++++DE +n+ a  +++ r+++
  gi|320100775|ref|YP_004176367.1| 117 RSRVVGEVPFKIVLLDEADNMTADAQQALRRLM 149
                                       457889999************987777666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   7.1e-05     0.031       2      25 ..      65      88 ..      64     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.1e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkk 25
                                      ++ Gp+g+GK+t+a+ La++l ++
  gi|320100775|ref|YP_004176367.1| 65 LFAGPPGTGKTTMAHCLAHDLYGD 88
                                      689*****************9833 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   0.00045       0.2       3      31 ..      64      92 ..      63     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklpq 31
                                      ++  G++G GKTt+++ la+++  +++++
  gi|320100775|ref|YP_004176367.1| 64 MLFAGPPGTGKTTMAHCLAHDLYGDDYKK 92
                                      5778*****************99888766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00011     0.048      37      57 ..      65      85 ..      62     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                            AAA_25 37 llaGapgtGKttlaldlalav 57
                                      l+aG+pgtGKtt+a  la+++
  gi|320100775|ref|YP_004176367.1| 65 LFAGPPGTGKTTMAHCLAHDL 85
                                      789**************9986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.049       5      85 ..      64     145 ..      62     154 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlks.ldadkfpdieswedfldevvelaaeladyktlviDt 73 
                                       +l  Gp+g+GKTt+a  l        +k  ++ ++++  + +++++++       +++++ +    + ++k++ +D 
  gi|320100775|ref|YP_004176367.1|  64 MLFAGPPGTGKTTMAHCLahdlygdDYKKYMLELNASDERkIEVIRGK-------VKEFARSRVVGEVPFKIVLLDE 133
                                       6789**************777776666666666666553313444433.......5555555577788899999999 PP

                            AAA_24  74 ideleelclaev 85 
                                       +d +   + + +
  gi|320100775|ref|YP_004176367.1| 134 ADNMTADAQQAL 145
                                       998877776655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00056      0.24      24      59 ..      46      81 ..      27      85 .. 0.79
   2 ?   -0.0   0.0       1.1   4.6e+02     186     228 ..     299     342 ..     249     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                                      EET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE 24 kei.sgnplvldlkkmashllvaGatgsGKStalntL 59
                                      kei ++ +  +++k+ + h+l aG +g+GK+t+ + L
  gi|320100775|ref|YP_004176367.1| 46 KEIvVRLKKFVEEKSIP-HMLFAGPPGTGKTTMAHCL 81
                                      45546666667788888.**************97765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                                       -B--.---EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCG CS
                      FtsK_SpoIIIE 186 rele.krpslvvivderieLrlaapkdssvlvedaivRlarkgr 228
                                        ++  + + l++ ++  i+ rl+ ++d+++     ++Rla  gr
  gi|320100775|ref|YP_004176367.1| 299 VKIPdEMRVLIADLAGEIQFRLVEGADDEIQLNAFLARLALIGR 342
                                       33333444445555555899999999999999999999997766 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 ?   13.1   0.0   0.00015     0.065      10     112 ..      51     151 ..      43     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                          ATPase_2  10 eleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal..gi 84 
                                       +l++ +e+++ + ++  Gp g GKt++   ++  l   d+y+ y+ +l+ +++ k++      ++k++++  +    
  gi|320100775|ref|YP_004176367.1|  51 RLKKFVEEKSIPHMLFAGPPGTGKTTMAHCLAHDLYG-DDYKKYMLELNASDERKIEVI--RGKVKEFARSRVvgEV 124
                                       68888888888888888*********99999999965.66899**************99..3333333333333222 PP

                          ATPase_2  85 avpkaeleeilk...eksklvfkaielllek 112
                                       +++ + l    +   + ++++++a+ +l+e 
  gi|320100775|ref|YP_004176367.1| 125 PFKIVLL----DeadNMTADAQQALRRLMEL 151
                                       3333333....23337778888888777665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00032      0.14       3      63 ..      63     123 ..      61     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                                       EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHH CS
                             KTI12   3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsa 63 
                                        +++ G P +GK+t+a+ La+ l   +++ ++++ ++   +k ++   +  + +Rs++  +
  gi|320100775|ref|YP_004176367.1|  63 HMLFAGPPGTGKTTMAHCLAHDLYGDDYKKYMLELNASDERKIEVIRGKVKEFARSRVVGE 123
                                       5799*********************999999999888876666677777777777766555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0014      0.63      11      31 ..      62      82 ..      53      94 .. 0.78
   2 ?   -0.5   0.0       3.1   1.4e+03     104     126 ..     127     149 ..      93     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                            AAA_19 11 kvllvtaGpGtGKTrvlkhiv 31
                                      +++l  ++pGtGKT++ ++  
  gi|320100775|ref|YP_004176367.1| 62 PHMLFAGPPGTGKTTMAHCLA 82
                                      67888999******9876654 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.1
                            AAA_19 104 ellivDEfqdvdelqyrLlkall 126
                                       ++++ DE+ +++  +++ l++l+
  gi|320100775|ref|YP_004176367.1| 127 KIVLLDEADNMTADAQQALRRLM 149
                                       37889999999865555555554 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00048      0.21       4      72 ..      67     135 ..      64     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00048
                   Viral_helicase1   4 hGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvks.tkgkililDEyl 72 
                                       +G pG GK+t+   l+++ l    +++    l+++ +++       v++f  ++v +   +ki++lDE+ 
  gi|320100775|ref|YP_004176367.1|  67 AGPPGTGKTTMAHCLAHD-LYGDDYKKYMLELNASDERKIEVIRGKVKEFARSRVVGeVPFKIVLLDEAD 135
                                       789*************99.77778888888888888777777777799999999999999********85 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00068       0.3       5      37 ..      64      96 ..      62     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00068
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLd 37
                                      ++++G  g+GK+t+a+ l++ L  + ++ y+L+
  gi|320100775|ref|YP_004176367.1| 64 MLFAGPPGTGKTTMAHCLAHDLYGDDYKKYMLE 96
                                      6799**********************9999986 PP

>> DUF4373  Domain of unknown function (DUF4373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       3.7   1.6e+03      41      72 ..     194     225 ..     186     233 .. 0.80
   2 ?    9.6   0.0    0.0035       1.5      11      57 ..     269     312 ..     263     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.7
                           DUF4373  41 gyyiewdeeqlllladkaklevdeeevkeive 72 
                                        y +++++ ++ + a ++ +e++e ++++ ++
  gi|320100775|ref|YP_004176367.1| 194 RYICNAEKVKCDERALETIYELSEGDMRRAIN 225
                                       68888888888888888899999999999998 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0035
                           DUF4373  11 dekierleaeyglkGygvyvkllekiykekgyyiewdeeqlllladk 57 
                                        +k++ l+ eygl G+ ++ ++ ++i+++ +   ++ +e+  l+ad 
  gi|320100775|ref|YP_004176367.1| 269 RNKLRTLMIEYGLSGVDIIRQIHKEIFSQ-EV--KIPDEMRVLIADL 312
                                       5799*************************.44..8999999999884 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     0.001      0.46       8     104 ..      46     159 ..      43     170 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHH..T-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H................HHHHH CS
                   Sigma54_activ_2   8 qelkerLeqaa..qsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp................ldlle 66 
                                       +e+  rL++ +  +s   ++ +G++G+gk+++A  L++   +++  + + +l ++                 ++++ 
  gi|320100775|ref|YP_004176367.1|  46 KEIVVRLKKFVeeKSIPHMLFAGPPGTGKTTMAHCLAHDLYGDDYKKYMLELNASDerkievirgkvkefarSRVVG 122
                                       5677788887732333458899**************99877766655555555433445556666665555555555 PP

                                       HTTTSEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEE CS
                   Sigma54_activ_2  67 qakggtLylkdiadlskaeqkeLlellakaeksslrlV 104
                                       ++   + +l + +++ +++q+ L  l++       r++
  gi|320100775|ref|YP_004176367.1| 123 EVPFKIVLLDEADNMTADAQQALRRLMELY-SATTRFI 159
                                       566677777777777777777776666554.5555665 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 ?   10.7   0.0   0.00094      0.41       9      78 ..      71     246 ..      64     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00094
                                       TSSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCHHTTEB-HHHH.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.............................. RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvD.aDpqannlaileglendiep.............................. 54 
                                       G+GKTt+a  La  l  + ++  ++     +    +++ g++++ ++                              
  gi|320100775|ref|YP_004176367.1|  71 GTGKTTMAHCLAHDLYGDDYKKYMLElNASDERKIEVIRGKVKEFARsrvvgevpfkivlldeadnmtadaqqalrr 147
                                       9*************************556666666667777777777999999999999999999999988888888 PP

                                       ..........................................................................CCH CS
                                       ..........................................................................xxx RF
                              CbiA  55 ..........................................................................dlk 57 
                                                                                                                  ++
  gi|320100775|ref|YP_004176367.1| 148 lmelysattrfiltanypskiiepiqsrtaifrfsplrkedvverlryicnaekvkcderaletiyelsegdmrRAI 224
                                       88888888888888888888888888888888888888888888888888888888888888888888888555555 PP

                                       CCCHHHHHHCHCHHHH...EEE CS
                                       xxxxxxxxxxxxxxxx.xxxxx RF
                              CbiA  58 rllellealgkkkall.lkiag 78 
                                        +l++ +alg++++ +  k++g
  gi|320100775|ref|YP_004176367.1| 225 NILQTTAALGEVVEEAvYKVIG 246
                                       5555557777776666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 2375.32
//
Query:       gi|320100776|ref|YP_004176368.1|  [L=200]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-05   23.8   0.2    7.1e-05   23.2   0.2    1.3  1  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.2     4e-09   7.1e-05       3     109 .]      53     173 ..      52     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4e-09
                                       EEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTS...SSSTTTTTTHHHHH.HHHHHHHT............. CS
                              Sld5   3 LPlWlaelLkrqrrveieppewlspesleailedetks...sdlpslpphflela.vkllelard............ 63 
                                       +P W+a++L+ +++++i + + + +e l+++l  e +    ++++ l+ +f++   +k+ e  ++            
  gi|320100776|ref|YP_004176368.1|  53 VPRWVARELAAKGYATITE-DGIDKERLAKLLFLEDRYksqPRFEELKGYFYRRLgEKIKETLEEhgksrdlrrlee 128
                                       79***************96.5668**********9999999999999999997666444444443444344555444 PP

                                       ....HCHHHHHHHHHHHHHHHHHHHTHCHHHHHHHTS-TCCHCCS-HHHH CS
                              Sld5  64 ....ldelkrllrdllevRlakirkfaenledaagggggellsglseeEk 109
                                           ++  +  l +l ++R++ki  f+   + +a     e+ ++ls eEk
  gi|320100776|ref|YP_004176368.1| 129 lsesVKMYRDALVSLTRLRAKKIVGFLTAPGYPA-----EAVNNLSLEEK 173
                                       43346666688*******************9999.....99999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1451.93
//
Query:       gi|320100777|ref|YP_004176369.1|  [L=700]
Description: replicative DNA helicase Mcm [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-99  331.8   0.0    1.9e-99  331.3   0.0    1.2  1  MCM              MCM P-loop domain
    3.2e-36  124.0   0.1    8.3e-36  122.6   0.0    1.7  2  MCM_OB           MCM OB domain
    4.1e-27   94.4   1.1    1.2e-26   92.9   1.1    1.9  1  MCM_lid          MCM AAA-lid domain
    5.6e-16   59.0   0.4    2.6e-15   56.9   0.0    2.3  2  MCM_N            MCM N-terminal domain
    3.6e-09   36.7   0.0    1.2e-08   35.1   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
    5.9e-06   25.8   0.0     0.0011   18.5   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00019   21.3   0.0    0.00049   20.0   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
     0.0075   16.0   0.2      0.084   12.6   0.1    2.5  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.046   14.1   0.1       0.19   12.1   0.1    2.0  1  AAA_16           AAA ATPase domain
      0.062   12.9   0.0       0.13   11.9   0.0    1.4  1  tRNA_anti-like   tRNA_anti-like


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 !  331.3   0.0  1.1e-102   1.9e-99       1     224 []     286     509 ..     286     509 .. 0.99

  Alignments for each domain:
  == domain 1  score: 331.3 bits;  conditional E-value: 1.1e-102
                                       HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHH CS
                               MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyv 77 
                                       ++e+i+ela+++ i ek+++siap iyg+ d+k+ai+l+l+ggv k l+d+t++rgdi+vllvgdpgtaKsqlL+++
  gi|320100777|ref|YP_004176369.1| 286 DEERIRELARDPWIREKIIASIAPGIYGYWDIKEAIALLLLGGVPKILQDGTRIRGDIHVLLVGDPGTAKSQLLQFT 362
                                       5799************************************************************************* PP

                                       HHHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEES CS
                               MCM  78 eklapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaK 154
                                       ++lapr+ ytsgkgs+aagLta+v rd++tge++leaGalv+ad+Gv+ciDe+dkm++edrsa+hEa+Eqqt+siaK
  gi|320100777|ref|YP_004176369.1| 363 SRLAPRGLYTSGKGSTAAGLTATVLRDKATGEYYLEAGALVIADGGVACIDEIDKMRDEDRSAIHEALEQQTVSIAK 439
                                       ***************************************************************************** PP

                                       SSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                               MCM 155 aGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                       aGiva Lnar+svlaA npk gryd++k++++ni+l++++LsrFDlif+++D ++ e+D++la++++ +h
  gi|320100777|ref|YP_004176369.1| 440 AGIVARLNARASVLAAGNPKDGRYDPTKPISKNIDLPPTILSRFDLIFTIKDLPNPEQDRKLARYVLGVH 509
                                       ******************************************************************9876 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.0   4.6e-39   8.3e-36       2     125 ..     115     247 ..     114     248 .. 0.91
   2 ?   -2.9   0.0       3.2   5.7e+03      72      85 ..     262     275 ..     261     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 4.6e-39
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EE.ES---..........-SB-..TTT-HHH-EEE CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktve.velee..........PrkCeekeCeskdpfkl 67 
                                       +Rd++s++igkl+ +eGivtr++++  +++ka++++ + ++ v+ +++ e          P+ C  + C++ ++f+l
  gi|320100777|ref|YP_004176369.1| 115 IRDISSDYIGKLIAIEGIVTRVTRIDARIVKATYRHADPETGVHeFHYPEegemgerlerPQLC--PVCGKPGRFEL 189
                                       8***********************************999887774533334555556666****..99********* PP

                                       -GGGSEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                            MCM_OB  68 etekskfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                        +eks+f+d+qk+ +QE+peevp G++Prs+ev+l++d+vd ++PGdrv v+Gi+r+ 
  gi|320100777|ref|YP_004176369.1| 190 IPEKSVFIDWQKIVVQEKPEEVPGGQIPRSIEVVLTGDIVDAARPGDRVVVIGILRVA 247
                                       *******************************************************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                                       SEEEEEEEEEEE-- CS
                            MCM_OB  72 skfvdfqklklQEs 85 
                                       s ++d  ++++QE+
  gi|320100777|ref|YP_004176369.1| 262 SFYIDANNVEVQEK 275
                                       6799********97 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   1.1   6.7e-30   1.2e-26       2      85 ..     523     609 ..     522     611 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 6.7e-30
                                       HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHH...TSS.TSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HH CS
                           MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkee...eds.krksipitvRqLesliRLseAlAklrlsevvtee 74 
                                       ll+kYi+yar+ ++P+l++ea++ ++e+Yv++Rk++       +  +i it+RqLe+l+RL+eA+A+l+l++ +t e
  gi|320100777|ref|YP_004176369.1| 523 LLKKYISYARRYVHPQLTPEAAKLIEEFYVSMRKSSipsD-PtRPVAIAITPRQLEALVRLTEAHARLSLKSKATLE 598
                                       89********************************997641.245789****************************** PP

                                       HHHHHHHHHHH CS
                           MCM_lid  75 dveeairllke 85 
                                       d+eeairl+  
  gi|320100777|ref|YP_004176369.1| 599 DAEEAIRLMLV 609
                                       ********975 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   1.4e-18   2.6e-15       2      86 ..      18      98 ..      17     124 .. 0.89
   2 ?   -2.1   0.1       3.3     6e+03       1      11 [.     640     650 ..     640     687 .. 0.66

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.4e-18
                             MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkkle 80
                                      e+F++F++++    ++++g +kY +++ +m  +++++L vd++dL  +++eLa+++++ p e l+ +++a++ +v++ +
  gi|320100777|ref|YP_004176369.1| 18 EAFKKFIDTY----RSKEGLRKYEERIGQMVGMGQRSLIVDFTDLIGYSRELANTLIDRPDEALESFSDAIRSIVERDY 92
                                      89********....678889*********************************************************** PP

                             MCM_N 81 psykdd 86
                                      p+y+++
  gi|320100777|ref|YP_004176369.1| 93 PEYARK 98
                                      *99998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                             MCM_N   1 qekFedFLeef 11 
                                       ++kF++FL + 
  gi|320100777|ref|YP_004176369.1| 640 KRKFREFLFSI 650
                                       68999999665 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 !   35.1   0.0   6.6e-12   1.2e-08       1     125 [.     344     463 ..     344     498 .. 0.86
   2 ?   -3.6   0.0       5.8     1e+04      61      83 ..     641     664 ..     629     668 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.6e-12
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlLvG+pGt+Ks+l +  +++  r + +    ++ t++ l+  +  +   g++ l+ ++lv  +  g ++++DE++
  gi|320100777|ref|YP_004176369.1| 344 HVLLVGDPGTAKSQLLQFTSRLAPRGLYT--SGKGSTAAGLTATVLRDkaTGEYYLEAGALV--IADGGVACIDEID 416
                                       79**************9999998766544..456677777777766556689999*******..99*********** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--... CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld..r 125
                                       ++++e  ++ +  le++++++++ g + + ++       +v+a++np d  +
  gi|320100777|ref|YP_004176369.1| 417 KMRDEDRSAIHEALEQQTVSIAKAGIVARLNAR-----ASVLAAGNPKDgrY 463
                                       ***********************9999999986.....89*******99431 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.8
                                       ----G-SEEEEESGGG--.HHHHH CS
                             AAA_5  61 raaregeilvlDEverae.sevln 83 
                                       r++re    +l+Ev +++ sev++
  gi|320100777|ref|YP_004176369.1| 641 RKFREFLFSILEEVSEISvSEVIK 664
                                       555666677899999999888876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0091        16      21      47 ..     341     367 ..     337     375 .. 0.85
   2 !   18.5   0.0   5.9e-07    0.0011      96     159 ..     396     459 ..     390     490 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0091
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllp 47 
                                       G  ++llvG pG+ K+ l +  + l p
  gi|320100777|ref|YP_004176369.1| 341 GDIHVLLVGDPGTAKSQLLQFTSRLAP 367
                                       7889************99887777666 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 5.9e-07
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                         + G++  a  Gv  +DE+ +++ +   ++ e le+++v+i++a   ++  ar  ++aa Np 
  gi|320100777|ref|YP_004176369.1| 396 YLEAGALVIADGGVACIDEIDKMRDEDRSAIHEALEQQTVSIAKAGIVARLNARASVLAAGNPK 459
                                       67889*********************************************************95 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 !   20.0   0.0   2.7e-07   0.00049       1     114 [.     344     460 ..     344     468 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.7e-07
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfan...llladeinra 74 
                                       hvll g PG+ak +l +  ++     +           + ++ t + ++++ e+ +++G+++     +   dei++ 
  gi|320100777|ref|YP_004176369.1| 344 HVLLVGDPGTAKSQLLQFTSRLAPRGLYT--SGKGSTAAGLTATVLRDKATGEYYLEAGALVIAdggVACIDEIDKM 418
                                       9************9999888876554432..233456789999999999**********976432448999****** PP

                             AAA_3  75 ppktqsalleameerqvtvege..thklpepflvlatqnPie 114
                                           +sa+ ea+e+++v+++++    +l+    vla+ nP +
  gi|320100777|ref|YP_004176369.1| 419 RDEDRSAIHEALEQQTVSIAKAgiVARLNARASVLAAGNPKD 460
                                       *****************9986522679************965 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.8   6.8e+03     130     145 ..     136     151 ..     134     160 .. 0.76
   2 !   12.6   0.1   4.7e-05     0.084      21     140 ..     341     455 ..     331     460 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.8
                                       EEE--EEEEEEESS-H CS
                   Sigma54_activat 130 eikvdvriiaatnedl 145
                                        +++d ri+ at ++ 
  gi|320100777|ref|YP_004176369.1| 136 VTRIDARIVKATYRHA 151
                                       56899******98765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.7e-05
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEE CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtl 97 
                                        d++vl++G+ Gt K+ l +   +  +   + + +   +++++ l ++ L   +    tG    ++G++  adgG+ 
  gi|320100777|ref|YP_004176369.1| 341 GDIHVLLVGDPGTAKSQLLQFTSRLAP---RGLYTSGKGSTAAGLTATVLRDKA----TGEYYLEAGALVIADGGVA 410
                                       567788888888888776666555554...445566666666666666654444....55556789*********** PP

                                       EEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEE CS
                   Sigma54_activat  98 fLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaa 140
                                        +Dei ++  e  + + ++l++++v   + G  +  ++   ++aa
  gi|320100777|ref|YP_004176369.1| 411 CIDEIDKMRDEDRSAIHEALEQQTVsiAKAGIVARLNARASVLAA 455
                                       ********************9997611566666666666666666 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   0.00011      0.19      26     125 ..     344     432 ..     333     473 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.............. 88 
                                        vll+G++G+ Ks l++    +l  + g++++gk          + l+ +  r++   +   e              
  gi|320100777|ref|YP_004176369.1| 344 HVLLVGDPGTAKSQLLQFTS-RLAPR-GLYTSGKGSTA------AGLTATVLRDKATGEYYLEagalviadggvaci 412
                                       79**************7666.67777.78888888777......333333334444444444423333444444444 PP

                            AAA_16  89 .aesaeleawrekleealaavpelagaeasrllellkr 125
                                        + ++ ++++r +++eal+                  +
  gi|320100777|ref|YP_004176369.1| 413 dEIDKMRDEDRSAIHEALE------------------Q 432
                                       4444444444444444444..................3 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   0.0   7.1e-05      0.13      82     120 ..     120     158 ..     117     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.1e-05
                                       HHHTT-EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S-- CS
                    tRNA_anti-like  82 kkYkGkiieVeGvvsdikkieassvvvlardddgltnVr 120
                                       ++Y Gk+i +eG+v+ +++i a+ v ++ r  d+ t+V 
  gi|320100777|ref|YP_004176369.1| 120 SDYIGKLIAIEGIVTRVTRIDARIVKATYRHADPETGVH 158
                                       79*****************************9*999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (700 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4767.99
//
Query:       gi|320100778|ref|YP_004176370.1|  [L=84]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.091   12.7   0.0       0.12   12.3   0.0    1.2  1  RuvB_C    RuvB C-terminal winged helix domain


Domain annotation for each model (and alignments):
>> 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   0.0   6.7e-06      0.12       7      36 ..      18      46 ..      16      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-06
                                      HHHHHHHHHHHT.TT--B-HHHHHHHTT-- CS
                            RuvB_C  7 ldikyLkllkekfkggpvglktlaailgee 36
                                      +d k L++l+ ++ ++p+gl+ la+ lg+e
  gi|320100778|ref|YP_004176370.1| 18 IDEKTLSILH-EYVKTPMGLEELAEKLGLE 46
                                      7999*****8.59***********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 662.40
//
Query:       gi|320100779|ref|YP_004176371.1|  [L=133]
Description: thioesterase superfamily protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-05   23.7   0.0    6.5e-05   23.2   0.0    1.2  1  4HBT      Thioesterase 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 !   23.2   0.0   3.6e-09   6.5e-05       4      71 ..      34     101 ..      32     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.6e-09
                                       B-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEE CS
                              4HBT   4 vhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevr 71 
                                       +  + + a+++++a  ++  +  +g+  v+   +i++l p+  g +++v a+++ + ++++ +ev+ +
  gi|320100779|ref|YP_004176371.1|  34 LSTPSMIAFMERTALRCVEPRLPEGYTTVGTMVNIKHLNPAPRGARVRVSAKLISVDGRRLLFEVKAY 101
                                       566778899*******************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 940.41
//
Query:       gi|320100780|ref|YP_004176372.1|  [L=85]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0038   17.6   1.0       0.39   11.1   0.1    2.3  2  zf-IS66         zinc-finger binding domain of transposase IS6
  ------ inclusion threshold ------
      0.011   15.6   2.2       0.35   10.8   0.2    2.5  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.02   15.0   1.1       0.79    9.9   0.2    2.2  2  Zn-ribbon_8     Zinc ribbon domain
      0.021   14.7   3.4        3.1    7.8   0.4    2.3  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.022   14.7   1.7        3.5    7.7   0.1    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.037   13.7   5.0       0.58    9.9   0.4    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.054   13.0   1.0        5.5    6.6   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.092   12.4   1.3        8.9    6.0   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.26   11.2   4.9       0.61   10.1   0.2    2.5  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.014        27      39      46 .]       4      11 ..       3      24 .. 0.85
   2 !   11.1   0.1    0.0002      0.39       3      29 ..      40      66 ..      39      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                           zf-IS66 39 kyaCpcCe 46
                                      +y+C++C+
  gi|320100780|ref|YP_004176372.1|  4 RYRCKRCG 11
                                      68888886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                           zf-IS66  3 tCpcCGgllkpigedrvreeldipPak 29
                                      +Cp C +ll+  g  ++r +++i Pa 
  gi|320100780|ref|YP_004176372.1| 40 VCPRCKSLLDIPGPGEIRSRIEIRPAV 66
                                      7******888888888********985 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00018      0.35      24      34 ..       4      14 ..       2      17 .. 0.85
   2 ?    4.2   0.1      0.02        41      27      33 ..      41      47 ..      39      50 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                    Zn_ribbon_SprT 24 nYrCrrCkgtL 34
                                      +YrC+rC+ +L
  gi|320100780|ref|YP_004176372.1|  4 RYRCKRCGFVL 14
                                      6******9776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.02
                    Zn_ribbon_SprT 27 CrrCkgt 33
                                      C+rCk+ 
  gi|320100780|ref|YP_004176372.1| 41 CPRCKSL 47
                                      7777765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2    0.0004      0.79       2      17 ..       2      16 ..       1      24 [. 0.72
   2 ?    4.0   0.0     0.028        55      28      34 ..      40      46 ..      31      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0004
                       Zn-ribbon_8  2 PiYeYrCeeCghefev 17
                                      Pi  YrC++Cg +  +
  gi|320100780|ref|YP_004176372.1|  2 PI-RYRCKRCGFVLFE 16
                                      55.7*******76555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.028
                       Zn-ribbon_8 28 aCPeCgs 34
                                      +CP+C+s
  gi|320100780|ref|YP_004176372.1| 40 VCPRCKS 46
                                      5****87 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4    0.0016       3.1      13      22 ..       6      15 ..       5      16 .. 0.92
   2 ?    7.7   0.2    0.0016       3.2       7      19 ..      34      46 ..      31      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                           DUF35_N 13 rCpdCGtvqf 22
                                      rC+ CG v f
  gi|320100780|ref|YP_004176372.1|  6 RCKRCGFVLF 15
                                      9*******98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                           DUF35_N  7 grLvgqrCpdCGt 19
                                      +rL g+ Cp C +
  gi|320100780|ref|YP_004176372.1| 34 YRLSGGVCPRCKS 46
                                      8999999999965 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0043       8.6      37      44 ..       4      11 ..       2      13 .. 0.85
   2 ?    7.7   0.1    0.0017       3.5      18      26 ..      38      46 ..      32      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0043
                     Zn_Tnp_IS1595 37 lfqCkeCr 44
                                      +++Ck+C+
  gi|320100780|ref|YP_004176372.1|  4 RYRCKRCG 11
                                      8******8 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0017
                     Zn_Tnp_IS1595 18 gfvCPhCgs 26
                                      g vCP+C+s
  gi|320100780|ref|YP_004176372.1| 38 GGVCPRCKS 46
                                      568****97 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00029      0.58       1       9 [.       5      13 ..       5      16 .. 0.92
   2 ?    5.8   0.4    0.0056        11      15      22 ..      39      46 ..      36      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00029
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y+C++CGf+
  gi|320100780|ref|YP_004176372.1|  5 YRCKRCGFV 13
                                      9******95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0056
                      Rubredoxin_2 15 GrCpsCgs 22
                                      G Cp C+s
  gi|320100780|ref|YP_004176372.1| 39 GVCPRCKS 46
                                      89****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 ?    6.6   0.1    0.0027       5.5      20      29 ..       5      14 ..       4      20 .. 0.79
   2 ?    5.3   0.1    0.0071        14       2       8 ..      40      46 ..      39      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0027
                                      EEESSSSBEE CS
                      TF_Zn_Ribbon 20 lvCtdCGlVl 29
                                      ++C++CG Vl
  gi|320100780|ref|YP_004176372.1|  5 YRCKRCGFVL 14
                                      6899999887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0071
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                      +CP C+s
  gi|320100780|ref|YP_004176372.1| 40 VCPRCKS 46
                                      7999998 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.007        14       3      10 ..       5      12 ..       4      17 .. 0.85
   2 ?    6.0   0.1    0.0044       8.9       4      12 ..      40      48 ..      37      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.007
                            zf_UBZ  3 ylCerCgk 10
                                      y C+rCg 
  gi|320100780|ref|YP_004176372.1|  5 YRCKRCGF 12
                                      89****96 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0044
                            zf_UBZ  4 lCerCgkei 12
                                      +C+rC++ +
  gi|320100780|ref|YP_004176372.1| 40 VCPRCKSLL 48
                                      8****9865 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0003      0.61      21      32 ..       3      14 ..       2      16 .. 0.86
   2 ?    2.8   0.4     0.055   1.1e+02      24      29 ..      40      45 ..      25      48 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                                      -EEEETTTTEEE CS
                         Nudix_N_2 21 eRlvCpaCgtih 32
                                       R++C++Cg++ 
  gi|320100780|ref|YP_004176372.1|  3 IRYRCKRCGFVL 14
                                      5*********96 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.055
                                      EETTTT CS
                         Nudix_N_2 24 vCpaCg 29
                                      vCp+C 
  gi|320100780|ref|YP_004176372.1| 40 VCPRCK 45
                                      999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 654.86
//
Query:       gi|320100781|ref|YP_004176373.1|  [L=271]
Description: Ser/Thr protein kinase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1962.15
//
Query:       gi|320100782|ref|YP_004176374.1|  [L=464]
Description: CCA-adding enzyme [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-38  129.7   0.0    9.1e-38  129.0   0.0    1.4  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    4.7e-11   42.8   0.0    1.3e-10   41.4   0.0    1.8  1  NTP_transf_2     Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.031   14.5   0.0    1.7  1  SMODS            Second Messenger Oligonucleotide or Dinucleo


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.0   1.5e-41   9.1e-38       1     112 [.     154     271 ..     154     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 1.5e-41
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE...........EEE...-SS CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekea.....llkkf.dep 71 
                                       d++rllKkf+kgi+vYG+e+k+kGfsGY +Ell+ +ygs+++vle+a++w+p+v+id+   ++       +k+ d+ 
  gi|320100782|ref|YP_004176374.1| 154 DQARLLKKFMKGINVYGAEVKTKGFSGYAVELLIAKYGSLRRVLEEASQWNPPVYIDTLGVDKgfwkeFRRKYpDSV 230
                                       789******************************************************88877777777666776889 PP

                                       -EEEETTEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
                   tRNA_NucTransf2  72 lvviDPvDpkRNvaaalsleklaefilaareflkkpseeff 112
                                       +++ DPvDp RNv+a++sl++l++++la+r+++++ps  f+
  gi|320100782|ref|YP_004176374.1| 231 VYMPDPVDPMRNVTANVSLKSLSTLTLASRCYMANPSPVFY 271
                                       999**********************************9887 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   2.1e-14   1.3e-10       5      94 ..      33     139 ..      29     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.1e-14
                                       HHHHHHHTT.TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH...............HHHEHHHHHHHHCCCEE CS
                      NTP_transf_2   5 leelkelep.vakvvlfGSyarGtalkg.SDiDllvvlpeevsre...............kkeegleklaeiikfle 64 
                                       l+++ ++++  a+v+l GS a +t+l+g  D+D++v++pe+ s e               +   +++++ae++++ +
  gi|320100782|ref|YP_004176374.1|  33 LKKVLSEHGvEAEVTLQGSIAHDTWLSGdRDMDIFVLYPESWSIEelktkgfkliveaagRLGGYELRYAEHPYVRV 109
                                       4444555555*******************************9999***************666778*********** PP

                                       ECTTEEEEEECEEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  65 ellglevdlvtrekledpllvksileerpl 94 
                                       ++  +e+d+v+   + dp +v+++++++p+
  gi|320100782|ref|YP_004176374.1| 110 RVSDVEADIVPAFNISDPARVRTAVDRTPF 139
                                       ***************************997 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.2e-06     0.031      11     134 ..       9     125 ..       6     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-06
                             SMODS  11 lsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegd 87 
                                       l+ i++s+++  ++   +++i   L+k  +e +   ae  l+GS a+dT + +  d d+ +  + +  + ++e + +
  gi|320100782|ref|YP_004176374.1|   9 LKLIKPSKEEYLHVLGVYETIAGTLKKVLSEHG-VEAEVTLQGSIAHDTWLSGDRDMDIFVLYPES--WSIEELKTK 82 
                                       566889999999999999999999999995544.5577889***********99999988888887..677777777 PP

                             SMODS  88 epsdlleklkkalkktyksseirqdrqvvvvelneikidvvPavenk 134
                                       + + ++e+  +     y+   +  +++ v+v++++++ d+vPa++ +
  gi|320100782|ref|YP_004176374.1|  83 GFKLIVEAAGRLG--GYEL--RYAEHPYVRVRVSDVEADIVPAFNIS 125
                                       7777777777664..4444..5577******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3506.72
//
Query:       gi|320100783|ref|YP_004176375.1|  [L=191]
Description: 2'-5' RNA ligase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-31  107.3   0.0      1e-17   64.1   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
    2.6e-10   40.4   0.0    3.1e-10   40.2   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    1.6e-08   34.7   0.0    2.6e-07   30.7   0.0    2.0  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
  ------ inclusion threshold ------
      0.017   14.6   0.0       0.53    9.7   0.0    2.0  2  HVSL             Uncharacterised conserved protein


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 !   64.1   0.0   2.3e-21     1e-17       4      87 .]      16      95 ..      12      95 .. 0.93
   2 !   41.5   0.0   2.5e-14   1.1e-10       5      87 .]      99     180 ..      97     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2.3e-21
                                      CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCS CS
                        LigT_PEase  4 peeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlr 82
                                      ++++ ++l + +++++    + +lkpv+++n H+TL+f+gev++++v+e++  + +i   ++pfe++v+g+g fps +r
  gi|320100783|ref|YP_004176375.1| 16 NRDVLRRLIEARDRVA--GVGVDLKPVEDENIHLTLRFIGEVPRSTVEEVCGIVTGI--SFKPFEMHVKGIGGFPSLER 90
                                      6677889999999999..77999**********************************..666**************99* PP

                                      CCEEE CS
                        LigT_PEase 83 prviy 87
                                      prvi+
  gi|320100783|ref|YP_004176375.1| 91 PRVIW 95
                                      ****9 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 2.5e-14
                                       HHHHHHHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEE CS
                        LigT_PEase   5 eeiaeelarlaaeleralaklglkpv.rpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfps 79 
                                       ee a el +l + +e+ l++lg+kp+ ++f+pHiTLa+++ ++  ek+ ++l ++++ ++g       vd+v + +s
  gi|320100783|ref|YP_004176375.1|  99 EEGAGELLELYRVVEAGLRRLGVKPErEEFTPHITLARVKGYRgLEKLVKVLLEMRDMDFGY----TPVDEVIVKKS 171
                                       566899*************************************97777778899999*99*8....66********* PP

                                       CC.SCCEEE CS
                        LigT_PEase  80 rl.rprviy 87 
                                        l + ++iy
  gi|320100783|ref|YP_004176375.1| 172 VLtPRGPIY 180
                                       *******99 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   6.9e-14   3.1e-10      19     129 ..      38     150 ..      18     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 6.9e-14
                   2_5_RNA_ligase2  19 kayprwppHitLlypfvededladlaellsrlaketepfevrldgfgvFeh.kks.vvylsv.sdsealqalraall 92 
                                       k++++   H+tL + ++ +++  + +  + +++ +++pfe +++g+g F++ +   v+++ + ++  +l +l + ++
  gi|320100783|ref|YP_004176375.1|  38 KPVEDENIHLTLRFIGEVPRSTVEEVCGIVTGI-SFKPFEMHVKGIGGFPSlERPrVIWAGIeEGAGELLELYRVVE 113
                                       66788889***********98655555666666.9*****************6666********************* PP

                   2_5_RNA_ligase2  93 ealpeagdkedsgeftPHlTiaqsadstsaaellekl 129
                                       ++l   g k +++eftPH+T+a+ +  +  ++l++ l
  gi|320100783|ref|YP_004176375.1| 114 AGLRRLGVKPEREEFTPHITLARVKGYRGLEKLVKVL 150
                                       ******999999**********988777777666655 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 !   30.7   0.0   5.8e-11   2.6e-07       4     184 ..       9     166 ..       8     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.8e-11
                                       EEEEE---HHHHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS- CS
                         AKAP7_NLS   4 FlsiplnsnklrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkp 80 
                                       F++i ++++++ ++l + + +v++ + +l++   ++ e++HlTl  +    ++ +++   +       ++ + + kp
  gi|320100783|ref|YP_004176375.1|   9 FIAIEVKNRDVLRRLIEARDRVAGVGVDLKP---VEDENIHLTLRFIGEVPRSTVEEVCGI-------VTGI-SFKP 74 
                                       9999999999999999999999996665554...679999999977654344444444322.......2222.349* PP

                                       -EEEEEEEEEE.....TTTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHT CS
                         AKAP7_NLS  81 lslrlkGletfnddpakarVlYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqak 157
                                       +++++kG++ f  +  + rV++a++ee    ++L+el +++   +   g++ e+++  +++H+Tl+ ++  ++ ++ 
  gi|320100783|ref|YP_004176375.1|  75 FEMHVKGIGGF-PSLERPRVIWAGIEEG--AGELLELYRVVEAGLRRLGVKPEREE--FTPHITLARVKGYRGLEKL 146
                                       ***********.79999********965..7******************9998874..6*******99977766665 PP

                                       T--S--GG.GGGGGTT-EEEEEE--EE CS
                         AKAP7_NLS 158 skesfdareilkqfkdfefgeekinei 184
                                        k       +l +++d +fg +++ e+
  gi|320100783|ref|YP_004176375.1| 147 VK-------VLLEMRDMDFGYTPVDEV 166
                                       55.......777788888887777765 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0    0.0094        42     137     174 ..       4      40 ..       1      67 [. 0.75
   2 ?    9.7   0.0   0.00012      0.53     119     189 ..      71     139 ..      54     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0094
                              HVSL 137 ektRsFlvlrvkspendeLkklleavnkvlee.fglppl 174
                                       e  RsF++++vk+   d L++l+ea ++v+   ++l+p 
  gi|320100783|ref|YP_004176375.1|   4 ELVRSFIAIEVKNR--DVLRRLIEARDRVAGVgVDLKPV 40 
                                       5569*****98666..7***********99765666655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00012
                              HVSL 119 akrrFevsfsglkwvsndektRsFlvlrvkspendeLkklleavnkvleefglpplykdeaFHiSiawslg 189
                                         ++Fe++++g+  +++ e+ R+ ++  ++ ++  eL +l + v++ l++ g++p  ++  +Hi +a   g
  gi|320100783|ref|YP_004176375.1|  71 SFKPFEMHVKGIGGFPSLERPRVIWAG-IE-EGAGELLELYRVVEAGLRRLGVKPEREEFTPHITLARVKG 139
                                       3469******************98877.44.4458*******************************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1404.24
//
Query:       gi|320100784|ref|YP_004176376.1|  [L=185]
Description: dephospho-CoA kinase, CoaE [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-16   59.7   0.1    5.3e-16   59.3   0.1    1.2  1  AAA_17         AAA domain
    5.8e-13   49.5   0.0    8.7e-13   48.9   0.0    1.3  1  AAA_18         AAA domain
    4.1e-06   27.0   0.0      9e-06   25.9   0.0    1.5  1  AAA_33         AAA domain
  ------ inclusion threshold ------
      0.022   15.1   0.1      0.037   14.4   0.1    1.8  1  AAA_16         AAA ATPase domain
      0.024   13.9   0.2       0.26   10.5   0.1    2.2  2  Zeta_toxin     Zeta toxin
       0.06   13.5   0.1       0.65   10.2   0.0    2.3  2  ApbA_C         Ketopantoate reductase PanE/ApbA C terminal
      0.078   13.4   0.1       0.14   12.6   0.1    1.5  1  AAA            ATPase family associated with various cellular
       0.09   12.4   0.0        1.1    8.8   0.0    2.3  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
       0.13   12.7   0.1       0.21   12.1   0.1    1.3  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae


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 !   59.3   0.1   2.7e-19   5.3e-16       2     131 ..       8     129 ..       7     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.7e-19
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHH..HHHHHHHHH.HSSEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqke..aaekiaeea.kkkgvl 75 
                                       G+PGsGK+ ++ + ++k+g++++++Gd++ree++r+  + + + m   + e ++++ ++  a ++i++   +++ v+
  gi|320100784|ref|YP_004176376.1|   8 GMPGSGKSIVV-EAARKLGLPVYTMGDVIREEVARRYGVVTPELMVSTSSELRRKHGENivAVRTIEKIGrENSVVV 83 
                                       9*******999.9***********************8877888887554444443333311444555544357789* PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-S CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddn 131
                                       vdg  ++ e ++    ++k         +i+ ++a+p + ++r+l+++  g++  +
  gi|320100784|ref|YP_004176376.1|  84 VDGVRSLIEVEE----FKK-----HGDVVIVAVHASPRTRFRRLLERKRPGDPS-S 129
                                       *****9877555....444.....33347899******9998888876544443.3 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   4.4e-16   8.7e-13       1     118 [.       4     125 ..       4     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 4.4e-16
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssal 71 
                                       Il++G+pG+GK+ + ++ +k+ g+     g+++r+ ++ ++ + + +    +++++r + +   ++++++e++    
  gi|320100784|ref|YP_004176376.1|   4 ILVAGMPGSGKSIVVEAARKL-GLpvytmGDVIREEVARRYGVVTPELMvSTSSELRRKHGENIVAVRTIEKIG--- 76 
                                       99****************998.6775888666666555554443333334555555555566666777777764... PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk...vvLtaspeelleRlekRgyeea 118
                                       +e++++v+dg+++  e e++k+++    v ++asp ++++Rl +R++ + 
  gi|320100784|ref|YP_004176376.1|  77 RENSVVVVDGVRSLIEVEEFKKHGDvviVAVHASPRTRFRRLLERKR-PG 125
                                       699999***************9888********************84.34 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.5e-09     9e-06       2     124 ..       4     127 ..       3     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.5e-09
                            AAA_33   2 vllvGlpGsGKstlaerllkklg......avllssdtlrr.rlfgtdqqsktdytrvldrlyqilnelarkalsagr 71 
                                       +l+ G+pGsGKs ++e  ++klg      + ++++ ++rr  ++  +    t +   +++  +i++ +  ++  +++
  gi|320100784|ref|YP_004176376.1|   4 ILVAGMPGSGKSIVVEA-ARKLGlpvytmGDVIREEVARRyGVVTPELMVSTSSELRRKHGENIVAVRTIEKIGREN 79 
                                       6899************8.88***988888888888888885444433333333333445566666666668899999 PP

                            AAA_33  72 nvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangdd 124
                                       +v++  + +s  e ++f k    +g  v iv+v+++++t  +Rl +R+++gd 
  gi|320100784|ref|YP_004176376.1|  80 SVVVVDGVRSLIEVEEFKK----HG-DVVIVAVHASPRTRFRRLLERKRPGDP 127
                                       9999999999999888755....55.699********************9763 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   0.1   1.8e-05     0.037      27      46 ..       4      23 ..       2     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                            AAA_16 27 vllsGesGvGKsslvrellr 46
                                      +l+ G++G+GKs +v+++++
  gi|320100784|ref|YP_004176376.1|  4 ILVAGMPGSGKSIVVEAARK 23
                                      89*************99885 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00013      0.26      18      38 ..       3      23 ..       2      41 .. 0.83
   2 ?    0.9   0.0      0.12   2.4e+02      40     108 ..      96     166 ..      87     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                        Zeta_toxin 18 lillgGqpGAGKselaellkd 38
                                       il++G pG+GKs + e++++
  gi|320100784|ref|YP_004176376.1|  3 FILVAGMPGSGKSIVVEAARK 23
                                      599**********99998765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                        Zeta_toxin  40 lerqgnvvrld.pDdlRelhPeyeeilka.dpkkaseltqkdaselvekllqeaiengyniivegtlrspd 108
                                       ++++g+vv +    + R+++++  e  +  dp+++ e  ++d++el+  l   ++ + y i+ e+  r+ +
  gi|320100784|ref|YP_004176376.1|  96 FKKHGDVVIVAvHASPRTRFRRLLERKRPgDPSSYEEFLKRDMTELGFGLGSVIALADYMIVNESSTREAE 166
                                       44566665554144568888888786664589999999999999998888888888888888887777665 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 ?    0.8   0.0      0.26   5.3e+02      95     113 ..      29      49 ..      18      56 .. 0.76
   2 ?   10.2   0.0   0.00032      0.65      63     109 ..     111     157 ..      57     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.26
                            ApbA_C  95 yinGavvkl..AeklgvetPv 113
                                       y+ G v++   A+++gv tP 
  gi|320100784|ref|YP_004176376.1|  29 YTMGDVIREevARRYGVVTPE 49 
                                       567888874449999999986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00032
                            ApbA_C  63 leeaveavlektaanrsSMlqDveagrktEidyinGavvklAeklgv 109
                                        +   +++le++++ ++S ++  +++  tE+ + +G v++lA+++ v
  gi|320100784|ref|YP_004176376.1| 111 PRTRFRRLLERKRPGDPSSYEEFLKRDMTELGFGLGSVIALADYMIV 157
                                       567778888999999***************************99866 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 ?   12.6   0.1     7e-05      0.14       1      98 [.       4      98 ..       4     123 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7e-05
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEE...ETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                               AAA  1 vllyGppGtGKTllakavakelgveflei...sgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76
                                      +l+ G pG GK+++++a a++lg +++++      e+   y   +++ +  + +e+++k +  i+ +  i+++++++  
  gi|320100784|ref|YP_004176376.1|  4 ILVAGMPGSGKSIVVEA-ARKLGLPVYTMgdvIREEVARRYGVVTPELMVSTSSELRRKHGENIVAVRTIEKIGREN-- 79
                                      699*********99998.67777664433100334444446666666666666666555544666666666665555.. PP

                                      CCCHHHHHHHHHHHHHHHHTTT CS
                               AAA 77 seseeeervvnqLlteldgvkk 98
                                        s +  + v  L++ ++++kk
  gi|320100784|ref|YP_004176376.1| 80 --SVVVVDGVRSLIE-VEEFKK 98
                                      ..4444444444433.233333 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00057       1.1       3      58 ..       4      71 ..       2     107 .. 0.81
   2 ?    1.9   0.0     0.075   1.5e+02     128     155 ..     138     165 ..      72     177 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00057
                                      EEEEESTTCCHHHHHHHHH.............CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETT CS
                              cobW  3 tvltGflGsGKTtLlnhll.............enraglklavivNefgevsiDaellretgveivelen 58
                                      ++++G +GsGK+ ++++               +++  +++ v++ e+  vs  +el r++g++iv + +
  gi|320100784|ref|YP_004176376.1|  4 ILVAGMPGSGKSIVVEAARklglpvytmgdviREEVARRYGVVTPELM-VSTSSELRRKHGENIVAVRT 71
                                      6899***********987666788888899888999999999999999.99999999999999887765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.075
                                       HCCHHHHHHHHHHTSSEEEEE-HHHHCH CS
                              cobW 128 eekieekaedqlaaadllvlnKtDllde 155
                                        ++    +++ +a ad +++n   + ++
  gi|320100784|ref|YP_004176376.1| 138 MTELGFGLGSVIALADYMIVNESSTREA 165
                                       4444445667789999999987655555 PP

>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0001      0.21      27      62 ..      54     110 ..      46     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                       xxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxx RF
                     Ribosomal_L26  27 LskeLrekygvrslpir.....................gvtrekangttvpvgihpS 62 
                                        s+eLr+k+g + + +r                     +v++ k+ g  v v +h+S
  gi|320100784|ref|YP_004176376.1|  54 TSSELRRKHGENIVAVRtiekigrensvvvvdgvrsliEVEEFKKHGDVVIVAVHAS 110
                                       599***********************************9****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1365.48
//
Query:       gi|320100785|ref|YP_004176377.1|  [L=132]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   59.3   0.0    7.6e-16   58.5   0.0    1.4  1  RNA_binding  RNA binding
  ------ inclusion threshold ------
      0.056   13.5   0.0      0.064   13.4   0.0    1.1  1  Pox_A22      Poxvirus A22 protein


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 !   58.5   0.0   8.5e-20   7.6e-16       1     118 [.       3     115 ..       3     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 8.5e-20
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.HHH CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.keL 76 
                                       ++ v+a+v++TEd ekV++a+ n++  +   + +++  G y    + +++++      ++lk l+el r +++   L
  gi|320100785|ref|YP_004176377.1|   3 RVVVEAEVRPTEDSEKVKKAVGNVFAGD---VVISDQGGGYR-LARGVSLTI------ESLKPLRELARVQQVePAL 69 
                                       589**********************977...56677777777.444555555......5588888888889983455 PP

                                       HHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS.....EEEEEEE CS
                       RNA_binding  77 lkeleervdekgklylrldKQaaylgklslvegdd.....vIkvkik 118
                                       ++ +  r  e+  +++ l+KQaay+gklslv++++     +I+++++
  gi|320100785|ref|YP_004176377.1|  70 RSYIH-RHRENRAITILLHKQAAYVGKLSLVDSEKesplgAIRITVE 115
                                       55555.5777************************9999999999986 PP

>> Pox_A22  Poxvirus A22 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.1e-06     0.064      40     118 ..      15      94 ..       1     105 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.1e-06
                           Pox_A22  40 dwerrvardilsynvdvvllEkqgrrsknvkfiyf.ikgllys.kktkvlvvkPvlkggsYrdRKkrsvevFlnlis 114
                                       d  ++v++ + ++ +  v++  qg + ++++ +   i++l    + ++v+ v+P+l+    r+R +r++ + l++ +
  gi|320100785|ref|YP_004176377.1|  15 D-SEKVKKAVGNVFAGDVVISDQGGGYRLARGVSLtIESLKPLrELARVQQVEPALRSYIHRHRENRAITILLHKQA 90 
                                       4.346778888888888999999999999998775266664333579************************999887 PP

                           Pox_A22 115 lfgi 118
                                        +  
  gi|320100785|ref|YP_004176377.1|  91 AYVG 94 
                                       7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1064.34
//
Query:       gi|320100786|ref|YP_004176378.1|  [L=249]
Description: RNAse Z [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   79.2   0.0    3.7e-22   78.8   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.5e-13   51.2   0.1    2.2e-13   50.7   0.1    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.8e-11   42.9   0.0    5.3e-11   42.0   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease
     0.0007   19.5   0.0     0.0016   18.4   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   8.3e-26   3.7e-22      27     201 .]      50     218 ..      32     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 8.3e-26
                                       -..SEEEEE-SS--HHHHGGGGCCCC.....C--EE..EEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEE CS
                     Lactamase_B_2  27 elppidaVllthaHyDHlaglltlre.....lrpkk..lplyapkgvlavleanfvylaleeepavnvheldwgesf 96 
                                       ++ +++aV++th H DH+ gl+ + +     +  +k  l+l+ p+++ ++ +  + +  l++ ++v+++ l+ ge  
  gi|320100786|ref|YP_004176378.1|  50 SPLKVKAVFVTHPHGDHYLGLPGVIQtmgltG--RKepLKLLLPRELDEYFRLILERKLLKPGFPVEFTVLANGEVY 124
                                       45589********************9998543..444599999999999888887777777779999********99 PP

                                       EECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHH CS
                     Lactamase_B_2  97 elgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemi 173
                                       + +  +++++a p++h+ +          +G+ ++ +gk+++y+gDt  ++    e  +g+d+l+++ t+++d  ++
  gi|320100786|ref|YP_004176378.1| 125 RDE--KISVRAYPVNHGVEA---------YGFHVAVAGKTLCYTGDTMPCSSV-VENCRGVDVLIHESTFTSDMGPE 189
                                       997..689********9998.........*********************955.66*****************9999 PP

                                       H.HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 174 r.hmgHltpeeaveaaadlgakrlvliHi 201
                                       + +++H+t ++a+ aa ++ga+ lvl+Hi
  gi|320100786|ref|YP_004176378.1| 190 AhEEYHSTTRDAASAALEAGAASLVLTHI 218
                                       99**************************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 !   50.7   0.1   4.9e-17   2.2e-13       8     197 .]      22     217 ..      18     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 4.9e-17
                                       EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                       Lactamase_B   8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                       ++ +  d   +L+D G + + ++++     +gl p++v+av++TH+H DH+ gl+g++++ +   +++++++  +++
  gi|320100786|ref|YP_004176378.1|  22 CIAVKADSNIYLFDVGEGCQSKMLK-----AGLSPLKVKAVFVTHPHGDHYLGLPGVIQTMGLTGRKEPLKLLLPRE 93 
                                       67788889999*************8.....8********************************************** PP

                                       HHHHHHHHHCCHH..TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                       Lactamase_B  85 eeaddaasrkgll..lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgr 159
                                         +++    +  l  + +++++ + +  e++ ++  ++ra++v   +g  + +++v   g+++++tGD+ + ++ + 
  gi|320100786|ref|YP_004176378.1|  94 LDEYFRLILERKLlkPGFPVEFTVLANGEVYRDEKISVRAYPVN--HGVEAYGFHVAVAGKTLCYTGDTMP-CSSVV 167
                                       99977666655556666666666666666666666666666655..5566777888899**********98.44444 PP

                                       CCC.............TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 160 idl............tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                         +            t ++++  +   ++ ++d++  + +  a+ lv++H
  gi|320100786|ref|YP_004176378.1| 168 ENCrgvdvlihestfTSDMGPEAHEEYHSTTRDAASAALEAGAASLVLTH 217
                                       44445666777777777777777777777777776666666666666555 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.2e-14   5.3e-11       7      63 .]      14      69 ..       9      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.2e-14
                     Lactamase_B_4  7 tsDtsg.PlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssigG 63
                                       + t+g P+++++ ds+ Ylf +vgEg+Q  + + +++  k++ +F+t+++  +++ G
  gi|320100786|ref|YP_004176378.1| 14 VPVTRGlPCIAVKADSNIYLF-DVGEGCQSKMLKAGLSPLKVKAVFVTHPH-GDHYLG 69
                                      566999***************.****************************9.776655 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 !   18.4   0.0   3.5e-07    0.0016      31     133 ..      48     177 ..      39     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.5e-07
                     Lactamase_B_3  31 eppaeeaDlvlisqaledHahletlkql......................................aenvkvleege 69 
                                       + ++ ++ +v +++ + dH+    l+++                                        +++vl++ge
  gi|320100786|ref|YP_004176378.1|  48 GLSPLKVKAVFVTHPHGDHYL--GLPGViqtmgltgrkeplklllpreldeyfrlilerkllkpgfPVEFTVLANGE 122
                                       556778999*********995..34555555799*********************999999999999999******* PP

                     Lactamase_B_3  70 slevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvl 133
                                        ++ +++++ra + +h         e +gf++ ++g t+++ G++     s+  ++   vDv++
  gi|320100786|ref|YP_004176378.1| 123 VYRDEKISVRAYPVNH-------GVEAYGFHVAVAGKTLCYTGDTMP--CSSVVENCRGVDVLI 177
                                       **************99.......356789****************96..899999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1976.93
//
Query:       gi|320100787|ref|YP_004176379.1|  [L=336]
Description: RNA methylase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-19   68.3   0.0    7.3e-18   65.0   0.0    2.0  1  UPF0020        Putative RNA methylase family UPF0020
    6.2e-09   35.9   0.0    1.8e-06   27.9   0.0    2.1  2  N6_N4_Mtase    DNA methylase
    8.6e-05   22.2   0.0    0.00014   21.6   0.0    1.3  1  Cons_hypoth95  Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.035   13.7   0.0      0.054   13.0   0.0    1.2  1  MTS            Methyltransferase small domain
       0.17   11.1   0.0       0.82    8.9   0.0    1.9  1  N6_Mtase       N-6 DNA Methylase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0     2e-21   7.3e-18       3     168 ..     159     295 ..     158     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 2e-21
                                       SS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--E CS
                           UPF0020   3 yRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelkl 79 
                                        R+f+   +L + +++ l++la++++g  llDP+ G+Gtil+Ea  +  +++                         
  gi|320100787|ref|YP_004176379.1| 159 HRPFKRSIALTPDVSRLLINLARVREGGILLDPFAGTGTILMEAWSMNIRAV------------------------- 210
                                       59999999************************************99999988......................... PP

                                       EEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHHHH CS
                           UPF0020  80 ygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelkrv 155
                                        g++ d+r+ +g +eN++ ++ + +  + +  + ++     +vd+i+t+pPYG+  +++++   +LY++fl ++  v
  gi|320100787|ref|YP_004176379.1| 211 -GIEVDWRLAHGMEENLRFYRANAIPVLGDSTFINVV----NVDAIATDPPYGRGASTHGQSqLALYDAFLGKAWDV 282
                                       .**************************9999999888....6***************9998879************* PP

                                       -TT..-EEEEEES CS
                           UPF0020 156 lrgggrlvlltse 168
                                       lr+g+ + ++t++
  gi|320100787|ref|YP_004176379.1| 283 LRSGSYMSFMTPA 295
                                       ***9988888875 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0     5e-10   1.8e-06     188     225 ..     181     218 ..     170     224 .. 0.86
   2 !    6.1   0.0    0.0023       8.2       1      39 [.     248     280 ..     248     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5e-10
                                       HS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHH CS
                       N6_N4_Mtase 188 stkkgdivlDpFaGSGtTavaakelgrkfiGieieeey 225
                                         ++g+i lDpFaG+Gt++++a +++ +++Gie++++ 
  gi|320100787|ref|YP_004176379.1| 181 RVREGGILLDPFAGTGTILMEAWSMNIRAVGIEVDWRL 218
                                       5689******************************9876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0023
                                       EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvl 39 
                                       vd i tdpPY+ g +      + ++++ + y  fl k +
  gi|320100787|ref|YP_004176379.1| 248 VDAIATDPPYGRGAS------THGQSQLALYDAFLGKAW 280
                                       799**********99......666666666666665555 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.8e-08   0.00014      41     128 ..     184     262 ..     173     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.8e-08
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       eg  +LD faG+G++ +EA S +  +av +e d + ++ ++enl+  ++++ + +l ++ + ++        ++d +
  gi|320100787|ref|YP_004176379.1| 184 EGGILLDPFAGTGTILMEAWSMN-IRAVGIEVDWRLAHGMEENLRFYRANA-IPVLGDSTFINVV-------NVDAI 251
                                       67789****************99.57899*******************774.5555555554442.......469** PP

                                       EE--SSSTTCH CS
                     Cons_hypoth95 118 flDPPyakell 128
                                         DPPy +++ 
  gi|320100787|ref|YP_004176379.1| 252 ATDPPYGRGAS 262
                                       ******99865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.054      20     133 ..     173     287 ..     170     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTT CS
                               MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleevee 95 
                                       s+lL++    ++ g +lD  +G+G + +++ +++   + + ++vd+r  +  +enl+  +++ + v+  + + +v  
  gi|320100787|ref|YP_004176379.1| 173 SRLLINLARVREGGILLDPFAGTGTILMEAWSMNI--RAVGIEVDWRLAHGMEENLRFYRANaIPVLGDSTFINVV- 246
                                       77888887887888899*******99877776655..589********************9977788777888888. PP

                                       S-EEEEEE---STTTC....HCHHHHHHHHHHHHHHHEEEEE CS
                               MTS  96 kkfdlivsNPPfhagk....atelavaeeliaeAkeaLkegG 133
                                        ++d+i + PP+ +g     + +la+ ++++ +A ++L++g 
  gi|320100787|ref|YP_004176379.1| 247 -NVDAIATDPPYGRGAsthgQSQLALYDAFLGKAWDVLRSGS 287
                                       .9**********998722224456788999999999999875 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00023      0.82      33      67 ..     171     205 ..     168     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                          N6_Mtase  33 evsklivellepksgesvyDpacGsggllvqaekv 67 
                                       +vs+l+++l+  ++g   +Dp +G+g +l++a ++
  gi|320100787|ref|YP_004176379.1| 171 DVSRLLINLARVREGGILLDPFAGTGTILMEAWSM 205
                                       69**************9*************99774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2604.04
//
Query:       gi|320100788|ref|YP_004176380.1|  [L=302]
Description: ribose-phosphate pyrophosphokinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-21   74.2   0.0    6.4e-19   68.0   0.0    2.3  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    1.2e-17   63.9   1.7    6.1e-17   61.6   0.8    2.1  2  Pribosyltran    Phosphoribosyl transferase domain
      3e-08   33.9   1.7    6.4e-08   32.8   0.4    2.1  3  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    0.00029   20.4   0.0    0.00052   19.5   0.0    1.4  1  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.034   13.6   0.0    1.4  1  PRTase_2        Phosphoribosyl transferase
      0.062   12.9   1.6        2.3    7.8   0.2    3.1  3  Amdase          Arylmalonate decarboxylase


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 !   68.0   0.0   2.2e-22   6.4e-19      17     116 .]      17     119 ..      12     119 .. 0.95
   2 ?    4.0   0.0     0.015        46      33      71 ..     195     233 ..     174     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 2.2e-22
                    Pribosyltran_N  17 akrlgvelgkakvsrfadgEikveiee..svrgkdvfiiqslskpvndnlmelllmidalrrasakritaViPylgy 91 
                                       a ++g e   +  + f+dgE +v+i+e  + +g++v+++ ++ +  +++++ ll++ dal r++a+   aViPyl+y
  gi|320100788|ref|YP_004176380.1|  17 AGEIGAETLGVVEKVFPDGEQYVRISEpeKAKGSKVVVVSTMYPMQDQAFIKLLMLGDALARSQAAMYLAVIPYLAY 93 
                                       66788888899999***********998899********************************************** PP

                    Pribosyltran_N  92 srqdrk.ksrepisaklvaklLeaaG 116
                                       srqd+  ++ ep+sa +v++ L+aaG
  gi|320100788|ref|YP_004176380.1|  94 SRQDKVfMPGEPVSALIVVNTLKAAG 119
                                       ************************99 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                    Pribosyltran_N  33 adgEikveiee.svrgkdvfiiqslskpvndnlmelllmi 71 
                                        +gE++++ +e  v g+dv+i+ ++++    ++ e  +m+
  gi|320100788|ref|YP_004176380.1| 195 VTGEVSYTPRElRVAGRDVIIVDDIVST-GGTIAEASRML 233
                                       5799999999989**********99855.45555555554 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.12   3.7e+02      66      93 ..      36      55 ..      10      58 .. 0.64
   2 !   61.6   0.8   2.1e-20   6.1e-17      16     135 ..     147     261 ..     139     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                                      TT--EE........EE----TTSEEEEE CS
                      Pribosyltran 66 dgseeaargssdesrlledpagkkVliV 93
                                      ++   +        + +e+ +g+kV++V
  gi|320100788|ref|YP_004176380.1| 36 EQYVRI--------SEPEKAKGSKVVVV 55
                                      222222........48999*******99 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 2.1e-20
                                       EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEE CS
                      Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVli 92 
                                        +l+ ++l++ + +++v++++++g++ +a   a+ ++v ++y+ k++ r  g  + ++        +  +ag+ V+i
  gi|320100788|ref|YP_004176380.1| 147 SDLLVKTLMS-DAERPVILAPDKGALERARFAANSIGVDYDYLVKSRDRVTGEVSYTP-------RELRVAGRDVII 215
                                       6777788888.899***********************999999888888877777775.......999********* PP

                                       E-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHHHHHH CS
                      Pribosyltran  93 VDDildtGgTllaalelLkekgpeevriavlv...dkpateeevdk 135
                                       VDDi++tGgT+ +a + L ++g+ ++++a+++     +a ++  d+
  gi|320100788|ref|YP_004176380.1| 216 VDDIVSTGGTIAEASRMLMKQGARRIHVATSHgllVGNALTRMLDA 261
                                       ******************************9866555555555555 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         1     3e+03      79     120 ..      18      58 ..      15      69 .. 0.74
   2 ?   -2.5   0.0       1.5   4.6e+03     103     121 ..     112     130 ..     104     153 .. 0.63
   3 !   32.8   0.4   2.1e-11   6.4e-08      81     149 ..     208     276 ..     206     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                                       S--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEE CS
                    Pribosyl_synth  79 GdvgGriaiivddliddvesfvaaaevlkerGaykiyvlath 120
                                       G++g     +v+ +  d e++v  +e  k++G+ k++v++t 
  gi|320100788|ref|YP_004176380.1|  18 GEIGAETLGVVEKVFPDGEQYVRISEPEKAKGS-KVVVVSTM 58 
                                       666666667888888888999999999999986.67777664 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                                       HHHHHHTT--EEEEEEEEE CS
                    Pribosyl_synth 103 aevlkerGaykiyvlathG 121
                                        ++lk+ G  k++v+  h 
  gi|320100788|ref|YP_004176380.1| 112 VNTLKAAGFRKLVVVDFHS 130
                                       5678888888888887774 PP

  == domain 3  score: 32.8 bits;  conditional E-value: 2.1e-11
                                       -TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HH CS
                    Pribosyl_synth  81 vgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntiphei 149
                                       v+Gr  iivdd++    ++ +a+++l ++Ga +i+v ++hGll  +a  ++ ++ +  + ++nt+   +
  gi|320100788|ref|YP_004176380.1| 208 VAGRDVIIVDDIVSTGGTIAEASRMLMKQGARRIHVATSHGLLVGNALTRMLDAGVRRIALANTLGVRV 276
                                       89***********************************************9999***********97766 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.7e-07   0.00052     116     157 ..     203     244 ..     186     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-07
                           UPRTase 116 Pkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                       P+++  a r v+++D +++TGg++a+a ++L ++g++  +I v+
  gi|320100788|ref|YP_004176380.1| 203 PRELrvAGRDVIIVDDIVSTGGTIAEASRMLMKQGAR--RIHVA 244
                                       5555448899***********************8876..55444 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.034     119     155 ..     208     243 ..     196     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                          PRTase_2 119 aaakelvLvDDEistGktalnliralqeklprkryvv 155
                                        a + +++vDD +stG t+++  r l ++  r+ ++v
  gi|320100788|ref|YP_004176380.1| 208 VAGRDVIIVDDIVSTGGTIAEASRMLMKQGARR-IHV 243
                                       45689*******************999987663.333 PP

>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.043   1.3e+02      88     124 ..     110     146 ..      91     163 .. 0.79
   2 ?   -2.1   0.0      0.81   2.4e+03      12      51 ..     174     214 ..     165     216 .. 0.79
   3 ?    7.8   0.2   0.00077       2.3      91     134 ..     231     274 ..     222     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.043
                            Amdase  88 avvealralgarRvAvataYidevnerLvayLeesgl 124
                                        vv++l+a g r++ v+   + ++ ++L +y+ +  +
  gi|320100788|ref|YP_004176380.1| 110 IVVNTLKAAGFRKLVVVDFHSSSLLSQLNDYIVNVMV 146
                                       47899************99999999999999876655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.81
                            Amdase  12 vrFeAeGLglk.elskegydevidrvveaArelaerGaqav 51 
                                       +rF+A+ +g++ +   ++ d v  +v  + rel+ +G +++
  gi|320100788|ref|YP_004176380.1| 174 ARFAANSIGVDyDYLVKSRDRVTGEVSYTPRELRVAGRDVI 214
                                       56777777775345667889999999999999999999988 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00077
                            Amdase  91 ealralgarRvAvataYidevnerLvayLeesglevaalesLdi 134
                                       + l + garR+ vat+    v ++L++ L++   ++a  ++L++
  gi|320100788|ref|YP_004176380.1| 231 RMLMKQGARRIHVATSHGLLVGNALTRMLDAGVRRIALANTLGV 274
                                       45778899999999999999999999999876666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2370.87
//
Query:       gi|320100789|ref|YP_004176381.1|  [L=358]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-19   70.3   0.0    1.6e-18   67.7   0.0    2.0  2  Radical_SAM     Radical SAM superfamily
     0.0014   18.6   1.0       0.69   10.0   0.0    2.9  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
     0.0029   17.9   0.1     0.0054   17.0   0.1    1.4  1  Fer4_12         4Fe-4S single cluster domain
     0.0059   16.0   2.9       0.16   11.4   0.1    2.7  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.013   14.9   5.5      0.093   12.3   0.0    3.1  3  TF_Zn_Ribbon    TFIIB zinc-binding
      0.068   13.0   0.0      0.068   13.0   0.0    3.3  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.28   11.2   0.0       0.28   11.2   0.0    2.7  3  DZR             Double zinc ribbon
       0.89    9.7   0.1       0.89    9.7   0.1    3.3  4  Zn-ribbon_8     Zinc ribbon domain
        3.3    7.5  11.2       0.56   10.0   0.1    3.0  3  zinc_ribbon_2   zinc-ribbon domain
        3.7    7.6  18.4       0.16   11.9   0.5    3.8  4  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        8.3    6.7   6.8        4.8    7.4   2.5    2.8  3  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   9.6e-22   1.6e-18       3     166 ..      87     243 ..      85     247 .. 0.91
   2 ?   -0.0   0.0      0.62     1e+03     128     147 ..     277     297 ..     258     307 .. 0.57

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 9.6e-22
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                        t gCn+ C+fC+++  +++++ g++  + e  e v+e+ +  g+ ++  +  ep++ ++f  ++++lak+  +g+ 
  gi|320100789|ref|YP_004176381.1|  87 STAGCNFYCRFCQNWVLSQSRRNGMFGKPYEPWEVVEEA-VGSGCQGISYTYNEPTVFYEFMYDVAKLAKE--KGLY 160
                                       799************************************.9******************************..7*** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                       +t++tng++  +e + +l  l  d  +++ +a  ++++ ++ ++ ++++ ++e+l  +++ g+  + ++ +++p + 
  gi|320100789|ref|YP_004176381.1| 161 NTMVTNGYMT-PEAIGKLGGLI-DAATVDFKASGNKDFYRRYMGVPDPSPIYESLIEMKKQGWW-IEVTNLIVPRVG 234
                                       *********8.99999999998.*********9999777777799*******************.777777777777 PP

                                       HHHHHHHHHH CS
                                       xxxxxxxxxx RF
                       Radical_SAM 157 deeleellel 166
                                       d+ +e++++l
  gi|320100789|ref|YP_004176381.1| 235 DR-IEDTVKL 243
                                       76.5666654 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHHTTSET.EEE CS
                                       xxxxxxxxxxxxxxxxx.xxx RF
                       Radical_SAM 128 eevlealeklreagikr.vvd 147
                                       e + +  e++r+ag+k   + 
  gi|320100789|ref|YP_004176381.1| 277 ETLEKHAEAARRAGLKHvYIG 297
                                       333334444444444443333 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 !   10.0   0.0   0.00042      0.69       2      11 ..     309     318 ..     308     328 .. 0.83
   2 !    6.3   0.2    0.0063        10       1       6 [.     334     339 ..     334     342 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00042
                    DNA_ligase_ZBD   2 CPvCGsavvR 11 
                                       CP CGs vv 
  gi|320100789|ref|YP_004176381.1| 309 CPKCGSLVVE 318
                                       ********94 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0063
                    DNA_ligase_ZBD   1 hCPvCG 6  
                                       +CPvCG
  gi|320100789|ref|YP_004176381.1| 334 KCPVCG 339
                                       6****9 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.3e-06    0.0054       6      98 ..      82     172 ..      78     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-06
                           Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeftkell.eeiiedlkkesiegltllGGEPllpenaeallelvkevke 81 
                                       + +s+ ++gCn+ C++C n  + + +++  f k+ +  e++e++  +  +g++++  EP +   +e +++++k  ke
  gi|320100789|ref|YP_004176381.1|  82 CAFSISTAGCNFYCRFCQNWVLSQSRRNGMFGKPYEpWEVVEEAVGSGCQGISYTYNEPTV--FYEFMYDVAKLAKE 156
                                       5678889**************999999999986665257888888999*************..89999********* PP

                           Fer4_12  82 ekpekdiwlytgytlee 98 
                                       +++  + ++++gy+  e
  gi|320100789|ref|YP_004176381.1| 157 KGL-YNTMVTNGYMTPE 172
                                       *99.58999***98655 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1    0.0001      0.16       2      13 ..     306     318 ..     305     320 .. 0.79
   2 ?    3.9   0.5     0.022        37      18      26 .]     334     342 ..     332     342 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                       zf-ribbon_3   2 tvrCPnCGa.pls 13 
                                        ++CP+CG+ +++
  gi|320100789|ref|YP_004176381.1| 306 NTYCPKCGSlVVE 318
                                       689******7776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.022
                       zf-ribbon_3  18 vCpyCGtkl 26 
                                       +Cp CG++l
  gi|320100789|ref|YP_004176381.1| 334 KCPVCGYRL 342
                                       477777765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       2.7   4.3e+03      20      25 ..      93      98 ..      92     100 .. 0.64
   2 ?   12.3   0.0   5.7e-05     0.093      19      41 ..     306     328 ..     300     329 .. 0.93
   3 ?    4.2   0.2     0.019        31       1       7 [.     333     339 ..     333     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                                      EEESSS CS
                      TF_Zn_Ribbon 20 lvCtdC 25
                                      ++C +C
  gi|320100789|ref|YP_004176381.1| 93 FYCRFC 98
                                      666666 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.7e-05
                                       CEEESSSSBEEEECCCCCCCHHH CS
                      TF_Zn_Ribbon  19 elvCtdCGlVlednsidegpewr 41 
                                       +++C++CG+++ ++   + ++wr
  gi|320100789|ref|YP_004176381.1| 306 NTYCPKCGSLVVERRGFYIVDWR 328
                                       899******************98 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.019
                                       EEETTTT CS
                      TF_Zn_Ribbon   1 ykCPnCg 7  
                                       +kCP+Cg
  gi|320100789|ref|YP_004176381.1| 333 FKCPVCG 339
                                       79****9 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.8      0.84   1.4e+03      23      34 ..      90      99 ..      89     112 .. 0.55
   2 ?   13.0   0.0   4.2e-05     0.068       3      16 ..     308     321 ..     306     323 .. 0.90
   3 ?    1.7   0.1      0.14   2.3e+02       3      10 ..     334     341 ..     332     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.84
                                      EESST.T----E CS
                    zf-C4_Topoisom 23 GCsnYPeCkftk 34
                                      GC+ Y  C+f  
  gi|320100789|ref|YP_004176381.1| 90 GCNFY--CRFCQ 99
                                      56665..65543 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.2e-05
                                       E-SSS--EEEEEE- CS
                    zf-C4_Topoisom   3 kCPkCggdLvlkrg 16 
                                        CPkCg+ +v++rg
  gi|320100789|ref|YP_004176381.1| 308 YCPKCGSLVVERRG 321
                                       7***********98 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.14
                                       E-SSS--E CS
                    zf-C4_Topoisom   3 kCPkCggd 10 
                                       kCP Cg  
  gi|320100789|ref|YP_004176381.1| 334 KCPVCGYR 341
                                       8****955 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.1   1.7e+03      30      38 ..      25      33 ..      14      49 .. 0.68
   2 ?   -1.6   0.8       1.8   2.9e+03      41      46 ..      94      99 ..      80     106 .. 0.65
   3 ?   11.2   0.0   0.00017      0.28       9      38 ..     303     342 ..     298     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                               DZR 30 rCpsCgekv 38
                                      rC  C++ +
  gi|320100789|ref|YP_004176381.1| 25 RCNLCHRRC 33
                                      455555543 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.8
                               DZR 41 earfCp 46
                                       +rfC+
  gi|320100789|ref|YP_004176381.1| 94 YCRFCQ 99
                                      344443 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00017
                               DZR   9 ppdarfCseCgtklkavaa..........edrCpsCgekv 38 
                                       p ++ +C++Cg+ + +               +Cp Cg+ +
  gi|320100789|ref|YP_004176381.1| 303 PLENTYCPKCGSLVVERRGfyivdwrlreGFKCPVCGYRL 342
                                       5678899999999975444999999999888999999875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   1.9       9.1   1.5e+04       7      13 ..      25      31 ..      23      33 .. 0.74
   2 ?   -2.5   0.3       3.5   5.7e+03       6      12 ..      93      99 ..      92     102 .. 0.81
   3 ?    9.7   0.1   0.00055      0.89      26      38 ..     306     319 ..     300     320 .. 0.79
   4 ?    1.4   0.1      0.21   3.4e+02       7      33 ..     334     339 ..     331     344 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9.1
                       Zn-ribbon_8  7 rCeeCgh 13
                                      rC+ C++
  gi|320100789|ref|YP_004176381.1| 25 RCNLCHR 31
                                      7888876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.5
                       Zn-ribbon_8  6 YrCeeCg 12
                                      + C+ C+
  gi|320100789|ref|YP_004176381.1| 93 FYCRFCQ 99
                                      7899998 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00055
                       Zn-ribbon_8  26 ltaCPeCgs.evrr 38 
                                       +t CP+Cgs  v+r
  gi|320100789|ref|YP_004176381.1| 306 NTYCPKCGSlVVER 319
                                       456******88887 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.21
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCg 33 
                                       +                     CP Cg
  gi|320100789|ref|YP_004176381.1| 334 K---------------------CPVCG 339
                                       3.....................66666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.1       6.3     1e+04       3      16 ..      96      98 ..      94     100 .. 0.42
   2 ?   10.0   0.1   0.00035      0.56      12      21 ..     305     314 ..     302     316 .. 0.81
   3 ?    4.4   0.5      0.02        32      16      22 ..     335     341 ..     331     342 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.3
                     zinc_ribbon_2  3 pnCGaelqdnakFC 16
                                                  FC
  gi|320100789|ref|YP_004176381.1| 96 R-----------FC 98
                                      3...........33 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00035
                     zinc_ribbon_2  12 nakFCpyCGt 21 
                                       ++++Cp+CG+
  gi|320100789|ref|YP_004176381.1| 305 ENTYCPKCGS 314
                                       6899999995 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.02
                     zinc_ribbon_2  16 CpyCGtp 22 
                                       Cp CG+ 
  gi|320100789|ref|YP_004176381.1| 335 CPVCGYR 341
                                       7777765 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 ?   -0.9   0.7         1   1.6e+03      36      45 ..      22      31 ..      13      33 .. 0.71
   2 ?   -0.4   0.3      0.74   1.2e+03      19      27 ..      93     101 ..      88     112 .. 0.71
   3 ?    6.8   0.5    0.0039       6.4      14      27 ..     299     315 ..     296     323 .. 0.76
   4 ?   11.9   0.5    0.0001      0.16      10      28 ..     324     343 ..     322     356 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1
                     Zn_Tnp_IS1595 36 glfqCkeCrk 45
                                      g+ +C+ C++
  gi|320100789|ref|YP_004176381.1| 22 GRVRCNLCHR 31
                                      5567777765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.74
                     Zn_Tnp_IS1595  19 fvCPhCgsr 27 
                                       f C +C++ 
  gi|320100789|ref|YP_004176381.1|  93 FYCRFCQNW 101
                                       779999975 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0039
                     Zn_Tnp_IS1595  14 rWpng...fvCPhCgsr 27 
                                       +W++      CP+Cgs 
  gi|320100789|ref|YP_004176381.1| 299 VWGHPlenTYCPKCGSL 315
                                       7888888555*****75 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.0001
                     Zn_Tnp_IS1595  10 LealrWpngfvCPhCgsr.k 28 
                                       + ++r ++gf CP Cg+r  
  gi|320100789|ref|YP_004176381.1| 324 IVDWRLREGFKCPVCGYRlN 343
                                       56899***********9852 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 ?   -2.3   0.0       3.3   5.4e+03      30      39 ..      20      29 ..      15      30 .. 0.79
   2 ?   -3.4   0.0       7.2   1.2e+04      17      25 ..      94     103 ..      92     110 .. 0.57
   3 ?    7.4   2.5     0.003       4.8      11      39 ..     302     338 ..     300     339 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.3
                     Auto_anti-p27 30 kggkvyCvaC 39
                                      ++g+v C +C
  gi|320100789|ref|YP_004176381.1| 20 GDGRVRCNLC 29
                                      6789999999 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.2
                     Auto_anti-p27  17 tCpvC.gvPL 25 
                                       +C  C + +L
  gi|320100789|ref|YP_004176381.1|  94 YCRFCqNWVL 103
                                       5666655555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.003
                     Auto_anti-p27  11 wtMLaetCpvCgvPLmrdr.....k...ggkvyCvaC 39 
                                       + + +++Cp+Cg+  ++ r     +   ++   C++C
  gi|320100789|ref|YP_004176381.1| 302 HPLENTYCPKCGSLVVERRgfyivDwrlREGFKCPVC 338
                                       567799*******999988665541444455567777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2607.06
//
Query:       gi|320100790|ref|YP_004176382.1|  [L=261]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-58  197.8   0.0    2.6e-58  197.6   0.0    1.0  1  ATP_bind_1   Conserved hypothetical ATP binding protein
    0.00027   20.8   0.0     0.0061   16.4   0.0    2.1  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
    0.00047   19.9   0.0       0.27   11.0   0.0    2.6  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0012   18.4   0.0     0.0097   15.5   0.0    2.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0016   18.5   0.0     0.0018   18.3   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0025   18.3   0.0      0.006   17.1   0.0    1.7  2  AAA_18       AAA domain
     0.0074   16.7   0.0     0.0096   16.3   0.0    1.5  1  AAA_16       AAA ATPase domain
     0.0096   15.5   0.1       0.32   10.5   0.0    2.7  3  FeoB_N       Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.012   15.3   0.0        0.1   12.2   0.0    2.1  2  SRP54        SRP54-type protein, GTPase domain
      0.013   14.8   0.1      0.058   12.7   0.1    1.9  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
      0.019   14.9   0.1         15    5.4   0.0    3.1  3  RsgA_GTPase  RsgA GTPase
      0.021   14.9   0.0      0.098   12.7   0.0    2.0  1  MMR_HSR1     50S ribosome-binding GTPase
      0.051   13.9   0.0       0.36   11.1   0.0    2.0  2  AAA_22       AAA domain
      0.057   13.5   0.0      0.088   12.9   0.0    1.4  1  DUF87        Helicase HerA, central domain
      0.063   13.0   0.0      0.093   12.4   0.0    1.3  1  AAA_24       AAA domain
      0.087   11.9   0.0       0.17   10.9   0.0    1.4  1  T2SSE        Type II/IV secretion system protein
       0.09   12.7   0.0       0.18   11.7   0.0    1.5  1  NACHT        NACHT domain
       0.11   11.9   0.0       0.25   10.8   0.0    1.5  2  PhoH         PhoH-like protein
       0.16   11.4   0.0        4.7    6.6   0.0    2.3  2  SRPRB        Signal recognition particle receptor beta subuni
       0.16   11.5   0.6        1.6    8.3   0.6    2.2  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.19   11.0   0.0       0.28   10.4   0.0    1.3  1  Zeta_toxin   Zeta toxin


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 !  197.6   0.0   3.1e-61   2.6e-58       1     239 [.       7     246 ..       7     248 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.6 bits;  conditional E-value: 3.1e-61
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflre 77 
                                       v+G+aGsGKt++++ l  +l + + + a+vNLDPA+eelpY++++d+r++++ +dvm + glgpngal+ ++++l  
  gi|320100790|ref|YP_004176382.1|   7 VLGTAGSGKTSLTSMLHTYLVSHQLDAAIVNLDPAVEELPYDPDIDVRDYVDARDVMRRRGLGPNGALIASIDMLLA 83 
                                       89*************************************************************************** PP

                        ATP_bind_1  78 sldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlr 154
                                       +++++++ +   +++y+l+DtPGQ+elf +++ ++++++++  + + v++yL+Ds++++ +++ +s+ll+a s+ +r
  gi|320100790|ref|YP_004176382.1|  84 NIQEIQDLVWSMKANYILIDTPGQMELFAFRDTGSIVLKSIVGDAKAVALYLIDSTYASRSSNIFSALLLAASTHAR 160
                                       *****999977799*************************************************************** PP

                        ATP_bind_1 155 lelPhvvvlnkfDllkek.lekeleffedvealslllekee.ekykklaeaiaelleefalvlrflplssekeesie 229
                                       l+ P+v+vl+k+Dll+e+   k    + d+++ls  + +e+     + +e+i+++le+     +++p+s+  +e+++
  gi|320100790|ref|YP_004176382.1| 161 LGYPQVNVLTKVDLLSEEaMGKLTGLLDDPDTLSVEIASEKqASLVWDEEEISSILEKLLVF-DIVPVSNTLGEGFD 236
                                       ****************997667777889999999988877768889***********99998.************** PP

                        ATP_bind_1 230 dllslideal 239
                                        l+++i+  l
  gi|320100790|ref|YP_004176382.1| 237 SLYAAIQRVL 246
                                       ******9865 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.1e-06    0.0061       1      36 [.       9      44 ..       9      47 .. 0.92
   2 ?    2.3   0.0      0.15   1.2e+02      92     115 ..      86     109 ..      72     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.1e-06
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                      G   sGK++l+ +L  y+++++   ++v+lD+   e
  gi|320100790|ref|YP_004176382.1|  9 GTAGSGKTSLTSMLHTYLVSHQLDAAIVNLDPAVEE 44
                                      7789***************************97665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                            CLP1_P  92 eekleenkkakasgliIntpGwvk 115
                                       +e  +   ++ka+ ++I+tpG ++
  gi|320100790|ref|YP_004176382.1|  86 QEIQDLVWSMKANYILIDTPGQME 109
                                       333333347899*********876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00031      0.27       4      28 ..       5      29 ..       3      44 .. 0.82
   2 ?    6.0   0.0     0.011       9.1      37     105 ..      98     178 ..      76     187 .. 0.65
   3 ?   -2.2   0.0       3.6   3.1e+03     114     142 ..     215     243 ..     203     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                         PduV-EutP  4 illiGkvgsGKttLtqalkgeelkY 28
                                      i+++G+ gsGKt+Lt  l+   ++ 
  gi|320100790|ref|YP_004176382.1|  5 IIVLGTAGSGKTSLTSMLHTYLVSH 29
                                      89**************998766555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                         PduV-EutP  37 sdeviDtPGe...ylenrklysalivtsaeadvialvq.d...ateeesvfppgf.....asvfnkeviGiitkidl 101
                                       +  +iDtPG+   ++   + + +l+++  +a+ +al + d   a++++++f++ +      + +  + + ++tk+dl
  gi|320100790|ref|YP_004176382.1|  98 NYILIDTPGQmelFAFRDTGSIVLKSIVGDAKAVALYLiDstyASRSSNIFSALLlaastHARLGYPQVNVLTKVDL 174
                                       44569****84333444445667889999999999853231224566777776541100033455577889999999 PP

                         PduV-EutP 102 aede 105
                                        ++e
  gi|320100790|ref|YP_004176382.1| 175 LSEE 178
                                       8554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.6
                         PduV-EutP 114 lLksaGaekifevsavekegieellkyle 142
                                        L++  +  i  vs++  eg+++l + ++
  gi|320100790|ref|YP_004176382.1| 215 ILEKLLVFDIVPVSNTLGEGFDSLYAAIQ 243
                                       55666677888999999999999988775 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 !   15.5   0.0   1.1e-05    0.0097       6     191 ..       5     245 ..       3     247 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                       EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHST...............HCHSHHHHHHTSCSSCEEEEEE. CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgeka..eeerv...............lDtlkeErergiTiksaaisle. 64 
                                       i+++g   +GKt+Lt  L +++   + +++    +   +               +D ++  r+rg+  + a i    
  gi|320100790|ref|YP_004176382.1|   5 IIVLGTAGSGKTSLTSMLHTYLVSHQLDAAIVnlD-P-AveelpydpdidvrdyVDARDVMRRRGLGPNGALIASId 79 
                                       7899999***********99887765543333331.2.1467789999999999***********877766655545 PP

                                       ............TTCSSEEEEEEEESSSGG.GHHHHHHH........HHT-SEEEEEEETTTB.STHHHHHHHHHHH CS
                          GTP_EFTU  65 ............ketkkylinliDtPGHvd.Fskevirg........lrvlDgavlvvdaveG.vepqteevlrlal 119
                                                     + k ++ liDtPG ++ F     +g          +  +a+ ++d++     ++    l la 
  gi|320100790|ref|YP_004176382.1|  80 mllaniqeiqdlVWSMKANYILIDTPGQMElFA-FRDTGsivlksivGDAKAVALYLIDSTYAsRSSNIFSALLLAA 155
                                       6688888998644888999*********99544.3333313433233334456888888875434445555555554 PP

                                       HTTTE....EEEEEESCGST...............HHHHHHHHHHHHHHHHHH............HHHHHHHHHTTT CS
                          GTP_EFTU 120 kegvp....iivfiNKmDrl...............kaelkeiveevkqklsrk............eeklekygekge 165
                                       + + +     + +++K+D l               +        +++     +            ee+++++ ek  
  gi|320100790|ref|YP_004176382.1| 156 STHARlgypQVNVLTKVDLLseeamgkltgllddpD--------TLSV----EiasekqaslvwdEEEISSILEKL- 219
                                       4433333439999******97777666444433222........2222....133334455556588888888887. PP

                                       TTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 166 kevpvvfgSalkgegvktllealvel 191
                                         + +v++S   geg+++l  a+ + 
  gi|320100790|ref|YP_004176382.1| 220 LVFDIVPVSNTLGEGFDSLYAAIQRV 245
                                       59999999999999999999988765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.1e-06    0.0018       2      55 ..       5      84 ..       4     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHH....................... CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx....................... RF
                              CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiep....................... 54
                                      +i+ ++ G+GKT+l+  L+++l  ++l+ + v +Dp  + l +   +       +                        
  gi|320100790|ref|YP_004176382.1|  5 IIVLGTAGSGKTSLTSMLHTYLVSHQLDAAIVNLDPAVEELPYdpdI-------DVrdyvdardvmrrrglgpngalia 76
                                      6788999*****************************98888744221.......1122333456666666666666666 PP

                                      .......C CS
                                      .......x RF
                              CbiA 55 .......d 55
                                             +
  gi|320100790|ref|YP_004176382.1| 77 sidmllaN 84
                                      55555552 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     7e-06     0.006       1      99 [.       5     121 ..       5     145 .. 0.60
   2 ?   -2.7   0.0       9.6   8.2e+03      28      43 ..     194     209 ..     160     227 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf......................gvnlrdvakenglllevdpealdeskrlded 55 
                                       I++ Gt+G+GKt+l+  L   l +                       + +rd               +d  +++++ 
  gi|320100790|ref|YP_004176382.1|   5 IIVLGTAGSGKTSLTSMLHTYL-VshqldaaivnldpaveelpydpDIDVRD--------------YVDARDVMRRR 66 
                                       9*****************5444.12344544333333333333344333333..............44444444444 PP

                            AAA_18  56 kldklldaleenss...........aleegknlvidghlaeleseaakdikkvvL 99 
                                        l  +  ++  ++             +    n+++ + ++++e  a++d + +vL
  gi|320100790|ref|YP_004176382.1|  67 GLGPNGALIASIDMllaniqeiqdlVWSMKANYILIDTPGQMELFAFRDTGSIVL 121
                                       4444444444443344444445555566666666666777777777777777555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.6
                            AAA_18  28 lrdvakenglllevdp 43 
                                       + ++a+e++ +l +d+
  gi|320100790|ref|YP_004176382.1| 194 SVEIASEKQASLVWDE 209
                                       3333333333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-05    0.0096      27      84 ..       5      65 ..       2     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekd...ggiflrgkcdqlesaipy..sa.laqalareellrq 84
                                      +++ G +G+GK+sl  +l+++l  +    +i+    +++    +py  ++ + ++ ++++++r 
  gi|320100790|ref|YP_004176382.1|  5 IIVLGTAGSGKTSLTSMLHTYLVSHqldAAIVNLDPAVEE---LPYdpDIdVRDYVDARDVMRR 65
                                      79******************99988553344444444444...788553335555555555555 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.86   7.3e+02       3      20 ..       5      22 ..       3      28 .. 0.85
   2 !   10.5   0.0   0.00037      0.32      46     118 ..      96     175 ..      85     188 .. 0.75
   3 ?    1.1   0.0       0.3   2.6e+02     129     156 .]     215     242 ..     196     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.86
                                      EEEEESTTSSHHHHHHHH CS
                            FeoB_N  3 valvGnpnvGkttlfnal 20
                                      ++++G   +Gkt+l   l
  gi|320100790|ref|YP_004176382.1|  5 IIVLGTAGSGKTSLTSML 22
                                      6789*********98776 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00037
                                       TEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGGGHHHHHHHHHHHH.......HTTSSEEEEEETH CS
                            FeoB_N  46 gkeveivDlPGiYslsayseeekvardflleeepdvvvnvvdatnlernLyLtlqll.......elgvpvvlalnmi 115
                                       + ++ ++D PG  +l a+    +++ + ++ +   v + ++d+t   r+  ++  ll        lg p v +l ++
  gi|320100790|ref|YP_004176382.1|  96 KANYILIDTPGQMELFAFRDTGSIVLKSIVGDAKAVALYLIDSTYASRSSNIFSALLlaasthaRLGYPQVNVLTKV 172
                                       57889**************************************9988875544443311111114556666666666 PP

                                       HHH CS
                            FeoB_N 116 dea 118
                                       d +
  gi|320100790|ref|YP_004176382.1| 173 DLL 175
                                       655 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.3
                                       HHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 129 kLsekLgvpvvktsakkkegieellkai 156
                                        L++ L +++v++s + +eg+++l +ai
  gi|320100790|ref|YP_004176382.1| 215 ILEKLLVFDIVPVSNTLGEGFDSLYAAI 242
                                       58899999**************998775 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012       0.1       3      38 ..       4      39 ..       2      41 .. 0.93
   2 ?    0.8   0.0      0.37   3.2e+02      82      96 ..      95     109 ..      80     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                       i+++G+ G+GKT+ ++ L  +l +++ ++++v +D
  gi|320100790|ref|YP_004176382.1|  4 FIIVLGTAGSGKTSLTSMLHTYLVSHQLDAAIVNLD 39
                                      7999**************************999988 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.37
                                       TTSSEEEEEE--SST CS
                             SRP54  82 ekidvvlvDTaGrlq 96 
                                        k++++l+DT G+++
  gi|320100790|ref|YP_004176382.1|  95 MKANYILIDTPGQME 109
                                       567899999999875 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.8e-05     0.058       2     129 ..       5     180 ..       4     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-05
                         Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnylardtlrlgati........................................... 35 
                                       ++ +G  gsGKts+ s+++  ++ ++     a+i                                           
  gi|320100790|ref|YP_004176382.1|   5 IIVLGTAGSGKTSLTSMLHTYLVSHQL---DAAIvnldpaveelpydpdidvrdyvdardvmrrrglgpngaliasi 78 
                                       6789*************9988887764...33333446677999999999999999999999999999999999999 PP

                         Gtr1_RagA  36 .......dveksevrflgnltlnlwDcgGqeafvee...ylssqkeeifrnvgvliyVfDvesreleedletlkeil 102
                                              + e +++  + + +  l+D +Gq ++++         k+ +    +v +y++D++    +++ + ++ +l
  gi|320100790|ref|YP_004176382.1|  79 dmllaniQ-EIQDLVWSMKANYILIDTPGQMELFAFrdtGSIVLKSIVGDAKAVALYLIDST--YASRSSNIFSALL 152
                                       99998643.3344446667778899****999886522122233333334444889999999..5555556666666 PP

                         Gtr1_RagA 103 ealrqysp..eakvfvlihKmDliqeder 129
                                        a++++ +    +v vl  K+Dl++e++ 
  gi|320100790|ref|YP_004176382.1| 153 LAASTHARlgYPQVNVL-TKVDLLSEEAM 180
                                       66655554113355554.68898888765 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     0.018        15     102     121 ..       5      24 ..       2      36 .. 0.86
   2 ?    1.4   0.0      0.32   2.7e+02     148     162 ..      94     108 ..      89     112 .. 0.79
   3 ?    4.3   0.0     0.039        33      47      74 ..     163     189 ..     129     238 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                                       EEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallp 121
                                       ++++G  G GK++L  +l+ 
  gi|320100790|ref|YP_004176382.1|   5 IIVLGTAGSGKTSLTSMLHT 24 
                                       6899**********999976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                                       EETTTEEEESS-SSS CS
                       RsgA_GTPase 148 elaegglliDtPGfr 162
                                       +++++ +liDtPG  
  gi|320100790|ref|YP_004176382.1|  94 SMKANYILIDTPGQM 108
                                       5677889******65 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.039
                                       -EEEEEEE-GGG--HHHHHHHHHHHHHH CS
                       RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeelea 74 
                                        + v vl+K+Dll+ee  + +l   l +
  gi|320100790|ref|YP_004176382.1| 163 YPQVNVLTKVDLLSEEA-MGKLTGLLDD 189
                                       356779*********99.4444444433 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.098       2      92 ..       5     142 ..       4     171 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE.............................. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke.............................. 47 
                                       ++++G   +GK++L + l    +++  d + + +d+  +++ ++  +                              
  gi|320100790|ref|YP_004176382.1|   5 IIVLGTAGSGKTSLTSMLHTYlVSHQLDAAIVNLDPAVEELPYDP-Didvrdyvdardvmrrrglgpngaliasidm 80 
                                       788999999999999999876567777888888888888777432.1344555666677777777777777777777 PP

                                       ..................EEEEECGGCSS...HHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHH CS
                          MMR_HSR1  48 ..................ielvDtpGlie...gaseekglgkaflaleeadlillvvdaseeklkp 92 
                                                         ++l+DtpG +e     +++  + k++    +  ++l+++d++   ++ 
  gi|320100790|ref|YP_004176382.1|  81 llaniqeiqdlvwsmkanYILIDTPGQMElfaFRDTGSIVLKSIVGDAK-AVALYLIDST---YAS 142
                                       888888888888888888********65443233344456666665444.8899999944...333 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   0.00042      0.36       6      33 ..       3      30 ..       2      65 .. 0.84
   2 ?    0.4   0.0      0.83   7.1e+02      70     118 ..     130     189 ..      76     207 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeea 33
                                      ++++v G +G+GKT l  +l+  l+ ++
  gi|320100790|ref|YP_004176382.1|  3 YFIIVLGTAGSGKTSLTSMLHTYLVSHQ 30
                                      689**************99998876654 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.83
                            AAA_22  70 a.........erlsseellealeqalrarav...ielliiDEaqhlrseealeeLrsllnl 118
                                       a         +  +s+ +++al  a++++a+   +++ ++  ++ l seea+ +L  ll++
  gi|320100790|ref|YP_004176382.1| 130 AvalylidstYASRSSNIFSALLLAASTHARlgyPQVNVLTKVDLL-SEEAMGKLTGLLDD 189
                                       2344455555445666666444444444444488888888888888.88887777666664 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.088      28      61 ..       7      41 ..       5      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                             DUF87 28 ilgsTGsGKSntvavLleelle.kkgatililDpH 61
                                      +lg++GsGK+ +++ L   l++ + +a i+ lDp 
  gi|320100790|ref|YP_004176382.1|  7 VLGTAGSGKTSLTSMLHTYLVShQLDAAIVNLDPA 41
                                      9********************999999***99996 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011     0.093       2      78 ..       2     109 ..       1     119 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            AAA_24   2 klkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie......................sw 49 
                                       ++ i++ G +g+GKT+l ++l       + ++++++++  + +l  d   d++                      s+
  gi|320100790|ref|YP_004176382.1|   2 PYFIIVLGTAGSGKTSLTSMLhtylvshQLDAAIVNLDPAVEELPYDPDIDVRdyvdardvmrrrglgpngaliaSI 78 
                                       56799****************88888887788888888888888888877777666666777777777777777777 PP

                            AAA_24  50 edfldevvel..aaeladyktlviDtidele 78 
                                       +++l  ++e+    +  + + + iDt +++e
  gi|320100790|ref|YP_004176382.1|  79 DMLLANIQEIqdLVWSMKANYILIDTPGQME 109
                                       7777777777655566677778888877766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.17     131     168 ..       4      43 ..       2      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks..derivtvEDpvE 168
                                        i+v G+ gsGKt l+ +l +++ ++  d  iv +  +vE
  gi|320100790|ref|YP_004176382.1|   4 FIIVLGTAGSGKTSLTSMLHTYLVSHqlDAAIVNLDPAVE 43 
                                       69**************999999998867777777766665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.18       3      30 ..       5      32 ..       3      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      +i+ G aGsGKT L   l++ + + +l+
  gi|320100790|ref|YP_004176382.1|  5 IIVLGTAGSGKTSLTSMLHTYLVSHQLD 32
                                      89************99998888777665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.25      22      60 ..       5      43 ..       2      58 .. 0.88
   2 ?   -3.3   0.0       5.8     5e+03      64      91 ..     160     187 ..     154     218 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                                      EEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S-- CS
                              PhoH 22 vfaiGpaGtGKtylavalavealkkkkvkriiltrpave 60
                                      ++++G aG+GKt l+ +l   +++++    i+ + pave
  gi|320100790|ref|YP_004176382.1|  5 IIVLGTAGSGKTSLTSMLHTYLVSHQLDAAIVNLDPAVE 43
                                      7899**************999999999999999999997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.8
                                       ---SS---------TTTHHHHHHHTTTS CS
                              PhoH  64 elGflpgdleekvdpylrplydaLkdll 91 
                                       +lG+ + ++ +kvd   +  + +L+ ll
  gi|320100790|ref|YP_004176382.1| 160 RLGYPQVNVLTKVDLLSEEAMGKLTGLL 187
                                       6677777777777766666666666555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0055       4.7       6      26 ..       5      25 ..       2      42 .. 0.84
   2 ?    2.2   0.0      0.12   1.1e+02      49      91 ..      97     144 ..      83     166 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0055
                                      EEEE-STTSSHHHHHHHHHHS CS
                             SRPRB  6 vllvGlsdsGKTslftrLttd 26
                                      ++++G   sGKTsl   L t 
  gi|320100790|ref|YP_004176382.1|  5 IIVLGTAGSGKTSLTSMLHTY 25
                                      7899**********9999875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                                       TT-SEEEETT-GCCSH.HHHHHHHHHGG...EEEE.EEEEETTS-HHH CS
                             SRPRB  49 skltliDfPGheklrq.klleklkakss...lkgl.vfvvDStidpke 91 
                                        +  liD PG+ +l   + + +++ ks    +k++ ++++DSt  ++ 
  gi|320100790|ref|YP_004176382.1|  97 ANYILIDTPGQMELFAfRDTGSIVLKSIvgdAKAVaLYLIDSTYASRS 144
                                       567799999998874312222222222112345443799999987775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.6    0.0018       1.6       3      33 ..       5      37 ..       3     189 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                                      EEEEESTTCCHHHHHHHHH..CT--SS-EEEEE CS
                              cobW  3 tvltGflGsGKTtLlnhll..enraglklaviv 33
                                      +++ G  GsGKT+L + l     +++l+ a++ 
  gi|320100790|ref|YP_004176382.1|  5 IIVLGTAGSGKTSLTSMLHtyLVSHQLDAAIVN 37
                                      68999*******997666544556666666654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00033      0.28      16      52 ..       2      39 ..       1      56 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                        Zeta_toxin 16 PklillgGqpGAGKselaellkdele.rqgnvvrldpD 52
                                      P  i++ G  G+GK++l ++l ++l  +q ++  ++ D
  gi|320100790|ref|YP_004176382.1|  2 PYFIIVLGTAGSGKTSLTSMLHTYLVsHQLDAAIVNLD 39
                                      88899****************99987666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 1812.87
//
Query:       gi|320100791|ref|YP_004176383.1|  [L=190]
Description: HAD-superfamily hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-09   37.6   0.3    4.2e-06   27.2   0.0    2.1  2  Hydrolase    haloacid dehalogenase-like hydrolase
    5.7e-09   36.6   0.1    9.9e-09   35.9   0.1    1.4  1  HAD          haloacid dehalogenase-like hydrolase
    3.7e-08   33.7   0.0    1.3e-07   31.9   0.0    1.9  1  HAD_2        Haloacid dehalogenase-like hydrolase
    6.2e-06   26.1   0.4    0.00019   21.3   0.0    2.2  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    0.00029   20.6   0.0     0.0011   18.7   0.0    1.8  1  NIF          NLI interacting factor-like phosphatase
  ------ inclusion threshold ------
      0.018   15.1   0.0       0.05   13.7   0.0    1.9  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
      0.032   14.1   0.0      0.061   13.2   0.0    1.5  1  NT5C         5' nucleotidase, deoxy (Pyrimidine), cytosolic t
       0.19   11.5   0.0        1.9    8.3   0.0    2.0  2  RF3_C        Class II release factor RF3, C-terminal domain


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00087         2       1      22 [.       4      22 ..       4      48 .. 0.79
   2 !   27.2   0.0   1.9e-09   4.2e-06     104     210 .]      64     163 ..      47     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00087
                                      SSEEEEESBTTTBCHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgepsvedv 22
                                      ++t+v D+dGTL+   ps++d+
  gi|320100791|ref|YP_004176383.1|  4 VRTIVVDVDGTLI---PSLVDF 22
                                      68***********...777665 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 1.9e-09
                                       TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 104 qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkv 180
                                       + ++l+ +++ dp  ++  + e +++L a g+++v++t  + et + ++++lG        ++++e+v      + v
  gi|320100791|ref|YP_004176383.1|  64 EEEELRTIALLDPEALRGNI-EGLRRLAAEGFRIVIATHRSMETLKPVIEKLG------LAGYITEAVTRDYSIDRV 133
                                       45889999999995555555.999*****************************......555566669999999999 PP

                                       HHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 181 aaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       + +r L+++  +++++GD+v D  a a+Ag
  gi|320100791|ref|YP_004176383.1| 134 EQLRYLKARYGDIVFIGDTVYDEDASARAG 163
                                       999**********************99998 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   4.4e-12   9.9e-09       1     183 [.       7     155 ..       7     159 .. 0.67

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 4.4e-12
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv 77 
                                       ++ D+DgTL+++    l ++  lr++ +r++   +e   l l  ++l l++++++++++ + +  + + +a l+   
  gi|320100791|ref|YP_004176383.1|   7 IVVDVDGTLIPS----LVDFEGLRERIRRELGVSHELKPLGLSLSRLPLSDEEKQKAWR-IVEEEELRTIALLDPEA 78 
                                       689*********....6666666666666666666664444444555555555555544.45555555555555555 PP

                               HAD  78 aevirpklldp..galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrg. 151
                                               l+   + l++la   a+G+r+v+ +    + ++p+ ++lg    la       ++t    +  + + + 
  gi|320100791|ref|YP_004176383.1|  79 --------LRGniEGLRRLA---AEGFRIVIATHRSMETLKPVIEKLG----LAG------YITEA--VTRDYSIDr 132
                                       ........333567888888...*************************....***......99999..555444440 PP

                               HAD 152 egkvaalrewlaaegegidleevvayGDspsD 183
                                        + ++ l++         ++ ++v++GD++ D
  gi|320100791|ref|YP_004176383.1| 133 VEQLRYLKA---------RYGDIVFIGDTVYD 155
                                       333344444.........5556*******998 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   5.8e-11   1.3e-07      59     176 ..      53     167 ..       7     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.8e-11
                             HAD_2  59 eekieellrkyneekkk....kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedv 131
                                       +e  ++ +r+++ee+ +       + + g +e L  L+++g+++ i+T +s e+++  +e+lg+  y++  vt +  
  gi|320100791|ref|YP_004176383.1|  53 DEEKQKAWRIVEEEELRtialLDPEALRGNIEGLRRLAAEGFRIVIATHRSMETLKPVIEKLGLAGYITEAVTRDYS 129
                                       2256788899999999967555667899**********************************************998 PP

                             HAD_2 132 ekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagikvi 176
                                         +        + l+ lk+   +++++GD+ +D  a+ +ag+++ 
  gi|320100791|ref|YP_004176383.1| 130 IDR-------VEQLRYLKARYGDIVFIGDTVYDEDASARAGVEFH 167
                                       877.......678999**************************986 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.037        83       1      11 [.       7      17 ..       7      25 .. 0.90
   2 !   21.3   0.0   8.4e-08   0.00019      19      58 ..      81     120 ..      73     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.037
                                      EEEEIIIIIS- CS
                       Hydrolase_3  1 ialDlDGTLln 11
                                      i++D+DGTL+ 
  gi|320100791|ref|YP_004176383.1|  7 IVVDVDGTLIP 17
                                      89*******86 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 8.4e-08
                                       HHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  19 ktkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                        ++e +++l ++g+ +viAT Rs+++++pv+e+lgl  ++
  gi|320100791|ref|YP_004176383.1|  81 GNIEGLRRLAAEGFRIVIATHRSMETLKPVIEKLGLAGYI 120
                                       58999******************************99665 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     5e-07    0.0011       2     129 ..       6     168 ..       5     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5e-07
                               NIF   2 tLVLDLDetLvhskleksk..................................klkvegek............vevs 32 
                                       t+V+D+D+tL+ s ++ ++                                                      +   
  gi|320100791|ref|YP_004176383.1|   6 TIVVDVDGTLIPSLVDFEGlrerirrelgvshelkplglslsrlplsdeekqkA------WriveeeelrtiaLLDP 76 
                                       899999999997775222234555566777777888888877555555444441......03333334555558888 PP

                               NIF  33 vlkRpgldefLkelsklyevvifTasseeyaeavidildpekkllshrlyrescvkkkgeyvKdLsllgrdlsrvvi 109
                                        ++R   + + + +++ + +vi T  s+e+ ++vi++l   + ++++ ++r+ ++    + v +L++l++   ++v+
  gi|320100791|ref|YP_004176383.1|  77 EALRGNIEGLRRLAAEGFRIVIATHRSMETLKPVIEKLGLAG-YITEAVTRDYSI----DRVEQLRYLKARYGDIVF 148
                                       99999999999999***************************9.7**********8....678899999999999999 PP

                               NIF 110 vDdspdsfelqpengipiks 129
                                       + d+ +   ++ + g++ ++
  gi|320100791|ref|YP_004176383.1| 149 IGDTVYDEDASARAGVEFHR 168
                                       98887777776666666665 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-05      0.05       1      55 [.       7     118 ..       7     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                                       EEEESTTTSE.........................................................ETTEE-TTHH CS
                       Hydrolase_6   1 flfDidGvLw.........................................................rgdkaipgaa 20 
                                       +++D+dG+L+                                                          + +a+ g  
  gi|320100791|ref|YP_004176383.1|   7 IVVDVDGTLIpslvdfeglrerirrelgvshelkplglslsrlplsdeekqkawriveeeelrtialLDPEALRGNI 83 
                                       5889999999999999999999999999999999999999999999999999999999999988888899******* PP

                                       HHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT CS
                       Hydrolase_6  21 ealnalraagkpvvllTNnsskseeeyakkleklg 55 
                                       e l++l a+g ++v+ T +s ++ + +++kl   g
  gi|320100791|ref|YP_004176383.1|  84 EGLRRLAAEGFRIVIATHRSMETLKPVIEKLGLAG 118
                                       ***********************999999986555 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 ?   13.2   0.0   2.7e-05     0.061      46      97 ..      52     108 ..       4     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                              NT5C  46 kPeqreslyrfltepgl....FadlepipgarevLeeladeg.rlvvitaallqfyd 97 
                                         e++++ +r + e +l      d e++ g  e L++la+eg r+v+ t++ +    
  gi|320100791|ref|YP_004176383.1|  52 SDEEKQKAWRIVEEEELrtiaLLDPEALRGNIEGLRRLAAEGfRIVIATHRSMETLK 108
                                       556777888888888873333457799************************998555 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00084       1.9      61     101 ..      22      62 ..      19      77 .. 0.76
   2 ?    2.0   0.0     0.076   1.7e+02      10      47 ..      66     103 ..      63     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHH---EEEEE-S--EEEEEE-SSH.HHHHHH CS
                             RF3_C  61 feVveeRlknEYgvevrleslpyslarwvesedekkkleel 101
                                       fe ++eR+++E gv+ +l++l +sl r   s++ek+k  ++
  gi|320100791|ref|YP_004176383.1|  22 FEGLRERIRRELGVSHELKPLGLSLSRLPLSDEEKQKAWRI 62 
                                       9999***********************99666665323333 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.076
                                       SEEEEEEESSGGGHHHHHHHHHHHHHCTSSEEEEET.T CS
                             RF3_C  10 ElfarvrlkdplkrkqlrkgleqLaeEGavqvfkeeea 47 
                                       E ++++ l dp   +   +gl+ La EG   v+ ++++
  gi|320100791|ref|YP_004176383.1|  66 EELRTIALLDPEALRGNIEGLRRLAAEGFRIVIATHRS 103
                                       56778888888888888999********8777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1416.79
//
Query:       gi|320100792|ref|YP_004176384.1|  [L=327]
Description: asparaginase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-74  248.9   0.0    6.5e-74  248.7   0.0    1.0  1  Asparaginase_2  Asparaginase


Domain annotation for each model (and alignments):
>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.7   0.0   3.6e-78   6.5e-74       2     303 ..       4     316 ..       3     319 .. 0.93

  Alignments for each domain:
  == domain 1  score: 248.7 bits;  conditional E-value: 3.6e-78
                                       EEEEEEEEESE-G-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEE CS
                    Asparaginase_2   2 vlvihGGAgsilktkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldA 78 
                                       +lv+hGGAgs  + ++ + ++++a+ e+++ ++++L+e+++al aV++avr +Ed+   naG+Gs l+  ge  ldA
  gi|320100792|ref|YP_004176384.1|   4 ALVLHGGAGSWRD-ESVRGRAEEAVGECTRLAWRLLDESNNALKAVVEAVRCMEDSGVLNAGYGSTLNLLGERSLDA 79 
                                       69*******8887.88899999******************************************************* PP

                                       EEEETTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHHHHHHTT----.-CGGG--HHHHHHHHHHHHCC CS
                    Asparaginase_2  79 simdgktlraGaVagvkrvknpislArlvmeksehvlLvgegAeefareqglelv.deesllteerlkelekakkek 154
                                        +m  + l +GaVa+vk  +npi lA++v e+++h+lL+ge A+++a  +gl  + ++ + + ++ ++++++ +  +
  gi|320100792|ref|YP_004176384.1|  80 GLMTSTGL-MGAVAAVKATRNPILLAKIVAEETPHILLAGEDADRLALLKGLPPLpPPPQHVVDRYIQAVRRLLGGE 155
                                       ***99988.*******************************************9886788999999999999999999 PP

                                       CHS..B-S-BS-TTT.............TT---EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTTSEEEETT CS
                    Asparaginase_2 155 aekkeaknvsekelk.............aklgTvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGaGtYAdnk 218
                                        ++++ k++ e ++              + + TvGaVa+D +g lAaaTSTgG+t kl+GRvGD+p++GaG YA ++
  gi|320100792|ref|YP_004176384.1| 156 LKQEYYKKIYEFASLhssvyyqmlkelvSVFDTVGAVAVDDKGVLAAATSTGGVTLKLPGRVGDTPVPGAGFYA-ST 231
                                       99888887776544478889888887777777******************************************.78 PP

                                       TEEEEEEE-HHHHCCTTHHHHHHHHHHTTT--HHHHHHHHHHCHHHHTTT.-EEEEEEETTS-EEEEECSCCCEEEE CS
                    Asparaginase_2 219 vgAvsaTGkGeeiirellaadivalmeykglsleeAaekvieeklkrvkg.sgGviavdkkGevaaefnsegmlray 294
                                         A saTG Ge+iir+++  +  +++ + g  l+eA  kv+++ + +v+   +G+i vd++G++  + n+egml++y
  gi|320100792|ref|YP_004176384.1| 232 NTACSATGIGEYIIRTMPCLRLDIEVSN-GVGLREALGKVMSHVNASVGLdALGFIGVDREGNIFYAYNTEGMLVGY 307
                                       89**************************.*****************9987799************************ PP

                                       EETTS--EE CS
                    Asparaginase_2 295 akedelkev 303
                                       +++ +  +v
  gi|320100792|ref|YP_004176384.1| 308 TRDGRDVYV 316
                                       998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2412.97
//
Query:       gi|320100793|ref|YP_004176385.1|  [L=439]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3331.71
//
Query:       gi|320100794|ref|YP_004176386.1|  [L=332]
Description: glucokinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-59  200.0   0.0    6.9e-59  199.7   0.0    1.0  1  ROK          ROK family
     0.0084   15.1   0.0      0.023   13.7   0.0    1.6  2  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 !  199.7   0.0   7.6e-63   6.9e-59       1     291 [.       6     314 ..       6     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 7.6e-63
                                       EEEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHH.HHHHCCCHCCHTEEEEEEEEESSEEETTCCEBS CS
                               ROK   1 tigidiGgtkialalvdeegeilarekvetptetteetlvdai.aelvdeaerkadeliavgigspGlisdksgkiv 76 
                                       +i++diG+ k+++al d  + il++  ++tp++    t+ +ai ++ +++  ++++++ avg++s G+++ ++g +v
  gi|320100794|ref|YP_004176386.1|   6 YIAVDIGASKTRIALCD-GSRILDKVVFSTPRTGDSRTIAEAIvSKTIEKWREELGSIEAVGVASIGPLDLERGRVV 81 
                                       79***************.889*************999999987367999999************************* PP

                                       SGGCGCCCCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT CS
                               ROK  77 stpnitwenfdlvekleerlnvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvag 153
                                       +tpn+  e+++l+e l+  l+v v+v nD+ a a++E+ fga   v+n++yvt++tGvG+Gv+++++l+ G++G+a 
  gi|320100794|ref|YP_004176386.1|  82 KTPNLPFEEIELLEPLSRMLGVKVYVVNDAVAGAWGEKHFGAGRHVRNLLYVTLSTGVGGGVVVDNHLLLGKQGNAH 158
                                       ***************************************************************************** PP

                                       -GGGSBS-.TTS-B-TTS-BSBHHHCCSHHHHHHCHTC...................CGTTS-HHHHHHHHCTT-HH CS
                               ROK 154 elGHiqld.pegekcgCGnqgClEtlasgralekraqq...................kgekleakeiiklaekgdev 210
                                       e+GHi +d + + +cgCG  g +E++a g  l ++a                     +g +++  +++ l + gd+ 
  gi|320100794|ref|YP_004176386.1| 159 EIGHIVVDyDSDLRCGCGGYGHWEAYAGGGNLPRVALWlleknpglyrgsvlaerlrSGIQVTSVDVFSLYRAGDPL 235
                                       ********888999******************9999888899*************999999**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH--SEEEEEHCCCTSTTHHHHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHHHH CS
                               ROK 211 aeevverlaeylakaiadlinlfdpqaivlgGgvseadklleairklvkkylnkklevpvveivaaklgdkagllGa 287
                                       a++vv  + ++ a+++a +in++dp+ +++gGgv   ++ +  + k vk++++k+  + + +i + +lgd+ gl Ga
  gi|320100794|ref|YP_004176386.1| 236 AADVVGHYIRATAAGLASAINVYDPELVIIGGGVFLNNADI--LLKPVKRRVLKEIVTRPPIIQPTSLGDDVGLYGA 310
                                       *********************************98655433..457777777777777777899************* PP

                                       HHHH CS
                               ROK 288 aaLa 291
                                       +a+a
  gi|320100794|ref|YP_004176386.1| 311 LAIA 314
                                       *998 PP

>> Glucokinase  Glucokinase
   #    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       2     112 ..       8     122 ..       7     132 .. 0.78
   2 ?   -1.9   0.0      0.14   1.3e+03     226     272 ..     232     277 ..     205     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-06
                       Glucokinase   2 agDiGGTkarlalveaeeeelelleiekyasadyaslee.alqaflaeaeaevkrpksavlAvAgpve...gdevel 74 
                                       a DiG  k+r+al++ ++    +   ++ ++ d  ++ e ++++ +++ ++e+ +++++ +A  gp++   g  v++
  gi|320100794|ref|YP_004176386.1|   8 AVDIGASKTRIALCDGSRIL-DKVVFSTPRTGDSRTIAEaIVSKTIEKWREELGSIEAVGVASIGPLDlerGRVVKT 83 
                                       67************998776.7777788888888877551678888888999999999999999*996332556888 PP

                       Glucokinase  75 tNlpWv.ise.eelakelgleaveliNDfeavayaiplle 112
                                        Nlp   i+  e l+++lg+ +v ++ND  a a++ ++++
  gi|320100794|ref|YP_004176386.1|  84 PNLPFEeIELlEPLSRMLGV-KVYVVNDAVAGAWGEKHFG 122
                                       9**98624432567777777.699**********977765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.14
                       Glucokinase 226 edplarealelFlailGsvagdlaLkllargGvyiaGGiapkilell 272
                                       +dpla+ ++  ++++ ++  +  a+++   + v i+GG+   + ++l
  gi|320100794|ref|YP_004176386.1| 232 GDPLAADVVGHYIRATAAGLA-SAINVYDPELVIIGGGVFLNNADIL 277
                                       567777777777776554443.4667777777889999887777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2381.89
//
Query:       gi|320100795|ref|YP_004176387.1|  [L=514]
Description: methionyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  322.3   0.7    1.8e-50  171.8   0.0    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
    2.8e-29  101.9   0.1    8.6e-16   57.3   0.1    3.8  3  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    2.8e-07   30.6   0.1    6.5e-07   29.4   0.1    1.6  1  Anticodon_1   Anticodon-binding domain of tRNA
    4.6e-07   29.5   0.7    0.00073   19.0   0.1    2.8  3  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    1.7e-05   23.9   0.2     0.0015   17.5   0.0    2.9  3  tRNA-synt_1f  tRNA synthetases class I (K)


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 !  150.5   0.2   1.5e-47   5.3e-44       2     138 ..      10     147 ..       9     154 .. 0.94
   2 !  171.8   0.0     5e-54   1.8e-50     166     390 ..     149     369 ..     145     370 .. 0.94

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 1.5e-47
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelf 78 
                                       +vtt+++Y+n+++H+Gh+++ + aD++aR++rl g++v+f++g+DehG +i+  Aek+g +p+e+v+++ + ++e +
  gi|320100795|ref|YP_004176387.1|  10 YVTTPIYYPNAPPHIGHAYTSVFADVLARFNRLIGNNVFFLTGNDEHGLKIQRVAEKAGKHPKEFVDEMASVYREYW 86 
                                       8**************************************************************************** PP

                                       HHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G.GG-EE. CS
                      tRNA-synt_1g  79 kklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpd.ryvegt 138
                                       ++l+is+d+++rtt+  h+++v+e f+ ++ kgliy+ +++++yc+++e+++++ +y+e+ 
  gi|320100795|ref|YP_004176387.1|  87 RTLGISYDHFIRTTDPYHEKAVKEAFSYIHGKGLIYKAKYSGMYCVDCEKYYSPgEYIEVD 147
                                       ***************************************************9762666653 PP

  == domain 2  score: 171.8 bits;  conditional E-value: 5e-54
                                       ...........EEE.EEEEEE-GGGGHHHHHHHH.HH-TT.SHHHHHHHH.HHHHT----EE-E...SS-SSS-EET CS
                      tRNA-synt_1g 166 npksaisgskpevketehlffklskfekklkewieeeeke.leenvkkivkewlkegLkdlais...rdldwGipvP 238
                                       +p++ i ++  e+ e+e ++fkls+f+++l + +e+++    ++ ++++++++ +egL+d++++    ++ wGipvP
  gi|320100795|ref|YP_004176387.1| 149 KPHCPIHNKPLEYLEEETYYFKLSEFKDYLLDILENKDVVyPQQYAREVASKIRNEGLRDVSVArpvERVGWGIPVP 225
                                       599****9999***********************87777778888899999999**********5555788****** PP

                                       TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHTT----S-E CS
                      tRNA-synt_1g 239 gaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillgaelklpkkv 315
                                        ++k v+YVW+dAl++Y+s +++      ++e+ + yW     ++++h+igkdi+ FHt +w +il++ +l  p++v
  gi|320100795|ref|YP_004176387.1| 226 FDDKYVIYVWFDALMNYLSGVGYPD----DKERLQLYW-----SNAHHVIGKDILWFHTAVWFSILKALDLPPPRRV 293
                                       ***********************96....788******.....459******************************* PP

                                       EEE--EEE--------------HHHHHHHH-.HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH CS
                      tRNA-synt_1g 316 vaheyltvegkKlSkSrgvvvkakealerld.adllRYylaaeapekkDldfswedfvervNseLadklgnlvnRv 390
                                       ++h+yl  +g K+ kS g+v+ ++e++ r++ +d +RY la+  +++kD++ s+e +   +NseLad++gnl++Rv
  gi|320100795|ref|YP_004176387.1| 294 IVHSYLINRGLKIGKSAGNVISIEELVSRYNgSDGVRYLLARIFNTDKDSEVSFELLDSIYNSELADTYGNLARRV 369
                                       *****************************6549*****************************************97 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.1   2.4e-19   8.6e-16      25     174 ..       9     139 ..       3     149 .. 0.87
   2 !    8.4   0.0   0.00015      0.55     363     433 ..     150     226 ..     142     229 .. 0.87
   3 !   31.0   0.0   2.3e-11   8.2e-08     485     598 ..     230     342 ..     227     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.4e-19
                       tRNA-synt_1  25 filvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefr 101
                                       f ++ +  y +  +HiGha++++  d++ r++r+ G++v +++G D +Gl i+ + ek  g++              
  gi|320100795|ref|YP_004176387.1|   9 FYVTTPIYYPNAPPHIGHAYTSVFADVLARFNRLIGNNVFFLTGNDEHGLKIQRVAEKA-GKHP------------- 71 
                                       6666777788899****************************************998887.4444............. PP

                       tRNA-synt_1 102 ekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktals 174
                                          +e+++e+a+ +r+ ++ lG+s+D  +   T d+  e+avke+f  ++ kgliy++k+   ++++++   s
  gi|320100795|ref|YP_004176387.1|  72 ---KEFVDEMASVYREYWRTLGISYD--HFIRTTDPYHEKAVKEAFSYIHGKGLIYKAKYSGMYCVDCEKYYS 139
                                       ...57788888999999*****9866..67889**********************************987666 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00015
                       tRNA-synt_1 363 pfcerskkpiiyrateqWfvrvkeladaalkave.kvqfvpkskekryaswlen..iqdWciSR...qrwWGhripl 433
                                       p+c  ++kp++y   e+++ +++e++d +l+ +e k   +p+++ ++ as ++n   +d  + R      WG ++p+
  gi|320100795|ref|YP_004176387.1| 150 PHCPIHNKPLEYLEEETYYFKLSEFKDYLLDILEnKDVVYPQQYAREVASKIRNegLRDVSVARpveRVGWGIPVPF 226
                                       99*******************************9777789************9944589999994423459999985 PP

  == domain 3  score: 31.0 bits;  conditional E-value: 2.3e-11
                       tRNA-synt_1 485 dvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillsl.altgsePfkevlvhglvrdee 560
                                        v+ vWF+  +   s +gyp+  +e l+ ++     + G Di+  W+++ + +s+ +  +  P ++v+vh+ ++ + 
  gi|320100795|ref|YP_004176387.1| 230 YVIYVWFDALMNYLSGVGYPDD-KERLQLYWSNAHHVIGKDIL--WFHTAVWFSIlKALDLPPPRRVIVHSYLI-NR 302
                                       57889****************9.999999999999******97..9999998885377788899*******987.57 PP

                       tRNA-synt_1 561 GrKmSKslgNvidpldvikky.gadalRltli.lsdvgrd 598
                                       G K+ Ks gNvi+ ++++++y g d +R+ l+   ++ +d
  gi|320100795|ref|YP_004176387.1| 303 GLKIGKSAGNVISIEELVSRYnGSDGVRYLLArIFNTDKD 342
                                       **************999988769*******9864444444 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 !   29.4   0.1   1.8e-10   6.5e-07      13      85 ..     399     465 ..     387     485 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.8e-10
                       Anticodon_1  13 kevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfit 85 
                                         + +++++y+ +ka+ +++e     +++ y++ +kp+ +    +++ +  ++lle++++ ++ll+P++P  +
  gi|320100795|ref|YP_004176387.1| 399 GAYIDSMKNYEVSKALEHAMEI--ARYANQYVNESKPWEKP---NPS-KELYTLLELIRAATILLHPVIPSAS 465
                                       56789****************6..8899**********743...333.234*******************765 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 !   19.0   0.1     2e-07   0.00073      13     125 ..      10     125 ..       3     147 .. 0.78
   2 !    7.7   0.0   0.00054       1.9     240     282 ..     293     335 ..     261     348 .. 0.73
   3 ?   -1.6   0.1      0.39   1.4e+03      70      97 ..     388     415 ..     375     430 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2e-07
                                       EEEEEBTTS-..-BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e  13 YvCGptvyda..shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdl 87 
                                       Yv  p  y +   h+Gha + v+ D+l+r+ + +g +v f+    +   ki + a++++k+ ke+++++ + + +  
  gi|320100795|ref|YP_004176387.1|  10 YVTTPIYYPNapPHIGHAYTSVFADVLARFNRLIGNNVFFLTGNDEHGLKIQRVAEKAGKHPKEFVDEMASVYREYW 86 
                                       5555555543126*****************************9999999**************************** PP

                                       HHTT----SB--BGGG..GHHHHHHHHHHHHHTTSEEE-T CS
                      tRNA-synt_1e  88 eaLnvlkptleprvse..kvdeiielvekliekgyaYavs 125
                                       ++L++   ++  r ++  + +++ e    +  kg  Y+++
  gi|320100795|ref|YP_004176387.1|  87 RTLGISYDHF-IRTTDpyHEKAVKEAFSYIHGKGLIYKAK 125
                                       ****998544.44444113345667777777788777776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00054
                                       EEEEE--EEETTBE--TTTT---BHHHHHTTS-HHH.HHHHHHS CS
                      tRNA-synt_1e 240 yflhnghlkiegekmsksLknfitikdvlkkfdprq.lRlllls 282
                                         +h+ +l   g k+ ks +n+i+i++++ +++++  +R+ll+ 
  gi|320100795|ref|YP_004176387.1| 293 VIVHS-YLINRGLKIGKSAGNVISIEELVSRYNGSDgVRYLLAR 335
                                       55555.4445789*******************986438888764 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.39
                                       S-HHHHHHHHHHHHHHHHHHTT----SB CS
                      tRNA-synt_1e  70 ksvkelaekfieefkkdleaLnvlkptl 97 
                                       k v++l+++++ ++ + +++ +v k+  
  gi|320100795|ref|YP_004176387.1| 388 KAVADLVATHVGAYIDSMKNYEVSKALE 415
                                       5678889999999999999999988643 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 ?    2.7   0.0     0.014        49      95     144 ..      61     112 ..      21     118 .. 0.86
   2 !   17.5   0.0   4.3e-07    0.0015     241     327 ..     267     351 ..     262     386 .. 0.71
   3 ?   -0.6   0.1      0.14     5e+02     134     165 ..     400     431 ..     380     447 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.014
                      tRNA-synt_1f  95 tsiPdpkgk.hesyaehfnaelvesLdelgieve.fisatelYksglydeai 144
                                       +++ +  gk  +++++ +++ ++e+ ++lgi ++ fi++t+ Y++ + +ea 
  gi|320100795|ref|YP_004176387.1|  61 QRVAEKAGKhPKEFVDEMASVYREYWRTLGISYDhFIRTTDPYHEKAVKEAF 112
                                       5666666773478******************9975799*****999988875 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.3e-07
                      tRNA-synt_1f 241 GkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwle.vaepevlrflilrrkPkka 316
                                       GkD+      + v   i + l+ ++P  v+    l++ g k+ +S Gnv+++e++++ +   + +r+l++r   ++ 
  gi|320100795|ref|YP_004176387.1| 267 GKDILW--FHTAVWFSILKALDLPPPRRVIVHSYLINRGLKIGKSAGNVISIEELVSrYNGSDGVRYLLAR-IFNTD 340
                                       566555..233344467899**********************************8752777999****999.55555 PP

                      tRNA-synt_1f 317 kkldldleilr 327
                                       k+ ++++e+l+
  gi|320100795|ref|YP_004176387.1| 341 KDSEVSFELLD 351
                                       55555554543 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.14
                      tRNA-synt_1f 134 lYksglydeaikealenrekikeilekyrgee 165
                                        Y + + + ++ +ale+  +i++  ++y +e+
  gi|320100795|ref|YP_004176387.1| 400 AYIDSMKNYEVSKALEHAMEIARYANQYVNES 431
                                       57777778888888888888888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3401.45
//
Query:       gi|320100796|ref|YP_004176388.1|  [L=493]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-17   62.6   0.2    2.8e-16   60.4   0.1    2.3  2  Radical_SAM  Radical SAM superfamily
    0.00013   21.9   0.0      0.085   12.9   0.0    2.5  2  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.26   2.3e+03      35      59 ..     143     166 ..     104     195 .. 0.71
   2 !   60.4   0.1   3.1e-20   2.8e-16       1     167 []     208     397 ..     208     397 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHTTSEEEEEESSTGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  35 leevkelkaekgvkevilgggepll 59 
                                       l e++ + +++gv++v+ g ge ++
  gi|320100796|ref|YP_004176388.1| 143 LYELELM-EKWGVDTVVDGEGEKIV 166
                                       4555666.66666666666666555 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 3.1e-20
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.........TTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.........pdfvelle 68 
                                       v+v+rgC+++C+fC+++      ++ r++++e+il+ev+ +  + g k++il++ ++lly         ++ v+l  
  gi|320100796|ref|YP_004176388.1| 208 VEVMRGCPRGCKFCSVT-----LRPLRFIPLEKILAEVDVN-IRAGLKGIILHSEDVLLYhadgvkpraDPVVKLHV 278
                                       689**************.....6******************.8**********************888733333333 PP

                                       HHHHTC.....CCTEEEEEEECSSCHG.................HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTC CS
                                       xxxxxx.....xxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  69 rlakla.....vpgiritvetngtlpd.................eeklerllelgvdrvslgleaaddekvlklmnr 123
                                       +  k+       ++ + ++                         e +l ++++  +  v++g+e+++ +  +++m+ 
  gi|320100796|ref|YP_004176388.1| 279 EVLKRIgerrsLAWSHASL-------AavkyaeenyrlisrlmnELVLNEHRK--FLGVEVGIETGSVRLAREIMRA 346
                                       3333323334533333333.......333333335333322222444445544..89************77777766 PP

                                       TSHH.......HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 124 ghtf.......eevlealeklreagikrvvdrivglpGendeeleellell 167
                                       + ++         v +a+++++e+ + +  ++i+g+pGe+ ++++e++el+
  gi|320100796|ref|YP_004176388.1| 347 KASPypveewpNIVEDAFRIMHENKVIPAATVILGFPGETPDDVVETIELI 397
                                       6666899999999999999999999888********************986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0     0.001         9      12      37 ..      45      70 ..      39      79 .. 0.87
   2 !   12.9   0.0   9.5e-06     0.085      73     120 ..     118     169 ..     107     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.001
                       B12-binding 12 lhplGlavlaaalrdagfeVqllgan 37
                                        p+G++ + a+lrdagf+  +++ +
  gi|320100796|ref|YP_004176388.1| 45 EAPYGMRKIEAVLRDAGFNAAIIDPD 70
                                      5699******************9976 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.5e-06
                       B12-binding  73 el...lkrirprvkvvvGGahp.s.ldpeetleaklgiddvvvgegedaleal 120
                                       e    ++++ ++vk+++GG+++ + l++ e++e+  g+d vv gege  + +l
  gi|320100796|ref|YP_004176388.1| 118 ESpavRRAKEKGVKIIAGGPAAwQwLYELELMEK-WGVDTVVDGEGEKIVVEL 169
                                       445555666779*******985322344455544.9***********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 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:                        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 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3671.29
//
Query:       gi|320100797|ref|YP_004176389.1|  [L=119]
Description: regulatory protein ArsR [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   30.3   0.6    6.2e-07   29.2   0.6    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
    9.7e-07   28.6   0.2    5.5e-06   26.2   0.0    2.0  2  MarR_2           MarR family
    8.3e-06   25.5   0.6    3.1e-05   23.7   0.0    2.1  2  HTH_IclR         IclR helix-turn-helix domain
    3.3e-05   23.7   1.9    4.1e-05   23.4   0.2    2.0  3  HTH_5            Bacterial regulatory protein, arsR family
    0.00019   21.4   1.2     0.0034   17.4   0.0    2.2  2  HTH_20           Helix-turn-helix domain
    0.00029   20.3   0.4    0.00071   19.1   0.4    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0027   18.1   0.7     0.0088   16.5   0.1    2.1  3  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.013   15.9   0.2      0.015   15.6   0.2    1.1  1  Penicillinase_R  Penicillinase repressor
      0.021   14.4   0.3       0.12   11.9   0.2    2.0  2  HTH_47           winged helix-turn-helix
      0.023   14.9   0.1      0.029   14.5   0.1    1.2  1  Peptidase_S78    Caudovirus prohead serine protease
      0.025   14.8   0.3      0.042   14.0   0.3    1.5  1  HTH_34           Winged helix DNA-binding domain
      0.036   14.0   0.0      0.064   13.2   0.0    1.4  1  PuR_N            Bacterial purine repressor, N-terminal
      0.041   14.4   1.0      0.059   13.9   1.0    1.3  1  HSCB_C           HSCB C-terminal oligomerisation domain
      0.073   13.1   0.0       0.12   12.5   0.0    1.4  1  HTH_Mga          M protein trans-acting positive regulator (M
      0.081   12.9   0.0       0.12   12.4   0.0    1.3  1  PepSY_2          Peptidase propeptide and YPEB domain
       0.39   10.9   0.1       0.39   10.9   0.1    1.9  3  DprA_WH          DprA 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 !   29.2   0.6   5.5e-10   6.2e-07       3      66 ..      10      74 ..       8      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.5e-10
                                      HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                              TrmB  3 klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                       +GL+ + a++ + Ll +++ ++ +e+ +++g  +s+v e++r Le kGlVe++  ++k Y  v 
  gi|320100797|ref|YP_004176389.1| 10 LIGLKPNMARIIAILLlSNKALSLSEVCNATGYAKSRVSEIMRILEAKGLVEVSIVKKKAYYKVR 74
                                      57888888999888888**************************************9998887665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.9e-09   5.5e-06       2      54 ..      12      63 ..      11      69 .. 0.91
   2 ?    0.3   0.1      0.57   6.4e+02      22      34 ..     105     118 ..      86     119 .] 0.68

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.9e-09
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      gl+p  ar++a L  +    l+ +e++ ++g+ ks+vs i + L+a+GLve +
  gi|320100797|ref|YP_004176389.1| 12 GLKPNMARIIAILLLSNKA-LSLSEVCNATGYAKSRVSEIMRILEAKGLVEVS 63
                                      7888889999999999875.9*****************************976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.57
                                       E.EHHHHHHHHTSS CS
                            MarR_2  22 l.tvgelarrlgls 34 
                                       +  ++e +rrl+++
  gi|320100797|ref|YP_004176389.1| 105 FmEIAEAVRRLQVK 118
                                       34677888888886 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 !   23.7   0.0   2.7e-08   3.1e-05       6      49 ..      18      61 ..      16      63 .. 0.93
   2 ?   -0.3   0.1      0.86   9.6e+02      22      22 ..      94      94 ..      76     117 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.7e-08
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      ++i+ +l   + +l+lse++++tg +kS v+ +++ L+  G+ve
  gi|320100797|ref|YP_004176389.1| 18 ARIIAILLLSNKALSLSEVCNATGYAKSRVSEIMRILEAKGLVE 61
                                      788899999999*******************************8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.86
                                      H CS
                          HTH_IclR 22 s 22
                                       
  gi|320100797|ref|YP_004176389.1| 94 E 94
                                      2 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 !   23.4   0.2   3.7e-08   4.1e-05       4      46 ..      19      61 ..      15      62 .. 0.93
   2 ?   -1.9   0.1       2.8   3.1e+03      32      39 ..      82      89 ..      76      92 .. 0.77
   3 ?   -2.9   0.0         6   6.7e+03      14      25 ..     101     112 ..      98     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.7e-08
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      R+  + lL+++ l+ +e ++++g  +s vS+  ++L+  GLVe
  gi|320100797|ref|YP_004176389.1| 19 RIIAILLLSNKALSLSEVCNATGYAKSRVSEIMRILEAKGLVE 61
                                      7777899999********************************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                                      HHHHHHHH CS
                             HTH_5 32 vShHLkkL 39
                                      + +HL +L
  gi|320100797|ref|YP_004176389.1| 82 IEEHLERL 89
                                      67899887 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6
                                       SSEEHHHHHHHH CS
                             HTH_5  14 gelcvcelaeel 25 
                                       g + + e+ae++
  gi|320100797|ref|YP_004176389.1| 101 GVRDFMEIAEAV 112
                                       556677888876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     3e-06    0.0034      10      56 ..      15      62 ..       7      66 .. 0.91
   2 ?    2.9   0.2       0.1   1.1e+02      11      33 ..      78      99 ..      73     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                                      HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 10 PvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      P  +ri + L  ++++l++se++ + + +k+ +s  +r+Le  gLvev
  gi|320100797|ref|YP_004176389.1| 15 PNMARIIAILlLSNKALSLSEVCNATGYAKSRVSEIMRILEAKGLVEV 62
                                      556788888889***********************************8 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.1
                                      HHHHHHHHHSTCTTB-HHHHHHH CS
                            HTH_20 11 vRrrilraLaraegltaselaer 33
                                       R  i+ +L ++ +++++e +++
  gi|320100797|ref|YP_004176389.1| 78 LRKHIEEHL-ERLARSLEEAHRE 99
                                      588999999.9999999998876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   6.4e-07   0.00071      11      48 .]      24      61 ..      18      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.4e-07
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lL  n  +s +e++ ++g  +s v++ ++ Le +Gl++
  gi|320100797|ref|YP_004176389.1| 24 LLLSNKALSLSEVCNATGYAKSRVSEIMRILEAKGLVE 61
                                      4555889*****************************96 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.9e-06    0.0088      19      49 ..      31      61 ..      18      69 .. 0.90
   2 ?   -1.1   0.1       2.4   2.7e+03      37      47 ..      76      86 ..      73     100 .. 0.75
   3 ?   -2.8   0.0       8.5   9.6e+03      35      42 ..     108     115 ..     101     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.9e-06
                            HTH_27 19 kkladlcgrlnvedshisyslkkLtekGLve 49
                                       +l+++c ++ + +s +s++++ L++kGLve
  gi|320100797|ref|YP_004176389.1| 31 LSLSEVCNATGYAKSRVSEIMRILEAKGLVE 61
                                      678***************************5 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                            HTH_27 37 yslkkLtekGL 47
                                      ++l+k++e +L
  gi|320100797|ref|YP_004176389.1| 76 EALRKHIEEHL 86
                                      67777777665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.5
                            HTH_27  35 isyslkkL 42 
                                       i++++++L
  gi|320100797|ref|YP_004176389.1| 108 IAEAVRRL 115
                                       67888887 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.2   1.4e-05     0.015      31      97 ..      40     107 ..      19     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                                       G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  31 kelaysTVktllrrLvkKgllsrekegrafiYsplvse.eeavasavkqlldklfegsvkelvaafve 97 
                                       +  a+s V  ++r L++Kgl++    +++  Y  +v+  ++ +++ ++ l ++l e ++++ v +f+e
  gi|320100797|ref|YP_004176389.1|  40 TGYAKSRVSEIMRILEAKGLVEVSIVKKKAYYKVRVEAlRKHIEEHLERLARSLEEAHRESGVRDFME 107
                                       3678999***************************9987356778888888888888888888888887 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00011      0.12      33      77 ..      17      61 ..       3      62 .. 0.91
   2 ?    0.4   0.0      0.42   4.7e+02      45      56 ..     101     112 ..      84     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 33 emallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                        +++ +L l+  + sL ++ + +g    rv +i+r L+++gl++
  gi|320100797|ref|YP_004176389.1| 17 MARIIAILLLSNKALSLSEVCNATGYAKSRVSEIMRILEAKGLVE 61
                                      5688999************************************86 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.42
                                       EEEEHHHHHHHH CS
                            HTH_47  45 GkrsLldiAeri 56 
                                       G r+ ++iAe +
  gi|320100797|ref|YP_004176389.1| 101 GVRDFMEIAEAV 112
                                       556666666654 PP

>> Peptidase_S78  Caudovirus prohead serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.6e-05     0.029     124     161 ..      49      86 ..      29      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                     Peptidase_S78 124 vvvrtikkveLlEvSvVtvPAyddtsvevsarsleavk 161
                                        ++r++++  L+EvS+V+  Ay + +ve+ ++++e++ 
  gi|320100797|ref|YP_004176389.1|  49 EIMRILEAKGLVEVSIVKKKAYYKVRVEALRKHIEEHL 86 
                                       3466677767******************9999998875 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 ?   14.0   0.3   3.8e-05     0.042       6      52 ..      21      68 ..      18      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.8e-05
                            HTH_34  6 lsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkg 52
                                      +++L+  ++  + +e+ +a++  +++ s  +++Le++g +ev++ +k+
  gi|320100797|ref|YP_004176389.1| 21 IAILLLsNKALSLSEVCNATGYAKSRVSEIMRILEAKGLVEVSIVKKK 68
                                      5555543889999*****************************998776 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 ?   13.2   0.0   5.7e-05     0.064       7      45 ..      18      55 ..      15      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-05
                             PuR_N  7 vaitkiLlenPnklisltyfaerfeaAKSsiSeDlaiik 45
                                      ++i+ iLl   nk +sl++ ++  + AKS +Se ++i++
  gi|320100797|ref|YP_004176389.1| 18 ARIIAILLL-SNKALSLSEVCNATGYAKSRVSEIMRILE 55
                                      556666665.4899*******************887765 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   5.3e-05     0.059      26      66 ..      73     116 ..      47     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT...-HHHHHHHHHHHH CS
                            HSCB_C  26 eeleelkaeveerieeleaeleeafekk...dleaaadllrrlr 66 
                                        ++e+l++ +ee++e l  +leea +++   d+ ++a+++rrl+
  gi|320100797|ref|YP_004176389.1|  73 VRVEALRKHIEEHLERLARSLEEAHRESgvrDFMEIAEAVRRLQ 116
                                       78999*******************9666899***********95 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 ?   12.5   0.0    0.0001      0.12       9      32 ..      19      42 ..      16      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                           HTH_Mga  9 kLlelLteneksltldelakeLgl 32
                                      +++++L+ ++k+l+l+e+++++g 
  gi|320100797|ref|YP_004176389.1| 19 RIIAILLLSNKALSLSEVCNATGY 42
                                      799999999***********9985 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.12       3      61 ..      18      77 ..      16      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                           PepSY_2  3 alalalallaaaAlAgrrdtdspkadwlpreklvakleaqGy.kvkkievddggcyEveg 61
                                      a ++a++ll+  Al  ++ +++        ++++++lea+G  +v+ ++ + + +  ve+
  gi|320100797|ref|YP_004176389.1| 18 ARIIAILLLSNKALSLSEVCNATGYAKSRVSEIMRILEAKGLvEVSIVKKKAYYKVRVEA 77
                                      5678999***9999966666666666667********************96665455555 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00035      0.39      20      56 ..      25      61 ..       5      62 .. 0.89
   2 ?   -2.7   0.0       5.9   6.6e+03      18      33 ..      83      98 ..      76     102 .. 0.51
   3 ?   -2.9   0.1       6.9   7.8e+03      49      58 ..     106     115 ..     106     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                           DprA_WH 20 aLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                      +L++ ++++ +++ +tg   ++vs +   LE +Glve
  gi|320100797|ref|YP_004176389.1| 25 LLSNKALSLSEVCNATGYAKSRVSEIMRILEAKGLVE 61
                                      5699*******************************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.9
                           DprA_WH 18 LaaLgpePvhvDqLvr 33
                                       ++L+  ++++++ +r
  gi|320100797|ref|YP_004176389.1| 83 EEHLERLARSLEEAHR 98
                                      4555555555555555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.9
                           DprA_WH  49 LELaGlverl 58 
                                       +E+a  v+rl
  gi|320100797|ref|YP_004176389.1| 106 MEIAEAVRRL 115
                                       5899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1473  (0.0821574); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 968.72
//
Query:       gi|320100798|ref|YP_004176390.1|  [L=139]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.9    8.6  10.5       0.27   11.3   3.9    2.3  2  SPC12     Microsomal signal peptidase 12 kDa subunit (SPC12)


Domain annotation for each model (and alignments):
>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.9   1.5e-05      0.27       1      57 [.      32      86 ..      32      87 .. 0.87
   2 ?    0.9   0.5     0.027   4.9e+02      21      32 ..     124     135 ..     108     139 .] 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.5e-05
                             SPC12  1 iDFeGQklaekllqvilvlsaviafivGyitqdlkltlyillagvvltllvvvPpWp 57
                                      iDF G  l++  +++++++  ++++++Gy+  +lk + yi+++ +v++l +v+  W+
  gi|320100798|ref|YP_004176390.1| 32 IDFLGKVLSNPRTYIVVIVQFLLGLALGYF--SLKALKYIVALILVVVLGMVLSVWS 86
                                      8****************************9..6788888888888888888887776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.027
                             SPC12  21 aviafivGyitq 32 
                                       ++++fi+G i+ 
  gi|320100798|ref|YP_004176390.1| 124 TTVGFIIGAILA 135
                                       567777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1138.92
//
Query:       gi|320100799|ref|YP_004176391.1|  [L=172]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   91.6   0.0    3.9e-26   91.4   0.0    1.0  1  DUF2299   Uncharacterized conserved protein (DUF2299)
  ------ inclusion threshold ------
       0.11   12.3   0.1        0.2   11.5   0.1    1.3  1  HTH_ParB  HTH domain found in ParB protein


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.0   4.3e-30   3.9e-26       2     136 ..       9     150 ..       8     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 4.3e-30
                                       HHHHHHHTT-EEEE--...-TTEEEEEEEE-STT..-EEEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHH CS
                           DUF2299   2 ikeWLkeeGlkveevp...danaefhilveppqpggvvvdvikpkgksdvvvvgmgvkvseehkkalsslkeeerke 75 
                                       i +WL++e ++ ++++   +a+++++++v++p   gv++ v+ p +k+d+++++ ++ +s+eh + l +lk+ er +
  gi|320100799|ref|YP_004176391.1|   9 ISKWLMDESFILRRFEappEARVKWGVNVSTPGTPGVNFTVVNPLDKPDRYILALAILISPEHARELDKLKPAERLR 85 
                                       889********99988888********************************************************** PP

                                       HHHHHHHHHTTTT-EEEEE-TTS--..-EEEEEEEEEGGG-...-HHHHHHHHHHHHHHHHHHHH CS
                           DUF2299  76 flselkrdLlrlcvdfqlipqdeel.pqsiqvskeiykdgl...tknelldavkrvrnakllviw 136
                                       +++++  + l++c d++++ q++ l pq i v  e++++++    k  +l  v r+ n +l +++
  gi|320100799|ref|YP_004176391.1|  86 VMHSILSKALTVCADCKIMVQPNILsPQAIAVNMELFEEEIhryGKPFFLRLVWRLLNTYLAIVS 150
                                       ***********************88****************999999**************9997 PP

>> HTH_ParB  HTH domain found in ParB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.2e-05       0.2      12      43 ..      67      97 ..      63      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                          HTH_ParB 12 iseGHARaLlslkdeelqlqlaekiieegLsV 43
                                      is  HAR L +lk   ++l +++ i+++ L+V
  gi|320100799|ref|YP_004176391.1| 67 ISPEHARELDKLKP-AERLRVMHSILSKALTV 97
                                      8999**********.9***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1458.42
//
Query:       gi|320100800|ref|YP_004176392.1|  [L=226]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   7.2    9.8e-08   32.5   7.2    2.4  2  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
        9.7    6.7  13.7        4.1    7.9   2.8    2.6  3  FtsX         FtsX-like permease family


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   7.2   1.1e-11   9.8e-08      16     118 ..      45     147 ..      24     149 .. 0.77
   2 ?    0.9   0.7     0.067     6e+02      27      37 ..     144     154 ..     137     220 .. 0.60

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.1e-11
                       SNARE_assoc  16 lll...gtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllpivPrdlvnyva 89 
                                       +++   ++  ++lga++G++l+y+lgr l    ++r  + ++++ +l++      f++++++  lpi P+d+v +++
  gi|320100800|ref|YP_004176392.1|  45 PWSlmlAVASSALGASIGKLLVYMLGRGLS--TFGRESRFKQNIAYLTSRHSTATFIMVFMAAALPI-PDDVVYIPV 118
                                       444333777789***************997..4455444445555544444478999*********6.8******** PP

                       SNARE_assoc  90 GltrvsfkrFflatfiGsipwalvyaylG 118
                                       G +r+++  Ff a  +G+++ +   a+ G
  gi|320100800|ref|YP_004176392.1| 119 GYARYNILLFFTALTAGKLVVTSMAAVYG 147
                                       *******************9988777766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.067
                       SNARE_assoc  27 allGaslayll 37 
                                       a+ G  +++l+
  gi|320100800|ref|YP_004176392.1| 144 AVYGRAFSFLF 154
                                       44444444433 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.59   5.3e+03      47      47 ..      20      20 ..       5      40 .. 0.47
   2 ?    6.3   0.4    0.0015        14      26      85 ..      48     106 ..      46     110 .. 0.75
   3 ?    7.9   2.8   0.00046       4.1      22      89 ..     121     186 ..     116     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.59
                              FtsX 47 l 47
                                      +
  gi|320100800|ref|YP_004176392.1| 20 V 20
                                      1 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0015
                              FtsX  26 llitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagl 85 
                                       l++++ ++++G  +g l+ ++l  +l+++   s+ k +i ++t     + +++++++a +
  gi|320100800|ref|YP_004176392.1|  48 LMLAVASSALGASIGKLLVYMLGRGLSTFGRESRFKQNIAYLTSRHSTATFIMVFMAA-A 106
                                       7889999999999999999999999999988777777777777666666666666666.3 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00046
                              FtsX  22 lteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsis 89 
                                          ++l+++ al +G ++ + +a +    + s++f  e +   ++ tv++ i++ ll + +ag +  +
  gi|320100800|ref|YP_004176392.1| 121 ARYNILLFFTALTAGKLVVTSMAAVYGRAF-SFLF-EEHPGIPSWVTVAAYIAITLLAMYIAGSIDWI 186
                                       56789**********444444444433333.3333.89999999999999999999999998766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1830.56
//
Query:       gi|320100801|ref|YP_004176393.1|  [L=209]
Description: mechanosensitive ion channel protein MscS [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.5e-16   58.1   4.2    8.5e-16   58.1   4.2    2.2  3  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
        2.9    8.1   5.1         16    5.7   0.2    2.6  2  DUF2749     Protein of unknown function (DUF2749)


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 ?   -2.2   0.5      0.28   2.5e+03       3      20 ..      16      33 ..      14      45 .. 0.59
   2 ?   -4.1   1.6         1   9.4e+03       9      26 ..      61      78 ..      57      83 .. 0.44
   3 !   58.1   4.2   9.5e-20   8.5e-16      28     106 ..     123     202 ..     115     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.28
                                      HHHHHHHHHHHHHHHHTT CS
                        MS_channel  3 ilkiliivvgilivlsll 20
                                      i+ + ++v +++ vl+++
  gi|320100801|ref|YP_004176393.1| 16 IIVYAVVVAVVMGVLQWF 33
                                      555566666666666555 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1
                                      HHHHHHHHHHTTT--SCC CS
                        MS_channel  9 ivvgilivlsllgvnvsa 26
                                      +++++l+  +++  +v+ 
  gi|320100801|ref|YP_004176393.1| 61 YIIVLLVLGWMIVSSVAQ 78
                                      333333333333333554 PP

  == domain 3  score: 58.1 bits;  conditional E-value: 9.5e-20
                                       HHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS.SEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHT CS
                        MS_channel  28 lavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig.dieGtVediglrttkirtfdgrivtiPnsslvt 103
                                       +a+ G++gl++g+a ++++ + vaG+++l+ +pfkiGD+v+++ + e  V+di++ +t +++ dg +v +P s+++ 
  gi|320100801|ref|YP_004176393.1| 123 VALGGFIGLVIGFATQQVLGQAVAGMFILLVRPFKIGDIVDVAgESEVVVKDISTMFTIVERKDGVEVLVPSSMIIG 199
                                       7999**************************************989999****************************9 PP

                                       S-E CS
                        MS_channel 104 sni 106
                                       ++i
  gi|320100801|ref|YP_004176393.1| 200 QKI 202
                                       887 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.0      0.01        90       6      23 ..      16      33 ..      13      39 .. 0.85
   2 ?    5.7   0.2    0.0018        16       6      37 ..      62      96 ..      59     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.01
                           DUF2749  6 lIvlviavaagagtilwl 23
                                      +Iv +++va++ g   w 
  gi|320100801|ref|YP_004176393.1| 16 IIVYAVVVAVVMGVLQWF 33
                                      8999999****9999997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0018
                           DUF2749  6 lIvlvia...vaagagtilwlvvqpragtsgsgea 37
                                      +Ivl ++   +  + +  +++++ p+ g+s++ + 
  gi|320100801|ref|YP_004176393.1| 62 IIVLLVLgwmIVSSVAQLFYVMLRPKYGASTAAAV 96
                                      7888888877666667788999****999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1249  (0.0696637); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1514.32
//
Query:       gi|320100802|ref|YP_004176394.1|  [L=399]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   17.2  45.5     0.0027   16.7   5.9    3.0  3  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 !   16.7   5.9   1.5e-07    0.0027     217     327 ..       7     116 ..       3     131 .. 0.88
   2 !    7.3  18.5   0.00011         2     143     309 ..     143     324 ..     137     331 .. 0.72
   3 !    5.5   5.1   0.00037       6.7     113     166 ..     338     391 ..     332     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-07
                             MFS_1 217 llfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglal 293
                                       +++   +s +  l+ l +++ +g++ ++++g+l a+  lv++++  +a +lsd       + l+ ++++l+ ++++l
  gi|320100802|ref|YP_004176394.1|   7 AFNIGLISVMDLLVNLVAVKYFGFN-AVELGILNAAWTLVFIPVVRVADKLSDAGRVGLLWRLGSFSMILLQALMCL 82 
                                       334446777999999999*******.8*****************99******9977788****************** PP

                             MFS_1 294 lavtssavllllvlvliGfglgfvfpsllalasd 327
                                         ++++++l+++++++  + l+ ++ ++++++ +
  gi|320100802|ref|YP_004176394.1|  83 SMWFDEKPLIYVAYMVHAVLLASTRLAVNTYIFE 116
                                       ************9999999999999999998866 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00011
                             MFS_1 143 llasslgWrav...fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl....... 209
                                       +l++++g+++v   ++ +a+++ la +l++l++ e++ + +r   + e  +t  ++++p  k ll+  +l       
  gi|320100802|ref|YP_004176394.1| 143 ALLAYIGFSSVlshYIYIAALFTLAHLLGILVIHEPALKIERILYRLE--STLSRAFIP-VKGLLTLSYLeiggstp 216
                                       445578888888877777777777777777777666666666655444..777777777.77777777666555554 PP

                             MFS_1 210 .....w........illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgr 273
                                            +        ++++al++f +g+ +l t lp yl  +lg++ + +++l+++++ +v+++l   +   sd + +
  gi|320100802|ref|YP_004176394.1| 217 lptriYaaaaastgVVVTALIGFRLGNEYLWTPLPYYLTYTLGMG-VSSVLLVYGIGRAVAFAL--YSMIKSDAVFS 290
                                       333321222233334666666666666669999999*********.99*************777..88888888554 PP

                             MFS_1 274 rrrlllallllllaalglallavtssavllllvlvl 309
                                         r ++al+ ++ ++++lal++v ++a+++ll+ ++
  gi|320100802|ref|YP_004176394.1| 291 --RGFFALSMMVRLTALLALINVRETALIGLLLGAI 324
                                       ..9*********************999988885544 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.00037
                             MFS_1 113 wfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv 166
                                       +f+k++ g ++gl+s+   + +++g + +g++ +slg  ++  + +++s+l++ 
  gi|320100802|ref|YP_004176394.1| 338 IFAKSRSGYGVGLYSLIGEAVSLVGSATSGYVFTSLGPLLTIAVTGLLSVLVIP 391
                                       7999*******************************************9999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2846.61
//
Query:       gi|320100803|ref|YP_004176395.1|  [L=291]
Description: dual specificity protein phosphatase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-11   41.8   0.0    1.6e-10   40.9   0.0    1.4  1  DSPc            Dual specificity phosphatase, catalytic domai
     0.0035   16.9   0.0     0.0044   16.6   0.0    1.2  1  Y_phosphatase   Protein-tyrosine phosphatase
  ------ inclusion threshold ------
      0.015   15.0   0.2      0.026   14.2   0.0    1.5  2  CDKN3           Cyclin-dependent kinase inhibitor 3 (CDKN3)
      0.027   14.4   0.0      0.047   13.6   0.0    1.4  1  Y_phosphatase3  Tyrosine phosphatase family


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 !   40.9   0.0   3.5e-14   1.6e-10      32     131 ..      46     145 ..      31     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.5e-14
                                       C..ECCTTTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEESSSSSHHHHHHHHHHHHHHTSCHHHH CS
                              DSPc  32 a..nalkkseieklripvedehetkiskyleeavefidkakqkgkkvlVHCqaGisRSatliiaYlmktknlslnea 106
                                       +   +l++++ie l+ip  d h  ++  +l +a+ fi+    +g+ vlVHC  G+ RS+ +++aYl   k+ls+ ea
  gi|320100803|ref|YP_004176395.1|  46 YylETLENHGIEALHIPTPDLHPVELL-DLLRASFFIERHVGEGGAVLVHCVGGLGRSGVVTAAYLV-FKGLSYYEA 120
                                       24667789999******9997777776.5667899******************************97.579****** PP

                                       HHHHHHHSTT-SSTHHHHHHHHHHH CS
                              DSPc 107 yeflkerrpaispnagfirqLleye 131
                                       +  +++  p   +n+ + r+++ ye
  gi|320100803|ref|YP_004176395.1| 121 VARVRSAVPGSIENPWQARMVRTYE 145
                                       *****99999999988888887776 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.9e-07    0.0044     162     225 ..      81     137 ..      39     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.9e-07
                                       HHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHTTSTTSS-SHHH CS
                     Y_phosphatase 162 vekskeaksgpvvVhCsaGvgRtgtfvaldillqqleaeeevdvlqivkelrkqRpgmvqtleq 225
                                       +e++   + g v+VhC  G gR+g++ a+ ++++ l+       +++v ++r+  pg++++  q
  gi|320100803|ref|YP_004176395.1|  81 IERHV-GEGGAVLVHCVGGLGRSGVVTAAYLVFKGLSY------YEAVARVRSAVPGSIENPWQ 137
                                       44444.67789*******************99999888......77777777777777777655 PP

>> CDKN3  Cyclin-dependent kinase inhibitor 3 (CDKN3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.7e-06     0.026     133     157 ..      88     112 ..      34     121 .. 0.73
   2 ?   -4.0   0.1       2.3     1e+04      34      43 ..     253     262 ..     250     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.7e-06
                                       T--EEEE-SSSSSHHHHHHHHHHHH CS
                             CDKN3 133 yrktlihcygglgrsclvaacllly 157
                                           l+hc gglgrs +v+a+ l++
  gi|320100803|ref|YP_004176395.1|  88 GGAVLVHCVGGLGRSGVVTAAYLVF 112
                                       45689*************9999987 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.3
                                       -GGGT-SSEE CS
                             CDKN3  34 lsrvncsqfl 43 
                                       l r ncsq+ 
  gi|320100803|ref|YP_004176395.1| 253 LCRDNCSQIA 262
                                       6789999975 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.047     116     149 ..      84     117 ..      43     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                    Y_phosphatase3 116 aladee.pvlfHCtaGKDRTGvlaalllsllGvde 149
                                       ++ + + +vl+HC  G  R Gv++a  l + G++ 
  gi|320100803|ref|YP_004176395.1|  84 HVGE-GgAVLVHCVGGLGRSGVVTAAYLVFKGLSY 117
                                       4555.469*****************9998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2093.74
//
Query:       gi|320100804|ref|YP_004176396.1|  [L=326]
Description: Thiamine-phosphate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-15   55.8   0.1    1.4e-14   54.5   0.0    1.8  2  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 !   54.5   0.0     8e-19   1.4e-14       6      93 ..      47     143 ..      10     144 .. 0.89
   2 ?   -2.5   0.0      0.49   8.8e+03      64      79 ..     265     282 ..     250     301 .. 0.52

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 8e-19
                                       EEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EE CS
                              AIRS   6 vvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvpl 73 
                                       + ++d     +l+ p ++   iG+ a+++++sD+++ G+ P ++++ l l+      ++ee+++gl+ea+e++gv +
  gi|320100804|ref|YP_004176396.1|  47 IYSMDAYRVRSLMLPWRTwrdIGWMALTGAVSDIVSKGGLPSVAMVGLGLSrdasieEVEELATGLREAGEHYGVRI 123
                                       5677777777777777778999********************99********************************* PP

                                       EEEEEEEESSEEEEEEEEEE CS
                              AIRS  74 vgGdtsfsneptisvtavGl 93 
                                       +gGdt+++ +p i+v+++G 
  gi|320100804|ref|YP_004176396.1| 124 TGGDTNEGGDPWIAVSVIGF 143
                                       ********99********96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.49
                                       HHHHHTT-EEE..EEEEE CS
                              AIRS  64 eaaeelgvplv..gGdts 79 
                                       +++ee+gv lv  gG +s
  gi|320100804|ref|YP_004176396.1| 265 AGGEEYGVVLVvdGGGLS 282
                                       555666665543333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2503.77
//
Query:       gi|320100805|ref|YP_004176397.1|  [L=520]
Description: polysaccharide biosynthesis protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-17   61.6  15.4    7.4e-17   61.6  15.4    2.6  2  Polysacc_synt    Polysaccharide biosynthesis protein
    2.3e-08   33.6  10.9    2.3e-08   33.6  10.9    2.6  2  Polysacc_synt_3  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6  15.4   8.2e-21   7.4e-17       8     271 ..      18     293 ..      13     296 .. 0.76
   2 ?   -2.7  18.2      0.33   2.9e+03      60     251 ..     292     480 ..     286     485 .. 0.72

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 8.2e-21
                     Polysacc_synt   8 lllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek........kelvsl 76 
                                       + +s++++ +l+  t+ +++r lgp ++G ++lal   t+l+i++d G++ +  r+i+ +++k        +++vsl
  gi|320100805|ref|YP_004176397.1|  18 YGASTITQIILQVATMMIVSRSLGPSNYGVYTLALLPSTILSIFSDPGVTSSMLRYISVAKAKgdecgvaeSYRVSL 94 
                                       5678889999*****************************************************99988777777777 PP

                     Polysacc_synt  77 illnvllvllvlvllfllllliaaflglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvveqlsr 152
                                       ++l+++ ++l+++++ l   l a +  +++  +  lila + + l++++   +  ++ g+e+    ++ q++    r
  gi|320100805|ref|YP_004176397.1|  95 LILSLVNAMLLVAIVLLPEELGAWL--AQREGLGELILATAPYpLATTIYGAVLTYYAGVEKAALRSILQLLAPALR 169
                                       7777777777777777777777545..555556666777777777******************************** PP

                     Polysacc_synt 153 vilvliavflfldivaavlgavlaalvggivslavlrkkfr...prfvilslklvrellsfsapltisslaillyty 226
                                       +ilv +a++l++++ +++++ v+ ++v ++ +lav+ +++r   p +  +   + + +ls ++ + +  la+ +  +
  gi|320100805|ref|YP_004176397.1| 170 LILVSLALMLGSSVHGVIAAHVATYVVMAVTGLAVSLRELRgfePCKGGF---DLKGFLSLALSIYMIGLAGAVVGR 243
                                       *************5555555555555555555555555554334444444...455555555555555555555555 PP

                     Polysacc_synt 227 idsillglllgaea......vGiYnaayqllvaisgllapivtaalfPvfs 271
                                       i  +l ++ +++        vG+Ynaa+ +l a+ ++l + +   l P+++
  gi|320100805|ref|YP_004176397.1| 244 IVGFLVAYSTSSMGeqgdfmVGNYNAANAFLGAVASILGSLTV-PLTPLLA 293
                                       55554444333333355699***************99998877.7777665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.33
                     Polysacc_synt  60 lvreiakyrekkelvslillnvllvll..vlvllfllllliaa.flglpe.lavlylilalmllllvgvasfrrglf 132
                                       l +  +++++  e ++l++ nvl++l+  v++ l+ +++ i + ++g+++ la l + ++++ ll+ + ++++++l+
  gi|320100805|ref|YP_004176397.1| 292 LAKKLNDNQA-GEASTLMI-NVLTALTipVAMYLVSFADAIIYsVYGRSYaLAPLFFSYMSISLLAWPLQAVYGSLY 366
                                       6666677777.35555555.555544401444455566666666777775245555556666669************ PP

                     Polysacc_synt 133 qglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrells 209
                                         l++ k++av  ++   + ++++l + + ++ + ++++++ l+ l+++ v++++ + ++r+r +++       +l 
  gi|320100805|ref|YP_004176397.1| 367 WVLNDRKPLAVYGLLLMATGLATSLPLSTVMG-LKGVAIAQGLYPLISSTVLAYYGYSRYRVRLNKS---GAAVILV 439
                                       **************999999999999999999.9***********************9999999988...4444443 PP

                     Polysacc_synt 210 fsapltisslaillytyidsillglllgaea.vGiYnaayqll 251
                                           lt+s+la l + +i ++l+++  g +     ++aa+ ll
  gi|320100805|ref|YP_004176397.1| 440 L--SLTLSQLARLATLRIPMYLAQAVVGFVIyTVLFTAAAGLL 480
                                       3..3677888888888888888888777766433455555555 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6  10.9   2.5e-12   2.3e-08       1     288 [.      35     339 ..      35     342 .. 0.80
   2 !    2.5   0.2    0.0078        70      51      82 ..     458     489 ..     454     515 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.5e-12
                   Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqkedltee..........dlstvftfnlvlgllialvlfl 67 
                                       +++R L p+++Gv+++al+  +++++f+d G+ s +++  +  ++          +  ++  ++lv ++l+ ++++l
  gi|320100805|ref|YP_004176397.1|  35 IVSRSLGPSNYGVYTLALLPSTILSIFSDPGVTSSMLRYISVAKAkgdecgvaesYRVSLLILSLVNAMLLVAIVLL 111
                                       68999*****************************9988776666645555544423334455555555666666666 PP

                   Polysacc_synt_3  68 lapliasfynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvi 144
                                         +l a++ + + l +++  +a  ++ ++++    ++++   k    ++ +l++ ++ +i+  ++ +lg +v  ++ 
  gi|320100805|ref|YP_004176397.1| 112 PEELGAWLAQREGLGELILATAPYPLATTIYGAVLTYYAGVEKAALRSILQLLAPALRLILVSLALMLGSSVHGVIA 188
                                       677889999999**********9999998888888888777777778888888888887776677788999****** PP

                   Polysacc_synt_3 145 gtllssllslvllwlaskwrprlkfslk...slkelfsfglklllsnllnylarnldnlliGkvlssa......aLG 212
                                         +++ ++++v  + +s   +r     k    lk  +s  l + + +l+  ++ ++  +l+++  ss        +G
  gi|320100805|ref|YP_004176397.1| 189 AHVATYVVMAVTGLAVSLRELRGFEPCKggfDLKGFLSLALSIYMIGLAGAVVGRIVGFLVAYSTSSMgeqgdfMVG 265
                                       ********9999888887776653333311268999999***********************987654222333699 PP

                   Polysacc_synt_3 213 lYsvakrlaslpvaeitsviakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqW 288
                                        Y+ a+ ++ ++ +++ s ++  l+P l++  +d ++  e+   ++++++ +++P+a++l+ +a+ ++  ++G+++
  gi|320100805|ref|YP_004176397.1| 266 NYNAANAFLGAVASILGS-LTVPLTPLLAKKLND-NQAGEASTLMINVLTALTIPVAMYLVSFADAIIYSVYGRSY 339
                                       ***999999988777665.666789*****9999.6778888899****************************998 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0078
                   Polysacc_synt_3  51 ftfnlvlgllialvlfllapliasfynqpelv 82 
                                       +  + v+g++i++vlf +a  + ++++++el 
  gi|320100805|ref|YP_004176397.1| 458 YLAQAVVGFVIYTVLFTAAAGLLKAIDEAELS 489
                                       67789**************9999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 3827.28
//
Query:       gi|320100806|ref|YP_004176398.1|  [L=219]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   13.2   2.1       0.22   11.9   2.1    1.7  1  BatA      Aerotolerance regulator N-terminal
       0.12   12.4   0.0       0.18   11.8   0.0    1.3  1  FIST_C    FIST C domain


Domain annotation for each model (and alignments):
>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.1   2.4e-05      0.22       1      30 [.       1      29 [.       1      31 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                              BatA  1 MlpFlnPllLlallllplpiillyllkrrp 30
                                      M +F+  l+Llal +l++ ++++y+  rr+
  gi|320100806|ref|YP_004176398.1|  1 M-EFADVLALLALSILAAAMVVWYYYWRRR 29
                                      8.9***************999999999986 PP

>> FIST_C  FIST C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     2e-05      0.18      29      79 ..     156     206 ..     120     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                            FIST_C  29 l..ggdflvrhllgvdpedgslaladdveeGqrlqlmlrdaealiedlerlle 79 
                                       +  ++d+lv +l++   + + + + +  ee+ +l+ m+++++a++e++++l++
  gi|320100806|ref|YP_004176398.1| 156 ReeDRDILVNTLMN--SGGKYIRISCIPEENAVLATMRAEPDAAVEAARDLPR 206
                                       04489999999999..46899*************************9999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1757.15
//
Query:       gi|320100807|ref|YP_004176399.1|  [L=83]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 675.83
//
Query:       gi|320100808|ref|YP_004176400.1|  [L=605]
Description: carbon starvation protein CstA [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-99  331.6  24.3    1.1e-98  330.6  24.3    1.4  1  CstA        Carbon starvation protein CstA
    4.8e-27   94.6   5.9    4.8e-27   94.6   5.9    3.3  4  CstA_5TM    5TM C-terminal transporter carbon starvation CstA
  ------ inclusion threshold ------
        1.3    8.9  11.3        3.6    7.5   1.4    2.7  2  60KD_IMP    60Kd inner membrane protein


Domain annotation for each model (and alignments):
>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.6  24.3  1.8e-102   1.1e-98       3     356 ..       5     366 ..       3     381 .. 0.88

  Alignments for each domain:
  == domain 1  score: 330.6 bits;  conditional E-value: 1.8e-102
                              CstA   3 avllvvvavvvfviayrfYgk.fiakkvlklddkraTPaerledgkdyvptnklvlfghhFasiagagPlvGpvlAa 78 
                                       a+ ++++ v+v+ ++y +Ygk  ++++v+++d +r TPa +  dg+dy p+nk+vlfghhFasiagagP++Gp++A+
  gi|320100808|ref|YP_004176400.1|   5 ALEVILIVVAVYGVSYYLYGKkVLEARVVRADGRRLTPAVEKFDGVDYAPANKWVLFGHHFASIAGAGPIIGPATAL 81 
                                       6678899999*********9637899*************************************************** PP

                              CstA  79 qfGylPgllWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallaillililvlavlalvvvkal 155
                                        +G+   l+W+l+G++f+gavhD+++l+asvr+ g s+ ++ +k++g++ak ++l  +++ lilvla++  v +++ 
  gi|320100808|ref|YP_004176400.1|  82 AWGWGLPLVWVLFGNIFIGAVHDYLSLMASVRHGGLSVMSISEKTMGRKAKYIFLAYVWFALILVLAAFLSVASNTY 158
                                       ****77799******************************************************************** PP

                              CstA 156 aespaavfsviltipialllGvllrklrkgvleasvigvvllllavvvgseveealaelltlsketlaivlivYvfv 232
                                       + +p a++ + +++p+al++G+l++++  +v++a++++++l l+ ++++ +       +l  +   +++vl++Y f+
  gi|320100808|ref|YP_004176400.1| 159 IGTPEASTMTWIFMPLALFFGILVYRFGLSVWKATAVALILELIGFIYSLNH------PLIADYGSWVAVLTIYSFL 229
                                       ********************************************99998877......******************* PP

                              CstA 233 AsvlPvwlllaPrdYlstflligtivllalgilvvape........lklpavtefvdgegpvfags...lfPllfit 298
                                       A++lPvw ll+PrdYl++++l + + +++lg l+va++        ++ +a  + v + g++ +++   ++P++ +t
  gi|320100808|ref|YP_004176400.1| 230 AAALPVWYLLQPRDYLNAYMLWAFVGTAVLGGLMVAGTplntkflyINWAAPGSVVGAIGDAAKSNfawFWPFVPLT 306
                                       *************************9999975554433111111113444455666667777665533279****** PP

                              CstA 299 iACGaiSGFHslvssgttskllekesdarlvgygamllEslvailalv..aaavlepaay 356
                                       iACGa+SGFHs+v+sgt+sk+l++e da lvgyg+ml+E+ v+ la++  aa+v++ +a+
  gi|320100808|ref|YP_004176400.1| 307 IACGALSGFHSVVASGTSSKQLANELDALLVGYGGMLTEGAVSSLAVLlpAAIVFDLTAF 366
                                       ******************************************988876223444455555 PP

>> CstA_5TM  5TM C-terminal transporter carbon starvation CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3      0.35   2.1e+03      59      74 ..      80      95 ..      47      97 .. 0.67
   2 ?   -2.3   0.1      0.97   5.8e+03      60      60 ..     153     153 ..     119     199 .. 0.61
   3 ?   -1.7   0.2       0.6   3.6e+03      51      75 ..     224     256 ..     192     262 .. 0.62
   4 !   94.6   5.9     8e-31   4.8e-27       3     116 .]     424     559 ..     422     559 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.35
                          CstA_5TM 59 llllwg.gintlWplFG 74
                                      + l+wg g+  +W lFG
  gi|320100808|ref|YP_004176400.1| 80 A-LAWGwGLPLVWVLFG 95
                                      2.244445889999998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.97
                          CstA_5TM  60 l 60 
                                       +
  gi|320100808|ref|YP_004176400.1| 153 V 153
                                       1 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.6
                          CstA_5TM  51 liavalavllllwg........gintlWplFGa 75 
                                       +i ++la++l +w         +  +lW   G+
  gi|320100808|ref|YP_004176400.1| 224 TIYSFLAAALPVWYllqprdylNAYMLWAFVGT 256
                                       233333334433335556666666777777776 PP

  == domain 4  score: 94.6 bits;  conditional E-value: 8e-31
                          CstA_5TM   3 vaytfailfvalfalTtlDtatRlaRyilqellgelk......kkaltnkyvatliavalavllllwg......... 64 
                                       v ++fa+ ++++f++TtlDta+RlaR+++ e+++++k      +k ltn+++a+li v+++++l++ +         
  gi|320100808|ref|YP_004176400.1| 424 VFKVFAATALTAFVVTTLDTANRLARFAWVEFFDWVKpkspslHKVLTNRWLASLIPVLAGYMLAIPQisdplnpgk 500
                                       7899*********************************877777777******************4444667777777 PP

                          CstA_5TM  65 ...gintlWplFGaaNQlLAalaLlvvtvwllktgr....kalvtliPmvfmlvvtlta 116
                                          +++++Wp+F+ +NQlLAa+aLl v++w +++++     a+++liP+ f++++++ a
  gi|320100808|ref|YP_004176400.1| 501 yiyAYQVVWPAFAGTNQLLAAIALLSVALWAWHEQKvrggIAWLILIPAGFLWLTVTLA 559
                                       8889****************************6666689999***********998765 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.8    0.0022        13      98     150 ..     122     191 ..      85     202 .. 0.63
   2 ?    7.5   1.4    0.0006       3.6     102     154 ..     496     570 ..     418     577 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0022
                          60KD_IMP  98 Lsapd..............lpillavttflqqkls....kskkmqkmmlyvmplmilffslsfpaglvlYw 150
                                       +s+++              ++++l+++ fl+   +    + ++ ++m+ ++mpl ++f  l +  gl+++ 
  gi|320100808|ref|YP_004176400.1| 122 ISEKTmgrkakyiflayvwFALILVLAAFLSVASNtyigTPEA-STMTWIFMPLALFFGILVYRFGLSVWK 191
                                       4443355666677777776455555555555444422232223.5688899****************9865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0006
                          60KD_IMP 102 d......................lpillavttflqqklskskkm..qkmmlyvmplmilffslsfpaglvlYwlvsn 154
                                                              l+ ++ +++ l ++    +k+      l+++p+ +l+++++++ +l lY++v +
  gi|320100808|ref|YP_004176400.1| 496 LnpgkyiyayqvvwpafagtnqlLAAIALLSVALWAWHE--QKVrgGIAWLILIPAGFLWLTVTLALALWLYYVVPS 570
                                       244455555555544444433332222222222222222..222223356789*********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4087.57
//
Query:       gi|320100809|ref|YP_004176401.1|  [L=100]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 735.46
//
Query:       gi|320100810|ref|YP_004176402.1|  [L=324]
Description: arsenite efflux ATP-binding protein ArsA [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-36  125.0   0.0    4.6e-36  124.6   0.0    1.1  1  ArsA_ATPase  Anion-transporting ATPase
    9.1e-09   35.5   0.0    1.8e-08   34.5   0.0    1.5  1  AAA_31       AAA domain
      6e-08   32.8   0.0    9.1e-08   32.2   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    4.2e-07   29.7   0.3    0.00081   18.9   0.1    2.2  2  ParA         NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.062   12.9   0.0    2.0  2  AAA_25       AAA domain
      0.038   13.5   0.0       0.24   10.8   0.0    1.9  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.091   12.5   0.0       0.16   11.7   0.0    1.3  1  IstB_IS21    IstB-like ATP binding protein
       0.14   11.5   0.3       0.99    8.6   0.1    2.1  2  MipZ         ATPase MipZ


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 !  124.6   0.0   2.1e-39   4.6e-36       6     260 ..      17     271 ..      13     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 2.1e-39
                                       EEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET..SSEEEEE--HHHHHHHHHCCH CS
                       ArsA_ATPase   6 vgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk..eNLsavEidpeveleeakqev 80 
                                         GKGGVGKtt + a+a++ls+ g ++ll s DPA  l   ++     e+ +++  +  +a   d e++  +  +e 
  gi|320100810|ref|YP_004176402.1|  17 ALGKGGVGKTTTAIALALELSRIG-RTLLASFDPAKHLLKYLEL---PEAGRIHsrNPFHAYQFDLEQATGKLLKEL 89 
                                       459*******************99.6899**********99998...4444555447899******95544444444 PP

                                       ...HGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHH CS
                       ArsA_ATPase  81 ...qkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevlekllek 154
                                           +   ++l++   e vl+ +  + PG++e ++  el++++  ++yd++v+D +PTG ++r+l lpe   ++l+ 
  gi|320100810|ref|YP_004176402.1|  90 rgnLESLAPSLKVLNAESVLKAARYT-PGLEEDAIIRELSRLYGLTDYDYLVVDMPPTGLAIRVLMLPELYTSWLDG 165
                                       00044555677888999999999988.************************************************** PP

                                       HHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 155 lvklkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLk 231
                                       l++++  + +l+ ++ ++ g+ +   + +l++l e  + +  +   l++pertsf++V +pE l+l+E +  +++L+
  gi|320100810|ref|YP_004176402.1| 166 LIDVRSRILSLKYTIGRVRGIRQEVSDPVLNRLIELRNMYSGLYTNLKNPERTSFIIVANPEPLPLYEMKEITRALA 242
                                       ******************999999999************************************************97 PP

                                       H.TT-EEEEEEEEEE-TTCSSSTSHHHHHH CS
                       ArsA_ATPase 232 k.ygikvdavivNkllpeeeqenCeflear 260
                                       + ++ +  ++++Nk+++  +++  e+lea 
  gi|320100810|ref|YP_004176402.1| 243 EsLDARPRLLVMNKVVNGMVRQ-AEYLEAL 271
                                       538999*********9999986.6888775 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   8.2e-12   1.8e-08       9     128 ..      19     146 ..      14     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 8.2e-12
                            AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne..iektlyevl.ieeknikeaiiktkvenld 82 
                                        KGGvGKTTt+++la  l++ g ++Ll  +Dp + +  +l++ +     +++ +++  ++ ++    + k+   nl+
  gi|320100810|ref|YP_004176402.1|  19 GKGGVGKTTTAIALALELSRIG-RTLLASFDPAKHLLKYLELPEAGriHSRNPFHAYqFDLEQATGKLLKELRGNLE 94 
                                       5*******************99.78999**********999965443434444444424666666667777788886 PP

                            AAA_31  83 lipssidLaeaeielvelekk....eeilkellekvk..deYDyiiiDcpPs 128
                                        +  s+++ +ae  l  ++ +    e+++ + l+++    +YDy ++D+pP+
  gi|320100810|ref|YP_004176402.1|  95 SLAPSLKVLNAESVLKAARYTpgleEDAIIRELSRLYglTDYDYLVVDMPPT 146
                                       66666888899999988777777766666677776642368**********7 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   4.1e-11   9.1e-08       2     110 ..      15     281 ..      14     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4.1e-11
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +ia +kGGvGKTt+a++La  l+r   r+ll  +Dp   +l++le  e  +                          
  gi|320100810|ref|YP_004176402.1|  15 FIALGKGGVGKTTTAIALALELSR-IGRTLLASFDPAKHLLKYLELPEAGRIHsrnpfhayqfdleqatgkllkelr 90 
                                       5889********************.889*********99999944444444435667999***9999********** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|320100810|ref|YP_004176402.1|  91 gnleslapslkvlnaesvlkaarytpgleedaiirelsrlygltdydylvvdmpptglairvlmlpelytswldgli 167
                                       **********************************************************9999999999999999999 PP

                                       .................................................................CCHCCCHHHHHH CS
                                       .................................................................xxxxxxxxxxxx RF
                              CbiA  55 .................................................................dlkrllelleal 66 
                                                                                                         +k + + l   
  gi|320100810|ref|YP_004176402.1| 168 dvrsrilslkytigrvrgirqevsdpvlnrlielrnmysglytnlknpertsfiivanpeplplyEMKEITRAL--- 241
                                       99999999999999999999999999999999999999999999999999999999999999555555555555... PP

                                       CHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                              CbiA  67 gkkkalllkiagvvlnrvdgeneetllkealeelkqry.gvpvlg 110
                                        +++    ++  +v n+v +     ++ e le l   y ++p+ +
  gi|320100810|ref|YP_004176402.1| 242 AESLD--ARPRLLVMNKVVNG--MVRQAEYLEALRD-YcEIPFPH 281
                                       44432..46777777777766..4555555555533.33666554 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   3.6e-07   0.00081       7      33 ..      15      41 ..      11      44 .. 0.88
   2 !    8.7   0.0   0.00048       1.1      97     122 ..     121     146 ..      99     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.6e-07
                              ParA  7 avlSgKGGVGKStvavnlAlaLakkgl 33
                                       ++ gKGGVGK+t+a+ lAl+L++ g 
  gi|320100810|ref|YP_004176402.1| 15 FIALGKGGVGKTTTAIALALELSRIGR 41
                                      5788******************98775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00048
                              ParA  97 skaikqllkdvewgelDyLiiDlPPG 122
                                       +++i++l +     + DyL++D+PP 
  gi|320100810|ref|YP_004176402.1| 121 DAIIRELSRLYGLTDYDYLVVDMPPT 146
                                       5678888888888999*********5 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   2.8e-05     0.062      30      67 ..       9      47 ..       5      94 .. 0.79
   2 ?   -0.3   0.0      0.31   6.9e+02      86     139 ..     201     247 ..     190     259 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava.tGkpwlgpv 67
                                      l + ++ +  G +g+GKtt a+ lal+++  G+ +l ++
  gi|320100810|ref|YP_004176402.1|  9 LGKPHTFIALGKGGVGKTTTAIALALELSrIGRTLLASF 47
                                      5556677889*****************996666665544 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                            AAA_25  86 lrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaiee 139
                                       lr+ ++ + ++l+ ++r  ++ +a+ e+lpL++++          +al++ +++
  gi|320100810|ref|YP_004176402.1| 201 LRNMYSGLYTNLKNPERTSFIIVANPEPLPLYEMKEIT-------RALAESLDA 247
                                       44444445566688999999988877999999876333.......334555544 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.24       6      37 ..      18      48 ..      13      56 .. 0.83
   2 ?    0.2   0.0      0.18   4.1e+02     141     204 ..     217     279 ..     206     295 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                         Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                       GkGG+Gk+tt+  l+  l++ g+ +l    D
  gi|320100810|ref|YP_004176402.1| 18 LGKGGVGKTTTAIALALELSRIGRTLL-ASFD 48
                                      6*********************98765.4455 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                         Fer4_NifH 141 aqevyivtsgelmalyaanniakgiekyaksgg.vrlgGliinsrkvddereliekfaeelgtkv 204
                                         + +iv++ e   ly   +i++++ +     + + +   ++n+   +++ e +e++ + ++++ 
  gi|320100810|ref|YP_004176402.1| 217 RTSFIIVANPEPLPLYEMKEITRALAESLDARPrLLVMNKVVNGM--VRQAEYLEALRDYCEIPF 279
                                       556799999999**********99988766655476777777744..778888888877777766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.9e-05      0.16      48      91 ..      13      58 ..       6      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                         IstB_IS21 48 enivllGpsGvGKshlaialgveavraglsv..lfvrvedLveelk 91
                                      + ++ lG  GvGK+  aial+ e  r g     +f  ++ L++ l+
  gi|320100810|ref|YP_004176402.1| 13 HTFIALGKGGVGKTTTAIALALELSRIGRTLlaSFDPAKHLLKYLE 58
                                      678999****************999877654115777777777666 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00044      0.99       7      31 ..      18      42 ..      14      54 .. 0.86
   2 ?    0.0   0.0      0.19   4.2e+02     208     231 ..     113     137 ..     100     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00044
                                      -SSTTSSHHHHHHHHHHHHHTTT-- CS
                              MipZ  7 nekGGsGksttavhvavaLlkkGar 31
                                        kGG Gk+tta+ +a  L++ G  
  gi|320100810|ref|YP_004176402.1| 18 LGKGGVGKTTTAIALALELSRIGRT 42
                                      569*****************99975 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.19
                                       EEE---B--GGGTTTG.GGT--GGG CS
                              MipZ 208 rvasGlserviyrelf.psGltlld 231
                                       r ++Gl+e  i rel  + Glt  d
  gi|320100810|ref|YP_004176402.1| 113 RYTPGLEEDAIIRELSrLYGLTDYD 137
                                       7789999999999996357888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2279.04
//
Query:       gi|320100811|ref|YP_004176403.1|  [L=414]
Description: molybdenum cofactor synthesis domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-42  144.8   1.0    3.3e-42  143.9   1.0    1.4  1  MoeA_N         MoeA N-terminal region (domain I and II)
    1.3e-25   89.7   0.1    2.2e-25   89.0   0.1    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
    3.7e-16   59.1   0.0    1.6e-15   57.0   0.0    2.2  1  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   1.0   5.5e-46   3.3e-42       1     157 []      10     178 ..      10     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 5.5e-46
                                       B-HHHHHHHHHHH-.HH...-EEEEEG....GCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...... CS
                            MoeA_N   1 lsveealaiilaal.el...eeeevpl....aaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep. 68 
                                       +sv++a+a++++ + ++   e     +     ++algr++a dv+A +dvPpf++Sa+DGYAv a +  +as  +p 
  gi|320100811|ref|YP_004176403.1|  10 ISVDDAVALLADVFkRTmelE-----VveerVLNALGRIAASDVTAGVDVPPFNRSAVDGYAVYAGDVVNASIYSPv 81 
                                       6899***98777774444432.....3334547899***********************************99999* PP

                                       ..............-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-T CS
                            MoeA_N  69 ........saageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedika 134
                                               s+ +++p++ l++g avr++TG+p+P gadaVv+ Ed+e +    ++v+v k+v+pg+nv r+Ged+++
  gi|320100811|ref|YP_004176403.1|  82 elalkgvvSPSDKPPSECLERGeAVRVHTGSPIPCGADAVVMDEDVEaS---GSRVTVfKPVSPGQNVSRRGEDFSS 155
                                       ********99999999*999999***********************532...3334447****************** PP

                                       TSEEE-TTBB--CCCHHHHHHCT CS
                            MoeA_N 135 GevllragtrltpaeigllasvG 157
                                       Gev++++gt l+p ++++l s+G
  gi|320100811|ref|YP_004176403.1| 156 GEVIVAKGTLLGPLHVAALSSIG 178
                                       ********************998 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.1   3.7e-29   2.2e-25       1     143 [.     191     329 ..     191     330 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 3.7e-29
                                       EEEEE-HHHH........TTSSGBHHHHHHHHHHHTTSE.EEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SS CS
                     MoCF_biosynth   1 avitvGdell........sgkieDtngpllaellkelgv.evskytvvpDdeeeikeallaaleeadviittGGtGp 68 
                                       +v+t+G+e+         +  ++++++ l+a+ll++ g+ +v+ y+v pDd++ i +a+ +a++e+d+++ttGGtG+
  gi|320100811|ref|YP_004176403.1| 191 GVLTTGSEVCepgvdsecPTIVYNSSARLIAALLRSTGFiDVRYYGVFPDDPAVIGDAVVEAVSENDLVVTTGGTGV 267
                                       69********999998888888****************99*******************9999************** PP

                                       STT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  69 tpdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       ++ Dv  +ala ++         +fr+v+++pg+p++++ +   ++   k++++L G+p+a++++ e il+pa +
  gi|320100811|ref|YP_004176403.1| 268 SEGDVLIDALAGVGR-------TVFRGVRMRPGRPTTLTLV---EG---KPVLNLSGYPVAAWTGYEAILMPAFK 329
                                       **************9.......6***********9888777...54...59*******************99876 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 !   57.0   0.0   2.6e-19   1.6e-15       2      72 .]     344     414 .]     343     414 .] 0.98

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.6e-19
                                       EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       arla++ +   g r+++Rv+l++ +  +vaep+  +gSg+Lssl ++ g+ivipe++eg+e+G+ V v+l+
  gi|320100811|ref|YP_004176403.1| 344 ARLARRTPNTVGYRSYIRVSLRDAGDMLVAEPYMLRGSGVLSSLLKSQGYIVIPENVEGFEKGDLVRVHLF 414
                                       89******************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3106.23
//
Query:       gi|320100812|ref|YP_004176404.1|  [L=284]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   60.0  37.5    1.5e-08   34.9  14.5    2.1  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9  14.5   8.6e-13   1.5e-08       9     134 ..      10     128 ..       4     131 .. 0.87
   2 !   31.3  15.0     1e-11   1.9e-07       2     136 ..     139     275 ..     138     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 8.6e-13
                              EamA   9 laalfwaiyfvls.killrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffy 84 
                                       l  ++w +   +s  + l+ v+    +f+r++++++lll++ l++++ +        +++ + + l+ +l f+l+++
  gi|320100812|ref|YP_004176404.1|  10 LLPVVWVAISSASiLVRLSGVPGEVCAFWRMFFSSLLLLPLWLHRGKGF--------KWYHVASGLALALHFILWMK 78 
                                       44455555444442555899999999***************99999999........8888999999********** PP

                              EamA  85 alkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                       +l  +s+ + +l++ l P+++li+ vl+ g +++  q+lg+  +++++ +
  gi|320100812|ref|YP_004176404.1|  79 SLFMVSVYTSTLLVVLYPLYSLIIDVLIHGYRPSMPQVLGFTAAVASLTV 128
                                       *********************************************99876 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 1e-11
                              EamA   2 lgillallaalfwaiyfvlskillrkv.spl.tltfvrfliagillliiallkegklaklslkd..wllllllgllg 74 
                                        g++l l a l+ a+yf + +++   v ++l  ++f ++  a+++ l++ ++++ ++  +++++  +l+++l++l++
  gi|320100812|ref|YP_004176404.1| 139 PGAILSLMAGLLVALYFEIGRYARGAVgESLsGYVFPTYASAAFFTLMYNMVSGVSI--FPVNPlsYLYFALMALIP 213
                                       6999******************95555344435666666667777777777777777..77777669999******* PP

                              EamA  75 tvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++l++ l++y+lk+ +a  ++ i++ eP  + +l++++lge + l ++l  v  +l+++ ++
  gi|320100812|ref|YP_004176404.1| 214 MMLGHTLMNYLLKHYPAYLVTSISLGEPFGAGLLAYFILGEGMALPSILTGVATVLSIVAVI 275
                                       *************************************************9999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2036.30
//
Query:       gi|320100813|ref|YP_004176405.1|  [L=754]
Description: arginine--tRNA ligase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-29  100.7   0.1    2.2e-13   49.9   0.1    2.1  2  tRNA-synt_1d     tRNA synthetases class I (R)
    8.6e-15   55.0   0.3    6.7e-14   52.1   0.1    2.6  2  DALR_1           DALR anticodon binding domain
    2.9e-05   23.6   0.1    7.2e-05   22.3   0.0    1.6  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
  ------ inclusion threshold ------
      0.048   14.2   0.0       0.11   13.0   0.0    1.6  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
        0.2   11.0   0.3        1.6    8.0   0.1    2.1  2  CorA             CorA-like Mg2+ transporter protein
       0.21   12.0   0.4         27    5.2   0.0    2.4  2  RXLR             RXLR phytopathogen effector protein, Avirule


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 !   48.4   0.0   2.2e-16   6.5e-13      16     153 ..     125     265 ..     110     319 .. 0.77
   2 !   49.9   0.1   7.5e-17   2.2e-13     112     296 ..     354     553 ..     338     567 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2.2e-16
                                       -SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS-. CS
                      tRNA-synt_1d  16 srekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqe. 91 
                                        +  + vvv+++s n   ++h+G  r  +iGd+ srll +lG++v rl +v D G+q  +L+ +++k   + ++ + 
  gi|320100813|ref|YP_004176405.1| 125 IGTGRSVVVEHTSANPVHPLHIGSGRNSVIGDTYSRLLKYLGFNVSRLFYVNDLGRQVAVLAYGVRKLRSQGVTPRp 201
                                       456789***********************************************************999988877542 PP

                                       .----SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHH.HHHHHHHHHHHHHHH CS
                      tRNA-synt_1d  92 .qelqdLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkl.lvditrtelqklydr 153
                                        +++++  ++       + ee+ +a++      +L    e+++++ ++ ++d   t l++ + r
  gi|320100813|ref|YP_004176405.1| 202 gMKIDHWYGVVYALTNILIEEDKLAHELDGLSRELARLVEELEEASRRlIMDKGVTGLERFHSR 265
                                       3788888776666666666777777777777777777666666655544677666666665554 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 7.5e-17
                                       HCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHH....HHHHHHHCT---EC--CCCCCCCHHHHHHHHHCTT-EE CS
                      tRNA-synt_1d 112 eifaerarnyvvkLqsgdedirklwkllvditrte....lqklydrldvtlierGeslykeslneivkelkkkglvk 184
                                       e  +++  +++ + ++gd+++r+l + +   + +     l+k++  +d +  e  + +  e   ++v+ + + g+++
  gi|320100813|ref|YP_004176405.1| 354 EAAEDEIADIMRRAEGGDPETRRLLREVSGEVLKGfletLSKINVSFDGFDYESSDEVL-ELSRKVVDRVIESGYAR 429
                                       55566777888899999999998888866555444000055555555555544443333.455799*********** PP

                                       ECTTCEEEEECCC............TSSCCE.ECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHH CS
                      tRNA-synt_1d 185 esdGalvvfldef............gkrlgv.vvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqq 248
                                       + dGa  v+l++              ++ g+ ++++sDG++ly t+Dia    + +  +a+kv  vi  +qs   +q
  gi|320100813|ref|YP_004176405.1| 430 VVDGAVEVDLNKAgedheyvknlfhPDQPGRfIIRRSDGTTLYVTRDIAYTLMKFTRHRAEKVYNVIAVEQSRAQKQ 506
                                       **********9888888889999886666777********************************************* PP

                                       HHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHH CS
                      tRNA-synt_1d 249 iflilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLd 296
                                       + ++l  +gy  e+ +l h ++ mv    + +++ r+G    +++lL 
  gi|320100813|ref|YP_004176405.1| 507 LKAVLYLLGYRREADNLVHFSYEMV-HLKGMRMSGRRGIYYTVDELLM 553
                                       *************************.6678899*****9988888885 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.54   1.6e+03      37      78 ..     285     324 ..     263     336 .. 0.72
   2 !   52.1   0.1   2.2e-17   6.7e-14       2     118 ..     623     753 ..     622     754 .] 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.54
                                       HHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHH CS
                            DALR_1  37 eLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnk 78 
                                       eL+k++  ++ +  +aa  l+  ++   l eLa+++ + Y++
  gi|320100813|ref|YP_004176405.1| 285 ELYKEIKGLETAGGDAAAYLS--EYRGRLRELASKYRELYKE 324
                                       555555555555555555444..6667799999999999986 PP

  == domain 2  score: 52.1 bits;  conditional E-value: 2.2e-17
                                       HHHHHHHHHHHHHTTCTTCCCCHCCHCC.............S-SH.HHHHHHHHHHTHHHHHHHHHHHT-THHHHHH CS
                            DALR_1   2 qyahaRiksilrkaeeegekleeealal.............leee.eekeLlkalaqfpevleeaaeelephklaey 64 
                                        y  +R++silr+    ++ +++   ++             l  + eek+Ll al  +p vl ea e ++p++l+ey
  gi|320100813|ref|YP_004176405.1| 623 TYGLVRAQSILRRLWGVEPLDDASIVKTrgldtlsslkqeeLGFNvEEKQLLEALVGYPMVLREAYEYMRPDRLLEY 699
                                       57777777777744433333333322225555666666666444459****************************** PP

                                       HHHHHHHHHHHHHHCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S- CS
                            DALR_1  65 lyeLaatfhkfYnkervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapek 118
                                       +  L+ +f+++Y+k+rv++e+++++++ R  L  av  vL++  d++G + p +
  gi|320100813|ref|YP_004176405.1| 700 ASGLSLAFNRMYEKHRVINEPDPVRKNIRVLLTIAVLLVLSDLADIMGFHKPRR 753
                                       *************************************************99987 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.4e-08   7.2e-05      23     135 ..     144     441 ..     136     457 .. 0.94
   2 ?   -4.1   0.1       2.6   7.7e+03     244     274 ..     528     558 ..     524     563 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.4e-08
                                       -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-............................ CS
                      tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks............................ 71 
                                        h+G +R+ v+ D   r+l++lg++v+ +  v D+  ++   a    k                             
  gi|320100813|ref|YP_004176405.1| 144 LHIGSGRNSVIGDTYSRLLKYLGFNVSRLFYVNDLGRQVAVLAYGVRKLrsqgvtprpgmkidhwygvvyaltnili 220
                                       7***********************************999888877766677999*********************** PP

                                       ............................................................................. CS
                      tRNA-synt_1e  72 ............................................................................. 71 
                                                                                                                    
  gi|320100813|ref|YP_004176405.1| 221 eedklaheldglsrelarlveeleeasrrlimdkgvtglerfhsriasirgmlslkhdtvkllrelykeikgletag 297
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                      tRNA-synt_1e  72 ............................................................................. 71 
                                                                                                                    
  gi|320100813|ref|YP_004176405.1| 298 gdaaaylseyrgrlrelaskyrelykeytgyvkaksalcreywevcrglasgfngyeaaedeiadimrraeggdpet 374
                                       ***************************************************************************** PP

                                       ...HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHH.HHHHHHHHTTSEEE-TTS-EEE-GGG CS
                      tRNA-synt_1e  72 ...vkelaekfieefkkdleaLnvlkptleprvsekvdeii.elvekliekgyaYavsdgdvyfdvsk 135
                                          ++e++ ++ + f + l+++nv    +    s++v e+  ++v+++ie gya +v+ g v  d +k
  gi|320100813|ref|YP_004176405.1| 375 rrlLREVSGEVLKGFLETLSKINVSFDGFDYESSDEVLELSrKVVDRVIESGYARVVD-GAVEVDLNK 441
                                       ************************************999973689**********999.777766543 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.6
                                       E--EEETTBE--TTTT---BHHHHHTTS-HH CS
                      tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdpr 274
                                        ++++++g +ms   + + t+ ++l  ++ +
  gi|320100813|ref|YP_004176405.1| 528 YEMVHLKGMRMSGRRGIYYTVDELLMDMENS 558
                                       5789999999999999999999999877765 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 ?   13.0   0.0   3.8e-05      0.11      18      83 ..      30      98 ..       6     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                                      -HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT....EEEEEEETT.EEEE CS
                   Arg_tRNA_synt_N 18 dleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei....iekvevagpGFiNf 83
                                         + +i+++ +++p +GDy + +   l +  +++  ei e ia kl +       ++++ +   G++N+
  gi|320100813|ref|YP_004176405.1| 30 YIRDGKIRVAPTPDPRMGDYGVALHAVLKNYPREKWGEIGESIAGKLVEYSAaecrVKRALFIN-GYVNV 98
                                      456678999999***********98888888888999999999999988864333455555544.78887 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00054       1.6     121     224 ..     223     320 ..     198     327 .. 0.74
   2 ?    0.4   0.0      0.11   3.2e+02      94     135 ..     360     401 ..     353     419 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00054
                              CorA 121 drlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdl 197
                                       d+l+++l+ l++el +l +ele+ +++ i+++ ++    l ++++ +a  r +l +l++  d+ +l +e  + ++ l
  gi|320100813|ref|YP_004176405.1| 223 DKLAHELDGLSRELARLVEELEEASRRLIMDKGVT---GLERFHSRIASIRGML-SLKH--DTVKLLRELYKEIKGL 293
                                       689999*************************9999...7777777777777777.6666..3333333333345666 PP

                              CorA 198 ldelerllemlealrerleslqdtyss 224
                                       +     ++ +l+ +r rl+ l + y  
  gi|320100813|ref|YP_004176405.1| 294 ETAGGDAAAYLSEYRGRLRELASKYRE 320
                                       666666888888888888887777754 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                              CorA  94 vikrlkdeggkpkspgellyrlldeivdrlfellekleeeld 135
                                       +++ +++++g+++   +ll ++  e+++ ++e+l+k++   d
  gi|320100813|ref|YP_004176405.1| 360 IADIMRRAEGGDPETRRLLREVSGEVLKGFLETLSKINVSFD 401
                                       3333335569999************************97666 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 ?    4.5   0.2     0.015        44     121     140 ..     312     331 ..     293     332 .. 0.89
   2 ?    5.2   0.0    0.0091        27      42      99 ..     366     454 ..     353     455 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.015
                              RXLR 121 rklkekYktlakqYaaylkr 140
                                       r+l +kY +l+k+Y+ y+k 
  gi|320100813|ref|YP_004176405.1| 312 RELASKYRELYKEYTGYVKA 331
                                       6799*************985 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0091
                              RXLR  42 eaesrdaadkRfLRshkae.......................eddeeseeraagknlld........vfvekklkkm 87 
                                        ae +d + +R+LR+   e                       +d+  +  r+   ++++        + ve  l+k+
  gi|320100813|ref|YP_004176405.1| 366 RAEGGDPETRRLLREVSGEvlkgfletlskinvsfdgfdyesSDEVLELSRKVVDRVIEsgyarvvdGAVEVDLNKA 442
                                       577888899999998887756666666677777777776653333333344554555549999998899******** PP

                              RXLR  88 lanekyakklFr 99 
                                        ++++y k+lF 
  gi|320100813|ref|YP_004176405.1| 443 GEDHEYVKNLFH 454
                                       **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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 0.28s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 5325.28
//
Query:       gi|320100814|ref|YP_004176406.1|  [L=654]
Description: glyceraldehyde-3-phosphate ferredoxin oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-30  106.5   0.0    2.2e-30  106.0   0.0    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma
    3.9e-15   55.7   0.0    4.1e-14   52.4   0.0    2.0  2  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 !  106.0   0.0   2.5e-34   2.2e-30       2     197 ..       7     230 ..       6     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 2.5e-34
                                       EEEEEETTTTEEEEEE--.HHHHHHH-SCHHHHHHHHHHHS-.TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEE CS
                            AFOR_N   2 kilrvdLstgkieveelp.eelaekylGgrglaakllldevp.pgvdplspenplvfatGpltgtpapgsgrlvvva 76 
                                       + l +d s+++ +vee++  e+      +  l++kl+++ ++ ++   ++p+n+lv+++G+++g+++ g++r+++v+
  gi|320100814|ref|YP_004176406.1|   7 RALFIDASSRRHWVEEYDlSEI----YSPISLGLKLHMEIYKsWSKPVYHPDNVLVLGAGLFAGSKMYGTHRFIAVF 79 
                                       6799**************5554....5899*********8776888889**************************** PP

                                       E-TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETT.....EEEEEE-..TTTTT........S-HH CS
                            AFOR_N  77 ksPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylviedd.....kveieda..edlwg........ldty 138
                                       +sPlt++l+ s++Gg ++ ++ r+  da+v+ G++e p ++++ d+      ve++++  + l+g         ++y
  gi|320100814|ref|YP_004176406.1|  80 RSPLTRGLHVSEMGG-AAFQF-RVNADALVVLGRSEVPLIVKVYDKgdgepVVEFHEIpdDTLEGvwrgykgyRGIY 154
                                       ***************.66665.8********************766567777******8766777888**9988*** PP

                                       HHHHHHHHHHTS.......EEEEE-HHHHTT-TTB-E.EE.........TTEEE-SSSHHHHHH.HTTEEEEEEE- CS
                            AFOR_N 139 ettealkeelgd.......kvaviGpaGenlvrfAsisvd.........dgraagrgGlGavmg.sKnlkaivvrg 197
                                       +++++l+++++        + + +Gpa + +  +A  s++         ++  a+r G G+v+  ++++ ai+  g
  gi|320100814|ref|YP_004176406.1| 155 ALQQYLSDSFTGfyeefngRSILVGPASKYTNIGALASITlskgrmdlgSEDFAARAGGGSVLYrAHGVAAIIYGG 230
                                       ********44444555655888*******9999998888888777766544478*********99*******9987 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 !   52.4   0.0   4.6e-18   4.1e-14      38     190 ..     294     465 ..     269     499 .. 0.73
   2 ?    1.2   0.0     0.017   1.5e+02     262     316 ..     543     593 ..     511     645 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 4.6e-18
                                       --BTTTTBS--TTG..GGGSH.......HHHHHH.TEEEE.E.-TT.-SS--EEEEE......ETEE---HHHHHHH CS
                            AFOR_C  38 lptknfqegtfeka..ekisg.......ealeek.ylvkneg.Cfs.CpiaCgrevkveegkkvkvegpeyetlaal 102
                                        p+ n++  + +ka  e++++       e ++++ ++ +  + C   Cp+aC+++     gk+      +ye + +l
  gi|320100814|ref|YP_004176406.1| 294 TPVFNWNMIYLPKAvrERLHElimkhiwEPFNKEaIESRSWKtCGEpCPLACKKVRL---GKY----KSDYEPYNGL 363
                                       56666666554444443344444433333333333555555569888******9976...443....239******* PP

                                       TGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHH............TS----TT-THHHHH CS
                            AFOR_C 103 GsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedt............dglelefgdaealle 167
                                       G+ +g+ d++   k+ el+d +G+D i++G++++f++e+  kGllk e++              +e +  +ae + +
  gi|320100814|ref|YP_004176406.1| 364 GPFIGVMDIHDAEKVVELADAYGFDAIELGQIVGFIFEALYKGLLKPEEVglpgkpffdpaaYTMEHSRVNAELATR 440
                                       *************************************************9777777777776666667777777777 PP

                                       HHHHHHTT-T.THHHHTT.-HHHHH CS
                            AFOR_C 168 llekiAkreg.igdllAe.Gvkrla 190
                                       ++e+ A + + + +l++e G +++a
  gi|320100814|ref|YP_004176406.1| 441 IVEQLAFGTNpVLRLIGEkGLRAAA 465
                                       7777777776666666652444444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.017
                                       HHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHHH CS
                            AFOR_C 262 talvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynleRl 316
                                        al++ +glC+f +++ e    + ++ ll+  +G++   e+ ++  +Ri   ++l
  gi|320100814|ref|YP_004176406.1| 543 EALISDAGLCRFHRGWAE----KAVPILLEKFYGVEKPLEKTRELYKRIAEYQKL 593
                                       6788999******95444....889999999999999999999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4517.13
//
Query:       gi|320100815|ref|YP_004176407.1|  [L=152]
Description: PadR family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-15   56.2   1.2    1.2e-14   54.0   0.2    2.1  2  PadR      Transcriptional regulator PadR-like family
    5.8e-05   23.2   0.0    0.00019   21.5   0.0    1.7  2  HTH_34    Winged helix DNA-binding domain
    0.00095   19.6   0.5     0.0037   17.7   0.1    2.2  3  HTH_27    Winged helix DNA-binding domain
     0.0011   18.8   1.1     0.0043   16.9   0.2    1.9  2  CK2S      Casein Kinase 2 substrate


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.2   2.6e-18   1.2e-14       1      74 [.      15      85 ..      15      86 .. 0.94
   2 ?    0.9   0.0       0.1   4.6e+02      31      46 ..     116     131 ..     101     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.6e-18
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      iL +++e+  +Gy + k+++e  +g l +++G +Yp+L+ + ++gl+++e++ + +g++r ++r+T++Grr+l 
  gi|320100815|ref|YP_004176407.1| 15 ILDMARENGFHGYYLLKKIREE-TG-LPVNPGLIYPLLRGMVRKGLLKAEESFE-KGRRRVLFRITEEGRRYLD 85
                                      799999****************.58.8***********************9985.9***************997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHTTS CS
                              PadR  31 eGslYpaLkrLekegl 46 
                                        G+l+  L+rL  ++l
  gi|320100815|ref|YP_004176407.1| 116 LGNLFERLDRLTSSQL 131
                                       5899999999988876 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 !   21.5   0.0   4.3e-08   0.00019      20      78 ..      33      93 ..      28      94 .. 0.86
   2 ?   -1.5   0.0      0.64   2.9e+03      26      42 ..     114     130 ..     111     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.3e-08
                            HTH_34 20 lkeale..atdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLks 78
                                      ++e+++  ++ g ++  l+ +  +g ++ + +f+++++r l+riT+eGr   ++ ++ L++
  gi|320100815|ref|YP_004176407.1| 33 IREETGlpVNPGLIYPLLRGMVRKGLLKAEESFEKGRRRVLFRITEEGRRYLDENKQDLEE 93
                                      5655442268899*************************************99999998875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.64
                            HTH_34  26 atdgnLsvhlkkLekag 42 
                                       at gnL   l+ L + +
  gi|320100815|ref|YP_004176407.1| 114 ATLGNLFERLDRLTSSQ 130
                                       67788888887776654 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.2   1.4e+04      34      45 ..      25      36 ..      18      39 .. 0.73
   2 !   17.7   0.1   8.2e-07    0.0037      38      68 .]      49      80 ..      45      80 .. 0.86
   3 ?   -1.8   0.0       1.1   4.7e+03      25      44 ..     120     139 ..     113     140 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.2
                            HTH_27 34 hisyslkkLtek 45
                                      h+ y lkk  e 
  gi|320100815|ref|YP_004176407.1| 25 HGYYLLKKIREE 36
                                      566888887765 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 8.2e-07
                            HTH_27 38 slkkLtekGLv.ertgdeadrrekrvrlTdkG 68
                                       l+ +++kGL+  ++  e+ rr++++r+T++G
  gi|320100815|ref|YP_004176407.1| 49 LLRGMVRKGLLkAEESFEKGRRRVLFRITEEG 80
                                      589********655555889999********9 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                            HTH_27  25 cgrlnvedshisyslkkLte 44 
                                        +rl++  s+    +kkL+e
  gi|320100815|ref|YP_004176407.1| 120 FERLDRLTSSQLDTVKKLVE 139
                                       45555555555566667665 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.097   4.4e+02      51      82 ..      63      94 ..      53     109 .. 0.77
   2 !   16.9   0.2   9.6e-07    0.0043      23      62 ..     109     147 ..     103     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.097
                              CK2S 51 rdfpdlqerLrekqlealeevlakLrekleel 82
                                      ++f++ + r++++++e+  + l++ +++lee 
  gi|320100815|ref|YP_004176407.1| 63 ESFEKGRRRVLFRITEEGRRYLDENKQDLEEA 94
                                      67888889999999999999988877777765 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 9.6e-07
                              CK2S  23 seslleslsnlaeqlqalqnvklygtplrdfpdlqerLre 62 
                                       + +ll++l+nl+e+l  l+ ++l+++  + ++dl++rLr 
  gi|320100815|ref|YP_004176407.1| 109 LIRLLATLGNLFERLDRLTSSQLDTV-KKLVEDLEQRLRG 147
                                       6789********************88.8**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1089.48
//
Query:       gi|320100816|ref|YP_004176408.1|  [L=238]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-35  121.4   0.0    4.7e-35  121.1   0.0    1.1  1  ABC_tran        ABC transporter
    6.9e-06   26.1   0.0        0.1   12.4   0.1    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    5.7e-05   22.8   0.2    0.00011   21.9   0.2    1.4  1  AAA_29          P-loop containing region of AAA domain
    0.00013   22.4   0.1    0.00019   21.9   0.1    1.4  1  AAA_16          AAA ATPase domain
    0.00028   20.8   0.0    0.00049   20.0   0.0    1.4  1  RsgA_GTPase     RsgA GTPase
    0.00042   19.8   0.0        0.7    9.3   0.1    2.1  2  SMC_N           RecF/RecN/SMC N terminal domain
     0.0012   19.1   0.1     0.0039   17.5   0.1    1.9  1  AAA_22          AAA domain
     0.0021   17.8   0.1       0.23   11.1   0.1    2.1  2  AAA_15          AAA ATPase domain
     0.0034   17.9   0.0     0.0051   17.3   0.0    1.3  1  AAA_23          AAA domain
     0.0067   16.0   0.0      0.011   15.3   0.0    1.4  1  AAA_25          AAA domain
  ------ inclusion threshold ------
      0.013   15.6   0.2      0.043   13.9   0.1    1.9  2  MMR_HSR1        50S ribosome-binding GTPase
      0.024   13.7   0.0      0.038   13.1   0.0    1.4  1  T2SSE           Type II/IV secretion system protein
      0.045   13.7   0.1       0.22   11.5   0.0    1.9  2  NACHT           NACHT domain
      0.059   13.1   0.0      0.097   12.4   0.0    1.4  1  AAA_30          AAA domain
      0.063   13.0   0.0      0.097   12.4   0.0    1.3  1  AAA_24          AAA domain
      0.077   12.9   0.0       0.12   12.2   0.0    1.4  1  Rad17           Rad17 P-loop domain
      0.079   12.7   0.4       0.45   10.2   0.1    2.0  2  Cytidylate_kin  Cytidylate kinase
      0.079   13.1   0.2      0.095   12.9   0.2    1.5  1  AAA_33          AAA domain
      0.079   13.2   0.0        1.5    9.1   0.0    2.2  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
       0.08   12.3   0.0       0.28   10.5   0.0    1.7  2  Mg_chelatase    Magnesium chelatase, subunit ChlI
       0.12   12.6   0.0       0.22   11.8   0.0    1.4  1  AAA_28          AAA domain
       0.16   11.7   0.1       0.41   10.3   0.0    1.7  2  IstB_IS21       IstB-like ATP binding protein
       0.16   12.5   0.0       0.27   11.8   0.0    1.4  1  AAA_18          AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.0   6.1e-38   4.7e-35       1     136 [.      24     173 ..      24     174 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 6.1e-38
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ v+l++++g +vai+G++G+GKStLl++l  l kpt+G+i ++g+d++     +   + +++ig+++q+ +l ++
  gi|320100816|ref|YP_004176408.1|  24 LRGVTLTVNRGDLVAIMGPSGSGKSTLLNMLGLLDKPTSGKIFIEGRDVTAlssnEVADVRNRKIGFVFQQFNLVNR 100
                                       6789***********************************************999888889999************** PP

                                       SBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ltv en           +  ++ ++++ l++ + +++ + ++p++LSgGq+qrva+ara++ +p+++l+DEpt
  gi|320100816|ref|YP_004176408.1| 101 LTVLENielpliprgiPRAIRVRRVVEALRMAGGDESWLPKRPNQLSGGQQQRVAIARAIVGEPEIILADEPT 173
                                       **************9999999************9999999999*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   0.00013       0.1       2      22 ..      37      57 ..      36      98 .. 0.80
   2 !   11.9   0.0   0.00018      0.14     235     302 ..     144     208 ..     139     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       ++ Gp gsGKS+LL  l ll
  gi|320100816|ref|YP_004176408.1| 37 VAIMGPSGSGKSTLLNMLGLL 57
                                      6899************99888 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00018
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                       ++lS G+++  a++ a+   +    ++l DEp  +L+ +  + ++e + k++++ g   i++TH+p++ 
  gi|320100816|ref|YP_004176408.1| 144 NQLSGGQQQRVAIARAIVGEP---EIILADEPTGNLDRASAKLVMETFiKLNNA-GLTTIIVTHDPEIA 208
                                       677888888877777777766...99*******************666266666.***********985 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   1.4e-07   0.00011      13      39 ..      25      51 ..      19      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.4e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      +g t+++++ + + ++GpsGsGKSTll
  gi|320100816|ref|YP_004176408.1| 25 RGVTLTVNRGDLVAIMGPSGSGKSTLL 51
                                      56788999777***************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   2.4e-07   0.00019       7      63 ..      19      74 ..      17     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.4e-07
                            AAA_16  7 eeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdql 63
                                       e+++L+ +  +v++g+  lv + G+sG+GKs+l+++l   l k   g if++g+ +  
  gi|320100816|ref|YP_004176408.1| 19 VETKALRGVTLTVNRGD--LVAIMGPSGSGKSTLLNMLG-LLDKPtsGKIFIEGRDVTA 74
                                      57788888888999885..8***************9998.5666655445555555444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.3e-07   0.00049      97     119 ..      32      54 ..       5      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.3e-07
                                       CTTSEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinal 119
                                        ++++++++G+SG GKStL+n+l
  gi|320100816|ref|YP_004176408.1|  32 NRGDLVAIMGPSGSGKSTLLNML 54 
                                       345999***************98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0009       0.7      26      42 ..      36      52 ..      19      59 .. 0.79
   2 !    8.6   0.0    0.0014       1.1     135     207 ..     144     213 ..      62     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0009
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlld 42
                                      + ai+Gp GSGKs ll+
  gi|320100816|ref|YP_004176408.1| 36 LVAIMGPSGSGKSTLLN 52
                                      789**********9986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0014
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH.HHHHCTTSEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael.lkeksknaQfivislreemlekadk 207
                                       ++LSgG+++ va+a       v    + l De   +LD +  k v e  +k ++     i+++++ e+ +  +k
  gi|320100816|ref|YP_004176408.1| 144 NQLSGGQQQRVAIARA----IVGEPEIILADEPTGNLDRASAKLVMETfIKLNNAGLTTIIVTHDPEIANCTRK 213
                                       49******99988743....3455568899**************998615555556999*****9998776655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1     5e-06    0.0039       6      29 ..      35      58 ..      31     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5e-06
                            AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                       +++++G+sG+GK+tll++l   +
  gi|320100816|ref|YP_004176408.1| 35 DLVAIMGPSGSGKSTLLNMLGLLD 58
                                      5789***************98876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00029      0.23      23      65 ..      33      72 ..      22     109 .. 0.71
   2 ?    5.1   0.0      0.02        16     322     369 .]     162     208 ..     144     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                            AAA_15 23 ee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedl 65
                                         l  + G+ +sGKS++l++l l+ + +    + +i+ie  d+
  gi|320100816|ref|YP_004176408.1| 33 RGdLVAIMGPSGSGKSTLLNMLGLLDKPT----SGKIFIEGRDV 72
                                      444999****************9998877....33344444333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                        ++ i+l +EP  +L     k +++++++l n +   +ii TH p i+
  gi|320100816|ref|YP_004176408.1| 162 GEPEIILADEPTGNLDRASAKLVMETFIKLNNAGL-TTIIVTHDPEIA 208
                                       478899999*********************99997.9********995 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.6e-06    0.0051      11      39 ..      25      54 ..       5      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.6e-06
                            AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAi 39
                                      r++++  ++  l++I Gp G+GK+T+l+ +
  gi|320100816|ref|YP_004176408.1| 25 RGVTLTVNRgDLVAIMGPSGSGKSTLLNML 54
                                      5556666553699**************977 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.4e-05     0.011      30     107 ..      31     105 ..      21     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                            AAA_25  30 lpagelallaGapgtGKttlaldlal..avatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarll 104
                                       + +g+l++++G++g+GK+tl+  l+l  + ++Gk +      e + V  +s  + +d  +r++  v++++++  rl+
  gi|320100816|ref|YP_004176408.1|  31 VNRGDLVAIMGPSGSGKSTLLNMLGLldKPTSGKIF-----IEGRDVTALSSNEVADVRNRKIGFVFQQFNLVNRLT 102
                                       5799****************8665541144455533.....378888888888888777778888888888888888 PP

                            AAA_25 105 vld 107
                                       vl 
  gi|320100816|ref|YP_004176408.1| 103 VLE 105
                                       875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.5e-05     0.043       2      19 ..      37      54 ..      36      91 .. 0.86
   2 ?   -1.8   0.0         4   3.1e+03      46      80 ..     164     198 ..     150     219 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      vai+G + +GKStL+n l
  gi|320100816|ref|YP_004176408.1| 37 VAIMGPSGSGKSTLLNML 54
                                      89**************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4
                                       EEEEEEECGG.CSSHHHHHHHHHHHHHHHHCTSEEE CS
                          MMR_HSR1  46 keielvDtpG.liegaseekglgkaflaleeadlil 80 
                                       +ei+l+D p   +++as +  + ++f +l++a l  
  gi|320100816|ref|YP_004176408.1| 164 PEIILADEPTgNLDRASAK-LVMETFIKLNNAGLTT 198
                                       4455555553122222222.2445555544444433 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.8e-05     0.038     114     164 ..      19      68 ..       4     105 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                             T2SSE 114 lkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvE 164
                                       ++ k  + +   v++  l+ + G+ gsGK+tll++ l  ++k +   + +E
  gi|320100816|ref|YP_004176408.1|  19 VETKALRGVTLTVNRGDLVAIMGPSGSGKSTLLNM-LGLLDKPTSGKIFIE 68 
                                       55556666677788888999*************96.556666555545555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.22       2      20 ..      36      54 ..      35      62 .. 0.89
   2 ?   -0.4   0.0       1.2   9.6e+02      49      88 ..     192     219 ..     178     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      lv++ G++GsGK+tLl  l
  gi|320100816|ref|YP_004176408.1| 36 LVAIMGPSGSGKSTLLNML 54
                                      799************9865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                       -...-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE CS
                             NACHT  49 gnarsladllfsqlpepaapvsevwavllelperlLlilD 88 
                                       +na +l ++++ + pe+a + ++           +Ll+ D
  gi|320100816|ref|YP_004176408.1| 192 NNA-GLTTIIVTHDPEIANCTRK-----------ILLLRD 219
                                       555.6666666666666666655...........444444 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   0.00012     0.097      14      45 ..      31      61 ..      22     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaa 45
                                      ++ g  ++++ Gp G+GK+t+l+ l  + +  
  gi|320100816|ref|YP_004176408.1| 31 VNRG-DLVAIMGPSGSGKSTLLNMLGLLDKPT 61
                                      3444.4999*************9886665555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.097       5      23 ..      37      57 ..      34      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_24  5 iliyGpsgiGKTtlakel..g 23
                                      ++i+Gpsg+GK+tl+++l   
  gi|320100816|ref|YP_004176408.1| 37 VAIMGPSGSGKSTLLNMLglL 57
                                      78*************998662 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   0.00016      0.12      33      66 ..      22      55 ..      11      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      ++l+  +L  ++  ++ i GPsG gkst +++L 
  gi|320100816|ref|YP_004176408.1| 22 KALRGVTLTVNRGDLVAIMGPSGSGKSTLLNMLG 55
                                      467788888888889**************99885 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00058      0.45       1      18 [.      37      54 ..      37      59 .. 0.89
   2 ?    0.1   0.0      0.74   5.8e+02     112     124 ..      62      74 ..      56      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                                      EEEE-STTSSHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaral 18
                                      +ai GP+gsGKs++  +l
  gi|320100816|ref|YP_004176408.1| 37 VAIMGPSGSGKSTLLNML 54
                                      799**********98776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.74
                                       SSBEEEEESSIII CS
                    Cytidylate_kin 112 karvvveGRDigt 124
                                       ++++ +eGRD+++
  gi|320100816|ref|YP_004176408.1|  62 SGKIFIEGRDVTA 74 
                                       5688999999986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00012     0.095       1      19 [.      36      54 ..      36     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_33  1 lvllvGlpGsGKstlaerl 19
                                      lv + G++GsGKstl+  l
  gi|320100816|ref|YP_004176408.1| 36 LVAIMGPSGSGKSTLLNML 54
                                      68899**********8765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0     0.002       1.5      18      88 ..     131     188 ..     120     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                           SbcCD_C  18 dedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       +++g e++l ++ ++lSGG++q +   a+a   +a +++       +++++ DE  ++lD  s++ ++e++
  gi|320100816|ref|YP_004176408.1| 131 MAGGDESWLPKRPNQLSGGQQQRV---AIA---RAIVGE-------PEIILADEPTGNLDRASAKLVMETF 188
                                       57889999999999******9643...333...223333.......6677777777777777777777765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00036      0.28      11      67 ..      23      79 ..      16      92 .. 0.78
   2 ?   -1.1   0.0       1.3     1e+03       5      31 ..     146     172 ..     144     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                      Mg_chelatase 11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkk 67
                                      a r +++++  g  + ++Gp+GsGK+ l + l  l  p s +  +e + ++++++++
  gi|320100816|ref|YP_004176408.1| 23 ALRGVTLTVNRGDLVAIMGPSGSGKSTLLNMLGLLDKPTSGKIFIEGRDVTALSSNE 79
                                      55666667777777889************9998888888888899999998888744 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                      Mg_chelatase   5 vkGqeeakraleiaaaGgHnlllvGpp 31 
                                       + G ++++ a+  a+ G+ +++l+  p
  gi|320100816|ref|YP_004176408.1| 146 LSGGQQQRVAIARAIVGEPEIILADEP 172
                                       678899999999999999999998665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.22       2      19 ..      37      54 ..      36      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                            AAA_28  2 ivitGgestGKTtlleaL 19
                                      ++i+G++++GK+tll+ L
  gi|320100816|ref|YP_004176408.1| 37 VAIMGPSGSGKSTLLNML 54
                                      89*************998 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00053      0.41      36      68 ..      22      55 ..      12      67 .. 0.80
   2 ?   -2.6   0.0       5.1     4e+03      96     118 ..     173     195 ..     151     208 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                         IstB_IS21 36 keLatlsf.iekkenivllGpsGvGKshlaialg 68
                                      k+L++    +++ + ++++GpsG GKs l   lg
  gi|320100816|ref|YP_004176408.1| 22 KALRGVTLtVNRGDLVAIMGPSGSGKSTLLNMLG 55
                                      5666555426788999***********9987777 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.1
                         IstB_IS21  96 dgklaralkrllkvdllilDdlg 118
                                        g+l ra ++l++ + + l + g
  gi|320100816|ref|YP_004176408.1| 173 TGNLDRASAKLVMETFIKLNNAG 195
                                       34444444444444444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00035      0.27       1      18 [.      37      54 ..      37     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      ++++G++G+GK+tl + L
  gi|320100816|ref|YP_004176408.1| 37 VAIMGPSGSGKSTLLNML 54
                                      689***********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1624.65
//
Query:       gi|320100817|ref|YP_004176409.1|  [L=1181]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   3.8        1.4    9.2   0.0    5.9  7  CARDB        CARDB
     0.0026   18.0  12.5        5.9    7.2   0.0    6.2  8  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
          2    8.7  10.4        2.2    8.5   0.5    5.3  6  He_PIG       Putative Ig domain


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.7     1e+04      53      90 ..      99     121 ..      93     132 .. 0.55
   2 ?    3.8   0.0     0.011        66      16      71 ..     172     232 ..     155     250 .. 0.75
   3 !    9.2   0.0   0.00024       1.4      23      83 ..     550     615 ..     537     632 .. 0.83
   4 ?    0.7   0.0      0.11   6.4e+02      57      86 ..     697     725 ..     682     741 .. 0.80
   5 ?   -3.3   0.0       1.8   1.1e+04      14      43 ..     781     810 ..     776     812 .. 0.73
   6 ?   -1.9   0.1      0.69   4.1e+03      13      65 ..     925     981 ..     915     991 .. 0.72
   7 ?    2.5   0.0     0.028   1.7e+02      12      72 ..    1043    1102 ..    1034    1121 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                                       EESEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT-SS CS
                             CARDB  53 tvpsLaagesttvsftwtteategevtltvvvDpdnev 90 
                                       ++  +++g+ +  sft+ ++               + v
  gi|320100817|ref|YP_004176409.1|  99 YIHVISPGDIARYSFTVDVA---------------SNV 121
                                       44455555555555554443...............333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                                       ETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE.....SEE-CTEEEEEEEEEE- CS
                             CARDB  16 fvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv.....psLaagesttvsftwtt 71 
                                          + ++++v++ N+G+ + +++ ++l l g+  +  +v      +++ g+++++ f+   
  gi|320100817|ref|YP_004176409.1| 172 AGSNPVSLYVKLVNKGNSSVTSMDLTLELPGDYFTPREVnssytGNIDYGDTASIVFSNIQ 232
                                       45567899999******************99999666665555588888888888777554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00024
                                       EEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEE.SEE-CTEEEEEEEEEE-S.-S-CEEEEEEE CS
                             CARDB  23 itvtvkNqGtaasgatkvalyldgelv....gtvtv.psLaagesttvsftwtte.ategevtltvv 83 
                                       +tv+v+N+G  ++ ++ ++l + g+l     + +t  ++La+g++ t  f    + a++g  t++v+
  gi|320100817|ref|YP_004176409.1| 550 LTVEVANTGVYQASNVILELNAPGDLIpltgN-ATCtAALAPGATCTAVFYLNLSrAQPGLKTFNVT 615
                                       79************************998844.44459**********9999998777776666655 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.11
                                       E-CTEEEEEEEEEE-S-S-CEEEEEEEEST CS
                             CARDB  57 LaagesttvsftwtteategevtltvvvDp 86 
                                       L  g+s+tv ++ + + + +++t+++vvD+
  gi|320100817|ref|YP_004176409.1| 697 LHEGSSRTVYVSGPLN-SLQTTTVSYVVDA 725
                                       7788888888888888.8888888888885 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 1.8
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEE CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvaly 43 
                                       ++++g+ ++  v v+N+G  +  +  ++ly
  gi|320100817|ref|YP_004176409.1| 781 PMEEGRGLSYMVVVRNNGFPSLSNPVLTLY 810
                                       5667777888899*****777666666665 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 0.69
                                       SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEE CS
                             CARDB  13 seafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttv 65 
                                          f++ ++ ++v+v N+ +a+ +++ val+   ++v    +  +++sL  ++ +  
  gi|320100817|ref|YP_004176409.1| 925 LIYFTNGSSMLEVEVVNEYNASVYNVYVALIPASNNVipqgAVKYIESLPGNSAARL 981
                                       556777788889999999999999999999888888777766667777766665555 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.028
                                        -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB   12 pseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72  
                                         ++ +vg  ++i+  v N+G a++++  v+ y  g++ g + +  ++++++t  ++   ++
  gi|320100817|ref|YP_004176409.1| 1043 TTAKYVGGRLSINGIVLNKGLAQARSLLVKAYYGGSS-GYSFIGDVDPSSQTPFRIDLYPA 1102
                                        566788889999999*******************999.77888888888888777776665 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 !    7.2   0.0     0.001         6      42      78 ..      98     134 ..      50     135 .. 0.78
   2 !    7.2   0.0   0.00098       5.9       7      77 ..     177     249 ..     173     251 .. 0.87
   3 ?   -2.6   0.1       1.2   6.9e+03      59      76 ..     472     489 ..     465     490 .. 0.83
   4 !    6.8   0.1    0.0013         8       8      77 ..     549     617 ..     542     619 .. 0.81
   5 ?   -2.8   0.0       1.4   8.1e+03       9      32 ..     670     693 ..     663     693 .. 0.83
   6 ?   -1.7   0.0       0.6   3.6e+03       2      35 ..     783     816 ..     782     832 .. 0.81
   7 ?   -1.6   0.0      0.56   3.4e+03       9      28 ..     935     954 ..     931     965 .. 0.90
   8 ?   -2.8   0.2       1.4   8.1e+03      52      76 ..    1132    1156 ..    1129    1158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                       NPCBM_assoc  42 asaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                       + +  + pG+ ++  ++V + ++  +G y+ t+++++
  gi|320100817|ref|YP_004176409.1|  98 TYIHVISPGDIARYSFTVDVASNVNPGGYPFTLNVSY 134
                                       445689****************************996 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00098
                       NPCBM_assoc   7 vtltltvtndgtaaatnvslslslPeGWtvvevspasaa..slapGetveatv.kVtppagaaaGdyevtakar 77 
                                       v+l + ++n+g++++t+  l+l+lP +   +  +++s     +++G+t++  + ++++ + + +G y+ ++k++
  gi|320100817|ref|YP_004176409.1| 177 VSLYVKLVNKGNSSVTSMDLTLELPGDYF-TPREVNSSYtgNIDYGDTASIVFsNIQIKPYTPPGVYTAVLKVS 249
                                       6677889*******************999.888777766679*******9887479999999999999999887 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                       NPCBM_assoc  59 VtppagaaaGdyevtaka 76 
                                       + + ++aa+G y  t+++
  gi|320100817|ref|YP_004176409.1| 472 IDVAPDAAPGVYAATMTL 489
                                       6788999*****999887 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0013
                       NPCBM_assoc   8 tltltvtndgtaaatnvslslslPeGWtvvevspasaa.slapGetveatvkVtppagaaaGdyevtakar 77 
                                        lt++v+n+g   a+nv l+l +P +     +  a+ + +lapG+t +a + +  + +a++G  +  ++ar
  gi|320100817|ref|YP_004176409.1| 549 GLTVEVANTGVYQASNVILELNAPGDLI-PLTGNATCTaALAPGATCTAVFYLNLS-RAQPGLKTFNVTAR 617
                                       5899********************9988.55555555569********99999886.57778877777777 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 1.4
                       NPCBM_assoc   9 ltltvtndgtaaatnvslslslPe 32 
                                       +t+t++n +  ++ +  +s+++P+
  gi|320100817|ref|YP_004176409.1| 670 YTVTLANLEPYPVYSMWVSVETPS 693
                                       689999999999999999999996 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 0.6
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWt 35 
                                       e G+  ++ ++v n+g  +++n  l+l lP+G  
  gi|320100817|ref|YP_004176409.1| 783 EEGRGLSYMVVVRNNGFPSLSNPVLTLYLPPGFL 816
                                       6788888899999*****************9965 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 0.56
                       NPCBM_assoc   9 ltltvtndgtaaatnvslsl 28 
                                       l+++v+n+ +a++ nv+++l
  gi|320100817|ref|YP_004176409.1| 935 LEVEVVNEYNASVYNVYVAL 954
                                       7899*************998 PP

  == domain 8  score: -2.8 bits;  conditional E-value: 1.4
                       NPCBM_assoc   52 tveatvkVtppagaaaGdyevtaka 76  
                                        + e tv+Vt p+    ++y +++++
  gi|320100817|ref|YP_004176409.1| 1132 YIEQTVTVTQPQAGGLSEYYIVIVV 1156
                                        6788999999998888888777665 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5   0.00038       2.2      24      46 ..     112     134 ..     109     137 .. 0.92
   2 ?    2.0   0.3     0.042   2.5e+02      24      47 ..     213     251 ..     211     252 .. 0.76
   3 ?   -2.5   0.0         1     6e+03      31      43 ..     476     488 ..     472     490 .. 0.72
   4 ?   -2.8   0.0       1.3   7.6e+03      34      44 ..     606     616 ..     603     617 .. 0.84
   5 ?   -1.7   0.0       0.6   3.6e+03      21      44 ..     880     890 ..     860     893 .. 0.77
   6 ?   -4.1   0.0         3   1.8e+04      25      35 ..    1083    1093 ..    1081    1099 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00038
                            He_PIG  24 titGtpdqtvapGsytftVtatd 46 
                                       ++t+++ ++v+pG y ft+ +++
  gi|320100817|ref|YP_004176409.1| 112 SFTVDVASNVNPGGYPFTLNVSY 134
                                       79*****************9986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.042
                            He_PIG  24 titGtpdqtvap...............GsytftVtatdg 47 
                                       ++tG++d++ ++               G+yt  + +++g
  gi|320100817|ref|YP_004176409.1| 213 SYTGNIDYGDTAsivfsniqikpytppGVYTAVLKVSAG 251
                                       577777777666777777777777777******999986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1
                            He_PIG  31 qtvapGsytftVt 43 
                                       +  apG+y  t t
  gi|320100817|ref|YP_004176409.1| 476 PDAAPGVYAATMT 488
                                       44469***99977 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.3
                            He_PIG  34 apGsytftVta 44 
                                       +pG  tf Vta
  gi|320100817|ref|YP_004176409.1| 606 QPGLKTFNVTA 616
                                       89999*****9 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 0.6
                            He_PIG  21 stGtitGtpdqtvapGsytftVta 44 
                                       s             +G+y+++ t 
  gi|320100817|ref|YP_004176409.1| 880 S-------------AGVYSVPFTL 890
                                       3.............4777777765 PP

  == domain 6  score: -4.1 bits;  conditional E-value: 3
                            He_PIG   25 itGtpdqtvap 35  
                                        + G++d+++++
  gi|320100817|ref|YP_004176409.1| 1083 FIGDVDPSSQT 1093
                                        77999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.44
# Mc/sec: 8116.06
//
Query:       gi|320100818|ref|YP_004176410.1|  [L=405]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-19   68.7   3.0    8.6e-19   68.7   3.0    2.2  3  MacB_PCD  MacB-like periplasmic core domain
    2.6e-14   53.4   4.0    2.6e-14   53.4   4.0    3.4  4  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
      0.017   15.1   0.0       0.59   10.2   0.0    2.5  2  NapD      NapD protein


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   3.0   1.4e-22   8.6e-19       2     194 ..      22     241 ..      21     242 .. 0.74
   2 ?   -2.8   1.0       1.1   6.6e+03      16      34 ..     266     283 ..     251     312 .. 0.52
   3 ?   -1.4   0.3      0.43   2.6e+03      10      46 ..     327     362 ..     321     394 .. 0.66

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.4e-22
                          MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsqisdl.gnlvtvtpgkgsgeslsdpdvealrrevp.veavapvv... 73 
                                       +lt++GiaiG +a+i+i+s+++g  + +  +i +l +nl++vtp++     l+++d+++lr  ++ v+ ++p++   
  gi|320100818|ref|YP_004176410.1|  22 ILTIIGIAIGPMALITIGSVTSGYGDFIVNSIMGLgQNLIVVTPSR--DYKLTQEDLDTLRS-IEgVVDASPFYstq 95 
                                       79*******************************9944566788865..56789999998854.667999***98766 PP

                          MacB_PCD  74 .tvrgggsgeeevtvvgvdpdyfk...vfglklaeGrffteadlrggpnvvvigeela...erlf....pvGdtirl 139
                                        +++ gg+  ++v ++gvd+ +f    + +l++ eG + + +d     + +++g+++a   +        +Gd++ +
  gi|320100818|ref|YP_004176410.1|  96 gEIYVGGE-RKTVFIYGVDA-EFIlkaLTSLTVMEGNPPSRSD----IGKALVGYRIAfndN--GereyDLGDVVAI 164
                                       53355543.45599*****5.5552544455667894443344....447999999995540..1444558888877 PP

                          MacB_PCD 140 ...............kpftVvGvledppgsgsalg.ddavylplttl.......qrrsitvrlkdgadleaaaaele 193
                                                       ++ V+G+l+++ g++++l+ d+ ++++++t+       + + i++ +++++ ++a++++++
  gi|320100818|ref|YP_004176410.1| 165 tvyqvqpggkiqvkrLSVAVSGILSKY-GGAAFLNpDQTIFVSMETVskmlgvkDWSGILLLAESPDRVDAVSEKIK 240
                                       77888888777779888*******777.66767777999****888744444434455****************998 PP

                          MacB_PCD 194 k 194
                                       +
  gi|320100818|ref|YP_004176410.1| 241 E 241
                                       6 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                          MacB_PCD  16 iaivslgeglqasvlsqis 34 
                                       + ++++ ++l+a     ++
  gi|320100818|ref|YP_004176410.1| 266 VNFITFAATLSAFAVA-VA 283
                                       4444444444433222.22 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.43
                          MacB_PCD  10 iGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk 46 
                                       iG     +++++g+ +++s   +is+ g+ +t+++++
  gi|320100818|ref|YP_004176410.1| 327 IGCVIGLSTGAIGAHVLSSRGLTISSGGA-FTLSIQA 362
                                       55555556779999999999999986664.7766654 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.13     8e+02      27      45 ..      22      40 ..      17      80 .. 0.60
   2 ?   -3.3   0.1       2.2   1.3e+04      41      69 ..     182     210 ..     180     216 .. 0.66
   3 ?    1.1   1.7     0.091   5.4e+02      16      45 ..     257     284 ..     246     295 .. 0.70
   4 !   53.4   4.0   4.4e-18   2.6e-14       2      96 .]     298     398 ..     297     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.13
                              FtsX 27 litlvalviGlglgllaaq 45
                                      ++t+++++iG  +++ +  
  gi|320100818|ref|YP_004176410.1| 22 ILTIIGIAIGPMALITIGS 40
                                      4555555555222222222 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                              FtsX  41 llaaqllsdvllssvfsselkisidlitv 69 
                                       ++++ +ls+++++ + ++  +i+++ +tv
  gi|320100818|ref|YP_004176410.1| 182 VAVSGILSKYGGAAFLNPDQTIFVSMETV 210
                                       55666677777777766777777777766 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.091
                              FtsX  16 qvlllllteillitlvalviGlglgllaaq 45 
                                       +++  +++ + +it+ a++++++++++   
  gi|320100818|ref|YP_004176410.1| 257 RIASSIVSAVNFITFAATLSAFAVAVA--G 284
                                       677778888888888888888555443..3 PP

  == domain 4  score: 53.4 bits;  conditional E-value: 4.4e-18
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs......selkisidlitvlii 72 
                                       reig+++alG+k+++vl l+++e++l +l+++viGl  g++ a +ls+ +l++ ++      +++++ i l+ ++++
  gi|320100818|ref|YP_004176410.1| 298 REIGVMKALGFKDREVLVLIIMEGVLMSLIGCVIGLSTGAIGAHVLSSRGLTISSGgaftlsIQASPKITLELLAET 374
                                       9********************************************9999999977566667799999********** PP

                              FtsX  73 ivlllllallagllsiskilkkep 96 
                                       + l +l+ +l +++++++++k+ p
  gi|320100818|ref|YP_004176410.1| 375 VSLTILTGILGSVFPAYRAMKIPP 398
                                       ********************9976 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0001      0.59      37      73 ..      58      94 ..      54      97 .. 0.92
   2 ?    2.2   0.0     0.032   1.9e+02      10      27 ..     226     244 ..     220     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0001
                              NapD 37 gklVvviEaesedeladtieaiealpgVlsaslvyhy 73
                                      ++l+vv  + + + + + ++++++++gV++as  y+ 
  gi|320100818|ref|YP_004176410.1| 58 QNLIVVTPSRDYKLTQEDLDTLRSIEGVVDASPFYST 94
                                      5799******************************986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.032
                              NapD  10 a.rperlaavkaalaalpg 27 
                                       a  p+r++av+++++++ g
  gi|320100818|ref|YP_004176410.1| 226 AeSPDRVDAVSEKIKEMYG 244
                                       4489************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3002.90
//
Query:       gi|320100819|ref|YP_004176411.1|  [L=339]
Description: PP-loop domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-17   62.3   0.0    2.5e-16   60.0   0.0    2.0  1  ATP_bind_3     PP-loop family
     0.0004   19.3   0.0    0.00053   18.9   0.0    1.1  1  tRNA_Me_trans  tRNA methyl transferase
    0.00043   19.7   1.8    0.00043   19.7   1.8    2.5  3  zn-ribbon_14   Zinc-ribbon
    0.00049   20.2   0.0    0.00079   19.5   0.0    1.4  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


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 !   60.0   0.0   5.6e-20   2.5e-16       1     145 [.      50     211 ..      50     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 5.6e-20
                                       EEEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H........ CS
                        ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv........ 68 
                                       +++vAvSgG DSmaLl++l kl++k    +++a+ vd g++   ++  + ++++++++++++++++++         
  gi|320100819|ref|YP_004176411.1|  50 HIIVAVSGGKDSMALLHFLRKLSRKIPGwRITAVLVDEGISGYREKTIRNLAKYAEENGVEYRVASFKEyigatlde 126
                                       589*******************9987544***************************************998666655 PP

                                       ..HHCTTSTCC....CHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT.. CS
                        ATP_bind_3  69 ..akkkgknle....eaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias.. 137
                                         +k ++++l          +R  vl++a+++ g +v+++Ah+ dD + tf+++la +s   +++ + +++   +  
  gi|320100819|ref|YP_004176411.1| 127 ivEKGRSRGLPylpcSYCGVFRRYVLNKAARELGGTVIATAHNMDDVVQTFIMNLASNSVD-KIYRLTPVTGNGEgg 202
                                       553333444431111234458999*******************************997764.555555554443311 PP

                                       .CCEE-CCC CS
                        ATP_bind_3 138 .irlvRPlL 145
                                        ir v P++
  gi|320100819|ref|YP_004176411.1| 203 fIRRVKPFY 211
                                       234444665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-07   0.00053       2     126 ..      50     170 ..      49     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-07
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78 
                                       +++va+SgG DS   ++ l++  +++ g  +  +   de   +   e+ +++  + ae+ g++++v +f+ ey  + 
  gi|320100819|ref|YP_004176411.1|  50 HIIVAVSGGKDSMALLHFLRKLSRKIPGWRITAVLV-DEGI-SGYREKTIRNLAKYAEENGVEYRVASFK-EYIGAT 123
                                       79**************************99988877.3333.678999*******************995.799999 PP

                     tRNA_Me_trans  79 feeflee.yeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHYa 126
                                       ++e++e+  ++G    P+  C    +  ++l+ka +elg   +at H  
  gi|320100819|ref|YP_004176411.1| 124 LDEIVEKgRSRGLPYLPCSYCGVFRR--YVLNKAARELGGTVIATAHNM 170
                                       9999987256899999*****86654..457777777********9965 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2      0.14   6.4e+02       2       7 ..       3       8 ..       2      11 .. 0.86
   2 ?   -3.4   0.5       1.6   7.1e+03       3       8 ..     141     146 ..     141     147 .. 0.84
   3 !   19.7   1.8   9.5e-08   0.00043       3      19 ..     285     301 ..     284     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.14
                      zn-ribbon_14 2 kCerCG 7
                                     kC+ CG
  gi|320100819|ref|YP_004176411.1| 3 KCSVCG 8
                                     8****9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.6
                      zn-ribbon_14   3 CerCGy 8  
                                       C+ CG 
  gi|320100819|ref|YP_004176411.1| 141 CSYCGV 146
                                       999*95 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 9.5e-08
                      zn-ribbon_14   3 CerCGylSSqkiCkACv 19 
                                       Ce CG  SS+++C+AC+
  gi|320100819|ref|YP_004176411.1| 285 CEICGEPSSHRVCRACL 301
                                       ****************6 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.8e-07   0.00079       2      57 ..      51     113 ..      50     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.8e-07
                                       EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEE CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglrlkv 57 
                                       ++v+vsgGkds++llh ++k  +++     + v vd g     ++ti+ + + +e+ g++  v
  gi|320100819|ref|YP_004176411.1|  51 IIVAVSGGKDSMALLHFLRKLSRKIpgwriTAVLVDEGISgyREKTIRNLAKYAEENGVEYRV 113
                                       799*********************777888999999987532466777777777777665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      799  (0.0445647); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2366.68
//
Query:       gi|320100820|ref|YP_004176412.1|  [L=221]
Description: metallophosphoesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   62.7   0.2    2.4e-12   46.7   0.0    2.2  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    4.3e-16   60.0   0.6    5.5e-16   59.7   0.6    1.1  1  Metallophos    Calcineurin-like phosphoesterase
    8.5e-15   55.3   0.0    2.3e-14   53.9   0.0    1.6  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.2e-06     0.019       7      43 ..       3      40 ..       1      48 [. 0.93
   2 !   46.7   0.0     4e-16   2.4e-12      80     254 ..      50     216 ..      42     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-06
                                      EEEEEE--TT-GGGHHHHHHHHHHH.--SEEEEES--- CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedk.dpDllvlvGdlv 43
                                      +vl +sd+++++  l+rl + +++  ++Dl++l Gd+ 
  gi|320100820|ref|YP_004176412.1|  3 RVLVLSDIHERTRSLPRLARRVRELgGVDLVLLAGDIT 40
                                      89***********************99*********95 PP

  == domain 2  score: 46.7 bits;  conditional E-value: 4e-16
                                       HHHHHHHT.T-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SSEEEEETTTEEEEEE-SEEESS--BSSSS-E CS
                     Metallophos_3  80 klfrelge.ldvpafvvPGkrDaPlevflreayeaevvfpnlkvvhesfaekeGevliaGmGGeivdgekeeefrLk 155
                                       k++re+ e ++ p+f+vPG+ D P  +   e  +      n+++ h      +G++++ G+GG    g  + ++ ++
  gi|320100820|ref|YP_004176412.1|  50 KILREIREsIGTPVFYVPGNCDDPRLTTDAESAG---DIVNIHGRH----VVHGDYVFYGVGGG---GISPFNTWIE 116
                                       666666442789************6443333333...233555554....46899*******96...45677899** PP

                                       EEHHHHHHHGGGGGGS---EEEEEESS--S-SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EEEEE..TTEE CS
                     Metallophos_3 156 YPaweveyrLkvlkelkdrrkvlllatpPigelvadkglkekgsevvaelvktlnPevvvvghavkeheel..gktl 230
                                       Y   +    L   k   + r v++ ++p  g ++  +g  + gse   e++ +++P + v gh++ +  ++  gkt 
  gi|320100820|ref|YP_004176412.1| 117 YGENDFKRLLENAKAHDPGRLVMVTHQPIKGFFDEVNG-VNIGSEAFREFLYSVQPLLWVTGHVHEHSGWVraGKTT 192
                                       **9999999*****999*********999999**9999.789**********************8888665449*** PP

                                       EEE--BGGGTEEEEEETTTTEEEE CS
                     Metallophos_3 231 vvnPGaleeGdfavvdleekkvel 254
                                       v+ PG +  G +a+v l++  v++
  gi|320100820|ref|YP_004176412.1| 193 VIHPGPFMRGYYALVSLSNSVVDT 216
                                       *******************99987 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.6   9.3e-20   5.5e-16       1     203 [.       2     181 ..       2     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 9.3e-20
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH.TSEEEEEC-TTS. CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky.pipvylllGNHe. 75 
                                       +r+lv++D+H     ++ ++l +l +++++  ++dlvllaGD+++  ++e   ++ l++  ++ ++pv+ ++GN++ 
  gi|320100820|ref|YP_004176412.1|   2 IRVLVLSDIH-----ERTRSLPRLARRVRELGGVDLVLLAGDITYFKPVEA-AVKILREIRESiGTPVFYVPGNCDd 72 
                                       59********.....9999999999999999****************9999.9999899999999***********4 PP

                                       ......CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESECEEETHHHHHHHHHHHSCHHH CS
                       Metallophos  76 ......gfeeellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGgspellvsldklgslnleleap 144
                                             +   e+           +++ + +  ++++   + g+g   +++++ +G+  ++                 
  gi|320100820|ref|YP_004176412.1|  73 prlttdA---ESAGDI------VNIHGRHVVHGDYVFYGVGGGGIspFNTWIEYGE-NDF----------------- 122
                                       4332110...111111......2222222222333333332233357788888887.333................. PP

                                       HCCHHHHHHHHHHTTCSEEEEEESSESS....CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 145 epgdewlkdlekrekadwvivlgHsply....rgsgylfgdealedllkkygvdlvisGHtHv 203
                                          + +l++  k  +   ++ ++H p+     + +g   g+ea++++l+  ++ l++ GH+H+
  gi|320100820|ref|YP_004176412.1| 123 ---KRLLEN-AKAHDPGRLVMVTHQPIKgffdEVNGVNIGSEAFREFLYSVQPLLWVTGHVHE 181
                                       ...566666.7778888888899***************************************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 !   53.9   0.0   3.8e-18   2.3e-14       2     151 ..       3     204 ..       2     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.8e-18
                     Metallophos_2   2 klaiiSDlHsnldaleavlealke.vgvdaiihaGDl.....eeeepevleellela..pvlaVrGNnD........ 62 
                                       +++++SD+H++ + l++++++++e  gvd++++aGD+      e++ ++l+e++e    pv +V+GN+D        
  gi|320100820|ref|YP_004176412.1|   3 RVLVLSDIHERTRSLPRLARRVRElGGVDLVLLAGDItyfkpVEAAVKILREIRESIgtPVFYVPGNCDdprlttda 79 
                                       799***************9999997789********865422233334555555544************99999999 PP

                     Metallophos_2  63 ...........................eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl........g 103
                                                                  ++  +   +   ++++++ l++++ ++ +g+ v ++H+           g
  gi|320100820|ref|YP_004176412.1|  80 esagdivnihgrhvvhgdyvfygvgggGISpFNTWIEYGENDFKRLLENAKAHD-PGRLVMVTHQP-IkgffdevnG 154
                                       988888888888888888888877775333333333444444555556777777.88889999997.45*****984 PP

                     Metallophos_2 104 vkdalaellkeaeegsd.vvvcGHtHvp.evekeggvlvvnPGsvgeprd 151
                                       v+ + ++ ++  ++++  + v GH H++ ++ + g+++v++PG   ++ +
  gi|320100820|ref|YP_004176412.1| 155 VNIGSEAFREFLYSVQPlLWVTGHVHEHsGWVRAGKTTVIHPGPFMRGYY 204
                                       444444444444456667*********9889999*********9888743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1670.90
//
Query:       gi|320100821|ref|YP_004176413.1|  [L=427]
Description: transporter, YbiR family [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-34  117.8  27.2    5.2e-34  117.8  27.2    1.9  2  CitMHS         Citrate transporter
    2.1e-06   27.1  24.4     0.0011   18.1   7.3    3.3  3  Na_sulph_symp  Sodium:sulfate symporter transmembrane region


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8  27.2   5.8e-38   5.2e-34       8     297 ..      18     370 ..       7     373 .. 0.79
   2 ?   -0.5   4.5     0.063   5.6e+02     118     168 ..     364     424 ..     345     427 .] 0.78

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 5.8e-38
                                       x.......xxxxxxxxxxxxxx......xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   8 k.......lrldvvallvlvll......vltiee....alsgiaspiillllgamiigaaleetGlfdrlaakllrl 67 
                                                +++v a+++++ +      +    e    +   i+ ++il+l+g++ ++++ +e+Gl   +a kl+++
  gi|320100821|ref|YP_004176413.1|  18 GlivrsrkPSIPVWAIMAAASTltvitgL----EpfneMGYSIDLDVILFLIGMFSLVGLADESGLLSLIAVKLVSK 90 
                                       24533333445555554444447753333....33445888899999****************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  68 aggkrdllvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaar 143
                                       a+  r ++++++l+ +llsaf+ nd+v+l+  p+v s+ak ++++ pl l+++la++  ig+++tp+G+p       
  gi|320100821|ref|YP_004176413.1|  91 ARDTREVFIATSLVLGLLSAFAVNDTVALMGPPVVYSMAK-ITGTDPLpLFLVLAFSVTIGSTMTPMGNP------- 159
                                       **9877*********************************9.6999999999*******************....... PP

                                       xxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 144 pglslpnlll......................lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsll 198
                                            +nll+                      + l+l+ l+++  +++  + l  ++++p+    +++ ++ia +++
  gi|320100821|ref|YP_004176413.1| 160 -----QNLLIaiesgltapfirfvtilsiptlVNLVLTPLIVMKMYGVGNRGLRGFIAVPEEHLRNRRDALIAGFFF 231
                                       .....9999988888888877777777755444445555577777777888899999999**************999 PP

                                       xxxxxxxxx....................................xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                            CitMHS 199 pvatillla....................................ykkveWsvlllfaGvfllvgaleqtG.ileal 238
                                       +v +ill+a                                    + +v+W+++++f+ +f+ ++++ ++G i  +l
  gi|320100821|ref|YP_004176413.1| 232 TVTVILLVAndvlelmgirlvehrgfipfvtaslayilssnprktLSRVDWGTIVFFITMFITMDGIWRSGvIQSWL 308
                                       877777666**************************************************************777888 PP

                                       xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                            CitMHS 239 adllga..ggplvalalvlgliallsafisnvavaalmapialgmapalgl..lspsplalal 297
                                       + ++    g  ++ ++ ++ ++ lls+++snv+++ l++  + +m  + g+  +++  la+ +
  gi|320100821|ref|YP_004176413.1| 309 SLFMPRvpGSRVLEYIELITVSLLLSQLLSNVPFVKLFINYMKSMGYT-GVeaSPWLTLAMGS 370
                                       888843543333333555666666**********87777766666552.33335565555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.063
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxx RF
                            CitMHS 118 iplalaaniggaltpiGtpttraaarpglslpnlll......................lalllvgllplvllf 168
                                       + la+++ i g lt+ G               n+++                      ++ ++++l++  +l+
  gi|320100821|ref|YP_004176413.1| 364 LTLAMGSTIAGNLTLLGAA------------SNIIIlevlesrygktisfieflrtgaVITAVNILVYTPFLL 424
                                       569999999999*******............****99999999999999999999777666666666666665 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   7.3   1.2e-07    0.0011     276     431 ..       7     163 ..       4     166 .. 0.73
   2 ?    1.8   3.4     0.011        98     208     352 ..     167     351 ..     163     364 .. 0.60
   3 !   16.4   0.6   3.9e-07    0.0035     178     237 ..     364     424 ..     358     426 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-07
                     Na_sulph_symp 276 fvlllllWifgeslnidattvaivvlvillllr.......vldWkDivkqktaWntllllgglialakllersglie 345
                                       + ll+l Wi g+ + +     +i v +i+   +       +   +  + +    +++l+l g+ +l  l ++sgl++
  gi|320100821|ref|YP_004176413.1|   7 IALLILAWIIGGLI-VRSRKPSIPVWAIMAAAStltvitgLEPFN-EMGYSIDLDVILFLIGMFSLVGLADESGLLS 81 
                                       56677777777755.444444444444444444333222144444.5666677799999****************** PP

                     Na_sulph_symp 346 wlgnklttslsglspavaiiiilslfvlvhylfaSatAttaal.lpillavaqaipgappllvalllalatslagfl 421
                                        ++ kl+++      +  ++i  sl++ +   fa +   +a +  p++ ++a+ + g +pl + l la+++ +++++
  gi|320100821|ref|YP_004176413.1|  82 LIAVKLVSKAR---DTREVFIATSLVLGLLSAFAVNDT-VALMgPPVVYSMAKIT-GTDPLPLFLVLAFSVTIGSTM 153
                                       *****999888...555667777777777777887754.4444158999999988.999****************** PP

                     Na_sulph_symp 422 lpyatgpnpi 431
                                       +p++ ++n +
  gi|320100821|ref|YP_004176413.1| 154 TPMGNPQNLL 163
                                       *******986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.011
                     Na_sulph_symp 208 ilgveitwasWflaaiptgvillllvplllyvlyppeikkke..........................eakavakte 258
                                        +g +  +++ + ++ ++ ++ l+l+pl++ ++y   +                                  va++ 
  gi|320100821|ref|YP_004176413.1| 167 ESGLTAPFIRFVTILSIPTLVNLVLTPLIVMKMYGVGNRGLRgfiavpeehlrnrrdaliagffftvtVILLVANDV 243
                                       56788888899999999999999999999999998888777756666666666666666666666553333444555 PP

                     Na_sulph_symp 259 lkelGpltarekallilfvlllllWifgesln.....idattvaivvlvillllr........vldWkDivkqktaW 322
                                       l+++G +   e++  i fv + l +i ++++      +d +t+ +++   ++++         + +W      + + 
  gi|320100821|ref|YP_004176413.1| 244 LELMG-IRLVEHRGFIPFVTASLAYILSSNPRktlsrVDWGTIVFFIT--MFITMdgiwrsgvIQSWLSLFMPRVPG 317
                                       55555.455555555566666666666665555544566555544443..333333466666555666666666666 PP

                     Na_sulph_symp 323 ntllllgglial....akllersgliewlgnklt 352
                                         +l +  li++    ++ll+++ +++ + n ++
  gi|320100821|ref|YP_004176413.1| 318 SRVLEYIELITVslllSQLLSNVPFVKLFINYMK 351
                                       6666665555432223555566666666666555 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 3.9e-07
                     Na_sulph_symp 178 ltvvqsasitsiaflTamApNllllglinsilgveitwasWfla.aiptgvillllvplll 237
                                       lt +++++i +  +l ++A N+++l++++s  g +i++++ + + a++t v +l+ +p+ll
  gi|320100821|ref|YP_004176413.1| 364 LTLAMGSTIAGNLTLLGAASNIIILEVLESRYGKTISFIEFLRTgAVITAVNILVYTPFLL 424
                                       5678999***********************************9878999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3210.22
//
Query:       gi|320100822|ref|YP_004176414.1|  [L=208]
Description: class II aldolase/adducin family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-52  175.8   0.5    9.3e-52  175.7   0.5    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 !  175.7   0.5   5.2e-56   9.3e-52       2     186 .]       8     184 ..       7     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 5.2e-56
                                       HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHH CS
                       Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHl 78 
                                       +++e++r l ++gl++g +GniS+r p+ +++litpsg+ +++l+ ed+vvvd++ g++veg    +kpsse+ lHl
  gi|320100822|ref|YP_004176414.1|   8 RIVEVARYLEEHGLNHGRSGNISLRIPGVNHVLITPSGLVKSRLSSEDIVVVDVN-GSIVEG---HRKPSSEVNLHL 80 
                                       799**********************99889999*********************9.****66...579********* PP

                                       HHHHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEE CS
                       Aldolase_II  79 aiykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavl 155
                                       aiy+ar d++av+H+H+ +a+al+ +a +++lpp+ +ea   + g+ev v++ a++gt +l+e++++al+  +ka+l
  gi|320100822|ref|YP_004176414.1|  81 AIYRARGDVNAVIHAHTVYATALA-VA-RRPLPPVIEEAIL-VIGGEVKVAEFAPYGTLQLAENVVKALE-GRKAAL 153
                                       ************************.65.799***9999998.66888**********************8.889*** PP

                                       ETTTEEEEEESSHHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 156 lrnHGlltvGetleeAvalaetleeaaeiql 186
                                       l+nHG+++vGe+leeA++ ++ le++ +++l
  gi|320100822|ref|YP_004176414.1| 154 LANHGVVAVGESLEEALEVLVSLERLSQVYL 184
                                       ***************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1552.37
//
Query:       gi|320100823|ref|YP_004176415.1|  [L=498]
Description: carboxypeptidase Pfu [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-161  537.0   0.0   4.9e-161  536.8   0.0    1.0  1  Peptidase_M32   Carboxypeptidase Taq (M32) metallopeptidase
  ------ inclusion threshold ------
       0.15   12.6   0.1         29    5.2   0.0    2.4  2  Ribosomal_L14e  Ribosomal protein L14


Domain annotation for each model (and alignments):
>> Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.8   0.0  5.5e-165  4.9e-161       3     488 .]      12     495 ..      10     495 .. 0.97

  Alignments for each domain:
  == domain 1  score: 536.8 bits;  conditional E-value: 5.5e-165
                     Peptidase_M32   3 kellkkvsalesasallewDketvmpkkgaearaeqlatLselahelltseevaellekleeekeeldekekavvee 79 
                                        e+++ ++a+ +a +l++wD+et+mp++g + ra + a L+ l+++l+ ++e+  l+ek+e+e+  l++ e+ vv+ 
  gi|320100823|ref|YP_004176415.1|  12 LEKYRVIWAIGHAGSLMSWDSETYMPEEGYRDRAVARAELEVLSQQLTLRPEFIGLVEKAEKEEG-LNDYERGVVRV 87 
                                       67888999*****************************************************8887.5567******* PP

                     Peptidase_M32  80 lkreykkakkvpaelvealakasakaeaaWreareandfalfepsLeevielkreiaelledlkkspYdaLldeyep 156
                                       lkr+++ a+++p  lv+++ak +++a+ aWrea+++ndf++f+p+Le++++l+r++a+ l + +++pYdaLld ye+
  gi|320100823|ref|YP_004176415.1|  88 LKRSIRIARSLPPWLVAEMAKTTQEAMVAWREAKARNDFEKFKPYLEKIFDLSRKTADFL-GWREHPYDALLDLYEE 163
                                       ************************************************************.**************** PP

                     Peptidase_M32 157 gltvekidalFeelkealvpllkkikeskekekkdksflereipeekqrelsrellkalgfdf.drgrldeseHPFt 232
                                       glt+ ++da+ ++l+++l++l++k+++++   +++  + + ++++ +++ +++++l++lg+   +r+rld+s+HPFt
  gi|320100823|ref|YP_004176415.1| 164 GLTTRDVDAILTRLRSDLKTLIEKVASESRFPRSHP-LESVKYDQGRMEIVNKKILEMLGYPLgKRARLDVSAHPFT 239
                                       ****************************99766655.99************************9************* PP

                     Peptidase_M32 233 tsfsrkDvRittryeednllsslfsvlHEaGHalYeqnlpeelsktplgggvslgihEsqSrlyEniigrskeFwev 309
                                       + ++ +DvRittrye  +++++++svlHE+GHalY+++++++l++tp+g gvslgihEsqSr++Eniigrs+eF+ev
  gi|320100823|ref|YP_004176415.1| 240 IDMGIHDVRITTRYEGVDFKRTMYSVLHEYGHALYQLQIDPALAYTPIGTGVSLGIHESQSRFWENIIGRSREFTEV 316
                                       ***************************************************************************** PP

                     Peptidase_M32 310 llpklkeafpeqlddvsleefyeavnkvepsliRveADEltYslHillRyelEkeliegklsvkdlpeaWnekykey 386
                                       ++p lke+  ++ +++++e++y ++n+v+psliRv+ADE+tY++Hi+lR +lEk +i g+++v++lpe+W + + e+
  gi|320100823|ref|YP_004176415.1| 317 VYPLLKEHL-DFIQGYTVEDLYLYFNTVRPSLIRVDADEVTYNMHIVLRAQLEKLVIGGEVKVSELPELWSQMMDEL 392
                                       *******85.56778************************************************************** PP

                     Peptidase_M32 387 LgidppddaeGvLQDvHWssgafGYFPtYalGniyaaqlfeamekdlpel..eiakgefseikkWLkenihqkGsly 461
                                       Lg++p++ +eG+LQD+HWs g++GYFPtY+lGn++aaq+++ ++ ++ +l  +i++++f++i++WL+e+ih++G++y
  gi|320100823|ref|YP_004176415.1| 393 LGVKPKTYSEGILQDIHWSMGSIGYFPTYTLGNLVAAQIRHVISGSM-DLreAISSKRFNDIQEWLRERIHRWGATY 468
                                       **********************************************9.666889*********************** PP

                     Peptidase_M32 462 sseellkkatgeslnaeyyidyLkeky 488
                                        ++ell+++ ge+ n+ey+i+y++eky
  gi|320100823|ref|YP_004176415.1| 469 PPKELLRRMIGEEYNPEYFIKYIREKY 495
                                       **************************9 PP

>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0033        29      51      73 ..      69      91 ..      66      93 .. 0.88
   2 ?    4.7   0.2    0.0047        42      51      69 ..     116     133 ..     102     137 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0033
                    Ribosomal_L14e 51 aarekraaltDFdRFkvmvakkq 73
                                      ++ ek + l+D++R  v+v+k+ 
  gi|320100823|ref|YP_004176415.1| 69 EKAEKEEGLNDYERGVVRVLKRS 91
                                      6789999*************986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0047
                    Ribosomal_L14e  51 aarekraaltDFdRFkvmv 69 
                                       a r   +a +DF++Fk ++
  gi|320100823|ref|YP_004176415.1| 116 AWR-EAKARNDFEKFKPYL 133
                                       333.44578******9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 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:                        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 0.24s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3742.12
//
Query:       gi|320100824|ref|YP_004176416.1|  [L=181]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   52.6   0.0    4.4e-14   52.4   0.0    1.1  1  LDcluster4       SLOG cluster4 family
    0.00072   19.7   0.0    0.00088   19.4   0.0    1.3  1  Lysine_decarbox  Possible lysine decarboxylase
  ------ inclusion threshold ------
      0.065   13.2   0.0       0.09   12.8   0.0    1.4  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
        0.2   11.1   0.2       0.44    9.9   0.1    1.6  2  TPALS            TIR- and PNP-associating SLOG family


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 !   52.4   0.0   9.7e-18   4.4e-14      34     130 ..      36     133 ..       3     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 9.7e-18
                        LDcluster4  34 avlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyTGlglagRnlilvlssdvviaiggrsGTl 110
                                       + +  Gg  G+m+    +a  + Gl v i p ++ +    +   +++ TGl  + R++ lv+ssd+++a+gg++GT+
  gi|320100824|ref|YP_004176416.1|  36 LAVAVGGYWGLMRIIVDAAL-TCGLKVLIYPYAEMEGLHYPEKAVVVKTGLTPEARSIPLVRSSDALVALGGGVGTM 111
                                       667789999***99999886.5699999***9888887777799********************************* PP

                        LDcluster4 111 sEialaleegkpvivlkgt..d 130
                                        E++la++ gkpv +l++   +
  gi|320100824|ref|YP_004176416.1| 112 IEVMLAYSMGKPVYLLRNGfpS 133
                                       ****************976552 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     2e-07   0.00088      43      74 ..      88     119 ..      47     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2e-07
                                       HHHHHHHHHHESEEEE-S-SHHHHHHHHHHHH CS
                   Lysine_decarbox  43 eeRkealveladafvilPGGiGTleElleilt 74 
                                       e R   lv+ +da+v+l GG+GT+ E++ +++
  gi|320100824|ref|YP_004176416.1|  88 EARSIPLVRSSDALVALGGGVGTMIEVMLAYS 119
                                       6788899*****************99986665 PP

>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05      0.09      57     104 ..      92     132 ..      59     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                       HHHHHC-SEEEEE--SSSSSS--HHHHHHHHHHHHCT-EEEEE-S-GC CS
                   Nuc_deoxyrib_tr  57 ialirqaDavianldpfrgpeaDsGtafEvGyavalgkpvlayttdar 104
                                       i l+r++Da++a   +        Gt++Ev  a+++gkpv+++++ + 
  gi|320100824|ref|YP_004176416.1|  92 IPLVRSSDALVALGGG-------VGTMIEVMLAYSMGKPVYLLRNGFP 132
                                       5567888888887766.......7*******************98765 PP

>> TPALS  TIR- and PNP-associating SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.54   2.4e+03     129     146 ..      26      45 ..      17      48 .. 0.66
   2 ?    9.9   0.1   9.9e-05      0.44     131     161 ..      94     124 ..      79     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.54
                             TPALS 129 eaqarv..gdalialGGgkG 146
                                       e+ +r+  gd  +a+GG  G
  gi|320100824|ref|YP_004176416.1|  26 EEICRCsnGDLAVAVGGYWG 45 
                                       55544433889999999766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 9.9e-05
                             TPALS 131 qarvgdalialGGgkGVsylAnkyhkagkPv 161
                                        +r +dal+alGGg G      +  + gkPv
  gi|320100824|ref|YP_004176416.1|  94 LVRSSDALVALGGGVGTMIEVMLAYSMGKPV 124
                                       57999***********999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1445.60
//
Query:       gi|320100825|ref|YP_004176417.1|  [L=86]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0047   17.2   0.8       0.01   16.1   0.8    1.7  1  DUF4129   Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.14   11.6   0.0    1.2  1  PSY3      Shu complex component Psy3, DNA-binding description


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.8   1.1e-06      0.01       4      61 ..      27      75 ..      24      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-06
                           DUF4129  4 allraLaer.gldrrpgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeey 61
                                      ++l++L+e+ g    ++ TprE+ar        +  l ++ae++e++ YG  ++++e++
  gi|320100825|ref|YP_004176417.1| 27 RILKRLREKyGC---TTCTPRELARLR-----MSGILKRFAEVYEDVVYG--AMDREDA 75
                                      677777777663...567******666.....6779*************7..4444433 PP

>> PSY3  Shu complex component Psy3, DNA-binding description
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.6e-05      0.14     151     171 ..      22      42 ..       4      43 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                              PSY3 151 lklLlkllkklrktfgcwvit 171
                                        + L ++lk lr+++gc+  t
  gi|320100825|ref|YP_004176417.1|  22 KEILWRILKRLREKYGCTTCT 42 
                                       5789*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 664.98
//
Query:       gi|320100826|ref|YP_004176418.1|  [L=297]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   18.8   0.1     0.0049   17.3   0.0    1.9  2  DUF4350        Domain of unknown function (DUF4350)
  ------ inclusion threshold ------
      0.027   14.3   0.4      0.048   13.4   0.4    1.4  1  Synaptobrevin  Synaptobrevin


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 !   17.3   0.0   5.5e-07    0.0049      15      69 .]      61     115 ..      50     115 .. 0.77
   2 ?   -3.3   0.0       1.4   1.3e+04      28      41 ..     253     274 ..     248     275 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.5e-07
                           DUF4350  15 eaqGvevrrvrkpfd..alegedgtllvvapdlrlteeela.allewvarGntlvlaa 69 
                                       e+   +v ++++ ++  +++++++ llvv+pd   t+ e+  +l  wv+ G+ lv+++
  gi|320100826|ref|YP_004176418.1|  61 ESLERRVNAIYSFSEveKYTPRNHALLVVGPD---TSLEWSpTLAHWVEEGGLLVVMD 115
                                       555666776666444548889***********...5545666*************985 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                           DUF4350  28 fdaleg........edgtllvv 41 
                                       ++ l++         ++tl+++
  gi|320100826|ref|YP_004176418.1| 253 ATSLTQsmywsnpvQRTTLIII 274
                                       5555555555555556677665 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   5.4e-06     0.048      49      86 ..     248     285 ..     238     288 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-06
                                       HHHHHHHHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXX CS
                     Synaptobrevin  49 qFkkqarklkrkmwwknmkliiililvvlililiiiiv 86 
                                        F + a+ l + m+w n   + +li++v+++ l ii++
  gi|320100826|ref|YP_004176418.1| 248 GFTTLATSLTQSMYWSNPVQRTTLIIIVIAVTLAIILL 285
                                       79999************866666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2307.18
//
Query:       gi|320100827|ref|YP_004176419.1|  [L=320]
Description: ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  209.5   0.1    1.9e-62  208.9   0.1    1.3  1  AAA_3            ATPase family associated with various cellul
    3.9e-20   71.5   0.6    6.8e-20   70.7   0.6    1.4  1  AAA_lid_2        AAA lid domain
    2.4e-17   63.2   0.0    1.1e-16   61.0   0.0    2.1  3  AAA_5            AAA domain (dynein-related subfamily)
    4.9e-07   30.2   0.0    1.4e-06   28.8   0.0    1.8  1  AAA              ATPase family associated with various cellul
    4.1e-06   26.6   0.0    3.3e-05   23.6   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
    7.2e-06   25.5   0.3      0.052   12.9   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.1e-05   23.7   0.0    5.4e-05   22.4   0.0    1.6  1  MCM              MCM P-loop domain
    0.00026   20.8   0.1     0.0038   17.0   0.1    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.018   15.4   0.2       0.28   11.6   0.1    2.3  2  AAA_16           AAA ATPase domain
      0.059   13.2   0.0         11    5.8   0.0    2.3  2  DUF4548          Domain of unknown function (DUF4548)


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.9   0.1   1.1e-65   1.9e-62       1     130 [.      48     177 ..      48     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.9 bits;  conditional E-value: 1.1e-65
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvllegvPG+aktll+k+la +l+l+fkriq tpdllPsdilG+++++ ++  f f+kGpvf+n+ll de+nrappk
  gi|320100827|ref|YP_004176419.1|  48 HVLLEGVPGTAKTLLAKTLAVTLGLDFKRIQATPDLLPSDILGVNIYDPATGGFMFRKGPVFTNILLFDEVNRAPPK 124
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                       tq+alleam+erqvtveg t++lpepflv+at nP+e+eGt+plpeaq+drfl
  gi|320100827|ref|YP_004176419.1| 125 TQAALLEAMQERQVTVEGVTYRLPEPFLVIATMNPVETEGTFPLPEAQVDRFL 177
                                       ****************************************************8 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.6   3.8e-23   6.8e-20       2      72 ..     241     312 ..     240     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 3.8e-23
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeivee 72 
                                       atr h++++lg+s+r +++all  +r lA+++gr yVtp+Dvk++a+ +L+HR++   e++ ++ t e+i++e
  gi|320100827|ref|YP_004176419.1| 241 ATRRHPMVKLGASPR-GAIALLLLSRSLALIHGRSYVTPDDVKQVAHAALSHRVIlrSEARLSKLTPESIIDE 312
                                       89*************.***************************************977777777777888776 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 !   61.0   0.0   6.4e-20   1.1e-16       1     138 []      48     176 ..      48     176 .. 0.94
   2 ?   -3.7   0.0       6.2   1.1e+04      80      95 ..     201     216 ..     199     224 .. 0.73
   3 ?   -1.2   0.0         1   1.8e+03      23      46 ..     263     286 ..     257     311 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 6.4e-20
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlL G pGt+K+ la+ la  l+  +  +q t d+ ++d++g   ++   g+  ++++p+        il++DEv+
  gi|320100827|ref|YP_004176419.1|  48 HVLLEGVPGTAKTLLAKTLAVTLGLDFKRIQATPDLLPSDILGVNIYDpaTGGFMFRKGPVF-----TNILLFDEVN 119
                                       79***************************************997666666************.....78******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll  + er++   eg ++   ++      f viat+np++  +  +l +a ++Rf
  gi|320100827|ref|YP_004176419.1| 120 RAPPKTQAALLEAMQERQVT-VEGVTYRLPEP------FLVIATMNPVEtEGTFPLPEAQVDRF 176
                                       *******************9.78888888888......***********999999999999998 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHHSSEEE CS
                             AAA_5  80 evlnsLlslleerrll 95 
                                       +vl+ L ++l+++++ 
  gi|320100827|ref|YP_004176419.1| 201 SVLDDLKPVLDRNTVI 216
                                       5788888888887765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1
                                       BS--EEEEE--TT--HHHHH--B- CS
                             AAA_5  23 lnreveyvqltrdtteedlkgrre 46 
                                       l r++  + ++++ t++d+k+  +
  gi|320100827|ref|YP_004176419.1| 263 LSRSLALIHGRSYVTPDDVKQVAH 286
                                       378888888888888888888655 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 !   28.8   0.0   7.6e-10   1.4e-06       1     129 [.      49     181 ..      49     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.6e-10
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                       vll G pGt KTllak +a +lg +f +i++ ++ll s+++g +  + +      ++    + il++DE+ +  ++ 
  gi|320100827|ref|YP_004176419.1|  49 VLLEGVPGTAKTLLAKTLAVTLGLDFKRIQAtPDLLpSDILGVNIYDPATGGFMFRKGPvFTNILLFDEVNRAPPKT 125
                                       79*************************998746888888888775554433223344444459**********9999 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEE CS
                               AAA  75 sgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkie 129
                                                  +++Ll+++++ +           ++++vi++ n         l++a + +Rf  +i 
  gi|320100827|ref|YP_004176419.1| 126 -----------QAALLEAMQERQVTvegvtyrlPEPFLVIATMNPvetegTFPLPEAQV-DRFLARIV 181
                                       ...........************999999999977799999988743333334555555.66666665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.9e-08   3.3e-05      13     142 ..      37     158 ..      29     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                                       HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBS.SSSSTTTSS-BEHH CS
                   Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhe.kGaFtGAekekkGl 88 
                                       + i ++  ++ +vl++G  Gt K+lla+++  +       f ++   + +++ll s++ G++     tG    +kG 
  gi|320100827|ref|YP_004176419.1|  37 QLILATLFSQGHVLLEGVPGTAKTLLAKTLAVTLGL---DFKRI---QATPDLLPSDILGVNiYDPATGGFMFRKGP 107
                                       455556667889****************99776653...33333...345666666666665234456666678887 PP

                                       HHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  89 fekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                       +      +l++De+++ p+++Q+ Ll+++qe++v+  G +   +  + +ia+ n
  gi|320100827|ref|YP_004176419.1| 108 VF---TNILLFDEVNRAPPKTQAALLEAMQERQVTVEGVTYRLPEPFLVIATMN 158
                                       75...469**************************99999988888887777654 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   2.9e-05     0.052       4      45 ..      28      69 ..      26      76 .. 0.86
   2 !   10.4   0.0   0.00017       0.3     108     161 ..     111     162 ..      99     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                      Mg_chelatase  4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsl 45
                                      +++G+++  + +  +   + ++ll G pG+ Kt+lak l+  
  gi|320100827|ref|YP_004176419.1| 28 KIIGKSREIQLILATLFSQGHVLLEGVPGTAKTLLAKTLAVT 69
                                      678888888888888889999****************99865 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00017
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpc 161
                                        +L++DE+     k+  +L e +++++vt++  ++  + p  f ++a+mNp  +
  gi|320100827|ref|YP_004176419.1| 111 NILLFDEVNRAPPKTQAALLEAMQERQVTVEGVTY--RLPEPFLVIATMNPVET 162
                                       5899**************************98765..56999*********865 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     3e-08   5.4e-05      54     175 ..      43     161 ..      23     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3e-08
                                       BCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSS...SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEE CS
                               MCM  54 lrgdinvllvgdpgtaKsqlLkyveklapravytsgkgssa...agLtaavvrdeetgefvleaGalvladkGvcci 127
                                       l ++ +vll g pgtaK+ l k+++ ++    +  ++++     +++      d++tg f++  G + +    +++ 
  gi|320100827|ref|YP_004176419.1|  43 LFSQGHVLLEGVPGTAKTLLAKTLA-VTLGLDFKRIQATPDllpSDILGVNIYDPATGGFMFRKGPVFTN---ILLF 115
                                       66788************98888877.444555555555443122566666678************99865...9*** PP

                                       ESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 128 DefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                       De+++   +++ al+Eam + ++++   G+++ L+    v+a +np++
  gi|320100827|ref|YP_004176419.1| 116 DEVNRAPPKTQAALLEAMQERQVTVE--GVTYRLPEPFLVIATMNPVE 161
                                       *********************99997..9*****************85 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 !   17.0   0.1   2.1e-06    0.0038      34     113 ..      47     138 ..      36     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklk.itsgPvlekagdlaallt.n.......lee....kdvlfideihrls 97 
                                        hvll G PG  kt lak +a  lg ++k i ++P l  ++d+ ++   +       +++    +++l+ de+ r  
  gi|320100827|ref|YP_004176419.1|  47 GHVLLEGVPGTAKTLLAKTLAVTLGLDFKrIQATPDLL-PSDILGVNIyDpatggfmFRKgpvfTNILLFDEVNRAP 122
                                       6*************************997245667664.44554432211111111122212224677888888888 PP

                            RuvB_N  98 raveevlysamedfrl 113
                                       ++++  l  am++ ++
  gi|320100827|ref|YP_004176419.1| 123 PKTQAALLEAMQERQV 138
                                       8888888888887766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00015      0.28       3      48 ..      30      70 ..      28     101 .. 0.77
   2 ?    1.5   0.0       0.2   3.5e+02     138     163 ..     112     137 ..     101     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellral 48
                                      +G+ +e++ +l++l    s+  + vll G +G+ K+ l+++l+  l
  gi|320100827|ref|YP_004176419.1| 30 IGKSREIQLILATL---FSQ--GHVLLEGVPGTAKTLLAKTLAVTL 70
                                      68888886665544...444..79***************9998555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                            AAA_16 138 vlvlDdlqwadeaslqllaaLlrlle 163
                                       +l++D++ +a + ++++l + +++++
  gi|320100827|ref|YP_004176419.1| 112 ILLFDEVNRAPPKTQAALLEAMQERQ 137
                                       799************99555555544 PP

>> DUF4548  Domain of unknown function (DUF4548)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.011        19      90     128 ..     108     148 ..     104     152 .. 0.82
   2 ?    5.8   0.0    0.0063        11      72     103 ..     266     296 ..     259     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.011
                           DUF4548  90 sfenivshremslhqpkaqttpkps..kddiptesihyrlP 128
                                        f ni+ + e+   +pk+q+   +   +  ++ e + yrlP
  gi|320100827|ref|YP_004176419.1| 108 VFTNILLFDEVNRAPPKTQAALLEAmqERQVTVEGVTYRLP 148
                                       5899999999*********98665511557999*******9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0063
                           DUF4548  72 evkmvqprtlkiPddlkasfenivshremslh 103
                                        + ++  r    Pdd k+  +  +shr++ l+
  gi|320100827|ref|YP_004176419.1| 266 SLALIHGRSYVTPDDVKQVAHAALSHRVI-LR 296
                                       667899999******************54.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2490.77
//
Query:       gi|320100828|ref|YP_004176420.1|  [L=411]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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      3e-15   56.3   0.0    1.7  1  DUF58     Protein of unknown function DUF58
  ------ inclusion threshold ------
      0.032   14.7   0.1       0.13   12.7   0.1    2.2  2  DUF4350   Domain of unknown function (DUF4350)


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 !   56.3   0.0   3.3e-19     3e-15       3      81 ..     195     270 ..     193     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 3.3e-19
                             DUF58   3 dfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqlld 79 
                                       d+a++ReY+pgD+ rrI Wk +A+tg+l+vre  +e ++ vllv+d ++e      + +++ t++++++ lar+ll+
  gi|320100828|ref|YP_004176420.1| 195 DLADIREYTPGDDTRRILWKHYAKTGRLLVREDYGEVKPVVLLVIDVRKELWG---IGTGVNTLAHIQLRLARSLLK 268
                                       8899**********************************************763...469*****************9 PP

                             DUF58  80 eg 81 
                                       e 
  gi|320100828|ref|YP_004176420.1| 269 EL 270
                                       74 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.4   3.6e+03      32      62 ..     284     311 ..     262     313 .. 0.70
   2 ?   12.7   0.1   1.5e-05      0.13      18      68 ..     315     369 ..     301     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.4
                           DUF4350  32 egedgtllvvapdlrlteeelaallewvarG 62 
                                       e+++ ++l+ + d    +++l all  +++G
  gi|320100828|ref|YP_004176420.1| 284 EQSPKVYLNAGGD---ADASLHALLSTLKAG 311
                                       4566677777777...778888888888877 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.5e-05
                           DUF4350  18 Gvevrrvrkpfdal.eg.edgtllvvapdlrlteeelaallewva..rGntlvla 68 
                                        +++++vr+++ a+ eg + + +lvva+ l++ +e +++l e++a  +G tlv+a
  gi|320100828|ref|YP_004176420.1| 315 EIPLSTVRQVLAAYgEGrRYDAVLVVANPLSILNEGVESLGELAAisPGRTLVVA 369
                                       678899999999995556788999999999*9998899998888777******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3043.78
//
Query:       gi|320100829|ref|YP_004176421.1|  [L=210]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1705.11
//
Query:       gi|320100830|ref|YP_004176422.1|  [L=60]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.8   6.0       0.19   11.6   6.0    1.0  1  DUF2721          Protein of unknown function (DUF2721)
        1.2    9.1   4.4        2.8    8.0   0.3    2.1  2  Gram_pos_anchor  LPXTG cell wall anchor motif
        2.6    8.0   4.2        2.7    8.0   4.2    1.0  1  RseC_MucC        Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   6.0   3.2e-05      0.19      66     114 ..      10      54 ..       4      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
                           DUF2721  66 ailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvsll 114
                                        i ll++s++++v++v ll++    +  l +l+++l +l ll++ +s+l
  gi|320100830|ref|YP_004176422.1|  10 FIGLLAASIFFLVVSVWLLYI----DRALPSLLSLLIGLTLLSTSLSIL 54 
                                       4789999**************....777788888888888888877776 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 ?    8.0   0.3   0.00047       2.8      12      35 ..       2      28 ..       2      32 .. 0.82
   2 ?    3.0   0.5     0.016        97      20      35 ..      39      54 ..      35      56 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00047
                                      XX...XXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 12 TG...engnifltaaGllallggllLl 35
                                      TG    ++ i+l+aa ++ l++++ Ll
  gi|320100830|ref|YP_004176422.1|  2 TGslvKAAFIGLLAASIFFLVVSVWLL 28
                                      6644348999*************9995 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.016
                                      XXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 20 ltaaGllallggllLl 35
                                       ++ Gl++l ++l +l
  gi|320100830|ref|YP_004176422.1| 39 SLLIGLTLLSTSLSIL 54
                                      5778888877777664 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.2   0.00044       2.7      61     115 ..       3      58 ..       1      60 [] 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00044
                         RseC_MucC  61 ksllkaallvYllPllllilgallgsall.gssellaalgallglvlgflivrlls 115
                                        sl+kaa++  l   ++++++ +   ++  +  +ll++l++l +l  ++ i+r+l+
  gi|320100830|ref|YP_004176422.1|   3 GSLVKAAFIGLLAASIFFLVVSVWLLYIDrALPSLLSLLIGLTLLSTSLSILRKLT 58 
                                       578999999988888887777777777778999****************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 445.15
//
Query:       gi|320100831|ref|YP_004176423.1|  [L=305]
Description: putative metallo-beta-lactamase superfamily hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   21.9   0.0    0.00017   21.2   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00055   19.9   0.0    0.00083   19.3   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0042   17.1   0.7      0.031   14.3   0.6    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.33   10.9   0.0    1.7  1  Arc_C          Arc C-lobe
       0.14   12.4   0.1        1.2    9.4   0.0    2.1  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 !   21.2   0.0   4.7e-08   0.00017      24     145 ..      59     178 ..      26     204 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.7e-08
                                       SS--..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEE.EEHHHHHHCCTTCGHHHCHTT.........TTEEEE CS
                     Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlre..lrpkklply.apkgvlavleanfvylaleee.........pavnvh 88 
                                          +  + d++++th HyDH  +  +l +  ++ +k+ +y  +++   + +++                  p  +  
  gi|320100831|ref|YP_004176423.1|  59 IEGKAYRADVIIITHYHYDHH-DPGFLIPieIYRDKV-VYiKDPQNNINASQRA-------RaarfikliePVAREI 126
                                       45556789*************.666666632444333.3312222222222222.......1222222343233333 PP

                                       EE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE....CTTEEEEEESS-S- CS
                     Lactamase_B_2  89 eldwgesfelgdggleitatparhksgrrldrnagdtlGlrie....gggkrvyyigDtgy 145
                                        ++ g + ++gd+   i++  a   ++          lG+++e    +g+++++y+ D++ 
  gi|320100831|ref|YP_004176423.1| 127 HVAEGSEARFGDTV--IRMSSAVPHGPS-------NKLGYVVEvsvkRGRESFLYTSDVEG 178
                                       34467778888644..444433333333.......57788877777689999******983 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.3e-07   0.00083       9      59 ..      17     122 ..      13     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.3e-07
                     Lactamase_B_3   9 sflletagarilvDPf.....................kanlgyeppaeeaDlvlisqaledHahletlkql...... 58 
                                       s  ++t++++i +DP                      +a+++ e +a +aD+++i++ + dH ++  l ++      
  gi|320100831|ref|YP_004176423.1|  17 STFVSTKDVKIHIDPAvslapkryglpphpreidrliQAGKEIEGKAYRADVIIITHYHYDHHDPGFLIPIeiyrdk 93 
                                       66788999********8877776666666666666554455666666******************999998888666 PP

                     Lactamase_B_3  59 ............................a 59 
                                                                    
  gi|320100831|ref|YP_004176423.1|  94 vvyikdpqnninasqraraarfikliepV 122
                                       66665555555555555554444444442 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.6   8.6e-06     0.031      34      57 ..      55      78 ..      12      79 .. 0.71
   2 ?    0.6   0.0      0.13   4.7e+02     129     195 ..     154     235 ..      88     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.6e-06
                                      HHHHHTSGGGGEEEEE-SBSSHHH CS
                       Lactamase_B 34 elaalglkpkdvdavilTHlHlDH 57
                                      + + ++ k  + d +i+TH+H+DH
  gi|320100831|ref|YP_004176423.1| 55 AGKEIEGKAYRADVIIITHYHYDH 78
                                      5566677777889*********** PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                                       TSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC................TTCEEE-SHCHHHHHHHHHHHHHHHCH CS
                       Lactamase_B 129 pghghghgvveygggkvlftGDallagetgridl...............tlrgaevrdpsdaekyldsllklaglka 190
                                        +   + ++v  g +++l+t D+  ++  +++++               t+  ++ +   + + +++ l+++++  +
  gi|320100831|ref|YP_004176423.1| 154 KLGYVVEVSVKRGRESFLYTSDVEGPCLDEHVGFileekprilvadgplTYMLGYRYSMKSLQASIANLKRIIDAGV 230
                                       55666778889999999999999999888888888888877777777777777777777777777777777777777 PP

                                       SEEEE CS
                       Lactamase_B 191 evlvp 195
                                       + ++ 
  gi|320100831|ref|YP_004176423.1| 231 KEIIV 235
                                       77666 PP

>> Arc_C  Arc C-lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.1e-05      0.33      57      79 ..      38      60 ..      28      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.1e-05
                             Arc_C 57 krflkpplpktleqliqkGkevq 79
                                      kr+  pp p+ ++ liq Gke+ 
  gi|320100831|ref|YP_004176423.1| 38 KRYGLPPHPREIDRLIQAGKEIE 60
                                      79999****************96 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.18   6.6e+02      49      57 ..      76      86 ..      53     119 .. 0.67
   2 ?    9.4   0.0   0.00033       1.2      32      57 ..     218     249 ..     198     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                                      EE-S---S..S CS
                                      xxxxxxxx..x RF
                               DHH 49 iDHHrlge..e 57
                                       DHH +g   +
  gi|320100831|ref|YP_004176423.1| 76 YDHHDPGFliP 86
                                      47777765551 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00033
                                       GGCGCCHHCCCSEEEEEEE-S---S......S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                               DHH  32 sqavegeakeeaedviiiDHHrlge......e 57 
                                       s a  +++++ +++ ii+DHH l +       
  gi|320100831|ref|YP_004176423.1| 218 SIANLKRIIDAGVKEIIVDHHLLRDlkygsrM 249
                                       55666779999***********9855544430 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2215.34
//
Query:       gi|320100832|ref|YP_004176424.1|  [L=457]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-51  175.7   1.2    1.6e-51  175.3   1.2    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.1e-16   61.2   1.0    1.6e-14   54.2   0.1    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    5.6e-09   35.7   0.5    3.4e-06   26.5   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    5.7e-08   31.9   0.2     0.0017   17.2   0.0    3.2  3  HI0933_like     HI0933-like protein
      1e-06   28.9   0.0    2.8e-06   27.6   0.0    1.7  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.2e-06   28.6   1.8      0.021   14.8   0.2    3.2  3  NAD_binding_9   FAD-NAD(P)-binding
    2.5e-06   27.3   8.5       0.02   14.5   0.4    3.5  3  DAO             FAD dependent oxidoreductase
    6.7e-06   25.7   0.7     0.0026   17.2   0.2    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
    1.9e-05   23.9   1.7    7.5e-05   22.0   0.1    2.5  3  FAD_binding_2   FAD binding domain
    0.00016   20.9   7.2      0.031   13.3   0.1    4.0  5  GIDA            Glucose inhibited division protein A
    0.00059   19.2   0.3       0.01   15.2   0.2    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0018   17.5   0.0      0.032   13.4   0.0    2.5  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0022   16.9   7.3        0.4    9.5   0.6    3.1  3  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.024   14.0   0.1      0.053   12.8   0.1    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
        0.8    8.7   3.5         11    5.0   0.6    2.8  3  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.3   1.2   1.3e-54   1.6e-51       1     294 []       5     309 ..       5     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 175.3 bits;  conditional E-value: 1.3e-54
                                       CSEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgiel 69 
                                       +d++viGgG+AG++aa+t++      kv++v +++  + + c l++a++g +   + +               g+e 
  gi|320100832|ref|YP_004176424.1|   5 YDILVIGGGAAGFTAAITAKIlyRDSKVLMVTKTDKSPIV-CALPYAIAGNRPLDDYLMpysyasS------LGVEI 74 
                                       699******************877*******999999999.6666666555554444444754322......47999 PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC..TTBEECCSECHHHHHHCCSS-T..S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv.aenvgklvrtldsaealklkllp..k 143
                                       l + evv+id+++ +v  +      +e+i +d+lv+AtGs+p     +Gv  ++v+ l ++++++ +l+++ ++   
  gi|320100832|ref|YP_004176424.1|  75 LVD-EVVDIDTEE-RVART----RGGEEIRFDNLVIATGSRPEAYMAEGVdLKGVYVLGKEYREVAELREAVNRdgV 145
                                       999.9*******9.77773....45789**********************888888899**************9999 PP

                                       EEEEES-SHHHHHHHHHH......HHHT-E.EEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxx......xxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaal......aklgke.vtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgn 212
                                       r+v vG+G++  ElA al      ++  k+ vt+v +r+ +l r +d+e+++ +e++le++Gv+++ +t+vk+i g+
  gi|320100832|ref|YP_004176424.1| 146 RVVLVGSGLTTAELADALsgipglTDHVKRyVTIVSRRKYILsRYFDEEFAELAERELEAKGVTIYSNTRVKRIHGH 222
                                       *****************74444446666677********************************************** PP

                                       TEEEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TEC CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxx RF
                       Pyr_redox_2 213 gekle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggk 281
                                       g+ +e v+l++ge+++ad vv+     p+tel+  ++gle+ +++givv++++rt+ p iya+GD++       +++
  gi|320100832|ref|YP_004176424.1| 223 GR-VEeVELDNGEVVKADVVVIVPTWVPNTELA-SRAGLEI-RGRGIVVNDYMRTSKPYIYAAGDCVekrdfltSDQ 296
                                       *8.667*****************99********.*******.9************************9999999999 PP

                                       CSS--HHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Pyr_redox_2 282 ggpelaqaAvqqG 294
                                       + ++la+ A +++
  gi|320100832|ref|YP_004176424.1| 297 RDIKLATLACEEA 309
                                       9999998887765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.039        47       2      28 ..       7      35 ..       6      41 .. 0.73
   2 !   54.2   0.1   1.3e-17   1.6e-14       1      79 [.     146     231 ..     146     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.039
                                      EEEECSSHHHHHHHHHHHHTT..SEEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvv 28
                                      ++v+GgG  g  +A +++ l   +kV +v
  gi|320100832|ref|YP_004176424.1|  7 ILVIGGGAAGFTAAITAKILYrdSKVLMV 35
                                      89**********99998765423555555 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 1.3e-17
                                       EEEEECSSHHHHHHHHHH......HHTT.SEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgal......aelg.kkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegs 69 
                                       +vv vG+G++  ElA al      +++    Vt+v r++ +l r++Dee++++ +++le++g++++ nt+v++i+g+
  gi|320100832|ref|YP_004176424.1| 146 RVVLVGSGLTTAELADALsgipglTDHVkRYVTIVSRRKYILsRYFDEEFAELAERELEAKGVTIYSNTRVKRIHGH 222
                                       799***************66666633223689********************************************* PP

                                       TTSEEEEEEE CS
                         Pyr_redox  70 edgvesvklk 79 
                                       ++ ve+v+l 
  gi|320100832|ref|YP_004176424.1| 223 GR-VEEVELD 231
                                       *9.9**9985 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0017         2       1      21 [.       8      28 ..       8      46 .. 0.84
   2 !   26.5   0.0   2.9e-09   3.4e-06     104     305 .]      76     283 ..      53     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl 21
                                      ++iG+G+aG +aai++k +  
  gi|320100832|ref|YP_004176424.1|  8 LVIGGGAAGFTAAITAKILYR 28
                                      69*************996655 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.9e-09
                       Pyr_redox_3 104 Vesvkkedegfevetske..tyeAkkviiAtGefdkPnklnipGeek.....lvkhyskvkefhkya...gqkvvVi 170
                                       V +v   d++ +v  +++  +++ ++++iAtG   +P+    +G +      l k y++v e+++     g +vv +
  gi|320100832|ref|YP_004176424.1|  76 VDEVVDIDTEERVARTRGgeEIRFDNLVIATGS--RPEAYMAEGVDLkgvyvLGKEYREVAELREAVnrdGVRVVLV 150
                                       556666666666665554369***********9..66665555555322222677888887665543122779**** PP

                       Pyr_redox_3 171 GgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke....ekikvlfnaevkeikekee 243
                                       G + + ++ A  l         v r  +i ++    +y l+ +  ++++el ++    + +++++n++vk+i+ + +
  gi|320100832|ref|YP_004176424.1| 151 GSGLTTAELADALSGIPGLTDHVKRYVTIVSR---RKYILSRYFDEEFAELAEReleaKGVTIYSNTRVKRIHGHGR 224
                                       ***************99999999888765555...69**************998898755***************99 PP

                       Pyr_redox_3 244 eykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                         +v+ ++g+ v++ d vv++  + p++++ +++++e+   gr  + ++ + t  p ++ aG
  gi|320100832|ref|YP_004176424.1| 225 VEEVELDNGEVVKA-DVVVIVPTWVPNTELASRAGLEI--RGRGIVVNDYMRTSKPYIYAAG 283
                                       99******988776.6666666699*****99999999..5555566788999999999998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0017       1      33 [.       5      39 ..       5      42 .. 0.85
   2 ?    3.8   0.0     0.016        19     131     165 ..      78     109 ..      64     140 .. 0.64
   3 !    7.2   0.0    0.0015       1.8     115     160 ..     199     243 ..     192     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                      -SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisa..akrgkrVlllekak 33
                                      +d++viGgGaAG+ aAi+a    r+++Vl++ k++
  gi|320100832|ref|YP_004176424.1|  5 YDILVIGGGAAGFTAAITAkiLYRDSKVLMVTKTD 39
                                      589***************96668999999887765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.016
                                       -EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 131 evksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       ev ++  ++++    +t+++ee++ d+lv+AtG+ 
  gi|320100832|ref|YP_004176424.1|  78 EVVDI--DTEE-RVARTRGGEEIRFDNLVIATGSR 109
                                       34445..3333.3445579**************85 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0015
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvl 160
                                        ++el+++gv+++ +t+vk++ + ++++ +v+++++e ++ad +v+
  gi|320100832|ref|YP_004176424.1| 199 AERELEAKGVTIYSNTRVKRI-HGHGRVEEVELDNGEVVKADVVVI 243
                                       5789*****************.55777799*************998 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 !   27.6   0.0   2.3e-09   2.8e-06      11     102 ..     341     435 ..     334     441 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.3e-09
                                       EEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEEC..TTHHHHHHHHHHHHHT CS
                     Pyr_redox_dim  11 vasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivG..pgageliqelavaika 85 
                                       +++ G+ e  A ++gi + vgk++  +   a++ +  ++ vKl++ + +g+++G +  G  ++++e+++ +a+ai+ 
  gi|320100832|ref|YP_004176424.1| 341 MGAAGYIESHALNEGISYIVGKARAVNRHPAWLPGGCEIQVKLLFLE-DGRLIGGQAAGrcNEVAEIVNSIALAIQG 416
                                       6889****************************************998.9**********88899************* PP

                                       TSBHHH..HHTSBSSSSST CS
                     Pyr_redox_dim  86 gltved..ladtihihPtl 102
                                        l ved  +  + + hP l
  gi|320100832|ref|YP_004176424.1| 417 SLRVEDliIGLQHGSHPLL 435
                                       *****63456677777765 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.37   4.4e+02       2      37 ..       9      44 ..       8      55 .. 0.64
   2 !   10.2   0.0   0.00047      0.56     115     155 ..      70     108 ..      63     109 .. 0.85
   3 !   14.8   0.2   1.8e-05     0.021      93     151 ..     184     243 ..     171     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.37
                     NAD_binding_9  2 ivGaGprGlavle..rLlarakkkspleitlfdpsepg 37
                                      ++G+G++G +++   ++l r  +++ l +t  d+s++ 
  gi|320100832|ref|YP_004176424.1|  9 VIGGGAAGFTAAItaKILYR--DSKVLMVTKTDKSPIV 44
                                      89**9999876641144444..4666777777776665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00047
                     NAD_binding_9 115 vtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       + ve++ +evvd++++++    ++++g+++++d++v+A+G 
  gi|320100832|ref|YP_004176424.1|  70 LGVEILVDEVVDIDTEER--VARTRGGEEIRFDNLVIATGS 108
                                       5789999******98865..56899**************95 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.8e-05
                     NAD_binding_9  93 RalyGrYlrdlfeellarlpegvtvevh.raevvdleeradgqavlladgaslaadaVvL 151
                                       + +++rY+++ f+el++r  e   v+++ +++v +++ +++  +v l++g+ ++ad Vv+
  gi|320100832|ref|YP_004176424.1| 184 KYILSRYFDEEFAELAERELEAKGVTIYsNTRVKRIHGHGRVEEVELDNGEVVKADVVVI 243
                                       45789**********9987555667766488**********99***************97 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.2    0.0014       1.6       1      18 [.       6      23 ..       6      45 .. 0.73
   2 !    7.7   0.1     0.002       2.4     155     203 ..      66     109 ..      64     147 .. 0.69
   3 !   14.5   0.4   1.6e-05      0.02     151     198 ..     198     243 ..     192     282 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0014
                                      EEEEECTSHHHHHHHHHH CS
                               DAO  1 dvviiGGGiiGlstAyeL 18
                                      d+++iGGG +G ++A  +
  gi|320100832|ref|YP_004176424.1|  6 DILVIGGGAAGFTAAITA 23
                                      8**************988 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                                       HHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                               DAO 155 aaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                        a +lGveil   ev++++ e     +v   t+ ge+ ++d +V+a+G  
  gi|320100832|ref|YP_004176424.1|  66 YASSLGVEILVD-EVVDIDTE----ERV-ARTRgGEEIRFDNLVIATGSR 109
                                       5889********.*****653....445.4455577644588******44 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEEEEEEEEEE CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgve..rttpgendaadavVn 198
                                          r++ea+Gv+i+ +t+v+++ +  g+v +ve  +   ge+++ad vV+
  gi|320100832|ref|YP_004176424.1| 198 LAERELEAKGVTIYSNTRVKRI-HGHGRVEEVEldN---GEVVKADVVVI 243
                                       44566****************9.5459999995433...88855577554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   2.2e-06    0.0026       1      31 [.       6      38 ..       6      40 .. 0.82
   2 !    6.9   0.0     0.003       3.5      83     140 ..     190     242 ..     143     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAa..raGakvlLveer 31
                                      D++V+GGg+aG++AAi+A+   ++ kvl+v ++
  gi|320100832|ref|YP_004176424.1|  6 DILVIGGGAAGFTAAITAKilYRDSKVLMVTKT 38
                                      9*****************722467788888776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.003
                      FAD_oxidored  83 tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfi 140
                                        f+ e+a +++e  l+ +gvt++ ntr+++++  g r+e+v++ +   +++++A+v++
  gi|320100832|ref|YP_004176424.1| 190 YFDEEFA-ELAERELEAKGVTIYSNTRVKRIHGHG-RVEEVELDN---GEVVKADVVV 242
                                       4555554.5677778888***************98.*******76...8999999875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   6.3e-08   7.5e-05       1      33 [.       6      40 ..       6      48 .. 0.89
   2 ?   -0.2   0.1      0.35   4.2e+02     146     186 ..     198     234 ..     171     257 .. 0.79
   3 ?   -1.8   0.0         1   1.2e+03      84     118 ..     304     338 ..     264     398 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.3e-08
                                      SEEEE--SHHHHHHHHHHHH..TTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaae..aGlkvavvekeqe 33
                                      D++ViG+G+AG +AA++a+   +  kv++v+k+++
  gi|320100832|ref|YP_004176424.1|  6 DILVIGGGAAGFTAAITAKIlyRDSKVLMVTKTDK 40
                                      99****************9766888******9986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.35
                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTC CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgr 186
                                          +++++ gv+++ +t+++++ +  grv  +++    +g+
  gi|320100832|ref|YP_004176424.1| 198 LAERELEAKGVTIYSNTRVKRI-HGHGRVEEVELD---NGE 234
                                       4455666667**********99.778899888877...444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1
                                       HHHHTHHHHHHHHHHTT----BCCTS..SB-EEE-TT CS
                     FAD_binding_2  84 afveaapeavdeLeelgvpfsrtedg..pvdvrelGg 118
                                       + +e+a++a++  +  gv +s  + g  pv v+++Gg
  gi|320100832|ref|YP_004176424.1| 304 LACEEARRAISAIK--GVTLSAGRMGriPVTVTRVGG 338
                                       22222222222222..444444223344455555554 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   2.6e-05     0.031       1      29 [.       6      36 ..       6      52 .. 0.77
   2 !    5.8   0.0    0.0052       6.3     111     150 ..      72     108 ..      65     122 .. 0.82
   3 ?   -1.3   0.0      0.75   8.9e+02     292     327 ..     137     172 ..     118     196 .. 0.74
   4 ?    2.8   0.2     0.043        51      95     146 ..     193     243 ..     149     246 .. 0.81
   5 ?   -1.6   0.1      0.94   1.1e+03     360     375 ..     336     351 ..     306     357 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                                      CEEEE-SSHHHHHHHHHHH..HTT--EEEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaa..rlGakvlLit 29
                                      d+ ViGgG AG+ AA++a+   +  kvl++t
  gi|320100832|ref|YP_004176424.1|  6 DILVIGGGAAGFTAAITAKilYRDSKVLMVT 36
                                      799*************987224577777774 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0052
                                       EEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 111 leiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       +ei+ +ev ++++   + ++ +t+ ge+i+ ++ viatG+
  gi|320100832|ref|YP_004176424.1|  72 VEILVDEVVDIDT---EERVARTRGGEEIRFDNLVIATGS 108
                                       7888899999977...667789*****************9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.75
                                       ESSTT--EEEEET----S-HHHHHHHHTTSTT-TT- CS
                              GIDA 292 pegleteliylvgfstslpeevqkevlrsipGLena 327
                                       +e ++ + + +v + + l++ +  + l+ ipGL + 
  gi|320100832|ref|YP_004176424.1| 137 REAVNRDGVRVVLVGSGLTTAELADALSGIPGLTDH 172
                                       457888888999999999999999999999999875 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-EEEECEEEE CS
                              GIDA  95 elyskevteklenepnleiiee.eveeliveekkvkgvvtedgetikakavvi 146
                                       e++++  +++le+ + ++i ++ +v+++   +++v+ v +++ge++ka++vvi
  gi|320100832|ref|YP_004176424.1| 193 EEFAELAERELEA-KGVTIYSNtRVKRI-HGHGRVEEVELDNGEVVKADVVVI 243
                                       5667777777887.88888765167778.669*****************9987 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 0.94
                                       E-CGGGTB-SHHHHHH CS
                              GIDA 360 lAGqinGteGYeEaaa 375
                                       + G + G  GY+E+ a
  gi|320100832|ref|YP_004176424.1| 336 VGGVVMGAAGYIESHA 351
                                       4567777777777766 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       0.1   1.2e+02     215     261 ..      65     107 ..      42     112 .. 0.79
   2 !   15.2   0.2   8.5e-06      0.01     216     258 ..     198     243 ..     189     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.1
                                       HHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
                     Amino_oxidase 215 alaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                                       + a+ ++g++i+++ +V +i++e+     +++ ge++++D  v+++ 
  gi|320100832|ref|YP_004176424.1|  65 SYAS-SLGVEILVD-EVVDIDTEE--RVARTRGGEEIRFDNLVIATG 107
                                       4445.899999999.899999944..445567*********999875 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.5e-06
                                       HHH...TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE CS
                     Amino_oxidase 216 lae...elrgldirlntrVkeikregdgvtvtledgevveaDaVvv 258
                                       lae   e++g++i  ntrVk+i+ +g    v+l +gevv+aD Vv+
  gi|320100832|ref|YP_004176424.1| 198 LAErelEAKGVTIYSNTRVKRIHGHGRVEEVELDNGEVVKADVVVI 243
                                       444566789**********************************997 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 ?    0.5   0.0      0.22   2.6e+02     191     221 ..       4      34 ..       2      66 .. 0.71
   2 !   13.4   0.0   2.7e-05     0.032     144     226 ..      94     184 ..      76     199 .. 0.73
   3 ?   -1.6   0.0      0.94   1.1e+03     283     334 ..     197     241 ..     182     243 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.22
                       K_oxygenase 191 kkriaVvGsGqSa..aeifedllrrqkkvelkl 221
                                       + +i+V+G+G  +  a i+ ++l r +  ++ +
  gi|320100832|ref|YP_004176424.1|   4 RYDILVIGGGAAGftAAITAKILYRDS--KVLM 34 
                                       568999999988533667777766644..3333 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.7e-05
                       K_oxygenase 144 eeelearnlvlgvGtepkiPevleklegkervvHsseylerkee....llakkriaVvGsGqSaaeifedllrr... 213
                                        ee++  nlv+++G++p+   ++e ++ k   v  +ey e  e     ++++ r++ vGsG ++ae+++ l      
  gi|320100832|ref|YP_004176424.1|  94 GEEIRFDNLVIATGSRPEA-YMAEGVDLKGVYVLGKEYREVAELreavNRDGVRVVLVGSGLTTAELADALSGIpgl 169
                                       56788899******99986.566777777788888888777655667788999**************9998665433 PP

                       K_oxygenase 214 ..qkkvelklvtrse 226
                                           k  +++v+r++
  gi|320100832|ref|YP_004176424.1| 170 tdHVKRYVTIVSRRK 184
                                       212346677777776 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.94
                       K_oxygenase 283 elyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdav 334
                                       el e+++ +++ +++++n++v++++ +g+   e++l+n      e++++d+v
  gi|320100832|ref|YP_004176424.1| 197 ELAEREL-EAKGVTIYSNTRVKRIHGHGR-VEEVELDN-----GEVVKADVV 241
                                       4444554.566799999999999999985.33344443.....455555555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.6   0.00033       0.4       1      34 [.       6      38 ..       6      45 .. 0.79
   2 ?   -0.0   0.0      0.25     3e+02     162     210 ..      65     109 ..      45     115 .. 0.75
   3 !    9.4   0.3   0.00035      0.42     155     204 ..     194     242 ..     187     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00033
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      +i+++GGG aG++aA++ +    ++ +v++v + 
  gi|320100832|ref|YP_004176424.1|  6 DILVIGGGAAGFTAAITAKILY-RDSKVLMVTKT 38
                                      699**********999876666.55788877664 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.25
                                       HHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
                    Trp_halogenase 162 rvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfr 210
                                        +a + Gv+++ ++v  v++d ++rv++ r   g+e+ +d  + ++G r
  gi|320100832|ref|YP_004176424.1|  65 SYASSLGVEILVDEV--VDIDTEERVARTR--GGEEIRFDNLVIATGSR 109
                                       356666*********..6667778888655..59999999888888877 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00035
                                       HHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEE CS
                    Trp_halogenase 155 lyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfi 204
                                       ++a++ +r  ea+Gvt+ + + v  +++ +grve+++l++g++v+ad ++
  gi|320100832|ref|YP_004176424.1| 194 EFAELAERELEAKGVTIYSNTRV-KRIHGHGRVEEVELDNGEVVKADVVV 242
                                       6899999999******9988764.57899******************987 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 ?   12.8   0.1   4.4e-05     0.053      27      56 ..       3      32 ..       1      43 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                                      ---EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                       AlaDh_PNT_C 27 epakvlviGgGvaGlqAiatakglgakVtv 56
                                      ++  +lviGgG aG  A+ tak l  + +v
  gi|320100832|ref|YP_004176424.1|  3 RRYDILVIGGGAAGFTAAITAKILYRDSKV 32
                                      56689*****************99766555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.6     0.009        11       1      30 [.       6      35 ..       6      48 .. 0.67
   2 ?   -1.4   0.0      0.79   9.4e+02     106     143 ..      73     109 ..      31     123 .. 0.64
   3 ?    3.3   0.1     0.028        33      87     136 ..     193     242 ..     167     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.009
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                      D++viG+G+Ag   A        + kv+++
  gi|320100832|ref|YP_004176424.1|  6 DILVIGGGAAGFTAAITAKILYRDSKVLMV 35
                                      9**********9877655333444444444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.79
                     Lycopene_cycl 106 eakvesveeeeageslvvleggrkirarlvvdarglas 143
                                       e  v++v++ +  e+++ + gg++ir    v a+g  +
  gi|320100832|ref|YP_004176424.1|  73 EILVDEVVDIDTEERVARTRGGEEIRFDNLVIATG-SR 109
                                       44466666666667799999999999999999999.33 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.028
                     Lycopene_cycl  87 krlkeellerlvengv.klleakvesveeeeageslvvleggrkirarlvv 136
                                       ++++e  +++l  +gv ++ + +v++++ +      v l++g+ ++a +vv
  gi|320100832|ref|YP_004176424.1| 193 EEFAELAERELEAKGVtIYSNTRVKRIHGHGR-VEEVELDNGEVVKADVVV 242
                                       56666667777755552678899999998877.889***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3211.54
//
Query:       gi|320100833|ref|YP_004176425.1|  [L=369]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-10   38.1  46.9    8.6e-10   38.1  46.9    2.1  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 !   38.1  46.9   4.8e-14   8.6e-10      26     351 ..      33     331 ..       4     333 .. 0.81
   2 !    6.6   3.8   0.00017       3.1     108     165 ..     303     362 ..     296     369 .] 0.87

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 4.8e-14
                             MFS_1  26 dlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagal 102
                                       + g + ++++ll++  +l  +++s+++G+l+d +Grrr+++lg+l+++ + +++ +  ++  l  l ++ G+ ++++
  gi|320100833|ref|YP_004176425.1|  33 EVGPDYAFMSLLVASETL-PGFFSVVGGVLGDMLGRRRMIVLGALSSIPF-IIAGM-GGVRSLPYLILMYGVLTSMA 106
                                       567777888887776665.9******************************.77778.67667888888889999999 PP

                             MFS_1 103 fpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepper 179
                                        p+++  + +++     g+ ++l++++ s+G ++g ++gg++a+sl+++a++ +la++   + + +++ +    p +
  gi|320100833|ref|YP_004176425.1| 107 SPNVYGGLLHYTGS--SGSSYSLIAVAGSIGWAIGGVIGGYMAESLSFTACMTVLAAMVSASYLAVYAAY----PGK 177
                                       9***********97..*********************************999999999888856555555....444 PP

                             MFS_1 180 krkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalv 256
                                        + +++ +             + +     +w l++a++l f+g+ ++++   l l++ l  + +++++++  ++a+ 
  gi|320100833|ref|YP_004176425.1| 178 VTYPGASL------------MEVVDGAGRVWPLFLASVLSFTGVRFFFSNYVLALRSMLTDP-VVYGLVVNTIPAIT 241
                                       44444444............667778888896666666666677776666666679999999.9************* PP

                             MFS_1 257 gailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf.glgfvfpsllalasdlappe 332
                                       ga++ +++gr+sd    r++ lla+++++  a+++a++ +       ++v+vl+ +  + +    l   +s+ +p +
  gi|320100833|ref|YP_004176425.1| 242 GAAIWPIIGRVSDN---RNPVLLAMIAVAEYAVLIAVFLNL---GDPVVVSVLWAIpIYPLLEQGLVISISRKLPGR 312
                                       ************99...788888888888888888888888...55556899**********99999999999999* PP

                             MFS_1 333 eagtasglfntagslggal 351
                                        +  asg+f+t  s++g+ 
  gi|320100833|ref|YP_004176425.1| 313 LQSLASGVFTTSLSVAGFA 331
                                       **************99985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00017
                             MFS_1 108 aliadwfpkeergraigllsagfslGailgpllgglla..sslgWravfyilaivsllaf 165
                                       + i++  p++ +++a g+++++ s++     llg +la   ++gW ++ +++a +sl+++
  gi|320100833|ref|YP_004176425.1| 303 ISISRKLPGRLQSLASGVFTTSLSVAGFAILLLGRVLAdiNAIGWYSISILAASLSLMLA 362
                                       667788899999*************************9767888***********99984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2977.33
//
Query:       gi|320100834|ref|YP_004176426.1|  [L=332]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-28   99.6   0.0      3e-28   99.0   0.0    1.3  1  ABC_tran  ABC transporter
    5.9e-16   59.1   1.1      2e-11   44.2   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.2e-09   37.9   0.0    6.5e-09   36.4   0.0    1.9  1  DUF4162   Domain of unknown function (DUF4162)
    0.00015   21.7   0.0    0.00022   21.2   0.0    1.2  1  Rad17     Rad17 P-loop domain
     0.0014   18.3   0.1     0.0028   17.4   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
     0.0046   16.8   0.0     0.0073   16.1   0.0    1.3  1  MukB      MukB N-terminal
     0.0047   16.7   0.0        2.4    7.8   0.0    2.1  2  AAA_15    AAA ATPase domain
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.034   14.5   0.0    1.5  1  AAA_16    AAA ATPase domain
       0.04   14.3   0.1      0.099   13.1   0.1    1.9  1  AAA       ATPase family associated with various cellular acti
      0.046   13.4   0.1      0.069   12.8   0.1    1.2  1  SRP54     SRP54-type protein, GTPase domain
      0.055   14.0   0.0      0.075   13.5   0.0    1.3  1  AAA_23    AAA domain
      0.099   13.2   0.0        0.2   12.2   0.0    1.6  1  AAA_18    AAA domain
       0.11   12.5   0.1       0.26   11.3   0.1    1.6  1  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts
       0.11   11.4   0.2       0.19   10.7   0.2    1.3  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.12   12.1   0.0       0.34   10.6   0.0    1.7  2  AAA_30    AAA domain
        0.2   11.1   0.0         19    4.6   0.0    2.1  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 !   99.0   0.0   2.7e-31     3e-28       1     136 [.      34     180 ..      34     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 2.7e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       lk vs+k+ +ge+v+++G+nGaGK+t +k+la ll p++G+ +++g ++ + +   +r++igvl+   + +  +lt 
  gi|320100834|ref|YP_004176426.1|  34 LKGVSFKIARGEVVGLLGPNGAGKTTTVKILATLLIPDSGDAWINGYHVVK-NVDDVRRSIGVLFSVeKGFYAKLTG 109
                                       799******************************************999999.9************99678888899* PP

                                       HHH.............HHHTCHHHHHHHSTTGG..TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglke..lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ren             e+d++++++l+ l+l++    d+      +++S G+k r+ larall++p++l+lDEpt
  gi|320100834|ref|YP_004176426.1| 110 RENlryfaalyglhgsEADARVDELLRLLELEKlgASDRL----FEEYSLGMKARLGLARALLRDPPVLILDEPT 180
                                       ******************************9993233444....5*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.4     4e-05     0.045       2      23 ..      47      68 ..      46      88 .. 0.82
   2 !   44.2   0.0   1.8e-14     2e-11     181     299 ..     100     212 ..      92     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +l GpNg+GK++  ++l  l 
  gi|320100834|ref|YP_004176426.1| 47 VGLLGPNGAGKTTTVKILATLL 68
                                      689***************7774 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 1.8e-14
                            AAA_21 181 ekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkk 257
                                       ek++  +l+++ +l+ + +   ++g+e  a+vde+l    +  le+ +  ++ + e S G+k  l+l+ allr++  
  gi|320100834|ref|YP_004176426.1| 100 EKGFYAKLTGRENLRYFAALYGLHGSEADARVDELL---RLLELEKLGASDRLFEEYSLGMKARLGLARALLRDP-- 171
                                       566777777777777777777777777777777776...445555555566666666******************.. PP

                            AAA_21 258 gsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        ++l++DEp +gL+P   r++ +l++e +rng  ++ tTH+ 
  gi|320100834|ref|YP_004176426.1| 172 -PVLILDEPTLGLDPPSARKIRGLVREMARNGKTILYTTHNM 212
                                       .***************************************96 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   5.8e-12   6.5e-09       1      78 [.     234     324 ..     234     327 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 5.8e-12
                                       E-HHHHHTTS.-SSEEEEE..--...-----..--.-EEE..E-TTS-EEEEE-..-.-----------.----EEE CS
                           DUF4162   1 GtleeiKrsy.gknrieve..ad...aeelleepg.veev..eeeggelelkle..d.eeaanellkal.tsgveir 64 
                                       Gt+ e+K+++ gk++i v+  +d   ++++l+e g    v  + e+++l+lkl   + e++a  ll++l ++g+ + 
  gi|320100834|ref|YP_004176426.1| 234 GTPGELKDKIgGKRTIIVKvrGDpslVSAVLRELGfMDAVaeSSEDDGLTLKLLtsSpEDDATMLLRELvRRGIGVS 310
                                       999*******5555555668844456777778888777776433336777777665679**********88****** PP

                                       EEEEE---HHHHHH CS
                           DUF4162  65 sFeeeePsLndIFi 78 
                                       s++ eeP+L+d+F+
  gi|320100834|ref|YP_004176426.1| 311 SLRIEEPTLEDVFM 324
                                       *************9 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.9e-07   0.00022      30     110 ..      29     111 ..      17     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.9e-07
                             Rad17  30 evkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvsl.kepdnqksdfkgltekesrfls 104
                                       +v e+lk  + + ++ +++ + GP G gk+t+vk+L+  l ++    w+n+  + k+ d  +  +  l+ +e+ f +
  gi|320100834|ref|YP_004176426.1|  29 QVIEALKGVSFKIARGEVVGLLGPNGAGKTTTVKILATLLIPDSgDAWINGYHVvKNVDDVRRSIGVLFSVEKGFYA 105
                                       466788999999998899999*******************9976267***987415555555555566666666666 PP

                             Rad17 105 qiesfk 110
                                       ++   +
  gi|320100834|ref|YP_004176426.1| 106 KLTGRE 111
                                       655555 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   0.1   2.5e-06    0.0028      13      50 ..      35      72 ..      28      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.5e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +g +++i + +++ l Gp+G+GK+T +  +++lL+p++
  gi|320100834|ref|YP_004176426.1| 35 KGVSFKIARGEVVGLLGPNGAGKTTTVKILATLLIPDS 72
                                      56788898777999**********************97 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.5e-06    0.0073      27      54 ..      45      72 ..      28     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.5e-06
                                      HHHHHHS--SHHHHHHHHHHHHHHS--T CS
                              MukB 27 lvttlsGgnGaGksttmaafvtaliPdl 54
                                       v  l G nGaGk+tt+  + t liPd 
  gi|320100834|ref|YP_004176426.1| 45 EVVGLLGPNGAGKTTTVKILATLLIPDS 72
                                      578899*********************6 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0022       2.4      25      48 ..      46      69 ..      33      93 .. 0.79
   2 !    6.8   0.0    0.0041       4.6     325     365 ..     172     211 ..     161     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0022
                            AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                                      +  l G+N++GK++ +++l  +l 
  gi|320100834|ref|YP_004176426.1| 46 VVGLLGPNGAGKTTTVKILATLLI 69
                                      66689**************88875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0041
                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +l+++EP + L p   + +  l +e+a+++k  +++tTH+
  gi|320100834|ref|YP_004176426.1| 172 PVLILDEPTLGLDPPSARKIRGLVREMARNGK-TILYTTHN 211
                                       57999**************************9.9******8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.1e-05     0.034      23     143 ..      43     178 ..      29     205 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysa.laqalareellrqllde.... 88 
                                       r+e+v l G+ G GK++ v+ l++ l  d      +g+ +  + d+ +++    + ++   ++ +++++l  +    
  gi|320100834|ref|YP_004176426.1|  43 RGEVVGLLGPNGAGKTTTVKILATLLIPDsgdawiNGYHVVKNVDDVRRS----IgVLFSVEK-GFYAKLTGRenlr 114
                                       448899*****************999888876666333344444444333....334444423.4444444441111 PP

                            AAA_16  89 ............aesaeleawrekleealaavpelagaea..srllellkrllallsrd.erplvlvlDd 143
                                                   a+++  e  r           +l ++++  +     +k+ l l++   ++p vl+lD+
  gi|320100834|ref|YP_004176426.1| 115 yfaalyglhgseADARVDELLRLLE------LEKLGASDRlfEEYSLGMKARLGLARALlRDPPVLILDE 178
                                       2211122111002222222222222......333333333443333333333322222102367777775 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   0.1   8.8e-05     0.099       3      22 ..      49      68 ..      47     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.8e-05
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      l Gp G GKT+++k +a+ l
  gi|320100834|ref|YP_004176426.1| 49 LLGPNGAGKTTTVKILATLL 68
                                      89**************9876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.2e-05     0.069       3      25 ..      46      68 ..      44      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                                      EEEEEESTTSSHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaall 25
                                      v+ l+G++GaGKTtt+  La ll
  gi|320100834|ref|YP_004176426.1| 46 VVGLLGPNGAGKTTTVKILATLL 68
                                      67799************999876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.7e-05     0.075      21      44 ..      46      69 ..      29     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-05
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLy 44
                                      ++ + GpNGaGKTT +  +   L 
  gi|320100834|ref|YP_004176426.1| 46 VVGLLGPNGAGKTTTVKILATLLI 69
                                      66789*********9988887775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017       0.2       1      25 [.      47      79 ..      47     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.........g 25
                                      ++l G+ G+GKtt  k L+ +l +         g
  gi|320100834|ref|YP_004176426.1| 47 VGLLGPNGAGKTTTVKILATLL-IpdsgdawinG 79
                                      6899**************9997.44556664552 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   0.1   0.00024      0.26      10      42 ..      37      67 ..      24      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                      HHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE 10 lgkklakalgdvilLeGdLGaGKTtlvrglaka 42
                                      +  k+a+  g+v+ L G+ GaGKTt v+ la  
  gi|320100834|ref|YP_004176426.1| 37 VSFKIAR--GEVVGLLGPNGAGKTTTVKILATL 67
                                      3334444..899****************99875 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 ?   10.7   0.2   0.00017      0.19      18      54 ..      33      69 ..      20      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                      HHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                              MeaB 18 llerllakaGraqvvGltGvPGaGkstlvealglelr 54
                                       l+ ++ k  r +vvGl G  GaGk t+v+ l++ l+
  gi|320100834|ref|YP_004176426.1| 33 ALKGVSFKIARGEVVGLLGPNGAGKTTTVKILATLLI 69
                                      56677788899*******************9998886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0003      0.34      19      42 ..      45      68 ..      37      97 .. 0.84
   2 ?   -2.1   0.0       2.3   2.6e+03      82     117 ..     164     203 ..     120     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                            AAA_30 19 rvavltGpAGtGKttalkalreaw 42
                                       v+ l Gp G+GKtt++k l+ ++
  gi|320100834|ref|YP_004176426.1| 45 EVVGLLGPNGAGKTTTVKILATLL 68
                                      488999************998765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                            AAA_30  82 grarlepgtllivDEagmv....dtkqlaallkaaekaga 117
                                       +ra l++  +li DE  +     ++++++ l+++++++g 
  gi|320100834|ref|YP_004176426.1| 164 ARALLRDPPVLILDEPTLGldppSARKIRGLVREMARNGK 203
                                       4455556678888887776666677777777777776444 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 ?    4.6   0.0     0.017        19      26      41 ..      46      61 ..      33      68 .. 0.81
   2 ?    4.1   0.0     0.023        26     150     203 ..     162     214 ..     151     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.017
                                      EEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnll 41
                                      +  ++GpNG+GK+  +
  gi|320100834|ref|YP_004176426.1| 46 VVGLLGPNGAGKTTTV 61
                                      56789*******9765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.023
                                       HHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 150 lfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                        +A    +  p+ +lDe    LD    +k+  l++e   n   i  + + +m+e
  gi|320100834|ref|YP_004176426.1| 162 GLARALLRDPPVLILDEPTLGLDPPSARKIRGLVREMARNGKTILYTTH-NMFE 214
                                       5666777889****************************99998887754.4554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2398.82
//
Query:       gi|320100835|ref|YP_004176427.1|  [L=270]
Description: ABC transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1965.11
//
Query:       gi|320100836|ref|YP_004176428.1|  [L=266]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   20.6  26.0     0.0005   19.6  26.0    1.5  1  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
        1.3    8.1  27.7      0.079   12.1  21.5    1.8  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6  26.0   5.5e-08    0.0005      31     209 ..      23     217 ..       9     218 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.5e-08
                     ABC2_membrane  31 llalvfgtvfgn..lgnsedglnr.....................pgllffsvlflafsaltsvapvferergvler 84 
                                       +++ ++g+  ++           +                     + + +fs  ++a+   ++  + ++ + gvle+
  gi|320100836|ref|YP_004176428.1|  23 FWISLLGFTLWGflF--------IgpvvlfspssmprslvagyalVAMTVFSSYMTATWDWSGH-LRWMLRSGVLEH 90 
                                       444444444443220........12222223333333455532334444444444443344455.99********** PP

                     ABC2_membrane  85 elvsplyslsayvlakvlvelpvsllqal...ifllivyflvgldlsrfflflllllltalaasslgllisalapsf 158
                                        lv++  s  +y+++ + v+l++ ++++    ++l++ y   g+++   +l+++ l+++++++++ +l+i+a +   
  gi|320100836|ref|YP_004176428.1|  91 ALVAGR-SIYVYFMGLLPVSLMWLMIEVGeiyLLLTVLYAQPGFNIADPVLLVASLIMLLVVLVAHSLIIGASVLAS 166
                                       ******.**********999999999875211444455555699998445555555555555555555555555556 PP

                     ABC2_membrane 159 edasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                        + s+++ l+  ++ + sG + p+ smp  +q +a + P++y  e+lr++l
  gi|320100836|ref|YP_004176428.1| 167 GTSSIVTELISWLIPIASGGMTPLASMPPQVQTLALMTPYSYPAELLRYSL 217
                                       789999999999999************77*******************987 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   2.6     0.084   7.5e+02     236     284 ..      21      69 ..       6      81 .. 0.56
   2 ?   12.1  21.5   8.8e-06     0.079     176     343 ..      65     244 ..      52     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.084
                   ABC2_membrane_3 236 gnlglllllfllfglayialgyll..sslfknsetaqilifivilllsgff 284
                                        ++++ ll f l g+++i  + l+  ss+ ++ +++++l+ ++++ +s ++
  gi|320100836|ref|YP_004176428.1|  21 HGFWISLLGFTLWGFLFIGPVVLFspSSMPRSLVAGYALV-AMTV-FSSYM 69 
                                       4666666666666666665555552334444444444432.2222.44444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.8e-06
                   ABC2_membrane_3 176 asfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill.l.afgl............gipfgnl 238
                                       +s  +++ ++   s+ +  +l sgv   +++ ++ + +++++ll++ l+ l + +               g+++ + 
  gi|320100836|ref|YP_004176428.1|  65 FS--SYMTATWDWSGHLRWMLRSGVLEHALVAGRSIYVYFMGLLPVSLMWLmIeVG-EiyllltvlyaqpGFNIADP 138
                                       33..334566667777889999***********************97754424422.2244456688889999999* PP

                   ABC2_membrane_3 239 glllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllr 315
                                       +ll+  +++ + +++a ++ +++ +  s+t +i++ ++++l+ +++gg+ pl ++p  +++++ + P ++p+++l  
  gi|320100836|ref|YP_004176428.1| 139 VLLVASLIMLLVVLVAHSLIIGASVLASGTSSIVTELISWLIPIASGGMTPLASMPPQVQTLALMTPYSYPAELLRY 215
                                       ***************************************************************************88 PP

                   ABC2_membrane_3 316 litgd.plweillsliilalfavvyllla 343
                                        + g+     ++  l++  l a +yl++a
  gi|320100836|ref|YP_004176428.1| 216 SLLGApMVLHTGDVLLYGSLYASLYLAAA 244
                                       88888334446666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1836.42
//
Query:       gi|320100837|ref|YP_004176429.1|  [L=116]
Description: AhpD family alkylhydroperoxidase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-18   64.1   0.1    1.3e-17   63.6   0.1    1.2  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.1   7.3e-22   1.3e-17      10      82 ..      30     101 ..      22     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 7.3e-22
                                       HHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHH CS
                               CMD  10 lreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaa 82 
                                       + + + + +  Ld+k++eLi+l++++a +ce C+  Ht aAl+aG++ +ei +v+ +a+ ++g+pa+++A +a
  gi|320100837|ref|YP_004176429.1|  30 YIQEAES-PAVLDAKTKELISLGIAIAVRCEPCIIWHTDAALKAGASLNEILDVIKVAVCMGGGPALMYASKA 101
                                       3333434.888**********************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 829.16
//
Query:       gi|320100838|ref|YP_004176430.1|  [L=141]
Description: putative signal transduction protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-34  115.9   4.2      4e-18   65.6   0.4    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.3   3.8e-18   6.8e-14       1      56 [.      14      69 ..      14      70 .. 0.92
   2 !   65.6   0.4   2.2e-22     4e-18       1      56 [.      79     134 ..      79     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.8e-18
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      ++dim+++++t+++++++e+a++lm e++ s++ VV++dg l Givt +D++ a++
  gi|320100838|ref|YP_004176430.1| 14 ISDIMSTPPITIKETEPVEKAAKLMFENNTSSVIVVNNDGVLTGIVTAKDVVAAVA 69
                                      58**********************6699999**999*9**888********99875 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 2.2e-22
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       Vg +m ++++t++pd+++ +ale+mre +v++lPVVd+d++++G+v+ rD++++ll
  gi|320100838|ref|YP_004176430.1|  79 VGRFMKENPLTISPDASITDALEKMREFNVRHLPVVDKDNRPIGMVSVRDIMDVLL 134
                                       899*************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1080.98
//
Query:       gi|320100839|ref|YP_004176431.1|  [L=169]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-31  106.8   0.0    1.2e-30  106.2   0.0    1.2  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 !  106.2   0.0   6.5e-35   1.2e-30      10     114 ..      27     137 ..      21     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 6.5e-35
                                       -.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-..SS--E-TT-........SS-E.EGGGS--S-SSS CS
                              TrmO  10 eeaeaeielepeynseealegleefshlwllfvfhenaekk.lkakvrpprl.......ggnervGvfatRsphRpn 78 
                                       +++++ ie+ pey  +++l+gle+fsh++++ ++h+   ++  + +v+p+rl       ++  +vGvfat sphRpn
  gi|320100839|ref|YP_004176431.1|  27 SSVRGYIEVLPEY--SQGLRGLEGFSHVIIIAYLHKVPYEArSTLLVKPRRLvtlglkpEELPEVGVFATDSPHRPN 101
                                       5689*********..********************983333123444444444444433445789************ PP

                                       -EEEEEEEEEEEETTEEEEES----TT-EEEEEEE- CS
                              TrmO  79 piglsvvklekvegnvlevsgvDlldgtpvlDiKPY 114
                                       pi+l++v+lek+e+++l+v+g+Dl dgtpvlDiKPY
  gi|320100839|ref|YP_004176431.1| 102 PIALTIVELEKIEEDRLYVRGLDLYDGTPVLDIKPY 137
                                       ************************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1243.22
//
Query:       gi|320100840|ref|YP_004176432.1|  [L=246]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1846.24
//
Query:       gi|320100841|ref|YP_004176433.1|  [L=321]
Description: NAD-dependent epimerase/dehydratase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-52  178.6   0.1    1.4e-52  178.6   0.1    1.5  2  Epimerase        NAD dependent epimerase/dehydratase family
    4.5e-51  174.2   0.0    5.7e-51  173.9   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      3e-20   72.5   0.0    1.5e-19   70.2   0.0    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.6e-19   69.3   0.1    3.1e-19   69.1   0.1    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.8e-17   61.7   0.0    7.1e-17   61.4   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    2.1e-11   43.5   0.1    3.3e-07   29.7   0.0    2.6  2  NAD_binding_4    Male sterility protein
    1.4e-09   38.1   0.0      2e-09   37.6   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
     0.0067   16.0   0.1      0.027   14.0   0.1    1.8  2  NmrA             NmrA-like family
  ------ inclusion threshold ------
       0.12   12.3   0.3       0.24   11.3   0.2    1.7  1  KR               KR domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6   0.1   6.9e-56   1.4e-52       2     241 .]       5     243 ..       4     243 .. 0.94
   2 ?   -2.3   0.2       1.3   2.5e+03     210     223 ..     245     258 ..     244     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 6.9e-56
                                       EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihl 71 
                                       +VtG++GfiGs+lv++l e+    evi +d+lss+s  + + +l     +lve+dl  + ++ ++f+  ++d+v+h 
  gi|320100841|ref|YP_004176433.1|   5 IVTGGAGFIGSHLVDYLVERLraEEVIIIDNLSSGSLVNIKGHLekgvaRLVEADLVREGEWVKAFR--DVDIVFHY 79 
                                       7******************999677*******999999999999***********************..89****** PP

                                       -S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHH CS
                         Epimerase  72 AavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKla 148
                                       Aa   v++s  +p   +++n++ t n+lea+r ++vk ++f+sSs+vYG++  +p+ e+    plkp s Y+a+Kla
  gi|320100841|ref|YP_004176433.1|  80 AANPEVRVSTVEPRIHFDNNVVATFNVLEAMRVSDVKGIVFASSSTVYGEPSVIPTPEDH---PLKPISVYGASKLA 153
                                       *******************************************************99999...************** PP

                                       HHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHH CS
                         Epimerase 149 geklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillv 225
                                       +e l++ay + yg++a+ilr+ n++G+r    ++++vi  +i+k+ +    + +lgdgt++  +l+v+D++ea +++
  gi|320100841|ref|YP_004176433.1| 154 SEALIQAYCELYGFKALILRYANIIGAR----SNHGVIVDFINKLRADPSRLEILGDGTQRKSYLHVSDAVEATMHL 226
                                       ****************************....***************999***********************7776 PP

                                       HHH.HTT-STTEEEEES CS
                         Epimerase 226 leh.vdagdkgeiyniG 241
                                       ++    a +  e+yniG
  gi|320100841|ref|YP_004176433.1| 227 VASrLGAARGAEVYNIG 243
                                       666044444466***99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                                       EEEEEHHHHHHHHH CS
                         Epimerase 210 RdflyveDvaeail 223
                                       Rd++ v ++a++++
  gi|320100841|ref|YP_004176433.1| 245 RDWVTVTEIADIVV 258
                                       9*********9986 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 !  173.9   0.0   2.9e-54   5.7e-51       1     331 [.       5     311 ..       5     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 2.9e-54
                                       EEETTTSHHHHHHHHHHHHC..T-CCEEEEEEESS-TTHHHH.HCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlek..gyevhgivrrsssfntgrie.hlakdpkeeleenlklhkgDltDssslerllaev 74 
                                       ++TG+aGfiGs+l+++L+e+    ev++i+++ss  ++ +i+ hl+       ++  +l+++Dl  + +  +++++v
  gi|320100841|ref|YP_004176433.1|   5 IVTGGAGFIGSHLVDYLVERlrAEEVIIIDNLSSG-SLVNIKgHLE-------KGVARLVEADLVREGEWVKAFRDV 73 
                                       59*****************8645677766666655.5445541554.......34679******************9 PP

                                       T-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----S CS
                     GDP_Man_Dehyd  75 qpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrs 151
                                         d v++ AA   V+vs  +P   +++nv++t+++Lea+r   ++    +++aS+s+vYG+++ +p  E++p++P s
  gi|320100841|ref|YP_004176433.1|  74 --DIVFHYAANPEVRVSTVEPRIHFDNNVVATFNVLEAMRVSDVK---GIVFASSSTVYGEPSVIPTPEDHPLKPIS 145
                                       ..89************************************98875...6889************************* PP

                                       HHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHH CS
                     GDP_Man_Dehyd 152 PYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkD 228
                                        Y+a+Kl+++ ++++y e yg+ a++ ++ n  + r  ++     i++++ +  ++     +lG++ ++++++hv+D
  gi|320100841|ref|YP_004176433.1| 146 VYGASKLASEALIQAYCELYGFKALILRYANIIGARS-NH---GVIVDFINKLRADPSRLEILGDGTQRKSYLHVSD 218
                                       ************************************5.44...569**********9999999************** PP

                                       HHHH.HHHHHHC....SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--S CS
                     GDP_Man_Dehyd 229 yvea.mwlmlqq....dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrp 300
                                        vea m+l+  +      +e y+i++ + ++v e++++ + e+g +          v+ +     ++ ++   +  p
  gi|320100841|ref|YP_004176433.1| 219 AVEAtMHLVASRlgaaRGAEVYNIGNRDWVTVTEIADIVVDEMGLKS---------VEYV----FKR-TTPDGRGWP 281
                                       ***95555554432223345566666666666666666666666532.........2221....222.33335566* PP

                                       S--SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 301 gevdlllgdaskakeeLgWkpkvsfeelvre 331
                                       g+v+l+l d+++++  LgW+pk s ++ vr+
  gi|320100841|ref|YP_004176433.1| 282 GDVKLMLLDTKRLE-SLGWRPKLSSRDAVRK 311
                                       *********99998.9********9999986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.0   7.7e-23   1.5e-19       2     251 ..       5     265 ..       4     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 7.7e-23
                                       EEETTTSHHHHHHHHHHHHH.B-SEEEEEES.-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkk.kpkkiiller.dElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                       +vtG++G iGs+lv+ ++++ +++++i++++ +  +l +i+ +le+ +++  l ve     +d+  + +  ka++  
  gi|320100841|ref|YP_004176433.1|   5 IVTGGAGFIGSHLVDYLVERlRAEEVIIIDNlSSGSLVNIKGHLEKGVAR--L-VE-----ADLVREGEWVKAFR-- 71 
                                       79****************99899999999973667999****99655554..4.34.....78888888889999.. PP

                                       T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE..............GGGSS--SHHH CS
                   Polysacc_synt_2  77 kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt..............DKAvnPtnvmG 139
                                       +vd+vfh AA  +V +   +p   +++Nv++t nv+ea   ++vk +v+ S+              D   +P++v+G
  gi|320100841|ref|YP_004176433.1|  72 DVDIVFHYAANPEVRVSTVEPRIHFDNNVVATFNVLEAMRVSDVKGIVFASSstvygepsviptpeDHPLKPISVYG 148
                                       9***********************************************9986456666666666779999******* PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTT.SSEEES-TT-EE.EEE-HHHHHH. CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeg.gpvtvTdpemtR.yfmtieeavq. 211
                                       a+K+++e l+qa+ +       k ++ R+ N++g  S+  vi  F ++++++ + + +      R  ++ +++av+ 
  gi|320100841|ref|YP_004176433.1| 149 ASKLASEALIQAYCELY---GFKALILRYANIIGarSNHGVIVDFINKLRADpSRLEILGDGTQRkSYLHVSDAVEa 222
                                       *************9999...8999*********93344568888888888887999987665555368889988753 PP

                                       ...HHHHHHHH--SS-EEEE--.-EEEHHHHHHHH........ CS
                   Polysacc_synt_2 212 ...LvlqalalakggeifvldmGepvkivdlakalielsglee 251
                                          Lv + l  a+g e++     + v+++++a  +++ +gl++
  gi|320100841|ref|YP_004176433.1| 223 tmhLVASRLGAARGAEVYNIGNRDWVTVTEIADIVVDEMGLKS 265
                                       3337888888999999998888899*******99999888765 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 !   69.1   0.1   1.5e-22   3.1e-19       1     230 [.       5     230 ..       5     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.5e-22
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskv..nvkkviegDvtdkdkleealegvdvvihlas 75 
                                       +vtGgaGF+G++lv  Lv++ +++ev ++D   s +l +   ++  +v+ ++e+D+  + +  +a ++vd+v+h a+
  gi|320100841|ref|YP_004176433.1|   5 IVTGGAGFIGSHLVDYLVERLRAEEVIIIDNLSSGSLVNIKGHLekGVARLVEADLVREGEWVKAFRDVDIVFHYAA 81 
                                       69****************************88888887765544116777*************************** PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                         +v+  +++     + nv  T nvlea + ++v+ +v+ Ss  v g+      ++   E+  ++ ++ ++y  sK 
  gi|320100841|ref|YP_004176433.1|  82 NPEVRVsTVEPRIHFDNNVVATFNVLEAMRVSDVKGIVFASSSTVYGE----PSVIPTPED--HPLKPISVYGASKL 152
                                       **999835555666899*****************************99....667767776..5667899******* PP

                         3Beta_HSD 152 laEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNv..awa 224
                                        +E+l+ +  +  l  g  +    LR a i G +++  ++v ++++l      l  +gd  + +++  v     a +
  gi|320100841|ref|YP_004176433.1| 153 ASEALIQAYCE--L-YG--FKALILRYANIIGARSNhgVIVDFINKLRADPSRLEILGDGTQRKSYLHVSDAveATM 224
                                       ******98877..3.33..6777899999999887633577888888888888888888888888888876524567 PP

                         3Beta_HSD 225 hilAar 230
                                       h++A+r
  gi|320100841|ref|YP_004176433.1| 225 HLVASR 230
                                       877776 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 !   61.4   0.0   3.6e-20   7.1e-17       2     249 ..       3     277 ..       2     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 3.6e-20
                                       EEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEE CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlae..eglevlaltre....................eldltdaeavaellkeakpdvvv 56 
                                       + +vtG+ G +Gs+L++ l e  +  ev+ +++                     e+dl ++ +  +++++   d+v 
  gi|320100841|ref|YP_004176433.1|   3 RFIVTGGAGFIGSHLVDYLVErlRAEEVIIIDNLssgslvnikghlekgvarlvEADLVREGEWVKAFRD--VDIVF 77 
                                       6789***********9988874445567776554689***9********999999999999999999999..899** PP

                                       E------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHH CS
                     RmlD_sub_bind  57 naAAytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaG 132
                                       + AA  +v     e++  +  n+ a+ ++ ea +  +++ +++ S+  V+      p  ed++ +P++vYG++Kla 
  gi|320100841|ref|YP_004176433.1|  78 HYAANPEVRVSTVEPRIHFDNNVVATFNVLEAMRVSDVKgIVFASSSTVYGEPSVIPTPEDHPLKPISVYGASKLAS 154
                                       ***********************************9997699********9999999******************** PP

                                       HHHHHHH-S....SEEEEEE-SEESSSSS-..HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCH CS
                     RmlD_sub_bind 133 Eqavlaagk....kalivRtswvygekgkn..fvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaa 201
                                       E  ++a+++    kali+R + + g++ +    v  + +l ++  +l++  D  q  s  ++ d  e++++l++ ++
  gi|320100841|ref|YP_004176433.1| 155 EALIQAYCElygfKALILRYANIIGARSNHgvIVDFINKLRADPSRLEILGDgtQRKSYLHVSDAVEATMHLVASRL 231
                                       ******66545559**********99544322667788888**********95566667789*************** PP

                                       H.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--S CS
                     RmlD_sub_bind 202 eekelagvyHlanegetswlefArailkeagadseevkpistaeyptp 249
                                        +++ a+vy ++n++ ++  e+A+ +++e+g +s  v+ + +   p+ 
  gi|320100841|ref|YP_004176433.1| 232 GAARGAEVYNIGNRDWVTVTEIADIVVDEMGLKS--VEYVFKRTTPDG 277
                                       98888*************************9955..665555555555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0     9e-05      0.18       1      22 [.       6      27 ..       6      39 .. 0.85
   2 !   29.7   0.0   1.7e-10   3.3e-07      80     216 ..      65     188 ..      61     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                                      EE-TTSHHHHHHHHHHHHHS-. CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpe 22
                                      +TG+ GF+G++L+  L+++ ++
  gi|320100841|ref|YP_004176433.1|  6 VTGGAGFIGSHLVDYLVERLRA 27
                                      7***************988764 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.7e-10
                                       HHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H CS
                     NAD_binding_4  80 dlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvye 153
                                       ++ +  + vd+++h aA+ ++  ++ e    ++ Nv +t +vle  + ++  k +++ S+++v+ge +         
  gi|320100841|ref|YP_004176433.1|  65 EWVKAFRDVDIVFHYAANPEVRVSTVEpriHFDNNVVATFNVLEAMR-VSDVKGIVFASSSTVYGEPS-V------- 132
                                       66677899*********9777665544333789***********777.66666**************9.3....... PP

                                       ......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST--- CS
                     NAD_binding_4 154 egekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwin 216
                                                 + +++  +    Y  sK ++E l++++ +  g++++i+R  +i+g +s  G+i 
  gi|320100841|ref|YP_004176433.1| 133 --------IPTPEDHPLKPISVYGASKLASEALIQAYCELYGFKALILRYANIIGaRSNHGVIV 188
                                       ........34566777788899****************************99999677778765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0     1e-12     2e-09       1     144 [.       8     175 ..       8     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1e-12
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH......HHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---T CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla......eleaeeglevvegdvtdvedlaealkgadaVvsalggg 71 
                                       G+ G +G++lv+ l++r   e ++++ n ++ +      +l ++  +++ve+d+  + +  +a++++d+V+  +++ 
  gi|320100841|ref|YP_004176433.1|   8 GGAGFIGSHLVDYLVERLRAEEVIIIDNLSSGSlvnikgHL-EKGVARLVEADLVREGEWVKAFRDVDIVFHYAANP 83 
                                       99***************99999999***8877633333333.468899***********************999877 PP

                                       CC.....HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHH...CCHHHHHHHHHHHHH CS
                    NAD_binding_10  72 gk.....deeg..........aknivdaakeagvkRfvlvsaigvgdevpgefgewnke...llkaylaakraaeel 130
                                       +      +             + n+++a++ ++vk +v+ s+  v+ e p+  ++  ++    ++ y a k a+e+l
  gi|320100841|ref|YP_004176433.1|  84 EVrvstvE--PrihfdnnvvaTFNVLEAMRVSDVKGIVFASSSTVYGE-PSVIPTPEDHplkPISVYGASKLASEAL 157
                                       77655551..04455555699************************964.5555555555111444455788888888 PP

                                       HHH....SSSEEEEEEE- CS
                    NAD_binding_10 131 lra....sgldwTivrpg 144
                                       ++a     g++  i+r +
  gi|320100841|ref|YP_004176433.1| 158 IQAycelYGFKALILRYA 175
                                       887655556666666655 PP

>> NmrA  NmrA-like 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     0.027       2      73 ..       5      81 ..       4     109 .. 0.79
   2 ?   -0.5   0.0      0.38   7.6e+02     163     232 ..     197     269 ..     181     270 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                      EESSTTSHHHHHHHHHHHH.HT-EEEEEES-S...-SHHHHHHHHSTT.EEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  2 lviGaTGrqGksvvrallk.aghkvralvRdt...kselakslkeaGv.elvkgdlddkeslvealkgvdvvfsvtg 73
                                      +v+G++G +G+++v++l++    +  +++ ++   +  ++k   e+Gv  lv++dl  +   v+a+++vd vf   +
  gi|320100841|ref|YP_004176433.1|  5 IVTGGAGFIGSHLVDYLVErLRAEEVIIIDNLssgSLVNIKGHLEKGVaRLVEADLVREGEWVKAFRDVDIVFHYAA 81
                                      69*****************544555556666655544555555566761677*********************8766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.38
                                       TS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHH.HHHHTTEEEEE..-SEEE-HHHHHHHHHHHHT.S-EEEE CS
                              NmrA 163 pedkvtllgpgnpkavlldaeeDiGafvikilkd.prklkgkrikl..agntlsgneivelfekkig.ktvkYt 232
                                       +   +++lg+g     +l ++ D  +++++++     ++ g  +      + ++++ei+++   ++g k+v+Y+
  gi|320100841|ref|YP_004176433.1| 197 DPSRLEILGDGTQRKSYL-HVSDAVEATMHLVASrLGAARGAEVYNigNRDWVTVTEIADIVVDEMGlKSVEYV 269
                                       444688999999888888.8889888888888773344455444431145679999999999988885568886 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00012      0.24       3      31 ..       4      33 ..       2     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                      EEEETTTSHHHHHHHHHHHHHH.S-EEEEE CS
                                KR  3 ylitGGlGgLGlelarwlaekg.arhlvll 31
                                      +++tGG+G +G +l++ l+e+  a++++++
  gi|320100841|ref|YP_004176433.1|  4 FIVTGGAGFIGSHLVDYLVERLrAEEVIII 33
                                      79******************9867777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2208.72
//
Query:       gi|320100842|ref|YP_004176434.1|  [L=405]
Description: cysteine synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-41  141.9   0.0    6.2e-41  140.7   0.0    1.6  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 !  140.7   0.0   3.5e-45   6.2e-41       7     292 ..     105     373 ..     101     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 3.5e-45
                                       S--EEEECCTCCCCCCEEEEEEGGGST.TSBTTHHHHHHHHHH..HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   7 pTPlvrlprlskelgvplflKlEslnp.tgSfKdRgaeyllar..lkegtgaktvveassGNhgralAaaaallGlk 80 
                                       pTPlv+l++ls +  v++++KlE+ +p + S+KdR a y+l+r  ++e    + + eass N+g+al   ++  G+k
  gi|320100842|ref|YP_004176434.1| 105 PTPLVKLKSLS-RGDVRVWAKLEWYHPfSLSIKDRVAWYMLHRllEEE-GNPRKLYEASSTNTGMALVGLGNYHGVK 179
                                       9*********9.55677*********99***************84444.59************************** PP

                                       EEEEEETTS-HHHHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHH... CS
                              PALP  81 vtivvpadaspekvallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEil... 151
                                       v++++p++a        +++Gae ++   + +     ++  e+ +  +ga++++qf+n ++++     ++ E     
  gi|320100842|ref|YP_004176434.1| 180 VRVYLPSTAQRCVDYVFQAMGAEARREstPITIGMLNKVLIEASR--DGAIVLNQFENDYNFLVhLRYTAKEADyql 254
                                       ***********99********988776335556666666445555..5*************************8444 PP

                                       HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTC CS
                              PALP 152 eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspsel 228
                                         +g +p avv+++G+ g ++++++++k+r + v+ igv+p++ +++ + +                 +++g   ++
  gi|320100842|ref|YP_004176434.1| 255 MSMGVRPSAVVAGLGTSGHFSALSFYFKHRYGRVKTIGVQPAQGSSIPGLR----------------RIETG---VK 312
                                       5556**************************************888888888................34444...44 PP

                                       CHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE CS
                              PALP 229 afelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvvil 292
                                        +  +    de+v v+ eeal+++ ++ar +gi+++ ss+a+  al kl+e g+l+++  v+v++
  gi|320100842|ref|YP_004176434.1| 313 WL--HSVEADEVVDVTLEEALKGVLHVARGDGIMPGFSSGAVAYALmKLVENGSLSGD--VIVVF 373
                                       44..4456789999***********************6666666666***********..66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2978.34
//
Query:       gi|320100843|ref|YP_004176435.1|  [L=373]
Description: MgtE integral membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-24   86.0  25.8    8.7e-13   48.7   3.3    3.0  3  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   7.9   1.2e-16   2.1e-12       1     123 [.      35     164 ..      35     165 .. 0.81
   2 ?    0.1   0.9     0.056     1e+03      52      66 ..     176     190 ..     161     235 .. 0.43
   3 !   48.7   3.3   4.9e-17   8.7e-13       2     121 ..     244     362 ..     243     365 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.2e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekk.lkkvllkelrvvlllgvilgllifllalllgwslllalvvglalv 76 
                                       iP +++l+G ++     r++talhlge+e++ + ++ l +++++ ++++i++l +++l  +l+  + +a++  ++l+
  gi|320100843|ref|YP_004176435.1|  35 IPGLMDLRGDVYGAIGYRLTTALHLGEVEPRfFTRFNLFNTLTGYVVSLIVSLELSILGAVLSYVFNMAMMDPVSLL 111
                                       799****************************9999999999999999999777777776666666666666666666 PP

                                       HHHHHHHHH........HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  77 lvllaaall......ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       ++++a++++       + ++ ++ l+k+g+DP  +++ ++t +gD l+ + l+
  gi|320100843|ref|YP_004176435.1| 112 FAVTASTIIvfailnPVVTASTITLFKKGVDPSGFVAVVVTGVGDALTPFTLL 164
                                       66666666655545533455557************************988875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHT-.CT CS
                              MgtE  52 llifllalllgwsll 66 
                                       l+ +++++ +  s+ 
  gi|320100843|ref|YP_004176435.1| 176 LVKAVFVVAVVASIG 190
                                       222222222111111 PP

  == domain 3  score: 48.7 bits;  conditional E-value: 4.9e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHT.TSS-GG.HHHHHHHHHHHHHHHHHH.HHHHHHHH.HHHHT-.CTSHHHHHHH CS
                              MgtE   2 PvilglgGnlgaqlasristalhl.gelekk.lkkvllkelrvvlllgvi.lgllifll.alllgwslllalvvgla 74 
                                       P++++l G+        +   lh+ g l+++ +++ +l e+++ ++  +   ++++++    +   ++  ++vv+l+
  gi|320100843|ref|YP_004176435.1| 244 PAFNALIGASMGHIGNIMNIELHIrGRLSHReYRRRILVEAAATFTSVLAaYVVVLASGsGST---WASSLMVVSLS 317
                                       8889999999999999999999*9568877776555555555544333330333333331223...3568889**** PP

                                       HHHHHHHHHHH..HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHH CS
                              MgtE  75 lvlvllaaallilgvllplllwklglDPdnaaiPlltalgDllgtll 121
                                       +++v++++a+   +++l+l ++k g+DPdn++ Pl+t+++D+ g l+
  gi|320100843|ref|YP_004176435.1| 318 FIIVYFLSAFT--TMYLTLESFKHGWDPDNIVFPLMTTFADFNGYLV 362
                                       ***********..*****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2683.95
//
Query:       gi|320100844|ref|YP_004176436.1|  [L=401]
Description: PhoU family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-07   29.8   1.6     0.0041   17.5   0.2    2.4  2  PhoU      PhoU domain
    3.1e-05   23.7   0.0     0.0035   17.1   0.0    2.4  2  TrkA_C    TrkA-C domain
     0.0083   15.5   1.4      0.048   13.0   0.4    2.5  3  PhoU_div  Protein of unknown function DUF47


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 !   11.2   0.1   6.6e-05       0.4      12      53 ..      43      84 ..      37     114 .. 0.81
   2 !   17.5   0.2   6.9e-07    0.0041       2      87 ..     223     303 ..     222     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.6e-05
                                      HHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU 12 lddalealeekdtelarevierddeidrlekeierslleala 53
                                      ld+a  a+++kd e+a++v++  + id+   +++ +   a++
  gi|320100844|ref|YP_004176436.1| 43 LDLAFYAYFSKDSEAAERVLDINKIIDENLAQFIMHTSLAYG 84
                                      78999**********************998888777555554 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 6.9e-07
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                        +++++++ m+d+a   l e d   ++ev +++  id  + +  ++l e  +k      d ++ ++l  + ++lE i
  gi|320100844|ref|YP_004176436.1| 223 IELKDYTRLMIDLAHYTLLEADPGVIEEVEDLEVYIDWRQLDTLNKLKEVSGKI-----DPDTFIGLSILLKELEDI 294
                                       6899***********************************999999954444444.....4567899*********** PP

                                       HHHHHHHHH CS
                              PhoU  79 gDhavniae 87 
                                       +D +  i+ 
  gi|320100844|ref|YP_004176436.1| 295 ADASNTISH 303
                                       ***999975 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.9e-07    0.0035      28      66 ..     161     199 ..     142     202 .. 0.85
   2 !    4.0   0.0    0.0071        43      26      65 ..     352     393 ..     343     398 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.9e-07
                                       EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C  28 lvvairRggeliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       +v++i+ g++++ p++dt++ ++ +++v g ++++ +l 
  gi|320100844|ref|YP_004176436.1| 161 IVLSIHAGKWMLAPGPDTIIPARSTIYVRGYRENVLRLL 199
                                       57788888**************************98875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0071
                                       S-EEEEEE-T.-EEES--T.T-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C  26 gvlvvairRg.geliipsg.dtvLeeGDvllvvgspsdlael 65 
                                       g +v+a++ g  ++  p   +  L++GD+l+++ + +  +e+
  gi|320100844|ref|YP_004176436.1| 352 GGMVLAVKIGdTWIAYPLAkNPALRPGDKLVIAYPTEFADEV 393
                                       66777775444677777777888*********9888766655 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.12     7e+02      87     103 ..     103     119 ..     100     146 .. 0.84
   2 !   13.0   0.4   8.1e-06     0.048     114     205 ..     213     302 ..     198     310 .. 0.85
   3 !    7.2   0.0   0.00049       2.9      81     130 ..     285     333 ..     283     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.12
                          PhoU_div  87 lDeildvlediamlvtl 103
                                       +D i+d+++di+ ++ +
  gi|320100844|ref|YP_004176436.1| 103 VDTIVDSVKDIVYTLLI 119
                                       799********998765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.1e-06
                          PhoU_div 114 deflallkktveaiealaevieele.klletalskkdiveeieslEdeiDqlqrklikklfsredasnplevlllve 189
                                       de++++lk+++e       +i+    +lle +     ++ee+e+lE  iD  q   ++kl++  + + p  ++ l+ 
  gi|320100844|ref|YP_004176436.1| 213 DELDQVLKRVIELKDYTRLMIDLAHyTLLEADPG---VIEEVEDLEVYIDWRQLDTLNKLKEVSGKIDPDTFIGLSI 286
                                       7888888888887777777777665256666666...9*************************************** PP

                          PhoU_div 190 iieklenvsdraedva 205
                                       + ++le ++d+++ ++
  gi|320100844|ref|YP_004176436.1| 287 LLKELEDIADASNTIS 302
                                       **********998876 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.00049
                          PhoU_div  81 lelveslDeildvlediamlvtlrkvefpeelkdeflallkktveaieal 130
                                       + l+++l +i+d  + i ++ +l + e+pe  +d f ++ +++ e i+ +
  gi|320100844|ref|YP_004176436.1| 285 SILLKELEDIADASNTISHIPSLLE-ELPEHYRDVFSKVFETVGERIKTV 333
                                       56899********************.6****************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3002.90
//
Query:       gi|320100845|ref|YP_004176437.1|  [L=151]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1242.72
//
Query:       gi|320100846|ref|YP_004176438.1|  [L=237]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1942.13
//
Query:       gi|320100847|ref|YP_004176439.1|  [L=480]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  113.8   0.0    6.2e-17   62.4   0.0    2.4  2  ABC_tran         ABC transporter
    2.6e-09   37.3   7.4    0.00026   20.9   0.1    3.8  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    8.8e-07   28.6   0.4       0.03   14.1   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
    1.1e-06   27.9   0.0    0.00087   18.4   0.0    2.3  2  T2SSE            Type II/IV secretion system protein
    1.4e-06   28.9   0.6     0.0073   16.8   0.0    2.2  2  AAA_23           AAA domain
    2.2e-06   28.0   0.3      0.036   14.3   0.0    2.4  2  AAA_28           AAA domain
    3.5e-06   27.5   0.7        0.1   13.0   0.4    2.5  2  AAA_16           AAA ATPase domain
      4e-06   25.8   0.1     0.0017   17.1   0.0    2.6  3  AAA_13           AAA domain
    4.4e-06   26.5   0.2      0.094   12.4   0.0    3.1  3  AAA_30           AAA domain
    1.1e-05   25.8   0.4        0.6   10.5   0.0    3.5  3  AAA              ATPase family associated with various cellul
    2.4e-05   24.0   0.1       0.08   12.5   0.0    2.5  2  AAA_25           AAA domain
    2.8e-05   24.4   1.5       0.23   11.7   0.3    3.3  3  AAA_22           AAA domain
    8.6e-05   22.9   0.3       0.52   10.6   0.0    2.7  2  AAA_19           AAA domain
    0.00012   22.6   0.0      0.052   14.1   0.0    2.6  2  AAA_18           AAA domain
    0.00013   21.9   2.1       0.28   11.1   0.1    2.4  2  NACHT            NACHT domain
    0.00037   20.5   0.1      0.021   14.7   0.0    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00039   20.2   3.4      0.083   12.6   0.0    2.7  2  AAA_24           AAA domain
     0.0012   18.2   0.3       0.21   10.9   0.1    2.3  2  Zeta_toxin       Zeta toxin
     0.0014   18.0   0.0       0.22   10.8   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0016   17.3   0.1       0.23   10.3   0.0    2.1  2  DLIC             Dynein light intermediate chain (DLIC)
     0.0022   17.7   0.3      0.094   12.5   0.1    2.3  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0029   17.6   0.8        3.5    7.6   0.1    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.003   17.9   0.4          2    8.8   0.0    3.0  2  RNA_helicase     RNA helicase
     0.0043   16.4   0.8       0.51    9.6   0.2    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0051   16.2   0.5       0.39   10.0   0.1    2.5  2  ATPase           KaiC
     0.0057   16.8   1.4        1.3    9.2   0.3    2.7  2  AAA_33           AAA domain
     0.0073   15.8   0.9       0.14   11.6   0.1    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0084   15.3   0.1        1.3    8.1   0.0    2.2  2  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
       0.01   15.4   1.8        2.3    7.8   0.1    2.3  2  SRP54            SRP54-type protein, GTPase domain
      0.013   15.2   0.1        6.9    6.4   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.026   13.4   0.6        3.8    6.3   0.1    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.035   13.5   1.8        1.9    7.9   0.0    3.4  4  SMC_N            RecF/RecN/SMC N terminal domain
      0.042   13.8   0.7         10    6.0   0.2    2.4  2  RsgA_GTPase      RsgA GTPase
      0.044   13.6   0.1        7.5    6.3   0.0    2.2  2  dNK              Deoxynucleoside kinase
      0.046   13.3   2.0        3.7    7.1   0.1    2.5  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.059   13.0   0.0        9.9    5.8   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.072   12.8   0.7       0.55    9.9   0.1    2.5  3  IstB_IS21        IstB-like ATP binding protein
      0.085   12.6   0.1        1.4    8.6   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
      0.087   12.0   0.5        1.3    8.1   0.1    2.2  2  PIF1             PIF1-like helicase
      0.088   12.5   0.4        1.4    8.6   0.0    2.0  2  AAA_15           AAA ATPase domain
      0.088   12.8   0.5        5.4    7.0   0.2    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
      0.093   11.5   4.0        7.2    5.3   0.2    3.1  3  ABC_ATPase       Predicted ATPase of the ABC class
      0.099   12.4   0.2       0.87    9.3   0.1    2.4  2  DEAD             DEAD/DEAH box helicase
       0.12   12.2   3.3        4.7    6.9   0.4    2.5  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.13   12.0   2.0        3.1    7.5   0.1    2.4  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.17   11.9   0.2       0.17   11.9   0.2    2.2  2  DUF87            Helicase HerA, central domain
       0.24    8.9   4.3       0.13    9.8   0.2    1.9  2  DUF3584          Protein of unknown function (DUF3584)
       0.24   11.3   1.6         14    5.6   0.1    2.6  2  MobB             Molybdopterin guanine dinucleotide synthesis
       0.29   10.6   1.6        9.6    5.6   0.1    2.4  2  Pox_A32          Poxvirus A32 protein
       0.29   11.0   1.0         26    4.7   0.1    2.7  2  NTPase_1         NTPase
       0.35   10.3   0.6        7.1    6.0   0.2    2.2  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
       0.53    9.9   1.4        3.3    7.3   0.0    2.3  2  Thymidylate_kin  Thymidylate kinase
       0.77   10.2   4.8         11    6.5   0.1    2.6  2  AAA_17           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 !   62.4   0.0   1.8e-19   6.2e-17       1     136 [.      24     174 ..      24     175 .. 0.86
   2 !   49.2   0.0   2.1e-15   7.2e-13       1     136 [.     277     407 ..     277     408 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1.8e-19
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe.pqlf 71 
                                       l+ v+l +++ge + +vG +G+GK+tL+++l g  k+      +G   +dg  ++e+e   l k+i v+ q+    f
  gi|320100847|ref|YP_004176439.1|  24 LRGVNLCVRRGESILVVGGTGSGKTTLARVLNGVAKWvyggeFKGYAVVDGLRVDETEPWLLAKRIHVVGQNpYMYF 100
                                       6789*********************************8777667777999999999999*************73344 PP

                                       TTSBHHHH............HHHTC....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                       xxxxxxxx............xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren............esdee....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                        +  vr+             e        + ka++++++++l d+       +LSgGq +r  +a++++  p+++++
  gi|320100847|ref|YP_004176439.1| 101 IDPLVRQDleayayslygsrE---LacraVRKAVESMNISGLLDKYF----FELSGGQARRALVAKSMIAGPEVIVF 170
                                       444477778899999966552...04446999999999999999998....************************** PP

                                       ESTT CS
                                       xxxx RF
                          ABC_tran 133 DEpt 136
                                       DEp 
  gi|320100847|ref|YP_004176439.1| 171 DEPL 174
                                       ***6 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 2.1e-15
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.v 76 
                                       lk v+l  +eg  + i G nG+GK+tLl++lag lkp +G++             + r    ++pq+ +lf++ + v
  gi|320100847|ref|YP_004176439.1| 277 LKGVHLVAREGDYTYIYGGNGSGKTTLLRILAGYLKPVKGKV-------------WRRGAAIYVPQNIHLFYTEEsV 340
                                       688999999*********************************.............7777777888887777777633 PP

                                       HHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHH.TSSEEEEESTT CS
                                       xxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                          ABC_tran  77 ren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallk.kpkllllDEpt 136
                                       +++            +  e+ +++l++lg++ l        p +LS+Gq +++a+  a l+ + +l+llDEp+
  gi|320100847|ref|YP_004176439.1| 341 AREienmckavgdraACLEKGKRVLEELGIDPLL------PPFNLSHGQMVKLAVSLAGLRdDVDLVLLDEPF 407
                                       3334445555554445555566666666665522......3489**********99886651689*******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 ?    7.4   0.3      0.01       3.5       3      23 ..      38      58 ..      36     116 .. 0.90
   2 ?   -0.8   0.0       3.1   1.1e+03     234     266 ..     144     173 ..     115     177 .. 0.86
   3 !   20.9   0.1   7.8e-07   0.00026       4      56 ..     292     338 ..     289     347 .. 0.73
   4 !   11.3   0.1   0.00067      0.23     224     272 ..     366     412 ..     336     433 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.01
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      +++G  gsGK++L + l ++a
  gi|320100847|ref|YP_004176439.1| 38 LVVGGTGSGKTTLARVLNGVA 58
                                      799**************9886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.1
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEp 266
                                       ++elS G+ r + ++ ++++ +    ++++DEp
  gi|320100847|ref|YP_004176439.1| 144 FFELSGGQARRALVAKSMIAGP---EVIVFDEP 173
                                       7899999999977777777766...9******9 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 7.8e-07
                            AAA_21   4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpei 56 
                                       ++G NgsGK++LL++l      ++++++ + + +++g  + +p  + l ++e+
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRIL------AGYLKPVKGKVWRRGAAIYVPQNIHLFYTEE 338
                                       9***************......6667777777777776666666655555555 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00067
                            AAA_21 224 lengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP 272
                                       +e g +  lp+++lS G+   la+ +a lr++   +l+l+DEp +gL +
  gi|320100847|ref|YP_004176439.1| 366 EELGIDPLLPPFNLSHGQMVKLAVSLAGLRDDV--DLVLLDEPFSGLTY 412
                                       5566677899*******9999888888888887..9**********966 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   0.1   0.00038      0.13      18      38 ..      30      50 ..      23      54 .. 0.82
   2 !   14.1   0.0   8.9e-05      0.03      20      39 ..     284     304 ..     275     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00038
                            AAA_29 18 eidlkgatlltGpsGsGKSTl 38
                                       +++ +++l++G +GsGK+Tl
  gi|320100847|ref|YP_004176439.1| 30 CVRRGESILVVGGTGSGKTTL 50
                                      5554559*************8 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.9e-05
                            AAA_29  20 dlkg.atlltGpsGsGKSTll 39 
                                        ++g  t + G +GsGK+Tll
  gi|320100847|ref|YP_004176439.1| 284 AREGdYTYIYGGNGSGKTTLL 304
                                       455679**************8 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.6e-06   0.00087     119     148 ..      24      53 ..       6      61 .. 0.80
   2 !    7.4   0.0    0.0061       2.1     134     155 ..     292     313 ..     207     319 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.6e-06
                             T2SSE 119 aevlrkavrerglilvsGgTgsGKttllya 148
                                        + ++  vr+  +ilv GgTgsGKttl+ +
  gi|320100847|ref|YP_004176439.1|  24 LRGVNLCVRRGESILVVGGTGSGKTTLARV 53 
                                       566777899999**************9865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0061
                             T2SSE 134 vsGgTgsGKttllyallkeink 155
                                       + Gg gsGKttll +l  +++ 
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILAGYLKP 313
                                       67***********999887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0023      0.78      22      39 ..      37      54 ..      26      70 .. 0.86
   2 !   16.8   0.0   2.1e-05    0.0073      22      39 ..     290     307 ..     275     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0023
                            AAA_23 22 tlItGpNGaGKTTildAi 39
                                       l++G +G+GKTT+ + +
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVL 54
                                      689***********8766 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.1e-05
                            AAA_23  22 tlItGpNGaGKTTildAi 39 
                                       t I+G NG+GKTT+l+ +
  gi|320100847|ref|YP_004176439.1| 290 TYIYGGNGSGKTTLLRIL 307
                                       78*************876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00082      0.28       2      21 ..      37      56 ..      36      87 .. 0.79
   2 !   14.3   0.0   0.00011     0.036       3      24 ..     291     323 ..     290     367 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00082
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      i ++Gg ++GKTtl++ L+ 
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVLNG 56
                                      789************99983 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00011
                            AAA_28   3 vitGgestGKTtlleaLa...........argy 24 
                                       +i Gg ++GKTtll+ La           +rg 
  gi|320100847|ref|YP_004176439.1| 291 YIYGGNGSGKTTLLRILAgylkpvkgkvwRRGA 323
                                       799***************555555444443344 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   0.4   0.00031       0.1      23      44 ..      33      54 ..      25      76 .. 0.85
   2 !   12.3   0.0   0.00049      0.17      23      67 ..     286     331 ..     275     425 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00031
                            AAA_16 23 rpelvllsGesGvGKsslvrel 44
                                      r+e++l++G  G+GK++l+r l
  gi|320100847|ref|YP_004176439.1| 33 RGESILVVGGTGSGKTTLARVL 54
                                      4589***************876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00049
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesai 67 
                                       ++ +++++G  G+GK++l+r l+ +l+  +g +  rg +   +++i
  gi|320100847|ref|YP_004176439.1| 286 EGDYTYIYGGNGSGKTTLLRILAGYLKPVKGKVwRRGAAIYVPQNI 331
                                       446899*************999976665543332333333333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.018       6.2      23      42 ..      41      60 ..      37      90 .. 0.81
   2 ?   -1.3   0.0       1.9   6.4e+02     522     554 ..     160     192 ..     155     207 .. 0.82
   3 !   17.1   0.0     5e-06    0.0017      18      39 ..     289     310 ..     283     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
                            AAA_13 23 GwNGaGKTtLSrllrslelg 42
                                      G  G+GKTtL+r+l+ + + 
  gi|320100847|ref|YP_004176439.1| 41 GGTGSGKTTLARVLNGVAKW 60
                                      788***********998765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                            AAA_13 522 seigkdkivviDDPvSSLDsnslfivfsliksr 554
                                       s i   +++v+D P   LD+n ++    l++s 
  gi|320100847|ref|YP_004176439.1| 160 SMIAGPEVIVFDEPLMWLDDNGVNEFLKLVESL 192
                                       5567889**************888777777765 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5e-06
                            AAA_13  18 iNliYGwNGaGKTtLSrllrsl 39 
                                       + +iYG NG+GKTtL r+l+  
  gi|320100847|ref|YP_004176439.1| 289 YTYIYGGNGSGKTTLLRILAGY 310
                                       679***************9875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2     0.002      0.67      20      53 ..      36      70 ..      27      74 .. 0.78
   2 ?    0.1   0.0       1.7   5.8e+02      68     114 ..     131     191 ..     109     202 .. 0.67
   3 !   12.4   0.0   0.00028     0.094      13      47 ..     282     329 ..     278     432 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.002
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.ggrviglA 53
                                        +++G+ G+GKtt+ ++l+ +++   gg+  g+A
  gi|320100847|ref|YP_004176439.1| 36 SILVVGGTGSGKTTLARVLNGVAKWVyGGEFKGYA 70
                                      5789**************99888766666666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.7
                            AAA_30  68 ieastiakllkrlk.............grarlepg.tllivDEagmv.dtkqlaallkaaek 114
                                       +e+++i  ll+++              + +++ +g ++++ DE  m  d + ++++lk +e+
  gi|320100847|ref|YP_004176439.1| 131 VESMNISGLLDKYFfelsggqarralvA-KSMIAGpEVIVFDEPLMWlDDNGVNEFLKLVES 191
                                       4455555555443377888888888854.44555559******9997777778888877765 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00028
                            AAA_30  13 lltsgdrvavltGpAGtGKttalkalreaweaag.............g 47 
                                       l++ +  ++ + G+ G+GKtt+l+ l+  ++  +             +
  gi|320100847|ref|YP_004176439.1| 282 LVAREGDYTYIYGGNGSGKTTLLRILAGYLKPVKgkvwrrgaaiyvpQ 329
                                       444455599****************99988877424444444444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1    0.0069       2.3       1      20 [.      37      56 ..      37      93 .. 0.85
   2 ?    2.8   0.0      0.44   1.5e+02      23      66 ..     128     172 ..     114     202 .. 0.82
   3 !   10.5   0.0    0.0018       0.6       2      23 ..     291     312 ..     290     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0069
                                      EEEESSTTSSHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavak 20
                                      +l++G  G GKT+la+ +  
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVLNG 56
                                      699*************8865 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.44
                                       THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  23 gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDE 66 
                                          + +++ s ll+ky+ e +   +     ak++  +p ++++DE
  gi|320100847|ref|YP_004176439.1| 128 RKAVESMNISGLLDKYFFELSGGQARRALVAKSMIaGPEVIVFDE 172
                                       455778999999999888877777777777787777999****99 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0018
                                       EEESSTTSSHHHHHHHHHHHHT CS
                               AAA   2 llyGppGtGKTllakavakelg 23 
                                       ++yG  G GKT+l + +a  l+
  gi|320100847|ref|YP_004176439.1| 291 YIYGGNGSGKTTLLRILAGYLK 312
                                       78****************9985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00024      0.08      23      63 ..      21      66 ..       8     121 .. 0.79
   2 !    9.0   0.0    0.0027      0.92      26      97 ..     280     355 ..     255     424 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                            AAA_25 23 rwlvkg...llpagelallaGapgtGKttla..ldlalavatGkpw 63
                                      +w+++g   ++++ge +l++G +g+GKttla  l+ +++++ G ++
  gi|320100847|ref|YP_004176439.1| 21 SWILRGvnlCVRRGESILVVGGTGSGKTTLArvLNGVAKWVYGGEF 66
                                      678887666789******************8223335555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0027
                            AAA_25  26 vkgllpagelallaGapgtGKttlaldlalava..tGkpwlg...pvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                       v+ + ++g+ + ++G  g+GKttl+  la  +   +Gk w     +++p+++   y   E  + e+++  +avg  +
  gi|320100847|ref|YP_004176439.1| 280 VHLVAREGDYTYIYGGNGSGKTTLLRILAGYLKpvKGKVWRRgaaIYVPQNIHLFY-TEESVAREIENMCKAVGDRA 355
                                       56678899****************98888666566888887777655455554333.33555667777777777444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   0.00068      0.23       4      25 ..      33      54 ..      31      63 .. 0.87
   2 ?   -1.3   0.0       7.4   2.5e+03      81      99 ..     151     172 ..     111     202 .. 0.75
   3 !    9.6   0.0    0.0031         1       7      28 ..     289     310 ..     284     374 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00068
                            AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                      +  +++v+G +G+GKTtl+r l
  gi|320100847|ref|YP_004176439.1| 33 RGESILVVGGTGSGKTTLARVL 54
                                      56789*************9965 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 7.4
                            AAA_22  81 aleqalrarav...ielliiDE 99 
                                       + ++al a+++   +e+++ DE
  gi|320100847|ref|YP_004176439.1| 151 QARRALVAKSMiagPEVIVFDE 172
                                       5667777777778889999999 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0031
                            AAA_22   7 ilvvtGesGtGKTtllrrlleq 28 
                                        ++++G  G+GKTtllr l+  
  gi|320100847|ref|YP_004176439.1| 289 YTYIYGGNGSGKTTLLRILAGY 310
                                       589*************988755 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2    0.0031       1.1      10      32 ..      34      56 ..      28      72 .. 0.77
   2 !   10.6   0.0    0.0015      0.52       9      39 ..     286     316 ..     280     431 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0031
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhiva 32
                                       + +lv++G G+GKT++ +    
  gi|320100847|ref|YP_004176439.1| 34 GESILVVGGTGSGKTTLARVLNG 56
                                      56799**********98766554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0015
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelgg 39 
                                       + +   + +G G+GKT++l+    +l+ ++g
  gi|320100847|ref|YP_004176439.1| 286 EGDYTYIYGGNGSGKTTLLRILAGYLKPVKG 316
                                       6677899************998888877665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   0.00015     0.052       1      45 [.      37      85 ..      37     140 .. 0.80
   2 ?    6.1   0.0     0.046        16       3      19 ..     292     308 ..     291     367 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00015
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe..a 45
                                      Il+ G  G+GKttla+ L+    +     g + + +a  +gl+ +++++   
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVLNG---VakwvyGGEFKGYAVVDGLRVDETEPwlL 85
                                      89****************33...33346788888888888888888877443 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.046
                            AAA_18   3 ltGtpGvGKttlakeLs 19 
                                       + G  G+GKttl + L+
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILA 308
                                       66888*********996 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.3    0.0016      0.55       3      20 ..      37      54 ..      35      72 .. 0.79
   2 !   11.1   0.1   0.00083      0.28       3      22 ..     290     309 ..     288     319 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      +++ G  GsGKTtL++ l
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVL 54
                                      799***********9865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00083
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                         + G +GsGKTtLl+ la 
  gi|320100847|ref|YP_004176439.1| 290 TYIYGGNGSGKTTLLRILAG 309
                                       6799***********98875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.22        75      22      39 ..      36      53 ..      25      59 .. 0.80
   2 !   14.7   0.0   6.3e-05     0.021      20      82 ..     287     348 ..     274     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.22
                          ATPase_2 22 iyfiYGpegsGKtaLlke 39
                                       +++ G  gsGKt+L + 
  gi|320100847|ref|YP_004176439.1| 36 SILVVGGTGSGKTTLARV 53
                                      46677999*******985 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.3e-05
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal 82 
                                        +  +iYG  gsGKt+Ll+ ++  l+   k +++      +  +++  f  ee++++++e++ 
  gi|320100847|ref|YP_004176439.1| 287 GDYTYIYGGNGSGKTTLLRILAGYLKP-VKGKVWRRGAAIYVPQNIHLFYTEESVAREIENMC 348
                                       45689**************98888865.45678888888888888888877888888877776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00025     0.083       3      49 ..      35      83 ..      33     101 .. 0.87
   2 ?    7.3   0.5      0.01       3.4       6      22 ..     291     307 ..     289     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                            AAA_24  3 lkiliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdiesw 49
                                       +il++G  g+GKTtla+ l    k ++   +kG++ +d+ ++++ e w
  gi|320100847|ref|YP_004176439.1| 35 ESILVVGGTGSGKTTLARVLngVAKWVYGGEFKGYAVVDGLRVDETEPW 83
                                      579****************997777788888889999999999988766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.01
                            AAA_24   6 liyGpsgiGKTtlakel 22 
                                        iyG +g+GKTtl++ l
  gi|320100847|ref|YP_004176439.1| 291 YIYGGNGSGKTTLLRIL 307
                                       59**********99865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00061      0.21      17      37 ..      35      55 ..      28      64 .. 0.87
   2 ?    5.0   0.0     0.039        13      23      41 ..     294     312 ..     287     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                        Zeta_toxin 17 klillgGqpGAGKselaellk 37
                                       +il++G++G+GK++la+ l+
  gi|320100847|ref|YP_004176439.1| 35 ESILVVGGTGSGKTTLARVLN 55
                                      579**************9876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.039
                        Zeta_toxin  23 GqpGAGKselaellkdele 41 
                                       G+ G+GK++l++ l+ +l+
  gi|320100847|ref|YP_004176439.1| 294 GGNGSGKTTLLRILAGYLK 312
                                       899*********9998876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00066      0.22      15      45 ..      27      57 ..      18      88 .. 0.84
   2 ?    4.8   0.0     0.046        16      19      50 ..     285     315 ..     270     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00066
                      Mg_chelatase 15 leiaaaGgHnlllvGppGsGKtmlakrlpsl 45
                                      +++++  g ++l+vG  GsGKt la+ l+++
  gi|320100847|ref|YP_004176439.1| 27 VNLCVRRGESILVVGGTGSGKTTLARVLNGV 57
                                      5666677789*****************9987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.046
                      Mg_chelatase  19 aaGgHnlllvGppGsGKtmlakrlpsllppls 50 
                                         G     ++G  GsGKt l + l++ l p++
  gi|320100847|ref|YP_004176439.1| 285 REGDY-TYIYGGNGSGKTTLLRILAGYLKPVK 315
                                       44444.4578999***********99998876 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00067      0.23      25      54 ..      34      63 ..      28      85 .. 0.78
   2 ?    4.9   0.0     0.029       9.9      30      55 ..     292     317 ..     285     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00067
                              DLIC 25 gksvlvlGedgsGkttliaklqGveeekkG 54
                                      g s+lv+G  gsGkttl   l Gv +   G
  gi|320100847|ref|YP_004176439.1| 34 GESILVVGGTGSGKTTLARVLNGVAKWVYG 63
                                      789********************9876654 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.029
                              DLIC  30 vlGedgsGkttliaklqGveeekkGr 55 
                                       + G +gsGkttl+  l G  ++ kG+
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILAGYLKPVKGK 317
                                       789***************99999997 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00028     0.094       3      23 ..      36      56 ..      34      63 .. 0.89
   2 ?    3.0   0.0      0.22        75       6      23 ..     292     309 ..     289     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                         PduV-EutP  3 killiGkvgsGKttLtqalkg 23
                                       il++G +gsGKttL++ l+g
  gi|320100847|ref|YP_004176439.1| 36 SILVVGGTGSGKTTLARVLNG 56
                                      699***************998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.22
                         PduV-EutP   6 liGkvgsGKttLtqalkg 23 
                                       + G  gsGKttL + l g
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILAG 309
                                       56999*******998876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1      0.01       3.5      19      39 ..      34      54 ..      21      60 .. 0.81
   2 ?    7.6   0.1     0.011       3.7      18      43 ..     286     311 ..     271     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                                      TEEEEEEESTTSSHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                      g+ il  G  G+GKTtl+r l
  gi|320100847|ref|YP_004176439.1| 34 GESILVVGGTGSGKTTLARVL 54
                                      667999************976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                                       HTEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  18 lgdvilLeGdLGaGKTtlvrglakal 43 
                                        gd  +++G  G+GKTtl r la  l
  gi|320100847|ref|YP_004176439.1| 286 EGDYTYIYGGNGSGKTTLLRILAGYL 311
                                       3777999*************998766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.049        17       1      18 [.      37      54 ..      37      75 .. 0.85
   2 !    8.8   0.0     0.006         2       2      23 ..     291     312 ..     290     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.049
                      RNA_helicase  1 iwlyGpsgeGKStlakeL 18
                                      i+++G +g GK+tla+ L
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVL 54
                                      6899***********984 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.006
                      RNA_helicase   2 wlyGpsgeGKStlakeLakall 23 
                                       ++yG +g GK+tl + La  l 
  gi|320100847|ref|YP_004176439.1| 291 YIYGGNGSGKTTLLRILAGYLK 312
                                       89*************9886665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2    0.0015      0.51      41      59 ..      36      54 ..      25      55 .. 0.87
   2 ?    4.8   0.0     0.046        16      43      59 ..     291     307 ..     274     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                                      SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE 41 hllvaGatgsGKStalntL 59
                                       +lv+G+tgsGK+t  ++L
  gi|320100847|ref|YP_004176439.1| 36 SILVVGGTGSGKTTLARVL 54
                                      58************88776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.046
                                       EEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  43 lvaGatgsGKStalntL 59 
                                        + G+ gsGK+t l+ L
  gi|320100847|ref|YP_004176439.1| 291 YIYGGNGSGKTTLLRIL 307
                                       699**********9966 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0012      0.39      17      36 ..      32      51 ..      28      66 .. 0.90
   2 ?    3.7   0.0       0.1        34      18      35 ..     286     303 ..     280     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                            ATPase 17 pegrvvlitGepGtGKtifa 36
                                       +g+++l++G++G+GKt++a
  gi|320100847|ref|YP_004176439.1| 32 RRGESILVVGGTGSGKTTLA 51
                                      6899**************98 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                            ATPase  18 egrvvlitGepGtGKtif 35 
                                       eg  + i+G+ G+GKt++
  gi|320100847|ref|YP_004176439.1| 286 EGDYTYIYGGNGSGKTTL 303
                                       678899**********97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.3    0.0038       1.3       2      19 ..      37      54 ..      37      62 .. 0.87
   2 ?    5.9   0.0      0.04        14       4      20 ..     292     308 ..     290     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0038
                            AAA_33  2 vllvGlpGsGKstlaerl 19
                                      +l+vG  GsGK+tla+ l
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVL 54
                                      689************965 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.04
                            AAA_33   4 lvGlpGsGKstlaerll 20 
                                       + G +GsGK+tl++ l+
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILA 308
                                       67899*******99876 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00042      0.14      27      51 ..      28      52 ..      24      60 .. 0.88
   2 ?    2.4   0.1       0.3     1e+02      27      52 ..     281     306 ..     271     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00042
                             AAA_7 27 elllknkkpvllvGptGtGKtviik 51
                                      +l+++++ ++l+vG tG+GKt++++
  gi|320100847|ref|YP_004176439.1| 28 NLCVRRGESILVVGGTGSGKTTLAR 52
                                      7899*****************9876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.3
                             AAA_7  27 elllknkkpvllvGptGtGKtviikd 52 
                                       +l+ +++  + ++G  G+GKt++++ 
  gi|320100847|ref|YP_004176439.1| 281 HLVAREGDYTYIYGGNGSGKTTLLRI 306
                                       566777888999*********99865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0     0.004       1.3      23      57 ..      37      72 ..      31     114 .. 0.77
   2 ?    5.0   0.0     0.036        12      22      38 ..     289     305 ..     276     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.004
                                      EEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE CS
                            NB-ARC 23 valvGmgGvGKttlakqilnksdeveg.rFdsvawv 57
                                      + +vG  G+GKttla+  +   + v g +F ++a v
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVLNGVAKWVYGgEFKGYAVV 72
                                      6799***********987776666655577776655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.036
                                       EEEEEESTTSSHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlak 38 
                                          ++G  G+GKttl++
  gi|320100847|ref|YP_004176439.1| 289 YTYIYGGNGSGKTTLLR 305
                                       5579***********87 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.015       5.1       3      18 ..      36      51 ..      35      62 .. 0.83
   2 ?    7.8   0.1    0.0068       2.3       5      31 ..     291     317 ..     288     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                                      EEEEEESTTSSHHHHH CS
                             SRP54  3 villvGlqGaGKTttl 18
                                       il+vG +G+GKTt +
  gi|320100847|ref|YP_004176439.1| 36 SILVVGGTGSGKTTLA 51
                                      589**********976 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0068
                                       EEEESTTSSHHHHHHHHHHHHHHTTS- CS
                             SRP54   5 llvGlqGaGKTttlaKLaallkkegkk 31 
                                        + G +G+GKTt l  La +lk  + k
  gi|320100847|ref|YP_004176439.1| 291 YIYGGNGSGKTTLLRILAGYLKPVKGK 317
                                       57899**************99876555 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 ?    6.0   0.0     0.027       9.2      35      53 ..      36      54 ..      27      60 .. 0.88
   2 ?    6.4   0.0      0.02       6.9      32      57 ..     286     311 ..     276     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                            RuvB_N 35 hvllyGpPGlGkttlakii 53
                                       +l++G  G Gkttla+++
  gi|320100847|ref|YP_004176439.1| 36 SILVVGGTGSGKTTLARVL 54
                                      689*************997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.02
                            RuvB_N  32 aldhvllyGpPGlGkttlakiiakel 57 
                                       + d++ +yG  G Gkttl +i+a  l
  gi|320100847|ref|YP_004176439.1| 286 EGDYTYIYGGNGSGKTTLLRILAGYL 311
                                       568999***************99755 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 ?    6.3   0.1     0.011       3.8      16      34 ..      35      53 ..      23      59 .. 0.81
   2 ?    5.3   0.0     0.023       7.6      13      35 ..     285     307 ..     277     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                     TrwB_AAD_bind 16 qhilivGttGsGKtqalek 34
                                      + il+vG+tGsGKt+ ++ 
  gi|320100847|ref|YP_004176439.1| 35 ESILVVGGTGSGKTTLARV 53
                                      4699**********98764 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.023
                     TrwB_AAD_bind  13 retqhilivGttGsGKtqalekl 35 
                                       re   + i G+ GsGKt+ l+ l
  gi|320100847|ref|YP_004176439.1| 285 REGDYTYIYGGNGSGKTTLLRIL 307
                                       6778899***********98755 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 ?    0.6   0.2      0.91   3.1e+02      28      41 ..      38      51 ..      31      64 .. 0.85
   2 ?    1.2   0.0      0.61   2.1e+02     136     186 ..     146     192 ..     102     208 .. 0.74
   3 ?    7.9   0.0    0.0055       1.9      25      41 ..     288     304 ..     279     317 .. 0.86
   4 ?   -1.9   0.0       5.4   1.8e+03     136     190 ..     378     429 ..     343     446 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.91
                                      EEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnll 41
                                       +vG  GSGK+ l 
  gi|320100847|ref|YP_004176439.1| 38 LVVGGTGSGKTTLA 51
                                      699*******9876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.61
                                       CS-HHH..HHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGe..ktLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                       +LSgG+  ++Lv      A  ++    + ++De  + LD++ v+++ +l+++ 
  gi|320100847|ref|YP_004176439.1| 146 ELSGGQarRALV------AKSMIAGPEVIVFDEPLMWLDDNGVNEFLKLVESL 192
                                       588998223344......44555555678999999999999999999988875 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0055
                                       SEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnll 41 
                                         t i+G NGSGK+ ll
  gi|320100847|ref|YP_004176439.1| 288 DYTYIYGGNGSGKTTLL 304
                                       5799**********987 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.4
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskna 190
                                       +LS G+  +v la+ +A    +   l+llDe  + L  + + ++ae l +  k+ 
  gi|320100847|ref|YP_004176439.1| 378 NLSHGQ--MVKLAVSLAGL-RDDVDLVLLDEPFSGLTYTDRVELAESLARLGKTI 429
                                       678887..45555555544.35667899999999999999999988888877544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2      0.03        10      99     121 ..      34      56 ..      28      64 .. 0.85
   2 ?    5.5   0.0     0.043        15      99     123 ..     287     311 ..     267     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.03
                                       TSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                       ++ +++vG +G GK+tL  +l++
  gi|320100847|ref|YP_004176439.1|  34 GESILVVGGTGSGKTTLARVLNG 56 
                                       567889************99987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.043
                                       TSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                       ++ + + G  G GK+tL+  l++ l
  gi|320100847|ref|YP_004176439.1| 287 GDYTYIYGGNGSGKTTLLRILAGYL 311
                                       478999*************998865 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.022       7.5       1      25 [.      37      61 ..      37      83 .. 0.85
   2 ?    5.1   0.0     0.052        18       5      23 ..     294     312 ..     291     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.022
                                      EEEEESTTSSHHHHHHHHHCCSTCE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvk 25
                                      i v G  g+GK+tl+ +L+  ++++
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVLNGVAKWV 61
                                      5677899***********9888776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.052
                                       ESTTSSHHHHHHHHHCCST CS
                               dNK   5 GnIgaGKstlvklLskklg 23 
                                       G  g+GK+tl+ +L+  l+
  gi|320100847|ref|YP_004176439.1| 294 GGNGSGKTTLLRILAGYLK 312
                                       6669**********98874 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.041        14       3      18 ..      37      52 ..      35      60 .. 0.83
   2 ?    7.1   0.1     0.011       3.7       3      20 ..     290     307 ..     288     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.041
                                      EEEEESTTCCHHHHHH CS
                              cobW  3 tvltGflGsGKTtLln 18
                                      ++++G  GsGKTtL +
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLAR 52
                                      5789999******965 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                                       EEEEESTTCCHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhl 20 
                                       t + G  GsGKTtLl+ l
  gi|320100847|ref|YP_004176439.1| 290 TYIYGGNGSGKTTLLRIL 307
                                       6688899********866 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.029       9.9      11      36 ..      31      56 ..      26     206 .. 0.85
   2 ?    5.4   0.0     0.037        13      13      39 ..     286     312 ..     279     436 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.029
                                      EBTT-EEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslsk 36
                                      + +G+ +l++g+ g Gkt++++ l  
  gi|320100847|ref|YP_004176439.1| 31 VRRGESILVVGGTGSGKTTLARVLNG 56
                                      568*****************976654 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.037
                                       TT-EEEEEESTTSSHHHHHHHHHHHSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  13 qGqrtlipgafgvGktvisqslskqsn 39 
                                       +G  t i g++g Gkt++++ l+ + +
  gi|320100847|ref|YP_004176439.1| 286 EGDYTYIYGGNGSGKTTLLRILAGYLK 312
                                       79999**************99998854 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0016      0.55      44      67 ..      31      54 ..      23      61 .. 0.88
   2 ?   -2.2   0.0       8.5   2.9e+03     106     136 ..     162     191 ..     123     203 .. 0.68
   3 ?   -0.5   0.0       2.6   8.8e+02      47      63 ..     287     303 ..     269     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0016
                         IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                      +++ e+i+++G++G GK+ la  l
  gi|320100847|ref|YP_004176439.1| 31 VRRGESILVVGGTGSGKTTLARVL 54
                                      7899****************9876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.5
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviek 136
                                       ++ +++++ D+  l  ld++  +++++++e+
  gi|320100847|ref|YP_004176439.1| 162 IAGPEVIVFDE-PLMWLDDNGVNEFLKLVES 191
                                       33346777776.5778888998988888875 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.6
                         IstB_IS21  47 kenivllGpsGvGKshl 63 
                                        +   + G+ G GK+ l
  gi|320100847|ref|YP_004176439.1| 287 GDYTYIYGGNGSGKTTL 303
                                       3557899********88 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0041       1.4      18      42 ..      30      54 ..      22      62 .. 0.83
   2 ?    1.4   0.0      0.68   2.3e+02      12      42 ..     277     307 ..     270     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0041
                                      HCTSSS-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat 18 vaktdlsvlitGesGtGKellarai 42
                                      +++   s+l++G +G+GK++lar +
  gi|320100847|ref|YP_004176439.1| 30 CVRRGESILVVGGTGSGKTTLARVL 54
                                      5566789***************987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.68
                                       HHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat  12 leqikkvaktdlsvlitGesGtGKellarai 42 
                                       l+ ++ va+    + i G +G+GK++l r +
  gi|320100847|ref|YP_004176439.1| 277 LKGVHLVAREGDYTYIYGGNGSGKTTLLRIL 307
                                       566677778888899*********9987765 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.38   1.3e+02      20      43 ..      32      55 ..      23      61 .. 0.84
   2 ?    8.1   0.1    0.0039       1.3      18      51 ..     283     316 ..     274     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.38
                                      HCTS-EEEEESTTSSCHHHHHHHH CS
                              PIF1 20 ekgklfFvtGsgGtgKtflwkall 43
                                      ++g+++ v G  G+gKt l + l 
  gi|320100847|ref|YP_004176439.1| 32 RRGESILVVGGTGSGKTTLARVLN 55
                                      67999************9988775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0039
                                       ..HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCC CS
                              PIF1  18 lnekgklfFvtGsgGtgKtflwkallkklrsegk 51 
                                       ++++g   +++G  G+gKt l++ l  +l++ + 
  gi|320100847|ref|YP_004176439.1| 283 VAREGDYTYIYGGNGSGKTTLLRILAGYLKPVKG 316
                                       5689999*******************99998654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.45   1.5e+02      26      44 ..      37      55 ..      34      60 .. 0.88
   2 ?    8.6   0.0     0.004       1.4      25      43 ..     289     307 ..     276     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.45
                            AAA_15 26 tvliGkNnsGKSsileald 44
                                       +++G  +sGK++++++l+
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVLN 55
                                      5799***********9986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.004
                            AAA_15  25 ltvliGkNnsGKSsileal 43 
                                       +t + G N+sGK+++l++l
  gi|320100847|ref|YP_004176439.1| 289 YTYIYGGNGSGKTTLLRIL 307
                                       79999***********998 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2     0.016       5.4       2      21 ..      37      56 ..      36      63 .. 0.85
   2 ?    3.3   0.0      0.22        74       4      23 ..     292     311 ..     290     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.016
                                      EEEE--SSSSHHHHHHHGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaa 21
                                      +l+vG +G+gK++la+ l  
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVLNG 56
                                      799************98865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.22
                                       EE--SSSSHHHHHHHGGGGB CS
                             AAA_5   4 LvGppGtgKselaerlaaal 23 
                                       + G  G+gK++l + la  l
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILAGYL 311
                                       57999*********999877 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.06        20     241     265 ..      30      55 ..      26      63 .. 0.82
   2 ?    2.0   0.0      0.21        71     368     432 ..     177     240 ..     168     254 .. 0.86
   3 ?    5.3   0.2     0.021       7.2     244     264 ..     286     307 ..     267     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.06
                                       EE-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAle 265
                                        +++G  +l+vGg   GK+TL + l+
  gi|320100847|ref|YP_004176439.1|  30 CVRRGeSILVVGGTGSGKTTLARVLN 55 
                                       567777789************99875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.21
                                       GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEEE-HHHHHHHHHCHT- CS
                        ABC_ATPase 368 kekepitplvdrvrelykklgvstilvvggsgdyldvAdtvilmeeykpkdvtekakeiaeelat 432
                                        ++++++ ++++v++l + +g ++i       ++l++ d+v+ +++    d t +a+ ++++ ++
  gi|320100847|ref|YP_004176439.1| 177 LDDNGVNEFLKLVESL-RFMGKTLIFMEHRFIQLLTIVDRVLILRNGVLVDETMEAHMLKHRAKS 240
                                       56789999*******9.89999999999*************************999998877655 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.021
                                       SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAl 264
                                       +G  t I Gg+  GK+TLL+ l
  gi|320100847|ref|YP_004176439.1| 286 EGdYTYIYGGNGSGKTTLLRIL 307
                                       555799*************976 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0026      0.87      13      31 ..      33      51 ..      24     170 .. 0.86
   2 ?   -0.1   0.0         2   6.6e+02      17      33 ..     290     306 ..     278     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                                      TTCEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                              DEAD 13 gggdvlvaaeTGsGKTlaf 31
                                      +g+++lv + TGsGKT+ +
  gi|320100847|ref|YP_004176439.1| 33 RGESILVVGGTGSGKTTLA 51
                                      7899************875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                                       EEEEESTTSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                              DEAD  17 vlvaaeTGsGKTlafli 33 
                                         + +  GsGKT+   i
  gi|320100847|ref|YP_004176439.1| 290 TYIYGGNGSGKTTLLRI 306
                                       5567778*****98554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4     0.014       4.7       1      17 [.      39      55 ..      39      61 .. 0.86
   2 ?    5.5   0.1     0.039        13       1      21 [.     292     312 ..     292     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.014
                        ATP_bind_1  1 vvGpaGsGKttfvgals 17
                                      vvG+ GsGKtt+ + l+
  gi|320100847|ref|YP_004176439.1| 39 VVGGTGSGKTTLARVLN 55
                                      89*********988776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.039
                        ATP_bind_1   1 vvGpaGsGKttfvgalseile 21 
                                       + G+ GsGKtt+ + l+ +l+
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILAGYLK 312
                                       679*********998887776 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 ?    3.7   0.3      0.14        48       1      14 [.      41      54 ..      41      59 .. 0.89
   2 ?    7.5   0.1    0.0092       3.1       1      19 [.     294     312 ..     294     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                            CLP1_P  1 GpkdsGKSTlarlL 14
                                      G++ sGK+Tlar+L
  gi|320100847|ref|YP_004176439.1| 41 GGTGSGKTTLARVL 54
                                      899*********99 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0092
                            CLP1_P   1 GpkdsGKSTlarlLlNyal 19 
                                       G++ sGK+Tl r+L+ y+ 
  gi|320100847|ref|YP_004176439.1| 294 GGNGSGKTTLLRILAGYLK 312
                                       7899************985 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00051      0.17      25      43 ..      36      54 ..      27      57 .. 0.91
   2 ?    0.6   0.4       1.5   4.9e+02      28      44 ..     292     308 ..     290     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00051
                             DUF87 25 HlAilgsTGsGKSntvavL 43
                                      +++++g TGsGK+++++vL
  gi|320100847|ref|YP_004176439.1| 36 SILVVGGTGSGKTTLARVL 54
                                      689**************98 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.5
                             DUF87  28 ilgsTGsGKSntvavLl 44 
                                       i g  GsGK+++ ++L 
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILA 308
                                       78889*******99985 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.5      0.29        99      20      37 ..      37      54 ..      24      55 .. 0.83
   2 ?    9.8   0.2   0.00038      0.13      18      37 ..     288     307 ..     270     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.29
                           DUF3584 20 tnieGtNaaGKTtLlrLi 37
                                        ++G  ++GKTtL r++
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARVL 54
                                      5688999********986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                           DUF3584  18 ghtnieGtNaaGKTtLlrLi 37 
                                       + t i G N++GKTtLlr++
  gi|320100847|ref|YP_004176439.1| 288 DYTYIYGGNGSGKTTLLRIL 307
                                       4689**************86 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.13        43       2      18 ..      37      53 ..      36      59 .. 0.83
   2 ?    5.6   0.1     0.041        14       4      24 ..     292     312 ..     290     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.13
                              MobB  2 lgivgksgsGKTtLlek 18
                                      + +vg  gsGKTtL   
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARV 53
                                      5689*********9765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.041
                              MobB   4 ivgksgsGKTtLleklipelk 24 
                                       i g +gsGKTtLl  l   lk
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRILAGYLK 312
                                       77999********99887776 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.028       9.6      16      29 ..      37      50 ..      31      63 .. 0.81
   2 ?    3.7   0.1      0.11        36      18      33 ..     292     307 ..     285     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.028
                           Pox_A32 16 lalvGgsGsGktvy 29
                                      + +vGg+GsGkt+ 
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTL 50
                                      6789********95 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                           Pox_A32  18 lvGgsGsGktvyLlsL 33 
                                       + Gg GsGkt+ L+ L
  gi|320100847|ref|YP_004176439.1| 292 IYGGNGSGKTTLLRIL 307
                                       78*********99765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.12        39       2      18 ..      37      53 ..      36      73 .. 0.83
   2 ?    4.7   0.1     0.077        26       3      24 ..     291     312 ..     289     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.12
                                      EEEE--TTSSHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkk 18
                                      +++ G  G+GKtTl + 
  gi|320100847|ref|YP_004176439.1| 37 ILVVGGTGSGKTTLARV 53
                                      7899*********9764 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.077
                                       EEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellk 24 
                                       +i G  G+GKtTl++ ++  lk
  gi|320100847|ref|YP_004176439.1| 291 YIYGGNGSGKTTLLRILAGYLK 312
                                       57799*********99988886 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 ?    6.0   0.2     0.021       7.1      13      28 ..      34      49 ..      27      59 .. 0.84
   2 ?    2.2   0.0      0.32   1.1e+02      13      30 ..     287     304 ..     280     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                                      SSEEEEEE-TTSSHHH CS
                     UvrD-helicase 13 ggpilveAsAGsGKTf 28
                                      g++ilv+ + GsGKT+
  gi|320100847|ref|YP_004176439.1| 34 GESILVVGGTGSGKTT 49
                                      789************7 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.32
                                       SSEEEEEE-TTSSHHHHH CS
                     UvrD-helicase  13 ggpilveAsAGsGKTfvl 30 
                                       g  + ++ + GsGKT+ l
  gi|320100847|ref|YP_004176439.1| 287 GDYTYIYGGNGSGKTTLL 304
                                       5667899********987 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4       0.9     3e+02       3      16 ..      41      54 ..      40      59 .. 0.84
   2 ?    7.3   0.0    0.0099       3.3       3      24 ..     294     315 ..     292     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.9
                                      ESTTSSHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaell 16
                                      G  G+GKtt a+ l
  gi|320100847|ref|YP_004176439.1| 41 GGTGSGKTTLARVL 54
                                      5679******9988 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0099
                                       ESTTSSHHHHHHHHHHHHHHTT CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeeg 24 
                                       G +G+GKtt +++l+ +lk  +
  gi|320100847|ref|YP_004176439.1| 294 GGNGSGKTTLLRILAGYLKPVK 315
                                       99*************9999765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.5     0.089        30       1      14 [.      40      53 ..      40      65 .. 0.87
   2 ?    6.5   0.1     0.032        11       1      15 [.     293     307 ..     293     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.089
                                      EE-TTSSHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqcek 14
                                      +Gg GsGK+t+++ 
  gi|320100847|ref|YP_004176439.1| 40 VGGTGSGKTTLARV 53
                                      7*********9965 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.032
                                       EE-TTSSHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqcekl 15 
                                       +Gg GsGK+t+++ l
  gi|320100847|ref|YP_004176439.1| 293 YGGNGSGKTTLLRIL 307
                                       7**********9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              53  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 3603.38
//
Query:       gi|320100848|ref|YP_004176440.1|  [L=195]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1634.05
//
Query:       gi|320100849|ref|YP_004176441.1|  [L=173]
Description: nitroreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-31  107.8   2.6    2.1e-19   70.2   0.5    2.0  2  Nitroreductase  Nitroreductase family
    4.1e-15   55.9   0.0    5.7e-06   26.0   0.0    3.0  3  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.037   13.8   0.0      0.058   13.1   0.0    1.3  1  PYC_OADA        Conserved carboxylase domain


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.5   3.5e-23   2.1e-19       1      60 [.       9      68 ..       9      86 .. 0.89
   2 !   38.7   0.1   1.6e-13   9.7e-10      89     170 .]      73     145 ..      66     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 3.5e-23
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalel 60
                                      +++RrSiR F+++pvp+e + k ++aar+aPsa+n+qpwrf++v+d ++r++l+e+ + +
  gi|320100849|ref|YP_004176441.1|  9 LKSRRSIRRFKPTPVPLELVLKAIDAARYAPSAKNSQPWRFIIVEDPAIRRRLGEIHAYA 68
                                      589**************************************************9986655 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 1.6e-13
                                       HSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEE CS
                    Nitroreductase  89 gapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivvl 165
                                       +ap+ +++           +e++    lld++ a   ++LaA+alGlg+++i ++ +   e+r++lglp +  +v +
  gi|320100849|ref|YP_004176441.1|  73 NAPLAVIV--------ACVSEESPTSYLLDCANATIYFMLAAHALGLGTVWIQTLRNIG-ELREILGLPANVTPVSM 140
                                       66666666........3445556666789**************************9887.6********99****** PP

                                       EEEE- CS
                    Nitroreductase 166 iavGy 170
                                       +avGy
  gi|320100849|ref|YP_004176441.1| 141 LAVGY 145
                                       ****9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0012       7.2       2      24 ..       5      27 ..       4      31 .. 0.87
   2 !   26.0   0.0   9.6e-10   5.7e-06     162     191 ..      30      59 ..      26      74 .. 0.83
   3 !   21.2   0.0     3e-08   0.00018      71     152 ..      81     165 ..      73     173 .] 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0012
                                      HHHHHHH--B---B--S---HHH CS
                    TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeel 24
                                      ++e ++ R+s+R++k ++++ el
  gi|320100849|ref|YP_004176441.1|  5 ILELLKSRRSIRRFKPTPVPLEL 27
                                      7899*************998765 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 9.6e-10
                                       HHHHHHHTS--GGG----EEE.E-SSEE.. CS
                    TM1586_NiRdase 162 eileaarlAPsAlNqqpwrfelkdddeiki 191
                                       ++++aar+APsA N+qpwrf +++d  i+ 
  gi|320100849|ref|YP_004176441.1|  30 KAIDAARYAPSAKNSQPWRFIIVEDPAIRR 59 
                                       799*******************99877655 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 3e-08
                                       E----SS.HHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST.............T-S-EEEEE-BS----.----- CS
                    TM1586_NiRdase  71 alvgekk.edleekaGYygeqlvLkltalGlgtcWvggtykk..kkakvelkkgeklvivIalGyaktklveakrkp 144
                                       a+v+e++ + ++  +      ++L + alGlgt W+    +    ++ + l+ + + v ++a+Gy+ ++  ++ rkp
  gi|320100849|ref|YP_004176441.1|  81 ACVSEESpTSYLLDCANATIYFMLAAHALGLGTVWIQTLRNIgeLREILGLPANVTPVSMLAVGYPGESPAPRPRKP 157
                                       55555555666666666777789*************987665446666999************************** PP

                                       HHHHBSS- CS
                    TM1586_NiRdase 145 leelcevk 152
                                       lee++ ++
  gi|320100849|ref|YP_004176441.1| 158 LEEIVFLN 165
                                       ***98655 PP

>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.7e-06     0.058      18      51 ..     106     139 ..     102     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.7e-06
                                       HHHTT-GGGHHHHHHHHHHHHHHTT----STTHH CS
                          PYC_OADA  18 akeqglldkfeevlkeyaevnkllGdivkVTPsS 51 
                                       a+++gl+  + + l+++ e +++lG +  VTP+S
  gi|320100849|ref|YP_004176441.1| 106 AHALGLGTVWIQTLRNIGELREILGLPANVTPVS 139
                                       6789*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.48
# Mc/sec: 1094.79
//
Query:       gi|320100850|ref|YP_004176442.1|  [L=447]
Description: rhomboid family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-37  127.5  19.2      4e-37  127.5  19.2    2.1  2  Rhomboid  Rhomboid family
     0.0023   18.4   0.2     0.0023   18.4   0.2    3.2  4  DUF1751   Eukaryotic integral membrane protein (DUF1751)
  ------ inclusion threshold ------
       0.05   13.2   0.1      0.094   12.4   0.1    1.4  1  HTH_33    Winged helix-turn helix


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 !  127.5  19.2   6.8e-41     4e-37       6     147 ..      63     217 ..      58     219 .. 0.94
   2 ?   -1.2   0.1      0.31   1.9e+03      46      66 ..     259     279 ..     244     301 .. 0.61

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 6.8e-41
                                       -TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S........-EESSHH CS
                          Rhomboid   6 elwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses.....plvGaSG 77 
                                        + r++t+mf Ha+++H++fNm++l++fG ++e+++Gs r+llly++sgla++l+++++ + +++     p+vGaSG
  gi|320100850|ref|YP_004176442.1|  63 GVVRIFTAMFTHADFFHIFFNMYFLWLFGRRIESVIGSRRYLLLYFASGLAAVLFHVAIIPVGGYdslvvPAVGASG 139
                                       578************************************************************99************ PP

                                       HHHHHHHHHHHHHHCCCCGS----HC............CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHH CS
                          Rhomboid  78 aifgllgallvlvprnrkllrkliia.........llllllfillnlvlgllpraggvsnlAHlgGllaGlllglll 145
                                       ai+g+lga+l+l+p +r ++  ++++          ++l+++++ ++++g+++  ggv+++AH+gG++aGl+l+++l
  gi|320100850|ref|YP_004176442.1| 140 AISGVLGAYLLLFPYARLMWCMFFLFlpycfpvstAVFLIIWFAEQVLYGYMRL-GGVAYFAHVGGFVAGLALTYVL 215
                                       ******************9998888899***99998999999999999999988.6*******************98 PP

                                       CC CS
                          Rhomboid 146 lr 147
                                        r
  gi|320100850|ref|YP_004176442.1| 216 TR 217
                                       76 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHH- CS
                          Rhomboid  46 flllyllsglagsllsllfsa 66 
                                       +ll+ +++g+a s+ + ++s+
  gi|320100850|ref|YP_004176442.1| 259 VLLVLVAAGFAYSVYYTVASP 279
                                       333444444444444444444 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.47   2.8e+03      55      76 ..      21      42 ..      16      52 .. 0.73
   2 !   18.4   0.2   3.9e-07    0.0023       9      95 ..      65     146 ..      53     149 .. 0.88
   3 ?   -2.5   0.3       1.3   7.6e+03      63      85 ..     172     195 ..     157     209 .. 0.48
   4 ?   -2.0   0.3      0.93   5.5e+03      54      84 ..     257     288 ..     253     303 .. 0.45

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.47
                           DUF1751 55 nvitnllvvlltlllylvtkse 76
                                       v++n++v+l+t   +++ +s 
  gi|320100850|ref|YP_004176442.1| 21 IVAANIVVYLYTSYRNMFLEST 42
                                      5778888888888777776655 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.9e-07
                           DUF1751   9 wtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllylvtkseelllvpisG 85 
                                         ++ta+f  + ++++ +++  l+l+g+ +E++ gs+ +l    ++ ++++l +vl+++++  v   ++ l+vp  G
  gi|320100850|ref|YP_004176442.1|  65 VRIFTAMFTHADFFHIFFNMYFLWLFGRRIESVIGSRRYL----LLYFASGLAAVLFHVAIIPVGGYDS-LVVPAVG 136
                                       679********************************99875....5678899999999999999999998.8899999 PP

                           DUF1751  86 lagilagflv 95 
                                       + g  +g+l 
  gi|320100850|ref|YP_004176442.1| 137 ASGAISGVLG 146
                                       9999999875 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.3
                           DUF1751  63 vlltlllylvtkseelll..vpisG 85 
                                       v ++++l + +++++ l+  +++ G
  gi|320100850|ref|YP_004176442.1| 172 VSTAVFLIIWFAEQV-LYgyMRLGG 195
                                       333333333333333.332345544 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.93
                           DUF1751  54 vnvitnllvvlltlllylvtkseelll.vpis 84 
                                       ++v+  l+++ +++ +y++ +s   ++ + + 
  gi|320100850|ref|YP_004176442.1| 257 LTVLLVLVAAGFAYSVYYTVASPPSTYlLSVT 288
                                       44444444444444444443333323324444 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.6e-05     0.094      15      42 ..     220     247 ..     215     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                            HTH_33  15 eerfgvsysvsgvyrlLkrlGfsyqkPr 42 
                                        e +++ y+   + r+L+++G+  +kPr
  gi|320100850|ref|YP_004176442.1| 220 VEHYRLNYTYDYIARWLQEIGIVVRKPR 247
                                       57899**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3086.97
//
Query:       gi|320100851|ref|YP_004176443.1|  [L=686]
Description: alpha amylase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-65  219.3   0.0    1.5e-64  218.8   0.0    1.2  1  Alpha-amylase    Alpha amylase, catalytic domain
    6.5e-06   26.5   0.1     0.0002   21.8   0.0    3.0  4  Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
     0.0011   17.3   0.0     0.0016   16.7   0.0    1.1  1  Glyco_hydro_70   Glycosyl hydrolase family 70
     0.0017   18.4   0.0     0.0041   17.2   0.0    1.7  1  Malt_amylase_C   Maltogenic Amylase, C-terminal domain
  ------ inclusion threshold ------
      0.076   13.6   0.2       0.14   12.7   0.2    1.4  1  GTA_holin_3TM    Holin of 3TMs, for gene-transfer release
       0.11   12.6   0.0       0.27   11.4   0.0    1.6  1  GHL6             Hypothetical glycosyl hydrolase 6
       0.44   10.4   1.3       0.72    9.8   1.3    1.3  1  TMEM154          TMEM154 protein family


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.0   5.7e-68   1.5e-64       1     335 [.     209     514 ..     209     523 .. 0.86

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 5.7e-68
                                       --CHHHHCTCCCCCCCT-SCEEE-B-CE-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC- CS
                     Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifkspqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHt 77 
                                       GDLkG++ekLdYlkeLGv  i+l+Pif s  + hgYd+ dy+++dp+fGt edlk+Li++ah++gikvi+D+V+ H 
  gi|320100851|ref|YP_004176443.1| 209 GDLKGVTEKLDYLKELGVGLIYLNPIFLSG-SVHGYDTYDYYTVDPKFGTLEDLKTLINEAHKRGIKVIFDFVPDHV 284
                                       9*****************************.********************************************** PP

                                       -TTSCCCHCCHHSTTSGGGCCC-E......ESS-STTC-TTTTCSCEECTTTTCEEESSS-TTS-BB-TTTCCCCCC CS
                     Alpha-amylase  78 sdehewfkeslkkkgepkrdyyiwkegkeekeppnnwkslfdgsaweydekaqeyylhlflkklpdLnteneevrke 154
                                       +  +  f++ +++    ++ y+ w           +w+ ++ g    y++++       ++ +lp+Ln  n evr++
  gi|320100851|ref|YP_004176443.1| 285 GLGFWAFQDVYRNG--RNSTYWSWFIV-------YKWR-FKLGDPTAYKCWW-------GIGSLPQLNVLNTEVRQY 344
                                       ****9999999944..48999999844.......6677.4445555667888.......599*************** PP

                                       CCCCCCCCCTTT-SEEEETTCCCTTTCCCCHCCHCCHHHHHHHHHHHTCCGTT-EEEEE-TT-SCCCHCCCC-CGG- CS
                     Alpha-amylase 155 lkdvvkfwlekgidGfRlDvvkhvskvealesngeflheftqalnetvasrkevmtvgEvssdasedlrvyttearl 231
                                       l +v+ +wl  g dG+R+D+   v        +  f +e ++a++     + ++++vgE+++   e+lr+ ++++ +
  gi|320100851|ref|YP_004176443.1| 345 LINVALYWLSIGFDGLRIDTPLDVID------SESFFRELREAVKSR---YPDAYIVGEIWDYRPEWLRGNAFDSLM 412
                                       ********************877766......468888889888866...5************************** PP

                                       SICECCITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-CCCTTCEEES--TTS--HHHHTTSSTTTT..... CS
                     Alpha-amylase 232 elemvldfphldvaqkakikeqlksisakklkellkkwlkaleeaaeeavtflgnHDqeRilsrlgddsaea..... 303
                                       ++    ++   +++ + +     +s++++++++ +  +      +a   ++++g+HD++R+l+ lg    +      
  gi|320100851|ref|YP_004176443.1| 413 NYYLGRNILLSYARGALN--GYTASMKLAEYYAGIGVN------VAGMGFNIIGSHDTSRVLTDLGGGGLNStpsne 481
                                       ***777777766666666..344443344443333333......345679****************98866578889 PP

                                       .HHHHHHHHHCCCTSSSEEEEETTCCCT----S CS
                     Alpha-amylase 304 .ekklklaaillltlrGvpviYyGeEigmtggk 335
                                        + +lkl+ +l+ t +G+pv+++G+E g+tg +
  gi|320100851|ref|YP_004176443.1| 482 sIARLKLLSTLQYTQPGMPVVFQGDERGITGRQ 514
                                       999***************************975 PP

>> Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         7   1.8e+04      75      92 ..     107     124 ..      94     127 .. 0.73
   2 ?   -3.5   0.0       5.9   1.5e+04       1      26 [.     179     203 ..     179     205 .. 0.67
   3 ?    0.7   0.0      0.29   7.3e+02      49      95 ..     501     557 ..     489     557 .. 0.65
   4 !   21.8   0.0   7.7e-08    0.0002      11      94 ..     564     626 ..     561     628 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7
                                       TCBSEEEEEEESTTEEEE CS
                   Alpha-amylase_C  75 dgransltltlpprsalv 92 
                                       +g++++++ltl  ++++ 
  gi|320100851|ref|YP_004176443.1| 107 RGLNYYFKLTLRNNTVVY 124
                                       788899999998887765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.9
                                       EEEEEETTSSEEEEEECTTT.EEEEEE CS
                   Alpha-amylase_C   1 wvsakdeenkviaFeRgdge.kllvvf 26 
                                       w++  +  + v +F R+dg    l ++
  gi|320100851|ref|YP_004176443.1| 179 WIN--EVSRGVPVFTRWDGPvTSLHCC 203
                                       666..6678899999999544455555 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.29
                                       ETTCTTSGCCTTT-SSTSS-EEEECT..........TCBSEEEEEEESTTEEEEEEE CS
                   Alpha-amylase_C  49 dvlntdaeeyggsglgntgkvvtvdd..........dgransltltlpprsalvlkv 95 
                                       +v+++d++ + g + +++++   +++           +r  +l+ t+p++s+++++v
  gi|320100851|ref|YP_004176443.1| 501 VVFQGDERGITGRQGNHDEQRYPIQWdrlnvevyehYKRLGELKNTIPALSTSIIHV 557
                                       678899999999875666664444443333332323225558899999999999885 PP

  == domain 4  score: 21.8 bits;  conditional E-value: 7.7e-08
                                       EEEEEECTTTEEEEEEE-SSSSEEECEEESSSSSEEEEETTCTTSGCCTTT-SSTSS-EEEECTTCBSEEEEEEEST CS
                   Alpha-amylase_C  11 viaFeRgdgekllvvfNfhpsnsrqdyrvgvpaagkyrdvlntdaeeyggsglgntgkvvtvdddgransltltlpp 87 
                                       ++a+ Rg  +++lv+ N++  ++ q y++  p +g+++ ++ +++++           +v+v+       +t+t+pp
  gi|320100851|ref|YP_004176443.1| 564 LLAYTRGYMDEVLVIANNDA-STPQSYEL--P-PGNWTLIYASNNWS-----------EVSVEH------NTVTVPP 619
                                       69****99448******887.6669****..*.********998886...........677775......69***** PP

                                       TEEEEEE CS
                   Alpha-amylase_C  88 rsalvlk 94 
                                       ++al+l 
  gi|320100851|ref|YP_004176443.1| 620 LTALILV 626
                                       ****996 PP

>> Glyco_hydro_70  Glycosyl hydrolase family 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.4e-07    0.0016     625     666 ..     244     284 ..     229     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.4e-07
                    Glyco_hydro_70 625 drydlglskpnkyGtaddlvdaikalhksGikviadwvpdqi 666
                                       d yd  ++ + k+Gt +dl   i   hk+Gikvi d+vpd +
  gi|320100851|ref|YP_004176443.1| 244 DTYDY-YTVDPKFGTLEDLKTLINEAHKRGIKVIFDFVPDHV 284
                                       77776.56677*****************************86 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.6e-06    0.0041      13      71 ..     564     620 ..     556     624 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                                       EEEEEEEETTEEEEEEEESS-EEEEE--GGGTT-EEEETTTTEE-----SS.EEEEE-TT CS
                    Malt_amylase_C  13 vlaYlReyedetilvvaNrsaqaveldlselagrvpvelfggeefpaigel.ytltLppy 71 
                                        laY+R y de +++++N +  +++ +l+    ++++ +  +++ + ++ +  t+t+pp 
  gi|320100851|ref|YP_004176443.1| 564 LLAYTRGYMDEVLVIANNDASTPQSYELP---PGNWTLIYASNNWSEVSVEhNTVTVPPL 620
                                       79***************************...5555555555555555544456777776 PP

>> GTA_holin_3TM  Holin of 3TMs, for gene-transfer release
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   5.4e-05      0.14      69     100 ..       2      33 ..       1      48 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                     GTA_holin_3TM  69 rwRPllgyvtlalllwaivldPllaaaialgl 100
                                       +wRP+ +y+tl+l+l+++   P++ a+i++ +
  gi|320100851|ref|YP_004176443.1|   2 GWRPVAVYATLILVLLQLTPLPIAGASIMEIY 33 
                                       7************************9999865 PP

>> GHL6  Hypothetical glycosyl hydrolase 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.27       7      64 ..     219     277 ..     214     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                              GHL6   7 eelkeagadtlvifardagg.vvyYrtkldfvtehpklk.rdllkelvkachregikvvv 64 
                                       ++lke+g+  + ++     g v  Y+t   ++t  pk    + lk l++++h++gikv+ 
  gi|320100851|ref|YP_004176443.1| 219 DYLKELGVGLIYLNPIFLSGsVHGYDTYD-YYTVDPKFGtLEDLKTLINEAHKRGIKVIF 277
                                       67788888877777766666577788875.89999999545666**************85 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.3   0.00028      0.72      19      74 ..     627     681 ..     607     683 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00028
                           TMEM154  19 eesadatsaasteseslkqeeakeslssaelsnesdqlelvlmiiiPlvllillll 74 
                                       +++   t+++st   s++++   e+++ +    e+d   l++++++Pl l  l+ll
  gi|320100851|ref|YP_004176443.1| 627 RNTVSETTTTSTAVTSFPGTMYTETTAIPG-RLEQDTRVLIIVVAVPLLLATLVLL 681
                                       456677888888888***888777777665.456778889*******998777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 5041.05
//
Query:       gi|320100852|ref|YP_004176444.1|  [L=297]
Description: cation diffusion facilitator family transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  11.7    3.6e-40  137.8  11.7    1.1  1  Cation_efflux  Cation efflux family
    8.7e-17   61.0   1.8    1.5e-16   60.3   1.7    1.5  1  ZT_dimer       Dimerisation domain of Zinc Transporter
     0.0052   16.9   0.1      0.012   15.8   0.1    1.7  1  YjcB           Family of unknown function
  ------ inclusion threshold ------
      0.011   16.1   2.7      0.011   16.1   2.7    2.1  2  DUF456         Protein of unknown function (DUF456)


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8  11.7     8e-44   3.6e-40       2     199 .]      19     211 ..      18     211 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 8e-44
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       ++s+++nlil+ v++ +gl++ S a++adafh+lsd++++l l+l++k++ kppde++pfG++r+e   ++v g ll
  gi|320100852|ref|YP_004176444.1|  19 WVSVAVNLILFTVKMYAGLVSSSIAVVADAFHTLSDCITSLALILGYKIAFKPPDEEHPFGHQRFEAATSIVIGTLL 95 
                                       689************************************************************************** PP

                     Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrkl.rsaalkaaalhvlgDaltslgvl 154
                                        ++++  +  +++kl+   e+++ +++a+vv+ vs+vv+ al++   r ++++ + ++++a+a+h+++Da+++l v+
  gi|320100852|ref|YP_004176444.1|  96 GVVGFEFINRSVDKLL-AREALVFSWIAVVVLTVSAVVKEALARWALRLAESVgGAESIRADAWHHRSDAVATLLVV 171
                                       ****************.9*************************98888888876999******************** PP

                     Cation_efflux 155 vsalvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                       +++++   +   +  ++D++++ll++ +i+y a++++k +++++l
  gi|320100852|ref|YP_004176444.1| 172 IGLMIGESV---W--WVDGLLGLLVSGLIIYVAYDIIKRASQDIL 211
                                       ****99998...4..9***********************999886 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   1.7   3.4e-20   1.5e-16       5      79 .]     219     292 ..     215     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.4e-20
                                       HHHHHHHHHTT-SS.-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE. CS
                          ZT_dimer   5 eeeeireiiksvpg.vkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHvePe 79 
                                       e+  +rei++ v g +++ h+++++++G++i v lhi++++ +++++aHe+a ++e++i++ + g  + +iHveP+
  gi|320100852|ref|YP_004176444.1| 219 EVSVLREIASGVSGdIRDLHHVHIHEYGDHIEVTLHIRLPPGMKLSDAHEVASRLEDAIRRTL-G-WEATIHVEPY 292
                                       677889999987755************************************************.7.468******7 PP

>> YjcB  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.7e-06     0.012      32      88 ..     160     216 ..     124     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-06
                              YjcB  32 rksdykalavvvsglGiaasCwfvtgllGitlaalalaeiwentkdvlvevmsktPa 88 
                                        +sd  a  +vv gl i+ s w+v gllG+ ++ l +   ++++k +  +++ ++P+
  gi|320100852|ref|YP_004176444.1| 160 HRSDAVATLLVVIGLMIGESVWWVDGLLGLLVSGLIIYVAYDIIKRASQDILGRAPS 216
                                       5788888889999********************999999999999999999998886 PP

>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   2.7   2.4e-06     0.011      28     131 ..      18     140 ..      12     145 .. 0.89
   2 ?    1.5   0.7     0.077   3.4e+02      64      95 ..     163     201 ..     143     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                            DUF456  28 gwlflavllvlallglvldylapalgakraGaskrgligaivGaivGffllp.p...............lGlllgpf 88 
                                       gw+ +av l+l+ + + + ++ + +++ +    + +  ++ +++i+G  + + p                 +++g +
  gi|320100852|ref|YP_004176444.1|  18 GWVSVAVNLILFTVKMYAGLVSSSIAVVADAFHTLSDCITSLALILGYKIAFkPpdeehpfghqrfeaaTSIVIGTL 94 
                                       699999999999999999999999999999999999999999*****9866664599999********99******* PP

                            DUF456  89 lgaflgEllrarkd...lreAlkaalgalvGfllgtlvklvlallm 131
                                       lg++  E++ +  d   +reAl  ++ a+v + ++++vk +la ++
  gi|320100852|ref|YP_004176444.1|  95 LGVVGFEFINRSVDkllAREALVFSWIAVVVLTVSAVVKEALARWA 140
                                       *******99888668999*********************9988665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.077
                            DUF456  64 ligaivGaivGffllp.p......lGlllgpflgaflgE 95 
                                        ++a++ +++G++++  +      lGll+  ++  ++ +
  gi|320100852|ref|YP_004176444.1| 163 DAVATLLVVIGLMIGEsVwwvdglLGLLVSGLIIYVAYD 201
                                       456777777777655553444555666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2322.62
//
Query:       gi|320100853|ref|YP_004176445.1|  [L=224]
Description: formylmethanofuran dehydrogenase subunit E [Desulfurococcus mucosus DSM 2162]
Scores for complete 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    6.4e-38  129.8   0.0    1.1  1  FmdE            FmdE, Molybdenum formylmethanofuran dehydroge
      5e-07   29.5   0.6    1.1e-06   28.5   0.6    1.5  1  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
  ------ inclusion threshold ------
      0.029   14.3   0.1      0.058   13.3   0.1    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.11   12.5   3.4        4.1    7.5   0.8    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.21   11.4   1.6       0.21   11.4   0.3    1.7  2  Hexapep         Bacterial transferase hexapeptide (six repeat


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 !  129.8   0.0   1.8e-41   6.4e-38       1     130 [.      13     156 ..      13     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 1.8e-41
                                       HHSS--CHHHHHHHHHHHHHHCC....-TT.....SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEE CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeeg.....deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkalt 72 
                                       fHGH+Cp+lvlG+rm+++al++lg++ + g      ee+ aive ++Cl+D++qv+tgctlG+++li++d+gk+alt
  gi|320100853|ref|YP_004176445.1|  13 FHGHVCPFLVLGLRMSEIALEKLGVR-RAGfreslHEEILAIVEANNCLVDGVQVATGCTLGNNSLIYVDTGKNALT 88 
                                       9***********************85.4557999******************************************* PP

                                       EEETTT-EEEEEEE-..........CCTHHHHHHHCCT--.GGGS-HHHHHHHHHHHHHHHHHS.HHHH CS
                              FmdE  73 fkkrktgkavrlklk..........eelpelreklakgka.keekeeeeleeeleeaikkilnapeeel 130
                                       ++kr+  k+vr++++          +e++el++k++++++ ++e e eel++++ee + +++n+peee+
  gi|320100853|ref|YP_004176445.1|  89 LVKRGLWKGVRIYVDherfsrkyipREASELFNKVVRERKgTPE-EVEELRRRWEEVGLSVRNLPEEEF 156
                                       ****************************************6666.9999******************97 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.6   2.9e-10   1.1e-06       2      32 ..     171     203 ..     170     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.9e-10
                      zf-dskA_traR   2 iygs..CeeCGEpIpeaRlralPgarlCveCqe 32 
                                        y s  C++CGE ++ +R + + g  lC++C+e
  gi|320100853|ref|YP_004176445.1| 171 VYPStrCSRCGELVMAPRAVEVNGHFLCKPCAE 203
                                       577778*************************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 ?   13.3   0.1   1.6e-05     0.058      16      53 ..     162     202 ..     154     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                    OrfB_Zn_ribbon  16 GikveevnpayTSktCseCgsknke...alsgrtfkCpnCg 53 
                                        ++ +e  p y S++Cs+Cg+ +        +  f C+ C 
  gi|320100853|ref|YP_004176445.1| 162 EVEAIEPAPVYPSTRCSRCGELVMApraVEVNGHFLCKPCA 202
                                       56777788899**********99887766667788888885 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.007        25       8      23 ..       5      20 ..       4      20 .. 0.89
   2 ?    7.5   0.8    0.0011       4.1      20      44 ..     176     202 ..     169     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.007
                     Zn_Tnp_IS1595  8 alLealrWpngfvCPh 23
                                      +l+e++ W +g+vCP+
  gi|320100853|ref|YP_004176445.1|  5 ELIERAKWFHGHVCPF 20
                                      688999*********6 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                     Zn_Tnp_IS1595  20 vCPhCgsr..kayriktrglfqCkeCr 44 
                                       +C +Cg     ++ ++  g f Ck C 
  gi|320100853|ref|YP_004176445.1| 176 RCSRCGELvmAPRAVEVNGHFLCKPCA 202
                                       4*****9999888888889*****995 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   5.8e-05      0.21       6      28 ..      57      78 ..      54      79 .. 0.87
   2 ?   -3.5   0.1       2.8     1e+04      20      24 ..     208     212 ..     207     213 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.8e-05
                                      TTEEE-TTEEEETTEEE-TTEEE CS
                           Hexapep  6 snvlIgpfaviggnVkIGdnvkI 28
                                      +n+l++ +++++ ++++G+n+ I
  gi|320100853|ref|YP_004176445.1| 57 NNCLVD-GVQVATGCTLGNNSLI 78
                                      799999.9999999999999877 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                                       EEE-T CS
                           Hexapep  20 VkIGd 24 
                                       +++G+
  gi|320100853|ref|YP_004176445.1| 208 AVVGR 212
                                       45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1659.70
//
Query:       gi|320100854|ref|YP_004176446.1|  [L=390]
Description: periplasmic-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-21   75.2   0.0    7.2e-21   74.8   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0     4e-25   7.2e-21       1     234 [.      70     319 ..      70     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 4e-25
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.............TS-BSBESSSB-HHHHHHH--SEEEE- CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee...........aivevgadgeidvEklaalkPDlvils 66 
                                       i++++p+  ++ + l at+ +vgv++  +++++  ++ +            i + g ++ +d E++a ++PDl+++s
  gi|320100854|ref|YP_004176446.1|  70 IVAIGPGALRLIVYLNATELLVGVEEVEKTWSPVGRDYAmaygdvlkalpVIGKGGPGNPPDPEAIASVRPDLIVMS 146
                                       899999999999999999999999999999998877777788888884444466666777777************** PP

                                       GGG....GGGHHHHHHHS-EEE----TTS....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT... CS
                      Peripla_BP_2  67 kgl.gltdedeellksgiptvivessntg....eslkeqiralgellgledeaeklvaeidsklaaaksaidse..k 136
                                       +++  l d de  ++ g+ +++v++s++     + +++ +r lge+lg+ d+ae+lv+  +s l +++s++  +  +
  gi|320100854|ref|YP_004176446.1| 147 AYYtTLKDPDELSRATGAAVIVVDYSPVTstnlSMFYRALRLLGEVLGRSDRAEALVNYTESLLKDLRSRTTGLntT 223
                                       ***99999999999*************999**9*****************************************633 PP

                                       -EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--.STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HH CS
                      Peripla_BP_2 137 pkpvlvfggadeggyvvagsnsyigdlldalgieniaaesk.kseyeeisaEqilasdpdvifvsgraeadnktgle 212
                                          v v + +++gg  ++g++    + l++lg+++ia++ + + ++ +++++ il ++pdv+fv+     + + +++
  gi|320100854|ref|YP_004176446.1| 224 SIRVYVGAVSYRGGQPFTGTQVPYPP-LSWLGMASIADTMAtTRGFLNVDFDSILMAQPDVVFVDEG---NLNIVVQ 296
                                       33344444556677777777776666.577******999999***********************99...9999999 PP

                                       HHT-SHH.HHTSHHHHTT-EEEE CS
                      Peripla_BP_2 213 flkenpl.laelpAvkngrVyal 234
                                       ++ ++p+ + +l A+  grVy+l
  gi|320100854|ref|YP_004176446.1| 297 DFSKDPGkYCALRAFTGGRVYGL 319
                                       99999875889999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3014.21
//
Query:       gi|320100855|ref|YP_004176447.1|  [L=344]
Description: transport system permease [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-67  228.1  42.1    1.5e-67  227.8  42.1    1.0  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
       0.14   11.6  29.7       0.52    9.8  29.7    1.9  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 !  227.8  42.1   1.7e-71   1.5e-67       2     311 ..      14     335 ..      13     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.8 bits;  conditional E-value: 1.7e-71
                             FecCD   2 lllllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilG 78 
                                       ll+++ll +++ga+++ + +++ ++ g+ d+  a +v++ r+ r+l+a+l+G  L+++ ++lQ+v+rNpLa+P +lG
  gi|320100855|ref|YP_004176447.1|  14 LLIAVLLDISMGAYPVGLRDLLGYIGGSLDDRIALVVIDARVRRILTAILAGSVLSLSTLVLQSVFRNPLASPFTLG 90 
                                       7899**********************999************************************************ PP

                             FecCD  79 issgaalgavlallll............lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsal 143
                                       ++++a+lga +a++ll            +   + f++++aafl  +   +lv++l+ + +g + ++liLa i++s+l
  gi|320100855|ref|YP_004176447.1|  91 LQHAASLGAGVAIMLLqagsilksstpgVYIGNPFTVSAAAFLATFGHGVLVITLS-SIAGLTVYSLILASIILSFL 166
                                       ***********************9999988899999999999999999********.******************** PP

                             FecCD 144 lsaltsllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnver 219
                                       ++++  l+++l+ ne +++++lfw +G+ls+ +w +++l++  lllll+++++ +  ldll ++de+A+s Gvn++ 
  gi|320100855|ref|YP_004176447.1| 167 TQSILYLMQYLFfNEISVSTLLFWSVGDLSRTTWCEIALIASSLLLLLVYAWWESMSLDLLGFSDELASSSGVNPAL 243
                                       **********999**************************************************************** PP

                             FecCD 220 vrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgi 296
                                       +rll +llv+l+++v+v+++G+igF GLi+    r+lvg ++r+ +p+  l+G+++++ ad+++r +l+p+ +pvg+
  gi|320100855|ref|YP_004176447.1| 244 TRLLSILLVSLAVGVTVSFTGIIGFAGLIALYASRILVGWSTRRCIPAVLLMGSIIMVSADIIGRSILKPVVIPVGV 320
                                       ***************************************************************************** PP

                             FecCD 297 vtaliGapffiylll 311
                                       vt+liG p++++l+l
  gi|320100855|ref|YP_004176447.1| 321 VTSLIGSPLLLLLML 335
                                       ************986 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  29.7   5.8e-05      0.52       5     251 ..      58     330 ..      54     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.8e-05
                             ABC-3   5 lqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvn..................lllgailv 63 
                                       ++ a+la+ ++sl + +l s      +s +  +l Haa  G ++a++l                     ++++a+l+
  gi|320100855|ref|YP_004176447.1|  58 ILTAILAGSVLSLSTLVLQSVFRNPLASPFTLGLQHAASLGAGVAIMLLQAgsilksstpgvyignpftVSAAAFLA 134
                                       56788888888888888888666667888888888888887777776655556778888888888876566777888 PP

                             ABC-3  64 gliaavalellkrktklkedtai..givlsvflalglv.lvslikkskvdldsyLfGniltisqedliliaiieavv 137
                                       ++   v +  l++ + l   ++i   i+ls fl  +++ l+++    + +++  Lf ++  +s++  + ia i+  +
  gi|320100855|ref|YP_004176447.1| 135 TFGHGVLVITLSSIAGLTVYSLIlaSIILS-FLTQSILyLMQYLFFNEISVSTLLFWSVGDLSRTTWCEIALIASSL 210
                                       888888888888877665544322144444.444444414455554999*******999999999988888887766 PP

                             ABC-3 138 llllllfwke...lllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaa...tArrltr 208
                                       llll++ w e   l l+ f+ elA ++g+++ l +ll ++l++lav v++ + G+i  + l+ + a+   +     r
  gi|320100855|ref|YP_004176447.1| 211 LLLLVYAWWEsmsLDLLGFSDELASSSGVNPALTRLLSILLVSLAVGVTVSFTGIIGFAGLIALYASrilVGWSTRR 287
                                       666666664322277899**************************************888887766652213333344 PP

                             ABC-3 209 slesllivAillglvsvvaGlllSyyldlatGavivlvatllf 251
                                        +  +l++ +++ + + ++G  +   + ++ G v  l+ + l+
  gi|320100855|ref|YP_004176447.1| 288 CIPAVLLMGSIIMVSADIIGRSILKPVVIPVGVVTSLIGSPLL 330
                                       4666666666666666666666666666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2735.78
//
Query:       gi|320100856|ref|YP_004176448.1|  [L=253]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-30  105.0   0.0    5.6e-30  104.7   0.0    1.1  1  ABC_tran     ABC transporter
    1.7e-13   51.1   0.5    1.1e-05   25.4   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    9.3e-08   31.8   0.2    1.9e-05   24.2   0.2    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    1.2e-05   25.3   0.0    0.00081   19.2   0.0    2.0  2  AAA_15       AAA ATPase domain
    5.3e-05   22.9   0.0    9.6e-05   22.0   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00012   22.6   0.0    0.00019   22.0   0.0    1.2  1  AAA_23       AAA domain
    0.00028   21.3   0.1    0.00063   20.2   0.1    1.6  1  AAA_16       AAA ATPase domain
     0.0019   15.8   0.1     0.0026   15.4   0.1    1.1  1  DUF3584      Protein of unknown function (DUF3584)
     0.0031   17.8   0.3      0.024   14.9   0.3    2.1  1  AAA_22       AAA domain
     0.0054   15.5   0.0      0.008   14.9   0.0    1.2  1  RNA12        RNA12 protein
     0.0078   15.1   0.0      0.022   13.6   0.0    1.6  2  AFG1_ATPase  AFG1-like ATPase
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.026   14.4   0.0    1.5  1  ATPase_2     ATPase domain predominantly from Archaea
      0.014   15.0   0.1      0.025   14.2   0.1    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.015   15.5   0.0       0.03   14.5   0.0    1.6  1  AAA_33       AAA domain
      0.016   14.0   0.1        2.7    6.7   0.1    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.019   15.4   0.0       0.41   11.1   0.0    2.2  2  AAA          ATPase family associated with various cellular a
      0.024   13.3   0.0        2.2    6.8   0.1    2.0  2  AAA_13       AAA domain
       0.03   14.6   0.1       0.53   10.5   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.032   14.1   0.2       0.22   11.4   0.1    2.0  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.064   13.2   0.1       0.62   10.1   0.0    2.2  2  AAA_5        AAA domain (dynein-related subfamily)
      0.075   12.9   0.1       0.25   11.2   0.0    1.8  1  DUF5591      Domain of unknown function (DUF5591)
      0.076   13.1   0.0      0.094   12.8   0.0    1.3  1  DUF87        Helicase HerA, central domain
      0.076   12.1   0.1       0.13   11.2   0.1    1.3  1  T2SSE        Type II/IV secretion system protein
      0.082   12.6   0.0       0.18   11.5   0.0    1.5  1  AAA_30       AAA domain
      0.087   12.9   0.0       0.17   11.9   0.0    1.6  2  AAA_14       AAA domain
       0.14   11.9   0.1       0.41   10.4   0.1    1.7  2  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.19   11.6   0.1       0.45   10.4   0.1    1.6  1  NACHT        NACHT domain
       0.19   11.0   0.0       0.33   10.2   0.0    1.3  1  Zeta_toxin   Zeta toxin
        0.2   11.4   0.1       0.72    9.5   0.0    1.8  2  AAA_24       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0     9e-33   5.6e-30       1     137 []      19     167 ..      19     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 9e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ vs+++k+++ ++ivG+nG+GK+tLl++++g lkp +G + +dgk + e ++++l +  g++pq       lt++
  gi|320100856|ref|YP_004176448.1|  19 LNGVSVEIKPSSFTGIVGPNGSGKTTLLRVMLGILKPRSGVVYIDGKAIGEYDRRRLASIYGYVPQRLDSITPLTLY 95 
                                       789****************************************************************7777777788 PP

                                       HH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +                  + e +++a++ +gl+e+  + +    ++LSgG+ qr  +aral+ +p+++llDEpt+
  gi|320100856|ref|YP_004176448.1|  96 DFvstgrrpyaslkglssRDHEAVARAIKAVGLEEKSSSLL----TELSGGELQRALIARALAAEPRIMLLDEPTS 167
                                       88999999*99999987666666999999999999999998....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.8e-08   1.1e-05       1      23 [.      31      53 ..      31      81 .. 0.79
   2 !   24.2   0.1     4e-08   2.5e-05     235     298 ..     137     197 ..     107     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.8e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      +++++GpNgsGK++LL+ + ++ 
  gi|320100856|ref|YP_004176448.1| 31 FTGIVGPNGSGKTTLLRVMLGIL 53
                                      79****************98884 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 4e-08
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +elS G ++  al++  l+a +  ++ l+DEp ++L+P  +  +++ll++l+rng+ v++t H+
  gi|320100856|ref|YP_004176448.1| 137 TELSGGELQR-ALIARALAAEP--RIMLLDEPTSNLDPYHQLMVMKLLRNLTRNGVTVVATLHD 197
                                       689*******.99999999998..**************7777777***************9665 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 !   24.2   0.2     3e-08   1.9e-05      24     198 ..      29     196 ..      10     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3e-08
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                       +sft ivGpNGSGK+ ll  +   LG      l+ ++    i   k+  + ++ +++ ++    ++   + + +++ 
  gi|320100856|ref|YP_004176448.1|  29 SSFTGIVGPNGSGKTTLLRVM---LGI-----LKPRSGVVYIDG-KAIGEYDRRRLASIYGYVPQR-LDSITPLTLY 95 
                                       46***************9998...884.....455554555555.444444444444444333333.2223445555 PP

                                       EEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtk.kevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                         v+++ +    ++g + +  + v++ ++ +g++++      +LSgGe + + +a  +A   ++p  ++llDe  ++
  gi|320100856|ref|YP_004176448.1|  96 DFVSTGRRPYASLKGLSSRDhEAVARAIKAVGLEEKssslltELSGGELQRALIARALA---AEP-RIMLLDEPTSN 168
                                       5555555555567777666645577777777777777777779****976544444433...344.4889******* PP

                                       S-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkeksknaQfivislr 198
                                       LD  +   v +ll++ + n   +v +l+
  gi|320100856|ref|YP_004176448.1| 169 LDPYHQLMVMKLLRNLTRNGVTVVATLH 196
                                       ***************9999888888876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.3e-06   0.00081      17      62 ..      22      64 ..      17      77 .. 0.75
   2 ?    4.1   0.0     0.051        31     322     360 ..     155     192 ..     143     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiek 62
                                      v+++++++ +t ++G+N+sGK+++l+++  +l+      + v++i+ 
  gi|320100856|ref|YP_004176448.1| 22 VSVEIKPSsFTGIVGPNGSGKTTLLRVMLGILKPR----SGVVYIDG 64
                                      677777777*****************997777755....45555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.051
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360
                                       +++ i l++EP  +L p +q +++kll++l +++   v+
  gi|320100856|ref|YP_004176448.1| 155 AEPRIMLLDEPTSNLDPYHQLMVMKLLRNLTRNGV-TVV 192
                                       56789*************************99985.455 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 !   22.0   0.0   1.6e-07   9.6e-05      13      50 ..      20      57 ..      17      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.6e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +g ++ei+++++t ++Gp+GsGK+Tll  +  +L p++
  gi|320100856|ref|YP_004176448.1| 20 NGVSVEIKPSSFTGIVGPNGSGKTTLLRVMLGILKPRS 57
                                      678999*********************88888888876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.1e-07   0.00019      20      39 ..      30      49 ..      12      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.1e-07
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       +t I+GpNG+GKTT+l+ +
  gi|320100856|ref|YP_004176448.1| 30 SFTGIVGPNGSGKTTLLRVM 49
                                      689*************9865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1     1e-06   0.00063      28     145 ..      33     166 ..      23     192 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1e-06
                            AAA_16  28 llsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa..laqalareellrqllde............. 88 
                                        ++G+ G+GK++l+r  l  l+ + g++ + gk+        y+   la++    +++ q ld              
  gi|320100856|ref|YP_004176448.1|  33 GIVGPNGSGKTTLLRVMLGILKPRSGVVyIDGKAIGE-----YDRrrLASIY---GYVPQRLDSitpltlydfvstg 101
                                       589***************9999885444488887777.....2111122222...3444444443333444444444 PP

                            AAA_16  89 .........aesaeleawrekleealaavpelagaea......srllellkrll.allsrderplvlvlDdlq 145
                                                +     ++++e+  +   a++++  +e+      +    +l+r+l a++   ++p +++lD+  
  gi|320100856|ref|YP_004176448.1| 102 rrpyaslkgL----SSRDHEAVAR---AIKAVGLEEKssslltELSGGELQRALiARALA-AEPRIMLLDEPT 166
                                       6544422222....2222222222...333333333343455544445566666577777.778999999755 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   4.1e-06    0.0026       7      36 ..      19      48 ..      14      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
                           DUF3584  7 lkGrvaeldldghtnieGtNaaGKTtLlrL 36
                                      l G+  e++++  t i+G N++GKTtLlr+
  gi|320100856|ref|YP_004176448.1| 19 LNGVSVEIKPSSFTGIVGPNGSGKTTLLRV 48
                                      568777***********************7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   3.9e-05     0.024       6      51 ..      30      68 ..      25     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51
                                      +++ ++G+ G+GKTtllr +l  l+       +r++vv+++ ++ +
  gi|320100856|ref|YP_004176448.1| 30 SFTGIVGPNGSGKTTLLRVMLGILK-------PRSGVVYIDGKAIG 68
                                      67789*************9999986.......47777777766555 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-05     0.008      15      55 ..      27      69 ..      21      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                             RNA12 15 nvntFivvkGPrGSGkkeL..vldrvlkdrkkvlvidCdelvk 55
                                      ++++F+ + GP GSGk+ L  v+  +lk r+ v++id +++ +
  gi|320100856|ref|YP_004176448.1| 27 KPSSFTGIVGPNGSGKTTLlrVMLGILKPRSGVVYIDGKAIGE 69
                                      6789**************97789999***********999976 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.9   1.2e+03      67      80 ..      34      47 ..      26      54 .. 0.85
   2 !   13.6   0.0   3.6e-05     0.022     108     164 ..     137     194 ..     128     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.9
                       AFG1_ATPase 67 lwGgvGrGKtylmd 80
                                      + G+ G GKt l+ 
  gi|320100856|ref|YP_004176448.1| 34 IVGPNGSGKTTLLR 47
                                      5799*******986 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.6e-05
                       AFG1_ATPase 108 tklrkekdplaivadrlaeearvlCfDEfevs.DiadamllsrLleaLfargvtlvaT 164
                                       t+l++++   a +a +la+e r++ +DE + + D+   +++ +Ll++L ++gvt+vaT
  gi|320100856|ref|YP_004176448.1| 137 TELSGGELQRALIARALAAEPRIMLLDEPTSNlDPYHQLMVMKLLRNLTRNGVTVVAT 194
                                       566666666778999*************76544************************9 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.3e-05     0.026      18      55 ..      27      63 ..      22      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyi 55
                                      +p+++  i Gp gsGKt+Ll+ ++  l+  +  v+y++
  gi|320100856|ref|YP_004176448.1| 27 KPSSFTGIVGPNGSGKTTLLRVMLGILKPRS-GVVYID 63
                                      67788889***************99996644.788875 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 ?   14.2   0.1     4e-05     0.025       3      21 ..      32      50 ..      30      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      t+++G+ GsGKTtLl+ +l
  gi|320100856|ref|YP_004176448.1| 32 TGIVGPNGSGKTTLLRVML 50
                                      89*************9987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.9e-05      0.03       4      96 ..      34     188 ..      32     202 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.9e-05
                            AAA_33   4 lvGlpGsGKstlaerllkklg....avllssdt............................................ 32 
                                       +vG++GsGK+tl++ +l  l+    +v ++  +                                            
  gi|320100856|ref|YP_004176448.1|  34 IVGPNGSGKTTLLRVMLGILKprsgVVYIDGKAigeydrrrlasiygyvpqrldsitpltlydfvstgrrpyaslkg 110
                                       69************997666556555556666677777777777777777777777777777777777777777777 PP

                            AAA_33  33 .........lrr.rlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat..nlsr.rer..arflklarr 94 
                                                +r  + +g +++s + +t+++    q+   +ar  +++ r ++ld +  nl++ ++   +++l+ + r
  gi|320100856|ref|YP_004176448.1| 111 lssrdheavARAiKAVGLEEKSSSLLTELSGGELQRA-LIARALAAEPRIMLLDEPtsNLDPyHQLmvMKLLRNLTR 186
                                       7777777753333333355556666666665544443.244444444455666766566666333333344444444 PP

                            AAA_33  95 lg 96 
                                        g
  gi|320100856|ref|YP_004176448.1| 187 NG 188
                                       44 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0044       2.7     234     263 ..      16      48 ..       6      53 .. 0.72
   2 ?    5.4   0.0     0.011       6.6     320     353 ..     136     169 ..     122     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0044
                                       TEEEEEEEE...-SSEEEEEE-TTSSHHHHHHH CS
                        ABC_ATPase 234 gkkvsGmgi...pkGvtlIvGggfhGKsTLLeA 263
                                       ++ ++G+ +   p   t IvG++  GK+TLL+ 
  gi|320100856|ref|YP_004176448.1|  16 TRVLNGVSVeikPSSFTGIVGPNGSGKTTLLRV 48 
                                       555566554222445899*************85 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                                       ESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 320 tedASGStsqAanimealeagakllLiDEDtsAt 353
                                        ++ SG   q a i++al a+ +++L+DE ts  
  gi|320100856|ref|YP_004176448.1| 136 LTELSGGELQRALIARALAAEPRIMLLDEPTSNL 169
                                       456799999********************99964 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00067      0.41       3      34 ..      34      67 ..      33      91 .. 0.81
   2 ?    2.1   0.0      0.39   2.4e+02      17      66 ..     118     164 ..     116     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00067
                                      EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTC CS
                               AAA  3 lyGppGtGKTllakavakelg..vefleisgsel 34
                                      ++Gp G GKT+l + +   l+  + ++ i+g+ +
  gi|320100856|ref|YP_004176448.1| 34 IVGPNGSGKTTLLRVMLGILKprSGVVYIDGKAI 67
                                      58*************9999975455777777766 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.39
                                       HHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  17 avakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDE 66 
                                       ava+ +++  le + s+ll  +   + +  r+l+++a + + p i+++DE
  gi|320100856|ref|YP_004176448.1| 118 AVARAIKAVGLEEKSSSLL--TELSGGELQRALIARALAAE-PRIMLLDE 164
                                       6666666666666666666..44556677778887776555.99999999 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0036       2.2      21      36 ..      34      49 ..      25      69 .. 0.87
   2 ?    4.4   0.0     0.019        12     526     556 ..     156     186 ..     147     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0036
                            AAA_13 21 iYGwNGaGKTtLSrll 36
                                      i G NG+GKTtL r++
  gi|320100856|ref|YP_004176448.1| 34 IVGPNGSGKTTLLRVM 49
                                      679*********8876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrll 556
                                       + +i  +D P S LD  ++ +v+ l+++ ++
  gi|320100856|ref|YP_004176448.1| 156 EPRIMLLDEPTSNLDPYHQLMVMKLLRNLTR 186
                                       789*************************984 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00086      0.53      62      89 ..     155     182 ..     113     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00086
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                         +r+++LDE  s+lD+  +  +++ll+
  gi|320100856|ref|YP_004176448.1| 155 AEPRIMLLDEPTSNLDPYHQLMVMKLLR 182
                                       3599*************99999999997 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00036      0.22       3      26 ..      33      56 ..      31      62 .. 0.88
   2 ?    0.2   0.0         1   6.3e+02      15      36 ..     176     197 ..     174     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                              MobB  3 givgksgsGKTtLleklipelkar 26
                                      givg +gsGKTtLl  ++ +lk r
  gi|320100856|ref|YP_004176448.1| 33 GIVGPNGSGKTTLLRVMLGILKPR 56
                                      79***************9999876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1
                              MobB  15 LleklipelkarglrvgtiKha 36 
                                       ++ kl++ l+++g++v +  h+
  gi|320100856|ref|YP_004176448.1| 176 MVMKLLRNLTRNGVTVVATLHD 197
                                       6789*********998655554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0     0.001      0.62       4      30 ..      34      62 ..      33      72 .. 0.82
   2 ?    0.7   0.0      0.77   4.8e+02      86     124 ..     159     199 ..     135     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.001
                                      EE--SSSSHHHHHHHGGGGB..S--EEEE CS
                             AAA_5  4 LvGppGtgKselaerlaaal..nreveyv 30
                                      +vGp G+gK++l + ++  l  ++ v+y+
  gi|320100856|ref|YP_004176448.1| 34 IVGPNGSGKTTLLRVMLGILkpRSGVVYI 62
                                      69**************9999755555555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.77
                                       HHHHHSSEEE..-SSSEEE---........-EEEEEESS-- CS
                             AAA_5  86 lslleerrllleeggelvkakndd.ller.frviatanpld 124
                                       ++ll+e +  l++ ++l+  k    l+++ ++v+at ++l+
  gi|320100856|ref|YP_004176448.1| 159 IMLLDEPTSNLDPYHQLMVMKLLRnLTRNgVTVVATLHDLN 199
                                       46777777777777777777765544444777777777665 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00041      0.25      57      84 ..      75     102 ..      64     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                                       E-SS-.EEEGGGTT-------------- CS
                           DUF5591  57 ltsPlGvvPreleevYPaaqYdiavtge 84 
                                       l s +G vP+ l+++ P++ Yd + tg+
  gi|320100856|ref|YP_004176448.1|  75 LASIYGYVPQRLDSITPLTLYDFVSTGR 102
                                       7899**********************96 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015     0.094      26      68 ..      32      74 ..      20     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                             DUF87 26 lAilgsTGsGKSntvavLleellekkgatililD..pHGEYgkal 68
                                      ++i+g  GsGK+++ +v+l  +l k+++ ++ +D  + GEY + +
  gi|320100856|ref|YP_004176448.1| 32 TGIVGPNGSGKTTLLRVMLG-IL-KPRSGVVYIDgkAIGEYDRRR 74
                                      699***************96.55.6*********55558999888 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 ?   11.2   0.1   0.00022      0.13     134     159 ..      34      58 ..      20      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                             T2SSE 134 vsGgTgsGKttllyallkeinksder 159
                                       + G+ gsGKttll ++l +++ +   
  gi|320100856|ref|YP_004176448.1|  34 IVGPNGSGKTTLLRVMLGILKPR-SG 58 
                                       56****************99987.44 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.18      20      43 ..      31      54 ..      24      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                            AAA_30 20 vavltGpAGtGKttalkalreawe 43
                                      ++ ++Gp G+GKtt+l+++  +++
  gi|320100856|ref|YP_004176448.1| 31 FTGIVGPNGSGKTTLLRVMLGILK 54
                                      7789*************9876665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027      0.17       5      53 ..      32      79 ..      29     141 .. 0.83
   2 ?   -2.6   0.0       8.6   5.3e+03      53      72 ..     145     164 ..     119     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekll 53
                                        i+G+  +GKTtll+ ++  l  +++ ++yi+ +   +++++  ++++
  gi|320100856|ref|YP_004176448.1| 32 TGIVGPNGSGKTTLLRVMLGILK-PRSGVVYIDGKAIGEYDRRRLASIY 79
                                      5799***********99997777.9999999999887777666555455 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.6
                            AAA_14  53 lelilek.lkeekktylflDE 72 
                                        +++ ++ l   + ++++lDE
  gi|320100856|ref|YP_004176448.1| 145 QRALIARaLA-AEPRIMLLDE 164
                                       4444444233.3667777777 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 ?   10.4   0.1   0.00066      0.41       1      23 [.      34      56 ..      34      66 .. 0.82
   2 ?   -1.6   0.0         3   1.9e+03     111     133 ..     177     199 ..     167     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00066
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelr 23
                                      +vGp GsGKtt+ + +  il+ r
  gi|320100856|ref|YP_004176448.1| 34 IVGPNGSGKTTLLRVMLGILKPR 56
                                      79************999888766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3
                        ATP_bind_1 111 lakiveeLesefalvvvyLvDsq 133
                                         k++++L++++ +vv  L D +
  gi|320100856|ref|YP_004176448.1| 177 VMKLLRNLTRNGVTVVATLHDLN 199
                                       45688899999999998888865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00072      0.45       5      19 ..      34      48 ..      31      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00072
                                      EEC-TTTCHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqk 19
                                      + G++GsGKTtLl+ 
  gi|320100856|ref|YP_004176448.1| 34 IVGPNGSGKTTLLRV 48
                                      78***********85 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00053      0.33      21      53 ..      34      66 ..      25      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00053
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                      ++G  G+GK++l++ +   l+++++vv +d+  
  gi|320100856|ref|YP_004176448.1| 34 IVGPNGSGKTTLLRVMLGILKPRSGVVYIDGKA 66
                                      67999************************9865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0012      0.72       7      24 ..      34      55 ..      31      91 .. 0.81
   2 ?   -0.9   0.0       1.9   1.2e+03     111     131 ..     177     197 ..     172     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                            AAA_24  7 iyGpsgiGKTtlakel....gp 24
                                      i+Gp+g+GKTtl++ +    +p
  gi|320100856|ref|YP_004176448.1| 34 IVGPNGSGKTTLLRVMlgilKP 55
                                      99**********9988776643 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                            AAA_24 111 frrllkklqelrknvifiahe 131
                                       +++ll++l+  + +v+++ h 
  gi|320100856|ref|YP_004176448.1| 177 VMKLLRNLTRNGVTVVATLHD 197
                                       6889999999999***99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1847.40
//
Query:       gi|320100857|ref|YP_004176449.1|  [L=193]
Description: TATA-binding protein of transcription factor TFIID [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-55  184.6   0.1    1.2e-26   92.5   0.0    2.0  2  TBP         Transcription factor TFIID (or TATA-binding prote
    4.7e-07   29.8   0.0      0.041   14.0   0.0    2.2  2  DUF3378     Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.044   13.5   1.3       0.19   11.4   0.1    2.5  3  Spore_YhaL  Sporulation protein YhaL
      0.084   12.9   0.0       0.17   11.8   0.0    1.4  1  DUF4865     Domain of unknown function (DUF4865)


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 !   90.5   0.0   1.1e-29   4.8e-26       2      84 ..      11      91 ..      10      92 .. 0.96
   2 !   92.5   0.0   2.6e-30   1.2e-26       2      84 ..     102     182 ..     101     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 1.1e-29
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++++N+va++ l+++ldLe ++++     ++Y+p++fpgl++rl++p++tal+F+sGk+v+tG+ks+++l ea+kki++
  gi|320100857|ref|YP_004176449.1| 11 YRVENIVATVILEHDLDLELIETRI--PSITYKPDQFPGLIFRLDKPRATALVFKSGKMVVTGTKSTQQLVEAVKKIIK 87
                                      68*******************9887..***************************************************9 PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                      ++ k
  gi|320100857|ref|YP_004176449.1| 88 VFMK 91
                                      9876 PP

  == domain 2  score: 92.5 bits;  conditional E-value: 2.6e-30
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       ++iqN+va  +++  ++Lek a+++  +++ Yepe+fpgl+ r+r+p+v++liFssGk+vitGak+e+e+++a+ +i
  gi|320100857|ref|YP_004176449.1| 102 VQIQNIVAGGDIHAYVNLEKAAYHL--EDSMYEPEQFPGLIHRMRDPRVVLLIFSSGKMVITGAKEESEVERAVVNI 176
                                       79********************998..************************************************** PP

                                       HHHHHH CS
                               TBP  79 apilkk 84 
                                       a+ l +
  gi|320100857|ref|YP_004176449.1| 177 ARQLYE 182
                                       *99975 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.2e-05     0.052      24      57 ..      42      75 ..      27      81 .. 0.89
   2 !   14.0   0.0   9.2e-06     0.041      23      61 ..     132     170 ..     120     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                           DUF3378 24 skkppyavfaakkndttItaYtSgKVlFQGknae 57
                                        + p+ +f+ +k+ +t  +++SgK ++ G++  
  gi|320100857|ref|YP_004176449.1| 42 PDQFPGLIFRLDKPRATALVFKSGKMVVTGTKST 75
                                      5689**************************9865 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.2e-06
                           DUF3378  23 rskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61 
                                       + ++ p+ + + +++ ++  ++ SgK ++ G++ e+e +
  gi|320100857|ref|YP_004176449.1| 132 EPEQFPGLIHRMRDPRVVLLIFSSGKMVITGAKEESEVE 170
                                       56789******************************9976 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.33   1.5e+03      20      35 ..      17      32 ..      15      33 .. 0.86
   2 ?   -1.5   0.0      0.46   2.1e+03      12      28 ..      61      77 ..      58      91 .. 0.71
   3 ?   11.4   0.1   4.3e-05      0.19       8      33 ..     148     173 ..     147     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.33
                        Spore_YhaL 20 vktakeEreldqefIE 35
                                      v t   E++ld e IE
  gi|320100857|ref|YP_004176449.1| 17 VATVILEHDLDLELIE 32
                                      7888999****99999 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                        Spore_YhaL 12 IlfSgymavktakeEre 28
                                      ++ Sg m+v+ +k  ++
  gi|320100857|ref|YP_004176449.1| 61 VFKSGKMVVTGTKSTQQ 77
                                      56688888887776655 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 4.3e-05
                        Spore_YhaL   8 viagIlfSgymavktakeEreldqef 33 
                                       v++ I+ Sg m+++ akeE e++++ 
  gi|320100857|ref|YP_004176449.1| 148 VVLLIFSSGKMVITGAKEESEVERAV 173
                                       8999******************9876 PP

>> DUF4865  Domain of unknown function (DUF4865)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.9e-05      0.17       8      39 ..      20      51 ..      16      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                           DUF4865  8 itLpadydmeiirkRvaekGhllDgfegLglK 39
                                      + L  d d+e i++R+ +  ++ D+f+gL ++
  gi|320100857|ref|YP_004176449.1| 20 VILEHDLDLELIETRIPSITYKPDQFPGLIFR 51
                                      7899*************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1427.08
//
Query:       gi|320100858|ref|YP_004176450.1|  [L=560]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-93  312.2   0.2    6.6e-93  311.9   0.2    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 !  311.9   0.2   3.7e-97   6.6e-93       2     563 ..      11     553 ..      10     553 .. 0.86

  Alignments for each domain:
  == domain 1  score: 311.9 bits;  conditional E-value: 3.7e-97
                           DUF2070   2 eklskyifrlPswk.vsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflall 77 
                                        ++++++f+lP+w+ +++++i++ a+++  l +++ +   +ll  l  +  +l  ++vl  +    ++kr + l+l+
  gi|320100858|ref|YP_004176450.1|  11 GRYYSVLFSLPHWEiLAVVFIVIAAAALISLGVNALP---FLLNSLIVI-VVLEAYRVLYPYTVFHKLKRIMGLSLT 83 
                                       589**********988888888888887777766655...333333322.222333444444444789999****** PP

                           DUF2070  78 telivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly....fs 150
                                       t+++++i            ++lvl  +vl++a++  +++ vl  +++++++++++ a++   ++i++++++      
  gi|320100858|ref|YP_004176450.1|  84 TLIYALI------------YNLVLRDWVLAVAASSTIVIAVLQGLDGTKWWRYIV-ATLPAGASIAISLWLtapvTL 147
                                       *******............7889999**************************993.344444444444444344444 PP

                           DUF2070 151 pesfllllllslifalavylfivvvdrplkrnlgvsaldllsaFlahilegskelEeffeeigeeadvpvkvlsfrr 227
                                            ++++l+l+f   ++ fi+++ +  +r+ g++a dl   Fl ++le++k++Ee+f++++++++v+ +++++  
  gi|320100858|ref|YP_004176450.1| 148 RGELSRAIILLLLF--SLADFIIYLAMGRHRINGYRAPDLGTLFLQNWLERRKNIEEVFDKLSTHENVHPRIVFL-- 220
                                       45555555555555..4579*******************************************************.. PP

                           DUF2070 228 edgekallvvPniHPGPlgeiGGsnLpkilaerldel...vlvlHgtatHdfNlvserevekiveavkealeele.y 300
                                          +++++v++++H+GP+++ G+s+Lp  l++ l++l   ++ lHg+++Hd+Nl+s+r+  ++++++ ++  ++e +
  gi|320100858|ref|YP_004176450.1| 221 ---GDLAVVYTDLHYGPFSNTGSSELPGELSSLLSKLgytAVTLHGFGSHDRNLASSRYLGEYLKKIYTTVMDAErE 294
                                       ...************************************9*******************************999977 PP

                           DUF2070 301 sskaskpvrvesgd.vkllgqrfgdslllvitrapegiDDiplsvglsimaeakaegfedvllVDaHNsfseeagev 376
                                       + +++++ r + +d ++ l+++f+  ++++++r+ +giDDip+++ l +   a+++g++dv+++D+HN++++e+  +
  gi|320100858|ref|YP_004176450.1| 295 ELRYHGALRLRGDDgWETLTLVFDRLSIVFVSRPGKGIDDIPYNLHLHYNVVARKKGLGDVVFIDSHNWEKQEEFHI 371
                                       77888*****************************************************************9998888 PP

                           DUF2070 377 lpgsedaeeliraaekalekleaaeeselkvgvarsetpkltpeeglGdlgiqvlvlevdg...qktayvliDgNNm 450
                                          +  ae ++++++kale   ++++ +++v    + +++    + +G      +++ev g   +++ ++++ gNNm
  gi|320100858|ref|YP_004176450.1| 372 ---DALAELIEETVNKALE--LKKSRPSVEVLSRYKCIKT----NAPGLINGDSCIIEVTGegrERVILLYLRGNNM 439
                                       ...8888888888888888..6666666666666666665....789*************9999************* PP

                           DUF2070 451 epglreeirealke.vdl.evevmTTDtHvvngvsl..gynpvGekvskdelielvlelvekAiadlepvevgyate 523
                                       epglr++++eal++   + +vev+T+D+H+++g++   +y pv+e+    el++ +le+++  + +  +  ++y+++
  gi|320100858|ref|YP_004176450.1| 440 EPGLRDRLVEALRGiTGAdHVEVFTNDEHSETGIRSslAYVPVHES---PELVRDILEATRGLMTEPYERGAQYSSS 513
                                       *************976669***************999*******55...577777777777777777777******* PP

                           DUF2070 524 rvevkvfgedrfeelvstvn.svvsvakilaaallllaill 563
                                       r  +kv+g +  + l + ++ ++++ +++l+ ++++l++ll
  gi|320100858|ref|YP_004176450.1| 514 RFDIKVMGYT-ASLLEKLLKdTYLEATVLLVSYAFILPLLL 553
                                       *********8.7888887762689**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3969.19
//
Query:       gi|320100859|ref|YP_004176451.1|  [L=175]
Description: PMT multi-domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 1255.74
//
Query:       gi|320100860|ref|YP_004176452.1|  [L=255]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  132.8   0.0    1.9e-38  132.6   0.0    1.0  1  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0025   18.1   0.0     0.0047   17.2   0.0    1.5  1  AAA_22       AAA domain
     0.0025   18.2   0.0     0.0051   17.2   0.0    1.5  2  AAA_16       AAA ATPase domain
      0.006   16.3   0.0     0.0093   15.7   0.0    1.2  1  AAA_24       AAA domain
  ------ inclusion threshold ------
      0.011   15.4   0.0       0.05   13.2   0.0    1.9  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.013   15.2   0.0      0.022   14.5   0.0    1.3  1  AAA_30       AAA domain
      0.014   15.3   0.0       0.17   11.7   0.0    2.1  1  NTPase_1     NTPase
       0.02   15.0   0.0       0.26   11.4   0.0    2.5  2  MMR_HSR1     50S ribosome-binding GTPase
      0.039   12.9   0.0       0.92    8.4   0.0    2.5  3  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.045   13.5   0.0      0.085   12.6   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.064   13.2   0.2        1.4    8.8   0.1    2.9  4  RsgA_GTPase  RsgA GTPase
      0.066   13.2   0.0       0.17   11.9   0.0    1.6  2  AAA_5        AAA domain (dynein-related subfamily)
      0.074   12.7   0.0        4.7    6.8   0.0    2.3  2  SRP54        SRP54-type protein, GTPase domain
      0.076   12.8   0.1        2.2    8.0   0.0    2.9  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.098   13.1   0.0       0.26   11.7   0.0    1.7  1  AAA          ATPase family associated with various cellular a
       0.11   11.5   0.0       0.19   10.8   0.0    1.3  1  T2SSE        Type II/IV secretion system protein
       0.13   12.1   0.0       0.26   11.2   0.0    1.5  1  NACHT        NACHT domain
       0.16   12.1   0.0       0.28   11.3   0.0    1.5  1  AAA_33       AAA domain
       0.18   11.6   0.0       0.55   10.0   0.0    1.7  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
       0.24   10.8   0.0       0.47    9.9   0.0    1.5  1  PhoH         PhoH-like protein


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 !  132.6   0.0   2.1e-41   1.9e-38       2     240 ..       8     249 ..       7     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 2.1e-41
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelr.grsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflre 77 
                                       +GpaGsGKt++v+a se+++ +   + a+vNLDP++ee  Y++++dir ++tl+dvm ++glgpnga + + e++ +
  gi|320100860|ref|YP_004176452.1|   8 TGPAGSGKTSLVKAYSEWVRRSlLLRTAIVNLDPGVEEPGYKPTLDIRWFFTLRDVMSKYGLGPNGAFIKSSELILD 84 
                                       7****************98765157899************************************************* PP

                        ATP_bind_1  78 sl.dwldeeleke.ed.dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsa 151
                                        l d l++    + ++ d++l+DtPGQ+e f ++++  +++++++  +++v  yL+D+  + ++t+ +s  ++ +  
  gi|320100860|ref|YP_004176452.1|  85 YLgDILARPPFSNmHQwDLVLIDTPGQMEAFIFRPASNILLKKIAGLGNTVLAYLIDASSIGSVTDAVSLWFIYVLL 161
                                       **888855554444778************************************************************ PP

                        ATP_bind_1 152 mlrlelPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesi 228
                                        ++++l +v v++k D +  +++     +e + +l  l+ +e++   + + ++ ++ ++++   r + +s+ ++e++
  gi|320100860|ref|YP_004176452.1| 162 QVKTGLITVPVISKSDAAG-RRDIVRALVEKPMDLPGLISDESGFALEIMPDLLNIASKTKGPFRAVEVSATRGEGL 237
                                       *****************55.7778888899999999999999999999999999999999999999**********9 PP

                        ATP_bind_1 229 edllslidealq 240
                                       + l  l+ ea++
  gi|320100860|ref|YP_004176452.1| 238 DSLHMLLHEAFC 249
                                       999998888775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.3e-06    0.0047       7      30 ..       4      27 ..       2      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.3e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                      i+v tG++G+GKT l++ + e+  
  gi|320100860|ref|YP_004176452.1|  4 IVVFTGPAGSGKTSLVKAYSEWVR 27
                                      7899******************73 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.7e-06    0.0051      25      50 ..       3      27 ..       1      68 [. 0.83
   2 ?   -2.8   0.0       8.2   7.3e+03     109     109 ..     196     196 ..     167     247 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.7e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralek 50
                                      ++v+++G++G+GK+slv++  + + +
  gi|320100860|ref|YP_004176452.1|  3 SIVVFTGPAGSGKTSLVKAYSE-WVR 27
                                      589**************99885.333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.2
                            AAA_16 109 p 109
                                       p
  gi|320100860|ref|YP_004176452.1| 196 P 196
                                       2 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     1e-05    0.0093       5      81 ..       5     116 ..       2     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                            AAA_24   5 iliyGpsgiGKTtlakel........gpkplfidtekGlksldadkfpdieswedfldevvel.............. 59 
                                       ++ +Gp+g+GKT+l+k +          ++++++++ G+ +   +   di+ + +++d + +               
  gi|320100860|ref|YP_004176452.1|   5 VVFTGPAGSGKTSLVKAYsewvrrslLLRTAIVNLDPGVEEPGYKPTLDIRWFFTLRDVMSKYglgpngafikssel 81 
                                       5779*******************99999***********************77777777777777788888888888 PP

                            AAA_24  60 .............aaeladyktlviDtideleelc 81 
                                                      + ++ + + iDt +++e ++
  gi|320100860|ref|YP_004176452.1|  82 ildylgdilarppFSNMHQWDLVLIDTPGQMEAFI 116
                                       88889999999998899999999999998888766 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.5e-05      0.05       2      32 ..       4      37 ..       3      45 .. 0.78
   2 ?   -0.2   0.0      0.73   6.6e+02      81     123 ..      99     144 ..      77     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.5e-05
                                      EEEEEESTTCCHHHHHHHHH...CT--SS-EEEE CS
                              cobW  2 vtvltGflGsGKTtLlnhll...enraglklavi 32
                                      ++v+tG+ GsGKT+L++++    +++  l++a++
  gi|320100860|ref|YP_004176452.1|  4 IVVFTGPAGSGKTSLVKAYSewvRRSLLLRTAIV 37
                                      6899************998766566666666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.73
                                       TT-SEEEEEECTTTTHHHH.HTTSHHHHH..CCCECEEEEEEETTT CS
                              cobW  81 erldviliEttGlaePapv.afteeelks..dltldavvavvDakn 123
                                       ++ d++li t G +e+      ++  lk+   l  +++ +++Da+ 
  gi|320100860|ref|YP_004176452.1|  99 HQWDLVLIDTPGQMEAFIFrPASNILLKKiaGLGNTVLAYLIDASS 144
                                       6788888888887777665322233333311333333345555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.4e-05     0.022      20      44 ..       4      28 ..       2      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                            AAA_30 20 vavltGpAGtGKttalkalreawea 44
                                      ++v tGpAG+GKt ++ka+ e +++
  gi|320100860|ref|YP_004176452.1|  4 IVVFTGPAGSGKTSLVKAYSEWVRR 28
                                      6799**************9998765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.17       2     110 ..       5     115 ..       4     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE..EEE-------EEEEEET.T--EEEEEETT.---SSEETTEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyt..eevreggrrigFkivdlasgeegiLarve.akreprvgkyv 75 
                                       v+ TGp G+GKt lvk  +e +++s +  + ++   + v e g +   +i       ++ +++ + +++++ +++  
  gi|320100860|ref|YP_004176452.1|   5 VVFTGPAGSGKTSLVKAYSEWVRRSLLLRTAIVNldPGVEEPGYKPTLDIRWF-FTLRDVMSKYGlGPNGAFIKSSE 80 
                                       678*************9999997764433333322256667777777777666.44556666666666677777777 PP

                                       E-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG CS
                          NTPase_1  76 vdvesfeelalealrkalseadviviDEiGkmElk 110
                                       + ++ + ++ ++     +++ d+++iD  G+mE +
  gi|320100860|ref|YP_004176452.1|  81 LILDYLGDILARPPFSNMHQWDLVLIDTPGQMEAF 115
                                       77777777777766666788888888888888876 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      0.26       2      86 ..       5     143 ..       4     175 .. 0.63
   2 ?   -1.2   0.0       2.3   2.1e+03      51      58 ..     193     200 ..     182     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                       EEEEESTTSSHHHHHHHHHT........STEEESSSTTS.......SSSEEEEEEEETTEE................ CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg........ekaivsdkpgt.......Trdinegrvklkgke................ 47 
                                       v++ G   +GK++L++a ++        ++aiv+  pg+       T+di+++                        
  gi|320100860|ref|YP_004176452.1|   5 VVFTGPAGSGKTSLVKAYSEwvrrslllRTAIVNLDPGVeepgykpTLDIRWF-------Ftlrdvmskyglgpnga 74 
                                       78999999999999999998664444433455555554322222224444443.......03334455677777788 PP

                                       ............................EEEEECGGCSS...HHHHHHHHHHHHHHHHCTSEEEEEEETT CS
                          MMR_HSR1  48 ............................ielvDtpGlie...gaseekglgkaflaleeadlillvvdas 86 
                                                                   ++l+DtpG +e       ++ l k+++ l +  ++++++das
  gi|320100860|ref|YP_004176452.1|  75 fiksselildylgdilarppfsnmhqwdLVLIDTPGQMEafiFRPASNILLKKIAGLGN-TVLAYLIDAS 143
                                       8888888888888888888888888888********54322211222234444444444.6666666655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.3
                                       EECGGCSS CS
                          MMR_HSR1  51 vDtpGlie 58 
                                       +D+pGli+
  gi|320100860|ref|YP_004176452.1| 193 MDLPGLIS 200
                                       799**986 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0     0.001      0.92      32      70 ..       5      44 ..       2      49 .. 0.85
   2 ?   -1.8   0.0       1.4   1.3e+03     122     158 ..     101     135 ..      97     139 .. 0.82
   3 ?    1.3   0.0      0.15   1.3e+02     206     224 ..     225     243 ..     164     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                                      EEEEE-TTSSHHHHHHHHHHHHHCTT.--EEEEEE----- CS
                              MeaB 32 vGltGvPGaGkstlvealglelrrrG.krvavlavDPssp 70
                                      v +tG  G+Gk  lv+a  + +rr    r a++ +DP+ +
  gi|320100860|ref|YP_004176452.1|  5 VVFTGPAGSGKTSLVKAYSEWVRRSLlLRTAIVNLDPGVE 44
                                      679***************9999887437*********976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                                       -SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTT CS
                              MeaB 122 fDvvlietvGvGqsevdvaevvdtfvvlllpeaGDel 158
                                       +D vli+t   Gq e  + + +  +++  +++ G+ +
  gi|320100860|ref|YP_004176452.1| 101 WDLVLIDTP--GQMEAFIFRPASNILLKKIAGLGNTV 135
                                       799999996..69999999999999988888888765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.15
                                       EEEEEBCCCTBSHHHHHHH CS
                              MeaB 206 kvlktsavegeGidelvda 224
                                       + +++sa++geG+d+l   
  gi|320100860|ref|YP_004176452.1| 225 RAVEVSATRGEGLDSLHML 243
                                       67899*********99765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.4e-05     0.085      25      43 ..       5      23 ..       1      26 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.4e-05
                            AAA_29 25 tlltGpsGsGKSTllDAiq 43
                                      +++tGp GsGK++l+ A++
  gi|320100860|ref|YP_004176452.1|  5 VVFTGPAGSGKTSLVKAYS 23
                                      689************9975 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0016       1.4     101     119 ..       4      22 ..       2      29 .. 0.88
   2 ?   -1.9   0.0       2.9   2.6e+03       4      17 ..      27      40 ..      24      43 .. 0.89
   3 ?   -0.1   0.0      0.82   7.4e+02     152     161 ..     102     111 ..      95     116 .. 0.76
   4 ?   -2.8   0.0       5.7   5.1e+03      78      99 ..     225     246 ..     216     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                                       EEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinal 119
                                       ++v+ G+ G GK++L++a 
  gi|320100860|ref|YP_004176452.1|   4 IVVFTGPAGSGKTSLVKAY 22 
                                       79*************9876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                                      -S-EETTTTEES-- CS
                       RsgA_GTPase  4 RknelvrpkvaNvd 17
                                      R+++l+r+++ N+d
  gi|320100860|ref|YP_004176452.1| 27 RRSLLLRTAIVNLD 40
                                      99**********99 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.82
                                       TEEEESS-SS CS
                       RsgA_GTPase 152 gglliDtPGf 161
                                       + +liDtPG 
  gi|320100860|ref|YP_004176452.1| 102 DLVLIDTPGQ 111
                                       4689*****5 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.7
                                       EEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkd 99 
                                       + + vsa+++egl++l+ ll++
  gi|320100860|ref|YP_004176452.1| 225 RAVEVSATRGEGLDSLHMLLHE 246
                                       5678899999999999988876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.17       2      28 ..       5      31 ..       4      38 .. 0.89
   2 ?   -2.5   0.0       5.4   4.8e+03      74      91 ..     229     246 ..     228     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                      EEEE--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreve 28
                                      v+  Gp G+gK++l++ +++ ++r+++
  gi|320100860|ref|YP_004176452.1|  5 VVFTGPAGSGKTSLVKAYSEWVRRSLL 31
                                      7889****************9988876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.4
                                       GGG--HHHHHHHHHHHHS CS
                             AAA_5  74 veraesevlnsLlsllee 91 
                                       v   + e l+sL++ll+e
  gi|320100860|ref|YP_004176452.1| 229 VSATRGEGLDSLHMLLHE 246
                                       55556677999****997 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0053       4.7       2      36 ..       3      38 ..       2      41 .. 0.78
   2 ?    3.6   0.0     0.051        45      82      96 ..      99     113 ..      94     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0053
                                      EEEEEEESTTSSHHHHHHHHHHHHHHT.TS-EEEEE CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkke.gkkvllva 36
                                      +++++ G+ G+GKT+ +   +++++++   ++++v 
  gi|320100860|ref|YP_004176452.1|  3 SIVVFTGPAGSGKTSLVKAYSEWVRRSlLLRTAIVN 38
                                      5799***********999888888877555666655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.051
                                       TTSSEEEEEE--SST CS
                             SRP54  82 ekidvvlvDTaGrlq 96 
                                       ++ d+vl+DT G+++
  gi|320100860|ref|YP_004176452.1|  99 HQWDLVLIDTPGQME 113
                                       678*********987 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0025       2.2       3      22 ..       4      23 ..       2      39 .. 0.89
   2 ?    0.7   0.1      0.45   4.1e+02      39      46 ..     104     111 ..      97     190 .. 0.74
   3 ?   -0.6   0.0       1.1     1e+03     121     142 ..     224     245 ..     212     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0025
                         PduV-EutP  3 killiGkvgsGKttLtqalk 22
                                       +++ G+ gsGKt+L +a +
  gi|320100860|ref|YP_004176452.1|  4 IVVFTGPAGSGKTSLVKAYS 23
                                      6899***********99865 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.45
                         PduV-EutP  39 eviDtPGe 46 
                                        +iDtPG+
  gi|320100860|ref|YP_004176452.1| 104 VLIDTPGQ 111
                                       56888886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.1
                         PduV-EutP 121 ekifevsavekegieellkyle 142
                                        +  evsa++ eg+++l   l+
  gi|320100860|ref|YP_004176452.1| 224 FRAVEVSATRGEGLDSLHMLLH 245
                                       56679***********988776 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   0.00029      0.26       1      19 [.       5      23 ..       5      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                      EEEESSTTSSHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakava 19
                                      v+++Gp G GKT+l+ka  
  gi|320100860|ref|YP_004176452.1|  5 VVFTGPAGSGKTSLVKAYS 23
                                      6899************965 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 ?   10.8   0.0   0.00021      0.19     131     156 ..       4      29 ..       2      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks 156
                                       +++++G+ gsGKt l+ a  +++  s
  gi|320100860|ref|YP_004176452.1|   4 IVVFTGPAGSGKTSLVKAYSEWVRRS 29 
                                       6889*************999998765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.26       2      19 ..       4      21 ..       3      32 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                      CEEEEC-TTTCHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqk 19
                                      +v+ +G+aGsGKT L++ 
  gi|320100860|ref|YP_004176452.1|  4 IVVFTGPAGSGKTSLVKA 21
                                      6899***********985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.28       1      20 [.       4      23 ..       4      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      +v++ G++GsGK+ l++ + 
  gi|320100860|ref|YP_004176452.1|  4 IVVFTGPAGSGKTSLVKAYS 23
                                      599************99875 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 ?   10.0   0.0   0.00061      0.55       1      36 [.       9      45 ..       9      52 .. 0.87
   2 ?   -1.4   0.0       1.9   1.7e+03     105     137 ..     103     139 ..      95     175 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00061
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgr.kpvyvDlDvGqse 36
                                      Gp  sGK++l++   +++ r+   ++++v+lD+G  e
  gi|320100860|ref|YP_004176452.1|  9 GPAGSGKTSLVKAYSEWVRRSLLlRTAIVNLDPGVEE 45
                                      899**************9988744999*******877 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                            CLP1_P 105 gliIntpGwvk....glgaellleliealepdvvvvl 137
                                        ++I+tpG ++      + ++ll++i+ l  +v+++l
  gi|320100860|ref|YP_004176452.1| 103 LVLIDTPGQMEafifRPASNILLKKIAGLGNTVLAYL 139
                                       5788888877622223344555555555555555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00052      0.47      20      39 ..       3      22 ..       1      46 [. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00052
                                      SEEEEE--TTSSTTHHHHHH CS
                              PhoH 20 divfaiGpaGtGKtylaval 39
                                      +iv+ +GpaG+GKt l  a+
  gi|320100860|ref|YP_004176452.1|  3 SIVVFTGPAGSGKTSLVKAY 22
                                      6999**********997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1808.37
//
Query:       gi|320100861|ref|YP_004176453.1|  [L=610]
Description: ATP-dependent DNA ligase I [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-64  214.9   0.1    1.2e-63  214.4   0.1    1.2  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    1.5e-40  139.3   0.5      8e-40  137.0   0.0    2.2  3  DNA_ligase_A_N   DNA ligase N terminus
    4.4e-27   94.6   0.0    8.7e-26   90.4   0.0    2.4  2  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    3.2e-05   24.3   1.0    5.3e-05   23.6   1.0    1.3  1  RNA_ligase       RNA ligase
     0.0012   18.8   0.4       0.12   12.4   0.0    3.0  3  DNA_ligase_OB_2  DNA ligase OB-like domain
  ------ inclusion threshold ------
       0.14   12.1   0.2        3.6    7.6   0.1    2.5  2  HTH_6            Helix-turn-helix domain, rpiR family


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 !  214.4   0.1   4.1e-67   1.2e-63       1     204 []     244     444 ..     244     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.4 bits;  conditional E-value: 4.1e-67
                                       -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEE CS
                    DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilD 77 
                                       pmLAe+l++  ++l+k+ ++++++E+KyDGeRaq+hk+gdkv +fSRrl++it+++p++v+ +++ +k+d  ++i++
  gi|320100861|ref|YP_004176453.1| 244 PMLAERLSDPGEILEKV-GGDAFIEYKYDGERAQIHKKGDKVWIFSRRLENITQQYPDVVELARNHLKAD--EAIVE 317
                                       9***************9.56666********************************************998..8**** PP

                                       EEEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEE CS
                    DNA_ligase_A_M  78 GElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrve 154
                                       GE+va+d+etge  pfq+l++r k+k+++++++ke+++ +f+FD+Lyl+g ++t e+l  Rr++Lee++  + +++ 
  gi|320100861|ref|YP_004176453.1| 318 GEIVAYDPETGELKPFQELMHR-KRKHDIHSAIKEYPVKVFLFDLLYLNGHDYTVETLPVRRSKLEEVV-DKVEEFT 392
                                       **********************.78899*****************************************.9999*** PP

                                       E--EEEESSHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 155 laeslevkdveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                       +ae +++++v+ele+++ +aiseg+EG++vK    ds+Y++g r++ w+K+K
  gi|320100861|ref|YP_004176453.1| 393 IAEYIRTNKVDELEKFFLKAISEGAEGVMVKAlhGDSIYQAGTRGWLWIKFK 444
                                       ********************************8889***************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 !  137.0   0.0   2.7e-43     8e-40       5     173 .]      13     193 ..      11     193 .. 0.96
   2 ?   -4.0   0.0       5.4   1.6e+04      86     102 ..     213     229 ..     206     235 .. 0.68
   3 ?   -0.5   0.0      0.45   1.3e+03       5      37 ..     381     416 ..     379     433 .. 0.69

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 2.7e-43
                                       HHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS-.-----HHHHHHHHHHHHT--H CS
                    DNA_ligase_A_N   5 laelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgr.eygigesllakalaealglsk 76 
                                       la++fe+ie+  ++r++++a+l  +f+++   +pe +  +++L    l+Pd++g  e+g+ge+ll+ka+a a+g+++
  gi|320100861|ref|YP_004176453.1|  13 LADVFERIEA-ITSRTQMTALLVGLFKQT---PPEIIDRVVYLiqgrLWPDWKGLpEIGVGEKLLVKAIALATGVTE 85 
                                       89********.88999**********664...799******************999********************* PP

                                       HHHHHHHHHHS-HHHHHHHHHCCHHHH..........------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHH CS
                    DNA_ligase_A_N  77 kkikdalakvgDlgevaeevlskrstl..........akkspltieevnelLdklaaa.gkgsedekkkilkkllkr 142
                                       ++++  ++++gDlg++ae+++sk++ +          ++ ++lt++ v+e+L ++a a g+gs+d k+++l++llk+
  gi|320100861|ref|YP_004176453.1|  86 ASVEGLSKSLGDLGKAAEQLKSKSTGRsqgvtllsytQQRTELTVNRVYETLVRVAMAqGEGSKDIKIRLLAGLLKE 162
                                       *99999999************999999999******99999***************999****************** PP

                                       S-HHHHHHHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 143 aspeEakyliriilkdlriglsektvldala 173
                                       asp+Eak+++r+++++lr+g++e t++dala
  gi|320100861|ref|YP_004176453.1| 163 ASPKEAKFIVRFVEGRLRVGIGEATIMDALA 193
                                       *****************************97 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.4
                                       HS-HHHHHHHHHCCHHH CS
                    DNA_ligase_A_N  86 vgDlgevaeevlskrst 102
                                         Dlgeva+ + sk  +
  gi|320100861|ref|YP_004176453.1| 213 RADLGEVAKILASKGLE 229
                                       47999998877776655 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.45
                                       HHHHHHHHCC..--..-HHHHHHHHHHHHHTS-..S CS
                    DNA_ligase_A_N   5 laelfekiee.stk..krlekrailanffrkvesag 37 
                                       l e+++k+ee +     r+ k++ l++ff k +s+g
  gi|320100861|ref|YP_004176453.1| 381 LEEVVDKVEEfTIAeyIRTNKVDELEKFFLKAISEG 416
                                       778889999965542456699999****96656533 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 ?    1.4   0.0      0.16   4.9e+02      21      58 ..      76     113 ..      64     154 .. 0.79
   2 !   90.4   0.0   2.9e-29   8.7e-26       1      99 []     469     578 ..     469     578 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.16
                                       EEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHH CS
                    DNA_ligase_A_C  21 vgkvgtGfsdaeleelrkklkelerkkppfaekvpeee 58 
                                       +   +tG ++a++e l k+l +l ++ +++++k   ++
  gi|320100861|ref|YP_004176453.1|  76 AIALATGVTEASVEGLSKSLGDLGKAAEQLKSKSTGRS 113
                                       55679***************999999888865555544 PP

  == domain 2  score: 90.4 bits;  conditional E-value: 2.9e-29
                                       GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEES CS
                    DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfa 75 
                                       rgg++g+ll+++y+  ++ +e+v+kvg+Gf+d++l++l + lk++ r++     +v ++ ++dvWveP+lv+e+ +a
  gi|320100861|ref|YP_004176453.1| 469 RGGKYGALLMAAYNdeKDVFETVCKVGSGFKDEDLDKLPEILKPYMRDRRHP--RVVANMEPDVWVEPALVAEIIGA 543
                                       6899**********65566************************888876666..4555556779************* PP

                                       EEECTSSSTT...........EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  76 eitasgkyka...........slRfPrfkrlReDk 99 
                                       e+t s+ +++           s+RfPrf+r+R+Dk
  gi|320100861|ref|YP_004176453.1| 544 ELTLSPVHTCaygkvksdagiSIRFPRFIRWRPDK 578
                                       **********************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.0   1.8e-08   5.3e-05       5     149 ..     266     428 ..     263     444 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.8e-08
                                       EEEE-SSEEEEEEEE..TTEEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES......... CS
                        RNA_ligase   5 vtEKlDGtnfriylv..kevgvasRsqil.pfgeekfkefkrwaaalrkklkeklaneelilyGElig......... 69 
                                       ++ K DG++++i++   k v ++sR+ +  +          +++ +  +  +++l+  e i+ GE++          
  gi|320100861|ref|YP_004176453.1| 266 IEYKYDGERAQIHKKgdK-VWIFSRRLENiT----------QQYPDVVELARNHLKADEAIVEGEIVAydpetgelk 331
                                       788***********9533.******999832..........3344445556678887789********998888887 PP

                                       ............SS....TTSS.EEEEEEEEEEE.CTTBECE--HHHH..HHHHHCCTB..EEEEE.SS.HHHHHCC CS
                        RNA_ligase  70 ...........hsi..kygglpkefyvFdifdir.dkeeqrylspdev..ealakglgtvpvlyegkfl.aaeelle 129
                                                  h i   ++++p + ++Fd++ ++ ++ + + l+ ++   e++ ++++   ++ e+ ++ + +el++
  gi|320100861|ref|YP_004176453.1| 332 pfqelmhrkrkHDIhsAIKEYPVKVFLFDLLYLNgHDYTVETLPVRRSklEEVVDKVEEFTIA-EYIRTnKVDELEK 407
                                       77777766666555655555777**********986665555554433224444433322233.2333335555555 PP

                                       C..HHHHTC--EEEEEESSSS CS
                        RNA_ligase 130 ll.lskgnkrEGlVikpesel 149
                                       ++ +  ++ +EG+ +k  ++ 
  gi|320100861|ref|YP_004176453.1| 408 FFlKAISEGAEGVMVKALHGD 428
                                       543433559*******88553 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   4.1e+03      42      51 ..     264     273 ..     261     276 .. 0.81
   2 !   12.4   0.0   4.1e-05      0.12       2      34 ..     465     503 ..     464     514 .. 0.78
   3 ?    3.1   0.0     0.034     1e+02      55      66 .]     563     575 ..     550     575 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                                       -EEEEEEE-T CS
                   DNA_ligase_OB_2  42 kiitykyqel 51 
                                       + i+yky+++
  gi|320100861|ref|YP_004176453.1| 264 AFIEYKYDGE 273
                                       579****997 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.1e-05
                                       ...EEEEEEEEEEEEE.TTEE......EEE-SS--HHHH CS
                   DNA_ligase_OB_2   2 GkGkykgmlGallvetkkgkr......fkiGsGlsdaqR 34 
                                       GkG+  g+ Gall+   ++++       k+GsG++d++ 
  gi|320100861|ref|YP_004176453.1| 465 GKGRRGGKYGALLMAAYNDEKdvfetvCKVGSGFKDEDL 503
                                       9*************99764423334459********985 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.034
                                       SS.-EEEEEEEE- CS
                   DNA_ligase_OB_2  55 gv.pRfPsflrvR 66 
                                       g+  RfP+f r+R
  gi|320100861|ref|YP_004176453.1| 563 GIsIRFPRFIRWR 575
                                       4457*******98 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 ?    7.6   0.1    0.0012       3.6      37      59 ..      74      96 ..      70     102 .. 0.91
   2 ?    1.6   0.0      0.09   2.7e+02      17      42 ..     389     415 ..     377     419 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                                      HHHHHHHTT--HHHHHHHH---S CS
                             HTH_6 37 ikalAkaaavSeativrfakkLG 59
                                      +ka+A a +v ea++  ++k+LG
  gi|320100861|ref|YP_004176453.1| 74 VKAIALATGVTEASVEGLSKSLG 96
                                      799*******************9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.09
                                       HHHHHHHHHHH-.S---TT--HHHHHH CS
                             HTH_6  17 sekkiaeyilas.pdkaielsikalAk 42 
                                        e++iaeyi+ + +d++ ++ +ka+++
  gi|320100861|ref|YP_004176453.1| 389 EEFTIAEYIRTNkVDELEKFFLKAISE 415
                                       589******976257777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4125.15
//
Query:       gi|320100862|ref|YP_004176454.1|  [L=611]
Description: serine protease-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   23.9   0.8    4.1e-05   23.2   0.8    1.3  1  Lon_C     Lon protease (S16) C-terminal proteolytic domain


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.8   2.3e-09   4.1e-05     106     168 ..     116     178 ..      45     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.3e-09
                                       GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEE CS
                             Lon_C 106 PkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvil 168
                                         +GPsa + ++  +++ll+g +v++  + tG i+  G v ++GGl  kl aa  ag+++v+ 
  gi|320100862|ref|YP_004176454.1| 116 KLEGPSATLLFTLVFTALLRGDRVNSSYTATGIIAPGGVVGAVGGLEAKLSAAAEAGLTRVVA 178
                                       568*********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 4051.99
//
Query:       gi|320100863|ref|YP_004176455.1|  [L=216]
Description: phage SPO1 DNA polymerase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-47  160.4   0.0    4.2e-47  160.0   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 !  160.0   0.0   2.3e-51   4.2e-47       1     153 [.      28     180 ..      28     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 160.0 bits;  conditional E-value: 2.3e-51
                                       HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCC CS
                               UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaei 77 
                                       pgeg+++++v++vGeaPg++ed+tg+pF+g+ag+ll +l++++g+kr     + +yitnvvkcrpp nr +p ++ei
  gi|320100863|ref|YP_004176455.1|  28 PGEGDTNSRVMLVGEAPGEREDETGRPFVGAAGKLLTELIESIGFKR-----ESLYITNVVKCRPPNNR-DPEDDEI 98 
                                       79*********************************************.....*****************.******* PP

                                       TCCHHHHHHHHHHHHSSEEEEESHHHHHH.......HH.HHSCESCCCSCT......SEEEEES-SSTTTTTTTTSH CS
                               UDG  78 kacaplleeeiellkprlivllGktaakall.....ge.klgklrgklleak.....irvlplphPsplnrnffksn 143
                                       kac p+l ++iellkpr+iv+lG++aa++l+     +  ++++ +gk ++a      + ++p++hP+++++n     
  gi|320100863|ref|YP_004176455.1|  99 KACLPYLLKQIELLKPRVIVALGRHAARTLFelgglKWvNMSSMHGKAFNAVingvhTVIIPTFHPAAALYN----- 170
                                       *****************************9667988445999********966678899*************..... PP

                                       HHHHHHHHHH CS
                               UDG 144 pelkaeawed 153
                                       p lk+e  +d
  gi|320100863|ref|YP_004176455.1| 171 PGLKDELRKD 180
                                       6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1616.29
//
Query:       gi|320100864|ref|YP_004176456.1|  [L=247]
Description: GtrA family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-19   70.0   5.6    2.8e-19   69.5   5.6    1.3  1  GtrA      GtrA-like protein


Domain annotation for each model (and alignments):
>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   5.6   1.6e-23   2.8e-19       1     117 []     120     242 ..     120     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.6e-23
                              GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaia....fivailfnFilnrrwtFkdrekakl..lkqflkFvlvs 71 
                                       rF++vG++g++v+la+  l  +ll+ ++l+An ia    f++++l+nF l++ wtFkd+  +++  l +++k++l+s
  gi|320100864|ref|YP_004176456.1| 120 RFIAVGASGVAVNLAVAELSHRLLQGNPLIANPIAstagFEASVLWNFTLHEEWTFKDAGLSSKgrLVRLIKYHLAS 196
                                       8******************999999999887755422228899*****************999999*********** PP

                              GtrA  72 llglllnllilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                       +++ + ++++ +++  +lg +++l ++vg++v++ +n++l  ++++
  gi|320100864|ref|YP_004176456.1| 197 IASWMSQVFFATVMPIYLGTPFWLGQAVGVLVGFTVNFILGYIYTW 242
                                       ****************************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1977.83
//
Query:       gi|320100865|ref|YP_004176457.1|  [L=77]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-26   91.2   0.6    3.6e-26   91.1   0.6    1.0  1  DUF5622   Domain of unknown function (DUF5622)


Domain annotation for each model (and alignments):
>> DUF5622  Domain of unknown function (DUF5622)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.6     2e-30   3.6e-26       1      66 []       3      76 ..       3      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 2e-30
                           DUF5622  1 lKHgKYvYVeredgwYvKvRvL.....ksree...vndpekYivlgkkvkkpprkakvlkeddlPeevreklkk 66
                                      lKHgKY+YV+r+dgwYvKvRvL     k++ e   + +p++Yiv+g k++ pp +a v++e+++P+ vr+ l++
  gi|320100865|ref|YP_004176457.1|  3 LKHGKYIYVKRSDGWYVKVRVLnvrfgKKQGEgvdASNPTRYIVTGSKTRIPPVHAVVVEEEAIPQPVRSSLYE 76
                                      8************************986666679999*********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 601.77
//
Query:       gi|320100866|ref|YP_004176458.1|  [L=95]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 718.64
//
Query:       gi|320100867|ref|YP_004176459.1|  [L=494]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-24   84.4   0.7    1.1e-22   80.3   0.7    2.3  1  DUF553          Transglutaminase-like domain
      0.004   17.0   0.0       0.01   15.6   0.0    1.7  1  Peptidase_C93   Bacterial transglutaminase-like cysteine prot
  ------ inclusion threshold ------
      0.038   14.5   0.0        0.1   13.1   0.0    1.7  1  Transglut_core  Transglutaminase-like superfamily


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 !   80.3   0.7   1.8e-26   1.1e-22       6     140 ..     250     365 ..     245     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.8e-26
                            DUF553   6 laekl....kkensketiinvlewvdenikYdyekaevvetllvlWatfftlskvdskilklietpkeilktkkgiC 78 
                                       ++++l     + +  ++ ++vl+w+den  Ydy+ka +                      ++i+ p ++ + kkgiC
  gi|320100867|ref|YP_004176459.1| 250 VSSILyqsgSEPSLPNATWRVLQWLDENASYDYDKAASN--------------------STYIYDPITFATLKKGIC 306
                                       556662222233456899******************998....................47899************* PP

                            DUF553  79 rDYaiLTaalLlnlniskvylvsvtfenskvgHaavavkidgtyfvlDqklpiikideylkk 140
                                       +DYa +Ta +L n     + lv  t   ++ gHa++ v ++g +f+lDq+lp++++d+y+ +
  gi|320100867|ref|YP_004176459.1| 307 TDYALFTATALVNISWDVYILVFNT---TNGGHAVAGVVVNGGFFILDQHLPPVEVDDYFRD 365
                                       ************9999876666555...4579***************************965 PP

>> Peptidase_C93  Bacterial transglutaminase-like cysteine proteinase BTLCP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-06      0.01      66     130 ..     294     354 ..     255     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                     Peptidase_C93  66 erWeypkdgaGdCedyallKrkeLieaGlpasallltvvrdekgegHavLtvrtdrGdlvLDNle 130
                                       +  ++++  +G C dyal     L++  +    l    v ++++ gHav  v ++ G ++LD   
  gi|320100867|ref|YP_004176459.1| 294 DPITFATLKKGICTDYALFTATALVNISWDVYIL----VFNTTNGGHAVAGVVVNGGFFILDQHL 354
                                       4446677779*******************97665....4567889*****************865 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.7e-05       0.1      16      63 ..     265     315 ..     253     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                    Transglut_core  16 ekakaiyewvrknveys...aprrtpgsrdaeavletgkGncedfaslfva 63 
                                        +  ++ +w+ +n +y+   a+ +++  +d+  + + +kG c+d+a   ++
  gi|320100867|ref|YP_004176459.1| 265 NATWRVLQWLDENASYDydkAASNSTYIYDPITFATLKKGICTDYALFTAT 315
                                       56667899***9999998777777777788999999*********976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3309.77
//
Query:       gi|320100868|ref|YP_004176460.1|  [L=471]
Description: transposase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-34  116.2   0.0    1.7e-33  115.4   0.0    1.4  1  OrfB_IS605      Probable transposase
    2.2e-19   69.1   0.0    4.6e-19   68.1   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.022   15.1   0.0    1.5  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.0   2.9e-37   1.7e-33       1     119 [.     171     286 ..     171     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 2.9e-37
                        OrfB_IS605   1 sipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       +ipveve  ++++ g  +a++DlGi nLatv++edg+w+++kg ++ s+y+y+ k+i ++q++l++++  +++ r+l
  gi|320100868|ref|YP_004176460.1| 171 HIPVEVEG-TTEAGGDLRASVDLGIVNLATVYVEDGDWYIFKGGSVLSQYEYYGKRISRVQKILSRHG--QRRGRRL 244
                                       799**998.9999******************************************************9..******* PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       a+l++kr+r+++h+l++++++++++lk + v++++vg++  i
  gi|320100868|ref|YP_004176460.1| 245 ALLYDKRRRFLRHALNSMVRRIMEELKGREVGEIIVGYPEGI 286
                                       **************************************9865 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0   7.7e-23   4.6e-19       2      68 ..     302     369 ..     301     370 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 7.7e-23
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       + ++++ e+  +e Gikv++vn+a+TSktCs Cg+ +++ ++++ +fkCp+ g ++++D+nAaiNil+
  gi|320100868|ref|YP_004176460.1| 302 DYVIRRFEEIGEELGIKVVKVNEAHTSKTCSLCGEAHDNgRVKRGLFKCPRMGRVINADLNAAINILH 369
                                       5678899999********************************************************96 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.7e-06     0.022      36     103 ..     259     332 ..     241     348 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHHHHHHHTT--EEEEE------SSS---S.......STTHHHHHHHHHT..T-EEEEE--S----XXX CS
                              RuvX  36 kekdleelkelvkeeeveeiVvGlPlnldgsegesa.......kkvrkfaeeLakrlkklpvelvDErlttveae 103
                                        ++ ++++ e +k +ev ei+vG+P  ++ s g++        + v +  ee+ ++l +++v+ v+E  t+++ +
  gi|320100868|ref|YP_004176460.1| 259 LNSMVRRIMEELKGREVGEIIVGYPEGISRSRGNKLtvnfwsyDYVIRRFEEIGEEL-GIKVVKVNEAHTSKTCS 332
                                       478899*******************77765555443111111133444445666676.99***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3241.09
//
Query:       gi|320100869|ref|YP_004176461.1|  [L=400]
Description: major facilitator superfamily protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-26   91.4  45.7    7.4e-26   90.9  45.7    1.3  1  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 !   90.9  45.7   4.1e-30   7.4e-26       1     351 [.      16     359 ..      16     391 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 4.1e-30
                             MFS_1   1 lllaaflsalarsilgpalpl..alaedlgispse.igllltlyalgaavaslplGrlsdrfGrrrvlllglllfal 74 
                                       ll+a++l+++ r+++g++ p+  ++a+ +g+++   +  + ++y+ ++av+++++G+l+d +G rrv  ++l+l+++
  gi|320100869|ref|YP_004176461.1|  16 LLVAYILVYFHRTMTGVMKPEvdHYARYYGVDANLlLAVMSSAYFYAYAVSQVFMGPLIDHYGVRRVGGVMLTLLGV 92 
                                       5789****************87778999999999867778899********************************** PP

                             MFS_1  75 glllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslgW 150
                                       ++l++++ ++   l+v+r l G+ a ++f + +   +  f +  +gr  +++  + +++++l+ ++l  +l   +g 
  gi|320100869|ref|YP_004176461.1|  93 ATLVMSL-PNPVSLIVGRTLIGVSATVAFLSYMRSSSLGFGPGSQGRLSSYALFAGGVSTVLAtYPLRLMLN-TAGI 167
                                       *666666.55447***********************************************888677777777.889* PP

                             MFS_1 151 ravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsgl 226
                                       + +f++la+++++++     +++ +p +        +      ++++  +k +  +p++w + l+a+++ ++g+++ 
  gi|320100869|ref|YP_004176461.1| 168 SMTFLALAALAFMLAA---SVYMISPDNGNGGGNGSL-----LRQVAM-LKDIAGSPHVWgVGLAAVASYGTGLAYQ 235
                                       **************77...555555555444444444.....233444.79**********6666666666788888 PP

                             MFS_1 227 ltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt.ssav 301
                                       +++  + l  v+ l+  +++++  l+lla+v++++++ +g+lsd+l++rr+ lla  l+++a+ +l++l+ + +s+ 
  gi|320100869|ref|YP_004176461.1| 236 SAWGQIHLARVFSLGkDAVSLY--LMLLAMVFVASSIPTGYLSDKLKKRRPFLLAATLVAVASWLLMFLSSYmDSTG 310
                                       9999998899999997447777..*********************************************99999999 PP

                             MFS_1 302 llllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggal 351
                                       lll++l l+G+ +g+  ++++++a + + p  +gta+++fn++   g+a+
  gi|320100869|ref|YP_004176461.1| 311 LLLVSLGLLGLSQGL-HVIAATMAKEPYDPAVSGTAVAFFNIILFMGIAV 359
                                       99999*********8.79999********************998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3015.43
//
Query:       gi|320100870|ref|YP_004176462.1|  [L=721]
Description: beta propeller domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-103  347.0   0.1   2.4e-103  346.7   0.1    1.0  1  Beta_propel  Beta propeller domain
     0.0068   15.7   0.2        0.9    8.9   0.0    3.7  3  LVIVD        LVIVD repeat
  ------ inclusion threshold ------
       0.18   12.0   0.1       0.66   10.3   0.0    1.9  2  CDC24        CDC24 Calponin


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 !  346.7   0.1    4e-107  2.4e-103       1     513 [.     115     711 ..     115     712 .. 0.93

  Alignments for each domain:
  == domain 1  score: 346.7 bits;  conditional E-value: 4e-107
                       Beta_propel   1 ySeTNvqvegVdEaDivktDGkyiyvvsgskvvivdaeaeelklvseikleekfkieelyldgdrLvvisseeeeee 77 
                                       yS+TNvqvegVdE D+vk+D +yiyv++g++v++ d  + + k vs+i l+e+++++ lyld+  Lvvi+ ++   +
  gi|320100870|ref|YP_004176462.1| 115 YSGTNVQVEGVDEEDVVKNDERYIYVATGGEVRVFD--TVSKKTVSRILLPENYQVHGLYLDKGYLVVIAGSRGVLQ 189
                                       9***********************************..889999****************************99999 PP

                       Beta_propel  78 seaeeeeepilskeetkvliyDisdkenpkllreleldGsyvssRkigdklylvsskeaeeeeenekeaeeakleel 154
                                       s +  ++  +l++ +t v++y++s++++p  +++  ++G +  sR+  + ly+vss       +     e+ +++ +
  gi|320100870|ref|YP_004176462.1| 190 SITLLYTGIALQHGSTLVVVYNVSNPSTPIEVGRAVISGIFTGSRLSSGILYVVSS------SSAYIIGENGSIKPF 260
                                       888877777777778*****************************************......333444555667899 PP

                       Beta_propel 155 lPkvseeeeklvacediylpdesesssyl.vvtsldlakdkavdskavlgsgeevYvseenlYlas........... 219
                                       +P++   +++   +edi +p++ +   y+ +v sl+l++ ++++ ++v+gs +++Y+s e+lY+as           
  gi|320100870|ref|YP_004176462.1| 261 IPSI---NGEP--VEDILIPEGLTLPLYMvTVYSLNLTSMDSSNLTVVTGSVDWIYMSRERLYIASkypvymvldvf 332
                                       ****...6665..799********9995549********************************************** PP

                       Beta_propel 220 ...........................................................eeyeeeeeksedkTeiyk 237
                                                                                                  +  +    + ed T +y 
  gi|320100870|ref|YP_004176462.1| 333 fqealvnasimsgafpedvlrdvssyasrgdynsayrriveylnsrsmeeasklidevnRVLSDLIPRVEDSTVFYM 409
                                       ********************************************************99844566678899******* PP

                       Beta_propel 238 falsdgkveyaasgeVpGtllnqFsldey..dg..yLRvatt................................... 275
                                       ++++++++++++s +V+G +l+qF+++e   dg   +  att                                   
  gi|320100870|ref|YP_004176462.1| 410 VDVNGTSLAFRGSIKVKGLILDQFAMEEMnlDGrrLFITATTlttaffkayytryqppmvvgdasnlqvnvvecves 486
                                       ****************************96655324677777*********************************** PP

                       Beta_propel 276 .......................leteeseaetsnnvyvLdek.lkevGkleglapgEriysvRFmgdraYlVTfrq 328
                                                              +    + ++tsn v+v d +  k+v+ l +lapgEriy++R +++++YlVT+r+
  gi|320100870|ref|YP_004176462.1| 487 rcvtipvflnasrmiqqpvawglW-YMLTGSDTSNLVAVVDLSvNKTVAVLSDLAPGERIYAARLVKNMFYLVTYRR 562
                                       ********************9953.56689***********775789999*************************** PP

                       Beta_propel 329 tDPLFviDLsdpanPkilGeLkIpGySeYLhpydenhLlGiGkeadeegeeeqglklslFDVsDpanpkevakvvig 405
                                       +DPL++iDLs+p+nP++lG+Lk pG+SeYLhp++ ++LlGiG       ++  glk+slFDVs p++p+e a +++ 
  gi|320100870|ref|YP_004176462.1| 563 IDPLYAIDLSNPENPRVLGYLKTPGFSEYLHPVSGDRLLGIGLG-----GN-GGLKISLFDVSRPEEPRESAYIEL- 632
                                       ******************************************76.....44.7*********************99. PP

                       Beta_propel 406 drgsdsealydhkAllfdkeknllaipvseesnsessssqgayvykvdaekgfklkgkitheelakeetlkkakdly 482
                                           +s++ +dh+A+++d+ ++  +ip+s       ++++g++v+kv  ++++ l++ ++h+               
  gi|320100870|ref|YP_004176462.1| 633 PG--WSPVFSDHHAFTWDPLRGNAYIPYS-------YTTSGVLVVKVG-DSSLHLVKILQHPG-------------- 685
                                       44..5************************.......99**********.9***********66.............. PP

                       Beta_propel 483 eysskvrRslyigdklytvseskiksadlet 513
                                              R++yig+ +ytvs s+i   + +t
  gi|320100870|ref|YP_004176462.1| 686 -----AIRAVYIGGSIYTVSWSSIAEWSADT 711
                                       .....89***************998887776 PP

>> LVIVD  LVIVD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.11   6.4e+02      11      24 ..     135     147 ..     131     156 .. 0.73
   2 !    8.9   0.0   0.00015       0.9      23      39 ..     206     223 ..     195     225 .. 0.76
   3 ?    1.3   0.0     0.037   2.2e+02      24      38 ..     567     581 ..     564     585 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.11
                             LVIVD  11 GnYaYvAdqdngLv 24 
                                       + Y YvA  +++  
  gi|320100870|ref|YP_004176462.1| 135 ERYIYVA-TGGEVR 147
                                       67*****.546655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00015
                             LVIVD  23 LvIv.DISNpSsptlkgs 39 
                                       Lv+v  +SNpS p+++g+
  gi|320100870|ref|YP_004176462.1| 206 LVVVyNVSNPSTPIEVGR 223
                                       6666579*********97 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.037
                             LVIVD  24 vIvDISNpSsptlkg 38 
                                         +D SNp +p   g
  gi|320100870|ref|YP_004176462.1| 567 YAIDLSNPENPRVLG 581
                                       569*****9997666 PP

>> CDC24  CDC24 Calponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.66      10      32 ..     200     222 ..     191     228 .. 0.88
   2 ?   -4.1   0.0         3   1.8e+04      70      83 ..     513     526 ..     513     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                             CDC24  10 lrqGspLlalfNalkpeeklevd 32 
                                       l++Gs L++++N+ +p++++ev 
  gi|320100870|ref|YP_004176462.1| 200 LQHGSTLVVVYNVSNPSTPIEVG 222
                                       89*******************94 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3
                             CDC24  70 lfsedttdlvkvlk 83 
                                       l+++dt++lv v++
  gi|320100870|ref|YP_004176462.1| 513 LTGSDTSNLVAVVD 526
                                       57899999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 5048.41
//
Query:       gi|320100871|ref|YP_004176463.1|  [L=137]
Description: transcriptional regulator TrmB [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   42.6   0.4    6.4e-11   42.0   0.4    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.6e-10   40.4   0.0    2.7e-10   39.6   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    5.9e-10   38.8   0.0    1.1e-09   38.0   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
    5.5e-06   26.2   0.0    1.2e-05   25.1   0.0    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
    5.6e-06   26.8   0.1      9e-06   26.1   0.1    1.3  1  HTH_27           Winged helix DNA-binding domain
    1.1e-05   25.4   0.0    1.8e-05   24.7   0.0    1.3  1  HTH_20           Helix-turn-helix domain
    1.5e-05   24.8   0.0    2.4e-05   24.1   0.0    1.4  1  MarR_2           MarR family
     0.0014   18.4   0.0     0.0026   17.5   0.0    1.4  1  LexA_DNA_bind    LexA DNA binding domain
     0.0024   17.7   0.0      0.004   17.0   0.0    1.4  1  MarR             MarR family
     0.0057   16.8   0.1       0.01   16.0   0.1    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.008   16.5   0.0      0.013   15.9   0.0    1.3  1  Rrf2             Transcriptional regulator
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.057   13.2   0.0    2.2  2  HTH_38           Helix-turn-helix domain
      0.017   14.8   0.1      0.069   12.8   0.0    2.1  2  Sigma70_r4_2     Sigma-70, region 4
      0.018   14.9   2.4      0.021   14.7   2.4    1.3  1  DUF1478          Protein of unknown function (DUF1478)
       0.02   14.8   0.1      0.065   13.2   0.1    1.9  1  HTH_12           Ribonuclease R winged-helix domain
      0.026   14.4   0.1        1.1    9.2   0.1    2.1  1  TBPIP            TBPIP/Hop2 winged helix domain
      0.027   14.3   0.1       0.11   12.3   0.0    2.0  3  HTH_23           Homeodomain-like domain
      0.046   13.8   0.0      0.075   13.1   0.0    1.4  1  FeoC             FeoC like transcriptional regulator
      0.056   13.8   0.0      0.077   13.4   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
      0.076   13.2   0.1       0.19   11.9   0.0    1.8  2  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.079   12.8   0.0       0.13   12.1   0.0    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.092   12.6   0.0       0.13   12.1   0.0    1.2  1  DUF742           Protein of unknown function (DUF742)
        0.1   13.1   0.0       0.27   11.7   0.0    1.7  1  HTH_40           Helix-turn-helix domain
       0.11   12.5   1.8       0.23   11.5   1.8    1.5  1  Ubiq-assoc       Ubiquitin-associated


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 !   42.0   0.4   8.6e-14   6.4e-11       5      57 ..       4      57 ..       2      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 8.6e-14
                                      HHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  5 GLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      +Lse+E ++Y++L+ k+ p+  +eia+e+++p s+v   Lr+L++kG+V ++ +
  gi|320100871|ref|YP_004176463.1|  4 DLSETELRIYVYLVeKRRPMGLREIAREVNLPVSTVHYNLRKLVEKGYVVKNLE 57
                                      79************99*********************************98765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   3.7e-13   2.7e-10       1      47 [.       5      52 ..       5      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 3.7e-13
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      l+et+++I+ +L ++ r +  re+A++++l++stv++ l++L+e+G++
  gi|320100871|ref|YP_004176463.1|  5 LSETELRIYVYLVEKRRpMGLREIAREVNLPVSTVHYNLRKLVEKGYV 52
                                      679***********9999*****************************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 !   38.0   0.0   1.4e-12   1.1e-09      12      51 ..      16      55 ..      10      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.4e-12
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      l e +++++l+e+Ar+  lp Stvh  L+ Lve Gyv ++
  gi|320100871|ref|YP_004176463.1| 16 LVEKRRPMGLREIAREVNLPVSTVHYNLRKLVEKGYVVKN 55
                                      66899********************************886 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.6e-08   1.2e-05       5      45 ..      10      52 ..       6      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.6e-08
                                      HHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      l+I  +L e  +++   e+a+e++l+ stv + L+kL e G+V
  gi|320100871|ref|YP_004176463.1| 10 LRIYVYLVEkrRPMGLREIAREVNLPVSTVHYNLRKLVEKGYV 52
                                      555445555599******************************9 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   1.2e-08     9e-06       9      51 ..      14      55 ..       8      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.2e-08
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                      + l++  rr++ l+++++ +n+  s+++y+l+kL+ekG+v+++
  gi|320100871|ref|YP_004176463.1| 14 VYLVE-KRRPMGLREIAREVNLPVSTVHYNLRKLVEKGYVVKN 55
                                      45566.99********************************775 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.3e-08   1.8e-05       9      56 ..       6      54 ..       5      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.3e-08
                                      -HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  9 hPvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +++ +ri+ +L   ++++ + e+a+++ l+ +t++y+Lr+L+e g+v  
  gi|320100871|ref|YP_004176463.1|  6 SETELRIYVYLvEKRRPMGLREIAREVNLPVSTVHYNLRKLVEKGYVVK 54
                                      567788999999999999***************************9865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   3.2e-08   2.4e-05      22      53 ..      23      54 ..       3      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.2e-08
                                      EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +  +e+ar+ +l+ s+v++ l++Lv++G+v++
  gi|320100871|ref|YP_004176463.1| 23 MGLREIAREVNLPVSTVHYNLRKLVEKGYVVK 54
                                      5678**************************86 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 !   17.5   0.0   3.5e-06    0.0026      21      56 ..      18      52 ..      10      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                                      HHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind 21 etgypPsireiaralglkSpsaveehLkaLerKGyi 56
                                      e+  p   reiar+++l   s+v+  L++L  KGy+
  gi|320100871|ref|YP_004176463.1| 18 EKRRPMGLREIAREVNLP-VSTVHYNLRKLVEKGYV 52
                                      55567779*********9.9***************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.4e-06     0.004       2      47 ..       6      52 ..       5      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.4e-06
                                      -HHHHHH.HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  2 tltqfvi.LrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      ++t+++i +++++ + p+ + e+a+ +++  stv   l++L++kG++
  gi|320100871|ref|YP_004176463.1|  6 SETELRIyVYLVEKRRPMGLREIAREVNLPVSTVHYNLRKLVEKGYV 52
                                      5556655467889999*****************************99 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   0.1   1.4e-05      0.01      17      53 ..      17      53 ..       6      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                                      HHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 17 seekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                       e++ + +  ++a++ n   s+V   l+kL ++Gyv+
  gi|320100871|ref|YP_004176463.1| 17 VEKRRPMGLREIAREVNLPVSTVHYNLRKLVEKGYVV 53
                                      4577888899**************************7 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.7e-05     0.013      11      55 ..      10      52 ..       1      58 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglv 55
                                      l++ +yL ++  ++p+ ++eia+++n++ s +   l+kL ++g+v
  gi|320100871|ref|YP_004176463.1| 10 LRIYVYLVEK--RRPMGLREIAREVNLPVSTVHYNLRKLVEKGYV 52
                                      5555666555..559****************************99 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.6e-05     0.057      21      42 ..      23      44 ..       9      46 .. 0.86
   2 ?   -1.5   0.0         3   2.2e+03      16      24 ..     122     130 ..     120     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.6e-05
                            HTH_38 21 lslreIArrLgrspsTIsRElk 42
                                      ++lreIAr+++   sT+++ l+
  gi|320100871|ref|YP_004176463.1| 23 MGLREIAREVNLPVSTVHYNLR 44
                                      99***************99887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3
                            HTH_38  16 llaeGlslr 24 
                                       +l eGl+lr
  gi|320100871|ref|YP_004176463.1| 122 MLHEGLTLR 130
                                       7899**999 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   9.2e-05     0.069      30      49 ..      26      45 ..      23      49 .. 0.87
   2 ?   -2.1   0.0       4.3   3.2e+03      21      30 ..      99     107 ..      96     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.2e-05
                                      HHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 30 kEIAellgisegtVksrlsR 49
                                      +EIA++ +++++tV ++l++
  gi|320100871|ref|YP_004176463.1| 26 REIAREVNLPVSTVHYNLRK 45
                                      8***************9987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                                       HHHTS---HH CS
                      Sigma70_r4_2  21 lryleglsyk 30 
                                       + y++g+s +
  gi|320100871|ref|YP_004176463.1|  99 M-YIQGYSSE 107
                                       6.99***975 PP

>> DUF1478  Protein of unknown function (DUF1478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.4   2.9e-05     0.021      82     138 ..      70     130 ..      13     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                           DUF1478  82 fldl.yrfiptltrtlltslgcgpggavvlr.sgyrs...lvlacslgvslllsyhqglipr 138
                                       f+ + yr+ip l    l  lg   gga+ +   gy s   +++a+sl  sll+  h+gl  r
  gi|320100871|ref|YP_004176463.1|  70 FIRVgYRVIPRLILYSLLYLGMSIGGAISMYiQGYSSerlMLIAVSLSSSLLM-LHEGLTLR 130
                                       554449*********************97643688554327789999988765.78998765 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 ?   13.2   0.1   8.7e-05     0.065       6      51 ..      15      55 ..      10      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-05
                            HTH_12  6 ilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrv 51
                                       l e+ +p+g +eia e+++        +v y Lrkl e+g++ ++
  gi|320100871|ref|YP_004176463.1| 15 YLVEKRRPMGLREIAREVNL-----PVSTVHYNLRKLVEKGYVVKN 55
                                      68899**********99976.....45789***********88776 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0015       1.1      19      47 ..      36      64 ..       7      70 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                             TBPIP 19 vqdvvanlqkklgKtavqkaLdeLvdegk 47
                                      v++v  nl+k + K  v+k L+  v++g 
  gi|320100871|ref|YP_004176463.1| 36 VSTVHYNLRKLVEKGYVVKNLEGYVAKGS 64
                                      45677788888888888888888777775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.11      21      45 ..      26      50 ..      23      55 .. 0.89
   2 ?   -2.9   0.0       8.8   6.6e+03      10      19 ..      96     105 ..      96     108 .. 0.78
   3 ?   -2.5   0.0       6.7     5e+03      11      21 ..     120     130 ..     120     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                            HTH_23 21 reIAreLgvsrrTvyrwlkryreeG 45
                                      reIAre + + +Tv   l++ +e+G
  gi|320100871|ref|YP_004176463.1| 26 REIAREVNLPVSTVHYNLRKLVEKG 50
                                      9**************8888888888 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.8
                            HTH_23  10 illllaeGls 19 
                                       ++ ++ +G+s
  gi|320100871|ref|YP_004176463.1|  96 AISMYIQGYS 105
                                       6889999998 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.7
                            HTH_23  11 llllaeGlsvr 21 
                                       ll+l eGl+ r
  gi|320100871|ref|YP_004176463.1| 120 LLMLHEGLTLR 130
                                       68999999987 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.075       9      53 ..      17      61 ..       8      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                              FeoC  9 leergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaatacc 53
                                      +e+r+   l+e++r+ +   +++   L  +v kG v k  ++  +
  gi|320100871|ref|YP_004176463.1| 17 VEKRRPMGLREIAREVNLPVSTVHYNLRKLVEKGYVVKNLEGYVA 61
                                      689999*******************************99887665 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0    0.0001     0.077       1      55 [.       5      56 ..       5      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                      ---S-SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEE CS
                   Penicillinase_R  1 lgelEaevmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrek 55
                                      l+e E+ ++ +l ek + +  +e+  e++ +     sTV+  lr+Lv+Kg++ ++ 
  gi|320100871|ref|YP_004176463.1|  5 LSETELRIYVYLVEKRRpMGLREIAREVNLP----VSTVHYNLRKLVEKGYVVKNL 56
                                      5788888888777776669999998888877....9***************98765 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   0.00025      0.19      23      51 ..      27      55 ..      18      92 .. 0.92
   2 ?   -1.5   0.0       3.8   2.9e+03      61      70 ..     115     124 ..      95     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                    B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvkq 51
                                      ++a+e++  ++ ++y l++L +kg++vk+
  gi|320100871|ref|YP_004176463.1| 27 EIAREVNLPVSTVHYNLRKLVEKGYVVKN 55
                                      667888888999***************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.8
                    B-block_TFIIIC  61 sistsllvlk 70 
                                       s s+sll+l+
  gi|320100871|ref|YP_004176463.1| 115 SLSSSLLMLH 124
                                       4566777766 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   0.0   0.00017      0.13      18      41 ..      23      46 ..       5      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                     HTH_AsnC-type 18 isyaeLAervGlSestvlrRvrrL 41
                                      +  +e+A++v+l  stv+  +r+L
  gi|320100871|ref|YP_004176463.1| 23 MGLREIAREVNLPVSTVHYNLRKL 46
                                      5679**************999888 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.13      51      88 ..      16      55 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                            DUF742 51 Lcre..plsVaelaAelklPvgvvrvLlsdLldaglltvr 88
                                      L+++  p+   e+a e++lPv++v+  l  L+++g+++ +
  gi|320100871|ref|YP_004176463.1| 16 LVEKrrPMGLREIAREVNLPVSTVHYNLRKLVEKGYVVKN 55
                                      55444478889************************99865 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.27      13      43 ..      23      53 ..      15      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                            HTH_40 13 lsieeIAkerglkesTIegHLaelieegeei 43
                                      + + eIA+e +l +sT+   L +l+e+g+ +
  gi|320100871|ref|YP_004176463.1| 23 MGLREIAREVNLPVSTVHYNLRKLVEKGYVV 53
                                      5689***********************9844 PP

>> Ubiq-assoc  Ubiquitin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.8   0.00031      0.23      13      37 ..      86     110 ..      83     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                       HHHH---SHHHHHHHHHH-SSHHHH CS
                        Ubiq-assoc  13 LMSLGLsidkAneyYekGilYedll 37 
                                       L  LG+si+ A + Y +G++ e+l+
  gi|320100871|ref|YP_004176463.1|  86 LLYLGMSIGGAISMYIQGYSSERLM 110
                                       6679******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1050.99
//
Query:       gi|320100872|ref|YP_004176464.1|  [L=83]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-12   45.8   2.4    3.3e-12   45.8   2.4    1.8  2  DUF131        Protein of unknown function DUF131
     0.0009   19.4   4.4    0.00098   19.2   4.4    1.0  1  CD20          CD20-like family
  ------ inclusion threshold ------
       0.98    9.2   4.8        3.5    7.4   0.6    2.1  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4      0.19   1.1e+03      55      55 ..      14      14 ..       1      24 [. 0.50
   2 !   45.8   2.4   5.6e-16   3.3e-12      13      62 .]      27      76 ..      16      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.19
                            DUF131 55 m 55
                                      +
  gi|320100872|ref|YP_004176464.1| 14 L 14
                                      2 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 5.6e-16
                            DUF131 13 eeaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllilf 62
                                        ++++ ++  gG Vv++GPIPI+ Gsd++  kt++iLaI l +++l+lf
  gi|320100872|ref|YP_004176464.1| 27 VGRREGGREFRGGFVVVVGPIPIVVGSDEETGKTLVILAIALSLVALALF 76
                                      46677788899999*********************************997 PP

>> CD20  CD20-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   4.4   1.6e-07   0.00098       2      80 ..       2      82 ..       1      83 [] 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-07
                              CD20  2 LGvvQillGllslvlGilllsvsss.tllasgypfWgGivfiisGvlgiaaekrst.kllvklslllnlvslvlalaGi 78
                                      ++++ +l+Gl+ l+ G++ll++ +    ++ g  f gG+v+++  +  ++ +   t k+lv+l ++l+lv l+l+l+ +
  gi|320100872|ref|YP_004176464.1|  2 MALLMLLTGLVLLAAGVILLVLEEAvGRREGGREFRGGFVVVVGPIPIVVGSDEETgKTLVILAIALSLVALALFLVPL 80
                                      577789******************966677777888888777777777666655555******************9988 PP

                              CD20 79 il 80
                                      il
  gi|320100872|ref|YP_004176464.1| 81 IL 82
                                      87 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.6   0.00059       3.5     119     142 ..       3      26 ..       1      37 [. 0.78
   2 ?    4.5   0.3    0.0045        27      37      58 ..      57      78 ..      39      83 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00059
                      Trp_oprn_chp 119 pvlalaggvllllagvllllrars 142
                                       ++l+l+ g++ll+agv+ll+  ++
  gi|320100872|ref|YP_004176464.1|   3 ALLMLLTGLVLLAAGVILLVLEEA 26 
                                       678899999999999999987654 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0045
                      Trp_oprn_chp 37 sGadwapaltalAlvllAaavA 58
                                      +G+++  ++ al+lv+lA ++ 
  gi|320100872|ref|YP_004176464.1| 57 TGKTLVILAIALSLVALALFLV 78
                                      7999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 666.65
//
Query:       gi|320100873|ref|YP_004176465.1|  [L=92]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.03   14.1   2.3       0.03   14.1   2.3    2.7  3  LapA_dom         Lipopolysaccharide assembly protein A domain
       0.53    9.5   3.4       0.59    9.4   3.4    1.1  1  Peptidase_U4     Sporulation factor SpoIIGA
        4.4    6.6   4.7       0.92    8.8   0.9    1.5  1  TssN             Type VI secretion system, TssN


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 ?   -4.0   8.2       2.3   1.3e+04      22      40 ..       6      24 ..       1      45 [. 0.57
   2 ?   -1.1   0.2      0.29   1.8e+03      22      27 ..      40      45 ..      26      53 .. 0.61
   3 ?   14.1   2.3   5.1e-06      0.03      21      44 ..      58      80 ..      58      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.3
                          LapA_dom 22 lllvafgiGallgwllslw 40
                                      ll++  +i ++ g++++++
  gi|320100873|ref|YP_004176465.1|  6 LLIAIGVILLITGGIVAVL 24
                                      4443333333333333332 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.29
                          LapA_dom 22 lllvaf 27
                                      +++v+f
  gi|320100873|ref|YP_004176465.1| 40 CIIVFF 45
                                      555555 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 5.1e-06
                          LapA_dom 21 llllvafgiGallgwllslwsylr 44
                                      +lllv+++iGa++++ll +  +++
  gi|320100873|ref|YP_004176465.1| 58 VLLLVSMVIGAVITLLLLWG-IIQ 80
                                      69***************995.444 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.4   9.8e-05      0.59      68     140 ..       8      85 ..       1      90 [. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 9.8e-05
                      Peptidase_U4  68 vsllmvliafgpkslkeflkalllfylvsfllgGilfalsyll...lkskn.......llvlllgalvaylllkllv 134
                                       +++ ++     + ++  +l+all    +s+ +gG++++++  l   +   +       l+ +++ga++++lll+ ++
  gi|320100873|ref|YP_004176465.1|   8 IAIGVI--LLITGGIVAVLEALLSSSGASISAGGCIIVFFIPLcfgV---GehhdvllLVSMVIGAVITLLLLWGII 79 
                                       333333..233456778999999999999999998777766565552...234566666677778888887777666 PP

                      Peptidase_U4 135 kiikkk 140
                                       ++ +++
  gi|320100873|ref|YP_004176465.1|  80 QASRSR 85 
                                       665555 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.9   0.00015      0.92      97     140 ..       7      50 ..       2      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00015
                              TssN  97 illtlivillglvlfvlvfnllselqygvwaatsllvfiipllf 140
                                       ++ + +++l+   +  ++  lls++   + a ++++vf+ipl+f
  gi|320100873|ref|YP_004176465.1|   7 LIAIGVILLITGGIVAVLEALLSSSGASISAGGCIIVFFIPLCF 50 
                                       45667788888889999999999999***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 668.71
//
Query:       gi|320100874|ref|YP_004176466.1|  [L=469]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-63  212.2   3.0    1.3e-62  211.7   3.0    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.6e-21   75.5   6.5    5.7e-18   65.3   0.0    3.7  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.1e-18   67.5   0.1    3.9e-18   65.7   0.0    2.0  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.5e-13   50.7   0.9    1.3e-12   47.6   0.8    2.0  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.1e-06   28.1   0.3    2.9e-06   26.7   0.3    1.7  1  Thi4            Thi4 family
    2.3e-06   27.3   1.1    2.3e-06   27.3   1.1    1.9  2  FAD_oxidored    FAD dependent oxidoreductase
    7.4e-06   25.3   8.4    8.6e-05   21.8   1.3    2.7  3  GIDA            Glucose inhibited division protein A
    9.1e-06   24.6   7.4     0.0014   17.4   0.0    3.1  3  HI0933_like     HI0933-like protein
    1.3e-05   25.0  15.4      0.076   12.6   3.3    3.9  4  DAO             FAD dependent oxidoreductase
    1.5e-05   24.9   2.9     0.0031   17.4   0.0    2.5  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    3.7e-05   23.9   2.7      0.014   15.7   0.5    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.3e-05   22.5   2.4    5.3e-05   22.5   2.4    3.3  2  FAD_binding_2   FAD binding domain
    0.00035   19.9   8.3      0.037   13.3   0.7    2.9  3  FAD_binding_3   FAD binding domain
     0.0025   18.2   0.4       0.48   10.9   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
     0.0033   16.8   2.6       0.11   11.8   0.0    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0039   16.6   0.5       0.97    8.7   0.1    2.2  2  ThiF            ThiF family
  ------ inclusion threshold ------
      0.023   14.0   0.5       0.23   10.7   0.0    2.5  3  Amino_oxidase   Flavin containing amine oxidoreductase
      0.049   13.0   0.1        2.1    7.7   0.0    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.049   13.2   2.7          4    7.0   0.0    2.5  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.13   12.2   7.6       0.14   12.2   0.0    3.6  4  NAD_binding_9   FAD-NAD(P)-binding
       0.31   10.0   6.8        3.2    6.7   0.4    2.9  3  Lycopene_cycl   Lycopene cyclase protein
       0.31    9.8   7.8       0.14   11.0   0.4    2.8  3  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   3.0   1.6e-65   1.3e-62       1     291 [.      16     324 ..      16     327 .. 0.96

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 1.6e-65
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias................. 57 
                                       +dvvv+G+G +G+ aa +la +g+kv++ve    +g+c n gc++ska+ ++ae+ + +                  
  gi|320100874|ref|YP_004176466.1|  16 YDVVVVGSGTGGYPAAVYLAGKGLKVAVVEehlIGGECTNYGCVPSKAFYQIAEAIRSIGkvggeasvkwgslvdwv 92 
                                       69***************************99*************************99989**************** PP

                                       .HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC....TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .evvkklnqgielllgeevvkidpgkkkvklekkke....gdeekiaydklvlAtGssprdlgipGvaenvgklvrt 129
                                          vk+ ++gi+ l ++++v++ +gk+ +k  ++      + +  i+++k++lA+Gs+p +   pGv   v++++  
  gi|320100874|ref|YP_004176466.1|  93 kSMVKESREGIQGLFESHGVNVLNGKAVLKTPHEIVveegSGKAVIEAGKVLLAPGSNPSTV--PGV---VFDGIGV 164
                                       98899999******************9999987766889877789***********999875..***...8889999 PP

                                       CHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 130 ldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsv 206
                                       l + eal  +++p++++++GgG+iGvElA a+++lg  +tlve +d++l+++d+++++al+ +l  +Gv++  +ts 
  gi|320100874|ref|YP_004176466.1| 165 LSNREALYMQEKPESMLIIGGGVIGVELANAFSSLGISITLVELMDHILPSMDRDIAQALKTHLSSRGVKILEKTST 241
                                       ***************************************************************************** PP

                                       EEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 207 keidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkg 282
                                         i + g+++  +l++ge++++d v+va+G++p+t++++  + g++ld+rg+i+++e+++t+vp +ya+GD +   g
  gi|320100874|ref|YP_004176466.1| 242 RSISRIGDRYVAELSNGERLEVDKVLVATGRTPRTSGIGlVENGVQLDRRGFIKINERQETTVPAVYAAGDAV---G 315
                                       *******9888************************************************************99...* PP

                                       SS--HHHHH CS
                                       xxxxxxxxx RF
                       Pyr_redox_2 283 gpelaqaAv 291
                                       gp la++A+
  gi|320100874|ref|YP_004176466.1| 316 GPLLAHKAI 324
                                       ******997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   1.1   0.00086       0.7       2      30 ..      18      46 ..      17      48 .. 0.95
   2 ?   -0.9   0.0         3   2.5e+03      41      65 ..      98     122 ..      90     131 .. 0.81
   3 !   65.3   0.0     7e-21   5.7e-18       2      73 ..     180     252 ..     179     257 .. 0.94
   4 ?   -1.9   0.0       6.5   5.3e+03      55      76 ..     349     370 ..     345     374 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00086
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      vvvvG+G+ g  +A +la  g kV vve 
  gi|320100874|ref|YP_004176466.1| 18 VVVVGSGTGGYPAAVYLAGKGLKVAVVEE 46
                                      8**************************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHTTEEEECSEEEEE CS
                         Pyr_redox  41 easkilqeklekngievllntkvee 65 
                                       e ++ +q  +e +g++vl ++ v +
  gi|320100874|ref|YP_004176466.1|  98 ESREGIQGLFESHGVNVLNGKAVLK 122
                                       5566778889999****99988765 PP

  == domain 3  score: 65.3 bits;  conditional E-value: 7e-21
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.v 73 
                                       ++++GgG+ig+ElA+a++ lg ++t+ve +d++l+ +D++++++l+++l+ +g+++l +t++ +i   +d  v
  gi|320100874|ref|YP_004176466.1| 180 MLIIGGGVIGVELANAFSSLGISITLVELMDHILPSMDRDIAQALKTHLSSRGVKILEKTSTRSISRIGDRyV 252
                                       79**************************************************************998887655 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 6.5
                                       EEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox  55 ievllntkveeiegsedgvesv 76 
                                       +++ ++ +v++i  se++++s+
  gi|320100874|ref|YP_004176466.1| 349 VTIFTGLEVASIGYSEKELTSI 370
                                       6677777777877777776665 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.8   5.5e+03      58      83 ..     178     203 ..     175     210 .. 0.83
   2 !   65.7   0.0   4.8e-21   3.9e-18       1     108 [.     347     454 ..     347     456 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.8
                                       TTTBEEEEEEECTTHHHHHHHHHHHH CS
                     Pyr_redox_dim  58 ktgkvlGahivGpgageliqelavai 83 
                                       ++  ++G  ++G + + +++ l + i
  gi|320100874|ref|YP_004176466.1| 178 ESMLIIGGGVIGVELANAFSSLGISI 203
                                       67789999999999999998887766 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 4.8e-21
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       ip ++ft +evas+G++e+e++  g++++ +++p   ++  ++++ ++ f+K++ d++ +kvlG+h+v+p+a+e+i+
  gi|320100874|ref|YP_004176466.1| 347 IPVTIFTGLEVASIGYSEKELTSIGVKYVKVRIPAYYLSAVKIKGGKQSFIKVLLDERLEKVLGIHVVAPNASEVIS 423
                                       799***********************999999***9***************************************** PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGHC CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealke 108
                                       ++  +   +l  +++a+t  +h t+se+l++
  gi|320100874|ref|YP_004176466.1| 424 AYIPLYLGKLCFREAARTPYPHLTVSESLRD 454
                                       ***************************9976 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 !   47.6   0.8   1.6e-15   1.3e-12       1     305 []      19     311 ..      19     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.6e-15
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypk..emtfispsftsekleipdlnaiseetspafslke 75 
                                       +++G G  G  aa+ l  +gl ++ ++E + ig   ++y    ++ f   ++  ++++  + +a +++ s    ++ 
  gi|320100874|ref|YP_004176466.1|  19 VVVGSGTGGYPAAVYLAGKGL-KVAVVEEHLIGGECTNYGCvpSKAFYQIAEAIRSIGKVGGEASVKWGSL---VDW 91 
                                       79*******************.79***************65225667777777777776666677777774...455 PP

                       Pyr_redox_3  76 eklsrkealeYlrevaksfelpiklfeeVesvkkedegfeve..tsketyeAkkviiAtGefdkPnklnipGeeklv 150
                                        k   ke  e  + + +s+ +++   + V +   + ++ +ve  + k+++eA kv++A G  +   ++++ +     
  gi|320100874|ref|YP_004176466.1|  92 VKSMVKESREGIQGLFESHGVNVLNGKAVLK---TPHEIVVEegSGKAVIEAGKVLLAPGS-NPSTVPGVVFDG-IG 163
                                       566678889999***********99988775...44556666115566************9.555667787777.88 PP

                       Pyr_redox_3 151 khyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeeki 227
                                       + +     +++ + + +++iGg+  +v+ A  + + g ++t+v   ++i         s+  di + l++ ++++ +
  gi|320100874|ref|YP_004176466.1| 164 VLSNREALYMQEKPESMLIIGGGVIGVELANAFSSLGISITLVELMDHILP-------SMDRDIAQALKTHLSSRGV 233
                                       88888888889999*****************************99975544.......578899999999888877* PP

                       Pyr_redox_3 228 kvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkk..slfeldedgrpvlteeteetnvpglf 302
                                       k+l+++++++i++   +y  + ++g+++ev d+v++atG +p +s +    ++++ld+ g+++++e + et+vp ++
  gi|320100874|ref|YP_004176466.1| 234 KILEKTSTRSISRIGDRYVAELSNGERLEV-DKVLVATGRTPRTSGIGLveNGVQLDRRGFIKINERQ-ETTVPAVY 308
                                       ***************************999.899*********988554449************9865.677***** PP

                       Pyr_redox_3 303 laG 305
                                        aG
  gi|320100874|ref|YP_004176466.1| 309 AAG 311
                                       999 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.3   3.6e-09   2.9e-06      14      56 ..      12      53 ..       6      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.6e-09
                                      HHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 14 kyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                      +++  Dvv+vG+G+ G  aa yla k +lkva++e+++  G  
  gi|320100874|ref|YP_004176466.1| 12 DIVRYDVVVVGSGTGGYPAAVYLAGK-GLKVAVVEEHLIGGEC 53
                                      78899*********************.**********965544 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   1.1   2.8e-09   2.3e-06       1      55 [.      17      70 ..      17     132 .. 0.86
   2 ?   -0.4   0.1      0.69   5.6e+02       3      33 ..     181     211 ..     180     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.8e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqv 55
                                      DvvVvG+g++G+ AA+  a +G kv++vee+  +GG  t+ +  +   +++ +++
  gi|320100874|ref|YP_004176466.1| 17 DVVVVGSGTGGYPAAVYLAGKGLKVAVVEEH-LIGGECTNYGCVPSKAFYQIAEA 70
                                      9***************************985.89******999998888854433 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.69
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergv 33 
                                       +++GGg+ Gv  A a    G +  Lve  ++
  gi|320100874|ref|YP_004176466.1| 181 LIIGGGVIGVELANAFSSLGISITLVELMDH 211
                                       79************************96665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.3   1.1e-07   8.6e-05       1      60 [.      17      78 ..      17      85 .. 0.79
   2 !    6.8   0.3    0.0037         3       3      33 ..     181     210 ..     179     225 .. 0.85
   3 ?   -1.0   0.0      0.87   7.1e+02      99     150 ..     222     272 ..     212     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G..GGTT--SSSSEEE-TTHHHHHHHHHHHT CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkl..dtiaelsCnpsiggiakgllvrEidalg 60
                                      dv+V+G G  G+ AA+ +a +G+kv+ + ++l  +++ + +C ps      ++  r i ++g
  gi|320100874|ref|YP_004176466.1| 17 DVVVVGSGTGGYPAAVYLAGKGLKVAVVEEHLigGECTNYGCVPSKAFYQIAEAIRSIGKVG 78
                                      79**************************66643389********986554444444444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0037
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkld 33 
                                        +iGgG  G+e A a + lG++++L+ + +d
  gi|320100874|ref|YP_004176466.1| 181 LIIGGGVIGVELANAFSSLGISITLV-ELMD 210
                                       79***********************9.4444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.87
                                       HHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA  99 kevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       ++++  l++   ++i+e++ ++ i + +   +  +++ge ++ ++v +atG 
  gi|320100874|ref|YP_004176466.1| 222 QALKTHLSS-RGVKILEKTSTRSISRIGDRYVAELSNGERLEVDKVLVATGR 272
                                       444555555.778888888777767667778889999999**********95 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.6    0.0006      0.49       1      32 [.      16      47 ..      16      52 .. 0.93
   2 ?    1.7   0.2       0.1        82       3      35 ..     180     212 ..     178     217 .. 0.91
   3 !   17.4   0.0   1.8e-06    0.0014     109     196 ..     218     305 ..     191     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0006
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dv+v+G G  G  aA+ +a +g +V+++e+ 
  gi|320100874|ref|YP_004176466.1| 16 YDVVVVGSGTGGYPAAVYLAGKGLKVAVVEEH 47
                                      59***************************975 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       +++iGgG  G+  A + ++ g +++l+e ++++
  gi|320100874|ref|YP_004176466.1| 180 MLIIGGGVIGVELANAFSSLGISITLVELMDHI 212
                                       78*************************988766 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS.-GGGT--SHHHHHHHHTT CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS.iPklGstgkgyklaeqfg 184
                                       +di +al+++l+++gvk+  +t+ +s+++  d+ +  +++++e+le dk+++AtG +     +G  ++g++l +   
  gi|320100874|ref|YP_004176466.1| 218 RDIAQALKTHLSSRGVKILEKTSTRSISRIGDR-YVAELSNGERLEVDKVLVATGRTPrTSGIGLVENGVQLDRRGF 293
                                       799************************999988.999999***************7641456777777777777766 PP

                                       --EEEEEEES-- CS
                       HI0933_like 185 htivplrpalvp 196
                                       ++i + + + vp
  gi|320100874|ref|YP_004176466.1| 294 IKINERQETTVP 305
                                       666666666555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   3.3   9.3e-05     0.076       1      37 [.      17      54 ..      17      58 .. 0.90
   2 ?   -0.4   0.0      0.84   6.9e+02     152     201 ..     103     148 ..      97     158 .. 0.65
   3 !    6.9   0.4    0.0051       4.1       3      27 ..     181     207 ..     179     211 .. 0.92
   4 !   11.5   0.0    0.0002      0.17     147     201 ..     219     271 ..     216     309 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.3e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaS 37
                                      dvv++G+G  G  +A +La +g  V+++e +  +g +++
  gi|320100874|ref|YP_004176466.1| 17 DVVVVGSGTGGYPAAVYLAGKGlkVAVVEEH-LIGGECT 54
                                      9******************999*********.6664655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.84
                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--G CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaG 201
                                       ++  +e++Gv++l+g  v +  +       v  ++  g    +a +v +a G
  gi|320100874|ref|YP_004176466.1| 103 IQGLFESHGVNVLNGKAVLKTPH----EIVV--EEGsGKAvIEAGKVLLAPG 148
                                       677899*********99988622....1223..2222332223344777776 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0051
                                       EEECTSHHHHHHHHHHHHTT..EEEEE CS
                               DAO   3 viiGGGiiGlstAyeLarrg..Vtlle 27 
                                       +iiGGG+iG+  A + +  g  +tl+e
  gi|320100874|ref|YP_004176466.1| 181 LIIGGGVIGVELANAFSSLGisITLVE 207
                                       8*************9999999999998 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--G CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaG 201
                                         ++al   + ++Gv+ile+t  +++++ ++    v + ++ge+ ++d+v +a+G
  gi|320100874|ref|YP_004176466.1| 219 DIAQALKTHLSSRGVKILEKTSTRSISRIGD--RYVAELSNGERLEVDKVLVATG 271
                                       6789999*******************88543..34422333877567*******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 !    6.7   1.2    0.0074         6       2      29 ..      18      45 ..      17      50 .. 0.93
   2 !   17.4   0.0   3.8e-06    0.0031       4      57 ..     182     237 ..     179     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0074
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvd 29
                                      v v+G+Gt G   a  +a +gl+V +v+
  gi|320100874|ref|YP_004176466.1| 18 VVVVGSGTGGYPAAVYLAGKGLKVAVVE 45
                                      89***********************997 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.8e-06
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-..H CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk..e 57 
                                       +iG G++G ++a++f s g++++lv+  +++l +  + i++ l+   +++ +k  e
  gi|320100874|ref|YP_004176466.1| 182 IIGGGVIGVELANAFSSLGISITLVELMDHILPSMDRDIAQALKTHLSSRGVKilE 237
                                       8****************************************999988877766333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   1.7e-05     0.014       1      38 [.      20      56 ..      20      65 .. 0.93
   2 !    7.6   0.1    0.0055       4.5       1      31 [.     182     212 ..     182     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                      +vG+G +G  aA +La +g++v ++e +  +GG ++ y
  gi|320100874|ref|YP_004176466.1| 20 VVGSGTGGYPAAVYLAGKGLKVAVVEEH-LIGGECTNY 56
                                      8*************************97.899999876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0055
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       I+G+G+ G  +A + +  g++++l+e  d++
  gi|320100874|ref|YP_004176466.1| 182 IIGGGVIGVELANAFSSLGISITLVELMDHI 212
                                       9*************************88876 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.4   6.5e-08   5.3e-05       1      30 [.      17      46 ..      17      53 .. 0.96
   2 ?    0.3   0.2      0.34   2.8e+02       2      31 ..     180     209 ..     179     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.5e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                      Dv+V+GsG +G+ AA+ +a +Glkvavve 
  gi|320100874|ref|YP_004176466.1| 17 DVVVVGSGTGGYPAAVYLAGKGLKVAVVEE 46
                                      9***************************96 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.34
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavveke 31 
                                        ++iG+G+ G   A + +  G ++++ve +
  gi|320100874|ref|YP_004176466.1| 180 MLIIGGGVIGVELANAFSSLGISITLVELM 209
                                       59*************************976 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.7   4.5e-05     0.037       2      33 ..      16      47 ..      15      49 .. 0.95
   2 !    9.1   1.0   0.00082      0.66       4      33 ..     180     209 ..     178     218 .. 0.91
   3 ?   -0.2   0.0      0.58   4.8e+02     107     144 ..     220     257 ..     213     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +dV++VG+G  G  +a  L+ +G +v +ve +
  gi|320100874|ref|YP_004176466.1| 16 YDVVVVGSGTGGYPAAVYLAGKGLKVAVVEEH 47
                                      79***************************987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00082
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                        lI+G+G  G+ la+  s+ G++ +lve +
  gi|320100874|ref|YP_004176466.1| 180 MLIIGGGVIGVELANAFSSLGISITLVELM 209
                                       59*************************976 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEE CS
                     FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvtaevrd 144
                                       + ++L  h+++rg+++ +kt ++s+ + ++   ae+ +
  gi|320100874|ref|YP_004176466.1| 220 IAQALKTHLSSRGVKILEKTSTRSISRIGDRYVAELSN 257
                                       66789999999999999999999999888877777665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.037        30       9      40 ..      17      48 ..      12     114 .. 0.76
   2 !   10.9   0.0   0.00059      0.48       1      39 [.     171     209 ..     171     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev 40
                                       v+vvG G+ ++  +  l+ +g kv vv + +
  gi|320100874|ref|YP_004176466.1| 17 DVVVVGSGTGGYPAAVYLAGKGLKVAVVEEHL 48
                                      69**************************9986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00059
                     NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvape 39 
                                       l+++ k +++l++GgG ++ + ++ + + g  +t+v   
  gi|320100874|ref|YP_004176466.1| 171 LYMQEKPESMLIIGGGVIGVELANAFSSLGISITLVELM 209
                                       577888899**************************8655 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 ?    3.7   1.5     0.041        33      29      58 ..      16      45 ..       8      51 .. 0.88
   2 !   11.8   0.0   0.00013      0.11      28      77 ..     177     226 ..     172     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.041
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlD 58
                                        v+v+G G+ G  A+   +g g kV v++
  gi|320100874|ref|YP_004176466.1| 16 YDVVVVGSGTGGYPAAVYLAGKGLKVAVVE 45
                                      579*******************99999987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev 77 
                                       p  +l+iGgGv G++ +++ ++lg ++t++++  + l  ++   a+ +++
  gi|320100874|ref|YP_004176466.1| 177 PESMLIIGGGVIGVELANAFSSLGISITLVELMDHILPSMDRDIAQALKT 226
                                       66789************************999888887777733333555 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0012      0.97      15      43 ..      12      40 ..       6      48 .. 0.87
   2 !    5.8   0.0    0.0094       7.7      20      49 ..     179     210 ..     165     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                      HHHTSEEEEE--SHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 15 kLrdskvllvGaGglGsellknLalsGvg 43
                                       + +  v++vG G+ G +++++La+ G++
  gi|320100874|ref|YP_004176466.1| 12 DIVRYDVVVVGSGTGGYPAAVYLAGKGLK 40
                                      567788*******************9986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0094
                                       EEEEE--SHHHHHHHHHHHHHTTT..EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                              ThiF  20 kvllvGaGglGsellknLalsGvg..kltlvD 49 
                                       ++l++G G +G el+ ++  +G++   ++l+D
  gi|320100874|ref|YP_004176466.1| 179 SMLIIGGGVIGVELANAFSSLGISitLVELMD 210
                                       689*******************9644555555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.1   9.3e+02       6      21 ..      30      45 ..      29      51 .. 0.93
   2 ?   10.7   0.0   0.00029      0.23     214     260 ..     222     270 ..     174     273 .. 0.87
   3 ?   -0.3   0.0      0.62   5.1e+02     414     448 ..     300     331 ..     295     334 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                                      HHHHHHHTTEEEEEEE CS
                     Amino_oxidase  6 aArqLlsaGfdVtvlE 21
                                      aA +L+ +G++V v+E
  gi|320100874|ref|YP_004176466.1| 30 AAVYLAGKGLKVAVVE 45
                                      8**************9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
                                       HHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S CS
                     Amino_oxidase 214 ealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTv 260
                                       +al    ++rg++i+  t  ++i+r gd +  +l++ge +e+D+V+v++
  gi|320100874|ref|YP_004176466.1| 222 QALKThlSSRGVKILEKTSTRSISRIGDRYVAELSNGERLEVDKVLVAT 270
                                       333335666**************************************97 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.62
                                       HCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHH CS
                     Amino_oxidase 414 akpegdprlffAGehtsreypgtvegAilSGlraA 448
                                       +++  +p ++ AG+++    p   ++Ail  ++aA
  gi|320100874|ref|YP_004176466.1| 300 QET-TVPAVYAAGDAVG--GPLLAHKAILESISAA 331
                                       556.89*********99..9999******999999 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   0.1     0.073        59      30      68 ..       9      47 ..       4      71 .. 0.84
   2 ?    7.7   0.0    0.0026       2.1      37      66 ..     178     207 ..     164     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.073
                                      SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C 30 lgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68
                                       g+++ +  v ++G G  G  +a +l++ g+kv +++ +
  gi|320100874|ref|YP_004176466.1|  9 EGRDIVRYDVVVVGSGTGGYPAAVYLAGKGLKVAVVEEH 47
                                      6778888899***********************999876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0026
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviayd 66 
                                       + + iiG G IG ++a+ ++++g+ ++ ++
  gi|320100874|ref|YP_004176466.1| 178 ESMLIIGGGVIGVELANAFSSLGISITLVE 207
                                       6789********************998876 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 ?    5.2   1.0     0.017        14       3      30 ..      18      45 ..      16      47 .. 0.93
   2 ?    7.0   0.0    0.0049         4       4      51 ..     181     228 ..     178     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.017
                                      EEEE--STTHHHHHHHHHHCTSEEEEE- CS
                    UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvD 30
                                      ++v+G+G  G + a+ la +g +v +v 
  gi|320100874|ref|YP_004176466.1| 18 VVVVGSGTGGYPAAVYLAGKGLKVAVVE 45
                                      89**********************9985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0049
                                       EEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTH CS
                    UDPG_MGDP_dh_N   4 sviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgL 51 
                                        +iG G +G+  a +++++g+ +++v   ++   ++ ++  +     L
  gi|320100874|ref|YP_004176466.1| 181 LIIGGGVIGVELANAFSSLGISITLVELMDHILPSMDRDIAQALKTHL 228
                                       59************************9988888777777666665555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.63   5.1e+02       1      40 [.      19      52 ..      19      64 .. 0.86
   2 ?   -0.6   0.0       1.4   1.1e+03     128     154 ..     121     148 ..      85     150 .. 0.72
   3 ?    0.7   0.6      0.58   4.7e+02       2      32 ..     182     207 ..     181     216 .. 0.81
   4 ?   12.2   0.0   0.00017      0.14     106     155 ..     223     272 ..     216     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.63
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                      ++vG G  G  ++  L+ +      l++ +++++ +g g 
  gi|320100874|ref|YP_004176466.1| 19 VVVGSGTGGYPAAVYLAGK-----GLKVAVVEEHLIG-GE 52
                                      6899999999999999988.....699*****99998.54 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                     NAD_binding_9 128 eeradgqavlladg.aslaadaVvLAlG 154
                                        +++ +  v + +g a ++a +V LA G
  gi|320100874|ref|YP_004176466.1| 121 LKTPHEIVVEEGSGkAVIEAGKVLLAPG 148
                                       4556666777767735679*****9998 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.58
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfd 32 
                                       i+G+G+ G+ +++++ +       ++itl++
  gi|320100874|ref|YP_004176466.1| 182 IIGGGVIGVELANAFSSL-----GISITLVE 207
                                       9**********9998877.....46666666 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00017
                     NAD_binding_9 106 ellarlpegvtvevh.raevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       +l   l++   v+++ +++  ++++ +d++   l++g++l++d+V +A+G 
  gi|320100874|ref|YP_004176466.1| 223 ALKTHLSS-RGVKILeKTSTRSISRIGDRYVAELSNGERLEVDKVLVATGR 272
                                       44444432.2455542668889****************************6 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4      0.01       8.2       1      31 [.      17      45 ..      17      55 .. 0.93
   2 ?    6.7   0.4    0.0039       3.2       3      36 ..     181     212 ..     179     218 .. 0.89
   3 ?   -0.1   0.0      0.46   3.8e+02      88     142 ..     219     273 ..     214     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.01
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      Dvvv+G+G  g   A  l  a +glkv ++e
  gi|320100874|ref|YP_004176466.1| 17 DVVVVGSGTGGYPAAVYL--AGKGLKVAVVE 45
                                      9*****************..*********97 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0039
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       ++iG+G  g+ lA+    +  g++++l+e  +++
  gi|320100874|ref|YP_004176466.1| 181 LIIGGGVIGVELANAF--SSLGISITLVELMDHI 212
                                       89**************..**********977665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.46
                     Lycopene_cycl  88 rlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdargla 142
                                       ++++ l+ +l + gvk le + ++       + ++ l++g++++   v++a+g  
  gi|320100874|ref|YP_004176466.1| 219 DIAQALKTHLSSRGVKILEKTSTRSISRIGDRYVAELSNGERLEVDKVLVATGRT 273
                                       5677888889999999888877665555554778899**************9933 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00017      0.14       1      37 [.      17      50 ..      17      75 .. 0.90
   2 ?    1.3   0.5      0.15   1.2e+02       2      32 ..     180     207 ..     179     213 .. 0.91
   3 ?    0.4   0.0      0.28   2.3e+02     156     209 ..     220     272 ..     216     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                      ++v+vG Gt G+ aA +la  +   l+v +ve   ig
  gi|320100874|ref|YP_004176466.1| 17 DVVVVGSGTGGYPAAVYLAGKG---LKVAVVEEHLIG 50
                                      69****************9998...99*****98887 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                                       EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlve 32 
                                       ++i+GGG  G   A+a++  +   +++tlve
  gi|320100874|ref|YP_004176466.1| 180 MLIIGGGVIGVELANAFSSLG---ISITLVE 207
                                       68****************999...99***99 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHCT-EEEE--EEEEEE-T.TS-EEEEEETTS-EEE-SEEEE-SGG CS
                    Trp_halogenase 156 yakfLrrvaearGvtrvegkvvevqlde.dgrveslrledgreveadlfiDcsGf 209
                                        a+ L+++  +rGv+++e +++    +  d +v++l    g+++e+d ++ ++G 
  gi|320100874|ref|YP_004176466.1| 220 IAQALKTHLSSRGVKILEKTSTRSISRIgDRYVAELSN--GERLEVDKVLVATGR 272
                                       688999999*********99988777776889998876..999999988877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 3369.08
//
Query:       gi|320100875|ref|YP_004176467.1|  [L=520]
Description: glycine dehydrogenase subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-11   42.2   0.0    1.3e-10   40.7   0.0    1.6  2  GDC-P            Glycine cleavage system P-protein
    3.6e-08   32.8   0.0    7.5e-08   31.7   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    1.9e-05   24.1   0.0    3.6e-05   23.1   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
     0.0063   15.8   0.0       0.01   15.1   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.21   10.3   0.0       0.63    8.7   0.0    1.6  2  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   3.5e-14   1.3e-10      30     280 ..      42     303 ..      37     312 .. 0.77
   2 ?   -2.2   0.0      0.39   1.4e+03     334     364 ..     358     388 ..     355     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.5e-14
                                       HS-GGGB--S---------HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SSGG.G CS
                             GDC-P  30 avPkeiklkkelkleapksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYqaE.i 104
                                       ++P+e++  +e  l++  sE e+++++++++++     +  +  G   ++  + i  +i   p  +t+  P q E  
  gi|320100875|ref|YP_004176467.1|  42 EIPSEMRRDREPGLPE-LSEVEVVRHFTNLSQAAFGvDNGPVPLGSCTMKYNPRIAWEIAGDP-RITNLHPLQDErT 116
                                       5888888888888776.7899999999999987665245567778776665444444466555.589******9945 PP

                                       -HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHH.HHHHHHHH-SSS--EEEEETT...S-HHHHH.HHHHHHG CS
                             GDC-P 105 sqGrLeallnfqtlvadltGldianasllDegtAaaE.Avllaaraskkkakkvvvdkk...vhpqtle.vlktrak 176
                                        qG Le l++ q+ +a++tG+d+    l   + A +E A +l+ r  ++   k  +d+k   v p++++ +    a 
  gi|320100875|ref|YP_004176467.1| 117 VQGLLEMLFELQKWLANITGMDTC--ILHPAAGAHGElAGVLTIRRYHEV--KGQIDRKteiVIPDSAHgTNPASAA 189
                                       7*********************75..688889999994445555544433..3333333112445554413346788 PP

                                       GGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEE.EE-TTGGGTB-- CS
                             GDC-P 177 glgieivevdlteekvtd.......kekevagvlvqypnteGried.lkelvekakkkkslvvv.aadllaLtllkp 244
                                         g+ +vev+++e++  d       + +++ag+++  p+t G  e+ +++++  ++++++l+    a+l  +   + 
  gi|320100875|ref|YP_004176467.1| 190 MAGFRVVEVPSAEDGNVDmealksiVGDSTAGLMITNPSTLGLFEEhITDIARLLHEHDALLYYdGANLNGIMGYAR 266
                                       899*******9999999999999988999*************9987689**********99987257777888899* PP

                                       HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGG CS
                             GDC-P 245 PgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkekl 280
                                       Pg++g Di+ +   + fG P g GGP ag + +k++ 
  gi|320100875|ref|YP_004176467.1| 267 PGDMGFDIAhINIHKTFGAPHGGGGPGAGPVCIKDRV 303
                                       ********94556788*************99888875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             GDC-P 334 lyavyhGkeglkeiarrihkkteilakelkk 364
                                       +y+   G++gl++ +++    t+++ k +++
  gi|320100875|ref|YP_004176467.1| 358 VYILSMGPQGLRKATEHAVLITNYFMKLMEN 388
                                       688999********99999999999887776 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.1e-11   7.5e-08      81     207 ..     164     288 ..     157     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.1e-11
                                       CCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B- CS
                       Aminotran_5  81 larslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iq 156
                                       ++ ++++++eiv+ ++ h  n   + +++   g++v+ +p  e+g++d+++l++ + + t+ ++it  s+ +G   +
  gi|320100875|ref|YP_004176467.1| 164 VKGQIDRKTEIVIPDSAHGTNP--ASAAM--AGFRVVEVPSAEDGNVDMEALKSIVGDSTAGLMITNPST-LGLfEE 235
                                       5556899********9999988..44443..59********************************98877.677589 PP

                                       -HHHHHHHHHHTT-EEEEE-TTTTTTS-.--HHHHTESEEEEETTTTTS.STT CS
                       Aminotran_5 157 pveeigklakkkgalvlvDaaqavghip.idvkklgvDflafsghKllg.PtG 207
                                        + +i++l+++++al+  D+a   g +      ++g D++ +  hK +g P G
  gi|320100875|ref|YP_004176467.1| 236 HITDIARLLHEHDALLYYDGANLNGIMGyARPGDMGFDIAHINIHKTFGaPHG 288
                                       9********************9887765156789************6551555 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     1e-08   3.6e-05      90     190 ..     168     257 ..     154     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-08
                                       HTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B-- CS
                     Aminotran_1_2  90 lnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvat 166
                                       +++++ei++pd  ++     + ++g+ vv++p  s+ed ++d+eal+  + +       t ++ +++   P+   + 
  gi|320100875|ref|YP_004176467.1| 168 IDRKTEIVIPDSAHGTNPASAAMAGFRVVEVP--SAEDGNVDMEALKSIVGD------STAGLMITN---PSTLGLF 233
                                       67999***************************..89***************9......778998886...5667789 PP

                                       HHHHHHHHHHHHHTTEEEEEEETT CS
                     Aminotran_1_2 167 leeleklldlakkynlllfvDeaY 190
                                       +e+++++++l +++ +ll+ D a 
  gi|320100875|ref|YP_004176467.1| 234 EEHITDIARLLHEHDALLYYDGAN 257
                                       *******************99775 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   2.9e-06      0.01      35     169 ..     125     256 ..     113     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHHTT-SEEEEES.-HHHHHHHHH.........HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE CS
                   Beta_elim_lyase  35 nrLedavaelfgkeaalfvp.qGtaAnsill.........killqrgeevivtepahihfdetgaiaelagvklrdl 101
                                       ++L++ +a+++g++  +  p  G  ++   +         k  + r++e+++ + ah+   ++ a a++ag +++++
  gi|320100875|ref|YP_004176467.1| 125 FELQKWLANITGMDTCILHPaAGAHGELAGVltirryhevKGQIDRKTEIVIPDSAHG---TNPASAAMAGFRVVEV 198
                                       6788888888888877766524666665555334555544445566666666666776...56778889******** PP

                                       -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       +++e+G++d+e+l++++ +       ++ +++t+      G  +  e++  +a + ++++  l +DgA
  gi|320100875|ref|YP_004176467.1| 199 PSAEDGNVDMEALKSIVGD------STAGLMITNPSTL--G--LFEEHITDIARLLHEHDALLYYDGA 256
                                       ***************9988......3556666666665..4..6899*******************99 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00018      0.63     140     236 ..     166     256 ..     155     282 .. 0.81
   2 ?   -1.8   0.0      0.28   9.9e+02     324     361 ..     357     394 ..     355     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00018
                                       HHHHCCEEEEEETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB.- CS
                     Pyridoxal_deC 140 aeildklvlytsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaF.d 215
                                        +i  k  ++  d ah      a+++g+++ ++p+ e+g++ ++al+  i  d  +Gl++     tl     g F +
  gi|320100875|ref|YP_004176467.1| 166 GQIDRKTEIVIPDSAHGTNPASAAMAGFRVVEVPSAEDGNVDMEALK-SIVGDSTAGLMI-TNPSTL-----GLFeE 235
                                       46788999999999****99*******************77777775.677788889999.444444.....45625 PP

                                       -HHHHHHHHHHCT-EEEEE-T CS
                     Pyridoxal_deC 216 dlkelgdicekydlwlHvDAA 236
                                       ++ +++ +++++d  l  D A
  gi|320100875|ref|YP_004176467.1| 236 HITDIARLLHEHDALLYYDGA 256
                                       899999999999999988877 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEE CS
                     Pyridoxal_deC 324 wfvlralGveglqnqirksvelakyleklirkderfei 361
                                       +  + ++G +gl++  ++ v + +y+ kl+++ + + i
  gi|320100875|ref|YP_004176467.1| 357 YVYILSMGPQGLRKATEHAVLITNYFMKLMENVKGYTI 394
                                       5667789********************99999877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3766.34
//
Query:       gi|320100876|ref|YP_004176468.1|  [L=473]
Description: glycine dehydrogenase subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.4e-114  383.3   0.0   1.7e-114  383.0   0.0    1.0  1  GDC-P        Glycine cleavage system P-protein
    0.00021   20.4   0.0    0.00055   19.0   0.0    1.7  1  Aminotran_5  Aminotransferase class-V


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.0   0.0  1.9e-118  1.7e-114       7     430 .]      14     463 ..       8     463 .. 0.90

  Alignments for each domain:
  == domain 1  score: 383.0 bits;  conditional E-value: 1.9e-118
                                       -HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S--......-------HHHHHHHHHHHHTTB--..-EE--BTTB- CS
                             GDC-P   7 sekdqkemLetlGlkslddliekavPkeiklkkel......kleapksEeellaelekiasknkv..vksfiGaGyy 75 
                                       +e+ +k+mLe++G+ s+ +l+ k++P+ei l ++        l  p sE e+ + +e+  s+nkv     f+G G+y
  gi|320100876|ref|YP_004176468.1|  14 TEESVKKMLEVIGVGSVSELF-KDIPSEILLGEDSwnkleiGLGRPLSEIEVKELVEEKLSRNKVfnPPPFMGGGVY 89 
                                       67889****************.9******98665411111134566************99****944458******* PP

                                       -----HHHHHHTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SS CS
                             GDC-P  76 dtilPaviqrnilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskk 152
                                        +++P+v+   i++++e++taYtPYqaEisqG ++al+++q+++a+l  +di nas++D ++  aEA+l+a+r+ k+
  gi|320100876|ref|YP_004176468.1|  90 PHYVPPVVRY-IISRGEFLTAYTPYQAEISQGLMQALFEYQSMMAELLEMDIVNASMYDWASSIAEAALMAFRVRKG 165
                                       *******987.*****************************************************************9 PP

                                       S--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-...........S-EEEEEEEES-TTSB---.-HHHH CS
                             GDC-P 153 kakkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd........kekevagvlvqypnteGried.lkelv 220
                                       + +k+++  +++p  ++v++t+ k++g+ i++ +   e  t         +  ++a+v vqypn++G ied +k++ 
  gi|320100876|ref|YP_004176468.1| 166 R-RKILLPGNMNPLHRRVVETYVKPQGLMIETIPFDRELGTVdaeavksmVDGDTAAVYVQYPNFFGIIEDnVKAIG 241
                                       9.99************************9999998766655558888888899*****************989**** PP

                                       HHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GG..GGGG--S-EEEEEEBT CS
                             GDC-P 221 ekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkek..lkRkiPGRlvGvskDa 295
                                       e a++k +l++  + ++aL+llkpPgelgaDi+vG++q +G+ + yGGPh g fAv+ +  l+R++PGR++G++   
  gi|320100876|ref|YP_004176468.1| 242 EIAHEKGALFITGVYPVALGLLKPPGELGADIAVGDGQSLGLGMNYGGPHLGIFAVRYDmnLVRQMPGRIIGLTTTI 318
                                       ********************************************************987679**************9 PP

                                       TS-.EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..T-EE CS
                             GDC-P 296 egk.ralrlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkk.leeel 370
                                       +g  +a+ ++ q+REqHirR+kAtsniCt+ aL+A+++a+y+ ++Gk+gl+++a+ ++ +++++++ +    l++++
  gi|320100876|ref|YP_004176468.1| 319 DGSsKAFAMVWQAREQHIRREKATSNICTNEALMAVASAVYMALLGKTGLRRLAELVYYRAHYASSRMSDIgLTRVF 395
                                       99638***************************************************************999899999 PP

                                       --SSBSSEEE....EE--TTTHHH.HHHHHHHTT..EE-EEESTTEEEE.E--TT--HHHHHHHHHHH CS
                             GDC-P 371 kkkkffdtll....ieveekaaek.vlkkaekeg..lnlrkvelktvgi.aldEtvtkedieallkvl 430
                                       k++ f+++ +    i v+  a+++ +l+++++ g  ++ ++ el++v++ a +E    + i+ l+++l
  gi|320100876|ref|YP_004176468.1| 396 KGEFFNEFPVsfnnIGVKYSAVHEkLLEHGIHGGlyIGSYYPELGEVALyAFTELHSVKAIDRLIETL 463
                                       999999987522224566656555499999999888899999*998876599**********999875 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.1e-08   0.00055     108     333 ..     186     426 ..     149     429 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.1e-08
                                       HHHHHTEEEEEEEBETT.SCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHHHHHHHHTT-EEEEE-TTTTTT CS
                       Aminotran_5 108 lakrtgakvkvipldee.geldldelekllnektklvaithvsnvtGt.iqpveeigklakkkgalvlvDaaqavgh 182
                                         k +g+ ++ ip+d+e g++d +++++ ++ +t++v+++   n  G+  + v++ig++a++kgal+++     ++ 
  gi|320100876|ref|YP_004176468.1| 186 YVKPQGLMIETIPFDRElGTVDAEAVKSMVDGDTAAVYVQ-YPNFFGIiEDNVKAIGEIAHEKGALFITGVYPVALG 261
                                       5567899******99655*******************886.689****5677***************9988888888 PP

                                       S---HHHHTESEEEEETTTT.....TSSTT-EEEEEEHH..HHHTS..SS.STTSEEEEETTEEE....EHCTTGGG CS
                       Aminotran_5 183 ipidvkklgvDflafsghKl.....lgPtGiGvlyvrke..llekleplllggemveevsleett....faeapskf 248
                                             +lg+D+++  g+ l     +g + +G+  vr +  l  +++   +g ++  + s +        +e+  + 
  gi|320100876|ref|YP_004176468.1| 262 LLKPPGELGADIAVGDGQSLglgmnYGGPHLGIFAVRYDmnLVRQMPGRIIGLTTTIDGSSKAFAmvwqAREQHIRR 338
                                       88888888888888777743222225555555555554311566665444443333332222211233366777777 PP

                                       S.SS--HHHHHHHHHHH.....HHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCS CS
                       Aminotran_5 249 eaGTpnvagiiglgaal.....eyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvh 320
                                       e  T n+    +l a++      +l ++gl++ ++     a+y+ +r+++++ +r+++   +  ++  vsfn  gv+
  gi|320100876|ref|YP_004176468.1| 339 EKATSNICTNEALMAVAsavymALLGKTGLRRLAELVYYRAHYASSRMSDIGLTRVFK--GEFFNEFPVSFNNIGVK 413
                                       7777777654444333311111444677777777777777777777777777777755..35667777777777777 PP

                                       HHHHHHHHHHTTE CS
                       Aminotran_5 321 aedvatlLdeegI 333
                                        + v   L e+gI
  gi|320100876|ref|YP_004176468.1| 414 YSAVHEKLLEHGI 426
                                       7777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3418.43
//
Query:       gi|320100877|ref|YP_004176469.1|  [L=369]
Description: aminomethyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-64  216.3   0.0    5.8e-64  215.9   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    7.4e-21   73.9   0.0    1.5e-20   72.9   0.0    1.5  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9   0.0   6.5e-68   5.8e-64       4     254 ..       9     255 ..       6     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 6.5e-68
                             GCV_T   4 rhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkat. 79 
                                         +++ga+ + f+ we+P  Y  +++++eh  vr+++glfDvShmg++ ++Gpd++ l q+++t+dis++k+ +++ 
  gi|320100877|ref|YP_004176469.1|   9 YYVEKGAETGLFGEWEVPYRY--TNAIEEHISVRTSVGLFDVSHMGRVLLKGPDVLPLAQYVYTKDISRTKEYSMSg 83 
                                       6789*****************..*************************************************98888 PP

                             GCV_T  80 ytlllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevlsk 156
                                        tl+ln+ ++v+dD ++++++++e+llv+na ++e++l++lek + +k+++ve+ d+t ++++lalqGP+a ev++ 
  gi|320100877|ref|YP_004176469.1|  84 PTLALNQWARVKDDEMLYKISDEEWLLVTNALTREHMLSYLEKVRSEKGFRVEIVDLTFNYSMLALQGPRAVEVMES 160
                                       9******************************************9999****************************** PP

                             GCV_T 157 llgadlselkffsfaevelaggkk.vlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtlRl 232
                                       l  +   +lk  +f+  e+ +g++ +lvsR+g+tGedGfei+ ++ e ++l++  l    ++gvk aGl ArdtlR+
  gi|320100877|ref|YP_004176469.1| 161 LGAKWAGDLKTLEFRMNEEIQGVRtFLVSRSGWTGEDGFEIWGESGELKRLVDLFL----SKGVKLAGLIARDTLRI 233
                                       **98999999999997777756655******************************6....5678************* PP

                             GCV_T 233 EaglrlyghdldeettPleagl 254
                                       E+g+ l gh+  e+ t + + l
  gi|320100877|ref|YP_004176469.1| 234 EMGFVLGGHEYGEDPTRFPCAL 255
                                       **********999977666555 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   1.7e-24   1.5e-20       4      79 ..     290     367 ..     289     368 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.7e-24
                           GCV_T_C   4 vgleld..dgapllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkpf 78 
                                       vgl+l    g+  +r+++ ++ ++  vG+vTSg+ysp l++ ia+Ayv++ +a  g+e++v++rgkr+pa++v+ pf
  gi|320100877|ref|YP_004176469.1| 290 VGLKLGkeAGRHFPRQDAGVYSEDVWVGWVTSGTYSPVLNRGIAMAYVDSRYALFGEELTVDIRGKRYPAKIVDFPF 366
                                       89999743448888**************************************************************9 PP

                           GCV_T_C  79 y 79 
                                        
  gi|320100877|ref|YP_004176469.1| 367 I 367
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2676.69
//
Query:       gi|320100878|ref|YP_004176470.1|  [L=448]
Description: serine hydroxymethyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-66  224.5   0.0    2.1e-66  224.2   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    6.7e-10   38.7   0.0    2.6e-09   36.8   0.0    1.7  1  Aminotran_1_2    Aminotransferase class I and II
      3e-09   36.6   0.0    6.8e-09   35.4   0.1    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
    3.1e-05   23.1   0.2    4.9e-05   22.5   0.2    1.3  1  Aminotran_5      Aminotransferase class-V
    0.00015   21.2   0.4    0.00029   20.3   0.2    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00053   18.6   0.2      0.002   16.7   0.1    1.9  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.052   13.3   0.6       0.51   10.1   0.1    2.3  2  XTBD             XRN-Two Binding Domain, XTBD
      0.088   11.8   0.0        0.2   10.6   0.0    1.5  1  SelA             L-seryl-tRNA selenium transferase


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 !  224.2   0.0   9.5e-70   2.1e-66       5     399 .]      22     398 ..      19     398 .. 0.93

  Alignments for each domain:
  == domain 1  score: 224.2 bits;  conditional E-value: 9.5e-70
                                       THHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT- CS
                              SHMT   5 dpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkl 81 
                                       d+ +   i + + r++++i++iasen++s+ ++ +    +  +yaeG P kr+y G  +vde+e  +q+   el ++
  gi|320100878|ref|YP_004176470.1|  22 DAVLNLTITHTMWRKRQTINMIASENVMSPLAMLVYLNDMMHRYAEGKPYKRFYQGLIYVDELEVKTQELMGELLGT 98 
                                       6666677889999**************************************************************** PP

                                       STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-H CS
                              SHMT  82 dpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidy 158
                                       +    +v+++p sG+ an++ + ++ +pgd+ +   + +G h++h        + a ++    +++ ++  +  id 
  gi|320100878|ref|YP_004176470.1|  99 K----HVDLRPISGTIANATAFRTFTKPGDKAVVAPVQAGAHVSHTKFG---TLGALGIEQIEMPFDIE--EWNIDV 166
                                       *....****************************************7554...46999998888998888..899*** PP

                                       HHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT CS
                              SHMT 159 delekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfey.advvtttthktl 234
                                       d+ +k  +e+kPk++  G s y      + + ++a+ vga ++ d+ah+ Glv++g   +P++  adv+t+ thkt+
  gi|320100878|ref|YP_004176470.1| 167 DKARKLIEEVKPKIVTLGGSLYLFPHPTKEIADVAHAVGAKVIHDVAHVLGLVVGGAWENPLKLgADVITSSTHKTF 243
                                       **************************************************************9659*********** PP

                                       -S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHH CS
                              SHMT 235 rGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknaka 311
                                        Gp+gg+i ++             +ee +k++ + vfP      + h +aa+av+  e ++    +y++qv++naka
  gi|320100878|ref|YP_004176470.1| 244 PGPQGGIIASS-------------NEEDYKEMGKVVFPMFVSNHHLHRLAAMAVTAIE-MKLWGSEYARQVVRNAKA 306
                                       ********998.............467788999*********************8654.6666789*********** PP

                                       HHHHHHHTT-EEGG...GS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS..STTTT-SEEEEESHHHH CS
                              SHMT 312 laealkekgyklvs...gGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd..ksalvtsGlrlGtpalt 383
                                       laeal  +g+++v    g t +h v+vd+ + g  G+r  k+le + i +nkn +P d  +    +sGlrlGt  lt
  gi|320100878|ref|YP_004176470.1| 307 LAEALAAEGFNVVMerkGYTTSHQVVVDVANLG-RGTRIAKLLEDAYIIVNKNMLPWDrpEDVKDPSGLRLGTQELT 382
                                       *************73325699********9998.7***********************75566779*********** PP

                                       HTT--HHHHHHHHHHH CS
                              SHMT 384 srgfkeedlekvakfi 399
                                       + g+ke +++++a+++
  gi|320100878|ref|YP_004176470.1| 383 RWGMKEGEMKEIARLM 398
                                       ************9875 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   1.1e-12   2.6e-09      39     306 ..      74     325 ..      63     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.1e-12
                                       ST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEE.E..ESS-THHHHH..H CS
                     Aminotran_1_2  39 eygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilv.p..dptyasykni..l 110
                                       +y+     +ele ++ +++g  e l +k+   +  +sG+ a++ a+ +++k  pgd+ +v p  +  + s+++   l
  gi|320100878|ref|YP_004176470.1|  74 FYQGLIYVDELEVKTQELMG--ELLGTKHV-DLRPISGTIANATAFRTFTK--PGDKAVVaPvqAGAHVSHTKFgtL 145
                                       67778888999999999999..77888888.*******************7..777755414224579999885226 PP

                                       HHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                     Aminotran_1_2 111 rlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                        + g+e +++p  + e++++d+++  ++++e      k+k++ + +        + +   ++++d+a++ ++ ++ D
  gi|320100878|ref|YP_004176470.1| 146 GALGIEQIEMP-FDIEEWNIDVDKARKLIEEV-----KPKIVTLGGS-----LYLFPHPTKEIADVAHAVGAKVIHD 211
                                       67788899999.569***************94.....8999999863.....34444556899999*********** PP

                                       ETTT.TCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEE.EHHHHHHHHHHHHHHTSSHHHHHHHH CS
                     Aminotran_1_2 188 eaYa.gfvfgsldavatranveeepnllivgslsKaf.GlaGeRvGyilg.naavvsqlrklsrpflsssllqaava 261
                                        a+  g+v g  +a+++ +++ +   ++i++s  K f G  G   G+i++ n++  + + k++ p+ +s++  + +a
  gi|320100878|ref|YP_004176470.1| 212 VAHVlGLVVG--GAWENPLKLGA---DVITSSTHKTFpGPQG---GIIASsNEEDYKEMGKVVFPMFVSNHHLHRLA 280
                                       ***9455666..78998888888...489999999999999*...*****999***************888888788 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 262 aalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       a++ +a +++ + +e ++++ +++k l ++La+ g++v+++  g+
  gi|320100878|ref|YP_004176470.1| 281 AMAVTAIEMKLWGSEYARQVVRNAKALAEALAAEGFNVVMERKGY 325
                                       88888787778********************999*****998876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.1     3e-12   6.8e-09      38     252 ..      89     331 ..      73     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3e-12
                                       HHHHHHHTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT......-HHHHSSTTHHHHCC--EEEEE-EBTTT CS
                   Beta_elim_lyase  38 edavaelfgkeaalfvp.qGtaAnsillkillqrgeevivtep......ahihfdetgaiaelagvklrdlknkeaG 107
                                       ++ + el+g++++   p +Gt An+ ++++++++g++ +v         +h+ f + ga+   +     +++++e  
  gi|320100878|ref|YP_004176470.1|  89 QELMGELLGTKHVDLRPiSGTIANATAFRTFTKPGDKAVVAPVqagahvSHTKFGTLGALGIEQI--EMPFDIEE-W 162
                                       556677888887655444******************99987666786667777777777754444..45666666.7 PP

                                       BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB--.-HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CH CS
                   Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvv.sleelrevaaiakkygiplhlDgARfanaakslgeivk 183
                                       ++d++k +++i+e      k+k+++l       gG  +  +   +e+a++a++ g +++ D A ++  +   g+   
  gi|320100878|ref|YP_004176470.1| 163 NIDVDKARKLIEE-----VKPKIVTL-------GGSLYlFPHPTKEIADVAHAVGAKVIHDVAHVLGLV-VGGAWEN 226
                                       7************.....56788866.......455551567799********************9877.4455555 PP

                                       HHHTTSSEEEEESSSTT--SS-EEEEE-HH.......................................HHHHHHHH CS
                   Beta_elim_lyase 184 emfsyvDsvtmslkKdllanvGgvlafrddel...................................edylaerveq 225
                                        +  ++D++t s  K    + Gg++a +++e                                     +y ++ v+ 
  gi|320100878|ref|YP_004176470.1| 227 PLKLGADVITSSTHKTFPGPQGGIIASSNEEDykemgkvvfpmfvsnhhlhrlaamavtaiemklwgSEYARQVVRN 303
                                       56678***********************99889**********************************9********* PP

                                       HHHHT---SSTHHHHH...HHHHHHHHS CS
                   Beta_elim_lyase 226 rkylggglrqagvlaa.leagiraleeg 252
                                       +k+l++ l   g+ ++ ++ g+ ++++ 
  gi|320100878|ref|YP_004176470.1| 304 AKALAEALAAEGFNVVmERKGYTTSHQV 331
                                       ************9888444555555444 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   2.2e-08   4.9e-05      70     207 ..     108     248 ..      86     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBE...TTSCBEGGGHHHH--.TTEEE CS
                       Aminotran_5  70 tteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipld...eegeldldeleklln.ektkl 142
                                       +t a++++ +++    kpgd++vv  +   a +    +      + ++ i++    ee+++d+d+++kl++  k+k+
  gi|320100878|ref|YP_004176470.1| 108 GTIANATAFRTF---TKPGDKAVVAPVQAGAHV-SHTKFGTLGALGIEQIEMPfdiEEWNIDVDKARKLIEeVKPKI 180
                                       444777777777...99******9877766665.566666666666666654322489************6346666 PP

                                       EEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTT....TTTS---HHHHTESEEEEETTT.TTSSTT CS
                       Aminotran_5 143 vaithvsnvtGtiqpveeigklakkkgalvlvDaaqa....vghipidvkklgvDflafsghK.llgPtG 207
                                       v++    +     +p++ei+++a+++ga v+ D a      vg +  +  klg+D++++s+hK + gP+G
  gi|320100878|ref|YP_004176470.1| 181 VTL--GGSLYLFPHPTKEIADVAHAVGAKVIHDVAHVlglvVGGAWENPLKLGADVITSSTHKtFPGPQG 248
                                       655..55666679**********************962222456778999*************999***9 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   1.3e-07   0.00029      45     191 ..     106     259 ..      77     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                                       SSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH.....HHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE CS
                   DegT_DnrJ_EryC1  45 ssGtaAlhlaLralgvgpgdeVIvpsltFvatan.....avlelgakpvfvDvdpdtynidpaaieaaitertkaIl 116
                                        sGt A++ a r +  +pgd+ +v+++   a ++     +   lg + + +  d++ +nid+++++++i+e    I+
  gi|320100878|ref|YP_004176470.1| 106 ISGTIANATAFRTFT-KPGDKAVVAPVQAGAHVShtkfgTLGALGIEQIEMPFDIEEWNIDVDKARKLIEEVKPKIV 181
                                       566666666666654.3455555544433333321111134556777777778999***************997776 PP

                                       EB..-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT...EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTH CS
                   DegT_DnrJ_EryC1 117 pV..hlyGqvadmdalkaiaakhglkvieDaAhAlGatykg...kkvGalgdaavfSFyptKnlttGeGGavvtnde 188
                                       +    ly  +   +++ ++a++ g kvi D Ah lG  + g    ++   +d+ + S +  K++    GG++ + +e
  gi|320100878|ref|YP_004176470.1| 182 TLggSLYLFPHPTKEIADVAHAVGAKVIHDVAHVLGLVVGGaweNPLKLGADVITSSTH--KTFPGPQGGIIASSNE 256
                                       5423678888899***********************99999775333333466666644..6677777777777777 PP

                                       HHH CS
                   DegT_DnrJ_EryC1 189 ela 191
                                       e  
  gi|320100878|ref|YP_004176470.1| 257 EDY 259
                                       655 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   9.1e-07     0.002      75     220 ..     107     260 ..      81     270 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.1e-07
                                       SHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHH..THHHTTCEEEEEST......TSHHHHHHHCCT.TEEEEE CS
                   Cys_Met_Meta_PP  75 sGmaAiaaailallkaGdeivvsddlYggtqrllkk..vlkklgievkfvdt......sdleelekaike.ntklvy 142
                                       sG+ A a+a++++ k Gd+ vv      g++   +k  +l  lgie   +         d+++ +k i+e + k+v 
  gi|320100878|ref|YP_004176470.1| 107 SGTIANATAFRTFTKPGDKAVVAPVQ-AGAHVSHTKfgTLGALGIEQIEMPFdieewnIDVDKARKLIEEvKPKIVT 182
                                       77778878888888888876654322.22222222201222233332222221122222333444444444445553 PP

                                       EESS-TTTT----HHHHHHHHHHTT-EEEEEGT.....TTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEES CS
                   Cys_Met_Meta_PP 143 lEtptnpllkvvDiekiaklakkagvlvvvDnt.....faspllqrplklgaDivvhSaTKylgGhsdvvaGvivvk 214
                                       l   ++  l  +  ++ia++a+++g+ v+ D +     ++ ++  +plklgaD+++ S+ K   G +   +G+i+++
  gi|320100878|ref|YP_004176470.1| 183 LG--GSLYLFPHPTKEIADVAHAVGAKVIHDVAhvlglVVGGAWENPLKLGADVITSSTHKTFPGPQ---GGIIASS 254
                                       32..23333334456777777777777777765111114567889****************999976...6888877 PP

                                       SCHHHH CS
                   Cys_Met_Meta_PP 215 gkeelk 220
                                       ++e+ k
  gi|320100878|ref|YP_004176470.1| 255 NEEDYK 260
                                       744444 PP

>> XTBD  XRN-Two Binding Domain, XTBD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00023      0.51      29      68 ..     275     314 ..     253     326 .. 0.85
   2 ?    0.7   0.1      0.19   4.3e+02      11      26 ..     413     428 ..     402     441 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                                       -HHHHHHHHHHHHHHHTT--B--HHHHHHHHHHHTTTTXX CS
                              XTBD  29 eedrLlsLsmvfanlvflGcrYprevmekvkelaegiaae 68 
                                       +++rL +++ + + +++ G +Y r+v+++ k lae +aae
  gi|320100878|ref|YP_004176470.1| 275 HLHRLAAMAVTAIEMKLWGSEYARQVVRNAKALAEALAAE 314
                                       789********************************98765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHGG CS
                              XTBD  11 eehWelrreFilrnke 26 
                                       ++  e+rreF++ +  
  gi|320100878|ref|YP_004176470.1| 413 QKVMEFRREFLEIHYG 428
                                       456789****999876 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     9e-05       0.2     178     225 ..     205     253 ..     193     267 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9e-05
                                       ES-B-S-GGG.GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE CS
                              SelA 178 GsGllvdlse.yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivG 225
                                       G+ ++ d+++  gl      ++ l+ G+d+++ s  k + gpq Gii  
  gi|320100878|ref|YP_004176470.1| 205 GAKVIHDVAHvLGLVVGGAWENPLKLGADVITSSTHKTFPGPQGGIIAS 253
                                       5555555544246777777888999**********************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3117.75
//
Query:       gi|320100879|ref|YP_004176471.1|  [L=141]
Description: glycine cleavage system H protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-41  138.9   0.3    8.9e-41  138.6   0.3    1.1  1  GCV_H            Glycine cleavage H-protein
    0.00022   21.1   0.1    0.00033   20.6   0.1    1.3  1  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0069   16.2   1.0       0.01   15.6   0.3    1.7  2  Biotin_lipoyl    Biotin-requiring enzyme
  ------ inclusion threshold ------
      0.065   13.1   0.1         15    5.5   0.0    2.3  2  Biotin_lipoyl_2  Biotin-lipoyl like
       0.11   12.0   0.1       0.16   11.4   0.1    1.3  1  NQRA             Na(+)-translocating NADH-quinone reductase s


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.6   0.3   2.5e-44   8.9e-41       1     121 [.      19     138 ..      19     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 2.5e-44
                                       -EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GG CS
                             GCV_H   1 lyytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNek 77 
                                       ++yt+ +ew   e++  +++Gitd+aq+el d+v+velpevg +vkkge+l++++s Ka s  yapvsG vvevNe+
  gi|320100879|ref|YP_004176471.1|  19 RRYTETDEWALLEGG-KVRIGITDYAQKELKDIVSVELPEVGRQVKKGEELGVIDSIKASSAYYAPVSGRVVEVNEE 94 
                                       58**********885.9************************************************************ PP

                                       GTT-TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHHHHH CS
                             GCV_H  78 leeepeliNkdpyeegWliklklsnleeleeLlsaeeyekllke 121
                                       l   pel+Nkdpy+ gW++ +++sn+ e e Ll+a +y++++k+
  gi|320100879|ref|YP_004176471.1|  95 LLSTPELVNKDPYGAGWIAVIEPSNPGEYEGLLDAGKYSEKIKS 138
                                       ***************************************99986 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 !   20.6   0.1   9.2e-08   0.00033      47      89 ..      57     100 ..      34     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.2e-08
                            RnfC_N  47 kvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvahgs 89 
                                       +vg +V+kG+ ++  ++   s++ +a+vsG+V+++++ l ++++
  gi|320100879|ref|YP_004176471.1|  57 EVGRQVKKGEELGVIDSiKASSAYYAPVSGRVVEVNEELLSTPE 100
                                       799************997679999***********999887776 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.3   4.7e+03      18      27 ..      26      35 ..       6      41 .. 0.61
   2 !   15.6   0.3   2.8e-06      0.01      22      57 ..      57      92 ..      42      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                                      SESSSTTCEE CS
                     Biotin_lipoyl 18 evlvkvGdkV 27
                                      e+   +G+kV
  gi|320100879|ref|YP_004176471.1| 26 EWALLEGGKV 35
                                      4444455554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.8e-06
                                      STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEES CS
                     Biotin_lipoyl 22 kvGdkVkagqvlaeveamKmemeieapkaGvvkeil 57
                                      +vG +Vk+g+ l ++ + K++    ap++G+v+e+ 
  gi|320100879|ref|YP_004176471.1| 57 EVGRQVKKGEELGVIDSIKASSAYYAPVSGRVVEVN 92
                                      89*******************************996 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.005        18      21      36 ..      59      74 ..      57      79 .. 0.88
   2 ?    5.5   0.0    0.0042        15       7      17 ..      82      92 ..      81      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.005
                   Biotin_lipoyl_2 21 GqrVkaGdvLaelDsr 36
                                      G +Vk+G  L ++Ds 
  gi|320100879|ref|YP_004176471.1| 59 GRQVKKGEELGVIDSI 74
                                      889***********96 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0042
                   Biotin_lipoyl_2  7 apvsGrVaqln 17
                                      apvsGrV+++n
  gi|320100879|ref|YP_004176471.1| 82 APVSGRVVEVN 92
                                      79*******98 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.5e-05      0.16      46      80 ..      57      92 ..      28      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.5e-05
                              NQRA 46 kegdkVkkGqvl.fedKknpgvlftspasGevvein 80
                                      ++g +VkkG+ l + d  + +  + +p+sG+vve+n
  gi|320100879|ref|YP_004176471.1| 57 EVGRQVKKGEELgVIDSIKASSAYYAPVSGRVVEVN 92
                                      5899*******956788889999***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1056.48
//
Query:       gi|320100880|ref|YP_004176472.1|  [L=233]
Description: deoxyribose-phosphate aldolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-09   35.7   0.8    9.1e-09   35.3   0.8    1.1  1  DeoC      DeoC/LacD family aldolase
    4.4e-05   22.9   1.3    6.8e-05   22.2   0.4    1.6  1  DHO_dh    Dihydroorotate dehydrogenase
      0.002   17.2   1.0      0.002   17.2   1.0    1.9  2  FMN_dh    FMN-dependent dehydrogenase
  ------ inclusion threshold ------
       0.13   12.4   0.1       0.78    9.9   0.0    2.1  2  DUF5448   Family of unknown function (DUF5448)


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 !   35.3   0.8     2e-12   9.1e-09      58     229 ..      62     219 ..      45     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2e-12
                                       T..TSEEEEETECSSCCTTSTTEEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHH...HHT CS
                              DeoC  58 k..diallvkldkgtyllkskqrdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeach...eeg 129
                                       +  +i+++v+++ g++ +++k      va++  a + G  ++++v+++++ +s + + + ++i+ v ea +      
  gi|320100880|ref|YP_004176472.1|  62 RtmEIGVVVGFPLGNTSTRTK------VAEAIDAAEHGVSEIDMVMNINMFKSRNYEYVKRDIRSVVEAVKpkgVKA 132
                                       3448*****************......*******************************************9444455 PP

                                       EEEEEE.EEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS CS
                              DeoC 130 lplile.lylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv 205
                                        ++i+e ++l de+    k      ++A+++ ae GaD +K+ ++  +  at  d+    ++ ++  +  v+ sGG+
  gi|320100880|ref|YP_004176472.1| 133 VKVIIEtGLLSDEE----K------KTATQLVAESGADYVKTCTGFLGSVATVHDVSLLYKASSGR-IS-VKASGGI 197
                                       67888888888888....3......68******************888888888888877777744.77.9*****9 PP

                                       SHHHHHHHHHH.HHHHHTH..CEEEES CS
                              DeoC 206 seedfletved.Avkeaga..sGvlsG 229
                                            ++ ++  A+++aga  +G +sG
  gi|320100880|ref|YP_004176472.1| 198 -----RRGLDAlAMIAAGAsrIGTSSG 219
                                       .....5555432455777777888887 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.4   1.5e-08   6.8e-05     232     272 ..     176     216 ..     169     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEE CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqv 272
                                       + +  lyk  +++i + ++GGi  g Dal +i aGAs +  
  gi|320100880|ref|YP_004176472.1| 176 HDVSLLYKASSGRISVKASGGIRRGLDALAMIAAGASRIGT 216
                                       456779*******************************8765 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1     0.088   3.9e+02     123     160 ..     116     153 ..      57     169 .. 0.63
   2 !   17.2   1.0   4.4e-07     0.002     254     297 ..     171     214 ..     166     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHHCTESEEEEESSTSS---BHHHHHCT- CS
                            FMN_dh 123 elteellkraeaagykalvltvDtpvlgkRerdlrngf 160
                                         ++++++ ++  g+ka+ + + t  l+  e+++ +++
  gi|320100880|ref|YP_004176472.1| 116 RDIRSVVEAVKPKGVKAVKVIIETGLLSDEEKKTATQL 153
                                       23566677777777777777777777766666666555 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.4e-07
                                       ---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEE CS
                            FMN_dh 254 apatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdav 297
                                       ++at++    + +a  gri v ++gGirrG D+l  +a GA+ +
  gi|320100880|ref|YP_004176472.1| 171 SVATVHDVSLLYKASSGRISVKASGGIRRGLDALAMIAAGASRI 214
                                       56677777777899999************************865 PP

>> DUF5448  Family of unknown function (DUF5448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.27   1.2e+03      60      80 ..      97     117 ..      74     132 .. 0.77
   2 ?    9.9   0.0   0.00017      0.78      67      95 ..     154     180 ..     132     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.27
                           DUF5448  60 vedliehvlespedreyvnkc 80 
                                       ++++++  +    + eyv + 
  gi|320100880|ref|YP_004176472.1|  97 IDMVMNINMFKSRNYEYVKRD 117
                                       688999888888899999874 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00017
                           DUF5448  67 vlespedreyvnkctgivgvklrveeval 95 
                                       v+e     +yv  ctg +g +  v +v+l
  gi|320100880|ref|YP_004176472.1| 154 VAE--SGADYVKTCTGFLGSVATVHDVSL 180
                                       555..5689*************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1755.14
//
Query:       gi|320100881|ref|YP_004176473.1|  [L=285]
Description: spermidine synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-45  153.4   0.0    5.8e-45  153.0   0.0    1.1  1  Spermine_synth   Spermine/spermidine synthase domain
    5.9e-07   29.3   0.1    1.8e-06   27.7   0.1    1.9  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
      7e-05   23.5   0.0    0.00016   22.3   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    0.00037   21.1   0.0    0.00075   20.1   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0021   18.7   0.0     0.0052   17.5   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.087   12.1   0.0       0.13   11.5   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
       0.14   12.0   0.0       0.19   11.5   0.0    1.3  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   0.0   2.3e-48   5.8e-45       2     178 ..      62     240 ..      61     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 2.3e-48
                                       HHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEE CS
                    Spermine_synth   2 faykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklv 78 
                                        +y+e ++h ++ lh+ p +vLiiGGg G +lrev+kh tv ++++vdiD  v++fskk+l  ++ ++fnd+r  ++
  gi|320100881|ref|YP_004176473.1|  62 AFYHESLVHPAMALHPDPVRVLIIGGGEGATLREVLKHGTVREAVMVDIDPVVVEFSKKYLEYMHQGSFNDPRSRVL 138
                                       68*************************************************************************** PP

                                       ESTCHHHHCTCSS.-EEEEEEECCSTTCSSCG..CSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHT CS
                    Spermine_synth  79 lgdgfkflkayek.kfdvvivdsldpvgpaen..lFskeffdllkkvlkedGviilqaekpelekelvinvdksgkq 152
                                       ++dg  ++k+     fdv i+d++dp     +  l+s+ef++ +k+vlk dGv+++qa +  +      +v+ ++  
  gi|320100881|ref|YP_004176473.1| 139 IMDGLRYVKEAPSdYFDVAIMDLTDPYAGDVAkpLYSEEFYRDVKRVLKRDGVMVTQAGSSYFYTSEYDYVLGNIGR 215
                                       ***********999***********875433337************************88888888999******** PP

                                       TSSCEEEEEEEETTTSCSCEEEEEEE CS
                    Spermine_synth 153 vfalqvepsavlvPtylsgminfvve 178
                                       v + ++  + + +P++  ++ ++v  
  gi|320100881|ref|YP_004176473.1| 216 VYR-YTAEYNIWIPSFGLNVNFIVAS 240
                                       *99.99999999***98876555443 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 !   27.7   0.1     7e-10   1.8e-06      10      53 .]      15      58 ..       9      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7e-10
                                      TEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
                   Spermine_synt_N 10 glalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                       + l++kV kv   ek+++Q+ +++e + fGk Lv+D+ +q tE
  gi|320100881|ref|YP_004176473.1| 15 TFKLQFKVLKVYAVEKTPHQEMMLVELEGFGKALVIDNFIQSTE 58
                                      57788999999999****************************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   6.1e-08   0.00016       1      97 []      82     190 ..      82     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.1e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH......TTTTEEEEESBCCGB..SSSTTTEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee......eglnvefvqgdaedl..pfedgsfDlvv 69 
                                       vL +G G+G ++++++k++   + ++vDi++  +e  ++ +e       ++++ +++ +d  ++  + +++ fD+ +
  gi|320100881|ref|YP_004176473.1|  82 VLIIGGGEGATLREVLKHGTVREAVMVDIDPVVVEFSKKYLEYmhqgsfNDPRSRVLIMDGLRYvkEAPSDYFDVAI 158
                                       789***************7689****************99987765555556*********7752246999****** PP

                                       EEST.GG...GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  70 ssga.lh...hlsdedlekalkeiarvLkpgG 97 
                                       +  +      + ++   e++++ ++rvLk +G
  gi|320100881|ref|YP_004176473.1| 159 MDLTdPYagdVAKPLYSEEFYRDVKRVLKRDG 190
                                       *44322222223333458999*******9998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.9e-07   0.00075       3      95 ..      85     193 ..      83     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.9e-07
                                       ET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-......EEEETTEECCC.T.SS-TT-EEEEEEES CS
                   Methyltransf_11   3 vGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl......kvefvvadaek.l.pfednsfDlvvsse 69 
                                       +G G G+ ++++ k+g  ++ v vD+++ +++ +k+  +  +       + +++ +d  + +   ++++fD+ ++  
  gi|320100881|ref|YP_004176473.1|  85 IGGGEGATLREVLKHGtvREAVMVDIDPVVVEFSKKYLEYMHQgsfndpRSRVLIMDGLRyVkEAPSDYFDVAIMDL 161
                                       89********************************999988888889999889999999985457999*********9 PP

                                       -CCC-......CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  70 vlhhv......edpekalkeiaRvLkpgGllv 95 
                                       +  +          e++ + ++RvLk +G++v
  gi|320100881|ref|YP_004176473.1| 162 TDPYAgdvakpLYSEEFYRDVKRVLKRDGVMV 193
                                       77777644443389***************987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     2e-06    0.0052       1      97 [.      83     190 ..      83     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg......ssfDlvv 71 
                                       L iG+G G++lr++l++    e + vDi+p ++e  k+ l   ++ ++n  + ++l  + l         ++fD+ +
  gi|320100881|ref|YP_004176473.1|  83 LIIGGGEGATLREVLKHGTVREAVMVDIDPVVVEFSKKYLEYMHQGSFNDPRSRVLIMDGLR-YvkeapsDYFDVAI 158
                                       569******************************99999999999999999998888765433.25889999****99 PP

                   Methyltransf_12  72 asnvlhhl......kdirevldnirklLkpgG 97 
                                       +  +  +          +e+ + ++++Lk +G
  gi|320100881|ref|YP_004176473.1| 159 MDLTDPYAgdvakpLYSEEFYRDVKRVLKRDG 190
                                       87666666555544444566667777777766 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.1e-05      0.13      68     111 ..      84     128 ..      51     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-05
                                       EET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-----T CS
                    Methyltransf_2  68 DvGGGtGalakaivsayPtikvivfDl.peVveaAkehlsageee 111
                                        +GGG Ga+++++ ++    ++++ D+ p Vve  k++l+  ++ 
  gi|320100881|ref|YP_004176473.1|  84 IIGGGEGATLREVLKHGTVREAVMVDIdPVVVEFSKKYLEYMHQG 128
                                       49*************************788899999998876665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.5e-05      0.19      16      71 ..      72     130 ..      56     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.5e-05
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.kakkaqkdqf 71 
                                       +++  + + rvL iG G+G +l++  ++g+  + ++vD++p+ ve  +     +++ +f
  gi|320100881|ref|YP_004176473.1|  72 AMALHPDPVRVLIIGGGEGATLREVLKHGTvrEAVMVDIDPVVVEFSKkYLEYMHQGSF 130
                                       4455667779***************9999999*********998876542333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2014.56
//
Query:       gi|320100882|ref|YP_004176474.1|  [L=489]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-153  510.5   0.0   2.4e-153  510.3   0.0    1.0  1  DUF2139   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2139  Uncharacterized protein conserved in archaea (DUF2139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  510.3   0.0  1.4e-157  2.4e-153       1     338 [.      27     367 ..      27     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 510.3 bits;  conditional E-value: 1.4e-157
                           DUF2139   1 lyytlafeaeahfikddsek.iYrfelvGkaPtsGGDtYnaveavDdkiyfGGWvhaPavykgreekkaeisfknkY 76 
                                       lyyt+a+eaeahfi+dd+ + +Yrf+ +G+ P+sGGDtYnav++vDd+i+fGGWvh+Pa ykg++++++ei+f+nkY
  gi|320100882|ref|YP_004176474.1|  27 LYYTVAMEAEAHFIHDDGFTeTYRFQGLGPGPASGGDTYNAVDVVDDEIFFGGWVHNPALYKGKTGGSGEIDFRNKY 103
                                       8****************9766******************************************************** PP

                           DUF2139  77 shvheydieekevkLlWkesihdeeeWagevseiiYdpledkLLlaraDGhanlGvyeidrktgearklsdkpalkG 153
                                       sh+h y ++e++vkLlW+esihde +Wagevs+i Ydp++d+LL+ raDGh+nlG+y++ r++g+++k+s++p lkG
  gi|320100882|ref|YP_004176474.1| 104 SHIHVYSVAEHSVKLLWSESIHDEYKWAGEVSQITYDPVNDRLLIGRADGHVNLGIYSLPRRGGRVEKVSETPGLKG 180
                                       ***************************************************************************** PP

                           DUF2139 154 alvldlacfdikedfkkgvegiecldliekkvvyeeledvekasvDgedvekresGavasaytrvfafvrGGilvgn 230
                                       al+ld+acfd+++++ +gv+gi+c+dl+++++v++++e+++++svDg++ve+r sG+ +saytr+ +f+rGG+lvgn
  gi|320100882|ref|YP_004176474.1| 181 ALFLDYACFDMQPNWLRGVDGIQCVDLVSGQLVKYSVESWSRISVDGGGVEMRGSGYGISAYTRYLHFFRGGVLVGN 257
                                       ***************************************************************************** PP

                           DUF2139 231 Pvee..eelrfvrllDfaetqyaplrsnalplgGGvlvafnaysealvrktneeeevvkkatntivgPsvLvYiaPp 305
                                       Pve+  +e rf+rl+Df+ ++yap+rsnal+lgGG+l++fnay+++ +++ +e ++v +k  nt+vgPsvLvYi+Pp
  gi|320100882|ref|YP_004176474.1| 258 PVEPwiDEPRFMRLFDFGRNPYAPQRSNALVLGGGILAPFNAYTHGFLHGYKEGDNVLAKHLNTVVGPSVLVYITPP 334
                                       ***************************************************************************** PP

                           DUF2139 306 vakivgalGaritslekvgdkvllatnttpnle 338
                                        a+iv alGar+ts+ k g+++l++ +ttpnl+
  gi|320100882|ref|YP_004176474.1| 335 QARIVMALGARVTSMAKRGGEILVGYSTTPNLG 367
                                       *******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3720.16
//
Query:       gi|320100883|ref|YP_004176475.1|  [L=446]
Description: Nodulation efficiency protein NfeD [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-09   38.2   3.4    1.4e-09   38.2   3.4    3.0  3  NfeD          NfeD-like C-terminal, partner-binding
     0.0011   18.9   0.0     0.0017   18.3   0.0    1.3  1  CLP_protease  Clp protease
  ------ inclusion threshold ------
      0.054   12.5   0.1       0.11   11.4   0.0    1.5  2  SDH_sah       Serine dehydrogenase proteinase
        0.1   12.8   2.2        1.9    8.8   0.7    3.0  2  HIG_1_N       Hypoxia induced protein conserved region
       0.11   11.1   0.0       0.15   10.6   0.0    1.1  1  DUF4127       Protein of unknown function (DUF4127)


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 ?   -1.0   0.2      0.66   2.4e+03      58      70 ..      25      37 ..       6      43 .. 0.49
   2 ?   -2.6   0.0       2.1   7.4e+03      67      76 ..     211     220 ..     204     222 .. 0.56
   3 !   38.2   3.4   3.8e-13   1.4e-09       2      84 .]     361     443 ..     358     443 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.66
                                      EE-.SSB-TT-EE CS
                              NfeD 58 arsegeiekgerV 70
                                      a+s+g++ + +rV
  gi|320100883|ref|YP_004176475.1| 25 AESQGQVRVVDRV 37
                                      3333334444444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                                       T-EEEEEEE- CS
                              NfeD  67 gerVrVveve 76 
                                       g+ VrV +ve
  gi|320100883|ref|YP_004176475.1| 211 GTHVRVNGVE 220
                                       4555555554 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 3.8e-13
                                       XXXXXXXXXXXXXXXS---SSS--S.S---.GGTTSEEEEEE-B..S.-EEEEETTEEEEEE-.SSB-TT-EEEEEE CS
                              NfeD   2 favvsvlllvllrplllkklkkkekktnae.aliGkegvvledi..g.tGrvkvdGeeWsarsegeiekgerVrVve 74 
                                        +v++ ++ v++++++  k++k      +e   +Gk+g+v+e++  g  G v ++Ge+W+a+s + + +ge+V+V e
  gi|320100883|ref|YP_004176475.1| 361 SIVLGGVFGVVIYKVINVKRRK-----PVEfLPVGKTGRVIEEVkpGqMGFVIIEGEYWRAVSSEHLLPGEEVVVEE 432
                                       5777788888888887777644.....456568***********99557**************999**********9 PP

                                       E.-SSSEEEEE CS
                              NfeD  75 v.eGltliVep 84 
                                       + eG  l+V++
  gi|320100883|ref|YP_004176475.1| 433 IlEGGVLKVRR 443
                                       87999999986 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.7e-07    0.0017      44      99 ..      65     121 ..      31     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.7e-07
                                       -SSS-EEEE.EEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-TT CS
                      CLP_protease  44 dpdkdilly.inspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagekg 99 
                                       +++  +l+y +ns GG ++ag++I d++ y k++ + ++   a S+++l+++ ++  
  gi|320100883|ref|YP_004176475.1|  65 ESTGSLLIYrVNSYGGLLDAGFTIGDAVLYSKTPTVAYVETKALSAATLIILPANIV 121
                                       33444555559***************************************9988755 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.2e-05      0.11      98     168 ..      75     145 ..      45     182 .. 0.84
   2 ?   -3.3   0.0      0.97   3.5e+03      66     269 ..     369     384 ..     366     392 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                           SDH_sah  98 ihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqypaasil 168
                                       + + GGl  a   i  a+   k++t   v   a+s  tli l a+ + l++ + +G ++p + +  +  i 
  gi|320100883|ref|YP_004176475.1|  75 VNSYGGLLDAGFTIGDAVLYSKTPTVAYVETKALSAATLIILPANIVALQRYSTIGDMQPVVVDPLTGRIQ 145
                                       45679****************************************************99988775555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.97
                           SDH_sah  66 GipiykfitiedseevlrairltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaad 142
                                       G+ iyk i++                                                                   
  gi|320100883|ref|YP_004176475.1| 369 GVVIYKVINV------------------------------------------------------------------- 378
                                       5555555554................................................................... PP

                           SDH_sah 143 eiildenavlGpvdpqlgqypaasilkvvekkeakdiddktliladiakkaikqveefvyellkdkydeekakeiak 219
                                                                                                                    
  gi|320100883|ref|YP_004176475.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                           SDH_sah 220 klteGrwthdypltveelkelGlevntnvpeevyellelyeqplgqrpsv 269
                                                                                   ++r++v
  gi|320100883|ref|YP_004176475.1| 379 --------------------------------------------KRRKPV 384
                                       ............................................344445 PP

>> HIG_1_N  Hypoxia induced protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.7   0.00052       1.9       2      19 ..     252     269 ..     251     274 .. 0.88
   2 ?    1.9   0.0     0.076   2.7e+02       6      27 ..     361     382 ..     358     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00052
                           HIG_1_N   2 eplvpiGilatvgalvrg 19 
                                       ++l  iG+lat  alv g
  gi|320100883|ref|YP_004176475.1| 252 NILATIGMLATIFALVAG 269
                                       799************998 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.076
                           HIG_1_N   6 piGilatvgalvrglrsmkrgd 27 
                                        i ++++ g++++ +++ kr++
  gi|320100883|ref|YP_004176475.1| 361 SIVLGGVFGVVIYKVINVKRRK 382
                                       5668999*************95 PP

>> DUF4127  Protein of unknown function (DUF4127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.2e-05      0.15     340     387 ..      36      93 ..      23     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.2e-05
                           DUF4127 340 pvalaDvayan.....gadkaLveaLkekg.....llsklaaYaGWNTasNtlGtala 387
                                        v ++D+a ++     g  +++++aL+e +     l++++ +Y G  +a+ t+G a+ 
  gi|320100883|ref|YP_004176475.1|  36 RVLVVDIAPPFdtidnGVAECFTDALREAEstgslLIYRVNSYGGLLDAGFTIGDAVL 93 
                                       5778888876554444************999999999*****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3027.03
//
Query:       gi|320100884|ref|YP_004176476.1|  [L=262]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-38  130.9   1.2    6.9e-38  130.4   1.2    1.2  1  Band_7        SPFH domain / Band 7 family
    0.00089   19.0   0.1     0.0014   18.4   0.1    1.4  1  Band_7_1      SPFH domain-Band 7 family
     0.0043   17.1   1.5     0.0043   17.1   1.5    1.6  2  ProSAAS       ProSAAS precursor
  ------ inclusion threshold ------
       0.13   13.1   0.2       0.26   12.1   0.2    1.6  1  GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fol


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 !  130.4   1.2   1.5e-41   6.9e-38       2     178 .]      27     197 ..      26     197 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 1.5e-41
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       i++e e+ vv+r G+l++ ++pGl +++Pf+++v++v++rv+t+dv++ ++++tkD+++v++d++v+yrv  d+  +
  gi|320100884|ref|YP_004176476.1|  27 IVREYERVVVFRLGRLVGAKGPGLILVIPFFDQVAKVDLRVITVDVPK-QEIITKDNVSVKVDAVVYYRV-VDPVLA 101
                                       799*********************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       +++v    an+   ++ + + +lr v+++ +l+ell++r+el+++++  l e    +G+ + +v+i+++++p+e+ +
  gi|320100884|ref|YP_004176476.1| 102 ITRV----ANYHYSVSLLGQTVLRDVLGQSELDELLQKRDELNKRITGILDELTMPWGIKISSVTIKSVELPEELMR 174
                                       ****....********************************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraeaea 178
                                       a+a+ ++ae+ ++a++ +ae+e+
  gi|320100884|ref|YP_004176476.1| 175 AMAKQAEAERWRRARVIEAEGER 197
                                       ********************995 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.1e-07    0.0014     145     209 ..     120     182 ..      79     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.1e-07
                          Band_7_1 145 lsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       l dvl++s++   +l  k +el ++++  l+e     G+++++++i++++lpee+ +a+ k+a++
  gi|320100884|ref|YP_004176476.1| 120 LRDVLGQSELD--ELLQKRDELNKRITGILDELTMPWGIKISSVTIKSVELPEELMRAMAKQAEA 182
                                       55666666543..6778999*****************************************9976 PP

>> ProSAAS  ProSAAS precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3         1   4.7e+03      16      34 ..       5      23 ..       3      31 .. 0.79
   2 !   17.1   1.5   9.5e-07    0.0043      71     113 ..     168     210 ..     146     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1
                           ProSAAS 16 gllvllllgllrppaalsa 34
                                      gll+ll++ l+  ++ lsa
  gi|320100884|ref|YP_004176476.1|  5 GLLILLIIILFIGVPLLSA 23
                                      8999999999999998887 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9.5e-07
                           ProSAAS  71 avqelaralahlleaerqeraraeaqeaedqqarvlaqllrvw 113
                                         +el ra+a+  eaer  rar    e e q +++la+  r++
  gi|320100884|ref|YP_004176476.1| 168 LPEELMRAMAKQAEAERWRRARVIEAEGERQASQILAEAARMY 210
                                       5579*******************999***********999987 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 ?   12.1   0.2   5.9e-05      0.26      74     117 ..     194     237 ..     157     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                                       GHHHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EE CS
                      GFO_IDH_MocA  74 theelakaaleagkhvllEKPlattveeakelvelaekkgklvs 117
                                       ++e+ a ++l+       E+P+a+ ++e++ l+e+a++k  +v 
  gi|320100884|ref|YP_004176476.1| 194 EGERQASQILAEAARMYEEHPVALRLRELQTLIEIAREKALVVV 237
                                       567778888888888889*********************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1869.24
//
Query:       gi|320100885|ref|YP_004176477.1|  [L=292]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   66.6  27.2    7.2e-12   45.6   8.3    2.2  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
        7.7    6.6   8.5        3.2    7.8   2.0    3.4  4  DUF1427   Protein of unknown function (DUF1427)


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 !   27.1  10.9   4.3e-10   3.9e-06       3     133 ..       9     136 ..       7     140 .. 0.85
   2 !   45.6   8.3     8e-16   7.2e-12       2     136 ..     151     289 ..     150     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.3e-10
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwlll.lllgllgtvla 78 
                                       g+l++ l++l+w++++ l+ +  ++++++t++++r l+ag+++l++++     +    + d+l   +llgl+g++++
  gi|320100885|ref|YP_004176477.1|   9 GLLYLGLSVLMWSLTPSLISMDKARYNSFTANGLRALLAGVVMLPFTAEIILEN----PVDYLTAgALLGLIGILVG 81 
                                       8889999***************************************98877777....77777777*********** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvl 133
                                        +l++  +++++++ a+++ +  ++ t +l  l+         +++ +++++G +
  gi|320100885|ref|YP_004176477.1|  82 DSLYILTIRRLGPGLAVVLCYSYVATTQLLKQLVAPGGSVYVAVAASLIAIVGMY 136
                                       ****************************999999544444444555555555554 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 8e-16
                              EamA   2 lgillallaalfwaiyfvlskil..lrkvspltltfvrfliagillliiallkegklaklslkd..wllllllgllg 74 
                                        g+l a l  ++wa++ ++s i    r ++ l+lt  rf+i g++l +++  + g ++ +++ +  + + +l gl g
  gi|320100885|ref|YP_004176477.1| 151 TGLLAAALTNISWAAWSLISWIYvkGRGLNVLALTSARFIIPGLILTVYSTRRHGARELFTHAPrkLRYTMLSGLTG 227
                                       68999***************888567888****************************7777777658888******* PP

                              EamA  75 tvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        +++  +++ +lk++++s+a+++t+ +Pv++ ++s+   g ++  ++l+g++l+ l++++ +
  gi|320100885|ref|YP_004176477.1| 228 YLVGGTAYLESLKYIDVSQATIATAAVPVLSQLISSTTTGSRIRRSELAGALLVALSIVISS 289
                                       **********************************************************9876 PP

>> DUF1427  Protein of unknown function (DUF1427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.0   0.00036       3.2      31      56 ..      71      97 ..      43     116 .. 0.76
   2 ?   -0.3   0.0      0.12   1.1e+03      27      48 ..     127     147 ..     121     173 .. 0.64
   3 ?   -1.0   0.1      0.19   1.7e+03      32      45 ..     222     235 ..     219     272 .. 0.59
   4 ?   -1.6   0.0       0.3   2.6e+03      44      66 ..     253     275 ..     241     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00036
                           DUF1427 31 aLvGLlGiLvGeqv.vPvakrllagee 56
                                      aL+GL+GiLvG+ + +  ++rl  g +
  gi|320100885|ref|YP_004176477.1| 71 ALLGLIGILVGDSLyILTIRRLGPGLA 97
                                      8**********9872344566655555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
                           DUF1427  27 PPvvaLvGLlGiLvGeqvvPva 48 
                                         ++a+vG+  i v eq+  ++
  gi|320100885|ref|YP_004176477.1| 127 ASLIAIVGMY-IAVREQLTFIV 147
                                       5577788765.67778865544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.19
                           DUF1427  32 LvGLlGiLvGeqvv 45 
                                       L GL G LvG    
  gi|320100885|ref|YP_004176477.1| 222 LSGLTGYLVGGTAY 235
                                       56777777775544 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.3
                           DUF1427  44 vvPvakrllageevatawakaec 66 
                                        vPv  +l++++++ + ++++e 
  gi|320100885|ref|YP_004176477.1| 253 AVPVLSQLISSTTTGSRIRRSEL 275
                                       68999999998888777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2238.31
//
Query:       gi|320100886|ref|YP_004176478.1|  [L=475]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-15   55.5   0.7    7.6e-15   54.9   0.7    1.4  1  DUF402     Protein of unknown function (DUF402)
    5.5e-05   22.7   0.0    7.9e-05   22.2   0.0    1.2  1  RNase_E_G  Ribonuclease E/G family


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.7   8.5e-19   7.6e-15       4      68 .]     372     435 ..     369     435 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 8.5e-19
                                       EEEE-TT-SEEEEEEEETTTEEEEEEEEEES--EE..E.EEE-EEEEEEESEEE......-HHHH CS
                            DUF402   4 lwllplglwynvfhfldgdgrlqglYvDiatppevgegawktiDlyLDlvvspdgevevlDedEL 68 
                                       ++++ lg+ y v+ +++g+ + +g Y++++tppev  +++k++Dl +D+ v+pdg+++vlD++EL
  gi|320100886|ref|YP_004176478.1| 372 YMVIMLGRPYIVHNYYRGN-TWLGSYINVNTPPEVSADTVKYHDLLVDVSVTPDGRINVLDREEL 435
                                       678889************8.***************779**************************8 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   8.8e-09   7.9e-05       2      90 ..     151     240 ..     150     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.8e-09
                         RNase_E_G   2 laGrylVllpegkkvgvSkkiedeeererlkell.eelkpeevGlIvRtaaegaseeelekdleelkkkweeileka 77 
                                       l G+ + ll  + +v++S+ i+d e ++rl +l+ ++l+ ++ G+ +R++a  a   el ++++ l  +++++++++
  gi|320100886|ref|YP_004176478.1| 151 LLGKLVALLHGEPRVTFSEHIRDPELKARLTTLAaSRLMGTGLGIHFRSSARFAGSGELLNEIDTLLGEYRRLMARV 227
                                       568888888777779*****************9967788999*********************************** PP

                         RNase_E_G  78 kkrkapsllyeee 90 
                                       k+++ p  ly+ e
  gi|320100886|ref|YP_004176478.1| 228 KEAEPPVKLYSGE 240
                                       *999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3405.43
//
Query:       gi|320100887|ref|YP_004176479.1|  [L=89]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-34  117.1   0.7    2.9e-34  117.0   0.7    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
  ------ inclusion threshold ------
      0.092   13.5   0.2        0.3   11.9   0.2    2.0  2  HEAT_PBS  PBS lyase HEAT-like repeat
       0.12   12.7   0.3        8.1    6.8   0.1    2.2  2  UPF0253   Uncharacterised protein family (UPF0253)


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.7   4.8e-38   2.9e-34       2      81 .]       8      87 ..       7      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 4.8e-38
                                      HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHH CS
                           UPF0147  2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEt 80
                                      e k++++i+lL +i++dt+vPrniRraa+ea+++L+de+ +++vraa+a+ +Ld++s+DpnmPl aRt+iw+v++ LEt
  gi|320100887|ref|YP_004176479.1|  8 EVKMRNAIYLLMSIVNDTAVPRNIRRAATEALNHLRDERYTPGVRAANAVGVLDQVSQDPNMPLSARTKIWQVIAILET 86
                                      67899*************************************************************************9 PP

                                      H CS
                           UPF0147 81 i 81
                                      i
  gi|320100887|ref|YP_004176479.1| 87 I 87
                                      8 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 ?   -2.1   0.0       1.7   9.9e+03       4      18 ..      13      27 ..      12      29 .. 0.58
   2 ?   11.9   0.2   4.9e-05       0.3       1      19 [.      31      49 ..      31      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                                      HHHHHHHHCTSGGGH CS
                          HEAT_PBS  4 aAakaLgqlgdeeai 18
                                      +A++ L  +  + a+
  gi|320100887|ref|YP_004176479.1| 13 NAIYLLMSIVNDTAV 27
                                      666666666555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHHHHHCTSGGGHH CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaip 19
                                      +RraA++aL  l+de++ p
  gi|320100887|ref|YP_004176479.1| 31 IRRAATEALNHLRDERYTP 49
                                      6*************88766 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0014       8.1      29      52 ..      13      36 ..       6      44 .. 0.83
   2 ?    4.2   0.0     0.009        54      29      49 ..      55      75 ..      43      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0014
                           UPF0253 29 calktLdevaanealpeevrekAA 52
                                       a+  L +++++ a+p+++r  A 
  gi|320100887|ref|YP_004176479.1| 13 NAIYLLMSIVNDTAVPRNIRRAAT 36
                                      57888999************8765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.009
                           UPF0253 29 calktLdevaanealpeevre 49
                                       a+ +Ld+v ++ ++p + r 
  gi|320100887|ref|YP_004176479.1| 55 NAVGVLDQVSQDPNMPLSART 75
                                      47899**********988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 635.40
//
Query:       gi|320100888|ref|YP_004176480.1|  [L=120]
Description: Sjogrens syndrome scleroderma autoantigen 1 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-12   47.3   0.3    2.3e-12   46.8   0.3    1.2  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.3   1.3e-16   2.3e-12       1      40 []       8      48 ..       8      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.3e-16
                     Auto_anti-p27  1 kkmgelLlkGwtMLaetCpv..CgvPLmrdrkggkvyCvaCd 40
                                      k m+elL  G+tML etCpv  C+ PL++ r +g+++C++++
  gi|320100888|ref|YP_004176480.1|  8 KVMAELLKSGATMLPETCPVegCNLPLFKLR-SGEIVCPVHG 48
                                      67****************************9.69*****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 836.56
//
Query:       gi|320100889|ref|YP_004176481.1|  [L=204]
Description: thymidylate kinase [Desulfurococcus mucosus DSM 2162]
Scores for 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-40  136.5   0.0    9.1e-40  136.3   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    1.5e-06   28.2   0.0      2e-05   24.5   0.0    2.0  1  dNK              Deoxynucleoside kinase
    5.8e-06   26.9   0.0    1.1e-05   26.0   0.0    1.5  1  AAA_18           AAA domain
    5.2e-05   23.5   0.0    8.5e-05   22.8   0.0    1.4  1  AAA_22           AAA domain
    7.5e-05   23.0   0.0     0.0001   22.6   0.0    1.2  1  AAA_28           AAA domain
    0.00011   22.7   0.0    0.00087   19.7   0.0    2.1  1  AAA_17           AAA domain
    0.00078   19.6   0.0      0.001   19.2   0.0    1.4  1  AAA_33           AAA domain
     0.0017   18.3   0.0      0.004   17.0   0.0    1.7  1  APS_kinase       Adenylylsulphate kinase
      0.003   17.0   0.0     0.0042   16.5   0.0    1.2  1  Arf              ADP-ribosylation factor family
     0.0035   16.9   0.0     0.0066   16.0   0.0    1.5  1  PPK2             Polyphosphate kinase 2 (PPK2)
     0.0083   17.1   0.0      0.014   16.4   0.0    1.4  1  LytR_C           LytR cell envelope-related transcriptional a
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.025   14.5   0.0    1.4  1  NTPase_1         NTPase
      0.021   14.8   0.0      0.047   13.6   0.0    1.6  1  NACHT            NACHT domain
      0.023   14.6   0.2      0.038   13.9   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
      0.031   14.1   0.2      0.077   12.8   0.2    1.6  1  DUF244           Uncharacterized protein family (ORF7) DUF
      0.037   14.4   0.0      0.051   14.0   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.046   13.6   0.0      0.078   12.9   0.0    1.3  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.051   13.7   0.0        9.4    6.3   0.0    2.2  2  SKI              Shikimate kinase
      0.057   13.1   0.0       0.11   12.2   0.0    1.6  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.087   12.1   0.0       0.11   11.8   0.0    1.1  1  KAP_NTPase       KAP family P-loop domain
      0.092   11.7   0.2       0.24   10.4   0.0    1.6  2  CP_ATPgrasp_1    A circularly permuted ATPgrasp
        0.1   12.3   0.0       0.15   11.7   0.0    1.3  1  AAA_30           AAA domain
       0.14   11.8   0.0       0.34   10.5   0.0    1.6  1  SRP54            SRP54-type protein, GTPase domain
       0.16   12.4   0.0       0.27   11.7   0.0    1.4  1  RNA_helicase     RNA helicase
       0.16   11.3   0.0       0.29   10.4   0.0    1.3  1  Zeta_toxin       Zeta toxin
       0.16   12.0   0.0       0.26   11.3   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


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 !  136.3   0.0   1.3e-42   9.1e-40       1     184 [.      10     187 ..      10     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 1.3e-42
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpal 77 
                                       +EGlDGaGKtt+a  l+e l+++g  ++ t ep+++ei + ++++ +     + +  al fa dr  h+ +++kp +
  gi|320100889|ref|YP_004176481.1|  10 LEGLDGAGKTTVAHRLVEELESRGFPAIYTYEPTDSEIVKAVKSIYS--DLRDAYIDALAFALDRLIHVKSLVKPFI 84 
                                       6***********************99*******************77..8889999********************* PP

                                       HTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHH CS
                   Thymidylate_kin  78 kqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrk 154
                                       ++g tv++dRy +Ss+aYq+a++   +d++l++n+ +l kPd+ ++ldvdpe++l R ++  +    e+e+++fl++
  gi|320100889|ref|YP_004176481.1|  85 EKGVTVVSDRYFYSSVAYQSASG-APFDWILEVNKYAL-KPDVAIYLDVDPEEGLSRKTTSTS-RFPEYEKKEFLHR 158
                                       ********************866.79**********99.********************9999.67899******** PP

                                       HHHHHHHHHHTTSTEEEEETTS-HHHHHHH CS
                   Thymidylate_kin 155 vrerylelakederiliidasksieevhee 184
                                       vre y ++++  + ++ +das+++ ev +e
  gi|320100889|ref|YP_004176481.1| 159 VREAYVRMVE-IGLLTRVDASRPLGEVYAE 187
                                       *********5.9999********9999765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     3e-08     2e-05       1     164 [.       8     164 ..       8     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3e-08
                                       EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSS...HHHHHHHHSHHH.H..HHHHHHHHHHHHHHHHHCH CS
                               dNK   1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqk...nlLekfYkdpsr.w..sfalqtyvllsrlkqqlea 71 
                                       iv+eG  gaGK+t++++L ++l+   f+ +  +++++ +   + ++ +Y d    +  ++a+    l +     + +
  gi|320100889|ref|YP_004176481.1|   8 IVLEGLDGAGKTTVAHRLVEELESRGFPAI-YTYEPTDSeivKAVKSIYSDLRDaYidALAFALDRLIHVKSLVKPF 83 
                                       89********************97777643.3454444455677777777776654334444444555544445556 PP

                                       HSSS-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCC CS
                               dNK  72 latkqvvvleRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgreee 148
                                       ++++ +vv +R  ys++        + +++s   ++   e+ + +l    kpd+ iYL++++e+ l r       + 
  gi|320100889|ref|YP_004176481.1|  84 IEKGVTVVSDRYFYSSV--------AYQSASGAPFDWILEVNKYAL----KPDVAIYLDVDPEEGLSRKTTSTSRFP 148
                                       68888999999999999........234455556666666666666....7*************9999777666666 PP

                                       TTS-HHHHHHHHHHHH CS
                               dNK 149 kkieldYlekLhekye 164
                                       +  ++++l ++ e y 
  gi|320100889|ref|YP_004176481.1| 149 EYEKKEFLHRVREAYV 164
                                       6667777777777775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.6e-08   1.1e-05       1     114 [.       8     144 ..       8     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.6e-08
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf............gvnlrdvakenglllevdpealdeskrldedkldklldale 65 
                                       I+l G  G+GKtt+a++L ++l++                ++++k   + +++  +a+ + + +  d+l  + ++++
  gi|320100889|ref|YP_004176481.1|   8 IVLEGLDGAGKTTVAHRLVEELESrgfpaiytyeptD---SEIVKAVKSIYSDLRDAYIDALAFALDRLIHVKSLVK 81 
                                       89******************99666777777775432...3333333333333333347888888888888888888 PP

                            AAA_18  66 enss...............aleegknlvidghlaeleseaakdikkvvLtaspeelleRlekRg 114
                                         ++               a+++++   +d++l+ + ++   d   ++L+++pee l R  +  
  gi|320100889|ref|YP_004176481.1|  82 PFIEkgvtvvsdryfyssvAYQSASGAPFDWILEVNKYALKPDVA-IYLDVDPEEGLSRKTTST 144
                                       887799999999999999977777777799999999999999988.**********99987755 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-07   8.5e-05       4      68 ..       4      66 ..       1      99 [. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-07
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst...sskdllrellralglel 68
                                      + +++v+ G  G+GKTt++ rl+e+l+ +      + + + +++++ s+     k+++++l  a+ + l
  gi|320100889|ref|YP_004176481.1|  4 KGYFIVLEGLDGAGKTTVAHRLVEELESR------GFPAIyTYEPTDSEivkAVKSIYSDLRDAYIDAL 66
                                      6789**********************876......8888856666666688888888888877766555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.5e-07    0.0001       2     147 ..       8     165 ..       7     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-07
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv..pEaareileeklakgedalpwv.edllafaervleeqleeeaaa. 70 
                                       iv+ G  ++GKTt++ +L ++    g+p +   E+    + +  ++   +l+++  d+lafa  +l + ++  +   
  gi|320100889|ref|YP_004176481.1|   8 IVLEGLDGAGKTTVAHRLVEElesrGFPAIytYEPTDSEIVKAVKSIYSDLRDAyIDALAFALDRLIHVKSLVKPFi 84 
                                       899**********9966664334449997777888887777788888888998889*******99976655555559 PP

                            AAA_28  71 aankvlfcDrglldtlaYarayggeaeaeleaaar.ekrydlvfllppap..ei..dddgeRredleereaiderlr 142
                                       +++ ++++Dr +  ++aY  a+g +    + +  + + + d  ++l+++p   +  +++ + r  + e +++ +r+r
  gi|320100889|ref|YP_004176481.1|  85 EKGVTVVSDRYFYSSVAYQSASGAP-FDWILEVNKyALKPDVAIYLDVDPeeGLsrKTTSTSRFPEYEKKEFLHRVR 160
                                       ***********************99.444333222244445555555555223342223333344455777777777 PP

                            AAA_28 143 ealre 147
                                       ea+ +
  gi|320100889|ref|YP_004176481.1| 161 EAYVR 165
                                       77765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-06   0.00087       2     120 ..      12     141 ..      11     156 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                                       E-TTSSHHHHHHHHHHHH...TEEEEEHHHHHHHHHHTT....TSHSSHHHHCTS..HHHHHHHHHHHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklveky...gfthlsaGdllreeakrg....glakardemrkl..pleekkelqkeaaekiaeea 69 
                                       G+ G+GK+t++ +lve++   gf+ + + +   +e+ +      ++  + +++ l   l++  ++  +++  i e  
  gi|320100889|ref|YP_004176481.1|  12 GLDGAGKTTVAHRLVEELesrGFPAIYTYEPTDSEIVKAvksiYSDLRDAYIDALafALDRLIHVKSLVKPFI-E-- 85 
                                       899**************99999999998555554444442111444444444444113333333333333333.3.. PP

                                       HSSEEEEEE-SEEEETTEEEESSHHHHH.....HHH..SEEEEEE--HHHHHHHHH CS
                            AAA_17  70 kkkgvlvdghprikeqagfldglpkevl.....eelkpdaiilleadpeeilerrl 120
                                       k  +v+ d ++      +  +g p + +       lkpd+ i+l++dpee l+r  
  gi|320100889|ref|YP_004176481.1|  86 KGVTVVSDRYFYSSVAYQSASGAPFDWIlevnkYALKPDVAIYLDVDPEEGLSRKT 141
                                       2455788888877777777888886553222225889************9888755 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.5e-06     0.001       2      25 ..       8      36 ..       7     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklg.....a 25
                                      ++l Gl G+GK+t+a+rl+++l      a
  gi|320100889|ref|YP_004176481.1|  8 IVLEGLDGAGKTTVAHRLVEELEsrgfpA 36
                                      6899***************9998666552 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.9e-06     0.004       2      33 ..       5      36 ..       4      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.9e-06
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisv 33
                                      g  + l Gl g+GK+t+a++l ++L+++g  +
  gi|320100889|ref|YP_004176481.1|  5 GYFIVLEGLDGAGKTTVAHRLVEELESRGFPA 36
                                      77899**********************99654 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.1e-06    0.0042      15      46 ..       6      37 ..       1      53 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.1e-06
                                      EEEEEEESTTSSHHHHHHHHHHSSCEECSSSS CS
                               Arf 15 lrilllGLDnaGKtTilkklkleelvttvPTi 46
                                      + i+l GLD+aGKtT+ ++l +e  ++  P i
  gi|320100889|ref|YP_004176481.1|  6 YFIVLEGLDGAGKTTVAHRLVEELESRGFPAI 37
                                      568999**************998777766654 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.5e-06    0.0066      30      73 ..       4      47 ..       1      57 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.5e-06
                                      -EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--HHHH CS
                              PPK2 30 kklvvifegrDaAGKgGaikrvtealnprvarvvalkaPteeEk 73
                                      k   +++eg D+AGK  + +r++e+l+ r+       +Pt+ E 
  gi|320100889|ref|YP_004176481.1|  4 KGYFIVLEGLDGAGKTTVAHRLVEELESRGFPAIYTYEPTDSEI 47
                                      55689**************************9999999**9995 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     2e-05     0.014       7      80 ..      13      91 ..      12      96 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-05
                            LytR_C  7 lNgtgvsGlAarvadaLeerGf.tvgevgnagnadee..ttivyreaaaaaak......alaaalglgelqedsvkdas 76
                                      l+g+g++ +A+r+ ++Le+rGf ++++ + +++  ++  ++i y ++ + +a+      al ++++++   ++++ +++
  gi|320100889|ref|YP_004176481.1| 13 LDGAGKTTVAHRLVEELESRGFpAIYTYEPTDSEIVKavKSI-Y-SDLR-DAYidalafALDRLIHVKS-LVKPFIEKG 87
                                      689*******************99998555554444474444.4.3333.3332211224444444333.333344444 PP

                            LytR_C 77 vtvv 80
                                      vtvv
  gi|320100889|ref|YP_004176481.1| 88 VTVV 91
                                      6665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.6e-05     0.025       2      30 ..       8      36 ..       7      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      +++ G  G GKtT+ ++++e+l+s+g++ 
  gi|320100889|ref|YP_004176481.1|  8 IVLEGLDGAGKTTVAHRLVEELESRGFPA 36
                                      6788999******************9875 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   6.9e-05     0.047       3      30 ..       8      35 ..       6      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.9e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      ++l+G  G GKTt +++l++++ ++  p
  gi|320100889|ref|YP_004176481.1|  8 IVLEGLDGAGKTTVAHRLVEELESRGFP 35
                                      89********************998765 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 ?   13.9   0.0   5.5e-05     0.038      22      70 ..       7      55 ..       2     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
                          ATPase_2 22 iyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie 70
                                      ++++ G  g GKt++  +++e+le+ ++  iy ++  +++i k+ ++i 
  gi|320100889|ref|YP_004176481.1|  7 FIVLEGLDGAGKTTVAHRLVEELESRGFPAIYTYEPTDSEIVKAVKSIY 55
                                      67888***************************99998888888777765 PP

>> DUF244  Uncharacterized protein family (ORF7) DUF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00011     0.077       2      63 ..      46     124 ..      45     138 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                            DUF244   2 eiinlkkdiysnyreeylmahnfnedtfik...lvedlver.....sd..fys.......sevefdwarefieyvdc 61 
                                       ei++  k iys+ r+ y+ a  f  d +i+   lv+ ++e+     sd  fys       s+  fdw+ e+ +y   
  gi|320100889|ref|YP_004176481.1|  46 EIVKAVKSIYSDLRDAYIDALAFALDRLIHvksLVKPFIEKgvtvvSDryFYSsvayqsaSGAPFDWILEVNKYALK 122
                                       899999********************998533467666665333333433665222222235668888877777655 PP

                            DUF244  62 ad 63 
                                        d
  gi|320100889|ref|YP_004176481.1| 123 PD 124
                                       55 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.4e-05     0.051      26      85 ..       7      58 ..       2     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.4e-05
                            AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrql 85
                                       ++l G  G GK++++ +l ++le +g+ ++++           s +++a  + +++ +l
  gi|320100889|ref|YP_004176481.1|  7 FIVLEGLDGAGKTTVAHRLVEELESRGFPAIYTYEPTD------SEIVKAV-K-SIYSDL 58
                                      58999*********************755555555555......2244444.3.344333 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 ?   12.9   0.0   0.00011     0.078       3      28 ..       9      34 ..       7      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                              MobB  3 givgksgsGKTtLleklipelkargl 28
                                       + g  g+GKTt  ++l++el++rg+
  gi|320100889|ref|YP_004176481.1|  9 VLEGLDGAGKTTVAHRLVEELESRGF 34
                                      566999******************96 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.014       9.4       2      17 ..      15      30 ..      14      54 .. 0.90
   2 ?    5.4   0.0     0.026        18      83     108 ..     121     146 ..     113     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                                      TSSHHHHHHHHHHHHT CS
                               SKI  2 GaGKstvGkllAkklg 17
                                      GaGK+tv+++l ++l+
  gi|320100889|ref|YP_004176481.1| 15 GAGKTTVAHRLVEELE 30
                                      9**********99986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.026
                                       HHHSEEEEEE--HHHHHHHHHHTTSS CS
                               SKI  83 kekgiviyLdvsleellerlkadkeR 108
                                        +  + iyLdv++ee l+r +  ++R
  gi|320100889|ref|YP_004176481.1| 121 LKPDVAIYLDVDPEEGLSRKTTSTSR 146
                                       447889************99888885 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.11       2      46 ..       8      52 ..       7     101 .. 0.81
   2 ?   -2.6   0.0       5.4   3.7e+03     130     147 ..     123     140 ..     115     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                               PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraek 46
                                      I + g  GaGkttva++l++ ++  + +a +     + ++++a k
  gi|320100889|ref|YP_004176481.1|  8 IVLEGLDGAGKTTVAHRLVEELESRGFPAIYTYEPTDSEIVKAVK 52
                                      6677889****************9999988875555555544444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.4
                               PRK 130 ldlkiyvdisidlelark 147
                                        d+ iy+d++ +  l+rk
  gi|320100889|ref|YP_004176481.1| 123 PDVAIYLDVDPEEGLSRK 140
                                       699999999887666666 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.11      19     111 ..       4      92 ..       1     107 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkllra 95 
                                       +++ ++L+g  G+GK+++  +l +el+++      ++ ++++  ++   +av+++++ L+da      +   +l+++
  gi|320100889|ref|YP_004176481.1|   4 KGYFIVLEGLDGAGKTTVAHRLVEELESR---GFPAIYTYEPTDSEI-VKAVKSIYSDLRDAYIDALAFALDRLIHV 76 
                                       68999************************...888999999999976.9999*********9999999999999999 PP

                        KAP_NTPase  96 kklkalkikgkiklrk 111
                                       k+l +++i +++  ++
  gi|320100889|ref|YP_004176481.1|  77 KSLVKPFIEKGVTVVS 92 
                                       9999999988877655 PP

>> CP_ATPgrasp_1  A circularly permuted ATPgrasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00035      0.24     193     236 ..      48      91 ..      41      94 .. 0.88
   2 ?   -1.8   0.0       1.8   1.2e+03      10      42 ..     165     196 ..     159     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                     CP_ATPgrasp_1 193 lkrvdviyRRvdddflDPlefrpdsvlGvpGlleayraGnvtla 236
                                        k v+ iy  + d+++D l+f  d  + v  l++   +  vt++
  gi|320100889|ref|YP_004176481.1|  48 VKAVKSIYSDLRDAYIDALAFALDRLIHVKSLVKPFIEKGVTVV 91 
                                       6899*****************************98877777776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                     CP_ATPgrasp_1  10 erlerGlkqRvraLnafLaDiYgdqeilkdGlv 42 
                                       +++e Gl  Rv+a    L ++Y +   + +G++
  gi|320100889|ref|YP_004176481.1| 165 RMVEIGLLTRVDA-SRPLGEVYAEVWSIVQGVI 196
                                       457999999*998.5678899988888888887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.15      19      48 ..       6      35 ..       1      55 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggr 48
                                       + vl+G  G+GKtt+   l+e +e++g++
  gi|320100889|ref|YP_004176481.1|  6 YFIVLEGLDGAGKTTVAHRLVEELESRGFP 35
                                      4789*******************9999965 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00049      0.34       4      29 ..       8      33 ..       6      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                                      EEEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkeg 29
                                      i+l Gl GaGKTt + +L + l+++g
  gi|320100889|ref|YP_004176481.1|  8 IVLEGLDGAGKTTVAHRLVEELESRG 33
                                      8899**************99988776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00038      0.27       1      43 [.       8      47 ..       8      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys.rnpeddf 43
                                      i+l G  g GK+t+a++L+++l+++      + +y+  ++++++
  gi|320100889|ref|YP_004176481.1|  8 IVLEGLDGAGKTTVAHRLVEELESRG----FPAIYTyEPTDSEI 47
                                      688999***********999999544....36677755555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00041      0.29      19      43 ..       8      32 ..       3      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00041
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerq 43
                                      i+l G  GAGK+++a+ l +ele++
  gi|320100889|ref|YP_004176481.1|  8 IVLEGLDGAGKTTVAHRLVEELESR 32
                                      788999***************9755 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      0.26      21      45 ..       7      31 ..       1      50 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                                      EEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE 21 vilLeGdLGaGKTtlvrglakalgv 45
                                      +i+LeG  GaGKTt ++ l+++l+ 
  gi|320100889|ref|YP_004176481.1|  7 FIVLEGLDGAGKTTVAHRLVEELES 31
                                      699*****************99953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1509.15
//
Query:       gi|320100890|ref|YP_004176482.1|  [L=111]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-27   93.2   0.2    8.5e-27   92.8   0.2    1.2  1  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.2   4.7e-31   8.5e-27       1      79 [.       5      80 ..       5      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 4.7e-31
                                      --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--E CS
                            DUF126  1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPl 79
                                      lSflg+vdp +G+v +++ ++   si g++Lv+++g+GStvgsyv+++++++g++P +++++ea+pil++G+++a+iPl
  gi|320100890|ref|YP_004176482.1|  5 LSFLGEVDPVRGVVKTESGEV---SIRGRVLVFKGGRGSTVGSYVIYAMRQQGSSPLCMVVKEAEPILIAGCVIAEIPL 80
                                      8**************988765...******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 945.79
//
Query:       gi|320100891|ref|YP_004176483.1|  [L=389]
Description: putative aconitase subunit 1 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-115  384.4   0.0   5.8e-115  384.2   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.2   0.0  3.3e-119  5.8e-115       1     401 []       1     385 [.       1     385 [. 0.96

  Alignments for each domain:
  == domain 1  score: 384.2 bits;  conditional E-value: 3.3e-119
                            DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvptt 77 
                                       m+Ltke+eaml+Ge+G+ ++kamei+v++Ge +gA+rLv++ +ahvsgvs ++ig  g +f++++ ekg+++rv+tt
  gi|320100891|ref|YP_004176483.1|   1 MYLTKEQEAMLRGEYGWSTAKAMEIIVRVGESMGADRLVEIVHAHVSGVSFSNIGVYGSRFIRDFYEKGGRARVYTT 77 
                                       9**************************************************************************** PP

                            DUF521  78 lnpigvdlerweelgvdeefaekqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTn 154
                                       +np +vd+  ++++ +d++++e+q+ i +a++++G+++ ftC+py + + p  Gehlaw+ESsav++aN+ +G  Tn
  gi|320100891|ref|YP_004176483.1|  78 VNPGCVDYGGLQSI-IDNSLLEQQSIIDDALVRMGFKPVFTCIPYWY-RPPAPGEHLAWGESSAVIFANTFYGGFTN 152
                                       *************9.*******************************9.***************************** PP

                            DUF521 155 reggpsalaaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKal 231
                                       reggp+alaaAitG+t+++Glh+  nR+++v v +  + +  +  g lG+++G++++ + P++    +    elK l
  gi|320100891|ref|YP_004176483.1| 153 REGGPIALAAAITGYTYHAGLHVLGNRRARVAVTLAPD-AYAYPAGTLGLWIGENLR-ETPFIPSAARLGMGELKVL 227
                                       **********************************7433.55555577*********9.99*****9999******** PP

                            DUF521 232 gAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElre 308
                                       +A++aasg++a+ +i g+TP   t+ e+l     +e++t++ +dle+++ e   ++ +   l ++GcPhlsl El e
  gi|320100891|ref|YP_004176483.1| 228 LASMAASGSHAMAVIPGLTPR-GTYIEEL-----EERVTVEGRDLERYVGEE--PPPGGRVLGYMGCPHLSLGELVE 296
                                       *********************.4443334.....79**************66..999999***************** PP

                            DUF521 309 laellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpg 385
                                        a+llk ++   + +l++t++ e+ ++++ l  +++l++ Gv++ + tC+vvs+l ++  +++v+tnSgKaa+Yl++
  gi|320100891|ref|YP_004176483.1| 297 TARLLKRHRYPRRGRLLLTIPAEYVSRYSWL--INELKARGVDIAAGTCPVVSRLRER--YDVVITNSGKAAFYLRK 369
                                       *****9999999*****************99..**********************994..9**************** PP

                            DUF521 386 ltgvkvalgsleecve 401
                                       ++g +v+++ ++e+ve
  gi|320100891|ref|YP_004176483.1| 370 IHGLRVRVAGVREVVE 385
                                       *************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3201.39
//
Query:       gi|320100892|ref|YP_004176484.1|  [L=426]
Description: carboxylyase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for 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  222.2   0.0    1.3e-65  221.9   0.0    1.0  1  UbiD         3-octaprenyl-4-hydroxybenzoate carboxy-lyase
  ------ inclusion threshold ------
       0.12   12.5   0.1         18    5.5   0.1    2.4  2  O_Spanin_T7  outer-membrane spanin sub-unit


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 !  221.9   0.0   1.4e-69   1.3e-65      18     405 ..      24     388 ..      20     389 .. 0.87

  Alignments for each domain:
  == domain 1  score: 221.9 bits;  conditional E-value: 1.4e-69
                                       -TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS..----EE- CS
                              UbiD  18 dpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkppippkvv 94 
                                       d  +Ei+ ia  +     ++++F+   g+ + +   tnl+  r+ v +++++ s ee+++ ++++l++    p   v
  gi|320100892|ref|YP_004176484.1|  24 DSSYEITRIAWSNR---DRVVVFKVR-GR-EWITGYTNLVTRRRDVYRLFNAGSDEELYKLMENALNN----PAGLV 91 
                                       66777777777776...678888654.44.578999****************999************7....34555 PP

                                       -GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCH CS
                              UbiD  95 esekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhwqihkgg 171
                                       ++     +  + +e     L+ LP+++++++DgG y+t+ ++i+ +  ++  n +++R++ + ++k+ l++++++  
  gi|320100892|ref|YP_004176484.1|  92 RD--EFHKYFRRIE---GLLDVLPFIKYYREDGGYYLTSSVIIACT--EEYCNSSFHRVMYHANDKATLRIVPRHLH 161
                                       33..2233222223...45666*********************987..5689**********9999******88774 PP

                                       HHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEE CS
                              UbiD 172 aehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivleGei 248
                                        + + + +++g ++ pva+++G +P   laA++  P g+ E+ + +al g ++ +++ +   ++vp d+ +v+eG+i
  gi|320100892|ref|YP_004176484.1| 162 YI-VSRNRERG-RDTPVALVLGLNPFQELAAAMNPPLGVFEVGVGAALGGGNM-VAETPLYRIPVPVDSSVVVEGVI 235
                                       44.66666777.8*******************************999998865.67777899*************** PP

                                       ECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEE.E-T.T-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTE CS
                              UbiD 249 dpgetapEGPfgdhtGyysevrdefpvfkVtait.hRk.dpiypttvvgkppeedallgkalealflpllkkqvpev 323
                                       +  e+  EGPf+d++   + +r+  pvfk  a++  R+ +p+++++v+g+  e++ l+g+++e++++ ++k+  p +
  gi|320100892|ref|YP_004176484.1| 236 TG-ERDREGPFTDILMLVDPERK-EPVFKPLAVYvARNgNPVFHAIVPGSW-EHQFLMGFPREPVIYSHVKRIAPGL 309
                                       98.689************88877.5*********545589******78876.********************9**** PP

                                       EEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CCCCEE CS
                              UbiD 324 kdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpdrDlv 400
                                       k+v+l+e g ++l++vvs+k+  pg+a+ ++ a++++++  s+ K+vivvD+d+dv+d+  v+waiatr++ ++Dl+
  gi|320100892|ref|YP_004176484.1| 310 KAVRLTEGGSGWLHVVVSLKQMSPGDARLAGLAVISAHP--SV-KHVIVVDDDIDVDDPLMVEWAIATRMRGSEDLI 383
                                       *******************999***************99..77.********************************* PP

                                       EECCC CS
                              UbiD 401 iiegt 405
                                       +++++
  gi|320100892|ref|YP_004176484.1| 384 VLRDV 388
                                       99876 PP

>> O_Spanin_T7  outer-membrane spanin sub-unit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.002        18      11      26 ..     223     238 ..     215     239 .. 0.89
   2 ?    4.3   0.0    0.0049        44      12      27 ..     361     376 ..     359     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.002
                       O_Spanin_T7  11 vsvDssLmvEPnLttE 26 
                                       v vDss++vE  +t E
  gi|320100892|ref|YP_004176484.1| 223 VPVDSSVVVEGVITGE 238
                                       78********999877 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0049
                       O_Spanin_T7  12 svDssLmvEPnLttEm 27 
                                        vD  LmvE  + t m
  gi|320100892|ref|YP_004176484.1| 361 DVDDPLMVEWAIATRM 376
                                       69********999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3065.03
//
Query:       gi|320100893|ref|YP_004176485.1|  [L=414]
Description: putative GTPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-36  125.9   0.0    2.4e-36  125.3   0.0    1.2  1  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
  ------ inclusion threshold ------
      0.034   13.9   0.0      0.061   13.0   0.0    1.3  1  AAA_24    AAA domain
      0.087   12.4   0.2       0.14   11.6   0.2    1.3  1  GTP_EFTU  Elongation factor Tu GTP binding 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 !  125.3   0.0     4e-40   2.4e-36       1     185 [.      99     273 ..      99     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 4e-40
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnp 77 
                                       G++dsGK+++++lL N+a+++g kp+++D DvGq +i+pPg+isl + +r++ ++++++  +  + f+Gd  p++  
  gi|320100893|ref|YP_004176485.1|  99 GGVDSGKTSFTTLLSNTAISAGLKPCVIDGDVGQADIGPPGFISLGIPDRQVLWNTEIPVYM--MRFIGDIRPQG-- 171
                                       899***************************************************99999887..78*******98.. PP

                            CLP1_P  78 slylalvkelareveekleenkkakasgliIntpGwvkglga.ellleliealepdvvvvldqeellnelkrdlpls 153
                                         y +++ + +r + ek+e   + + s+++I+t+Gw+++ ga  ++++lie++epd+vv+l++ +l   +kr +++ 
  gi|320100893|ref|YP_004176485.1| 172 --YTHVIPRELRWLAEKSE---SLGCSIIVIDTDGWIRDPGAvYYKQRLIEIVEPDAVVILGD-DLSRYFKR-FEKI 241
                                       ..66666666666664444...57****************97366799**************7.45555555.5559 PP

                            CLP1_P 154 kvkvvklpkspgvvqrsreerrelreerireY 185
                                       +vkv +lp+    + rsreerr lr++r+r +
  gi|320100893|ref|YP_004176485.1| 242 GVKVYELPEPTVRRTRSREERRLLRSMRYRDF 273
                                       **********9999***************987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.061       3      80 ..      93     206 ..      92     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie..........swedfldevvel... 59 
                                       ++++++G   +GKT++ + l       g kp +id + G +++ +  f ++            ++  +         
  gi|320100893|ref|YP_004176485.1|  93 RRVVVIGGVDSGKTSFTTLLsntaisaGLKPCVIDGDVGQADIGPPGFISLGipdrqvlwntEIPVYMM----Rfig 165
                                       589**************9999999*9999******************9987777888866663333333....1334 PP

                            AAA_24  60 ....................aaeladyktlviDtideleel 80 
                                                           + e  +++++viDt +++ + 
  gi|320100893|ref|YP_004176485.1| 166 dirpqgythviprelrwlaeKSESLGCSIIVIDTDGWIRDP 206
                                       46777999999999999999999999********9998765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   2.4e-05      0.14       3      24 ..      92     113 ..      90     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                                       EEEEEEEESTTSSHHHHHHHHH CS
                          GTP_EFTU   3 irnigiighvDhGKtTLtdrLl 24 
                                       +r +++ig vD+GKt++t  L 
  gi|320100893|ref|YP_004176485.1|  92 HRRVVVIGGVDSGKTSFTTLLS 113
                                       99**************997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3097.36
//
Query:       gi|320100894|ref|YP_004176486.1|  [L=214]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       291  (0.0162307); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1820.89
//
Query:       gi|320100895|ref|YP_004176487.1|  [L=206]
Description: AAA ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-07   28.6   0.2    0.00012   21.5   0.2    2.7  1  Rad51            Rad51
    1.3e-05   24.7   0.0     0.0002   20.8   0.0    2.2  2  ATPase           KaiC
    0.00036   20.2   0.0     0.0027   17.3   0.0    2.0  1  AAA_25           AAA domain
    0.00053   19.8   0.0     0.0018   18.0   0.0    1.7  2  AAA_24           AAA domain
    0.00074   19.9   0.0    0.00087   19.7   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0076   16.8   0.0      0.011   16.2   0.0    1.3  1  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.019   14.7   0.0    1.2  1  AAA_30           AAA domain
      0.028   14.2   0.5      0.055   13.2   0.5    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.035   13.8   0.0       0.05   13.3   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.042   14.3   0.5      0.068   13.7   0.5    1.2  1  AAA_23           AAA domain
      0.044   14.2   0.0      0.096   13.1   0.0    1.7  1  AAA              ATPase family associated with various cellul
      0.045   13.3   0.1      0.078   12.5   0.1    1.4  1  AAA_7            P-loop containing dynein motor region
      0.045   13.7   0.0       0.08   12.8   0.0    1.4  1  NACHT            NACHT domain
      0.047   13.7   0.0      0.057   13.5   0.0    1.3  1  AAA_14           AAA domain
      0.083   11.8   0.1       0.12   11.2   0.1    1.3  1  Kinesin          Kinesin motor domain
       0.11   12.4   0.0       0.15   11.9   0.0    1.2  1  RsgA_GTPase      RsgA GTPase
       0.11   12.5   0.0       0.13   12.3   0.0    1.3  1  AAA_5            AAA domain (dynein-related subfamily)
       0.14   12.3   0.2       0.27   11.4   0.2    1.7  1  AAA_33           AAA domain
       0.14   12.0   0.0        0.2   11.5   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
       0.17   11.5   0.1       0.24   11.0   0.1    1.2  1  SRP54            SRP54-type protein, GTPase domain
       0.21   11.2   0.0       0.29   10.7   0.0    1.2  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.24   10.4   0.1       0.41    9.7   0.1    1.3  1  T2SSE            Type II/IV secretion system 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 !   21.5   0.2   1.4e-07   0.00012      18     253 ..       5     204 ..       2     206 .] 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.4e-07
                                       EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHH CS
                             Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaer 94 
                                        l tG +++D+l    ie+ s t  +G  +sGkt + +t++        +   ++ ++y++te t++ er+ +  er
  gi|320100895|ref|YP_004176487.1|   5 GLYTGHQTIDSL----IESSSTTLFYGVAGSGKTTMLMTIAG-------NYCRNRVCLYVSTEETLHYERVARDPER 70 
                                       577888888888....7999***************9999974.......456899********************** PP

                                       TT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHH CS
                             Rad51  95 ykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrk 171
                                       y          v    +y   +    l  +a+ +  + f  + +Ds+ +l+R +  g + l+    +l+ ++ +Lrk
  gi|320100895|ref|YP_004176487.1|  71 YR--------GVLFTEIYDFGR----LVDLATFIYLHGFEAVFIDSLNSLFRLEPLGENSLS----RLAYIVASLRK 131
                                       94........244445555544....445677778889999999999999999999998887....58889999999 PP

                                       HHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEE.EEE CS
                             Rad51 172 ladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleav.fai 247
                                         ++ +  ++ + qv a  +           kP+g  vl     + ++l  g g++R +++v+ P+  e  +  f i
  gi|320100895|ref|YP_004176487.1| 132 TVENNSGKLFASAQVRAGEGE---------DKPVGEPVLDYYFDVVVSLSIG-GDGRYARIVKPPEADEGRVFpFRI 198
                                       999988888888888776554.........7899999999999999998876.678999999999998877643888 PP

                                       ETTEEE CS
                             Rad51 248 geeGie 253
                                       +e+Gie
  gi|320100895|ref|YP_004176487.1| 199 TESGIE 204
                                       888885 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.5e-07    0.0002      16      81 ..      17      83 ..       6      91 .. 0.76
   2 ?    2.2   0.0      0.12        98     117     225 ..      94     204 ..      84     206 .] 0.47

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-07
                            ATPase 16 ipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa..edlrenak.slGwdlekleeeg 81
                                      i + +++l +G++G+GKt++ ++ + + +++  + +++v++ee+   e + ++ +   G+ ++++ + g
  gi|320100895|ref|YP_004176487.1| 17 IESSSTTLFYGVAGSGKTTMLMTIAGNYCRN--RVCLYVSTEETLhyERVARDPErYRGVLFTEIYDFG 83
                                      577899*****************99999887..**********86556666555424466666666655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                            ATPase 117 eikakrvviDsitglayeekeavaReilrqlvrvlk......klgvTailvsekss...seeaaggygveefivdgv 184
                                         + ++v iDs+++l + e   +  + l +l+++++      +++   ++ s +     +e++  g  v  +  d v
  gi|320100895|ref|YP_004176487.1|  94 LHGFEAVFIDSLNSLFRLE--PLGENSLSRLAYIVAslrktvENNSGKLFASAQVRageGEDKPVGEPVLDYYFDVV 168
                                       5566777788887772222..12222222222222200001123344455554333355555555666666666666 PP

                            ATPase 185 ivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       + L          R+ +ivk   ++ + +++pf Ite+gi+
  gi|320100895|ref|YP_004176487.1| 169 VSLSI---G-GDGRYARIVKPPEAD-EGRVFPFRITESGIE 204
                                       66662...2.223555555554433.456677777777775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.3e-06    0.0027      25     170 ..      12     127 ..       9     142 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.3e-06
                            AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrdda 101
                                        ++ l+   +++l++G  g+GKtt+++ +a  +++ +            +lyvs+E++  + +r +r   +     +
  gi|320100895|ref|YP_004176487.1|  12 TIDSLIESSSTTLFYGVAGSGKTTMLMTIAGNYCRNR-----------VCLYVSTEETL-HYERVARDPERY----R 72 
                                       578899999*************************866...........58999999998.555544433333....3 PP

                            AAA_25 102 rllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg...densnsdvgalve 170
                                       ++l++ + ++                + + +l+  i   +g + v iD+l+++++    +ens s  + +v+
  gi|320100895|ref|YP_004176487.1|  73 GVLFTEIYDF----------------GRLVDLATFIYL-HGFEAVFIDSLNSLFRLeplGENSLSRLAYIVA 127
                                       4455544443................222234544555.677777777777777665555555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0018       5      80 ..      23     111 ..      19     112 .. 0.84
   2 ?   -1.0   0.0       1.5   1.2e+03     157     185 ..     158     182 ..     124     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                            AAA_24   5 iliyGpsgiGKTtlakel......gpkplfidtekGlksldadkfpdie.........swedfldevvelaaelady 66 
                                        l yG +g+GKTt++ ++          l++ te+ l+   +++ p+            +  ++d ++++   l+++
  gi|320100895|ref|YP_004176487.1|  23 TLFYGVAGSGKTTMLMTIagnycrNRVCLYVSTEETLHYERVARDPERYrgvlfteiyDFGRLVDLATFI--YLHGF 97 
                                       578*******************9888889******99999999977555899888777777777777776..799** PP

                            AAA_24  67 ktlviDtideleel 80 
                                       + ++iD+++ l +l
  gi|320100895|ref|YP_004176487.1|  98 EAVFIDSLNSLFRL 111
                                       *********99875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                            AAA_24 157 anelkeevDlvlranlkredkvgervlkt 185
                                        + l + +D+v+ +++    ++++r+   
  gi|320100895|ref|YP_004176487.1| 158 EPVLDYYFDVVVSLSI----GGDGRYARI 182
                                       4678899999999998....567776655 PP

>> AAA_16  AAA ATPase 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   0.00087      22      69 ..      19      61 ..      10     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipy 69
                                      ++ + +l++G +G+GK++++ +++  +++++ +++++++ + +     y
  gi|320100895|ref|YP_004176487.1| 19 SS-STTLFYGVAGSGKTTMLMTIAGNYCRNRvCLYVSTEETLH-----Y 61
                                      33.789***********************95333344444444.....3 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   1.4e-05     0.011       8      37 ..      17      46 ..      11      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                                      EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkp 37
                                      ++ ++++ + G  G+GK+t+l+++ag++  
  gi|320100895|ref|YP_004176487.1| 17 IESSSTTLFYGVAGSGKTTMLMTIAGNYCR 46
                                      7889999*******************9865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.3e-05     0.019       9      40 ..      12      42 ..       9      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                            AAA_30  9 avealltsgdrvavltGpAGtGKttalkalre 40
                                       +++l++s+  +++  G+AG+GKtt+l +++ 
  gi|320100895|ref|YP_004176487.1| 12 TIDSLIESSS-TTLFYGVAGSGKTTMLMTIAG 42
                                      6777888886.99**************99875 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   0.5   6.8e-05     0.055      19      39 ..      17      37 ..       5      41 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-05
                            AAA_29 19 idlkgatlltGpsGsGKSTll 39
                                      i+ +++tl+ G  GsGK+T+l
  gi|320100895|ref|YP_004176487.1| 17 IESSSTTLFYGVAGSGKTTML 37
                                      344449*************98 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 ?   13.3   0.0   6.1e-05      0.05       4      35 ..      26      52 ..      23      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-05
                   Viral_helicase1  4 hGvpGcGKStlirkllrtsliltvnrptaell 35
                                       Gv+G+GK+t++ +++ +       r++++l+
  gi|320100895|ref|YP_004176487.1| 26 YGVAGSGKTTMLMTIAGN-----YCRNRVCLY 52
                                      6*************9988.....445555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   8.4e-05     0.068       9      39 ..       6      40 ..       3      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.4e-05
                            AAA_23  9 sf.rdqeidF...skgltlItGpNGaGKTTildAi 39
                                       + ++q+id    s+  tl++G  G+GKTT l  i
  gi|320100895|ref|YP_004176487.1|  6 LYtGHQTIDSlieSSSTTLFYGVAGSGKTTMLMTI 40
                                      565679999999999***************99766 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   0.00012     0.096       2      45 ..      24      70 ..      23     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                      EEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCS.SSSTTHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel..gvefleisgsell.skyvgesekk 45
                                      l+yG  G GKT++   +a +   ++ +l +s  e l  + v   +++
  gi|320100895|ref|YP_004176487.1| 24 LFYGVAGSGKTTMLMTIAGNYcrNRVCLYVSTEETLhYERVARDPER 70
                                      8*****************99643344566666666633444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.6e-05     0.078      25      57 ..      12      44 ..       8      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-05
                             AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkl 57
                                       ++ l++++  +l++G +G+GKt++++++  ++
  gi|320100895|ref|YP_004176487.1| 12 TIDSLIESSSTTLFYGVAGSGKTTMLMTIAGNY 44
                                      57899********************99866554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.9e-05      0.08       2      21 ..      22      41 ..      21      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.9e-05
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      + +  G aGsGKTt+l  +a
  gi|320100895|ref|YP_004176487.1| 22 TTLFYGVAGSGKTTMLMTIA 41
                                      67889************998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     7e-05     0.057       6      50 ..      24      69 ..      19     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                            AAA_14  6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkk..ladpe 50
                                      +  G+  +GKTt+l +++ ++  +++ +ly++ ++   ++  ++dpe
  gi|320100895|ref|YP_004176487.1| 24 LFYGVAGSGKTTMLMTIAGNYC-RNRVCLYVSTEETLHYErvARDPE 69
                                      5679999***********9998.9999*****999777542244554 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00015      0.12      64      94 ..      10      38 ..       5      90 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                      HHHHHHHHTTSEEEEEEEESTTSSHHHHHTB CS
                           Kinesin 64 kplvesvleGynatifaYGqtgsGKTyTmeg 94
                                      ++ ++s++e  ++t+f YG+ gsGKT Tm  
  gi|320100895|ref|YP_004176487.1| 10 HQTIDSLIESSSTTLF-YGVAGSGKT-TMLM 38
                                      6788999988887777.*********.4433 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   0.00019      0.15      89     122 ..       9      43 ..       3      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       g++++ +l+++ +t+++ G  G GK+t++ +++++
  gi|320100895|ref|YP_004176487.1|   9 GHQTIDSLIESsSTTLFYGVAGSGKTTMLMTIAGN 43 
                                       6788899999889****************999987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.13       3      42 ..      24      65 ..      22     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      EEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH CS
                             AAA_5  3 lLvGppGtgKselaerlaaal..nreveyvqltrdtteedlk 42
                                      l  G  G+gK+++ + +a  +  nr  +yv   + + +e + 
  gi|320100895|ref|YP_004176487.1| 24 LFYGVAGSGKTTMLMTIAGNYcrNRVCLYVSTEETLHYERVA 65
                                      789******************888888888877777777664 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00034      0.27       3      25 ..      24      48 ..      23     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                            AAA_33  3 llvGlpGsGKstlaerllkklg..a 25
                                      l+ G++GsGK+t +  ++ +     
  gi|320100895|ref|YP_004176487.1| 24 LFYGVAGSGKTTMLMTIAGNYCrnR 48
                                      799**********999876655552 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   0.0   0.00025       0.2      16      56 ..      18      55 ..      11     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviyyia 56
                                      e+  ++  + YG  gsGKt++l+ i+ n    +   +y++ 
  gi|320100895|ref|YP_004176487.1| 18 ES--SSTTLFYGVAGSGKTTMLMTIAGNYCR-NRVCLYVST 55
                                      44..566788***************999833.334445444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00029      0.24       3      28 ..      22      47 ..      20      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                      EEEEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                                       +l+ G+ G+GKTt l  +a  + ++
  gi|320100895|ref|YP_004176487.1| 22 TTLFYGVAGSGKTTMLMTIAGNYCRN 47
                                      679*************9999877665 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   0.00036      0.29       3      23 ..      23      43 ..      21      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                                      EEEEESTTCCHHHHHHHHHCT CS
                              cobW  3 tvltGflGsGKTtLlnhllen 23
                                      t++ G  GsGKTt+l ++  n
  gi|320100895|ref|YP_004176487.1| 23 TLFYGVAGSGKTTMLMTIAGN 43
                                      77889***********99844 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00051      0.41     120     151 ..      11      42 ..       7      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00051
                             T2SSE 120 evlrkavrerglilvsGgTgsGKttllyallk 151
                                       +++ + +++  + l+ G  gsGKtt+l ++  
  gi|320100895|ref|YP_004176487.1|  11 QTIDSLIESSSTTLFYGVAGSGKTTMLMTIAG 42 
                                       5677788888999**************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 00:00:00.37
# Mc/sec: 1653.37
//
Query:       gi|320100896|ref|YP_004176488.1|  [L=170]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-33  115.9   6.8      9e-33  113.7   6.8    1.8  1  CarS-like     CDP-archaeol synthase
    4.2e-07   30.0   1.0    4.2e-07   30.0   1.0    2.1  2  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   6.8     1e-36     9e-33       6     175 .]       8     170 .]       1     170 [] 0.87

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1e-36
                         CarS-like   6 lksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilaldssg 82 
                                       +  i + lpa vanas vlv G   +d G+ ++dGr + G+ +t+ G+  Gv+   ++g   g++            
  gi|320100896|ref|YP_004176488.1|   8 VWLIKYYLPAMVANASPVLVKGRIAIDRGRLFIDGRPVFGNHKTWEGFTIGVVNAFITGSAIGVV---------LRD 75 
                                       3445677************************************************9999988887.........345 PP

                         CarS-like  83 svlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp....vkllpieliilivlitl 155
                                       + ++  +l+l  ++ ++lGd++G+fikrrl+i  Gkp +i+dql+f l++ +l        ++  +++++l +l+ l
  gi|320100896|ref|YP_004176488.1|  76 PWIQ--VLSLAAGVSSMLGDLAGAFIKRRLGIAPGKPLPIVDQLNFALATTILYIAlrveDVVGRMDFVALTLLLIL 150
                                       5555..466778999********************************9987766332322345579*********** PP

                         CarS-like 156 vlhlsaniiayklglkdvwy 175
                                       +lh+++n +ay lglkd w+
  gi|320100896|ref|YP_004176488.1| 151 ILHVATNSLAYLLGLKDTWW 170
                                       *******************9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   1.0   4.7e-11   4.2e-07     170     232 ..      49     105 ..      42     112 .. 0.91
   2 !    3.4   0.8    0.0062        56     113     155 ..     124     164 ..     109     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.7e-11
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGDLveSglKRafgi 232
                                        KT+eGf  G+v a++ g+++  vl +     +  + +lsl +++++++GDL    +KR++gi
  gi|320100896|ref|YP_004176488.1|  49 HKTWEGFTIGVVNAFITGSAIGVVLRDP----W--IQVLSLAAGVSSMLGDLAGAFIKRRLGI 105
                                       5*************************94....3..34689999******************98 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0062
                                       HHHHTHHHH.TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      CTP_transf_1 113 allyvvlllqslllienikeglllvllllalvvaaDigaYffG 155
                                        +ly++l  ++  ++ + +  +l++ll+l+l va+ + aY+ G
  gi|320100896|ref|YP_004176488.1| 124 TILYIAL--RVEDVVGRMDFVALTLLLILILHVATNSLAYLLG 164
                                       3334444..458888888888888999999999999****999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1443.71
//
Query:       gi|320100897|ref|YP_004176489.1|  [L=407]
Description: SufBD protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-45  153.0   1.0    1.8e-44  152.0   0.1    1.7  2  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.05   8.9e+02     186     205 ..      61      80 ..      60      83 .. 0.86
   2 !  152.0   0.1     1e-48   1.8e-44       2     218 .]     155     378 ..     154     378 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.05
                           UPF0051 186 gAtvGkideeqlfYLmsRGl 205
                                       +A+  ++de +l+ Lm R l
  gi|320100897|ref|YP_004176489.1|  61 AASYIQLDETALYRLMERVL 80 
                                       578889**********9966 PP

  == domain 2  score: 152.0 bits;  conditional E-value: 1e-48
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       q+ ++++ v+egae++++   +gc            gv+e++v +nA+l++++++ w++++++ +++++++++ a++
  gi|320100897|ref|YP_004176489.1| 155 QYAHNIVFVDEGAEAHVV---TGCavphgvregvhiGVSEFYVSRNARLTFTMMHAWADGMHVRPRTAVRVEEGAEY 228
                                       678***************...999999999999999*********************************99999999 PP

                           UPF0051  67 elttvslggkltrk.epsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgki 142
                                        ++++  +   +++ +p++el+  g++a l +++ ++g+   d+++ + ++g+++s++++s+ v++d+a++  r+ i
  gi|320100897|ref|YP_004176489.1| 229 VSYYIIYSPVASLQtYPRTELS-AGGKAYLASIVAGSGRGIYDQGSAAVLAGKGSSAEVVSRVVASDHAEVYARSSI 304
                                       9999999998665549999998.9***************************************************** PP

                           UPF0051 143 kvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                          +  ++t++h+e+  Llls ka +++iP +  ++  + +sH+A++G i+e+++ YLms+G++e+eA++++vrgf
  gi|320100897|ref|YP_004176489.1| 305 --DAYDAETRGHIECLGLLLSGKAMVSSIPVITSRKPGALLSHEAAIGMIAEKEIQYLMSKGFTEDEAKSVLVRGF 378
                                       ..6667*********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2976.75
//
Query:       gi|320100898|ref|YP_004176490.1|  [L=243]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-20   74.2   0.0      2e-20   73.7   0.0    1.2  1  ABC_tran     ABC transporter
    3.1e-11   43.7   0.6    5.9e-06   26.3   0.2    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    7.3e-08   32.1   0.0     0.0024   17.4   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0001   22.0   0.0    0.00016   21.3   0.0    1.2  1  AAA_27       AAA domain
    0.00024   20.8   0.0    0.00048   19.8   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0035   17.9   0.0     0.0051   17.3   0.0    1.2  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.078   12.5   0.0    2.0  2  AAA_25       AAA domain
      0.017   15.4   0.2       0.51   10.6   0.0    2.1  2  AAA_22       AAA domain
       0.02   14.8   0.1      0.036   14.0   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.03   14.0   0.0       0.25   11.0   0.0    2.1  2  AAA_30       AAA domain
      0.031   14.2   0.0      0.058   13.3   0.0    1.4  1  NACHT        NACHT domain
      0.052   13.3   0.0       0.18   11.5   0.0    1.7  2  AAA_15       AAA ATPase domain
      0.065   13.4   0.0       0.11   12.6   0.0    1.4  1  AAA_33       AAA domain
      0.067   13.6   0.1       0.13   12.6   0.0    1.5  2  AAA_16       AAA ATPase domain
       0.14   12.1   0.0       0.32   10.9   0.0    1.5  2  ATPase_2     ATPase domain predominantly from Archaea
       0.22   11.1   0.3       0.56    9.8   0.1    1.7  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.28    9.9   0.0       0.38    9.5   0.0    1.1  1  Adeno_IVa2   Adenovirus IVa2 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 !   73.7   0.0   1.9e-23     2e-20       1     136 [.      18     160 ..      18     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.9e-23
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       l++vsl++++ge+++++G+nG+GKStLl+ ++gl      +G+i + g+d+++  + e++r  i+  +q+p   +++
  gi|320100898|ref|YP_004176490.1|  18 LRDVSLTVQHGELHVVMGPNGSGKSTLLASIMGLPYLkvVSGKIYFGGRDITDlPPYERARLGIALAHQNPPEVKGV 94 
                                       689******************************9766559*************99***************9999999 PP

                                       BHHHH......HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx......xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren......esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++r+       +++ e +++ skl  ++ l ++ +      +SgG+k+r +l  +ll+ pkl +lDEp 
  gi|320100898|ref|YP_004176490.1|  95 KLRDVarfmleKYRCEDSAMFSKLLRVDpLLERDL---FLGFSGGEKKRAELFLSLLQSPKLAMLDEPD 160
                                       99999999988444444444444444432444444...59***************************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 !   15.9   0.0     8e-06    0.0084       2      19 ..      31      48 ..      30      85 .. 0.87
   2 !   26.3   0.2   5.6e-09   5.9e-06     237     297 ..     133     190 ..     113     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8e-06
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       v+ GpNgsGKS+LL  +
  gi|320100898|ref|YP_004176490.1| 31 HVVMGPNGSGKSTLLASI 48
                                      6899***********877 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 5.6e-09
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +S G k+ + l+++ll+ +   +l  +DEp++g + +   +++ ++++l+r+g+ vil+TH
  gi|320100898|ref|YP_004176490.1| 133 FSGGEKKRAELFLSLLQSP---KLAMLDEPDSGVDIESADSIAHVIDLLTRKGSSVILVTH 190
                                       699999999*******999...99************************************* PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.3e-06    0.0024      24      44 ..      28      48 ..      18      57 .. 0.85
   2 !   12.9   0.0     5e-05     0.053     137     212 ..     133     205 ..      92     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                       ++ +++GpNGSGKs ll +i
  gi|320100898|ref|YP_004176490.1| 28 GELHVVMGPNGSGKSTLLASI 48
                                      46789**************99 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5e-05
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH.HHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk.eksknaQfivislreemlekadklvgvt 212
                                       +SgGek+ + l L   +   +   l +lDe d+  D +    +a++++  ++k + +i ++++  +++k +++ +v 
  gi|320100898|ref|YP_004176490.1| 133 FSGGEKKRAELFLS--L--LQSPKLAMLDEPDSGVDIESADSIAHVIDlLTRKGSSVILVTHTGLITNKLSRIDRVH 205
                                       69999998876554..3..34445899*********************445556********999999888887765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.5e-07   0.00016      19      50 ..      21      52 ..      16      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +++  ++ +lh+++GpN +GKst+l++i  l 
  gi|320100898|ref|YP_004176490.1| 21 VSLTVQHGELHVVMGPNGSGKSTLLASIMGLP 52
                                      455556899*****************998775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.5e-07   0.00048      17      42 ..      23      48 ..      16      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.5e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAi 42
                                      ++++  + ++++Gp+GsGKSTll +i
  gi|320100898|ref|YP_004176490.1| 23 LTVQHGELHVVMGPNGSGKSTLLASI 48
                                      5566445999************9666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.8e-06    0.0051      20      40 ..      29      49 ..      16      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.8e-06
                            AAA_23 20 gltlItGpNGaGKTTildAik 40
                                       l ++ GpNG+GK+T+l  i 
  gi|320100898|ref|YP_004176490.1| 29 ELHVVMGPNGSGKSTLLASIM 49
                                      477999***********9985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.4e-05     0.078      31      54 ..      26      49 ..      21      78 .. 0.86
   2 ?    0.2   0.0      0.43   4.6e+02     169     190 ..     171     192 ..     153     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.4e-05
                            AAA_25 31 pagelallaGapgtGKttlaldla 54
                                        gel++++G+ g+GK+tl+ +++
  gi|320100898|ref|YP_004176490.1| 26 QHGELHVVMGPNGSGKSTLLASIM 49
                                      5799***************99875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.43
                            AAA_25 169 vealeriarrtgaavllvhHvg 190
                                       ++++ ++ +r+g  v+lv H+g
  gi|320100898|ref|YP_004176490.1| 171 IAHVIDLLTRKGSSVILVTHTG 192
                                       44455555789999******97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00048      0.51       6      24 ..      29      47 ..      24      53 .. 0.84
   2 ?    2.9   0.0      0.12   1.2e+02      92     133 ..     151     193 ..      91     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                            AAA_22  6 gilvvtGesGtGKTtllrr 24
                                       + vv+G+ G+GK+tll+ 
  gi|320100898|ref|YP_004176490.1| 29 ELHVVMGPNGSGKSTLLAS 47
                                      5679************986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                            AAA_22  92 ielliiDEaqh.lr..seealeeLrsllnlsrkgvqliLvGtpel 133
                                       ++l ++DE +  ++  s++ + ++ +ll   rkg ++iLv +++l
  gi|320100898|ref|YP_004176490.1| 151 PKLAMLDEPDSgVDieSADSIAHVIDLLT--RKGSSVILVTHTGL 193
                                       47889999999998988999999999999..********988776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.4e-05     0.036      91     121 ..      19      50 ..       2      64 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       ++++  +++ ++ v++G+ G GKStL+ ++++
  gi|320100898|ref|YP_004176490.1|  19 RDVSLTVQHgELHVVMGPNGSGKSTLLASIMG 50 
                                       555555555599***************99987 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   0.00024      0.25      16      38 ..      26      48 ..      20      52 .. 0.82
   2 ?    0.3   0.0      0.48     5e+02      35      63 ..     171     199 ..     150     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                            AAA_30 16 sgdrvavltGpAGtGKttalkal 38
                                      ++  ++v+ Gp G+GK+t+l+++
  gi|320100898|ref|YP_004176490.1| 26 QHGELHVVMGPNGSGKSTLLASI 48
                                      444699**************987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                            AAA_30  35 lkalreaweaaggrviglAptgkaAkvLa 63 
                                       ++++ ++++++g +vi++++tg   ++L+
  gi|320100898|ref|YP_004176490.1| 171 IAHVIDLLTRKGSSVILVTHTGLITNKLS 199
                                       56777778888888888888887777776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.5e-05     0.058       3      21 ..      31      49 ..      29      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-05
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                       ++ G++GsGK+tLl++++
  gi|320100898|ref|YP_004176490.1| 31 HVVMGPNGSGKSTLLASIM 49
                                      5899*************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.18      16      43 ..      20      48 ..      17      52 .. 0.79
   2 ?   -0.9   0.0      0.97     1e+03     324     367 ..     151     193 ..     143     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsileal 43
                                      dv++ ++   l v+ G+N+sGKS++l  +
  gi|320100898|ref|YP_004176490.1| 20 DVSLTVQHGeLHVVMGPNGSGKSTLLASI 48
                                      555555555599*************9877 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.97
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       +++ +++EP+    ++   ++++ +  l ++++  vi+ TH+  
  gi|320100898|ref|YP_004176490.1| 151 PKLAMLDEPDSGVDIESADSIAHVIDLLTRKGS-SVILVTHTGL 193
                                       678889999999999999999999999999998.9******865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001      0.11       1      22 [.      30      50 ..      30      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            AAA_33  1 lvllvGlpGsGKstlaerllkk 22
                                      l ++ G++GsGKstl+ +++  
  gi|320100898|ref|YP_004176490.1| 30 LHVVMGPNGSGKSTLLASIM-G 50
                                      57899**********99988.4 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012      0.13      22      45 ..      28      49 ..      15      87 .. 0.85
   2 ?   -2.4   0.0       5.2   5.5e+03     120     135 ..     168     183 ..     106     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                            AAA_16 22 grpelvllsGesGvGKsslvrell 45
                                      g  el ++ G+ G+GKs+l+ +++
  gi|320100898|ref|YP_004176490.1| 28 G--ELHVVMGPNGSGKSTLLASIM 49
                                      3..6778*************9876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.2
                            AAA_16 120 lellkrllallsrder 135
                                       ++ +++ ++ll+r+++
  gi|320100898|ref|YP_004176490.1| 168 ADSIAHVIDLLTRKGS 183
                                       3444455555555444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00031      0.32      20      41 ..      28      49 ..      19      64 .. 0.85
   2 ?   -2.3   0.0       3.3   3.5e+03     104     123 ..     169     188 ..     108     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeii 41
                                       e  ++ Gp gsGK++Ll  i+
  gi|320100898|ref|YP_004176490.1| 28 GELHVVMGPNGSGKSTLLASIM 49
                                      6789**************9876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.3
                          ATPase_2 104 kaielllekikkkgkkiiii 123
                                        +i+ +++ +++kg  +i++
  gi|320100898|ref|YP_004176490.1| 169 DSIAHVIDLLTRKGSSVILV 188
                                       35778888888888877775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00053      0.56       3      21 ..      31      49 ..      29      58 .. 0.88
   2 ?   -1.8   0.0       1.9     2e+03      72      95 ..     173     195 ..     166     209 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00053
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                       v+ G+ GsGK+tLl +++
  gi|320100898|ref|YP_004176490.1| 31 HVVMGPNGSGKSTLLASIM 49
                                      6899***********9986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                                       HHHHHHHHHTT-SEEEEEECTTTT CS
                              cobW  72 elealeereerldviliEttGlae 95 
                                       ++ +l++r+   +vil+  tGl +
  gi|320100898|ref|YP_004176490.1| 173 HVIDLLTRK-GSSVILVTHTGLIT 195
                                       555566666.57888888888654 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00036      0.38      90     142 ..      31      83 ..      20      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                        Adeno_IVa2  90 GviyGPtGsGksqllrnlissklisPiPetvifitPekdmipPeelkaWelql 142
                                        v+ GP GsGks ll +++    ++ +   ++f   +   +pP e+    + l
  gi|320100898|ref|YP_004176490.1|  31 HVVMGPNGSGKSTLLASIMGLPYLKVVSGKIYFGGRDITDLPPYERARLGIAL 83 
                                       699****************9999999999999999999999998887665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1680.88
//
Query:       gi|320100899|ref|YP_004176491.1|  [L=38]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       104  (0.00580066); expected 358.6 (0.02)
Passed bias filter:                      103  (0.00574488); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 295.04
//
Query:       gi|320100900|ref|YP_004176492.1|  [L=271]
Description: pyrroline-5-carboxylate reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-31  106.1   0.0    1.7e-30  105.3   0.0    1.4  1  P5CR_dimer      Pyrroline-5-carboxylate reductase dimerisatio
    1.1e-18   67.6   0.1    1.8e-18   66.9   0.1    1.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0001   22.0   0.2    0.00031   20.4   0.2    1.7  1  ApbA            Ketopantoate reductase PanE/ApbA
    0.00058   19.9   1.3      0.028   14.4   1.0    2.5  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00059   19.3   0.0    0.00093   18.6   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0015   18.1   0.0     0.0023   17.5   0.0    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0063   16.6   0.0      0.012   15.7   0.0    1.5  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.023   14.9   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.014   15.5   0.0      0.028   14.5   0.0    1.5  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
      0.049   13.6   0.0       0.12   12.3   0.0    1.7  1  ADH_zinc_N      Zinc-binding dehydrogenase
      0.065   13.5   0.0       0.12   12.6   0.0    1.4  1  TrkA_N          TrkA-N domain
       0.12   12.3   0.0       0.22   11.4   0.0    1.4  1  KR              KR domain


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 !  105.3   0.0   1.1e-33   1.7e-30       1     102 [.     153     256 ..     153     257 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 1.1e-33
                                       CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS..HHHHHHHH--TTSHHHH CS
                        P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese..paelrdkvtspgGtTia 75 
                                       E++lda+tal+GsgpA+++ +++al+ +gv  Gl+r+ A + +  +++G+a+ l++++  pa lrd+vt+p+GtTi+
  gi|320100900|ref|YP_004176492.1| 153 EELLDAWTALAGSGPAFIAEIVDALVMSGVLVGLPRDLACDAVLDVLEGTARFLRNNDihPAILRDEVTTPAGTTIR 229
                                       899**************************************************9977789***************** PP

                                       HHHHHHHTTHHHHHHHHHHHHHHHHHH CS
                        P5CR_dimer  76 glkeleegglraavieaveaaakrske 102
                                       gl ++e++g++aa+++++ea++krs e
  gi|320100900|ref|YP_004176492.1| 230 GLITMESEGVKAALMKTIEASYKRSME 256
                                       ************************987 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 !   66.9   0.1   1.2e-21   1.8e-18       1      97 []       2      93 ..       2      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.2e-21
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      +i+++G+G++g a+++ l+++g   ++iv a+ r  e++   a++lg+ vt  dn  a++++dv++++vkp++++++++
  gi|320100900|ref|YP_004176492.1|  2 RIAVLGSGRIGTAVVKSLISCG--YSDIV-ATGRRDETLSN-AKSLGAHVTR-DNDLAVKSSDVIFVTVKPYHFPALAK 75
                                      79********************..77777.98999998865.588899***9.************************** PP

                                      HCGHHHHTTSEEEEESSS CS
                     F420_oxidored 80 elakdalkgklvisvlag 97
                                      ++ ++++ gk+++s +ag
  gi|320100900|ref|YP_004176492.1| 76 QVNRSSWVGKIIVSFMAG 93
                                      ***************997 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   2.1e-07   0.00031       1     120 [.       3     108 ..       3     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                                       EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE- CS
                              ApbA   1 iailGaGaiGsllaakLak.agadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivt 75 
                                       ia+lG+G iG+ +  +L      d++  +r++  l + k+ G ++t+++       + a+ ++        d+++vt
  gi|320100900|ref|YP_004176492.1|   3 IAVLGSGRIGTAVVKSLIScGYSDIVATGRRDeTLSNAKSLGAHVTRDN-------DLAVKSS--------DVIFVT 64 
                                       89***************9978888********99999999999999999.......6666666........****** PP

                                       SSGGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEE CS
                              ApbA  76 vKayqteealeeikplldpntvvlllqNGlgheeelrealpkprv 120
                                       vK y+  + ++++++      +++++  G++   +++ ++++++v
  gi|320100900|ref|YP_004176492.1|  65 VKPYHFPALAKQVNRSSWVGKIIVSFMAGVRIN-TIKLIVGNSHV 108
                                       ************999999999999999998764.45555555555 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.0   1.9e-05     0.028       2     115 ..       3     103 ..       2     132 .. 0.76
   2 ?   -2.4   0.0       2.8   4.2e+03     119     141 ..     153     175 ..     106     183 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                       EEEE--SHHHHHHHHHHHTTT.--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE-- CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaeng.hevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvv 77 
                                       iavlG+G  Gta+ k+l + g ++++  +r++e       +  n k L      ++++  +dl  a+k +d+i++ v
  gi|320100900|ref|YP_004176492.1|   3 IAVLGSGRIGTAVVKSLISCGySDIVATGRRDE-------TLSNAKSL-----GAHVTRDNDL--AVKSSDVIFVTV 65 
                                       999**********99999999344444444433.......33455555.....4556555555..899********* PP

                                       -HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHH CS
                    NAD_Gly3P_dh_N  78 PsqalrevlkklkgllkkkailvsliKGieegtlklls 115
                                          ++   +k+++      +i+vs + G+  +t kl+ 
  gi|320100900|ref|YP_004176492.1|  66 KPYHFPALAKQVNRSSWVGKIIVSFMAGVRINTIKLIV 103
                                       *****************************999999984 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                                       HHHH-S--EEEEESS--HHHHHT CS
                    NAD_Gly3P_dh_N 119 eeelkeekvavlsGpslAeEvak 141
                                       ee l+  +    sGp +  E+++
  gi|320100900|ref|YP_004176492.1| 153 EELLDAWTALAGSGPAFIAEIVD 175
                                       33333333334467777777765 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 !   18.6   0.0   6.2e-07   0.00093      38      99 ..       2      65 ..       1      70 [. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.2e-07
                                      EEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeeelgvelv.sleellaesDivslhl 99
                                      +++++G GrIG+av k l + g  +++a+ r+ ++ +++++lg++++ + + ++++sD++++++
  gi|320100900|ref|YP_004176492.1|  2 RIAVLGSGRIGTAVVKSLISCGYsDIVATGRRDETLSNAKSLGAHVTrDNDLAVKSSDVIFVTV 65
                                      789*******************97788888887776799*****8886888899******9987 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.5e-06    0.0023       6      99 ..       2      96 ..       1     113 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                      -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHH.HHHT-SEEEE-S-HHHHHHHHHHHTGG CS
                              IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvae.avkkadvvmiliPDelqkevyeeeiep 83
                                      +iav+G G  G a  + l   g   +v+  + ++++++Ak+ g +v++ ++ avk++dv+++ +   +  ++  ++++ 
  gi|320100900|ref|YP_004176492.1|  2 RIAVLGSGRIGTAVVKSLISCGYSDIVATGRRDETLSNAKSLGAHVTRDNDlAVKSSDVIFVTVKPYHFPALA-KQVNR 79
                                      69*********************99999999999************988874789999999987655555555.44444 PP

                                      G--TT-.EEEESSSHHH CS
                              IlvN 84 nlkegk.alafahGfni 99
                                      +   gk +++f  G  i
  gi|320100900|ref|YP_004176492.1| 80 SSWVGKiIVSFMAGVRI 96
                                      43333315566666665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.7e-06     0.012      14      84 ..       2      66 ..       1      85 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.7e-06
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisata 84
                                      ++ ++G G++++ v+k L++ g+ ++v ++R  e  ++ a++l+++   +++ ++l   ++++dv+++ ++
  gi|320100900|ref|YP_004176492.1|  2 RIAVLGSGRIGTAVVKSLISCGYSDIVATGRRDETLSN-AKSLGAH---VTRDNDLA--VKSSDVIFVTVK 66
                                      789****************************8776655.5777555...66656665..899999998766 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.5e-05     0.023       1      65 [.       2      67 ..       2     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                      EEEEE--SHHHHHHHHHHHHTT-E.EEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSS CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagyk.vavynrtkekveelvaegakaaesieelvasldvvitmvka 65
                                      +i+++G G +G+  ++ l++ gy+ +++  r+ e + ++ + ga+++ +   +v+s dv+++ vk 
  gi|320100900|ref|YP_004176492.1|  2 RIAVLGSGRIGTAVVKSLISCGYSdIVATGRRDETLSNAKSLGAHVTRDNDLAVKSSDVIFVTVKP 67
                                      59********************97255566899999999999*********************984 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.9e-05     0.028       1      71 [.       1      61 [.       1      75 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEE CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvl 71
                                      +++av+G  Gr+G++vvk + +     +va   r+e         +l + ++lg  vt d + +++++dv+
  gi|320100900|ref|YP_004176492.1|  1 MRIAVLGS-GRIGTAVVKSLISCGYSDIVATGRRDE---------TLSNAKSLGAHVTRDNDLAVKSSDVI 61
                                      89*****8.*************99999999988887.........56667788888888888888888876 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.1e-05      0.12       2      41 ..      11      51 ..      11      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-05
                                      HHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEET CS
                        ADH_zinc_N  2 vGlaavqlAkalGa.eviavdsseeklelakklGadeviny 41
                                      +G+a+v+ +  +G   ++a+ + +e l  ak+lGa+++ ++
  gi|320100900|ref|YP_004176492.1| 11 IGTAVVKSLISCGYsDIVATGRRDETLSNAKSLGAHVTRDN 51
                                      79**********************************99887 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     8e-05      0.12       1      44 [.       3      47 ..       3      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8e-05
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEE CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglev 44
                                      i+++G Gr+G+++++ L + g++d+v+  +++e++ +++  g++v
  gi|320100900|ref|YP_004176492.1|  3 IAVLGSGRIGTAVVKSLIScGYSDIVATGRRDETLSNAKSLGAHV 47
                                      79*****************99999****99999999999998887 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.22       8      51 ..       7      43 ..       3      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      TTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT CS
                                KR  8 GlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal 51
                                      G G +G+++++ l++ g + +v ++R+ ++ +++k+       l
  gi|320100900|ref|YP_004176492.1|  7 GSGRIGTAVVKSLISCGYSDIVATGRRDETLSNAKS-------L 43
                                      78*************************544444332.......2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        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: 1955.24
//
Query:       gi|320100901|ref|YP_004176493.1|  [L=884]
Description: Lhr family ATP dependent helicase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-51  175.4   0.0    1.9e-51  174.6   0.0    1.4  1  DEAD_assoc  DEAD/H associated
    1.7e-27   96.3   0.0      1e-26   93.8   0.0    2.2  2  DEAD        DEAD/DEAH box helicase
    5.9e-16   58.8   0.7    1.8e-15   57.2   0.7    1.9  1  Helicase_C  Helicase conserved C-terminal domain
      5e-10   39.6   0.0      1e-08   35.4   0.0    2.3  2  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.02   15.3   3.3          5    7.6   0.5    3.6  2  AAA         ATPase family associated with various cellular ac
      0.093   13.1   0.0       0.98    9.8   0.0    2.5  2  AAA_16      AAA ATPase domain
        0.2   10.3   0.0          1    8.0   0.0    2.1  1  SNF2_N      SNF2 family N-terminal 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 !  174.6   0.0   7.5e-55   1.9e-51       1     191 []     654     842 ..     654     842 .. 0.96

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 7.5e-55
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +P+d+ +l+E +++ + +++++vhs fGr++n+ala+l+a+ + +r+g++v+++++D+g++l++p + r +    e+
  gi|320100901|ref|YP_004176493.1| 654 VPSDELILIEIYDEPT-RRNIIVHSIFGRKANDALARLYAYIVGQRLGVNVKLTVTDNGFMLTVPGHPRGE--WLEW 727
                                       8***********7655.99*******************************************996555643..4479 PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavre 154
                                       ++++  +++ e+le+ + +++l+krrFr+ A r+++l+rry++ +k+ ++ +++a++Ll++++e+p+fp+l+e++re
  gi|320100901|ref|YP_004176493.1| 728 FRTIPVEKAWEILEKVVRRTDLLKRRFRHTAVRSFMLLRRYRDTEKSINKLQVNAEELLKAVEEIPGFPVLKETYRE 804
                                       ***************************************************************************** PP

                        DEAD_assoc 155 vledqlDlerlaellrriaageirvveve.tprpSpfA 191
                                       +l d++ ++++ e+l+++++gei+v+ +  ++ pSpfA
  gi|320100901|ref|YP_004176493.1| 805 ILMDYMHIDEAVEVLEKVRSGEIKVALMGpVDVPSPFA 842
                                       ***************************999*******9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0     4e-30     1e-26       1     170 [.      38     223 ..      38     229 .. 0.86
   2 ?   -0.8   0.0      0.45   1.2e+03      45      72 ..     287     314 ..     257     359 .. 0.57

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 4e-30
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS.....TTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet.....kgktgpkalivePtreLaeqtlnnlkkfkk 72 
                                       t++Q+++ipl+ +g +vlv+ +TG+GKTla ++ +++ +y++     +  +g  +++v+P+r+L +++ +nl +  +
  gi|320100901|ref|YP_004176493.1|  38 TPVQRRTIPLVKQGCNVLVSSPTGTGKTLAVFLGIIDDIYRQyeetgRMPDGVYVVYVSPLRALNNDMRKNLLEPVE 114
                                       79***************************************9999999999*************************9 PP

                                       TST............SEEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHH CS
                                       xxx............xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                              DEAD  73 yid............lrvlliiggvaardqlskldng.vdivvgtpgrlddllstgkln..lsqvrflVlDEadrll 134
                                        i             ++v ++ +++++ +++++++++ ++i+++tp+ l+  l+  +++  l + r+l++DE+++l 
  gi|320100901|ref|YP_004176493.1| 115 GIVeearsmglelprIKV-AVRTSDSTPSEKQRMNRDpPHILITTPESLAIALNAPRFRerLANARILIVDEVHELA 190
                                       744466677777744444.3455778888888885448*************9966666556**************** PP

                                       HTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 135 dqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +++++ ++   +++l++   + +lq   i lSAT+ 
  gi|320100901|ref|YP_004176493.1| 191 SSKRGSHLAVSVERLEHLAGR-RLQ--RIGLSATIA 223
                                       ***************766554.345..9******96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.45
                                       STS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  45 ktgpkalivePtreLaeqtlnnlkkfkk 72 
                                       k++  +li + tr+ +e ++ +l+k+++
  gi|320100901|ref|YP_004176493.1| 287 KRHRTTLIFTNTRSSTERVVFKLRKIFE 314
                                       3333455555555555555555555555 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 !   57.2   0.7   7.2e-19   1.8e-15       6     108 ..     278     389 ..     273     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 7.2e-19
                                       HHHHH.HHTTTTSEEEEEESSHHHHHH.....HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEE CS
                        Helicase_C   6 llell.kleeeggkilifvntidrlek.....vklllekk....gikvavlhgelpqnereeileqfnkgesdvLia 72 
                                       ++++l    ++++++lif+nt+++ e+      k++ ek+       + ++h++l+ + r+ei ++ ++ge + +++
  gi|320100901|ref|YP_004176493.1| 278 IYDELrRIIKRHRTTLIFTNTRSSTERvvfklRKIF-EKEgvidIDDIEAHHSSLSRDVRIEIENKLKNGELRAIVS 353
                                       555555455899999********7776666644555.6665775356778*************************** PP

                                       SGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  73 tdvaerGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                       ++ +e Gidi  +++V+ ++ p++vt++ qr+GR+g
  gi|320100901|ref|YP_004176493.1| 354 STSLELGIDIGYIDVVVLLSSPKSVTRLLQRVGRAG 389
                                       ***********************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0     4e-12     1e-08      23     169 ..      50     222 ..      21     224 .. 0.77
   2 ?    1.0   0.4      0.14   3.7e+02      83     147 ..     272     332 ..     251     356 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 4e-12
                                       TTSEEEEEESTTSTHHHHH.HHHHHHH-S............-EEEEESSHHHHHHHHHHGGGGTGG........... CS
                            ResIII  23 rdkrglikmaTGtGKTlva.aklierllkkgkee.......kflflvprkslleqtleefkkflseayke....... 84 
                                       +  ++l+  +TGtGKTl   + +i+ ++++++e         ++ + p ++l + +++++ +  +  ++e       
  gi|320100901|ref|YP_004176493.1|  50 QGCNVLVSSPTGTGKTLAVfLGIIDDIYRQYEETgrmpdgvYVVYVSPLRALNNDMRKNLLEPVEGIVEEarsmgle 126
                                       5557899*********98889********98888******999**************99977777766666666777 PP

                                       .......GEEEESSS-B--............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T. CS
                            ResIII  85 .......igkkvsgdkkka.....kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk. 148
                                              +    ++d   +     ++ +++  +il+tt +sl  ++   +  + + +  +  ++i+DE+H l+++k 
  gi|320100901|ref|YP_004176493.1| 127 lprikvaV---RTSD---StpsekQRMNRDPPHILITTPESLAIAL---NAPRFRERLANARILIVDEVHELASSKr 194
                                       76542221...2222...22335556778889**************...7777777778888************866 PP

                                       ......TTHHHHHT-..--SEEEEEESS- CS
                            ResIII 149 ......swreilekf..keavllglTATp 169
                                             s+++ le++  ++  ++gl+AT+
  gi|320100901|ref|YP_004176493.1| 195 gshlavSVER-LEHLagRRLQRIGLSATI 222
                                       6555555555.5555456699*******7 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                                       ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEE..TGGGTTS. CS
                            ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiD..EaHrlgak 147
                                       +ei++ + ++ +++  ++++ + +++t++ s +++       + ++  +++ vi iD  EaH+++ +
  gi|320100901|ref|YP_004176493.1| 272 EEINEAIYDELRRI--IKRHRTTLIFTNTRSSTERV----VFKLRKIFEKEGVIDIDdiEAHHSSLS 332
                                       33444444444444..58889999999999988888....99999999999999999899***9875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.5    0.0019         5       2      76 ..      55     195 ..      54     215 .. 0.59
   2 ?    4.0   0.1     0.025        65      46      90 ..     305     344 ..     269     393 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                                       EEESSTTSSHHHHH.HHHHHHH............THEEEEEETTTCSSS............................ CS
                               AAA   2 llyGppGtGKTlla.kavakel............gvefleisgsellsk............................ 37 
                                       l++ p GtGKTl++   ++ ++            gv+++ +s  + l++                            
  gi|320100901|ref|YP_004176493.1|  55 LVSSPTGTGKTLAVfLGIIDDIyrqyeetgrmpdGVYVVYVSPLRALNNdmrknllepvegiveearsmglelprik 131
                                       67777777777765234555543333333333333556666666666444666666666666666666666666666 PP

                                       ......................STTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTT CS
                               AAA  38 ......................yvgesekkirelfkeakeka...kpsilfiDEidalaksrsg 76 
                                                             ++  ++++++  +++ +  +   +  il++DE+++la+s++g
  gi|320100901|ref|YP_004176493.1| 132 vavrtsdstpsekqrmnrdpphILITTPESLAIALNAPRFRErlaNARILIVDEVHELASSKRG 195
                                       6666666666677777777777555555555555555332223445589999999999998833 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                               AAA  46 irelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLl 90 
                                       +   ++++ ek    ++ iD+i+a ++s    +++++ ++ n+L 
  gi|320100901|ref|YP_004176493.1| 305 VVFKLRKIFEK--EGVIDIDDIEAHHSSL---SRDVRIEIENKLK 344
                                       33333334444..49**********9999...8888888888885 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00038      0.98      23     152 ..      50     194 ..      44     218 .. 0.56
   2 ?   -0.4   0.0       0.5   1.3e+03      43     143 ..     281     405 ..     267     419 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00038
                            AAA_16  23 rpelvllsGesGvGKsslv.....rellralekd.....ggiflrgkcdqlesaipysalaqalareellrqlldea 89 
                                       ++++vl+s + G+GK+  v     + ++r++e++     g+++++               ++al +   +r+ l e+
  gi|320100901|ref|YP_004176493.1|  50 QGCNVLVSSPTGTGKTLAVflgiiDDIYRQYEETgrmpdGVYVVYVS------------PLRAL-N-NDMRKNLLEP 112
                                       4489*************996555566666666664444333333332............33444.3.3333333333 PP

                            AAA_16  90 esaeleawrekleeala.............avpelagaea...............srllellkrllallsrderplv 138
                                        +  +e++r   +e  +             +        +               ++l+ +l++   + +r +   +
  gi|320100901|ref|YP_004176493.1| 113 VEGIVEEARSMGLELPRikvavrtsdstpsE--------KqrmnrdpphilittpESLAIALNAPR-FRERLANARI 180
                                       3334444444333333344444333333330........234555556666888877777777666.3333344579 PP

                            AAA_16 139 lvlDdlqwadeasl 152
                                       l++D+++ + ++ +
  gi|320100901|ref|YP_004176493.1| 181 LIVDEVHELASSKR 194
                                       *****998887554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.5
                            AAA_16  43 ellralekdggiflrgkcdqlesaipy..salaqalareellr..qlldeaesaeleawrekleeala......... 106
                                       el+r +++++  ++ ++++++   +++    l +++++e+++   +++++  s++ ++ r ++e  l+         
  gi|320100901|ref|YP_004176493.1| 281 ELRRIIKRHRTTLIFTNTRSS---TERvvFKLRKIFEKEGVIDidDIEAH-HSSLSRDVRIEIENKLKngelraivs 353
                                       555555555544455555555...22211124444444444330033333.33355555666666666665555444 PP

                            AAA_16 107 .......avpelagaea................srllellkrllallsrderplvlvlDd 143
                                              +                         +rll+ + r+   ++++++  v+v+D 
  gi|320100901|ref|YP_004176493.1| 354 stslelgI--------DigyidvvvllsspksvTRLLQRVGRAGHHIRETSKGRVIVVDR 405
                                       33333330........14444444444444445788888888886666667788888885 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00039         1     148     201 ..     150     201 ..      29     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00039
                                       ----EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 148 adydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavs 201
                                          +++itt + l+   + +  r+ l + +   +++DE h l +s++  + avs
  gi|320100901|ref|YP_004176493.1| 150 DPPHILITTPESLAIALNAPRFRERLANAR--ILIVDEVHELASSKRGSHLAVS 201
                                       34589************9999999998765..699**********876666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (884 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.43
# Mc/sec: 6183.64
//
Query:       gi|320100902|ref|YP_004176494.1|  [L=464]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-19   69.7   0.6    3.1e-19   69.7   0.6    2.0  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    6.5e-17   62.2   0.0    9.4e-17   61.7   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.3e-13   51.2   0.0    1.8e-13   50.6   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    7.1e-06   25.6   0.0     0.0029   17.1   0.0    2.5  3  Glyco_transf_21  Glycosyl transferase family 21
     0.0004   20.9   0.0    0.00081   19.9   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.13   13.6   0.0       0.23   12.8   0.0    1.3  1  RNR_inhib        Ribonucleotide reductase inhibitor


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 !   69.7   0.6     1e-22   3.1e-19       1     196 [.     130     339 ..     130     345 .. 0.79
   2 ?   -2.3   0.7       1.2   3.6e+03     156     186 ..     412     443 ..     360     456 .. 0.41

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 1e-22
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsg 76 
                                       +++++D D +l+   l++++  l+ +++va+v g   + n  + l+e   + ++  +  + + r+ +g  v+  G g
  gi|320100902|ref|YP_004176494.1| 130 YVYVVDVDAMLDKCLLEKAIGVLEaNGNVAAVVGRWEPLNLDTRLSEALGYSMKFIIDAIYRGRSCMGLSVFPLGTG 206
                                       799*********************669*************************98777788888889999******** PP

                   Glyco_trans_2_3  77 aflrrsalqevg.gwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc......el 146
                                       +++r+++l+ +  gwd   + + +D+++g r++ +G+ v +++e +v+ + p+t+ra + Q +RwayG+        
  gi|320100902|ref|YP_004176494.1| 207 TLFRARVLKGILkGWD--QERIQDDMEIGARMMYHGLGVKYIDECAVYVENPSTYRALRIQQSRWAYGAtdvlvtR- 280
                                       *********7777***..9*************************************************96544330. PP

                   Glyco_trans_2_3 147 eklil........lvrllgylgsllwsalplhl.allllfsllalalvlllllllaall 196
                                         +il        ++  l++l ++++ +l+++  ++l ++ +++ + vl+ +++l+ ll
  gi|320100902|ref|YP_004176494.1| 281 LSHILrskqgflgKMEALAFLSQYIVPSLVFLGsLVLAVQVVVRPVDVLWEYAYLLLLL 339
                                       22222455555555555577777777665544325666666666444443333333332 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                   Glyco_trans_2_3 156 lgylgsllwsalplhl.allllfsllalalvl 186
                                       l+ ++ l+++a++ +  +l l+ + + + l+l
  gi|320100902|ref|YP_004176494.1| 412 LRAPWELVFAAFFTATgLLGLTRGAVVTGLWL 443
                                       23334444444332221222333333322222 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 !   61.7   0.0   3.2e-20   9.4e-17       4     230 .]      44     272 ..      41     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.2e-20
                   Glyco_tranf_2_3   4 lavlVptfneed.vlgevlesllaqeyprvevvvvv.desdaetl..evaeelaaalpdvrvrvvvnarnlgstgks 76 
                                       +++++p+ +e+  +l++ ++ +      ++e++vv  d +d + +  e++   + + ++v v++v+++   g   + 
  gi|320100902|ref|YP_004176494.1|  44 VSFIIPVRREPIeYLERAVNYIHGLGVEDYEIIVVSdDDEDVGEVlfERLV--EWRRKGVNVWLVRRSIPEG--YRT 116
                                       899****9998778888999999988899******9644554433134443..45777889**998876445..444 PP

                   Glyco_tranf_2_3  77 ralnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvflln.rstlvsal.galefaerhlrfla 150
                                        a+n +l   ++d+v +vD D+ +++++l+++  ++ +  +v+av ++ + ln +++l  al + ++f ++ +++ +
  gi|320100902|ref|YP_004176494.1| 117 GAVNTGLWLSRGDYVYVVDVDAMLDKCLLEKAIGVLeANGNVAAVVGRWEPLNlDTRLSEALgYSMKFIIDAIYRGR 193
                                       56689999****************************75557877777766665266666666777799999995444 PP

                   Glyco_tranf_2_3 151 arralgvltlnGsgslirrevlkele.gldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnR 226
                                           l+ +++ G+g+l+r++vlk +  g+d    + dD e+g r++ +g  ++y  + av+ + ps+  a++ q  R
  gi|320100902|ref|YP_004176494.1| 194 SCMGLS-VFPLGTGTLFRARVLKGILkGWDQ-ERIQDDMEIGARMMYHGLGVKYIDECAVYVENPSTYRALRIQQSR 268
                                       444444.6679**************867999.********************************************* PP

                   Glyco_tranf_2_3 227 wvyg 230
                                       w+yg
  gi|320100902|ref|YP_004176494.1| 269 WAYG 272
                                       **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 !   50.6   0.0     6e-17   1.8e-13       1     167 [.      45     215 ..      45     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 6e-17
                                       EEEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH...C-TTEEEEEESSS-.HHHHHHH CS
                   Glycos_transf_2   1 svviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelak...edprvrvirreenv.Gkagaln 72 
                                       s +ip+  e  ++l+++++ +      +d+eiivv D ++D  + + e+l++   ++ +v ++rr+  +    ga+n
  gi|320100902|ref|YP_004176494.1|  45 SFIIPVRREpIEYLERAVNYIHGL-GVEDYEIIVVSDDDEDVGEVLFERLVEwrrKGVNVWLVRRSIPEgYRTGAVN 120
                                       78*****************99999.****************************999999999*******66789*** PP

                                       HHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCC CS
                   Glycos_transf_2  73 aglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkg 149
                                       +gl  ++gdy+ ++D D   d+  lek ++ le++g+ +++++r      +++ + +++++ + ++    r rs  g
  gi|320100902|ref|YP_004176494.1| 121 TGLWLSRGDYVYVVDVDAMLDKCLLEKAIGVLEANGNVAAVVGRWEPLNLDTRLSEALGYSMKFIIDAIYRGRSCMG 197
                                       ************************************************9999*999**999999999999******* PP

                                       CSTTCSTCCCEEEEHHHH CS
                   Glycos_transf_2 150 nlsfeigsaallrreale 167
                                        + f  g+ +l+r ++l+
  gi|320100902|ref|YP_004176494.1| 198 LSVFPLGTGTLFRARVLK 215
                                       ************999986 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 !    6.2   0.0    0.0022       6.5       9      56 ..      51      98 ..      43     117 .. 0.81
   2 !   17.1   0.0   9.8e-07    0.0029      21     172 ..     118     270 ..     100     271 .. 0.81
   3 ?   -4.1   0.0       3.1   9.3e+03      62      84 ..     277     300 ..     277     310 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0022
                   Glyco_transf_21  9 sgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaale 56
                                       ++p ++  + +n +++l    y+++v+sD+d  v +  +e+l++  +
  gi|320100902|ref|YP_004176494.1| 51 RREPIEYLERAVNYIHGLGVEDYEIIVVSDDDEDVGEVLFERLVEWRR 98
                                      466777778899********************9999999999986444 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9.8e-07
                   Glyco_transf_21  21 nllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntl...agvlqa. 93 
                                       +++++l   + d++ + D d+++++  Le+  + le    g V +++   ++ +l ++l  a+ + +     ++++ 
  gi|320100902|ref|YP_004176494.1| 118 AVNTGLWLSRGDYVYVVDVDAMLDKCLLEKAIGVLEA--NGNVAAVVGRWEPLNLDTRLSEALGYSMkfiIDAIYRg 192
                                       55666666789*******************9999996..799999999***********888875551224444445 PP

                   Glyco_transf_21  94 ..klsglgfavGksmalrreaLeai.GGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaR 167
                                          ++   f +G   ++r ++L+ i  G  +  + + +D+++g+++  +Gl v   ++ ++ ++ p  s++ral  +
  gi|320100902|ref|YP_004176494.1| 193 rsCMGLSVFPLGTGTLFRARVLKGIlKGWDQ--ERIQDDMEIGARMMYHGLGVKYIDECAVYVENP--STYRALRIQ 265
                                       5334566899*************87244444..789**********************98887766..599****** PP

                   Glyco_transf_21 168 qlrWa 172
                                       q rWa
  gi|320100902|ref|YP_004176494.1| 266 QSRWA 270
                                       ****8 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 3.1
                   Glyco_transf_21  62 lVtslpvgsdak.glaaaleaafl 84 
                                       lVt l+   + k g+ +++ea+ +
  gi|320100902|ref|YP_004176494.1| 277 LVTRLSHILRSKqGFLGKMEALAF 300
                                       567766655544389999988776 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.7e-07   0.00081       3      84 ..      54     140 ..      52     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.7e-07
                   Glyco_tranf_2_4   3 eadiLpeflahhlalgfdr..ilvydndstDgtrailke...l..pevkllhvdksyederrqvellkallaryaea 72 
                                       + ++L++ + ++  lg+++  i+v+++d++D    + ++   +  + v+++ v+ s+ + +r  ++ + l    +++
  gi|320100902|ref|YP_004176494.1|  54 PIEYLERAVNYIHGLGVEDyeIIVVSDDDEDVGEVLFERlveWrrKGVNVWLVRRSIPEGYRTGAVNTGLW--LSRG 128
                                       5679*************7445*********9986666664445324499********87666666666555..4589 PP

                   Glyco_tranf_2_4  73 dwvlvvDaDEfl 84 
                                       d+v+vvD+D +l
  gi|320100902|ref|YP_004176494.1| 129 DYVYVVDVDAML 140
                                       *********776 PP

>> RNR_inhib  Ribonucleotide reductase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.8e-05      0.23       9      23 ..     106     120 ..     104     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                         RNR_inhib   9 VRKsVpeGYktgsvy 23 
                                       VR+s+peGY+tg v 
  gi|320100902|ref|YP_004176494.1| 106 VRRSIPEGYRTGAVN 120
                                       9***********964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3354.31
//
Query:       gi|320100903|ref|YP_004176495.1|  [L=215]
Description: Zn-dependent hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-40  137.9   0.1    4.4e-40  137.2   0.1    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
    2.1e-13   50.3   1.6    4.8e-09   36.0   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.1   4.9e-44   4.4e-40       1     163 []       3     167 ..       3     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 4.9e-44
                     Lactamase_B_3   1 eltwlghnsfllet.agarilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee.geslevg 74 
                                       +++w+gh+++ +   +g +i +DP ++ ++g ++p+++aDlvl+++++ dH++++ + +   +++vl++  +++ v+
  gi|320100903|ref|YP_004176495.1|   3 RVSWHGHACVSILRdNGYTITIDPHDGySIGIKRPEVKADLVLVTHDHFDHNAVDVVSK-SGKTRVLKSfRGEAVVD 78 
                                       589*******9877479********999*******************************.99******988999*** PP

                     Lactamase_B_3  75 gleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealela 151
                                       +++ir+++t hd+ +g++rgen+++++e+dg +i+hlG+l+  ++ + l +l+ vD+++tPvgg++t+++ ea  ++
  gi|320100903|ref|YP_004176495.1|  79 DVRIRGFRTFHDKYKGKRRGENTVYIVEVDGKRIAHLGDLGDIPDASVLSALKGVDLLITPVGGTFTIEPGEAWSII 155
                                       ***************************************************************************** PP

                     Lactamase_B_3 152 krLkpklvlPmh 163
                                       +++kp  vlP+h
  gi|320100903|ref|YP_004176495.1| 156 EEVKPLNVLPIH 167
                                       ***********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 !   12.6   1.5   8.1e-06     0.072      30      48 ..      40      57 ..      22      71 .. 0.80
   2 !   36.0   0.0   5.4e-13   4.8e-09      99     201 .]      78     168 ..      64     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-06
                                      SEEEEE-SS--HHHHGGGG CS
                     Lactamase_B_2 30 pidaVllthaHyDHlagll 48
                                      + d+Vl+th+H+DH a ++
  gi|320100903|ref|YP_004176495.1| 40 KADLVLVTHDHFDHNA-VD 57
                                      78************73.44 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 5.4e-13
                                       CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHHCT-SEEEEE-S-SSTTHHHH CS
                     Lactamase_B_2  99 gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerlggadllllditayeddemir 174
                                       +  +++i+ +   h++ +  ++++g++  +++e +gkr++++gD+g ip +++   l+g+dll+ +++         
  gi|320100903|ref|YP_004176495.1|  78 D--DVRIRGFRTFHDKYK--GKRRGENTVYIVEVDGKRIAHLGDLGDIPdASVLSALKGVDLLITPVG--------- 141
                                       4..467888877777777..99***************************66699**************......... PP

                                       HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 175 hmgHltpeeaveaaadlgakrlvliHi 201
                                       + +++ p+ea+ +++++++  +++iH+
  gi|320100903|ref|YP_004176495.1| 142 GTFTIEPGEAWSIIEEVKPLNVLPIHY 168
                                       889999********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1529.30
//
Query:       gi|320100904|ref|YP_004176496.1|  [L=66]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 455.54
//
Query:       gi|320100905|ref|YP_004176497.1|  [L=94]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 731.39
//
Query:       gi|320100906|ref|YP_004176498.1|  [L=277]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-05   24.2   0.0    2.6e-05   23.7   0.0    1.1  1  PfkB      pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.094   12.7   0.0       0.14   12.0   0.0    1.3  1  IL2       Interleukin 2


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 !   23.7   0.0   2.9e-09   2.6e-05     176     283 ..     155     258 ..     139     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.9e-09
                                       HHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SEEEEEEGGGEEEEEETTEEEEEEE.SSSS- CS
                              PfkB 176 allellaladllkpneeElealtgekledieealaalhklkakga.ktvvvtlGkeGalvvekdgelkvpavpkvkv 251
                                       + l+ll+++d++ +  +El+a t     d+  al++l +       + vvvt   ++  vv+++    ++   +  v
  gi|320100906|ref|YP_004176498.1| 155 RALHLLRYFDVVHMDVDELKAATCVW--DELRALEKLLN---IVRgTRVVVTGRLKPIHVVDHGSLESINIDDSPLV 226
                                       56899***************988888..55444444433...3334899999999******9666666666577799 PP

                                       SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                              PfkB 252 vDttGAGDsfvggflaallegksleealrfan 283
                                        D tGAGD f g +l++ l+ +++ +a++ a+
  gi|320100906|ref|YP_004176498.1| 227 SDKTGAGDYFLGTLLVNMLSHEDFTKAVEKAH 258
                                       9***************************9997 PP

>> IL2  Interleukin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05      0.14      59      88 ..     165     194 ..     120     207 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                                       E-BSS--SGGGHHHHHHTHHHHHHHHHHHH CS
                               IL2  59 ylPkkatelkhlqcleeelkpleevlnlaq 88 
                                        +  ++ elk   c+ +el++le++ln+ +
  gi|320100906|ref|YP_004176498.1| 165 VVHMDVDELKAATCVWDELRALEKLLNIVR 194
                                       2445789********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2116.26
//
Query:       gi|320100907|ref|YP_004176499.1|  [L=122]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-05   24.7   0.0    2.8e-05   24.1   0.0    1.3  1  Thioredoxin_3  Thioredoxin 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 !   24.1   0.0   1.6e-09   2.8e-05      16      74 ..      29      88 ..      24      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.6e-09
                                      HHHHHHHHCHCCTCECEEECC.TTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHH CS
                     Thioredoxin_3 16 lekavkeaaaekgikaevekv.tdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkl 74
                                      l ++++e++++kgi +e++     f++  + + m  P+++++gk+++ G+vps  e+++ 
  gi|320100907|ref|YP_004176499.1| 29 LFQVAEELLDRKGIWVEIIPEhVWFNDPLEAESMDLPQIYVNGKLRFIGRVPSISELKSA 88
                                      678999**********88877688999999999***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 941.38
//
Query:       gi|320100908|ref|YP_004176500.1|  [L=459]
Description: seryl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  106.2   0.0    3.1e-30  105.5   0.0    1.3  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    5.7e-21   74.8   4.6      1e-20   73.9   4.6    1.4  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   0.0   3.5e-34   3.1e-30       7     179 .]     245     423 ..     238     423 .. 0.93

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 3.5e-34
                                       TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeasldds 79 
                                       ++++++L++t+e+ +++l+  e + +++LPlk++ +++++R+E+     d++G++Rv++Fh+ ++yv+ +++++++ 
  gi|320100908|ref|YP_004176500.1| 245 EGEDLYLIATAEHSLAALHAFEEIPEEELPLKYVGVSPCFRKEAGagnrDLKGIFRVHQFHKVEQYVYAKPEESWSL 321
                                       4689***************999899999****************778899*************************** PP

                                       HHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS.S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                      tRNA-synt_2b  80 lrdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn.r 155
                                       +++li  ++++f+ l l++r +    ++  a +++k+++e +++ ++ ++e++++++  + +s rl+++ +++ +  
  gi|320100908|ref|YP_004176500.1| 322 MEELIGNAEELFRGLELPYRIVNIASGDLGAPAAKKYDLETWMPAQGLFREMVSCSNTTDWQSFRLKTRLIRRRGmI 398
                                       ******************885555599999******************************************99944 PP

                                       EEEEEEEEEE.EEHHHHHHHHHHHH CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxx RF
                      tRNA-synt_2b 156 eksvimicaa.igveRllsaileqn 179
                                       ++ v++++ + i+ +R +  ile++
  gi|320100908|ref|YP_004176500.1| 399 KEYVHTLNSTaIASTRAITSILENH 423
                                       5679****999***********986 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 !   73.9   4.6   1.2e-24     1e-20       5     107 ..       7     107 ..       6     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.2e-24
                                       HHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHH CS
                      Seryl_tRNA_N   5 klirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelke 81 
                                        l+renpe++ke++kkR+ d+++vde + ld ++r++ ++++el++++N +s+ I+++ +   +++  i+e+kel  
  gi|320100908|ref|YP_004176500.1|   7 TLLRENPEQLKEHVKKRFMDPSLVDEAYRLDLEWRKMLSQVQELRHRHNVISRDISRLPEP--ERSLRINEAKELLS 81 
                                       79*********************************************************86..79************ PP

                                       HHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  82 elkaleaelkeleaeleklllaiPNi 107
                                       +l++le++l+ele+  +++ll++PN+
  gi|320100908|ref|YP_004176500.1|  82 QLEELEKKLRELEELRDEALLKLPNT 107
                                       *************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3277.09
//
Query:       gi|320100909|ref|YP_004176501.1|  [L=119]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-17   61.0   0.5    1.3e-16   60.6   0.5    1.2  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.5     7e-21   1.3e-16       1      66 [.       6      73 ..       6      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 7e-21
                                      HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC..STT CS
                    FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalr.alpg 66
                                      k++v +aL+tVtDPe+g+d+++lgl+++i++ +  +V+++++lt++ c+la+ +   +++ l+ +l  
  gi|320100909|ref|YP_004176501.1|  6 KKKVIEALETVTDPEIGIDVYNLGLIYDIRVVDeKTVKIAMSLTTMFCPLAATLPLMIIDVLKeKLGV 73
                                      5789***************************999****************************955544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 918.14
//
Query:       gi|320100910|ref|YP_004176502.1|  [L=96]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.019   15.2   0.0       0.03   14.5   0.0    1.4  1  Viral_DNA_bi  Viral DNA-binding protein, all alpha domain
      0.041   14.2   0.0      0.044   14.1   0.0    1.1  1  PTH2          Peptidyl-tRNA hydrolase PTH2
       0.15   12.2   0.0        3.4    7.9   0.0    2.0  2  PI3K_rbd      PI3-kinase family, ras-binding domain


Domain annotation for each model (and alignments):
>> Viral_DNA_bi  Viral DNA-binding protein, all alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.1e-06      0.03      30      60 ..      35      65 ..      21      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-06
                      Viral_DNA_bi 30 siveklaatylrkkhkelrLTfsSsksfatv 60
                                      si+ekl a + r++ k++ L ++S++ + ++
  gi|320100910|ref|YP_004176502.1| 35 SIMEKLIAEWERNQQKGIPLDYASEEELKAM 65
                                      89***********************999887 PP

>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.4e-06     0.044      39      72 ..      31      70 ..       4      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.4e-06
                                      H......HHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHH CS
                              PTH2 39 e......kellkeWeeegqkkivlkveseeeLlelaakak 72
                                      +      ++l+ eWe+++qk i l   seeeL+ +++ a 
  gi|320100910|ref|YP_004176502.1| 31 PtvasimEKLIAEWERNQQKGIPLDYASEEELKAMYTIAV 70
                                      13444455899*********************99988775 PP

>> PI3K_rbd  PI3-kinase family, ras-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00058       3.4      25      65 ..      17      56 ..       6      59 .. 0.82
   2 ?    2.7   0.0     0.023   1.4e+02      26      46 ..      61      81 ..      57      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00058
                                      SS-SEEEEEEEETTS-HHHHHHHHHHCHH----------GE CS
                          PI3K_rbd 25 enkqqkvtlkvnpnstpesllaealrkklsvldqedvtddy 65
                                      e  +q +++ +  + t++s++++++++ +++++++ +  dy
  gi|320100910|ref|YP_004176502.1| 17 ESREQAYKIAFYSDPTVASIMEKLIAEWERNQQKGIPL-DY 56
                                      467899*********************77777777666.55 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.023
                                      S-SEEEEEEEETTS-HHHHHH CS
                          PI3K_rbd 26 nkqqkvtlkvnpnstpeslla 46
                                      + +  +t+ v++++tp  +l+
  gi|320100910|ref|YP_004176502.1| 61 ELKAMYTIAVKISETPPHVLM 81
                                      567889*********988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 736.03
//
Query:       gi|320100911|ref|YP_004176503.1|  [L=333]
Description: ribose 1,5-bisphosphate isomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-87  293.1   0.6    2.1e-87  292.9   0.6    1.0  1  IF-2B            Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.098   12.6   0.0       0.93    9.4   0.0    2.2  2  Pyrid_oxidase_2  Pyridoxamine 5'-phosphate oxidase


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 !  292.9   0.6   2.4e-91   2.1e-87       1     282 []      21     298 ..      21     298 .. 0.98

  Alignments for each domain:
  == domain 1  score: 292.9 bits;  conditional E-value: 2.4e-91
                                       SS-SHHHHHHHHHHHHHHHHHHCC.CSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdak.tskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeak 76 
                                       k+rG+ +i++aa+e+l+++++++    + + +k+++ + +d L+++rPtavsl na+ ++     +lk+ +d+++a+
  gi|320100911|ref|YP_004176503.1|  21 KIRGAGKIGRAAAEALKIAAEEYAgPRDLQVFKKYIGRVADILISTRPTAVSLPNAVMFVVS---ALKNAQDYESAR 94 
                                       69*********************944566777****************************99...89********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHH CS
                             IF-2B  77 ksliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltake 153
                                       +s+i  ++++i+e + a +ki+++aa +ik++ ++lT+c+s+++ +++ +a ++++ +kV+ +E+rP  qGr ta++
  gi|320100911|ref|YP_004176503.1|  95 SSIIGSANRFIEESLSAVKKISEMAARRIKENSIVLTHCHSSVAVSTITEAYRQGRVVKVYSTETRPFYQGRITATQ 171
                                       ***************************************************************************** PP

                                       HHHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGG CS
                             IF-2B 154 LvqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlde 230
                                       L ++g+pv  i+dsav+yvm e vd+v++GAd++++nGa++nkiGTs++A++Ake+++ v+vvaes+kfs+ + ++e
  gi|320100911|ref|YP_004176503.1| 172 LINNGVPVVQIPDSAVRYVMGE-VDYVVIGADTVASNGAVVNKIGTSQVALAAKEARVRVYVVAESYKFSPVTLVGE 247
                                       **********************.****************************************************** PP

                                       GSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 231 difieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                        + ie+rdp e+++ +  +  +  +kv+np fDvtPpe+I++i+Te+Gv+pp
  gi|320100911|ref|YP_004176503.1| 248 LVPIEFRDPTEVVPEDWLKQHP-GVKVLNPSFDVTPPEYIDAIVTEIGVIPP 298
                                       ****************999888.***************************98 PP

>> Pyrid_oxidase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.052   4.7e+02      91     118 ..      85     112 ..      76     123 .. 0.78
   2 ?    9.4   0.0    0.0001      0.93      78     135 ..     219     277 ..     168     296 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.052
                                       --TTSTTS-EEEEEEEEEE--TTTHHHH CS
                   Pyrid_oxidase_2  91 vdpesptcarvsltGklekveseekkla 118
                                        +++++++ar s++G+ ++  +e  +++
  gi|320100911|ref|YP_004176503.1|  85 KNAQDYESARSSIIGSANRFIEESLSAV 112
                                       578999*********9987765555444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0001
                                       EEGGGSSHHHHHT--TTSTTS-EEEEEEEEEE--.TTTHHHHHHHHHHH-GGGGGS-GG CS
                   Pyrid_oxidase_2  78 iseeqtptckkkkvdpesptcarvsltGklekve.seekklaekcllsrHpdakkWlpg 135
                                       +  + ++   +  v +es++ + v+l+G+l+++e ++  +++ +  l++Hp  k   p+
  gi|320100911|ref|YP_004176503.1| 219 VALAAKEARVRVYVVAESYKFSPVTLVGELVPIEfRDPTEVVPEDWLKQHPGVKVLNPS 277
                                       4444444444556888999999************88888999*********98876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2660.21
//
Query:       gi|320100912|ref|YP_004176504.1|  [L=313]
Description: initiation factor 2B-like protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-53  179.5   0.0      1e-52  179.1   0.0    1.0  1  IF-2B        Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.085   12.5   0.0       0.14   11.7   0.0    1.4  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi


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 !  179.1   0.0   1.1e-56     1e-52      14     282 .]      24     280 ..      14     280 .. 0.94

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 1.1e-56
                                       HHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHHHHHH CS
                             IF-2B  14 evllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikelikei 90 
                                        +l+++++  +   ++ + +   + ++ L++ rP+++   na+rr+ +          +++  k + e+i+ l++e 
  gi|320100912|ref|YP_004176504.1|  24 STLRKAASSGD---AKAFAKMFVELYEKLMAERPSSMASLNALRRIGT--------YFLENGLKGIEEYIDALASEY 89 
                                       44554444444...66667777788999********************........457999999***********9 PP

                                       HHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXEEEEEEGG CS
                             IF-2B  91 eeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagipvtlitds 167
                                        e+    +++aa+++ dgd+++T +ns t+ ++++++++++ k+kV+v+EsrP l+G  +a+ L++ g++v li+ds
  gi|320100912|ref|YP_004176504.1|  90 DESVTRAAEMAAKRVVDGDALMTNSNSLTLRRLFKTLVDSGVKVKVYVAESRPGLEGLAMAEYLEKLGVEVYLIVDS 166
                                       9999999********************************************************************** PP

                                       GHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHHE CS
                             IF-2B 168 avayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeelln 244
                                       a++++m++ +dkv++GA+++++nGa++ k+G+s +A+ A+e+++ v+vva+++kfs ++  +e     e+d + l+ 
  gi|320100912|ref|YP_004176504.1| 167 AARFFMKN-IDKVVLGAEAVAANGAVVGKAGSSIIALDAHEARVRVFVVAPTMKFSIETIYGELLKLPEGDWRLLMD 242
                                       ********.******************************************************************** PP

                                       ETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 245 itgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                        + +r+ +e+     p++DvtPpe+I++i Te G+++p
  gi|320100912|ref|YP_004176504.1| 243 EDTRRTLPENYMATAPLYDVTPPEYIDVIATERGLFAP 280
                                       ***********************************987 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 ?   11.7   0.0   1.6e-05      0.14      91     118 ..     144     171 ..     110     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHTTSEEEEEEETHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  91 ytgitlAEyfrdqgknvlliadslsrwa 118
                                       + g+++AEy+ + g +v li+ds  r+ 
  gi|320100912|ref|YP_004176504.1| 144 LEGLAMAEYLEKLGVEVYLIVDSAARFF 171
                                       579**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2291.61
//
Query:       gi|320100913|ref|YP_004176505.1|  [L=289]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-07   30.2   0.1    6.2e-05   22.9   0.0    2.5  2  AAA_26    AAA domain
  ------ inclusion threshold ------
       0.18   11.9   0.0        0.7   10.0   0.0    1.8  2  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


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 !   22.9   0.0     7e-09   6.2e-05       5      42 ..       5      42 ..       2      91 .. 0.69
   2 !    4.6   0.0    0.0029        26     117     138 ..     201     222 ..     183     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7e-09
                            AAA_26  5 vtgt.dtgvGKTvvslgLvralkrkgvkvgyfKPiqtgi 42
                                      +tg+  +++GKT+v+lgL+r l  + +k+ yfKP++  +
  gi|320100913|ref|YP_004176505.1|  5 ITGMlPHDSGKTTVALGLAREL-GRRFKTYYFKPVAGHS 42
                                      55541468**************.9***********7544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0029
                            AAA_26 117 ellnadiaknlgapvilVargg 138
                                       +++ a  a++l+a+v+lVa++ 
  gi|320100913|ref|YP_004176505.1| 201 NNSSAPTAASLDADVVLVAAPS 222
                                       56667789***********875 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   7.8e-05       0.7      10      30 ..      13      32 ..      12      42 .. 0.84
   2 ?   -1.3   0.0      0.24   2.2e+03      54      70 ..     194     243 ..     131     258 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.8e-05
                                      SSHHHHHHHHHHHHHHTT--E CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA 10 vGKTtlaanLaralarrglrV 30
                                      +GKTt+a++Lar l r ++++
  gi|320100913|ref|YP_004176505.1| 13 SGKTTVALGLARELGR-RFKT 32
                                      8*************99.5555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.24
                                       H.................................CCHCCCHHHHHHCHCH CS
                                       x.................................xxxxxxxxxxxxxxxx RF
                              CbiA  54 p.................................dlkrllellealgkkk 70 
                                                                         d  r+++ +eal+++ 
  gi|320100913|ref|YP_004176505.1| 194 IvltesynnssaptaasldadvvlvaapsklliyDGRRYKRAVEALSIGR 243
                                       24455555555555555555555555555555555566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 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:                        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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2124.37
//
Query:       gi|320100914|ref|YP_004176506.1|  [L=491]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0046   16.7   0.3     0.0062   16.3   0.3    1.1  1  DUF4201         Domain of unknown function (DUF4201)
  ------ inclusion threshold ------
      0.041   12.1   0.9      0.058   11.6   0.9    1.1  1  EzrA            Septation ring formation regulator, EzrA
      0.043   13.2   0.7      0.063   12.7   0.7    1.1  1  Cluap1          Clusterin-associated protein-1
      0.044   13.2   0.1      0.061   12.7   0.1    1.1  1  Tropomyosin     Tropomyosin
      0.052   12.4   1.2      0.077   11.9   1.2    1.1  1  Spc7            Spc7 kinetochore protein
      0.081   13.0   0.2       0.13   12.4   0.2    1.2  1  Nup54           Nucleoporin complex subunit 54
       0.14   12.5   3.0       0.22   11.8   3.0    1.3  1  GAT             GAT domain
       0.14   12.8   0.3       0.22   12.2   0.3    1.2  1  YabA            Initiation control protein YabA
       0.14   12.5   0.5       0.21   12.0   0.5    1.2  1  V-SNARE         Vesicle transport v-SNARE protein N-terminus
       0.15   11.6   1.3       0.22   11.1   1.3    1.1  1  HAUS-augmin3    HAUS augmin-like complex subunit 3
       0.21   11.6   1.1       0.31   11.1   1.1    1.2  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.22   12.2   0.2       0.41   11.3   0.2    1.4  1  SlyX            SlyX
       0.24   11.4   3.6       0.36   10.8   3.6    1.3  1  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
        0.3    9.3   2.8       0.42    8.8   2.8    1.1  1  COG6            Conserved oligomeric complex COG6
        0.4   10.8   1.5       0.61   10.2   1.5    1.1  1  Tropomyosin_1   Tropomyosin like
       0.43   10.7   3.9       0.63   10.1   3.9    1.2  1  ADIP            Afadin- and alpha -actinin-Binding


Domain annotation for each model (and alignments):
>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   5.6e-06    0.0062      23     117 ..     367     461 ..     357     464 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.6e-06
                           DUF4201  23 akiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkke 99 
                                       + ++++l  +   g  Lt   + +l +  q+ + +I + n ++++l +++t+  +++++l  kl + +se+  l+++
  gi|320100914|ref|YP_004176506.1| 367 SLTSSQLVAFILAGSSLTPLGYSNLLNLLQQRKLEIGDLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSR 443
                                       5555566666666667777778888899999999******************************************* PP

                           DUF4201 100 lkekeerlaklrkelykv 117
                                       + + +++l+k ++  +++
  gi|320100914|ref|YP_004176506.1| 444 ITQVNAELEKAKALYTQA 461
                                       **********99877765 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   5.2e-05     0.058     100     171 ..     399     470 ..     391     473 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                                       THHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHH CS
                              EzrA 100 kkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqle 171
                                       k ++ +l+ +++e+ +++ ++++ ++elt +    ++e + l+++  +++ +l++ ++ y +a++++ + l+
  gi|320100914|ref|YP_004176506.1| 399 KLEIGDLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKAKALYTQAYTYITLGLA 470
                                       667888999999****************************************************99987765 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   5.6e-05     0.063     160     214 ..     399     456 ..     389     462 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                            Cluap1 160 qleleeie...kalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqk 214
                                       +le+ +++   ++l+++++++++++++++ +l++++s+++ L+++i++ ++ele+a+ 
  gi|320100914|ref|YP_004176506.1| 399 KLEIGDLNvkvNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKAKA 456
                                       55555554111456789999***********************************986 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.4e-05     0.061       7      62 ..     406     461 ..     401     466 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                       Tropomyosin   7 eeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleea 62 
                                       + +++e ++  +++++ ++e + k +   +E + ln ri+++++ele+++   ++a
  gi|320100914|ref|YP_004176506.1| 406 NVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKAKALYTQA 461
                                       56889999999**************************************9887776 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.2   6.9e-05     0.077     202     261 ..     396     455 ..     390     462 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                              Spc7 202 eelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                       ++ + e+ +l+++++e+++ ++++++ ++el+ k+++ +++ + l+++i + +  le+ k
  gi|320100914|ref|YP_004176506.1| 396 QQRKLEIGDLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKAK 455
                                       455555555555555555555555555555555555555555555555555555555444 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00011      0.13      30      98 ..     387     454 ..     382     464 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  30 GFedLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleil 98 
                                       G++ L + +++ + e+  ++ +++e+++ +++++ +   e++ +l+++ ++++ l +R++++ + le +
  gi|320100914|ref|YP_004176506.1| 387 GYSNLLNLLQQRKLEIGDLNVKVNELNNTVTSMN-QTINELTGKLATCSSENTLLNSRITQVNAELEKA 454
                                       5666666677788899999***************.9999***********************9999866 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.0    0.0002      0.22      26      74 ..     409     461 ..     390     464 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                               GAT  26 lkeLyetckamqpriqklieet...adeedllae.lLqlNDeLnnvlerYerl 74 
                                       ++eL++t+ +m ++i +l +++   + e+ ll+  + q+N eL ++ + Y+++
  gi|320100914|ref|YP_004176506.1| 409 VNELNNTVTSMNQTINELTGKLatcSSENTLLNSrITQVNAELEKAKALYTQA 461
                                       79*******************98875555455545***********9999987 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3    0.0002      0.22       5      56 ..     404     455 ..     400     468 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXX CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeee 56 
                                       +l  k++el++++++++++++el  +la++  en+ L+   +++  +le+++
  gi|320100914|ref|YP_004176506.1| 404 DLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKAK 455
                                       5777899999999999999999999999999999999999999988886554 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   0.00019      0.21      21      77 ..     396     458 ..     387     460 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                           V-SNARE  21 eerkaalreiekkldeaeelldqMelEvrnlps......serasykaklreykselkklkkel 77 
                                       ++rk  + ++  k++e+++ + +M+  +++l        se + +++++++ ++el+k+k  +
  gi|320100914|ref|YP_004176506.1| 396 QQRKLEIGDLNVKVNELNNTVTSMNQTINELTGklatcsSENTLLNSRITQVNAELEKAKALY 458
                                       799999*************************5556789899999**************99755 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   0.00019      0.22      74     142 ..     396     464 ..     388     479 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                      HAUS-augmin3  74 eeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenae 142
                                       ++ +  + +L+ +++eL ++  + ++  n+L+   a+ ++e+  l+++ ++++ +l++a++  +++   
  gi|320100914|ref|YP_004176506.1| 396 QQRKLEIGDLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKAKALYTQAYTY 464
                                       566777889**************************************************9987776655 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00028      0.31      52      97 ..     407     452 ..     393     462 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                    CENP-F_leu_zip  52 aevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervs 97 
                                        +v++l++ +  ++++ +el+ +L++++se+  L+  + + + + +
  gi|320100914|ref|YP_004176506.1| 407 VKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELE 452
                                       56899*****************************999998887655 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00037      0.41       5      55 ..     402     452 ..     399     460 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX   5 leeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       + +L +k+  + +t+ ++n+++ e   +++    +  ll+ r+ +++++ +
  gi|320100914|ref|YP_004176506.1| 402 IGDLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELE 452
                                       668899999999999999999999999999999999999999988887766 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 ?   10.8   3.6   0.00032      0.36      23      73 ..     404     454 ..     389     461 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                        TMF_DNA_bd  23 kLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkea 73 
                                       +L  k ++lnnt+ +++++++el+ ++++ ++++  l++ +++ +++l++a
  gi|320100914|ref|YP_004176506.1| 404 DLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKA 454
                                       445555556666666666666666555555555555555555555555444 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.8   0.00037      0.42      39      92 ..     402     455 ..     390     457 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00037
                              COG6  39 fqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkle 92 
                                        + ++ ++++++++v+++n++++e++ kl ++++e++ l++ +++ ++e++k++
  gi|320100914|ref|YP_004176506.1| 402 IGDLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKAK 455
                                       567788999****************************************99875 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   0.00054      0.61      32      93 ..     397     455 ..     391     463 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00054
                     Tropomyosin_1  32 ekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeeleesd 93 
                                       ++  ei +L+ k+++l++ v  ++++++e + k+    + +++n  l+ +i ++  ele++ 
  gi|320100914|ref|YP_004176506.1| 397 QRKLEIGDLNVKVNELNNTVTSMNQTINELTGKLA---TCSSENTLLNSRITQVNAELEKAK 455
                                       56668999999999999999999999988887775...455667788999999999999886 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.9   0.00056      0.63      49     109 ..     396     456 ..     389     461 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                              ADIP  49 drdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleq 109
                                       ++ + +   ln ++++l+++ ++++++i+ l+ +l+   +e++l++++ +q +++l+++++
  gi|320100914|ref|YP_004176506.1| 396 QQRKLEIGDLNVKVNELNNTVTSMNQTINELTGKLATCSSENTLLNSRITQVNAELEKAKA 456
                                       4444444568999*******************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      763  (0.0425568); expected 358.6 (0.02)
Passed Vit filter:                       178  (0.00992805); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 3441.07
//
Query:       gi|320100915|ref|YP_004176507.1|  [L=166]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.098   12.6   0.0        0.2   11.6   0.0    1.4  1  DUF2415    Uncharacterised protein domain (DUF2415)
       0.16   12.2   0.2       0.16   12.2   0.2    1.8  2  YbgT_YccB  Membrane bound YbgT-like protein


Domain annotation for each model (and alignments):
>> DUF2415  Uncharacterised protein domain (DUF2415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.2e-05       0.2      19      33 ..      60      74 ..      58      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                           DUF2415 19 visEhvgrvHlvDlR 33
                                      v+sE+ g++Hl+ lR
  gi|320100915|ref|YP_004176507.1| 60 VWSEEAGHSHLAPLR 74
                                      9***********999 PP

>> YbgT_YccB  Membrane bound YbgT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   1.7e-05      0.16      15      26 ..      42      53 ..      42      54 .. 0.89
   2 ?   -3.4   0.1       1.3   1.1e+04      11      15 ..     156     160 ..     156     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                         YbgT_YccB 15 lfgilnalwlEk 26
                                      ++++lna+w+E+
  gi|320100915|ref|YP_004176507.1| 42 SLATLNAMWIEA 53
                                      68*********8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                         YbgT_YccB  11 lLAvl 15 
                                       l+A++
  gi|320100915|ref|YP_004176507.1| 156 LFACS 160
                                       79996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1297.22
//
Query:       gi|320100916|ref|YP_004176508.1|  [L=466]
Description: SSS sodium solute transporter superfamily protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-48  164.8  29.8    4.2e-48  164.2  29.8    1.3  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2  29.8   2.4e-52   4.2e-48       2     406 .]      36     416 ..      35     416 .. 0.88

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 2.4e-52
                               SSF   2 flagrsltgfvlglslaasnisaasfvGlaGava.asGlavvllelgalllvlllllllaerlrnagalTlpdylsk 77 
                                       +lagr+l+ + +++sl a+ni+++s vG+a+ ++   Gl+ +++ l a ++ ++ l l+  rlr++ + Tlp+++  
  gi|320100916|ref|YP_004176508.1|  36 ILAGRNLGVILVAASLSANNIGGGSTVGVAAKAYgDWGLSAGWYILTAAIA-MIPLALVLARLRRSLVWTLPEVIGR 111
                                       79*******************************9458*******9998775.678889999**************** PP

                               SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlm 154
                                       R++  +   +l ++  ++ +++  + ++++ + +i  + Gl ye++v++ +++ ++Yt++GGl A  +td  q  ++
  gi|320100916|ref|YP_004176508.1| 112 RYGTPS--YLLTSILQIVSLVCLSAMQVLASGTIIAALTGLPYEVGVVIAGGISTVYTIMGGLWADAFTDLFQWAII 186
                                       ****99..555666667777778899*************************************************** PP

                               SSF 155 lvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakda 231
                                        +g l  l +v+++vGg+e++v+kl   +    dl+++++        t+ sl +  +   ++   ++ R + akd 
  gi|320100916|ref|YP_004176508.1| 187 FFGMLAALPFVISNVGGFETMVSKLPPGHF---DLFKAGGG-------TIVSLLIMYIVTFIMGSEMITRAFGAKDE 253
                                       ***********************9976666...****8884.......333443334444444467899******** PP

                               SSF 232 kailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaimst 308
                                       k++ +g l + ++ +++ +    i+            a+ +++++s+ ay + +  l p+++aGl l+++l a ms+
  gi|320100916|ref|YP_004176508.1| 254 KTAFRGSLLSAVFQGMFAFIPALIG--------LAALAAFPNIKASD-AYATAMLRLAPPWIAGLGLSAILGATMSS 321
                                       ********99999999988844444........44445557777777.899999*********************** PP

                               SSF 309 ltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavi 385
                                        +s +l ass+f+kD+Y+k++r + a+++e++ + r  + v++ ++il+a+   +  +++++ +af   a+  +a +
  gi|320100916|ref|YP_004176508.1| 322 ADSDMLCASSIFSKDIYQKFIRPK-ASDREIILITRAGIAVIGGISILIALLRLD--IITVNTFAFMLRAAGPFAPF 395
                                       *******************99988.888888888888888899999998888765..69****************** PP

                               SSF 386 llalfwkrvneqGAlagliiG 406
                                       l+++f ++v ++  ++++i+G
  gi|320100916|ref|YP_004176508.1| 396 LFGIFREKVSRNAGIVAIIAG 416
                                       ***********9999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3704.73
//
Query:       gi|320100917|ref|YP_004176509.1|  [L=210]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1196  (0.0667076); expected 358.6 (0.02)
Passed bias filter:                      849  (0.0473534); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 1761.26
//
Query:       gi|320100918|ref|YP_004176510.1|  [L=145]
Description: membrane-bound metal-dependent hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-18   66.8  10.2    4.4e-17   61.9  10.2    2.0  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 !   61.9  10.2   2.4e-21   4.4e-17       1     165 [.       1     133 [.       1     141 [. 0.81

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.4e-21
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllfla 77 
                                       M+  tH+ll+aalg  +++ ++++   ++l+va l++l+PDiD         +   +      ++HR   H +++l 
  gi|320100918|ref|YP_004176510.1|   1 MKKTTHVLLAAALGSYIGSDIASSL--TALTVAGLASLIPDID---------V---H------FKHRRTLHNIFALS 57 
                                       8899******************984..899999999*******.........1...1......46************ PP

                              YdjM  78 llalvlllllrlfgrsalrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltllsrrglval 154
                                       l+ l++++llr ++ ++  +  ++++g lsH+l+D+l+ +Gv+ll Pfs++ ++l++      +        ++v l
  gi|320100918|ref|YP_004176510.1|  58 LCILGAAFLLRYLKVYNTLILEAIAVGWLSHILADMLNIQGVRLLHPFSDASFSLKIARS---N--------NPV-L 122
                                       **************994444444*************************966666555444...3........445.5 PP

                              YdjM 155 elvllvlylvi 165
                                       ++ l++l +++
  gi|320100918|ref|YP_004176510.1| 123 NITLSLLSITL 133
                                       55555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 00:00:00.39
# Mc/sec: 1109.79
//
Query:       gi|320100919|ref|YP_004176511.1|  [L=240]
Description: ribose-5-phosphate isomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-49  165.4   0.0    1.1e-48  165.2   0.0    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.2   0.0   5.9e-53   1.1e-48       2     173 .]      56     231 ..      55     231 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.2 bits;  conditional E-value: 5.9e-53
                                       EEESSHHHHHHHHHTT--.BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBES CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgip.llsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlve 77 
                                        vp+S +t  ++++ g + ll+   v+e+d++iDGaDev ++l+++KG+Gga+ rEK +a  +++ i+++d++K++ 
  gi|320100919|ref|YP_004176511.1|  56 LVPSSADTMLHLASIGYTvLLDPAGVDEVDVYIDGADEVSSKLDMVKGRGGAFAREKTLALRSRERIYVVDYTKYTG 132
                                       69***************856788****************************************************86 PP

                                       S..TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTT CS
                    Rib_5-P_isom_A  78 k..lgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipG 152
                                          l ++p+PveVlp++l++v r+l +l  g+p+lR ++gkdgpvv+dngn+i+D k++++++dp +l+++lk ++G
  gi|320100919|ref|YP_004176511.1| 133 VdyLYAKPIPVEVLPVSLRYVVRKLGELGYGEPVLRVGSGKDGPVVSDNGNYIVDYKLSKPVRDPLALHNALKLLHG 209
                                       653668********************98679***************************9999*************** PP

                                       EEEESEE-S.--SEEEEEETTC CS
                    Rib_5-P_isom_A 153 VvetGlFlg.ladkvlvgkedg 173
                                       V+etG+F + l+d v+vg+++g
  gi|320100919|ref|YP_004176511.1| 210 VIETGVFPSeLVDMVIVGEPSG 231
                                       ********77********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1780.52
//
Query:       gi|320100920|ref|YP_004176512.1|  [L=282]
Description: D-aminopeptidase DppA [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-88  295.3   0.0    4.4e-88  295.1   0.0    1.0  1  Peptidase_M55  D-aminopeptidase
  ------ inclusion threshold ------
      0.097   12.1   0.0       0.15   11.5   0.0    1.3  1  Creatininase   Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Peptidase_M55  D-aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.1   0.0   4.9e-92   4.4e-88       1     262 [.       1     264 [.       1     266 [. 0.99

  Alignments for each domain:
  == domain 1  score: 295.1 bits;  conditional E-value: 4.9e-92
                     Peptidase_M55   1 MkvyISaDiEGvagvvsweqvepgeaeyerarrlmteevnaaiegalaagatevlVnDsHgsmrNllpeeLdervrl 77 
                                       Mk yIS+D+EG+ gv+s ++++pg+++++r  r++t+ +n +++++ ++g++ ++V+DsHg m+N+++ eLd+r++l
  gi|320100920|ref|YP_004176512.1|   1 MKAYISVDLEGLPGVSSLTMLNPGNTQFNRPVRVLTKLLNTVVDELSNHGFETIYVADSHGLMTNIDYLELDSRAEL 77 
                                       9**************************************************************************** PP

                     Peptidase_M55  78 isGkpkplsmmegldesfdavlfvGyHaragtekgvlaHTysgsaieevrlngkevgEfglnaalagelgVPvvlvs 154
                                       i+G+p+p+sm++ ld+sfda+lf+GyH++agt +g+l+HT+sg++++e+++ng++++Ef +n+++age +VPv+l++
  gi|320100920|ref|YP_004176512.1|  78 IQGYPRPFSMVTLLDSSFDAALFIGYHSAAGTIHGILDHTMSGRTFAEIKVNGEKASEFIINSLYAGEQDVPVILLA 154
                                       ***************************************************************************** PP

                     Peptidase_M55 155 GDdalceeakellpevetvavkeglgrfaakslspeeaeeaireavkeavekake..akplkleepvelevefksta 229
                                       GD++l  e++++ p++++v++k+gl+r++a++  +++++ea+re+v++av+k+k+  ++plk+e+p+++e++++++ 
  gi|320100920|ref|YP_004176512.1| 155 GDEHLGGEVEKHSPWTVFVPLKKGLSRYSAIYPGIDKVTEALREGVAKAVKKLKKgeMQPLKWEKPYRVELNLRDSL 231
                                       *****************************************************9999******************** PP

                     Peptidase_M55 230 lAdaaslvpgveridartvefeaedveellral 262
                                        Ad ++ +p  +r+da++vef+a+++ e+l ++
  gi|320100920|ref|YP_004176512.1| 232 IADILEALPVFKRVDAYRVEFSATTAREMLGYI 264
                                       ****************************99776 PP

>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.7e-05      0.15      82     111 ..      33      62 ..      14      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.7e-05
                      Creatininase  82 etliavlrdileslarhGfrrivlvngHgg 111
                                        +l+++l  ++++l++hGf+ i +  +Hg 
  gi|320100920|ref|YP_004176512.1|  33 RVLTKLLNTVVDELSNHGFETIYVADSHGL 62 
                                       57999***********************94 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:                      398  (0.0221987); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2015.73
//
Query:       gi|320100921|ref|YP_004176513.1|  [L=184]
Description: metal dependent phosphohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-17   61.9   0.0    1.9e-16   60.5   0.0    1.7  1  HD_3      HD domain
    8.2e-13   48.5   0.0    1.1e-12   48.1   0.0    1.2  1  HD_2      HD containing hydrolase-like enzyme
      7e-06   26.3   0.5    2.2e-05   24.7   0.5    1.8  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 !   60.5   0.0   3.1e-20   1.9e-16       3     130 ..       8     134 ..       6     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 3.1e-20
                              HD_3   3 kLKfqkRqgwlqtgrvr..eesvaeHmwrvalmalllseelk...ekvdiarvikmfLiHDlvEiltgDiispde.l 73 
                                       +L++++R+gw+  g+ +  +esva+H + + l+a+ ++e l+    ++d+arv+ m++iHD++E++tgD++  ++  
  gi|320100921|ref|YP_004176513.1|   8 NLRHIPRTGWVLRGVPPavAESVADHIFLTTLIAMDIAERLGsmgVRIDKARVLAMSIIHDIPEAVTGDVVRQVKhG 84 
                                       69***********9755336*******************99865579***********************8877523 PP

                              HD_3  74 akeekeeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllq 130
                                        +e+ +  e +a+e++         + +++l +E  ++ + ea ++k+ D + ++l 
  gi|320100921|ref|YP_004176513.1|  85 VEEYFSMVESKAIEEL----GL---QGYSELYDELSKAGSLEALVVKAADDIATILE 134
                                       3333444555555544....22...36899999999999999999999999999885 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 !   48.1   0.0   1.9e-16   1.1e-12       4     166 ..       4     160 ..       2     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.9e-16
                              HD_2   4 allsrlkyieRwalmrn....treenvaeHslevaliahalal.ienkkfggkldaerlallalyHDasEiitGDlp 75 
                                       +++ +l+ i R + +      +  e+va+H + ++lia+ +a  +++  +g ++d  r+++++++HD++E++tGD+ 
  gi|320100921|ref|YP_004176513.1|   4 KYILNLRHIPRTGWVLRgvppAVAESVADHIFLTTLIAMDIAErLGS--MGVRIDKARVLAMSIIHDIPEAVTGDVV 78 
                                       677788888886654432233678999**********9998874444..578************************* PP

                              HD_2  76 tpvKyanpeireaykevEeeaeekllelLpeelreeyeelladeeaeeeekklvkaaDklsalikcleelkagnkeF 152
                                        +vK+    ++e ++ vE++a e+l  +    + e y+el ++ +    e  +vkaaD + ++++  + +++g ++ 
  gi|320100921|ref|YP_004176513.1|  79 RQVKHG---VEEYFSMVESKAIEELGLQ---GYSELYDELSKAGSL---EALVVKAADDIATILEGSRLVDTGYRQV 146
                                       ****97...6678999****99998754...566667776644455...889*************999999999999 PP

                              HD_2 153 eeakkeieeklkel 166
                                       ee+  +++++l +l
  gi|320100921|ref|YP_004176513.1| 147 EEIVVNVRDHLYRL 160
                                       88888888877766 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.5   3.7e-09   2.2e-05       2     120 ..      31     130 ..      30     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.7e-09
                                       HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlg 75 
                                       ++H++ +  +a  +ae+lg    + d+ ++l++ ++HDi + ++gd   +   +++ +++ + v  + ++e+++   
  gi|320100921|ref|YP_004176513.1|  31 ADHIFLTTLIAMDIAERLGSmgvRIDKARVLAMSIIHDIPEAVTGDVVRQ--VKHGVEEYFSMVESKAIEELGLQG- 104
                                       79*******************************************93332..223343344444444444444444. PP

                                       HHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                                HD  76 ldledvaklirehheswegkkrprglaerqlslearivklaDrla 120
                                             ++l+ e ++                slea++vk+aD +a
  gi|320100921|ref|YP_004176513.1| 105 -----YSELYDELSKAG--------------SLEALVVKAADDIA 130
                                       .....566666666666..............58888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1334.73
//
Query:       gi|320100922|ref|YP_004176514.1|  [L=462]
Description: carboxylase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-52  178.8   0.0    1.9e-52  177.9   0.0    1.4  1  PYC_OADA    Conserved carboxylase domain
    5.3e-42  144.2   0.0    7.4e-42  143.7   0.0    1.2  1  HMGL-like   HMGL-like
  ------ inclusion threshold ------
       0.06   13.3   0.1         12    5.9   0.0    2.9  3  ADH_zinc_N  Zinc-binding dehydrogenase
      0.064   12.4   0.1          2    7.5   0.0    2.2  2  DUF561      Protein of unknown function (DUF561)


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 !  177.9   0.0   4.2e-56   1.9e-52       1     166 [.     290     446 ..     290     456 .. 0.94

  Alignments for each domain:
  == domain 1  score: 177.9 bits;  conditional E-value: 4.2e-56
                                       HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TT CS
                          PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegry 77 
                                       V++h++PGG++tn   q+k++g++dk+ evl+e+++v+++lG +++VTPsS++vg +Av+nv n          gry
  gi|320100922|ref|YP_004176514.1| 290 VLEHQVPGGMITNFIMQLKQLGAEDKLGEVLEEVRRVREDLGWPPLVTPSSQIVGAQAVLNVIN----------GRY 356
                                       89**************************************************************..........79* PP

                                       SS--HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHH CS
                          PYC_OADA  78 kdipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleeka..kteedvlsyalypk 152
                                       k ++++v+d++kG +G+pp++ +ee+vk +l  e+pi++rpad+l+p  +e++ k ++ek   ++eedvl+y+l+p+
  gi|320100922|ref|YP_004176514.1| 357 KVVTKEVRDYVKGLYGRPPAPLKEEVVKLILGSEKPIDVRPADLLKP-MYEECVKTVKEKGyyTKEEDVLTYCLFPD 432
                                       ***********************************************.78*********9855599*********** PP

                                       HHHHHHHHHHHHHH CS
                          PYC_OADA 153 vaekflkfreeygd 166
                                       va++f+++++++ +
  gi|320100922|ref|YP_004176514.1| 433 VATEFFEKNRRQAS 446
                                       ******97776544 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.7   0.0   1.7e-45   7.4e-42       2     256 ..       2     259 ..       1     266 [. 0.93

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 1.7e-45
                                       -EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B.... CS
                         HMGL-like   2 vkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkkar... 66 
                                       v+ivdttLRD++q+l +++l++e+++++ ++ d+ g+ +iE+         ++ + ed++e++r i + vk  +   
  gi|320100922|ref|YP_004176514.1|   2 VEIVDTTLRDAHQSLlATRLKTEDMIPLLDKIDRTGFYSIEMwggatfdvMIRYLNEDPWERLRIIRERVKRVKlqm 78 
                                       79************99*********************************9********************9996666 PP

                                       .......--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT CS
                         HMGL-like  67 ......ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..vel 135
                                             +++++++ +++++++ve    +g ++++vf+a ++              +++++  ++ a++lg+    ++
  gi|320100922|ref|YP_004176514.1|  79 llrgqnLVGYRHYPDDVVEKFVELSYRNGIDIFRVFDALND--------------VRNMKTSIRKAKELGAIvqGTI 141
                                       666778*****************99****************..............9**************9844567 PP

                                       -BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHH CS
                         HMGL-like 136 sledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaA 212
                                        ++ ++ +++e  ++++e+++++G++ i+i+D++G+l+P  a+ l++a+ke+ k  +++ vH H + GlAva  ++A
  gi|320100922|ref|YP_004176514.1| 142 TYTISPVHTVEHYLKIAEELISLGVDHIAIKDMSGILDPYTAYSLVKAIKENFK--IPVDVHSHYTGGLAVATYVKA 216
                                       788899************************************************..********************* PP

                                       HHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT-B----HHH CS
                         HMGL-like 213 veaGadrvdgtvnGlGeraGnaaleelvaalealgvdtgldlqk 256
                                       veaGad +d++++ l  ++G + + ++ +al+   + + +dl+ 
  gi|320100922|ref|YP_004176514.1| 217 VEAGADFIDTSISPLAFGTGQPGIQTVYYALHPD-ARPRIDLSV 259
                                       ******************************9854.455566555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.76   3.4e+03      62      81 ..      40      58 ..      38      59 .. 0.79
   2 ?    5.9   0.0    0.0027        12      45      89 ..      94     140 ..      72     156 .. 0.86
   3 ?    4.1   0.0    0.0095        43      32      84 ..     163     222 ..     143     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.76
                                      EEESSCSHHHHHHHHHCEEE CS
                        ADH_zinc_N 62 vfecvGsgatleaalkllkp 81
                                      ++e+ G gat++  +++l++
  gi|320100922|ref|YP_004176514.1| 40 SIEMWG-GATFDVMIRYLNE 58
                                      688889.9999998888875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHTTTSSEEE..EEESSCSHHHHHHHHHCEEEEEEEEECS CS
                        ADH_zinc_N  45 dlverikeltggegvdv..vfecvGsgatleaalkllkpgGrlvvvG 89 
                                       d+ve+  el   +g+d+  vf+++++ + ++++++ +k+ G +v   
  gi|320100922|ref|YP_004176514.1|  94 DVVEKFVELSYRNGIDIfrVFDALNDVRNMKTSIRKAKELGAIVQGT 140
                                       7999999999999***999***********************99765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0095
                                       HTTESEEEET........TTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEE CS
                        ADH_zinc_N  32 klGadeviny........kea.dlverikeltggegvdvvfecvGsgatleaalkllkpgGr 84 
                                       +lG+d++            +a +lv++ike + + +vdv   ++G g ++ +++k++  g  
  gi|320100922|ref|YP_004176514.1| 163 SLGVDHIAIKdmsgildpYTAySLVKAIKENF-KIPVDVHSHYTG-GLAVATYVKAVEAGAD 222
                                       44666655444555555567779*********.88**********.********99988865 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.013        58     117     150 ..     137     170 ..     113     177 .. 0.80
   2 ?    7.5   0.0   0.00046         2      48      86 ..     182     225 ..     170     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.013
                            DUF561 117 PktdlsvtiPyiLkleeqvkLakkLeslgvdliq 150
                                        + +++ ti  + ++e+ +k+a++L slgvd i 
  gi|320100922|ref|YP_004176514.1| 137 VQGTITYTISPVHTVEHYLKIAEELISLGVDHIA 170
                                       45679999999********************985 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00046
                            DUF561  48 adpklvkkvksvsniPiCvsa.....veakllleavkaGadlve 86 
                                       ++  lvk +k++ +iP+ v +     +   + ++av aGad+++
  gi|320100922|ref|YP_004176514.1| 182 TAYSLVKAIKENFKIPVDVHShytggLAVATYVKAVEAGADFID 225
                                       56789************9964233337889999********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3278.86
//
Query:       gi|320100923|ref|YP_004176515.1|  [L=425]
Description: class I/II aminotransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-48  165.8   0.0    1.8e-48  165.6   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.018   13.9   0.0        0.2   10.4   0.0    2.1  2  Aminotran_MocR   Alanine-glyoxylate amino-transferase
      0.042   12.4   0.0      0.062   11.8   0.0    1.1  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 !  165.6   0.0     3e-52   1.8e-48      33     361 ..      86     416 ..      57     418 .. 0.88

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 3e-52
                                       HHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHH CS
                     Aminotran_1_2  33 aggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasykni 109
                                       +  +  +y  ++glpel++a+ + l++  +++++++ +++v++G   ++++ i  l l+ gd  l+ dp+y+ y + 
  gi|320100923|ref|YP_004176515.1|  86 DPFKHFRYVSTQGLPELRTAISEDLRKYGGVDVEPS-NILVTTGGADGLVLSIYTL-LDEGDTLLLLDPSYSVYWDL 160
                                       5556679***************9999889*******.6666666555555556566.56****************** PP

                                       HHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEE CS
                     Aminotran_1_2 110 lrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfv 186
                                       +rl+g+ v +++   e++f+ d e ++++l +        k il++sp NPt  v++ e  ++++d+a++++++++ 
  gi|320100923|ref|YP_004176515.1| 161 ARLAGLRVETCRQLYENGFNPDPECIKDKLGS------SAKAILLASPDNPTSRVINSEVAKTIVDVAYERKAWIIY 231
                                       ************999*****************......779************************************ PP

                                       EETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHH CS
                     Aminotran_1_2 187 DeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaav 260
                                       D aY ++v++ + ++    ++++  + l++vgs+sK+ +++G R+Gy++g ++ +  ++kl+  + +  + ++q+++
  gi|320100923|ref|YP_004176515.1| 232 DVAYKHLVYEGEHVW--FEKLAPSMDrLVVVGSFSKDIAIPGGRLGYVYGPSNAIAEMTKLKGVLGIvaPVPMQWMA 306
                                       **********76433..4666777668**********************************99776669******** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHH......CHHHHHHHHHHTCT CS
                     Aminotran_1_2 261 aaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasqsgmflltdlsae......takelskkLleevg 329
                                          ls   + +++l e    + +rr+  +++L++      vl++ + m+l+ d+ ++      ++  +  kL+ee+g
  gi|320100923|ref|YP_004176515.1| 307 YYYLSGGFK-EKYLREVIPVYRRRRDAAYEALKKNlpRARVLKPAASMYLFPDMAHYirekglDDVGFTMKLIEEKG 382
                                       ******775.57********************999**********************98888888888888****** PP

                                       EEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 330 vyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                       v+++pg++f+   +++lRit+ +++e++l e +e
  gi|320100923|ref|YP_004176515.1| 383 VAMLPGSIFGEsgSNHLRITFVTMDEKNLVEGIE 416
                                       ************999******9****99987766 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.021   1.3e+02      49      73 ..      97     121 ..      91     128 .. 0.82
   2 ?   10.4   0.0   3.3e-05       0.2     132     283 ..     152     297 ..     125     395 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.021
                                       --CCC-EE.TTEETTSSS-TT--HH CS
                    Aminotran_MocR  49 lGeedlraadGtdlrnyGGlaGlpe 73 
                                        G  +lr+a   dlr yGG++  p+
  gi|320100923|ref|YP_004176515.1|  97 QGLPELRTAISEDLRKYGGVDVEPS 121
                                       566788899999********98886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3.3e-05
                                       S--HHHHHHHHHHT-EEEEE.EEETTE..E-HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SS CS
                    Aminotran_MocR 132 pGydrhfllleelGielltv.dlqddG..pdvdaveklvaedasvkGilavpkysnptGetiseevarrlaalkaaa 205
                                       p y  ++ l +  G+++ t  +l ++G  pd + ++   +  +s k il      npt  +i +eva+ ++ +    
  gi|320100923|ref|YP_004176515.1| 152 PSYSVYWDLARLAGLRVETCrQLYENGfnPDPECIKDKLG--SSAKAILLA-SPDNPTSRVINSEVAKTIVDVAYER 225
                                       5555556666666665554324555554466677765554..355666543.347***************9997666 PP

                                       TT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTT.TS-TTSS-EEEEE-HHHHHHHHHHHHHC- CS
                    Aminotran_MocR 206 pdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastsk.itfaGaGvafvassedniawlkkylGlqs 281
                                           i +d ay+  +lv e+++    v   + a   dr +v+ s sk i+  G  +++v   ++ ia ++k  G+  
  gi|320100923|ref|YP_004176515.1| 226 KA-WIIYDVAYK--HLVYEGEH----VWFEKLAPSMDRLVVVGSFSKdIAIPGGRLGYVYGPSNAIAEMTKLKGVLG 295
                                       55.577899996..78888875....5566667788*********9989***********************99987 PP

                                       S- CS
                    Aminotran_MocR 282 iG 283
                                       i 
  gi|320100923|ref|YP_004176515.1| 296 IV 297
                                       74 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     1e-05     0.062      70     173 ..     123     232 ..     108     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                                       EEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST...TSHHHHHHHCCTTEEEEEE CS
                   Cys_Met_Meta_PP  70 alavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt...sdleelekaikentklvyl 143
                                        l+++ G   + ++i +ll +Gd +++ d  Y+   +l +    +++   + ++     d+e ++ ++ +  k+++l
  gi|320100923|ref|YP_004176515.1| 123 ILVTTGGADGLVLSIYTLLDEGDTLLLLDPSYSVYWDLARLAGLRVETCRQLYENgfnPDPECIKDKLGSSAKAILL 199
                                       678888999999*****************99999999988888887776666665455699**************** PP

                                       ESS-TTTT----...HHHHHHHHHHTT-EEEEE CS
                   Cys_Met_Meta_PP 144 EtptnpllkvvD...iekiaklakkagvlvvvD 173
                                        +p np+ +v+     ++i+++a ++++ ++ D
  gi|320100923|ref|YP_004176515.1| 200 ASPDNPTSRVINsevAKTIVDVAYERKAWIIYD 232
                                       **********98332346888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3176.55
//
Query:       gi|320100924|ref|YP_004176516.1|  [L=450]
Description: tRNA(Ile2) 2-agmatinylcytidine synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-37  125.6   0.0    1.6e-36  124.9   0.0    1.3  1  DUF1743         Domain of unknown function (DUF1743)
     0.0029   17.5   2.1     0.0061   16.4   2.1    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.24   11.4   1.4       0.47   10.5   1.4    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.31   11.0   4.2       0.66   10.0   4.2    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.0   3.6e-40   1.6e-36       2     116 .]     150     264 ..     149     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 3.6e-40
                                       THHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEE CS
                           DUF1743   2 rgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlf 77 
                                       rg+iG++aa+g+++   d+tyEl+aYr +e++g +r+vde+s++e+de+t  +t+ n+D++ +++++ P++pdpvl+
  gi|320100924|ref|YP_004176516.1| 150 RGVIGSLAAIGNQMLSGDYTYELIAYRTREYIGkPRMVDEDSIVEMDEATRGRTILNYDYESGRPLVIPRGPDPVLY 226
                                       8*************999************************************************************ PP

                                       EEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  78 Girgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       G+rge+p ++++a k i+   e++e mavfrtnq+td+h
  gi|320100924|ref|YP_004176516.1| 227 GVRGETPLDVIEASKLIRV-LEPIEYMAVFRTNQHTDSH 264
                                       *******************.*****************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 !   16.4   2.1   1.4e-06    0.0061      31      55 ..     370     394 ..     361     396 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                    OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfe 55 
                                       C++Cg++++ a  g+ fkC++Cgf+
  gi|320100924|ref|YP_004176516.1| 370 CPVCGRRMESAGRGKGFKCRHCGFR 394
                                       ***********************96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.4   0.00011      0.47      60      99 ..     357     398 ..     337     405 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                                       -EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS-EEE CS
                              HypA  60 aeLeieevpvkvrCreCgkefeleek..alrCpkCgsadvei 99 
                                       +eL+ +++  +  C +Cg+++e++ +   ++C +Cg + +e+
  gi|320100924|ref|YP_004176516.1| 357 KELSKKTITRNPLCPVCGRRMESAGRgkGFKCRHCGFRTTEL 398
                                       5677888888899*********88844589******988776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.2   0.00015      0.66      19      45 ..     368     393 ..     355     394 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayriktrglfqCkeCrk 45 
                                       + CP Cg r  +a r    + f+C++C+ 
  gi|320100924|ref|YP_004176516.1| 368 PLCPVCGRRmeSAGRG---KGFKCRHCGF 393
                                       77*****775444444...55******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3505.06
//
Query:       gi|320100925|ref|YP_004176517.1|  [L=326]
Description: deoxyhypusine synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-101  339.4   0.0   1.9e-101  339.1   0.0    1.1  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.1   0.0  1.1e-105  1.9e-101       1     286 [.      32     316 ..      32     318 .. 0.97

  Alignments for each domain:
  == domain 1  score: 339.1 bits;  conditional E-value: 1.1e-105
                                DS   1 ellesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlik 76 
                                       +l+e+++++ gf+a ++++a +il +m +d+++t +l++t+n++s+G+r+++a++++e+++  ++tT+g +++D+++
  gi|320100925|ref|YP_004176517.1|  32 DLVEQLGNAhGFMAGHVYRASQILYEMIADSDATRLLAFTGNIVSTGIRGLLAEMIREGFFHGVITTCGAVDHDIAR 108
                                       5899999999******************************************************************* PP

                                DS  77 algkktylgdfelddeeLrekginRignllvpneny.ckfedwvreildkleeeqkvwspselikelGkeindeeSi 152
                                        +g+ +y+gd+ +dd++Lr  +i+R+gn+l+p eny  ++e+++r++l++l + +k+ws+sel++e Gk+i+de+Si
  gi|320100925|ref|YP_004176517.1| 109 GTGHAYYKGDWLYDDTMLRALEIHRLGNILIPLENYgLAVEKFTRPLLEDLAKVKKKWSVSELLYEAGKRIRDENSI 185
                                       ************************************99*************************************** PP

                                DS 153 lywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanl 229
                                       l++Ay+++ipvf+p++ Dgs+G q+++ +     + +++di++D +++ d+++ akk ga+i+GGG++Khh++++++
  gi|320100925|ref|YP_004176517.1| 186 LRAAYEKNIPVFVPGVFDGSFGSQIVFNQ---VSTGIEVDIISDEKKIIDMVFAAKKLGALIIGGGISKHHTIWWAQ 259
                                       ***********************666666...34459**************************************** PP

                                DS 230 mrngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                       +r+g+dyavy+tta e+dGslsga+++Ea+Swgk+k++ ++v vyaDaTi+lPL+v 
  gi|320100925|ref|YP_004176517.1| 260 LRDGLDYAVYVTTAVEYDGSLSGAQPREAISWGKLKPSGRHVVVYADATIALPLIVG 316
                                       *******************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2587.49
//
Query:       gi|320100926|ref|YP_004176518.1|  [L=223]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-05   24.0   0.0    5.1e-05   23.3   0.0    1.4  1  Mrr_cat   Restriction endonuclease
    0.00034   21.0   0.0    0.00057   20.3   0.0    1.4  1  NERD      Nuclease-related domain
  ------ inclusion threshold ------
      0.053   13.3   0.1       0.35   10.7   0.0    2.2  2  DUF3136   Protein of unknown function (DUF3136)


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 !   23.3   0.0   8.6e-09   5.1e-05       2      78 ..      77     161 ..      76     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.6e-09
                                       TTT-TTCHHHHHHHHHHHHSSS...EEE---B-TTSSB--EEEETTEEEEEEEEEEE--T.......S-B-HHHHHH CS
                           Mrr_cat   2 dkmspkeFeklvaellealGyk...eveltgrsgDggiDliakkdplgserilvqaKryk.......nkvgvkeVqe 68 
                                       +++++++Fe+l+  ++ ++Gy    +++lt +     iD++    + g   i+v +K+++        + g ++V++
  gi|320100926|ref|YP_004176518.1|  77 RAVDWRDFEQLASYVMSEHGYLvesNITLT-TPVRLEIDVVGVDTASG-LGIAVDCKHWShntrgklIEAGTRHVER 151
                                       5789*****************974333333.355889****7655545.77********654444222589999999 PP

                                       HHHHCTTS.. CS
                           Mrr_cat  69 ligalkkrga 78 
                                       l +al ++ +
  gi|320100926|ref|YP_004176518.1| 152 LEKALSHYDY 161
                                       9999999764 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.6e-08   0.00057       6      92 ..      85     166 ..      81     196 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.6e-08
                              NERD   6 EravakeLkelkedeylvlhdvrlrpgtg.eiDhlvispk.gifv.iEvKnwsGwifgdkegrwtqkikkgfknple 79 
                                       E+ + ++++   e++ylv ++++l++  + eiD++ + +  g+ + +++K+ws +++g+      +   +++   le
  gi|320100926|ref|YP_004176518.1|  85 EQLASYVMS---EHGYLVESNITLTTPVRlEIDVVGVDTAsGLGIaVDCKHWSHNTRGK----LIEAGTRHV-ERLE 153
                                       455555555...679*********888668*****99988899888*******988888....333323333.6677 PP

                              NERD  80 qakrhakalkksl 92 
                                       +a  h ++lk+++
  gi|320100926|ref|YP_004176518.1| 154 KALSHYDYLKEKY 166
                                       7777777776666 PP

>> DUF3136  Protein of unknown function (DUF3136)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.18   1.1e+03       3      12 ..      21      30 ..      19      54 .. 0.68
   2 ?   10.7   0.0   5.9e-05      0.35      17      43 ..      63      88 ..      60      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.18
                           DUF3136  3 igeLEAgysl 12
                                      ++eLEA y +
  gi|320100926|ref|YP_004176518.1| 21 LDELEALYRV 30
                                      5778887754 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.9e-05
                           DUF3136 17 lrlLvkegrslkeikRtvCWdrLerLh 43
                                      lr L+++g s++ i R+v W   e+L 
  gi|320100926|ref|YP_004176518.1| 63 LR-LLEQGVSIERISRAVDWRDFEQLA 88
                                      54.789*****************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.38
# Mc/sec: 1757.11
//
Query:       gi|320100927|ref|YP_004176519.1|  [L=245]
Description: DNA polymerase sliding clamp subunit A [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   44.2   0.1    2.1e-10   40.4   0.0    2.2  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    5.9e-11   42.6   0.6    3.8e-08   33.6   0.1    2.9  3  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    1.2e-06   28.2   0.1    2.3e-05   24.0   0.0    2.5  3  Rad9      Rad9
    0.00015   20.9   0.1       0.22   10.6   0.0    2.1  2  Rad1      Repair protein Rad1/Rec1/Rad17
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.046   13.7   0.0    1.5  1  HTH_46    Winged helix-turn-helix DNA binding
       0.14   12.3   1.2        2.4    8.3   0.0    2.8  3  VIGSSK    Helicase-associated putative binding domain, C-term


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 !   40.4   0.0   6.9e-14   2.1e-10       5      93 ..       5      93 ..       1     121 [. 0.90
   2 ?    1.7   0.0     0.066     2e+02      12      89 ..     139     215 ..     130     228 .. 0.64

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 6.9e-14
                                      EESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTST CS
                            PCNA_N  5 rleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcan 83
                                       l +a ++k ++ a+  l +e+++++  +Gis++alD  + + +++ l s+ f +y  + + ++g++ +++ k+lk   
  gi|320100927|ref|YP_004176519.1|  5 VLPEAKIFKEIIGAVGKLADEVALNITREGISIKALDIDQSSYIEIVLPSDMFLEYTVENEEVVGISTSNIKKVLKHLR 83
                                      57799************************************************************************** PP

                                      TTSEEEEEEE CS
                            PCNA_N 84 nedsvtlkae 93
                                      + +++t+++ 
  gi|320100927|ref|YP_004176519.1| 84 KGENLTIETS 93
                                      *****99875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.066
                                       HHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEE CS
                            PCNA_N  12 lkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsv 88 
                                       +kk +e +  + + + +d++++ +  +a+ ss+   v ++  s +  +     +     ++  l+ +l +a+ +d+v
  gi|320100927|ref|YP_004176519.1| 139 VKKAIEDVESVGSVIEVDASSDTLVFRAVGSSRAE-VRFTQGSPALISLEVREPSKSTYDVVKLATVLGVAEMSDMV 214
                                       67777777777777888888888888888888743.44555555555555544555555555555555555555555 PP

                                       E CS
                            PCNA_N  89 t 89 
                                       t
  gi|320100927|ref|YP_004176519.1| 215 T 215
                                       5 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 !    5.7   0.0    0.0053        16      15      45 ..       9      39 ..       2      54 .. 0.84
   2 ?   -0.2   0.0      0.36   1.1e+03       8      44 ..      65     100 ..      59     105 .. 0.80
   3 !   33.6   0.1   1.3e-11   3.8e-08       4     127 ..     125     241 ..     120     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHHTTT-SEEEEEEETTEEEEEE CS
                            PCNA_C 15 ssefaricrdlsqlsdsvvisvtkegvkfsa 45
                                      +  f+ i+  + +l d+v +++t+eg+  +a
  gi|320100927|ref|YP_004176519.1|  9 AKIFKEIIGAVGKLADEVALNITREGISIKA 39
                                      45599999999****************8876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.36
                                       SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEE CS
                            PCNA_C   8 davvklpssefaricrdlsqlsdsvvisvtkegvkfs 44 
                                       + vv +++s+ +++ + l + +++++i  + e v f+
  gi|320100927|ref|YP_004176519.1|  65 EEVVGISTSNIKKVLKHLRK-GENLTIETSGEYVGFT 100
                                       56888999999999999976.7788888888888775 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 1.3e-11
                                       -SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEE CS
                            PCNA_C   4 dseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtlt 80 
                                       +++++ + +l+ss  ++ + d+ +++  + + ++ +++ f+a    Gs+     +v+  + +   + le++ep + t
  gi|320100927|ref|YP_004176519.1| 125 NLDFKVTAQLTSSGVKKAIEDVESVGSVIEVDASSDTLVFRAV---GSSRA---EVRFTQGSPALISLEVREPSKST 195
                                       36899999*********************************95...56633...44555667889************ PP

                                       EEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  81 falkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                       + +  la++   + +s+ vtl +ss +Pl++e++i ++  ++yl a+
  gi|320100927|ref|YP_004176519.1| 196 YDVVKLATVLGVAEMSDMVTLGFSSKMPLKMEFHIGSG-RITYLTAP 241
                                       ***********************************875.56677666 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   7.6e-09   2.3e-05       4      72 ..      15      84 ..      12     133 .. 0.87
   2 ?    0.8   0.0     0.092   2.7e+02       3      34 ..     141     172 ..     139     178 .. 0.85
   3 ?   -0.6   0.0      0.25   7.5e+02      19      43 ..     179     203 ..     172     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.6e-09
                              Rad9  4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqircki.lvKsvlsvfrs 72
                                      ++ ++ ++ de+ l+i+++g+++++++  +S+y  + l +++F +y+ e +e + +++ ++K vl+ +r 
  gi|320100927|ref|YP_004176519.1| 15 IIGAVGKLADEVALNITREGISIKALDIDQSSYIEIVLPSDMFLEYTVENEEVVGISTsNIKKVLKHLRK 84
                                      677889****************************************999888888887358999999883 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.092
                              Rad9   3 ralqclsrigdelyleisedglelrtvnssrS 34 
                                       +a++ +  +g  + +++s d l +r+v ssr+
  gi|320100927|ref|YP_004176519.1| 141 KAIEDVESVGSVIEVDASSDTLVFRAVGSSRA 172
                                       677777889999999***************97 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.25
                              Rad9  19 isedglelrtvnssrSayalvtlkk 43 
                                        s+ +++l+  + s+S+y +v+l+ 
  gi|320100927|ref|YP_004176519.1| 179 GSPALISLEVREPSKSTYDVVKLAT 203
                                       5667788888899999999999975 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   7.2e-05      0.22      12      64 ..      12      66 ..       5     101 .. 0.81
   2 !    8.5   0.0   0.00032      0.96     168     260 ..     131     215 ..     102     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.2e-05
                              Rad1 12 LatlLksiafkd.kalvqissdGlkfiv.ednrvlqaqafldkalFtsYtfenaq 64
                                      + +++ +++    ++ ++i+++G+++ + +  ++  ++ +l++++F +Yt+en++
  gi|320100927|ref|YP_004176519.1| 12 FKEIIGAVGKLAdEVALNITREGISIKAlDIDQSSYIEIVLPSDMFLEYTVENEE 66
                                      666777777655389***********7637789999***************8765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00032
                              Rad1 168 kvilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksvlekfevsslsessessYkfa 244
                                       +  l s+  ++a+++ +++ +++++ ass     ++ ++a g+ +++ev f++ +  l ++ev    e+s+s Y++ 
  gi|320100927|ref|YP_004176519.1| 131 TAQLTSSGVKKAIEDVESVGSVIEVDASSD----TLVFRAVGS-SRAEVRFTQGSPALISLEVR---EPSKSTYDVV 199
                                       556889999*****************9994....9******97.689*****************...888888**99 PP

                              Rad1 245 llkkaakalalssKvs 260
                                        l+ +  + ++s  v 
  gi|320100927|ref|YP_004176519.1| 200 KLATVLGVAEMSDMVT 215
                                       9999988887776665 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.046      34      57 ..      69      92 ..      65      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                            HTH_46 34 nLSrSsimkvLseLkkggyIeier 57
                                       +S S i kvL +L+kg++++ie 
  gi|320100927|ref|YP_004176519.1| 69 GISTSNIKKVLKHLRKGENLTIET 92
                                      68******************9986 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 ?    8.3   0.0   0.00081       2.4      39      51 ..      59      71 ..      45      77 .. 0.90
   2 ?   -0.6   0.1      0.51   1.5e+03      29      50 ..     130     151 ..     129     158 .. 0.81
   3 ?    0.7   0.0       0.2   5.8e+02      48      56 ..     167     175 ..     165     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00081
                            VIGSSK 39 eYTHenseViGsS 51
                                      eYT en+eV+G S
  gi|320100927|ref|YP_004176519.1| 59 EYTVENEEVVGIS 71
                                      9**********88 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.51
                            VIGSSK  29 iqAILasaGVeYTHenseViGs 50 
                                       + A L+s+GV+   e  e +Gs
  gi|320100927|ref|YP_004176519.1| 130 VTAQLTSSGVKKAIEDVESVGS 151
                                       6788999999987777777775 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.2
                            VIGSSK  48 iGsSkvEeq 56 
                                       +GsS++E +
  gi|320100927|ref|YP_004176519.1| 167 VGSSRAEVR 175
                                       9*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1867.68
//
Query:       gi|320100928|ref|YP_004176520.1|  [L=210]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1594.81
//
Query:       gi|320100929|ref|YP_004176521.1|  [L=382]
Description: PhoH family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-45  155.5   0.0    1.6e-45  155.1   0.0    1.2  1  PhoH           PhoH-like protein
    5.4e-07   29.4   2.1    2.5e-05   24.0   0.6    2.5  2  KH_2           KH domain
    6.2e-07   29.2   0.1    0.00025   20.8   0.1    2.7  2  KH_1           KH domain
    1.9e-05   24.6   0.2       0.01   15.9   0.0    2.7  2  KH_5           NusA-like KH domain
  ------ inclusion threshold ------
       0.11   13.1   0.0       0.24   11.9   0.0    1.5  1  ABC_tran       ABC transporter
       0.12   10.8   0.0       0.17   10.4   0.0    1.1  1  Terminase_GpA  Phage terminase large subunit (GpA)
       0.17   11.6   0.0       0.25   11.1   0.0    1.3  1  DEAD           DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.1   0.0   6.3e-49   1.6e-45       1     201 [.       8     210 ..       8     214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 6.3e-49
                                       .----SHHHHHHHHHHH..H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T..T----SS----- CS
                              PhoH   1 kikpktkeQkeylealk..kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpavea..geelGflpgdle 73 
                                       ki+p+t +Q+e+++al+  +++i+  +Gp+G+GK+++++ ++v+ + ++++kr+i++rp +++  g+el++ +   +
  gi|320100929|ref|YP_004176521.1|   8 KISPQTPGQEEIVNALSdkRYEIIGLFGPTGSGKSLISILYGVDSVLNNRYKRFIISRPLIDVvsGKELTAADLG-D 83 
                                       599*************988899***************************************8888******9995.8 PP

                                       ----TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EEE CS
                              PhoH  74 ekvdpylrplydaLkdllgaekvekllekgkievaplaymRGrTlndafvilDEAQnttkeqmkmfltRlGenskvv 150
                                        +++   +++ d  + +++ + +++l+ekg i +a+ +y+RGrT++d++++lD+AQ++  e+  ++++R+G+ns+++
  gi|320100929|ref|YP_004176521.1|  84 SYYQLASSYIQDITSGVVEWSLIRELMEKGLIVIADSHYLRGRTFDDSIIFLDDAQSIPVESAIEIVMRIGRNSRLI 160
                                       9**************************************************************************** PP

                                       EEE--------------THHHHHHTTT-TTEEEEE--GGG----HHHHHHH CS
                              PhoH 151 vtGdvtqidlpkgkksGlaealevlknvegieivelkkkdvvRhplvkkiv 201
                                       ++Gd+ ++ +  + ++  + ++e+l +++++++++l  kd+vR ++ + i 
  gi|320100929|ref|YP_004176521.1| 161 IAGDPVFQRTVGS-RDSASMLREILLGEDSAKVIDLGLKDIVRPGARRGIK 210
                                       *******988766.788899************************9988876 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.6   9.6e-09   2.5e-05      19      64 ..     256     302 ..     242     331 .. 0.77
   2 ?    4.3   0.0     0.014        36      29      59 ..     334     364 ..     320     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 9.6e-09
                                       EEECCS.CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTT CS
                              KH_2  19 eIerta.nrviiviresqpgivIGkgGsnikkigkelrkdieklegk 64 
                                        I  +   +++i+++e+  g+++GkgG++i  i+k+ +++++++e +
  gi|320100929|ref|YP_004176521.1| 256 GITGEGsPDAVIIVKEGYIGRLVGKGGERITGIEKDTGYRLRAVELS 302
                                       5555444688999****************************988866 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.014
                                       EEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2  29 iviresqpgivIGkgGsnikkigkelrkdie 59 
                                       + ++++  g  +G++Gs i+ ++   +k ++
  gi|320100929|ref|YP_004176521.1| 334 VKVTSEGYGAFVGQKGSHIRFLEDVMKKLLG 364
                                       66777778999*********99999998884 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   9.8e-08   0.00025       3      34 ..     266     297 ..     265     305 .. 0.89
   2 !    5.3   0.0    0.0067        17       4      27 ..     334     357 ..     331     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9.8e-08
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEE CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIk 34 
                                       +i+v+  ++gr++GkgG++I  I+++tg + +
  gi|320100929|ref|YP_004176521.1| 266 VIIVKEGYIGRLVGKGGERITGIEKDTGYRLR 297
                                       589999*********************98766 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0067
                                       EEEGGGHHHHHHTGGGHHHHHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIre 27 
                                       ++v s+ +g+ +G +Gs+I+ +++
  gi|320100929|ref|YP_004176521.1| 334 VKVTSEGYGAFVGQKGSHIRFLED 357
                                       566777799***********9987 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.9e-06      0.01       5      61 ..     265     314 ..     263     318 .. 0.90
   2 !    5.8   0.0    0.0058        15       9      35 ..     336     357 ..     328     373 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-06
                              KH_5   5 tkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsP 61 
                                       ++++Vk++      +G +vgk+G+ri  ++++  g + + ve s D++ +i  a++P
  gi|320100929|ref|YP_004176521.1| 265 AVIIVKEGY-----IGRLVGKGGERITGIEKDT-GYRLRAVELSLDFKPLIR-AIHP 314
                                       799******.....******************9.************999995.5555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0058
                              KH_5   9 VkshnpnvdpvGaivgkkGsrikavss 35 
                                       V s+       Ga+vg+kGs i+ +++
  gi|320100929|ref|YP_004176521.1| 336 VTSEG-----YGAFVGQKGSHIRFLED 357
                                       45555.....8***********97665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.4e-05      0.24      10      34 ..      27      50 ..      22      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.4e-05
                                      TTSEEEEEESTTSSHHHHHHHHTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 10 egekvaivGenGaGKStLlkllagl 34
                                      + e+++++G++G+GKS L+++l+g 
  gi|320100929|ref|YP_004176521.1| 27 RYEIIGLFGPTGSGKS-LISILYGV 50
                                      5699***********9.67777775 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.5e-05      0.17      13      49 ..       9      44 ..       2      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.5e-05
                     Terminase_GpA 13 wrtdrtPylreimdalsdreveevvfvkpaqvGkTel 49
                                      +++ +tP + ei++alsd+++e + + +p+ +Gk+ +
  gi|320100929|ref|YP_004176521.1|  9 ISP-QTPGQEEIVNALSDKRYEIIGLFGPTGSGKSLI 44
                                      544.79****************************986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.9e-05      0.25       1      58 [.      13      69 ..      13     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.9e-05
                                      -HHHHHHHHHHHTTC.EEE.EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHH CS
                                      xxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  1 tdiQaeaiplilggg.dvl.vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtre 58
                                      t+ Q+e+++++ +++ +++ + ++TGsGK+l+ ++  +++v++   ++ ++ +i  P+  
  gi|320100929|ref|YP_004176521.1| 13 TPGQEEIVNALSDKRyEIIgLFGPTGSGKSLISILYGVDSVLN---NRYKRFIISRPLID 69
                                      67899999999977644444679******************86...55567777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2792.84
//
Query:       gi|320100930|ref|YP_004176522.1|  [L=442]
Description: transglutaminase domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-11   44.8   0.0    2.4e-11   44.0   0.0    1.4  1  Transglut_core  Transglutaminase-like superfamily
  ------ inclusion threshold ------
       0.17   11.4   0.3        0.4   10.2   0.0    1.7  2  Stevor          Subtelomeric Variable Open Reading frame


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 !   44.0   0.0   2.7e-15   2.4e-11      28     111 ..     192     284 ..     172     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.7e-15
                    Transglut_core  28 nveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsgeeekeq............svase 92 
                                        ++   +++++ +r++++v+ +++G+c d++ ++v ll   Gipa +++gy++ ++ +++             ++++
  gi|320100930|ref|YP_004176522.1| 192 YFT---YNASDLPRTIDEVVDSRQGDCDDMSRVLVELLSYYGIPAVIASGYVYIRDIGVNgvlstkignvtyVFKHN 265
                                       334...459999999****************************************99999***99999999999999 PP

                    Transglut_core  93 daHawvevylegygWvplD 111
                                       + Ha v +y++g gW++lD
  gi|320100930|ref|YP_004176522.1| 266 GPHAFVLAYIPGLGWISLD 284
                                       99***************99 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.59   5.3e+03     161     202 ..      12      56 ..       6      79 .. 0.56
   2 ?   10.2   0.0   4.5e-05       0.4     238     264 ..     410     436 ..     370     438 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.59
                            Stevor 161 vlltliglaaakaaavaa...kvalsaealkklasslsilnlfse 202
                                       v+l+l++  +a+ +++     ++ ++ +a+k + s+++ + ++++
  gi|320100930|ref|YP_004176522.1|  12 VMLSLLSNLYATPTVAVPetcETLYFINAIKVYNSTINETLMLET 56 
                                       555555555554333222124556666666666676666666654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 4.5e-05
                            Stevor 238 iaalvllilavvliiLYiwlyrRRKnS 264
                                        ++lv+l +av  +++ iwl rRR  S
  gi|320100930|ref|YP_004176522.1| 410 PVILVVLAVAVFTLLVAIWLSRRRLTS 436
                                       46788888888889999*******776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3369.62
//
Query:       gi|320100931|ref|YP_004176523.1|  [L=73]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       167  (0.00931452); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 581.55
//
Query:       gi|320100932|ref|YP_004176524.1|  [L=286]
Description: methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-54  183.2   0.0    6.2e-54  182.8   0.0    1.1  1  Met_10           Met-10+ like-protein
    2.7e-07   30.1   0.0    3.6e-07   29.7   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
      7e-06   25.7   0.0      1e-05   25.2   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    7.8e-06   25.5   0.0    1.2e-05   24.8   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00082   19.2   0.0     0.0012   18.6   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
     0.0076   16.2   0.0      0.013   15.5   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.008   15.7   0.0      0.013   15.1   0.0    1.3  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.011   16.5   0.0      0.022   15.4   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
      0.042   13.5   0.0      0.063   12.9   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   0.0   3.1e-57   6.2e-54       4     194 ..      28     223 ..      25     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 3.1e-57
                                       EEETTEEEEEB-TTSSHHH.HHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEET CS
                            Met_10   4 eiiGdvvilnlreelkeyk.kvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDv 78 
                                       e iGd+++++++  +++++ k ++e +l++   vk+v+     veg +R ++  +laG++++eti +E+gc fk+D+
  gi|320100932|ref|YP_004176524.1|  28 EFIGDLALIRVPLGMEPWElKPLAEELLKRFnFVKSVWAAIPGVEGPYRLRSHVLLAGEERSETIYREHGCVFKVDI 104
                                       679*********999997635577777777659******************************************** PP

                                       TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEE CS
                            Met_10  79 skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkp 155
                                        kvy s+ l+ E+ r+a+l ++ge+V+++fAG G f+i ia+++ +++v++id+nP++++y+ eni+lN+ve++v+p
  gi|320100932|ref|YP_004176524.1| 105 NKVYISPSLNYEHLRIARLTRPGETVLNMFAGAGLFSIIIARHAAPRKVYSIDINPYAYQYMVENIRLNHVEDIVEP 181
                                       ***************************************************************************** PP

                                       EES-GGG---...TT-EEEEEE--TTTGGGGHHHHHHHEEEE CS
                            Met_10 156 ileDgrevir...eqladrvvmnlpksaieFldkvlaalkdg 194
                                       il+D+ ev+    ++  drv+m++p+ a ++ldk+l+al+ g
  gi|320100932|ref|YP_004176524.1| 182 ILGDAGEVVDsrlSNSSDRVLMPYPELALDYLDKALKALRGG 223
                                       ********9977888999*******************99976 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.8e-10   3.6e-07      51     145 ..     128     222 ..      86     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.8e-10
                                       EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC.--SS-EEEEEE CS
                               TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvlla.ekkkrfdviDl 126
                                        +vl+ ++++Gl +i  a   +  ++v+  Di++ A++ + eN++ln+ve+iv++  +dA  ++  + ++  d + l
  gi|320100932|ref|YP_004176524.1| 128 ETVLNMFAGAGLFSIIIARH-AAPRKVYSIDINPYAYQYMVENIRLNHVEDIVEPILGDAGEVVDsRLSNSSDRV-L 202
                                       5799**************99.8899***********************************999986677777777.7 PP

                                       --SS-.-GGGHHHHHHHEEE CS
                               TRM 127 DPfGs.papfldsavqsvke 145
                                        P+   + ++ld+a+++++ 
  gi|320100932|ref|YP_004176524.1| 203 MPYPElALDYLDKALKALRG 222
                                       79976266899999998875 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 !   25.2   0.0   5.2e-09     1e-05       2      89 ..     128     215 ..     127     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.2e-09
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvf 76 
                                       +++l +f+GaG  +i +a++   +kv++i+in+   + + +N ++  v+d + ++lgd  e++ +  +++   d v+
  gi|320100932|ref|YP_004176524.1| 128 ETVLNMFAGAGLFSIIIARHaaPRKVYSIDINPYAYQYMVENIRLNHVEDIVEPILGDAGEVVDSRLSNSS--DRVL 202
                                       5799**************9866689**************************************99777777..9999 PP

                   Methyltransf_15  77 lSpPwGGpsYkkq 89 
                                       +  P    +Y ++
  gi|320100932|ref|YP_004176524.1| 203 MPYPELALDYLDK 215
                                       9999888888775 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   6.2e-09   1.2e-05     157     215 ..     122     181 ..     117     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.2e-09
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLga.kkvvavDiDevAvkvakeNaelNkveaklev 215
                                       +l ++ge+vl + +G+G+ +i  a+ +a +kv+ +Di++ A +   eN++lN+ve+ +e 
  gi|320100932|ref|YP_004176524.1| 122 RLTRPGETVLNMFAGAGLFSIIIARHAApRKVYSIDINPYAYQYMVENIRLNHVEDIVEP 181
                                       67899***************98887666389************************98864 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.9e-07    0.0012      46     167 ..     126     241 ..     104     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.9e-07
                   Methyltransf_16  46 sklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWgeeleedllekeev 121
                                        + +vl + +G+Gl+ +++a+++ + kv+  D++  + + + +ni ln+  +++ v+    d ge + +  l+++  
  gi|320100932|ref|YP_004176524.1| 126 PGETVLNMFAGAGLFSIIIARHAAPRKVYSIDINPyAYQYMVENIRLNH--VEDIVEPILGDAGE-VVDSRLSNS-S 198
                                       56799****************************99799*********55..66555554445555.545555554.6 PP

                   Methyltransf_16 122 DlilaaDcvYledslelLvkvLkellkkeskvlvaykkrreaekkF 167
                                       D +l+    Y e +l+ L k Lk l    + + v ++ +  + +++
  gi|320100932|ref|YP_004176524.1| 199 DRVLMP---YPELALDYLDKALKALRGGRGWIHVYLHVKTLKGEHY 241
                                       999985...8888888888888888887777666655555555555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.4e-06     0.013       8      79 ..     120     191 ..     116     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                   Methyltransf_18   8 iaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk 79 
                                       ia+l ++g++v+   +  g+ +i ++++   +kv+ +Din+ +++   eni+ +++ed +e +l+d  e+++
  gi|320100932|ref|YP_004176524.1| 120 IARLTRPGETVLNMFAGAGLFSIIIARHAAPRKVYSIDINPYAYQYMVENIRLNHVEDIVEPILGDAGEVVD 191
                                       788888999999999999***********************************************9877765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.5e-06     0.013      31      88 ..     126     185 ..     111     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.5e-06
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasd 88 
                                         ++vl + +GaG+ ++ +a++    +v  +d++ +A +   en++ n++e  ve +  d
  gi|320100932|ref|YP_004176524.1| 126 PGETVLNMFAGAGLFSIIIARHAAPRKVYSIDINPYAYQYMVENIRLNHVEdiVEPILGD 185
                                       567899*******************************************99765555555 PP

>> Methyltransf_25  Methyltransferase 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     0.022       1      72 [.     130     205 ..     130     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS..SSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp..fedgsfDlvvssg 72 
                                       vL + +G G +++ +a++    kv+ +Di++ + +++ e+++ +++   ve + gda ++     ++s D v++ +
  gi|320100932|ref|YP_004176524.1| 130 VLNMFAGAGLFSIIIARHAAPRKVYSIDINPYAYQYMVENIRLNHVedIVEPILGDAGEVVdsRLSNSSDRVLMPY 205
                                       89999*************967********************99988988999999997753125677888888754 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-05     0.063      42     119 ..     127     203 ..     117     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                                       C-EEEETT-TTSHHHHHHHHTT-..SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRga..kkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                       g++vL++faG G  ++  + R a  +k++ ++ ++ a++ + en++  ++e+ ++ +  da e ++++ ++  + d 
  gi|320100932|ref|YP_004176524.1| 127 GETVLNMFAGAGLFSI-IIARHAapRKVYSIDINPYAYQYMVENIRLNHVEDIVEPILGDAGEVVDSRLSN--SSDR 200
                                       6889********9999.688888345899********************9999999999999999887544..3466 PP

                                       EEE CS
                     Cons_hypoth95 117 vfl 119
                                       v +
  gi|320100932|ref|YP_004176524.1| 201 VLM 203
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2245.14
//
Query:       gi|320100933|ref|YP_004176525.1|  [L=223]
Description: DNA-(apurinic or apyrimidinic site) lyase [Desulfurococcus mucosus DSM 2162]
Scores for 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   0.0    7.2e-16   58.6   0.0    1.3  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.5e-06   28.3   5.8    2.4e-06   27.7   5.8    1.3  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
    0.00012   21.8   0.0    0.00027   20.6   0.0    1.6  1  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.033   14.8   0.0      0.092   13.4   0.0    1.8  2  HHH_5          Helix-hairpin-helix domain
      0.057   13.8   0.6       0.62   10.5   0.1    2.6  2  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 !   58.6   0.0     2e-19   7.2e-16       1      96 [.      29     166 ..      29     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2e-19
                                       HHHHHHTTS-HHHHHHHHHHHHHHHS..HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfg..fptpedladadeekLrelirelGfyrrKakyikelArilv......... 66 
                                       v+++lsq+tsd +a ++i+rl+e  g   +tp+ ++++++  L+ ++r++G+yr++a+ +++lA+ ++         
  gi|320100933|ref|YP_004176525.1|  29 VAVVLSQNTSDRNAVKAIARLREI-GqgRITPQVILSMEQHMLEGILRPAGMYRNRARVLRKLAELFQepgfterlt 104
                                       789********************9.5599************************************************ PP

                                       ...................................S-SSS--TTSHHHHHHHHHHTTSSSSTTHH CS
                                       ...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ...................................gkpdvlivvDvhvrrilkrlrsikekktkk 96 
                                                                          g   ++++vD+h++ri +r++++++   ++
  gi|320100933|ref|YP_004176525.1| 105 aevtragdvnearrrlmelpgvgektadvvllryfG--IPVFPVDTHISRITRRMGFTETG-RYS 166
                                       ********************************6555..59***************999874.555 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 !   27.7   5.8   6.6e-10   2.4e-06       1      17 []     196     212 ..     196     212 .. 1.00

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.6e-10
                     EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                       C+ARkP C++C+L+DlC
  gi|320100933|ref|YP_004176525.1| 196 CKARKPLCDECVLRDLC 212
                                       ***************** PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   7.6e-08   0.00027      13      28 ..     120     135 ..     112     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.6e-08
                                       HHTSTT-SHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIl 28 
                                       L++lPGVG+ktA+++l
  gi|320100933|ref|YP_004176525.1| 120 LMELPGVGEKTADVVL 135
                                       99************98 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.7   1.7e+04      33      44 ..      42      53 ..      39      56 .. 0.66
   2 ?   13.4   0.0   2.6e-05     0.092      32      52 ..     115     135 ..      89     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.7
                                      -HHHHHTSTTS- CS
                             HHH_5 33 dveeLakipGiG 44
                                      +v+++a++  iG
  gi|320100933|ref|YP_004176525.1| 42 AVKAIARLREIG 53
                                      466677766666 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.6e-05
                                       S-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  32 adveeLakipGiGkktAerii 52 
                                       +++ +L ++pG+G+ktA+ ++
  gi|320100933|ref|YP_004176525.1| 115 EARRRLMELPGVGEKTADVVL 135
                                       45667************9766 PP

>> HHH_8  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      0.85     3e+03      29      39 ..      40      50 ..      40      55 .. 0.72
   2 ?   10.5   0.1   0.00017      0.62      41      63 ..     112     134 ..      77     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.85
                                      HHHHCCCCC-S CS
                             HHH_8 29 rrAaraiealp 39
                                      r+A++ai++l 
  gi|320100933|ref|YP_004176525.1| 40 RNAVKAIARLR 50
                                      67888887775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00017
                                       -HHHHTTHCTTSTT--HHHHHHH CS
                             HHH_8  41 eitsleeeltklpgiGkkiaaki 63 
                                       ++++++ +l +lpg+G+k+a+++
  gi|320100933|ref|YP_004176525.1| 112 DVNEARRRLMELPGVGEKTADVV 134
                                       344543379***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1676.17
//
Query:       gi|320100934|ref|YP_004176526.1|  [L=432]
Description: asparaginyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-87  292.5   0.0    3.8e-87  292.3   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.6e-11   44.0   0.2    2.6e-11   43.3   0.2    1.3  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.032   13.7   0.0       0.17   11.4   0.0    1.9  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.3   0.0   6.3e-91   3.8e-87       3     313 ..     113     426 ..     111     427 .. 0.96

  Alignments for each domain:
  == domain 1  score: 292.3 bits;  conditional E-value: 6.3e-91
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                       e++l+nr+l +r+++  k+l++++tv++a r+y+++ng+ e+++PiL+ s++e+ga+lF v       ++f    +L
  gi|320100934|ref|YP_004176526.1| 113 EYLLDNRHLWIRSPRFAKILKVKHTVLEAGREYFTSNGWWEVNPPILTASACEGGATLFPV-------DYFgqkaYL 182
                                       67899********************************************************.......67777778* PP

                                       -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                        qs qlyle+li   +++v++++++FRaE+srt+rhlaE++++e e ++ ++ed+m+v+eel++++v++vle+ ++d
  gi|320100934|ref|YP_004176526.1| 183 SQSAQLYLEALIYV-LEKVWSLTPSFRAERSRTRRHLAEYWHLEPEAAWYTMEDMMRVAEELVSHIVRRVLEERRGD 258
                                       **************.*********************************************************99999 PP

                                       CCHTTTTTS..EE-SSS.-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBB CS
                                       xxxxxxxxx..xxxxxx.xxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 153 iefvirrns..kdlkkp.fkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyark 220
                                       +    r+ +  k+ ++p ++r+ y+ea+e+l+++      g+dl  ++er+l+  e  +p+fvt+fP+++k+Fy++ 
  gi|320100934|ref|YP_004176526.1| 259 LIDLGRNIErlKPAAEPpYPRIRYDEAVEILQKKgvnikwGDDLGADEERILTM-EFEKPFFVTHFPRQIKSFYMKV 334
                                       877777666777777777***************9*******************9.899******************* PP

                                       STTSTTBBSEEEEEET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHH CS
                                       xxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 221 eeddkkltesyDllin.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlv 295
                                       +  +++++ ++Dll + g+ E++gG  R++++++l++k+ ++gl+   ++ ++wyl++++yG++ph+G+glG++R +
  gi|320100934|ref|YP_004176526.1| 335 DPSNPNVVLGFDLLAPeGYgEIIGGGEREDNYDVLYQKIVEQGLN---PDDYKWYLDLRRYGSVPHSGFGLGVERAT 408
                                       ***************9889**************************...***************************** PP

                                       HHHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 296 mlllgsesIrdviaFPkl 313
                                       m+++g+++Ird+++FP+ 
  gi|320100934|ref|YP_004176526.1| 409 MWIAGLDHIRDTLPFPRF 426
                                       ****************95 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 !   43.3   0.2   4.4e-15   2.6e-11       1      75 [.      19      97 ..      19      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 4.4e-15
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkvee 72
                                      V+++G++ ++     g+ +fi +rD +g iqvv+++    ee  + ++n+  +  v + G+v++    pgg +el +e+
  gi|320100934|ref|YP_004176526.1| 19 VCIRGWIYRR--SVVGGKAFIRVRDSSGVIQVVVDSgrlgEELVNELKNIGLEASVMACGTVREEpraPGG-YELEAES 94
                                      89********..9999*************************************************999999.******9 PP

                                      EEE CS
                   tRNA_anti-codon 73 iel 75
                                      +++
  gi|320100934|ref|YP_004176526.1| 95 FKI 97
                                      886 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 ?   -0.9   0.0      0.15     9e+02     109     152 ..     205     247 ..     198     255 .. 0.77
   2 ?   11.4   0.0   2.8e-05      0.17     210     233 ..     396     419 ..     388     423 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.15
                                       EEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHH CS
                      tRNA-synt_2d 109 rvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellkkl 152
                                         fR +    ++hlae+  +e  ++   ++++d++ v+eel++++
  gi|320100934|ref|YP_004176526.1| 205 PSFRAERsRTRRHLAEYWHLEPEAA--WYTMEDMMRVAEELVSHI 247
                                       5689988678889999999997655..489999999999999887 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.8e-05
                                       EEEEEEEEHHHHHHHHHT-SSGHH CS
                      tRNA-synt_2d 210 sgfafGlGveRlamlkygieDiRe 233
                                       +  +fGlGveR +m   g++ iR+
  gi|320100934|ref|YP_004176526.1| 396 PHSGFGLGVERATMWIAGLDHIRD 419
                                       5678*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 2914.11
//
Query:       gi|320100935|ref|YP_004176527.1|  [L=183]
Description: (30S ribosomal protein S18P)-alanine acetyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for 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   59.0   0.2    8.4e-16   58.3   0.2    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.4e-11   43.9   0.1    3.7e-11   43.3   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      1e-08   35.2   0.1    1.6e-08   34.5   0.1    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.3e-08   33.4   0.0    7.3e-08   32.3   0.0    1.5  1  FR47             FR47-like protein
    3.2e-06   27.3   0.1    2.8e-05   24.2   0.5    2.3  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    4.9e-05   23.5   0.3      9e-05   22.6   0.3    1.5  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    5.4e-05   22.9   0.0    9.7e-05   22.1   0.0    1.4  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0024   18.5   0.0     0.0036   18.0   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.18   11.3   0.0    1.3  1  GNAT_acetyltran  GNAT acetyltransferase


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 !   58.3   0.2   4.2e-19   8.4e-16       2     117 .]      39     159 ..      38     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 4.2e-19
                                       HHHHHHHHHHTHHHHHHHHHHH.HHHHHHSTTCEEEEEEET.TEEEEEEEEEEEET........TSTTEEEEEEEEE CS
                    Acetyltransf_1   2 rdlvellvesffppnedaseee.feesfsleaegllvaeed.geliGfisllkipd........ekggvayieslaV 68 
                                       +++ e+ +   ++++++ ++ee +e++     + ++vae   ge++G+i+ +  +            + +++ s+aV
  gi|320100935|ref|YP_004176527.1|  39 DRVIEINMVALPEHYPRGFFEElYEDY----GKAFYVAEAPsGEVVGYIMTRVEWKpgffhrflA--RSGHVVSIAV 109
                                       567788888888999999999955555....556666554459*******999999889988752..668888**** PP

                                       SGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  69 speyrgkGlGsaLlealeeraree.gikkivlaveedndaairlYeklGF 117
                                        +e+rgk lG aL+ ++++ +  e  +++ +l+v+++n++ai lYeklG+
  gi|320100935|ref|YP_004176527.1| 110 LSEHRGKSLGYALMAHAMRSMYYEyKCNETYLEVRVSNTPAISLYEKLGY 159
                                       ******************9999999**999*******************8 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.1   1.9e-14   3.7e-11       4      75 ..      68     160 ..      64     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.9e-14
                                       EEEEEEET.TEEEEEEEEEEES............TCTEE...EEE-GGGTTSSHHHHHHHHTT......SEEEEEEE CS
                    Acetyltransf_7   4 evfVaedd.gkivGfialslld............aeitr...laVdpeyrgkGiGraLleaae......kgiileql 58 
                                        ++Vae   g++vG+i   +++            +   +   +aV+ e+rgk +G aL+++a        +++  ++
  gi|320100935|ref|YP_004176527.1|  68 AFYVAEAPsGEVVGYIMTRVEWkpgffhrflarsG---HvvsIAVLSEHRGKSLGYALMAHAMrsmyyeYKCN--ET 139
                                       599998889999**99988888*998887765444...1556******************8333344322243..23 PP

                                       EE....THHHHHHHHHHTTEE CS
                    Acetyltransf_7  59 el....naekaikfYeklGFe 75 
                                       +l    ++++ai++YeklG+ 
  gi|320100935|ref|YP_004176527.1| 140 YLevrvSNTPAISLYEKLGYS 160
                                       4433434459*********97 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   8.1e-12   1.6e-08      29     112 ..      66     165 ..      47     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 8.1e-12
                   Acetyltransf_10  29 gealllvaeeggkivGvielrdgs.............hisllfVdpeyrgqGigkaLleaveee.aekdgikl.elt 90 
                                       g+a++++   +g++vG+i +r ++             h+  ++V +e+rg+ +g aL+ ++ +  + + + ++  l+
  gi|320100935|ref|YP_004176527.1|  66 GKAFYVAEAPSGEVVGYIMTRVEWkpgffhrflarsgHVVSIAVLSEHRGKSLGYALMAHAMRSmYYEYKCNEtYLE 142
                                       5555555556799999996677777788999999999**********************999986556666668*** PP

                   Acetyltransf_10  91 vnasp.yavpfYeklGFkavgee 112
                                       v+ s+  a+++YeklG+ +v+ e
  gi|320100935|ref|YP_004176527.1| 143 VRVSNtPAISLYEKLGYSKVKVE 165
                                       *****9************99554 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   3.7e-11   7.3e-08      21      81 ..     101     163 ..      95     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.7e-11
                                       TSSEEEEEE-GGG-SSSHHHHHHH.HHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEEE CS
                              FR47  21 ggelgalqvlpehrrrGlgsrlvk.alakeiae.rgktvllvvvasNtpsirlyeklGfekie 81 
                                       +g + ++ vl ehr++ lg  l + a+     e + ++  l v+ sNtp+i+lyeklG+ k +
  gi|320100935|ref|YP_004176527.1| 101 SGHVVSIAVLSEHRGKSLGYALMAhAMRSMYYEyKCNETYLEVRVSNTPAISLYEKLGYSKVK 163
                                       688999*************9886615555556689999*********************9984 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.92   1.8e+03      87     104 ..       6      23 ..       4      26 .. 0.87
   2 !   24.2   0.5   1.4e-08   2.8e-05       2     127 ..      30     161 ..      29     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.92
                                       TS-HHHHHHHHHHHHHHH CS
                    Acetyltransf_9  87 grgvlskLlaraleemre 104
                                       gr ++ +L ++ale++r 
  gi|320100935|ref|YP_004176527.1|   6 GRPHVDALFNTALERLRN 23 
                                       789999********9996 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.4e-08
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTT..SEEEEEEE.TTEEEEEEEEEEEEEEETT.EEEEE. CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrkllee..srvlgaed.ngelvgqlallplelnvpG.ktlka. 73 
                                       ir++t++d+d v+e+   a  ++ ++      +f++l+e+  + +++ae   ge+vg + ++++e++ +   ++ a 
  gi|320100935|ref|YP_004176527.1|  30 IRNATSSDIDRVIEINMVALPEHYPRG-----FFEELYEDygKAFYVAEApSGEVVG-YIMTRVEWKPGFfHRFLAr 100
                                       9**************999999999985.....5666666543467777778999999.5578999986556666554 PP

                                       .EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  74 .agvtgVavapehrgrgvlskLlaraleemree.gqplsllfP.....ssipiYrrfGyei 127
                                        + v+++av  ehrg+ +  +L+a+a++ m+ e + + ++l        +i++Y+++Gy++
  gi|320100935|ref|YP_004176527.1| 101 sGHVVSIAVLSEHRGKSLGYALMAHAMRSMYYEyKCNETYLEVrvsntPAISLYEKLGYSK 161
                                       59**************************999885555555544433332378999999975 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.3   4.5e-08     9e-05      48     149 ..      66     174 ..      30     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.5e-08
                    Acetyltransf_4  48 keyvflvae.sdrivGyaylg.q.....fkkr..akdwkaelsvylaerdnnkeglgrelidaleqvl.keqnienl 114
                                       ++ ++ ++  s+++vGy   + +     f+ r  a+++++     l     + ++lg +l+++ +  +  e+  ++ 
  gi|320100935|ref|YP_004176527.1|  66 GKAFYVAEApSGEVVGYIMTRvEwkpgfFH-RflARSGHVVSIAVLS--EHRGKSLGYALMAHAMRSMyYEYKCNET 139
                                       5666666669*******9877323333233.4478888887666664..58899999999999997777******** PP

                    Acetyltransf_4 115 laeiaspnensiqfhkalGFelvgifkkcikkngr 149
                                       + e+ ++n+++i ++++lG+++v+ +k+++ ++  
  gi|320100935|ref|YP_004176527.1| 140 YLEVRVSNTPAISLYEKLGYSKVKVEKGYYLDGED 174
                                       ***************************99877665 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   4.9e-08   9.7e-05      89     141 ..     111     163 ..     100     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.9e-08
                                       HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                        e+rgk l+ al+ + ++ +  + +++   +E +v+N+ ai+l+ek+G+ k+k
  gi|320100935|ref|YP_004176527.1| 111 SEHRGKSLGYALMAHAMRSMYYEYKCNETYLEVRVSNTPAISLYEKLGYSKVK 163
                                       5799*********************************************9986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.8e-06    0.0036      45     137 ..      58     159 ..      15     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                    Acetyltransf_3  45 waeeseeegygwaivlkdtgv.iGsvglrdleeedee.........aelgymlapsfwgkGyateavralleyafee 111
                                       ++e +e+ g  + + + ++g+ +G+++ r +e+++++           +++ + ++++gk ++   ++ +++ ++ e
  gi|320100935|ref|YP_004176527.1|  58 FEELYEDYGKAFYVAEAPSGEvVGYIMTR-VEWKPGFfhrflarsgHVVSIAVLSEHRGKSLGYALMAHAMRSMYYE 133
                                       4444444554577878777766****655.78887778889*999888889999******99999999999999999 PP

                    Acetyltransf_3 112 lglerlvavidkeNeaSirvleklGf 137
                                        + ++ + ++  +N+  i ++eklG+
  gi|320100935|ref|YP_004176527.1| 134 YKCNETYLEVRVSNTPAISLYEKLGY 159
                                       99***********************7 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.2e-05      0.18     177     238 ..      98     163 ..      81     168 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.2e-05
                   GNAT_acetyltran 177 vyekgieieidTkedyrrkgLAtivaaalileclk....rglyPsWDaaneaSvaLaekLGYefek 238
                                         ++g+ ++i+  +++r+k L +++ a+  +        ++ y +    n+++++L+ekLGY  +k
  gi|320100935|ref|YP_004176527.1|  98 LARSGHVVSIAVLSEHRGKSLGYALMAHAMRSMYYeykcNETYLEVRVSNTPAISLYEKLGYSKVK 163
                                       67899***************99988777665444301113444444445*************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1306.04
//
Query:       gi|320100936|ref|YP_004176528.1|  [L=404]
Description: phosphopantothenoylcysteine decarboxylase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-56  188.9   0.0    2.1e-54  184.2   0.0    2.2  2  DFP           DNA / pantothenate metabolism flavoprotein
    2.6e-31  108.5   0.0    4.7e-31  107.7   0.0    1.4  1  Flavoprotein  Flavoprotein


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 ?    2.6   0.0     0.012   1.1e+02      23      62 ..      22      63 ..      18      97 .. 0.67
   2 !  184.2   0.0   2.3e-58   2.1e-54       1     185 [.     188     373 ..     188     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.012
                                      EEE----HHHHHHHHHHHHTT-EEEEEE-S-SS--..-TT-E CS
                               DFP 23 isNrSSGkmGyalAeaaaarGaeVtlvsgpvslet..pegve 62
                                      ++ +SS    + lA++++++G +V++v  + sl+   p+ v+
  gi|320100936|ref|YP_004176528.1| 22 LTASSSIYKSIDLARRLIRMGGSVRVVLTKRSLTLigPDLVH 63
                                      677888889999***************999776642244444 PP

  == domain 2  score: 184.2 bits;  conditional E-value: 2.3e-58
                                       TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHH CS
                               DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleave 77 
                                       l+g++vlvtaGpTrE+iDpVR+i+N+SSG mG+ +A+++a rGa+V lv+gp++++ p +v+   vesa+em+++++
  gi|320100936|ref|YP_004176528.1| 188 LRGRRVLVTAGPTREHIDPVRVITNPSSGLMGVLVARELACRGASVDLVHGPMAVKPPYTVRAFGVESASEMADKIR 264
                                       689*****************************************************9*9****************** PP

                                       HHH..TT-SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-S.S..-HH CS
                               DFP  78 eal..keadivimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaet.e..ell 149
                                       e +   + d++++aAA aDy+p+++ ++Ki+  +e+  l+l+le++p+ ++ +   k + ++lv+Faaet    el+
  gi|320100936|ref|YP_004176528.1| 265 ELTsiVNYDAAVFAAAPADYKPATTMQTKIST-REKPVLELRLEPTPKTIRAIV--K-RPRVLVAFAAETcGgeELV 337
                                       88733566***********************7.77889***************4..3.456********97367*** PP

                                       HHHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE CS
                               DFP 150 enareklerkgldlivaNdvskeeagfgsdenevtl 185
                                       e+a +k ++ g+dl+v N+vs+++agfg+d  +v++
  gi|320100936|ref|YP_004176528.1| 338 ERALHKAADYGADLVVGNNVSSSNAGFGKDMLDVVM 373
                                       *****************************9988876 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0   5.3e-35   4.7e-31       2     150 ..      17     174 ..      16     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 5.3e-35
                                       EEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG.......GS....TCSSHHHHHHCTTESEEEEE CS
                      Flavoprotein   2 killgiTGsvaaikalellekLkkegievqvvltkaAkkfiske.......klklaaredpilhielrrwadllvia 71 
                                       +++lg+T s++++k ++l ++L++ g +v+vvltk +  +i ++       +  +++++++ +hi+l+rw d+++ia
  gi|320100936|ref|YP_004176528.1|  17 NLVLGLTASSSIYKSIDLARRLIRMGGSVRVVLTKRSLTLIGPDlvhwatgSKPFHEMSGETEHIDLARWGDAMIIA 93 
                                       689***************************************996655555555555******************** PP

                                       EEEHHHHHHHHTT--SSHHHHHH..HTHCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT................GH CS
                      Flavoprotein  72 PasantlakianGiadnlltlil..ratakkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkgkma 145
                                       Pa+ nt+akia G+ d lltl++  ++++ k+++++Pamn +++++pq ++   +l e g +++ P   +++k+k++
  gi|320100936|ref|YP_004176528.1|  94 PATLNTMAKIAGGVLDELLTLTAvtMMGSGKKVMLVPAMNLRLMNSPQYKRITGILeEYGAIIVPPM-VEEDKAKYP 169
                                       *******************999854559****************************669****9999.556666655 PP

                                       HHHHH CS
                      Flavoprotein 146 eieei 150
                                        ++++
  gi|320100936|ref|YP_004176528.1| 170 PLDDL 174
                                       54444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3285.39
//
Query:       gi|320100937|ref|YP_004176529.1|  [L=312]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2607.38
//
Query:       gi|320100938|ref|YP_004176530.1|  [L=258]
Description: pantothenate synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-78  261.5   3.1    3.3e-78  261.3   3.1    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
      0.083   13.7   0.1       0.14   13.0   0.1    1.3  1  Sfi1_C    Spindle body associated protein C-terminus


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 !  261.3   3.1   3.7e-82   3.3e-78       1     176 []      65     242 ..      65     242 .. 0.99

  Alignments for each domain:
  == domain 1  score: 261.3 bits;  conditional E-value: 3.7e-82
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleeda..ripeles 75 
                                       +llak+pvisvNGNtaaLv++eiveLae++gak+evNlfyrt+eR+e++a+ l e+ga evlg+ eda  +ipel s
  gi|320100938|ref|YP_004176530.1|  65 MLLAKHPVISVNGNTAALVPREIVELAETVGAKIEVNLFYRTREREEAVARQLLEHGAVEVLGVGEDAsaTIPELFS 141
                                       699*************************************************************9999889****** PP

                            PPS_PS  76 eRakvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkks 152
                                       eR++vs +Gi+ aDvvlvplEDGDR+eaL++mgK+via+DLNPlsRtar+a++tivdn+vRa+p +++++k+lk+++
  gi|320100938|ref|YP_004176530.1| 142 ERRRVSPRGILIADVVLVPLEDGDRTEALRRMGKTVIAVDLNPLSRTARAASVTIVDNIVRAIPLMIKEAKQLKSME 218
                                       ***************************************************************************** PP

                            PPS_PS 153 keeleeivkefdnkkvlkealkei 176
                                       k++lee+++++dn++vl+eal++i
  gi|320100938|ref|YP_004176530.1| 219 KARLEEMIRSYDNNAVLQEALRAI 242
                                       ********************9876 PP

>> Sfi1_C  Spindle body associated protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05      0.14      42      89 ..     201     248 ..     197     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                            Sfi1_C  42 rraiPSPiKsssvldstvKkklekeektaakeskakeppklslerink 89 
                                        raiP  iK +++l s  K++le++ +++ ++   +e+ +  ler   
  gi|320100938|ref|YP_004176530.1| 201 VRAIPLMIKEAKQLKSMEKARLEEMIRSYDNNAVLQEALRAILERLRE 248
                                       59***********************99999998888888887777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2171.25
//
Query:       gi|320100939|ref|YP_004176531.1|  [L=293]
Description: GHMP kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.017   15.3   2.5      0.033   14.4   2.5    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.5   1.8e-06     0.033       5      66 .]      75     134 ..      71     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-06
                                       EESSHTTSSSCHHHHHHHHHHHHHHHHTTEH.HHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   5 kseiPvgaGLGSSAAlavalvaAllallgls.leeaklaleaerlaqggngsggDvaasvyGg 66 
                                       +s + +g+G+G SA l  a ++A++++ gl+ l   +  ++a+ l ++ +++ gDv   + Gg
  gi|320100939|ref|YP_004176531.1|  75 YSPVSLGSGFGLSAGLLIAHALAAYRAKGLPsL---RAFQVAHVLEVKYSTGLGDVLSEYTGG 134
                                       577889***********************9955...556666655566779999997777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 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:                        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 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2322.16
//
Query:       gi|320100940|ref|YP_004176532.1|  [L=425]
Description: phosphoglycerate mutase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-50  171.0   0.0    2.6e-50  170.6   0.0    1.2  1  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    2.5e-29  102.4   0.0    3.1e-29  102.1   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
     0.0071   16.0   0.0      0.011   15.4   0.0    1.2  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


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 !  170.6   0.0   4.4e-54   2.6e-50       1     170 []      36     226 ..      36     226 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 4.4e-54
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-.EEEEEEEEEEC..TTCEEETT CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgd.vafRcnlvtvdeedgiiidrr 76 
                                       A+++++Gl++tv +giap+Sd A++silGydp+++ytGRGplEAlg+Gle+++g  vafR+n++t+d+++++iidrr
  gi|320100940|ref|YP_004176532.1|  36 ARNSKCGLMYTVGKGIAPESDEAVISILGYDPHEVYTGRGPLEALGAGLEIREGYeVAFRANFATIDPSTRVIIDRR 112
                                       89****************************************************77********************* PP

                                       GGG-..-TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE......--S-B--S--..SSTTS..........- CS
                      PhosphMutase  77 agri.steeakeLikalneel.e.egvevkfypgveyrhllvl......lsdkitdtdpphdkegk..........e 134
                                        gr  st eakeL+ka+++     ++ ++k+ +++++r+++v+      ls ++ + dp+++++g           +
  gi|320100940|ref|YP_004176532.1| 113 VGRSlSTAEAKELAKAVDGLElGiHEGYAKVVATIGHRAVVVIgsrrhrLSPMVDNNDPAYKRHGMvsvavpspsrK 189
                                       ***99**************99966899**************************************999999999999 PP

                                       -----BS..SGGGHHHHHHHHHHHHHHHHHHHHSHHH CS
                      PhosphMutase 135 ikellpl.kseeaketaellnelieksqeiLedhpvN 170
                                       + +++pl +++eak  ae+ ne+ e+s eiL++hpvN
  gi|320100940|ref|YP_004176532.1| 190 VPKIMPLdDTAEAKVAAEIANEFFERSLEILSKHPVN 226
                                       9999999889999***********************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0   5.1e-33   3.1e-29       3     237 ..       5     409 ..       3     417 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 5.1e-33
                                       EEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                     Metalloenzyme   3 vvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel............ 67 
                                       ++ +vlDG+G++ +d++  ++++ +P ld  + +       +++g+++++ +++ + s+ + +++            
  gi|320100940|ref|YP_004176532.1|   5 LLYLVLDGMGDRLSDPVTTLELSVKPGLDWVARN-------SKCGLMYTVGKGIAPESDEAVISIlgydphevytgr 74 
                                       5679******************************.......89****************999999999999999*** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|320100940|ref|YP_004176532.1|  75 gplealgagleiregyevafranfatidpstrviidrrvgrslstaeakelakavdglelgihegyakvvatighra 151
                                       ***************************************************************************** PP

                                       ............................................................................H CS
                                       ............................................................................x RF
                     Metalloenzyme  68 ............................................................................l 68 
                                                                                                                    
  gi|320100940|ref|YP_004176532.1| 152 vvvigsrrhrlspmvdnndpaykrhgmvsvavpspsrkvpkimplddtaeakvaaeianeffersleilskhpvnaE 228
                                       ****************************************************************************9 PP

                                       HHHTT-----EEEEEEEE-S---SS.HHHHHT--EEEE--SHH....................STT--HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxx RF
                     Metalloenzyme  69 risetvkfahvtffwnggrsgyfnp.leereeipsdtvitfdl....................qpemkavevaekal 124
                                       r  ++  +a+ ++++++g s +    l e+++ + ++++++ +                    +p+ ++++  e al
  gi|320100940|ref|YP_004176532.1| 229 RARKGLLPANAILMRDAGGSLPRAVkLPEKYGCRFAVLAEMPVevgigrafgaetiimepptgNPARDYEARLETAL 305
                                       99*************9887765555588899999998888888********************************** PP

                                       HHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHH.HHHHHHTTS-TTTEEEEEE-SSB--TTTSS....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 125 dailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDe.avkeildaieqvdgilvvtADHgnaedmvkrdkqplT 200
                                       +a+  g+  +v+v++k +D+ GH+gd+e + + ie++D+  v+ ++d+++++   l+vtADH ++++++        
  gi|320100940|ref|YP_004176532.1| 306 KAL--GDNHIVYVHLKGPDEPGHDGDVESKKKRIEEIDRyFVQPLIDEVRDKY-ALIVTADHATPPSVKA------- 372
                                       ***..6679******************************89********9998.****************....... PP

                                       .-----EEEEEESTT----S--S.SHHHHTT-TTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                     Metalloenzyme 201 sHtlepVPilivgkglapdkvke.gakfrekggLanva 237
                                        Ht +pVP++++ +g++pd v++ +++ + kg+L+ ++
  gi|320100940|ref|YP_004176532.1| 373 -HTDDPVPVAFYMPGIEPDGVSRfTERDCGKGSLGLIE 409
                                       .********************999999999***99886 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-06     0.011     170     238 ..     305     370 ..     254     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                                       T...SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHH.HHHHHHHHHHHTTGTTTEEEEEEES---EEEH CS
                      Phosphodiest 170 l...ekpdlllvyleetDtvgHkfGpdspevedalrrvDk.aigdLlealderglsaetniilvSDHGmadvs 238
                                       l   ++   ++v+l ++D  gH    +s   ++ ++++D+ +++ L+++++++     +++i+++DH   +  
  gi|320100940|ref|YP_004176532.1| 305 LkalGDNHIVYVHLKGPDEPGHDGDVES--KKKRIEEIDRyFVQPLIDEVRDK-----YALIVTADHATPPSV 370
                                       1334888899************763333..4589*****956999********.....*********988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3311.25
//
Query:       gi|320100941|ref|YP_004176533.1|  [L=256]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-24   85.5   0.0      6e-24   85.1   0.0    1.2  1  ABC_tran  ABC transporter
    3.7e-15   56.5   0.1    4.5e-08   33.2   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00023   20.7   0.4      0.017   14.6   0.4    2.1  1  SMC_N     RecF/RecN/SMC N terminal domain
     0.0037   17.8   0.1     0.0076   16.8   0.1    1.5  1  AAA_23    AAA domain
     0.0045   16.7   0.0      0.011   15.5   0.0    1.6  2  AAA_30    AAA domain
     0.0056   16.4   0.1      0.011   15.5   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.017   15.5   0.0    1.3  1  AAA_16    AAA ATPase domain
      0.031   13.9   0.1      0.055   13.1   0.1    1.3  1  SRP54     SRP54-type protein, GTPase domain
      0.036   13.8   0.0       0.15   11.8   0.0    1.5  2  AAA_15    AAA ATPase domain
      0.036   14.5   0.0      0.068   13.6   0.0    1.5  1  AAA       ATPase family associated with various cellular acti
       0.11   12.8   0.2       0.19   12.0   0.2    1.7  1  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   3.7e-27     6e-24       2     136 ..      33     174 ..      32     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 3.7e-27
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++s++++ ge+++++G+nG+GK+t l+++a l kp +Ge+l+ g +  + e  ++r+ i +lp+e+   ++lt  +
  gi|320100941|ref|YP_004176533.1|  33 RDLSFNVRSGEIYGLIGPNGSGKTTTLRIVATLIKPSSGEVLVYGVNAVK-EPLKARQLINYLPEEAGAYRDLTGLD 108
                                       689*****************************************988888.4667899***************9989 PP

                                       H.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 + ++  e++ + +g+ +   + +++  +++S+G+k+ +al  +l++kpkl++lDEpt
  gi|320100941|ref|YP_004176533.1| 109 FirfmlslrfKGKALEETVEEAVGIAD-LGNSLRKPVRTYSKGMKRILALSVVLASKPKLMILDEPT 174
                                       89****998744444455555556555.555555666*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   8.4e-08   0.00014       2      80 ..      45     120 ..      44     132 .. 0.68
   2 !   33.2   0.0   2.8e-11   4.5e-08     233     300 ..     143     208 ..     108     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.4e-08
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        +liGpNgsGK++ L++   l    +++        + ++++  ++ l +y pe+++++++  ++++ +r+  +lr+
  gi|320100941|ref|YP_004176533.1|  45 YGLIGPNGSGKTTTLRIVATLI--KPSSGEVLVYGVNAVKEPLKARQLINYLPEEAGAYRDL-TGLDFIRFMLSLRF 118
                                       68****************8885..45555555555555666666666666677766666666.66666666666666 PP

                            AAA_21  79 er 80 
                                       + 
  gi|320100941|ref|YP_004176533.1| 119 KG 120
                                       55 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 2.8e-11
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpl 300
                                       p+r  S G+kr+lal + l++ +   +l ++DEp +gL+ ++   + +l+ k++++ g  v+l++H+ l
  gi|320100941|ref|YP_004176533.1| 143 PVRTYSKGMKRILALSVVLASKP---KLMILDEPTTGLDVERSIYVRDLVkKYNRELGLTVLLSSHNML 208
                                       67888***************988...9*************9999999***666666**********976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.4     1e-05     0.017      27     207 ..      45     213 ..      33     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                       EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSC...EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekee...vsis 100
                                         ++GpNGSGK+  l  +        a+ ++ ++ + l++  ++ ++  ka+  i +  e++ +  + +    +  +
  gi|320100941|ref|YP_004176533.1|  45 YGLIGPNGSGKTTTLRIV--------ATLIKPSSGEVLVYGVNAVKEPLKARQLINYLPEEAGAYRDLTGldfIRFM 113
                                       568999999999988777........335788888999999888888999988888866665545555551113444 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                        ++  kg+   +++++  +   +++l +s +    + S G k ++al++++A +   p  l++lDe    LD ++  
  gi|320100941|ref|YP_004176533.1| 114 LSLRFKGK---ALEETVEEAVGIADLGNSLRKPVRTYSKGMKRILALSVVLASK---P-KLMILDEPTTGLDVERSI 183
                                       44444444...55555555566666666666667889*************9964...3.4899************** PP

                                       HHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkeksknaQfivislreemlekadk 207
                                        v +l+k+ + +  + v   +++mle  + 
  gi|320100941|ref|YP_004176533.1| 184 YVRDLVKKYNRELGLTVLLSSHNMLEVERL 213
                                       *******99999988888888888876654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   4.6e-06    0.0076      10      37 ..      30      60 ..      16      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.6e-06
                            AAA_23 10 f..rdqeidF.skgltlItGpNGaGKTTild 37
                                      +  rd +++  s  ++ ++GpNG+GKTT l+
  gi|320100941|ref|YP_004176533.1| 30 IgvRDLSFNVrSGEIYGLIGPNGSGKTTTLR 60
                                      444556666677789*************987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.7e-06     0.011      20      53 ..      44      77 ..      37     102 .. 0.87
   2 ?   -2.5   0.0       2.1   3.4e+03      69      96 ..     143     172 ..     115     175 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.7e-06
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglA 53
                                      +  l Gp G+GKtt+l+ ++ +++ + g+v+++ 
  gi|320100941|ref|YP_004176533.1| 44 IYGLIGPNGSGKTTTLRIVATLIKPSSGEVLVYG 77
                                      77899*******************9988888765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                            AAA_30  69 eastiakllkrlk..grarlepg.tllivDE 96 
                                       + +t  k +kr    + + l+++ +l+i DE
  gi|320100941|ref|YP_004176533.1| 143 PVRTYSKGMKRILalS-VVLASKpKLMILDE 172
                                       3333333333332543.23334447777777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   6.5e-06     0.011      19      50 ..      37      70 ..      22      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                            AAA_29 19 idlkg..atlltGpsGsGKSTllDAiqalLvpak 50
                                      +++++  ++ l+Gp+GsGK+T l  +++l+ p++
  gi|320100941|ref|YP_004176533.1| 37 FNVRSgeIYGLIGPNGSGKTTTLRIVATLIKPSS 70
                                      4433336899***********9988888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0     1e-05     0.017      18      88 ..      38      97 ..      23     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqllde 88
                                      +vrsg  e+  l+G+ G+GK++ +r +++ ++ + g + ++g +             + l++++l++ l +e
  gi|320100941|ref|YP_004176533.1| 38 NVRSG--EIYGLIGPNGSGKTTTLRIVATLIKPSSGEVlVYGVNAVK----------EPLKARQLINYLPEE 97
                                      45666..78899****************9999884444355544444..........555666666666666 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.4e-05     0.055       6      34 ..      47      75 ..      43      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvll 34
                                      l+G++G+GKTttl  +a l+k +  +vl+
  gi|320100941|ref|YP_004176533.1| 47 LIGPNGSGKTTTLRIVATLIKPSSGEVLV 75
                                      89***************999988777776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     9e-05      0.15      27      49 ..      46      68 ..      33      73 .. 0.83
   2 ?   -1.5   0.0      0.94   1.5e+03     288     313 ..     138     163 ..      80     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9e-05
                            AAA_15 27 vliGkNnsGKSsilealdlFlnn 49
                                       liG+N+sGK++ l++   +++ 
  gi|320100941|ref|YP_004176533.1| 46 GLIGPNGSGKTTTLRIVATLIKP 68
                                      59************998777765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.94
                            AAA_15 288 ddeelplnknGsGvqrllllillile 313
                                       +  + p+   + G++r+l l++ +++
  gi|320100941|ref|YP_004176533.1| 138 NSLRKPVRTYSKGMKRILALSVVLAS 163
                                       55666777888999999998877665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.2e-05     0.068       3      23 ..      47      67 ..      45     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      l+Gp G GKT++ + va+ ++
  gi|320100941|ref|YP_004176533.1| 47 LIGPNGSGKTTTLRIVATLIK 67
                                      89***************9875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00012      0.19       7      28 ..      44      65 ..      39     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                            AAA_22  7 ilvvtGesGtGKTtllrrlleq 28
                                      i  ++G+ G+GKTt+lr ++  
  gi|320100941|ref|YP_004176533.1| 44 IYGLIGPNGSGKTTTLRIVATL 65
                                      6669************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1739.00
//
Query:       gi|320100942|ref|YP_004176534.1|  [L=417]
Description: Na+ ABC transporter permease [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   67.1  31.6    1.8e-18   66.8  31.6    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    4.3e-08   32.8  43.7    9.2e-08   31.7  43.7    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein
    8.8e-05   22.0  21.2    8.8e-05   22.0  21.2    3.4  3  ABC2_membrane    ABC-2 type transporter
     0.0042   17.1  12.2     0.0042   17.1  12.2    3.4  4  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8  31.6   4.1e-22   1.8e-18       3     343 ..      20     398 ..      18     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 4.1e-22
                   ABC2_membrane_3   3 fliitlllPiilvlllglifsnsve....ddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalk 75 
                                       f+ +++++ +++++ lg i+ +sve    ++++++i+vv e++++l +ql++ l+ + + +   +++s++ea +   
  gi|320100942|ref|YP_004176534.1|  20 FI-MSIIILVVFYASLGGIMRTSVEsavrEASSISIGVVKEEDTPLVNQLIAVLNHYTNGS-LGFYSSLDEAVE--- 91 
                                       66.99999999999999999*999977778**************************99999.99******9974... PP

                   ABC2_membrane_3  76 ngdidgilvipkgfskdll..........kgesatvtvlinssnlnsskailnalnsllqqlnasalvlqseatsts 142
                                         ++  ++ ip gf+ +++            +  +++ +i+++ l+++++i+++l++ll   +           s+ 
  gi|320100942|ref|YP_004176534.1|  92 --KAGVAILIPRGFTVNATtpgrslmlkgGVKIESLSPIISQARLSVVSSIASTLSNLLPVAI-----------SQL 155
                                       ..44456789*****998898888888874444556667777777777888888888654433...........333 PP

                   ABC2_membrane_3 143 aninvestqleeelsnvasf...................lvgliliilifitasfiavsiveEkesrikelqlvsgv 200
                                        n++ve   ++   +n++++                   + +li + ++ i a+++a++ + Ek  ++ e++l  ++
  gi|320100942|ref|YP_004176534.1| 156 YNVSVEP-GKQVVVDNYVRIygrtmtvaefnavvgvlsmIPTLIGL-VVGINAAYAAQATAIEKVEKAFEMLLAQPI 230
                                       4444433.22222233333333333333334422211104444444.3556688899999***************** PP

                   ABC2_membrane_3 201 splqywlskilgdflvyllqlllill...lafgl...................gipfg...nlglllllfllfglay 252
                                        + + +++ki+g +++++++   +++   l++++                   +  +     + l+++ ++l+++ +
  gi|320100942|ref|YP_004176534.1| 231 PRRSVVVAKIIGAVVASMIMGTAYMVamlLMLASvvpsgmvgnessqliqstmS--VAgpfVIALIIFSMVLGLIYS 305
                                       ********************988776543588889**************88542..332223345668999999999 PP

                   ABC2_membrane_3 253 ialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrli.tgdplweil.l 327
                                        a+g l++++++++++a +l +++ill++g+ ++++ l  + +++  ++s + ++ ++ + ++ + +g++ +  l  
  gi|320100942|ref|YP_004176534.1| 306 GAMGVLVGAVVSDERMAGVLSTPIILLFMGVGFAVMYLGMPLNTITAVLSGLSIVPIAFVVINASlSGQYVYAALsV 382
                                       9***********************************999777**********************7566644443336 PP

                   ABC2_membrane_3 328 sliilalfavvyllla 343
                                       s+++la +av +++++
  gi|320100942|ref|YP_004176534.1| 383 SIAVLATLAVMLIAIV 398
                                       6666666666665554 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7  43.7     2e-11   9.2e-08       5     285 ..       8     402 ..       5     404 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2e-11
                   ABC2_membrane_2   5 kkEfrdlvrsrrfllltvllpli....................dvalaylkdlgsslqseakaikeatlaleyveaa 61 
                                        +E++ +++++ f+   ++l+++                       + ++k+ ++ l ++  a+             
  gi|320100942|ref|YP_004176534.1|   8 VREVKSFLKNPAFIMSIIILVVFyaslggimrtsvesavreasSISIGVVKEEDTPLVNQLIAVL------------ 72 
                                       57999999999999999999999555555555555554444443333333333333333333333............ PP

                   ABC2_membrane_2  62 sasdeaedtdqdlkv.............................................................. 76 
                                                     +                                                              
  gi|320100942|ref|YP_004176534.1|  73 --------------Nhytngslgfyssldeavekagvailiprgftvnattpgrslmlkggvkieslspiisqarls 135
                                       ..............244444444455555555555666777999999999999999999999999999999999999 PP

                   ABC2_membrane_2  77 .......................................................vstimavlipvi..aalfgada 96 
                                                                                              +s+i ++++ v+   a+ +a+a
  gi|320100942|ref|YP_004176534.1| 136 vvssiastlsnllpvaisqlynvsvepgkqvvvdnyvriygrtmtvaefnavvgvLSMIPTLIGLVVgiNAAYAAQA 212
                                       999999999999999999999999999999*********************99987777777777773334566788 PP

                   ABC2_membrane_2  97 iagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll.............alaiilalgivlaled 160
                                        a Ek ++  + lL++P++R++++++K+ig +++++++  a+++++ll             +     ++ +++a+  
  gi|320100942|ref|YP_004176534.1| 213 TAIEKVEKAFEMLLAQPIPRRSVVVAKIIGAVVASMIMGTAYMVAMLLmlasvvpsgmvgnESSQLIQSTMSVAGPF 289
                                       999**********************************9999999999988888888777665555555556666666 PP

                   ABC2_membrane_2 161 llllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflslls 237
                                       ++ l+++s++l+l+    a+g+l+ +v+ + r a  l+  ++++++ +   v   ++++l+      +i+  ls ls
  gi|320100942|ref|YP_004176534.1| 290 VIALIIFSMVLGLIY-SGAMGVLVGAVVSDERMAGVLSTPIILLFMGVGFAVM-YLGMPLN------TITAVLSGLS 358
                                       666677777777766.59***********888887777777777754443333.4445554......35668***** PP

                   ABC2_membrane_2 238 ptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                                       +     +++n+ l+g+    + ++a ++ i +l +++++ +++v+F+r
  gi|320100942|ref|YP_004176534.1| 359 IVPIAFVVINASLSGQ----YVYAALSVSIAVLATLAVMLIAIVVFNR 402
                                       ****************....7999999999999999999999999998 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.02        91       7      38 ..       7      37 ..       3      58 .. 0.56
   2 !   22.0  21.2     2e-08   8.8e-05      52     182 ..     190     342 ..     135     354 .. 0.80
   3 ?   -2.2  11.0      0.51   2.3e+03     108     165 ..     352     408 ..     338     413 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.02
                     ABC2_membrane  7 lkreflqrwrdpslgllwrliqplllalvfgt 38
                                      + re+++++++p+ + ++ +i  +++a + g 
  gi|320100942|ref|YP_004176534.1|  7 VVREVKSFLKNPAFI-MSIIILVVFYASLGGI 37
                                      556666666666444.4444444444444333 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2e-08
                     ABC2_membrane  52 r....pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv. 123
                                            p l++  v  +a  a +++a+ +e+ ++ +e +l+ p+ ++ ++v+ak+++ ++ s+++++++++ +++++ 
  gi|320100942|ref|YP_004176534.1| 190 VlsmiPTLIGLVVGINA--AYAAQATAIEKVEKAFEMLLAQPI-PRRSVVVAKIIGAVVASMIMGTAYMVAMLLMLa 263
                                       03334888888888888..8888889*****************.**************************9999765 PP

                     ABC2_membrane 124 ........gldls...........rf..flflllllltalaasslgllisalapsfedasqlaslvllpllllsGff 179
                                               g + s            f  +l+++ ++l ++++ ++g+l++a+++++++a++l++ ++l+++ + Gf 
  gi|320100942|ref|YP_004176534.1| 264 svvpsgmvGNESSqliqstmsvagPFviALIIFSMVLGLIYSGAMGVLVGAVVSDERMAGVLSTPIILLFMGV-GFA 339
                                       5555544433333666666766543388999999999*******************************99866.555 PP

                     ABC2_membrane 180 ipi 182
                                       +++
  gi|320100942|ref|YP_004176534.1| 340 VMY 342
                                       555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.51
                     ABC2_membrane 108 sllqalifllivyflvgldlsrfflflllllltalaasslgllisalapsfedasqla 165
                                       ++l +l ++ i++++++  ls + +++++l +++ ++ +l+++++a+++  +d+++l+
  gi|320100942|ref|YP_004176534.1| 352 AVLSGLSIVPIAFVVINASLS-GQYVYAALSVSIAVLATLAVMLIAIVVFNRDIVVLG 408
                                       344445555588888888887.888888888888888889999988888888887765 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 ?   -2.4   0.1      0.86   3.8e+03     166     175 ..      21      30 ..      13      45 .. 0.54
   2 !   17.1  12.2   9.3e-07    0.0042      57     159 ..     198     299 ..     165     317 .. 0.59
   3 ?   -1.6  11.2      0.49   2.2e+03     100     174 ..     291     367 ..     274     372 .. 0.60
   4 ?   -6.1  13.6         4   1.8e+04     101     164 ..     339     403 ..     324     412 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.86
                   ABC2_membrane_4 166 vlpliltlvy 175
                                       ++++i+ +v+
  gi|320100942|ref|YP_004176534.1|  21 IMSIIILVVF 30 
                                       2222222111 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9.3e-07
                   ABC2_membrane_4  57 llllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvg.fsvk 132
                                       + l++ i + +a++    E+ ++ +  Ll  P+ r+++++aK+i  ++ s+++  + + +++l+ l s  ++ + ++
  gi|320100942|ref|YP_004176534.1| 198 IGLVVGINAAYAAQATAIEKVEKAFEMLLAQPIPRRSVVVAKIIGAVVASMIMGTAYM-VAMLLMLASVVPSgMVGN 273
                                       223333444567788899**************************99888876665444.444443444443313333 PP

                   ABC2_membrane_4 133 lvlellkkclelgllvffavlpiialv 159
                                          + l ++++ +++ f++ l i+ +v
  gi|320100942|ref|YP_004176534.1| 274 ESSQ-LIQSTMSVAGPFVIALIIFSMV 299
                                       3333.3444445555555555443332 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.49
                   ABC2_membrane_4 100 ivllllsvllmlvtflitvlfallsgfvgfs....vklvlellkkclelgllvffavlpiialvl.lkksyvlplil 171
                                       i+l+++s++l l+    + ++++l+g v+ +    + l + ++  ++ +g  v+++ +p+  +++ l   +++p+++
  gi|320100942|ref|YP_004176534.1| 291 IALIIFSMVLGLI---YSGAMGVLVGAVVSDermaGVLSTPIILLFMGVGFAVMYLGMPLNTITAvLSGLSIVPIAF 364
                                       3344444444444...4444555555554331100334445666777888888888889988865255568999998 PP

                   ABC2_membrane_4 172 tlv 174
                                        ++
  gi|320100942|ref|YP_004176534.1| 365 VVI 367
                                       776 PP

  == domain 4  score: -6.1 bits;  conditional E-value: 4
                   ABC2_membrane_4 101 vllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpi.ialvllkks 164
                                       +++ l + l  +t++++ l  + + fv+++++l  + +   l + + v+++++++ ia+v++++ 
  gi|320100942|ref|YP_004176534.1| 339 AVMYLGMPLNTITAVLSGLSIVPIAFVVINASLSGQYVYAALSVSIAVLATLAVMlIAIVVFNRD 403
                                       34444444555555555566666666677777767777766666666665555543556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1340  (0.0747392); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2729.19
//
Query:       gi|320100943|ref|YP_004176535.1|  [L=268]
Description: ketopantoate hydroxymethyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-108  359.6   0.5   9.7e-108  359.5   0.5    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    9.5e-06   25.2   4.5    0.00018   21.1   1.7    2.8  3  PEP_mutase       Phosphoenolpyruvate phosphomutase
  ------ inclusion threshold ------
      0.071   12.6   0.1       0.15   11.6   0.1    1.5  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.5   0.5  1.6e-111  9.7e-108       1     259 []       4     259 ..       4     259 .. 0.99

  Alignments for each domain:
  == domain 1  score: 359.5 bits;  conditional E-value: 1.6e-111
                   Pantoate_transf   1 kvtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakra 77 
                                       ++tv+d+ kmk + ekiam+Tayd+++Aklvd+agvdviLVGDs+gmvv+g ++t+pv++++m+ h+++V+r+ +ra
  gi|320100943|ref|YP_004176535.1|   4 RITVRDIVKMKGR-EKIAMVTAYDYAMAKLVDQAGVDVILVGDSVGMVVHGFDTTIPVSMDMMLIHVASVSRARPRA 79 
                                       689********88.*************************************************************** PP

                   Pantoate_transf  78 lvvadlPfgsyeaskeqalenAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqg 154
                                       lvvad+Pf+sye+s e+a++nA+ l+k+ gadavKlegg e+ ++v+alv+agipVmgHiGltPq+   +ggy+ +g
  gi|320100943|ref|YP_004176535.1|  80 LVVADMPFLSYETSVEEAVRNAGLLMKA-GADAVKLEGGGEMSDVVRALVRAGIPVMGHIGLTPQRSFLIGGYRRRG 155
                                       ***************************9.************************************************ PP

                   Pantoate_transf 155 kteeeaeklledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvk 231
                                        +e+e +++leda++le+aG+f++v+E + a++a e+t++l++ptI+IG+G+ cdGqvlvlhDllglt ++ p f+k
  gi|320100943|ref|YP_004176535.1| 156 LSEKERDRILEDARELERAGVFSIVIEYTAADVAGEVTRELNVPTICIGSGPFCDGQVLVLHDLLGLT-EHPPPFAK 231
                                       *******************************************************************9.779***** PP

                   Pantoate_transf 232 kyaelaesieeavkaYaeevkegsFPae 259
                                        ya+l+++i +av +Ya+evk+g FP+e
  gi|320100943|ref|YP_004176535.1| 232 AYADLRSMIIKAVGEYAKEVKAGVFPEE 259
                                       **************************85 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.7     3e-08   0.00018       7     107 ..      16     117 ..      10     125 .. 0.89
   2 !    9.6   0.1   9.5e-05      0.57     151     190 ..      90     130 ..      83     146 .. 0.82
   3 ?    2.1   0.0     0.018   1.1e+02      84     107 ..     161     184 ..     150     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3e-08
                        PEP_mutase   7 kgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevv.slPlivDle.dGyg 81 
                                       + e + ++ a+D + ak+v +ag++ + ++      ++G++ +  ++++ +l +v+++ ++  +  + +D+    y+
  gi|320100943|ref|YP_004176535.1|  16 R-EKIAMVTAYDYAMAKLVDQAGVDVILVGDSVGMVVHGFDTTIPVSMDMMLIHVASVSRARpRALVVADMPfLSYE 91 
                                       3.67999***********************99999*************************99445668999745999 PP

                        PEP_mutase  82 espeevaetvrrliaaGvvgvniEDk 107
                                        s+ee  ++   l++aG+ +v +E  
  gi|320100943|ref|YP_004176535.1|  92 TSVEEAVRNAGLLMKAGADAVKLEGG 117
                                       9999999****************965 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 9.5e-05
                        PEP_mutase 151 agagleeaieRaraYaeAGAdgvfvpglqkdae.iaelvaa 190
                                        + ++eea++ a + ++AGAd+v   g+ + ++ +++lv+a
  gi|320100943|ref|YP_004176535.1|  90 YETSVEEAVRNAGLLMKAGADAVKLEGGGEMSDvVRALVRA 130
                                       56789***********************9999967888765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.018
                        PEP_mutase  84 peevaetvrrliaaGvvgvniEDk 107
                                        +++ e  r+l++aGv  ++iE +
  gi|320100943|ref|YP_004176535.1| 161 RDRILEDARELERAGVFSIVIEYT 184
                                       567888999************976 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.5e-05      0.15     109     148 ..       6      45 ..       1      56 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                   Glyco_transf_21 109 rreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspa 148
                                       + +++ ++ G e++a   A Dya++kl+ +aG+ v+l+ +
  gi|320100943|ref|YP_004176535.1|   6 TVRDIVKMKGREKIAMVTAYDYAMAKLVDQAGVDVILVGD 45 
                                       567888999***************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1804.23
//
Query:       gi|320100944|ref|YP_004176536.1|  [L=310]
Description: ketopantoate reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-26   91.8   0.0      5e-26   91.3   0.0    1.2  1  ApbA_C          Ketopantoate reductase PanE/ApbA C terminal
    9.7e-21   74.0   0.0    1.6e-20   73.3   0.0    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.002   18.7   0.0     0.0041   17.7   0.0    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0022   17.7   4.7      0.003   17.2   3.6    1.7  2  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.013   14.7   0.2      0.018   14.3   0.2    1.2  1  FAD_binding_3   FAD binding domain
      0.037   14.3   1.2      0.094   13.0   1.2    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
       0.36   10.8   1.1        1.9    8.5   0.4    2.6  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


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 !   91.3   0.0     2e-29     5e-26       1     123 [.     181     299 ..     181     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 2e-29
                            ApbA_C   1 dirlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan 77 
                                       +i+  rw Kl++na++nplta+++++n+ +l ++ + +l++ +l E  +va+++g+ +++ rl +++   ++ ta+n
  gi|320100944|ref|YP_004176536.1| 181 NIDYYRWLKLALNAVVNPLTAIARSRNRVVL-TGPGLELAKLILSEFTEVARRHGYLFEPRRLLDYIVSNVRSTADN 256
                                       68899************************99.77799**************************************** PP

                            ApbA_C  78 rsSMlqDveagrktEidyinGavvklAeklgvetPvnellyellka 123
                                       +sSM qDv+ag +tE+dyinG+++   ++lg e  vn l++ ++++
  gi|320100944|ref|YP_004176536.1| 257 HSSMAQDVAAGSPTEVDYINGFIA---RELGREPSVNGLITLMIHL 299
                                       **********************85...5666666666666666665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   6.3e-24   1.6e-20       1     148 [.       5     153 ..       5     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 6.3e-24
                                       EEEES-SHHHHHHHHHHHHHTHC..EEEE-SCHHHHH.HHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE CS
                              ApbA   1 iailGaGaiGsllaakLakagad..vtlilrsrrlea.lkknGlrltseggeeilrppealsaeekselepidlviv 74 
                                       ++i+G Ga+G ++a+ L++ag    ++ ++r++ +++ l++ G+r++++ + + +++p+++++  +s   ++  v+ 
  gi|320100944|ref|YP_004176536.1|   5 VCIIGGGAVGATIAYFLYRAGFSgiPVYYGREETVKTvLQQGGIRVHDRVEGVDILVPVVPRHY-ESPVDECRFVFN 80 
                                       69*********************99999999999**99************55555555555555.599********* PP

                                       -SSGGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEEEECS--EEEEE CS
                              ApbA  75 tvKayqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgevhhagkgeikig 148
                                       +vKay++ + +  ++++l+++ v l+lqNG+g++e  +e++  ++  ggv+++ga+r +p ++  +g  +i  g
  gi|320100944|ref|YP_004176536.1|  81 SVKAYSVPATMVLAEEILASDGVLLMLQNGFGSLELAEEKF-GSKAAGGVVYFGAERVSPAHIVYHGGRTIIAG 153
                                       *****************************************.55*******************99887777655 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   0.0   1.6e-06    0.0041       2      81 ..       5      94 ..       4     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.6e-06
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.............-EEECECHHHHHHH-SEEEE CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.............vkvtavdneeaaeeadvvvl 67
                                      ++iiG+G +g+++a  l +ag++   ++ +    +e+++   ++ g             v v ++++e  ++e+ +v+ 
  gi|320100944|ref|YP_004176536.1|  5 VCIIGGGAVGATIAYFLYRAGFSGIPVYYG---REETVKTVLQQGGirvhdrvegvdilVPVVPRHYESPVDECRFVFN 80
                                      79*******************888888855...6777888888888899**********999999************** PP

                                      -S-HHHHHHHHHHC CS
                     F420_oxidored 68 avkpedveevlsel 81
                                      +vk + v++++  +
  gi|320100944|ref|YP_004176536.1| 81 SVKAYSVPATMVLA 94
                                      *******9987555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.6   1.2e-06     0.003       1      22 [.       4      25 ..       4      33 .. 0.87
   2 ?   -2.0   0.0      0.82   2.1e+03     192     227 ..      74     107 ..      36     155 .. 0.47

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-06
                                      EEEEECTSHHHHHHHHHHHHTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg 22
                                      dv+iiGGG +G+++Ay+L r+g
  gi|320100944|ref|YP_004176536.1|  4 DVCIIGGGAVGATIAYFLYRAG 25
                                      9*****************9887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.82
                                       EEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEE CS
                               DAO 192 aadavVnaaGawsdllgllkeldlpispvrgqvlvl 227
                                       +++ v n+  a+s  + ++  l   i +  g  l+l
  gi|320100944|ref|YP_004176536.1|  74 ECRFVFNSVKAYSVPATMV--LAEEILASDGVLLML 107
                                       3455666655554211222..122344444444444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   7.2e-06     0.018       2      26 ..       3      27 ..       2      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.2e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHH CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvr 26
                                       dV+I+G+G +G++ a +L +aG +
  gi|320100944|ref|YP_004176536.1|  3 SDVCIIGGGAVGATIAYFLYRAGFS 27
                                      59*********************76 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   3.7e-05     0.094       1      21 [.       7      27 ..       7      32 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                                      EE--SHHHHHHHHHHHCCTEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfd 21
                                      I+G+G+ G+++Ay+L +agf+
  gi|320100944|ref|YP_004176536.1|  7 IIGGGAVGATIAYFLYRAGFS 27
                                      9***************99985 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4   0.00073       1.9       2      35 ..       5      39 ..       4     113 .. 0.86
   2 ?   -3.3   0.0       3.2   8.1e+03      95     135 ..     205     216 ..     191     229 .. 0.54
   3 ?   -1.8   0.0         1   2.6e+03     134     147 ..     259     272 ..     258     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00073
                                      EEEE--SHHHHHHHHHHHTTT.--EEEE-S-HHHH CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaeng.hevrlwvreeeli 35
                                      ++++G+G+ G ++A  l ++g + + ++  +ee++
  gi|320100944|ref|YP_004176536.1|  5 VCIIGGGAVGATIAYFLYRAGfSGIPVYYGREETV 39
                                      9****************999964444444444333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                                       TT-EEEE---SEET.TTEEHHHHHHHHH-S--EEEEESS-- CS
                    NAD_Gly3P_dh_N  95 kkailvsliKGieegtlkllsevieeelkeekvavlsGpsl 135
                                                                      + +vl+Gp l
  gi|320100944|ref|YP_004176536.1| 205 S-----------------------------RNRVVLTGPGL 216
                                       3.............................33456666543 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1
                                       --HHHHHTT--EEE CS
                    NAD_Gly3P_dh_N 134 slAeEvakgkptav 147
                                       s+A+ va+g pt+v
  gi|320100944|ref|YP_004176536.1| 259 SMAQDVAAGSPTEV 272
                                       89**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2189.16
//
Query:       gi|320100945|ref|YP_004176537.1|  [L=291]
Description: phosphomethylpyrimidine kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-39  135.4   0.0      2e-39  134.8   0.0    1.2  1  ThiP_synth  Thiamine-phosphate synthase
     0.0052   16.5   0.0      0.012   15.4   0.0    1.5  1  HTH_23      Homeodomain-like domain
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.021   14.2   0.0    1.4  1  FAM35_C     Protein family FAM35, C-terminal
      0.032   14.2   0.1      0.069   13.1   0.1    1.5  1  HTH_37      Helix-turn-helix domain
      0.047   13.7   0.0      0.098   12.7   0.0    1.5  1  FPL         Uncharacterised conserved protein


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0   5.6e-43     2e-39       5     163 ..     131     283 ..     128     285 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 5.6e-43
                                       HHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT- CS
                        ThiP_synth   5 alelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpev 81 
                                       al +++++e+++++iPevgsN++ya + + s+ ++++++GRI+r+ ++v v gep++g+s+h++r+ll++   +p  
  gi|320100945|ref|YP_004176537.1| 131 ALLRITSIEGLHRVIPEVGSNLVYAPRPPASVYEIIGLTGRITRTLNGVAVTGEPMYGGSRHLSRLLLTVSTLNPAK 207
                                       78899************************************************************************ PP

                                       -EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCCS-ECEEEE--BCTB--EEEEEESSHHH CS
                        ThiP_synth  82 raainirydekilealeelglkvvefdreeepeevgstmewgvaeaieelevpdviydeGgvGkEpmiyvlgkdaee 158
                                       r+  n ry+e ++eal++lglk +  +++e+ e+      w+  e+ +++  pd+i d Gg+G+Ep++y+++ d +e
  gi|320100945|ref|YP_004176537.1| 208 RVGFNTRYEEVYVEALRDLGLKLAVSGPHEDVEG-----FWKRVEMAARE-KPDAIADLGGKGLEPVVYIFTTDFNE 278
                                       **********************************.....69666665555.59************************ PP

                                       HHHHH CS
                        ThiP_synth 159 vvekv 163
                                       + + +
  gi|320100945|ref|YP_004176537.1| 279 LERIL 283
                                       98876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.3e-06     0.012      12      40 ..      22      50 ..      14      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-06
                            HTH_23 12 lllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      +l ++Gls+++I+ +L+vs+  v + lk+
  gi|320100945|ref|YP_004176537.1| 22 RLSRQGLSQHRISSLLHVSQPMVNKLLKK 50
                                      45567********************9997 PP

>> FAM35_C  Protein family FAM35, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     6e-06     0.021      64     105 ..     110     153 ..     104     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-06
                           FAM35_C  64 kiykqCysCLpltavkryyRpalltvk..dgssevcvqvgsell 105
                                       +i++ C + Lp+     yyR all+++  +g ++v  +vgs+l+
  gi|320100945|ref|YP_004176537.1| 110 EIFTSCSEGLPVDPDVEYYRVALLRITsiEGLHRVIPEVGSNLV 153
                                       7************************9988999***999999986 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.9e-05     0.069      23      54 ..      19      50 ..       7      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT CS
                            HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrg 54
                                      +a  + +++lsq  +  ll+++qP v++ll+ 
  gi|320100945|ref|YP_004176537.1| 19 LAHRLSRQGLSQHRISSLLHVSQPMVNKLLKK 50
                                      6778899**********************984 PP

>> FPL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-05     0.098      66     119 ..      37      99 ..      26     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                               FPL  66 yllSnnhinelielefdf.........edeellayYislLktlslkldketvqfffnekaaeF 119
                                       + +S+ ++n+l++ +++           + e+++yY+ +L +l+++  ++ +++   +  ++ 
  gi|320100945|ref|YP_004176537.1|  37 LHVSQPMVNKLLKKPMEEylrqlhevgLEREVVEYYVEILCSLAFRAPRDRFELASYQVVNTL 99 
                                       5679999*****99998889999999999*****************99998888666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2005.32
//
Query:       gi|320100946|ref|YP_004176538.1|  [L=222]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   12.0   0.1      0.064   11.8   0.1    1.2  1  DUF3589   Beta-mannosyltransferases


Domain annotation for each model (and alignments):
>> DUF3589  Beta-mannosyltransferases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.6e-06     0.064     132     205 ..      79     147 ..      22     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-06
                           DUF3589 132 kkkfkklkfPsflpipfyhnlkktkkryyGpEDpRillvknekgyeEPlivfNskhrkikkakekedkklevkl 205
                                       + + k+ ++ +f  i    ++ +  +   G EDpR+ l   +    EPl + N+ h+   k k      +ev+ 
  gi|320100946|ref|YP_004176538.1|  79 SYTSKNQTWWRFRDIDSVRDAIEAYTGSRGEEDPRLKLLAIKYRSMEPLKMLNTLHKLAVKDK-----LSEVDK 147
                                       566677777778888877777777777889************************998887744.....333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1629.14
//
Query:       gi|320100947|ref|YP_004176539.1|  [L=242]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-29  101.4   0.0    8.2e-29  100.9   0.0    1.2  1  ABC_tran    ABC transporter
    7.4e-13   49.0   0.8    1.6e-05   24.9   0.2    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
     0.0019   18.7   0.1     0.0029   18.1   0.1    1.2  1  AAA_23      AAA domain
     0.0046   16.7   0.0     0.0081   15.9   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
     0.0089   14.7   0.0        0.3    9.7   0.0    2.0  2  AAA_13      AAA domain
  ------ inclusion threshold ------
      0.022   14.5   0.2      0.032   13.9   0.2    1.6  1  AAA_30      AAA domain
      0.025   15.0   0.0      0.032   14.6   0.0    1.3  1  AAA_16      AAA ATPase domain
      0.032   13.7   0.0          2    7.8   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
      0.048   14.1   0.0      0.082   13.3   0.0    1.4  1  AAA         ATPase family associated with various cellular ac
      0.066   13.5   0.1        0.2   11.9   0.0    1.8  2  AAA_28      AAA domain
      0.072   12.7   0.0       0.13   11.9   0.0    1.3  1  SRP54       SRP54-type protein, GTPase domain
      0.098   11.9   0.0       0.19   11.0   0.0    1.4  1  Zeta_toxin  Zeta toxin
       0.11   12.2   0.0       0.92    9.2   0.0    2.0  2  AAA_24      AAA domain
       0.12   12.0   0.0        0.2   11.3   0.0    1.3  1  AAA_15      AAA ATPase domain
       0.16   12.0   0.3         18    5.3   0.1    2.1  2  MutS_V      MutS domain V
       0.18    9.3   0.0       0.23    8.9   0.0    1.1  1  DUF3584     Protein of unknown function (DUF3584)
        0.2   11.2   0.2       0.44   10.1   0.2    1.6  1  cobW        CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   7.8e-32   8.2e-29       2     137 .]      21     161 ..      20     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 7.8e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + vs+++++ge+++++G+nGaGK+tLl+++ag +kpt G++++ g+d  + e e++r+ ig+lp+e++  ++lt  e
  gi|320100947|ref|YP_004176539.1|  21 RGVSFTVRPGEIYGLIGPNGAGKTTLLRIIAGIVKPTRGTVKVYGRDPYR-EFEETRRLIGYLPEEANTYQRLTGLE 96 
                                       689********************************************999.9**********************999 PP

                                       H......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +       +  ++e +++    +    +++++++ ++S+G+k+r+ l ++l++kp l +lDEpt+
  gi|320100947|ref|YP_004176539.1|  97 HllfyarLYGGDVESMVEYGARITGLGDRLHDEAGTYSHGMKRRLLLGAVLMRKPMLAILDEPTS 161
                                       9999988555556666666666666777777888*****************************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 !   24.9   0.2   1.5e-08   1.6e-05       2      22 ..      33      53 ..      32      86 .. 0.81
   2 !   23.0   0.0   5.7e-08     6e-05     235     301 ..     131     195 ..      87     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.5e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +liGpNg+GK++LL+++ ++
  gi|320100947|ref|YP_004176539.1| 33 YGLIGPNGAGKTTLLRIIAGI 53
                                      68****************876 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5.7e-08
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                          S G+kr   ll a+l + +   l ++DEp +gL+ ++  ++ + +  + +++g+ vil++H+ l 
  gi|320100947|ref|YP_004176539.1| 131 GTYSHGMKRR-LLLGAVLMRKP--MLAILDEPTSGLDVHASVSVRRTIrQYVAETGSTVILSSHNMLE 195
                                       44599*****.66666666555..899***********888888888853334469********9875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.7e-06    0.0029      21      40 ..      32      51 ..      18      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                            AAA_23 21 ltlItGpNGaGKTTildAik 40
                                      ++ ++GpNGaGKTT+l+ i 
  gi|320100947|ref|YP_004176539.1| 32 IYGLIGPNGAGKTTLLRIIA 51
                                      77899***********9886 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.6e-06    0.0081      13      39 ..      21      47 ..      10      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.6e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      +g ++++++ +++ l+Gp+G+GK+Tll
  gi|320100947|ref|YP_004176539.1| 21 RGVSFTVRPGEIYGLIGPNGAGKTTLL 47
                                      45678888888999************9 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00028       0.3      23      39 ..      37      53 ..      27      68 .. 0.85
   2 ?    3.0   0.0      0.03        32     528     571 ..     152     193 ..     146     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G NGaGKTtL r+++ +
  gi|320100947|ref|YP_004176539.1| 37 GPNGAGKTTLLRIIAGI 53
                                      89************976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.03
                            AAA_13 528 kivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnl 571
                                          ++D P S LD  ++ +v   i++++  ++  + ++++ Hn+
  gi|320100947|ref|YP_004176539.1| 152 MLAILDEPTSGLDVHASVSVRRTIRQYV--AETGSTVILSSHNM 193
                                       55689**********************9..788999******96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     3e-05     0.032      19      51 ..      31      63 ..      22     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvig 51
                                       +  l Gp G+GKtt+l+ ++ +++   g+v +
  gi|320100947|ref|YP_004176539.1| 31 EIYGLIGPNGAGKTTLLRIIAGIVKPTRGTVKV 63
                                      567799***************999988666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.1e-05     0.032      25      89 ..      31      86 ..      16     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqlldea 89
                                      e+  l+G+ G GK++l+r ++  ++ ++g + ++g+              +  ++++l+  l +ea
  gi|320100947|ref|YP_004176539.1| 31 EIYGLIGPNGAGKTTLLRIIAGIVKPTRGTVkVYGRDPYR----------EFEETRRLIGYLPEEA 86
                                      77789****************6666655444455444333..........3344445666666554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0019         2      26      42 ..      32      48 ..      13      53 .. 0.82
   2 ?    3.8   0.0     0.032        34     153     203 ..     146     195 ..     138     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0019
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlld 42
                                      +  ++GpNG+GK+ ll 
  gi|320100947|ref|YP_004176539.1| 32 IYGLIGPNGAGKTTLLR 48
                                      5579*********9986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.032
                                       HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 153 iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                       + + k   l +lDe  + LD +    v + +++   ++   vi  +++mle
  gi|320100947|ref|YP_004176539.1| 146 VLMRK-PMLAILDEPTSGLDVHASVSVRRTIRQYVAETGSTVILSSHNMLE 195
                                       44444.45899*********************9988877777777777766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.8e-05     0.082       3      23 ..      35      55 ..      33      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-05
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      l+Gp G GKT+l + +a  ++
  gi|320100947|ref|YP_004176539.1| 35 LIGPNGAGKTTLLRIIAGIVK 55
                                      89***************9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019       0.2       4      34 ..      35      72 ..      33      93 .. 0.77
   2 ?   -2.7   0.0       5.8   6.1e+03      81      98 ..      94     111 ..      93     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                            AAA_28  4 itGgestGKTtlleaLa.....argypvv..pEaarei 34
                                      ++G+ ++GKTtll+ +a      rg++ v  ++++re+
  gi|320100947|ref|YP_004176539.1| 35 LIGPNGAGKTTLLRIIAgivkpTRGTVKVygRDPYREF 72
                                      79**************9776655565533366666665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.8
                            AAA_28  81 glldtlaYarayggeaea 98 
                                       gl   l+Yar ygg++e 
  gi|320100947|ref|YP_004176539.1|  94 GLEHLLFYARLYGGDVES 111
                                       5566789*****999665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.13       6      41 ..      35      70 ..      31      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                      l+G++GaGKTt l  +a ++k    +v +   D +R
  gi|320100947|ref|YP_004176539.1| 35 LIGPNGAGKTTLLRIIAGIVKPTRGTVKVYGRDPYR 70
                                      89*******************999999999999998 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.19      21      57 ..      35      72 ..      28      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrld.pDdlRel 57
                                      l G  GAGK++l++ ++  ++++++ v+++ +D +Re+
  gi|320100947|ref|YP_004176539.1| 35 LIGPNGAGKTTLLRIIAGIVKPTRGTVKVYgRDPYREF 72
                                      56889****************99999999735888886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00088      0.92       6      66 ..      34      89 ..      31      93 .. 0.62
   2 ?    0.7   0.0      0.35   3.7e+02     145     172 ..     181     208 ..     159     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00088
                            AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvelaaelady 66
                                       ++Gp+g+GKTtl++ +   + ++   +G+ ++++++    + +e+ +  + +l++e ++y
  gi|320100947|ref|YP_004176539.1| 34 GLIGPNGAGKTTLLRII---AGIVKPTRGTVKVYGRD--PYREFEETRRLIGYLPEEANTY 89
                                      589**********9987...44444444454444444..2345555555555555555555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.35
                            AAA_24 145 ytrlepklgkktanelkeevDlvlranl 172
                                        t+ +  l++  + e+++ +D v+ ++ 
  gi|320100947|ref|YP_004176539.1| 181 ETGSTVILSSHNMLEIEYLCDRVGLISK 208
                                       3566778888888899999998888764 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019       0.2      28      44 ..      35      51 ..      26      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            AAA_15 28 liGkNnsGKSsileald 44
                                      liG+N++GK+++l+++ 
  gi|320100947|ref|YP_004176539.1| 35 LIGPNGAGKTTLLRIIA 51
                                      9*************995 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.017        18       4      21 ..      36      53 ..      34      55 .. 0.87
   2 ?    4.9   0.0     0.023        24      50     133 ..     122     206 ..     108     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                                      E-STTSSHHHHHHHHHHH CS
                            MutS_V  4 tGpnmaGkstylrqvali 21
                                       Gpn aGk t+lr +a i
  gi|320100947|ref|YP_004176539.1| 36 IGPNGAGKTTLLRIIAGI 53
                                      6************99866 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.023
                                       -------SS-HHHHHHHHHHHHHTT.--TTSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES.-GGGG CS
                            MutS_V  50 asDdlakgkstFmvEmlEtasilkn.atekslvilDElGRGtstydGlaialavaeyllekikaktlfatH.yhelt 124
                                        +D+l  +  t+   m+    +    + +  l ilDE   G  +   +++  ++ +y++e + ++++++ H   e+ 
  gi|320100947|ref|YP_004176539.1| 122 LGDRLHDEAGTYSHGMKRRLLLGAVlMRKPMLAILDEPTSGLDVHASVSVRRTIRQYVAE-TGSTVILSSHnMLEIE 197
                                       566677777777666665433322212355689************************998.6788888888245666 PP

                                       GHHHHSTTE CS
                            MutS_V 125 klaekleev 133
                                        l +++  +
  gi|320100947|ref|YP_004176539.1| 198 YLCDRVGLI 206
                                       666655555 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00022      0.23      21      37 ..      34      50 ..      16      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00022
                           DUF3584 21 nieGtNaaGKTtLlrLi 37
                                       + G N+aGKTtLlr+i
  gi|320100947|ref|YP_004176539.1| 34 GLIGPNGAGKTTLLRII 50
                                      57899**********98 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00042      0.44       3      20 ..      33      50 ..      31      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                                      EEEEESTTCCHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhl 20
                                      ++l G+ G+GKTtLl+ +
  gi|320100947|ref|YP_004176539.1| 33 YGLIGPNGAGKTTLLRII 50
                                      6799***********866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1723.31
//
Query:       gi|320100948|ref|YP_004176540.1|  [L=423]
Description: ABC transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   79.6  14.6    2.6e-22   79.4  14.6    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.7e-13   50.5  25.2    4.1e-13   49.3  25.2    1.6  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0011   18.9   9.7     0.0011   18.9   9.7    2.4  3  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4  14.6   4.3e-26   2.6e-22       3     344 ..      24     410 ..      22     411 .. 0.77

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 4.3e-26
                   ABC2_membrane_3   3 fliitlllPiilvlllglifs.nsveddentpiavvdedn..........sslsqqlv..........ealeaspsv 58 
                                        li+t+llP+i +  +gl+   + v  +++++iavvded           +      v          e l+ s+ +
  gi|320100948|ref|YP_004176540.1|  24 ALITTILLPLIAMPAIGLLTVfLMV--QQPVNIAVVDEDAsthvspvfniT------VssrdlaagirEHLSRSG-F 91 
                                       577********99777766542666..8***********985555555553......044333344435555543.6 PP

                   ABC2_membrane_3  59 elvyevdseeeakkalkngdidgilvipkgfskdllkgesatvtvlinssnlnsskailnalnsllqqlnasalv.. 133
                                       + vy + ++  a   l n  id ++vip gf +++++  +   + +i  +n++++++++ ++ +++  + a+  +  
  gi|320100948|ref|YP_004176540.1|  92 N-VYMYGDKWTA---LSNSSIDLVVVIPRGFAENASSIDRVASVDIIRRANVQAAQQAEGTVRGFIDYYSAQLSGrk 164
                                       6.7888887755...89******************977777777788*****************9888887777788 PP

                   ABC2_membrane_3 134 .lqseatstsaninvestql...................eeelsnvasflvgliliilifitasfiavsiveEkesr 190
                                        +   ++ +  +++v+ + +                   ee l++ +  l++l + ++++  as+++ +++ E+e++
  gi|320100948|ref|YP_004176540.1| 165 lEALAKLASVGPVDVNALRNpivvgsvvlvspsgaevgaEEALKSLVARLLVLSFSFVVTPAASYVIDGVIGERERK 241
                                       87777777778888888777889998888999888555555555555555555555556666999999********* PP

                   ABC2_membrane_3 191 ikelqlvsgvsplqywlskilgdflvyllql..........llill.l..afgl..gipfg..nlglll..llfllf 248
                                       ++e++l+s+ s+++ +lsk+++  ++++l +          +     +  afg      +    +++++  +  +l 
  gi|320100948|ref|YP_004176540.1| 242 TMEMLLTSPASVSEVFLSKLVAASMLGVLASladlggilayV---TlIimAFGGgiL--VVmdPVLVCIhvVTAFLT 313
                                       *******************************66655543321...121236666542..333144555578999999 PP

                   ABC2_membrane_3 249 glayialgyllsslfknsetaqilifivilllsgffgglfp..ledlpsalkwifsiiPffapglgllrlitgdplw 323
                                       +l+++++++ + + ++  ++a+ +++iv+++ ++ff++ ++  +++lp ++ + ++++P ++ +l++   ++g+ l+
  gi|320100948|ref|YP_004176540.1| 314 ILVTVSIATPFIARSSGLRSASNVAGIVSSIGLVFFIIGWMidFPKLPPSIMYPLMLVPYTHSILAIQGYVYGE-LA 389
                                       999999999999999999************99999999988677778899999999999999999999999999.88 PP

                   ABC2_membrane_3 324 eillsliilalfavvylllal 344
                                        +++sli+l + ++v +++a+
  gi|320100948|ref|YP_004176540.1| 390 VVARSLIVLPAVSLVSMIIAI 410
                                       899****************98 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 !   49.3  25.2   6.8e-17   4.1e-13       2     286 ..       9     416 ..       8     418 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 6.8e-17
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli................................................... 27 
                                       ++++kE  ++ r+r+ l++t+llpli                                                   
  gi|320100948|ref|YP_004176540.1|   9 VLLWKEALEISRDRKALITTILLPLIampaiglltvflmvqqpvniavvdedasthvspvfnitvssrdlaagireh 85 
                                       689***********************999988888877777755555555555444444444444444444444444 PP

                   ABC2_membrane_2  28 ........dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkv.................... 76 
                                                                                               +                    
  gi|320100948|ref|YP_004176540.1|  86 lsrsgfnvY-----------------------------------------------Mygdkwtalsnssidlvvvip 115
                                       444444440...............................................044445555555555555666 PP

                   ABC2_membrane_2  77 ............................................................................. 76 
                                                                                                                    
  gi|320100948|ref|YP_004176540.1| 116 rgfaenassidrvasvdiirranvqaaqqaegtvrgfidyysaqlsgrklealaklasvgpvdvnalrnpivvgsvv 192
                                       6666666666666666666666666666777777******************************************* PP

                   ABC2_membrane_2  77 .....................vstimavlipvi.......aalfgadaiagEkergTlkllLskPvsRdeillgKfi 125
                                                            +       +++        aa   +d + gE+er+T++ lL++P+s +e+ l+K++
  gi|320100948|ref|YP_004176540.1| 193 lvspsgaevgaeealkslvarL-------LVLSfsfvvtpAASYVIDGVIGERERKTMEMLLTSPASVSEVFLSKLV 262
                                       **************77775543.......33333333446999999******************************* PP

                   ABC2_membrane_2 126 gglaigla..iavallatvllalaiilalgivlaledllllvvasvlllllv....vflalglllSsvarssreaaa 196
                                       + +++g++  +a + ++   ++l+i++ +g  l ++d +l+ + +v+ +l++      ++ +++ Ss +rs+++ a 
  gi|320100948|ref|YP_004176540.1| 263 AASMLGVLasLADLGGILAYVTLIIMAFGGGILVVMDPVLVCIHVVTAFLTIlvtvSIATPFIARSSGLRSASNVAG 339
                                       ***996443555555555555****************9999998888888777433334446899999999999999 PP

                   ABC2_membrane_2 197 lalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlnalgstatnllillllla 273
                                       ++ ++ +v++i+  ++ ++        + p++i+  l l+++t+++ ++ + ++        ++ a +l++l ++ +
  gi|320100948|ref|YP_004176540.1| 340 IVSSIGLVFFIIGWMIDFP--------KLPPSIMYPLMLVPYTHSILAIQGYVYGEL-----AVVARSLIVLPAVSL 403
                                       9999999998877777766........333455667999*****9999999998888.....688888888888888 PP

                   ABC2_membrane_2 274 vllvlgyvlFkrk 286
                                       v++++++ + +++
  gi|320100948|ref|YP_004176540.1| 404 VSMIIAIRFIDKE 416
                                       8888887776666 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.16   9.7e+02      14      31 ..      23      42 ..      10      65 .. 0.49
   2 !   18.9   9.7   1.9e-07    0.0011      57     177 ..     216     350 ..     187     352 .. 0.63
   3 ?   -2.6   0.3      0.76   4.5e+03      58     118 ..     396     402 ..     363     417 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.16
                   ABC2_membrane_4 14 ivwllvlaall..vpllall 31
                                        +++ +++ l  +p ++ll
  gi|320100948|ref|YP_004176540.1| 23 KALITTILLPLiaMPAIGLL 42
                                      33333332222013333332 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.9e-07
                   ABC2_membrane_4  57 llllplilgiiasylif...rEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtf.....litvlfallsg 125
                                       +l + ++++  asy+i     E++ +t+  Llt P s  +++l+Kl++  +l vl +l+ +      +t+++  + g
  gi|320100948|ref|YP_004176540.1| 216 VLSFSFVVTPAASYVIDgviGERERKTMEMLLTSPASVSEVFLSKLVAASMLGVLASLADLggilaYVTLIIMAFGG 292
                                       4555556666788887633359999*****************************99998763222233333333334 PP

                   ABC2_membrane_4 126 fvgfsvkl..vlellkkclelgllvffavlpiialvl..lkksyvlpli..ltlvyti 177
                                       ++ + +++  v++ ++  ++++l+++ + +p ia ++     s+v++++  + lv++i
  gi|320100948|ref|YP_004176540.1| 293 GILVVMDPvlVCIHVVTAFLTILVTVSIATPFIARSSglRSASNVAGIVssIGLVFFI 350
                                       4443344411333333444455555555666666533213445566666555555555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.76
                   ABC2_membrane_4  58 lllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitv 118
                                       ++lp++                                                       
  gi|320100948|ref|YP_004176540.1| 396 IVLPAV------------------------------------------------------S 402
                                       122211......................................................1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3135.33
//
Query:       gi|320100949|ref|YP_004176541.1|  [L=163]
Description: regulatory protein MarR [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   40.3   3.4    5.4e-09   35.9   0.2    2.8  3  HTH_45           Winged helix-turn-helix
    1.5e-07   30.8   0.1    3.7e-07   29.6   0.1    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.1e-06   27.7   0.2    5.5e-06   26.4   0.1    1.8  2  DprA_WH          DprA winged helix domain
    4.6e-06   26.5   0.1      1e-05   25.4   0.1    1.6  1  HTH_36           Helix-turn-helix domain
    1.5e-05   24.8   0.2    4.1e-05   23.4   0.2    1.8  1  HTH_11           HTH domain
    2.1e-05   24.3   0.2      6e-05   22.8   0.2    1.8  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00013   22.0   0.1    0.00031   20.7   0.1    1.6  1  HemN_C           HemN C-terminal domain
    0.00013   21.7   0.1    0.00031   20.5   0.1    1.7  1  HTH_IclR         IclR helix-turn-helix domain
     0.0002   21.1   0.2    0.00064   19.5   0.2    1.9  1  HTH_5            Bacterial regulatory protein, arsR family
    0.00021   21.1   0.1    0.00047   20.0   0.1    1.6  1  MarR_2           MarR family
    0.00045   18.7   1.3     0.0031   16.0   0.0    1.9  2  DUF505           Protein of unknown function (DUF505)
    0.00052   19.9   0.1     0.0011   18.9   0.1    1.6  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0021   18.4   0.4      0.005   17.1   0.2    1.9  1  Rrf2             Transcriptional regulator
     0.0021   17.9   0.7     0.0051   16.7   0.5    1.7  1  HTH_12           Ribonuclease R winged-helix domain
     0.0025   17.8   0.0     0.0049   16.8   0.0    1.6  1  HTH_29           Winged helix-turn helix
     0.0025   17.5   0.1     0.0051   16.5   0.1    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0037   17.4   0.2       0.29   11.3   0.1    2.4  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0042   17.1   0.5      0.011   15.8   0.2    1.9  1  HTH_20           Helix-turn-helix domain
     0.0046   16.9   0.2     0.0093   15.9   0.2    1.4  1  MarR             MarR family
     0.0047   17.4   0.3     0.0093   16.4   0.3    1.5  1  HTH_27           Winged helix DNA-binding domain
     0.0064   17.1   0.0      0.011   16.4   0.0    1.3  1  RPA_C            Replication protein A C terminal
     0.0084   16.2   0.0      0.019   15.1   0.0    1.6  1  HTH_28           Helix-turn-helix domain
     0.0093   15.7   0.0      0.021   14.6   0.0    1.6  1  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.022   14.4   0.0    1.5  1  RP-C             Replication protein C N-terminal domain
      0.011   15.7   3.0      0.021   14.9   0.2    2.3  2  HTH_Mga          M protein trans-acting positive regulator (M
      0.012   15.3   0.6      0.052   13.3   0.1    1.9  2  DUF4423          Domain of unknown function (DUF4423)
      0.029   14.0   0.1      0.057   13.1   0.1    1.5  1  GntR             Bacterial regulatory proteins, gntR family
      0.032   14.6   0.1       0.08   13.3   0.0    1.6  1  Penicillinase_R  Penicillinase repressor
      0.038   14.1   0.0      0.083   13.0   0.0    1.6  1  HTH_7            Helix-turn-helix domain of resolvase
      0.043   13.7   0.3       0.17   11.8   0.3    2.0  1  HxlR             HxlR-like helix-turn-helix
      0.056   14.0   1.1        2.9    8.5   0.1    3.0  3  ANAPC2           Anaphase promoting complex (APC) subunit 2
      0.084   13.0   0.2       0.16   12.1   0.2    1.5  1  DUF2250          Uncharacterized protein conserved in archaea
      0.084   12.7   0.1       0.26   11.1   0.0    1.8  1  HTH_10           HTH DNA binding domain
       0.12   12.2   0.0       0.27   11.0   0.0    1.6  1  LexA_DNA_bind    LexA DNA binding domain
       0.13   11.3   0.0       0.16   10.9   0.0    1.2  1  TnsD             Tn7-like transposition protein D
       0.14   11.8   0.1        5.4    6.6   0.0    2.0  2  EcoR124_C        Type I restriction and modification enzyme -


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 !   35.9   0.2   1.1e-11   5.4e-09      11      73 ..       7      69 ..       3      73 .. 0.91
   2 ?   -0.7   0.0         3   1.5e+03      35      59 ..      94     122 ..      87     124 .. 0.54
   3 ?    4.1   0.1     0.095        47      37      53 ..     130     146 ..     124     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.1e-11
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkele 73
                                      +L+ ++e++    k+  +  Ls +++++YL  L ekgl+++++e Y lT+ Gl+l ++l+ l+
  gi|320100949|ref|YP_004176541.1|  7 LLSLMDENGVAIDKLSSETGLSTRTVKRYLRELEEKGLVEQRGELYALTAAGLKLKKSLQALR 69
                                      68888888889999999****************************************999876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3
                            HTH_45  35 llnkYLdm....LvekglikkskekYvlT 59 
                                       + ++ L +    L +k +++++  kY  T
  gi|320100949|ref|YP_004176541.1|  94 NYKQLLAIidagLADKSVLEEHMRKYLAT 122
                                       55544432111355566667777777665 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.095
                            HTH_45  37 nkYLdmLvekglikksk 53 
                                       ++YL +L+e g ik+ +
  gi|320100949|ref|YP_004176541.1| 130 DEYLAYLLETGAIKNLD 146
                                       68***********9833 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 !   29.6   0.1   7.5e-10   3.7e-07      11      48 .]       9      46 ..       2      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 7.5e-10
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       L+++ +  +  L+ ++glS  tv+r+l++Lee+Gl++
  gi|320100949|ref|YP_004176541.1|  9 SLMDENGVAIDKLSSETGLSTRTVKRYLRELEEKGLVE 46
                                      46666889999*************************96 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   1.1e-08   5.5e-06      16      58 ..       6      48 ..       2      50 .. 0.95
   2 ?   -2.0   0.0       8.2   4.1e+03      15      24 ..     153     162 ..     145     163 .] 0.79

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.1e-08
                           DprA_WH 16 rvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverl 58
                                      ++L+++    v++D L+ +tgl++++v + L eLE +Glve++
  gi|320100949|ref|YP_004176541.1|  6 KLLSLMDENGVAIDKLSSETGLSTRTVKRYLRELEEKGLVEQR 48
                                      699**************************************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.2
                           DprA_WH  15 rrvLaaLgpe 24 
                                       +++L aLg +
  gi|320100949|ref|YP_004176541.1| 153 ETILKALGDQ 162
                                       7899999976 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1     2e-08     1e-05      14      55 .]       7      45 ..       2      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2e-08
                            HTH_36 14 lasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      l+s+ ++ng      + l++ +gls +Tv r+++eLe++G++
  gi|320100949|ref|YP_004176541.1|  7 LLSLMDENGV---AIDKLSSETGLSTRTVKRYLRELEEKGLV 45
                                      6777766666...8899***********************85 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   8.3e-08   4.1e-05       6      43 ..       5      43 ..       2      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.3e-08
                            HTH_11  6 lelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      l+lL   +++ + +++L+ e+++S+rtv r++++Lee+g
  gi|320100949|ref|YP_004176541.1|  5 LKLLSLMDENgVAIDKLSSETGLSTRTVKRYLRELEEKG 43
                                      55655556666***************************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 !   22.8   0.2   1.2e-07     6e-05      15      56 ..       8      49 ..       5      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-07
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      l L+ +    +d++++e+g++  +v ++Lr+Le+kGlVe + 
  gi|320100949|ref|YP_004176541.1|  8 LSLMDENGVAIDKLSSETGLSTRTVKRYLRELEEKGLVEQRG 49
                                      5788899999*****************************875 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   6.2e-07   0.00031      13      65 ..       8      59 ..       7      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.2e-07
                            HemN_C 13 lgLRlreGldlaafeqrfgldleellaaaleklqeqGLLeldggrlrltprGr 65
                                      l L+   G+ ++++  ++gl+   +++  l++l+e+GL+e++g+ + lt +G+
  gi|320100949|ref|YP_004176541.1|  8 LSLMDENGVAIDKLSSETGLS-TRTVKRYLRELEEKGLVEQRGELYALTAAGL 59
                                      6677788**************.5556999*********************995 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   6.3e-07   0.00031      19      52 .]      16      49 ..       5      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.3e-07
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      + +  l+ +tgl+  tv R+L+ L+e G+veq g
  gi|320100949|ref|YP_004176541.1| 16 VAIDKLSSETGLSTRTVKRYLRELEEKGLVEQRG 49
                                      4677899*************************75 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 !   19.5   0.2   1.3e-06   0.00064       5      46 ..       5      46 ..       3      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      lk+L+l+ e+   +  l+ e+gls  tv ++L+ L+e GLVe
  gi|320100949|ref|YP_004176541.1|  5 LKLLSLMDENGVAIDKLSSETGLSTRTVKRYLRELEEKGLVE 46
                                      788888888999999**************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   9.5e-07   0.00047      11      54 ..       7      48 ..       4      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.5e-07
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      L+ L ++ g  +++  l  ++gls  +v r l++L+++GLve+r
  gi|320100949|ref|YP_004176541.1|  7 LLSLMDENG--VAIDKLSSETGLSTRTVKRYLRELEEKGLVEQR 48
                                      566777888..9999***************************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 !   16.0   0.0   6.2e-06    0.0031     473     540 ..       5      70 ..       2      79 .. 0.85
   2 ?    1.8   0.2      0.12        59     206     266 ..     100     159 ..      95     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.2e-06
                            DUF505 473 lkvlkkiPkrgvsveelveevdeleeeevrealeklearglvevlpdgnvvlTeaGelikrAlsgvpe 540
                                       lk+l+ + + gv++++l +e+ +l  + v++ l++le +glve    + + lT aG ++k+ l++ + 
  gi|320100949|ref|YP_004176541.1|   5 LKLLSLMDENGVAIDKLSSET-GLSTRTVKRYLRELEEKGLVEQ-RGELYALTAAGLKLKKSLQALRA 70 
                                       577888889999****98888.9999999************997.678999*********99988665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                            DUF505 206 alrkggvaeelvlsedilealakvvdgeeleeeekeaLealgyvddegeltpaGeklleay 266
                                       a+ ++g a+++vl+e++ + la++v +  l +e ++ L + g +++ ++l +  e +l+a+
  gi|320100949|ref|YP_004176541.1| 100 AIIDAGLADKSVLEEHMRKYLATWVKD-SLGDEYLAYLLETGAIKNLDDLKNYLETILKAL 159
                                       5566778899*************9998.89999************9999999999888875 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 !   18.9   0.1   2.2e-06    0.0011      26      59 ..      20      53 ..       7      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-06
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEEE CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.rgrriri 59
                                       l+s  Gl+  tv r l+eL+++gl++ rg  +  
  gi|320100949|ref|YP_004176541.1| 20 KLSSETGLSTRTVKRYLRELEEKGLVEqRGE-LYA 53
                                      689999*********************4454.555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2     1e-05     0.005      15      57 ..       6      47 ..       1      68 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-05
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                        L++ +e++ v+++++++++++s + +++ l++L+++glv+ 
  gi|320100949|ref|YP_004176541.1|  6 KLLSLMDENG-VAIDKLSSETGLSTRTVKRYLRELEEKGLVEQ 47
                                      5566677777.******************************85 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.5     1e-05    0.0051      28      64 ..      25      60 ..      14      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-05
                            HTH_12 28 ydigeravRyrLrkleergltrrvgyagreltEkGle 64
                                        +++r+v + Lr lee+gl+++ g     lt  Gl+
  gi|320100949|ref|YP_004176541.1| 25 TGLSTRTVKRYLRELEEKGLVEQRGEL-YALTAAGLK 60
                                      56899*****************99854.448888876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.9e-06    0.0049       7      41 ..      10      44 ..       5      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.9e-06
                            HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      l++e +  +  +   +gls rtv r+l+  ee+Gl
  gi|320100949|ref|YP_004176541.1| 10 LMDENGVAIDKLSSETGLSTRTVKRYLRELEEKGL 44
                                      5555444699************************5 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     1e-05    0.0051      11      45 ..      12      46 ..       6      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-05
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      ++  + +++l+ + g S+ T+ R L+eLee+gl++
  gi|320100949|ref|YP_004176541.1| 12 DENGVAIDKLSSETGLSTRTVKRYLRELEEKGLVE 46
                                      556699**************************975 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 !   11.3   0.1   0.00059      0.29      23      54 ..      16      47 ..       7      51 .. 0.85
   2 ?    3.8   0.0      0.13        67       7      20 ..     149     162 ..     145     163 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00059
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyvey 54
                                      v   +l+++ + s  +V   l++Le++G+ve 
  gi|320100949|ref|YP_004176541.1| 16 VAIDKLSSETGLSTRTVKRYLRELEEKGLVEQ 47
                                      445789************************86 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHH CS
                    Fe_dep_repress   7 EdYLetIYtlseek 20 
                                        +YLetI+++ +++
  gi|320100949|ref|YP_004176541.1| 149 KNYLETILKALGDQ 162
                                       68******998765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   2.2e-05     0.011      15      59 ..       7      50 ..       3      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-05
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +l++  ++ g+    l  + +ls  t+ + Lr+Lee gLve+++e
  gi|320100949|ref|YP_004176541.1|  7 LLSLM-DENGVAIDKLSSETGLSTRTVKRYLRELEEKGLVEQRGE 50
                                      55555.888999999999999*********************997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.9e-05    0.0093       9      48 ..       7      46 ..       3      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-05
                                      HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      L +l ++++  + +L +  g+s+ tv r l++Le+kGl+e
  gi|320100949|ref|YP_004176541.1|  7 LLSLMDENGVAIDKLSSETGLSTRTVKRYLRELEEKGLVE 46
                                      5566777788899**************************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 !   16.4   0.3   1.9e-05    0.0093      14      68 .]      11      58 ..       3      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-05
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      + ++++++  l+  + ++  ++   l++L+ekGLv     e  +r  +++lT++G
  gi|320100949|ref|YP_004176541.1| 11 MDENGVAIDKLSSETGLSTRTVKRYLRELEEKGLV-----E--QRGELYALTAAG 58
                                      46788888999999999999999************.....5..8888******99 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 !   16.4   0.0   2.2e-05     0.011      63      97 ..      11      45 ..       3      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.2e-05
                                      XSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 63 eseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                       +e+Gv +d ++ +++ls ++vk+ ++eL+++G++
  gi|320100949|ref|YP_004176541.1| 11 MDENGVAIDKLSSETGLSTRTVKRYLRELEEKGLV 45
                                      6799*****************************86 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.7e-05     0.019       6      45 ..       8      45 ..       5      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                            HTH_28  6 iklla.aGhsvreaArelgisrrtvyrWikryeegGiagLv 45
                                      + l+  +G++++ ++ e g+s rtv+r ++ +ee G+   v
  gi|320100949|ref|YP_004176541.1|  8 LSLMDeNGVAIDKLSSETGLSTRTVKRYLRELEEKGL---V 45
                                      566775688*************************775...4 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   0.0   4.2e-05     0.021      10      46 ..       7      44 ..       5      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.2e-05
                            HTH_23 10 illllae.GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                       l l +e G  + + + e g s rTv r+l+  +e+Gl
  gi|320100949|ref|YP_004176541.1|  7 LLSLMDEnGVAIDKLSSETGLSTRTVKRYLRELEEKGL 44
                                      56677778999999999****************99996 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.4e-05     0.022      76     104 ..      20      48 ..      17      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-05
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirr 104
                                       +Ls+++gls++t++r l++L e Gl+  r
  gi|320100949|ref|YP_004176541.1|  20 KLSSETGLSTRTVKRYLRELEEKGLVEQR 48 
                                       799**********************9766 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 ?   14.9   0.2   4.2e-05     0.021      16      45 ..      12      40 ..       2      44 .. 0.82
   2 ?    0.7   0.3       1.1   5.7e+02      11      32 ..     133     154 ..     131     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.2e-05
                           HTH_Mga 16 eneksltldelakeLglseltlqsdiseLn 45
                                      + e+   +d+l++e+gls +t++ +++eL 
  gi|320100949|ref|YP_004176541.1| 12 D-ENGVAIDKLSSETGLSTRTVKRYLRELE 40
                                      4.4666789*******************97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                           HTH_Mga  11 lelLteneksl.tldelakeLgl 32 
                                       l++L+e ++++ +ld+l+++L +
  gi|320100949|ref|YP_004176541.1| 133 LAYLLE-TGAIkNLDDLKNYLET 154
                                       789999.9999569999999865 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1    0.0001     0.052      28      95 ..       6      71 ..       2     104 .. 0.88
   2 ?    0.4   0.0      0.92   4.6e+02      40      76 ..     114     151 ..      97     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                           DUF4423 28 ellplkdf.kadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevkseavr 95
                                      +ll+l+d+    +++l+  ++  +s+  v++ l+ L++ gl+++ ++  y  t + l+ +++ +++ +r
  gi|320100949|ref|YP_004176541.1|  6 KLLSLMDEnGVAIDKLSSETG--LSTRTVKRYLRELEEKGLVEQRGE-LYALTAAGLKLKKSLQALRAR 71
                                      577788774568999******..***********************8.**********99998887666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.92
                           DUF4423  40 eelakrlrpkisaeevekalefLlklgllkkded.gky 76 
                                       e + k l   ++ +   + l +Ll++g +k   d ++y
  gi|320100949|ref|YP_004176541.1| 114 EHMRKYLATWVKDSLGDEYLAYLLETGAIKNLDDlKNY 151
                                       45555566666666667788999999999988776666 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00012     0.057      28      57 ..      19      48 ..       8      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverr 57
                                       +L++e g s+ tv + Lr+Le++glve r
  gi|320100949|ref|YP_004176541.1| 19 DKLSSETGLSTRTVKRYLRELEEKGLVEQR 48
                                      6899***********************976 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00016      0.08      24      54 ..      18      48 ..      14      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00016
                                      HHT--GGG---HHHHHHHHHHHHHTTS-EEE CS
                   Penicillinase_R 24 veeleeekelaysTVktllrrLvkKgllsre 54
                                      +++l++e+ l+  TVk  lr L++Kgl++++
  gi|320100949|ref|YP_004176541.1| 18 IDKLSSETGLSTRTVKRYLRELEEKGLVEQR 48
                                      68999***********************875 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00017     0.083      16      44 ..      10      38 ..       4      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                                      SSTTTT--STTTSSSS---SSSS--SS-- CS
                             HTH_7 16 kLleeGisiskIAkevnisRsTvYRylad 44
                                       + e+G +i k+  e+++s  Tv+Ryl++
  gi|320100949|ref|YP_004176541.1| 10 LMDENGVAIDKLSSETGLSTRTVKRYLRE 38
                                      57799*********************986 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00034      0.17      30      80 ..      26      69 ..       7      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                                      TS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                              HxlR 30 kisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80
                                      ++s+++  + LreLe++gl+e++      +   Y lt++G +l++ lq+l 
  gi|320100949|ref|YP_004176541.1| 26 GLSTRTVKRYLRELEEKGLVEQRG-----E--LYALTAAGLKLKKSLQALR 69
                                      68999**************98653.....3..6999999999999999986 PP

>> ANAPC2  Anaphase promoting complex (APC) subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0058       2.9      30      60 .]      24      54 ..       3      54 .. 0.89
   2 ?   -0.2   0.0       2.9   1.5e+03      35      49 ..     113     127 ..     105     128 .. 0.84
   3 ?    2.3   0.0      0.48   2.4e+02      28      46 ..     138     156 ..     131     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0058
                            ANAPC2 30 gydisdeeLkefLdelvkegkLelsgGkYkL 60
                                      ++  s +++k++L el ++g +e  g+ Y L
  gi|320100949|ref|YP_004176541.1| 24 ETGLSTRTVKRYLRELEEKGLVEQRGELYAL 54
                                      4558999**********************87 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.9
                            ANAPC2  35 deeLkefLdelvkeg 49 
                                       +e ++++L ++vk+ 
  gi|320100949|ref|YP_004176541.1| 113 EEHMRKYLATWVKDS 127
                                       578999******985 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.48
                            ANAPC2  28 degydisdeeLkefLdelv 46 
                                       ++g  ++ ++Lk++L++  
  gi|320100949|ref|YP_004176541.1| 138 ETGAIKNLDDLKNYLETIL 156
                                       56677899*******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 ?   12.1   0.2   0.00033      0.16      13      55 ..       7      48 ..       2      70 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00033
                           DUF2250 13 vlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerv 55
                                      +l  +++ +v   k ++ e+ ++   v+++l++Lee GL+e+ 
  gi|320100949|ref|YP_004176541.1|  7 LLSLMDENGVAIDK-LSSETGLSTRTVKRYLRELEEKGLVEQR 48
                                      55555555555554.567899*******************975 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00051      0.26      24      50 ..      16      42 ..      13      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                            HTH_10 24 vtlkeLAkelGIskstlsehLrkaesk 50
                                      v +++L+ e G+s  t++ +Lr+ e+k
  gi|320100949|ref|YP_004176541.1| 16 VAIDKLSSETGLSTRTVKRYLRELEEK 42
                                      67899******************9998 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   0.00054      0.27      31      58 ..      21      47 ..       8      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00054
                                      HHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 31 iaralglkSpsaveehLkaLerKGyier 58
                                      ++ + gl+ +++v+  L+ Le KG++e 
  gi|320100949|ref|YP_004176541.1| 21 LSSETGLS-TRTVKRYLRELEEKGLVEQ 47
                                      56666775.*****************96 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00032      0.16     190     233 ..       6      46 ..       1      80 [. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                              TnsD 190 rlkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqk 233
                                       +l  L++e+g+ +++ ++e g++++tV+ry+++l++     +++
  gi|320100949|ref|YP_004176541.1|   6 KLLSLMDENGVAIDKLSSETGLSTRTVKRYLRELEEKG---LVE 46 
                                       66778889************************999765...333 PP

>> EcoR124_C  Type I restriction and modification enzyme - subunit R C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.092        46     190     236 ..      17      62 ..      11      81 .. 0.73
   2 ?    6.6   0.0     0.011       5.4     189     250 ..      96     154 ..      91     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.092
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX CS
                         EcoR124_C 190 eleelieeegldeealkkfikeilkrgkfdalgteilklllspkklg 236
                                       ++++l++e gl++  +k+++ e  ++g +++ g+    l ++++kl+
  gi|320100949|ref|YP_004176541.1|  17 AIDKLSSETGLSTRTVKRYLRELEEKGLVEQRGEL-YALTAAGLKLK 62 
                                       799************************99555543.44444444444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         EcoR124_C 189 keleelieeegldeealkkfikeilkrgkfdalgteilklllspkklglkerrkkkkkvmek 250
                                       k+l ++i+    d++ l++ + ++l ++  d+lg+e l +ll+   ++   +  + k++ e 
  gi|320100949|ref|YP_004176541.1|  96 KQLLAIIDAGLADKSVLEEHMRKYLATWVKDSLGDEYLAYLLETGAIK---NLDDLKNYLET 154
                                       678889997666788*************************96555444...44444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 1305.16
//
Query:       gi|320100950|ref|YP_004176542.1|  [L=475]
Description: alpha amylase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   13.9   0.1       0.29   11.7   0.0    2.1  2  ArdA      Antirestriction protein (ArdA)


Domain annotation for each model (and alignments):
>> ArdA  Antirestriction protein (ArdA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.083   1.5e+03      90     122 ..     244     290 ..     228     305 .. 0.61
   2 ?   11.7   0.0   1.6e-05      0.29      10      74 ..     275     365 ..     269     409 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.083
                              ArdA  90 fgdleeledafeeeylgeydsle..............dyAeelveel 122
                                        gd+e++++++e  y ++++ l               +y ++++e++
  gi|320100950|ref|YP_004176542.1| 244 DGDVEKWRARLERMYSSSLKRLDelvsserdnvgneaAYWRDMLEKT 290
                                       45788888888888877777776555666665554444444444444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.6e-05
                              ArdA  10 nnGelhGeWldlpadaeelqealkai.s.....................aeeedeEwaihDyeglpeaslge....y 60 
                                       n G+    W d+  ++  + e+ +++                       +e+  e++ i+D+eg p++s++e     
  gi|320100950|ref|YP_004176542.1| 275 NVGNEAAYWRDMLEKTRGIVEDAASMlDeyvglmkarthqdlhlaqmiyVESPAEDFIITDFEGEPGRSIDErlwkE 351
                                       6666667777777777777777777752455677777788888877766668999*****************98776 PP

                              ArdA  61 esidelnelaklle 74 
                                       + i +l+ + +   
  gi|320100950|ref|YP_004176542.1| 352 PPIRDLASMIRSFH 365
                                       66777776663333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3653.41
//
Query:       gi|320100951|ref|YP_004176543.1|  [L=514]
Description: alpha-amylase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-65  219.4   0.0    1.3e-64  218.5   0.0    1.5  1  Glyco_hydro_57  Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.5   0.0   7.2e-69   1.3e-64       2     325 .]       6     309 ..       5     309 .. 0.89

  Alignments for each domain:
  == domain 1  score: 218.5 bits;  conditional E-value: 7.2e-69
                                       EEEEE-----TTS-.SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-H..HHHHHHHHH CS
                    Glyco_hydro_57   2 fvfhqHqplykkpg.kgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylnge..kksylpate 75 
                                       ++f++Hqp++ +++ + ++ ++ +  +     ++ al  ++++++                       +++y+pat+
  gi|320100951|ref|YP_004176543.1|   6 LMFEVHQPYRLRRDiHYRLLEKALAGRVEPGDVEEALFDNELNRLV-----------------VERasERCYIPATR 65 
                                       6778888888777733333333333333333344444444444444.................33346********* PP

                                       HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-..H CS
                    Glyco_hydro_57  76 ellelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpd..s 150
                                       ++le  ++     + +k       ++++sg +leq+q+w ++ev +lfrel+++g +E++ ++yyH+++++lp+   
  gi|320100951|ref|YP_004176543.1|  66 IILENVKRYAGGSRGFK------ASFSVSGVFLEQAQRW-KPEVVDLFRELAGTGMIEFVEQTYYHSMAAFLPYfgF 135
                                       *****966666677777......****************.**********************************999 PP

                                       HHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-E CS
                    Glyco_hydro_57 151 edieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggia 227
                                       +++++qv ++r+l+ee++g++P+ + ++E+++s++++ ++  +G+++++t++++++l ++   sp+++y++   +i 
  gi|320100951|ref|YP_004176543.1| 136 DELREQVVEHRKLVEELIGYRPTSIENTEFTYSNDVACFFDSMGYRVVLTEGVERVLGWR---SPNYVYKAYGCDIR 209
                                       9***********************************************************...************** PP

                                       EEE--CHH-TTTSGGG-................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHH CS
                    Glyco_hydro_57 228 vffRdreLsddigFrys....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeel 298
                                       v+ R+++LsddigFr+s    +qypl ++d+++ w+ ++   +++++ ia+d+E++g  h+pe+g+ eFl++++ e+
  gi|320100951|ref|YP_004176543.1| 210 VLTRNYRLSDDIGFRFSdktwDQYPL-TADKYASWIAST---PGDLIFIAVDYETFGehHWPESGIHEFLKWMPGEV 282
                                       **************************.**********98...*********************************** PP

                                       HHHHHHHHHHHHHHHHHHSS-EEEEEE CS
                    Glyco_hydro_57 299 eenglielvtpsefikklkpkgliklp 325
                                        + g++++ tpse++++++ ++++++p
  gi|320100951|ref|YP_004176543.1| 283 LKYGHLNFSTPSEVVERHPVRDVLDVP 309
                                       *********************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3665.56
//
Query:       gi|320100952|ref|YP_004176544.1|  [L=643]
Description: alpha-amylase [Desulfurococcus mucosus DSM 2162]
Scores for 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  116.5   0.4      9e-34  115.6   0.4    1.4  1  DUF1925         Domain of unknown function (DUF1925)
    7.2e-32  110.9   0.0    1.2e-31  110.1   0.0    1.3  1  Glyco_hydro_57  Glycosyl hydrolase family 57
    4.2e-26   92.2   0.0    2.9e-12   46.8   0.0    2.1  2  DUF1926         Domain of unknown function (DUF1926)


Domain annotation for each model (and alignments):
>> DUF1925  Domain of unknown function (DUF1925)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.4   1.5e-37     9e-34       1      78 [.     281     356 ..     281     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 1.5e-37
                           DUF1925   1 GiwknFlvkYeesnemhkrmlevskklkklaskkeaeealeallraqandaYWhGlFGGiYlphLRravyenlikae 77 
                                       G+++nFlvkY+esn+mhk+ml+v++kl +l  +   ee++  +l +q+ndaYWhGlFGGiYl+hLR+a+ye+li+ e
  gi|320100952|ref|YP_004176544.1| 281 GFFRNFLVKYRESNNMHKKMLWVRRKLGSL--DSVPEEVRTGYLLSQCNDAYWHGLFGGIYLAHLRQAIYEELIRTE 355
                                       9*****************************..778999*************************************99 PP

                           DUF1925  78 a 78 
                                       a
  gi|320100952|ref|YP_004176544.1| 356 A 356
                                       7 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   2.1e-35   1.2e-31      62     323 ..      18     266 ..       5     268 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 2.1e-35
                                       HHT-H.HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE CS
                    Glyco_hydro_57  62 ylnge.kksylpateellelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvEllts 137
                                       +l+g  +k++ + +++ll+ +    +++ +lk      f++++sgpll ++ k+ ++e le++ +l + g +E+++ 
  gi|320100952|ref|YP_004176544.1|  18 QLKGVnEKIFVNSYRLLLDVF----KSFADLK------FTVHVSGPLLLYLAKN-HPEWLEELFKLGDLGVLEFMAG 83 
                                       567778999999999999996....999****......****************.********************** PP

                                       -TT-B-GGG-S-HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------ CS
                    Glyco_hydro_57 138 pyyHpllpllpdsedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskes 214
                                       +  +++lp++p+ ed eaq+++ + l+e++ g +P+g+wlpE++++p ++e+l +lG ey+f d++  +  ++ ++ 
  gi|320100952|ref|YP_004176544.1|  84 SLGEAILPIIPR-EDREAQIREYIALFERLSGFKPKGLWLPERVWEPGLPEVLGKLGVEYVFIDDSTLTKTGHPQDL 159
                                       ************.****************************************************88888888778* PP

                                       TTS-EE-TTS...-EEEE--CHH-TTTSGGG-............TTSB............-TT---TTT--BB-TT- CS
                    Glyco_hydro_57 215 pyrpyllkngg..iavffRdreLsddigFryseqypleavddfinwlkkvkka..ksevvtialdgEnwghypetgk 287
                                        y+++ ++++g  + vff+d  +++ ++++         +++++++l +  ++  + ++v+ + d+E++g++     
  gi|320100952|ref|YP_004176544.1| 160 AYYAWNTEDSGqlVRVFFIDAGIRYILPWE--------PPERVLEYLVSKGREgdQARLVLWGSDAEKFGEWMDPER 228
                                       *****************************6........99*******96556689***************9988887 PP

                                       S---H.HHHH..HHHHHH..HHHHHHHHHHHHHHSS-EEEE CS
                    Glyco_hydro_57 288 keFle.klye..eleeng..lielvtpsefikklkpkglik 323
                                           + +ly+  el +++   + + +pse++ ++  +gl++
  gi|320100952|ref|YP_004176544.1| 229 S---RsWLYSflELMRRSrdRVSMTHPSEYLMEHGVRGLLY 266
                                       6...44999955444555899**********9999998876 PP

>> DUF1926  Domain of unknown function (DUF1926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   4.9e-16   2.9e-12       1      55 [.     376     432 ..     376     436 .. 0.94
   2 !   43.9   0.0   3.8e-15   2.3e-11      89     279 ..     436     635 ..     431     637 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 4.9e-16
                           DUF1926   1 DfdlDgreEvlleseklvavlkpaqGGsliElddrk..kefNllntLtRrpEaYHek 55 
                                       Dfd+Dg++Evl+e+++ ++++kp+ GG l+E+d++    e+Nl++t+ R  E+Y +k
  gi|320100952|ref|YP_004176544.1| 376 DFDYDGEPEVLVETPSQNLYVKPDDGGTLFEYDVKSrgLEHNLQDTMSRYGEPYINK 432
                                       9********************************9875589**************776 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 3.8e-15
                           DUF1926  89 vyDwyerkslvDhfldeeltlesfvqg.elkeegDFanqpyeiekk.kvevvlkrdGgvy.....kkeitlrKeytl 158
                                       + Dwy+r s   h+   ++ l+++ ++  +k+ +D a +++++ +   +e++l+  Gg y        + ++K++ l
  gi|320100952|ref|YP_004176544.1| 436 HPDWYRRVSWRIHLWSDDTGLYDWINNtPFKDMSDLALKKHHVAVGeGNEITLRALGGFYqygstPVTVMVEKKINL 512
                                       78*********************988747*************8877799***********88866667789****** PP

                           DUF1926 159 eekseleveyeltneske.iellfavElNlallaleaddr..ylllndkk..lgeeleleevkefeleDevlkkkle 230
                                       ++k +  v+y+++n  ++  +++ ++E  +a     ++d   y+++++ +  ++e+  ++  +  + + ++   ++ 
  gi|320100952|ref|YP_004176544.1| 513 TDK-GHAVTYRIRNMGDKtFSTRLGIEYHVAWKIDRENDEkpYYVVEGVSrdVSESGVFHTERITVGSAGY--PSIV 586
                                       666.99*********99999*******99998755554441144444444556666666555555555555..99** PP

                           DUF1926 231 lelsepaelwafPveTVSqsekgfelvyQgvavvllwpvdlkekeewkl 279
                                       le+s+p e w   + ++S  ekgf  + Qg+ v+ + ++ lk++ee + 
  gi|320100952|ref|YP_004176544.1| 587 LEASKPHEAWIAQLASLSRTEKGFKEMPQGLGVMFTRQLVLKPGEEYEA 635
                                       *****************************************99999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.79 Elapsed: 00:00:00.38
# Mc/sec: 5114.39
//
Query:       gi|320100953|ref|YP_004176545.1|  [L=516]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-24   84.5   0.0    1.1e-23   83.6   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    6.4e-22   78.4   0.0    9.3e-22   77.9   0.0    1.3  1  Glyco_transf_5   Starch synthase catalytic domain
    8.5e-21   74.8   0.0    1.6e-20   73.9   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.5e-09   38.1   0.1    5.7e-09   36.2   0.0    2.1  2  Glyco_transf_4   Glycosyltransferase Family 4
    2.6e-09   37.7   0.0    1.1e-08   35.7   0.0    2.0  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.9e-07   31.4   0.0    4.1e-07   30.3   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.15   10.6   0.1       0.57    8.7   0.0    1.9  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 !   83.6   0.0   4.3e-27   1.1e-23       9     159 ..     307     466 ..     302     484 .. 0.81

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 4.3e-27
                                       TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHH.CTTCGGGEE.EC CS
                   Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeel.elsdnvifl.ge 80 
                                       ++++++ ++il  gr +k+Kg+d l+k++++l  +  p++++v+a    +   e+ l++ +e      dn+++l g+
  gi|320100953|ref|YP_004176545.1| 307 EPFKQDGPLILLTGRSTKQKGIDILLKSMDKLVSE-IPRARVVLAVipvS-GTEELLREIIEYVaLFPDNLRVLpGY 381
                                       5788999*************************997.77777776666532.33344444444331457888875388 PP

                                       CHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT......SEEEE-TT-HHHHHHH CS
                   Glycos_transf_1  81 vsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge......tGllvkpnnaealaea 151
                                       v++e   +l+ +a++f++ps++E+fG+v+lEAma+g+pv+asn+gg+++++ d        tG l+ p + e ++ea
  gi|320100953|ref|YP_004176545.1| 382 VDYEHYLTLYYSASVFLAPSRYEPFGLVVLEAMASGTPVVASNTGGFRDLILDVRryglngTGMLFTPLDREGMIEA 458
                                       99999************************************************99999***********99999999 PP

                                       HHHHHHSH CS
                   Glycos_transf_1 152 irkllede 159
                                       ++ +l+  
  gi|320100953|ref|YP_004176545.1| 459 LTLMLDIV 466
                                       98776543 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 !   77.9   0.0   3.6e-25   9.3e-22       2     240 ..       3     229 ..       2     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 3.6e-25
                    Glyco_transf_5   2 ilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkvak 78 
                                        ++++ E     k+GGLa+v   L++a++ +g dv++ +P++g+ ke+  + +ev+++  +          ++++++
  gi|320100953|ref|YP_004176545.1|   3 TWMLTFESIYTRKVGGLAEVPPRLAEAMKSMGEDVEIYTPSHGFKKENT-TGKEVFKTWING--------SEYSIWE 70 
                                       589***************************************8888876.777777743222........4455555 PP

                    Glyco_transf_5  79 lkkdgvdvyfldnpeffdreglYgdkgedyednaerfalfsraalellekl...gwkpdvihahDWhtalvpallke 152
                                        ++  v++y+++   + + + +Y+       +   +  +f+r + e+ +++   g  pd++h hDWh+  + + +++
  gi|320100953|ref|YP_004176545.1|  71 YNA-PVKHYIVSGGVL-EEPIVYSR------NLLFKSLVFARIVREYFNHVagrGETPDIVHGHDWHSYPALLAVNA 139
                                       554.999999999884.46779954......5555566999*******997654556************99777777 PP

                    Glyco_transf_5 153 lykerglfkkiktvftiHNlayqgrfpkdel.aalglp.a......edfekldglefygkvnflk.agivyadavtt 220
                                         ++ g    + +v+ iH l  +  ++ + l + +g+  +         + l+++ +++   +++  + +++d+v+t
  gi|320100953|ref|YP_004176545.1| 140 ESTRMG--IPVGIVYQIH-LLSRTLIDLEALaKGIGVSgDdylrggLGVKPLKEY-YERSGGWVErLAALTSDKVLT 212
                                       654444..4499******.666667887777566787733444444222233333.3446777777*********** PP

                    Glyco_transf_5 221 VSptyakEiltpefgggleg 240
                                       VS+ y +++++     gl++
  gi|320100953|ref|YP_004176545.1| 213 VSKGYTRDVVRIV---GLDN 229
                                       *********9976...7766 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 !   73.9   0.0   6.3e-24   1.6e-20       2     132 ..     314     463 ..     313     464 .. 0.74

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 6.3e-24
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.H...EEEEEES.---....HHHHHHHTT-T.T.EEEE---..THHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d...vrlvivG.dgprp..eeleelaagleer.veftGfv..edlae 68 
                                       p il +Gr   ++kg+d+ll+ + +l ++ +   v l ++  +g+++  +e+ e++a + ++  ++ G+v  e    
  gi|320100953|ref|YP_004176545.1| 314 PLILLTGRS-TKQKGIDILLKSMDKLVSEiPrarVVLAVIPvSGTEEllREIIEYVALFPDNlRVLPGYVdyEHYLT 389
                                       7899*****.567**********666645534343333332223222122333344433466467789997666889 PP

                                       HHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--......T..TSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  69 llaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv......g..engllvppgdpealaeailrLl 132
                                       l+ +a+vf+aPs  e fgl++lEama+g+pvVa+++gg+++++      g   +g+l+ p d e ++ea+  +l
  gi|320100953|ref|YP_004176545.1| 390 LYYSASVFLAPSryEPFGLVVLEAMASGTPVVASNTGGFRDLIldvrryGlnGTGMLFTPLDREGMIEALTLML 463
                                       9***********999****************************977666433467*************997665 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   2.2e-12   5.7e-09       1     164 [.      16     238 ..      16     241 .. 0.78
   2 ?   -3.1   0.0       2.7     7e+03     141     168 ..     357     384 ..     340     386 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.2e-12
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.............................elvvrvprvpl 48 
                                       vGG + +  +La+a+  +G +V+++tp+++ + e+                                    ++ +  
  gi|320100953|ref|YP_004176545.1|  16 VGGLAEVPPRLAEAMKSMGEDVEIYTPSHGFKKENTTgkevfktwingseysiweynapvkhyivsG--GVLEEPIV 90 
                                       5888888889********************999999999**************99988877654321..12222222 PP

                    Glyco_transf_4  49 pllkrllrslaflrrlrrllkre.........kpDvvHahspaalgaallalrr...rlgipl..VltvHglye... 108
                                        +++ l +sl f+r +r+    +          pD+vH h++++   alla  +   r gip+  V+ +H l     
  gi|320100953|ref|YP_004176545.1|  91 YSRNLLFKSLVFARIVRE----YfnhvagrgeTPDIVHGHDWHSY-PALLAVNAestRMGIPVgiVYQIHLLSRtli 162
                                       222222233444443333....2333466679*********9996.5555555568899999877999999999*** PP

                    Glyco_transf_4 109 ...................krllkarlkplsrllralerrllrradrviavSeatadelrerygvpp.ekitVipn 164
                                                             +k+ +  ++r   ++er ++  +d+v++vS+   +++++  g+++  k+  + n
  gi|320100953|ref|YP_004176545.1| 163 dlealakgigvsgddylrgGLGVKPLKEYYERSGGWVERLAALTSDKVLTVSKGYTRDVVRIVGLDNaTKVDYVFN 238
                                       ***************99886667778888889999999999************99999999999998777777776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                    Glyco_transf_4 141 SeatadelrerygvppekitVipnGvDl 168
                                       +e++ +e++e+  + p++++V+p  vD 
  gi|320100953|ref|YP_004176545.1| 357 TEELLREIIEYVALFPDNLRVLPGYVDY 384
                                       5677788888777777999999988885 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 !   35.7   0.0   4.2e-12   1.1e-08       1     150 [.      17     228 ..      17     238 .. 0.70
   2 ?   -2.0   0.0       1.7   4.3e+03      72      72 ..     392     392 ..     341     455 .. 0.62

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4.2e-12
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvlt.......papapg.........................apeleedgvrvhrl 45 
                                       gG + +  +la+a+   G +V+++t            +                          + ++ +gv     
  gi|320100953|ref|YP_004176545.1|  17 GGLAEVPPRLAEAMKSMGEDVEIYTpshgfkkE----NttgkevfktwingseysiweynapvKHYIVSGGVL-EE- 87 
                                       6677777799***************55555440....034455566666655544444432222223333332.22. PP

                   Glyco_trans_4_4  46 p.vprrpspladlaalralrrll...rqrrerpdvvhahspt..aglaarlar.rrrgipl..vvtlh......... 104
                                       p v+ r  ++++l ++r +r+++   + r e pd+vh h+++   +l+a+ a   r gip+  v+ +h         
  gi|320100953|ref|YP_004176545.1|  88 PiVYSRNLLFKSLVFARIVREYFnhvAGRGETPDIVHGHDWHsyPALLAVNAEsTRMGIPVgiVYQIHllsrtlidl 164
                                       3244444589999999*****9999888************974445555555534569**777******99999999 PP

                   Glyco_trans_4_4 105 ...........glllrrg..sgavrrly....ralerrllrradavlvvseaeaeelra.lgvp 150
                                                  ++ lr+g    +++ +y     ++er+++   d vl+vs +  +++++  g++
  gi|320100953|ref|YP_004176545.1| 165 ealakgigvsgDDYLRGGlgVKPLKEYYersgGWVERLAALTSDKVLTVSKGYTRDVVRiVGLD 228
                                       99999888874344555566777888998888899****************9999999967765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                   Glyco_trans_4_4  72 e 72 
                                       +
  gi|320100953|ref|YP_004176545.1| 392 Y 392
                                       1 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.6e-10   4.1e-07       1      91 [.     396     497 ..     396     498 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.6e-10
                   Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltddaegleelftpgk......evilfe..dleelaekirylla...npeer 66 
                                       ++L+psr+e + l+++Ea+a+G++++++ + g+++l+ + +      +++lf   d e ++e++  +l+   n++e 
  gi|320100953|ref|YP_004176545.1| 396 VFLAPSRYEPFGLVVLEAMASGTPVVASNTGGFRDLILDVRryglngTGMLFTplDREGMIEALTLMLDiveNEDES 472
                                       589***************************999999888888888889999999**********9998765577887 PP

                   Glyco_trans_1_2  67 raiaeaarervlaehtydhraeqll 91 
                                       +a+ ++   ++ + +t+ + a++ll
  gi|320100953|ref|YP_004176545.1| 473 SARLRRRCVEYSSSFTWSNSAARLL 497
                                       777777777778999****999987 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.3   7.6e+02     122     174 ..     100     155 ..      96     163 .. 0.70
   2 ?    8.7   0.0   0.00022      0.57     460     519 ..     382     440 ..     370     499 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHCT----EEEEEEETGGGHHHHHHHHHTT....-SEEEEEEES CS
                      Glycogen_syn 122 iilGflvalflkefreleekkavvahfhewlaGvgliltrkrk....ldvatvftth 174
                                       +++  +v ++++++    e++ +v h h+w +  +l+ + +      ++v  v+  h
  gi|320100953|ref|YP_004176545.1| 100 LVFARIVREYFNHVAGRGETPDIV-HGHDWHSYPALLAVNAEStrmgIPVGIVYQIH 155
                                       788889999999999999999987.88999988888766543211226667777666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00022
                                       --HHHHHHH-S.EEE-..--SSBSS-HHHHHHHHTT--EEEETTBHHHHHHHHH-TTGGGGTE CS
                      Glycogen_syn 460 ldyeefvrGch.lGvf..psyyepwGytpaectvmGipsvttnlsGfGcfmeeliedakdyGi 519
                                       +dye+++   +   vf  ps yep+G    e    G p v++n  Gf    ++li d + yG+
  gi|320100953|ref|YP_004176545.1| 382 VDYEHYLTLYYsASVFlaPSRYEPFGLVVLEAMASGTPVVASNTGGF----RDLILDVRRYGL 440
                                       5777776533213344449***************************9....466666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 4162.26
//
Query:       gi|320100954|ref|YP_004176546.1|  [L=624]
Description: glycoside hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-33  114.6   4.3    7.3e-30  104.3   0.0    2.5  3  Glyco_hydro_57  Glycosyl hydrolase family 57
  ------ inclusion threshold ------
      0.054   13.3   0.0       0.12   12.2   0.0    1.5  1  NifZ            NifZ domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   1.5e-05      0.13       1      59 [.     111     177 ..     111     184 .. 0.68
   2 !  104.3   0.0   8.1e-34   7.3e-30     116     321 ..     203     426 ..     198     431 .. 0.80
   3 ?   -2.6   0.1      0.28   2.5e+03      92     121 ..     464     504 ..     447     507 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.5e-05
                                       EEEEEE-----TTS-...SSSSSH.....HHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHH CS
                    Glyco_hydro_57   1 afvfhqHqplykkpg...kgeytl.....pwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqL 59 
                                       a+v+h Hq   + p+   +g++++     + +r  +   Y   a++lek ++ h t++Ls+sLi+q 
  gi|320100954|ref|YP_004176546.1| 111 ALVWHHHQAPNYLPDgsiHGPWAFiyvygNSLRPYGNAPYSYHAAMLEKHRDYHATYNLSPSLIKQW 177
                                       688999997666666455333333000012334445556888999*******************995 PP

  == domain 2  score: 104.3 bits;  conditional E-value: 8.1e-34
                                       TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-....HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHH CS
                    Glyco_hydro_57 116 nkevlelfrelqesgqvElltspyyHpllpllpd....sedieaqvkkarelyeeyfgqePrgfwlpElavspeile 188
                                       ++++  ++    e+gq+ +lts y+H +  +l d    ++ i+ +v+ ++++ +e +g++P g w pE+a+s +++ 
  gi|320100954|ref|YP_004176546.1| 203 IEDTVAKYVRAYERGQIDVLTSIYAHTIGGFLIDvlgmEDVIRDEVRYGISITKEVLGVTPLGAWTPEMAFSMKLID 279
                                       666777777788********************8888856677889******************************** PP

                                       HHHHTT--EEEE-C.------------TTS-EE-TTS.....-EEEE--CHH-TTTSGGG-...............T CS
                    Glyco_hydro_57 189 ilaelGfeylftde.laeiledkskespyrpyllkngg....iavffRdreLsddigFrys...eqypleavddfin 257
                                       i++++G+ey++ d+  ++  ++  k s+y py + n++    i v+fR++eLsd ++F+     e     a +++ +
  gi|320100954|ref|YP_004176546.1| 280 IYYDNGIEYTVLDDkCHFEGAEGEKTSSYEPYIALNKEsgkhIVVYFRNHELSDVLSFKNNftsE---VHALRNAYE 353
                                       **************745555555566888888777777778*****************9885552...444444444 PP

                                       TSB..............-TT---TTT-....-BB-TT-S---HHHHHHHHHHH...HHHHHHHHHHHHHHSS-EE CS
                    Glyco_hydro_57 258 wlkkvkka....ksevvtialdgEnwg....hypetgkkeFleklyeeleeng...lielvtpsefikklkpkgl 321
                                          +++k      ++++t+aldgEnw+    + p t    +l kl  +le+ +    ++l++++e++++l+++++
  gi|320100954|ref|YP_004176546.1| 354 MSLTIAKRilesSGRILTLALDGENWMvfsgNPPLTAF--YLDKLLLFLESLSdagFLRLMSLREVYSELPATRI 426
                                       444444444445***************66655555553..9***999777776666**************99987 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.28
                                       H............HHHHHHHHHHHHHHHHHHHHHT.TT-HHH CS
                    Glyco_hydro_57  92 k............ldlavlfnlaisgplleqiqkwlnkevle 121
                                       k            +++a + + +  ++ +++++ w  +++++
  gi|320100954|ref|YP_004176546.1| 464 KtyeymvggrdpySEKARWALWHALDSDYWWAEFW-SPKIID 504
                                       34444455556667888999999999999999999.999987 PP

>> NifZ  NifZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.3e-05      0.12      22      67 ..      24      70 ..      15      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.3e-05
                              NifZ 22 fpgkeigelLvkkGdvGvvvsvGtflqnqeiYlVeF.leeglvVGcl 67
                                      +pg e    L++ G++G v++v +f +++ iY+ +  + e  +VG+ 
  gi|320100954|ref|YP_004176546.1| 24 MPGEEAKIHLLASGEKGKVIHVSVFDDEKTIYEGDLtIGETPIVGVI 70
                                      588899999***********************977766666777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.38
# Mc/sec: 4900.59
//
Query:       gi|320100955|ref|YP_004176547.1|  [L=309]
Description: phosphoesterase DHHA1 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00067   20.1   0.2      0.003   18.0   0.2    2.0  1  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   1.7e-07     0.003       6     136 ..     190     300 ..     185     301 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-07
                                       HHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC..TCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEEC CS
                             DHHA1   6 eerkelekeleelkealaklkaeellekaeevk..gvkvlvaevgeewdagalgiaadklksklkkpvivfvakeeg 80 
                                        e k++++ l   +ea+a+++    +      +  gvk+lv ++   +d+++  +    + +  k+ +   v+  + 
  gi|320100955|ref|YP_004176547.1| 190 LEVKNVYENL--IREAIARAEL---V------ErrGVKILVFQD---VDPRVHPGELIHVAE--KNGIFSHVYIVRY 250
                                       5666666666..6666666532...2......222777777666...666666666666666..5566666666666 PP

                                       TEEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEETCEEE..EEEEHCH.HHHHHHHHHH CS
                             DHHA1  81 dkvkvsarskkdgvdagelakeaaaklgggGGGHdlAaG..agipaek.leealealee 136
                                           +s+rs    +d+++la +      +gGGGH+  aG  ++i+ e  l e+++ +ee
  gi|320100955|ref|YP_004176547.1| 251 -PRGLSLRSE--YIDVSKLALK------YGGGGHRRIAGipGKINLETlLGEIVKSVEE 300
                                       .55699***9..9*********......******9999989999988888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2286.54
//
Query:       gi|320100956|ref|YP_004176548.1|  [L=161]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-05   24.3   0.0    4.1e-05   23.7   0.0    1.4  1  Thioredoxin_7  Thioredoxin-like
     0.0042   17.3   0.0     0.0063   16.7   0.0    1.3  1  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.017   14.5   0.0    1.2  1  DUF929         Domain of unknown function (DUF929)


Domain annotation for each model (and alignments):
>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   6.8e-09   4.1e-05      19      82 ..      66     136 ..      48     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.8e-09
                                       -EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG..........-TT-.......--SSEEE CS
                     Thioredoxin_7  19 pvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani.........lelde.......qgvPvva 79 
                                         ++ffg+++c++C+++ ++f  +      + +k+ +l+vdv++  +++             +        gvP+ +
  gi|320100956|ref|YP_004176548.1|  66 IRIIFFGSTTCPHCHRQSEFFNAT------MPGKVLYLWVDVDQDAGSVfskvvnlevS---KgipfnyaGGVPHML 133
                                       579******************999......999*********99999987777663330...2555534445****9 PP

                                       EE- CS
                     Thioredoxin_7  80 fld 82 
                                       +l+
  gi|320100956|ref|YP_004176548.1| 134 VLG 136
                                       986 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0063       1      35 [.      68     105 ..      68     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                                       EEEEESTSSHHHHHHHHHHHHTT...GGEEEEEGCCSH CS
                      Glutaredoxin   1 vvlftkptCpyCkkakrlLkelg...vkfeeidvdkde 35 
                                       ++ f+++tCp+C++  ++++      v +  +dvd+d+
  gi|320100956|ref|YP_004176548.1|  68 IIFFGSTTCPHCHRQSEFFNATMpgkVLYLWVDVDQDA 105
                                       678****************877666788********97 PP

>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.8e-06     0.017       3      76 ..       2      82 ..       1      84 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-06
                            DUF929  3 liviaiivliivvivvvslsai..........vsnalvelskqvyaseplstkfvkvsnqdlasngkvevyfvswegCP 71
                                      +++++i+++ii+++v++ + ++          +s + v  +    +  +  + +  +s +    n ++ ++f ++  CP
  gi|320100956|ref|YP_004176548.1|  2 ILLVPIVAFIIIIAVMLLMWHQptgsggtpfyLSTERV--AGVSFTGDEWRSIYSEISLKT-PLNDSIRIIFFGSTTCP 77
                                      67899999999999888888888998888854444444..333344444443477777666.6699************* PP

                            DUF929 72 vgaae 76
                                      ++  +
  gi|320100956|ref|YP_004176548.1| 78 HCHRQ 82
                                      **765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1235.72
//
Query:       gi|320100957|ref|YP_004176549.1|  [L=228]
Description: transmembrane electron transport protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       723  (0.0403257); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1763.22
//
Query:       gi|320100958|ref|YP_004176550.1|  [L=379]
Description: Heat shock protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-42  143.9   1.4    1.8e-41  142.1   0.0    2.3  2  Peptidase_M48  Peptidase family M48
    1.8e-05   24.1   0.6    4.4e-05   22.8   0.1    1.8  2  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.077   11.3   2.1        0.1   10.9   2.1    1.3  1  OATP           Organic Anion Transporter Polypeptide (OATP) f
        0.7    9.6  19.3        3.5    7.3  13.1    2.4  2  Yip1           Yip1 domain
        6.3    6.2   6.7       0.41   10.1   0.8    2.0  3  DUF3087        Protein of unknown function (DUF3087)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.6       1.2   4.3e+03     101     124 ..      32      55 ..      10      97 .. 0.60
   2 !  142.1   0.0     5e-45   1.8e-41       3     195 ..     114     371 ..     112     372 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                                       HTT-SHHHHHTT--S---HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 101 lisraeedaagafldalavligll 124
                                       + ++a+++ +  +l++ ++++gll
  gi|320100958|ref|YP_004176550.1|  32 APRVARGFSNRFALKSSMIIVGLL 55 
                                       333344444444444444444444 PP

  == domain 2  score: 142.1 bits;  conditional E-value: 5e-45
                                       -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                         ++l+++v+e+a+++g+ ++++k + vnsp  NAFa+g+  +  +i+++++L   +lseeel+aV+GHElGH+ hr
  gi|320100958|ref|YP_004176550.1| 114 HSEDLQRIVNEVAAKLGV-NRPPKAMLVNSPP-NAFAYGNILSGrYIAVSRELA-GMLSEEELKAVIGHELGHHIHR 187
                                       5789**************.9999********5.**********99*********.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH............HTT-SHHHHHTT--S--.-HHHHHHHHHHTT...HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx...xxxxxxxxx RF
                     Peptidase_M48  79 hsvvslivsllasillllglal............lisraeedaagafldal.avliglliillfl...alSRkrEyq 139
                                       +++++l+++ l+si+++lg++l            l+sr +++a+g+f+  + ++++++l++++++   a+SR rEy+
  gi|320100958|ref|YP_004176550.1| 188 DNTIMLFMGILPSIIYYLGVFLiraglvsssvsrLTSRRRDNASGGFILVIaGIAAVALSFIVQVlvlAFSRLREYY 264
                                       ******************99762222222222223455666666666544303344444444444899********* PP

                                       HHHHHHHTTT.HHHHHHHHHHHHHHTT--S---HHHH........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                     Peptidase_M48 140 ADeagvellkrakdlvraliklakdlerqdvsaslrs........................................ 176
                                       AD  g+++ + + +++ral+kl+  +e+ +++ ++ s                                        
  gi|320100958|ref|YP_004176550.1| 265 ADTSGARASS-PLNMQRALAKLHLYYEGSSYAREAVSasklktlfiyaftetvaspfyhyktppriawervdidevi 340
                                       **********.*****************999999999999999********************************** PP

                                       ............HHS-SS--HHHHHHHHHH- CS
                                       ............xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 177 ............ellstHPplleRiqalkel 195
                                                   e++stHPp+++R++ l++l
  gi|320100958|ref|YP_004176550.1| 341 eelkrrevnsvqEFFSTHPPTPKRLRFLDTL 371
                                       ***************************9975 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.2e-08   4.4e-05      31     227 ..      14     204 ..       8     207 .. 0.77
   2 ?   -1.9   0.0      0.41   1.5e+03     107     137 ..     235     263 ..     229     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-08
                     Peptidase_M56  31 iaaYalWlivllallipfipesavslpvkfetskinsaaskaplasaaskvlddkas....alatdvkkvewktilk 103
                                       + aYa+ ++v++++ + ++p       v   +s+ ++ +s++ ++   +++ +             ++ +  +  l+
  gi|320100958|ref|YP_004176550.1|  14 MLAYAVGFVVMMSMAALIAP------RVARGFSNRFALKSSMIIVGLLAAASSI--AgiclVAYLLTSYFGAALTLD 82 
                                       67788888888888888877......3445667777777777776665554222..233545555556666677788 PP

                     Peptidase_M56 104 illliWivgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemqlkrnikirlsssidsPavlgll..k 178
                                       ++++i +++ l+ l+  + + ++++  ++  ++++++  l+++++e   + ++ r++k +l +s  + +  g +   
  gi|320100958|ref|YP_004176550.1|  83 FVAAIAVFVLLANLFTYLISPFMIN--LFYGAKHSED--LQRIVNEVAAKLGVNRPPKAMLVNSPPNAFAYGNIlsG 155
                                       9999999999998888888888888..7777777777..99****************99998876666666644114 PP

                     Peptidase_M56 179 prIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqclfwf 227
                                        +I ++ +++  ls+eel+ ++ HEl H  ++D  + l++ +l  ++++
  gi|320100958|ref|YP_004176550.1| 156 RYIAVSRELAGMLSEEELKAVIGHELGHHIHRDNTIMLFMGILPSIIYY 204
                                       69**********************************9999999888776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                     Peptidase_M56 107 liWivgalilllyliaallvlkkrfvrklgk 137
                                       +++i+g+++++l +i  +lvl   f r ++ 
  gi|320100958|ref|YP_004176550.1| 235 ILVIAGIAAVALSFIVQVLVLA--FSRLREY 263
                                       5667777777777777777776..4444443 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.1   2.9e-05       0.1       9     101 ..      21     116 ..      11     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.9e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP   9 lglvqamvsgyfkstittiEkrFklpssts..gliassneignilli..lfvsYfggrghrPrwigigallmalgsl 81 
                                       ++++  m+  +   +   +  rF l+ss +  gl+a+++ i+ i+l+  l+ sYfg+      + +i+++++    +
  gi|320100958|ref|YP_004176550.1|  21 FVVMMSMAALIAPRVARGFSNRFALKSSMIivGLLAAASSIAGICLVayLLTSYFGAALTLDFVAAIAVFVLLANLF 97 
                                       33334677777888999999********8555*********99887722567******9999999999988888888 PP

                                       xxxxxxxxxxxxxxxxxxxx RF
                              OATP  82 llalPhfisgkyeyeeeese 101
                                       ++ +  f+ +   y  ++se
  gi|320100958|ref|YP_004176550.1|  98 TYLISPFMINL-FYGAKHSE 116
                                       87777777642.33333333 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  13.1   0.00097       3.5      60     146 ..       8      95 ..       3     128 .. 0.72
   2 ?    5.6   0.4    0.0032        11      26      81 ..     192     256 ..     166     269 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00097
                              Yip1  60 ssllgaiiggylglllgllllalllhliakllggkgsfkqtlsvvgyallPlilgaliaillllllgt......... 127
                                       +++++ ++++++g++++    al+   +a+ + ++  +k ++ +vg+ ++++ ++++++++ ll ++          
  gi|320100958|ref|YP_004176550.1|   8 FTMIALMLAYAVGFVVMMSMAALIAPRVARGFSNRFALKSSMIIVGLLAAASSIAGICLVAYLLTSYFgaaltldfv 84 
                                       57788888888888888888888888899999999999999999999999999999987776666555644444443 PP

                              Yip1 128 llllvgllaliWslvllyl 146
                                       +        +i ++vll++
  gi|320100958|ref|YP_004176550.1|  85 A--------AIAVFVLLAN 95 
                                       2........3333333332 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0032
                              Yip1  26 llllalltlllgllas.lnlgqtlasg........eevqgltlssllgaiiggylglllglllla 81 
                                       +l++ +l+ +  +l+  l+ ++ ++s+        ++ ++ +++ ++++i++ +l +++ +l+la
  gi|320100958|ref|YP_004176550.1| 192 MLFMGILPSIIYYLGVfLIRAGLVSSSvsrltsrrRDNASGGFILVIAGIAAVALSFIVQVLVLA 256
                                       55666666666666663333344444466665554333344444444444444444444444444 PP

>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00011      0.41      19      97 ..      48     126 ..      41     140 .. 0.78
   2 ?   -2.3   0.1      0.76   2.7e+03      26      68 ..     241     256 ..     201     267 .. 0.54
   3 ?   -3.7   0.0         2   7.2e+03     108     121 ..     279     292 ..     274     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                           DUF3087  19 ivalvallavlsllfstllialfg.eeevsnfhlnllGvvlalvltaailrklktkpfmaevvYvWrLKqllnkiyr 94 
                                        +++v lla+ s + +  l+a++  +  ++ ++l+++ ++ a+++++a l  +  +pfm ++ Y+ +    l++i +
  gi|320100958|ref|YP_004176550.1|  48 SMIIVGLLAAASSIAGICLVAYLLtSYFGAALTLDFVAAI-AVFVLLANLFTYLISPFMINLFYGAKHSEDLQRIVN 123
                                       5678888888888888777765552666779999999776.566666777788899***********9999999998 PP

                           DUF3087  95 klk 97 
                                       +++
  gi|320100958|ref|YP_004176550.1| 124 EVA 126
                                       765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.76
                           DUF3087  26 lavlsllfstllialfgeeevsnfhlnllGvvlalvltaailr 68 
                                       +a+                           v l++++ +++l 
  gi|320100958|ref|YP_004176550.1| 241 IAA---------------------------VALSFIVQVLVLA 256
                                       222...........................3334444444444 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2
                           DUF3087 108 enAlkilrFyyqgl 121
                                       ++Al  l+ yy+g+
  gi|320100958|ref|YP_004176550.1| 279 QRALAKLHLYYEGS 292
                                       67999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2761.40
//
Query:       gi|320100959|ref|YP_004176551.1|  [L=655]
Description: serine protease-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-11   43.2   0.0    5.7e-11   42.3   0.0    1.3  1  Lon_C     Lon protease (S16) C-terminal proteolytic domain
  ------ inclusion threshold ------
      0.053   13.6   1.6       0.26   11.4   0.1    2.7  3  SecG      Preprotein translocase SecG subunit


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 !   42.3   0.0   6.4e-15   5.7e-11     101     171 ..     108     179 ..      93     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6.4e-15
                                       -S-B-GG.GGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGG CS
                             Lon_C 101 PeGavPk.dGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPke 171
                                        e ++P   GPs+G  ++  ++sllt+++ +  v+mtG i   G + p+GGlkekl aa  +g k  ++P  
  gi|320100959|ref|YP_004176551.1| 108 TESSTPIiGGPSSGGLMTIGFLSLLTNRSLQPWVTMTGMINPDGTIGPVGGLKEKLDAAASNGFKMFLIPFG 179
                                       5666774269***********************************************************965 PP

>> SecG  Preprotein translocase SecG subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.14   1.2e+03      40      57 ..      41      61 ..       6      62 .. 0.67
   2 ?   -2.7   0.0      0.72   6.4e+03      38      50 ..     395     414 ..     385     418 .. 0.65
   3 ?   11.4   0.1   2.9e-05      0.26      32      69 ..     592     630 ..     574     631 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.14
                                      -...-SSCCCHHCCHHHHHHH CS
                              SecG 40 f...gsrgaekfLtkiTvila 57
                                      +    s + +++L+k+T i+a
  gi|320100959|ref|YP_004176551.1| 41 YapaVSGSGQGVLSKTTLIVA 61
                                      455445677889999999987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.72
                                       SS-.......-SSCCCHHCC CS
                              SecG  38 slf.......gsrgaekfLt 50 
                                       +l+        +r+ae+fL+
  gi|320100959|ref|YP_004176551.1| 395 KLMylahtlsYARQAEAFLN 414
                                       34446666668999999998 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 2.9e-05
                                       ....SS-SS--SSCCCHHCCHHHHHHHHHHHHHHHHHHC CS
                              SecG  32 ggg.asdslfgsrgaekfLtkiTvilavlFfvlslvlal 69 
                                       ggg  ++++ +s +a+ +L k  +i+++ ++++s+vlal
  gi|320100959|ref|YP_004176551.1| 592 GGGsTNNTSGSSGSANTMLVKYLAIVGAMLAIVSIVLAL 630
                                       55546666779999999********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (655 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4803.79
//
Query:       gi|320100960|ref|YP_004176552.1|  [L=300]
Description: phosphoesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-08   34.4   0.0    9.6e-08   32.4   0.1    1.9  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    4.6e-06   27.3   0.1    1.5e-05   25.6   0.1    1.8  1  Metallophos    Calcineurin-like phosphoesterase
      0.001   19.5   0.1     0.0015   19.0   0.1    1.3  1  HAD            haloacid dehalogenase-like hydrolase


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 !   32.4   0.1   1.6e-11   9.6e-08       3     130 ..      30     183 ..      29     212 .. 0.71
   2 ?   -1.1   0.0      0.32   1.9e+03     133     150 ..     240     257 ..     235     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.6e-11
                     Metallophos_2   3 laiiSDlH.............................snldaleavlealkevgvdaiihaGDleeeep........ 42 
                                       +++++DlH                             + ++a+e +++a +  ++d++++ GDl + ++        
  gi|320100960|ref|YP_004176552.1|  30 MLVMADLHlgfeeaasrgltyslrgsssyagvflpriQLRRAIEYLVKASSVLDIDRVVVNGDL-KHAFdrllrqer 105
                                       567777777777777777777777777777777766666788888899999999*********5.222244455555 PP

                     Metallophos_2  43 ....evleellela..pvlaVrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkdalaellk 113
                                           e++ +l+e    +v++VrGN+D ++++  +     +l+ +l ++ e++++ +++l++Hg+     ++++ + +
  gi|320100960|ref|YP_004176552.1| 106 devvEFVTWLREKGirEVEVVRGNHD-NYLKPVLR----RLNVELVNSIEVTADSRRILIVHGH-----EDVDVAGR 172
                                       4444566666665599**********.43444444....44445556678888999*******9.....67777777 PP

                     Metallophos_2 114 eaeegsdvvvcGHtHvp 130
                                       +      +vv GH H  
  gi|320100960|ref|YP_004176552.1| 173 D------IVVIGHEHPS 183
                                       7......9999999965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                     Metallophos_2 133 ekeggvlvvnPGsvgepr 150
                                       ek+g ++ vn Gsv ++ 
  gi|320100960|ref|YP_004176552.1| 240 EKTGLITWVNLGSVDQAT 257
                                       56677899******9874 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   2.5e-09   1.5e-05       2     123 ..      29     164 ..      28     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.5e-09
                                       EEEEEESBTB.......................TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS........ CS
                       Metallophos   2 rilvigDlHl.......................algggqlddllkllddllreekpdlvllaGDlvdrg........ 47 
                                       + lv++DlHl                        l   ql++++++l ++ +  ++d v+++GDl +          
  gi|320100960|ref|YP_004176552.1|  29 KMLVMADLHLgfeeaasrgltyslrgsssyagvFLPRIQLRRAIEYLVKASSVLDIDRVVVNGDLKHAFdrllrqer 105
                                       789**************999988888877755544445555555555444555899********7776666688766 PP

                                       HHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHH.HCEEETSEEEEEETTE..EEEEEEE CS
                       Metallophos  48 dlekellellaalvkypipvylllGNHegfeeellnkygylgifsepwrsd.aevfnnlplaslgsgs..lkvlllh 121
                                       d   e++ +l++++     v +++GNH+    ++l +         + r+  +e +n + +          ++l++h
  gi|320100960|ref|YP_004176552.1| 106 DEVVEFVTWLREKGI--REVEVVRGNHD----NYLKP---------VLRRLnVELVNSIEVT-----AdsRRILIVH 162
                                       555556666677777..589********....44444.........2222202222222222.....2456999999 PP

                                       SE CS
                       Metallophos 122 Gg 123
                                       G+
  gi|320100960|ref|YP_004176552.1| 163 GH 164
                                       99 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.5e-07    0.0015      67     151 ..      91     171 ..      33     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-07
                               HAD  67 eelaaelerfvaevirpklldpgalellaahraaGd.rvvvvSgglrplvepllaelgadevlat.elevdd.rltg 140
                                       ++l++ ++r++++++       +++e++ + r++G+ +v vv g+++ +++p+l++l+  e++++ e+  d  r+  
  gi|320100960|ref|YP_004176552.1|  91 GDLKHAFDRLLRQER------DEVVEFVTWLREKGIrEVEVVRGNHDNYLKPVLRRLN-VELVNSiEVTADSrRILI 160
                                       333334444442222......59*************9*********************.555555355555576666 PP

                               HAD 141 elglegkpvrg 151
                                        +g+e+ +v+g
  gi|320100960|ref|YP_004176552.1| 161 VHGHEDVDVAG 171
                                       66667766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2296.12
//
Query:       gi|320100961|ref|YP_004176553.1|  [L=211]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.3   0.0       0.22   11.0   0.0    1.1  1  Rhabdo_ncap_2  Rhabdovirus nucleoprotein


Domain annotation for each model (and alignments):
>> Rhabdo_ncap_2  Rhabdovirus nucleoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.2e-05      0.22      48     185 ..      17     163 ..       5     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.2e-05
                     Rhabdo_ncap_2  48 lvinakkpgpaseeellllvakaleaevvgikelstggln.......drleaaeekklaeilekelaeelakavcfl 117
                                       +++++++ ++++e++ +++  + +e++ +gi+e+++ +l        + + a  ++ +++   +   ++++ ++ ++
  gi|320100961|ref|YP_004176553.1|  17 MAPKSRASEEPREPQPQPKESGQQERQETGIDEIKEIILRktraaqkSSRDAVNRETVETPVQDNVNGKIMSTIEAI 93 
                                       67889999999**9999***********************9998887555555566666666666666777777777 PP

                     Rhabdo_ncap_2 118 aa.lllrlvaKseesveraiknfkeryaklyktsldikatvlfnee.alesireafqkrsslrntvllil 185
                                       aa + +r v   ++ v++ ++ + e++ + y+++   + + +++   +l+ i e+ +++++l+++++++ 
  gi|320100961|ref|YP_004176553.1|  94 AAsSHVRIVECDQQGVCNDGRRIGEVFTDEYGLKRQRGFINTTRLPiFLDFIVEEAEANPVLKKAYVVRT 163
                                       7725789999999****************999988876555555547******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1509.03
//
Query:       gi|320100962|ref|YP_004176554.1|  [L=119]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 864.00
//
Query:       gi|320100963|ref|YP_004176555.1|  [L=637]
Description: indolepyruvate ferredoxin oxidoreductase subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for 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   69.9   0.0    4.4e-19   68.8   0.0    1.6  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      5e-16   59.2   0.1    8.2e-16   58.4   0.1    1.3  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    1.1e-10   40.8  10.9    7.4e-07   28.7   2.3    3.0  2  Fer4          4Fe-4S binding domain
    4.9e-09   35.9  12.7    3.3e-05   23.8   1.7    2.8  2  Fer4_6        4Fe-4S binding domain
    2.2e-07   30.9  11.3    8.9e-06   25.7  11.9    2.5  2  Fer4_21       4Fe-4S dicluster domain
    5.5e-06   26.2  19.1     0.0013   18.7   3.8    2.9  2  Fer4_2        4Fe-4S binding domain
    7.8e-06   26.0   8.8    1.9e-05   24.7   8.8    1.7  1  Fer4_9        4Fe-4S dicluster domain
    1.4e-05   25.5  10.1     0.0004   20.9  11.2    2.5  3  Fer4_7        4Fe-4S dicluster domain
    1.6e-05   24.9  10.9     0.0022   18.1  12.0    2.6  2  Fer4_10       4Fe-4S dicluster domain
    5.6e-05   22.9   0.1    0.00013   21.7   0.1    1.6  1  Transket_pyr  Transketolase, pyrimidine binding domain
    0.00026   21.9   9.4     0.0017   19.2   0.8    2.5  2  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
       0.02   14.5   2.3      0.023   14.3   0.3    2.1  3  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
      0.037   14.5   2.2      0.037   14.5   2.2    3.0  2  Fer4_4        4Fe-4S binding domain
      0.057   13.9   7.8       0.64   10.5   0.9    2.5  2  Fer4_8        4Fe-4S dicluster domain
        1.5    9.6   7.8         11    6.8   0.9    2.8  2  Fer4_15       4Fe-4S single cluster domain
        1.9    9.1  11.9        2.1    9.0   2.0    2.6  3  Fer4_17       4Fe-4S dicluster domain
        3.3    8.6   7.3        4.7    8.1   0.7    2.5  2  Fer4_22       4Fe-4S dicluster domain
        6.5    7.4  12.5        5.5    7.6   1.5    2.7  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 !   68.8   0.0   4.4e-22   4.4e-19       1     151 [.     404     547 ..     404     548 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4.4e-22
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHH.HSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakl.akpdrevvaivGDGgflmi.lqelatavrrnlpi 75 
                                       diGc+tl      ++++p ++++  ++  mG +l++A+G    +  +++v+a++GD++f++  ++  +++v++n  +
  gi|320100963|ref|YP_004176555.1| 404 DIGCYTL------GYQKPFETQM--TCFEMGGSLGIAHGFGKvL--RQTVIAVIGDSTFFHAgIPPAINIVYNNSRV 470
                                       89*****......8999988877..9**************8734..46***************************** PP

                                       EEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EE....EESSH.HHHHHHHHHHHHCSSS CS
                      TPP_enzyme_C  76 tvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.ga....rvekadveeleealkealekkg 147
                                       + +vl+N++++mtg+q++p +g + +g +   ++ + ++ + + +G k ++    rv+++ ++ l +alk+ l+ ++
  gi|320100963|ref|YP_004176555.1| 471 IPLVLDNSTTAMTGHQPHPGTGVTAMGLE---TRRILPEDILREAGFKtVVinplRVKES-IDLLTQALKDYLKGER 543
                                       **********************9999988...999*************655677766666.6777777777778877 PP

                                       EEEE CS
                      TPP_enzyme_C 148 pali 151
                                        a++
  gi|320100963|ref|YP_004176555.1| 544 IAIV 547
                                       7765 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 !   58.4   0.1   8.2e-19   8.2e-16       2     171 ..      23     187 ..      22     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 8.2e-19
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a ++ag+ v++aYP TPs+ei+e+l+e + ++++   +v    +E  a++++ GAa++G+r++Ta    G+  +++ 
  gi|320100963|ref|YP_004176555.1|  23 ASLEAGICVATAYPGTPSTEIIEALSEVAGECGI---YVEWSINEKVAFETAYGAAITGVRSLTAMKHVGVNVASDI 96 
                                       6789999**********************99996...888889********************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                       l+  a + + + +vvv    p    s +++q    +     + v+ ++++ +a+ l+ +Af l+++++ Pvi+ +  
  gi|320100963|ref|YP_004176555.1|  97 LMSSAYSGVKAGFVVVSADDPGA-HSSQNEQDNRWYGMLAHIPVVEPSSARDAYYLTKEAFELSTRYEHPVILRT-T 171
                                       *9998777776666665444444.67889999999999999******************************9987.5 PP

                                       HHH.HEEEEEEC-SGG CS
                             POR_N 156 fllshevekvelpdee 171
                                       +++sh++++vel  + 
  gi|320100963|ref|YP_004176555.1| 172 TRVSHTRQPVELNGDI 187
                                       7778*******98765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.5     8e-06    0.0079       1      16 [.     570     585 ..     570     586 .. 0.90
   2 !   28.7   2.3   7.4e-10   7.4e-07       1      24 []     601     624 ..     601     624 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8e-06
                                       EEEETTTSSS-THHHH CS
                              Fer4   1 vvideekCigCGaCve 16 
                                       ++++e+kC+gC+aC++
  gi|320100963|ref|YP_004176555.1| 570 YTVIEDKCTGCNACIN 585
                                       5799**********85 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 7.4e-10
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       +vi ee+C gCG+C+++CP+ AI+
  gi|320100963|ref|YP_004176555.1| 601 PVILEELCAGCGLCASICPFKAIS 624
                                       6899******************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 !   16.5   3.7   6.6e-06    0.0065       3      24 .]     571     594 ..     571     594 .. 0.91
   2 !   23.8   1.7   3.3e-08   3.3e-05       1      24 []     600     623 ..     600     623 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-06
                            Fer4_6   3 eidpdkCigCgdC..vrvCPegai 24 
                                       ++ +dkC+gC++C   ++CP+ +i
  gi|320100963|ref|YP_004176555.1| 571 TVIEDKCTGCNACinLTACPAIVI 594
                                       6899*********9999***9876 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3.3e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +++i +++C gCg C+++CP++ai
  gi|320100963|ref|YP_004176555.1| 600 KPVILEELCAGCGLCASICPFKAI 623
                                       689999***************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 !   14.0   3.3   4.2e-05     0.042      33      52 ..     569     590 ..     552     594 .. 0.79
   2 !   25.7  11.9   8.9e-09   8.9e-06       4      58 ..     573     624 ..     571     625 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                           Fer4_21  33 vlkvvedeCvGCnlCss..vCP 52 
                                       v++v+ed+C+GCn C++   CP
  gi|320100963|ref|YP_004176555.1| 569 VYTVIEDKCTGCNACINltACP 590
                                       46899**********8522688 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 8.9e-09
                           Fer4_21   4 dedkCigCgkCl..iaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPvedcie 58 
                                        edkC gC+ C+  +aC+     ai i + ++ +v+ e+ C GC lC+s+CP  ++i+
  gi|320100963|ref|YP_004176555.1| 573 IEDKCTGCNACInlTACP-----AIVIPTGSRKPVIlEELCAGCGLCASICPF-KAIS 624
                                       479********8334666.....999988888888659**************7.7775 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   3.8   1.3e-06    0.0013       2      22 .]     569     591 ..     568     591 .. 0.86
   2 !   18.5   1.2   1.5e-06    0.0015       2      21 ..     600     619 ..     599     620 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                            Fer4_2   2 pvvvdtdrCigCgaCv..saCPa 22 
                                       ++ v +d+C+gC+aC+  +aCPa
  gi|320100963|ref|YP_004176555.1| 569 VYTVIEDKCTGCNACInlTACPA 591
                                       57899**********666****8 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.5e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++v+ ++ C gCg C s CP
  gi|320100963|ref|YP_004176555.1| 600 KPVILEELCAGCGLCASICP 619
                                       68999*************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   8.8   1.9e-08   1.9e-05       1      51 []     576     623 ..     576     623 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.9e-08
                            Fer4_9   1 kCtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgC+aC   +aCpa v+   + +  +  +      C gCg C+ +Cp +ai
  gi|320100963|ref|YP_004176555.1| 576 KCTGCNACinLTACPAIVIPTGSRKPVILEE-----LCAGCGLCASICPFKAI 623
                                       7*******66678******888888887763.....6************9887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   2.6   0.00042      0.42      29      50 ..     568     591 ..     551     593 .. 0.74
   2 !   20.9  11.2     4e-07    0.0004       1      52 []     576     622 ..     576     622 .. 0.88
   3 !   15.8   1.7   1.6e-05     0.016       2      21 ..     608     627 ..     607     632 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                            Fer4_7  29 ekveidpekClgCgaCva..vCPt 50 
                                       + +++ ++kC+gC+aC++  +CP+
  gi|320100963|ref|YP_004176555.1| 568 PVYTVIEDKCTGCNACINltACPA 591
                                       6789999*********97668995 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4e-07
                            Fer4_7   1 rCigCgaCv..aaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC+aC    aCp+ +i +  +       k++i +e C gCg C++ CP++a
  gi|320100963|ref|YP_004176555.1| 576 KCTGCNACInlTACPAIVIPTGSR-------KPVILEELCAGCGLCASICPFKA 622
                                       7*******94468**999998665.......789*****************986 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.6e-05
                            Fer4_7   2 CigCgaCvaaCpvkaielde 21 
                                       C gCg C++ Cp kai++++
  gi|320100963|ref|YP_004176555.1| 608 CAGCGLCASICPFKAISVKN 627
                                       99*************99875 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  12.0   2.2e-06    0.0022       6      56 .]     574     619 ..     570     619 .. 0.88
   2 !   16.7   0.8   5.9e-06    0.0059       2      31 ..     601     630 ..     600     635 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                           Fer4_10   6 ddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d+C++C++C +  aCPa       + + +++ +  +  e C gcg C+++CP
  gi|320100963|ref|YP_004176555.1| 574 EDKCTGCNACINltACPA-------IVIPTGSRKPVILEELCAGCGLCASICP 619
                                       69*********9779***.......8888888888888899***********9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.9e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakge 31 
                                       +vi ++ C +Cg C + CP+++ sv++++ 
  gi|320100963|ref|YP_004176555.1| 601 PVILEELCAGCGLCASICPFKAISVKNQPS 630
                                       6788999*************8888777765 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.3e-07   0.00013      50     171 ..      57     171 ..       6     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                       EEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTS CS
                      Transket_pyr  50 vidsgisEqavlgfavGaalagpllviveaqFgdFangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehq 125
                                       +++ +i E+ +  +a+Gaa++g   +   a+  + +n    +a++ ++  +a +++k+g vv+ +    +  + + q
  gi|320100963|ref|YP_004176555.1|  57 YVEWSINEKVAFETAYGAAITG--VRSLTAMKHVGVN----VASDILM-SSAYSGVKAGfVVVSA-D--DPGAHSSQ 123
                                       78999*****************..8888888888899....8888888.8999999999555433.2..33344555 PP

                                       BSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SEEEEEE- CS
                      Transket_pyr 126 saeleaflrlipglkvvrPsdpaetkhllrrairr..edrkPvvlrlp 171
                                         ++ +++ +++ + vv Ps++ +++ l ++a +   ++++Pv+lr++
  gi|320100963|ref|YP_004176555.1| 124 NEQDNRWYGMLAHIPVVEPSSARDAYYLTKEAFELstRYEHPVILRTT 171
                                       55799****************************9977889*****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 ?    6.4   2.1     0.017        17       1      20 [.     576     597 ..     576     605 .. 0.78
   2 !   19.2   0.8   1.7e-06    0.0017       2      25 ..     608     631 ..     607     636 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                           Fer4_16   1 rCgtCgkCae..vCPtnaikek 20 
                                       +C++C++C++  +CP+ +i + 
  gi|320100963|ref|YP_004176555.1| 576 KCTGCNACINltACPAIVIPTG 597
                                       5*******85449**9999776 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.7e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekei 25 
                                       C +Cg Ca++CP +ai+ k++++ 
  gi|320100963|ref|YP_004176555.1| 608 CAGCGLCASICPFKAISVKNQPST 631
                                       *****************9977665 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   2.3e-05     0.023       3     157 ..      16     168 ..      14     184 .. 0.71
   2 ?   -2.1   0.1       2.6   2.6e+03      49     106 ..     426     483 ..     415     496 .. 0.70
   3 ?   -3.4   0.0       6.2   6.2e+03       9      23 ..     507     521 ..     507     529 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa 76 
                                       + ea++ra  ++g+ ++ ++pG+ ++++++alse     gi v  + +E +a   A g a    +   ++ ++g+++
  gi|320100963|ref|YP_004176555.1|  16 GNEAIARASLEAGICVATAYPGTPSTEIIEALSEVAgecGIYVEWSINEKVAFETAYGAAITGVRSLTAMKHVGVNV 92 
                                       6799999999*************************9999999999*************9877777777777779888 PP

                                       HHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS-- CS
                      TPP_enzyme_N  77 tnaltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpg 153
                                       ++ +      +  +   +v+s+d p ++ +q+ + +     ++++++   +++++s++++  + ++A++ + ++   
  gi|320100963|ref|YP_004176555.1|  93 ASDILMSSAYSGVKAGFVVVSADDPGAHSSQNEQDN--RWYGMLAHIP--VVEPSSARDAYYLTKEAFELS-TRYEH 164
                                       876655555555566678888888888887444443..3344444444..445555555555555555555.55555 PP

                                       EEEE CS
                      TPP_enzyme_N 154 Pvyl 157
                                       Pv l
  gi|320100963|ref|YP_004176555.1| 165 PVIL 168
                                       5555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH CS
                      TPP_enzyme_N  49 qgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg 106
                                       +g  ++A+g+ ++ ++ ++++    + +  +++ +++  ++++ ++ l+ d++t+   
  gi|320100963|ref|YP_004176555.1| 426 GGSLGIAHGFGKVLRQTVIAVIGDSTFFHAGIPPAINIVYNNSRVIPLVLDNSTTAMT 483
                                       5667889999998766555555444566667777888888888888888887776655 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.2
                                       HHHHHCT--EEEE-- CS
                      TPP_enzyme_N   9 raLkalgvehvfgvp 23 
                                       ++L+++g ++v+++p
  gi|320100963|ref|YP_004176555.1| 507 DILREAGFKTVVINP 521
                                       689*********998 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.1    0.0057       5.7       2      15 ..     575     590 ..     574     593 .. 0.83
   2 ?   14.5   2.2   3.7e-05     0.037       2      16 ..     606     620 ..     605     621 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0057
                            Fer4_4   2 erCigCgsCvaa..CP 15 
                                       ++C+gC +C++   CP
  gi|320100963|ref|YP_004176555.1| 575 DKCTGCNACINLtaCP 590
                                       89*******9865566 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.7e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e C gCg C ++CP+
  gi|320100963|ref|YP_004176555.1| 606 ELCAGCGLCASICPF 620
                                       67************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 ?    6.4   1.0     0.012        12       3      17 ..     575     591 ..     573     601 .. 0.81
   2 ?   10.5   0.9   0.00064      0.64       5      17 ..     608     620 ..     606     633 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                            Fer4_8   3 ekCieCgaCq..saCpv 17 
                                       +kC++C aC   +aCp+
  gi|320100963|ref|YP_004176555.1| 575 DKCTGCNACInlTACPA 591
                                       58999999997778985 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00064
                            Fer4_8   5 CieCgaCqsaCpv 17 
                                       C +Cg+C s Cp+
  gi|320100963|ref|YP_004176555.1| 608 CAGCGLCASICPF 620
                                       9999999999994 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0     0.028        28       5      17 ..     574     586 ..     571     596 .. 0.83
   2 ?    6.8   0.9     0.011        11       6      19 ..     606     619 ..     602     625 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.028
                           Fer4_15   5 rdaCigcglCvae 17 
                                       +d+C+gc++C+ +
  gi|320100963|ref|YP_004176555.1| 574 EDKCTGCNACINL 586
                                       699*******865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                           Fer4_15   6 daCigcglCvaeap 19 
                                       ++C gcglC+  +p
  gi|320100963|ref|YP_004176555.1| 606 ELCAGCGLCASICP 619
                                       79*********998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.3     0.064        64       1      15 [.     576     592 ..     576     605 .. 0.74
   2 ?    9.0   2.0    0.0021       2.1      44      57 ..     606     619 ..     596     623 .. 0.80
   3 ?    8.3   2.3    0.0033       3.3       2      15 ..     608     621 ..     607     632 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.064
                           Fer4_17   1 rCiqCgyClp..eCpsy 15 
                                       +C++C +C++  +Cp  
  gi|320100963|ref|YP_004176555.1| 576 KCTGCNACINltACPAI 592
                                       58888888877778765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0021
                           Fer4_17  44 slCieCgeCerkCP 57 
                                       +lC++Cg+C++ CP
  gi|320100963|ref|YP_004176555.1| 606 ELCAGCGLCASICP 619
                                       57888888888888 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0033
                           Fer4_17   2 CiqCgyClpeCpsy 15 
                                       C++Cg C+  Cp+ 
  gi|320100963|ref|YP_004176555.1| 608 CAGCGLCASICPFK 621
                                       66666666666654 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.0      0.13   1.3e+02      79      93 ..     574     590 ..     548     593 .. 0.76
   2 ?    8.1   0.7    0.0048       4.7      79      94 ..     605     620 ..     598     622 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                           Fer4_22  79 esgCvGCgRCie..acp 93 
                                       e +C+GC+ Ci+  acp
  gi|320100963|ref|YP_004176555.1| 574 EDKCTGCNACINltACP 590
                                       6789****998622455 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0048
                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                       e+ C GCg C + cp 
  gi|320100963|ref|YP_004176555.1| 605 EELCAGCGLCASICPF 620
                                       5789*******99986 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 ?    3.9   3.7     0.078        77       2      15 ..     574     586 ..     573     592 .. 0.78
   2 ?    7.6   1.5    0.0055       5.5       4      17 ..     606     619 ..     604     620 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.078
                           Fer4_13   2 DrdtCiacgaCvel 15 
                                       + d+C++c+aC +l
  gi|320100963|ref|YP_004176555.1| 574 E-DKCTGCNACINL 586
                                       5.9********985 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0055
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                       + C +cg+C++++P
  gi|320100963|ref|YP_004176555.1| 606 ELCAGCGLCASICP 619
                                       78***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4667.93
//
Query:       gi|320100964|ref|YP_004176556.1|  [L=199]
Description: Pyruvate/ketoisovalerate oxidoreductase, catalytic domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-31  107.4   0.0    9.8e-31  107.2   0.0    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   0.0   5.5e-35   9.8e-31       1     177 []      13     192 ..      13     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 5.5e-35
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG++t+g++++  +++ G +v+ ++++g+++rGg++++hvri++  ++p i+v +a+ ++a+++ +  + l + +
  gi|320100964|ref|YP_004176556.1|  13 GGQGIITLGRLIGLGCMHRGVDVSVAEVHGMSQRGGSVVVHVRIGEG-ESPIIPVAGAHSIIAMEMLESVRSLVYAN 88 
                                       9********************************************98.89****************5555******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH..T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-H.... CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl..gvrvygvdatkiakeiggneraaNtvmlGalaallg.lpl.... 147
                                       +++++++n   ++p+ l k++++e+ l   +  g+r y+ da+k   e  g+++  N+++lG+++a+ + l+     
  gi|320100964|ref|YP_004176556.1|  89 NDTTLVINDFLWPPP-LSKYPSREAILTAISgkGLRHYVYDANKASMEVTGSPISSNVALLGFTLAVDKeLSKyisl 164
                                       *********765555.55666667766666689*******************************7764444444444 PP

                                       HHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 148 ealeeaikkrfpkkkeviekNlkafragye 177
                                       e++e ai ++f++  +v+e N++ +r+ ye
  gi|320100964|ref|YP_004176556.1| 165 EDVEWAIGRAFRG--AVAEINKRLLRKSYE 192
                                       ************9..7*********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1525.59
//
Query:       gi|320100965|ref|YP_004176557.1|  [L=65]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 474.92
//
Query:       gi|320100966|ref|YP_004176558.1|  [L=154]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1108.34
//
Query:       gi|320100967|ref|YP_004176559.1|  [L=317]
Description: iron-sulfur cluster protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   0.0       0.51   10.4   0.0    2.3  2  Ribosomal_S16  Ribosomal protein S16
      0.025   14.2   0.0      0.062   12.9   0.0    1.6  2  Q_salvage      Potential Queuosine, Q, salvage protein family
      0.072   13.2   0.1        3.8    7.6   0.1    2.6  2  Lambda_CIII    Lambda Phage CIII
       0.22   12.0   0.0       0.63   10.5   0.0    1.9  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p


Domain annotation for each model (and alignments):
>> Ribosomal_S16  Ribosomal protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.061   2.8e+02      12      27 ..      53      68 ..      47      70 .. 0.87
   2 ?   10.4   0.0   0.00011      0.51      24      58 ..      89     117 ..      85     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.061
                                      EEEEETTSSTTSSESE CS
                     Ribosomal_S16 12 ivvadsrkprdgrpiE 27
                                      +v++d r  r g+p E
  gi|320100967|ref|YP_004176559.1| 53 MVAMDHRLSRPGKPYE 68
                                      799***********98 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                                       SESEEEEEEETTTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16  24 rpiEklGtYdPlakkkekkevelneerikyWlgvG 58 
                                       +++E  G+++P     e +  ++ ++ ++ Wl+vG
  gi|320100967|ref|YP_004176559.1|  89 KYMEDPGFFNP-----E-HLASIRVDEVEAWLSVG 117
                                       8999*******.....2.24899***********9 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 ?   12.9   0.0   1.4e-05     0.062      10     123 ..      46     155 ..      37     183 .. 0.80
   2 ?   -2.3   0.0       0.6   2.7e+03     183     217 ..     205     239 ..     201     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                         Q_salvage  10 tvdfifvvdlLNFsFWsekeeeerfaveykgkkytgYwsLvaalkraleegipitdpeflsketeeelkkvfrsate 86 
                                       ++++ +v+ ++ +      +  + ++ e ++  y g + L     r+  e+  +++pe l++++ +e++ +++  + 
  gi|320100967|ref|YP_004176559.1|  46 VARYFIVMVAMDHRLS---RPGKPYEAELEDGVYRGAELLYRLGMRKYMEDPGFFNPEHLASIRVDEVEAWLSVGN- 118
                                       5555555555555532...2456677777777777877788777899999**********************9885. PP

                         Q_salvage  87 eeiplleeRlellreagkvllekfdgsfvnlikkank 123
                                        + p +e R+ llr++g  +++ f+g++ ++i+++ +
  gi|320100967|ref|YP_004176559.1| 119 AKPPDIEVRTLLLRDMGLKITRLFNGNVKDIIEASGG 155
                                       57899***************************99765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.6
                         Q_salvage 183 mfADyrvpqvLrqlgvLeyseeLekklkekelles 217
                                       +  D+ + ++ + lg+++ s +L +k++ + +++ 
  gi|320100967|ref|YP_004176559.1| 205 IPVDNHLSRIAYRLGIVMVSGSLWAKIRGHVEVTR 239
                                       55788999999999999999999999998877655 PP

>> Lambda_CIII  Lambda Phage CIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1   0.00086       3.8       9      32 ..       3      25 ..       1      30 [. 0.85
   2 ?    2.7   0.0      0.03   1.3e+02      10      25 ..     203     218 ..     200     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00086
                       Lambda_CIII  9 vaGvpqESlLdRitrklRegwkrl 32
                                      v+G+  E   +R++r lR+   r+
  gi|320100967|ref|YP_004176559.1|  3 VIGLD-EGIVERVARTLRNNPERI 25
                                      78999.************988887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.03
                       Lambda_CIII  10 aGvpqESlLdRitrkl 25 
                                        G+p +  L+Ri+ +l
  gi|320100967|ref|YP_004176559.1| 203 LGIPVDNHLSRIAYRL 218
                                       699999*******998 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014      0.63      22      88 ..      91     220 ..      10     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                       HHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                           HhH-GPD  22 ferfgfptpedladadeekLrelirelGfyrrKakyikelArilv................................ 66 
                                       +e  gf++pe la++  +++++    l +++ K + i+     l                                 
  gi|320100967|ref|YP_004176559.1|  91 MEDPGFFNPEHLASIRVDEVEAW---LSVGNAKPPDIEVRTLLLRdmglkitrlfngnvkdiieasggrlygslgdp 164
                                       33334999999999999999999...555555555555444444466666666666666666666666669****** PP

                                       ..................................S-SSS--TTSHHHHHHHHHHTT CS
                                       ..................................xxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ..................................gkpdvlivvDvhvrrilkrlrs 88 
                                                                          + + +i+vD h++ri+ rl++
  gi|320100967|ref|YP_004176559.1| 165 glidllrvfrafedpvekkplllakflsrrgvitLREKLGIPVDNHLSRIAYRLGI 220
                                       **********************************777899***********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2258.79
//
Query:       gi|320100968|ref|YP_004176560.1|  [L=118]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.1   0.2      0.084   10.9   0.2    1.0  1  HPS6      Hermansky-Pudlak syndrome 6 protein
       0.13   12.2   0.0       0.14   12.0   0.0    1.1  1  SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex


Domain annotation for each model (and alignments):
>> HPS6  Hermansky-Pudlak syndrome 6 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   9.3e-06     0.084     462     516 ..      37      92 ..      17      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.3e-06
                              HPS6 462 lvsL.eelkaslvkasekeveavceeLveqEvsRllsseldkenLlylnsiFslfP 516
                                       +++L ee++ ++ +++++ v++     +e+Ev+R+l   + k  L y n ++sl P
  gi|320100968|ref|YP_004176560.1|  37 VMDLrEEVRRRVREGEKDLVQENESVFIEREVMRVLMELVRKGVLYYRNGVYSLSP 92 
                                       555536788888888888899999999*************************9987 PP

>> SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05      0.14     129     188 ..      42      92 ..      11      97 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                          SMC_Nse1 129 lelarilaaaraerr....stelsqeeaaadkgLtaseaeklLkrLveegWleksreGfysLdl 188
                                        e+ r         r    +++l    +++++ +   e+ ++L +Lv++g l++ r+G ysL++
  gi|320100968|ref|YP_004176560.1|  42 EEVRR---------RvregEKDLV---QENESVFIEREVMRVLMELVRKGVLYY-RNGVYSLSP 92 
                                       33333.........1222233333...456788999****************98.69*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 911.25
//
Query:       gi|320100969|ref|YP_004176561.1|  [L=288]
Description: methyltransferase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   15.4   0.0      0.019   14.6   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.039   14.7   0.0       0.13   12.9   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
      0.055   12.8   0.0          4    6.7   0.0    2.7  3  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.092   12.6   0.0       0.29   11.0   0.0    1.9  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
       0.13   12.0   0.0        3.7    7.2   0.0    2.1  2  N6_N4_Mtase      DNA methylase


Domain annotation for each model (and alignments):
>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.2e-06     0.019      41     125 ..     134     218 ..     117     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.2e-06
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkeefdi 116
                                       +g +vLD + G G  ++  l  +a  ++ +e d+++v i ++n  +  l++ ++++ ++d +e +++l+  +e+f  
  gi|320100969|ref|YP_004176561.1| 134 RGMSVLDTCMGLGYTAIASLEKDAGFVHTFEVDENVVWIAERNPWSRSLSSgRIRIEIRDVVEGVSTLP--SESFGR 208
                                       6789***************************************8777777669************9995..678*** PP

                                       EEE--S.SST CS
                     Cons_hypoth95 117 vflDPP.yak 125
                                       +  DPP + +
  gi|320100969|ref|YP_004176561.1| 209 IIHDPPrFTR 218
                                       ******4443 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.8     1e+04      21      39 ..     111     129 ..      96     135 .. 0.65
   2 ?   12.9   0.0   3.7e-05      0.13       1      97 []     138     240 ..     138     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                                       SSEEEEEESSHHHHHHHHH CS
                   Methyltransf_25  21 kakvtgvDiseemleaare 39 
                                        +++ g+D+ +++l ++r+
  gi|320100969|ref|YP_004176561.1| 111 MHRIQGTDPWHDALVKVRA 129
                                       6788899998888877765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.7e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBC.CGBS.SSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgda.edlp.fedgsfDlvvssg 72 
                                       vLd + G G +++a +++  ++ v+ ++++e+ + +a+++  +++l   +++++  d+ e ++ ++++sf  ++   
  gi|320100969|ref|YP_004176561.1| 138 VLDTCMGLGYTAIASLEK-DAGFVHTFEVDENVVWIAERNPWSRSLssgRIRIEIRDVvEGVStLPSESFGRIIHDP 213
                                       9***********999999.689****************999998788889999999995445437999*****9954 PP

                                       T.GGG.SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  73 a.lhh.lsdedlekalkeiarvLkpgG 97 
                                         +   + +    +++ e++rvL+pgG
  gi|320100969|ref|YP_004176561.1| 214 PrFTRsTGELYSLDFYIELYRVLQPGG 240
                                       4444324444456799**********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 ?    6.7   0.0    0.0011         4      33      89 ..     118     174 ..     106     207 .. 0.73
   2 ?    2.0   0.0     0.031   1.1e+02     138     150 ..     231     243 ..     219     247 .. 0.89
   3 ?   -0.0   0.0      0.13   4.5e+02     204     228 ..     261     285 ..     250     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHH..--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHH CS
                   Ubie_methyltran  33 rlWkkfvekl..vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvge 89 
                                       + W++ + k+    v+rg +vlD + G g  a++ +   ++ g v+  +++en++ ++e
  gi|320100969|ref|YP_004176561.1| 118 DPWHDALVKVraAKVRRGMSVLDTCMGLGYTAIASL--EKDAGFVHTFEVDENVVWIAE 174
                                       45888555541155789************9887544..456677777777777776666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.031
                                       HHHHHEEEEEEEE CS
                   Ubie_methyltran 138 eayrvlkpGGrlv 150
                                       e+yrvl+pGG l+
  gi|320100969|ref|YP_004176561.1| 231 ELYRVLQPGGVLF 243
                                       79********985 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.13
                                       HHHHHHHTTEEEEEEEEEGGGTEEE CS
                   Ubie_methyltran 204 lkeliedaGfksveyesltgGvvai 228
                                       +++ +  aGf+++ y+  + G v++
  gi|320100969|ref|YP_004176561.1| 261 IRNRLSRAGFENIFYDPDAQGFVCV 285
                                       5666889********9999999987 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.1e-05      0.29      32      90 ..     186     246 ..     172     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                                       EEEEEES-HHHHHHHC-.T-EEEEEE-SS-TTT.SGGGCSHHHHHHHHHHEEEEEEEEES- CS
                   Methyltransf_30  32 tlklligdarealkeld.ekadawFlDgFsPak.nPelwseellkelarllkkkgtlatys 90 
                                       ++++ i d+ e +++l+ e++  + +D+   ++   el+s +++ el+r+l+++g+l  y+
  gi|320100969|ref|YP_004176561.1| 186 RIRIEIRDVVEGVSTLPsESFGRIIHDPPRFTRsTGELYSLDFYIELYRVLQPGGVLFHYT 246
                                       677888899999999988899999999854444167**********************998 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.001       3.7     191     229 ..     134     173 ..     124     175 .. 0.85
   2 ?    2.7   0.0     0.025        90      39      58 ..     229     248 ..     224     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                                       TT-EEEETT-TTTHHHHHHHHTT-EEEE.EESSHHHHHHH CS
                       N6_N4_Mtase 191 kgdivlDpFaGSGtTavaakelgrkfiG.ieieeeyvela 229
                                        g +vlD  +G G+Ta+a +e +  f+  +e++e+ v +a
  gi|320100969|ref|YP_004176561.1| 134 RGMSVLDTCMGLGYTAIASLEKDAGFVHtFEVDENVVWIA 173
                                       5779*****************9999998888888877665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.025
                                       HHHHHHHEEEEEEEEEEE-C CS
                       N6_N4_Mtase  39 lkevrrvLkddgsifinidd 58 
                                         e++rvL+++g++f   ++
  gi|320100969|ref|YP_004176561.1| 229 YIELYRVLQPGGVLFHYTGE 248
                                       5799**********987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2196.22
//
Query:       gi|320100970|ref|YP_004176562.1|  [L=133]
Description: CopG family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   0.0    0.00026   20.9   0.0    1.5  1  RHH_3            Ribbon-helix-helix domain
    0.00098   19.0   0.0     0.0016   18.3   0.0    1.4  1  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.094   12.8   0.0       0.19   11.8   0.0    1.5  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.4e-08   0.00026       2      40 ..       6      44 ..       5      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.4e-08
                             RHH_3  2 ktrttvsidpelaekLkaLSekTrIprSklldeAiellL 40
                                      k+r+++si+ ++ae+L++L e +   rS ++  A+ +++
  gi|320100970|ref|YP_004176562.1|  6 KRRFGISIPSNIAERLDNLAELLHCDRSTIVSNALNEYI 44
                                      89***********************99999999998886 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 !   18.3   0.0   2.7e-07    0.0016       1      37 [.       8      44 ..       8      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-07
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                      r+ i+++++++erLd la+ ++  rS ++  Al ey+
  gi|320100970|ref|YP_004176562.1|  8 RFGISIPSNIAERLDNLAELLHCDRSTIVSNALNEYI 44
                                      899*************************999999997 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 ?   11.8   0.0   3.2e-05      0.19      89     121 ..       6      38 ..       2      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                   HicB_lk_antitox  89 aeriNitlpervlkriDaavkaagesRSgflak 121
                                       + r+ i++p+++ +r+D++++  +  RS  +++
  gi|320100970|ref|YP_004176562.1|   6 KRRFGISIPSNIAERLDNLAELLHCDRSTIVSN 38 
                                       57999***********************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 962.30
//
Query:       gi|320100971|ref|YP_004176563.1|  [L=293]
Description: ABC-3 protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-17   63.0  24.0    4.4e-17   62.4  24.0    1.2  1  ABC-3     ABC 3 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 !   62.4  24.0   2.5e-21   4.4e-17      12     256 ..      35     285 ..      29     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.5e-21
                             ABC-3  12 silvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrk..tk.lkedta 85 
                                         l +la + +g ++  r+  +l+++  H ++  v l+yll++ + +++  +++ + +al++++    ++ l+ + +
  gi|320100971|ref|YP_004176563.1|  35 YWLTGLALSSVGLLTYYRGLEFLVAGSTHGSFLAVTLGYLLASLFNTSIYYSAIPIGLALVYIAGYfiYRgLDPNKV 111
                                       5678999999*******************************999888888888888888888776411332678899 PP

                             ABC-3  86 igivlsvflalglvlvslikk...skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAk 159
                                         +++s++ + g+++  ++ +   ++ +l+s+++G+ + ++ +d+i  + i+ +vl+l+ll++ e ++i++d+  Ak
  gi|320100971|ref|YP_004176563.1| 112 SSFMVSFTSSAGVIAAYYVLTafpARYSLSSIMLGDPVLMTVNDMIAASTISFIVLALVLLIYEETVFISIDPVSAK 188
                                       99*****99*99998888777778***************************************************** PP

                             ABC-3 160 veglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyld 236
                                        +gl+v l+++  ++ i+la    l++ G i+   ++ +P  +  r++ + ++ l    l++  s+++G l+ +   
  gi|320100971|ref|YP_004176563.1| 189 IAGLRVWLYDFASFTAIGLATIGLLRVSGYIMEHVMILLPPLIGARISGNSREHLFSTLLVSTASSALGYLVAIEQG 265
                                       ***************************************************************************** PP

                             ABC-3 237 latGavivlvatllfllall 256
                                       l++ +   l+++llfl  ++
  gi|320100971|ref|YP_004176563.1| 266 LSPVGASGLILVLLFLYTVF 285
                                       88877778888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2283.68
//
Query:       gi|320100972|ref|YP_004176564.1|  [L=333]
Description: periplasmic solute-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-22   78.2   0.0    7.7e-22   77.9   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 !   77.9   0.0   4.3e-26   7.7e-22       3     224 ..      35     265 ..      33     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 4.3e-26
                                       ESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESS.TTTSGTHHHHHHHH.TTCCCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxx RF
                              ZnuA   3 attsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvyng.lelEtwldkllass.sqatrvev 77 
                                       + ++ + + v+ +  d+  v  Lvppg+dpH+y+++ +d  kl +A l+v++g  ++E  +++l+ +   +at +++
  gi|320100972|ref|YP_004176564.1|  35 TVFPSMVNDVKSLLCDNDSVDYLVPPGVDPHEYQLSTSDYDKLRKATLIVSTGhTGVEMQISELVMQGgLNATLINI 111
                                       5555555567788888999*********************************9778998899997444133344366 PP

                                       EETTT...TCCSEBCSSESTG.GGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS CS
                                       xxxxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  78 idlse...gveeeeeeeDpHi.WlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeip 150
                                       ++      ++++ + +e+ H+  ++p n+  +ven++++Lv+++p +ad y+a+a ++i++L +l ++ + +   +p
  gi|320100972|ref|YP_004176564.1| 112 LEIPGlriAINPSTGQENLHMpIYDPLNYLLFVENLTSTLVALNPSKADCYRAKAMDVIASLARLISKSHGRYMGVP 188
                                       65441222357788888***7589**************************************************999 PP

                                       GTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS....HHHHHHHHHHHHHTT-SEEEEET..TS.-THHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx..xx.xxxxxxxxxxxx RF
                              ZnuA 151 eekrklvtthdafgylarayglevagiagiste....aaqiaalieeikeagvkaifvep..la.spklaetlaeea 220
                                             v++ ++++y  + +g++v+++   +++    + +++ +   +++  ++++f+ +  ++ +++++ +l +++
  gi|320100972|ref|YP_004176564.1| 189 -----TVVDTPVLQYAVEWMGFKVVKSLIPEHDvqpsPLDLSTVEGLLRNGTIPIVFYTSppVSsESNTLVELSRRY 260
                                       .....79******************986333336677********************98765334777788888888 PP

                                       T.-EE CS
                                       x.xxx RF
                              ZnuA 221 g.vkv 224
                                       g v v
  gi|320100972|ref|YP_004176564.1| 261 GvVAV 265
                                       83444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2354.05
//
Query:       gi|320100973|ref|YP_004176565.1|  [L=254]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-21   76.4   0.0      4e-21   76.0   0.0    1.2  1  ABC_tran    ABC transporter
    8.4e-10   38.9   0.1    0.00052   19.9   0.2    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    7.7e-05   22.2   0.0       0.29   10.5   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
     0.0094   16.5   0.5      0.015   15.8   0.5    1.2  1  AAA_23      AAA domain
  ------ inclusion threshold ------
      0.062   13.1   0.0       0.12   12.2   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
       0.16   11.2   0.1       0.25   10.6   0.1    1.2  1  Zeta_toxin  Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   1.3e-24     4e-21       2     136 ..      19     170 ..      18     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.3e-24
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB..H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt..v 76 
                                       ++v+  +k   +v+++G+nGaGK+tL+ +++g  +p  G ++++g +++  +  +l + ++++pq   + ++    +
  gi|320100973|ref|YP_004176565.1|  19 RDVNSIIKGPGLVQVIGPNGAGKTTLFLTILGVIRPVRGVVRVNGVEVNG-DPGKLGEMVSYVPQRFYMPRDAPlsL 94 
                                       5667777777899*************************************.88999**********44433332115 PP

                                       HHH...................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren...................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                        e                    +     +k+ s l+ + l+ +v++++ s+LSgGq qr  +aral  ++++ll+DE
  gi|320100973|ref|YP_004176565.1|  95 WEFvemyaktysrrggargsldYV---RSKVSSALETVRLPREVWQRRVSELSGGQLQRALIARALSVDAEILLMDE 168
                                       555888998777777777644444...5555555555556668888888**************************** PP

                                       TT CS
                                       xx RF
                          ABC_tran 135 pt 136
                                       p 
  gi|320100973|ref|YP_004176565.1| 169 PL 170
                                       *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 !   17.1   0.0   1.2e-06    0.0037       4      24 ..      33      53 ..      31      93 .. 0.78
   2 !   19.9   0.2   1.8e-07   0.00052     234     302 ..     140     204 ..     130     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                            AAA_21  4 liGpNgsGKSnLLdaldllar 24
                                      +iGpNg+GK++L+ ++ ++ r
  gi|320100973|ref|YP_004176565.1| 33 VIGPNGAGKTTLFLTILGVIR 53
                                      7**************988754 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.8e-07
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSplll 302
                                       ++elS G+++  al++  l+ +    +ll DEp ++++P+    l++++ elsr   ++ ++++H+p ll
  gi|320100973|ref|YP_004176565.1| 140 VSELSGGQLQR-ALIARALSVDA--EILLMDEPLSNIDPEGRGILADIIGELSR--EKLlLVSSHDPMLL 204
                                       6799*******.88888888886..9*************888888888888888..6666******9765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00015      0.44      24      44 ..      28      48 ..      20      58 .. 0.84
   2 !   10.5   0.0   9.9e-05      0.29     136     199 ..     142     201 ..      64     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                      +++  ++GpNG+GK+ l+  i
  gi|320100973|ref|YP_004176565.1| 28 PGLVQVIGPNGAGKTTLFLTI 48
                                      567889*********999777 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.9e-05
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                       +LSgG+ + + +a  ++      a + l+De  +++D + + ++a+++ e s +  ++v s++ 
  gi|320100973|ref|YP_004176565.1| 142 ELSGGQLQRALIARALS----VDAEILLMDEPLSNIDPEGRGILADIIGELSREKLLLVSSHDP 201
                                       89999865444443333....456799*************************999999999875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   4.9e-06     0.015      18      36 ..      27      45 ..      14      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.9e-06
                            AAA_23 18 skgltlItGpNGaGKTTil 36
                                      ++gl+ ++GpNGaGKTT++
  gi|320100973|ref|YP_004176565.1| 27 GPGLVQVIGPNGAGKTTLF 45
                                      6899999***********8 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.9e-05      0.12      24      45 ..      30      51 ..      19      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                            AAA_29 24 atlltGpsGsGKSTllDAiqal 45
                                       + ++Gp+G+GK+Tl+  i  +
  gi|320100973|ref|YP_004176565.1| 30 LVQVIGPNGAGKTTLFLTILGV 51
                                      56799**********8555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   8.3e-05      0.25      14      51 ..      26      63 ..      17      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.3e-05
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51
                                      + P l+++ G  GAGK++l   +   +++ ++vvr+++
  gi|320100973|ref|YP_004176565.1| 26 KGPGLVQVIGPNGAGKTTLFLTILGVIRPVRGVVRVNG 63
                                      56999******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1927.96
//
Query:       gi|320100974|ref|YP_004176566.1|  [L=279]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2162.20
//
Query:       gi|320100975|ref|YP_004176567.1|  [L=800]
Description: xanthine dehydrogenase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-177  589.3   0.2   7.7e-177  589.1   0.2    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    5.3e-26   91.1   0.0    1.1e-25   90.2   0.0    1.5  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  589.1   0.2  8.6e-181  7.7e-177       1     550 []     172     728 ..     172     728 .. 0.97

  Alignments for each domain:
  == domain 1  score: 589.1 bits;  conditional E-value: 8.6e-181
                                       STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlv 75 
                                       +h+e+++ +l   ki+ G++++af++a ++ve+e+rt++qeh+ylE++aa+a+p + dg +t+y++tq+p+ +rr+v
  gi|320100975|ref|YP_004176567.1| 172 IHDERGSDILSryKIRVGNIDEAFRNASVIVENEYRTPMQEHAYLEPEAAIAIP-EPDGGVTIYAKTQCPFDTRRAV 247
                                       58888888888888999***********99************************.77******************** PP

                                       HHHHT--GGGEEEE-SB-S--TTTT.SS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TT CS
                     Ald_Xan_dh_C2  76 aevlglpenkvrvivprvGGGFGgK.tqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkd 151
                                       ++vlglp n vrvi+p +GGGFGg       +++ aalaA+ t+rp  +  +Ree+++ ++krhp++++y+ +a++d
  gi|320100975|ref|YP_004176567.1| 248 SNVLGLPFNMVRVIAPALGGGFGGAeDVGNEIAAKAALAAMYTKRPAVVLHTREESIIGHTKRHPMIARYRHAAKRD 324
                                       *************************88888889999***************************************** PP

                                       S-EEEEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 152 GkitaldvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdel 228
                                       G++++++++++ d+Gaya+l+p+v +ra++h++gpYk+ n++v+  vvytN++p++afRGfG+pq++fa+Er+md l
  gi|320100975|ref|YP_004176567.1| 325 GTLLGVEAEIVLDTGAYASLGPFVGWRAIVHSTGPYKVYNAKVDLAVVYTNRVPAGAFRGFGNPQVTFAVERQMDIL 401
                                       ***************************************************************************** PP

                                       HHHHT--HHHHHHHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS CS
                     Ald_Xan_dh_C2 229 AeelgldplelRrrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegig 305
                                       Aeelg+dp+e+R rN+++pg++t +gq + +  +l e+++++ e s+++e+r+ + +   g ++rGig+a++++g +
  gi|320100975|ref|YP_004176567.1| 402 AEELGIDPVEIRLRNALRPGDRTVHGQLLDHGVGLVEAIERAVELSKWHEKRKLYSQIS-GSMRRGIGIAVFYHGNS 477
                                       **********************99***98889************************999.5689************6 PP

                                       --S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HH CS
                     Ald_Xan_dh_C2 306 lgftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrst 382
                                       +g+  +  + ++a++ ++ dGs++ +tg+t+mGqG+   l+ iaae Lgvp++  +v+  dt+++p++++t+aSrst
  gi|320100975|ref|YP_004176567.1| 478 IGA--EGADYSSATIIIQRDGSILFRTGLTDMGQGSIQGLVNIAAEILGVPPNYFKVELPDTASTPDSGPTVASRST 552
                                       665..568899****************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTS.-CCCEEEETTEEEET...EEEECHHHHHHHHHHTTSSEEEEEEE.... CS
                     Ald_Xan_dh_C2 383 dlngnAvkkAaeklrerllkiaaellev.spedleledgkvvvk...eksvslaelaaaaylervslsatgfykt.. 453
                                       +++gnA++ Aa klr+rl ++a+++l++ sped+ ++  kv+++   +++++++el+++a++++v+l++ g+y++  
  gi|320100975|ref|YP_004176567.1| 553 AMGGNATLVAAYKLRRRLNELASSMLGCkSPEDVVIDAPKVYCRddpGHHITWKELVEQAFWKGVPLQEFGYYRApp 629
                                       ***************************9459*************9988889**********************99** PP

                                       ...EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEE CS
                     Ald_Xan_dh_C2 454 ..ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvyd 528
                                         ++eetg+g+p+++++yga v+ VevD+etg v+v+++v+v+D+G++iN++ +e    GG+ qG+G+almE++  +
  gi|320100975|ref|YP_004176567.1| 630 aeWHEETGTGQPYFTYTYGAIVSDVEVDMETGVVRVKEAVTVYDIGRVINRTGAEHHGVGGYLQGMGYALMEDTYHS 706
                                       ***************************************************************************** PP

                                       TTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 529 edGqlltasladYkiPtaadiP 550
                                       +dG++ +++l++Y+iPt +diP
  gi|320100975|ref|YP_004176567.1| 707 PDGHVYNTNLSTYHIPTGMDIP 728
                                       *********************9 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.0   1.2e-29   1.1e-25       1     109 [.      42     149 ..      42     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 1.2e-29
                                       TT-SCCGGG.CC-TTTE.EEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SS CS
                      Ald_Xan_dh_C   1 tGeavYvdD.ipapgal.ylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaed 75 
                                       tG+ +Y+ D i + ++  +++ vrS +ahA+i+sidvs+a + pGVv vit  d+p++n+ +  +l d++  l+a++
  gi|320100975|ref|YP_004176567.1|  42 TGKPIYTADfIRLLKNPvFVYSVRSRYAHAWIKSIDVSEAARYPGVVRVITSRDIPGINDVGY-VLPDQP--LIADR 115
                                       89*******445555557****************************************88874.666665..***** PP

                                       EESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                      Ald_Xan_dh_C  76 kvrsvgqavaavvAedeetArkAaklvkveYeel 109
                                       kvr+ g++va+vvAe+ e Ar+A + v+v+Ye+l
  gi|320100975|ref|YP_004176567.1| 116 KVRYIGDTVALVVAESLENARDAGERVHVDYEPL 149
                                       ********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (800 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.41
# Mc/sec: 5907.36
//
Query:       gi|320100976|ref|YP_004176568.1|  [L=178]
Description: purine hydroxylase subunit delta apoprotein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-25   88.0   0.0    4.9e-25   87.4   0.0    1.3  1  Fer2_2      [2Fe-2S] binding domain
      2e-07   30.9   0.3      2e-07   30.9   0.3    2.0  2  Fer2        2Fe-2S iron-sulfur cluster binding domain
    5.4e-05   23.2   0.1    8.4e-05   22.5   0.1    1.5  1  Fer2_3      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.019   15.0   0.4      0.078   13.0   0.4    2.1  1  Fer2_4      2Fe-2S iron-sulfur cluster binding domain
      0.076   12.9   0.0       0.15   11.9   0.0    1.5  1  PDEase_I_N  3'5'-cyclic nucleotide phosphodiesterase N-termin
       0.12   12.5   0.0       0.34   11.1   0.0    1.7  1  SAM_2       SAM domain (Sterile alpha motif)


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   1.6e-28   4.9e-25       1      75 [.      77     149 ..      77     150 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 1.6e-28
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       T+egl+ e  +lh++q af+e  ++qCG+CtpGf+m ++all++n p+p+ ee++e+ls  lCRC++Y+ +++A+
  gi|320100976|ref|YP_004176568.1|  77 TLEGLAPE-GKLHAIQVAFIETRGVQCGFCTPGFMMMTKALLDHN-PNPSFEEVKEWLSSTLCRCGSYHYYFAAA 149
                                       89***966.68**********************************.99999******************999997 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 !   30.9   0.3   6.6e-11     2e-07       2      50 ..      10      57 ..       9      78 .. 0.81
   2 ?   -1.8   0.2         1   3.1e+03      38      44 ..      99     106 ..      95     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 6.6e-11
                                      ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEES CS
                              Fer2  2 tidgkevevevadgettlldaaeenggidipysCggggCgtClvevleg 50
                                      +++g e+ +ev+++e+++     + g + ++ +Cg g CgtC v v+ g
  gi|320100976|ref|YP_004176568.1| 10 EVNGVEHILEVPPHERLIDTLRYRLGLTSVKEGCGRGECGTCIVLVN-G 57
                                      799*************5555555799******************998.3 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                                       SS.SSTTE CS
                              Fer2  38 gg.CgtCl 44 
                                       g  Cg C+
  gi|320100976|ref|YP_004176568.1|  99 GVqCGFCT 106
                                       344****6 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 !   22.5   0.1   2.8e-08   8.4e-05      49      91 ..      40      81 ..      10     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.8e-08
                            Fer2_3 49 rasCregiCGscavainGkptlaCtatikdlakqkseielepl 91
                                      +  C+ g CG+c v +nG p+  C + +++l+  k  ++le l
  gi|320100976|ref|YP_004176568.1| 40 KEGCGRGECGTCIVLVNGLPRHSCLTLTSTLDGAK-VTTLEGL 81
                                      578***********************999988765.4555554 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 ?   13.0   0.4   2.6e-05     0.078      44      79 ..      41      77 ..       4      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                            Fer2_4 44 elcaggeCrnClVevegepnvracs..tpvedGlkvet 79
                                      e c +geC +C+V v+g p   +c   t   dG kv+t
  gi|320100976|ref|YP_004176568.1| 41 EGCGRGECGTCIVLVNGLP-RHSCLtlTSTLDGAKVTT 77
                                      5799**************9.556651156678888887 PP

>> PDEase_I_N  3'5'-cyclic nucleotide phosphodiesterase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     5e-05      0.15      19      33 ..     126     140 ..     120     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
                        PDEase_I_N  19 seVrdWLastFtrqq 33 
                                       +eV++WL+st+ r  
  gi|320100976|ref|YP_004176568.1| 126 EEVKEWLSSTLCRCG 140
                                       69*********9954 PP

>> SAM_2  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.34       3      29 ..     122     150 ..     121     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                       GHHHHHHHHHHHHT..TTGGGHHHHHHTT CS
                             SAM_2   3 swsledvaeWLrsi..glkqytdnFrdag 29 
                                       + s+e+v eWL+s+  +++ y ++F  a+
  gi|320100976|ref|YP_004176568.1| 122 NPSFEEVKEWLSSTlcRCGSYHYYFAAAK 150
                                       789*********987899*******9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1323.73
//
Query:       gi|320100977|ref|YP_004176569.1|  [L=258]
Description: molybdopterin dehydrogenase FAD-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   93.2   0.0    2.5e-26   92.4   0.0    1.3  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    1.1e-13   51.2   0.0    1.9e-13   50.4   0.0    1.4  1  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai


Domain annotation for each model (and alignments):
>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.0   2.8e-30   2.5e-26      44     167 ..      10     135 ..       2     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 2.8e-30
                                       -SEEEEGTTSG.GGS-EEEESSEEEEETTSBHHHHHHHHHHHH.HHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT CS
                     FAD_binding_5  44 pehliditgip.elkeieeteggleiGAavtlselaaealvre.rypalsealekiAspqiRnvaTiGGNlataspi 118
                                       p+ l+d++ ++ +l++++ ++g ++iGA++tl e+ ++ l r+ ry  +++ ++k++ ++iR  aTiGGN+a a++ 
  gi|320100977|ref|YP_004176569.1|  10 PRFLVDLSPLKkDLSYVKIENGVVRIGALTTLWEISRSTLHRDiRYAGFTDVFKKFGTMAIRFNATIGGNIASATQY 86 
                                       66789999985379*********************755555444677888*************************** PP

                                       -SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEESS-TT-EEEEEE CS
                     FAD_binding_5 119 sDlapaLlaldAevelrsaegerevpleeflkgpgktalepgelitave 167
                                       sD++++Ll++dA++ l+sa+g rev leefl + ++t ++p+elit+++
  gi|320100977|ref|YP_004176569.1|  87 SDYITLLLVYDARLRLESASGVREVSLEEFLVDKRTTIIKPNELITEIS 135
                                       ***********************************************97 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   2.2e-17   1.9e-13       2     101 ..     146     247 ..     145     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.2e-17
                                       EE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS..-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTC CS
                     CO_deh_flav_C   2 ay.klsrrrendiaivnaAfrveleedgkiedariafggvapt..pvraekaeaaLiGkplseelleeaakaleeel 75 
                                       a+ k+ rr      iv+ Af ++ e++ +++d+riaf  v+++  p ra+ +e+ +iGk lse++l ea + le+e+
  gi|320100977|ref|YP_004176569.1| 146 AFiKFDRRELIIAGIVTGAFYLTKEGE-RVKDVRIAFDMVKERriPGRARMTEECVIGKTLSESVLREAESCLEREM 221
                                       787888888877779********9877.*************998999****************************** PP

                                       HHHTCTTC-HHHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  76 spasdprasaeYRrslavsllfrfll 101
                                       + +sd+  s eYR ++ ++ l+r ll
  gi|320100977|ref|YP_004176569.1| 222 KRISDWWTSDEYRLDMSKTSLRRGLL 247
                                       *******************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2015.05
//
Query:       gi|320100978|ref|YP_004176570.1|  [L=335]
Description: cysteine synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-70  235.8   0.1    7.5e-70  235.7   0.1    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.7   0.1   4.2e-74   7.5e-70       2     294 .]       8     306 ..       7     306 .. 0.93

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 4.2e-74
                                       GGCSSS--EEEECCTC.CCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprls.kelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaa 74 
                                       t  ig+TP+vrl r+  + + ++++ K+E++nptgS+KdR a y+++r+ e+   ++++t+v+ ++GN+g+a +a a
  gi|320100978|ref|YP_004176570.1|   8 TECIGGTPIVRLSRILpEGFTAEIWGKMEFTNPTGSVKDRMALYMIKRAVEKgelKPGMTIVVPTTGNTGIAFSALA 84 
                                       6789**********996777778*************************99999************************ PP

                                       HHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCH...HHHHHHHHHHHHHH.STTCEE--TTTSHHHHHH.HHTH CS
                              PALP  75 allGlkvtivvpadaspekvallrllGaevvevggd...ydeavaaaaelaae.gegaylvsqfdnptvieg.ygti 146
                                       ++lG+kv iv+p+ +s+e+  l+rl+Gae  +++g+     +a+++a++l ae  +++yl +q++++++i++ y+t+
  gi|320100978|ref|YP_004176570.1|  85 SVLGFKVLIVIPEEMSAERFMLMRLFGAEFYFTPGGeadAGTALETARRLVAEnPDKYYLFDQWGDEANIQAhYETT 161
                                       *********************************666233666666699988887899999***************** PP

                                       HHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS CS
                              PALP 147 glEileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg 223
                                       g Ei+eq+g  p+a+v+ vG+Gg++ Gia+ lke+  dv v g+ep++++  a+ +++g++ ++   ++ ++g++ g
  gi|320100978|ref|YP_004176570.1| 162 GREIIEQVG-CPKAFVAEVGTGGTLIGIARRLKEECKDVIVAGAEPAECPVAAEWFKTGKPGPWG--RHEIEGVGDG 235
                                       ********8.999*******************************************999996655..9********* PP

                                       CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 224 spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                          ++ ++  + l+d++vtvs+eea++++r+ ar eg+ v+ ss+a++ a+ kl++ ++l+ gd+vv+il++
  gi|320100978|ref|YP_004176570.1| 236 -FIPDIIARNKHLLDDFVTVSSEEAIQMARKIARLEGLPVGISSGANVVAAiKLARTRKLESGDKVVTILPD 306
                                       .77888888899*********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2696.24
//
Query:       gi|320100979|ref|YP_004176571.1|  [L=421]
Description: major facilitator superfamily protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   50.9  32.0    1.3e-12   47.3  23.9    2.0  2  MFS_1        Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.087   13.1   3.5        4.6    7.5   0.1    3.5  3  Mpv17_PMP22  Mpv17 / PMP22 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 !   47.3  23.9   1.5e-16   1.3e-12      16     317 ..      28     335 ..      13     344 .. 0.74
   2 !    8.0   3.0   0.00014       1.2      99     183 ..     332     417 ..     326     421 .] 0.83

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.5e-16
                             MFS_1  16 gpalpl.alaedlgispseigllltlyalgaavaslplGrlsd..rfGrrrvlllglllfalg.lllll..fa...s 83 
                                       ++ l   +l + + +  +e+g l+ +  l++a ++lp+++l++  r+ r++++l + ++  +g +l++l  f     
  gi|320100979|ref|YP_004176571.1|  28 SMGLVYaLLIKMYSYGIHELGVLTIARLLAYASSQLPAAWLVEehRHLRKKIWLYMGIVNRVGwALVILalFMpreY 104
                                       22222224455566789**************************5554499966666666666645555544324644 PP

                             MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......Wravf 154
                                        l++++vl +++ +++g++  a++ ++ d++p +e + +++ ++  +  +++++ +l+ +l + l       ++ ++
  gi|320100979|ref|YP_004176571.1| 105 VLPYVAVLSFIAQFAGGVAGVAAMDVLGDLVPFKESTTVFSRANQLAYSSILVAHGLSIVLFA-LPieialkYTTAY 180
                                       4559****************************************9999999999999999994.4447999999999 PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp...awkallkdpvlwillialllfffgfsg... 225
                                       +i+ +v++ + +   ll++ ++p r+ +s  +      p+++++   a+k + +d+ l      l+l++f++++   
  gi|320100979|ref|YP_004176571.1| 181 LIALVVAIASSI---LLYFIPDPGRSLQSINTT----SPSGMSEidkALKNIIHDQGL---RGYLFLITFFNFAvni 247
                                       999999999999...888899999999999888....888888888999999999966...3333333344444011 PP

                             MFS_1 226 .lltllplylqevlglsglllaglllallalvgail.allagrlsdrlgrrrrlllallllllaalglallavtssa 300
                                        + ++  +  + + g +   l ++l  +++l + i+   +++ l++r g rr+++ ++++ +l+ +++ ++a++   
  gi|320100979|ref|YP_004176571.1| 248 pAPFWDYIV-MNTTGGN--ELFVVLKNFAGLSSKIFgTRMWSTLMRRRGVRRAMIAGIASSSLIPVAYSYIAMP--- 318
                                       355555554.4444444..444444777777776666779*********************************9... PP

                             MFS_1 301 vllllvlvliGfglgfv 317
                                       + ++ v +  Gf ++ +
  gi|320100979|ref|YP_004176571.1| 319 FEIIGVEAYSGFVWASI 335
                                       44444444444444444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00014
                             MFS_1  99 agalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpe 174
                                        +++  +++++   ++p + r++++++l+ +++  a l+  lg+++a s ++ + v ++ + +  l+++l++ +lpe
  gi|320100979|ref|YP_004176571.1| 332 WASIDISSNIYNIYLSPSTLRPLYLSMLGFTTNTVAGLASTLGSIIAvSTGNITPVLILSGTMRGLSALLAYKVLPE 408
                                       56666677777777899999***************************77777*****************98888887 PP

                             MFS_1 175 epperkrks 183
                                       +  ++ + +
  gi|320100979|ref|YP_004176571.1| 409 PGETPVKAA 417
                                       776665555 PP

>> Mpv17_PMP22  Mpv17 / PMP22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.7    0.0086        77      26      56 ..      87     115 ..      72     119 .. 0.71
   2 ?   -1.6   0.0      0.36   3.2e+03      28      42 ..     184     198 ..     171     204 .. 0.65
   3 ?    7.5   0.1   0.00052       4.6      34      60 ..     340     366 ..     328     367 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0086
                       Mpv17_PMP22  26 nwkvWppaqlinFyfvPlkfRvlfvnvvslg 56 
                                       n + W    +i+  f+P ++ +++v v+s++
  gi|320100979|ref|YP_004176571.1|  87 NRVGWA--LVILALFMPREYVLPYVAVLSFI 115
                                       444454..46778899************998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.36
                       Mpv17_PMP22  28 kvWppaqlinFyfvP 42 
                                        v  +a+ i+ yf+P
  gi|320100979|ref|YP_004176571.1| 184 LVVAIASSILLYFIP 198
                                       356678889999999 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00052
                       Mpv17_PMP22  34 qlinFyfvPlkfRvlfvnvvslgWnty 60 
                                       +++n y+ P+ +R l+ +++++  nt+
  gi|320100979|ref|YP_004176571.1| 340 NIYNIYLSPSTLRPLYLSMLGFTTNTV 366
                                       689*******************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3078.90
//
Query:       gi|320100980|ref|YP_004176572.1|  [L=429]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.1e-105  352.4   0.0   2.6e-105  352.1   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    1.1e-32  112.3   0.0    1.7e-32  111.6   0.0    1.3  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.1   0.0  2.9e-109  2.6e-105       1     270 []      32     300 ..      32     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 352.1 bits;  conditional E-value: 2.9e-109
                             Nre_N   1 LcglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglsledii 77 
                                       Lcgl++cpi+ ++ a+ k+   + s+ +eGsspPsvf+GrygYP V++gp vpp +gd+ v+d+pe+w+g ++e+i+
  gi|320100980|ref|YP_004176572.1|  32 LCGLSYCPIIARAMASLKLGMVSGSRVIEGSSPPSVFIGRYGYPYVRAGPGVPPLSGDTLVYDHPESWIGRRIEEIL 108
                                       8*****************999889***************************************************** PP

                             Nre_N  78 klrlslvrgekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkv 154
                                       ++r+slv+g+++v+v+++  ++++ee++ ++ls+kpvdv vel+k+p++ l+f+e+++P Gp++++e+++v +np++
  gi|320100980|ref|YP_004176572.1| 109 DYRWSLVTGYTSVDVRRPF-NRIIEETRLVVLSSKPVDVRVELSKPPRPMLSFSEEEPPQGPRSPMERMQVLGNPSI 184
                                       ******************8.********************************************************* PP

                             Nre_N 155 prkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpei 231
                                       pr+vek+++Dtdl A +avv+Ly+sg+ v++iq+++SvG+LG+k++rrlVPTrWsITAvd+i+++el+k++k+++++
  gi|320100980|ref|YP_004176572.1| 185 PRPVEKAFNDTDLPAGRAVVYLYESGIPVSHIQKIFSVGALGVKEQRRLVPTRWSITAVDSILSRELLKDVKSYESL 261
                                       ***************************************************************************** PP

                             Nre_N 232 devevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       +e+ev++ ++++N f+ iL+P kwsfe++Eaw+pgs+wn
  gi|320100980|ref|YP_004176572.1| 262 NEIEVYVLRHYDNLFVSILYPAKWSFEWMEAWWPGSTWN 300
                                       **************************************8 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.0   1.9e-36   1.7e-32       1     110 []     313     423 ..     313     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 1.9e-36
                             Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkp.kefesleea 76 
                                       e+y+gr++y++i+G+Yya+ la+le+L++++rqa++++lrei+p++++P+GvW+vRe++r+++++ p  ++++l e+
  gi|320100980|ref|YP_004176572.1| 313 EDYHGRTTYPSIGGCYYASMLATLEHLSRVRRQATAVLLREIYPGFNLPIGVWFVRESIREMYRRGPvLKTSNLGEV 389
                                       789*************************************************************99889******** PP

                             Nre_C  77 leevseklklplkkllkkskllkelkkqktLddF 110
                                          +++ ++l + k+ ++s+llk++ + k+++dF
  gi|320100980|ref|YP_004176572.1| 390 AMLLDKVTRLGAGKWFDSSRLLKRISRSKSIRDF 423
                                       *******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3188.07
//
Query:       gi|320100981|ref|YP_004176573.1|  [L=265]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   56.8   0.0    6.1e-15   56.0   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
     0.0017   18.1   2.9        4.4    6.9   0.0    2.4  2  DUF1848      Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   6.8e-19   6.1e-15       2     159 ..      29     194 ..      28     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 6.8e-19
                                       EEESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakl 73 
                                       +++ gC+++C++C+ +       v+ ++ + +l +e+i++ +k+  ++      ++g g++++ +  ve++ rl ++
  gi|320100981|ref|YP_004176573.1|  29 NPYTGCAHACIYCYARMYtrnreVSENWGSIVLVKENIVDVLKRE-VST-HPRGTVGVGTVTDAYQPVEAVYRLTRR 103
                                       6789************99************************999.566.444444455555555555555555555 PP

                                       C.....CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSE CS
                                       x.....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  74 a.....vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagik 143
                                             + g++ ++ t  +l+  + ++ l +++ +  v +++ ++d+e v + ++ r + + ++++alekl e gi+
  gi|320100981|ref|YP_004176573.1| 104 SlelllKHGFHASIQTKNPLI-LRDIDILTRYRgLVDVGFTVTTLDSE-VSRFIEpRAPPPGARVRALEKLSEEGIP 178
                                       566******************.**************************.**************************** PP

                                       TEEEEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 144 rvvdrivglpGendee 159
                                       + v+  +++pG n +e
  gi|320100981|ref|YP_004176573.1| 179 VWVFYGPIIPGLNSDE 194
                                       7666679999999886 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   5.6     0.001       9.1     253     265 .]      31      43 ..      27      43 .. 0.93
   2 !    6.9   0.0   0.00049       4.4      55     124 ..     119     189 ..     114     213 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.001
                           DUF1848 253 yntClhgCvYCYA 265
                                       y  C h C+YCYA
  gi|320100981|ref|YP_004176573.1|  31 YTGCAHACIYCYA 43 
                                       999*********9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00049
                           DUF1848  55 tknpkpllkkleelkergiklyfqfTltdyeke....lepnvpsleerietfkelseklgkerviwRyDPillt 124
                                       tknp  +l+ ++ l++ +  + + fT+t+ ++e    +ep+ p+   r++++++lse+  +  v + y Pi+  
  gi|320100981|ref|YP_004176573.1| 119 TKNPL-ILRDIDILTRYRGLVDVGFTVTTLDSEvsrfIEPRAPPPGARVRALEKLSEEGIP--VWVFYGPIIPG 189
                                       66665.56666666665444444555554433322359******************98654..44557777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2043.46
//
Query:       gi|320100982|ref|YP_004176574.1|  [L=257]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-88  295.7   0.5    2.4e-88  295.5   0.5    1.0  1  DUF2192   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.057   13.3   0.0        6.6    6.7   0.0    2.3  2  YfdX      YfdX protein


Domain annotation for each model (and alignments):
>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.5   0.5   2.7e-92   2.4e-88       1     229 []       2     233 ..       2     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 295.5 bits;  conditional E-value: 2.7e-92
                           DUF2192   1 kelykkrievlvdllsklleee.kltReelvellkkvYeekgiePlrGlskPediYdkElatlYvvgkyGlgleeel 76 
                                       k+++kkri+v+v++ls++ ++  +l+R++lv++l+++Ye++g++P+rG++ P+diYdkEl+tlYv+gkyGlgl +++
  gi|320100982|ref|YP_004176574.1|   2 KQPHKKRIQVAVSILSEATKKLdELDRSKLVDYLRRTYEKTGLSPIRGKALPPDIYDKELTTLYVIGKYGLGLLDDY 78 
                                       689******************99****************************************************** PP

                           DUF2192  77 kelfdkifsvEekleealeiilskkkeeavekvkevl..gkidenkvarvlrlvltkvvlgfadeeelikllrklee 151
                                       + +f+kif++Ee+leeal+++l++k +ea+e++k+v+  g id n++ar+lr+ ltk+vlgf++e++++++l+ + +
  gi|320100982|ref|YP_004176574.1|  79 PAMFSKIFYIEERLEEALNLLLQGKVDEARERIKSVSpsGVIDGNMIARLLRIPLTKLVLGFMSEDDFTRILHVVFK 155
                                       ***********************************9999************************************** PP

                           DUF2192 152 afpelektvkkyarfyiAfkiaekiaegeirnrlekealkkalalrlgiekalPsdeyiaeiakevfkvpkkvlkkv 228
                                       afpe+ektv++y+rf+i+fk+ae+i++geir+r+ kealk+ala+r+g++k++P d+y+++ia++vf++p++ l+kv
  gi|320100982|ref|YP_004176574.1| 156 AFPEEEKTVRSYVRFFIGFKLAEAIYRGEIRSREYKEALKRALAIRVGFPKTTPGDDYVKAIAEAVFNIPEEELSKV 232
                                       ****************************************************************************9 PP

                           DUF2192 229 l 229
                                       l
  gi|320100982|ref|YP_004176574.1| 233 L 233
                                       7 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0037        34      14      36 ..       6      28 ..       4      58 .. 0.81
   2 ?    6.7   0.0   0.00073       6.6     114     140 ..      89     115 ..      84     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0037
                                      TT-HHHHHHHHHHHHHHHTS-HH CS
                              YfdX 14 qgdtkeAkkllekAqgkleaala 36
                                      ++ ++ A++ l++A++kl+++  
  gi|320100982|ref|YP_004176574.1|  6 KKRIQVAVSILSEATKKLDELDR 28
                                      678899*************9854 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00073
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              YfdX 114 paavkkAaelleegkyyeAkeaLkeal 140
                                       ++ + +A++ll +gk++eA e +k++ 
  gi|320100982|ref|YP_004176574.1|  89 EERLEEALNLLLQGKVDEARERIKSVS 115
                                       678899999999999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2008.20
//
Query:       gi|320100983|ref|YP_004176575.1|  [L=94]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 662.66
//
Query:       gi|320100984|ref|YP_004176576.1|  [L=128]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 983.31
//
Query:       gi|320100985|ref|YP_004176577.1|  [L=119]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-05   23.7   0.1    5.2e-05   23.2   0.1    1.4  1  HTH_3           Helix-turn-helix
    0.00057   20.0   0.0     0.0012   18.9   0.0    1.6  1  HTH_28          Helix-turn-helix domain
     0.0013   18.2   0.0     0.0023   17.3   0.0    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0039   17.5   0.0     0.0069   16.7   0.0    1.4  1  HTH_Tnp_1       Transposase
      0.009   16.0   0.0      0.021   14.8   0.0    1.5  1  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.4   0.1      0.019   14.5   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.013   15.4   0.2      0.026   14.5   0.2    1.5  1  HTH_11          HTH domain
      0.028   14.2   0.0      0.053   13.3   0.0    1.4  1  MerR            MerR family regulatory protein
      0.035   13.9   1.2      0.051   13.4   0.2    1.8  2  HTH_23          Homeodomain-like domain
      0.035   14.5   0.0      0.056   13.9   0.0    1.3  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.047   14.1   0.0       0.11   12.9   0.0    1.6  2  Linker_histone  linker histone H1 and H5 family
      0.092   12.8   0.0       0.18   11.8   0.0    1.5  1  HTH_29          Winged helix-turn helix
       0.11   12.3   0.4       0.88    9.4   0.0    2.4  3  HTH_10          HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   3.8e-08   5.2e-05      11      48 ..      36      73 ..      24      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.8e-08
                                      HHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHH CS
                             HTH_3 11 sqeeLAeklGvsrstisriEnGernPsletlkklakaL 48
                                      s+ eL++ lG+s+++i+++ + e+ Ps e+l++ ++ L
  gi|320100985|ref|YP_004176577.1| 36 SIIELSRDLGISPTAIRKYVKKEAYPSDEVLQRALEKL 73
                                      778*****************************998877 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.1e-07    0.0012       2      35 ..      24      57 ..      23      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.1e-07
                            HTH_28  2 RleiikllaaGhsvreaArelgisrrtvyrWikr 35
                                      R++ i+l+++ +s+ e++r lgis++ +++ +k+
  gi|320100985|ref|YP_004176577.1| 24 RAKLIELMLSTRSIIELSRDLGISPTAIRKYVKK 57
                                      99***************************99987 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.6e-06    0.0023      12      48 ..      19      55 ..      17      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-06
                      HTH_Tnp_ISL3 12 iTlrleayilelllesrsvkavArqlgvSwtTVwril 48
                                       ++  +a+ +el+l++rs+ + +r+lg+S+t ++ ++
  gi|320100985|ref|YP_004176577.1| 19 VSKETRAKLIELMLSTRSIIELSRDLGISPTAIRKYV 55
                                      688999*************************998766 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     5e-06    0.0069       8      49 ..      20      63 ..      17      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                         HTH_Tnp_1  8 sdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...e 49
                                      s+e +a+++++   + +s+ e+ r++g+sp + +k +++     +
  gi|320100985|ref|YP_004176577.1| 20 SKETRAKLIELM-LSTRSIIELSRDLGISPTAIRKYVKKEAypsD 63
                                      789999*****9.889*********************99644433 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.5e-05     0.021      17      52 ..      39      73 ..      35      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                            HTH_19 17 elaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                      el+++lgis++ i+++ + +  +ps e+l++++e+l
  gi|320100985|ref|YP_004176577.1| 39 ELSRDLGISPTAIRKYVKKEA-YPSDEVLQRALEKL 73
                                      89*****************99.*********99987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.4e-05     0.019      19      40 ..      36      57 ..      33      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                            HTH_24 19 sqreLAerlglSpstvnrrlkr 40
                                      s+ eL++ lg+Sp+++++++k+
  gi|320100985|ref|YP_004176577.1| 36 SIIELSRDLGISPTAIRKYVKK 57
                                      778*****************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   1.9e-05     0.026       4      38 ..      26      57 ..      23      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIka 38
                                      +++el l++r   s+ eL++ L++S +++r+++k+
  gi|320100985|ref|YP_004176577.1| 26 KLIELMLSTR---SIIELSRDLGISPTAIRKYVKK 57
                                      5555555555...799*****************95 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.053       1      22 [.      36      57 ..      36      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                                      EHHHHHHHHTTTHHHHHHHHHT CS
                              MerR  1 tIgevAeltGvsprtLRyYEre 22
                                      +I e+++ +G+sp ++R Y ++
  gi|320100985|ref|YP_004176577.1| 36 SIIELSRDLGISPTAIRKYVKK 57
                                      688****************886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   3.7e-05     0.051       3      40 ..      20      57 ..      18      60 .. 0.93
   2 ?   -3.1   0.1       5.7   7.9e+03       4      15 ..      80      91 ..      79      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                            HTH_23  3 sereRlrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      s++ R++ + l +   s+ e +r Lg+s+  +++++k+
  gi|320100985|ref|YP_004176577.1| 20 SKETRAKLIELMLSTRSIIELSRDLGISPTAIRKYVKK 57
                                      7899**********99*******************997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                            HTH_23  4 ereRlrilllla 15
                                      e +R+ il l+ 
  gi|320100985|ref|YP_004176577.1| 80 EAMRMIILDLVE 91
                                      567888888765 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-05     0.056      12      45 ..      36      68 ..      28      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                            HTH_26 12 tkseLargtgisaatlsrlvkgkpervsldtLdk 45
                                      ++ eL+r++gis + + ++vk+++ ++s ++L++
  gi|320100985|ref|YP_004176577.1| 36 SIIELSRDLGISPTAIRKYVKKEA-YPSDEVLQR 68
                                      5689*******************5.999999975 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.1e-05      0.11      10      52 ..      35      72 ..      30      77 .. 0.77
   2 ?   -2.5   0.0       5.1     7e+03      40      57 ..     102     119 .]      93     119 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-05
                    Linker_histone 10 eAIkalkerkGsSrqaIkkyikakykvvdvskfksllkkalkk 52
                                        I++l    G+S +aI ky+k++ +  +    +  l++al+k
  gi|320100985|ref|YP_004176577.1| 35 RSIIELSRDLGISPTAIRKYVKKEAYP-S----DEVLQRALEK 72
                                      5799999999***********988764.2....3346666666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.1
                    Linker_histone  40 skfksllkkalkkgvekg 57 
                                       +k + +l+ +l++ +++g
  gi|320100985|ref|YP_004176577.1| 102 EKHREFLRETLRSIISQG 119
                                       455678888888877765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.18       1      34 [.      24      56 ..      24      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlk 34
                                      Ra+ + l+    s + ++ + lg+s++ +++++k
  gi|320100985|ref|YP_004176577.1| 24 RAKLIELMLSTRS-IIELSRDLGISPTAIRKYVK 56
                                      8889999999998.******************98 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00064      0.88      26      46 ..      37      57 ..      34      59 .. 0.88
   2 ?   -0.1   0.0      0.59   8.1e+02      42      52 ..      64      74 ..      62      75 .. 0.82
   3 ?   -3.3   0.0       5.9   8.1e+03      44      51 ..     108     115 ..     103     117 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00064
                            HTH_10 26 lkeLAkelGIskstlsehLrk 46
                                      + eL+ +lGIs++++ ++++k
  gi|320100985|ref|YP_004176577.1| 37 IIELSRDLGISPTAIRKYVKK 57
                                      669*************99986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.59
                            HTH_10 42 ehLrkaeskli 52
                                      e L++a +kl+
  gi|320100985|ref|YP_004176577.1| 64 EVLQRALEKLA 74
                                      78999999985 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.9
                            HTH_10  44 Lrkaeskl 51 
                                       Lr+  + +
  gi|320100985|ref|YP_004176577.1| 108 LRETLRSI 115
                                       44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 908.85
//
Query:       gi|320100986|ref|YP_004176578.1|  [L=292]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2346.95
//
Query:       gi|320100987|ref|YP_004176579.1|  [L=404]
Description: 2-aminoadipate aminotransferase apoenzyme [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-34  119.1   0.0    2.9e-34  118.8   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    1.1e-06   27.8   0.0    1.7e-06   27.1   0.0    1.3  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
  ------ inclusion threshold ------
      0.053   12.8   0.0        0.1   11.9   0.0    1.5  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.091   12.0   0.0       0.13   11.5   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.0   6.5e-38   2.9e-34      34     363 .]      63     397 ..      37     397 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 6.5e-38
                                       HTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHH CS
                     Aminotran_1_2  34 ggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknil 110
                                       g ++ +y+ ++g  e++e+l +fl r+ ++ +++e  ++v+sG++++++++ + l ++pgd ++  +p+y     ++
  gi|320100987|ref|YP_004176579.1|  63 GDNALQYSETKGIIEVRETLSDFLARKREIHVDAE-DIIVTSGSQSGLDIVSRTL-IDPGDIVVTESPSYLAALGAF 137
                                       667899*****************************.*******************.********************* PP

                                       HHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS.-TTT--B--HHHHHHHHHHHHHTTEEEEE CS
                     Aminotran_1_2 111 rlsggevvryplyseedfhldlealeealkeapegnkktkvilvesp.hNPtGtvatleeleklldlakkynlllfv 186
                                       +++g+ ++ ++++   + ++  + le+ lk++  +  ++k+i+v  + +NP Gt ++++  + ll++a +y ll++ 
  gi|320100987|ref|YP_004176579.1| 138 KMNGARLIGVKVD---EHGMRTDLLEDRLKQLGDDVRRVKFIYVIPVgQNPAGTTMDKDRKKHLLEIASRYDLLVVE 211
                                       ***********65...9999***********998888*****8776648**************************** PP

                                       EETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHH CS
                     Aminotran_1_2 187 DeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaava 261
                                       D+ Y+   +++   va +  +++e  ++ ++++sK + ++G+R+G+i++ +++++  +++++ +    ++l q +va
  gi|320100987|ref|YP_004176579.1| 212 DDPYSYIIYEEGAEVASLKSMDKEGRVIYMSTVSKIL-APGLRIGWIAAEKELIRRFEIVKQYVDLhsPTLNQFIVA 287
                                       **********6633333777777777*********98.6************99999999998876666888888888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...TEEEECCSCSSEEEEEETHH..CHHHHHHHHHHTCTEEEE CS
                     Aminotran_1_2 262 aalsdallkqseleemrqrlqkrrkelrdeLael...glkvlasqsgmflltdlsae..takelskkLleevgvyvt 333
                                       +a+++   +++ ++ ++  ++++r+++ ++++e    ++ ++++ +g+f++  + +   +a +l +k +++++v+ +
  gi|320100987|ref|YP_004176579.1| 288 EAIKTGV-IDDVVSRAVPYYKAKRDTMLKAIQENfpeYVWYTKPIGGLFVFAYVHKPgfDAGALLEKAVKQYKVAYV 363
                                       8888765.5679************************666666666****9998888899****************** PP

                                       EGGGGTS....TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 334 pgtsftv....pgrlRitvAglteeeleelveal 363
                                       pg sf+      ++ Ri+++  ++e+++e + +l
  gi|320100987|ref|YP_004176579.1| 364 PGGSFHPegdgVNSMRINFSYPSHEQIREGIARL 397
                                       *******9999889**************999876 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   3.9e-10   1.7e-06     128     403 ..     124     395 ..     101     404 .] 0.75

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.9e-10
                                       EEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHHH....HHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT CS
                    Aminotran_MocR 128 lvtvpGydrhfllleelGielltvdlqddGpdvdave....klvaedasvkGilavpkysnptGetiseevarrlaa 200
                                       +  +p y   +   +  G +l+ v++++ G   d +e    +l  +   vk i+++p   np+G+t+ +++ ++l  
  gi|320100987|ref|YP_004176579.1| 124 VTESPSYLAALGAFKMNGARLIGVKVDEHGMRTDLLEdrlkQLGDDVRRVKFIYVIPVGQNPAGTTMDKDRKKHLLE 200
                                       45678888888889999*************8776654211166666678*********************9999998 PP

                                       ---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHH...H CS
                    Aminotran_MocR 201 lkaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawl...k 274
                                       +  +  d+ +  dd y+   ++ e+ + a      ++     r + +++ ski   G  ++ +a+ ++ i+ +   k
  gi|320100987|ref|YP_004176579.1| 201 IA-SRYDLLVVEDDPYSY-IIYEEGAEVAS----LKSMDKEGRVIYMSTVSKILAPGLRIGWIAAEKELIRRFeivK 271
                                       84.568**********74.56677666444....4555666799999999******************998761115 PP

                                       HHHHHC-S---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..TTSSEEE---SBSS-EEEEE CS
                    Aminotran_MocR 275 kylGlqsiGpdkveqlrhvkflkdyeGlealmrdhaeliapkfeavlevleaelg..gaevatwteprGGyfisldt 349
                                       +y+ l+s   +++  +  +k         + + d      p ++a  +++ + +     e+  +t+p GG f+   +
  gi|320100987|ref|YP_004176579.1| 272 QYVDLHSPTLNQFIVAEAIK--------TGVIDDVVSRAVPYYKAKRDTMLKAIQenFPEYVWYTKPIGGLFVFAYV 340
                                       66666665544444444333........334445555556777777777666666445699999*********9999 PP

                                       SSS-HHHHHHH...HHHCTEE---TTTTSSTT--SSS-EEEE--SSS-HHHHHHHHH CS
                    Aminotran_MocR 350 ldgvakrvvkl...aeeaGvsltaaGatypaGedpkdrnirlaptlppleevetamd 403
                                        ++  +    l    ++  v+  + G+ +p+G+  +   +r+  + p+ e++++ + 
  gi|320100987|ref|YP_004176579.1| 341 HKPGFDAGALLekaVKQYKVAYVPGGSFHPEGDGVN--SMRINFSYPSHEQIREGIA 395
                                       9998766544411145668999**********8764..5899999******998775 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.3e-05       0.1      22     144 ..      79     212 ..      59     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                                       SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSS CS
                   DegT_DnrJ_EryC1  22 gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtyn 98 
                                        ++ ++F ++ ++ + ++  i v+sG+++ + + +   ++pgd V++ s +++a   a   +ga+ + v vd++ + 
  gi|320100987|ref|YP_004176579.1|  79 RETLSDFLARKREIHVDAEDIIVTSGSQSGLDIVSRTLIDPGDIVVTESPSYLAALGAFKMNGARLIGVKVDEHGMR 155
                                       56666666666777777777888888877666667777**************************9988888866555 PP

                                       B-..GGGCGGG--TTE..EEEEEB-GGGB--..-HH.....HHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1  99 id..paaieaaitert..kaIlpVhlyGqva..dmd.....alkaiaakhglkvieD 144
                                        d   ++++++    +  k I ++ +  ++a   md     +l +ia++++l v+eD
  gi|320100987|ref|YP_004176579.1| 156 TDllEDRLKQLGDDVRrvKFIYVIPVGQNPAgtTMDkdrkkHLLEIASRYDLLVVED 212
                                       441135555555443356777666665555544676334446999999999999999 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     3e-05      0.13      28     167 ..      69     212 ..      59     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                                       CT--HHHHHHHHHHHHHTT-SEEEE.......ES-HHHHH.HHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC-- CS
                   Beta_elim_lyase  28 YgedktvnrLedavaelfgkeaalf.......vpqGtaAn.sillkillqrgeevivtepahihfdetgaiaelagv 96 
                                       Y e k++ ++ +++ + +  +  +        v++G ++   i  ++l+ +g+ v+ ++p+  +    ga   ++g+
  gi|320100987|ref|YP_004176579.1|  69 YSETKGIIEVRETLSDFLARKREIHvdaediiVTSGSQSGlDIVSRTLIDPGDIVVTESPS--YLAALGAF-KMNGA 142
                                       5555555555555555444444444444444488888766258889999998866666555..66677777.79*** PP

                                       EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase  97 klrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                       +l+ +k +e   m  + le+ +k+ g+   ++k+i++    +  +G+ +  +  + + +ia +y++ ++ D
  gi|320100987|ref|YP_004176579.1| 143 RLIGVKVDE-HGMRTDLLEDRLKQLGDDVRRVKFIYVIPVGQNPAGTTMDKDRKKHLLEIASRYDLLVVED 212
                                       *********.78************9998899****998777778*********************999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3134.07
//
Query:       gi|320100988|ref|YP_004176580.1|  [L=523]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   38.0   0.0    5.2e-09   36.7   0.0    1.7  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.04   13.9   0.1       0.22   11.5   0.0    2.1  2  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   5.8e-13   5.2e-09       2     165 ..     211     370 ..     210     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 5.8e-13
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavp 76 
                                       +v+rgC++ CsfC+ ++      ++r++s+  ++++v+ +  a+    ++v+ +   p    ++ +lle l  +   
  gi|320100988|ref|YP_004176580.1| 211 EVSRGCRFWCSFCIESR---VFQPYRERSLPLLKRLVEDGVsASIWgRRVVLYSLSFPVTSTHL-KLLEYLGSE--- 280
                                       689*************8...7*******************765444366666666666665544.777777776... PP

                                       TEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdri 149
                                         +i+ + + ++++    e+le+ +  g  +++l  e++++   ++ +    + ++e +e+++ + e g+++  ++i
  gi|320100988|ref|YP_004176580.1| 281 --NIRASLPSIRLSalsSEVLELVKSVGQRTLTLAPETFTPV-LQRVFFkYVDIVDEMIESVKHALEEGFNVKLYMI 354
                                       ..3444444444444569999********************8.666664588889********************** PP

                                       EEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 150 vglpGendeeleelle 165
                                       +g++Ge  +++++ le
  gi|320100988|ref|YP_004176580.1| 355 YGVKGEGVDDVKANLE 370
                                       **********988776 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      59     120 ..      81     143 ..      68     144 .. 0.73
   2 ?   -0.9   0.0      0.18   1.6e+03      18      41 ..     337     363 ..     330     383 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                       B12-binding  59 alltsqleavkelvel....lkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       +++   + +  +l++     +kr+ + +++v+GG+++   p         id+ v+ge+e +le +
  gi|320100988|ref|YP_004176580.1|  81 LHYEPDIVNLIRLLNSggipVKREQRATPIVAGGPVVMENPIP--FS-GIIDVFVIGEAEATLEGI 143
                                       445555555555555599998999999*******995555555..43.567999********9977 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.18
                       B12-binding  18 avlaaalrdagfeVqll...ganven.e 41 
                                        +++ al++ gf+V+l+   g++ e  +
  gi|320100988|ref|YP_004176580.1| 337 ESVKHALEE-GFNVKLYmiyGVKGEGvD 363
                                       678888998.999986644444333343 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3690.50
//
Query:       gi|320100989|ref|YP_004176581.1|  [L=254]
Description: 3-hydroxy-3-methylglutaryl-coenzyme A reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.0   0.0       0.22   10.5   0.0    1.2  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
        0.2   11.9   0.0       0.43   10.9   0.0    1.5  1  Clr5         Clr5 domain


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 ?   10.5   0.0   2.5e-05      0.22       4      62 ..      35     100 ..      32     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHS-HHHHHHHTT----.HHHHHHHSSS---------EEEE..EEEETTE....EEEEEE CS
                       HMG-CoA_red   4 eRrklleelteeeleelkeesld.eevadkmiEnviGyvqlPlGvag..pllingk....eylvPm 62 
                                       +Rr +++e+t+ +l++++++ ld +e  +    nv+G++q+PlG++g  +l in+k    ++l P+
  gi|320100989|ref|YP_004176581.1|  35 IRRLYIQEKTGLSLSAIGSTILDfTEGDHYRGYNVVGALQVPLGIVGviQLSINNKsresYLLAPL 100
                                       689999999999999999999996555555567************983356677776664555555 PP

>> Clr5  Clr5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.43       6      28 ..      29      53 ..      24      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
                              Clr5  6 eahkatIrrLYleen..rsLkdvme 28
                                      e+ ka+IrrLY++e+   sL+ +++
  gi|320100989|ref|YP_004176581.1| 29 ENVKALIRRLYIQEKtgLSLSAIGS 53
                                      689***********63356666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1932.64
//
Query:       gi|320100990|ref|YP_004176582.1|  [L=135]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-11   43.0   0.1    4.3e-11   42.7   0.1    1.2  1  OB_aCoA_assoc    DUF35 OB-fold domain, acyl-CoA-associated
    3.9e-09   36.2   1.8    5.2e-09   35.8   1.8    1.2  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.024   14.6   0.1      0.075   13.0   0.0    1.8  2  DUF2767          Protein of unknown function (DUF2767)
      0.043   14.1   0.7        8.9    6.6   0.1    2.5  3  Methyltransf_13  Putative zinc binding domain
      0.068   13.2   0.3       0.13   12.3   0.3    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met


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 !   42.7   0.1   1.2e-14   4.3e-11       5      64 ..      52     112 ..      47     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.2e-14
                                       -GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT....-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc   5 sgrGtvysftvvhrappgfaeeaPyvvgvVeLde.gvrimarlvgvdpdevriGmrVravf 64 
                                         ++++ ++tv++ a +gf+e++P+++gv e  e   ri+a l++v p+e++ G +++ v 
  gi|320100990|ref|YP_004176582.1|  52 NEKARLLTWTVIYSAMEGFEEKRPVIIGVLETVEsKARITAPLTDVLPEELKPGIEMEPVL 112
                                       459*******************************9999*******************9886 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 !   35.8   1.8   1.5e-12   5.2e-09       4      37 .]      13      46 ..      10      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.5e-12
                           DUF35_N  4 aaegrLvgqrCpdCGtvqfPPravCphCgsddle 37
                                       +++rL ++rC+dCG+  +P+  +C+ Cgs++ e
  gi|320100990|ref|YP_004176582.1| 13 IDRYRLKASRCKDCGRTGYPASSICRFCGSRNIE 46
                                      589**************99999*********986 PP

>> DUF2767  Protein of unknown function (DUF2767)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.4   1.4e+03      14      34 ..      36      56 ..      34      64 .. 0.79
   2 ?   13.0   0.0   2.1e-05     0.075      13      50 ..      53      90 ..      42      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.4
                           DUF2767 14 vCRvvGdvVlvlaelGqetkr 34
                                      +CR  G   ++ +el  e  r
  gi|320100990|ref|YP_004176582.1| 36 ICRFCGSRNIEYVELVNEKAR 56
                                      799999998888887776655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.1e-05
                           DUF2767 13 EvCRvvGdvVlvlaelGqetkriviadvlrTrlarkkd 50
                                      E  R++   V+  a +G+e kr vi +vl T  +++++
  gi|320100990|ref|YP_004176582.1| 53 EKARLLTWTVIYSAMEGFEEKRPVIIGVLETVESKARI 90
                                      556777778999999****************9999887 PP

>> Methyltransf_13  Putative zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0066        24      35      48 ..      14      27 ..       6      29 .. 0.87
   2 ?    6.6   0.1    0.0025       8.9       1      10 [.      37      46 ..      37      51 .. 0.86
   3 ?   -2.9   0.0       2.4   8.6e+03      18      31 ..      92     103 ..      91     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0066
                   Methyltransf_13 35 pfyplrlvvCedCg 48
                                       +y+l++  C+dCg
  gi|320100990|ref|YP_004176582.1| 14 DRYRLKASRCKDCG 27
                                      579**********8 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0025
                   Methyltransf_13  1 CRiCgselle 10
                                      CR+Cgs+++e
  gi|320100990|ref|YP_004176582.1| 37 CRFCGSRNIE 46
                                      *******987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.4
                   Methyltransf_13  18 qplansflkpeqld 31 
                                       +pl++++  pe+l+
  gi|320100990|ref|YP_004176582.1|  92 APLTDVL--PEELK 103
                                       5888888..77665 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   0.3   3.7e-05      0.13      71     100 ..      21      48 ..      12      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                       EEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
                              HypA  71 vrCreCgkefeleekalrCpkCgsadveiv 100
                                        rC++Cg+++  +++   C  Cgs+++e v
  gi|320100990|ref|YP_004176582.1|  21 SRCKDCGRTGYPASS--ICRFCGSRNIEYV 48 
                                       58*****99998855..7*******99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1001.51
//
Query:       gi|320100991|ref|YP_004176583.1|  [L=352]
Description: hydroxymethylglutaryl-CoA synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-12   46.1   0.0      3e-11   43.3   0.0    2.3  2  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    4.2e-06   26.3   0.0    1.1e-05   24.9   0.1    1.6  2  Thiolase_N      Thiolase, N-terminal domain
     0.0014   18.4   0.4     0.0049   16.7   0.2    2.0  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.069   12.8   0.0    1.9  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C 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 ?   -0.5   0.0      0.32   1.4e+03      25      42 ..      95     112 ..      66     117 .. 0.51
   2 !   43.3   0.0   6.7e-15     3e-11       1      81 [.     223     303 ..     223     312 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                                       HHHHHHHT--GGGB--TH CS
                     ACP_syn_III_C  25 davakklglpeekvvvnl 42 
                                         +a+ lg++++ ++++l
  gi|320100991|ref|YP_004176583.1|  95 TIIAEALGITPDTMATDL 112
                                       336677777777766665 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 6.7e-15
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEE CS
                     ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllv 75 
                                       Lek+gl+ped+++ v+hq n ++   va+ lg+p+ekv+  l    +Gn   +s ++ L++ ++  k kpg+++ll+
  gi|320100991|ref|YP_004176583.1| 223 LEKTGLKPEDFNYAVFHQPNGTFPLRVARMLGIPKEKVLPGLvtPYIGNSYNSSALIGLSRILD--KAKPGERILLA 297
                                       799************************************98866789*****************..99********* PP

                                       EEETTT CS
                     ACP_syn_III_C  76 gfGaGl 81 
                                        fG G 
  gi|320100991|ref|YP_004176583.1| 298 PFGSGA 303
                                       *99996 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   2.6e-09   1.1e-05      19     114 ..      50     145 ..      41     163 .. 0.92
   2 ?   -2.1   0.0      0.45     2e+03      30      50 ..     218     238 ..     217     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.6e-09
                                       TTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHH CS
                        Thiolase_N  19 kdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavala 95 
                                       +d  a+ ++ ea++++l +ag+dp+++  v +G+  +  + +  a  +a ++gi  +++a+ ++ +c  + +a+   
  gi|320100991|ref|YP_004176583.1|  50 ADEDAVTMGWEAARNALRRAGIDPKKIGAVWFGTESKPYAVKPSATIIAEALGITPDTMATDLEFACRAASEALRIS 126
                                       6778999********************************************************************** PP

                                       HHHHHTTSHSEEEEEEEEE CS
                        Thiolase_N  96 aqsiaageadvvvagGvEs 114
                                       +++ia+g ++ ++++G  +
  gi|320100991|ref|YP_004176583.1| 127 IGAIASGLINYALIIGSDT 145
                                       **************99765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.45
                                       HHHHHHHHHTS-GGGCCEEEE CS
                        Thiolase_N  30 alkallekagvdpeevdeviv 50 
                                       a+k llek+g++pe+ ++ ++
  gi|320100991|ref|YP_004176583.1| 218 AVKMLLEKTGLKPEDFNYAVF 238
                                       68999*********9998776 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 !   16.7   0.2   1.1e-06    0.0049       2      43 ..     111     150 ..     110     182 .. 0.78
   2 ?   -1.5   0.0      0.52   2.3e+03      37      57 ..     281     304 ..     280     307 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                                       EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-T CS
                       ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDw 43 
                                       Dl+ aC ++  al +  ++i+sg ++++L+ig++t     ++
  gi|320100991|ref|YP_004176583.1| 111 DLEFACRAASEALRISIGAIASGLINYALIIGSDTAQA--NP 150
                                       8999******************************9544..44 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.52
                                       GGGCS-TTT...HHHHTTB-EEEE CS
                       ACP_syn_III  37 lskilDwkd...rstavlfGDGAg 57 
                                       ls+ilD ++   r     fG GAg
  gi|320100991|ref|YP_004176583.1| 281 LSRILDKAKpgeRILLAPFGSGAG 304
                                       699999986433555557888887 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 ?   -0.1   0.0      0.13   5.9e+02      66      79 ..     229     242 ..     209     253 .. 0.78
   2 ?   12.8   0.0   1.5e-05     0.069     141     208 ..     257     319 ..     248     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                                       -GGG-SEEEE--SS CS
                    HMG_CoA_synt_C  66 tlddfdyvifhsPf 79 
                                         +df+y +fh P 
  gi|320100991|ref|YP_004176583.1| 229 KPEDFNYAVFHQPN 242
                                       4579********96 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.5e-05
                                       HHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STT CS
                    HMG_CoA_synt_C 141 kkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsed 208
                                       k+kv p l+ p  +Gn Y +s+   l  +l    ++   g+ri+l  +GsG  +  +s+ v++   e+
  gi|320100991|ref|YP_004176583.1| 257 KEKVLPGLVTP-YIGNSYNSSALIGLSRIL----DKAKPGERILLAPFGSGAGSDAYSIIVTDRIVEK 319
                                       67788877666.69************9999....4444699*******************99876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2644.45
//
Query:       gi|320100992|ref|YP_004176584.1|  [L=369]
Description: oligopeptide/dipeptide ABC transporter ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-29  102.9   0.0    2.7e-29  102.4   0.0    1.2  1  ABC_tran   ABC transporter
      5e-18   65.4   0.1    9.2e-18   64.5   0.1    1.5  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
     0.0029   17.5   0.3        0.1   12.4   0.0    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
  ------ inclusion threshold ------
      0.013   14.9   0.3          1    8.6   0.1    2.2  2  ATPase     KaiC
       0.02   15.2   0.3      0.045   14.0   0.3    1.8  1  AAA_22     AAA domain
       0.15   12.4   0.0       0.22   11.9   0.0    1.4  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 !  102.4   0.0     9e-33   2.7e-29       2     136 ..      48     220 ..      47     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 9e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE......................EETTCEGGGB-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGei......................lldgkdlkeqeles 56 
                                       + vs+++ +ge+ a+ Ge+G+GK+t  k++++l kpteG+i                      +++ ++++e+ l+ 
  gi|320100992|ref|YP_004176584.1|  48 DGVSFDVMKGEVFALAGESGCGKTTTGKTILRLNKPTEGQIgylpskevveelgdveriseygHINVTSIDERHLRP 124
                                       78*************************************************************************** PP

                                       CCHCEEEE-SS..--S-TTSBHHHH............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHH CS
                                       xxxxxxxxxxx..xxxxxxxxxxxx............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  57 lrkeigvlpqe..pqlfpeltvren............esdee...iekalsklglkelkdtvvksspssLSgGqkqr 116
                                       lrk ++++ q+   +l+p+ t++e              ++++   ++kal++++l+  +d+ +++ p+ LSgGq+qr
  gi|320100992|ref|YP_004176584.1| 125 LRKDVQMIWQDpfGSLNPRRTIYEIleeplaihgvgvSREDRydiVAKALESVKLTP-PDEYMDRYPHMLSGGQRQR 200
                                       ***********8778*********9**********9833333457999999999999.9****************** PP

                                       HHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 117 valarallkkpkllllDEpt 136
                                       v++aral+ +pk++++DEp 
  gi|320100992|ref|YP_004176584.1| 201 VVIARALILNPKFVVADEPV 220
                                       *******************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 !   64.5   0.1   3.1e-21   9.2e-18       1      59 [.     272     333 ..     272     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 3.1e-21
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd...klekikgeapslerldeGCpFapRCp 59 
                                       vE g++++++++plHPYT+aL++++p++++ ++   + + ikge+ps+ + ++GC+F+pRC 
  gi|320100992|ref|YP_004176584.1| 272 VELGDARRVIENPLHPYTRALVEAIPEPEPSRRltiREVPIKGEVPSPINVPSGCRFHPRCV 333
                                       8*********************************9999***********************5 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.017        50       2      24 ..      60      82 ..      59     156 .. 0.81
   2 !   12.4   0.0   3.4e-05       0.1     231     300 ..     187     254 ..     104     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.017
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       +l G  g+GK++  +++  l  
  gi|320100992|ref|YP_004176584.1| 60 FALAGESGCGKTTTGKTILRLNK 82
                                      6899**************88843 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.4e-05
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                       ++ ++ lS G+++   +++  l +++  ++++ DEp + L+ ++ +++l+l+ el++  g   ++ TH+  
  gi|320100992|ref|YP_004176584.1| 187 DRYPHMLSGGQRQR-VVIARALILNP--KFVVADEPVSMLDVSIRAEILQLMMELKNkLGLTYLFITHDLA 254
                                       55666678888888.67777777776..79999*******************5555559*********976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00035         1      17      38 ..      55      76 ..      43      86 .. 0.89
   2 ?    4.2   0.0    0.0077        23     138     164 ..     225     252 ..     209     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00035
                            ATPase 17 pegrvvlitGepGtGKtifalq 38
                                      ++g+v  ++Ge+G+GKt+ +++
  gi|320100992|ref|YP_004176584.1| 55 MKGEVFALAGESGCGKTTTGKT 76
                                      67999*************9976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0077
                            ATPase 138 avaReilrqlvrvl.kklgvTailvsek 164
                                         +R+++ ql+++l +klg+T ++++  
  gi|320100992|ref|YP_004176584.1| 225 VSIRAEILQLMMELkNKLGLTYLFITHD 252
                                       569***********999*******9874 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   1.5e-05     0.045       7      34 ..      59      86 ..      54     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeak 34
                                      + ++ GesG+GKTt+ +++l+ ++  + 
  gi|320100992|ref|YP_004176584.1| 59 VFALAGESGCGKTTTGKTILRLNKPTEG 86
                                      67899**************999864444 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   7.4e-05      0.22      25      52 ..      58      86 ..      42     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.4e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekd..g 52
                                      e+  l GesG+GK++  +++lr l+k   g
  gi|320100992|ref|YP_004176584.1| 58 EVFALAGESGCGKTTTGKTILR-LNKPteG 86
                                      67889***************95.6665341 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2816.01
//
Query:       gi|320100993|ref|YP_004176585.1|  [L=321]
Description: oligopeptide/dipeptide ABC transporter ATPase [Desulfurococcus mucosus DSM 2162]
Scores for 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  103.8   0.0    1.4e-29  103.4   0.0    1.2  1  ABC_tran      ABC transporter
    1.6e-18   67.0   0.0    2.6e-18   66.3   0.0    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    6.5e-07   29.5   0.0    9.4e-06   25.6   0.0    2.0  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.1e-05   22.5   0.9    0.00092   18.7   0.1    2.0  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00021   20.7   0.5     0.0062   16.0   0.3    2.2  2  TniB          Bacterial TniB protein
     0.0019   17.8   0.0      0.032   13.8   0.0    2.1  2  AAA_25        AAA domain
     0.0091   16.3   0.7       0.24   11.7   0.7    2.1  1  AAA_22        AAA domain
     0.0099   15.6   0.0       0.02   14.6   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.019   14.6   0.1      0.026   14.2   0.1    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
      0.022   15.2   0.1       0.16   12.4   0.1    2.1  1  AAA           ATPase family associated with various cellular 
      0.041   14.3   0.0      0.081   13.3   0.0    1.5  1  RNA_helicase  RNA helicase
      0.065   13.1   0.1       0.19   11.6   0.0    1.7  2  RsgA_GTPase   RsgA GTPase
      0.072   12.4   0.1          8    5.7   0.0    2.1  2  DnaB_C        DnaB-like helicase C terminal domain
       0.11   12.9   0.0       0.18   12.2   0.0    1.4  1  AAA_16        AAA ATPase domain
       0.16   11.3   0.0        0.8    9.0   0.0    1.9  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.17   11.6   0.0       0.23   11.2   0.0    1.2  1  PRK           Phosphoribulokinase / Uridine kinase family
       0.21   11.5   0.1       0.35   10.8   0.1    1.3  1  NACHT         NACHT domain
       0.25   11.0   0.6        0.6    9.8   0.1    1.8  2  AAA_24        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.0   1.4e-32   1.4e-29       2     136 ..      26     182 ..      25     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.4e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx.. RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke.....qeleslrkeigvlpqe.. 67 
                                       + vs++l++ge ++i Ge+G+GKStL+  l++l+ p    + G+i ++gk++ e      ++e+  k i++++q   
  gi|320100993|ref|YP_004176585.1|  26 DGVSFTLNKGESLGIAGESGCGKSTLAYSLIRLVPPpgkiAGGQIIFKGKNVLEmseeeFRREVRWKGISMVFQGam 102
                                       78*********************************9999999******999999777766677777899******99 PP

                                       --S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       + l+p +t++++            ++e +e+a + l++++++ +++ks p++LSgG+kqrv++a+al+ +p+++++D
  gi|320100993|ref|YP_004176585.1| 103 NALNPVYTIGDQiaevlmlhqgySKKEALETAGKMLQMVGIDVRRLKSYPHELSGGMKQRVVIAMALALNPPVVIAD 179
                                       99*******************97777779999********************************************* PP

                                       STT CS
                                       xxx RF
                          ABC_tran 134 Ept 136
                                       Ept
  gi|320100993|ref|YP_004176585.1| 180 EPT 182
                                       **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 !   66.3   0.0   2.6e-21   2.6e-18       1      65 []     234     298 ..     234     298 .. 0.99

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 2.6e-21
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E+gps+++ ++p HPYT +Ll s+prl+ e + l+ i+g +p+l + + GC+FapRCp a ++C
  gi|320100993|ref|YP_004176585.1| 234 IEYGPSEAVYNNPMHPYTVGLLGSIPRLHGELRDLTWIPGFPPDLANPPPGCRFAPRCPRAFNKC 298
                                       7***************************************************************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 ?    1.8   0.0      0.18   1.7e+02       4      20 ..      40      56 ..      38      99 .. 0.77
   2 !   25.6   0.0   9.4e-09   9.4e-06     234     303 .]     152     219 ..     124     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.18
                            AAA_21  4 liGpNgsGKSnLLdald 20
                                      + G  g+GKS+L + l 
  gi|320100993|ref|YP_004176585.1| 40 IAGESGCGKSTLAYSLI 56
                                      8899********88774 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 9.4e-09
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpllld 303
                                       ++elS G+k+   ++++ l++++  ++++ DEp + L+  +++ ++ llk+l++  g+ +il +H+ +l++
  gi|320100993|ref|YP_004176585.1| 152 PHELSGGMKQR-VVIAMALALNP--PVVIADEPTTALDVVVQAQIMNLLKRLKKeLGISIILISHDLSLIA 219
                                       6899*****99.44444444444..************************888888************9986 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 ?    2.6   0.1     0.076        76      28      44 ..      39      55 ..      24      59 .. 0.85
   2 !   18.7   0.1   9.2e-07   0.00092     126     206 ..     137     222 ..      76     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.076
                                      EEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnlldAi 44
                                       i G+ G+GKs l  ++
  gi|320100993|ref|YP_004176585.1| 39 GIAGESGCGKSTLAYSL 55
                                      599********998876 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 9.2e-07
                                       HHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEE CS
                                       xxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                             SMC_N 126 llesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfi 193
                                       +l+++gi+         +LSgG k+ v +a+ +A++     p+++ De   aLD    +++ +llk+ +k+    +i
  gi|320100993|ref|YP_004176585.1| 137 MLQMVGIDVRrlksyphELSGGMKQRVVIAMALALN----PPVVIADEPTTALDVVVQAQIMNLLKRLKKElgISII 209
                                       445555544455666669*************99996....59************************99999556778 PP

                                       EE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxx RF
                             SMC_N 194 vislreemlekad 206
                                        is++  ++++  
  gi|320100993|ref|YP_004176585.1| 210 LISHDLSLIAEIA 222
                                       8888877766653 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.077        76      36      59 ..      36      59 ..      30      71 .. 0.81
   2 !   16.0   0.3   6.2e-06    0.0062     107     160 ..     160     211 ..     136     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.077
                              TniB 36 pnlllvGdsnnGKtmivekFarlh 59
                                      ++l ++G+s +GK++++ +  rl 
  gi|320100993|ref|YP_004176585.1| 36 ESLGIAGESGCGKSTLAYSLIRLV 59
                                      57889**********987766655 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.2e-06
                              TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       +++ v+++  +l++ v+i DE   +l   +  q +++n+lk+L+ el i+i+l+
  gi|320100993|ref|YP_004176585.1| 160 KQRVVIAMALALNPPVVIADEPTTAL--DVVVQAQIMNLLKRLKKELGISIILI 211
                                       56677888889999********9999..7888999*****************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.2e-05     0.032      30      89 ..      32      92 ..      23     145 .. 0.76
   2 ?    1.9   0.0      0.15   1.4e+02     166     188 ..     191     213 ..     176     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava.tGkpwlg...pvapeqgkVlyvsaEdsedelrrR 89
                                      l +ge   +aG +g+GK+tla++l   v   Gk  +g   +   +  +Vl  s E+ + e+r++
  gi|320100993|ref|YP_004176585.1| 32 LNKGESLGIAGESGCGKSTLAYSLIRLVPpPGK-IAGgqiI--FKGKNVLEMSEEEFRREVRWK 92
                                      678888899***************998886555.4455433..477788877777777777765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.15
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       +++++ l+r+++++g+ ++l+ H
  gi|320100993|ref|YP_004176585.1| 191 AQIMNLLKRLKKELGISIILISH 213
                                       78999*****************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.7   0.00024      0.24       8     128 ..      38     211 ..      33     217 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee......................................erpevvfvt 46 
                                       l + GesG+GK+tl+  l +  +   k++                                       +        
  gi|320100993|ref|YP_004176585.1|  38 LGIAGESGCGKSTLAYSLIRLVPPPGKIAGgqiifkgknvlemseeefrrevrwkgismvfqgamnalN-------- 106
                                       5689***********999998877666666777774444444444444444444333333333333331........ PP

                            AAA_22  47 lpsstsskdllrellralglelka...........................................erlsseelle 80 
                                                                                                          ++++++  + 
  gi|320100993|ref|YP_004176585.1| 107 -----------------------PvytigdqiaevlmlhqgyskkealetagkmlqmvgidvrrlksYPHELSGGM- 159
                                       .......................12333333333333333333333333333333333333443322222222222. PP

                            AAA_22  81 aleqalrarav....ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                          q +  +++    ++++i DE    l+   ++++++ L++l +  + g+++iL+
  gi|320100993|ref|YP_004176585.1| 160 --KQRVVIAMAlalnPPVVIADEPTTaLDvvvQAQIMNLLKRLKK--ELGISIILI 211
                                       ..2222222223446777777777776666655777777777777..777777776 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 !   14.6   0.0     2e-05      0.02      13      49 ..      26      62 ..      23      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      dg +++++  ++  ++G+sG GKSTl  +++ l  p+
  gi|320100993|ref|YP_004176585.1| 26 DGVSFTLNKGESLGIAGESGCGKSTLAYSLIRLVPPP 62
                                      66778888555899************87777776665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.6e-05     0.026       3      37 ..      23      58 ..      21     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                                      HHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHH CS
                                      xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  3 rvlDal.fpivqGqrtlipgafgvGktvisqslskq 37
                                      +++D + f++ +G+ ++i g++g+Gk++++ sl++ 
  gi|320100993|ref|YP_004176585.1| 23 KAVDGVsFTLNKGESLGIAGESGCGKSTLAYSLIRL 58
                                      566754399*********************999986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00016      0.16       3      56 ..      40     104 ..      38     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                       EESSTTSSHHHHHHHHHHHH..............THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHT CS
                               AAA   3 lyGppGtGKTllakavakel..............gvefleisgsellskyvgesekkirelfkeakek 56 
                                       + G  G+GK++la ++++ +              g ++le+s  e++    + + k i+++f+ a + 
  gi|320100993|ref|YP_004176585.1|  40 IAGESGCGKSTLAYSLIRLVpppgkiaggqiifkGKNVLEMSEEEFR---REVRWKGISMVFQGAMNA 104
                                       5799***************7666655555555556889999999999...566777777777776443 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   8.2e-05     0.081       3      21 ..      40      58 ..      38      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLaka 21
                                      + G+sg+GKStla++L++ 
  gi|320100993|ref|YP_004176585.1| 40 IAGESGCGKSTLAYSLIRL 58
                                      68*************9985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.19      88     119 ..      23      55 ..       7      65 .. 0.79
   2 ?   -1.8   0.0       2.6   2.6e+03      56     102 ..     185     226 ..     160     231 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       ++++ ++  l++ +   ++G+SG GKStL  +l
  gi|320100993|ref|YP_004176585.1|  23 KAVDGVSFTLNKgESLGIAGESGCGKSTLAYSL 55 
                                       56677777787768889************8776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                                       GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEE CS
                       RsgA_GTPase  56 iDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkts 102
                                       +D++ +++ ++ lk   ++lg++++l+s +      +l ++++dk++
  gi|320100993|ref|YP_004176585.1| 185 LDVVVQAQIMNLLKRLKKELGISIILISHD-----LSLIAEIADKIA 226
                                       566666665555556666778888777666.....344444555555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.008         8       8      45 ..      24      61 ..      20      98 .. 0.74
   2 ?    4.9   0.1     0.015        14      90     137 ..     161     213 ..     101     226 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.008
                                      HHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  8 dLDkltsGlqkgdliiiAarpsmGktalalniaenaav 45
                                       +D +   l+kg+ + iA+ +++Gk++la ++++ +  
  gi|320100993|ref|YP_004176585.1| 24 AVDGVSFTLNKGESLGIAGESGCGKSTLAYSLIRLVPP 61
                                      56777888999999****************99987664 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHSEEEEEEXSSX.....CHHHHHHHHHHHHHHTTEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  90 eklteaieelseaklfiddtpal.....tvseirskarrlkkekglgliviDy 137
                                       +++  a++   + +++i d+p++       ++i + ++rlkke g+++i+i +
  gi|320100993|ref|YP_004176585.1| 161 QRVVIAMALALNPPVVIADEPTTaldvvVQAQIMNLLKRLKKELGISIILISH 213
                                       45555555555666666666654222222345566666676666677666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.18      25      48 ..      36      59 ..      25     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                            AAA_16 25 elvllsGesGvGKsslvrellral 48
                                      e++ + GesG+GKs+l+ +l r +
  gi|320100993|ref|YP_004176585.1| 36 ESLGIAGESGCGKSTLAYSLIRLV 59
                                      78889***********98877544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00081       0.8      22      49 ..      35      62 ..      15      71 .. 0.82
   2 ?   -0.6   0.0      0.71     7e+02     175     199 ..     145     169 ..     133     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00081
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllppl 49
                                      g +l ++G +G+GK+ la  l  l+pp 
  gi|320100993|ref|YP_004176585.1| 35 GESLGIAGESGCGKSTLAYSLIRLVPPP 62
                                      5677899******************985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.71
                      Mg_chelatase 175 ekeierYlsklsgplldRidlqvev 199
                                        ++ ++Y + lsg +  R+ + +++
  gi|320100993|ref|YP_004176585.1| 145 VRRLKSYPHELSGGMKQRVVIAMAL 169
                                       567899************9988765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.23       3      22 ..      39      58 ..      37     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                               PRK  3 gvagsSGaGkttvarkleki 22
                                      g+ag+SG+Gk+t+a  l  +
  gi|320100993|ref|YP_004176585.1| 39 GIAGESGCGKSTLAYSLIRL 58
                                      9***********99877655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00036      0.35       5      23 ..      40      58 ..      37      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                                      EEC-TTTCHHHHHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqklala 23
                                      + Ge+G+GK+tL+ +l+++
  gi|320100993|ref|YP_004176585.1| 40 IAGESGCGKSTLAYSLIRL 58
                                      78***********999875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0006       0.6       4      22 ..      37      55 ..      34      84 .. 0.86
   2 ?   -1.4   0.1       1.6   1.6e+03     108     130 ..     190     213 ..     187     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                      ++ i G+sg GK+tla++l
  gi|320100993|ref|YP_004176585.1| 37 SLGIAGESGCGKSTLAYSL 55
                                      6789************998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                            AAA_24 108 aeefrrllkklq.elrknvifiah 130
                                       ++++++llk+l+ el+  +i+i+h
  gi|320100993|ref|YP_004176585.1| 190 QAQIMNLLKRLKkELGISIILISH 213
                                       56666777775414555*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2232.58
//
Query:       gi|320100994|ref|YP_004176586.1|  [L=350]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-19   71.2   0.0    2.5e-19   70.3   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 !   70.3   0.0   1.4e-23   2.5e-19       3     166 ..      43     210 ..      42     211 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.4e-23
                                       EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklav 75 
                                       +t  C++rC+fC++     +++++ ++ + +  i++ v+e   ++ g v++++ ++g++l yp +vel+++l+ +  
  gi|320100994|ref|YP_004176586.1|  43 PTTLCPQRCIFCSVDAGisSSNRWAEYLVEPGLIVKGVEETVnVKSGgVEVLLDSMGDVLTYPWLVELVRELKSIP- 118
                                       5788***********99**************************99999***************************7. PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHH.TTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklre.agikrvvdriv 150
                                         +++++et g+l++   ++rl ++g+drv+l+++ +++ek   + + r +++++v+++ e++ +  +i+   ++ +
  gi|320100994|ref|YP_004176586.1| 119 GVYSVALETHGLLLSTNLIDRLNDAGLDRVNLSIDVTSNEKAYYIYGtRYYDVSRVMRLAEYIVReTDID-LHVTPL 194
                                       ****************************************8888888899***********986515566.9***** PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                        lpG nde+++ ++e+
  gi|320100994|ref|YP_004176586.1| 195 WLPGLNDEDVVTIVEW 210
                                       **********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2718.68
//
Query:       gi|320100995|ref|YP_004176587.1|  [L=644]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-25   87.9  15.6    6.6e-25   87.9  15.6    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.065   13.3   0.1       0.15   12.1   0.1    1.6  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2      0.49   4.4e+03     159     172 ..      37      47 ..      24      58 .. 0.49
   2 !   87.9  15.6   7.3e-29   6.6e-25       1     184 [.     447     642 ..     447     643 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.49
                      BPD_transp_1 159 lalviavlllnlva 172
                                       + +++++l+   v+
  gi|320100995|ref|YP_004176587.1|  37 ALILLLFLV---VV 47 
                                       222222222...22 PP

  == domain 2  score: 87.9 bits;  conditional E-value: 7.3e-29
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrli 71 
                                       g+++Gi+++ ++++++d++++++i++l  +P++ l+i++  ++        +++l+   l+++il+++s+a++++++
  gi|320100995|ref|YP_004176587.1| 447 GVIAGIVSG-YYGGWIDEVIQRVIDILNNIPFLPLMIIVGTAAqktlppGSQKSLYIILLYLAILIIFSWAGLAIVV 522
                                       899******.************************9999998889****6666666666666**************** PP

                      BPD_transp_1  72 rraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgy 148
                                       r++ l++ ++ ++eaara+Gas  +i++++++P+++ +++++l++++++++   + l+ lg  +G   +++ a l+ 
  gi|320100995|ref|YP_004176587.1| 523 RSMTLSIKEEPYIEAARAMGASNSRIIFYHIFPQVMMYAVATLVYNVPSAILTEAGLSVLGLRHG--WPTWGAVLSE 597
                                       *************************************************************8875..4444444444 PP

                      BPD_transp_1 149 dyseis.........nggvlalviavlllnlvadilqrlldprvr 184
                                         ++++           + + l i  l ++l+  ++ ++++pr+r
  gi|320100995|ref|YP_004176587.1| 598 ARAAGIagyaawwwiLPPGILLSITSLTFVLLGLAVEKIVEPRLR 642
                                       444444555557777****************************98 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.7e-05      0.15      20      83 ..     261     325 ..     258     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                      Baculo_PEP_C  20 nvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt.rldtlltnLtdalnalqdtl 83 
                                       + L+ ir+++v+i+a ++++ + +   +++ +++++ +++++d+  +++l ++L++  ++l+++ 
  gi|320100995|ref|YP_004176587.1| 261 PKLEEIRSKLVNISAYITEDPAGLRAIIGQAESNITYAISNIDKiSFSDLYSTLDAVSKTLSTAY 325
                                       5699***************************************9988888888888888877332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 4838.20
//
Query:       gi|320100996|ref|YP_004176588.1|  [L=368]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  103.5  16.4    1.1e-29  103.5  16.4    2.6  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.4     0.013   2.3e+02      51      79 ..      19      47 ..       7      54 .. 0.79
   2 !  103.5  16.4   6.2e-34   1.1e-29       7     184 ..     157     366 ..     151     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.013
                      BPD_transp_1 51 hlilpviillllsaapyvrlirraalrsl 79
                                      + ++ +ii+++l + +y+  i++a++++l
  gi|320100996|ref|YP_004176588.1| 19 YVAIIIIIAAILELSGYASQIYEAMVNEL 47
                                      55666899999999999999999998876 PP

  == domain 2  score: 103.5 bits;  conditional E-value: 6.2e-34
                      BPD_transp_1   7 laa......lnrnkkldkllrpliivllslPsfvlaillvlvf...........................vilsilg 50 
                                        +a      ++++  +d+l+  +  v++++P  +la+l++ vf                            + sil+
  gi|320100996|ref|YP_004176588.1| 157 ALAlapriaYRHGTLVDRLVVAYAAVTSAVPLWWLAMLFIRVFgyqlgwfptslrgvttplnqfwanpgqNFVSILW 233
                                       3334477779***********************************************************87777777 PP

                      BPD_transp_1  51 hlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavl 127
                                       +   p+++ +++ ++++ + +r+++lr++ +d+v +a+a+G++++ i rk++++ +l pi+t +ila++g lgg ++
  gi|320100996|ref|YP_004176588.1| 234 YITPPLVVFTIIALGGWLYGVRAMVLRIVREDYVMVAKAKGLPEKDITRKYIMRPSLAPILTNVILALAGTLGGMII 310
                                       77777************************************************************************ PP

                      BPD_transp_1 128 leflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       +e ++ wpG+gtl   ai   d+  i  ++++++v ++l+  +++ il+ l+dprvr
  gi|320100996|ref|YP_004176588.1| 311 TESVFDWPGMGTLYYAAIVTGDTETIV-ALFVVYVGVYLIARFILEILYVLVDPRVR 366
                                       ***************************.****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2884.54
//
Query:       gi|320100997|ref|YP_004176589.1|  [L=983]
Description: solute-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   50.9   7.0    2.8e-10   39.7   0.1    2.6  2  SBP_bac_5       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.012   15.4   1.8      0.024   14.5   1.8    1.4  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
      0.021   14.1   1.1      0.037   13.4   1.1    1.3  1  CorA            CorA-like Mg2+ transporter protein
      0.037   13.8   0.1       0.16   11.7   0.1    2.1  1  HTH_psq         helix-turn-helix, Psq domain
       0.05   13.9   0.8       0.12   12.6   0.8    1.7  1  DUF4064         Protein of unknown function (DUF4064)
       0.27   11.3   6.2       0.79    9.8   1.3    2.7  2  DUF1664         Protein of unknown function (DUF1664)
       0.61   10.3   3.9        1.8    8.9   0.2    2.5  2  WXG100          Proteins of 100 residues with WXG
       0.65    7.9   4.9       0.94    7.3   4.9    1.2  1  Prominin        Prominin
       0.87    9.6  14.8        2.5    8.2  14.8    1.8  1  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
        1.6    8.1   8.6       0.47    9.8   0.5    2.8  3  DUF4618         Domain of unknown function (DUF4618)
        1.6    9.2  10.0        0.1   13.0   0.4    3.3  3  NPV_P10         Nucleopolyhedrovirus P10 protein
        3.9    7.7   5.2        2.6    8.2   2.2    2.1  2  Fib_alpha       Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.1   1.9e-13   2.8e-10     152     365 ..      36     307 ..      31     319 .. 0.79
   2 !   12.3   3.0   4.1e-05     0.061      27     143 ..     518     718 ..     517     737 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.9e-13
                                       SSEEEEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT............. CS
                         SBP_bac_5 152 ldriefkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtk............. 214
                                       +d+i++    + +   +al sG id +  +++p++++ql+ ++g+++  +s+++g   l++N +             
  gi|320100997|ref|YP_004176589.1|  36 VDKITVVRK-TIEEVPDALTSGAIDAYmFSLKPAQAAQLQGKQGITL--YSAPAGLIELTLNPApvyvavlngsvsi 109
                                       555555443.5666668889999986668999999999999999999..778888888899999999999999999* PP

                                       ....................................STGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTT CS
                         SBP_bac_5 215 ....................................kppfddkrvRqAlsyAiDreeivkavlegyatpansllpps 255
                                                                            +p++  ++R Al+y iDr + + ++++g a+p++++l++ 
  gi|320100997|ref|YP_004176589.1| 110 teaasklgvpavaitniyttsegktvvelgaypgkgVNPLAFREIRFALNYLIDRVAAASTIMRGFAVPMYTFLSQY 186
                                       **********************************9999*************************************99 PP

                                       STTCCSCHCCCSHH...SHHHHHHHH....HHHTT-BCSSTSCEETC....EEEEEEEEETTSHHHH.HHHHHHHHH CS
                         SBP_bac_5 256 spgadeeykpayka...ydpekAkkl....LkeaGykdgdggglrek....klkltlllasgspaek.aiaeliqqq 320
                                        p +  + +   k+   y+p    +     L + G  + +g     k    ++++tl +   +++e+ +i  ++ ++
  gi|320100997|ref|YP_004176589.1| 187 DPDYAVIADIIAKYeftYNPGYVDQVitdvLSKVGAVKIGG-----KwtyeGQPITLKFIIRQEDERrDIGYMFSSE 258
                                       99998777776555778776666555000044555444444.....3555555555555545444444********* PP

                                       HHHTTEEEEEEEECHH....HHHHHHHHCTTESEEEEEEECTTSTTHHH CS
                         SBP_bac_5 321 lkkiGikvevktvdwa....atylervkdgdfdmillgwgadypdpdnf 365
                                       lkk+G++v+   + ++      y ++  + ++ ++  gwg + +d +++
  gi|320100997|ref|YP_004176589.1| 259 LKKLGFEVNEMEMTFSqainIIYGTDPAAFEWHIYTAGWGKGGIDRYDS 307
                                       *************77669997777889*************999997766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.1e-05
                                       T-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC........................................ CS
                         SBP_bac_5  27 gvkFsDGtpltAeDvvfsferlldpdtasgyasllee........................................ 63 
                                       g+kF++G  +t +Dvv  + +l d  + ++y+sl                                           
  gi|320100997|ref|YP_004176589.1| 518 GAKFHNGITITWADVVGYLAYLFDLIYDPNYSSLEPRlsssskpwadtvkgfefdfnnkkvtvyidywhfdenyias 594
                                       89***************988888888888887776557766777777777777777777777777777777777777 PP

                                       ..TCTEEEEEEEETTEEEEEESSETTTTTTHCHHHHHHHGC.................................... CS
                         SBP_bac_5  64 ..dqdikkveavddytvrftlkkpnalfltllaavpasiak.................................... 102
                                         + ++++   +   t+++ l +   + + l ++  +  ++                                    
  gi|320100997|ref|YP_004176589.1| 595 waSFSPVNPIEIHAATFELALDRRSETKYVLYQKKGYEWFSlvwpshvakvketlqsyknnnnvlskvnkyamgllk 671
                                       776666666667777777777777664444444444444447777777789999999******************** PP

                                       ......CHTCTCTTTTTGTTTSE-BSSSEEEEEEET.TTEEEEEE-TT CS
                         SBP_bac_5 103 ......kaaekeddkdkdtnekpvgtGPYklkefkp.gqkivlernpd 143
                                             + +++ ++  +++n + ++ GP++l++ +  +q ++l+++ d
  gi|320100997|ref|YP_004176589.1| 672 mdewnaRIDADINW-INTYNLAWISYGPFMLTKLDTqNQVLELKAFRD 718
                                       **997544444555.79999999**********777356777888766 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.8   1.6e-05     0.024      75     171 ..     853     946 ..     840     959 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                                       CCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..----- CS
                    Apolipoprotein  75 lapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveer 151
                                       la+  +   ++++  + el+eq av  + lr++l+++++ +      +v++ ++ ++  ++++++  ++ a  + ++
  gi|320100997|ref|YP_004176589.1| 853 LANVRSSAIAQINTIVSELKEQKAVDLDTLRDQLASALSGVAGV---LVDQYVSLIGTAMDNMNRLSQTTASTINSQ 926
                                       55555555567788888888888888888888888886666554...458888888888888888888888888888 PP

                                       SSSHHHHHHHTS-TTSHHHH CS
                    Apolipoprotein 152 lssrveelrekleeqaeelr 171
                                       +ss+++++r+ +++  e++ 
  gi|320100997|ref|YP_004176589.1| 927 VSSQIQQIRTDMAALSEKVD 946
                                       99999888888887444443 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.1   2.5e-05     0.037      71     179 ..     844     957 ..     824     972 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                              CorA  71 lsillgdnflitvrreplealdevikrlk.....deggkpkspgellyrlldeivdrlfellekleeeldeledele 142
                                       lsi    ++l  vr++ +  +++++++lk     d +  +++ ++ l  +   +vd++  l+ +  +++++l+++  
  gi|320100997|ref|YP_004176589.1| 844 LSIQNVSDVLANVRSSAIAQINTIVSELKeqkavDLDTLRDQLASALSGVAGVLVDQYVSLIGTAMDNMNRLSQTTA 920
                                       566666677888999999999999999999999999999999999999****************************9 PP

                              CorA 143 dstkkeilrelaqlrrrlvklrralapnrevlkrlla 179
                                       + ++ +  +++ q+r++++ l + + +++++l++l +
  gi|320100997|ref|YP_004176589.1| 921 STINSQVSSQIQQIRTDMAALSEKVDATQNTLNSLQT 957
                                       9999999999999****99999988888888877654 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 ?   11.7   0.1   0.00011      0.16      11      30 ..     101     120 ..     100     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                           HTH_psq  11 avvnGkmSirkAArkYgiPr 30 
                                       av+nG++Si +AA+k g+P+
  gi|320100997|ref|YP_004176589.1| 101 AVLNGSVSITEAASKLGVPA 120
                                       89*****************8 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   8.1e-05      0.12      40      80 ..     922     978 ..     888     982 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-05
                           DUF4064  40 tee................qalsgedasavleflstllivlgvialiaivlgivgal 80 
                                       t++                 +  +++++++l +l+t++++ + + +iai+l+iv++l
  gi|320100997|ref|YP_004176589.1| 922 TINsqvssqiqqirtdmaaLSEKVDATQNTLNSLQTYIFANIALTIIAIILSIVALL 978
                                       44444455555555667665556788999*************************987 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.061        90      49      85 ..     845     881 ..     835     899 .. 0.81
   2 ?    9.8   1.3   0.00053      0.79      67     121 ..     901     956 ..     879     958 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.061
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskei 85 
                                       ++++vs+ la+++    ++i+++ ++l+eqk++  ++
  gi|320100997|ref|YP_004176589.1| 845 SIQNVSDVLANVRSSAIAQINTIVSELKEQKAVDLDT 881
                                       5899*************************99986544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00053
                           DUF1664  67 ridrvdkkldeqkeiskeikeevt.evredlseigedvesvkeaveglesklerie 121
                                        +  +++ +d+++++s+ +++ ++ +v++++++i++d+ +++e v   +++l++++
  gi|320100997|ref|YP_004176589.1| 901 YVSLIGTAMDNMNRLSQTTASTINsQVSSQIQQIRTDMAALSEKVDATQNTLNSLQ 956
                                       56677889999********999963799*****************99999999986 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 ?    8.9   0.2    0.0012       1.8      11      76 ..     859     925 ..     854     929 .. 0.94
   2 ?    2.2   0.6      0.14   2.1e+02      51      76 ..     929     954 ..     925     962 .. 0.45

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHH.HHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  11 qaaarfqkqaeeledelq.rlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkq 76 
                                       +a+a+++++ +el+++ + +l+   d+l+s+ sG a++  ++    +  a+++++++ +++++++++
  gi|320100997|ref|YP_004176589.1| 859 SAIAQINTIVSELKEQKAvDLDTLRDQLASALSGVAGVLVDQYVSLIGTAMDNMNRLSQTTASTINS 925
                                       6889999999***999999*******************************************99986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  51 aefeewkqaaqklvdaLeeisealkq 76 
                                       +++++++  ++ l ++ + ++++l++
  gi|320100997|ref|YP_004176589.1| 929 SQIQQIRTDMAALSEKVDATQNTLNS 954
                                       33444444444444444444444433 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.9   0.00063      0.94     298     423 ..     863     960 ..     831     978 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00063
                          Prominin 298 kilssleiekldtskcldql.pnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgre 373
                                       +i++ ++  k +   +ld+l +++ + l+++ +vl +++ s++  +++++n ++++ +                   
  gi|320100997|ref|YP_004176589.1| 863 QINTIVSELKEQKAVDLDTLrDQLASALSGVAGVLVDQYVSLIGTAMDNMNRLSQTTA------------------- 920
                                       2222222211122223344433344455555555555555555555555555554444................... PP

                          Prominin 374 qikklakkiprealdavisdlenterssktfddvvekyekyrwliglivc 423
                                                 +++ ++v+s+++++ +++ + +++v+  +++ + + +++ 
  gi|320100997|ref|YP_004176589.1| 921 ----------STINSQVSSQIQQIRTDMAALSEKVDATQNTLNSLQTYIF 960
                                       ..........4444444444444444444444444444444444444433 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 ?    8.2  14.8    0.0017       2.5      17     115 ..     848     959 ..     833     974 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                      Baculo_PEP_C  17 dLtnvLnairlqn.vqilaqlatlldaietqLnalsedlksllaeldt............rldtlltnL.tdalnal 79 
                                       ++++vL+ +r+   +qi + +++l+++ +  L++l ++l s+l+ ++             +  +++++L +++  ++
  gi|320100997|ref|YP_004176589.1| 848 NVSDVLANVRSSAiAQINTIVSELKEQKAVDLDTLRDQLASALSGVAGvlvdqyvsligtA-MDNMNRLsQTTASTI 923
                                       5678899996543145555555566666667999999999999999998888777766633.333444413455677 PP

                      Baculo_PEP_C  80 qdtlrneLtnlnsiltnLlssvtNinstLnnllqal 115
                                       + +++++++ + ++++ L  +v  +++tLn+l + +
  gi|320100997|ref|YP_004176589.1| 924 NSQVSSQIQQIRTDMAALSEKVDATQNTLNSLQTYI 959
                                       8******************************97765 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         1   1.5e+03     137     228 ..     245     278 ..     239     282 .. 0.52
   2 ?   -2.0   0.1       1.3   1.9e+03       5      23 ..     646     664 ..     642     676 .. 0.81
   3 ?    9.8   0.5   0.00032      0.47      73     110 ..     921     958 ..     901     963 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1
                           DUF4618 137 qdeldeleelikevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLk 213
                                       +de  ++                                                             +  e+++L 
  gi|320100997|ref|YP_004176589.1| 245 EDERRDIG----------------------------------------------------------YMFSSELKKLG 263
                                       44444444..........................................................44555556666 PP

                           DUF4618 214 aeveqLqaqaeepre 228
                                        ev+++++   +  +
  gi|320100997|ref|YP_004176589.1| 264 FEVNEMEMTFSQAIN 278
                                       666666555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                           DUF4618   5 kksleelkkheaeLtklnk 23 
                                       k++l+ +k++++ L+k nk
  gi|320100997|ref|YP_004176589.1| 646 KETLQSYKNNNNVLSKVNK 664
                                       7899999999999999987 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00032
                           DUF4618  73 qeweekeekklekLeqqleqlnakvqklqeelnvLstY 110
                                        ++++++++++++++ ++ +l +kv  +q+ ln L+tY
  gi|320100997|ref|YP_004176589.1| 921 STINSQVSSQIQQIRTDMAALSEKVDATQNTLNSLQTY 958
                                       467889999***************************** PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.6   3.8e+03      22      48 ..      21      50 ..      12      57 .. 0.53
   2 ?   -0.1   0.6       0.9   1.4e+03       7      26 ..     854     874 ..     830     897 .. 0.58
   3 ?   13.0   0.4     7e-05       0.1       7      32 ..     932     957 ..     926     964 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                           NPV_P10 22 alqqqvddvqenlpdvteln...ekLdaqs 48
                                       +q+ v++ ++  p v++++   + +++ +
  gi|320100997|ref|YP_004176589.1| 21 PIQTTVAQTTQPGPAVDKITvvrKTIEEVP 50
                                      566666666666555554431113344444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.9
                           NPV_P10   7 lvIr.adikavddkVdalqqq 26 
                                         +r ++i+++++ V+ l++q
  gi|320100997|ref|YP_004176589.1| 854 ANVRsSAIAQINTIVSELKEQ 874
                                       333312444444444444332 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 7e-05
                           NPV_P10   7 lvIradikavddkVdalqqqvddvqe 32 
                                        +Ir+d +a+++kVda q+ ++++q+
  gi|320100997|ref|YP_004176589.1| 932 QQIRTDMAALSEKVDATQNTLNSLQT 957
                                       79*******************99987 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.2   1.8e+03      37      62 ..     642     667 ..     639     687 .. 0.66
   2 ?    8.2   2.2    0.0017       2.6      22     111 ..     864     959 ..     851     968 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                                       HCCCCCCCCCCCCHHHHHHHHHHHHH CS
                         Fib_alpha  37 lekleneleeisnstkeaeelvkeik 62 
                                       ++k++++l++++n+++  +++ k+ +
  gi|320100997|ref|YP_004176589.1| 642 VAKVKETLQSYKNNNNVLSKVNKYAM 667
                                       56666677777776666666655554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHH..HHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHCCCH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstke..aeelvkeikdslrekqkskkdn....dnvikksskeleeeilr 92 
                                       +++++++ +++   dl++l+++l+++ +      ++++v+ i + + + ++ ++ +    ++ +++  ++++++++ 
  gi|320100997|ref|YP_004176589.1| 864 INTIVSELKEQKAVDLDTLRDQLASALSGVAGvlVDQYVSLIGTAMDNMNRLSQTTastiNSQVSSQIQQIRTDMAA 940
                                       56666666777777788888888777665543225777776666666555555543322366666666778889999 PP

                                       HHHHHHCCHHHHHHHHHHH CS
                         Fib_alpha  93 lketidaqesnirvLqnvl 111
                                       l e++da+ ++++ Lq+ +
  gi|320100997|ref|YP_004176589.1| 941 LSEKVDATQNTLNSLQTYI 959
                                       ***************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (983 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1252  (0.069831); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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: 0.85u 0.30s 00:00:01.14 Elapsed: 00:00:00.43
# Mc/sec: 6819.39
//
Query:       gi|320100998|ref|YP_004176590.1|  [L=162]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.047   13.9   0.2      0.064   13.4   0.2    1.2  1  Adeno_E3    Adenovirus E3 protein
       0.42    9.6   6.5       0.19   10.7   3.3    1.7  2  XK-related  XK-related protein


Domain annotation for each model (and alignments):
>> Adeno_E3  Adenovirus E3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   7.2e-06     0.064      28     109 ..      73     153 ..      53     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-06
                          Adeno_E3  28 tktlpliqnttnstlplpetnkletnlkqrfsrdllesntttktGGelrGlptedpwvvvGlvtlGlvaGGlvlilc 104
                                       + tl ++   +++++ +   + ++  l++ f   ++  ntt  t   l Gl++ +p+    +++l     G vl+  
  gi|320100998|ref|YP_004176590.1|  73 SSTLMVFDRIVEYSVTVKPGEAVNLTLNHPFYSIMSMENTT-LTSITLTGLRAVKPFMALSILSLVTFIVGTVLMAT 148
                                       44555555555555555556666777888887666667777.899********************99999999**** PP

                          Adeno_E3 105 ylylp 109
                                       y+yl 
  gi|320100998|ref|YP_004176590.1| 149 YIYLR 153
                                       ***85 PP

>> XK-related  XK-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1     0.062   5.6e+02     161     179 ..      15      33 ..       5      49 .. 0.68
   2 ?   10.7   3.3   2.2e-05      0.19     285     334 ..     103     149 ..      98     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.062
                        XK-related 161 avsavlSlvslawalvsyq 179
                                       ++s+ lSlvs++   ++y+
  gi|320100998|ref|YP_004176590.1|  15 VASIPLSLVSMTTHYIEYS 33 
                                       4555566666666555554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.2e-05
                        XK-related 285 yyllmllenillvllwyylkkdslesdvlalvllvvlvsfllGivfmllY 334
                                       +y++m +en++l+++ ++  +    ++++al  ++ lv+f++G v+m  Y
  gi|320100998|ref|YP_004176590.1| 103 FYSIMSMENTTLTSITLTGLRAV--KPFMAL-SILSLVTFIVGTVLMATY 149
                                       8**************75555554..666666.7779************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1183.99
//
Query:       gi|320100999|ref|YP_004176591.1|  [L=80]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   12.9   0.4       0.14   12.2   0.4    1.4  1  PspB      Phage shock protein B


Domain annotation for each model (and alignments):
>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   7.8e-06      0.14       8      25 ..      10      27 ..       2      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-06
                              PspB  8 pliifvlfVapiWLiLHY 25
                                      ++ +f  f++  WL+LH 
  gi|320100999|ref|YP_004176591.1| 10 MVFVFASFIMRNWLWLHV 27
                                      6789*************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 589.46
//
Query:       gi|320101000|ref|YP_004176592.1|  [L=334]
Description: NADH dehydrogenase subunit H [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-48  165.3  20.3    2.5e-48  164.9  20.3    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 !  164.9  20.3   1.4e-52   2.5e-48       8     297 ..      20     324 ..      11     327 .. 0.87

  Alignments for each domain:
  == domain 1  score: 164.9 bits;  conditional E-value: 1.4e-52
                                       HHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHC.CS-----TTS-HHHHHHHHHHHHHHHHCTT CS
                            NADHdh   8 vvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKll.lKediipkkadkllfllapvlalilallaf 83 
                                       ++++++ +++++l Rk++Ar+q+R+GP +vGp+G+lqp++D+ Kll +Ke + +k + + +  ++ ++ +++++ a+
  gi|320101000|ref|YP_004176592.1|  20 LFTVILSLFTQYLVRKISARFQRRMGPSYVGPYGVLQPFMDFWKLLrVKELVKSKYSMQRVAEISLLIGIACITGAI 96 
                                       34455555**************************************89***************************** PP

                                       TTS-SSSSSS--TTHHHHHHHHHH.HCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..H-SS CS
                            NADHdh  84 aviPfgevladlnvglllilalss.lgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvll..agsl 157
                                       +++P+g   +   ++ l++++++s + v++++la++++  +Y+ lG  R +++++  E ++++ l++++++  ags 
  gi|320101000|ref|YP_004176592.1|  97 ILLPIGLFNVRSPLDYLVFFYMASvMPVLALVLASLSTPGPYTSLGVSRLLSILTISEPVYFTGLFVPCFIatAGSP 173
                                       ******433333556666665555167899****************************9998877776665337888 PP

                                       -HHHHHHCCCTT...-C....CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHH CS
                            NADHdh 158 slseiveaqeei...wf....illqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyan 227
                                        l +i +a +++   w     +++ ll+++++++al  ++   PF++peae+EL+aGf tE+sg  +al+ l + + 
  gi|320101000|ref|YP_004176592.1| 174 MLLSIGSASTRVmelWShpvtAVILLLSLLALIVALQSKAMYPPFNIPEAEQELIAGFETEFSGPLLALVSLLHDMD 250
                                       88888776665567765677744459999************************************************ PP

                                       HHHHHHHHHHHCT.SS-HCCS.....HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                            NADHdh 228 mvlvsalavllFlgGwllpfs.....gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                       +++  + +v++ lgG  +pf+     g++++++K+++ll++ + i++++ R+R++q++    k+    ala+ ll
  gi|320101000|ref|YP_004176592.1| 251 LTVSLLAVVYIVLGGP-APFPhfslgGVVMVAFKYVALLIVSVAIKNIFGRYRLEQALIQLLKYGAAPALAATLL 324
                                       **************96.577778999*******************************999999988888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2090.52
//
Query:       gi|320101001|ref|YP_004176593.1|  [L=118]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 862.78
//
Query:       gi|320101002|ref|YP_004176594.1|  [L=532]
Description: membrane bound hydrogenase subunit MbhH [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-49  168.4  23.3      2e-49  168.4  23.3    2.1  3  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
       0.66   10.2  11.9        5.8    7.2   0.0    5.3  5  DUF3493          Low psii accumulation1 / Rep27


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.4      0.33   2.9e+03      38      54 ..      44      60 ..      10      62 .. 0.53
   2 !  168.4  23.3   2.3e-53     2e-49       3     283 ..     137     436 ..     135     448 .. 0.85
   3 ?   -2.4   0.1      0.24   2.2e+03      37      93 ..     474     491 ..     453     499 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.33
                   Proton_antipo_M 38 lflltllgsliLLlgil 54
                                        +l +++s+i+L+++ 
  gi|320101002|ref|YP_004176594.1| 44 GSMLAAFSSVIILIAVY 60
                                      23445566666666655 PP

  == domain 2  score: 168.4 bits;  conditional E-value: 2.3e-53
                   Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal......e 73 
                                       d + l++ lE+ +++ y L+ + k +++++eA+ k++l+++++  + + ++++ly   g+l++  ls +        
  gi|320101002|ref|YP_004176594.1| 137 DAFNLFVMLEVLSISAYGLVSYHKGRAEAVEAAAKYALIGAVATNMYFGALVILYVTHGSLNMGLLSAISqyyrfaG 213
                                       567899****************************************9999*************99999986666544 PP

                   Proton_antipo_M  74 lglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.......vss 143
                                        g+++ +l ++++ l   +  Ksa++p h+Wlpda+ eaPtpvsa l++++v++gv++++r++  l+        + 
  gi|320101002|ref|YP_004176594.1| 214 EGVKYAGLIVVAFSLW-VFTYKSALFPNHFWLPDAHPEAPTPVSAALSGMVVNVGVYAVMRFMYTLFgpssylaGYR 289
                                       4445555444444444.3789*****************************************998877554444566 PP

                   Proton_antipo_M 144 neisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav........atqygveaaiihllthalfk 212
                                       +++   l+il+++s ++g+l+ ++q+d+KrllAyS+ish+G++ i+l++        a +++v++a++h+++h+l k
  gi|320101002|ref|YP_004176594.1| 290 EAVLVALFILGSVSGVVGALLMMSQRDVKRLLAYSTISHIGIIYIGLSAgfltgtgeAVKIAVAGAVTHIVSHGLAK 366
                                       7888999***************************************998666532222357899************* PP

                   Proton_antipo_M 213 allFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslill 283
                                       ++lF+++g +  +   +rd+++++g     P+ + +++ ++lslaGl p++gF+sk+li ++    + il 
  gi|320101002|ref|YP_004176594.1| 367 SMLFMASGVF-IDAAGSRDMDEMRGVGRLYPLASFAWVAGFLSLAGLLPFLGFYSKLLIYYGYAYSGFILG 436
                                       *******777.5666******************************************99876655554443 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.24
                   Proton_antipo_M  37 klflltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgll 93 
                                                                                 + ++++++ll++g+l
  gi|320101002|ref|YP_004176594.1| 474 VEW---------------------------------------MLFTIAMVLLVLGAL 491
                                       333.......................................333444444444444 PP

>> DUF3493  Low psii accumulation1 / Rep27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.037   3.4e+02      32      75 ..      17      60 ..      14      63 .. 0.75
   2 ?    1.0   0.0     0.053   4.8e+02      22      43 ..      80     101 ..      78     115 .. 0.84
   3 ?    7.2   0.0   0.00064       5.8      50      76 ..     250     277 ..     228     278 .. 0.86
   4 ?    1.2   0.1     0.045   4.1e+02      21      40 ..     295     314 ..     287     320 .. 0.84
   5 ?    1.0   1.4     0.056     5e+02      19      42 ..     421     444 ..     414     454 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.037
                           DUF3493 32 iGalifllrllaaragaesapeleealenlaiqvgavalfvfLl 75
                                      +++++f++ l+++++g+++a+ l     ++   +  v+++++++
  gi|320101002|ref|YP_004176594.1| 17 LALIVFVIPLIEKLTGSRRATYLLALTGSMLAAFSSVIILIAVY 60
                                      78899999999999999999888777777766666666666655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.053
                           DUF3493  22 lYlafaaSaliGalifllrlla 43 
                                       +Y + +  aliGa+++l+ l+ 
  gi|320101002|ref|YP_004176594.1|  80 VYEVDGLNALIGAYTALTMLAV 101
                                       56777899********998875 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.00064
                           DUF3493  50 sa.peleealenlaiqvgavalfvfLlr 76 
                                       +a ++++ al+++ ++vg+ a++ f++ 
  gi|320101002|ref|YP_004176594.1| 250 EApTPVSAALSGMVVNVGVYAVMRFMYT 277
                                       4447899******************985 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.045
                           DUF3493  21 flYlafaaSaliGalifllr 40 
                                       +l++   +S+++Gal ++++
  gi|320101002|ref|YP_004176594.1| 295 ALFILGSVSGVVGALLMMSQ 314
                                       57888899*******99887 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.056
                           DUF3493  19 RlflYlafaaSaliGalifllrll 42 
                                       +l++Y + a S++i + i+++ + 
  gi|320101002|ref|YP_004176594.1| 421 KLLIYYGYAYSGFILGGIMIIVIS 444
                                       6899**********6666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); 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:                         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 0.28s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 3768.97
//
Query:       gi|320101003|ref|YP_004176595.1|  [L=167]
Description: membrane bound protein complex subunit MbxA [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-40  136.8   1.1      5e-40  136.6   1.1    1.0  1  MNHE      Na+/H+ ion antiporter subunit
  ------ inclusion threshold ------
       0.19   12.0   2.7       0.47   10.8   2.7    1.6  1  DUF2929   Protein of unknown function (DUF2929)


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   1.1   5.5e-44     5e-40       2     146 .]      11     165 ..      10     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 5.5e-44
                              MNHE   2 lllflvWllltgs..lgelllGlllallvalllrrll.......lplrrvllrllayl.lvflweivkanldVakrv 68 
                                       +l+f+++++++gs  + +l++G+++al++ +l++++        l++ r+++ ll+y+  +f ++ +ka++dV+kr+
  gi|320101003|ref|YP_004176595.1|  11 ALSFITYIVFSGSiqPYDLVTGVVVALVTGVLFANITvsepwkvLNPARWFW-LLRYAvRYFTIDETKAHIDVIKRI 86 
                                       678******************************9999988876666666655.7777736889************** PP

                              MNHE  69 lrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldv.edeeeeareeikgrlErrll 144
                                       l+pk p++p+ivkvp++  sd+ ++ +ansit tPGT++v+v+ed++++yvH++d+ + e++ea++ei+  +E++ +
  gi|320101003|ref|YP_004176595.1|  87 LHPKTPVNPAIVKVPYEAVSDYTVASIANSITNTPGTVVVEVREDEKAFYVHWIDAkTIEPAEAKKEISLVFEEYSR 163
                                       ********************************************************7777**************998 PP

                              MNHE 145 ei 146
                                       +i
  gi|320101003|ref|YP_004176595.1| 164 KI 165
                                       76 PP

>> DUF2929  Protein of unknown function (DUF2929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.7   5.2e-05      0.47      17      49 ..      15      47 ..       8      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.2e-05
                           DUF2929 17 vgYIgsaLtgvtydfttalilavvfgvlvilii 49
                                      ++YI+ + + ++yd +t +++a+v+gvl+++i 
  gi|320101003|ref|YP_004176595.1| 15 ITYIVFSGSIQPYDLVTGVVVALVTGVLFANIT 47
                                      67777777788********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1313.51
//
Query:       gi|320101004|ref|YP_004176596.1|  [L=134]
Description: NADH-ubiquinone oxidoreductase subunit 4L [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-22   77.7   0.4    6.4e-22   77.2   0.4    1.2  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
       0.11   10.8   4.9       0.14   10.4   4.9    1.1  1  DUF2070      Predicted membrane protein (DUF2070)
       0.23   11.9   1.4       0.44   11.0   1.4    1.5  1  Curto_V3     Curtovirus V3 protein


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 !   77.2   0.4   1.1e-25   6.4e-22       4     105 .]      15     131 ..       8     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 1.1e-25
                                       HHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC............................TTSC CS
                       Oxidored_q2   4 lliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi...............tnpatefadpl 65 
                                       + +++ f+i+lyg++++++ +k++i+l + s  +n + + +g++++   v                +++ ++++dpl
  gi|320101004|ref|YP_004176596.1|  15 FSLIFNFAISLYGLFFKSHYIKKVIALTIFSDTINAFAIYLGYRKWVDGVNprppvlvteptpsalKEFVARAVDPL 91 
                                       567888*************************************9954333378999********************* PP

                                       GGHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG--X CS
                       Oxidored_q2  66 pqalvLtaivigaaetavgLallvrlyreygtddvqelrr 105
                                       pqalvLta+vig+a+t +++ l ++ly++y+t+d++e+rr
  gi|320101004|ref|YP_004176596.1|  92 PQALVLTAVVIGLAVTLFLVFLGYQLYKHYHTLDMREIRR 131
                                       *************************************975 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.9   2.4e-05      0.14      76     184 ..      10     122 ..       3     129 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.4e-05
                           DUF2070  76 lltelivviisllaillsall.qalvllalvlslalvfalrllvlvavsdesllkavlpaliq..pllailllvly. 148
                                       ++ +l+++i+ ++ +l+ +++ + ++   ++l++++ +++ + +++ + ++  +    p ++   p  ++l    + 
  gi|320101004|ref|YP_004176596.1|  10 FALTLFSLIFNFAISLYGLFFkSHYIKKVIALTIFSDTINAFAIYLGYRKWVDGVNPRPPVLVtePTPSALKE--Fv 84 
                                       3445555666666666665556777777777777777777777777777777777764444330033333333..34 PP

                           DUF2070 149 ..fspesfllllllslifalavylfivvvdrplkrnlg 184
                                           +     l+l+ ++++lav lf+v++ ++l + ++
  gi|320101004|ref|YP_004176596.1|  85 arAVDPLPQALVLTAVVIGLAVTLFLVFLGYQLYKHYH 122
                                       55334455667777888999999***999999998664 PP

>> Curto_V3  Curtovirus V3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.4   7.4e-05      0.44       4      40 ..       5      41 ..       3      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.4e-05
                          Curto_V3  4 lpdwlfllfvfsillqsginfygtfqserisaklssl 40
                                      + ++lf l +fs++++  i +yg f   +  +k+ +l
  gi|320101004|ref|YP_004176596.1|  5 IVNYLFALTLFSLIFNFAISLYGLFFKSHYIKKVIAL 41
                                      5689*******************98655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1064.32
//
Query:       gi|320101005|ref|YP_004176597.1|  [L=270]
Description: Na+/H+ antiporter MnhB subunit-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-21   74.9  14.3    6.8e-21   74.9  14.3    2.0  2  MnhB            Domain related to MnhB subunit of Na+/H+ anti
  ------ inclusion threshold ------
      0.085   12.8   0.6      0.085   12.8   0.6    3.2  3  FixQ            Cbb3-type cytochrome oxidase component FixQ
       0.21   11.7   4.9      0.056   13.6   1.0    2.0  2  Cytochrom_B561  Eukaryotic cytochrome b561


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.42   2.5e+03      11      82 ..      10      22 ..       3      46 .. 0.54
   2 !   74.9  14.3   1.1e-24   6.8e-21       1     123 [.     115     251 ..     115     252 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.42
                              MnhB 11 plillvslylllrGhnsPGGGFqgGlilaaalillylafgleelekllrvklaprileglglllavltgllg 82
                                      +l+                                                           +l+ l+ l+g
  gi|320101005|ref|YP_004176597.1| 10 ILT-----------------------------------------------------------ILFGLSLLAG 22
                                      222...........................................................2333333333 PP

  == domain 2  score: 74.9 bits;  conditional E-value: 1.1e-24
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafglee..lekllrvklaprileglgllla 75 
                                       i++tv++l +p+i++v++++ l+Gh++PGGGFqgG+++a+a ++ +++f++++  ++ l++ +  + +l ++gl+ +
  gi|320101005|ref|YP_004176597.1| 115 IVKTVSKLTLPMIITVGASIGLHGHLTPGGGFQGGATAAVAPMVAIIVFSVAFlvERGLSKEN--MLVLRSIGLTGI 189
                                       79***************************************************9555555656..56********** PP

                              MnhB  76 vltgllglllgfltslflel.el.............llgevelgtallfdlgVylvVvggll 123
                                        lt++l +++g+l+  ++++ ++             + g    gt+++f+l+ +++V++g++
  gi|320101005|ref|YP_004176597.1| 190 GLTAVLLFFVGLLYGVNAYVfQNmakpfspvsfpweVNGALISGTLWFFNLFEFIAVTAGFT 251
                                       ********9997777777665555666666677765444556****************9986 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.6      0.26   1.6e+03      12      28 ..       9      25 ..       6      29 .. 0.87
   2 ?   12.8   0.6   1.4e-05     0.085       8      31 ..     188     211 ..     186     216 .. 0.85
   3 ?   -3.8   2.2       2.2   1.3e+04       7       7 ..     248     248 ..     231     259 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.26
                              FixQ 12 swgllflvllfygvviy 28
                                      +++++++ l +++ +++
  gi|320101005|ref|YP_004176597.1|  9 IILTILFGLSLLAGIAW 25
                                      67899999999999998 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.4e-05
                              FixQ   8 gfadswgllflvllfygvviyafr 31 
                                       g++ +++llf+v+l+ygv +y+f 
  gi|320101005|ref|YP_004176597.1| 188 GIGLTAVLLFFVGLLYGVNAYVFQ 211
                                       5666899***************96 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.2
                              FixQ   7 r 7  
                                       +
  gi|320101005|ref|YP_004176597.1| 248 A 248
                                       1 PP

>> Cytochrom_B561  Eukaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       0.7   4.2e+03      78      95 ..      10      27 ..       7      32 .. 0.67
   2 ?   13.6   1.0   9.4e-06     0.056      44     110 ..     154     224 ..     150     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.7
                                      HHHHHHHHHHHHHHHHHT CS
                    Cytochrom_B561 78 vtvilfllqlvlGfvlfl 95
                                      +  ilf l+l++G++  +
  gi|320101005|ref|YP_004176597.1| 10 ILTILFGLSLLAGIAWQW 27
                                      556777777777776655 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.4e-06
                                       HHHHHHHHHHHHHHHHHHHHT--SS-SHHHH....HHHHHHHHHHHHHHHHHHHHTSS---HHHHHHHHHH CS
                    Cytochrom_B561  44 lalilavvgllavfksknekeianlyslHsw....lGlvtvilfllqlvlGfvlfllpklskklralllpl 110
                                       +a ++a++ + ++f  ++   ++n+  l s+    +Gl++v+lf++ l++G+ ++++++++k ++++  p+
  gi|320101005|ref|YP_004176597.1| 154 VAPMVAIIVFSVAFLVERGLSKENMLVLRSIgltgIGLTAVLLFFVGLLYGVNAYVFQNMAKPFSPVSFPW 224
                                       555566666666666666677777777777666669******************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2178.41
//
Query:       gi|320101006|ref|YP_004176598.1|  [L=87]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.9e-12   45.2   2.6    7.9e-12   45.2   2.6    1.6  2  DUF4040     Domain of unknown function (DUF4040)
     0.0024   16.2   6.6     0.0024   16.2   6.6    1.0  1  DUF2070     Predicted membrane protein (DUF2070)
     0.0048   16.9   0.1     0.0048   16.9   0.1    1.7  2  Trep_Strep  Hypothetical bacterial integral membrane protein 
  ------ inclusion threshold ------
      0.016   15.5   0.9      0.024   14.9   0.7    1.4  1  DUF5438     Family of unknown function (DUF5438)
      0.063   12.1   5.4      0.065   12.0   5.4    1.0  1  CreD        Inner membrane protein CreD


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.13   4.6e+02      33      47 ..       8      22 ..       5      24 .. 0.72
   2 !   45.2   2.6   2.2e-15   7.9e-12       4      67 .]      20      83 ..      17      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.13
                           DUF4040 33 lfvllgAPDvAlTqa 47
                                      +++l+ A  vA T a
  gi|320101006|ref|YP_004176598.1|  8 IYILMAASSVASTIA 22
                                      678888888887765 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 2.2e-15
                           DUF4040  4 vlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlpr 67
                                       +a+++a++ +d++++vi++++++ ++++lf+ll APD+ l ++ v  gl++ +lll +++++r
  gi|320101006|ref|YP_004176598.1| 20 TIAVYFAIVEKDLVKSVIYSAIQSGFYTILFYLLMAPDIVLVYLPVSVGLIPGVLLLLISKTER 83
                                      6899*********************************************************986 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   6.6   6.8e-07    0.0024     104     177 ..       9      82 ..       1      87 [] 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.8e-07
                           DUF2070 104 lvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfivvvdr 177
                                       ++l  a+++a ++ v++a+ +++l k+v+ ++iq+ ++ +l++l+++p+ +l++l +s+ ++ +v+l+++  + 
  gi|320101006|ref|YP_004176598.1|   9 YILMAASSVASTIAVYFAIVEKDLVKSVIYSAIQSGFYTILFYLLMAPDIVLVYLPVSVGLIPGVLLLLISKTE 82 
                                       4555689999***********************************99999999999998888888888776555 PP

>> Trep_Strep  Hypothetical bacterial integral membrane protein (Trep_Strep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.0      0.49   1.8e+03     159     171 ..      10      22 ..       1      28 [. 0.37
   2 !   16.9   0.1   1.3e-06    0.0048       2      53 ..      30      80 ..      29      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.49
                        Trep_Strep 159 vlliltivgallG 171
                                       +l+++  v++ ++
  gi|320101006|ref|YP_004176598.1|  10 ILMAASSVASTIA 22 
                                       2222222222222 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.3e-06
                        Trep_Strep  2 kDlitigiftalyfvvvfvvgmlglispvlmlllpaivallagivymllvak 53
                                      kDl+  +i++a+   ++++   l +   +++++lp+ v+l+ g+  +l+ +k
  gi|320101006|ref|YP_004176598.1| 30 KDLVKSVIYSAIQSGFYTILFYLLMAPDIVLVYLPVSVGLIPGVLLLLI-SK 80
                                      9*********************88888****************876664.44 PP

>> DUF5438  Family of unknown function (DUF5438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.7   6.8e-06     0.024       5      50 ..      21      67 ..      17      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.8e-06
                           DUF5438  5 iphsftmtlkeinrsiiysttnsvisallmynllt.iisttylsvsf 50
                                      i   f++  k++ +s+iys+  s   ++l y l++  i   yl vs 
  gi|320101006|ref|YP_004176598.1| 21 IAVYFAIVEKDLVKSVIYSAIQSGFYTILFYLLMApDIVLVYLPVSV 67
                                      666799999**********************9997358889999885 PP

>> CreD  Inner membrane protein CreD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   5.4   1.8e-05     0.065     355     406 ..      11      62 ..       4      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                              CreD 355 liaalavvllislYlssvlkskkrgllfaallallYgllyvlLqledyALLl 406
                                       l+aa++v   i++Y++ v k+  ++++ +a+ + +Y++l+ lL + d+ L+ 
  gi|320101006|ref|YP_004176598.1|  11 LMAASSVASTIAVYFAIVEKDLVKSVIYSAIQSGFYTILFYLLMAPDIVLVY 62 
                                       6799999*************************************99998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 652.54
//
Query:       gi|320101007|ref|YP_004176599.1|  [L=123]
Description: MnhG/PhaG subunit monovalent cation/proton antiporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-16   59.7  10.6    3.6e-16   59.2  10.6    1.3  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
  ------ inclusion threshold ------
       0.78    9.8   8.8          3    7.9   1.3    3.1  3  DUF1656         Protein of unknown function (DUF1656)


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2  10.6     4e-20   3.6e-16       1      79 []      13     100 ..      13     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 4e-20
                    PhaG_MnhG_YufB   1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaa........slkllliilfllltaP 68 
                                       ll lGa+ +l+gaig+ r++++y Rlhaat+++ +G +  ++G+ l + +           ++  +++++++l+ aP
  gi|320101007|ref|YP_004176599.1|  13 LLSLGAVASLIGAIGMHRFRNFYLRLHAATVSTIWGGVYPIVGASLLAiTMPElgvyrwfmAGAGFVTAFIVLILAP 89 
                                       689****************************************99977555449******9999************* PP

                    PhaG_MnhG_YufB  69 vaahliaraay 79 
                                        ++h++ara++
  gi|320101007|ref|YP_004176599.1|  90 AGSHALARAVH 100
                                       ********986 PP

>> DUF1656  Protein of unknown function (DUF1656)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4    0.0081        73      13      38 ..       6      31 ..       3      34 .. 0.89
   2 ?    7.9   1.3   0.00034         3      25      55 ..      58      88 ..      52      89 .. 0.86
   3 ?    7.6   0.4   0.00041       3.7       6      37 ..      75     106 ..      73     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0081
                           DUF1656 13 lvlallAllltlllrrllarlglyrl 38
                                      l ++ +All   ++  l+ ++g +r+
  gi|320101007|ref|YP_004176599.1|  6 LEYIGVALLSLGAVASLIGAIGMHRF 31
                                      5688999***************9998 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00034
                           DUF1656 25 llrrllarlglyrlvWhpaLfdlAlfvcllg 55
                                      ll   +  lg+yr++   a f +A  v++l+
  gi|320101007|ref|YP_004176599.1| 58 LLAITMPELGVYRWFMAGAGFVTAFIVLILA 88
                                      666677789*******************996 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00041
                           DUF1656   6 GvyvPpllvlallAllltlllrrllarlglyr 37 
                                       G+ + + +++++lA + + +l r  +r g++r
  gi|320101007|ref|YP_004176599.1|  75 GAGFVTAFIVLILAPAGSHALARAVHRSGISR 106
                                       66677899**********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 908.25
//
Query:       gi|320101008|ref|YP_004176600.1|  [L=90]
Description: multiple resistance and pH regulation protein F [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   45.8   7.9    5.7e-12   45.8   7.9    2.0  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M
  ------ inclusion threshold ------
      0.017   15.3   4.8      0.018   15.2   4.8    1.0  1  RDD        RDD family
        2.3    7.7   8.7        2.5    7.6   8.7    1.0  1  Pox_P21    Poxvirus P21 membrane protein
        2.4    8.6  10.2        2.9    8.3  10.2    1.1  1  MgtE       Divalent cation transporter
        8.8    5.2   5.8       0.64    8.9   1.2    1.4  2  Pex24p     Integral peroxisomal membrane peroxin


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.0      0.64   2.3e+03      32      47 ..       4      19 ..       1      26 [. 0.61
   2 !   45.8   7.9   1.6e-15   5.7e-12       2      53 .]      33      84 ..      32      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.64
                         MrpF_PhaF 32 dvalvlAllgFvgtva 47
                                      d+++ + +l +  +++
  gi|320101008|ref|YP_004176600.1|  4 DIVVPVTILVYALSII 19
                                      5555555555555554 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 1.6e-15
                         MrpF_PhaF  2 DRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfle 53
                                      D v+A+D++++ +v l++l+ai++++++++ va+ lAl+ +   +++a++le
  gi|320101008|ref|YP_004176600.1| 33 DQVLAIDVMTYATVTLMVLIAIYLREAILVVVAIPLALWVYALDIYVAKYLE 84
                                      99************************************************97 PP

>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   4.8   5.1e-06     0.018      49     125 ..       5      80 ..       1      89 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                               RDD  49 lllllvlllvllvyqllllsk.kgqTlGklllglkvvd.edgrklglaqaliRalllllllvlglslvlllllligf 123
                                       +++ +  l+++l ++++++ + kg T+G ++l + v + ++ + + l +  +R+ +l+++    ++l+l+++ l ++
  gi|320101008|ref|YP_004176600.1|   5 IVVPVTILVYALSIIIVFVRAlKGPTIGDQVLAIDVMTyATVTLMVLIAIYLREAILVVVA---IPLALWVYALDIY 78 
                                       5666667777777777777778****************9999999999*******877765...9999888888777 PP

                               RDD 124 lf 125
                                       + 
  gi|320101008|ref|YP_004176600.1|  79 VA 80 
                                       65 PP

>> Pox_P21  Poxvirus P21 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.7   0.00071       2.5      91     169 ..       2      82 ..       1      89 [. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00071
                           Pox_P21  91 iaslllPlpsLviaYClalqilnpsnantvg...msivcvllsivtivvnsvsvsktlktisyivLavlfciYvlkl 164
                                       i  +++P++ Lv a  + +  +++ ++ t+g   ++i +++ + vt++v  +++     +++ + + + + +Y+l +
  gi|320101008|ref|YP_004176600.1|   2 IVDIVVPVTILVYALSIIIVFVRALKGPTIGdqvLAIDVMTYATVTLMVL-IAIYLREAILVVVAIPLALWVYALDI 77 
                                       56799*************99999999999983335555566677777776.44433333333334444567899999 PP

                           Pox_P21 165 trakk 169
                                       + ak+
  gi|320101008|ref|YP_004176600.1|  78 YVAKY 82 
                                       87766 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  10.2   0.00081       2.9      41     101 ..      11      76 ..       2      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00081
                                       HHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHTTS- CS
                              MgtE  41 rvvlllgvilgllifllalllgwslllalvvglalvlvllaaall.....ilgvllplllwklglD 101
                                       ++v  l++i++++++l   ++g ++l++ v+++a v+++++ a++     ++ v++pl+lw + lD
  gi|320101008|ref|YP_004176600.1|  11 ILVYALSIIIVFVRALKGPTIGDQVLAIDVMTYATVTLMVLIAIYlreaiLVVVAIPLALWVYALD 76 
                                       34556666666666666666777777777888888888888888889998999********99998 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2      0.65   2.3e+03      62      72 ..      12      20 ..       4      29 .. 0.41
   2 ?    8.9   1.2   0.00018      0.64      48      89 ..      38      79 ..      32      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.65
                            Pex24p 62 lvvlplllllf 72
                                      lv  ++l +++
  gi|320101008|ref|YP_004176600.1| 12 LV--YALSIII 20
                                      22..1111111 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00018
                            Pex24p 48 llvytficlvpylelvvlplllllfvvmvpaylyrhplrkss 89
                                      + v+t+ ++ +++ ++++    +l+vv +p +l+ + l++ +
  gi|320101008|ref|YP_004176600.1| 38 IDVMTYATVTLMVLIAIYLREAILVVVAIPLALWVYALDIYV 79
                                      55899999999999999******************9666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 670.64
//
Query:       gi|320101009|ref|YP_004176601.1|  [L=133]
Description: NADH-ubiquinone oxidoreductase subunit I [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   54.3  10.9    1.2e-07   31.2   2.7    2.2  2  Fer4      4Fe-4S binding domain
    1.6e-11   44.6   4.8    2.2e-11   44.1   4.8    1.3  1  Fer4_7    4Fe-4S dicluster domain
    1.8e-10   40.8   4.2    1.8e-05   24.8   0.5    2.2  2  Fer4_21   4Fe-4S dicluster domain
      4e-10   39.6  17.9    3.7e-07   30.2  10.4    2.0  2  Fer4_10   4Fe-4S dicluster domain
    7.7e-10   38.4  11.7    5.3e-05   23.1   2.0    2.2  2  Fer4_6    4Fe-4S binding domain
    1.1e-09   38.4  26.7    1.9e-06   27.9   9.1    1.9  3  Fer4_9    4Fe-4S dicluster domain
    9.6e-08   32.9   6.1     0.0014   19.5   0.2    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    1.2e-07   31.4  10.2     0.0019   18.2   1.9    2.3  2  Fer4_2    4Fe-4S binding domain
    9.4e-07   29.2   2.8       0.01   16.3   0.2    2.1  2  Fer4_8    4Fe-4S dicluster domain
    1.4e-06   28.7   3.9     0.0052   17.3   0.2    2.2  2  Fer4_17   4Fe-4S dicluster domain
     0.0021   18.9  14.7      0.066   14.2   3.4    2.3  2  Fer4_3    4Fe-4S binding domain
     0.0022   18.2   2.4       0.16   12.1   0.2    2.1  2  Fer4_18   4Fe-4S dicluster domain
     0.0022   18.8   4.3       0.81   10.6   0.2    2.1  2  Fer4_22   4Fe-4S dicluster domain
     0.0079   16.6  11.8       0.29   11.7   3.0    2.2  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.022   15.5   6.7        2.2    9.1   0.0    2.7  2  Fer4_15   4Fe-4S single cluster domain
       0.22   12.1   8.4        3.8    8.1   0.4    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.26   11.4   0.2       0.26   11.4   0.2    2.0  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   1.3   9.5e-10     1e-06       4      24 .]      41      61 ..      38      61 .. 0.92
   2 !   31.2   2.7   1.2e-10   1.2e-07       2      23 ..      82     103 ..      81     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.5e-10
                                      ETTTSSS-THHHHHSTTTEEE CS
                              Fer4  4 deekCigCGaCvevCPvgAIt 24
                                      d +kC+gC +C   CP +AI+
  gi|320101009|ref|YP_004176601.1| 41 DLSKCTGCSLCSIECPADAIK 61
                                      899*****************6 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.2e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        id+ kC++C +C++vCP++A 
  gi|320101009|ref|YP_004176601.1|  82 LIDYGKCVYCYRCISVCPFNAY 103
                                       59******************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 !   44.1   4.8   2.1e-14   2.2e-11       1      52 []      44     102 ..      28     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2.1e-14
                            Fer4_7   1 rCigCgaCvaaCpvkaielde.......eenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC  C   Cp++ai++++        ++++++ ++ id+ kC++C++C++vCP++a
  gi|320101009|ref|YP_004176601.1|  44 KCTGCSLCSIECPADAIKMTPipegydvPKSNPRRIYPLIDYGKCVYCYRCISVCPFNA 102
                                       7******************964444333223334466789*****************97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.5   1.7e-08   1.8e-05      37      59 .]      41      62 ..      28      62 .. 0.84
   2 !   17.7   0.2   2.8e-06     0.003      31      57 ..      77     104 ..      67     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-08
                           Fer4_21 37 vedeCvGCnlCssvCPvedciem 59
                                        ++C+GC lCs+ CP  d+i+m
  gi|320101009|ref|YP_004176601.1| 41 DLSKCTGCSLCSIECPA-DAIKM 62
                                      4579************5.***99 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.8e-06
                           Fer4_21  31 ktvlkvv.edeCvGCnlCssvCPvedci 57 
                                       +++++++   +Cv C  C+svCP + +i
  gi|320101009|ref|YP_004176601.1|  77 RRIYPLIdYGKCVYCYRCISVCPFNAYI 104
                                       5556665246999999999999998777 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2  10.4   3.5e-10   3.7e-07       4      56 .]      40      99 ..      37      99 .. 0.97
   2 !   20.4   0.8   3.9e-07   0.00041       3      24 ..      82     105 ..      80     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.5e-10
                           Fer4_10  4 idddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       d ++C++C  C   CPad+       +++++ + + +     ++++kC  c  C+++CP
  gi|320101009|ref|YP_004176601.1| 40 ADLSKCTGCSLCSIECPADAikmtpipEGYDVPKSNPRRIYPLIDYGKCVYCYRCISVCP 99
                                      6899*******************************************************9 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.9e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadl..t 24 
                                        id  +C+ C +C ++CP+++  +
  gi|320101009|ref|YP_004176601.1|  82 LIDYGKCVYCYRCISVCPFNAyiH 105
                                       68999**************66421 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   2.4   2.8e-07    0.0003       5      24 .]      41      60 ..      39      60 .. 0.93
   2 !   23.1   2.0     5e-08   5.3e-05       3      24 .]      82     103 ..      80     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.8e-07
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d +kC+gC  C + CP++ai
  gi|320101009|ref|YP_004176601.1| 41 DLSKCTGCSLCSIECPADAI 60
                                      789***************98 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 5e-08
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                        id+ kC+ C++C++vCP++a+
  gi|320101009|ref|YP_004176601.1|  82 LIDYGKCVYCYRCISVCPFNAY 103
                                       69*****************996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.4   4.5e-06    0.0047      27      51 .]      35      60 ..      18      60 .. 0.71
   2 !   27.9   9.1   1.8e-09   1.9e-06       1      50 [.      44     102 ..      44     103 .. 0.94
   3 !   16.5   1.5   6.6e-06    0.0069       1      25 [.      87     111 ..      87     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.5e-06
                            Fer4_9 27 rlraase.eaCigCgaCveaCpkgai 51
                                      r r++ + ++C+gC  C   Cp +ai
  gi|320101009|ref|YP_004176601.1| 35 RGRHYADlSKCTGCSLCSIECPADAI 60
                                      3333333689************9987 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.8e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.........eaCigCgaCveaCpkga 50 
                                       kCtgC  C   Cpa+++++   ++   + + +           +C+ C +C+ +Cp +a
  gi|320101009|ref|YP_004176601.1|  44 KCTGCSLCSIECPADAIKMTPIPEGYDVPKSNPrriyplidyGKCVYCYRCISVCPFNA 102
                                       7**********************99999888779********99************875 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 6.6e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerk 25 
                                       kC+ C +C+++Cp+++++  +  r 
  gi|320101009|ref|YP_004176601.1|  87 KCVYCYRCISVCPFNAYIHTNEYRL 111
                                       7**************9988776665 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.5   2.1e-05     0.022       1      21 [.      44      64 ..      44      78 .. 0.85
   2 !   19.5   0.2   1.4e-06    0.0014       1      24 [.      87     110 ..      87     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                      +C++C  C   CP++aik++ 
  gi|320101009|ref|YP_004176601.1| 44 KCTGCSLCSIECPADAIKMTP 64
                                      5****************9874 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.4e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkeke 24 
                                       +C+ C +C++vCP na  +++e++
  gi|320101009|ref|YP_004176601.1|  87 KCVYCYRCISVCPFNAYIHTNEYR 110
                                       5**************976665555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.5   2.1e-06    0.0022       4      22 .]      39      57 ..      36      57 .. 0.89
   2 !   18.2   1.9   1.8e-06    0.0019       3      21 ..      81      99 ..      79     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                      ++d  +C+gC+ C   CPa
  gi|320101009|ref|YP_004176601.1| 39 YADLSKCTGCSLCSIECPA 57
                                      78999********888**8 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.8e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      + +d  +C+ C  C+s+CP
  gi|320101009|ref|YP_004176601.1| 81 PLIDYGKCVYCYRCISVCP 99
                                      789**************** 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   0.2   9.6e-06      0.01      45      63 ..      39      57 ..      11      64 .. 0.73
   2 !   13.5   0.3   7.2e-05     0.076       4      17 ..      87     102 ..      84     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.6e-06
                            Fer4_8 45 eealwsCttcgaCtevCpv 63
                                      +  l +Ct+c  C+ +Cp 
  gi|320101009|ref|YP_004176601.1| 39 YADLSKCTGCSLCSIECPA 57
                                      6678888888888888886 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.2e-05
                            Fer4_8   4 kCieCgaCqsaCp..v 17 
                                       kC+ C +C s Cp  +
  gi|320101009|ref|YP_004176601.1|  87 KCVYCYRCISVCPfnA 102
                                       7889999999998443 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   4.9e-06    0.0052      41      59 ..      40      58 ..      11      59 .. 0.71
   2 !   12.8   0.4   0.00012      0.13       1      27 [.      87     113 ..      87     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-06
                           Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                         s+C++C +C+ +CP++
  gi|320101009|ref|YP_004176601.1| 40 ADLSKCTGCSLCSIECPAD 58
                                      46799************86 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00012
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllr 27 
                                       +C  C  C+ +Cp+++ + +++ +l+ 
  gi|320101009|ref|YP_004176601.1|  87 KCVYCYRCISVCPFNAYIHTNEYRLAD 113
                                       699**********98887777776665 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   3.6   0.00096         1       1      15 []      45      59 ..      45      59 .. 0.94
   2 !   14.2   3.4   6.3e-05     0.066       1      15 []      88     102 ..      88     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00096
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      CtgC++C   CP +A
  gi|320101009|ref|YP_004176601.1| 45 CTGCSLCSIECPADA 59
                                      ************877 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.3e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C++C  vCP +A
  gi|320101009|ref|YP_004176601.1|  88 CVYCYRCISVCPFNA 102
                                       999*********998 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.011        11      52      74 ..      36      58 ..      15      64 .. 0.80
   2 !   12.1   0.2   0.00016      0.16      58      77 ..      85     104 ..      77     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                           Fer4_18 52 erkekgagdcidcescvkvcPtg 74
                                       r+ ++ ++c+ c+ c   cP +
  gi|320101009|ref|YP_004176601.1| 36 GRHYADLSKCTGCSLCSIECPAD 58
                                      456778899***********975 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00016
                           Fer4_18  58 agdcidcescvkvcPtgidi 77 
                                        g+c+ c  c++vcP +  i
  gi|320101009|ref|YP_004176601.1|  85 YGKCVYCYRCISVCPFNAYI 104
                                       589************87655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.5    0.0013       1.4      78      94 ..      41      57 ..      30      59 .. 0.81
   2 !   10.6   0.2   0.00077      0.81      78      94 ..      84     100 ..      74     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      + s+C+GC  C+  cp+
  gi|320101009|ref|YP_004176601.1| 41 DLSKCTGCSLCSIECPA 57
                                      67899999999999997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00077
                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       +  +Cv C RCi++cp 
  gi|320101009|ref|YP_004176601.1|  84 DYGKCVYCYRCISVCPF 100
                                       56689999999999985 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   1.6     0.001       1.1       2      16 ..      43      57 ..      42      63 .. 0.91
   2 !   11.7   3.0   0.00028      0.29       3      17 .]      87     101 ..      85     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C+gC  C + CP 
  gi|320101009|ref|YP_004176601.1| 43 SKCTGCSLCSIECPA 57
                                      69************6 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00028
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       +C+ C +C+++CP++
  gi|320101009|ref|YP_004176601.1|  87 KCVYCYRCISVCPFN 101
                                       8************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 ?    6.3   3.7     0.016        16       4      19 ..      41      56 ..      39      62 .. 0.89
   2 ?    9.1   0.0    0.0021       2.2       3      36 ..      83     118 ..      82     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                           Fer4_15  4 DrdaCigcglCvaeap 19
                                      D ++C+gc lC  e+p
  gi|320101009|ref|YP_004176601.1| 41 DLSKCTGCSLCSIECP 56
                                      8899*******99998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                           Fer4_15   3 vDrdaCigcglCvaea..pevfeldedglasvlldd 36 
                                       +D  +C  c +C+ ++    ++  +e+ la+++++d
  gi|320101009|ref|YP_004176601.1|  83 IDYGKCVYCYRCISVCpfNAYIHTNEYRLADHVISD 118
                                       8999************66678888888888888765 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 ?    7.3   2.5    0.0063       6.7       2      17 ..      41      56 ..      40      62 .. 0.92
   2 ?    8.1   0.4    0.0036       3.8       1      17 [.      83      99 ..      83     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0063
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D ++C++c +C   +P
  gi|320101009|ref|YP_004176601.1| 41 DLSKCTGCSLCSIECP 56
                                      6789***********9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0036
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      +D  +C+ c  C +++P
  gi|320101009|ref|YP_004176601.1| 83 IDYGKCVYCYRCISVCP 99
                                      68889***********9 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00025      0.26      71     102 ..      41      73 ..      18      75 .. 0.84
   2 ?    0.4   0.3      0.67   7.1e+02      71      81 ..      84      94 ..      78     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                       -CCC--S--HHHHH-TT--EEE-.--STT-C-- CS
                            ETF_QO  71 naqnCvhCktCdikdpsqniewv.vPeGggGPk 102
                                       + + C  C  C+i  p + i+ + +PeG + Pk
  gi|320101009|ref|YP_004176601.1|  41 DLSKCTGCSLCSIECPADAIKMTpIPEGYDVPK 73 
                                       5678*****************9845***99987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.67
                                      -CCC--S--HH CS
                            ETF_QO 71 naqnCvhCktC 81
                                      +   Cv+C  C
  gi|320101009|ref|YP_004176601.1| 84 DYGKCVYCYRC 94
                                      55689999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 962.66
//
Query:       gi|320101010|ref|YP_004176602.1|  [L=406]
Description: NADH-ubiquinone oxidoreductase subunit 49kDa [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-63  212.4   0.5    1.9e-60  204.3   0.5    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    6.1e-12   45.2   3.9    1.1e-09   37.8   0.4    3.4  4  NiFeSe_Hases    Nickel-dependent hydrogenase
  ------ inclusion threshold ------
       0.14   12.5   0.3         28    5.2   0.0    3.1  3  DUF2369         Uncharacterised conserved protein (DUF2369)


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.3   0.5   3.2e-64   1.9e-60       2     271 .]     127     374 ..     126     374 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.3 bits;  conditional E-value: 3.2e-64
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkk 78 
                                       +G   +f+ ++ +Re+++++ e vtG R+ a+y+++GGv+rD+++   ++++++l+el+ +++ ++k++ +++++ k
  gi|320101010|ref|YP_004176602.1| 127 IGFENLFMNIMLDRERVMKAKEIVTGGRVLADYMMVGGVRRDIDDVKRDRLRKLLTELKPRVEYYRKVFEEDETILK 203
                                       678889*********************************************************************** PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       R++gvg l+  ++++ gl Gpv+RasGvk+D R +++Y+aYde++f+v++++egD+++R++vr +E  +S+++   +
  gi|320101010|ref|YP_004176602.1| 204 RLVGVGRLKPVDVTSHGLLGPVARASGVKIDARASDKYDAYDEVSFNVVTRTEGDSWARMMVRWDETLESIEMALFI 280
                                       ***************************************************************************** PP

                                       HHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS.-SEEE CS
                    Complex1_49kDa 156 leklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgssk.pyrlk 231
                                       l+klp++          +p+++++ ++                 p+ge+y++vEa +Gel +y++sdg+ + pyr+k
  gi|320101010|ref|YP_004176602.1| 281 LDKLPSDGSP-------VPDEKKLPRK----------------FPPGEAYTRVEAQRGELAYYVMSDGKGMnPYRVK 334
                                       *****75533.......3444455444................59************************988***** PP

                                       EE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 232 irapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       ir+ps +n+  +  l  g+++ D+++il sld+++++++R
  gi|320101010|ref|YP_004176602.1| 335 IRTPSVNNIINTGFLYVGYTIPDLPVILTSLDPCVSCMER 374
                                       ***********************************99987 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.4   1.8e-13   1.1e-09       1      68 [.      51     118 ..      51     120 .. 0.97
   2 !    5.3   0.0    0.0012       7.4     160     220 ..     140     200 ..     125     207 .. 0.82
   3 ?    0.2   0.0     0.045   2.7e+02     410     450 ..     293     332 ..     231     340 .. 0.71
   4 ?   -1.5   0.4      0.14   8.5e+02     493     502 ..     362     371 ..     359     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.8e-13
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhiv 68 
                                       RG+E++ +        ++v R+CG+C  vH+   vra+e  lg+++++ a+++r l +  + +h+h++
  gi|320101010|ref|YP_004176602.1|  51 RGIEKLCERNSFYKDIFIVGRVCGICNAVHTNVYVRALEAILGVTPNRRAKYLRVLAMELERIHSHML 118
                                       9*******9999999***************************************************86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0012
                                       HHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHHHHHTHHHHHH CS
                      NiFeSe_Hases 160 qrkaakivaifggknPhpqslvvGGvtcaidllnaerlaevkslikevkefveevylpDvl 220
                                       +++++k+  i +g    +  ++vGGv   id ++ +rl+++ + +k   e+ ++v+ +D +
  gi|320101010|ref|YP_004176602.1| 140 RERVMKAKEIVTGGRVLADYMMVGGVRRDIDDVKRDRLRKLLTELKPRVEYYRKVFEEDET 200
                                       45566777777666667777********************************999999865 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.045
                                       -TT-SGGGS-SEEEEEEEEEETTEEEEEEEEEETTEEEEEE CS
                      NiFeSe_Hases 410 eekldkkevpkeakGvglveapRGaLsHwikikdgkienYq 450
                                       +ek  ++++p   + +  vea RG L+ ++  + + ++ Y 
  gi|320101010|ref|YP_004176602.1| 293 DEKKLPRKFPP-GEAYTRVEAQRGELAYYVMSDGKGMNPYR 332
                                       33344555665.789999*********99987776666665 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.14
                                       HHHT--BHHH CS
                      NiFeSe_Hases 493 ihSfDPClAC 502
                                       + S DPC++C
  gi|320101010|ref|YP_004176602.1| 362 LTSLDPCVSC 371
                                       679******* PP

>> DUF2369  Uncharacterised conserved protein (DUF2369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.051   3.1e+02      11      36 ..      53      78 ..      45     116 .. 0.79
   2 ?    5.2   0.0    0.0046        28      10      27 ..     180     197 ..     174     204 .. 0.86
   3 ?    1.4   0.1     0.071   4.2e+02       2      23 ..     368     389 ..     367     390 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.051
                           DUF2369 11 lseLkpdtqYyfdVFvvdqkrntssa 36
                                      +++L  + ++y d+F+v +  +   a
  gi|320101010|ref|YP_004176602.1| 53 IEKLCERNSFYKDIFIVGRVCGICNA 78
                                      8899999**********998884433 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0046
                           DUF2369  10 tlseLkpdtqYyfdVFvv 27 
                                       +l+eLkp+ +Yy  VF  
  gi|320101010|ref|YP_004176602.1| 180 LLTELKPRVEYYRKVFEE 197
                                       799*************65 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.071
                           DUF2369   2 CvgkktkvtlseLkpdtqYyfd 23 
                                       Cv  ++ vt+ +L++++ Y+++
  gi|320101010|ref|YP_004176602.1| 368 CVSCMERVTVVDLEKNSVYRVS 389
                                       9999***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2818.37
//
Query:       gi|320101011|ref|YP_004176603.1|  [L=151]
Description: NADH dehydrogenase (ubiquinone) 30 kDa subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-20   74.2   0.0    1.5e-20   74.0   0.0    1.0  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 !   74.0   0.0   8.4e-25   1.5e-20       1     116 [.      29     149 ..      29     151 .] 0.89

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 8.4e-25
                                       EE--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-ST CS
                    Complex1_30kDa   1 lvvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsleknerirvkvevdeeepevpSvtdlfpg 76 
                                       lvv+pe++++v + + ++   +  +ls+++a D k e+r+++ y+++ l ++e+i++++++++++p+v+S++d++pg
  gi|320101011|ref|YP_004176603.1|  29 LVVKPENVKQVFAEMLEKIGRENMYLSTIVATDMKdEGRIRLDYYVVLLPEEETIVIRTHLPRDNPVVDSIIDVIPG 105
                                       5799******88888877778889*********77799****9999999999************************* PP

                                       HHHHHHHHHHHSHHBCTTSSTSS-SSS.STTS...SS-TTSTTS CS
                    Complex1_30kDa  77 adwyEREayDmfGivfeghpdlrrill.pedf...eghPLRkdf 116
                                       a   E Ea+D++G+vf+g+p lrr +  p d     ++PLRkd 
  gi|320101011|ref|YP_004176603.1| 106 ALAGECEAHDLLGVVFQGNPFLRRGFFvPRDLveqGKYPLRKDS 149
                                       **********************9866559997564456****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1191.19
//
Query:       gi|320101012|ref|YP_004176604.1|  [L=161]
Description: NADH-quinone oxidoreductase subunit B [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-29  100.6   0.4    6.9e-29  100.3   0.4    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.4   3.9e-33   6.9e-29       1     131 []      32     143 ..      32     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 3.9e-33
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C+Gc+i++la+ ++l+d      +r++ +l+ + +         + d+lvv+Gavt+k+ e+l++l+e+++ +k+vi
  gi|320101012|ref|YP_004176604.1|  32 CNGCDIEVLAAITPLYDP-----ERFGVRLAPSIR---------HGDILVVTGAVTKKSGERLKRLYEQMPCPKFVI 94 
                                       ******************.....*******99999.........99******************************* PP

                                       EESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetllal 131
                                       avG+CA++GG+++ +    ++    ++++vvpv ++ipGCPp+peail+++++l
  gi|320101012|ref|YP_004176604.1|  95 AVGACACSGGVFSKSY---TV--LAGADKVVPVSMYIPGCPPRPEAILDGIVKL 143
                                       ************4333...33..4699***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1214.75
//
Query:       gi|320101013|ref|YP_004176605.1|  [L=767]
Description: (NiFe) hydrogenase maturation protein HypF [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-44  150.3   0.0    5.8e-44  149.7   0.0    1.3  1  Sua5_yciO_yrdC   Telomere recombination
      4e-31  106.5  10.3    3.2e-15   55.6   1.3    2.4  2  zf-HYPF          HypF finger
    1.1e-23   83.9   0.0    2.6e-23   82.6   0.0    1.6  2  HypF_C           HypF Kae1-like domain
    2.2e-19   69.6   0.1    5.4e-19   68.4   0.0    1.7  2  Acylphosphatase  Acylphosphatase
     0.0008   19.2   0.0       0.32   10.7   0.0    2.5  3  Peptidase_M22    Glycoprotease family
  ------ inclusion threshold ------
        1.1    8.9   4.9       0.13   11.8   0.4    1.8  2  zf-MYST          MYST family zinc finger 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 !  149.7   0.0   1.9e-47   5.8e-44       2     178 ..     210     384 ..     209     385 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 1.9e-47
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-.TC--HHHHHHHHCT-SSS CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklae.seveeealkllerfwPGp 77 
                                       ++++G iva++++++Y++a  at++++v+rlre+K+rp +kp+av+  + + l+ l+  +e ++e+l+++++    p
  gi|320101013|ref|YP_004176605.1| 210 LIDEGYIVAVKGLGGYHIASLATDDDVVQRLRERKRRP-RKPFAVMGLDTSILELLVYmDEADREVLESPQA----P 281
                                       689***********************************.*********************************....* PP

                                       CEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHC.TS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-S CS
                    Sua5_yciO_yrdC  78 itlllkrskeklpkevapglktvGvrlPdtplarlLleal.geplvaTSanlsgepsitdaeeveeelgeivdlild 153
                                       i ll kr+++++++ v+pgl++ Gv++++tpl+  Ll  + ++ lv+TS+n+sgep++ d e ++++l++ivd++l 
  gi|320101013|ref|YP_004176605.1| 282 ILLLPKREDSPVSRLVSPGLSHEGVFIAYTPLHFILLMHTrDKFLVMTSGNVSGEPMCRDDECARSKLSQIVDFFLV 358
                                       *******9999**********************87665552678********************************* PP

                                       S-.--SSS---EEEETTSSTSSECEX CS
                    Sua5_yciO_yrdC 154 gg.eiavgvdstVvdltegkpkilRr 178
                                       ++ +i ++vd++V++ t+g++ +lRr
  gi|320101013|ref|YP_004176605.1| 359 HDrDIVNRVDDSVLRKTGGEYVLLRR 384
                                       *************************8 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   1.3   1.1e-18   3.2e-15       1      33 [.     107     139 ..     107     140 .. 0.96
   2 !   55.6   2.0   1.1e-18   3.3e-15       1      34 []     157     191 ..     157     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.1e-18
                                       --HHHHHHHC-TTSTTTT-TT---TTTS--EEE CS
                           zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsl 33 
                                       +C+ Cl+E+ dp++RR+ ++f+sC +CGPr+s+
  gi|320101013|ref|YP_004176605.1| 107 VCKHCLEEVLDPSNRRYMYPFNSCAWCGPRFSM 139
                                       6******************************98 PP

  == domain 2  score: 55.6 bits;  conditional E-value: 1.1e-18
                                       --HHHHHHHC-TTS.TTTT-TT---TTTS--EEEE CS
                           zf-HYPF   1 lCedClrEykdpld.RRfhaqfisCtnCGPrlsli 34 
                                       lCedC rEy+dp++ RR+haq+isC++ GPrl+l+
  gi|320101013|ref|YP_004176605.1| 157 LCEDCMREYRDPSNvRRHHAQGISCPRDGPRLTLY 191
                                       7********************************96 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.6   1.1e+04      87      99 ..     169     181 ..     150     183 .. 0.79
   2 !   82.6   0.0   8.8e-27   2.6e-23       3     100 ..     400     499 ..     398     501 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.6
                            HypF_C  87 ievqHHhAHllav 99 
                                        +v  HhA  +++
  gi|320101013|ref|YP_004176605.1| 169 SNVRRHHAQGISC 181
                                       6799999999887 PP

  == domain 2  score: 82.6 bits;  conditional E-value: 8.8e-27
                            HypF_C   3 ekevLAlGaelkntfalakggqallsqhlGdlenletleayeealeeleklleik..pevivcDlhpdylstklaee 77 
                                       e+ev+A+G++l+nt  +  +++++l+q++Gdle+++++ ++ +a+e + + ++++   +viv+D+hp y+s++l  e
  gi|320101013|ref|YP_004176605.1| 400 EREVVAFGGDLNNTGGVGFEDKVVLTQYIGDLESYNAQVELLNAIEYMVRNYGVSlrDSVIVVDKHPLYHSRRLGVE 476
                                       689*************************************************9862267****************** PP

                            HypF_C  78 laekeklelievqHHhAHllavl 100
                                       +ae+++++++evqHH+AH+l ++
  gi|320101013|ref|YP_004176605.1| 477 YAERHGIPVVEVQHHYAHVLGAA 499
                                       *******************9876 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.0   1.8e-22   5.4e-19       2      85 .]       5      88 ..       4      88 .. 0.92
   2 ?   -3.7   0.0       5.8   1.7e+04      17      32 ..     494     509 ..     493     514 .. 0.78

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.8e-22
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppk.arvdeveveeleeeee 79
                                      r++vtG VQgvgFR+f+ rl +++gl+G+vrN    +Vei +eg+ee + +fl++l +++p+ a +dev +ee++  + 
  gi|320101013|ref|YP_004176605.1|  5 RIVVTGLVQGVGFRPFIDRLVRQIGLNGFVRNVGGSEVEIWVEGDEEGLYEFLAALFNEKPPpALIDEVVFEEESPLGY 83
                                      799*****************************************************9966666********99766666 PP

                   Acylphosphatase 80 fkdFei 85
                                       ++F+i
  gi|320101013|ref|YP_004176605.1| 84 -NGFTI 88
                                      .88887 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.8
                   Acylphosphatase  17 fvrrlAkelglkGyvr 32 
                                       +v  +A ++gl+G v 
  gi|320101013|ref|YP_004176605.1| 494 HVLGAAIDRGLSGRVA 509
                                       5667899999999885 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.1   6.2e+03     151     192 ..     214     264 ..     197     270 .. 0.62
   2 !    5.7   0.0    0.0034        10      71     101 ..     476     502 ..     434     517 .. 0.71
   3 !   10.7   0.0   0.00011      0.32     132     246 ..     606     732 ..     594     745 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.1
                                       .S......SCCHHHHHHHCTC...S.......EET...TEEE.CHHHHHHHHHH CS
                     Peptidase_M22 151 py......pggpkieklakeg...kkiefprplkg...ldfsfsGlktavlkel 192
                                       +y       gg +i +la +    ++++     k    ++f  +Gl+t++l++l
  gi|320101013|ref|YP_004176605.1| 214 GYivavkgLGGYHIASLATDDdvvQRLR---ERKRrprKPFAVMGLDTSILELL 264
                                       4444433347778888888773333322...22335668899999999998776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHCT--EEEEEHHHHHHHCCHCTS CS
                     Peptidase_M22  71 sfAkglalalnkPlvgVnhleahalaarlee 101
                                            +a  +++P+v V+h  ah+l a ++ 
  gi|320101013|ref|YP_004176605.1| 476 E----YAERHGIPVVEVQHHYAHVLGAAIDR 502
                                       4....45689***************998874 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00011
                                       ESSSEHHHHHHHHHHHHT..S....SCCH..HHHHHHCTC.S.......EET.........TEEE.CHHHHHHHHHH CS
                     Peptidase_M22 132 tlddaagealdkvarllglpy....pggp..kieklakeg.kkiefprplkg.........ldfsfsGlktavlkel 192
                                       tl   +g  +d va ll+ ++    +g+p   +e+la++g       r l g         + + + Gl t++++  
  gi|320101013|ref|YP_004176605.1| 606 TLASSTGRLIDMVAALLNPSIersfEGEPaiWLESLAHSGtP-----RLLEGvrffiddgvMRLDYYGLVTNIIEMR 677
                                       556667788888888886555666545553366888888842.....44434444455888999999**9*999988 PP

                                       ST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCH CS
                     Peptidase_M22 193 ek.evedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeee 246
                                        + e   laasf  +      e  +  +k ++++++v++GG a n++L ++l+e 
  gi|320101013|ref|YP_004176605.1| 678 GAvEPGVLAASFLYSLGYYYGELIAGTVKGEGVSSVVVSGGAAVNEYLYKGLKER 732
                                       555688899999999888888889999999********************99854 PP

>> zf-MYST  MYST family zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4       2.7     8e+03      34      40 ..     107     113 ..     107     113 .. 0.88
   2 ?   11.8   0.4   4.5e-05      0.13      17      52 ..     140     175 ..     136     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.7
                           zf-MYST  34 vCefClk 40 
                                       vC++Cl+
  gi|320101013|ref|YP_004176605.1| 107 VCKHCLE 113
                                       8****95 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.5e-05
                           zf-MYST  17 WYfSpYPeelankekLyvCefClkYmksakelerHk 52 
                                        Y SpY +e ++ +k  +Ce C++ +++ ++++rH 
  gi|320101013|ref|YP_004176605.1| 140 MYRSPYDRENTSMAKYVLCEDCMREYRDPSNVRRHH 175
                                       6*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 5188.33
//
Query:       gi|320101014|ref|YP_004176606.1|  [L=75]
Description: hydrogenase assembly chaperone HypC/HupF [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-22   77.5   0.4    6.9e-22   77.4   0.4    1.0  1  HupF_HypC  HupF/HypC family
  ------ inclusion threshold ------
       0.11   13.0   0.0       0.12   12.9   0.0    1.1  1  UPF0113_N  UPF0113 Pre-PUA 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 !   77.4   0.4   7.7e-26   6.9e-22       1      65 []       1      68 [.       1      68 [. 0.94

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 7.7e-26
                                      CCEEEEEEEEEEET....TEEEEECTTEEEEEEGTTCTTB-TT-EEEEETTEEEEEE-HHHHHHHHHHH CS
                         HupF_HypC  1 MCLaiPgkvveied....elAlvdvgGvrrevslalveevkvGdyVLvhvGfAiekideeeaeetlell 65
                                      MCL++Pg+v+++++    ++ +v+vgGv r+v  al e+vk+GdyV+vh+G+Ai +i++eeaeet++ll
  gi|320101014|ref|YP_004176606.1|  1 MCLGVPGEVLSVDEdkglRILKVKVGGVVRQVISAL-EDVKPGDYVIVHAGVAIGRINKEEAEETMRLL 68
                                      **************88877*************7777.67***************************986 PP

>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05      0.12      31      76 ..      13      60 ..       6      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                         UPF0113_N 31 dgtycfrlkkkrVyyvseellklaetikpen..lisaGtclGkftktk 76
                                      d+++ +r+ k +V  v  +++ ++e +kp    ++ aG+ +G+++k++
  gi|320101014|ref|YP_004176606.1| 13 DEDKGLRILKVKVGGVVRQVISALEDVKPGDyvIVHAGVAIGRINKEE 60
                                      3467899999******************998899**********9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 543.48
//
Query:       gi|320101015|ref|YP_004176607.1|  [L=345]
Description: hydrogenase expression/formation protein HypE [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   81.9   0.2    8.3e-23   81.2   0.2    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.4e-14   53.8   0.9    7.4e-14   52.2   0.9    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 !   81.2   0.2   9.2e-27   8.3e-23       1     152 [.     168     317 ..     168     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 9.2e-27
                                       STTEEEEEEETSSCTCCHHHHH.HHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslk.rkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       kpGd++++t  +  +ga+++++  ++le+++       ++d+  + + i  +++  ++  +v+aa+D T+GGL+ +l
  gi|320101015|ref|YP_004176607.1| 168 KPGDKIVVTNYIAEHGATILAAqLGMLEDAKGL-----RSDAKPLVKTILPVLEKYRD--GVNAARDPTRGGLAATL 237
                                       79***************9655403444444444.....99999999999999999996..***************** PP

                                       HHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
                            AIRS_C  77 aemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                                       +e+a+ sg+++ +d   +p++ e++     ++ ++l  +++G+ +++v++   d v+++l++ g+ + +vIGev++ 
  gi|320101015|ref|YP_004176607.1| 238 NEWARSSGLTIIVDRGSIPVRIEVAeflemLGVDPLTLASEGVAVLSVRSSIVDDVVEELRRNGE-NPSVIGEVVEP 313
                                       ***********************995555555555555***************************.79*******98 PP

                                       SSEE CS
                            AIRS_C 149 eels 152
                                       ++++
  gi|320101015|ref|YP_004176607.1| 314 RSSE 317
                                       8765 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 !   52.2   0.9   8.2e-18   7.4e-14       2      93 ..      55     157 ..      43     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 8.2e-18
                                       SSEEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHH CS
                              AIRS   2 Daavvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaee 68 
                                       D  +v+t d    ++ v+p+ f    iG +a+ ++l+Dl++mGArP+a+++++ ++      +le+vv ++ + +  
  gi|320101015|ref|YP_004176607.1|  55 DSFIVFTSD----SYTVKPIFFpggdIGGLAASGVLNDLVMMGARPVAFMDNIVVEegfplrDLEAVVGSMVKTLVD 127
                                       344799999....889999999******************************************************* PP

                                       TT-EEEEEEEEEESS.....EEEEEEEEEE CS
                              AIRS  69 lgvplvgGdtsfsne.....ptisvtavGl 93 
                                        +v+l+gGd +++++     ++is +a+G+
  gi|320101015|ref|YP_004176607.1| 128 NNVALIGGDFKVMPRgevdgIVISGFAIGV 157
                                       *************98999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2505.27
//
Query:       gi|320101016|ref|YP_004176608.1|  [L=515]
Description: dihydropteroate synthase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-12   45.2   0.1    5.6e-05   23.2   0.1    2.9  3  DUF4346          Domain of unknown function (DUF4346)
     0.0002   20.2   0.0    0.00034   19.4   0.0    1.2  1  CdhD             CO dehydrogenase/acetyl-CoA synthase delta s
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.065   12.9   0.1    2.1  2  Pterin_bind      Pterin binding enzyme
      0.076   12.8   0.0       0.22   11.3   0.0    1.7  2  RETICULATA-like  Protein RETICULATA-related


Domain annotation for each model (and alignments):
>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.48   2.1e+03      86     104 ..      35      53 ..      26      59 .. 0.80
   2 !   18.4   0.0   3.7e-07    0.0017       8      36 ..     424     452 ..     418     458 .. 0.91
   3 !   23.2   0.1   1.3e-08   5.6e-05      85     118 .]     476     509 ..     468     509 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.48
                           DUF4346  86 elpvtkldhaaYlGRelqr 104
                                       + pv+ +  + Yl Rel r
  gi|320101016|ref|YP_004176608.1|  35 PIPVAAMMSSEYLERELPR 53 
                                       678999999*******987 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.7e-07
                           DUF4346   8 kRaielDpaGYflikvdreaklivakhys 36 
                                       +R   +DpaG+f i+vd+e+++iv++hy+
  gi|320101016|ref|YP_004176608.1| 424 RRRTGMDPAGFFKIHVDHESGNIVVEHYK 452
                                       68889***********************7 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.3e-08
                           DUF4346  85 eelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                       e+   ++ dh  YlG el +a +aL++gkeY+qD
  gi|320101016|ref|YP_004176608.1| 476 ERRLASMHDHFFYLGYELSKAYIALKTGKEYVQD 509
                                       45667999*************************9 PP

>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.6e-08   0.00034      62     198 ..     181     318 ..     166     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.6e-08
                                       .ETTEEEE--EEEEE--SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHH CS
                              CdhD  62 krvgekltldaiairlistdPakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiae 138
                                       k+v    ++d++++    + P +  ++++++v++ +  p+ + + dp  l++a+   +d   ll + t   +ke+ e
  gi|320101016|ref|YP_004176608.1| 181 KAVAD--GADIVVLGFSMGKPQACIREVIAEVKERTRRPVGVDAPDPGLLREAAGWGAD---LLMSFTYSALKELGE 252
                                       55666..899***********999*****************************998884...9************** PP

                                       HHHHTT--EEEE...-.SSHHHHHHHHHH...HHCTT---EEEE---SH.....HHHHHHHHHHHH CS
                              CdhD 139 laleykvpvvll...sindleelkelark...llkagvkdivldPttaalGegleetidnvvriRr 198
                                       +    +v vvl+   +  + ++l++l +     l+ g ++i+ldP+  +  +gl  ++ +  ++Rr
  gi|320101016|ref|YP_004176608.1| 253 AWFPGDVGVVLVpepGAGGQDSLRSLLEAyrlALEKGATRIILDPVLSPPLNGLTASLWRYSEVRR 318
                                       ********999722234556666666433111356788*********9999******999999998 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.4e-05     0.065      19      96 ..     171     238 ..     166     253 .. 0.75
   2 ?   -0.9   0.0      0.24   1.1e+03     165     209 ..     291     334 ..     273     356 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSE CS
                       Pterin_bind  19 dldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagad 95 
                                       +ld ++a+a k v++GAdi+ +g   ++P+a  +          +v+++++++++ p+ +D  ++  +++A   gad
  gi|320101016|ref|YP_004176608.1| 171 SLDHIVARAVKAVADGADIVVLGFSMGKPQACIR----------EVIAEVKERTRRPVGVDAPDPGLLREAAGWGAD 237
                                       7899***********************9986544..........455555555566666666666666666666666 PP

                                       E CS
                       Pterin_bind  96 i 96 
                                       +
  gi|320101016|ref|YP_004176608.1| 238 L 238
                                       5 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.24
                                       GGEEEETTTTS.STTHHHHHHHHHTHHHHHHTTS.SEBEEEGTTGHH CS
                       Pterin_bind 165 erillDpgigf.gkteehnlellrrldelreale.vpvllGvSrksf 209
                                       +ri+lDp + +       +l    r +e+r++l  vp+l+Gv ++  
  gi|320101016|ref|YP_004176608.1| 291 TRIILDPVLSPpLNGLTASLW---RYSEVRRMLPgVPLLMGVGNITE 334
                                       568888877764222223333...33444444444999999888765 PP

>> RETICULATA-like  Protein RETICULATA-related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.9e-05      0.22     102     162 ..     177     237 ..     171     242 .. 0.94
   2 ?   -3.4   0.0       1.7   7.6e+03      11      34 ..     348     371 ..     345     375 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                   RETICULATA-like 102 qRvaafvykgaklaavGfiaglvgtglsnalialrkkldpsfesevkvppvlksalvygaf 162
                                       +R++  v  ga ++++Gf +g  +  + +++++++++ +  +  +++ p +l+ a+++ga 
  gi|320101016|ref|YP_004176608.1| 177 ARAVKAVADGADIVVLGFSMGKPQACIREVIAEVKERTRRPVGVDAPDPGLLREAAGWGAD 237
                                       799999*****************************************************85 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.7
                   RETICULATA-like  11 fkvllEevigvsasllaevekRke 34 
                                       + +++E+ +++  ++ a v++R++
  gi|320101016|ref|YP_004176608.1| 348 ASIGVEIGVEAYLTTEASVKTRGS 371
                                       456677777777777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3845.03
//
Query:       gi|320101017|ref|YP_004176609.1|  [L=237]
Description: flavoprotein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   67.5   0.1    1.8e-18   66.8   0.1    1.3  1  Flavoprotein  Flavoprotein
    2.2e-10   39.9  11.6    1.1e-06   28.2   2.2    3.1  2  Fer4          4Fe-4S binding domain
    2.9e-07   30.2  12.1    0.00081   19.4   3.1    2.3  2  Fer4_6        4Fe-4S binding domain
      1e-06   29.2   9.7    1.9e-06   28.4   9.7    1.5  1  Fer4_7        4Fe-4S dicluster domain
    4.9e-06   27.4   5.1     0.0036   18.2   0.3    2.2  2  Fer4_16       4Fe-4S double cluster binding domain
    6.1e-06   26.3  22.7    0.00065   19.8  12.9    2.1  2  Fer4_10       4Fe-4S dicluster domain
    2.1e-05   24.6   6.0    3.1e-05   24.0   6.0    1.3  1  Fer4_21       4Fe-4S dicluster domain
    0.00025   21.2   9.9    0.00038   20.5   9.9    1.3  1  Fer4_9        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.029   14.4  14.1      0.088   13.0   3.5    2.4  2  Fer4_2        4Fe-4S binding domain
      0.056   14.2  11.7        1.2    9.9   1.5    3.2  3  Fer4_15       4Fe-4S single cluster domain
       0.54   10.8  12.4         78    3.9  12.6    2.3  2  Fer4_17       4Fe-4S dicluster domain
        0.6   10.6  12.5       0.18   12.3   2.7    2.2  2  Fer4_8        4Fe-4S dicluster domain
        3.5    8.8  12.6        3.5    8.8   3.5    2.6  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.1   1.3e-21   1.8e-18       1     112 [.       3     133 ..       3     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.3e-21
                                       EEEEEEE-SSCGGGCH.HHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...............TCSSHHHHHHCT.. CS
                      Flavoprotein   1 kkillgiTGsvaaika.lellekLkkegievqvvltkaAkkfiskeklklaa...........redpilhielrr.. 63 
                                       k +++g+TG+ a + + ++++ +L + g++++ ++++aA+ ++s     l +           r             
  gi|320101017|ref|YP_004176609.1|   3 KSVAWGVTGAGAFMREsIDVMASLTETGVSITAYVSRAARSILSMY--GLLErlvavlqgpypR----------Gvv 67 
                                       5799***********99***************************44..4444344555555550..........044 PP

                                       ..................TESEEEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHC CS
                      Flavoprotein  64 ..................wadllviaPasantlakianGiadnlltlilra..takkpiliaPamnpam 112
                                                          +d+ v+ Pas+nt+aki+nGiad+l++++++   ++++ +li+P     +
  gi|320101017|ref|YP_004176609.1|  68 fedeeapgfpstgrlykgVYDIAVVSPASMNTVAKIVNGIADSLVSNMVMHaiKNNMRVLILP---VDL 133
                                       444555556666666666***************************99995568999*******...555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   2.2   1.9e-05     0.026       1      23 [.     142     166 ..     142     167 .. 0.85
   2 !   28.2   2.2   7.7e-10   1.1e-06       2      24 .]     175     197 ..     174     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                       EEEETTTSSS-THHHHH..STTTEE CS
                              Fer4   1 vvideekCigCGaCvev..CPvgAI 23 
                                       +vid  kC  C+ C+ +  CP+gA+
  gi|320101017|ref|YP_004176609.1| 142 IVIDRGKCSLCNWCAAAdsCPTGAL 166
                                       69************86544999997 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 7.7e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        +d +kC++C  C + CP+gAI+
  gi|320101017|ref|YP_004176609.1| 175 RVDASKCTRCYVCKDRCPYGAIS 197
                                       79*******************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 !   16.2   1.7     6e-06    0.0083       2      24 .]     142     166 ..     141     166 .. 0.94
   2 !   19.4   3.1   5.9e-07   0.00081       2      24 .]     174     196 ..     173     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
                            Fer4_6   2 veidpdkCigCgdCvrv..CPegai 24 
                                       ++id+ kC  C+ C+++  CP+ga+
  gi|320101017|ref|YP_004176609.1| 142 IVIDRGKCSLCNWCAAAdsCPTGAL 166
                                       89************99999****97 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 5.9e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       v++d++kC+ C+ C + CP+gai
  gi|320101017|ref|YP_004176609.1| 174 VRVDASKCTRCYVCKDRCPYGAI 196
                                       89********************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   9.7   1.4e-09   1.9e-06       1      52 []     148     195 ..     142     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.4e-09
                            Fer4_7   1 rCigCgaCvaa..CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C  C+ C+aa  Cp++a++ d++      ++v++d++kC+ C++C ++CP+ga
  gi|320101017|ref|YP_004176609.1| 148 KCSLCNWCAAAdsCPTGALRHDPY------HRVRVDASKCTRCYVCKDRCPYGA 195
                                       799*****97777********998......789*******************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.7   0.00039      0.54       1      24 [.     148     173 ..     148     179 .. 0.77
   2 !   18.2   0.3   2.6e-06    0.0036       1      27 [.     180     206 ..     180     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                           Fer4_16   1 rCgtCgkCa..evCPtnaikekkeke 24 
                                       +C  C+ Ca  ++CPt+a++++ + +
  gi|320101017|ref|YP_004176609.1| 148 KCSLCNWCAaaDSCPTGALRHDPYHR 173
                                       5999****73367*******996555 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.6e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiea 27 
                                       +C++C  C + CP +ai+ + e ++++
  gi|320101017|ref|YP_004176609.1| 180 KCTRCYVCKDRCPYGAISFDVEITVKP 206
                                       5*****************997777665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  12.9   4.7e-07   0.00065       2      56 .]     142     192 ..     141     192 .. 0.93
   2 !   19.2   2.2   7.2e-07     0.001       2      23 ..     174     195 ..     173     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.7e-07
                           Fer4_10   2 vvidddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +vid+ +C  C+ C +a  CP+      +    ++  +vr++ +kCt+c  C + CP
  gi|320101017|ref|YP_004176609.1| 142 IVIDRGKCSLCNWCAAAdsCPT------GALRHDPYHRVRVDASKCTRCYVCKDRCP 192
                                       799************9666***......999999999999****************9 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.2e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                       v++d+++C+rC  C++ CP+ +
  gi|320101017|ref|YP_004176609.1| 174 VRVDASKCTRCYVCKDRCPYGA 195
                                       6889***************933 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   6.0   2.2e-08   3.1e-05       2      58 ..     143     197 ..     142     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                           Fer4_21   2 ridedkCigCgkClia..CedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +id+ kC  C+ C+ a  C+   + a++ d+ ++++v +++C+ C +C + CP  ++i+
  gi|320101017|ref|YP_004176609.1| 143 VIDRGKCSLCNWCAAAdsCP---TGALRHDPYHRVRVDASKCTRCYVCKDRCPY-GAIS 197
                                       69***********9863377...799***************************5.8885 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   9.9   2.8e-07   0.00038       1      51 []     148     196 ..     148     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.8e-07
                            Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC  C+ C +a  Cp+g+ + d  +r +        +C+ C  C ++Cp gai
  gi|320101017|ref|YP_004176609.1| 148 KCSLCNWCAAAdsCPTGALRHDPYHRVRVDAS----KCTRCYVCKDRCPYGAI 196
                                       7*******66555*********9999988654....7*************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 ?    6.9   2.9    0.0054       7.4       2      22 .]     141     163 ..     141     163 .. 0.84
   2 ?   13.0   3.5   6.4e-05     0.088       3      22 .]     174     193 ..     171     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0054
                            Fer4_2   2 pvvvdtdrCigCgaCvsa..CPa 22 
                                       p+v+d+ +C  C+ C  a  CP+
  gi|320101017|ref|YP_004176609.1| 141 PIVIDRGKCSLCNWCAAAdsCPT 163
                                       689************75555**7 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.4e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       v vd+ +C++C  C + CP+
  gi|320101017|ref|YP_004176609.1| 174 VRVDASKCTRCYVCKDRCPY 193
                                       789***********999*95 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.2     0.003       4.1       1      18 [.     142     159 ..     142     160 .. 0.92
   2 ?    4.5   0.0     0.044        61      55      65 ..     157     167 ..     156     168 .. 0.89
   3 ?    9.9   1.5    0.0009       1.2       1      19 [.     174     192 ..     174     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.003
                           Fer4_15   1 VvvDrdaCigcglCvaea 18 
                                       +v+Dr +C  c+ C+a++
  gi|320101017|ref|YP_004176609.1| 142 IVIDRGKCSLCNWCAAAD 159
                                       89*************986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.044
                           Fer4_15  55 AaraCPvdAIr 65 
                                       Aa++CP++A+r
  gi|320101017|ref|YP_004176609.1| 157 AADSCPTGALR 167
                                       9*******985 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0009
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V+vD ++C+ c +C +++p
  gi|320101017|ref|YP_004176609.1| 174 VRVDASKCTRCYVCKDRCP 192
                                       89***************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 ?    3.5   1.9     0.075     1e+02      45      58 ..     148     163 ..     140     166 .. 0.75
   2 ?    3.9  12.6     0.056        78      41      59 ..     176     194 ..     148     196 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.075
                           Fer4_17  45 lCieCgeCe..rkCPq 58 
                                       +C+ C+ C+   +CP 
  gi|320101017|ref|YP_004176609.1| 148 KCSLCNWCAaaDSCPT 163
                                       6888888875566775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.056
                           Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                         as+C+ C  C+ +CP+g
  gi|320101017|ref|YP_004176609.1| 176 VDASKCTRCYVCKDRCPYG 194
                                       35899************97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2  13.5      0.18   2.4e+02       5      63 ..     149     193 ..     145     194 .. 0.55
   2 ?   12.3   2.7   0.00013      0.18       2      17 ..     178     193 ..     177     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                            Fer4_8   5 CieCgaCq..saCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       C  C  C   ++Cp+   +    +d+++++       +       + +Ct c  C+++Cp 
  gi|320101017|ref|YP_004176609.1| 149 CSLCNWCAaaDSCPTGALR----HDPYHRVRV-----D-------ASKCTRCYVCKDRCPY 193
                                       6666666555556643333....444444333.....1.......3567777777777775 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                            Fer4_8   2 lekCieCgaCqsaCpv 17 
                                       ++kC++C  C++ Cp 
  gi|320101017|ref|YP_004176609.1| 178 ASKCTRCYVCKDRCPY 193
                                       7899999999999994 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.8     0.049        67       1      15 []     149     165 ..     149     165 .. 0.84
   2 ?    8.8   3.5    0.0025       3.5       1      15 []     181     195 ..     181     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.049
                            Fer4_3   1 CtgCg..aCvevCPvgA 15 
                                       C  C+  a  ++CP+gA
  gi|320101017|ref|YP_004176609.1| 149 CSLCNwcAAADSCPTGA 165
                                       778877789999***98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct C+ C + CP+gA
  gi|320101017|ref|YP_004176609.1| 181 CTRCYVCKDRCPYGA 195
                                       **************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1846.74
//
Query:       gi|320101018|ref|YP_004176610.1|  [L=130]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-34  118.1   0.0    2.7e-34  117.9   0.0    1.0  1  DHNA           Dihydroneopterin aldolase
  ------ inclusion threshold ------
       0.16   12.4   0.0       0.19   12.1   0.0    1.2  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain


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 !  117.9   0.0   3.1e-38   2.7e-34       1     108 []      15     123 ..      15     123 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 3.1e-38
                                       -HHHHHHHHHHHHHHHHHHHHTT-EE.STTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTT CS
                              DHNA   1 tdrerAvFEagiklgalyHqfvGtPv.seesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgem 76 
                                       t+r+rAvFEagi+lg++ Hqf+G+Pv ++e+ e l ++ie+++++QPf ed++v+i+ +   e  + ++Yt+L++++
  gi|320101018|ref|YP_004176610.1|  15 TERDRAVFEAGIALGMIAHQFTGIPVrRREDLELLRRVIENAVKAQPFKEDARVEIKMDLQGEGGNPYDYTTLKTRH 91 
                                       79************************77899***************************987777777********** PP

                                       EEEEEEEEETTEEEEEEEEEETTTTEEEEEEE CS
                              DHNA  77 ldveitvkyeeaevkarleyieeldYplmkve 108
                                       +d++++v+y++++v+arl+yi eld++l+++e
  gi|320101018|ref|YP_004176610.1|  92 IDATVVVRYGGTRVTARLRYIPELDFNLAYIE 123
                                       ******************************96 PP

>> 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 ?   12.1   0.0   2.1e-05      0.19      14      69 ..      30      92 ..      22     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                                      HHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC.......EEGGGC CS
                     RNA_pol_A_bac 14 vvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge.......vtagdl 69
                                      ++aH ++ ip+++ ++le+l  + e + + + ++e+  ve+k++ +g+g          ++++
  gi|320101018|ref|YP_004176610.1| 30 MIAHQFTGIPVRRREDLELLRRVIENAVKAQPFKEDARVEIKMDLQGEGGnpydyttLKTRHI 92
                                      79****************665555554478999999999999999998866676666444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 943.57
//
Query:       gi|320101019|ref|YP_004176611.1|  [L=239]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-25   89.4   0.0    2.8e-25   89.0   0.0    1.1  1  MAF_flag10     Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.038   14.0   0.0    1.7  2  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.0   3.2e-29   2.8e-25       2     166 ..      37     192 ..      36     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 3.2e-29
                        MAF_flag10   2 nllknlkenlkpslkellnkfkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lD 77 
                                       +ll+++++  +  ++e+++   g+k a+++g G  L  +l ll +  + +++iaad+a+++Ll +g+kPDivv+ lD
  gi|320101019|ref|YP_004176611.1|  37 RLLEEMDNTVE--FDEVKRMADGKKAAVVFGCGRNLVRDLGLLMDA-STLLLIAADGATTVLLGHGVKPDIVVTdLD 110
                                       56677777776..788888666789******************755.89**************************** PP

                        MAF_flag10  78 pqeasyevfkeaekkgdiplvfasgvnpellkkykgpki.flvtgstqa..lelleeekneilfgGgsvantaldlA 151
                                       +  + y+ +++a+ +g +++v+a+g+n + ++k+ +  +  l+  stq+   + +       +fgG++++++a +lA
  gi|320101019|ref|YP_004176611.1| 111 G--YIYD-LQKASAEGAVTVVHAHGDNMHRVEKFVKGFKgPLIG-STQVepRPHV------YNFGGFTDGDRAAFLA 177
                                       *..5555.88999989*****************99888856554.5555345555......9*************** PP

                        MAF_flag10 152 vklgfkeIiliGqDl 166
                                       + lg++eI+l+G+Dl
  gi|320101019|ref|YP_004176611.1| 178 YALGIREIYLAGFDL 192
                                       **************9 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.3   2.7e+03      61      80 ..      26      46 ..      13      68 .. 0.55
   2 ?   14.0   0.0   4.3e-06     0.038       8      73 ..      82     142 ..      75     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.3
                     TPK_catalytic 61 kpdqdstDl.ekaialvleke 80
                                      ++dq++tD+    ++ + +  
  gi|320101019|ref|YP_004176611.1| 26 EKDQEATDVlSRLLEEMDNTV 46
                                      458888885133334444444 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.3e-06
                     TPK_catalytic   8 aslrvcaDgGanrlyeeekerlellpdvivGDlDSirpevkefyeskgteivkkpdqdstDlekai 73 
                                       + l ++aDg++  l+      ++++pd++v DlD    + ++  ++ ++++v+ +  + + +ek +
  gi|320101019|ref|YP_004176611.1|  82 TLLLIAADGATTVLL-----GHGVKPDIVVTDLDGYIYDLQKASAEGAVTVVHAHGDNMHRVEKFV 142
                                       34689**********.....9********************9999999***999977776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1751.13
//
Query:       gi|320101020|ref|YP_004176612.1|  [L=281]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  103.6   0.0    1.6e-29  103.2   0.0    1.1  1  GCHY-1    Type I GTP cyclohydrolase folE2


Domain annotation for each model (and alignments):
>> GCHY-1  Type I GTP cyclohydrolase folE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   8.9e-34   1.6e-29       1     255 [.       5     263 ..       5     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 8.9e-34
                                       .XXXXXXXXXX----SEEEEEEEEEE.EEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH...HS-SSEE CS
                            GCHY-1   1 lpDvqsekderkipldrVGvkgvklp.vkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevle...eaeeele 73 
                                       +pD++sek+++++ +drVG+ +++ p ++v+d      t+   +++fv+Lp  ++G+h+SR++e+     + + el+
  gi|320101020|ref|YP_004176612.1|   5 IPDIHSEKPSVELGVDRVGLLKLRAPpMRVED-----YTVLPVFKAFVNLPGYARGAHLSRIYEAYVrvvKPHGELS 76 
                                       59*********************986267776.....5899**********************98663323448999 PP

                                       GGGHHHHHHHHHHHTT.-SEEEEEEEEEEEEEE...E-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEEEEE- CS
                            GCHY-1  74 eksleeileellekleyaeraevelkfeyfiek...kapvsgkeglesyevtleaelerkeevkltvgvevpvttlC 147
                                        + l++++eell+  +y+++a v+++ +++ +    + p  + +g+ ++ +t++  +    +++ + g  v + ++C
  gi|320101020|ref|YP_004176612.1|  77 LDLLRTLAEELLRVNDYSDTALVSMRGRLYYTVargNVPEYSGNGFIYAGLTFKRGVG---SLREYSGGGVYGLSTC 150
                                       9*************************98765440014455555566666666666662...59************** PP

                                       HHHHHHS.....SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHHHHHHHHTS---HH CS
                            GCHY-1 148 PCskeisrell.eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEkavtekayenpkFvE 223
                                       PC+k+++r+l+ e  +H+Q+ ++   +e+  ++ +ve  ++++ +   +  +  + lKR DE+ ++++ ye   F E
  gi|320101020|ref|YP_004176612.1| 151 PCAKAVARHLYgEPYTHMQKVRIDALLES--RRLRVEPVEVFKRLSGIVHVP-RNHLKRIDEASFVREVYEDSSFTE 224
                                       ********9999788*********99994..567788899999998888887.5789******************** PP

                                       HHHHHHHHHHHS-TTEEEE..........EEEEEEE-TTTSS CS
                            GCHY-1 224 DvvRevaaaleeeerveef..........sveveneESiHnH 255
                                       D++R++  +l + ++               v+v+++E iH++
  gi|320101020|ref|YP_004176612.1| 225 DIARRASLELARLAA---SrgdtgldgvlYVRVRSYETIHEY 263
                                       **********54433...23468999999***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2166.10
//
Query:       gi|320101021|ref|YP_004176613.1|  [L=181]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   12.1   0.0       0.25   11.6   0.0    1.2  1  DUF5055   Domain of unknown function (DUF5055)


Domain annotation for each model (and alignments):
>> DUF5055  Domain of unknown function (DUF5055)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.4e-05      0.25       6      72 ..      96     166 ..      91     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                           DUF5055   6 kftyedkeytle....ftrrtvkemekkgfvaadieekpmttlpalfagaflahhrfekkdvineiysklt 72 
                                         t++d ++++     ftr   +   ++ f   di+  p t+l ++ +ga +a  ++e  + i+++  +++
  gi|320101021|ref|YP_004176613.1|  96 GHTFKDAHFIIVlcdwFTRECNSSAARNSFEHFDIHASPTTLLLSVENGAVKAMRKLEGVKRIDQLVEEVS 166
                                       56888888876333449999999**********************************99998988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1462.41
//
Query:       gi|320101022|ref|YP_004176614.1|  [L=125]
Description: desulfoferrodoxin ferrous iron-binding region [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-30  103.5   0.0    8.4e-30  103.2   0.0    1.0  1  Desulfoferrodox  Desulfoferrodoxin
    5.1e-10   39.6   0.0    6.5e-10   39.2   0.0    1.1  1  SoxY             Sulfur oxidation protein SoxY
  ------ inclusion threshold ------
       0.16   12.1   0.3       0.36   11.0   0.3    1.6  1  RS4NT            RS4NT (NUC023) domain


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   0.0   1.4e-33   8.4e-30       3      95 ..      19     117 ..      17     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.4e-33
                                       HTTTHTTSEEEEEESEEEETTEEEEEEEESSSS--BSSSS-EEEEEEEEEETTSS.......EEEE-TBS.ESEEEE CS
                   Desulfoferrodox   3 dekeekHvPvieadevvkagelfevkvkvgkipHpneeeHyIewielyleeegek.......rvelsaed.epevtf 71 
                                        +k e+H+P iea+++vk ge+f+vkv+vg  pHpn+ eH+I+wiely+eeeg++       r+e+++ + ep v +
  gi|320101022|ref|YP_004176614.1|  19 ISKVETHTPRIEAPDHVKPGEVFRVKVSVG--PHPNTVEHSIRWIELYFEEEGRAfnpvligRYEFTPVYsEPVVEV 93 
                                       57899*************************..************************************9956***** PP

                                       EEEESSSEEEEEEEEETTTEEEEE CS
                   Desulfoferrodox  72 tvklkkekklvalsyCnlHGlWes 95 
                                        +k++k ++l+a++yCnlHGlWes
  gi|320101022|ref|YP_004176614.1|  94 YLKIQKPGRLIAVEYCNLHGLWES 117
                                       **********************97 PP

>> SoxY  Sulfur oxidation protein SoxY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   1.1e-13   6.5e-10      17     108 ..      27     124 ..      13     125 .] 0.84

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.1e-13
                              SoxY  17 vkldaPeiAengavVpvtvsvd.lpgteadkvksiallvdkN...papl.aatfelgp.ageaevstrirlaetsnv 87 
                                        +++aP+ ++ g+v+ v+vsv  +p+t +++++ i l+ ++     +p+ + ++e++p   e+ v++ +++++   +
  gi|320101022|ref|YP_004176614.1|  27 PRIEAPDHVKPGEVFRVKVSVGpHPNTVEHSIRWIELYFEEEgraFNPVlIGRYEFTPvYSEPVVEVYLKIQKPGRL 103
                                       489*****************9525666666777799999986222456669*******99***************** PP

                              SoxY  88 ravaetsdgklyvaskeVkvt 108
                                       +av +++ + l+++ keVkv+
  gi|320101022|ref|YP_004176614.1| 104 IAVEYCNLHGLWESYKEVKVS 124
                                       ********************8 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3     6e-05      0.36       6      35 ..      25      51 ..      23      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6e-05
                                      -EETTTS-TTS---SSSSSEE----SSSS- CS
                             RS4NT  6 HLKrlaAPkhWpldkkegvfavkPspGPHk 35
                                      H  r+ AP+h    k + vf vk s GPH+
  gi|320101022|ref|YP_004176614.1| 25 HTPRIEAPDH---VKPGEVFRVKVSVGPHP 51
                                      6678999999...999*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1026.83
//
Query:       gi|320101023|ref|YP_004176615.1|  [L=100]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       468  (0.026103); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 798.67
//
Query:       gi|320101024|ref|YP_004176616.1|  [L=152]
Description: AsnC family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-13   48.6   0.1    1.4e-12   47.3   0.0    1.8  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.2e-10   40.3   0.0      4e-10   39.5   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    9.1e-10   37.9   1.7      1e-09   37.8   0.2    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00074   19.4   0.0     0.0015   18.5   0.0    1.5  1  HTH_11          HTH domain
     0.0029   18.1   0.1     0.0065   16.9   0.0    1.6  2  HTH_27          Winged helix DNA-binding domain
     0.0083   16.0   0.1       0.03   14.2   0.0    1.9  2  MarR_2          MarR family
     0.0097   15.7   0.1      0.018   14.9   0.1    1.4  1  HxlR            HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.021   14.9   0.0    1.3  1  NapD            NapD protein
      0.025   14.5   0.0       0.11   12.5   0.1    2.0  3  MarR            MarR family
      0.051   13.5   0.8       0.21   11.5   0.1    2.0  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.052   13.2   0.0        0.1   12.2   0.0    1.5  1  HTH_50          Helix-turn-helix domain
       0.06   13.5   0.6        0.1   12.8   0.1    1.6  2  HTH_34          Winged helix DNA-binding domain
       0.11   12.1   0.0        1.1    8.9   0.0    2.2  2  HTH_47          winged helix-turn-helix


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 !   47.3   0.0   9.8e-16   1.4e-12       1      42 []       9      50 ..       9      50 .. 0.99
   2 ?   -3.5   0.0       7.3     1e+04      16      21 ..      70      75 ..      63      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 9.8e-16
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDeiD  I+++L+e+aR +++e+A ++ lS  +v++Rv++Le
  gi|320101024|ref|YP_004176616.1|  9 LDEIDMFIIKELMENARKPFREIALKLKLSDVAVIKRVKKLE 50
                                      8****************************************8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.3
                     HTH_AsnC-type 16 aRisya 21
                                      +Risy+
  gi|320101024|ref|YP_004176616.1| 70 GRISYT 75
                                      799986 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 !   39.5   0.0   2.9e-13     4e-10       2      68 ..      76     138 ..      75     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.9e-13
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvarte 68 
                                       ++++ep++   l e++ +l+e ++V+ +   +Gd+d+l+ +++rd e+l+r+++e + s++gv ++ 
  gi|320101024|ref|YP_004176616.1|  76 GINVEPNK---LFEVAYRLKEKEYVKYLALASGDHDLLAVIWARDGEELQRIHEE-IKSIEGVVNIY 138
                                       69999999...*****************************************999.*******9986 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 !   37.8   0.2   7.3e-13     1e-09       1      48 []       9      56 ..       9      56 .. 0.98
   2 ?   -2.0   0.1       1.9   2.6e+03      40      48 .]      90      98 ..      90      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 7.3e-13
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lde+d  I+++L++n+r + re+A +l lS  +v +r+k+Le+ G+Ik
  gi|320101024|ref|YP_004176616.1|  9 LDEIDMFIIKELMENARKPFREIALKLKLSDVAVIKRVKKLESRGVIK 56
                                      7999*******************************************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                            HTH_24 40 rLeeeGlIk 48
                                      rL+e++++k
  gi|320101024|ref|YP_004176616.1| 90 RLKEKEYVK 98
                                      899****97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.1e-06    0.0015       5      54 ..      16      69 ..      14      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgr.GY 54
                                      i++ L+e+    +  e+A +L++S  +v +++k+Le+ g    + ++ +p + GY
  gi|320101024|ref|YP_004176616.1| 16 IIKELMENAR-KPFREIALKLKLSDVAVIKRVKKLESRGvikkYALIVDPASlGY 69
                                      7777777776.4889************************7777666666555565 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 !   16.9   0.0   4.7e-06    0.0065      11      50 ..      16      57 ..       7      73 .. 0.88
   2 ?   -3.1   0.0       8.7   1.2e+04      41      48 ..      90      97 ..      84      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.7e-06
                            HTH_27 11 lir..hrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                       i+  ++++rk  ++++ +l+++d ++++ +kkL+ +G++++
  gi|320101024|ref|YP_004176616.1| 16 IIKelMENARKPFREIALKLKLSDVAVIKRVKKLESRGVIKK 57
                                      4445569999*****************************954 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.7
                            HTH_27 41 kLtekGLv 48
                                      +L ek++v
  gi|320101024|ref|YP_004176616.1| 90 RLKEKEYV 97
                                      68888888 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.2e-05      0.03      23      53 ..      27      57 ..      13      63 .. 0.87
   2 ?   -1.4   0.0       1.6   2.2e+03       6      20 ..     105     119 ..     100     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLver 53
                                        +e+a +l+ls  av +++k+L+++G + +
  gi|320101024|ref|YP_004176616.1| 27 PFREIALKLKLSDVAVIKRVKKLESRGVIKK 57
                                      689************************9975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHCTTTS CS
                            MarR_2   6 aqarvLaaLgrrpgr 20 
                                        ++++La++ +r+g+
  gi|320101024|ref|YP_004176616.1| 105 GDHDLLAVIWARDGE 119
                                       578999999999886 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.3e-05     0.018       8      73 ..      14      80 ..       9      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEE.EE-TCGGGGH CS
                              HxlR  8 llilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveY.sltekGrsle 73
                                      + i+ el++  +k f e++ +l k+s    ++r ++Le+ g+i++ ++   P    Y +++ +G ++e
  gi|320101024|ref|YP_004176616.1| 14 MFIIKELMEnARKPFREIALKL-KLSDVAVIKRVKKLESRGVIKKYALIVDPASLGYgRISYTGINVE 80
                                      78999999967788********.*************************99999998844566666555 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.5e-05     0.021       8      68 ..      77     138 ..      76     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                              NapD   8 VqarperlaavkaalaalpgvEv.hasdeegklVvviEaesedeladtieaiealpgVlsas 68 
                                       +++ p++l +v+ +l++ + v + + ++++  l  vi a + +el ++ e+i++++gV+++ 
  gi|320101024|ref|YP_004176616.1|  77 INVEPNKLFEVAYRLKEKEYVKYlALASGDHDLLAVIWARDGEELQRIHEEIKSIEGVVNIY 138
                                       6789999**************972557777*****************************985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.7e-05      0.11      13      50 ..      21      58 ..      13      63 .. 0.84
   2 ?   -2.5   0.0       3.8   5.2e+03      28      47 ..      78      97 ..      77      98 .. 0.75
   3 ?   -1.7   0.0       2.1   2.9e+03      22      39 ..     130     147 ..     106     148 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.7e-05
                                      HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                       e+      e+a kl++s  +v + +++Le +G i+++
  gi|320101024|ref|YP_004176616.1| 21 MENARKPFREIALKLKLSDVAVIKRVKKLESRGVIKKY 58
                                      5555667789*************************997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                                      TS-HHHHHHHHHHHHHTTSE CS
                              MarR 28 gvskstvtrvldrLekkGli 47
                                      +v++  + +v+ rL +k+++
  gi|320101024|ref|YP_004176616.1| 78 NVEPNKLFEVAYRLKEKEYV 97
                                      66677778888899999987 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.1
                                       HHHHHHTS-HHHHHHHHH CS
                              MarR  22 eLakklgvskstvtrvld 39 
                                        +   +++ ++ +t v++
  gi|320101024|ref|YP_004176616.1| 130 SIEGVVNIYPAVLTDVIK 147
                                       444455666666666665 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   0.00015      0.21      14      54 ..      17      57 ..       9      60 .. 0.88
   2 ?   -0.3   0.0      0.75     1e+03      37      53 ..      82      98 ..      75     105 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                      CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                       + L+++ ++  +eia +l+++   v + +++Le++G++++
  gi|320101024|ref|YP_004176616.1| 17 IKELMENARKPFREIALKLKLSDVAVIKRVKKLESRGVIKK 57
                                      46799*********************************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.75
                                      HCHHHHHHHHHHCTSEE CS
                              TrmB 37 skvYevLrsLedkGlVe 53
                                      +k  ev  +L++k +V+
  gi|320101024|ref|YP_004176616.1| 82 NKLFEVAYRLKEKEYVK 98
                                      55555566666666664 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.4e-05       0.1       8      46 ..       9      48 ..       7      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                            HTH_50  8 veefErelikkayek.YpStRklAkrLGvShtaianklrk 46
                                      ++e++  +ik+++e+  + +R +A +L +S  a++++++k
  gi|320101024|ref|YP_004176616.1|  9 LDEIDMFIIKELMENaRKPFREIALKLKLSDVAVIKRVKK 48
                                      6778888888888873588*******************98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.3e-05       0.1       3      45 ..      14      56 ..      12      61 .. 0.93
   2 ?   -3.3   0.1       7.8   1.1e+04      38      46 ..      91      99 ..      84     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                            HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      ++++  L+++ +  f+e+  +l+++d +  + +kkLe+ g i+
  gi|320101024|ref|YP_004176616.1| 14 MFIIKELMENARKPFREIALKLKLSDVAVIKRVKKLESRGVIK 56
                                      689999********************************99886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.8
                            HTH_34 38 LekagYiev 46
                                      L++++Y+++
  gi|320101024|ref|YP_004176616.1| 91 LKEKEYVKY 99
                                      777778764 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.24   3.3e+02      51      77 ..      30      56 ..      25      57 .. 0.89
   2 ?    8.9   0.0   0.00079       1.1      30      52 ..      90     112 ..      74     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.24
                                      HHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 51 diAeriglpfdrvaaiaraLaeaglla 77
                                      +iA +++l+  +v++ +++L+  g+++
  gi|320101024|ref|YP_004176616.1| 30 EIALKLKLSDVAVIKRVKKLESRGVIK 56
                                      7899999999999999********997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00079
                                       ---HHHHHHHHHH-EEEEEHHHH CS
                            HTH_47  30 kqaemallwvLnlaDGkrsLldi 52 
                                       + +e++++++L+la G+++Ll +
  gi|320101024|ref|YP_004176616.1|  90 RLKEKEYVKYLALASGDHDLLAV 112
                                       5568999*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1134.42
//
Query:       gi|320101025|ref|YP_004176617.1|  [L=297]
Description: auxin efflux carrier [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-09   34.4  15.7    3.5e-05   22.4   1.8    2.1  2  Mem_trans  Membrane transport protein
  ------ inclusion threshold ------
        0.1   11.8   0.4       0.25   10.5   0.4    1.6  1  TraP       TraP protein


Domain annotation for each model (and alignments):
>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.8   3.9e-09   3.5e-05      62     134 ..      64     139 ..      24     149 .. 0.76
   2 !   17.3   7.2   1.4e-07    0.0013     240     385 ..     149     291 ..     140     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.9e-09
                         Mem_trans  62 rfiladvlvklivlillllgallskifkgslewtitlfslstlpNtlvlgipllkalyge......ygvslmvqvvv 132
                                       ++++a ++++  ++++ ++  l+++   ++ e+   lf+ st+pN ++lg+p+  al+g       yg+  +v+ v 
  gi|320101025|ref|YP_004176617.1|  64 DTWIAFSFIVF-TFVSAVSLSLIAR--GRPREYYGALFLASTFPNAVFLGFPVSMALFGSihvasiYGLVTLVLNVL 137
                                       56666666555.5556666666668..8999*****************************99888888888887777 PP

                         Mem_trans 133 lq 134
                                       l 
  gi|320101025|ref|YP_004176617.1| 138 LP 139
                                       65 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.4e-07
                         Mem_trans 240 lrklirnPntyssllglilslvsfkwnvimpkiiqksisilgdaglpmalfslGlfLalqpkkiacgnsvatfalav 316
                                       lr+ ++ P++++ + gl  +  ++ w   + + i++++    +a +  a+ +lG+ L l++  +    ++  + ++ 
  gi|320101025|ref|YP_004176617.1| 149 LRRILLMPALLGFIAGLGGHYAAPSW---FVNWITSALWWAPQALSYTATAVLGARLPLRMDVLRRNRRFLGVVALY 222
                                       55555555555555555555555555...46889999999999999999************9999999999999*** PP

                         Mem_trans 317 RlilgPlvmlvavlavgLrgslllvaivqaAlPqgivlfviAkeynvherelstllifgmlialpitlv 385
                                       R+++ P+v ++++l+  +   l  +a+++  +P++++ + iA++ +  ++++++  ++ +l  ++ +++
  gi|320101025|ref|YP_004176617.1| 223 RFLISPAVTALVLLVSRVDVGLSIQAVTVSLMPPAVMNTLIAERHGWMPELVASTTFLLTLAVVLCLPL 291
                                       **************9999999999*************************99776665555555555555 PP

>> TraP  TraP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   2.8e-05      0.25     122     155 ..     182     215 ..     173     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.8e-05
                              TraP 122 llLWallallytavavvigkrPvrrgklkkirvv 155
                                        l Wa  al yta av+  + P+r + l+++r +
  gi|320101025|ref|YP_004176617.1| 182 ALWWAPQALSYTATAVLGARLPLRMDVLRRNRRF 215
                                       456899***********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2320.12
//
Query:       gi|320101026|ref|YP_004176618.1|  [L=303]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-21   75.1  20.9    5.5e-21   75.1  20.9    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
    1.3e-06   28.2   0.2    1.3e-06   28.2   0.2    2.6  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 ?   -2.0   0.3      0.28   2.5e+03     161     179 ..      35      53 ..      18      55 .. 0.67
   2 !   75.1  20.9   6.1e-25   5.5e-21       1     183 [.     111     295 ..     111     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.28
                      BPD_transp_1 161 lviavlllnlvadilqrll 179
                                       +++ vll+ +++ il+ ++
  gi|320101026|ref|YP_004176618.1|  35 AGLTVLLIYVSLSILAPYI 53 
                                       5677777777777777666 PP

  == domain 2  score: 75.1 bits;  conditional E-value: 6.1e-25
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g+ +G++++ ++++ +d++l+ ++++ll++Ps+vl+i++       silg+  l+ ++i++lls+ p++r++r+++l
  gi|320101026|ref|YP_004176618.1| 111 GLAAGLVSG-YYGGLVDEILMHVVNFLLAMPSIVLMIVIG------SILGSNTLSvILIIGLLSWSPIARIVRSMVL 180
                                       7899*****.******************************......*********99******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       + ++  ++++ar lGa++  i+ +++lP+++p++i+  +l++  ++   ++l f+g ++ +g + +  il++ y ++
  gi|320101026|ref|YP_004176618.1| 181 SLREWAFIQVARSLGAGDSWIITRHILPAVAPVAIANTVLSVSTAIFSHAALVFMGVGN-IGEWNWGLILYNAYVSG 256
                                       ******************************************99988888888888444.77777777777777766 PP

                      BPD_transp_1 154 s.........nggvlalviavlllnlvadilqrlldprv 183
                                       +         + + ++l+ +  +++lv + + r ldpr+
  gi|320101026|ref|YP_004176618.1| 257 AlaagmwwyfIPPGVMLISLAYAVMLVGYGIERELDPRM 295
                                       677777666655555555555556666666666666665 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 !   28.2   0.2   1.5e-10   1.3e-06       4      51 .]      21      70 ..      18      70 .. 0.85
   2 ?   -2.6   0.4      0.65   5.8e+03      15      21 ..     107     113 ..      98     121 .. 0.54
   3 ?   -2.4   0.6      0.57   5.1e+03      30      32 ..     150     152 ..     137     168 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.5e-10
                            OppC_N  4 qdawrrFkrNklAvvglvilllllliaifaPliaPydp..qdliqnllpP 51
                                      ++++   + N+   +gl +ll+ + ++i+aP+i+Py+p  +d++  l+pP
  gi|320101026|ref|YP_004176618.1| 21 ARMLTIIRGNRSVKAGLTVLLIYVSLSILAPYITPYKPsdTDPSSILQPP 70
                                      566677789999**************************77666556***9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.65
                            OppC_N  15 lAvvglv 21 
                                       +Av+gl+
  gi|320101026|ref|YP_004176618.1| 107 TAVIGLA 113
                                       2444443 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.57
                            OppC_N  30 aif 32 
                                       +i+
  gi|320101026|ref|YP_004176618.1| 150 SIL 152
                                       333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2319.54
//
Query:       gi|320101027|ref|YP_004176619.1|  [L=321]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-40  137.5   8.4    4.2e-40  137.5   8.4    2.0  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2     0.045     8e+02     112     127 ..      12      27 ..       1      58 [. 0.57
   2 ?   -3.3   0.2      0.36   6.5e+03      14      36 ..      88     111 ..      79     114 .. 0.47
   3 !  137.5   8.4   2.3e-44   4.2e-40       1     184 [.     115     320 ..     115     321 .] 0.99

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.045
                      BPD_transp_1 112 tglilafggllggavl 127
                                       ++++ +f++l  +++l
  gi|320101027|ref|YP_004176619.1|  12 SSVASVFMLLTIAFIL 27 
                                       2222222222222222 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.36
                      BPD_transp_1  14 kkldkllrpliivll.slPsfvla 36 
                                        +   ll +l ++ll  +P +++ 
  gi|320101027|ref|YP_004176619.1|  88 PVAEVLLERLLNTLLlLVPAVLIS 111
                                       444444544444443145555543 PP

  == domain 3  score: 137.5 bits;  conditional E-value: 2.3e-44
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......................vilsilghlil 54 
                                       g+l+G+++a +r+++l k+l++   +l++lP+++l+ llvl+                         i++ l h++l
  gi|320101027|ref|YP_004176619.1| 115 GVLTGVVSAWKRGSRLEKALSGTALALYTLPTYWLGGLLVLASinylhlpvtgmgdygvgyssfmdHIKDLLSHMVL 191
                                       899*************************************888***********************9999******* PP

                      BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                       p+ +l+l+ ++++++l+r+++l++l +d+++++ra G ++ +i++k+ l+na+ p++t + ++++ ++ gavl+e++
  gi|320101027|ref|YP_004176619.1| 192 PLSTLVLVNYGGFTLLVRASMLDVLAEDYIRTYRAVGFGEGRILFKYGLKNAMLPTLTAISISIATSVSGAVLTETI 268
                                       ***************************************************************************** PP

                      BPD_transp_1 132 gswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       ++wpG+g+l+ ea  ++dy++ + g++l+++++v+l nl+adil+ l+dprvr
  gi|320101027|ref|YP_004176619.1| 269 FAWPGVGRLIYEAVFNRDYPLLQ-GAFLTVTVSVVLANLLADILYGLIDPRVR 320
                                       ***********************.****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2419.31
//
Query:       gi|320101028|ref|YP_004176620.1|  [L=587]
Description: family 5 extracellular solute-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-71  239.8   0.3    6.4e-71  239.3   0.3    1.2  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.3   0.3   3.6e-75   6.4e-71       1     362 [.      85     451 ..      85     465 .. 0.93

  Alignments for each domain:
  == domain 1  score: 239.3 bits;  conditional E-value: 3.6e-75
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       ++vp+LA+s we   D  t++f+L  +++F+DG p+tA+Dv+fsf  l+++ ++s++a+       ++++  +d+yt
  gi|320101028|ref|YP_004176620.1|  85 TYVPDLAAS-WE-YLDPHTVRFHLVSNATFHDGVPVTASDVEFSFH-LANQSWSSRSANVK----VVESMRILDNYT 154
                                       68*******.46.567778**************************6.8999******9999....6*********** PP

                                       EEEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TT.STTT.SCSSS CS
                         SBP_bac_5  78 vrftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpd.Ywgg.gkpkl 152
                                       v+ft ++  +lf+++ a +++ ++k+ ++  +d+++++  ++vg+GP +l+e+k gq++vle     Y+ +  +pk+
  gi|320101028|ref|YP_004176620.1| 155 VEFTVSSI-PLFFAMAASTIPIVPKHIWAGLSDPSTYSGYPVVGSGPLRLTEYKEGQYLVLEPYSGfYY-PwYLPKV 229
                                       ****9998.9999999999999999*****************************************654.669**** PP

                                       SEEEEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT.....STGGGSHHH CS
                         SBP_bac_5 153 driefkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtk.....kppfddkrv 223
                                       +ri++k++pd +++a+al++G++d v  ++p ++   l  ++g kv  +spg++++y+afN +     +p ++d +v
  gi|320101028|ref|YP_004176620.1| 230 NRIIVKFYPDVTSAANALLAGDVDAVgPYIPMAMYTVLASNPGFKV-FTSPGTTYFYIAFNVDpngtgNPTLRDLNV 305
                                       ***********************88877788888888899999999.****************************** PP

                                       HHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC...EE CS
                         SBP_bac_5 224 RqAlsyAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek...kl 297
                                       R+Al+yA +   + +++ +gy +pa+s+lp+s  +++++ kp+  ++++  A + L++aGyk g++g++ +    +l
  gi|320101028|ref|YP_004176620.1| 306 RKALAYATNISYLCDTAWHGYSKPATSVLPSSNIYHNKNLKPY--DFNLSRAVEVLESAGYKLGPNGVRVSGegtPL 380
                                       ***************************************9997..89********************99999***** PP

                                       EEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH........HHHHHHHHCTTESEEEEEEECTTSTT CS
                         SBP_bac_5 298 kltlllasgspaekaiaeliqqqlkkiGikvevktvdwa........atylervkdgdfdmillgwgadypdp 362
                                         tll++s  p +  +a++i++ +++iGi ++vk++d+         +   + v +  +dm l++w  d+ d 
  gi|320101028|ref|YP_004176620.1| 381 AYTLLVPSRFPEAVNAAQVIADWWRQIGISLTVKAMDTGsmsaiiwsN--VNGVVRLGHDMDLWDWIVDPNDV 451
                                       ************************************877899999642..34688999999999999996664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4101.49
//
Query:       gi|320101029|ref|YP_004176621.1|  [L=240]
Description: amino acid-binding ACT domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-10   39.6   2.6      5e-08   32.6   0.4    2.4  2  ACT_7     ACT domain
    0.00062   19.5   5.2     0.0016   18.2   0.2    3.0  3  ACT       ACT domain


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 !    6.9   0.1   0.00062       5.5      14      48 ..      76     113 ..      64     114 .. 0.81
   2 !   32.6   0.4   5.5e-12     5e-08       4      64 ..     165     226 ..     163     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00062
                                       -.---SS--HHHHHHHHHHTTT---...EEEE-SS-EE CS
                             ACT_7  14 sglpfdvtGivaklaspLaeagIsi...fqiStyrtdy 48 
                                       s++++ ++  ++k++++Lae  I++   ++i+ty++ +
  gi|320101029|ref|YP_004176621.1|  76 SRMNTTTPSPMSKVFRVLAESSIELktsLVIATYDSNI 113
                                       6788999999**************95556777888865 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 5.5e-12
                                       EEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   4 dgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLh 64 
                                        +++++ v+++  +++++G+v+ +++ La+ +++i+qi   + + +i+V+  d+ +A +aL+
  gi|320101029|ref|YP_004176621.1| 165 ADVSAIVVISPVENIETPGFVSYITTLLARRKVNILQIMsAHSDTIIVVDRGDALEAFKALE 226
                                       678999999996666***********************956666677889999999999997 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.55     5e+03      25      31 ..      17      23 ..      12      29 .. 0.82
   2 ?    2.5   0.0     0.014   1.2e+02      14      33 ..      86     105 ..      86     118 .. 0.77
   3 !   18.2   0.2   1.8e-07    0.0016      10      60 ..     181     226 ..     171     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.55
                                      TSEEEEE CS
                               ACT 25 giNidsi 31
                                      g+Ni si
  gi|320101029|ref|YP_004176621.1| 17 GVNISSI 23
                                      8999998 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHTTSEEEEEEE CS
                               ACT  14 LarvfgaladrgiNidsieq 33 
                                       +++vf++la+  i +    +
  gi|320101029|ref|YP_004176621.1|  86 MSKVFRVLAESSIELKTSLV 105
                                       589*******9887766655 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.8e-07
                                       STTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHH CS
                               ACT  10 rPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevle 60 
                                        PG  + ++++la+r +Ni  i ++ s     + ++vv+ +d+ ++ ++le
  gi|320101029|ref|YP_004176621.1| 181 TPGFVSYITTLLARRKVNILQIMSAHS-----DTIIVVDRGDALEAFKALE 226
                                       69*************************.....6799999999888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1804.80
//
Query:       gi|320101030|ref|YP_004176622.1|  [L=269]
Description: glutamine amidotransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  116.2   0.0    1.3e-33  116.1   0.0    1.0  1  GATase_4  Glutamine amidotransferases class-II
    1.1e-11   45.0   0.0      2e-11   44.2   0.0    1.5  1  GATase_6  Glutamine amidotransferase domain
     0.0068   16.3   0.0      0.011   15.6   0.0    1.4  1  GATase_7  Glutamine amidotransferase domain
  ------ inclusion threshold ------
       0.15   10.0   0.0       0.19    9.6   0.0    1.0  1  Nckap1    Membrane-associated apoptosis protein


Domain annotation for each model (and alignments):
>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.0   2.9e-37   1.3e-33       1     254 [.       1     259 [.       1     269 [] 0.82

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 2.9e-37
                          GATase_4   1 mceLLgmssnvptdisfsftgfaarg..gltdahadGwGiafyegkaarvfkdpepsaesplaelvreypiksknvv 75 
                                       mc+L+g+ +n p+d+ fsf     +     +++  +GwGia+ ++ + +v k+p p  +s+ a+ v +   + ++vv
  gi|320101030|ref|YP_004176622.1|   1 MCRLFGLYANRPVDVYFSFFESPMGSmvEFSHENPSGWGIAWLDEGGWHVYKEPLPLYSSAKAREVIQRRARGRIVV 77 
                                       9*****************976554441145667789***************************9999999******* PP

                          GATase_4  76 aHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl...egrfePv.GsTDsElafCelleelasrfeka 148
                                       +H+R a+ G+ +  nthp    +  r+w+fAHnG++++ +  l   ++r++ + G+TDsE  f  +++e +++    
  gi|320101030|ref|YP_004176622.1|  78 SHVRLASVGDRRRGNTHP----WLYRSWVFAHNGTIHDRRALLgllDERHRSLdGDTDSEAFFHLVVQEAEEYG--- 147
                                       *****************9....5689**********996666677766666666******99998888877776... PP

                          GATase_4 149 epsaeeleralaelakeiaelGvfnlllsdgralfa..hastrLvy...ilRkaPfgeaelk..dedlevdfeevtt 218
                                          +e + ra++++++e      +n++ sdg+ l+a  +a+t+L y     R+ P +  el    ++ +  ++ +  
  gi|320101030|ref|YP_004176622.1| 148 -DPVEGIRRAVEKIIAEGIGFSSLNFIASDGERLYAlrYATTSLDYytlYYRERPGEGFELRklSKETRQLIAMKLA 223
                                       .5789999***************************944555666441114599997666665323444445677788 PP

                          GATase_4 219 kedrvavvatepLtrdetWkklepGellvfrdGalv 254
                                        ++r+++va+ep++++  W+ +++ +l+v+++G  +
  gi|320101030|ref|YP_004176622.1| 224 YRERAVLVASEPMSDEPYWNPIPNKHLIVVNSGLDI 259
                                       8999***************************99544 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   4.6e-15     2e-11      11      87 ..      72     151 ..      59     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 4.6e-15
                          GATase_6  11 edevalaHvRlaivglaeeega.qPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall....e 82 
                                       ++++++ HvRla+vg + + g+ +P    ++ ++++hNG+i++ ++l   l + + +++ +++D+e  ++l+    e
  gi|320101030|ref|YP_004176622.1|  72 RGRIVVSHVRLASVGDR-RRGNtHPW--LYRSWVFAHNGTIHDRRALLGLLDE-RHRSLDGDTDSEAFFHLVvqeaE 144
                                       567*************8.88888***..*****************99999999.88899***********8866666 PP

                          GATase_6  83 elG..ee 87 
                                       e+G   e
  gi|320101030|ref|YP_004176622.1| 145 EYGdpVE 151
                                       6665533 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.6e-06     0.011      10      93 ..      90     183 ..      79     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                          GATase_7  10 eagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.............ewgeealer 73 
                                        ++  P +    ++ v+++nG+i + + l   L +++ + ++++D+e   +l+ +             + +e+++ +
  gi|320101030|ref|YP_004176622.1|  90 RGNTHPWL---YRSWVFAHNGTIHDRRALLGLLDERHRSLDGDTDSEAFFHLVVQeaeeygdpvegirRAVEKIIAE 163
                                       55556666...36899***********************************99886777777774444444444444 PP

                          GATase_7  74 lnGmfAfaiwdeeekrllla 93 
                                         G  ++  + ++ +rl++ 
  gi|320101030|ref|YP_004176622.1| 164 GIGFSSLNFIASDGERLYAL 183
                                       45555555555555555555 PP

>> Nckap1  Membrane-associated apoptosis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   4.3e-05      0.19     141     185 ..     108     154 ..     102     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 4.3e-05
                            Nckap1 141 riedrkavlglynaayellkgqsdps..ypRlgqlildydePlkkLq 185
                                        i+dr+a+lgl++  +  l g+ d++  ++ ++q  ++y +P+ ++ 
  gi|320101030|ref|YP_004176622.1| 108 TIHDRRALLGLLDERHRSLDGDTDSEafFHLVVQEAEEYGDPVEGIR 154
                                       599*******************9999989*************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1997.13
//
Query:       gi|320101031|ref|YP_004176623.1|  [L=364]
Description: tRNA synthetase class II (D K and N) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-41  140.2   0.0    9.5e-41  139.9   0.0    1.0  1  tRNA-synt_2  tRNA synthetases class II (D, K and N)


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 !  139.9   0.0   5.3e-45   9.5e-41       7     312 ..      44     357 ..      40     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 5.3e-45
                                       HTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT..TEEE-E-S-SHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       tRNA-synt_2   7 knryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrek.ekeffaLtqspqly 82 
                                       +n ++ +r+++v + +++ s v+ka+r++l+e+gf+e   Pi+       g r   vk + k  ++ +  + s  +y
  gi|320101031|ref|YP_004176623.1|  44 RNYHVYVRHPRVLRAVKTYSMVLKAMRSILDEHGFTELPSPIIGYVS-DPGLRG-AVKASIKmYGKVYEVQSSVIMY 118
                                       6789999************************************9994.333333.33334443679999******** PP

                                       HHHHHHCTHSEEEEEEEEE--S--B...TTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  83 lellivagidrvfqiaraFRaEdsr...tdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefv 156
                                       ++l+++  +++++  ar+ R E ++   t rhlaEFtq+++e s ++ +d+m ++ee +   vk++l+ + + +++ 
  gi|320101031|ref|YP_004176623.1| 119 KQLYASL-LGKIYYAARNLRVEPVEnasTGRHLAEFTQLDVEASLTTADDVMMLAEETLYGAVKHLLNYHSGLLTRE 194
                                       *****99.************9765444499************************************88887776666 PP

                                       TTTTS.EE-SSS.-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTST CS
                                       xxxxx.xxxxxx.xxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 157 irrns.kdlkkp.fkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddk 225
                                        +r   ++++kp ++r++y+ a+e l+ +      g +l+ + e al +     pv++  fP + + Fy   +  ++
  gi|320101031|ref|YP_004176623.1| 195 EERFLeETIIKPpYPRIDYDSAVELLRRKgftvehGRELSFDAEAALGD-IYGTPVWIQGFPTSSRGFYYIPDPGKP 270
                                       6665466666777*************98866665555555555555555.8889****************999999* PP

                                       TBBSEEEEEETTE..EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--.SEEEEEEEHHHHHHHHC CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 226 kltesyDllingv..ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGap.phgGlglGldRlvmlll 299
                                            y+l+++    E++ G  R+ ++e l +++k++g       k++w+le+ e Ga  p++G+glG++Rlv ++ 
  gi|320101031|ref|YP_004176623.1| 271 GYNVDYNLILPSRagEVLDGGCREYRYEHLVDRIKHHGEP---LGKYKWFLELAEAGAIqPTCGWGLGVERLVRYIH 344
                                       ***********7669***********************99...9************97549**************** PP

                                       T-SSGGGCSSS-X CS
                                       xxxxxxxxxxxxx RF
                       tRNA-synt_2 300 gsesIrdviaFPk 312
                                        ++++  +++ P+
  gi|320101031|ref|YP_004176623.1| 345 RLPHVAYASPHPR 357
                                       *****99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2832.24
//
Query:       gi|320101032|ref|YP_004176624.1|  [L=261]
Description: metal dependent phosphohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.7   0.0        0.1   12.8   0.0    1.5  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.8e-06       0.1      30     120 ..      98     175 ..      95     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-06
                                       HHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHH.H.....H CS
                                HD  30 laaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldledvaklirehheswegkkrp.r.....g 100
                                       l+ LlHD+G+ +++d              He +ga i+  ++ r       + kli   + +   +++  +     +
  gi|320101032|ref|YP_004176624.1|  98 LGSLLHDVGNSVHRD-------------MHERIGAVIAMPILDRV------LGKLIQDQSIRVKLRQEVmHaiyctS 155
                                       678*********999.............49999999988887776......66666666666665555541344557 PP

                                       HHCCTSCHHHHHHHHHHHHH CS
                                HD 101 laerqlslearivklaDrla 120
                                       ++++ l+ ea +vk+ D ++
  gi|320101032|ref|YP_004176624.1| 156 YDVECLTYEAGCVKVGDGVD 175
                                       77778888888888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1915.99
//
Query:       gi|320101033|ref|YP_004176625.1|  [L=255]
Description: PA14 domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   63.7   0.0    2.1e-17   63.3   0.0    1.2  1  PA14      PA14 domain
  ------ inclusion threshold ------
       0.13   12.8   0.1        1.2    9.7   0.1    2.2  1  GLEYA     GLEYA domain


Domain annotation for each model (and alignments):
>> PA14  PA14 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0   2.4e-21   2.1e-17      22     146 ..      52     166 ..      24     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 2.4e-21
                                       EESSSCTSBEGCCCTTT-GCGCCSCEEEEEEEEEBSSSEEEEEEETTCCCEEEEETTCCCEETT-TTS--TT----S CS
                              PA14  22 edtdkdiafawdtevpgegeaadnfsarwtGylkppesGtYtFkvasddgvrlsidgelvidnngqqekksnadast 98 
                                       e+ ++ i+f w + +p e+++  +f a++ G +k++ +GtY F v s+dg++ls+dg++++d +        +d ++
  gi|320101033|ref|YP_004176625.1|  52 ETISPRIDFTWFD-KPHEKVPSKRFIAEFKGFIKIDYPGTYRFYVVSSDGAILSVDGRVLVDAW--------FDQPP 119
                                       6677888999988.9*************************************************........66779 PP

                                       -EEEEEEE-TT-EE.EEEEEEEESSSSCCE..BEEEE-TTS-EEESBGC CS
                              PA14  99 eesatlyltaGkkY.pirieyfhagtdgsvhislswtspdgkeeeidee 146
                                       ++ ++ + + G+ Y  ir+ y+++++ g+v  +l w +pdg +e+i+++
  gi|320101033|ref|YP_004176625.1| 120 RLHSSPEIVLGRGYrRIRLLYYNRDGIGEV--TLGWIRPDGVAESIPSD 166
                                       9999999999999955**************..*********99999876 PP

>> GLEYA  GLEYA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00013       1.2       1      43 [.      75     117 ..      75     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                       EEEEEEEEE--SSSEEEEEEE.EEESEEEEEESBT.TBBTTBHH CS
                             GLEYA   1 falelrGYfyapktgtYtfslsnaDdiallwlGdk.Afscwtra 43 
                                       f+ e++G++  +  gtY f + ++D  a+l +     ++ w  +
  gi|320101033|ref|YP_004176625.1|  75 FIAEFKGFIKIDYPGTYRFYVVSSD-GAILSVDGRvLVDAWFDQ 117
                                       67899****************6555.555555444366666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1835.52
//
Query:       gi|320101034|ref|YP_004176626.1|  [L=290]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   17.1   0.1     0.0094   15.8   0.1    1.7  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0048   16.5   0.1      0.013   15.1   0.1    1.7  1  GntR             Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.053   13.3   0.4       0.21   11.4   0.0    2.0  2  SKA2             Spindle and kinetochore-associated protein 2
      0.085   12.8   0.0        0.2   11.7   0.0    1.6  1  PadR             Transcriptional regulator PadR-like family
       0.19   12.2   1.8        2.2    8.8   0.5    2.7  3  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.21   10.7   0.3        9.5    5.3   0.0    2.1  2  AI-2E_transport  AI-2E family transporter
        0.9    9.6   4.3         12    5.9   0.2    2.2  2  DUF1664          Protein of unknown function (DUF1664)


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.7e-06    0.0094      34      53 ..     267     286 ..     262     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.7e-06
                                       SSCHCHHHHHHHHHHCTSEE CS
                              TrmB  34 vprskvYevLrsLedkGlVe 53 
                                       v r kvYe+Lr+Le+kGl++
  gi|320101034|ref|YP_004176626.1| 267 VARDKVYEALRRLEEKGLIK 286
                                       7899**************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     5e-06     0.013      19      57 ..     251     288 ..     240     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-06
                                       -TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR  19 rpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57 
                                         G +L    +  a++ V r  v eALrrLe++gl+  +
  gi|320101034|ref|YP_004176626.1| 251 GNGGIL-DIPHFTAKYRVARDKVYEALRRLEEKGLIKLK 288
                                       556666.67777899********************9865 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 ?   -0.8   0.1      0.51   1.3e+03      48      72 ..      28      52 ..      22      65 .. 0.60
   2 ?   11.4   0.0   8.3e-05      0.21       4      75 ..      83     152 ..      80     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.51
                              SKA2 48 kkvkeelqaLkeqceellaekkeli 72
                                      k++ e +  +++ ++ + a+kk l 
  gi|320101034|ref|YP_004176626.1| 28 KNIEESIVLMERMIRSIEASKKGLE 52
                                      4555555566666666666666544 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.3e-05
                              SKA2   4 vdklealFqkaesdLdyvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidki 75 
                                       +++  alF+k   dL+ v+ rLe   q + p +a  + ++l +lk++  e+++++ q+  l  + ++ + +i
  gi|320101034|ref|YP_004176626.1|  83 ISGYIALFTKVLYDLTRVKLRLETITQIQEPMKA--LPEVLDELKRIEPEVEKINPQLVSLIRAIEQKVGSI 152
                                       677889****************987777666665..99****************999988877666555555 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.7e-05       0.2      26      48 ..     264     286 ..     257     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-05
                                       -CCTTHHHHHHHHHHHHHTTSEE CS
                              PadR  26 llelseGslYpaLkrLekeglve 48 
                                        +++   ++Y aL+rLe++gl++
  gi|320101034|ref|YP_004176626.1| 264 KYRVARDKVYEALRRLEEKGLIK 286
                                       46777789*************97 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         1   2.7e+03      14      66 ..      28      77 ..      26      85 .. 0.62
   2 ?    8.8   0.5   0.00087       2.2      27      63 ..      97     136 ..      81     153 .. 0.76
   3 ?    1.9   0.0      0.12   3.2e+02      13      34 ..     142     163 ..     136     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                           NPV_P10 14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                      k++++ +  ++  + ++++  +    l+  L++ + ++++  ++ ++Iq i  
  gi|320101034|ref|YP_004176626.1| 28 KNIEESIVLMERMIRSIEASKKG---LEMTLEEHTRKVKSSGAQDKEIQRIID 77
                                      56666666666666666665555...556677777766666666666666654 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00087
                           NPV_P10  27 vddvqenlpdvtelnekLdaqsaqLaelet...kvenIqd 63 
                                       +++v+  l+++t+++e + a+++ L+el+    +ve+I+ 
  gi|320101034|ref|YP_004176626.1|  97 LTRVKLRLETITQIQEPMKALPEVLDELKRiepEVEKINP 136
                                       5778888888888888888888888888776666777764 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.12
                           NPV_P10  13 ikavddkVdalqqqvddvqenl 34 
                                       i+a+++kV ++q + d+ ++  
  gi|320101034|ref|YP_004176626.1| 142 IRAIEQKVGSIQVSTDSSSAPY 163
                                       8999******999887766655 PP

>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0037       9.5      73     134 ..      31      91 ..      25     104 .. 0.77
   2 ?    3.7   0.0     0.011        28      75     128 ..     106     159 ..     100     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0037
                   AI-2E_transport  73 plliaqltqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsll 134
                                        + i+ ++++++s++a+ ++l+  l+e++++++    +++++++ +++  +ni ++i+  ++
  gi|320101034|ref|YP_004176626.1|  31 EESIVLMERMIRSIEASKKGLEMTLEEHTRKVKSSGAQDKEIQRIIDEESRNISGYIAL-FT 91 
                                       56677788999999999999999999999999999746999999999999999999842.33 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.011
                   AI-2E_transport  75 liaqltqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilss 128
                                        i+q+++ +k lp ++d+l++i  e++++ ++l +li+a++q++ +i  + +ss
  gi|320101034|ref|YP_004176626.1| 106 TITQIQEPMKALPEVLDELKRIEPEVEKINPQLVSLIRAIEQKVGSIQVSTDSS 159
                                       589999999************999999999999657888888877777666665 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   0.9     0.012        30      50      97 ..      37      84 ..      23      94 .. 0.85
   2 ?    5.9   0.2    0.0049        12      68     121 ..      97     153 ..      91     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                           DUF1664 50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls 97
                                      +e++  s++a k+ L+  +++  +k++++ +  kei++ ++e ++++s
  gi|320101034|ref|YP_004176626.1| 37 MERMIRSIEASKKGLEMTLEEHTRKVKSSGAQDKEIQRIIDEESRNIS 84
                                      78899999***********99999999999999999998888777765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0049
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvk....eaveglesklerie 121
                                       + rv  +l+  ++i++ +k  + ev ++l++i+ +ve+++    ++++ +e+k+ +i+
  gi|320101034|ref|YP_004176626.1|  97 LTRVKLRLETITQIQEPMK-ALPEVLDELKRIEPEVEKINpqlvSLIRAIEQKVGSIQ 153
                                       5677778888888877775.58888888999999988887322245566677777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2161.60
//
Query:       gi|320101035|ref|YP_004176627.1|  [L=386]
Description: AAA ATPase [Desulfurococcus mucosus DSM 2162]
Scores for 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  113.9   0.0    1.1e-32  113.2   0.0    1.3  1  AAA              ATPase family associated with various cellul
    6.1e-15   55.0   1.5    1.4e-14   53.9   1.5    1.6  1  MIT              MIT (microtubule interacting and transport) 
    1.9e-08   34.0   0.0    3.7e-08   33.0   0.0    1.5  1  AAA_lid_3        AAA+ lid domain
    6.6e-06   26.0   0.0    1.9e-05   24.6   0.0    1.9  1  Vps4_C           Vps4 C terminal oligomerisation domain
    7.5e-06   26.2   0.0    1.5e-05   25.1   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
      4e-05   23.4   0.0    0.00013   21.8   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00014   22.3   0.1       0.18   12.2   0.0    2.5  2  AAA_16           AAA ATPase domain
    0.00015   22.1   0.0     0.0099   16.2   0.0    3.0  2  AAA_22           AAA domain
    0.00022   21.8   0.0     0.0016   18.9   0.0    2.2  2  AAA_18           AAA domain
     0.0003   20.6   0.0    0.00053   19.8   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00035   19.9   0.2      0.012   14.9   0.0    2.4  3  TIP49            TIP49 P-loop domain
    0.00039   20.2   0.0    0.00067   19.4   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
    0.00042   20.0   1.4     0.0016   18.2   1.4    2.1  1  TPR_1            Tetratricopeptide repeat
    0.00063   19.8   0.0     0.0031   17.5   0.0    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0011   19.0   0.4        1.1    9.1   0.1    2.7  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0017   18.3   2.6     0.0034   17.4   0.7    2.6  2  TPR_2            Tetratricopeptide repeat
     0.0036   17.4   2.9     0.0089   16.2   1.1    2.8  2  TPR_8            Tetratricopeptide repeat
     0.0096   16.3   0.0      0.034   14.6   0.0    2.0  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.027   14.5   0.0    1.7  1  AAA_14           AAA domain
      0.015   14.9   0.1       0.14   11.8   0.0    2.2  2  AAA_25           AAA domain
      0.016   14.9   0.0      0.043   13.5   0.0    1.7  1  AAA_24           AAA domain
      0.018   14.9   0.0      0.053   13.4   0.0    1.8  1  Rad17            Rad17 P-loop domain
      0.026   14.8   0.0       0.05   13.8   0.0    1.6  1  AAA_28           AAA domain
      0.028   13.9   0.0      0.098   12.2   0.0    1.8  2  AAA_7            P-loop containing dynein motor region
      0.037   14.2   0.0      0.072   13.2   0.0    1.5  1  AAA_33           AAA domain
      0.056   13.1   0.0      0.093   12.4   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.075   12.8   0.4       0.16   11.8   0.4    1.5  1  DUF5113          Domain of unknown function (DUF5113)
      0.075   12.2   0.0       0.14   11.3   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.088   12.2   0.0       0.15   11.4   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.12   13.1   4.9        4.5    8.1   0.6    4.1  3  TPR_6            Tetratricopeptide repeat
       0.12   11.6   0.0       0.64    9.3   0.0    2.0  2  Zeta_toxin       Zeta toxin
       0.13   12.0   1.3       0.32   10.7   1.3    1.7  1  TPR_11           TPR repeat
       0.15   13.0   0.0        1.4    9.9   0.1    2.6  1  TPR_14           Tetratricopeptide repeat
       0.18   11.7   0.0        3.1    7.7   0.0    2.2  2  NACHT            NACHT domain
       0.19   12.4   0.4       0.89   10.3   0.3    2.2  2  TPR_16           Tetratricopeptide repeat
       0.21   11.9   0.0       0.38   11.0   0.0    1.4  1  Hydin_ADK        Hydin Adenylate kinase-like domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.0   2.2e-35   1.1e-32       1     131 [.     142     276 ..     142     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 2.2e-35
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksr 74 
                                       +ll+GppG+GKT la a+a+e+++ ++++s ++++sk++g++ek+++++f++a+e a   kp+i+fiDE+d+l +  
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEIDAVLINVSPATIMSKWLGDAEKNVKKVFDKAREYAsqdKPVIIFIDEVDSLLQPL 218
                                       69******************************************************9**999***********9999 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTS...SSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkk...eskvivigatnrpdkldpallrgRfdrkieie 131
                                        g+e + e+r+ nq+l e+dg+k+k   + +++v+gatn+p++ld  ++ +Rf+++i+++
  gi|320101035|ref|YP_004176627.1| 219 -GNEVGGEKRMRNQFLIEMDGLKSKenkKMPLFVVGATNKPWTLDIGFI-RRFEKRIYVP 276
                                       .99*********************97765669*****************.7******997 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 !   53.9   1.5   2.8e-17   1.4e-14       2      64 ..       8      71 ..       7      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.8e-17
                               MIT  2 dkAlelvkkAveeDnagnyeeAlelYkealelLlqalke.kneerrellrekieeYleRaeeLk 64
                                      dk++e+++kAv +D+ag+ye A+++Y  a++lL++ lk   ++   e++r  i++Y +R+  L+
  gi|320101035|ref|YP_004176627.1|  8 DKGIEYAHKAVSADKAGDYESAIKYYNAAIDLLSKYLKLyPDSPLAETYRDLIQKYRNRVSILE 71
                                      8*************************************55999****************99887 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   7.5e-11   3.7e-08       1      33 [.     302     334 ..     302     359 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 7.5e-11
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr 33 
                                       ++d+++LAe+Te+yS AD+a++++e   +  ++
  gi|320101035|ref|YP_004176627.1| 302 SIDYDKLAELTENYSPADIASIVKEVQNNVAEE 334
                                       58***********************88777666 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 !   24.6   0.0   3.8e-08   1.9e-05      26      61 .]     349     384 ..     319     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.8e-08
                            Vps4_C  26 ePpvtlkDflkalkkarptVskeDLekheeFTkefG 61 
                                        +p+t +Df+k+++k +p++ ++ Le ++e+ +++G
  gi|320101035|ref|YP_004176627.1| 349 LRPLTTDDFIKVIEKRKPSIDPSWLEAYKEWQDKYG 384
                                       459****************************99998 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   3.1e-08   1.5e-05       6      81 ..     142     215 ..     139     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.1e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                       ill gp g+Gktela ala+ +++     li +   +++     ++e+ v++   ++  y ++++  i+++DE+d  
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEIDA----VLINVSPATIMSkwLGDAEKNVKKVFDKAREYASQDKPVIIFIDEVDSL 214
                                       7899******************96....33333333333334449******************************76 PP

                                       - CS
                             AAA_2  81 h 81 
                                        
  gi|320101035|ref|YP_004176627.1| 215 L 215
                                       5 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.6e-07   0.00013      35      70 ..     141     176 ..     105     271 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.6e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                                        +ll+GpPG Gkt la  +a+e+++ l   s  ++ 
  gi|320101035|ref|YP_004176627.1| 141 GILLFGPPGCGKTELAIALANEIDAVLINVSPATIM 176
                                       59*********************9877665544432 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00036      0.18      25      48 ..     140     163 ..     110     173 .. 0.82
   2 !    7.5   0.0    0.0099       4.9     117     146 ..     185     213 ..     170     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00036
                            AAA_16  25 elvllsGesGvGKsslvrellral 48 
                                       + +ll G++G+GK+ l+ +l++++
  gi|320101035|ref|YP_004176627.1| 140 QGILLFGPPGCGKTELAIALANEI 163
                                       789*************98888776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0099
                            AAA_16 117 srllellkrllallsrderplvlvlDdlqw 146
                                       + +  ++ ++ +++s+ ++p+++++D+++ 
  gi|320101035|ref|YP_004176627.1| 185 KNVKKVFDKAREYASQ-DKPVIIFIDEVDS 213
                                       6667778888899999.999*******995 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     2e-05    0.0099       8     105 ..     142     219 ..     139     257 .. 0.66
   2 ?   -1.5   0.0       5.7   2.8e+03      51      70 ..     318     337 ..     270     358 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                       ++++G++G+GKT l+  l+++            + v+++++  t    ++++ l + +    +   + + ++++ ++
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEI-----------DAVLINVSPAT----IMSKWLGDAE----K---NVKKVFDKARE 196
                                       799*****************75...........67888887777....5555555555....3...77778888888 PP

                            AAA_22  85 alraravielliiDEaqhlr...s 105
                                       ++++ +  +++ iDE++ l     
  gi|320101035|ref|YP_004176627.1| 197 YASQDKP-VIIFIDEVDSLLqplG 219
                                       8888888.8999999999643441 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.7
                            AAA_22  51 tsskdllrellralglelka 70 
                                        + +++ +e+ +++ +el++
  gi|320101035|ref|YP_004176627.1| 318 ADIASIVKEVQNNVAEELNE 337
                                       24445555555555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.3e-06    0.0016       1      44 [.     142     203 ..     142     246 .. 0.75
   2 ?    0.1   0.0       2.3   1.1e+03      25      67 ..     299     338 ..     266     356 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.3e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe 44 
                                       Ill G+pG+GKt+la +L+++  ++                   n+++v+ + + + ++d++
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEIdAVlinvspatimskwlgdaEKNVKKVFDKAREYASQDKP 203
                                       99****************99975557777888777777877777777777777766666666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.3
                            AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                       ++ ++d+ k  +l + + p+   +   +++++++++ ++l+e 
  gi|320101035|ref|YP_004176627.1| 299 SIDSIDYDKLAELTENYSPA---DIASIVKEVQNNVAEELNEK 338
                                       66677777777777777777...77777788888888887775 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 !   19.8   0.0   1.1e-06   0.00053       3      71 ..     144     211 ..     142     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                   Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                         G pGcGK+ l   l+++   +l  ++p a + ++++ +++++  + +d++ + ++++ k  i+++DE 
  gi|320101035|ref|YP_004176627.1| 144 LFGPPGCGKTELAIALANEIdAVLINVSP-ATIMSKWLGDAEKNVKKVFDKAREYASQD-KPVIIFIDEV 211
                                       5688*************999766666666.99******9999999999**999999997.6889999*96 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-05     0.012      51      76 ..     140     165 ..     136     180 .. 0.87
   2 ?   -2.7   0.0       5.1   2.5e+03     263     288 ..     184     212 ..     169     214 .. 0.58
   3 ?    2.0   0.0      0.19        96     202     266 ..     270     335 ..     258     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelge 76 
                                       +++Ll Gp+g Gkt laia+++e+ +
  gi|320101035|ref|YP_004176627.1| 140 QGILLFGPPGCGKTELAIALANEIDA 165
                                       68*********************974 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                                       XXXXXXXXXXXX...XXXXXXXXXXXXXX CS
                             TIP49 263 nkkvakyveegk...aeivpGvlfiDevh 288
                                       +k v+k  ++ +   ++  p ++fiDev 
  gi|320101035|ref|YP_004176627.1| 184 EKNVKKVFDKAReyaSQDKPVIIFIDEVD 212
                                       44454444433211134457789999996 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                                       S--------S---S----XXXXXXXXXXXXXXXXXXXXXXXX....XXX.XXXXXXXXXXXXXXXX CS
                             TIP49 202 ekdefvelPkGevekkkevvqevtLhdlDvanarpqdllslllqllksk.kteiteklreeinkkv 266
                                       ek  +v+ P+ ev+k+  +     L d+  +++   d l+ l+++ ++   + i +++++++ + +
  gi|320101035|ref|YP_004176627.1| 270 EKRIYVPPPNKEVRKQLFIHYIGKLKDVYSIDSIDYDKLAELTENYSPAdIASIVKEVQNNVAEEL 335
                                       66789999*****988765555579**********9999999888776414555555555554443 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 !   19.4   0.0   1.4e-06   0.00067      47      70 ..     139     162 ..     100     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                         IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                       +++i+l+Gp+G GK+ laial+ e
  gi|320101035|ref|YP_004176627.1| 139 SQGILLFGPPGCGKTELAIALANE 162
                                       689******************987 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.4   3.1e-06    0.0016       4      31 ..      13      40 ..      11      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-06
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1  4 lynlGnayfklgkydeAleyyekALeln 31
                                      +  +++   k g+y+ A++yy+ A+ l 
  gi|320101035|ref|YP_004176627.1| 13 YAHKAVSADKAGDYESAIKYYNAAIDLL 40
                                      7789999******************985 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 !   17.5   0.0   6.3e-06    0.0031       2      76 ..     142     213 ..     141     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.3e-06
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                       +lL GppG+gK+ela  la  + + +  ++ +  t  ++ +g  e kn ++++ +   + +  ++ i+++DEv+ 
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEIDAVL--INVSPATIMSKWLGDAE-KNVKKVFDKAREYASQDKPVIIFIDEVDS 213
                                       89************999998776543..44444444444444444.34444444444443333888888888875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0     0.007       3.5      23      42 ..     142     161 ..     134     166 .. 0.84
   2 !    9.1   0.1    0.0023       1.1      93     131 ..     174     215 ..     157     234 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.007
                          ATPase_2  23 yfiYGpegsGKtaLlkeiie 42 
                                       ++++Gp g+GKt L   +++
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALAN 161
                                       689**********9877666 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                          ATPase_2  93 eilkeksklvfkaielllekikkkgkk...iiiiiDelqkli 131
                                       +i+++   +++k+++++++k ++ + +   +ii+iDe+  l 
  gi|320101035|ref|YP_004176627.1| 174 TIMSKWLGDAEKNVKKVFDKAREYASQdkpVIIFIDEVDSLL 215
                                       345555666777777777777776666666999*****8876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.7   6.8e-06    0.0034       4      30 ..      13      39 ..      10      43 .. 0.88
   2 ?   -1.5   0.0       7.7   3.8e+03      17      24 ..     191     198 ..     179     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.8e-06
                             TPR_2  4 lynlGlayyklgdyeeAleafekAlel 30
                                      +   + ++ k+gdye A++++++A+ l
  gi|320101035|ref|YP_004176627.1| 13 YAHKAVSADKAGDYESAIKYYNAAIDL 39
                                      667899999****************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.7
                             TPR_2  17 yeeAleaf 24 
                                       +++A+e+ 
  gi|320101035|ref|YP_004176627.1| 191 FDKAREYA 198
                                       37777775 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.1   1.8e-05    0.0089       4      30 ..      13      39 ..      13      49 .. 0.93
   2 ?   -1.7   0.0       9.3   4.6e+03       8      28 ..      53      74 ..      52      75 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekalel 30
                                      y +++   +k gdye+A++yy+ a++l
  gi|320101035|ref|YP_004176627.1| 13 YAHKAVSADKAGDYESAIKYYNAAIDL 39
                                      778899999***************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 9.3
                                      HHHH.HHTT-HHHHHHHHHHHH CS
                             TPR_8  8 gsiy.lklgdyeeAkeyyekal 28
                                      + +y +  ++y + ++ +ek++
  gi|320101035|ref|YP_004176627.1| 53 AETYrDLIQKYRNRVSILEKYV 74
                                      5566455678899999999987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.7e-05     0.034       1      26 [.     142     167 ..     142     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.7e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i+l+Gp+g+GK+ la  La+++   l
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEIDAVL 167
                                       689****************9997655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.3e-05     0.027       5      75 ..     142     213 ..     139     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikell.....vkkesilyinldderdkkladpekllelileklkeekktylflDEiqe 75 
                                       +++ G+  +GKT l+  l++e       v++  i+   l d ++  ++    + +  +e ++++k  ++f+DE+  
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEIDavlinVSPATIMSKWLGDAEKNVKK----VFDKAREYASQDKPVIIFIDEVDS 213
                                       6899***********999976664444444444444434443333333....3344444333368899*****976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00027      0.14      36      54 ..     142     160 ..     131     164 .. 0.89
   2 ?    0.1   0.0         1   5.1e+02     123     159 ..     184     219 ..     167     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pg+GKt la+ la
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALA 160
                                       79***************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                            AAA_25 123 gtlltadvdaleaaieevegvrlvviDplsralggde 159
                                       ++ ++ ++d+ ++ + +  +++ + iD ++++l+   
  gi|320101035|ref|YP_004176627.1| 184 EKNVKKVFDKAREYASQ-DKPVIIFIDEVDSLLQPLG 219
                                       44467788888888888.67*******9999988733 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   8.7e-05     0.043       5      89 ..     142     226 ..     139     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.7e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidelee 79 
                                       il++Gp+g GKT la  l  + ++++i++   +  +  + ++  ++++++ d++ e a +++   +++iD +d l +
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALanEIDAVLINVSP-ATIMSKWLGDAEKNVKKVFDKAREYASQDK-PVIIFIDEVDSLLQ 216
                                       89*************9998888899999988.448888888866688888888888766555.56999******999 PP

                            AAA_24  80 lclaevirqn 89 
                                          +ev   +
  gi|320101035|ref|YP_004176627.1| 217 PLGNEVGGEK 226
                                       9999886554 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   0.00011     0.053      28     106 ..     113     201 ..      89     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                             Rad17  28 ieevkewlkadvLesrkkr.........iLLisGPsGCgkstvvkvLskelgiklrewlnpvslke.pdnqksdfkg 94 
                                       +eevk++lk +v+   k            +L+ GP+GCgk+     L+ e    l++ + ++ + +     ++++k 
  gi|320101035|ref|YP_004176627.1| 113 LEEVKQALKRSVIYPVKTPqlyplgwsqGILLFGPPGCGKTELAIALANEIDAVLINVSPATIMSKwLGDAEKNVKK 189
                                       677778877776644433235665555556789********999999999988887766555443312336667777 PP

                             Rad17  95 ltekesrflsqi 106
                                       +++k  ++ sq 
  gi|320101035|ref|YP_004176627.1| 190 VFDKAREYASQD 201
                                       777777666665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0    0.0001      0.05       2      23 ..     142     164 ..     141     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                            AAA_28   2 ivitGgestGKTtlleaLaar.g 23 
                                       i ++G++++GKT l+ aLa++ +
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEiD 164
                                       789****************8654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002     0.098      35     110 ..     141     212 ..     136     216 .. 0.81
   2 ?   -2.3   0.0       5.5   2.7e+03      89     101 ..     269     281 ..     265     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr.rkgvygPpggkklvvFvDDln 110
                                        +ll Gp G+GKt ++  l +++d      + in+s  t  ++     e++++k   k    + + k +++F+D+++
  gi|320101035|ref|YP_004176627.1| 141 GILLFGPPGCGKTELAIALANEID-----AVLINVSPATIMSKWLGDAEKNVKKVfDKAREYASQDKPVIIFIDEVD 212
                                       689****************99999.....788888888888888877888887762344456778999******986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.5
                             AAA_7  89 rrkgvygPpggkk 101
                                        +k++y+Pp++k+
  gi|320101035|ref|YP_004176627.1| 269 FEKRIYVPPPNKE 281
                                       5799******997 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   0.00014     0.072       2      30 ..     142     170 ..     142     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllss 30 
                                       +ll G+pG+GK+ la  l+++ +avl++ 
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEIDAVLINV 170
                                       6899****************999999875 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 ?   12.4   0.0   0.00019     0.093       8      75 ..     133     206 ..     131     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                                       HS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS......SEEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   8 lfpivqGqrtlipgafgvGktvisqslskqsnsd......daiiyvgiGergnevaevleefpegtimkrtvlv 75 
                                       l+p++  q +l++g  g+Gkt+++ +l+++ ++        +i     G  +++v++v+++ +e    ++ v++
  gi|320101035|ref|YP_004176627.1| 133 LYPLGWSQGILLFGPPGCGKTELAIALANEIDAVlinvspATIMSKWLGDAEKNVKKVFDKAREYASQDKPVII 206
                                       7899999*********************9974445555422444455888888888888888886655555554 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00031      0.16       9      49 ..      11      51 ..       4      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                           DUF5113  9 ndYanlayylnvegeyeeALeyldsaleylNahyekYakkk 49
                                       +Ya+ a  +   g+ye+A++y + a+++l ++ + Y ++ 
  gi|320101035|ref|YP_004176627.1| 11 IEYAHKAVSADKAGDYESAIKYYNAAIDLLSKYLKLYPDSP 51
                                      58********************************9998776 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.14      15      84 ..      95     170 ..      88     212 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                            DUF815  15 alepveevdevklddLvgidkqkealven......teqfleglpannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                        lep ++ ++ +++dLv++++ k+al++       t q+     ++ +LL+G  G+GK  l  al ne+ +  + +
  gi|320101035|ref|YP_004176627.1|  95 VLEPDKRSNKNTFKDLVDLEEVKQALKRSviypvkTPQLYPLGWSQGILLFGPPGCGKTELAIALANEIDAVLINV 170
                                       57777888999999***********999722222255666666799*********************998765333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00031      0.15      25      43 ..     142     160 ..     137     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt la +l+
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALA 160
                                       89**********9987765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.6    0.0091       4.5      17      33 .]      34      50 ..      14      50 .. 0.59
   2 ?    1.2   0.1       1.5   7.3e+02      21      30 ..      54      63 ..      53      65 .. 0.87
   3 ?   -1.4   0.0       9.8   4.9e+03       6      23 ..     180     198 ..     179     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0091
                                      HHHHHHHHHHHHH-TT- CS
                             TPR_6 17 dkAlealerlikeYPdS 33
                                       +A+++l + +k YPdS
  gi|320101035|ref|YP_004176627.1| 34 NAAIDLLSKYLKLYPDS 50
                                      35666666777777766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.5
                                      HHHHHHHHH- CS
                             TPR_6 21 ealerlikeY 30
                                      e++++li++Y
  gi|320101035|ref|YP_004176627.1| 54 ETYRDLIQKY 63
                                      79*******9 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 9.8
                                       HHHHHHH.HHHHHHHHHHH CS
                             TPR_6   6 lalsyrk.lgdtdkAleal 23 
                                       l+ + ++  +  dkA+e+ 
  gi|320101035|ref|YP_004176627.1| 180 LGDAEKNvKKVFDKAREYA 198
                                       67777777778999*9986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0013      0.64      19      41 ..     142     164 ..     138     175 .. 0.85
   2 ?   -0.9   0.0       1.7   8.5e+02       3      21 ..     189     208 ..     187     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                        Zeta_toxin  19 illgGqpGAGKselaellkdele 41 
                                       ill G pG+GK+ela +l++e++
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEID 164
                                       7899**************99983 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                        Zeta_toxin   3 ellkdkk.ypsqerPklill 21 
                                       +++++++ y sq++P++i++
  gi|320101035|ref|YP_004176627.1| 189 KVFDKAReYASQDKPVIIFI 208
                                       56788888999*****9996 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.3   0.00064      0.32       7      26 ..      23      42 ..      22      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00064
                            TPR_11  7 qGkyeeAieaYkkAlkldPd 26
                                       G+ye Ai+ Y++A++l ++
  gi|320101035|ref|YP_004176627.1| 23 AGDYESAIKYYNAAIDLLSK 42
                                      59*************99655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0028       1.4      14      37 ..      23      53 ..      13      61 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0028
                            TPR_14 14 lGdpdeAiallrrala.......laPddaea 37
                                      +Gd++ Ai+++++a++       l+Pd++ a
  gi|320101035|ref|YP_004176627.1| 23 AGDYESAIKYYNAAIDllskylkLYPDSPLA 53
                                      6777777777777766444444377777654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0062       3.1       3      24 ..     142     163 ..     140     169 .. 0.88
   2 ?    1.8   0.0      0.39     2e+02      54     100 ..     172     225 ..     165     290 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0062
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       ++l G++G+GKT L+  la ++
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEI 163
                                       6789***********9999876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.39
                                       HCHHHCCCCTS--SSS-C...CHHHHCCSCCCEEEEEE-STT-SS-TCH..... CS
                             NACHT  54 ladllfsqlpepaapvse...vwavllelperlLlilDglDelvtdlgq....k 100
                                       +a+++ + l + +++v++   +  + +++ + + + +D +D l + lg+    +
  gi|320101035|ref|YP_004176627.1| 172 PATIMSKWLGDAEKNVKKvfdKAREYASQDKPVIIFIDEVDSLLQPLGNevggE 225
                                       5555666666677777774445567889999999*********99999966553 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3    0.0018      0.89      41      62 ..      17      38 ..      13      51 .. 0.58
   2 ?    4.3   0.1      0.13        65      13      32 ..      33      52 ..      33      57 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0018
                            TPR_16 41 gdaalrqgrlaeAaalyraalr 62
                                      +++a ++g+++ A+ +y+aa++
  gi|320101035|ref|YP_004176627.1| 17 AVSADKAGDYESAIKYYNAAID 38
                                      4455555555555555555552 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                            TPR_16 13 yddAaaaleaalkrdpssPd 32
                                      y +A+ +l  +lk++p+sP+
  gi|320101035|ref|YP_004176627.1| 33 YNAAIDLLSKYLKLYPDSPL 52
                                      56777888888888877775 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00077      0.38       2      30 ..     142     170 ..     141     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00077
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       i++ G+P  GKt+ a++La + +a l+++
  gi|320101035|ref|YP_004176627.1| 142 ILLFGPPGCGKTELAIALANEIDAVLINV 170
                                       7789*******************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      781  (0.0435607); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); 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: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 2769.01
//
Query:       gi|320101036|ref|YP_004176628.1|  [L=61]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-33  114.6   2.6    1.5e-33  114.5   2.6    1.0  1  Cren7     Chromatin protein Cren7
  ------ inclusion threshold ------
      0.036   14.1   0.1      0.065   13.3   0.0    1.5  2  DUF4585   Domain of unknown function (DUF4585)


Domain annotation for each model (and alignments):
>> Cren7  Chromatin protein Cren7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   2.6   1.6e-37   1.5e-33       1      58 []       1      58 [.       1      58 [. 0.99

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 1.6e-37
                                      XSS-S-EEEE-TTS-EEEE--SEEEEESSTTS--EEEEEEE-TTT--EEEEEE-TTS- CS
                             Cren7  1 eackkpvkVktpeGkeleLvPvKvWqLaPkgkkGvkvgLFkdPetgkyfRakvpddyP 58
                                      ++c+++vkVktp+G+eleLvPvKvWqL+P+g+kGvkvgLF+dPe g+yfR+kvp++yP
  gi|320101036|ref|YP_004176628.1|  1 MPCTEKVKVKTPSGRELELVPVKVWQLNPRGRKGVKVGLFQDPESGRYFRTKVPENYP 58
                                      79*******************************************************9 PP

>> DUF4585  Domain of unknown function (DUF4585)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.72   6.4e+03      45      47 ..      11      13 ..       4      25 .. 0.51
   2 ?   13.3   0.0   7.2e-06     0.065       9      25 ..      39      55 ..      33      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.72
                           DUF4585 45 vps 47
                                       ps
  gi|320101036|ref|YP_004176628.1| 11 TPS 13
                                      332 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.2e-06
                           DUF4585  9 lLlDpesGqyfvvdlPv 25
                                      l +DpesG+yf   +P 
  gi|320101036|ref|YP_004176628.1| 39 LFQDPESGRYFRTKVPE 55
                                      67899999999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 461.03
//
Query:       gi|320101037|ref|YP_004176629.1|  [L=403]
Description: dihydroorotate dehydrogenase family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-33  114.2   0.0      4e-28   98.5   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
    3.4e-12   45.6  18.1      2e-07   30.5   1.0    2.7  3  Fer4          4Fe-4S binding domain
    7.9e-12   45.1   8.0    2.2e-11   43.7   7.9    1.8  1  Fer4_21       4Fe-4S dicluster domain
    2.4e-11   44.0  10.2    5.2e-11   43.0  10.2    1.6  1  Fer4_7        4Fe-4S dicluster domain
    1.7e-09   37.7   8.9      3e-09   36.9   8.9    1.4  1  Fer4_9        4Fe-4S dicluster domain
    2.4e-09   36.7  12.2    0.00022   21.1   2.4    2.7  2  Fer4_2        4Fe-4S binding domain
    1.9e-08   34.0  17.1    0.00012   22.0   1.3    2.7  2  Fer4_6        4Fe-4S binding domain
    7.5e-07   29.2  11.6    2.4e-06   27.6  10.7    2.3  2  Fer4_10       4Fe-4S dicluster domain
    5.2e-06   27.3   7.6     0.0035   18.3   2.0    2.5  2  Fer4_16       4Fe-4S double cluster binding domain
    1.5e-05   24.6   0.4    2.3e-05   24.0   0.4    1.3  1  NMO           Nitronate monooxygenase
    0.00026   21.8   6.4       0.17   12.7   0.3    2.3  2  Fer4_22       4Fe-4S dicluster domain
    0.00028   21.3  12.1     0.0015   19.0  11.5    2.4  2  Fer4_8        4Fe-4S dicluster domain
     0.0014   18.1   0.0      0.011   15.2   0.0    2.3  3  His_biosynth  Histidine biosynthesis protein
     0.0033   17.9   9.0       0.36   11.4   1.1    2.6  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
     0.0092   15.0   4.3      0.038   13.0   3.4    2.4  2  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.012   16.1  18.8      0.067   13.7   2.9    2.7  2  Fer4_4        4Fe-4S binding domain
      0.015   15.8  12.6        2.3    8.8  12.7    2.4  1  Fer4_17       4Fe-4S dicluster domain
      0.022   15.5  13.2       0.71   10.6   1.7    3.0  2  Fer4_15       4Fe-4S single cluster domain
       0.04   14.9  20.9      0.055   14.4   4.6    3.0  2  Fer4_3        4Fe-4S binding domain
      0.047   12.7   0.1       0.13   11.2   0.0    1.7  2  IMPDH         IMP dehydrogenase / GMP reductase domain
       0.17   11.0   0.1       0.27   10.3   0.1    1.2  1  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   2.9e-05     0.025       2      57 ..       4      59 ..       3      70 .. 0.83
   2 !   98.5   0.0   4.7e-31     4e-28     154     295 .]     173     312 ..     161     312 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                                      G-EEETTEEESSSEEE-TT.SSTTSSSHHHHHCTTSSEEEEEEE-SS-B--S-S--E CS
                            DHO_dh  2 latkvlglkfknpiglAaG.fdkegeeilkllklgfgaieigsvtpkpqeGnpkPrv 57
                                      l+++++glk+knp+++Aa  +  + e++ +l+++g+ga+  +++  kp    p+P +
  gi|320101037|ref|YP_004176629.1|  4 LSVELAGLKLKNPLMNAACpVSRDYEAMRELVDAGVGAVVAKTISVKPAI-VPRPSM 59
                                      7899************996488899999****************999865.455555 PP

  == domain 2  score: 98.5 bits;  conditional E-value: 4.7e-31
                                       HHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTT..SSEEEEEGGGHH CS
                            DHO_dh 154 lkvvkevskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkan..ktGGlsGkalkd 228
                                       +k+++e  ++p++ Kl+P  +  ++ + +++l + ++dgi++tNt+   l+id+++  ++     + G +sG+alk+
  gi|320101037|ref|YP_004176629.1| 173 AKALRESVSIPIFPKLSP--FTPNIPELVKELEKVGVDGIVATNTIGPALHIDVETGMPIVGGpyGYGWMSGPALKP 247
                                       577788889*********..8889999*****************************999987668999********* PP

                                       HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       +al+v+ + + ++k  +p+IgvGGi+ g D++e+++aGAs+vq+ ta   egp ++ +i ke++e L
  gi|320101037|ref|YP_004176629.1| 248 LALAVVSQAALNTK--LPVIGVGGISRGLDVIEYFMAGASAVQICTAALVEGPGVFTRILKEVNEWL 312
                                       *******9988888..***********************************************9865 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       9.3     8e+03      17      20 ..      21      24 ..      20      24 .. 0.83
   2 !   25.3   4.1     1e-08     9e-06       1      22 [.     343     364 ..     343     366 .. 0.90
   3 !   30.5   1.0   2.4e-10     2e-07       2      23 ..     377     398 ..     376     399 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.3
                                      HSTT CS
                              Fer4 17 vCPv 20
                                      +CPv
  gi|320101037|ref|YP_004176629.1| 21 ACPV 24
                                      8**7 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1e-08
                                       EEEETTTSSS-THHHHHSTTTE CS
                              Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                       +v+de kCigCG C++vC ++A
  gi|320101037|ref|YP_004176629.1| 343 PVVDEKKCIGCGFCEQVCNYDA 364
                                       69****************7777 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 2.4e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        id  kC gCG+C +vCP+ AI
  gi|320101037|ref|YP_004176629.1| 377 RIDLTKCYGCGLCTSVCPTRAI 398
                                       69*******************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 !   43.7   7.9   2.5e-14   2.2e-11       2      57 ..     344     398 ..     343     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 2.5e-14
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       ++de+kCigCg C ++C+  ++   +  +k+v+++   +C GC lC+svCP+  +i
  gi|320101037|ref|YP_004176629.1| 344 VVDEKKCIGCGFCEQVCNYDAVHVEDAGGKRVARIDLTKCYGCGLCTSVCPT-RAI 398
                                       69****************5555544566788999999**************7.666 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0  10.2     6e-14   5.2e-11       1      52 []     349     397 ..     349     397 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 6e-14
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +CigCg+C+++C ++a+ ++++    g++ ++id +kC+gCg C +vCPt a
  gi|320101037|ref|YP_004176629.1| 349 KCIGCGFCEQVCNYDAVHVEDA---GGKRVARIDLTKCYGCGLCTSVCPTRA 397
                                       7******************887...567789******************976 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   8.9   3.5e-12     3e-09       1      51 []     349     398 ..     349     398 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3.5e-12
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC+gCg C+++C++++v  ++a++k+  r++  ++C+gCg C+ +Cp+ ai
  gi|320101037|ref|YP_004176629.1| 349 KCIGCGFCEQVCNYDAVHVEDAGGKRVARID-LTKCYGCGLCTSVCPTRAI 398
                                       7****************99999999998775.459*************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 !   21.1   2.4   2.6e-07   0.00022       2      20 ..     342     360 ..     341     362 .. 0.93
   2 !   20.2   2.5     5e-07   0.00043       3      22 .]     376     395 ..     374     395 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.6e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                       p+vvd+ +CigCg C ++C
  gi|320101037|ref|YP_004176629.1| 342 PPVVDEKKCIGCGFCEQVC 360
                                       799**************** PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       + +d  +C gCg C+s+CP+
  gi|320101037|ref|YP_004176629.1| 376 ARIDLTKCYGCGLCTSVCPT 395
                                       568999*************7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   4.2   3.1e-07   0.00026       2      23 ..     343     364 ..     342     365 .. 0.93
   2 !   22.0   1.3   1.4e-07   0.00012       1      24 []     375     398 ..     375     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.1e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       +++d+ kCigCg C+ vC ++a
  gi|320101037|ref|YP_004176629.1| 343 PVVDEKKCIGCGFCEQVCNYDA 364
                                       89****************9887 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.4e-07
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       v++id  kC gCg C++vCP+ ai
  gi|320101037|ref|YP_004176629.1| 375 VARIDLTKCYGCGLCTSVCPTRAI 398
                                       6899*****************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 ?   -1.1   0.0       2.5   2.1e+03      17      32 ..      20      30 ..      19      49 .. 0.63
   2 !   27.6  10.7   2.8e-09   2.4e-06       3      56 .]     344     394 ..     342     394 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.5
                           Fer4_10 17 kaCPadltsvgakgea 32
                                      +aCP+     +  +ea
  gi|320101037|ref|YP_004176629.1| 20 AACPV-----SRDYEA 30
                                      68*99.....333333 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.8e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v+d+++Ci+Cg C ++C +     +  + a ++ + r+++ kC gcg C+++CP
  gi|320101037|ref|YP_004176629.1| 344 VVDEKKCIGCGFCEQVCNY---DAVHVEDAGGKRVARIDLTKCYGCGLCTSVCP 394
                                       789**************33...5555666777888888***************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 !   11.8   0.3   0.00042      0.36      51      66 ..     347     362 ..     322     368 .. 0.71
   2 !   18.3   2.0     4e-06    0.0035       1      19 [.     382     400 ..     382     403 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00042
                           Fer4_16  51 qeaitgCdiCqdvCPa 66 
                                       +++++gC+ C++vC +
  gi|320101037|ref|YP_004176629.1| 347 EKKCIGCGFCEQVCNY 362
                                       5789999999999965 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                       +C +Cg C++vCPt+ai+ 
  gi|320101037|ref|YP_004176629.1| 382 KCYGCGLCTSVCPTRAIHF 400
                                       5****************86 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.4   2.7e-08   2.3e-05     123     227 ..     193     295 ..     151     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-08
                               NMO 123 lpteevvarlkeagvvliptissvkearkv.earGaDalivqGpeaGG.hqGtpevgdkglfaLvpqvldavdiPvi 197
                                       ++ +e+v++l+++gv  i+ + ++  a  +  + G+   iv Gp + G + G p+ +    +a+v q++   ++Pvi
  gi|320101037|ref|YP_004176629.1| 193 PNIPELVKELEKVGVDGIVATNTIGPALHIdVETGM--PIVGGPYGYGwMSG-PALK-PLALAVVSQAALNTKLPVI 265
                                       555677888888888888888887766554145555..47788776551555.4442.456788888888888**** PP

                               NMO 198 AaGGiidrrgvaaaLalGAsgvqigtrfLl 227
                                         GGi ++ +v   + +GAs+vqi t+ L+
  gi|320101037|ref|YP_004176629.1| 266 GVGGISRGLDVIEYFMAGASAVQICTAALV 295
                                       **************************9886 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   0.3    0.0002      0.17      76      93 ..     344     361 ..     330     364 .. 0.84
   2 !   11.6   1.3   0.00046      0.39      81      94 ..     382     395 ..     372     401 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                           Fer4_22  76 kfgesgCvGCgRCieacp 93 
                                        ++e++C+GCg C+++c+
  gi|320101037|ref|YP_004176629.1| 344 VVDEKKCIGCGFCEQVCN 361
                                       468999***********7 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00046
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                       +C GCg C+++cp+
  gi|320101037|ref|YP_004176629.1| 382 KCYGCGLCTSVCPT 395
                                       55555555555554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.1   5.2e+03      13      23 ..      20      31 ..      19      46 .. 0.71
   2 !   19.0  11.5   1.7e-06    0.0015       3      63 ..     348     395 ..     346     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.1
                            Fer4_8 13 saCpvlrrtk.k 23
                                      +aCpv r+   +
  gi|320101037|ref|YP_004176629.1| 20 AACPVSRDYEaM 31
                                      579998887643 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.7e-06
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       +kCi+Cg+C++ C   +  + h  da g++ +   +         l +C +cg Ct+vCp+
  gi|320101037|ref|YP_004176629.1| 348 KKCIGCGFCEQVC---NYDAVHVEDAGGKRVA---R-ID------LTKCYGCGLCTSVCPT 395
                                       69*********99...4455789999999777...2.23......689************7 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   1.1e+03      83     107 ..      26      50 ..      26      56 .. 0.85
   2 ?   -2.6   0.0       3.5     3e+03     151     167 ..     197     213 ..     193     215 .. 0.81
   3 !   15.2   0.0   1.3e-05     0.011      60     120 ..     248     309 ..     243     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                                       SSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  83 rsledveelleagadkviigtaavk 107
                                       r++e+++el++ag+  v+  t  vk
  gi|320101037|ref|YP_004176629.1|  26 RDYEAMRELVDAGVGAVVAKTISVK 50 
                                       6889999999999999999888776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                                       HHHHHHHHTT-SEEEEE CS
                      His_biosynth 151 elakkleelgageillt 167
                                       el+k+le++g+  i+ t
  gi|320101037|ref|YP_004176629.1| 197 ELVKELEKVGVDGIVAT 213
                                       78999999999999887 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH.H-THHHHHHHHHHC CS
                      His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaav.knpelikelaekfg 120
                                         l++v++ a ++++pv   GGI++  dv e++ aga+ v i taa+ + p ++++++++++
  gi|320101037|ref|YP_004176629.1| 248 LALAVVSQAALNTKLPVIGVGGISRGLDVIEYFMAGASAVQICTAALvEGPGVFTRILKEVN 309
                                       56899***************************************986488999999999887 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 !   10.2   1.4     0.001      0.85       1      16 [.     345     360 ..     345     373 .. 0.94
   2 !   11.4   1.1   0.00042      0.36       1      17 [.     378     394 ..     378     396 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       VD+++Ci+cg C +++
  gi|320101037|ref|YP_004176629.1| 345 VDEKKCIGCGFCEQVC 360
                                       9************999 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00042
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D  +C +cg+C +++P
  gi|320101037|ref|YP_004176629.1| 378 IDLTKCYGCGLCTSVCP 394
                                       7999************* PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.5   4.3e+02      46      70 ..       2      26 ..       1      48 [. 0.80
   2 !   13.0   3.4   4.5e-05     0.038     263     303 ..     252     293 ..     146     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.5
                                      -B--EEETTEEESSSEEE--BSTGG CS
                            FMN_dh 46 vdlsttllGqklslPvliaPvglak 70
                                      +dls++l G kl+ P++ a++ +++
  gi|320101037|ref|YP_004176629.1|  2 ADLSVELAGLKLKNPLMNAACPVSR 26
                                      599**************99876554 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.5e-05
                                       HH.HHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 263 ei.veavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                        + ++a++ +++v+  gGi+rG Dv+     GA+av +  ++
  gi|320101037|ref|YP_004176629.1| 252 VVsQAALNTKLPVIGVGGISRGLDVIEYFMAGASAVQICTAA 293
                                       2335677889**************************987655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.1    0.0005      0.43       2      15 ..     348     361 ..     347     363 .. 0.88
   2 ?   13.7   2.9   7.8e-05     0.067       3      17 .]     382     396 ..     380     396 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0005
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       ++CigCg C+ +C 
  gi|320101037|ref|YP_004176629.1| 348 KKCIGCGFCEQVCN 361
                                       69***********6 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.8e-05
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       +C gCg C+++CP++
  gi|320101037|ref|YP_004176629.1| 382 KCYGCGLCTSVCPTR 396
                                       899**********85 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  12.7    0.0027       2.3       1      58 [.     349     395 ..     349     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0027
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       +Ci+Cg+C+++C + + + ++    + a           +    +C +Cg+C+++CP 
  gi|320101037|ref|YP_004176629.1| 349 KCIGCGFCEQVCNYDAVHVEDAGGKRVA-----------RIDLTKCYGCGLCTSVCPT 395
                                       6************999987743322222...........335689************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 ?   10.6   3.1   0.00086      0.74       2      31 ..     344     375 ..     344     379 .. 0.81
   2 ?   10.6   1.7   0.00084      0.71       2      20 ..     377     395 ..     376     398 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00086
                           Fer4_15   2 vvDrdaCigcglCvaea..pevfeldedglas 31 
                                       vvD+++Cigcg C +++  + v ++d  g+ +
  gi|320101037|ref|YP_004176629.1| 344 VVDEKKCIGCGFCEQVCnyDAVHVEDAGGKRV 375
                                       69**************9877888888777765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00084
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       ++D ++C gcglC  ++p+
  gi|320101037|ref|YP_004176629.1| 377 RIDLTKCYGCGLCTSVCPT 395
                                       59***************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 ?    9.6   3.7    0.0023         2       1      14 [.     350     363 ..     350     364 .. 0.87
   2 ?   14.4   4.6   6.4e-05     0.055       1      15 []     383     397 ..     383     397 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0023
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gCg C++vC ++
  gi|320101037|ref|YP_004176629.1| 350 CIGCGFCEQVCNYD 363
                                       ***********665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.4e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg+C  vCP++A
  gi|320101037|ref|YP_004176629.1| 383 CYGCGLCTSVCPTRA 397
                                       99**********998 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   1.5e+03      96     122 ..      19      44 ..      12      50 .. 0.68
   2 ?   11.2   0.0   0.00015      0.13     195     249 ..     249     301 ..     243     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                                       EEEE-SSTTHHHHHHHHHHTT-SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  96 gaavgvkedalervkalveagvdvlvv 122
                                        aa+ v++ + e +++lv+agv ++v 
  gi|320101037|ref|YP_004176629.1|  19 NAACPVSR-DYEAMRELVDAGVGAVVA 44 
                                       56666664.466777888888877765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgev 249
                                       A+a v++aa +++ pvi  GGi+   d++  + aGa+av +    a+  E pg +
  gi|320101037|ref|YP_004176629.1| 249 ALAVVSQAALNTKLPVIGVGGISRGLDVIEYFMAGASAVQIC--TAALVEGPGVF 301
                                       78889999*******************************985..47777777755 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 ?   10.3   0.1   0.00031      0.27     265     308 ..     252     295 ..     239     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                       HHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHH CS
                      Glu_synthase 265 tlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaali 308
                                       ++ +  l  ++ +i  Gg+  g dv+   + GA av+i taal+
  gi|320101037|ref|YP_004176629.1| 252 VVSQAALNTKLPVIGVGGISRGLDVIEYFMAGASAVQICTAALV 295
                                       567788999999******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2951.52
//
Query:       gi|320101038|ref|YP_004176630.1|  [L=412]
Description: phosphoglycerate kinase [Desulfurococcus mucosus DSM 2162]
Scores for 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-94  315.6   0.0    4.6e-94  315.5   0.0    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.5   0.0   2.6e-98   4.6e-94       1     377 [.      12     393 ..      12     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 315.5 bits;  conditional E-value: 2.6e-98
                                       GGGS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHT.T-EEEEEE--S--TTS-GGG-SHHHHHHH CS
                               PGK   1 vkdldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllek.gakvvllsHlgrpkgekeklslkpvaerL 75 
                                       v+d++++gk+v++R+D+Nvp++ e g i dd+ri+ +   ik++le+ + ++vl+sH+grp g+++ ++++++ae L
  gi|320101038|ref|YP_004176630.1|  12 VRDVNISGKKVFMRIDVNVPIDPEtGDILDDRRIKIHSMFIKKMLEDyQPALVLASHQGRP-GDDDFTTMEKHAELL 87 
                                       689******************9989*********************97788**********.89************* PP

                                       HHHHTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H...H....HHHHHHHT-SEEEE--GGGTT CS
                               PGK  76 sellgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde...e....lakklasladvyVnDAFgtah 145
                                       s+++g+++++v+d++g+++ e+i++lk+ge llL+N+r  +eE  + +   +    +ak+l++++++yVnDAF+tah
  gi|320101038|ref|YP_004176630.1|  88 SKYTGRDIRYVPDIIGPRALEEINNLKPGEALLLDNLRLLSEEVIEAPperQaltiMAKRLSAVFNIYVNDAFATAH 164
                                       *******************************************5444443414567********************* PP

                                       S--TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHH CS
                               PGK 146 rahaStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantF 220
                                       r++ S+vg++ ++++++G l+e+E++a+++v+++ e p +++lGG+kv + ++vienL+++   d+++++G++a  F
  gi|320101038|ref|YP_004176630.1| 165 RSQPSIVGLPLLMPSCMGPLFEQEIAAVRRVFNSAESPRIYVLGGSKVRELLRVIENLMRNKlaDRILTTGLLAQLF 241
                                       *************99********************************************98778************* PP

                                       HHHTT-B-TTSS-...-GGG.....HHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE CS
                               PGK 221 lkaqgleigkslv...eedk.....lelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDi 289
                                       l+a+g++ig++ +   ee k     +  a+ +l +       i +pvD+ v+ +    + + + +  i  +  a Di
  gi|320101038|ref|YP_004176630.1| 242 LAAKGVNIGTENMkilEE-KgllplVPRARYILLRG----APIETPVDLRVEVN---GDVRNTYIGGI--TGVAKDI 308
                                       *********988855444.23555578888887765....69**********72...22334444444..55899** PP

                                       -HHHHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEES CS
                               PGK 290 gpktielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvSt 366
                                       g++t++ +++ i++a+++v+ Gp+Gv+e e+f++GT  i++a+ +++  a++++ Gg+ a++v++ +l++++ hvSt
  gi|320101038|ref|YP_004176630.1| 309 GENTMQIYSDLIRDARIIVMRGPAGVIEDERFREGTLRILDAVYSSN--AFTLIAGGHLASMVDESKLTSRI-HVST 382
                                       *********************************************84..6******************8875.**** PP

                                       SSHHHHHHHCT CS
                               PGK 367 GGgAsLelLeg 377
                                       GG A+L +L+g
  gi|320101038|ref|YP_004176630.1| 383 GGNALLLFLSG 393
                                       *********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2971.94
//
Query:       gi|320101039|ref|YP_004176631.1|  [L=356]
Description: glyceraldehyde-3-phosphate dehydrogenase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   47.1   0.0    2.6e-12   46.6   0.0    1.2  1  Gp_dh_C   Glyceraldehyde 3-phosphate dehydrogenase, C-termina
    6.3e-06   26.5   0.0    1.6e-05   25.2   0.0    1.7  1  Gp_dh_N   Glyceraldehyde 3-phosphate dehydrogenase, NAD bindi
     0.0002   21.5   0.0     0.0004   20.5   0.0    1.6  1  DapB_N    Dihydrodipicolinate reductase, N-terminus


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 !   46.6   0.0   4.4e-16   2.6e-12       3     137 ..     147     279 ..     145     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 4.4e-16
                                       HHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEEEE CS
                           Gp_dh_C   3 plakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldglAv 77 
                                       +l+  l+ ++g+k++l +++++++++         k+ +r+++++   ++  ++++++ +  +V p    ++ + A 
  gi|320101039|ref|YP_004176631.1| 147 RLLCTLHREYGVKRALSVIIRRAADP---------KEDQRGPVNSilLDPPSIPSHHGLDARTVAPW--LDIVTAAA 212
                                       78889*********************.........8999******999******************6..689***** PP

                                       EESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH.....TTTTTTEEEEHSHHHGGGGTTGCS..SE CS
                           Gp_dh_C  78 rVPtpnvsvvdlvvelekevtveevnaalkeaae.....galkgilsyteeelvssDlvgdph..ss 137
                                        VPt+ +++  + vel+ +v++ +v ++l+   +     +a +gi s+++ ++ ++D  + +   ++
  gi|320101039|ref|YP_004176631.1| 213 VVPTTLMHMQFIEVELSTQVNRGDVVELLDGINRfllveSASTGIDSTSKVMELARDSGRPRGdiYE 279
                                       *********************************99**999*****************8765544444 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 !   25.2   0.0   2.6e-09   1.6e-05       1      43 [.       3      44 ..       3      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.6e-09
                                      CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHHHHHHH CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindltdletlayll 43
                                      vk+a+nG+G IG+ ++ a+l++k++++v i +   +++ ayl 
  gi|320101039|ref|YP_004176631.1|  3 VKIAVNGYGTIGKRIVDAVLSNKDFRLVGIAK-YRVDYSAYLA 44
                                      69****************************99.5666777765 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.6e-08    0.0004       1      36 [.       3      37 ..       3     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.6e-08
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke 36
                                      +k+av+G+ G++Gk++v+av +++d++lv+  + + 
  gi|320101039|ref|YP_004176631.1|  3 VKIAVNGY-GTIGKRIVDAVLSNKDFRLVGIAKYRV 37
                                      69******.********************9877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2684.35
//
Query:       gi|320101040|ref|YP_004176632.1|  [L=138]
Description: UspA domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-19   68.7   0.1    4.4e-17   62.9   0.1    2.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1   2.5e-21   4.4e-17       2     141 .]      13     138 .]      12     138 .] 0.89

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 2.5e-21
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       +++IlV++Dgse+s kAle+Al+lak++g++++++++ +  +s   + ++   + +++ l                +
  gi|320101040|ref|YP_004176632.1|  13 FRKILVPIDGSENSLKALEFALDLAKHYGSKIVVAYAKPKGDSRGDPFERARIKIAREGLNV--------------Q 75 
                                       79**********************************99888776666666555555555555..............4 PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        ++ e +  + +   +++++  e ++d +V+G+rg+s   ++ +GS++ +++ ++p++V ++r
  gi|320101040|ref|YP_004176632.1|  76 YKVIEYDPSNSNTPSTLVREIIEGGYDAVVLGARGLSLTTDIPIGSTALSLVINSPVSVFIIR 138
                                       77899999999999**********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1029.45
//
Query:       gi|320101041|ref|YP_004176633.1|  [L=513]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   39.9   0.0    2.5e-09   36.0   0.0    2.2  2  Phosphorylase    Carbohydrate phosphorylase
      7e-10   38.7   0.0    1.3e-09   37.9   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    6.6e-05   23.3   0.0    0.00012   22.5   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.011        68     339     376 ..     224     265 ..     213     325 .. 0.80
   2 !   36.0   0.0   4.1e-13   2.5e-09     524     627 ..     370     475 ..     363     494 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.011
                                       SHHHHHHHHHT....TTHHHHHHSGGGEEE----B-CHHHCC CS
                     Phosphorylase 339 aalhsellkke....vlkdfyelypekfnnktnGitprrwll 376
                                       ++l+s ++ ++    v+ +       kf+ +tnGi   rw++
  gi|320101041|ref|YP_004176633.1| 224 SRLKSAIVVSKkqedVVGKIFPAHAGKFRGITNGIYLPRWMH 265
                                       566666665440000444444556789*************96 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 4.1e-13
                                       EEEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESSTCHHHHHHHH-GGGSEEES-BHHH CS
                     Phosphorylase 524 kvvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDGanvEiaeevgeenifiFGltaee 600
                                       + v+l++yn+ +a  i  ++dl      +g eA GT+ mk  +nG  ++++ DG  +Ei e   +   ++FG++  +
  gi|320101041|ref|YP_004176633.1| 370 NTVYLQDYNIETARLIAQGSDLWLFTPFSGWEACGTSFMKAQVNGVPVLSSRDGGALEIIEDGVT--GWLFGQDLRD 444
                                       569********************************************************997544..4789999999 PP

                                       HHHHHHHT....--HHHHHHH-HHHHHHHHH CS
                     Phosphorylase 601 veelkkkg....ynpkelyekdpelkevlda 627
                                        ++++++      +++e+ e +++l  ++d+
  gi|320101041|ref|YP_004176633.1| 445 FTNIYTDPrageIDEREYQEFRNKLLWIIDM 475
                                       9988877533334444555544555444444 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 !   37.9   0.0   2.1e-13   1.3e-09       8     141 ..     302     439 ..     298     445 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.1e-13
                                       HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.........STTHHHHHHHHHHHCTTCGGG CS
                   Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG........ngeeekelkklaeelelsdnvi 76 
                                       +++ ++++ i+    rl ++K++  + + +++ +   + n+ +++aG        +  ++k++++l   l+l ++v 
  gi|320101041|ref|YP_004176633.1| 302 SNVNADGRIIVAWTRRLARYKRPYFAARFIEENP---DVNAFFILAGkphprdndGLGYLKKFREL--DLKLANTVY 373
                                       5666788889999999999999999999999776...89***********9966555666666666..555544444 PP

                                       EEECCHSSSHHHHHHC.ESEEEEEESS..BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE- CS
                   Glycos_transf_1  77 flgevsredleellkn.adifvlpsis..EgfGivllEAmaaglpviasnaggpaevvkdgetGllvk 141
                                       +  +    +   l+ + +d+ +++  s  E+ G++ + A   g+pv++s  gg++e+++dg+tG+l+ 
  gi|320101041|ref|YP_004176633.1| 374 LQDYNI--ETARLIAQgSDLWLFTPFSgwEACGTSFMKAQVNGVPVLSSRDGGALEIIEDGVTGWLFG 439
                                       444444..555555556999888877677*************************************86 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 !   22.5   0.0     2e-08   0.00012       4     125 ..     312     446 ..     309     450 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2e-08
                                       EEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...........HHHHHHHT.T-T.TEEEE---.THHHHH CS
                   Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp..rp.......eeleelaa.gleerveftGfv.edlael 69 
                                       + ++ rl +++k+  + ++ +++  + ++ ++++G+ p  r+       ++++el + +l+++v +  +  e  + +
  gi|320101041|ref|YP_004176633.1| 312 VAWTRRL-ARYKRPYFAARFIEENPDVNAFFILAGK-PhpRDndglgylKKFREL-DlKLANTVYLQDYNiETARLI 385
                                       5566667.4556666666666666644588*****4.433337788566555533.358888899999887888888 PP

                                       HHH-SEEEE--....---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHH CS
                   Glyco_trans_1_4  70 laaadvfvaPs....egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpeala 125
                                        + +d+ +++     e +g + + a   g+pv +++ gg+ e++  g++g+l+  +d  +++
  gi|320101041|ref|YP_004176633.1| 386 AQGSDLWLFTPfsgwEACGTSFMKAQVNGVPVLSSRDGGALEIIedGVTGWLFG-QDLRDFT 446
                                       9999**99988899999******************99999*****9******95.5777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3732.33
//
Query:       gi|320101042|ref|YP_004176634.1|  [L=554]
Description: aminopeptidase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   27.5   0.2    0.00025   20.8   0.0    2.4  2  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
       0.01   14.7   0.1       0.24   10.3   0.0    2.2  2  DUF4910        Domain of unknown function (DUF4910)


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.1    0.0041        36      15      44 ..     237     259 ..     224     277 .. 0.76
   2 !   20.8   0.0   2.7e-08   0.00025      94     191 ..     301     410 ..     297     417 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0041
                                       EEEEEE--B-TTTTCCT---TTTTHHHHHH CS
                     Peptidase_M28  15 lllgAHyDsvgvgrgpifvGAdDnAsgvaa 44 
                                       ++l +H+ +      p   GA DnAsg +a
  gi|320101042|ref|YP_004176634.1| 237 VVLVSHICHPR----P---GAHDNASGSVA 259
                                       56666665554....6...********986 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.7e-08
                                       EEEECS-SSSS--EEE.............HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEES...STT-STTHHHH CS
                     Peptidase_M28  94 vlnlDmvgsggkellf.............esgdkssselekelkalakpvgraaaedpfders...grgrsDhspfl 154
                                       v+nlDmvgs++    +             ++ + +  ++++ l+++ +  g      p  + s   ++  sDh +fl
  gi|320101042|ref|YP_004176634.1| 301 VVNLDMVGSKQWITGStlnivnaplymdsTIVPYTYLAVKAVLDTAPSFSGFDL---PGSRYSlspYTAGSDHDVFL 374
                                       799999999988877777788777666666666666666666666666666653...2222223235666******* PP

                                       TTT--EEEECTSSS-TTTTSTTSSGGGB-HHHHHHHH CS
                     Peptidase_M28 155 kagvpvldlaetgfpevyHtprDtldnidkdtlaria 191
                                         gv ++ l +++  ++yHt  Dt++ +++++l ++a
  gi|320101042|ref|YP_004176634.1| 375 SWGVDTVML-NEWPSKYYHTDMDTAETLSQRSLTDTA 410
                                       *********.99999999************9998876 PP

>> DUF4910  Domain of unknown function (DUF4910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.6e-05      0.24      70     124 ..     237     290 ..     227     297 .. 0.80
   2 ?    2.0   0.0    0.0088        79     184     233 ..     366     410 ..     356     419 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.6e-05
                                       EEEEEE----S-.TTTTHHHHHHHHHHHHHHTTS--.SSEEEEEEE-TTHHHHHHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4910  70 vllsahvChPsl.andnlsGiavatalakalaerkerrysyrllfvPetiGsityl 124
                                       v+l++h+ChP   a dn sG +va  +a  +++  +       ++vPe  G++ yl
  gi|320101042|ref|YP_004176634.1| 237 VVLVSHICHPRPgAHDNASG-SVANYVAAFISHVMRLDIPLCHVWVPEFTGTV-YL 290
                                       899*******7538899999.57778888888887778888889999988876.55 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.0088
                                       -SSTHHHHTSTTT---EEEEESS-TT.-TTTTBTTSSGGG--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4910 184 ygyDerqycsPgvdlpvgslaRskygeypeYhtsaDnldfvkpealeesf 233
                                        g+D   + s gvd  +  l  ++    + Yht  D  + +++++l+++ 
  gi|320101042|ref|YP_004176634.1| 366 AGSDHDVFLSWGVDTVM--LNEWPS---KYYHTDMDTAETLSQRSLTDTA 410
                                       57888888888888644..444442...349***************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3917.48
//
Query:       gi|320101043|ref|YP_004176635.1|  [L=554]
Description: phenylalanyl-tRNA synthetase subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-40  136.5   0.0    1.4e-39  135.8   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
      1e-18   67.4   0.1    1.4e-13   50.9   0.1    3.6  3  B5               tRNA synthetase B5 domain
    5.8e-13   48.9   0.0    9.9e-13   48.1   0.0    1.3  1  B3_4             B3/4 domain
    7.8e-05   22.8   0.0      0.015   15.5   0.0    3.3  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
    0.00038   20.0   0.0     0.0014   18.2   0.0    1.8  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.0   3.8e-43   1.4e-39      11     213 ..     359     547 ..     352     548 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 3.8e-43
                   tRNA_synthFbeta  11 tegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevla 87 
                                         g+l++ + ++r++rd+l+g+G++Ev +y + s +    l      r++  ++nP se +++lR+ L+pglLe++ 
  gi|320101043|ref|YP_004176635.1| 359 SVGRLHPLEYASRRIRDILVGMGFTEVSNYMMSSVEAQTSL--LGGGREVFIVENPKSEKYTALRSWLTPGLLETIV 433
                                       34559999*********************************..599******************************* PP

                   tRNA_synthFbeta  88 rNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekve 163
                                       +N  ++ + +++FEig+v+++d s e++++ er+l+++l++++           +   d  ++v+all+ lg+ k  
  gi|320101043|ref|YP_004176635.1| 434 ENTGKRPR-IAVFEIGDVVIPDaSRETGARVERRLCVALSHEK-----------ATLTDGLAVVKALLRDLGV-KPL 497
                                       ****9988.**********************************...........*******************.888 PP

                   tRNA_synthFbeta 164 fepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                       fe a+ + + +gr+A i+vd+ +vG++Ge+ p +l ++++ ++v+++E+ 
  gi|320101043|ref|YP_004176635.1| 498 FEGATIAGFLQGRTAVIRVDDDNVGFVGEVEPGILYRLGVVNPVVIAEMV 547
                                       ************************************************95 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   9.2e-05      0.33       2      53 ..       5      56 ..       4      61 .. 0.91
   2 !   50.9   0.1     4e-17   1.4e-13       1      67 []     278     344 ..     278     344 .. 0.98
   3 ?    0.4   0.0      0.23   8.1e+02      15      32 ..     367     397 ..     359     499 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.2e-05
                                      EEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--S CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  2 slrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDler 53
                                      +++++ +++ll   l+ ee  k L+rl+ce+++  +d+++ +  + R+Dl  
  gi|320101043|ref|YP_004176635.1|  5 RVSMSDLESLLAKRLTLEELYKGLTRLKCEIENIAGDTVEYEANHDRPDLFS 56
                                      6889999************************************999***965 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 4e-17
                                       EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       ++++++ +++llG++ls ee  k+L++  +++++  +++++V+ P++R D++  +D++E++a  yGY
  gi|320101043|ref|YP_004176635.1| 278 ITVDLGDVSRLLGVELSVEEALKLLQQHYYRVKSVSGKVFSVEAPAYRIDVKTWVDVAEDIAVSYGY 344
                                       6899**************************************************************9 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.23
                                       ---HHHHHHHHHHTT-E.............. CS
                                       xxxxxxxxxxxxxxxxx.............x RF
                                B5  15 dlseeeiikiLkrlgce.............r 32 
                                       ++ + +i +iL  +g++             +
  gi|320101043|ref|YP_004176635.1| 367 EYASRRIRDILVGMGFTevsnymmssveaqT 397
                                       5667789999999999855555555555540 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   2.8e-16   9.9e-13       4     132 ..      95     235 ..      92     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.8e-16
                                       EEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE.--TTE CS
                              B3_4   4 ryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiqgdivvrl.akege 74 
                                       + a +v+r+v   ++                i+ +  +++++ + +g+      ++++Dld i+++i  r   +++ 
  gi|320101043|ref|YP_004176635.1|  95 YIALAVVRDVVLSEEA---------------ISQIMQLQEKLASTYGRgrrkaSIGVYDLDLIKPPIYYRAvDPDKA 156
                                       5555555555555555...............99999********************************666266778 PP

                                       EEEBTTS-.EEEE-T...................TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HH CS
                              B3_4  75 klvtldgk.erelde...................edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpv 130
                                       k ++l++k e +l+e                   +++v +dse+ + sla++ + +  kv+ +T+n+++ +++++p 
  gi|320101043|ref|YP_004176635.1| 157 KYIPLNEKrEMTLREvlsktdkgrlygyiiehmeRYPVLMDSEERIlSLAPILNADYNKVTTKTRNILVDSTGLSPD 233
                                       ******9878888889****************************999**************************9997 PP

                                       HH CS
                              B3_4 131 si 132
                                        +
  gi|320101043|ref|YP_004176635.1| 234 IV 235
                                       66 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 !   15.5   0.0   4.2e-06     0.015       1      82 [.       1      69 [.       1      70 [. 0.88
   2 ?    1.6   0.0     0.092   3.3e+02      46      69 ..     307     330 ..     275     342 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.2e-06
                         PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglaralkv 79
                                      MP+i v+ ++L ++l k+lt eel + l ++  E+ +i  ++                +    r+DL + eglaral+ 
  gi|320101043|ref|YP_004176635.1|  1 MPVIRVSMSDLESLLAKRLTLEELYKGLTRLKCEIENIAGDTV-------------EYEANHDRPDLFSSEGLARALRP 66
                                      9999999999999999999999999999999999999988887.............3456677***************9 PP

                         PhetRS_B1 80 Flg 82
                                      Flg
  gi|320101043|ref|YP_004176635.1| 67 FLG 69
                                      987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.092
                         PhetRS_B1  46 kadkkseeviykidipAnryDLLc 69 
                                        + k+ + +++ ++ pA r D+  
  gi|320101043|ref|YP_004176635.1| 307 YRVKSVSGKVFSVEAPAYRIDVKT 330
                                       355667788999999999999855 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.9e-07    0.0014       9     155 ..     356     494 ..     351     499 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.9e-07
                                       SCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-S CS
                      tRNA-synt_2d   9 krieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRt 85 
                                       ++i+ g+lhpl+  +++i++i++ +gf+ev++  + s     + L            ++F++++p++  e+ + LR+
  gi|320101043|ref|YP_004176635.1| 356 PSISVGRLHPLEYASRRIRDILVGMGFTEVSNYMMSSVEAQTSLLG--------GGREVFIVENPKS--EKYTALRS 422
                                       578899*************************999966555555554........34579***99999..8899**** PP

                                       STHHHHHHHH...TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTS CS
                      tRNA-synt_2d  86 httavqirtl...ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfga 155
                                         t+  + t+   + k+p i ++ ig v   da   t   +   +   +  e+ +l+d ++v+++ll++l g 
  gi|320101043|ref|YP_004176635.1| 423 WLTPGLLETIvenTGKRPRIAVFEIGDVVIPDASRETGARVERRLCVALSHEKATLTDGLAVVKALLRDL-GV 494
                                       ********9987555667899999**99999998888888888887888888999999999999999988.65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3882.22
//
Query:       gi|320101044|ref|YP_004176636.1|  [L=385]
Description: sodium/hydrogen exchanger [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-30  105.2  46.3    4.2e-30  104.8  46.3    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8  46.3   2.3e-34   4.2e-30       2     377 ..       8     379 ..       6     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 2.3e-34
                                       HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTH CS
                    Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknl 76 
                                       +l+ill+ +vg l+rr  ++e+ g++i+G++lG  +      +   +dl+++s +  i+ +F+aG+  +l+++ +n 
  gi|320101044|ref|YP_004176636.1|   8 FLGILLSKVVGHLLRRHSIGEVAGYLIVGIILGVTVGR----DeyIHDLSLVSSIAAIFVVFYAGVTSSLEDVVENS 80 
                                       67777788888889*******************99877....33569****************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHH CS
                    Na_H_Exchanger  77 ksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDa 153
                                        s+l+++l++v++tv++  +l+  ++ lg+++  all++++ls t + +++ ++    r+p ++ ++l+++s ++D+
  gi|320101044|ref|YP_004176636.1|  81 ASALAVSLTSVAVTVIT--VLAI-VMYLGYSFETALLVALLLSNTATEMASMLV---ERLPLHVKSMLVSASFIDDL 151
                                       ***************99..3333.246799************************...999***************** PP

                                       HCCCCCHHHHHHTX..XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 154 vavvllavllalak..eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaal 228
                                       ++v++++ +         + + +s + +l ++lvv+ ++   +l++  ++ +++    ++ + ++ ++l+++ l+ l
  gi|320101044|ref|YP_004176636.1| 152 FMVLATSAYYMWRLtgHVNEALVSTVVALAATLVVFTLITRQRLILNPVFNYMS----RNMAYFTDASLIMLSLLLL 224
                                       ********9988854323333333333333344444444444444444444444....678999999********** PP

                                       HHHTSXXXHHHHHHHHHHHHH..HHHHHTTHHHH.........HHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHH CS
                    Na_H_Exchanger 229 laellgvsgilgaflaGlvls..eyefsnklsek.........lesfreglfnplfFvlvGlsldlkvlnnhlsvli 294
                                       la   g+s i++a laG+++s   + ++ +l+ +         l s+++glf plf ++vGl++ ++++      + 
  gi|320101044|ref|YP_004176636.1| 225 LAFESGMSYIIAAYLAGILVSggLGMKDPMLRYRarvsdftniLGSVIDGLFTPLFMLYVGLHIRISAV-----DPV 296
                                       *********************7644444445555775565555555555****************9988.....688 PP

                                       HHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHH CS
                    Na_H_Exchanger 295 lvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvq 371
                                       l++++l+a ++++ l+ f++l++ g +++  +++gf++++rg + l l++ g  lgl + e+++++++v+l t+++ 
  gi|320101044|ref|YP_004176636.1| 297 LLAALLAAGIATKMLSYFAFLKARGEDTSVGVTAGFSMTGRGVLELTLLVKGFELGLVSVEVFNTIVAVALSTIVIS 373
                                       899999999999***************************************************************88 PP

                                       HHHHHH CS
                    Na_H_Exchanger 372 Glslkp 377
                                        + +++
  gi|320101044|ref|YP_004176636.1| 374 VIAVSV 379
                                       877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2831.79
//
Query:       gi|320101045|ref|YP_004176637.1|  [L=313]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.78    9.7   4.7        1.3    8.9   4.7    1.4  1  MSA-2c    Merozoite surface antigen 2c
        3.6    7.0  15.5        5.7    6.3  15.5    1.3  1  CAP_N     Adenylate cyclase associated (CAP) N terminal


Domain annotation for each model (and alignments):
>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.7   0.00015       1.3     152     195 ..     134     181 ..      75     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00015
                            MSA-2c 152 kkPsr.tssaetPaPsdae..saaaqPPes.kpaqaPaPtspsqsees 195
                                       kkP +   ++  PaP+ a+  +a+ +PPe+ kpa  PaP+ p++  + 
  gi|320101045|ref|YP_004176637.1| 134 KKPIQpMIKPPKPAPQAAKpvEAVVKPPEApKPAAPPAPQPPPPPRQV 181
                                       45543134555788888753368999**999********999987765 PP

>> CAP_N  Adenylate cyclase associated (CAP) N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  15.5   0.00064       5.7     233     283 ..     152     203 ..     126     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00064
                                       ....SSC--XXXXXXX.....XXXXXXXX.....XXXXXXXXXXXXXXXXXXXX CS
                             CAP_N 233 k..aaaaaasaaaagg.pppPpPpPppasvfeeesaaasasaaaggmsavFaeL 283
                                       k  +a  ++++a++ + pp+P+PpPpp +v+   ++ a ++++a +++ +F+e+
  gi|320101045|ref|YP_004176637.1| 152 KpvEAVVKPPEAPKPAaPPAPQPPPPPRQVQ--PEKPAPQEKEAVDVTKLFDEV 203
                                       3333334444444444255577777777664..3335788889999*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2274.03
//
Query:       gi|320101046|ref|YP_004176638.1|  [L=122]
Description: transcriptional regulator-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   17.7   0.0     0.0053   16.8   0.0    1.4  1  HTH_3           Helix-turn-helix
      0.007   16.0   0.1      0.015   15.0   0.1    1.5  1  Sigma70_r4_2    Sigma-70, region 4
  ------ inclusion threshold ------
      0.027   14.5   0.0       0.67   10.0   0.0    2.2  2  HTH_19          Helix-turn-helix domain
      0.071   13.5   0.0       0.11   12.8   0.0    1.4  1  HTH_31          Helix-turn-helix domain
       0.13   12.1   0.0       0.26   11.2   0.0    1.5  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-06    0.0053       7      37 ..      27      57 ..      22      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                                      HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSB CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPs 37
                                      + g +q e+A+ l++++s+++    G+r+P 
  gi|320101046|ref|YP_004176638.1| 27 EYGFTQLEVARILDMKQSAVNYVLTGRRKPK 57
                                      59**************************995 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   4.2e-06     0.015      18      44 ..      21      47 ..      18      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.2e-06
                                      HHHHHHTS---HHHHHHHHT--HHHHH CS
                      Sigma70_r4_2 18 ifllryleglsykEIAellgisegtVk 44
                                      ++ l ++ g+++ E+A++l+++ ++V+
  gi|320101046|ref|YP_004176638.1| 21 AVKLVREYGFTQLEVARILDMKQSAVN 47
                                      78999*********************8 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00019      0.67      10      43 ..      27      60 ..      22      80 .. 0.84
   2 ?    2.4   0.0     0.045   1.6e+02      41      61 ..      98     118 ..      91     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                            HTH_19 10 elgltqeelaerlgisrskisaiEngkkdvps.ae 43
                                      e+g+tq e+a+ l++ +s  +   +g++ +p+ +e
  gi|320101046|ref|YP_004176638.1| 27 EYGFTQLEVARILDMKQSAVNYVLTGRR-KPKyYE 60
                                      89*************9999999999999.887544 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.045
                            HTH_19  41 saelllkiaealgidleyllq 61 
                                        ++l++++ ea+g ++++l++
  gi|320101046|ref|YP_004176638.1|  98 LRGLYRSVIEAVGEPVDELIS 118
                                       567789999*********986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.2e-05      0.11      14      43 ..      29      57 ..      10      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                            HTH_31 14 GLsqeevAerlgvsestlsrlEqGrrgrps 43
                                      G +q evA+ l + +s ++ + +Grr  p+
  gi|320101046|ref|YP_004176638.1| 29 GFTQLEVARILDMKQSAVNYVLTGRRK-PK 57
                                      99************************5.74 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.1e-05      0.26      11      34 ..      32      55 ..      23      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.1e-05
                    YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlkgkkq 34
                                      q ++A+ l+++q+aV+++l g+++
  gi|320101046|ref|YP_004176638.1| 32 QLEVARILDMKQSAVNYVLTGRRK 55
                                      7789****************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 866.42
//
Query:       gi|320101047|ref|YP_004176639.1|  [L=215]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1151  (0.0641977); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1636.52
//
Query:       gi|320101048|ref|YP_004176640.1|  [L=240]
Description: purine phosphorylase family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-42  143.1   0.5      1e-41  142.8   0.5    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 !  142.8   0.5   5.6e-46     1e-41       4     209 ..      17     211 ..      16     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 142.8 bits;  conditional E-value: 5.6e-46
                                       EEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEE CS
                         PNP_UDP_1   4 iivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaG 80 
                                       i vg+pg+v+ll+   le+ ++ +++rg k+vtG +kgk+v+i+++GiG+p+a+ +   +l + +g+++i+r+Gt G
  gi|320101048|ref|YP_004176640.1|  17 IAVGDPGRVDLLSGI-LEDARVVNTHRGLKTVTGFYKGKRVTIATHGIGAPSAS-IVFEELYQ-LGARRIVRVGTTG 90 
                                       789************.**************************************.66666666.45*********** PP

                                       ESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSE.E--HHHHHHHHHCHHTTTTTEEEEEEEEESESS- CS
                         PNP_UDP_1  81 glnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsyda.padpelrallkeaaealgikvhrGvvatadgfya 156
                                       g++ d+++GDvv+++ a++ +++++l +      y p+ + a  +dp l++++ ea++++g +++ G+v ++d fya
  gi|320101048|ref|YP_004176640.1|  91 GIRRDTRIGDVVVATGAMYVQNGCGLGQ------YIPGLCGAsSPDPVLTTRIMEALSKNGLNFKKGPVFSSDAFYA 161
                                       ************************9875......44444444368******************************** PP

                                       CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTC CS
                         PNP_UDP_1 157 eteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaea 209
                                       e +  ++ ++ +g+ aveME+aa+++l   +g +  ++ vvsd++ g   +ea
  gi|320101048|ref|YP_004176640.1| 162 EDPSFAEKMSHYGVVAVEMEAAALFTLGWMRGFDTSCVLVVSDVLHG---EEA 211
                                       *******************************************8776...222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1771.02
//
Query:       gi|320101049|ref|YP_004176641.1|  [L=484]
Description: cysteinyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-122  406.1   0.0   1.2e-121  405.8   0.0    1.1  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    2.2e-11   43.1   1.9    1.5e-08   33.9   0.9    2.1  2  tRNA-synt_1g  tRNA synthetases class I (M)
    4.3e-09   36.7   0.8    1.1e-08   35.4   0.1    2.0  2  DALR_2        DALR domain
    8.9e-06   24.2   0.3    0.00034   19.0   0.0    2.1  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    0.00077   18.5   0.3     0.0028   16.6   0.0    2.0  3  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d


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 !  405.8   0.0  3.3e-125  1.2e-121       4     300 ..      23     318 ..      20     319 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.8 bits;  conditional E-value: 3.3e-125
                                       -SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHH CS
                      tRNA-synt_1e   4 pleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfi 80 
                                       p+e + v++YvCGptvyd++h+Gh++++v++D ++r+l  +gY+v +v n+tDidDkii+r++ee++ ++e++e++ 
  gi|320101049|ref|YP_004176641.1|  23 PVEPGIVKMYVCGPTVYDYTHIGHGKTYVIYDAFKRYLSLRGYHVVHVMNITDIDDKIIRRSHEEGRDWNEIVEEYT 99 
                                       678899*********************************************************************** PP

                                       HHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT---- CS
                      tRNA-synt_1e  81 eefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaege 157
                                       +++ ++le+Lnv+  + +prvse++deii++++ li+kgyaY++ +g vyfdv k+e+Yg+ls +++ +   g+e+e
  gi|320101049|ref|YP_004176641.1| 100 RDYISALEKLNVKV-DHHPRVSEHIDEIIRFIQGLIDKGYAYVAPSGSVYFDVDKYEDYGRLSGRESRDTW-GQEQE 174
                                       ************97.99***********************************************9998765.55555 PP

                                       S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSS CS
                      tRNA-synt_1e 158 vseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaafd 234
                                         +ekk++ DfaLWka+k+gep w+sPwgkGRPGWhieCsvm+s++lgs++dih+GG+DL+fPhhene aqsea+f+
  gi|320101049|ref|YP_004176641.1| 175 FLSEKKNPYDFALWKAAKPGEPYWESPWGKGRPGWHIECSVMSSRYLGSRFDIHGGGTDLIFPHHENERAQSEAYFG 251
                                       6689************************************************************************* PP

                                       .S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 235 .kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                        k++v +++h+g +++ ++kmsksLkn++ +k+++ k+ p+ lRl  ls+hyr++l f ee+le+a+
  gi|320101049|ref|YP_004176641.1| 252 sKPWVSIWMHSGLVMVGKDKMSKSLKNIVPLKEAFDKWGPMPLRLWYLSTHYRKPLYFFEEALENAV 318
                                       99*************************************************************9986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.9   4.1e-12   1.5e-08      12     122 ..      40     148 ..      31     156 .. 0.87
   2 !    8.2   0.0   0.00026      0.93     318     356 ..     262     300 ..     246     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.1e-12
                                       S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEE CS
                      tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdky 88 
                                       + +H+Gh  ++++ D+f Ry  lrg++v++v        +i  + ++eg + +e+ve++++ + + ++kln++ d++
  gi|320101049|ref|YP_004176641.1|  40 DYTHIGHGKTYVIYDAFKRYLSLRGYHVVHVMNITDIDDKIIRRSHEEGRDWNEIVEEYTRDYISALEKLNVKVDHH 116
                                       568****************************9999999*************************************** PP

                                       EETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                      tRNA-synt_1g  89 grttseehkelvqeifkklkekgliyekeieqly 122
                                        r +++   +   ++++ l +kg+ y   +  +y
  gi|320101049|ref|YP_004176641.1| 117 PRVSEHI--DEIIRFIQGLIDKGYAYVAPSGSVY 148
                                       9987654..4455788888888888876665555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00026
                                       E--EEE--------------HHHHHHHH-HHHHHHHHHH CS
                      tRNA-synt_1g 318 heyltvegkKlSkSrgvvvkakealerldadllRYylaa 356
                                       ++ ++v  +K+SkS +++v  kea ++  +  lR ++++
  gi|320101049|ref|YP_004176641.1| 262 SGLVMVGKDKMSKSLKNIVPLKEAFDKWGPMPLRLWYLS 300
                                       567788899******************999999966554 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.1   7.5e+03      36      56 ..     315     335 ..     311     339 .. 0.72
   2 !   35.4   0.1     3e-12   1.1e-08       1      61 [.     361     422 ..     361     424 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHGGGT-S- CS
                            DALR_2  36 aaasalkallrelaevLGllq 56 
                                       + a +l ++l++ a++LG l 
  gi|320101049|ref|YP_004176641.1| 315 ENAVKLYERLVTAAQLLGKLS 335
                                       455667899999999999655 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 3e-12
                                       HHHHHHTBT--HHHHHHHHHHHHHHHHHHHHTT-HHHH.HHHHHHHHHHHGGGT-S-S-HHH CS
                            DALR_2   1 kFeeaMdDDFNTaeAiavlFelakeiNralkeedkaaa.salkallrelaevLGllqeepea 61 
                                       +F ea+ DDFNTaeA+a++ e    + r+ +++ ++ + s+  +llre+ +vLG+l +e ea
  gi|320101049|ref|YP_004176641.1| 361 RFHEALSDDFNTAEAMAAVNEYLTILFRDIQHNPRHLLvSTSIKLLREFNSVLGVLDKELEA 422
                                       7********************9999998555554444425556**************99886 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 !    3.1   0.1    0.0061        22      32      66 ..      36      70 ..      29      81 .. 0.87
   2 !   19.0   0.0   9.5e-08   0.00034     518     597 ..     226     305 ..     219     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0061
                       tRNA-synt_1 32 PyvtGslHiGhalaktlkdivirykrmkGkevlyv 66
                                      P v    HiGh  + ++ d   ry +++G++v +v
  gi|320101049|ref|YP_004176641.1| 36 PTVYDYTHIGHGKTYVIYDAFKRYLSLRGYHVVHV 70
                                      7777789************************9776 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 9.5e-08
                       tRNA-synt_1 518 dmlleGlDiirgWvarlillslaltgsePfkevlvh.glvrdeeGrKmSKslgNvidpldvikkygadalRltlils 593
                                       d+   G D i+   ++   +s a +gs+P+ ++ +h glv+ ++  KmSKsl+N++  ++  +k g   lRl+ +++
  gi|320101049|ref|YP_004176641.1| 226 DIHGGGTDLIFPHHENERAQSEAYFGSKPWVSIWMHsGLVMVGK-DKMSKSLKNIVPLKEAFDKWGPMPLRLWYLST 301
                                       5666788999999999999999***********99945777665.69**************************9999 PP

                       tRNA-synt_1 594 dvgr 597
                                       ++ +
  gi|320101049|ref|YP_004176641.1| 302 HYRK 305
                                       8865 PP

>> 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 ?   -2.3   0.0      0.45   1.6e+03      13      24 ..      41      52 ..      36      83 .. 0.76
   2 !   16.6   0.0   7.9e-07    0.0028      49      97 ..      95     142 ..      86     148 .. 0.90
   3 ?   -2.8   0.0      0.61   2.2e+03     230     266 ..     257     294 ..     248     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.45
                                      S-BHHHHHHHHH CS
                      tRNA-synt_1c 13 yLHiGhakaall 24
                                      y HiGh k+ ++
  gi|320101049|ref|YP_004176641.1| 41 YTHIGHGKTYVI 52
                                      678888887654 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7.9e-07
                                       -HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE CS
                      tRNA-synt_1c  49 keeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvc 97 
                                       +ee++   + +l+ l++k d+   + s++ de+ ++++ Li kG+AYv+
  gi|320101049|ref|YP_004176641.1|  95 VEEYTRDYISALEKLNVKVDH-HPRVSEHIDEIIRFIQGLIDKGYAYVA 142
                                       689999*************77.5689*********************97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.61
                                       EEEEE.--EEETTSB-SHHHHHHHHHTTSSSSTT-TTS CS
                      tRNA-synt_1c 230 fihey.lrlnlekkklSKRklsllvdekqvkewddlre 266
                                        i++   ++ + k k+SK  ++++  ++++++w+  ++
  gi|320101049|ref|YP_004176641.1| 257 SIWMHsGLVMVGKDKMSKSLKNIVPLKEAFDKWGPMPL 294
                                       555541466678899***99999999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3549.25
//
Query:       gi|320101050|ref|YP_004176642.1|  [L=229]
Description: endonuclease (RecB family)-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   22.1   0.7    0.00034   20.8   0.7    1.7  1  UPF0102   Uncharacterised protein family UPF0102
     0.0016   18.3   0.5      0.023   14.6   0.0    2.8  4  MarR_2    MarR family
  ------ inclusion threshold ------
      0.014   15.7   2.7      0.018   15.3   2.7    1.5  1  MlaD      MlaD protein
      0.065   12.9   0.3        0.3   10.7   0.1    1.8  2  DUF3394   Domain of unknown function (DUF3394)
       0.13   12.7   0.0       0.27   11.7   0.0    1.6  1  NERD      Nuclease-related domain
       0.27   11.3   1.3        0.8    9.8   0.0    2.6  4  HTH_20    Helix-turn-helix domain


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 !   20.8   0.7   1.1e-07   0.00034       2      44 ..      13      64 ..      12      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-07
                                      HHHHHHHHHHTT-EEEEEEEEETT.....EEEEEEE...TTEEEEEEEEE.- CS
                           UPF0102  2 EelaaeyLekkgyeilernwrcra.....gEiDiia...tevlvfvEVKt.R 44
                                      E +a eyLe++g++i e + + ++     gE+D +a   + v   vEVK+ R
  gi|320101050|ref|YP_004176642.1| 13 ELIALEYLERQGFRIEEARKKIKVegveiGEVDAVAvsrNGVKYAVEVKAgR 64
                                      889***************999977777779*********8899******944 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   9.1e+03      10      18 ..      16      24 ..      12      33 .. 0.55
   2 ?    0.3   0.0      0.22   6.6e+02      22      33 ..      94     105 ..      76     106 .. 0.80
   3 ?   -3.4   0.0       3.3   9.8e+03      38      46 ..     133     141 ..     130     143 .. 0.62
   4 !   14.6   0.0   7.6e-06     0.023       3      51 ..     146     190 ..     144     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                                      HHHHHHCTT CS
                            MarR_2 10 vLaaLgrrp 18
                                      +L +L r +
  gi|320101050|ref|YP_004176642.1| 16 ALEYLERQG 24
                                      344444443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.22
                                       EEHHHHHHHHTS CS
                            MarR_2  22 ltvgelarrlgl 33 
                                        ++++la++lg+
  gi|320101050|ref|YP_004176642.1|  94 DSAAALAKELGV 105
                                       49999*****98 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.3
                                       HHHHHHHHH CS
                            MarR_2  38 vsrilkrLv 46 
                                       + ril+ Lv
  gi|320101050|ref|YP_004176642.1| 133 IRRILDVLV 141
                                       556777666 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 7.6e-06
                                       --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51 
                                       ++p+++ v+ aL+r+      ++e a++l+ s  ++ r+++r +a+GL+
  gi|320101050|ref|YP_004176642.1| 146 VPPQDLEVIDALARSR----DIKEFADALKTSVENAMRHVRRIQAKGLL 190
                                       5789999999**9996....7***************************8 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.7   5.9e-06     0.018      17      50 ..      30      61 ..      23     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.9e-06
                              MlaD 17 vgapVryrGvtvGrVtsitldpdtrrvtvtvdld 50
                                      ++ ++++ Gv++G+V+++ ++   ++v++ v+++
  gi|320101050|ref|YP_004176642.1| 30 ARKKIKVEGVEIGEVDAVAVSR--NGVKYAVEVK 61
                                      5799***************955..4444444444 PP

>> DUF3394  Domain of unknown function (DUF3394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.21   6.2e+02     107     143 ..      18      54 ..      12      87 .. 0.68
   2 ?   10.7   0.1    0.0001       0.3     102     164 ..      92     156 ..      57     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.21
                           DUF3394 107 erLeaaGltlleedgkvlvdevefgspaekagldfdf 143
                                       e Le+ G  + e  +k++v+ ve+g   + a   ++ 
  gi|320101050|ref|YP_004176642.1|  18 EYLERQGFRIEEARKKIKVEGVEIGEVDAVAVSRNGV 54 
                                       6688889999999999999999988765544444444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0001
                           DUF3394 102 eatgeerL.eaaGltlleedgkvlvdevefgspaekagldfdfeivevevpa.drppkelvyipA 164
                                       ++++++ L +++G++++e +++ lvd+ e++  +e+a   f  +i++v v+  + pp++l  i A
  gi|320101050|ref|YP_004176642.1|  92 ADDSAAALaKELGVEVIELGDQYLVDAEELEVIVESAVQGFIRRILDVLVKDeSVPPQDLEVIDA 156
                                       56677777799****************************************95556666666655 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.1e-05      0.27       6      56 ..      13      63 ..       8     107 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.1e-05
                              NERD  6 EravakeLkelked..eylvlhdvrlrpg.tgeiDhlvispkgi.fviEvKnwsG 56
                                      E  ++++L+++  +       + +++++   ge+D +++s++g+ + +EvK+  G
  gi|320101050|ref|YP_004176642.1| 13 ELIALEYLERQ--GfrIEEARKKIKVEGVeIGEVDAVAVSRNGVkYAVEVKA--G 63
                                      55566666633..2111122233444333444**********97366****9..4 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.4   7.1e+03      27      45 ..      41      58 ..      37      60 .. 0.64
   2 ?   -3.8   0.0       4.8   1.4e+04      26      35 ..      95     104 ..      95     106 .. 0.76
   3 ?    9.8   0.0   0.00027       0.8      13      54 ..     151     190 ..     133     196 .. 0.79
   4 ?   -3.1   0.1       2.8   8.3e+03      41      53 ..     202     215 ..     201     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.4
                                      HHHHHHHHTS-HHHHHHHH CS
                            HTH_20 27 aselaerldlskntlsyHL 45
                                       +e+++   +s+n + y +
  gi|320101050|ref|YP_004176642.1| 41 IGEVDAVA-VSRNGVKYAV 58
                                      56666666.7888887765 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.8
                                       -HHHHHHHHT CS
                            HTH_20  26 taselaerld 35 
                                       +a++la++l+
  gi|320101050|ref|YP_004176642.1|  95 SAAALAKELG 104
                                       6788898886 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00027
                                       HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54 
                                       +++ +aL  a+ +  +e+a++l +s  ++ +H+r  +  gL+
  gi|320101050|ref|YP_004176642.1| 151 LEVIDAL--ARSRDIKEFADALKTSVENAMRHVRRIQAKGLL 190
                                       4456666..************************998777776 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.8
                                       HHHHHHHHHH.CTT CS
                            HTH_20  41 lsyHLrvLee.agL 53 
                                       l+ +L vL+e + L
  gi|320101050|ref|YP_004176642.1| 202 LYAQLTVLREkVKL 215
                                       67889999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1708.29
//
Query:       gi|320101051|ref|YP_004176643.1|  [L=393]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   33.5   0.1    5.6e-07   30.1   0.0    2.6  3  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.24   11.1   0.0    1.4  1  FAD_binding_4  FAD 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 !   30.1   0.0   6.3e-11   5.6e-07       5     166 ..      52     218 ..      48     219 .. 0.76
   2 ?   -1.1   0.0      0.24   2.2e+03      80     103 ..     225     248 ..     220     252 .. 0.85
   3 ?   -1.2   0.0      0.27   2.4e+03      46      93 ..     261     306 ..     240     317 .. 0.61

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 6.3e-11
                                       SEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH.HHTT..SEEEEEESSTGGGS...TTHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxx..xxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet..vrregrgrslsveeileevkelk.aekg..vkevilgggeplly...pdfvellerlakl 73 
                                        gC+++C +C+++ +    +  +++ ls  +++  +  ++ + +g  +  + lg+ +  l+    + + ++ +++k+
  gi|320101051|ref|YP_004176643.1|  52 IGCTMGCLYCYIGDMgfPIDSIKPYPLSGVQLVYALLNNRyFLPGreGSLIALGSVTEPLHpavLERTLEYIEAVKR 128
                                       69***********9999888888888888888888888887777753444444444444443443444444444444 PP

                                       CCCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  74 avpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdri 149
                                          g +i ++t +++  +  +++l+e        +++ ++ +  +l+++   + ++ + e+++++ eag+k+  +  
  gi|320101051|ref|YP_004176643.1| 129 -YMGNHIQFSTKAYVS-KTTAAKLAEIDpGISPLVTIVSLRYSSILERN--APKPDLRFESIRTMSEAGLKPLLFLR 201
                                       .4999**********8.*********99555555555555555666666..689*********************** PP

                                       EEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                       Radical_SAM 150 vglpGendeeleellel 166
                                       +++pG ++ e+ee++++
  gi|320101051|ref|YP_004176643.1| 202 PVIPGITEWEFEEIIDE 218
                                       **************986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.24
                                       EEEEECSSCHGHHHHHHHHHTT-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvd 103
                                       i v++ g+++++ +++rl++ gvd
  gi|320101051|ref|YP_004176643.1| 225 IGVVAGGLRVSRGIIDRLRDTGVD 248
                                       6788899999999*******9988 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.27
                                       T.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHH CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  46 g.vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeek 93 
                                       g  +  ++ g e+++ ++++ +++r++ l  + +  ++ +n +++  e 
  gi|320101051|ref|YP_004176643.1| 261 GkLRAGVQYGVEVSDIKEKIAAYARRKGL--KYFPSACMANLYTH-GET 306
                                       33666666677777777777777777777..46666666666666.554 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.7e-05      0.24      11      89 ..     210     288 ..     203     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHHHHHTT CS
                     FAD_binding_4  11 eevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlvealaakgl 86 
                                        e ++++  a+e+g  + v++gG  ++++ + + +++ +dl+++++ ++i   + +a v+ Gv ++d+ e +aa+ +
  gi|320101051|ref|YP_004176643.1| 210 WEFEEIIDEAAEHG-AIGVVAGGLRVSRGIIdRLRDTGVDLREIEKRIKIPLGKLRAGVQYGVEVSDIKEKIAAYAR 285
                                       577899999**999.78999999999977777999******999999************************999887 PP

                                       ECS CS
                     FAD_binding_4  87 llg 89 
                                         g
  gi|320101051|ref|YP_004176643.1| 286 RKG 288
                                       766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2889.53
//
Query:       gi|320101052|ref|YP_004176644.1|  [L=195]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   15.5   0.0       0.29   11.0   0.0    2.4  2  RelB_N    RelB Antitoxin alpha helical domain


Domain annotation for each model (and alignments):
>> RelB_N  RelB Antitoxin alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.6e-05      0.29       1      30 [.      53      82 ..      53      99 .. 0.83
   2 ?    2.1   0.0    0.0097   1.7e+02      12      24 ..     121     133 ..     118     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.6e-05
                                      --EEE-CHHHHHHHHHH.HHHHHHHHHTTT CS
                            RelB_N  1 iaVqIdieeyekIeEiLEDyGLaklMeevk 30
                                      iaV++  +++ +I +iLE  G   l++e  
  gi|320101052|ref|YP_004176644.1| 53 IAVFLKSDIFTRIVDILESSGFSSLLTEIL 82
                                      79*****************99988888865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.0097
                                       HHHHHH.HHHHHH CS
                            RelB_N  12 kIeEiLEDyGLak 24 
                                        Ie +L + GL+k
  gi|320101052|ref|YP_004176644.1| 121 TIESMLRNTGLFK 133
                                       59*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1389.85
//
Query:       gi|320101053|ref|YP_004176645.1|  [L=224]
Description: phosphoserine phosphatase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-16   59.6   0.0    6.7e-16   59.2   0.0    1.2  1  HAD              haloacid dehalogenase-like hydrolase
    1.3e-13   51.7   0.0    5.3e-12   46.5   0.0    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
      1e-08   35.5   0.0      9e-08   32.4   0.0    2.0  1  HAD_2            Haloacid dehalogenase-like hydrolase
      1e-05   25.4   0.0    7.9e-05   22.5   0.0    2.1  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
     0.0036   16.7   0.0       0.01   15.3   0.0    1.6  2  Put_Phosphatase  Putative Phosphatase
  ------ inclusion threshold ------
       0.12   12.5   0.4       0.82    9.8   0.4    2.3  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase


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 !   59.2   0.0   2.3e-19   6.7e-16       1     188 []       6     178 ..       6     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.3e-19
                               HAD   1 alfDfDgTLldg.dslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaeler 75 
                                       ++fD Dg L+ + +s  +l ++++ r+ +  ++++r+ l  +l     ++++ ++a ++ +  ++ +   +++ l r
  gi|320101053|ref|YP_004176645.1|   6 VVFDCDGVLTENhSSWQVLHEYFGSRDNKYFADLYRRGLISYL-----DWMKIDIALMIHSWGKPITrVNVEDALSR 77 
                                       79**********5555588887777777666666666666666.....44444689999999999996666666666 PP

                               HAD  76 fvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd..rltgelglegkpvr 150
                                                  +p+a+++++a  + G+ v+vvS+g++ lve++++e+g+d +  ++l+++d   + g+   e  +  
  gi|320101053|ref|YP_004176645.1|  78 VK--------VKPEARRVVEALNEMGYIVAVVSSGIDVLVERVCREVGVDLCFYNKLRFEDgeLVPGG---EALVPL 143
                                       66........89*******************************************9999999555555...443333 PP

                               HAD 151 gegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                        ++k++++r+   ae+  i++++++++GDs++D+  +r
  gi|320101053|ref|YP_004176645.1| 144 -REKPRVIRS--IAENLSIRISDTYYVGDSEWDIDVFR 178
                                       .47*******..**********************8765 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   1.8e-15   5.3e-12       3     210 .]       5     181 ..       4     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.8e-15
                                       EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlta 79 
                                       +vvfD+dG+Lt+ ++s   + ++                           r  + + fa       y +g   +l++
  gi|320101053|ref|YP_004176645.1|   5 LVVFDCDGVLTENHSSWQVLHEYF------------------------GSR--DNKYFAD-----LYRRGLISYLDW 50 
                                       69*********9996655555555........................444..4467999.....999999999999 PP

                                       HHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  80 ldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG 156
                                       +    d    i+s+ +    v ++  +al         kvkpea+ +v++L+++g+ v++++++    +er+ +++G
  gi|320101053|ref|YP_004176645.1|  51 M--KIDIALMIHSWGKPITRVNVE--DAL------SRVKVKPEARRVVEALNEMGYIVAVVSSGIDVLVERVCREVG 117
                                       9..666777777777777777777..333......3445************************************** PP

                                       .GGGESEEEEHHCES...STTT........SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       .xxxxxxxxxxxxxx...xxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 157 .ddyfdaviasdiet...vakp........spegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        d +f +++  ++ +               +p+  + +++ L ++++++  VGD+ +D+  ++ +g
  gi|320101053|ref|YP_004176645.1| 118 vDLCFYNKLRFEDGElvpG--GealvplreKPRVIRSIAENLSIRISDTYYVGDSEWDIDVFRSVG 181
                                       *999988888888888652..335778999*****************************9988765 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0     3e-11     9e-08       1     172 [.       6     181 ..       6     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3e-11
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee.kieellrkyneekkkk 76 
                                       ++FD Dg+l      +     ++l ey +++ ++++++ l+   l  +l+ ++++      ++ + + ++n e    
  gi|320101053|ref|YP_004176645.1|   6 VVFDCDGVLTENHSSW-----QVLHEY-FGSRDNKYFADLYRRGLISYLDWMKIDIALMIhSWGKPITRVNVEDALS 76 
                                       7899***999876655.....445455.5677888888888888888888887754432235555555555555558 PP

                             HAD_2  77 evkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk.........KPdpevieka 144
                                        vk+ ++++ ++e L+e+gy +++v+s+ +  ve+  +++g++  F   +  ed e             +p+vi+ +
  gi|320101053|ref|YP_004176645.1|  77 RVKVKPEARRVVEALNEMGYIVAVVSSGIDVLVERVCREVGVDLCFYNKLRFEDGELVpggealvplREKPRVIRSI 153
                                       9******************************************88855444333332212223333344599***** PP

                             HAD_2 145 leklklkkeeviyvGDsptDieaakkag 172
                                        e+l +  +++ yvGDs  Di   + +g
  gi|320101053|ref|YP_004176645.1| 154 AENLSIRISDTYYVGDSEWDIDVFRSVG 181
                                       *********************8777666 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   4.2e+03       3      72 ..       8      22 ..       5      43 .. 0.51
   2 ?   -0.3   0.0      0.24     7e+02      15      55 ..      79     119 ..      75     134 .. 0.83
   3 !   22.5   0.0   2.7e-08   7.9e-05     188     229 ..     146     187 ..     144     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                                      EEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTE CS
                       Hydrolase_3  3 lDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgk 72
                                      +D                                                        + G l+ ++++++
  gi|320101053|ref|YP_004176645.1|  8 FD--------------------------------------------------------CDGVLTeNHSSWQ 22
                                      34........................................................4444443333333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       k++++++++++ l e g+ v++ +    + v++v +e+g+d
  gi|320101053|ref|YP_004176645.1|  79 KVKPEARRVVEALNEMGYIVAVVSSGIDVLVERVCREVGVD 119
                                       68899999999999999999999988888888888888877 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 2.7e-08
                                       HHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET CS
                       Hydrolase_3 188 KgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmg 229
                                       K   ++ +a++l+i  ++++ +GD+e Di  +  +g+++A++
  gi|320101053|ref|YP_004176645.1| 146 KPRVIRSIAENLSIRISDTYYVGDSEWDIDVFRSVGHSIAVE 187
                                       6667899*********************************97 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.4e-06      0.01       2     117 ..       5     123 ..       4     128 .. 0.85
   2 ?   -1.6   0.0      0.48   1.4e+03     166     182 ..     158     174 ..     146     178 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.4e-06
                   Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkgl..wnelmdr.vlkelheqgvsea..dikkvlrsipls 73 
                                       lvvfD D  + ++ s   v +e   ++  +   + +r+gl  + ++m+  +   +h+ g+ ++  +++++l ++ ++
  gi|320101053|ref|YP_004176645.1|   5 LVVFDCDGVLTENHSSWQVLHEYFGSRDNKYFADLYRRGLisYLDWMKIdIALMIHSWGKPITrvNVEDALSRVKVK 81 
                                       89***********99999999988888889999999987534888887514455688886655116799******** PP

                   Put_Phosphatase  74 pglvelikslakkkleldliiiSDaNsffieeileaagledlFs 117
                                       p+  +++++l  ++ ++ + ++S    + +e + +  g+  +F 
  gi|320101053|ref|YP_004176645.1|  82 PEARRVVEAL--NEMGYIVAVVSSGIDVLVERVCREVGVDLCFY 123
                                       **********..8899***********************99996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.48
                   Put_Phosphatase 166 gveyerliYvGDganDl 182
                                       +++ +   YvGD+  D+
  gi|320101053|ref|YP_004176645.1| 158 SIRISDTYYVGDSEWDI 174
                                       56777889****98875 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   0.00027      0.82       1      37 [.       6     102 ..       6     146 .. 0.72
   2 ?   -3.5   0.0       3.9   1.2e+04      60      70 ..     196     206 ..     189     217 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00027
                                       EEEESTTTSE............................................................ETTEE-T CS
                       Hydrolase_6   1 flfDidGvLw............................................................rgdkaip 17 
                                       ++fD+dGvL                                                                k+ p
  gi|320101053|ref|YP_004176645.1|   6 VVFDCDGVLTenhsswqvlheyfgsrdnkyfadlyrrglisyldwmkidialmihswgkpitrvnvedalSRVKVKP 82 
                                       69*******96666666666666666666666666666666666666666666666666666666666655666666 PP

                                       THHHHHHHHHHTT-EEEEEE CS
                       Hydrolase_6  18 gaaealnalraagkpvvllT 37 
                                       +a ++++al+++g+ v++++
  gi|320101053|ref|YP_004176645.1|  83 EARRVVEALNEMGYIVAVVS 102
                                       66666666666666666665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.9
                                       GGGEEEHHHHH CS
                       Hydrolase_6  60 eeqvvtsataa 70 
                                       +eqvv+s   +
  gi|320101053|ref|YP_004176645.1| 196 AEQVVSSLREI 206
                                       45555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1663.69
//
Query:       gi|320101054|ref|YP_004176646.1|  [L=106]
Description: transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00092   19.3   0.9     0.0017   18.4   0.9    1.4  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.015   16.0   1.0      0.022   15.5   1.0    1.2  1  FYDLN_acid      Protein of unknown function (FYDLN_acid)
       0.02   14.9   0.0      0.024   14.7   0.0    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.095   12.7   0.1       0.15   12.1   0.1    1.2  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
        0.1   12.9   0.0       0.13   12.5   0.0    1.2  1  TFIIE_beta      TFIIE beta subunit core domain
       0.15   12.0   0.5       0.22   11.5   0.5    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.17   12.0   6.2       0.23   11.6   0.2    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.49   10.2   4.5        3.2    7.6   0.1    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.54   10.2   5.9        3.4    7.7   0.7    2.3  2  zinc_ribbon_4   zinc-ribbon domain
        1.5    8.7   3.7        6.7    6.7   1.2    2.1  2  HalOD2          Halobacterial output domain 2
        5.9    6.9   5.8        1.7    8.7   0.7    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9     1e-06    0.0017       7      34 ..      68      93 ..      68      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgs 34
                                      rC++Cg +f  l +     ++  CP+C+s
  gi|320101054|ref|YP_004176646.1| 68 RCRKCGYVFKDLGRPR---KPSrCPRCKS 93
                                      8*********999655...6666****98 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.0   1.3e-05     0.022      12      36 ..      69      95 ..      67     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                        FYDLN_acid 12 CpscgakFYDLnk..dPivcpkcgeef 36
                                      C +cg  F DL++  +P  cp c++e+
  gi|320101054|ref|YP_004176646.1| 69 CRKCGYVFKDLGRprKPSRCPRCKSEW 95
                                      ************8889********998 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 ?   14.7   0.0   1.4e-05     0.024      72      96 ..      68      95 ..      27      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      EETTTS-EEE.CHH.H.HHS-TTTSSS- CS
                              HypA 72 rCreCgkefe.lee.k.alrCpkCgsad 96
                                      rCr+Cg+ f+ l + +   rCp+C+s+ 
  gi|320101054|ref|YP_004176646.1| 68 RCRKCGYVFKdLGRpRkPSRCPRCKSEW 95
                                      8*********5554434669*****975 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 ?   12.1   0.1     9e-05      0.15      17      45 ..      66      96 ..      59     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9e-05
                          zf-C2HC5 17 apnClnCGkiiCakegls..kpCsfCgspll 45
                                       p C +CG +     ++   ++C+ C+s+ +
  gi|320101054|ref|YP_004176646.1| 66 PPRCRKCGYVFKDLGRPRkpSRCPRCKSEWI 96
                                      599********99999998999*****9876 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.1e-05      0.13       8      35 ..      12      37 ..      10      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-05
                        TFIIE_beta  8 iveylKkkdgplsleeIlsylslqldls 35
                                      i   l++ ++pl+++eI s l+l  + +
  gi|320101054|ref|YP_004176646.1| 12 IARLLREVERPLTVDEIISMLQL--NAT 37
                                      55679999**************9..443 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 ?   11.5   0.5   0.00013      0.22      30      55 ..      68      94 ..      54      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                    OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgfe 55
                                      +C +Cg++ k+  + ++  +Cp+C+ e
  gi|320101054|ref|YP_004176646.1| 68 RCRKCGYVFKDlGRPRKPSRCPRCKSE 94
                                      6***********99**********977 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00014      0.23      16      25 ..      68      77 ..      67      78 .. 0.91
   2 ?    2.8   1.6     0.079   1.3e+02       2       8 ..      87      93 ..      87      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                           UPF0547 16 fCphCGyvFq 25
                                      +C+ CGyvF+
  gi|320101054|ref|YP_004176646.1| 68 RCRKCGYVFK 77
                                      5********7 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.079
                           UPF0547  2 vCPeCea 8 
                                      +CP+C +
  gi|320101054|ref|YP_004176646.1| 87 RCPRCKS 93
                                      6****86 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0019       3.2       2      10 ..      68      76 ..      68      79 .. 0.85
   2 ?    3.7   1.3     0.031        51      16      22 ..      87      93 ..      87      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                      Rubredoxin_2  2 vCsqCGfes 10
                                      +C++CG+++
  gi|320101054|ref|YP_004176646.1| 68 RCRKCGYVF 76
                                      8******87 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.031
                      Rubredoxin_2 16 rCpsCgs 22
                                      rCp C+s
  gi|320101054|ref|YP_004176646.1| 87 RCPRCKS 93
                                      8****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 ?    7.7   0.7    0.0021       3.4      27      36 .]      68      77 ..      68      77 .. 0.93
   2 ?    5.1   0.4     0.013        21       4      10 ..      87      93 ..      86      96 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                     zinc_ribbon_4 27 rCskCghvFr 36
                                      rC kCg vF+
  gi|320101054|ref|YP_004176646.1| 68 RCRKCGYVFK 77
                                      8*******96 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
                     zinc_ribbon_4  4 tCpsCka 10
                                      +Cp+Ck+
  gi|320101054|ref|YP_004176646.1| 87 RCPRCKS 93
                                      4555554 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1       0.1   1.6e+02      33      40 ..      68      75 ..      65      79 .. 0.63
   2 ?    6.7   1.2    0.0041       6.7       1      12 [.      84      95 ..      84      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.1
                            HalOD2 33 kCtrCGev 40
                                      +C +CG v
  gi|320101054|ref|YP_004176646.1| 68 RCRKCGYV 75
                                      56666655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0041
                            HalOD2  1 rPekCseCsldW 12
                                      +P +C+ C+ +W
  gi|320101054|ref|YP_004176646.1| 84 KPSRCPRCKSEW 95
                                      69********** PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.39   6.3e+02       3       9 ..      67      73 ..      62      73 .. 0.79
   2 ?    8.7   0.7     0.001       1.7      22      29 ..      88      95 ..      85      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.39
                    PhnA_Zn_Ribbon  3 pkCplCa 9 
                                      p C +C+
  gi|320101054|ref|YP_004176646.1| 67 PRCRKCG 73
                                      8999995 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.001
                    PhnA_Zn_Ribbon 22 CpeCahEw 29
                                      Cp C++Ew
  gi|320101054|ref|YP_004176646.1| 88 CPRCKSEW 95
                                      77777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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):              11  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 848.93
//
Query:       gi|320101055|ref|YP_004176647.1|  [L=138]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-18   65.4   0.0    6.4e-18   64.6   0.0    1.3  1  DUF167    Uncharacterised ACR, YggU family COG1872


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0   3.6e-22   6.4e-18       1      74 [.      49     117 ..      49     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 3.6e-22
                                       EEEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEE CS
                            DUF167   1 gvilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvv 74 
                                       g+il++rvkPg ++d ++     +++++l +  ++pp++G+AN+al+kf+++ l++p s+++iv+G++s  K++
  gi|320101055|ref|YP_004176647.1|  49 GIILSIRVKPGESEDFLT-----VEGDELVFYTSEPPERGRANAALVKFFSRELKIPVSRIDIVYGHRSTLKKL 117
                                       689***************.....56677********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1047.07
//
Query:       gi|320101056|ref|YP_004176648.1|  [L=396]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-78  262.6   0.0    7.5e-78  262.3   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    1.2e-06   28.3   0.0    1.9e-06   27.6   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    1.6e-05   24.8   0.0    2.3e-05   24.2   0.0    1.3  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.044   13.3   0.0      0.081   12.5   0.0    1.4  1  MTS              Methyltransferase small domain
      0.044   13.2   0.0      0.072   12.5   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.066   12.9   0.0       0.25   11.1   0.0    1.8  2  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.3   0.0   2.5e-81   7.5e-78      17     375 ..      35     389 ..      16     390 .. 0.93

  Alignments for each domain:
  == domain 1  score: 262.3 bits;  conditional E-value: 2.5e-81
                                       T--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHH CS
                               TRM  17 keeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeN 93 
                                        ++VFYNP   + RD +vlv+r   +l+    + ++ +d+L+++G+R+iR a+E +g + ++ ND+ ++Av  i++N
  gi|320101056|ref|YP_004176648.1|  35 WMPVFYNPSAVVSRDATVLVLR---VLHGS--HGFTFIDSLAGTGVRGIRIAVE-SGGEGIV-NDVDPRAVYYIRKN 104
                                       589*****************55...55555..4689******************.6766666.************** PP

                                       HHHTT--G.GEEEE-S-HHHHHC...--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHH CS
                               TRM  94 vklnevee.ivvineddAnvlla...ekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspek 166
                                       ++ln+  +  v++ +++Anvll+    +   fd++DlDP+Gspapflds+ + +++k+++ v aTDta+L+ ++ +k
  gi|320101056|ref|YP_004176648.1| 105 IQLNKLGNgKVEVYSQEANVLLNnltFTGIPFDYVDLDPYGSPAPFLDSVFKPLAKKAVIGVSATDTAPLTCSHFRK 181
                                       *******889999999******965556667********************************************** PP

                                       HHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHH.HTTEEEEEEE CS
                               TRM 167 clrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkv.leklglvlhC 242
                                        lr+Y  + + +++  E++ R+l++++ ++aa  +  v+pll +++ +Y+rvf++++++a ++ ++ +e lg++ +C
  gi|320101056|ref|YP_004176648.1| 182 TLRRYWFTCVDTDFEKEIGARLLITYIFKRAAALDTSVKPLLVFMHRHYYRVFLETRRNAGEAYRLsTECLGYIWYC 258
                                       ************************************************************99987616678****** PP

                                       TTT--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--S CS
                               TRM 243 sgClseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldap 319
                                        + l+++ vk+l  ++   +  g+k   +G +w+  l dk+fv+++ +ea +   + l+k+++++L+++k+E+  + 
  gi|320101056|ref|YP_004176648.1| 259 PSTLERGYVKTLSDLNDVTCMSGEKPVPIGKIWICGLGDKDFVNRLHDEAGS--VNWLTKDTRRILSMLKNEVELNN 333
                                       ***************999999999**************************99..5677**************96667 PP

                                       S-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
                               TRM 320 lyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                                        y  +++l+s+l  ++p+ +++++ l+++g ++srtH+ p+++k +a++ a++evl
  gi|320101056|ref|YP_004176648.1| 334 PYVRVDKLCSILGRNMPKYEELIDTLRSIGIKASRTHFDPRGLKIEADTRALIEVL 389
                                       7889**************************************************98 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   6.4e-10   1.9e-06      41     142 ..      62     164 ..      47     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.4e-10
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkeefdi 116
                                       +g +++D  aG+G+ g+  +     + ++ + d++av  +++n++  kl + +++++ ++a   l++l+ ++ +fd+
  gi|320101056|ref|YP_004176648.1|  62 HGFTFIDSLAGTGVRGIRIAVESGGEGIVNDVDPRAVYYIRKNIQLNKLGNgKVEVYSQEANVLLNNLTFTGIPFDY 138
                                       67789*************9999999*********************999999************************* PP

                                       EEE--SSSTTCH..HHHHHHHHHTT-E CS
                     Cons_hypoth95 117 vflDPPyakell.ieevlelleekkll 142
                                       v lDP y + +  +  v++ l++k ++
  gi|320101056|ref|YP_004176648.1| 139 VDLDP-YGSPAPfLDSVFKPLAKKAVI 164
                                       ****7.555432366666666666555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   7.8e-09   2.3e-05     101     163 ..      63     125 ..      38     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.8e-09
                                       T-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT.CEEEEES-GGG- CS
                            Met_10 101 gevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek.vvkpileDgrev 163
                                       g + +d +AG G   i ia+ s ++  + +d++P++v y+++ni+lNk+ + +v+++ ++++ +
  gi|320101056|ref|YP_004176648.1|  63 GFTFIDSLAGTGVRGIRIAVESGGEG-IVNDVDPRAVYYIRKNIQLNKLGNgKVEVYSQEANVL 125
                                       5567999************9777665.569******************9752676666655544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.7e-05     0.081      19      86 ..      50     119 ..      43     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE CS
                               MTS  19 GsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevva 86 
                                       ++ l l+ l+ ++  + +D  +G+Gv g+ +a es   e  + dvd rA+   ++n++ nkl    vev+ 
  gi|320101056|ref|YP_004176648.1|  50 ATVLVLRVLHGSHGFTFIDSLAGTGVRGIRIAVESGG-EGIVNDVDPRAVYYIRKNIQLNKLGngkVEVYS 119
                                       6788899999999999*****************9999.56679*****************99765555554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05     0.072     162     219 ..      63     121 ..      49     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalse 219
                                       g +++D  +G+G+  i  a     + +  D+D+ Av   ++N++lNk+ + k+ev+ +e
  gi|320101056|ref|YP_004176648.1|  63 GFTFIDSLAGTGVRGIRIAVESGGEGIVNDVDPRAVYYIRKNIQLNKLGNgKVEVYSQE 121
                                       45889999999999998877777777789*******************99899997543 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.3e-05      0.25      55     102 ..      71     117 ..      59     141 .. 0.82
   2 ?   -1.6   0.0      0.63   1.9e+03      75      94 ..     315     334 ..     303     345 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
                   Methyltransf_16  55 sGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkv 102
                                       +GtG+ G+ +a   ++ + i+ D++  ++  ++kni+lnk + + kv+v
  gi|320101056|ref|YP_004176648.1|  71 AGTGVRGIRIAVE-SGGEGIVNDVDPrAVYYIRKNIQLNK-LGNGKVEV 117
                                       8***********9.8888999**9987999********88.66777766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.63
                   Methyltransf_16  75 ltDleellellkknielnkn 94 
                                         D+  +l +lk+ +eln+ 
  gi|320101056|ref|YP_004176648.1| 315 TKDTRRILSMLKNEVELNNP 334
                                       45889999999*****9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2994.81
//
Query:       gi|320101057|ref|YP_004176649.1|  [L=186]
Description: nucleoside-triphosphatase [Desulfurococcus mucosus DSM 2162]
Scores for 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  165.5   0.1    1.2e-48  165.2   0.1    1.0  1  NTPase_1         NTPase
    8.1e-06   25.0   0.2    1.5e-05   24.1   0.2    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    1.3e-05   24.9   0.0    1.8e-05   24.4   0.0    1.1  1  DUF2478          Protein of unknown function (DUF2478)
    0.00014   22.4   0.0    0.00039   21.0   0.0    1.8  1  AAA_18           AAA domain
    0.00028   20.8   0.0    0.00039   20.3   0.0    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
    0.00042   20.6   0.0     0.0015   18.8   0.0    1.9  1  AAA_22           AAA domain
    0.00044   20.3   0.0    0.00076   19.6   0.0    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
    0.00071   19.8   0.0      0.002   18.3   0.0    1.7  1  AAA_33           AAA domain
     0.0029   17.4   0.0     0.0067   16.2   0.0    1.6  1  AAA_30           AAA domain
     0.0034   17.1   0.0      0.023   14.4   0.0    2.0  2  AAA_24           AAA domain
     0.0048   16.8   0.0     0.0098   15.8   0.0    1.5  1  NACHT            NACHT domain
     0.0062   16.9   0.3      0.011   16.1   0.3    1.8  1  AAA_16           AAA ATPase domain
     0.0066   15.9   0.0      0.011   15.2   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.021   15.3   0.0    1.4  1  AAA              ATPase family associated with various cellul
      0.013   16.0   0.0      0.021   15.3   0.0    1.4  1  ABC_tran         ABC transporter
      0.024   14.9   0.0      0.054   13.7   0.0    1.6  1  AAA_28           AAA domain
      0.028   14.4   0.1        1.5    8.8   0.0    2.5  3  AAA_5            AAA domain (dynein-related subfamily)
      0.036   13.7   0.0       0.07   12.7   0.0    1.6  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.038   14.4   0.2       0.15   12.5   0.0    1.9  2  AAA_17           AAA domain
      0.038   13.7   0.1      0.077   12.7   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.046   13.3   0.0      0.076   12.5   0.0    1.2  1  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.049   12.5   0.1      0.095   11.6   0.1    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.075   12.3   0.0       0.14   11.4   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.076   13.4   0.0       0.12   12.8   0.0    1.3  1  RNA_helicase     RNA helicase
      0.083   12.8   0.0       0.13   12.1   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.084   13.1   0.0       0.16   12.2   0.0    1.6  1  DUF1611_N        Domain of unknown function (DUF1611_N) Rossm
       0.12   11.6   0.0       0.13   11.5   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.13   12.0   0.0       0.18   11.5   0.0    1.2  1  PRK              Phosphoribulokinase / Uridine kinase family
       0.14   12.1   0.0       0.22   11.4   0.0    1.3  1  APS_kinase       Adenylylsulphate kinase
       0.15   11.7   0.0       0.22   11.2   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.16   12.3   0.1        1.8    8.9   0.1    2.1  2  AAA_19           AAA domain
       0.19   12.2   0.0       0.34   11.4   0.0    1.3  1  AAA_23           AAA domain
        0.2   11.9   0.0       0.35   11.1   0.0    1.3  1  Roc              Ras of Complex, Roc, domain of DAPkinase


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 !  165.2   0.1   2.2e-51   1.2e-48       1     163 [.       5     165 ..       5     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.2 bits;  conditional E-value: 2.2e-51
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE- CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvd 77 
                                       k++iTG+pG GK+T++++++++l+ +g+ vgGf ++evre++ r+gFkivdl sg+e++La+++a+ ++rvg+y+v 
  gi|320101057|ref|YP_004176649.1|   5 KIVITGHPGAGKSTFFERLVSELRARGLVVGGFKAPEVREHDVRVGFKIVDLLSGDEAWLAKRGAHGSIRVGSYTVM 81 
                                       699************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEE CS
                          NTPase_1  78 vesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvf 153
                                       +e++++l+ +al++al+eadvi +DE+G+mElk++ fk  + e+L+s+kpv+ v+h r  d +++ +++   d++ +
  gi|320101057|ref|YP_004176649.1|  82 LEEASRLIGNALQRALREADVIGVDEVGPMELKIPLFKPLILEALESGKPVVLVVHYRLsDREILGRLE---DAERI 155
                                       **********************************************************88877777777...57889 PP

                                       E--TTTTTTH CS
                          NTPase_1 154 evteenrdal 163
                                        +t enr+ +
  gi|320101057|ref|YP_004176649.1| 156 VITVENREIM 165
                                       99*****976 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 !   24.1   0.2   2.8e-08   1.5e-05      30      60 ..       4      34 ..       2      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.8e-08
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--E CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrv 60
                                       ++ +tG PGaGkst+ e+l+ elr+rG  v
  gi|320101057|ref|YP_004176649.1|  4 SKIVITGHPGAGKSTFFERLVSELRARGLVV 34
                                      5688************************877 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.4e-08   1.8e-05       4     134 ..       8     140 ..       6     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.4e-08
                           DUF2478   4 vvyadgeavdalLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeririsqdlgsgsqgCrLdpeaLa 80 
                                       + +++g+   +++++++++lra+Gl v+G+   + +e++  +   +++dl +g++  + ++  +gs      +  L+
  gi|320101057|ref|YP_004176649.1|   8 ITGHPGAGKSTFFERLVSELRARGLVVGGFKAPEVREHD-VRVGFKIVDLLSGDEAWLAKRGAHGSIRVGSYTVMLE 83 
                                       677888999999******************988888775.678****************999999877777778899 PP

                           DUF2478  81 eaaaaverala...egadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVsekl 134
                                       ea++ + +al+   ++ad++ v   G  E +   + + i +al++g Pv+ +V+ +l
  gi|320101057|ref|YP_004176649.1|  84 EASRLIGNALQralREADVIGVDEVGPMELKIPLFKPLILEALESGKPVVLVVHYRL 140
                                       999988888852226799***********************************9876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   7.2e-07   0.00039       1      87 [.       6     144 ..       6     171 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.2e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf...................gvnlrdvakenglllevdpe...........al 46 
                                       I++tG pG+GK+t+ ++L ++l +                    g+++ d+++ ++  l    +           +l
  gi|320101057|ref|YP_004176649.1|   6 IVITGHPGAGKSTFFERLVSELrARglvvggfkapevrehdvrvGFKIVDLLSGDEAWLAKRGAhgsirvgsytvML 82 
                                       99****************88874447788777888888877777777777777766666666655555333333222 PP

                            AAA_18  47 deskrldedkldklldaleenss............................aleegknlvidghlaele 87 
                                       +e  rl  + l+++l       +                             ++++ +lv+  +l++ e
  gi|320101057|ref|YP_004176649.1|  83 EEASRLIGNALQRAL-------ReadvigvdevgpmelkiplfkplilealESGKPVVLVVHYRLSDRE 144
                                       222222222222222.......12222334555555555555555555543333444445555555444 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 !   20.3   0.0   7.2e-07   0.00039       2      35 ..       6      39 ..       5     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.2e-07
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKh 35
                                      + i+g+ g+GK t+ e+l++el+argl vg  K 
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELRARGLVVGGFKA 39
                                      6799*************************99885 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.7e-06    0.0015       8      55 ..       6      55 ..       2     144 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-06
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskd 55
                                      +v+tG++G+GK+t  +rl+++l ++       + pev + ++ ++ +  d
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELRARGLVVGgfKAPEVREHDVRVGFKIVD 55
                                      89*******************96544333365333333444444444444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.4e-06   0.00076       1      24 [.       5      29 ..       5     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-06
                                      EEEEEESTTSSHHHHHHHHHTS.TE CS
                          MMR_HSR1  1 evaivGrpNvGKStLinaltge.ka 24
                                      +++i G+p +GKSt++ +l+ e +a
  gi|320101057|ref|YP_004176649.1|  5 KIVITGHPGAGKSTFFERLVSElRA 29
                                      699****************998554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.6e-06     0.002       2      24 ..       6      28 ..       6      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.6e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                      +++ G+pG+GKst+ erl+ +l 
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELR 28
                                      5788**************99987 PP

>> AAA_30  AAA 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    0.0067      21     114 ..       6     127 ..       1     137 [. 0.56

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrvigl.AptgkaAkv.La........eelgieastiakllkrlk...... 81 
                                        v+tG +G+GK+t  + l+  ++a+g  v g+ Ap+ +  +v ++                  + +l + +      
  gi|320101057|ref|YP_004176649.1|   6 IVITGHPGAGKSTFFERLVSELRARGLVVGGFkAPEVREHDVrVGfkivdllsG--------DEAWLAKRGahgsir 74 
                                       689**********************97666653555544444344222222220........222222222333333 PP

                            AAA_30  82 ..................grarlepgtllivDEagmv..dtkqlaallkaaek 114
                                                          + +l++++++ vDE+g +   +  ++ l+ +a +
  gi|320101057|ref|YP_004176649.1|  75 vgsytvmleeasrlignaLQRALREADVIGVDEVGPMelKIPLFKPLILEALE 127
                                       33333333344456777633567777888888888763344455555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   4.2e-05     0.023       4      29 ..       5      34 ..       3     115 .. 0.59
   2 ?    0.5   0.0      0.79   4.3e+02     115     170 ..     122     179 ..     115     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel....gpkplfi 29
                                      ki+i+G +g+GK+t+  +l      + l++
  gi|320101057|ref|YP_004176649.1|  5 KIVITGHPGAGKSTFFERLvselRARGLVV 34
                                      9**************999966654444444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.79
                            AAA_24 115 lkklqelrknvifiah..ektrkdedpegeakytrlepklgkktanelkeevDlvlra 170
                                       +    e +k v+++ h  +  r++  + ++a+   ++ + ++  +  +k+++D++lr 
  gi|320101057|ref|YP_004176649.1| 122 ILEALESGKPVVLVVHyrLSDREILGRLEDAERIVITVENREIMGSRVKQIADVILRG 179
                                       5566666776777766223455555666667777777788888899999999999986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.8e-05    0.0098       3      29 ..       6      32 ..       4      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                      ++++G +G GK+t+ ++l+++++++ l
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELRARGL 32
                                      89********************98865 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   0.3     2e-05     0.011      27      63 ..       6      42 ..       1     178 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      ++++G++G GKs+  ++l  +l+++g ++   k+ + 
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELRARGLVVGGFKAPEV 42
                                      78*****************9***99766644444444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.1e-05     0.011       4      30 ..       6      32 ..       4      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                      EEEE--TTSSHHHHHHHHHHHHHHTT- CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekr 30
                                      +v+tG+P +GKst+ ++L ++l++++ 
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELRARGL 32
                                      8*********************99765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.8e-05     0.021       2      68 ..       7     109 ..       6     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.8e-05
                                       EEESSTTSSHHHHHHHHHHHHTHE...EEEEETTTCSSS...................................STT CS
                               AAA   2 llyGppGtGKTllakavakelgve...fleisgsellsk...................................yvg 40 
                                       +++G pG GK+++ + +++el ++   +  ++++e++++                                   +++
  gi|320101057|ref|YP_004176649.1|   7 VITGHPGAGKSTFFERLVSELRARglvVGGFKAPEVREHdvrvgfkivdllsgdeawlakrgahgsirvgsytvMLE 83 
                                       689*****************975533355667777775578888888888888999999999999999999999999 PP

                                       HHHHHHHHHHHHHHHTSTSEEEEEETGG CS
                               AAA  41 esekkirelfkeakekakpsilfiDEid 68 
                                       e+++ i + +++a ++a   ++ +DE+ 
  gi|320101057|ref|YP_004176649.1|  84 EASRLIGNALQRALREA--DVIGVDEVG 109
                                       9***********98888..9*****986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.9e-05     0.021      12      36 ..       4      28 ..       2      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.9e-05
                                      SEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllk 36
                                      +k++i+G+ GaGKSt+++ l  +l+
  gi|320101057|ref|YP_004176649.1|  4 SKIVITGHPGAGKSTFFERLVSELR 28
                                      6899*************99988876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0    0.0001     0.054       1      21 [.       5      25 ..       5      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
                            AAA_28  1 kivitGgestGKTtlleaLaa 21
                                      kivitG +++GK+t  e+L +
  gi|320101057|ref|YP_004176649.1|  5 KIVITGHPGAGKSTFFERLVS 25
                                      79************9998863 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 ?    8.8   0.0    0.0028       1.5       2      28 ..       6      32 ..       5      63 .. 0.87
   2 ?    3.2   0.0      0.15        81      46      74 ..      79     108 ..      71     115 .. 0.80
   3 ?   -2.5   0.0       8.6   4.7e+03      21      46 ..     124     150 ..     121     162 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                                      EEEE--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreve 28
                                      +++ G pG gKs++ erl + l+++ +
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELRARGL 32
                                      6899**************988866655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                                       --..........--------G-SEEEEESG CS
                             AAA_5  46 eik.ngttslvdsplvraaregeilvlDEv 74 
                                        ++ ++  +l  ++l ra re++++ +DEv
  gi|320101057|ref|YP_004176649.1|  79 TVMlEEASRLIGNALQRALREADVIGVDEV 108
                                       555566777888999**************9 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.6
                                       GGB.S--EEEEE--TT--HHHHH--B- CS
                             AAA_5  21 aal.nreveyvqltrdtteedlkgrre 46 
                                       +al   + ++   + +++ ++++gr+e
  gi|320101057|ref|YP_004176649.1| 124 EALeSGKPVVLVVHYRLSDREILGRLE 150
                                       555544444555566677777777766 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 ?   12.7   0.0   0.00013      0.07       3      24 ..       6      27 ..       4      60 .. 0.85
   2 ?   -2.0   0.0       4.1   2.3e+03      81      92 ..      98     109 ..      68     158 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                      EEEEESTTCCHHHHHHHHHCT- CS
                              cobW  3 tvltGflGsGKTtLlnhllenr 24
                                      +v+tG +G+GK+t+ ++l+++ 
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSEL 27
                                      79****************9553 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                                       TT-SEEEEEECT CS
                              cobW  81 erldviliEttG 92 
                                       ++ dvi +  +G
  gi|320101057|ref|YP_004176649.1|  98 READVIGVDEVG 109
                                       344444444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00027      0.15       1      20 [.       9      28 ..       9      45 .. 0.85
   2 ?   -0.4   0.0       2.5   1.4e+03      93     119 ..     142     168 ..      79     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                                      EE-TTSSHHHHHHHHHHHHT CS
                            AAA_17  1 lGgPGsGKgtqceklvekyg 20
                                      +G PG+GK+t  e+lv ++ 
  gi|320101057|ref|YP_004176649.1|  9 TGHPGAGKSTFFERLVSELR 28
                                      699*************9985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.5
                                       HHHHHHHH..SEEEEEE--HHHHHHHH CS
                            AAA_17  93 pkevleelkpdaiilleadpeeilerr 119
                                       ++e+l  l+    i++ +++ ei+  r
  gi|320101057|ref|YP_004176649.1| 142 DREILGRLEDAERIVITVENREIMGSR 168
                                       233444444445566666666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00014     0.077      24      39 ..       5      20 ..       1      27 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                            AAA_29 24 atlltGpsGsGKSTll 39
                                       +++tG+ G+GKST++
  gi|320101057|ref|YP_004176649.1|  5 KIVITGHPGAGKSTFF 20
                                      478***********97 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.076       5      28 ..       5      28 ..       3      33 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                      EEEEEESTTSSHHHHHHHHHHHTT CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktg 28
                                      +i+i gh  +GK+T+ +rL+ ++ 
  gi|320101057|ref|YP_004176649.1|  5 KIVITGHPGAGKSTFFERLVSELR 28
                                      689****************98765 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 ?   11.6   0.1   0.00017     0.095      16      43 ..       4      31 ..       2      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                     TrwB_AAD_bind 16 qhilivGttGsGKtqalekllrairarg 43
                                      ++i+i+G  G+GK++ +e l+ ++rarg
  gi|320101057|ref|YP_004176649.1|  4 SKIVITGHPGAGKSTFFERLVSELRARG 31
                                      5799**********************98 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   0.00026      0.14      19      46 ..       6      33 ..       4      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnv 46
                                      i++ G pGAGKs+  e l  el+++g v
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELRARGLV 33
                                      7899*****************9755544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00022      0.12       1      23 [.       6      28 ..       6      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      i+++G++g GKSt+ ++L+++l 
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELR 28
                                      789***************99987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.13     101     125 ..       5      29 ..       1      48 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                       EEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelel 125
                                        +v+ G+ G+GKSt+ ++l++el++
  gi|320101057|ref|YP_004176649.1|   5 KIVITGHPGAGKSTFFERLVSELRA 29 
                                       5799****************99765 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00029      0.16      36      84 ..     103     153 ..      82     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00029
                         DUF1611_N  36 iGiapeggklp..eswreavkeAleaGldvvsGlHerLsddpelaalakkk 84 
                                       iG+   g +    +  ++ + eAle G  vv   H+rLsd + l +l + +
  gi|320101057|ref|YP_004176649.1| 103 IGVDEVGPMELkiPLFKPLILEALESGKPVVLVVHYRLSDREILGRLEDAE 153
                                       5555555443324678999*********************99888877665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.13       4      26 ..       6      37 ..       3     108 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                           DUF2075  4 vlVtGvaGtGKtvvllnllael.........e 26
                                      +++tG +G+GK+    +l+ el          
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELrarglvvggF 37
                                      89***********9999999995555555550 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.18       2      29 ..       6      33 ..       5      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                               PRK  2 IgvagsSGaGkttvarklekifgrekvk 29
                                      I ++g  GaGk+t+ ++l++ ++  ++ 
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSELRARGLV 33
                                      789*****************99976655 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0004      0.22       4      43 ..       5      44 ..       2      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTT CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRh 43
                                       + +tG  g+GKst  ++l ++L+++g  v      +vR+
  gi|320101057|ref|YP_004176649.1|  5 KIVITGHPGAGKSTFFERLVSELRARGLVVGGFKAPEVRE 44
                                      5899**********************99888777777775 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0004      0.22       1      21 [.       6      26 ..       6      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrt 21
                                      iv+ G pG+GKSt   +l+++
  gi|320101057|ref|YP_004176649.1|  6 IVITGHPGAGKSTFFERLVSE 26
                                      79************9999987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0034       1.8      11      37 ..       4      30 ..       1      36 [. 0.86
   2 ?    1.4   0.0      0.69   3.8e+02      94     115 ..      91     112 ..      65     136 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0034
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvel 37
                                      + +++t+ pG GK++  +  v++l ++
  gi|320101057|ref|YP_004176649.1|  4 SKIVITGHPGAGKSTFFERLVSELRAR 30
                                      6789*************9999998776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.69
                            AAA_19  94 aeeekklqeeellivDEfqdvd 115
                                       ++ ++ l+e++++ vDE+  ++
  gi|320101057|ref|YP_004176649.1|  91 NALQRALREADVIGVDEVGPME 112
                                       35567887788******96543 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00063      0.34      23      37 ..       7      21 ..       3      25 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00063
                            AAA_23 23 lItGpNGaGKTTild 37
                                      +ItG+ GaGK+T+++
  gi|320101057|ref|YP_004176649.1|  7 VITGHPGAGKSTFFE 21
                                      9************98 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 ?   11.1   0.0   0.00065      0.35       1      22 [.       5      26 ..       5      32 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00065
                                      EEEEESSTTSSHHHHHHCHCT- CS
                               Roc  1 KvvlvGdsgvGKtsllkrfved 22
                                      K+v+ G  g+GK+++++r+v++
  gi|320101057|ref|YP_004176649.1|  5 KIVITGHPGAGKSTFFERLVSE 26
                                      9******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); 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: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1299.97
//
Query:       gi|320101058|ref|YP_004176650.1|  [L=294]
Description: XRE family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-12   46.7   0.2    1.9e-11   43.8   0.1    2.5  2  HTH_3      Helix-turn-helix
    2.8e-07   30.4   2.4    2.9e-07   30.4   0.4    2.1  2  HTH_19     Helix-turn-helix domain
    5.1e-06   26.7   0.1    1.8e-05   25.0   0.0    2.0  2  HTH_31     Helix-turn-helix domain
     0.0001   22.2   1.0    0.00068   19.6   0.0    2.9  4  HTH_Crp_2  Crp-like helix-turn-helix domain
    0.00029   20.7   0.1     0.0041   17.0   0.0    2.8  3  HTH_11     HTH domain
     0.0011   18.8   0.1     0.0046   16.7   0.0    2.1  2  HTH_23     Homeodomain-like domain
     0.0012   18.5   0.0     0.0029   17.3   0.0    1.7  1  MerR       MerR family regulatory protein
     0.0046   17.1   0.1      0.014   15.5   0.0    1.9  2  HTH_17     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.059   13.5   0.0    1.9  1  HTH_22     HTH domain
       0.02   15.0   0.0      0.095   12.9   0.0    2.1  2  UPF0180    Uncharacterised protein family (UPF0180)
      0.062   13.4   0.0       0.16   12.1   0.0    1.7  1  MerR_1     MerR HTH family regulatory protein
      0.083   13.1   1.2        1.5    9.1   0.1    3.0  3  PCP_red    Proto-chlorophyllide reductase 57 kD subunit
       0.11   12.6   0.0       0.34   11.0   0.0    1.9  1  HTH_7      Helix-turn-helix domain of resolvase
       0.12   12.4   0.0       0.32   11.0   0.0    1.8  1  HTH_29     Winged helix-turn helix
       0.13   11.9   1.6        2.2    8.0   0.1    3.5  3  Crp        Bacterial regulatory proteins, crp 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 !   43.8   0.1   1.6e-14   1.9e-11       1      51 [.     137     187 ..     137     190 .. 0.95
   2 ?   -0.4   0.0       1.1   1.3e+03      38      49 ..     265     276 ..     264     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.6e-14
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSE CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvs 51 
                                       l e+Rk+ gl++ eLAe+lGvsr ti+++E+Ge ++sl++ ++la++ g +
  gi|320101058|ref|YP_004176650.1| 137 LHEKRKEIGLTRGELAEMLGVSRKTIYMYEKGELMISLQKGIELARVIGED 187
                                       679********************************************9965 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHT CS
                             HTH_3  38 letlkklakaLg 49 
                                       le+++k+a++ g
  gi|320101058|ref|YP_004176650.1| 265 LENAEKIARTTG 276
                                       79999***9987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.4   2.4e-10   2.9e-07       2      41 ..     135     173 ..     134     188 .. 0.85
   2 ?   -2.0   0.1       3.2   3.9e+03      15      33 ..     265     283 ..     259     289 .. 0.60

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.4e-10
                            HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvps 41 
                                        rL e R+e glt  elae+lg+sr+ i+++E+g+  ++s
  gi|320101058|ref|YP_004176650.1| 135 SRLHEKRKEIGLTRGELAEMLGVSRKTIYMYEKGEL-MIS 173
                                       589999****************************75.665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                            HTH_19  15 qeelaerlgisrskisaiE 33 
                                       +e  ++ ++++ s++  iE
  gi|320101058|ref|YP_004176650.1| 265 LENAEKIARTTGSRLVTIE 283
                                       4444455666677777777 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       6.4   7.6e+03      33      45 ..       2      13 ..       2      27 .. 0.56
   2 !   25.0   0.0   1.5e-08   1.8e-05       4      55 ..     135     185 ..     134     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.4
                            HTH_31 33 rlEqGrrgrpspa 45
                                      r+E+G+ +   ++
  gi|320101058|ref|YP_004176650.1|  2 RWETGAGN-IAED 13
                                      67777763.4333 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.5e-08
                            HTH_31   4 alLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55 
                                        +L++ R++ GL++ e+Ae lgvs+ t+  +E G+    s++    lar+ g
  gi|320101058|ref|YP_004176650.1| 135 SRLHEKRKEIGLTRGELAEMLGVSRKTIYMYEKGELM-ISLQKGIELARVIG 185
                                       689999******************************5.99999888888876 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 ?   -3.2   0.0       7.3   8.8e+03      36      44 ..      12      20 ..      11      20 .. 0.82
   2 ?   -2.3   0.0       3.8   4.5e+03      44      67 ..      89     111 ..      88     112 .. 0.77
   3 !   19.6   0.0   5.7e-07   0.00068       5      38 ..     127     162 ..     126     163 .. 0.80
   4 ?   -1.5   0.0       2.1   2.6e+03      36      47 ..     219     230 ..     218     257 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.3
                                      HHHHHHHHH CS
                         HTH_Crp_2 36 etvsrilse 44
                                      e vsr+l++
  gi|320101058|ref|YP_004176650.1| 12 EDVSRTLRR 20
                                      779***985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.8
                                       HHHHTTSEEETEEEEES-HHHHHH CS
                         HTH_Crp_2  44 eLkreglisrgrririldleaLra 67 
                                       +L+++ +  r++ + i  +e L++
  gi|320101058|ref|YP_004176650.1|  89 KLEDDVVYVRNG-VNIVTPELLNN 111
                                       778887877886.99999999987 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 5.7e-07
                                       HHHHHHHCT.TTC.EEEEEHHHHHHHHHTTSSHHHH CS
                         HTH_Crp_2   5 rfLlrlaer.agg.eielpltqeelAsmlGltretv 38 
                                       ++Ll+l++    + + e+ lt+ elA+mlG++r t+
  gi|320101058|ref|YP_004176650.1| 127 NYLLKLSASrLHEkRKEIGLTRGELAEMLGVSRKTI 162
                                       589999554133457899***************997 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHH CS
                         HTH_Crp_2  36 etvsrilseLkr 47 
                                       et+ r+l++L++
  gi|320101058|ref|YP_004176650.1| 219 ETIWRLLNRLSN 230
                                       566666666654 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.7   9.2e+03      38      47 ..      17      26 ..      16      29 .. 0.81
   2 !   17.0   0.0   3.4e-06    0.0041      15      33 ..     144     163 ..     134     165 .. 0.83
   3 ?   -0.5   0.0         1   1.2e+03      30      45 ..     219     234 ..     218     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.7
                            HTH_11 38 aLeelgvpIe 47
                                      +L+ +g+++e
  gi|320101058|ref|YP_004176650.1| 17 TLRRAGFRVE 26
                                      7999999998 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.4e-06
                            HTH_11  15 p.isgeeLAeeLnvSrrtvr 33 
                                         ++  eLAe L+vSr+t++
  gi|320101058|ref|YP_004176650.1| 144 IgLTRGELAEMLGVSRKTIY 163
                                       358999*************9 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1
                            HTH_11  30 rtvrrdIkaLeelgvp 45 
                                        t++r + +L+ l v+
  gi|320101058|ref|YP_004176650.1| 219 ETIWRLLNRLSNLVVK 234
                                       5999999999988744 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.8e-06    0.0046       7      35 ..     131     163 ..     127     169 .. 0.83
   2 ?   -1.8   0.0       2.5     3e+03      32      40 ..     219     227 ..     218     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                            HTH_23   7 Rlrillllae....GlsvreIAreLgvsrrTvy 35 
                                       +l++ +l+ +    Gl++ e A++Lgvsr T+y
  gi|320101058|ref|YP_004176650.1| 131 KLSASRLHEKrkeiGLTRGELAEMLGVSRKTIY 163
                                       66666777756679******************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                            HTH_23  32 rTvyrwlkr 40 
                                        T++r l+r
  gi|320101058|ref|YP_004176650.1| 219 ETIWRLLNR 227
                                       69****999 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.4e-06    0.0029       3      22 ..     149     168 ..     147     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHTTTHHHHHHHHHT CS
                              MerR   3 gevAeltGvsprtLRyYEre 22 
                                       ge+Ae++Gvs +t+  YE+ 
  gi|320101058|ref|YP_004176650.1| 149 GELAEMLGVSRKTIYMYEKG 168
                                       9*****************95 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.5   8.9e+03      10      16 ..     129     135 ..     114     143 .. 0.59
   2 !   15.5   0.0   1.2e-05     0.014       2      19 ..     146     163 ..     146     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.5
                            HTH_17  10 lLgvsrs 16 
                                       lL++s s
  gi|320101058|ref|YP_004176650.1| 129 LLKLSAS 135
                                       4555555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
                            HTH_17   2 ltveEaAelLgvsrstvy 19 
                                       lt  E+Ae+Lgvsr+t+y
  gi|320101058|ref|YP_004176650.1| 146 LTRGELAEMLGVSRKTIY 163
                                       6778*************9 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.9e-05     0.059      47      61 ..     151     165 ..     148     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-05
                            HTH_22  47 vAekLgiSraTvYry 61 
                                       +Ae Lg+Sr T+Y y
  gi|320101058|ref|YP_004176650.1| 151 LAEMLGVSRKTIYMY 165
                                       7************99 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-05     0.095      10      51 ..      12      53 ..      11      68 .. 0.93
   2 ?   -2.6   0.0       5.4   6.5e+03       8      32 ..     264     288 ..     262     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                           UPF0180 10 snvkeaLrekGYeVvdleteedaqsvdaiVvtGqdtnvmgie 51
                                      ++v++ Lr+ G++V+ l+  + a+s+d++ ++G+++ +m+i+
  gi|320101058|ref|YP_004176650.1| 12 EDVSRTLRRAGFRVELLSYPHVARSIDIVACKGDTRVFMKIS 53
                                      5899***************999**************999986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.4
                           UPF0180   8 gLsnvkeaLrekGYeVvdleteeda 32 
                                       +L+n ++  r+ G + v++et++d 
  gi|320101058|ref|YP_004176650.1| 264 KLENAEKIARTTGSRLVTIETKSDL 288
                                       6888888888889999999986665 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.16       4      25 ..     149     170 ..     146     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                       HHHHHHHTS-HHHHHHHHHHTT CS
                            MerR_1   4 gevakilgvtthtlrywekegl 25 
                                       ge+a++lgv+ +t+ ++ek  l
  gi|320101058|ref|YP_004176650.1| 149 GELAEMLGVSRKTIYMYEKGEL 170
                                       8*****************9766 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 ?    0.4   0.0      0.64   7.7e+02      31      42 ..      99     110 ..      97     111 .. 0.87
   2 ?   -0.4   0.0       1.2   1.4e+03      30      42 ..     244     256 ..     243     257 .. 0.85
   3 ?    9.1   0.1    0.0013       1.5      23      40 ..     267     284 ..     266     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.64
                                       HT-SEE-HHHHH CS
                           PCP_red  31 rGleeVtvevve 42 
                                       +G + Vt+e+++
  gi|320101058|ref|YP_004176650.1|  99 NGVNIVTPELLN 110
                                       899******986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                       HHT-SEE-HHHHH CS
                           PCP_red  30 erGleeVtvevve 42 
                                       ++G++++tv +++
  gi|320101058|ref|YP_004176650.1| 244 AKGRDTITVTRLD 256
                                       589******9875 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHT-SEE-HHH CS
                           PCP_red  23 aaEklArerGleeVtvev 40 
                                       +aEk Ar  G + Vt+e+
  gi|320101058|ref|YP_004176650.1| 267 NAEKIARTTGSRLVTIET 284
                                       8***************97 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.34      21      41 ..     145     165 ..     133     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                       T--STTTSSSS---SSSS--S CS
                             HTH_7  21 GisiskIAkevnisRsTvYRy 41 
                                       G ++ ++A+ +++sR T+Y y
  gi|320101058|ref|YP_004176650.1| 145 GLTRGELAEMLGVSRKTIYMY 165
                                       88999**************65 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.32      14      30 ..     147     163 ..     137     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                            HTH_29  14 tvsqiAkllglsrrtvy 30 
                                       t  ++A++lg+sr+t+y
  gi|320101058|ref|YP_004176650.1| 147 TRGELAEMLGVSRKTIY 163
                                       7789************9 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.81   9.7e+02      17      25 ..      12      20 ..      11      20 .. 0.79
   2 ?    8.0   0.1    0.0018       2.2       3      19 ..     146     162 ..     144     162 .. 0.90
   3 ?   -0.5   0.0      0.87     1e+03      17      26 ..     219     228 ..     219     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.81
                                      HHHHHHHHH CS
                               Crp 17 ETVSRlLtr 25
                                      E VSR+L r
  gi|320101058|ref|YP_004176650.1| 12 EDVSRTLRR 20
                                      569***965 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0018
                                       --HHHHHHHHTS-HHHH CS
                               Crp   3 mSRqdIAdylGlTrETV 19 
                                       ++R ++A+ lG +r T+
  gi|320101058|ref|YP_004176650.1| 146 LTRGELAEMLGVSRKTI 162
                                       8************9886 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.87
                                       HHHHHHHHHH CS
                               Crp  17 ETVSRlLtrL 26 
                                       ET+ RlL rL
  gi|320101058|ref|YP_004176650.1| 219 ETIWRLLNRL 228
                                       9999****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2018.46
//
Query:       gi|320101059|ref|YP_004176651.1|  [L=235]
Description: rRNA 2'-O-methyltransferase fibrillarin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.1e-102  342.0   0.0   1.3e-102  341.8   0.0    1.0  1  Fibrillarin  Fibrillarin
      0.006   16.4   0.0      0.011   15.5   0.0    1.5  1  PCMT         Protein-L-isoaspartate(D-aspartate) O-methyltran
  ------ inclusion threshold ------
      0.089   12.5   0.0       0.18   11.4   0.0    1.4  1  GCD14        tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.8   0.0  2.1e-106  1.3e-102       1     225 [.       7     232 ..       7     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 341.8 bits;  conditional E-value: 2.1e-106
                                       EEEECSSTTEEEEE.TTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEE CS
                       Fibrillarin   1 veeheklegvyivk.ekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLY 76 
                                       v++hek++gvy+v+ e+g+ +lat+nlvpg++vYgEkl +v++ EyR+Wn +rsKla+a+ +gl++ pi++g+++LY
  gi|320101059|ref|YP_004176651.1|   7 VKPHEKYYGVYVVElEDGSLKLATRNLVPGRRVYGEKLYRVGDVEYREWNLYRSKLAGALANGLSDQPIREGHRILY 83 
                                       789************************************************************************** PP

                                       ESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTH CS
                       Fibrillarin  77 lGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdq 153
                                       lG+asGtt+sH+sDi+g +g++y+vef+prv+rel+ va+ R+ni+Pil+DArkP++Yr++ve+vD ++aDvaqp+q
  gi|320101059|ref|YP_004176651.1|  84 LGIASGTTASHISDIIGLKGRIYGVEFAPRVMRELVLVAEVRRNIYPILGDARKPHEYRHVVETVDGLYADVAQPEQ 160
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEEE CS
                       Fibrillarin 154 arilaknaklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgkyk 225
                                       a+i+a+na+lflk+ggyll+++karsidvtkep+e++++e+e+lk++g++++++v+lepy++dha+++++y+
  gi|320101059|ref|YP_004176651.1| 161 ASIVADNASLFLKDGGYLLLAVKARSIDVTKEPSEIYRREIETLKQRGFEIVDVVHLEPYDRDHAMIYATYR 232
                                       *********************************************************************997 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-06     0.011      71     137 ..      75     139 ..      59     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                                       --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTT CS
                              PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGy 137
                                       +++g r+L +G  sG  +  ++ ++g kgr+ ++e  +++++e    l ++ ++n+  + gD rk +
  gi|320101059|ref|YP_004176651.1|  75 IREGHRILYLGIASGTTASHISDIIGLKGRIYGVEFAPRVMREL--VLVAEVRRNIYPILGDARKPH 139
                                       889*********************************99988764..344445556666666666655 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.18      38     128 ..      75     162 ..      66     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                             GCD14  38 lkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgkv 114
                                       +++G +++  G  sg+ ++ i+  ++ +G+++ +ef   r+   re     e+  ++     D+ k    ++v ++v
  gi|320101059|ref|YP_004176651.1|  75 IREGHRILYLGIASGTTASHISDIIGLKGRIYGVEFAP-RV--MRELVLVAEVRRNIYPILGDARKPHEYRHVVETV 148
                                       899*********************************65.43..3445566777788888888888765557788999 PP

                             GCD14 115 DavfLDlPaPweai 128
                                       D ++ D+ +P +a 
  gi|320101059|ref|YP_004176651.1| 149 DGLYADVAQPEQAS 162
                                       99999999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1776.25
//
Query:       gi|320101060|ref|YP_004176652.1|  [L=406]
Description: rRNA biogenesis protein Nop56/Nop58 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-69  233.7   0.0    2.4e-69  233.3   0.0    1.1  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.3   0.0   1.4e-73   2.4e-69       2     229 ..     150     375 ..     149     376 .. 0.93

  Alignments for each domain:
  == domain 1  score: 233.3 bits;  conditional E-value: 1.4e-73
                                       HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.......HHHHHHHHHHHHCHH CS
                               Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkee......deelakevimaakvta 72 
                                       +d+idk+in ++ r+rewYs hFpEL++lvk++ eYak+v ++g +r++ + + +        e+a++  +aa+   
  gi|320101060|ref|YP_004176652.1| 150 IDDIDKTINLYVARLREWYSIHFPELDELVKEHPEYAKLVYELG-DRSNYTVE-NlvklgyGREKAEKLADAARS-- 222
                                       79******************************************.88998555.336455533366667777777.. PP

                                       HH-SSS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHH CS
                               Nop  73 stsmgaelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPast 149
                                         s ga+ls+ d++ ik l+  +l+l++lr++l eY++  m+++APN++aLvG++++arL+s aGgL++Lak+Past
  gi|320101060|ref|YP_004176652.1| 223 --SIGADLSDFDMNYIKVLAGIILDLYRLRDTLDEYIDAVMKEVAPNIAALVGPKLGARLLSLAGGLEKLAKLPAST 297
                                       ..*************************************************************************** PP

                                       HTTTT-HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHH CS
                               Nop 150 iqilGaekalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeie 225
                                       iq+lGaekalfral+ +++ pk+G+i++++ ++k+ p+++++kiaR+laaK+++aa++D f  +   +G+kl +e e
  gi|320101060|ref|YP_004176652.1| 298 IQVLGAEKALFRALRtGGKPPKHGVIFQHPHIHKS-PRWQRGKIARALAAKLSIAAKVDYF--SGRLVGDKLVKEFE 371
                                       ***************777***************88.************************9..67899********* PP

                                       HHHH CS
                               Nop 226 kklk 229
                                       ++++
  gi|320101060|ref|YP_004176652.1| 372 ERVE 375
                                       9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 3165.04
//
Query:       gi|320101061|ref|YP_004176653.1|  [L=50]
Description: 30S ribosomal protein S30E [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   51.1   1.7    1.3e-13   50.9   1.7    1.0  1  Ribosomal_S30  Ribosomal protein S30


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   1.7     7e-18   1.3e-13       3      44 ..       4      44 ..       3      50 .] 0.80

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 7e-18
                                      BX-STTTTHHHHHS------.-------THHHHHHHHHHHTTS CS
                     Ribosomal_S30  3 hGsLarAGKVrnqTPKveKq.ekkKkptGRakkRlqYnrRfvn 44
                                      hGsL++AGKVr+qTPK+  + +k K p+ R k+   Y rR +n
  gi|320101061|ref|YP_004176653.1|  4 HGSLTKAGKVRSQTPKIPPKpKKNKPPRVRNKW--EYVRRVEN 44
                                      ****************99993466666555555..*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.20s 00:00:00.51 Elapsed: 00:00:00.34
# Mc/sec: 436.03
//
Query:       gi|320101062|ref|YP_004176654.1|  [L=327]
Description: L-threonine 3-dehydrogenase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  104.2   0.0    8.6e-30  104.0   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.9e-22   80.2   0.0    6.5e-22   78.4   0.0    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.3e-14   54.0   0.0      2e-14   53.4   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    3.1e-09   36.3   0.0    4.1e-09   35.8   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.6e-09   35.8   0.1    9.4e-08   31.5   0.1    2.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      7e-08   32.6   0.0    1.1e-07   31.9   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    1.1e-06   28.0   0.0      8e-06   25.2   0.0    2.2  2  NAD_binding_4    Male sterility protein
    0.00025   20.7   0.0    0.00042   19.9   0.0    1.3  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.19   12.1   0.0    1.3  1  Peripla_BP_3     Periplasmic binding protein-like domain
       0.15   12.8   0.0       0.39   11.4   0.0    1.8  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


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 !  104.0   0.0   4.8e-33   8.6e-30       1     230 [.      10     236 ..      10     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 4.8e-33
                                       EEEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekg..yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.v 74 
                                       +lV+G tG+iGsalv al ++   y+v++  + ++ ++ ++l+   + ++d++d+ +le++++++++d+++hlAa  
  gi|320101062|ref|YP_004176654.1|  10 VLVLGSTGQIGSALVPALRDRYgkYNVVAGYHSRKPEAPELLDG-PVEQVDVLDKGSLEKVIERYNVDTIYHLAAiL 85 
                                       79*******************98999888888866666665554.9***************************9966 PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHH CS
                         Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlagek 151
                                       +  ++   +p   ++ n+ g  n+leaar++g+ ++   sS + +G++a+  k  t +++ + p++ Y+++K+age 
  gi|320101062|ref|YP_004176654.1|  86 SAAGE--RNPMLAWRVNMDGLINVLEAAREHGI-KVFWPSSIAAFGPSAP--KYNTPQYTVMDPTTMYGITKYAGEL 157
                                       66555..889999********************.*************999..5555555677*************** PP

                                       HHHHHHHHHT-EEEEEEESEEESTTS-TTS.TTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHH CS
                         Epimerase 152 lveayaaqyglnaiilrlfnlyGprngege.vsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvle 227
                                       l ++y  +yg+++  +r+  +++    +g   +     +   +legk + + +   +   + +y  D+++a + ++e
  gi|320101062|ref|YP_004176654.1| 158 LGRYYFLKYGVDVRGVRYPGIISSEALPGGgTTDYAVEIFYYALEGK-KYKCYLRKDTMLPMMYMPDAVKAAIQLME 233
                                       *************************4444447777777778889999.89999999999*****************9 PP

                                       HHT CS
                         Epimerase 228 hvd 230
                                       + +
  gi|320101062|ref|YP_004176654.1| 234 ADR 236
                                       933 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 !   78.4   0.0   3.6e-25   6.5e-22       1     332 []      11     312 ..      11     312 .. 0.77

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 3.6e-25
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+ G +G+iGs l+  L +++   +++v    s + +  e l + p         + ++D+ D+ sle++++++++d
  gi|320101062|ref|YP_004176654.1|  11 LVLGSTGQIGSALVPALRDRYG-KYNVVAGYHSRKPEAPE-LLDGP---------VEQVDVLDKGSLEKVIERYNVD 76 
                                       899***************9954.44555544444445444.44444.........569******************* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSS.B-TTS-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevp.qtEttpfyPrsPY 153
                                       ++y+LAA    +    +P   ++vn+ G +++Lea+r++g    ++++  S+   +G  +        t ++P+  Y
  gi|320101062|ref|YP_004176654.1|  77 TIYHLAAILSAAG-ERNPMLAWRVNMDGLINVLEAAREHG----IKVFWPSSIAAFGPSAPKYnTPQYTVMDPTTMY 148
                                       *******955444.378*********************98....5899*********9986551456799******* PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS.-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprr.getfvtrkitravarialgkqevlylGnldakRdwghvkDy 229
                                       +++K + + + + y  +yg+ +   ++    s         t   +++   +++gk+ + yl   d      +  D 
  gi|320101062|ref|YP_004176654.1| 149 GITKYAGELLGRYYFLKYGVDVRGVRYPGIISSEAlPGGGTTDYAVEIFYYALEGKKYKCYLR-KDTMLPMMYMPDA 224
                                       ********************9887666554333330334566777788888899998888765.56678899***** PP

                                       HHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--S.S--SB CS
                     GDP_Man_Dehyd 230 veamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrp.gevdl 305
                                       v+a  +++++d+++   +     ++v  f   + ++l ++i +               + +ve++p +++  ++   
  gi|320101062|ref|YP_004176654.1| 225 VKAAIQLMEADRSR---LKLMVGYNVAAFS-FTPEQLANEIRKY------------IPSFEVEYEPDFRQAiADSWP 285
                                       *********99853...4444455554433.3445555554433............234567787777766566777 PP

                                       --B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 306 llgdaskakeeLgWkpkvsfeelvrem 332
                                          d s a+ee gW+p ++fe +v++m
  gi|320101062|ref|YP_004176654.1| 286 KSLDDSVAREEWGWRPDWGFEAMVKDM 312
                                       799**********************98 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   1.1e-17     2e-14       2     134 ..       9     157 ..       8     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.1e-17
                                       EEEEESTTSHHHHHHHHHCTTT..SEEEEEE-TT..............T--TTSHHHHHHHHHHH--SEEEE----- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaee..glevlaltre..............eldltdaeavaellkeakpdvvvnaAAyt 62 
                                       ++lv+G++Gq+Gs+L+ +l+ +  +++v+a   +              ++d+ d+ +++++++  + d ++++AA  
  gi|320101062|ref|YP_004176654.1|   9 RVLVLGSTGQIGSALVPALRDRygKYNVVAGYHSrkpeapelldgpveQVDVLDKGSLEKVIERYNVDTIYHLAAIL 85 
                                       79*****************98532567777744457***************************************98 PP

                                       -HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TT..S----SSHHHHHHHHHHH CS
                     RmlD_sub_bind  63 avDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeed..detsPlnvYGrtKlaGEq 134
                                          + E ++ +a +vn+++  ++ eaa+++g+++   S+   F  ++++ Y++     ++P ++YG tK+aGE 
  gi|320101062|ref|YP_004176654.1|  86 SA-AGERNPMLAWRVNMDGLINVLEAAREHGIKVFWPSSIAAFGPSAPK-YNTPqyTVMDPTTMYGITKYAGEL 157
                                       75.67**************************************999766.5443013458************95 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   2.3e-12   4.1e-09       1     122 [.      11     129 ..      11     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.3e-12
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleeale..gvdvvihlas 75 
                                       +v+G++G +G+alv +L ++  + +v +     +pe   el       v ++Dv+dk +le+++e  +vd + hla+
  gi|320101062|ref|YP_004176654.1|  11 LVLGSTGQIGSALVPALRDRYGKYNVVAGYHSRKPEA-PELLDGP---VEQVDVLDKGSLEKVIEryNVDTIYHLAA 83 
                                       6999************998887666644333333333.3444444...569*************94457789***** PP

                         3Beta_HSD  76 lvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgp 122
                                       +   ag+ +     +vn+ G  nvlea++++g++v+ + Ss+ + gp
  gi|320101062|ref|YP_004176654.1|  84 ILSAAGERNPMLAWRVNMDGLINVLEAAREHGIKVF-WPSSIAAFGP 129
                                       *********************************987.8999999998 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   5.3e-11   9.4e-08       2     123 ..      11     119 ..      10     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 5.3e-11
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                       lv G++G iGs+lv  + ++  k  ++   +  k  e  + l     +  +         dv dk +lek++e+++v
  gi|320101062|ref|YP_004176654.1|  11 LVLGSTGQIGSALVPALRDRYGKYNVVAGYHSRKP-EAPELL-----DGPV------EQVDVLDKGSLEKVIERYNV 75 
                                       66666666666666665555444333333322222.112212.....1112......2369**************** PP

                                       SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEE CS
                   Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkv 123
                                       d+++h AA+    + e+np+ a++ N+ g  nv+eaa e+g+k +
  gi|320101062|ref|YP_004176654.1|  76 DTIYHLAAILS-AAGERNPMLAWRVNMDGLINVLEAAREHGIKVF 119
                                       ********976.589***************************977 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 !   31.9   0.0   6.3e-11   1.1e-07       1     108 [.      14     134 ..      14     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6.3e-11
                                       TTTSHHHHHHHHHHHHC-.T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHT........T-SEEEES CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRn.peklaeleaeeglevvegdvtdvedlaealk........gadaVvsa 67 
                                       G tG++G++lv  l +r  +++v+a   + + +++el +     v ++dv+d+ +l+++++        +  a++sa
  gi|320101062|ref|YP_004176654.1|  14 GSTGQIGSALVPALRDRYgKYNVVAGYHSrKPEAPELLD---GPVEQVDVLDKGSLEKVIErynvdtiyHLAAILSA 87 
                                       89***************999****985442445555654...35778999**********96644444344456666 PP

                                       ---TCC......HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCH CS
                    NAD_binding_10  68 lggggk......deegaknivdaakeagvkRfvlvsaigvgdevpge 108
                                       +g ++       + +g +n+++aa+e+g+k f   s +  g ++p+ 
  gi|320101062|ref|YP_004176654.1|  88 AGERNPmlawrvNMDGLINVLEAAREHGIKVFWPSSIAAFGPSAPKY 134
                                       6666558888777777*************999998888888766653 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.23   4.2e+02       3      33 ..      14      44 ..      12      69 .. 0.81
   2 !   25.2   0.0   4.4e-09     8e-06      86     241 ..      73     213 ..      49     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.23
                                      -TTSHHHHHHHHHHHHHS-.TEEEEEE-SSS CS
                     NAD_binding_4  3 GaTGFLGkvLlekLLrttpevkiyllvRaks 33
                                      G+TG +G+ L+  L ++  ++++++  ++++
  gi|320101062|ref|YP_004176654.1| 14 GSTGQIGSALVPALRDRYGKYNVVAGYHSRK 44
                                      99*********99988777667776666655 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 4.4e-09
                                       HH--EEEE--SS-S.STTSSE..EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......H CS
                     NAD_binding_4  86 eevdviihsaAtvnfdepyke..llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeek 160
                                        +vd i+h aA ++  ++ +   ++rvN++G  +vle a++   + v+   S a++ +                   
  gi|320101062|ref|YP_004176654.1|  73 YNVDTIYHLAAILSAAGERNPmlAWRVNMDGLINVLEAAREHGIK-VFWPSSIAAFGPSAP---------------- 132
                                       48************999777655899**************99888.666666588888888................ PP

                                       HH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEE.E-EEE--SSST---TTSHHHHHHHHHHHH-EEES CS
                     NAD_binding_4 161 ldederaklkglpntYeqsKalaEklvrearrrsglpvvivR.psiitgesktGwingsdlgirgllgliakgvlpe 236
                                       ++++ + +  + ++ Y  +K+++E l r ++ + g+ v  vR p+ii +e  +G   ++   ++ + ++ + +++++
  gi|320101062|ref|YP_004176654.1| 133 KYNTPQYTVMDPTTMYGITKYAGELLGRYYFLKYGVDVRGVRyPGIISSEALPGGGTTDY-AVEIFYYALEGKKYKC 208
                                       5678889999999*************************87776899999****9988888.8999988888888887 PP

                                       -SB-- CS
                     NAD_binding_4 237 ilgdk 241
                                        l ++
  gi|320101062|ref|YP_004176654.1| 209 YLRKD 213
                                       77664 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.3e-07   0.00042       1     104 [.      10     126 ..      10     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                                       EEESSTTSHHHHHHHHHHHH..HT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHT..T-SEEEE--- CS
                              NmrA   1 IlviGaTGrqGksvvrallk..aghkvralvRdtkselakslkeaGvelvkgdlddkeslvealk..gvdvvfsvtg 73 
                                       +lv+G+TG++G+++v al +   +++v a  +  ++ +a +l + +ve v  d+ dk sl+++++  +vd+++   +
  gi|320101062|ref|YP_004176654.1|  10 VLVLGSTGQIGSALVPALRDryGKYNVVAGYHS-RKPEAPELLDGPVEQV--DVLDKGSLEKVIEryNVDTIYHLAA 83 
                                       79******************8889999999886.677899999****966..999*********8445899998877 PP

                                       GG............S-HHHHHHHHHHHHHHHS-SEEEEEE--- CS
                              NmrA  74 fy............skeiedgkklvdAakeaGvkhfiySslgd 104
                                       +             + +++   ++ +Aa e G+k f +Ss+++
  gi|320101062|ref|YP_004176654.1|  84 ILsaagernpmlawRVNMDGLINVLEAAREHGIKVFWPSSIAA 126
                                       66788999999988888888899****************9865 PP

>> Peripla_BP_3  Periplasmic binding protein-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.19      74     130 ..      92     147 ..       4     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                       -SE.EEEESSCCHHHHHHHHHCCTT--TTTTEEEEBSS--SCC.CSSSS--EEEE--HH CS
                      Peripla_BP_3  74 lPt.AviaasDelAlgvlqalreaglrvPedlsvigfddsela.alssPplTtvrqple 130
                                       +P  A+ ++ D   + vl+a+re+g++v +  s+ +f   + a ++ +P+ T++++ ++
  gi|320101062|ref|YP_004176654.1|  92 NPMlAWRVNMDG-LINVLEAAREHGIKVFWPSSIAAFG--PSApKYNTPQYTVMDPTTM 147
                                       565355554444.466**********************..8888*********998765 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.39       1      35 [.      10      44 ..      10     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEESST CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaagsn 35
                                      v++LGsTG IG++ +  ++++  k++vva + +++
  gi|320101062|ref|YP_004176654.1| 10 VLVLGSTGQIGSALVPALRDRYGKYNVVAGYHSRK 44
                                      78*******************99***998666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2176.28
//
Query:       gi|320101063|ref|YP_004176655.1|  [L=396]
Description: 2-amino-3-ketobutyrate coenzyme A ligase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-66  224.1   0.0    3.5e-66  223.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.4e-07   29.6   0.0    3.5e-07   29.1   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.002   17.2   0.0     0.0034   16.4   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.029   13.1   0.0       0.41    9.3   0.0    2.4  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
      0.048   12.9   0.0      0.085   12.1   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.9   0.0   9.6e-70   3.5e-66       2     361 ..      43     384 ..      42     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: 223.9 bits;  conditional E-value: 9.6e-70
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsG 76 
                                       +v+ L+sn+yl +++ p l+ +a ++ e  g + g  +++ g  ++l++l  ++a+f +        +eaa+v+ +G
  gi|320101063|ref|YP_004176655.1|  43 EVVVLASNNYLNLANDPRLKQAAVEAMEkyGWGPGAVWAIAGYHEILDALHRKIAEFKR--------TEAALVFPTG 111
                                       799**********9998888887777777*99999999999999***************........9********* PP

                                       HHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEE CS
                     Aminotran_1_2  77 agaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvil 153
                                       +  ++ +++++ +   gd+il+++++++s+++++rls++e v y+       h+d  +le++l++ + +  k+ +i+
  gi|320101063|ref|YP_004176655.1| 112 FAVNAGTIPAIVE--QGDVILSDELNHGSIIDGIRLSRAEKVIYK-------HCDPSDLEDKLRQVHGKY-KKILIV 178
                                       ************8..******************************.......************966555.5999** PP

                                       EESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 154 vesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRv 230
                                       + ++++++G++a+l e+ kl   a++yn++l+vD+a++++v+g+ +  +++++veee++ + vg++sKa+G+ G   
  gi|320101063|ref|YP_004176655.1| 179 TDGVFSMDGDIAPLREIAKL---AREYNAMLYVDDAHGEGVLGEGRGSPAHLGVEEEVD-FHVGTFSKALGSSG--- 248
                                       ********************...********************8866667*********.**************... PP

                                       EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCS CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqs..eleemrqrlqkrrkelrdeLaelglkvlasqsg 305
                                       G+i ++ +v++++r+ +r++l s+  ++avaaa  +al++    e  e+ +rl+++r++++++L+ +g++  +sq+ 
  gi|320101063|ref|YP_004176655.1| 249 GMIGSDHEVIEYIRNRARSWLLSTGFPPAVAAANLKALEIVMsdEGRERIRRLWENREYFKKGLEGIGFNTGKSQTP 325
                                       **************************999999988888876669********************************* PP

                                       SEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelve 361
                                       ++++  ++ ++  el+++L +e gv v+p+ ++ v   ++r+R  v Ag+t+++l++++ 
  gi|320101063|ref|YP_004176655.1| 326 IVPVIIGDTKKTRELARSLFDE-GVFVVPIVYPMVargTERIRNQVnAGHTRDDLDKALA 384
                                       **********************.**********************************986 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   9.8e-11   3.5e-07      55     181 ..      90     217 ..      87     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.8e-11
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHH CS
                   Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleele 131
                                       ++l ++ia+ +++eaal++++G a  a +i a++++Gd i++++  +g+  + ++ + +  ++ +k++d+sdle+  
  gi|320101063|ref|YP_004176655.1|  90 DALHRKIAEFKRTEAALVFPTGFAVNAGTIPAIVEQGDVILSDELNHGSIIDGIR-LSRAEKVIYKHCDPSDLEDKL 165
                                       6899**********************************88887777777777765.5566779999*******9999 PP

                                       HHCCTTEEEEEEESS-TTTT..----HHHHHHHHHHTT-EEEEEGTTTHTTT CS
                   Cys_Met_Meta_PP 132 kaikentklvylEtptnpll..kvvDiekiaklakkagvlvvvDntfaspll 181
                                       ++++ + k +++ t +   +  +++ +++iakla++ ++++ vD +   ++l
  gi|320101063|ref|YP_004176655.1| 166 RQVHGKYKKILIVTDGVFSMdgDIAPLREIAKLAREYNAMLYVDDAHGEGVL 217
                                       999999999998888766662269999*****************99887776 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.5e-07    0.0034      44     177 ..      88     211 ..      60     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.5e-07
                                       HHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEE CS
                       Aminotran_5  44 aveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvip 120
                                       ++++ + k+ae+  +e    ++f   t+ a+n+  + +   +++gd i+  e++h + +          g+++  ++
  gi|320101063|ref|YP_004176655.1|  88 ILDALHRKIAEFKRTEA--ALVFP--TGFAVNAGTIPA--IVEQGDVILSDELNHGSII---------DGIRLSRAE 149
                                       56666667777776664..56664..455566665555..3899999999999999999.........688888888 PP

                                       BETTSCBEGGGHHHH-....-TTEEEEEEE.SBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 121 ldeegeldldelekll....nektklvait.hvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                       +   ++ d+++le++l     +  k++++t  v ++ G i p+ ei+kla++++a++ vD a
  gi|320101063|ref|YP_004176655.1| 150 KVIYKHCDPSDLEDKLrqvhGKYKKILIVTdGVFSMDGDIAPLREIAKLAREYNAMLYVDDA 211
                                       88889999999999985554345566666526889*************************87 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 ?    9.3   0.0   0.00011      0.41     100     207 ..     120     213 ..     106     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00011
                                       HHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--EB-TTS-BE---GGGGSHHHHHHHHHHSTTTGSESEEEEES CS
                          OKR_DC_1 100 navltpgdlvlvdRNcHKSiehalvlsgatPvylepernalgiiggidlkefeeetlkekikevpdakaprlavitn 176
                                        a++++gd++l d  +H Si  ++ ls a+ v          i ++ d     ++ l+ k+++v  + + + +++t 
  gi|320101063|ref|YP_004176655.1| 120 PAIVEQGDVILSDELNHGSIIDGIRLSRAEKV----------IYKHCD-----PSDLEDKLRQVHGKYK-KILIVTD 180
                                       56777788888888888888777777776654..........333333.....3677777777765544.7889998 PP

                                       S-T..TSEEE-HHHHHHHHTTSESEEEEE-TT- CS
                          OKR_DC_1 177 sTY..dGvlynakeivdkleklsdrilfDeAwv 207
                                       + +  dG ++ ++ei +++ +++  +++D+A++
  gi|320101063|ref|YP_004176655.1| 181 GVFsmDGDIAPLREIAKLAREYNAMLYVDDAHG 213
                                       876558999999999999999999999999996 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.4e-05     0.085      35     169 ..      90     211 ..      81     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-H CS
                   Beta_elim_lyase  35 nrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdl 111
                                        +L  ++ae   +eaal +p+G a n+  + +++++g+ ++ +e +h+       ++  + v       k+    d+
  gi|320101063|ref|YP_004176655.1|  90 DALHRKIAEFKRTEAALVFPTGFAVNAGTIPAIVEQGDVILSDELNHGSIIDGIRLSRAEKV-----IYKH---CDP 158
                                       56888899999999********************9998888888888877666555444444.....4444...788 PP

                                       HHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 112 ekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                        +le+++++v    +  k++++t  + ++ G + +   lre+a++a++y+  l +D A
  gi|320101063|ref|YP_004176655.1| 159 SDLEDKLRQVHG--KYKKILIVTDGVFSMDGDIAP---LREIAKLAREYNAMLYVDDA 211
                                       88*******655..999999999999999998876...68999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2761.36
//
Query:       gi|320101064|ref|YP_004176656.1|  [L=451]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   0.0    2.6e-55  186.9   0.0    1.4  1  Asparaginase    Asparaginase, N-terminal
    5.7e-34  116.7   0.0    3.3e-33  114.3   0.0    2.1  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    1.2e-18   66.1   0.1    2.7e-18   65.0   0.1    1.6  1  GatD_N          GatD N-terminal domain
     0.0058   16.2   0.0       0.14   11.7   0.0    2.1  2  Peripla_BP_4    Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.9   0.0   5.9e-59   2.6e-55       1     180 [.      98     284 ..      98     294 .. 0.97

  Alignments for each domain:
  == domain 1  score: 186.9 bits;  conditional E-value: 5.9e-59
                                       EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHC.CT- CS
                      Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.eey 76 
                                       +v +l+tGGTias++d+++g ++p l+  e+le +pel++ia +++++++++ S++++p++w  + +++++++ +++
  gi|320101064|ref|YP_004176656.1|  98 RVTLLGTGGTIASKVDYETGGVTPVLTPGEILEWVPELADIAVFNAREVMSVFSEDIEPSHWTLISREVYKEIlSGV 174
                                       799**********************************************************************888* PP

                                       SEEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.... CS
                      Asparaginase  77 dgfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.... 149
                                       dg+V++hGTD ++y+AsaL++ +++ ++pvv++Gsqr++++++sD++ Nl +A+++a++  ++a+ ++v++g+    
  gi|320101064|ref|YP_004176656.1| 175 DGVVIAHGTDMMSYSASALAFSITGKPVPVVFVGSQRSSDRPSSDSAFNLRAAFITASKA-PFAESVIVMHGEtsdt 250
                                       **********************************************************99.**************** PP

                                       ...EEETTTEEE-BSSSSS-EEETTT--SEEEET CS
                      Asparaginase 150 ...llranrvtKvhtssldaFespnlgplaeveg 180
                                           +r+ +++K+hts++daF+s+n +pla+++ 
  gi|320101064|ref|YP_004176656.1| 251 yalAHRGVKARKMHTSRRDAFQSINDKPLARINP 284
                                       *******************************943 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.24   1.1e+03      13      31 ..     164     181 ..     160     265 .. 0.78
   2 !  114.3   0.0   7.4e-37   3.3e-33       1     114 []     314     428 ..     314     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.24
                                       HHHHHHHHHTT--EEEEEE CS
                    Asparaginase_C  13 tkvlkallkkgakGvvleg 31 
                                        +v k++l +g++Gvv++ 
  gi|320101064|ref|YP_004176656.1| 164 REVYKEIL-SGVDGVVIAH 181
                                       56777777.5999999985 PP

  == domain 2  score: 114.3 bits;  conditional E-value: 7.4e-37
                                       -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HH CS
                    Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkel 77 
                                       +V+++k++pg++++vl+ l++kg  G+vleg G G++p++l++++++a+++gi+vv+tsqc++g+v+ ++y++g++l
  gi|320101064|ref|YP_004176656.1| 314 KVALVKVYPGLQGEVLETLIDKGFHGIVLEGSGLGHMPNKLVPTIARAVDNGIPVVMTSQCLFGRVNLHVYSTGRRL 390
                                       7**************************************************************************** PP

                                       HHHTEEE-TT--HHHHHHHHHHHCTT.---HHHHHHHH CS
                    Asparaginase_C  78 erlgvisaddmtpeaarikLmlllgk.gldpaevrklf 114
                                        ++gvi + d+ pe+a++kL ++lg+  +dp+evrk+f
  gi|320101064|ref|YP_004176656.1| 391 LEAGVIPGLDILPETAYVKLSWILGSiSRDPEEVRKVF 428
                                       **************************566*******98 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.1   6.1e-22   2.7e-18       1      55 []      20      76 ..      20      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 6.1e-22
                                      --TT-EEEEE-SS.-EEEEEE----.TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  1 ievGDlikvekkg.reyeGilmPrs.elsdddiivlKLdnGYNiGikieeiekiell 55
                                      +e+GD+++v+ k+ +++eGilmPr+  +s++ i+vlKLdnGYNiG++i ei +++ll
  gi|320101064|ref|YP_004176656.1| 20 AEPGDRLRVVLKDgSVFEGILMPRQaLYSSRPILVLKLDNGYNIGLNIGEIGEVRLL 76
                                      689*******9999***********99************************999987 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 ?    2.2   0.0     0.025   1.1e+02      51     159 ..     169     293 ..     165     308 .. 0.66
   2 !   11.7   0.0   3.1e-05      0.14      44      85 ..     325     370 ..     323     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.025
                                       HHHTT-SEEEE--SSH..HHHHHHHHH.HHHTT-EEEEESTT...GCTTT-CEEEEEC-HHHHHHHHH..HHHHHHC CS
                      Peripla_BP_4  51 aiakgvdgiivapvds..talapalkk.akaaGIpVvafdsd...dapsgerlayvgfdneaaGelqa..eylaekl 119
                                        i +gvdg+++a      +  a+al+  ++ + +pVv++ s+   d ps++ + +  + + +a ++     +++ + 
  gi|320101064|ref|YP_004176656.1| 169 EILSGVDGVVIAHGTDmmSYSASALAFsITGKPVPVVFVGSQrssDRPSSDSAFNLRAAFITASKAPFaeSVIVMHG 245
                                       57789998888877775544445555448999999999999966666666666655555555544433445666666 PP

                                       TTH.EEEEEE.TSCCCHHHHHHHHHHHHHHHHH.......-T.TCEECC CS
                      Peripla_BP_4 120 ggkkgkvvil.aGspgdpnaeeriegfrkvlke.......yp.gikiva 159
                                        ++  ++++  +G+   + ++ r ++f ++ ++       ++ +i i++
  gi|320101064|ref|YP_004176656.1| 246 ETS-DTYALAhRGVKARKMHTSRRDAFQSINDKplarinpDTgEIRIIG 293
                                       666.666665689999999999999998886665555666444666666 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHTT-SEEEE--SSH....HHHHHHHHHHHHTT-EEEE CS
                      Peripla_BP_4  44 Qvaqiedaiakgvdgiivapvds....talapalkkakaaGIpVva 85 
                                       Q +++e++i+kg+ gi++         + l p++++a ++GIpVv 
  gi|320101064|ref|YP_004176656.1| 325 QGEVLETLIDKGFHGIVLEGSGLghmpNKLVPTIARAVDNGIPVVM 370
                                       6789*************99776455569****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3393.21
//
Query:       gi|320101065|ref|YP_004176657.1|  [L=638]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-70  237.4   0.0    2.6e-70  236.9   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    1.3e-24   86.7   0.3    2.7e-24   85.7   0.3    1.6  1  GatB_Yqey  GatB domain
    4.3e-19   68.6   0.0    1.2e-18   67.1   0.0    1.9  1  GAD        GAD domain
    0.00013   22.1   0.4    0.00026   21.1   0.4    1.5  1  YqeY       Yqey-like protein


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.9   0.0   5.9e-74   2.6e-70       2     272 ..      12     450 ..      11     451 .. 0.96

  Alignments for each domain:
  == domain 1  score: 236.9 bits;  conditional E-value: 5.9e-74
                                       EEEEEEEEEB--SB-SSSSSBSSSSCE...........STTSS--TTTTTS.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxx.......................... RF
                            GatB_N   2 viGlEiHaqlktksKlFssasteeege...........epnsevsevdlal.......................... 41 
                                       ++GlEiH+ql+t++KlF++++t+ +++            ++se++evd+a+                          
  gi|320101065|ref|YP_004176657.1|  12 KVGLEIHVQLDTARKLFCKCPTTLSDAqgvpeftrylrPAKSETGEVDAAAllewrkskryeyeapqessclveade 88 
                                       89*******************88333346677888884599**********************************99 PP

                                       .TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEE CS
                                       .xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                            GatB_N  42 .PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihl 115
                                        P   P+ +++ea+ +a+++a a+n++i +e++++RK+++++++ +g+Q+t+    +a +G +   + k++i++++l
  gi|320101065|ref|YP_004176657.1|  89 eP---PHeISEEALLTALAVARAMNMRIIDEIHVMRKIVIDGSNVSGFQRTA---LVAVNGFILDeDGKIGIQTLCL 159
                                       98...999********************************************...6669997754489********* PP

                                       EE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 116 EeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvre 192
                                       EeDaa++++e+++ + ++++R+G+pLiE++t+pd+ +pe+a++v+ k+++l+r +g ++ ++  G++R+D+N+S+r 
  gi|320101065|ref|YP_004176657.1| 160 EEDAARKISESEDATRYRIDRLGIPLIEVATAPDIYDPEQAMRVALKIGQLIRLTGRAKHGL--GTIRQDLNISIRG 234
                                       **********999*************************************************..************4 PP

                                       SETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                            GatB_N 193 eekgeeegtrvEiKnlnslksiekaieyeierqiell........................................ 229
                                              g++vE+K++++l  i k++e+e+ rq++ll                                        
  gi|320101065|ref|YP_004176657.1| 235 -------GAKVEVKGVQHLYLIPKVVENEALRQLRLLglrdelvkrgvrpedivfnivdvtevfkntaskiirrvls 304
                                       .......59******************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|320101065|ref|YP_004176657.1| 305 tpgggvyavvlpgfkgllgmelqpgrrfgteladyarvwggvggifhtdelpnygiteeevralygkthaspdrdai 381
                                       ***************************************************************************** PP

                                       .............................-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHHH CS
                                       .............................xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 .............................qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseeli 272
                                                                    +eTr++++d g+t+++R+++ +a   r++pe+d+pp+ ++ el+
  gi|320101065|ref|YP_004176657.1| 382 vivadasekavealkavverarmaltgvpEETRAANPD-GTTRYMRPRPgSA---RMYPETDIPPIYVTPELV 450
                                       **************************************.**********555...*************99986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.3     6e-28   2.7e-24       1     148 []     489     633 ..     489     633 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 6e-28
                                       HHHHHHHHHSS...HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TX CS
                         GatB_Yqey   1 dffeevvkegad..aklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gk 74 
                                       d++e++vk+++   ++++++ +l++++ +l++ g+++e+  + +++++ +l+++a+g ++k+++ e+l+ ++ + gk
  gi|320101065|ref|YP_004176657.1| 489 DLYEKLVKKYSGriPASVIASTLVNVIPSLRRDGVPVEN--IDDDSIEGVLDMVARGAVAKEAIPEILAGVARNpGK 563
                                       789*******6678*************************..9*********************************** PP

                                       XHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  75 speeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                        +e+i++e gL  +s  eel kl++e+ia+n    e+++++ eka+++++ +vMk  +Gk+d+ lv e +kekL
  gi|320101065|ref|YP_004176657.1| 564 LVEDIVRELGLSTVSL-EELDKLIDEAIARN---REKIEARREKAFQIIMSEVMKTARGKVDGGLVAERVKEKL 633
                                       ***************7.9*************...9999**********************************98 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   2.8e-22   1.2e-18       2      95 .]     300     395 ..     299     395 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.8e-22
                                       HHHHHS.TEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT-- CS
                               GAD   2 sealks.ggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgae 76 
                                       + +l+  gg v a+++pg +++l ++e++++++f++el++++++w +v+g ++t++++ + +teeev+ l+ ++ a+
  gi|320101065|ref|YP_004176657.1| 300 RRVLSTpGGGVYAVVLPG-FKGLLGMELQPGRRFGTELADYARVWGGVGGIFHTDELPNYgITEEEVRALYGKTHAS 375
                                       6678888***********.8********************************************************* PP

                                       TT.EEEEEEEEEHHHHHHHH CS
                               GAD  77 eg.DillfvAdkkktvnkal 95 
                                       ++ D++++vAd  +++++al
  gi|320101065|ref|YP_004176657.1| 376 PDrDAIVIVADASEKAVEAL 395
                                       999*********99999987 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.4   5.7e-08   0.00026      91     143 .]     577     633 ..     567     633 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.7e-08
                                       --HHHHHHHHHHHHHHT....T--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH- CS
                              YqeY  91 lseeeiealvkeaiaev....gaesmkdmGkvmkalkpkvkGkaDgkkvsalvkekL 143
                                       +s ee+++l++eaia+     +a+  k++  +m+ ++++++Gk+Dg+ v + vkekL
  gi|320101065|ref|YP_004176657.1| 577 VSLEELDKLIDEAIARNrekiEARREKAFQIIMSEVMKTARGKVDGGLVAERVKEKL 633
                                       67799*********86533337779******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 4884.14
//
Query:       gi|320101066|ref|YP_004176658.1|  [L=116]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   15.7   0.1       0.17   12.5   0.0    1.9  2  TIR_2           TIR domain
      0.046   13.9   0.1        1.3    9.2   0.0    2.2  2  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05      0.17      11      59 ..       5      56 ..       3      67 .. 0.75
   2 ?    1.1   0.0     0.067     6e+02      17      31 ..      75      89 ..      66     109 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                             TIR_2 11 ewa.eklaeaLeaagirvwl.drwd.lkpgedweeeieeaiessdvvlvvls 59
                                      e++ e ++e L ++g+rv + d ++   +g+  ++++ +++++s+v+++ +s
  gi|320101066|ref|YP_004176658.1|  5 EVVeEAIVELLSRNGYRVSVkDVEErTLKGGISRARLIHGVKNSSVFMARIS 56
                                      5665779***********642655443555555555669*********9888 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.067
                             TIR_2 17 aeaLeaagirvwldr 31
                                      a+ Le++g+rv + +
  gi|320101066|ref|YP_004176658.1| 75 ASSLEEKGWRVDVAE 89
                                      678999999994433 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00015       1.3      19      51 ..       9      42 ..       3      43 .. 0.87
   2 ?    2.7   0.0     0.015   1.4e+02      22      38 ..      75      91 ..      63     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00015
                                      HHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHT CS
                    HGTP_anticodon 19 kklaeeLraagirveldd.snesigkkireadll 51
                                      + + e L+++g+rv ++d ++++++  i++a+l+
  gi|320101066|ref|YP_004176658.1|  9 EAIVELLSRNGYRVSVKDvEERTLKGGISRARLI 42
                                      568899************9999999999999875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.015
                                      HHHHHTTTSEEEEESSS CS
                    HGTP_anticodon 22 aeeLraagirvelddsn 38
                                      a+ L+++g+rv++ +++
  gi|320101066|ref|YP_004176658.1| 75 ASSLEEKGWRVDVAEDE 91
                                      77899999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 823.99
//
Query:       gi|320101067|ref|YP_004176659.1|  [L=302]
Description: helix-turn-helix Fis-type protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-05   25.1   0.4    1.9e-05   24.4   0.4    1.4  1  HTH_8       Bacterial regulatory protein, Fis family
    4.4e-05   23.2   0.3    0.00014   21.6   0.3    1.9  1  HTH_IclR    IclR helix-turn-helix domain
    0.00012   22.1   0.0    0.00029   20.9   0.0    1.6  1  HTH_28      Helix-turn-helix domain
    0.00014   21.7   0.6      0.014   15.3   0.1    2.5  2  HTH_Crp_2   Crp-like helix-turn-helix domain
    0.00025   20.7   0.0    0.00072   19.3   0.0    1.7  1  HTH_23      Homeodomain-like domain
    0.00071   19.4   0.4     0.0018   18.1   0.1    1.7  2  MarR_2      MarR family
     0.0011   18.5   0.3     0.0011   18.5   0.3    2.1  3  HTH_24      Winged helix-turn-helix DNA-binding
     0.0077   16.0   0.0      0.027   14.2   0.0    1.9  2  HTH_psq     helix-turn-helix, Psq domain
       0.01   15.9   0.1      0.027   14.5   0.1    1.7  1  HTH_3       Helix-turn-helix
  ------ inclusion threshold ------
      0.013   15.5   0.1      0.027   14.5   0.1    1.5  1  HTH_29      Winged helix-turn helix
      0.015   15.4   0.7      0.039   14.0   0.1    1.9  2  HTH_20      Helix-turn-helix domain
      0.025   14.5   0.1      0.057   13.4   0.1    1.5  1  HTH_1       Bacterial regulatory helix-turn-helix protein, ly
       0.03   14.2   0.1      0.085   12.8   0.1    1.7  1  TrmB        Sugar-specific transcriptional regulator TrmB
      0.051   14.0   0.6      0.084   13.3   0.6    1.3  1  DEC-1_C     Dec-1 protein, C terminal region
      0.085   12.4   0.1       0.18   11.3   0.1    1.5  1  Sigma70_r4  Sigma-70, region 4
       0.14   12.0   0.3       0.67    9.9   0.1    2.1  2  HTH_5       Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.4   1.7e-08   1.9e-05      13      40 ..      12      39 ..      10      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.7e-08
                                      HHHHTTT-HHHHHHHHTS-HHHHHHHHH CS
                             HTH_8 13 ALertgGnkskAArlLGisRrtLyrKLk 40
                                      AL  +g  +++A+r+LGisR++L r+L 
  gi|320101067|ref|YP_004176659.1| 12 ALLNNGVSLAEASRMLGISRSQLSRRLN 39
                                      78889999******************95 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   1.3e-07   0.00014      12      48 ..      11      47 ..       9      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.3e-07
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      +a  + +++l+e +r +g+++S  +R L+tL+++G v
  gi|320101067|ref|YP_004176659.1| 11 IALLNNGVSLAEASRMLGISRSQLSRRLNTLMKRGAV 47
                                      56677899***************************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 !   20.9   0.0   2.6e-07   0.00029       4      34 ..       9      39 ..       8      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.6e-07
                            HTH_28  4 eiikllaaGhsvreaArelgisrrtvyrWik 34
                                      e i ll +G+s +ea+r lgisr++++r ++
  gi|320101067|ref|YP_004176659.1|  9 ETIALLNNGVSLAEASRMLGISRSQLSRRLN 39
                                      7899999*******************99876 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 !   15.3   0.1   1.3e-05     0.014      22      51 ..      18      47 ..       3      58 .. 0.84
   2 ?    4.1   0.0      0.04        45      34      51 ..     234     251 ..     231     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkregli 51
                                      ++ +e ++mlG++r+++sr l+ L ++g +
  gi|320101067|ref|YP_004176659.1| 18 VSLAEASRMLGISRSQLSRRLNTLMKRGAV 47
                                      6778889********************987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.04
                                       SHHHHHHHHHHHHHTTSE CS
                         HTH_Crp_2  34 tretvsrilseLkregli 51 
                                       t et+  +ls+Lk+ g++
  gi|320101067|ref|YP_004176659.1| 234 TLETLATLLSQLKESGIL 251
                                       679*************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.5e-07   0.00072       9      42 ..       9      42 ..       7      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.5e-07
                            HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkryr 42
                                      + + ll +G s +e++r+Lg+sr++++r l++  
  gi|320101067|ref|YP_004176659.1|  9 ETIALLNNGVSLAEASRMLGISRSQLSRRLNTLM 42
                                      56778888********************988765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.6e-06    0.0018      15      51 ..      14      47 ..      10      53 .. 0.88
   2 ?   -2.6   0.0       4.9   5.5e+03      36      54 ..     203     221 ..     201     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                                      HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                       +++   ++ +e  r lg+s+s +sr+l+ L ++G v
  gi|320101067|ref|YP_004176659.1| 14 LNNG---VSLAEASRMLGISRSQLSRRLNTLMKRGAV 47
                                      5555...999************************977 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHTTSEEEE CS
                            MarR_2  36 savsrilkrLvaaGLverr 54 
                                       + + r+++ L  + +v r 
  gi|320101067|ref|YP_004176659.1| 203 HHMVRHVNALTLRRYVYRG 221
                                       5667999999999999875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   9.9e-07    0.0011      15      45 ..      15      45 ..       7      47 .. 0.92
   2 ?   -3.1   0.0       5.2   5.8e+03      35      43 ..     182     190 ..     182     190 .. 0.89
   3 ?   -2.9   0.0       4.6   5.2e+03      34      46 ..     238     250 ..     235     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.9e-07
                            HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeG 45
                                      n + s +e +++lg+S+s ++rrl+ L++ G
  gi|320101067|ref|YP_004176659.1| 15 NNGVSLAEASRMLGISRSQLSRRLNTLMKRG 45
                                      7899*************************99 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.2
                            HTH_24  35 nrrlkrLee 43 
                                       n+rl+ L++
  gi|320101067|ref|YP_004176659.1| 182 NWRLNDLVK 190
                                       89***9986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.6
                            HTH_24  34 vnrrlkrLeeeGl 46 
                                       + + l +L+e+G+
  gi|320101067|ref|YP_004176659.1| 238 LATLLSQLKESGI 250
                                       5566788999998 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 !   14.2   0.0   2.4e-05     0.027       3      39 ..       5      40 ..       3      44 .. 0.85
   2 ?   -1.9   0.0       2.6   2.9e+03      28      39 ..     209     221 ..     209     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                           HTH_psq  3 ealaaAleavvnGkmSirkAArkYgiPrsTLwrrkrg 39
                                      ++la+ ++   nG +S+++A+r  gi+rs L+rr+++
  gi|320101067|ref|YP_004176659.1|  5 DTLAETIALLNNG-VSLAEASRMLGISRSQLSRRLNT 40
                                      6677777777799.******************99876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                           HTH_psq  28 iPrsTLw.rrkrg 39 
                                       +++ TL+ +++rg
  gi|320101067|ref|YP_004176659.1| 209 VNALTLRrYVYRG 221
                                       56679**888876 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.4e-05     0.027       6      30 ..      14      38 ..      11      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                                      HHTTHHHHHHHHHHTSSHHHHHHHH CS
                             HTH_3  6 kqlglsqeeLAeklGvsrstisriE 30
                                      + +g s++e++++lG+srs++sr  
  gi|320101067|ref|YP_004176659.1| 14 LNNGVSLAEASRMLGISRSQLSRRL 38
                                      57899*****************965 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.4e-05     0.027       3      32 ..       9      37 ..       8      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                            HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrw 32
                                      + ++ll+ Gvs  +++ ++lg+sr++  r 
  gi|320101067|ref|YP_004176659.1|  9 ETIALLNNGVS-LAEASRMLGISRSQLSRR 37
                                      56899*****8.*************99885 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.5e-05     0.039      21      54 ..      14      47 ..      10      49 .. 0.90
   2 ?   -3.0   0.0       7.1   7.9e+03      45      53 ..     242     250 ..     233     255 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLv 54
                                       + g++++e  + l++s+++ls++L++L + g+v
  gi|320101067|ref|YP_004176659.1| 14 LNNGVSLAEASRMLGISRSQLSRRLNTLMKRGAV 47
                                      3789************************999987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.1
                                       HHHHHHCTT CS
                            HTH_20  45 LrvLeeagL 53 
                                       L +L e g+
  gi|320101067|ref|YP_004176659.1| 242 LSQLKESGI 250
                                       556666666 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     5e-05     0.057       9      37 ..      12      41 ..       9      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5e-05
                                      HHHHHS.SHHHHHHHHTS-HHHHHHHHHHH CS
                             HTH_1  9 avaeeg.sftrAAeeLglsqpavsrqikrL 37
                                      a+  +g s+++A + Lg+s + +sr++++L
  gi|320101067|ref|YP_004176659.1| 12 ALLNNGvSLAEASRMLGISRSQLSRRLNTL 41
                                      56677889*******************998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.6e-05     0.085      16      52 ..      12      47 ..      11      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-05
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlV 52
                                      aLl++g +   e +++lg++rs+  + L+ L+++G V
  gi|320101067|ref|YP_004176659.1| 12 ALLNNGVSL-AEASRMLGISRSQLSRRLNTLMKRGAV 47
                                      677666655.567**********************99 PP

>> DEC-1_C  Dec-1 protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   7.5e-05     0.084      55      96 ..      81     122 ..      63     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-05
                           DEC-1_C  55 sappavinyyyaapqrpvvqsyg.tsyggggygsnaygvprpv 96 
                                        +pp+vi yy  a  rpv  sy    y g   gs   g  r v
  gi|320101067|ref|YP_004176659.1|  81 GSPPTVISYYSYA-ARPVTISYVrDDYSGVDAGSIVAGTCRAV 122
                                       47*****998544.59*****972579*******999999987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00016      0.18      20      46 ..      17      43 ..      11      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                      T--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4 20 glTleEIgerlgiSrerVrqiekrAlr 46
                                      g +l+E +++lgiSr+  +++++  ++
  gi|320101067|ref|YP_004176659.1| 17 GVSLAEASRMLGISRSQLSRRLNTLMK 43
                                      789**************9999887666 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 ?    9.9   0.1    0.0006      0.67      21      43 ..      23      45 ..      12      49 .. 0.87
   2 ?   -0.7   0.0       1.2   1.3e+03      36      45 ..     242     251 ..     239     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0006
                                      HHHHHTS-HHHHHHHHHHHHHTT CS
                             HTH_5 21 laeelglsqstvShHLkkLreaG 43
                                       +++lg+s+s +S+ L+ L++ G
  gi|320101067|ref|YP_004176659.1| 23 ASRMLGISRSQLSRRLNTLMKRG 45
                                      5899****************988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                       HHHHHHTTSE CS
                             HTH_5  36 LkkLreaGLV 45 
                                       L++L+e+G++
  gi|320101067|ref|YP_004176659.1| 242 LSQLKESGIL 251
                                       899*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2169.13
//
Query:       gi|320101068|ref|YP_004176660.1|  [L=132]
Description: translation initiation factor 5A precursor (eIF-5A) [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   25.9   1.3    1.2e-05   25.2   1.3    1.4  1  EFP       Elongation factor P (EF-P) OB domain
      4e-05   23.6   0.2     0.0011   19.0   0.0    2.3  2  EFP_N     Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> 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 !   25.2   1.3   1.4e-09   1.2e-05      10      35 ..      82     107 ..      79     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.4e-09
                                       TTEEEEEETTT--EEEEEHHHHTTGC CS
                               EFP  10 gdeyvFMdnetYeqielpkeqlgdaa 35 
                                       g +y +Md+etYe +e++k+++++++
  gi|320101068|ref|YP_004176660.1|  82 GTMYQVMDMETYETFEVEKDAVEEDV 107
                                       899*******************9887 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.2e-07    0.0011       4      32 ..      10      38 ..       7      41 .. 0.92
   2 ?    2.4   0.0     0.018   1.6e+02       6      24 ..      73      91 ..      69      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-07
                                      G--TT-EEEETTEEEEEEEEEEEEETTS- CS
                             EFP_N  4 elkkGlvieidgklyvVlefehvkpGkGq 32
                                      +lk G +i idg++++++e    k Gk +
  gi|320101068|ref|YP_004176660.1| 10 NLKIGSFIVIDGEPCRIVEMSRAKTGKHG 38
                                      799***********************987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.018
                                      -TT-EEEETTEEEEEEEEE CS
                             EFP_N  6 kkGlvieidgklyvVlefe 24
                                      + G++i   g  y+V++ e
  gi|320101068|ref|YP_004176660.1| 73 RVGQIIADMGTMYQVMDME 91
                                      899*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1013.71
//
Query:       gi|320101069|ref|YP_004176661.1|  [L=117]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 901.17
//
Query:       gi|320101070|ref|YP_004176662.1|  [L=298]
Description: amidohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-05   24.1   0.0    2.5e-05   23.7   0.0    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.4e-09   2.5e-05      58     249 ..      85     260 ..      46     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.4e-09
                                       HSSSHHHHHHHHHHHHHTEEEEEE.EEEEECCTTEEEEEEEEEEEETTSEE.EEEEE-SS--EECTTSCECCGHHTS CS
                      CN_hydrolase  58 aglgetlallaalarkngiavvig.liereltngklqayntavlldldgkl.vgkyrKlhLfpgeprpptaverelf 132
                                         + + l+ l+ l++++g  ++ + lier  ++ ++  y + v++  ++     ++rK+          ++ e+++ 
  gi|320101070|ref|YP_004176662.1|  85 DSEHQYLKTLRYLSANYGLNIISPaLIER--AGSRY--YISSVFVPYGNGEePVSQRKIL--------VSSEEKKIG 149
                                       55567899****************88888..9****..9999988654444377777777........689999999 PP

                                       CS.-SSS-EEEETTEEEEEEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHH..HHHHHHHHTSEE CS
                      CN_hydrolase 133 ep.gdgipvfdtpvgkiGaaiCyeigfpellralalkgaeilvnlserapvpksmgppqwell..graralengcfv 206
                                        + g++i v+   + k  +++  ei  pel r+  ++g +++v ++       s+ +p+++++   ra a+ +g++v
  gi|320101070|ref|YP_004176662.1| 150 IRpGHEISVLNDYYLKYVVLVSNEIVVPELGRVGVAQGCNMVVSTI-------SPLKPVRNYVdiVRALAQILGVWV 219
                                       886776999999999*****************************89.......999999999722566666688898 PP

                                       EEEEBEEEHCETTEEEE--EEEE-TTS-EEEECCSSSTEEEEE CS
                      CN_hydrolase 207 iaanqvggyeqlilwpvghSaiidpdGrilaglgeeeegvlia 249
                                       + +  + +   ++  +v++S +++p+G++++  +e + g++++
  gi|320101070|ref|YP_004176662.1| 220 LHVGGIFI--VNDDRYVLNSLVVNPQGELVVMYSEATPGLVTV 260
                                       88888888..9999***********************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2268.16
//
Query:       gi|320101071|ref|YP_004176663.1|  [L=1326]
Description: reverse gyrase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-80  271.3   0.0    2.3e-80  270.6   0.0    1.3  1  Topoisom_bac  DNA topoisomerase
    2.8e-24   85.3   0.1    1.3e-23   83.1   0.0    2.2  2  Toprim        Toprim domain
    7.5e-11   42.4   0.0     0.0027   18.0   0.0    3.6  3  Helicase_C    Helicase conserved C-terminal domain
    1.1e-10   41.5   0.0    4.5e-10   39.6   0.0    2.0  2  DEAD          DEAD/DEAH box helicase
      7e-10   38.2   0.5    2.6e-09   36.3   0.5    2.0  1  zf_Rg         Reverse gyrase zinc finger
    4.2e-05   23.6   0.0    9.7e-05   22.4   0.0    1.5  1  ResIII        Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.046   13.9   0.0    1.9  1  Helicase_C_2  Helicase C-terminal domain
       0.19   11.0   0.0       0.33   10.3   0.0    1.3  1  Ofd1_CTDD     Oxoglutarate and iron-dependent oxygenase degra
          1    9.2   5.2         29    4.5   0.0    4.1  4  HTH_IclR      IclR helix-turn-helix domain
        2.8    8.0   5.8       0.48   10.4   1.5    2.0  2  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
        3.8    7.1   5.2        8.3    6.0   0.7    2.4  2  zf-ribbon_3   zinc-ribbon domain


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 !  270.6   0.0   1.4e-83   2.3e-80       3     412 ..     867    1293 ..     865    1294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 270.6 bits;  conditional E-value: 1.4e-83
                      Topoisom_bac    3 nenlvdaaeaRrelDwliGinlsrlltk.......klk...............g.kkvlsaGRVqtptLaliveR 54  
                                        + +lv+++ +Rr+ D+++G++ls+ ++k         +               + ++++saGRVqtp+L+ i+e 
  gi|320101071|ref|YP_004176663.1|  867 DIRLVESQIVRRIDDRWLGFSLSEKVQKyawmdycL-RylfhkrglvekstccRpNGNMSAGRVQTPVLGYIIEE 940 
                                        6799********************999876666550.0555666677666655279******************9 PP

                      Topoisom_bac   55 ereienFvpeey.weveatlkkekkekekkkkkkkerikdkeeaeaileklkk.k.eakvesvekkekkkppplp 126 
                                        ++++ +  pe y ++ ++ +++ ++      + +   i+  +  + i+ ++kk    ++ve v+++e + +pp p
  gi|320101071|ref|YP_004176663.1|  941 TDARSR--PERYvYRMKIYIERIGDL----VEVSIPYID-AK-NAGIVDTVKKrPhPVEVEVVSEEEVQLNPPPP 1007
                                        998875..676636777665444433....345555454.33.34577777776459*************8888* PP

                      Topoisom_bac  127 fdtttLqkeasrklglsakktlsiaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllk 201 
                                        f+t++L++easr lgl a +t++iaq+L+e+ glitY+RTdstr+s++  +k ++++l++k    y e+a++ +k
  gi|320101071|ref|YP_004176663.1| 1008 FTTDSLLEEASRTLGLPATRTMEIAQDLFET-GLITYHRTDSTRVSDTG-VKIARQYLEDK----YGEKAPHYFK 1076
                                        ******************************7.*****************.9********97....6667777776 PP

                      Topoisom_bac  202 ktkkksvvknkkveaHeAIrPteelpklkels...............ddekklYelIvrrflaslmkdakyeett 261 
                                         ++ +    ++  +aHeAIrPt+ +++ ++l                +d+ +lY+l++rrf+as+m++ak ++  
  gi|320101071|ref|YP_004176663.1| 1077 -PRTW----GEG-GAHEAIRPTRPIDS-DRLVelvkegvlslplrltRDHVRLYDLVFRRFIASQMEAAKLRKLV 1144
                                        .6655....555.8********99994.4555566888999*****988888*********************** PP

                      Topoisom_bac  262 vkleveeeefkasg.ktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleekkTkppkryteasLikam 335 
                                        +++ +++++++++  ++ + kG+++vy++ +   +e     lk ge+v   e+e+++++   p+r+   ++i++m
  gi|320101071|ref|YP_004176663.1| 1145 LRVYIGDRSYETEIyTEAVWKGYLEVYENVRLLGRE---LGLKPGERV---EAEIHDGNRVTPPRLRSHDVIRWM 1213
                                        *****999999997256678*******877776665...589*****8...6789******************** PP

                      Topoisom_bac  336 ekagiGtpaTraeiieklvergYverk.k.kslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkad 407 
                                        ++ giG+p+T+a+i+++l++rgYv++  k k+l+pte G+++ ++l +++ ++vs+++T++lee +++I++++ +
  gi|320101071|ref|YP_004176663.1| 1214 KEQGIGRPSTYAKIVQTLIDRGYVRVTgKvKALIPTERGRSVFNFLgKYYGNVVSVDTTRRLEELMEDISKNTVE 1288
                                        **************************9779****************6666**********************999 PP

                      Topoisom_bac  408 akevl 412 
                                        +++ l
  gi|320101071|ref|YP_004176663.1| 1289 YQSAL 1293
                                        88765 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.8   4.5e+03      48      67 ..     643     662 ..     611     663 .. 0.86
   2 !   83.1   0.0   8.2e-27   1.3e-23       2     103 .]     679     851 ..     678     851 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.8
                                       TTHHHHHHHHHHHHHHSEEE CS
                            Toprim  48 dkkkvlkalkelakradeii 67 
                                       + ++ +k ++e+++r++e+i
  gi|320101071|ref|YP_004176663.1| 643 NLEELMKQIEEERRRVSEVI 662
                                       56788999*********998 PP

  == domain 2  score: 83.1 bits;  conditional E-value: 8.2e-27
                                       EEEESSHHHHHHHHHTHT...................STEEEEEEESSSSEEEHS.....................T CS
                            Toprim   2 lvivEgpsdaktiakalg...................sgfqavtaslGhildlet.....................e 38 
                                       l++vE+p++a+tia ++g                   s  + +tas Gh++dl+t                     +
  gi|320101071|ref|YP_004176663.1| 679 LMVVESPNKARTIAGFFGkpsvrivgnilqvyevtigSYVLSITASAGHVYDLVTdkslpeaegaealygvlrvdgR 755
                                       9***************************************************************************8 PP

                                       TEEEEE................................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHH CS
                            Toprim  39 fkpvye................................eiedkkkvlkalkelakradeiilatDpDreGeaiawel 83 
                                       f pvy+                                 +  k +v+kal+ela+++d +++ tDpD eGe+iaw+l
  gi|320101071|ref|YP_004176663.1| 756 FIPVYTdikkcsnghqfteelggntvecprckmdnkqsHVIRKLDVIKALRELAEEVDVVFIGTDPDAEGEKIAWDL 832
                                       8888888999999999999999999999999999998899999999999**************************** PP

                                       HHHHTHHHTTTEEEEEESSS CS
                            Toprim  84 levlkellenkigrvefsei 103
                                       + +l++++++ ++r+ef+e+
  gi|320101071|ref|YP_004176663.1| 833 RVLLEPYANE-VRRIEFHEV 851
                                       *999999999.*******96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.7e-06    0.0027      40      75 ..     199     234 ..     172     260 .. 0.90
   2 !   15.9   0.0   7.8e-06     0.013      16      96 ..     384     468 ..     374     478 .. 0.79
   3 ?    3.8   0.0     0.043        71      95     110 ..     585     600 ..     579     601 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                                       TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG CS
                        Helicase_C  40 gikvavlhgelpqnereeileqfnkgesdvLiatdv 75 
                                        i+++++hg l +++re ++++ ++g++d+L++t++
  gi|320101071|ref|YP_004176663.1| 199 CIRILCIHGHLGKRDRETAMNRLKEGSFDILLTTSA 234
                                       599*******************************87 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 7.8e-06
                                       TSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG....GTSSSTST. CS
                        Helicase_C  16 ggkilifvntidrlek....vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdv....aerGidip. 83 
                                       ++ +l+fv+  + +e     v+ll ++kg+++ ++h+    +  +e l++f kg+++vL+        + rGid+p 
  gi|320101071|ref|YP_004176663.1| 384 RDGVLVFVPVDKGVEYaeriVELL-REKGLRAEAFHS----KTSIELLDAFAKGDVNVLVGVATyygvMVRGIDLPe 455
                                       567899999999665555555555.6668********....78899*************76654445599*****97 PP

                                       TESEEEESSSSSS CS
                        Helicase_C  84 kvnlVinfdlprn 96 
                                       +v++V++ ++pr 
  gi|320101071|ref|YP_004176663.1| 456 RVKYVVFAGVPRH 468
                                       79****9999965 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.043
                                       SSHHHHHHHHTTSSST CS
                        Helicase_C  95 rnvtsyiqriGRtgRa 110
                                        +v++yiq++GR+ R 
  gi|320101071|ref|YP_004176663.1| 585 PDVATYIQASGRASRL 600
                                       5799*********996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   2.8e-13   4.5e-10       3     138 ..     110     264 ..     108     286 .. 0.84
   2 ?   -3.0   0.1       3.3   5.4e+03      57      94 ..    1276    1317 ..    1272    1321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.8e-13
                                       HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                              DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet...kgktgpkalivePtreLaeqtlnnlkkfkkyid. 75 
                                        Q+     +l+g ++ + a+TG+GKT   l+ +l i  +     + +g +  +v Pt+ L  q  ++l+ f ++++ 
  gi|320101071|ref|YP_004176663.1| 110 AQKTWARRVLKGLSFSIIAPTGMGKTVFSLVTALYITQRArreGDPRGWRSYLVFPTTPLLLQAERKLRAFAENLGv 186
                                       57888888999999*************999999977766577557778899**********************8777 PP

                                       .............SEEEEEET...TSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHH CS
                                       .............xxxxxxxx...xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 .............lrvlliig...gvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlld 135
                                                    +r+l+i g   + +++  +++l++g  di+++t   +++    + l+ + +r++V+D +d +l+
  gi|320101071|ref|YP_004176663.1| 187 sicsndnwdngdcIRILCIHGhlgKRDRETAMNRLKEGsFDILLTTSAFIHRNY--ELLKGKGFRLIVMDDVDAVLK 261
                                       788888999999999998855442677788888887779********9999955..578899**************9 PP

                                       TTT CS
                                       xxx RF
                              DEAD 136 qgf 138
                                       +g+
  gi|320101071|ref|YP_004176663.1| 262 SGR 264
                                       854 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.3
                                        HHHHHHHHHHHHHHTTTST...SEEE.EEETTSSHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx...xxxx.xxxxxxxxxxxxxxx RF
                              DEAD   57 reLaeqtlnnlkkfkkyid...lrvl.liiggvaardqlskl 94  
                                        +eL+e++ +n+ ++ + ++    +v  ++ig+++ ++ l+k+
  gi|320101071|ref|YP_004176663.1| 1276 EELMEDISKNTVEYQSALEgiyREVTtAVIGNHRVNELLEKM 1317
                                        699999999999999976556333335678887777766665 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.5   1.6e-12   2.6e-09       5      35 ..      19      49 ..      16      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.6e-12
                             zf_Rg  5 vfeklCPNCgGdisdeRlekGLpCkrClPke 35
                                      v+++ CPNCgG+isd+Rl    pC++Cl +e
  gi|320101071|ref|YP_004176663.1| 19 VYRHACPNCGGPISDYRLIFKAPCEKCLRDE 49
                                      899*************************887 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 !   22.4   0.0     6e-08   9.7e-05       6     139 ..     109     254 ..      89     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6e-08
                                       HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S...........-EEEEESSHHHHHHHHHHGGG CS
                            ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee......kflflvprkslleqtleefkk 76 
                                       + Q++  +++l+ l       + i ++TG+GKT+ ++ ++ ++++ +++e      +  ++ p++ ll q++++++ 
  gi|320101071|ref|YP_004176663.1| 109 SAQKTWARRVLKGL------SFSIIAPTGMGKTVFSLVTALYITQRARREgdprgwRSYLVFPTTPLLLQAERKLRA 179
                                       45555555555554......47899********************99999*************************99 PP

                                       GTGG....GEEEESSS-B--.............................-SEEEEEHHHHHHTH........HHHTT CS
                            ResIII  77 flseaykeigkkvsgdkkka......................kekdstnkkilvttiqsldadseeeeeeseellrd 131
                                       f+++   +i+ +   d+ ++                      ++ ++ + +il+tt   ++++        e l+ +
  gi|320101071|ref|YP_004176663.1| 180 FAENLGVSICSN---DNWDNgdcirilcihghlgkrdretamNRLKEGSFDILLTTSAFIHRNY-------ELLKGK 246
                                       999986553333...2222211122344444444444445566667777777777777666666.......777777 PP

                                       T-SEEEEE CS
                            ResIII 132 rfdviiiD 139
                                        f +i++D
  gi|320101071|ref|YP_004176663.1| 247 GFRLIVMD 254
                                       77777777 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.8e-05     0.046       2      99 ..     377     471 ..     376     627 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                      Helicase_C_2   2 lellevvpggvlvffp...Syklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcr..Gk 73 
                                       ++l+   ++gvlvf+p     ++ e++ve l+e++   ++e f++   +++ ++l+ + +  ++  +l++v+   G 
  gi|320101071|ref|YP_004176663.1| 377 VKLVLTLRDGVLVFVPvdkGVEYAERIVELLREKGL--RAEAFHS---KTSIELLDAFAK--GDVNVLVGVATyyGV 446
                                       67788899*******933346799999999999997..7788987...88999*******..6666666665555** PP

                      Helicase_C_2  74 lsEGidfsddllraviivglPfpnpk 99 
                                       +  Gid++ ++++ v+  g+P   ++
  gi|320101071|ref|YP_004176663.1| 447 MVRGIDLP-ERVKYVVFAGVPRHRFS 471
                                       ********.899********975554 PP

>> Ofd1_CTDD  Oxoglutarate and iron-dependent oxygenase degradation C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002      0.33     102     184 ..      79     162 ..      63     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                                       HHHHHHHH.HHHHSHHHHHHHHHHHSE.EE-EEEEEEEEE-TTT-EE--BE----G..EEEEEEEEE---S-TTTST CS
                         Ofd1_CTDD 102 eeklkeLlekllkskafrkwlalitgldlltsesilarRfrpGkdytLatsteeee..avLevtlnltptkgWesge 176
                                       e +l eL++     + f+ + +++tg+++ ++++  arR  +G ++ ++  t   +  + L   l++t  +   +g+
  gi|320101071|ref|YP_004176663.1|  79 EGALRELVKREEMLRDFEAFFEKATGFKMWSAQKTWARRVLKGLSFSIIAPTGMGKtvFSLVTALYITQ-RARREGD 154
                                       5677778777777789******************************98776665554789999999999.4444455 PP

                                       T---EEEE CS
                         Ofd1_CTDD 177 vGGyelym 184
                                         G+  y+
  gi|320101071|ref|YP_004176663.1| 155 PRGWRSYL 162
                                       56666665 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 ?   -0.8   0.1      0.87   1.4e+03       6      27 ..      67      88 ..      67      91 .. 0.91
   2 ?   -3.7   0.1       6.8   1.1e+04       3      16 ..     483     496 ..     482     500 .. 0.78
   3 ?    4.0   0.2     0.027        44      21      50 ..    1014    1043 ..    1009    1045 .. 0.91
   4 ?    4.5   0.0     0.018        29      33      50 ..    1222    1239 ..    1217    1241 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.87
                                      HHHHCT-CTTBSS-BHHHHHHH CS
                          HTH_IclR  6 laiLdalaeapqeltlselArr 27
                                      +++L++ ae  +e  l+el +r
  gi|320101071|ref|YP_004176663.1| 67 FQLLRLYAESSREGALRELVKR 88
                                      799***************9876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.8
                                       HHHHHHHCT-CTTB CS
                          HTH_IclR   3 dRalaiLdalaeap 16 
                                        R la+L+ +ae+ 
  gi|320101071|ref|YP_004176663.1| 483 LRVLAVLRDIAEGE 496
                                       58999999888865 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.027
                                        HHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   21 lselArrtglpkStvhRlLqtLvelGyveq 50  
                                        l e +r +glp + +  + q L e G++++
  gi|320101071|ref|YP_004176663.1| 1014 LEEASRTLGLPATRTMEIAQDLFETGLITY 1043
                                        7799***********************986 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.018
                                        HHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   33 StvhRlLqtLvelGyveq 50  
                                        St   ++qtL+ +Gyv+ 
  gi|320101071|ref|YP_004176663.1| 1222 STYAKIVQTLIDRGYVRV 1239
                                        5556799*********95 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 ?   10.4   1.5    0.0003      0.48       1      21 [.      18      39 ..      18      47 .. 0.83
   2 ?   -4.0   0.2       9.2   1.5e+04      13      20 ..     651     658 ..     650     659 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                      zf-dskA_traR  1 giygs.CeeCGEpIpeaRlral 21
                                      g y++ C  CG pI + Rl   
  gi|320101071|ref|YP_004176663.1| 18 GVYRHaCPNCGGPISDYRLIFK 39
                                      67999*************9765 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9.2
                      zf-dskA_traR  13 IpeaRlra 20 
                                       I e+R+r+
  gi|320101071|ref|YP_004176663.1| 651 IEEERRRV 658
                                       99***996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.7    0.0051       8.3      19      26 .]      24      31 ..      22      33 .. 0.68
   2 ?    2.8   0.3     0.053        86       2       9 ..     780     787 ..     779     792 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0051
                       zf-ribbon_3 19 CpyCGtkl 26
                                      Cp+CG+++
  gi|320101071|ref|YP_004176663.1| 24 CPNCGGPI 31
                                      77777765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.053
                       zf-ribbon_3   2 tvrCPnCG 9  
                                       tv+CP+C+
  gi|320101071|ref|YP_004176663.1| 780 TVECPRCK 787
                                       89*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      852  (0.0475208); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.99u 0.34s 00:00:01.33 Elapsed: 00:00:00.50
# Mc/sec: 7957.38
//
Query:       gi|320101072|ref|YP_004176664.1|  [L=479]
Description: Na+/solute symporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   50.9  36.5    1.1e-13   50.9  36.5    2.2  2  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9  36.5     6e-18   1.1e-13       1     393 [.      31     408 ..      31     425 .. 0.81
   2 ?    0.7   2.0      0.01   1.9e+02     109     160 ..     417     469 ..     413     474 .. 0.71

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 6e-18
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvllllllla.erlr...nagalTlpd 73 
                                       y++ag++++++v   + aa+  sa  ++Gl G+++  G++ + +el  ll+ +++l  ++ +++r   ++g +T  +
  gi|320101072|ref|YP_004176664.1|  31 YIIAGGRVGSLVSFGTYAATTYSAFMMLGLVGLAYSTGVGALGFELLYLLVTVIILSTIGfKIWRlsrEKGWITPSQ 107
                                       99********************************************99999888888776255558889******** PP

                               SSF  74 ylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiq 150
                                       +l   + ++ + ++++ l l   ++ ++++++ g  + + +  Gl+  ++ l+ aa+  l++++ G+ ++  td  q
  gi|320101072|ref|YP_004176664.1| 108 MLGDIYSSRLLGILVAGLYL-FTMIPYVAAQIQGLTIVF-TYAGLDPVAGTLVSAAVAYLWILFAGMWSIATTDLYQ 182
                                       *******9996666666655.5667899***98777666.678********************************** PP

                               SSF 151 avlmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRfla 227
                                       a+lml g l+     +l +  l  +   ++ a + + + + + +  ++  p   l   + +++     p +++R++ 
  gi|320101072|ref|YP_004176664.1| 183 AILMLTGGLLYITQLMLPAPWLPGASPSQAIALV-GEKGYLGLT--DFWTPHVFLAYTVPWIFFALTNPQVVMRLYI 256
                                       ********99888888888766655555444444.322233222..3455555555555577777899********* PP

                               SSF 228 akdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAa 304
                                         d +a +++v       +l  + +++ +l a  +a a     ++++   + + + L+  l+++++  l+   ++Aa
  gi|320101072|ref|YP_004176664.1| 257 QRDEAAYRRSVALFSFYGLLYTLIAVTAGLLARGFAEA---GFIPANLKRDEVTIYLI-RLFNPFVGSLIAVSIVAA 329
                                       *****9999987766666666667799******99998...67888888899999996.79*******99999**** PP

                               SSF 305 imstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasav 381
                                        +st++s++ + +s+    +Y +++ +     ++++ ++  ++lv+i+l+ +la       +++l  + + +l  + 
  gi|320101072|ref|YP_004176664.1| 330 AVSTVNSIVHAVASS----IYREVIGSP----RRQLALLNAVSLVIIALSSFLAYARVAY-IVDLSVMTSVYL-LPL 396
                                       *********988876....588888777....6667778888999999999999888888.777766655555.456 PP

                               SSF 382 lavillalfwkr 393
                                       +++  ++l+  r
  gi|320101072|ref|YP_004176664.1| 397 APITAIGLYLAR 408
                                       778778888777 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.01
                               SSF 109 aklielalGlnyetavllla.altalYtviGGllAvvytdtiqavlmlvgali 160
                                       a+l+ la G  + +a  ll  ++ a   v  G  A+ ++ t+ ++++l+g ++
  gi|320101072|ref|YP_004176664.1| 417 AALLSLATGETVAVASTLLNrGSRAFTSVYAGVPASLWVLTVSTLVLLAGFML 469
                                       6666666776666655544414444555889*****************99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); 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:                         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 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3404.42
//
Query:       gi|320101073|ref|YP_004176665.1|  [L=56]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.1   1.0       0.04   14.0   1.0    1.1  1  MARVEL    Membrane-associating domain


Domain annotation for each model (and alignments):
>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.0   2.2e-06      0.04      61     103 ..      11      56 .]       3      56 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-06
                            MARVEL  61 vlylfk...nsaftsilwplidlivdalaallwlvafialaaglrd 103
                                       +  l++      f ++++ l ++++  l++l w++a+i++   +++
  gi|320101073|ref|YP_004176665.1|  11 ITILSSyvvPYVFLRNSRGLELFLFWTLLTLAWITASIVYLRRVQQ 56 
                                       3333333333357899999999******************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 438.67
//
Query:       gi|320101074|ref|YP_004176666.1|  [L=340]
Description: MarR family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-06   26.0   0.5    2.4e-05   24.1   0.3    2.0  2  MarR_2          MarR family
     0.0001   22.7   0.1    0.00033   21.1   0.1    1.8  1  HTH_27          Winged helix DNA-binding domain
    0.00026   20.9   0.2    0.00064   19.6   0.2    1.6  1  MarR            MarR family
     0.0011   18.8   0.2     0.0034   17.3   0.2    1.9  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0016   18.5   0.2     0.0051   16.9   0.3    1.7  1  DprA_WH         DprA winged helix domain
      0.002   18.0   0.5     0.0056   16.6   0.2    2.0  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0029   17.5   0.0      0.006   16.5   0.0    1.5  1  TBPIP           TBPIP/Hop2 winged helix domain
     0.0048   16.9   1.0      0.017   15.1   0.3    2.1  2  HTH_46          Winged helix-turn-helix DNA binding
     0.0057   16.2   0.6      0.021   14.4   0.3    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.011   15.7   0.3      0.095   12.7   0.1    2.7  3  HTH_36          Helix-turn-helix domain
      0.013   15.4   0.7      0.042   13.7   0.7    2.0  1  HTH_5           Bacterial regulatory protein, arsR family
      0.013   15.7   0.1      0.027   14.6   0.1    1.5  1  HTH_34          Winged helix DNA-binding domain
      0.016   15.5   0.1      0.063   13.6   0.1    1.9  1  Rrf2            Transcriptional regulator
      0.018   15.0   0.1      0.053   13.5   0.1    1.7  1  Cdc6_C          CDC6, C terminal winged helix domain
      0.041   14.0   0.9      0.092   12.8   0.6    1.8  1  HTH_20          Helix-turn-helix domain
      0.044   13.6   0.2       0.12   12.2   0.2    1.8  1  HTH_IclR        IclR helix-turn-helix domain
      0.045   14.0   0.3       0.22   11.7   0.1    2.2  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.071   13.1   0.1        1.6    8.8   0.0    2.6  2  RHH_3           Ribbon-helix-helix domain
      0.078   13.1   0.1       0.13   12.4   0.1    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.3   2.5e-08   2.4e-05       9      54 ..       8      53 ..       5      58 .. 0.90
   2 ?   -2.0   0.0       3.8   3.5e+03      33      45 ..     307     319 ..     306     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.5e-08
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       +L  L    g+++ ++ l r+l+ sks++s il +L++ GL+err
  gi|320101074|ref|YP_004176666.1|  8 ALLELLSSMQGKEVPQSYLHRALNASKSRISEILSELEKEGLIERR 53
                                      5667788888889*******************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.8
                                       SSHHHHHHHHHHH CS
                            MarR_2  33 lsksavsrilkrL 45 
                                       ++  +v ri+++L
  gi|320101074|ref|YP_004176666.1| 307 IDGETVRRIVAKL 319
                                       5667888999887 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 !   21.1   0.1   3.5e-07   0.00033       7      50 ..       8      52 ..       4      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.5e-07
                            HTH_27  7 lvLhlir.hrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                      ++L+l+  +++ ++ ++ l+++ln ++s is++l++L++ GL+er
  gi|320101074|ref|YP_004176666.1|  8 ALLELLSsMQGKEVPQSYLHRALNASKSRISEILSELEKEGLIER 52
                                      567778889999999****************************87 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   6.8e-07   0.00064      10      50 ..      11      53 ..       8      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.8e-07
                                      HHHHHSTT..EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 10 rilyeqgp..lsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++l+++++    +s L ++l+ sks ++++l +Lek+GlieR+
  gi|320101074|ref|YP_004176666.1| 11 ELLSSMQGkeVPQSYLHRALNASKSRISEILSELEKEGLIERR 53
                                      5555555534678899**************************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 !   17.3   0.2   3.6e-06    0.0034      27      58 ..      25      56 ..       7      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                                      HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       ++++l+ ++s++ e+L++Le+ Gl+er+   
  gi|320101074|ref|YP_004176666.1| 25 YLHRALNASKSRISEILSELEKEGLIERRVIG 56
                                      57899***********************9744 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   5.4e-06    0.0051      12      58 ..       4      53 ..       3      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.4e-06
                           DprA_WH 12 dlerrvLaaLgpe...PvhvDqLvrrtglpaaevsaaLleLELaGlverl 58
                                      dl+r++L++L++     v+   L+r++ ++ +++s +L+eLE +Gl+er+
  gi|320101074|ref|YP_004176666.1|  4 DLRRALLELLSSMqgkEVPQSYLHRALNASKSRISEILSELEKEGLIERR 53
                                      789999***97633459*******************************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 !   16.6   0.2     6e-06    0.0056      23      54 ..      22      53 ..       5      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6e-06
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrg 54
                                       q  l + l+++ + +s ilseL++egli+r+
  gi|320101074|ref|YP_004176666.1| 22 PQSYLHRALNASKSRISEILSELEKEGLIERR 53
                                      5666667899********************54 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.4e-06     0.006      24      59 ..      24      61 ..      19      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.4e-06
                             TBPIP 24 anlqk..klgKtavqkaLdeLvdegkiieKeyGKqkiY 59
                                      ++l++  + +K  + ++L eL++eg+i  +++G +ki 
  gi|320101074|ref|YP_004176666.1| 24 SYLHRalNASKSRISEILSELEKEGLIERRVIGRSKIV 61
                                      589998899**************************884 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.8e-05     0.017      27      55 ..      24      52 ..       5      65 .. 0.84
   2 ?   -0.8   0.0       1.7   1.6e+03      12      54 ..     266     308 ..     264     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                            HTH_46 27 kyIqkrtnLSrSsimkvLseLkkggyIei 55
                                      +y ++  n S+S+i ++LseL k+g Ie 
  gi|320101074|ref|YP_004176666.1| 24 SYLHRALNASKSRISEILSELEKEGLIER 52
                                      788999999*****************985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                            HTH_46  12 LielpeelreninvlkyIqkrtnLSrSsimkvLseLkkggyIe 54 
                                       +++ +e +r+    l+y +  t +  S   + +s+ k   yI+
  gi|320101074|ref|YP_004176666.1| 266 MASISEYSRNPYRFLEYYSAVTGIPVSILREAVSAYKPSPYID 308
                                       7888999999999999999999999999999999999888886 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   0.3   2.2e-05     0.021       4      48 .]       5      51 ..       3      51 .. 0.84
   2 ?   -2.9   0.0       5.4   5.1e+03      30      48 .]     166     184 ..     166     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                            HTH_24  4 tdrkILelLqk.npr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++r++LelL   +++  +q+ L ++l+ S+s +++ l +Le+eGlI+
  gi|320101074|ref|YP_004176666.1|  5 LRRALLELLSSmQGKeVPQSYLHRALNASKSRISEILSELEKEGLIE 51
                                      5677777777776666888888899*********************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.4
                            HTH_24  30 SpstvnrrlkrLeeeGlIk 48 
                                       Sps+++ +  rL  + +++
  gi|320101074|ref|YP_004176666.1| 166 SPSATLVYSSRLSTMDYVR 184
                                       8999999999999999986 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   0.1    0.0001     0.095      27      55 .]      22      50 ..       6      50 .. 0.83
   2 ?   -2.2   0.0       4.6   4.3e+03       8      23 ..      89     104 ..      87     106 .. 0.72
   3 ?   -1.9   0.0       3.5   3.3e+03      40      49 ..     310     319 ..     307     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                       q++l ++l+ sk+ +s ++ eLe+ G+i
  gi|320101074|ref|YP_004176666.1| 22 PQSYLHRALNASKSRISEILSELEKEGLI 50
                                      699************************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.6
                            HTH_36   8 klllgslasfankngg 23 
                                        l+lg+ as  n++g+
  gi|320101074|ref|YP_004176666.1|  89 YLFLGYFASRMNEKGY 104
                                       5778888888877776 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.5
                            HTH_36  40 nTvsraikeL 49 
                                       +Tv+r++++L
  gi|320101074|ref|YP_004176666.1| 310 ETVRRIVAKL 319
                                       69*****999 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   4.4e-05     0.042       6      46 ..      11      51 ..       4      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++L++++ +e   + l ++l+ s+s +S+ L+ L+++GL+e
  gi|320101074|ref|YP_004176666.1| 11 ELLSSMQGKEVPQSYLHRALNASKSRISEILSELEKEGLIE 51
                                      444444446666677999*********************97 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.9e-05     0.027       2      47 ..       6      53 ..       5      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-05
                            HTH_34  2 RlavlsyLas..vdeadfvelkealeatdgnLsvhlkkLekagYievd 47
                                      R a+l +L+s   +e+  ++l  al+a+++++s  l+ Lek g ie++
  gi|320101074|ref|YP_004176666.1|  6 RRALLELLSSmqGKEVPQSYLHRALNASKSRISEILSELEKEGLIERR 53
                                      6678888888667889999*************************9986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.7e-05     0.063      12      56 ..       7      51 ..       4      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-05
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +all+L +  +++ v  + +++  n s+s ++ il++L+k+gl++
  gi|320101074|ref|YP_004176666.1|  7 RALLELLSSMQGKEVPQSYLHRALNASKSRISEILSELEKEGLIE 51
                                      68888888888888******************************8 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 ?   13.5   0.1   5.6e-05     0.053      38      65 ..      33      58 ..      28      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                      -HHHHHHHHHHHHHTTSEEEEEEE-CC. CS
                            Cdc6_C 38 tqrevsdllseLemlgileleksskGrr 65
                                      + +++s++lseLe+ g++e+++   Gr+
  gi|320101074|ref|YP_004176666.1| 33 SKSRISEILSELEKEGLIERRVI--GRS 58
                                      679******************99..553 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   9.8e-05     0.092      11      61 .]       5      57 ..       1      57 [. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.8e-05
                                      HHHHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 11 vRrrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                       Rr++l +L  ++++++  s l+++l  sk+ +s  L +Le+ gL+e++  gr
  gi|320101074|ref|YP_004176666.1|  5 LRRALLELLssMQGKEVPQSYLHRALNASKSRISEILSELEKEGLIERRVIGR 57
                                      699*********************************************97775 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 ?   12.2   0.2   0.00013      0.12       8      50 ..       9      52 ..       8      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      HHCT-CTTBSS.-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqe.ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +L++l++ ++  +  s l+r++  +kS  + +L+ L+++G++e+
  gi|320101074|ref|YP_004176666.1|  9 LLELLSSMQGKeVPQSYLHRALNASKSRISEILSELEKEGLIER 52
                                      78888877766369999*************************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 ?   11.7   0.1   0.00024      0.22      23      53 ..      21      51 ..       9      53 .. 0.86
   2 ?   -1.7   0.0       3.7   3.5e+03      44      53 ..     175     184 ..     168     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyve 53
                                      v ++ l ++Ln s+s +se l++Lek+G++e
  gi|320101074|ref|YP_004176666.1| 21 VPQSYLHRALNASKSRISEILSELEKEGLIE 51
                                      556778899*******************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.7
                                       HHHHHTTSEE CS
                    Fe_dep_repress  44 kkLekdGyve 53 
                                       ++L+ + yv 
  gi|320101074|ref|YP_004176666.1| 175 SRLSTMDYVR 184
                                       5899999995 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.43     4e+02      28      35 ..     184     191 ..     183     191 .. 0.94
   2 ?    8.8   0.0    0.0017       1.6      17      39 ..     280     301 ..     274     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.43
                             RHH_3  28 rSklldeA 35 
                                       rS+++++A
  gi|320101074|ref|YP_004176666.1| 184 RSEYVEKA 191
                                       8******9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                             RHH_3  17 LkaLSekTrIprSklldeAiell 39 
                                       L+ +S+ T+Ip+S +l+eA++ +
  gi|320101074|ref|YP_004176666.1| 280 LEYYSAVTGIPVS-ILREAVSAY 301
                                       7889*********.99****976 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00014      0.13       3      53 ..       5      55 ..       3      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                    B-block_TFIIIC  3 dqfklLelIassRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                      ++++lLel++s   + + qs L+++++ +++ +  +l  Lek gLI+++ i
  gi|320101074|ref|YP_004176666.1|  5 LRRALLELLSSMQGKEVPQSYLHRALNASKSRISEILSELEKEGLIERRVI 55
                                      67899999999999999*******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2675.01
//
Query:       gi|320101075|ref|YP_004176667.1|  [L=221]
Description: uracil phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-41  141.5   0.1    2.8e-41  141.3   0.1    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    5.6e-07   29.2   0.8    9.7e-07   28.4   0.8    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00046   19.7   0.1     0.0007   19.2   0.1    1.4  1  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 !  141.3   0.1   4.6e-45   2.8e-41       2     206 ..       7     220 ..       6     221 .] 0.94

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 4.6e-45
                           UPRTase   2 sshpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysg.elldeekialVpilRa 77 
                                       ++++ ++a lt+lRd++ts+ +fr+ + r++r+l+ e++++ +++e++ v+tplg+  +g +++d ++i+++ +lRa
  gi|320101075|ref|YP_004176667.1|   7 VNRKYAQAVLTTLRDKNTSQIEFRKGLVRLGRILGLELIED-FECEKTVVETPLGARVDGcRIKDLDNIVVITVLRA 82 
                                       678899***********************************.******************8888999********** PP

                           UPRTase  78 Gegmeealrellpearvghlglqreeet......lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkerg 148
                                         +++e+l ++l +a+ g +   r ee+       e ++ y k P+  +++ v++ D ++aTG+++++++++L+e+g
  gi|320101075|ref|YP_004176667.1|  83 AWPLTEGLIKVLFTAKQGVVAARRVEEKgmkagsFEIEISYVKTPRITSRDVVVISDVMVATGSTLVSVLEKLREKG 159
                                       *********************999998877777777889*******99***************************** PP

                           UPRTase 149 vgeekIlvlsvlaseegv...krlaeefp.kvkvvtaavDeeldekgyivpGlGDfGDRlFg 206
                                       +  ++  v+sv+  + ++   k+ aee   ++k++t a+D+e+dekgyivpGlGD+GDR Fg
  gi|320101075|ref|YP_004176667.1| 160 IA-KRYYVASVITTPHAIgrlKKYAEEAGiDLKLYTIAIDPEIDEKGYIVPGLGDAGDRAFG 220
                                       95.89***********986667777788789******************************8 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.8   1.6e-10   9.7e-07      29     128 ..      72     174 ..      64     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.6e-10
                                       GGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE..........EE----TTSEEEEE-S.EESSSH CS
                      Pribosyltran  29 kpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdes..rlledpagkkVliVDD.ildtGg 101
                                        + vv++++r ++p+   l++ L +++  +v +++++++g+   +  ++  +   +++ +  + V+++ D +++tG+
  gi|320101075|ref|YP_004176667.1|  72 DNIVVITVLRAAWPLTEGLIKVLfTAKQGVVAARRVEEKGMKAGSFEIE--IsyVKTPRITSRDVVVISDvMVATGS 146
                                       589********************96677777777777777666653333..1346777777777777777258**** PP

                                       HHHHHHHHHHCC-BS.EEEEEEEEE-HH CS
                      Pribosyltran 102 TllaalelLkekgpe.evriavlvdkpa 128
                                       Tl  +le L+ekg + +  +a +++ p+
  gi|320101075|ref|YP_004176667.1| 147 TLVSVLEKLREKGIAkRYYVASVITTPH 174
                                       ************9875555555555555 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.2e-07    0.0007     113     183 ..     124     192 ..      50     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-07
                          PRTase_2 113 edeellaaakelvLvDDEistGktalnliralqeklprkryvvvslvdwrseedeaafaaleeelgiriev 183
                                        ++ ++++++ +v+ D  ++tG+t++ ++++l+ek  +kry v+s++   +  +  + ++ +ee gi++++
  gi|320101075|ref|YP_004176667.1| 124 VKTPRITSRDVVVISDVMVATGSTLVSVLEKLREKGIAKRYYVASVITTPH--AIGRLKKYAEEAGIDLKL 192
                                       4444556667778888899**************************986544..458888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1652.39
//
Query:       gi|320101076|ref|YP_004176668.1|  [L=261]
Description: nucleotidyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-26   93.3   0.0    2.2e-26   93.0   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
      1e-09   38.9   0.0    1.3e-09   38.7   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   2.5e-30   2.2e-26       2     240 ..       7     234 ..       6     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 2.5e-30
                                       EEEE--S--GGGTTCCTTSSGGGSEETTET.ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgke.rliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       av+LaGG+G+R++P t  ++k+++pv+++e ++++ +++ l ++g+ +i++ ++ ++   + +++++gs+f+v++++
  gi|320101076|ref|YP_004176668.1|   7 AVVLAGGQGERFRPYTEIIPKPMIPVGNNEkPVLELVVKWLRRHGVSRIVFLVN-YKWRYIYNYFGDGSRFDVSITY 82 
                                       8***********************************************777777.556667789************* PP

                                       EEESS--..BGGHHHHHTHH.HHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEE CS
                   NTP_transferase  78 alepegk..gtAdAvalaae.lledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvi 151
                                       ++ +eg   +t +A+++a +  l +      +l+  gD+l   ++ ++++ +  +++  ++t++++++ +    Gv+
  gi|320101076|ref|YP_004176668.1|  83 SIDEEGGysNTGGAILKAYRdGLIKGR----ALIWYGDILAPLDVPDLLRYHSGAGS--DLTLVVTNRYR-VPVGVV 152
                                       ******999******998651455444....7*************************..56666555544.557*** PP

                                       EECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE- CS
                   NTP_transferase 152 eadeegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaey 228
                                       ++d++ +v ++ EKP+ +     a  G+ v +  v+ + ++  +el r  d++++++p ++++g++  a++ ++   
  gi|320101076|ref|YP_004176668.1| 153 KVDNDYNVVEMREKPELDI---NATIGVAVAELRVFSEGLE--RELGRDFDFMGNLVPWLINNGYRVKAYIYSG--E 222
                                       *****************98...57888889999****9999..*******************************..5 PP

                                       EEEXSSHHHHHH CS
                   NTP_transferase 229 WsDvGtldslle 240
                                       W DvG+l+ + +
  gi|320101076|ref|YP_004176668.1| 223 WFDVGSLERYKK 234
                                       ******998866 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   1.4e-13   1.3e-09       1     125 [.       7     144 ..       7     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.4e-13
                                       EEEEEESS-TTTTT.....THHHHCC..CCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-EEE- CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallpl..ggkpllervldalraagvdevvvvggd..eevlaal...arlgvrvved 65 
                                       av+LAGG++ R+       +K+++p+  ++kp+le v++ lr++gv+++v  +++  + +++++    r++v++++ 
  gi|320101076|ref|YP_004176668.1|   7 AVVLAGGQGERFRPyteiiPKPMIPVgnNEKPVLELVVKWLRRHGVSRIVFLVNYkwRYIYNYFgdgSRFDVSITYS 83 
                                       79**********8444689*******98899***********************95557777663335667888777 PP

                                       TTSS...-SHHHHHHHHHHH.H.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSS CS
                      NTP_transf_3  66 edpg...kgplaslaaalra.aadadavlvlacDmPlltpelverllaaaaasgadvvvptyeg 125
                                        d++    +++++++ a r  +  + ++l+  +D+  l p  v  ll+ +  +g+d + ++++ 
  gi|320101076|ref|YP_004176668.1|  84 IDEEggySNTGGAILKAYRDgL-IKGRALIWYGDI--LAPLDVPDLLRYHSGAGSDLTLVVTNR 144
                                       7776012455566666666632.689999999998..557777777777777777776666553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1917.76
//
Query:       gi|320101077|ref|YP_004176669.1|  [L=328]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   29.2   2.9    9.5e-05   22.9   0.1    2.2  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    5.4e-06   26.5   0.6     0.0067   16.5   0.0    2.2  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.1e-05   25.5   0.0    1.7e-05   24.8   0.0    1.3  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
     0.0093   16.0   0.0      0.018   15.1   0.0    1.4  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.19   11.6   0.0    1.3  1  YjeF_N           YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> 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 !   22.9   0.1   2.7e-08   9.5e-05       2     121 ..      16     138 ..      15     146 .. 0.79
   2 !    6.7   0.4    0.0025       8.8      48     111 ..     211     273 ..     193     298 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.7e-08
                   Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrps...pladlaalralrrllrqrrerpd 75 
                                       G +  ++ + + La+rG e+++l+p+++   +e++ +  rv+ + +pr+p+    ++ +++++al++ +r+ r ++ 
  gi|320101077|ref|YP_004176669.1|  16 GHAGFAYTVGHYLAERGIELDILVPRGYSWVRERMMRLGRVIEMTLPRKPAepiYRGLPRWIQALKESIRVCRNKYT 92 
                                       666666777899*************************************96544445589999998888889***** PP

                   Glyco_trans_4_4  76 vvhahspt....aglaarlarrrrgiplvvtlhg.lllrrgsgavrrlyra 121
                                       vv a ++      +l ++la        ++t+ + + ++++s+av  lyr 
  gi|320101077|ref|YP_004176669.1|  93 VVFASGSNfsipPSLTCMLAG-----SMILTIEDvARFTERSRAVSTLYRL 138
                                       ***998763333556666666.....6788888845588888888888865 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0025
                   Glyco_trans_4_4  48 prrpsplad..laalralrrllrqrrerpdvvhahsp.taglaarlarrrrgiplvvtlhgll.lrrg 111
                                       p+r++++ +   +++ +  r++     +  +v++h+p t++l arla  ++ +  v++++ +l  +rg
  gi|320101077|ref|YP_004176669.1| 211 PYRRGHPEWvvFQYTSDIHRWI----AGASLVVTHYPgTTALTARLAY-GKPVVMVYSPRHTLaAPRG 273
                                       4444445542234667778887....8899******835777777777.6666667777654414444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.9e-06    0.0067       1      92 [.      14     110 ..      14     148 .. 0.81
   2 !    8.7   0.1   0.00046       1.6      49     107 ..     213     269 ..     185     299 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev...elvvrvprvplpllkrllrslaflrrlrrllkre..k 72 
                                       +GG + +++++ ++La+rG+e ++++p++    +e+     +v++++ ++ p  + ++  ++ +++l++ ++    k
  gi|320101077|ref|YP_004176669.1|  14 YGGHAGFAYTVGHYLAERGIELDILVPRGYSWVRERMmrlGRVIEMTLPRKPAEPIYRGLPRWIQALKESIRVCrnK 90 
                                       6999999******************999998888887877777788888888888888888888888887774455* PP

                    Glyco_transf_4  73 pDvvHahspaalgaallalr 92 
                                       + vv a ++ + +   l ++
  gi|320101077|ref|YP_004176669.1|  91 YTVVFASGSNFSIPPSLTCM 110
                                       ***98887776665555554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00046
                    Glyco_transf_4  49 pllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltv...Hgly 107
                                       +   + +  +++ +++ r++   +  +v +h+p++    +l +r+++g+p+V  +   H+l+
  gi|320101077|ref|YP_004176669.1| 213 RRGHPEWVVFQYTSDIHRWIA--GASLVVTHYPGTT---ALTARLAYGKPVVMVYsprHTLA 269
                                       334444455666666777776..9********8887...44455569999998854447777 PP

>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.8e-09   1.7e-05      33     144 ..     199     305 ..     176     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.8e-09
                                       CHHHCCT-EEC---STT-TTTTCEEEEEESSSSHHHHHHHH-EEEEC.S-CHHHHHHHHTT--EEEE--TT....S- CS
                   Glyco_tran_28_C  33 qvlhqtGkreleevkikveeltlkvevfefidkmaeaikaadLvIsR.AGagtiaEllalgkplIlvplpeaaenhq 108
                                        v+ qtG+ + e+ +  ++e      vf+++ ++   i+ a+Lv+++  G++++   la+gkp ++v +p+++    
  gi|320101077|ref|YP_004176669.1| 199 RVVMQTGDVDPEPYRRGHPEW----VVFQYTSDIHRWIAGASLVVTHyPGTTALTARLAYGKPVVMVYSPRHTLAAP 271
                                       688888877777766655555....69********************77**********************999999 PP

                                       HHHHHHHHHHHHHHSSEEEE-STTCHHHHHHHHCCS CS
                   Glyco_tran_28_C 109 dnNakelekagaalvleqkeltpekLeeallelaae 144
                                       +    +l++++ a +le+  ++p +L+ea++e + +
  gi|320101077|ref|YP_004176669.1| 272 RGDSSKLAEKLNAVYLEE--VDPARLAEAIEEARGM 305
                                       999999999999988865..4579999999987765 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 !   15.1   0.0   4.9e-06     0.018       2     118 ..       8     120 ..       8     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.9e-06
                                       EEEE-SSHHHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHH CS
                   Glyco_transf_28   2 vllggGTgGhvfPalAlakeLkkegheVrylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavv 78 
                                       vll+ G gGh   a  + ++L+++g+e   +  +rg+  + v+e+ + + ++   +l+rk  ++  + +++ ++a++
  gi|320101077|ref|YP_004176669.1|   8 VLLIAGYGGHAGFAYTVGHYLAERGIELD-ILVPRGYS-W-VRERMMRLGRVIEMTLPRKPAEPIYRGLPRWIQALK 81 
                                       6889999**********************.99999974.5.59999*999977778********************* PP

                                       HHHHHHHHHHHCCCCCCCCCCCHCCCCCHCCCTTHCCCCC CS
                   Glyco_transf_28  79 kakkilkeakpdavvgtggyvslpaviaaplaripviihE 118
                                       +++++ +++  ++v+++g ++s+p+ +   la+  + + E
  gi|320101077|ref|YP_004176669.1|  82 ESIRVCRNK-YTVVFASGSNFSIPPSLTCMLAGSMILTIE 120
                                       ****99875.68899*********9998888777666555 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.19      27      60 ..       6      39 ..       3      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                            YjeF_N 27 kkvlvlvGsgnnGgdglaaArhLaqegakVtvll 60
                                       kvl+++G g + g ++ ++ +La++g++ ++l+
  gi|320101077|ref|YP_004176669.1|  6 DKVLLIAGYGGHAGFAYTVGHYLAERGIELDILV 39
                                      589**************************99843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2202.18
//
Query:       gi|320101078|ref|YP_004176670.1|  [L=306]
Description: cation diffusion facilitator family transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-18   66.3  23.9    3.5e-18   66.1  23.9    1.1  1  Cation_efflux    Cation efflux family
    8.4e-09   35.4   0.8    1.6e-08   34.6   0.1    1.8  2  ZT_dimer         Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
      0.015   15.2   0.3      0.048   13.5   0.3    1.8  1  DUF502           Protein of unknown function (DUF502)
        1.9    8.9   6.4         12    6.3   5.0    2.8  3  Phage_holin_5_2  Phage holin family Hol44, in holin superfami


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1  23.9   7.8e-22   3.5e-18       2     198 ..      21     211 ..      20     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 7.8e-22
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       i+s l+ ++ ++ el+v+l++ S  l+ d +h+ +d+v + + ll+++l+++  ++rfp+ +  +e +   + +l++
  gi|320101078|ref|YP_004176670.1|  21 IASALLSFTGLVLELAVALIAPSIILITDLLHWTVDTVLEAVFLLVVYLASRF-SKRFPWSIVMIEGVTVTTAILVI 96 
                                       7899999*******************************************997.89********************* PP

                     Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlv 155
                                       lgl  +++l+ i ++   ++ +  + + lv +l++ v+++a+++i rr+  ++r ++l+++a h+l+D ++s+ + +
  gi|320101078|ref|YP_004176670.1|  97 LGLYGYIFLDYISSTA--EGVSTRSLIPLVATLAGGVITVAMYIIQRRNYLRYRIELLRVDAAHALIDFIASILASI 171
                                       ****************..99999****************************************************** PP

                     Cation_efflux 156 salvillfnlksgplaDpvaslligliilysalkllkeslseL 198
                                       ++ ++++   +s   ++ +++++ +++++ s ++++k+ ++ L
  gi|320101078|ref|YP_004176670.1| 172 GIALTYWSGSHS---VELLFTFMSMMFVVHSLFEVFKDIVRTL 211
                                       *******96665...**********************998877 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.4   1.1e+04      47      58 ..     153     164 ..     152     168 .. 0.76
   2 !   34.6   0.1   3.5e-12   1.6e-08       4      72 ..     219     287 ..     216     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
                                       -HHHHHHHHHHH CS
                          ZT_dimer  47 svkeaHeiadev 58 
                                        v  aH+++d +
  gi|320101078|ref|YP_004176670.1| 153 RVDAAHALIDFI 164
                                       688999998866 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 3.5e-12
                                       .HHHHHHHHH.TT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EE CS
                          ZT_dimer   4 eeeeeireii.ksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadv 72 
                                       e +++i++ + ++  + ++v d+ +rk+Gs ++v+ +i vd+d++++e H++ +++ ++i +  + + +v
  gi|320101078|ref|YP_004176670.1| 219 ELRARIKDSLiEDFSN-VEVGDVDARKIGSFYVVSAKILVDPDMTMREIHRLRKRIVRSITSCSELIYHV 287
                                       6788999888456665.67***************************************998665444444 PP

>> DUF502  Protein of unknown function (DUF502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.1e-05     0.048       6      53 ..     167     214 ..     163     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                            DUF502   6 lillvGllasnligrkllklgerllkriPlvksiYsalkqvvetfsse 53 
                                       ++  +G+ ++ + g+  ++l+  +++ + +v s+++++k++v t+ ++
  gi|320101078|ref|YP_004176670.1| 167 ILASIGIALTYWSGSHSVELLFTFMSMMFVVHSLFEVFKDIVRTLTGS 214
                                       56789***************************************9865 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.46   2.1e+03      22      28 ..      92      98 ..      61     117 .. 0.64
   2 ?    6.3   5.0    0.0027        12      21      68 ..     119     173 ..      93     177 .. 0.73
   3 ?    2.2   0.2      0.05   2.3e+02      21      40 ..     162     177 ..     154     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.46
                   Phage_holin_5_2 22 yIPlilg 28
                                       I +ilg
  gi|320101078|ref|YP_004176670.1| 92 AILVILG 98
                                      2344444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0027
                   Phage_holin_5_2  21 kyIPlilgiiGiilgvvivfta..dfqaedilifg.....aiiqGilsggastgl 68 
                                        +IPl+ ++ G++++v++++++  ++    i ++      a+i  i s +as+g+
  gi|320101078|ref|YP_004176670.1| 119 SLIPLVATLAGGVITVAMYIIQrrNYLRYRIELLRvdaahALIDFIASILASIGI 173
                                       79*************8888876685544444444455666777777777777775 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.05
                   Phage_holin_5_2  21 kyIPlilgiiGiilgvvivf 40 
                                        +I  il+ iGi+l+    +
  gi|320101078|ref|YP_004176670.1| 162 DFIASILASIGIALT----Y 177
                                       58999********99....2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2130.47
//
Query:       gi|320101079|ref|YP_004176671.1|  [L=100]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 729.09
//
Query:       gi|320101080|ref|YP_004176672.1|  [L=276]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.4   0.1       0.32   10.3   0.0    1.5  1  VirC1     VirC1 protein


Domain annotation for each model (and alignments):
>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   1.8e-05      0.32     102     133 ..      47      79 ..      43     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.8e-05
                             VirC1 102 iiassdllliPtmltpld.idealatyryviel 133
                                       ++ +s lll+P mltp++ i   l+ yry+  +
  gi|320101080|ref|YP_004176672.1|  47 VVDASSLLLVPPMLTPVEpISRLLKFYRYLAGF 79 
                                       788999**********98688889999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2081.21
//
Query:       gi|320101081|ref|YP_004176673.1|  [L=315]
Description: PfkB domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  158.3   0.1    3.6e-46  157.8   0.1    1.0  1  PfkB          pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.069   12.5   0.0       0.13   11.6   0.0    1.4  1  Amidohydro_1  Amidohydrolase family
      0.071   12.3   0.0      0.097   11.9   0.0    1.1  1  AvrB_AvrC     Avirulence protein
      0.094   12.1   0.0       0.15   11.4   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.1   8.1e-50   3.6e-46       5     299 ..      10     288 ..       7     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 8.1e-50
                                       EEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEE CS
                              PfkB   5 vviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdt 79 
                                       v++G  +id+  +++k    +e+v++++v  ++GGa+ N Ava+++ g+++++i  v   +++++ le+ ++ gvd+
  gi|320101081|ref|YP_004176673.1|  10 VSVGNFNIDVAVYVDKMpgLDESVNAREVDIRPGGAATNYAVAVSHYGHRSSLIASVSSNPLAKMGLETVRDMGVDV 86 
                                       79****************999999***************************************************** PP

                                       TTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHH CS
                              PfkB  80 dyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaak 156
                                       ++v    d+++g+ + +v  dg r+++  +ga+a lt++++  +++ll +++++++++l+++    ++le  +  + 
  gi|320101081|ref|YP_004176673.1|  87 SHVS-YVDAQPGMVVSIVYPDGSRSMIRSLGANAYLTPDKV--SQELLDSSSVVHMATLHPA----KALEISRRTRA 156
                                       ****.6667*****************************976..***************5555....77777777777 PP

                                       HTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEE CS
                              PfkB 157 nggtfdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGal 233
                                       +++ +dp ++ ++    +++l+e+l+++d+l++n+ E + ltg+   d+ e+ ++       g++ +vv+lG +Ga+
  gi|320101081|ref|YP_004176673.1| 157 AMKSYDPGVYVHTD---VSELREVLRHIDVLFLNRQEYAVLTGKV--DVRELFNL-------GVNIIVVKLGGKGAV 221
                                       77778888888888...689*************************..77777777.......899************ PP

                                       EEE.TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCS CS
                              PfkB 234 vve.kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiasl 299
                                       + +  +g++++ ++p+ k+vDttGAGD+f++ f aa+ +  s++ealr++  ++al + +kg++ ++
  gi|320101081|ref|YP_004176673.1| 222 ALTrDGGVYHAYTAPQGKPVDTTGAGDAFNAFFNAAYIDTGSVREALRYGASAGALKTLCKGSMLCW 288
                                       ***9999999****************************************************99876 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.8e-05      0.13     249     301 ..      95     152 ..      46     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                                       T..............TSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TT CS
                      Amidohydro_1 249 a..............asgnslnlleelrlalklqrgllye.deegglslkealrmaTingAkalgldd 301
                                       +              ++++sl     +++a+     l  + +++  l+ + ++ maT+++Akal +++
  gi|320101081|ref|YP_004176673.1|  95 QpgmvvsivypdgsrSMIRSL-----GANAY-----LTPDkVSQELLDSSSVVHMATLHPAKALEISR 152
                                       353332222222223455555.....88888.....4444577888******************9986 PP

>> AvrB_AvrC  Avirulence protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.2e-05     0.097     200     243 ..     143     187 ..     111     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                                       HHHHHHH.HHHHHHHHHHH-SSEEE---GGGHHHHHHHHHHHHHH CS
                         AvrB_AvrC 200 dlykdlk.rrglkdllaagePnlithtsaeyvpkikdhlesLykq 243
                                       ++ k l+ +r+++  +++++P +  ht+ ++++++  h++ L+ +
  gi|320101081|ref|YP_004176673.1| 143 HPAKALEiSRRTRAAMKSYDPGVYVHTDVSELREVLRHIDVLFLN 187
                                       4445554257778899**************************986 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.4e-05      0.15     110     223 ..     172     270 ..     164     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                                       HHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEE CS
                      Phos_pyr_kin 110 ealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveel 186
                                       + l+e +l++ +v+  N +E+++L+g         k   ++l +lg++ +++k g    + av   +  dg+ ++ +
  gi|320101081|ref|YP_004176673.1| 172 SELRE-VLRHIDVLFLNRQEYAVLTG---------KVDVRELFNLGVNIIVVKLGG---KGAV--ALTRDGGVYHAY 233
                                       55665.88889999999999999999.........667899************776...3555..555599999*** PP

                                       EEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHH CS
                      Phos_pyr_kin 187 eaerietknthGtGCtlssaiaaelakgesleeAvkk 223
                                       +a++ +  +t G+G+++ +   a      s++eA++ 
  gi|320101081|ref|YP_004176673.1| 234 TAPQGKPVDTTGAGDAFNAFFNAAYIDTGSVREALRY 270
                                       **************************99999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 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:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2282.76
//
Query:       gi|320101082|ref|YP_004176674.1|  [L=287]
Description: uridine phosphorylase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-38  131.5   0.3    3.4e-38  131.2   0.3    1.1  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.28   11.2   0.1    1.8  1  YLP        YLP motif


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 !  131.2   0.3   3.8e-42   3.4e-38       2     228 ..      33     251 ..      32     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 3.8e-42
                                       EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEE CS
                         PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGt 78 
                                       ++++ g+p++v+ +a+   e+     ++r++ ++ G +kg+ v+++stGiG+p +a +a+ +l   +  +++ir+Gt
  gi|320101082|ref|YP_004176674.1|  33 YILLPGDPERVPWIASF-WEKSWLVARHREYVTYSGYYKGVFVSATSTGIGAPATA-IAVEELARVG-GDTFIRVGT 106
                                       7899*************.5555555557****************************.9999999977.6******** PP

                                       EEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS CS
                         PNP_UDP_1  79 aGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfy 155
                                        G+l++d++vGD+vi++ a++++g+s+        +y+ ++y+a a+ + + +l+eaa  lg+++h+G++a++d+fy
  gi|320101082|ref|YP_004176674.1| 107 TGALRSDIRVGDIVISTGAVRLEGTSR--------HYVMPEYPAVASYDVVMALVEAADSLGVRYHVGLTASSDSFY 175
                                       ***************************........****************************************** PP

                                       -CH.............HHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHH CS
                         PNP_UDP_1 156 aet.............eaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaq 219
                                         +             +  +++lr+ ++ + eME++ +++lA+ +g++++a+++     ++        e++e+  +
  gi|320101082|ref|YP_004176674.1| 176 VGQerpgfrdylppfqRGLVSYLRSINVLNFEMEASLIFTLANIYGLRAGAVCAAIA--NR--------ETEEFIVN 242
                                       *******99999888666666********************************9833..33........44444444 PP

                                       HHHHHHHHH CS
                         PNP_UDP_1 220 eaaknaaal 228
                                       + + +a ++
  gi|320101082|ref|YP_004176674.1| 243 AGVGDAIRV 251
                                       444444444 PP

>> YLP  YLP motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   3.2e-05      0.28       2       9 .]     184     191 ..     184     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                               YLP   2 nEYLPPve 9  
                                       ++YLPP++
  gi|320101082|ref|YP_004176674.1| 184 RDYLPPFQ 191
                                       79*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2186.32
//
Query:       gi|320101083|ref|YP_004176675.1|  [L=172]
Description: phosphodiesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-30  106.8   0.0    1.5e-30  106.6   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    1.7e-08   35.2   0.3    1.1e-05   26.0   0.3    2.1  1  Metallophos    Calcineurin-like phosphoesterase
     0.0011   18.4   0.0      0.046   13.0   0.0    2.1  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   2.5e-34   1.5e-30       1     164 [.       1     163 [.       1     164 [. 0.83

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 2.5e-34
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela...pvlaVrGNnDeevveedvlrea 74 
                                       M ++++SD+H+n++a++ ++e++ e+gv++ ih+GD+  ++p +l+ +++ a   ++++ +GNnD++v  + ++r +
  gi|320101083|ref|YP_004176675.1|   1 MLIGVLSDTHDNVSATRSIVERMVEQGVELAIHLGDV--VSPFTLRFMRDSArglKFIILKGNNDGDV--HLLSRIS 73 
                                       99**********************************9..7775444444444555**********666..5555555 PP

                     Metallophos_2  75 aelgtdlp.eeaelelagekvlliHgdpl.gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgep 149
                                       a +g d+  e  +le++g+++l +Hg  + ++++++ ++l + + ++d+v++GHtHv+++e  +g lv nPG++++ 
  gi|320101083|ref|YP_004176675.1|  74 ASYGWDYYsEPVFLEIGGRRMLALHGYGDiAATNKMVDALAR-SLDVDMVLYGHTHVARAEFLEGKLVFNPGEACGY 149
                                       555555533*****************9778555555555555.47778***************************** PP

                     Metallophos_2 150 rdgdpetyaildtde 164
                                        +g++ +y i+dtd+
  gi|320101083|ref|YP_004176675.1| 150 ITGRR-SYGIVDTDT 163
                                       99998.*******97 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.3   1.8e-09   1.1e-05       3     203 ..       3     129 ..       1     130 [. 0.66

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.8e-09
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee 79 
                                       i v++D+H      + ++++ ++++  ++ ++ l +++GD+v        +l++++   + + ++++l+GN +  + 
  gi|320101083|ref|YP_004176675.1|   3 IGVLSDTH-----DNVSATRSIVERMVEQ-GVELAIHLGDVVSPF-----TLRFMRDSAR-GLKFIILKGNND-GDV 66 
                                       88******.....*************999.**********99988.....5555443333.3568********.333 PP

                                       HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHHHHH CS
                       Metallophos  80 ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkdlek 156
                                        ll++       s +w ++    + +   ++g+   + l lhG                              d   
  gi|320101083|ref|YP_004176675.1|  67 HLLSRISA----SYGWDYY----SEPVFLEIGGR--RMLALHGY----------------------------GD--- 102
                                       44444333....4455555....44444445555..55555554............................12... PP

                                       HTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 157 rekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                              i+ +             ++ ++ l +  +vd+v++GHtHv
  gi|320101083|ref|YP_004176675.1| 103 -------IAAT-------------NKMVDALARSLDVDMVLYGHTHV 129
                                       .......3333.............33333667888888888888886 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.0    0.0065        39      11      45 ..       6      40 ..       2      49 .. 0.90
   2 !   13.0   0.0   7.7e-06     0.046     197     249 ..     105     163 ..      93     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0065
                                      EE--TT-GGGHHHHHHHHHHH--SEEEEES----- CS
                     Metallophos_3 11 isdlkgevellerlveviedkdpDllvlvGdlvka 45
                                      +sd +++v    ++ve + +++++l + +Gd+v++
  gi|320101083|ref|YP_004176675.1|  6 LSDTHDNVSATRSIVERMVEQGVELAIHLGDVVSP 40
                                      688899999999********************986 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.7e-06
                                       -S-HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--B...GGGTE..EEEEETTT CS
                     Metallophos_3 197 kgsevvaelvktlnPevvvvghavkeh.eelgktlvvnPGa...leeGd..favvdlee 249
                                       +++++v  l ++l+ ++v+ gh++ ++ e l+  lv nPG+   +  G+  + +vd++ 
  gi|320101083|ref|YP_004176675.1| 105 ATNKMVDALARSLDVDMVLYGHTHVARaEFLEGKLVFNPGEacgYITGRrsYGIVDTDT 163
                                       5678999******************999************8322234433366666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1332.22
//
Query:       gi|320101084|ref|YP_004176676.1|  [L=192]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   43.8   0.1    3.2e-11   42.6   0.1    1.7  2  ArsA_HSP20       HSP20-like domain found in ArsA
    2.6e-10   40.4   2.2    1.1e-08   35.2   2.2    2.3  1  HSP20            Hsp20/alpha crystallin family
    9.9e-05   22.5   0.1    0.00016   21.8   0.1    1.3  1  GvpH             GvpH
    0.00013   22.9   0.5    0.00023   22.1   0.5    1.4  1  CS               CS domain
     0.0012   18.3   0.1     0.0019   17.6   0.1    1.3  1  DPCD             DPCD protein family
  ------ inclusion threshold ------
      0.046   14.1   1.5       0.37   11.2   0.7    2.7  2  DUF3696          Protein of unknown function (DUF3696)
       0.14   11.7   0.0       0.64    9.5   0.0    1.8  2  T4BSS_DotI_IcmL  Type-IV b secretion system, inner-membrane c


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 ?    1.7   0.0     0.075   1.9e+02      18      30 ..     104     116 ..      99     118 .. 0.85
   2 !   42.6   0.1   1.3e-14   3.2e-11       1      63 []     110     177 ..     110     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.075
                        ArsA_HSP20  18 idlsrsgdeLtIk 30 
                                       id+++sgde t+ 
  gi|320101084|ref|YP_004176676.1| 104 IDVFESGDEVTVI 116
                                       9*********995 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 1.3e-14
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrs..gdeLtIkignfrRq....itLPsvlarkevtsAkfedgvLeIrF 63 
                                       +de+ + +++P+v+k++id+  s  g +++I++ + +R+    i LP +++   + +A++++gvLe+++
  gi|320101084|ref|YP_004176676.1| 110 GDEVTVIAEIPGVEKDKIDVKVSddGRTIVINASDTNRKyykeIELPAKVDPASA-KASYKNGVLEVKL 177
                                       589999**********877777655999999999666655566**********77.***********86 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   2.2   4.2e-12   1.1e-08       2     100 ..     106     190 ..     105     192 .] 0.83

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 4.2e-12
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTE..EEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEE CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednr..vlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkasl 76 
                                       + e+ +e +v +++pg++k+ ++vkv d+   +++++  +              +rk+ ++++LP  vd+ + kas+
  gi|320101084|ref|YP_004176676.1| 106 VFESGDEVTVIAEIPGVEKDKIDVKVSDDGrtIVINASDT--------------NRKYYKEIELPAKVDPASAKASY 168
                                       667889999***********99999988754477777776..............4789999**************** PP

                                       ETTEEEEEEEBSS--..------- CS
                             HSP20  77 kdGvLtvtvpkkepekkkkerkiq 100
                                       k+GvL+v+++k+ +e   k  ki+
  gi|320101084|ref|YP_004176676.1| 169 KNGVLEVKLKKTGRED--KGVKIK 190
                                       ***********99984..444454 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   6.4e-08   0.00016      98     170 ..     108     184 ..      95     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.4e-08
                              GvpH  98 ddsdelvvvadlpGvtdedvdvaletdeqaltlrvdddv...verlvl.ddpdvaitdltlrnqvlelrlarsedsd 170
                                       +++de+ v+a++pGv  +++dv +  d +++ ++  d      + + l  + d a ++ + +n vle++l ++   d
  gi|320101084|ref|YP_004176676.1| 108 ESGDEVTVIAEIPGVEKDKIDVKVSDDGRTIVINASDTNrkyYKEIELpAKVDPASAKASYKNGVLEVKLKKTGRED 184
                                       689**********************9999999998886411133344423456677888889999999998887666 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.5     9e-08   0.00023       7      76 .]     108     179 ..     104     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9e-08
                                       EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                                CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliegeLfgpIdpeesswtieskkveitLkK 76 
                                       ++ deV+v  ++++v+++k dvkv+   r++ ++  +  +k ++e eL +++dp +++ + ++  +e++LkK
  gi|320101084|ref|YP_004176676.1| 108 ESGDEVTVIAEIPGVEKDKIDVKVSDDGRTIVINAsDTnRKYYKEIELPAKVDPASAKASYKNGVLEVKLKK 179
                                       6789***********99999999998888888888855588889999************************9 PP

>> DPCD  DPCD protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   7.5e-07    0.0019     108     139 ..     124     157 ..     118     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.5e-07
                              DPCD 108 kevysvtvdeeereivvrT..tNkKYyKklsipd 139
                                       k+  +v+v+++ r+iv+    tN+KYyK++++p 
  gi|320101084|ref|YP_004176676.1| 124 KDKIDVKVSDDGRTIVINAsdTNRKYYKEIELPA 157
                                       67889************86447*********993 PP

>> DUF3696  Protein of unknown function (DUF3696)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   0.00014      0.37      37      48 ..      14      25 ..      10      30 .. 0.86
   2 ?   -0.1   0.0      0.49   1.2e+03      28      36 ..      79      88 ..      75      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                           DUF3696 37 nWPeGFFDqaek 48
                                       W+eGFFD++++
  gi|320101084|ref|YP_004176676.1| 14 FWEEGFFDEIDR 25
                                      6********997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.49
                           DUF3696 28 p.iddnGris 36
                                      p i+++G+++
  gi|320101084|ref|YP_004176676.1| 79 PvIKEFGNVR 88
                                      56******97 PP

>> T4BSS_DotI_IcmL  Type-IV b secretion system, inner-membrane complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00025      0.64      75     121 ..      38      82 ..      34      92 .. 0.76
   2 ?   -0.1   0.0      0.22   5.6e+02     104     159 ..     123     177 ..     118     192 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00025
                   T4BSS_DotI_IcmL  75 Lqkaseefteegwesfaqslkssgnlkavkdkklvltavptgapvir 121
                                       + ++s+ ft+eg+e+f   l+++g+   v   ++ +   p g pvi+
  gi|320101084|ref|YP_004176676.1|  38 MRRLSRGFTPEGFEEFERELERKGVKPYVYGFSITI--GPDGKPVIK 82 
                                       77899******************9866665554444..566666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                   T4BSS_DotI_IcmL 104 kdkklvltavptgapvirqeglvkGryaWrvqlPllltyesaskstsqtllvtlvi 159
                                       +++k+ ++    g  ++ +++ ++ +y  +++lP  +   sa+ s ++  ++++ +
  gi|320101084|ref|YP_004176676.1| 123 EKDKIDVKVSDDGRTIVINASDTNRKYYKEIELPAKVDPASAKASYKNG-VLEVKL 177
                                       5566666677778889999999999999999999888877776655543.445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1379.60
//
Query:       gi|320101085|ref|YP_004176677.1|  [L=138]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-34  116.8   0.1    6.4e-34  116.6   0.1    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 !  116.6   0.1   3.5e-38   6.4e-34       1     115 []      20     135 ..      20     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 3.5e-38
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT..T-GGGTTS..THHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee..eYrhnaegpdnadaHlkss 75 
                                       dit  veeav++sgv +G+v+++++h+ta++++nEn ++++ +D+ + l++l  ++  ++rhn   +dna+aH+ s+
  gi|320101085|ref|YP_004176677.1|  20 DITGIVEEAVEKSGVANGIVVIHAPHATAAIVLNEN-EEGLINDIVDKLKDLTEPDsgRWRHN-RIDDNAHAHIGSA 94 
                                       79**********************************.****************7777******.6778********* PP

                                       HH-SEEEEEEETTEE---TTEEEEEEESS-SSE.EEEEEEE CS
                           UPF0047  76 llgssltipvedgklalGtwqsiylveldgpre.Rkvvvqv 115
                                       ++g++ +ipv++g++a Gtwq+++++e+dgpr+ R+v+++v
  gi|320101085|ref|YP_004176677.1|  95 IIGAERVIPVVNGRVARGTWQNVFFIEMDGPRSsREVIITV 135
                                       *******************************888***9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1076.49
//
Query:       gi|320101086|ref|YP_004176678.1|  [L=392]
Description: Nicotinate phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-27   94.6   0.0    1.4e-26   93.3   0.0    1.6  2  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
    3.5e-06   27.0   0.0    1.3e-05   25.2   0.0    1.9  2  QRPTase_N   Quinolinate phosphoribosyl transferase, N-termina
    1.1e-05   25.8   0.0    2.6e-05   24.6   0.0    1.5  1  NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal d
    1.6e-05   25.3   0.0      0.074   13.4   0.0    2.3  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 !   93.3   0.0   3.1e-30   1.4e-26       1     167 [.     114     300 ..     114     302 .. 0.95
   2 ?   -2.0   0.0       0.6   2.7e+03      44      58 ..     329     343 ..     314     353 .. 0.81

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 3.1e-30
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveav 70 
                                       iA+++ar+++ a ++++ +++ R  +P+++++  +A++iGG+d       +++lgL+   +++++ i  +g+++ea+
  gi|320101086|ref|YP_004176678.1| 114 IASKAARVKRLAMDKTILFFGLRAVHPAIAPMVDRAAYIGGVDavsgvlsEKYLGLKPSGTMPHALILTFGDQREAW 190
                                       8**************************************************************************** PP

                                       HHHHHHHTTTSE..EEEEESSHHHHHHHHHHT.....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEE CS
                         QRPTase_C  71 ksvreavdkevk..ievevesleeleevleae.....adiimLDnfsv..eelkkaveel.keknkr....vlievS 133
                                       k+++e+v+ +v+  + v++  +e  e+ ++a+       +++LD++s+   ++k++vee+ +  +++    v+i vS
  gi|320101086|ref|YP_004176678.1| 191 KAFDEVVEPNVPriMLVDTLYDEREEALMAARllggrLYGVRLDTPSSrrGDMKHIVEEVrWTLDINgfknVKIVVS 267
                                       *******99999999*****99999999998888877999******997899*******988888888999****** PP

                                       SS--TTTHHHHHCTT-SEEEECHHCHTB----EE CS
                         QRPTase_C 134 GgvtlenveeyaksgvdvisvgalthsvkalDis 167
                                       Gg+ ++++  +++ + d+++vg+ ++  +++Dis
  gi|320101086|ref|YP_004176678.1| 268 GGLDEKEIVRLRDLV-DAFGVGTSISMPPSVDIS 300
                                       *************98.*****************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.6
                                       --TSSTTTSEEE-HH CS
                         QRPTase_C  44 nhrlgLsdmvlikdn 58 
                                        +r gL+d+v + dn
  gi|320101086|ref|YP_004176678.1| 329 RKRPGLNDIVALMDN 343
                                       79999****999999 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 ?   -1.2   0.0      0.49   2.2e+03      23      44 ..       5      31 ..       2      44 .. 0.66
   2 !   25.2   0.0   2.9e-09   1.3e-05      25      89 .]      50     112 ..      34     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.49
                                      EESSSEEE-SHH...HHHHHHHHH..T CS
                         QRPTase_N 23 iakeegvvaGle...vaeevfell..p 44
                                      ia+ee ++ Gl+   ++ ++f++l  +
  gi|320101086|ref|YP_004176678.1|  5 IAREEEILGGLAtdvYFTRTFKVLkaK 31
                                      899999999987333566666666542 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 2.9e-09
                                       SSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  25 keegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrlS 89 
                                        e++v+aGle++  +++    ++v + +++G+ +++g+ ll ieG + ++  +E  +L +l ++S
  gi|320101086|ref|YP_004176678.1|  50 YEWAVYAGLEEVIYLLKGK-PVTV-YSMPEGTLFKAGEPLLIIEGYYDDFALYETPVLGILRHYS 112
                                       689*************966.5555.566***********************************98 PP

>> NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.7e-09   2.6e-05      49      88 ..     348     387 ..     345     390 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.7e-09
                        NAPRTase_C  49 psrvekLlkkvfkdGklvyelpsleeireyvkeqlaelrp 88 
                                       p++  +Ll k++++G+ v elpsle+ir+yv eql+e+++
  gi|320101086|ref|YP_004176678.1| 348 PEDYTPLLLKYLDNGEPVRELPSLEDIRRYVLEQLREVPE 387
                                       677899******************************9986 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 !   10.0   0.0   0.00019      0.84       1      52 [.      15      66 ..      15      71 .. 0.92
   2 !   13.4   0.0   1.7e-05     0.074      88     124 ..      72     108 ..      65     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                        NAPRTase_N  1 LdtDlYkltmaqavfkkgpdvevvfelffRkkpfkgeyaivagleevieyle 52
                                      L tD+Y     +++  kg +++v++e+ + k p+++e a++agleevi  l+
  gi|320101086|ref|YP_004176678.1| 15 LATDVYFTRTFKVLKAKGVRKKVRMEFHVMKLPKGYEWAVYAGLEEVIYLLK 66
                                      7899999999999999999*****************************9886 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.7e-05
                        NAPRTase_N  88 evaveeeevvfpgepeirveGpwieaillEtplLaiv 124
                                       +++++e++ ++ gep + +eG   +  l+Etp+L i+
  gi|320101086|ref|YP_004176678.1|  72 VYSMPEGTLFKAGEPLLIIEGYYDDFALYETPVLGIL 108
                                       367888888*************************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2763.72
//
Query:       gi|320101087|ref|YP_004176679.1|  [L=226]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.1   0.0       0.15   11.5   0.0    1.2  1  DUF2608   Protein of unknown function (DUF2608)


Domain annotation for each model (and alignments):
>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.5e-06      0.15     172     200 ..     149     177 ..     144     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-06
                           DUF2608 172 lLdkigrepksviFiDDkkknlasveeal 200
                                       +L  i +++++v+++DDk  nla +++ l
  gi|320101087|ref|YP_004176679.1| 149 ALLEILEDYDAVVYVDDKPVNLAVIDQGL 177
                                       45566789***************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1614.13
//
Query:       gi|320101088|ref|YP_004176680.1|  [L=346]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0077   16.5   0.0      0.019   15.3   0.0    1.6  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-06     0.019      14      45 ..     146     178 ..     133     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-06
                                       TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCH CS
                      NTP_transf_2  14 vakvvlfGSyarGtalkg.SDiDllvvlpeevs 45 
                                         +v ++GS   G +++  SDiDl+v++ +   
  gi|320101088|ref|YP_004176680.1| 146 LDDVGVTGSLLPGIHNPLfSDIDLVVYGWRKGL 178
                                       56899**********************977743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2615.22
//
Query:       gi|320101089|ref|YP_004176681.1|  [L=194]
Description: phosphoesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0012   19.1   0.0     0.0015   18.7   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
     0.0089   15.4   0.1        3.3    6.9   0.0    2.2  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-07    0.0015       5      71 ..       9      75 ..       5     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-07
                     Metallophos_2  5 iiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela..pvlaVrGNnDeevveedvl 71
                                      ++ Dl ++  + + +  +++  gvda+i++GD   ++p ++++l e++  p + V G+ D+  v + + 
  gi|320101089|ref|YP_004176681.1|  9 AVYDLEASKTLSRILCVIARTLGVDAVILLGDT--VSPVIIDWLVERCviPTYGVLGRLDDASVSQSLR 75
                                      555666555555666667777889********8..***********99************333333333 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0   0.00037       3.3       7      45 ..       6      44 ..       1      47 [. 0.75
   2 !    6.5   0.0   0.00052       4.7     198     249 ..     126     174 ..     120     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00037
                                      EEEEEE--TT-GGGHHHHHHHHHHH.--SEEEEES----- CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedk.dpDllvlvGdlvka 45
                                      ++la+ dl+ +   l r++ vi+   ++D+++l+Gd v++
  gi|320101089|ref|YP_004176681.1|  6 RLLAVYDLEASKT-LSRILCVIARTlGVDAVILLGDTVSP 44
                                      7899999987765.566665555444**********9875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00052
                                       S-HHHHHHHHHH--SEEEE-SS--EEEEETTEEEEE--BGGGTEEEEEETTT CS
                     Metallophos_3 198 gsevvaelvktlnPevvvvghavkeheelgktlvvnPGaleeGdfavvdlee 249
                                       +s++v e v +l+P+++++g  v   e   +   ++PG+  + +f  v +e+
  gi|320101089|ref|YP_004176681.1| 126 SSDIVGEAVESLKPRLILAGACV---EPCVEGNLISPGSALKNHFMYVAIEG 174
                                       899****************9983...44444445789988888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1392.21
//
Query:       gi|320101090|ref|YP_004176682.1|  [L=461]
Description: branched-chain acyl-CoA synthetase (ADP-forming) subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  179.9   0.1    4.4e-53  178.8   0.1    1.6  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    2.3e-25   89.3   0.3    1.3e-24   86.9   0.1    2.2  2  CoA_binding_2  CoA binding domain
    1.9e-19   70.1   0.3    8.5e-19   68.0   0.2    2.2  2  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
      0.037   13.3   0.1      0.079   12.2   0.1    1.4  1  MCH            Cyclohydrolase (MCH)
       0.14   12.7   0.9        4.2    8.0   0.3    2.9  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8   0.1   1.2e-56   4.4e-53       1     138 []     149     288 ..     149     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 1.2e-56
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsird..grkflsaa 75 
                                       +G+ialisqSGal++al+ w+  +++g+s ++s+Gn+ad+dva+l eyla+dp+t+vi++ylE+i+   g +f++ +
  gi|320101090|ref|YP_004176682.1| 149 KGNIALISQSGALGIALMGWTIMNEIGLSALLSVGNMADLDVAELSEYLADDPNTRVITIYLEGIKPgkGGEFVEKM 225
                                       69***************************************************************9855789***** PP

                      Succ_CoA_lig  76 rraarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       r+++ kkpvvv+k+Grs++ga+aaashtg+lagsd++++aaf+q+G++r++++ee+fd+a+++
  gi|320101090|ref|YP_004176682.1| 226 RKVTLKKPVVVIKAGRSRRGAAAAASHTGSLAGSDNLYEAAFKQSGIIRAYTVEEMFDIARAF 288
                                       ************************************************************986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.1   3.6e-28   1.3e-24       1     109 [.       9     127 ..       9     134 .. 0.94
   2 ?   -0.6   0.0      0.51   1.8e+03      82     103 ..     408     429 ..     353     435 .. 0.62

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 3.6e-28
                                       --EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivke 74 
                                       r+iaV+Gas +pgk gy vlr+++     g +v+pVnp+++eilg k+y+s+ + p +vd++ v +p++a+p++++e
  gi|320101090|ref|YP_004176682.1|   9 RSIAVIGASRTPGKIGYVVLRNIKGygfPG-KVYPVNPQADEILGYKAYPSILDVPDEVDVAIVTVPADAVPKVMEE 84 
                                       79***********************66666.8*********************758********************* PP

                                       HHHH--SEEEE-TT........---HHHHHHHHHTT-EEE.ES CS
                     CoA_binding_2  75 alalgakavwlqpg........sedeeaaelaeeagirvvgdr 109
                                       ++++g+k++++  +        + ++ ++e a+++g+r++g++
  gi|320101090|ref|YP_004176682.1|  85 CGRKGVKVAVIITSgfsevgnvELENRIVETARKYGMRILGPN 127
                                       *******99999999*******9*****************998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.51
                                       EEEE-TT---HHHHHHHHHTT- CS
                     CoA_binding_2  82 avwlqpgsedeeaaelaeeagi 103
                                       ++ +  g+   ea++++++++i
  gi|320101090|ref|YP_004176682.1| 408 VAGFVGGEDTYEAIKYLNRHNI 429
                                       4444444444444444444444 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.2   2.4e-22   8.5e-19       4      96 .]       9      99 ..       6      99 .. 0.97
   2 ?   -2.3   0.0       2.2   7.7e+03      55      70 ..     191     208 ..     183     226 .. 0.59

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 2.4e-22
                                      EEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  4 tkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80
                                       +++viGa+++ ++++ ++ ++ ++yg++ +v++vnp+  ++e+lg ++y+s+ +++++  vdva++tvPa+++ ++++
  gi|320101090|ref|YP_004176682.1|  9 RSIAVIGASRTPGKIGyVVLRNIKGYGFPgKVYPVNPQ--ADEILGYKAYPSILDVPDE--VDVAIVTVPADAVPKVME 83
                                      689*************999*******************..*******************..****************** PP

                                      HHHHTT-SEEEEESST CS
                       CoA_binding 81 elveagikgiviiteg 96
                                      e+ ++g+k++viit+g
  gi|320101090|ref|YP_004176682.1| 84 ECGRKGVKVAVIITSG 99
                                      **************86 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                                       HHHHHHC.T.TTEEEEES CS
                       CoA_binding  55 deleekt.e.vdvavitv 70 
                                       +el+e + + +++ vit+
  gi|320101090|ref|YP_004176682.1| 191 AELSEYLaDdPNTRVITI 208
                                       555555552366666654 PP

>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.2e-05     0.079     135     185 ..      72     116 ..      54     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                       EEESSS---HHHHHHHHHHHTS-GGGEEEEEE-SSSHHHHHHHHTTHHHHH CS
                               MCH 135 vlesdklPdeevvekvaeecgvepenvtllvaptaSlaGsvqvaaRvveva 185
                                       ++      ++++v kv eecg +  +v +++++  S +G v+   R+ve+a
  gi|320101090|ref|YP_004176682.1|  72 TV------PADAVPKVMEECGRKGVKVAVIITSGFSEVGNVELENRIVETA 116
                                       44......4556678**********************************98 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3    0.0012       4.2      48      92 ..      53      96 ..      10      99 .. 0.80
   2 ?    1.9   0.0     0.093   3.3e+02      28      87 ..     235     295 ..     218     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                                      -EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEE CS
                     F420_oxidored 48 vkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvi 92
                                       k+ + +  ++ +e dv +++v+  +v++v++e  ++  k  ++i
  gi|320101090|ref|YP_004176682.1| 53 YKAYP-SILDVPDEVDVAIVTVPADAVPKVMEECGRKGVKVAVII 96
                                      55555.667888999*****************9966666666655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.093
                                       EEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC.GHHHHT CS
                     F420_oxidored  28 ivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel.akdalk 87 
                                       +v+ + r+   a+++a++ g  + + +  eaa ++  ++ a   e + +++++  a+ + k
  gi|320101090|ref|YP_004176682.1| 235 VVIKAGRSRRGAAAAASHTGSLAGSDNLYEAAFKQSGIIRAYTVEEMFDIARAFaAQPLPK 295
                                       5566799999999999999999888888999999999999999999999999884344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3488.60
//
Query:       gi|320101091|ref|YP_004176683.1|  [L=108]
Description: t-RNA-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-26   92.1   0.0    2.1e-26   91.9   0.0    1.0  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   1.1e-30   2.1e-26       1      95 [.      14     105 ..      14     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.1e-30
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       lrvG v +ae++p+++kL++l+vd+Ge   rqi++g+ ++y+pe  ++k+v+vvanlkpkk++G eS+GM+l+++  
  gi|320101091|ref|YP_004176683.1|  14 LRVGLVKSAERVPGSEKLIRLIVDLGELGERQIIAGLGKWYQPEFFQGKHVIVVANLKPKKMMGLESQGMLLATD-- 88 
                                       79*************************999********************************************9.. PP

                                       ESSCEEEEEESST--TTC CS
                         tRNA_bind  78 dekevgilelpadveaGe 95 
                                         +   ++++++ v++G+
  gi|320101091|ref|YP_004176683.1|  89 -TDPPVLATVEKPVKPGA 105
                                       .58889999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 799.20
//
Query:       gi|320101092|ref|YP_004176684.1|  [L=232]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  104.3   0.0    1.2e-29  103.2   0.0    1.5  1  TYW3      Methyltransferase TYW3


Domain annotation for each model (and alignments):
>> TYW3  Methyltransferase TYW3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   6.7e-34   1.2e-29       7     212 ..      14     193 ..       8     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 6.7e-34
                                       HHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEES CS
                              TYW3   7 LeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkwlfvsH 83 
                                       ++++     ++ + G++D++ ++l+ ++n+  +++T+SSCsGR++             ++++  +++ +++++f++H
  gi|320101092|ref|YP_004176684.1|  14 WRRM----WEDLEIGYLDKDLLPLLILLNTERKVYTMSSCSGRIVAS-----------DSETPWERGVDSTVIFKKH 75 
                                       5555....677899******************************998...........4555566666789****** PP

                                       S---HHHHHHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEECTT. CS
                              TYW3  84 dpvkeeellaelfgleeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivslkkk. 159
                                        pv+  ell+ ++  +              +r i++++  +I+H+ +r+l++A+++l++A+ +G+++SGi+sl+++ 
  gi|320101092|ref|YP_004176684.1|  76 VPVEPGELLRLYSIPV--------------NRKIWLNVTGPIIHLSARDLQTAARILRIARLSGYKHSGIISLSRSk 138
                                       ********99999987..............799***************************************99876 PP

                                       EEEEEEE---EEEEEEE...STS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                              TYW3 160 kvivairsglklevpig...kellvseeylkllvklanerfeenkkrierfeealk 212
                                        vi+++++g+ l++p+    +  +v  e ++ lv+lan  + e kkr++r++ +lk
  gi|320101092|ref|YP_004176684.1| 139 GVILELTTGVYLSIPLRtrgG-DVVGSESIDGLVELANATLYEGKKRLSRLYMELK 193
                                       899**************9632.89****************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1775.00
//
Query:       gi|320101093|ref|YP_004176685.1|  [L=272]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-64  216.9   0.1    2.5e-64  216.6   0.1    1.0  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.6   0.1   1.4e-68   2.5e-64       5     203 ..      65     268 ..      62     270 .. 0.97

  Alignments for each domain:
  == domain 1  score: 216.6 bits;  conditional E-value: 1.4e-68
                                       -SEEEEEEEEE-TT---EEEEE--B-SS-.-TTSS-TT-B--B-HHHHHHHHHHHHGGG..GGSTT-EEEE--S-SS CS
                    tRNA_deacylase   5 vdliiflSrHssesgkplLTvHvtGnlge.aelGGkpeelapaaPrllkallralkkia..ekleefevtlEatHHG 78 
                                       ++++i+lSrHsse+g++++TvH+tGn+g  a +GGkp+el++a+P ++ +llr lk+++  +  +e+ev++EatHHG
  gi|320101093|ref|YP_004176685.1|  65 ASEYIVLSRHSSEAGVKSYTVHHTGNFGGeAAYGGKPGELGVASPLTAWRLLRLLKTLRdsYGRSEYEVSYEATHHG 141
                                       689*************************99*****************************99999************* PP

                                       -----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH--.----EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-G CS
                    tRNA_deacylase  79 PtelkvPslFvEiGSteeeWkdedaaeavaeavlellese.eekekvlvgiGGgHYaprftklvletevavGhilsk 154
                                       Pt++++P++FvEiGSt  eW+de ++++v eav +ll++   +++++++giGGgHY +++t+l+l++ v++Ghi++k
  gi|320101093|ref|YP_004176685.1| 142 PTSISKPLVFVEIGSTLGEWRDEVNHRVVGEAVARLLKEPgGDECNPAIGIGGGHYPRKHTELALSEPVCYGHIMAK 218
                                       *************************************9998899********************************* PP

                                       GGGGG--HHHHHHHHHHH..T-SEEEE-TTT--HHHHHHHHHHHHHHT-E CS
                    tRNA_deacylase 155 yaleelkeevikqaleks.egadvalidkkslkseqkeaieelleelgie 203
                                       yal++l+ +++++++++s  + ++++++kk++++e++  +ee+++++g++
  gi|320101093|ref|YP_004176685.1| 219 YALGALSMDTLDKMVHRSaVKPSIIVVEKKGTRQEHRVLVEEYASNKGLT 268
                                       ******************999***********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2175.88
//
Query:       gi|320101094|ref|YP_004176686.1|  [L=340]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.019   14.6   0.0    1.3  1  DUF3344   Protein of unknown function (DUF3344)


Domain annotation for each model (and alignments):
>> DUF3344  Protein of unknown function (DUF3344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-06     0.019     110     167 ..      86     147 ..      53     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-06
                           DUF3344 110 sdYligllayDvtdlisgs...gnnvlvltnkggtssdgrikgitLvvayedss.gtetqyw 167
                                        d l+   +yDvt+l++++   g+  + lt +++++s +r+  + L+++yed++ +t+ +yw
  gi|320101094|ref|YP_004176686.1|  86 RDKLVSKFVYDVTSLLNTEdsmGKDWVNLTFRHEGGSPVRLRKAQLIAVYEDPDaSTSLKYW 147
                                       4556666689*****9988333455666777765566*************966626778888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2495.84
//
Query:       gi|320101095|ref|YP_004176687.1|  [L=72]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.039   14.0   0.0      0.039   14.0   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.2e-06     0.039      66     122 ..       1      49 [.       1      67 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-06
                                       EEEE--SSSSSS--HHHHHHHHHHHHCT-EEEEE-S-GCGHHHHHTSSB.TTS.B-T CS
                   Nuc_deoxyrib_tr  66 vianldpfrgpeaDsGtafEvGyavalgkpvlayttdarelrervealrdadgllve 122
                                       +i+ ++++r  + D+ +  E Gy  ++ k v++y++d   +        dad++ ve
  gi|320101095|ref|YP_004176687.1|   1 MIVHIKKTRERGFDASVFSEYGYPFSRYKSVMVYVDDKAIM--------DADEVFVE 49 
                                       58899999999***********************9998864........55555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 557.08
//
Query:       gi|320101096|ref|YP_004176688.1|  [L=427]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.3   0.0    1.8e-14   53.6   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    4.1e-10   40.2   0.0    6.7e-10   39.5   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0     2e-18   1.8e-14       9     143 ..     245     379 ..     239     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2e-18
                                       TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflgevsr 83 
                                       ++k e+k i+++ gr  + Kg+   i af +l ++  +++klv+ G  + ++++++ + ae+l+++++v f+g++sr
  gi|320101096|ref|YP_004176688.1| 245 TVK-ERKGIVVFGGRPIPSKGLIEGILAFSKLVRE-LSDLKLVFTGyiGRQNKARVLAFAEKLGIREKVLFTGYISR 319
                                       444.8999************************997.**********9999999999********************* PP

                                       SSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT CS
                   Glycos_transf_1  84 edleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn 143
                                       ++   l ++a ++++ps+ ++   ++lEA  +g+pv  + ++ +  ++   ++  l +++
  gi|320101096|ref|YP_004176688.1| 320 KERLRLVRRAMLMLYPSHEDSYSYAVLEATLLGTPVAGYGIPALQTYFGGLDNVRLAPEG 379
                                       ************************************877666666666555555555555 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 !   39.5   0.0   7.5e-14   6.7e-10       3     132 ..     252     392 ..     249     394 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 7.5e-14
                                       EEEEES---GG.GTHHHHHHHH.HHHH.H..HEEEEEES---....HHHHHHHT..T-T.TEEEE---..THHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleav.pllrkk..dvrlvivGdgp..rpeeleelaa..gleerveftGfv..edlaell 70 
                                       +++f Gr   + kg+   + a+ +l+r +  d++lv+ G     +++++ + a+  g++e+v ftG++  ++  +l+
  gi|320101096|ref|YP_004176688.1| 252 IVVFGGRPI-PSKGLIEGILAFsKLVR-ElsDLKLVFTGYIGrqNKARVLAFAEklGIREKVLFTGYIsrKERLRLV 326
                                       567777875.559**999****66666.5456*******42222224444455468999*********87779999* PP

                                       HH-SEEEE--.-.--SHHHHHHHHTT-EEEE-TGGGTTT--.T.TSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  71 aaadvfvaPs.e.gfglkllEamaaglpvVatdvggiaevv.g.engllvppgdpealaeailrLl 132
                                       ++a +++ Ps e + ++++lEa  +g+pv    +++++ +  g +n  l+p+gd e l++   +L+
  gi|320101096|ref|YP_004176688.1| 327 RRAMLMLYPShEdSYSYAVLEATLLGTPVAGYGIPALQTYFgGlDNVRLAPEGDLEGLVQDAMDLI 392
                                       **********9559********************99888887656669**********99988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3047.72
//
Query:       gi|320101097|ref|YP_004176689.1|  [L=418]
Description: group 1 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-24   85.9   0.0    3.8e-24   85.1   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    6.5e-12   45.8   0.9    9.1e-12   45.3   0.2    1.6  2  Glyco_transf_4   Glycosyltransferase Family 4
    6.9e-11   42.7   0.0    1.3e-10   41.8   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
     0.0099   16.3   1.2      0.019   15.4   0.3    2.1  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.011   15.8   0.0       0.02   14.9   0.0    1.4  1  ALG11_N          ALG11 mannosyltransferase N-terminus
      0.015   15.7   0.0      0.033   14.6   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   1.3e-27   3.8e-24       9     161 ..     226     376 ..     223     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.3e-27
                                       TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES......STTHHHHHHHHHHHCTTCGGGEEEC CS
                   Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.....ngeeekelkklaeelelsdnviflge 80 
                                       +g+ne+++ i++vgr++ eK++d +ika+  l    +++ ++ ++G     n  ++++l+kla ++++  +++++++
  gi|320101097|ref|YP_004176689.1| 226 KGFNERDNSIVMVGRISSEKRHDDVIKAVGML----DDKPVVRVIGaltrgNLGYLAYLRKLASKHNV--RLEVYFN 296
                                       689***************************99....78899999999**99*****************..9999999 PP

                                       CHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  81 vsredleellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairkll 156
                                        +r  l e l +++++v+ +i E+fGi+++EAmaag pvi+   +g +++++  g  Gl +   ++e+l+e i  +l
  gi|320101097|ref|YP_004176689.1| 297 APRRTLAETLCSSKALVHAAIGEHFGIAVVEAMAAGAPVIVNReSGSYRDILGGGYYGLGY--SSIEELSESIYLIL 371
                                       9*99**************************************************9966544..46799999999999 PP

                                       HSHHH CS
                   Glycos_transf_1 157 edeel 161
                                       +d+ l
  gi|320101097|ref|YP_004176689.1| 372 HDSSL 376
                                       99844 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.2     3e-15   9.1e-12       1     169 [.      16     218 ..      16     219 .. 0.79
   2 ?   -2.6   0.0       1.6   4.9e+03      75      99 ..     312     335 ..     268     338 .. 0.59

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3e-15
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvv..tpgddgpleeev..elvvrvprvpl..pllkrllrslaflrrlrrllkre 71 
                                       vGG+e +  e +r L+ +G+ V++   t+   ++l+  v      ++ +  +  p   +l++   +++++ ++++ +
  gi|320101097|ref|YP_004176689.1|  16 VGGAELVKAEASRVLCNMGYSVVLAglTHVELRHLPVDVsaTGCMEFNYLLPwfPQALGLYQVHLASKAVEKAIRLH 92 
                                       79***********************65444444444444763333333333300333445566677889999***** PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrr.rlgiplVltvHglye.....................krllkarlkplsrllral 126
                                       +p +v + s+++ +  +l+ r+  + +++++  H+ly                      ++  k+++++++r ++a 
  gi|320101097|ref|YP_004176689.1|  93 RPCLVFIDSEGSRVIDGLKERMgFKLVKYIHFPHSLYLatrncsrtgsrvlslycrdalSYSRKYFSSMFWRTYWAT 169
                                       *************9999999976666666777777777*********************777777777777777776 PP

                    Glyco_transf_4 127 errl.........lrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       + ++         +++ad v ++Se+t+d lre+ygv++   +V++++v +e
  gi|320101097|ref|YP_004176689.1| 170 YLKVlestlpenpFQHADLVMVNSEYTRDLLRELYGVKA---RVVYPPVHIE 218
                                       66667888****************************997...******9876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                    Glyco_transf_4  75 vvHahspaalgaallalrrrlgipl 99 
                                       +vHa     +g a++ +++  g+p+
  gi|320101097|ref|YP_004176689.1| 312 LVHAAIGEHFGIAVVEAMA-AGAPV 335
                                       4555544444555555554.55555 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   4.5e-14   1.3e-10       2     132 ..     233     371 ..     232     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 4.5e-14
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---........HHHHHHHT..T-T.TEEEE---THHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprp......eeleelaa..gleerveftGfvedlaell 70 
                                       + i++vGr++  +k++d +++av  l +k+  + ++G  + +      + l++la+  +++ +v f   +  lae l
  gi|320101097|ref|YP_004176689.1| 233 NSIVMVGRIS-SEKRHDDVIKAVGMLDDKP-VVRVIGALT-RgnlgylAYLRKLASkhNVRLEVYFNAPRRTLAETL 306
                                       579******5.55**************775.578888432.1234455677766643555556777777788***** PP

                                       HH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGG.TTT--..TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  71 aaadvfvaPs..egfglkllEamaaglpvVatdvgg.iaevv..gengllvppgdpealaeailrLl 132
                                        +++ +v     e fg++++Eamaag pv++ + +g  ++++  g  gl  +  + e+l e i  +l
  gi|320101097|ref|YP_004176689.1| 307 CSSKALVHAAigEHFGIAVVEAMAAGAPVIVNRESGsYRDILggGYYGLGYS--SIEELSESIYLIL 371
                                       *********99*********************98762688777556666555..6777777766665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   6.3e-06     0.019     127     156 ..     183     212 ..      17     215 .. 0.78
   2 ?   -2.2   0.0       1.7     5e+03      76     101 ..     312     337 ..     262     346 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.3e-06
                   Glyco_trans_4_4 127 lrradavlvvseaeaeelra.lgvpadrvvv 156
                                       +++ad+v+v+se+ +++lr+ +gv  +rvv+
  gi|320101097|ref|YP_004176689.1| 183 FQHADLVMVNSEYTRDLLRElYGVK-ARVVY 212
                                       699*****************66665.67664 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                   Glyco_trans_4_4  76 vvhahsp.taglaarlarrrrgiplvv 101
                                       +vha    + g+a++ a  ++g+p++v
  gi|320101097|ref|YP_004176689.1| 312 LVHAAIGeHFGIAVVEAM-AAGAPVIV 337
                                       444443202333333333.66777766 PP

>> ALG11_N  ALG11 mannosyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   6.9e-06      0.02     107     209 .]      93     204 ..      67     204 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.9e-06
                           ALG11_N 107 lvpdvfidtmGyaftyplvkllagvkvvaYvHYP...tistdmlkrvkereaky..nnkeavakskllsllkllYyk 178
                                           vfid+ G      l +  +g k v Y+H+P    + t   +r  +r  +   +++ +++++ + s++  +Y+ 
  gi|320101097|ref|YP_004176689.1|  93 RPCLVFIDSEGSRVIDGLKER-MGFKLVKYIHFPhslYLATRNCSRTGSRVLSLycRDALSYSRKYFSSMFWRTYWA 168
                                       45679******9888777765.67**********4444677777777666655411334444556666777777887 PP

                           ALG11_N 179 lfallYslv.....gsladvvmvnssWTknhikslw 209
                                       +  ++ + +      ++ad+vmvns +T++ +++l+
  gi|320101097|ref|YP_004176689.1| 169 TYLKVLESTlpenpFQHADLVMVNSEYTRDLLRELY 204
                                       766666544233235789***********9999886 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.033      10      71 ..     320     382 ..     294     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                   Glyco_trans_1_2  10 spnlrlfEaaacGafaltdda.egleelftpgkevilfedleelaekiryllanpeerraiae 71 
                                        +   ++Ea+a+Ga++++++   ++++++  g  ++ +++ eel e i   l +  ++ +  e
  gi|320101097|ref|YP_004176689.1| 320 HFGIAVVEAMAAGAPVIVNREsGSYRDILGGGYYGLGYSSIEELSESIYLILHDSSLWTKYHE 382
                                       5666789************98899***********************9877777777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3125.04
//
Query:       gi|320101098|ref|YP_004176690.1|  [L=255]
Description: ParB domain-containing protein nuclease [Desulfurococcus mucosus DSM 2162]
Scores for 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   84.6   0.0      8e-24   84.0   0.0    1.3  1  DUF5603   Domain of unknown function (DUF5603)
    6.1e-13   48.9   0.0      1e-12   48.1   0.0    1.3  1  ParBc     ParB-like nuclease domain
    9.4e-06   24.7   0.0      0.098   11.5   0.0    2.1  2  DUF1015   Protein of unknown function (DUF1015)


Domain annotation for each model (and alignments):
>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.0   1.3e-27     8e-24       1     105 []     107     213 ..     107     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.3e-27
                                       --EEEEES-HHHHHHHHHHTT---EE-TTHHHH......HHCTSSSEEEES..SSEEEE--SHHHHHHHHHHHHHHH CS
                           DUF5603   1 twypaikgdlnklleelkkeglrveedkekeeklkd...eelgkiafvlvgkneksykiygsleeqkkvskvldkls 74 
                                       tw p i+gd+  +lee  + gl v e++   +   d   + l + +f+++g  + + +i g++e qk+vs+vl++l+
  gi|320101098|ref|YP_004176690.1| 107 TWLPGIIGDVKPVLEEAARRGLGVAECRYSVDTSGDidaKLLEESSFIVLG-RDLCRAISGGVEGQKIVSQVLNELN 182
                                       8**************************9887775541114467899*****.899********************** PP

                                       HTTSSEEEEESSHHHHHHHHHTTS-SEEEE- CS
                           DUF5603  75 legkielvyygekeealrdlekgkidylflr 105
                                       ++g ++lvyyge  eal+dl+ g + ylf+r
  gi|320101098|ref|YP_004176690.1| 183 MKGLFTLVYYGELSEALEDLKSGWLHYLFIR 213
                                       ******************************8 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   1.7e-16     1e-12       9      76 ..      33      98 ..      21     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.7e-16
                             ParBc  9 rpnplqprkdspekieelvasIkk.kGllqPiivrktr.qgryeiiaGerRlrAakrlglkevpvivlei 76
                                        n   ++   + +++el++ I++ + +  Pi+v++ +  ++y i++G++R+ A+k lg++++p+i+++ 
  gi|320101098|ref|YP_004176690.1| 33 V-NHEELV---DARLRELMDKIRSeNAVDMPIVVTPIPgTDKYLIVDGHHRWAAVKALGYRKIPCIIIDY 98
                                      3.333333...779*********955666**************************************985 PP

>> DUF1015  Protein of unknown function (DUF1015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   1.6e-05     0.098     201     221 ..      67      87 ..      28      92 .. 0.74
   2 !   11.4   0.0   1.8e-05      0.11     317     380 ..     173     236 ..     132     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.6e-05
                           DUF1015 201 adkklyIADGHHRyatalavr 221
                                        ++k++I DGHHR+a+ +a++
  gi|320101098|ref|YP_004176690.1|  67 GTDKYLIVDGHHRWAAVKALG 87 
                                       67899***********99986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 1.8e-05
                           DUF1015 317 llepilgiedprkderidyvhgleeavekvdsgeagvafllnptsveelfavadagevmPrKST 380
                                       +++++l+  +++   ++ y ++l+ea+e+++sg  ++ f+ +  ++e++++ +++g+v  +K+T
  gi|320101098|ref|YP_004176690.1| 173 IVSQVLNELNMKGLFTLVYYGELSEALEDLKSGWLHYLFIRKSLTKEDVMRYVRNGGVYAPKTT 236
                                       55555555555555667899*************88****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1868.09
//
Query:       gi|320101099|ref|YP_004176691.1|  [L=316]
Description: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-73  243.5   0.0    1.3e-72  242.9   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    8.9e-36  122.5   0.0    1.1e-35  122.3   0.0    1.0  1  2-Hacid_dh       D-isomer specific 2-hydroxyacid dehydrogenas
      2e-06   28.0   0.0      6e-05   23.3   0.0    2.3  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00019   21.7   0.2       0.82   10.0   0.0    3.1  3  Nitro_FeMo-Co    Dinitrogenase iron-molybdenum cofactor
     0.0018   17.9   0.0      0.013   15.1   0.0    2.2  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0059   16.7   0.0      0.015   15.3   0.0    1.6  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
     0.0069   16.6   0.6       0.54   10.5   0.0    3.4  4  TrkA_N           TrkA-N domain
     0.0075   16.3   0.0      0.017   15.2   0.0    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.014   15.9   0.0      0.076   13.6   0.0    2.2  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.022   15.6   0.0        0.1   13.4   0.0    2.2  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.029   14.6   0.0       0.38   11.0   0.0    2.7  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


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 !  242.9   0.0   7.7e-76   1.3e-72       1     178 []     111     287 ..     111     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 242.9 bits;  conditional E-value: 7.7e-76
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeee 76 
                                       ++l+++++r++a  d+++r gew  +k+  g el+gkt+Gi+G+GrIG++va++++ +f+m++i+yd++++++  e+
  gi|320101099|ref|YP_004176691.1| 111 VGLMISVARKIAFSDRRMRMGEW-PKKHAVGVELHGKTLGIVGAGRIGSTVARICRfGFNMNIIYYDPYRNEQL-EK 185
                                       689********************.9999*****************************************99776.99 PP

                                       HHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES- CS
                      2-Hacid_dh_C  77 elgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDv 153
                                       e+g+++v+l++ll+esD+vs+h+pltp+t+hlin+e+l++mkk+ailiNt+RG++vd++aL++aLk+g+iaga+lDv
  gi|320101099|ref|YP_004176691.1| 186 EVGARYVDLDTLLRESDVVSIHVPLTPQTQHLINEEKLRLMKKTAILINTSRGQVVDTNALVKALKEGWIAGAGLDV 262
                                       99*************************************************************************** PP

                                       -SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 154 feeeplpedspllelpnviltPHia 178
                                       feeeplp+ +pll l+nv+ltPHi+
  gi|320101099|ref|YP_004176691.1| 263 FEEEPLPKGHPLLGLENVVLTPHIG 287
                                       ***********************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 !  122.3   0.0   6.5e-39   1.1e-35       1     127 [.       9     312 ..       9     315 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 6.5e-39
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vl+ ++++e++le+l+++g+ev+v++e+ ++el++ +k+++alivrs+  v+++v+  +++L++iaragvG Dn+D+
  gi|320101099|ref|YP_004176691.1|   9 VLVASHIHEKALETLRANGFEVVVREEPGEDELASLIKGFHALIVRSKPLVSRRVIYSADSLRIIARAGVGLDNIDV 85 
                                       789999***********999********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       +aa+erGi V n+p++st svAEl+                                                    
  gi|320101099|ref|YP_004176691.1|  86 EAARERGIEVINAPASSTMSVAELAvglmisvarkiafsdrrmrmgewpkkhavgvelhgktlgivgagrigstvar 162
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|320101099|ref|YP_004176691.1| 163 icrfgfnmniiyydpyrneqlekevgaryvdldtllresdvvsihvpltpqtqhlineeklrlmkktailintsrgq 239
                                       ***************************************************************************** PP

                                       ................................................T-BHHHHHHHHHHHHHHHHHHHTTC CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ................................................aaTeeaqeniaeeaaenlvaflkge 127
                                                                                       a+T eaqe+++ e+ae++v+++k +
  gi|320101099|ref|YP_004176691.1| 240 vvdtnalvkalkegwiagagldvfeeeplpkghpllglenvvltphigASTVEAQERAGIEVAEKIVEYFKKH 312
                                       *********************************************************************9975 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.11   1.8e+02     102     133 ..      86     116 ..      81     130 .. 0.84
   2 !   23.3   0.0   3.7e-08     6e-05       2     106 ..     148     252 ..     147     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                                       HHHHHTT-EEEEEEEESHHHHHHHT-EEEEEE CS
                     NAD_binding_2 102 kelkekglkfldaPVSGGeegAekGtLsimvG 133
                                       ++++e+g+++++aP S +   Ae +   +m++
  gi|320101099|ref|YP_004176691.1|  86 EAARERGIEVINAPASSTMSVAELAV-GLMIS 116
                                       67899************999999888.88877 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.7e-08
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g++G G +Gs  a+ + + g+++ ++  ++ + e+l +e    + ++  l+++ dvv + v+ +++++++i++  l
  gi|320101099|ref|YP_004176691.1| 148 LGIVGAGRIGSTVAR-ICRFGFNMNIIYYDPYRNEQLEKEVGARYVDLDTLLRESDVVSIHVPLTPQTQHLINEeKL 223
                                       79*********9875.88999999999999999*****9999999999*************************9999 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelke 106
                                       + +kk +ili++s  ++ dt+ l k+lke
  gi|320101099|ref|YP_004176691.1| 224 RLMKKTAILINTSRGQVVDTNALVKALKE 252
                                       9*************************997 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 !   10.0   0.0   0.00051      0.82      54      91 ..       6      42 ..       2      46 .. 0.83
   2 ?   -0.7   0.0       1.1   1.8e+03      69      85 ..      86     103 ..      84     110 .. 0.72
   3 !    7.7   0.0    0.0027       4.5      56      80 ..     279     303 ..     276     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00051
                                      T-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHHH CS
                     Nitro_FeMo-Co 54 gvdvvivgkiGpralakleaagievykgaggtveealk 91
                                      g +v+++++i ++al+ l+a+g ev++ ++++ e+ l+
  gi|320101099|ref|YP_004176691.1|  6 GYRVLVASHIHEKALETLRANGFEVVV-REEPGEDELA 42
                                      6689**********************9.6666665555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                                       HHHCTTTSEEEES.-SSB CS
                     Nitro_FeMo-Co  69 akleaagievykg.aggt 85 
                                       ++ +++giev+ + a+ t
  gi|320101099|ref|YP_004176691.1|  86 EAARERGIEVINApASST 103
                                       567899*****9854444 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0027
                                       SEEEESSSCHHHHHHHCTTTSEEEE CS
                     Nitro_FeMo-Co  56 dvvivgkiGpralakleaagievyk 80 
                                       +vv++ +iG + +++ e+agiev +
  gi|320101099|ref|YP_004176691.1| 279 NVVLTPHIGASTVEAQERAGIEVAE 303
                                       79********************976 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.48   7.7e+02      30      56 ..       9      35 ..       5      48 .. 0.61
   2 !   15.1   0.0     8e-06     0.013       2      92 ..     143     233 ..     142     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.48
                                      EEEEE-TT-HHHHHHHHTT-EEEEHHH CS
                              IlvN 30 vvvglregsksvkkAkeegfevltvae 56
                                      v v+ + ++k +++ +++gfev+  +e
  gi|320101099|ref|YP_004176691.1|  9 VLVASHIHEKALETLRANGFEVVVREE 35
                                      556666666666666666666654444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8e-06
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHH.HHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqk.evy 77 
                                       l+gk++ ++G G  G + a+  r  g+++ +  ++  ++ +  ke g + ++++ + +++dvv i +P + q+ +++
  gi|320101099|ref|YP_004176691.1| 143 LHGKTLGIVGAGRIGSTVARICR-FGFNMNIIYYDPYRNEQLEKEVGARYVDLDTLLRESDVVSIHVPLTPQTqHLI 218
                                       789****************9988.89***99999999999****************************876641455 PP

                                       HHHTGGG--TT-EEE CS
                              IlvN  78 eeeiepnlkegkala 92 
                                       +ee    +k+ ++l 
  gi|320101099|ref|YP_004176691.1| 219 NEEKLRLMKKTAILI 233
                                       555556666666553 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.8   9.5e+03      40      56 ..      21      37 ..      10      54 .. 0.65
   2 !   15.3   0.0   9.4e-06     0.015      16     111 ..     138     237 ..     135     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.8
                                      HHHHHCT-EEEEE-S-H CS
                     AdoHcyase_NAD 40 aslkglGarvivtevdP 56
                                      ++l++ G  v+v e   
  gi|320101099|ref|YP_004176691.1| 21 ETLRANGFEVVVREEPG 37
                                      56777777777766544 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 9.4e-06
                                       HH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCT.T-EE--HHHCTTT-SEE...EE-S.S CS
                     AdoHcyase_NAD  16 atdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaame.Gfevvtleevvkkadiv...vttt.G 87 
                                       a  v l Gk+  ++G G +G   a+    +G  + +   dP    q   e G + v l+++++++d+v   v  t  
  gi|320101099|ref|YP_004176691.1| 138 AVGVELHGKTLGIVGAGRIGSTVARI-CRFGFNMNIIYYDPYRNEQLEKEvGARYVDLDTLLRESDVVsihVPLTpQ 213
                                       6678899*************988875.569*************9999887799***********9987333444426 PP

                                       SSSSB-HHHHCCS-TTEEEEE-SS CS
                     AdoHcyase_NAD  88 nkdiitlehlkkmkddaivcniGh 111
                                       ++ +i+ e+l+ mk++ai+ n   
  gi|320101099|ref|YP_004176691.1| 214 TQHLINEEKLRLMKKTAILINTSR 237
                                       789****************99865 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.59   9.6e+02      30      46 ..      16      32 ..       4      44 .. 0.69
   2 ?    1.2   0.0      0.26   4.2e+02      33      58 ..      84     109 ..      68     117 .. 0.85
   3 !   10.5   0.0   0.00033      0.54       3      48 ..     150     195 ..     148     201 .. 0.86
   4 ?   -2.8   0.0       4.4   7.2e+03      56      65 ..     295     304 ..     287     314 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.59
                                      SHHHHHHHHHTTSEEEE CS
                            TrkA_N 30 deerveelreeglevvv 46
                                       e+++e+lr++g+evvv
  gi|320101099|ref|YP_004176691.1| 16 HEKALETLRANGFEVVV 32
                                      46667777777777665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.26
                                       HHHHHHHTTSEEEES-TTSHHHHHHT CS
                            TrkA_N  33 rveelreeglevvvgdatdeevLeea 58 
                                        ve +re+g+ev+++ a+++  ++e+
  gi|320101099|ref|YP_004176691.1|  84 DVEAARERGIEVINAPASSTMSVAEL 109
                                       58999**********99998877766 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00033
                                       EES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES- CS
                            TrkA_N   3 iiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgd 48 
                                       i+G+Gr+G+++a+  + g  ++ +i  d+ r e+l++e  +++v  d
  gi|320101099|ref|YP_004176691.1| 150 IVGAGRIGSTVARICRFGF-NMNIIYYDPYRNEQLEKEVgARYVDLD 195
                                       9**************9998.599********9999988767777655 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 4.4
                                       HHTTGGGESE CS
                            TrkA_N  56 eeagiekada 65 
                                       e+agie a+ 
  gi|320101099|ref|YP_004176691.1| 295 ERAGIEVAEK 304
                                       4444444433 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     1e-05     0.017       9      99 ..     142     227 ..     135     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEE...EE- CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvv...isa 82 
                                       +l++k+  ++GaG++++ va+ +++ g++ + ++  +  r ++l +e+++    +++l+   +ll+e+dvv   +  
  gi|320101099|ref|YP_004176691.1| 142 ELHGKTLGIVGAGRIGSTVAR-ICRFGFN-MNIIYYDPYRNEQLEKEVGAR---YVDLD---TLLRESDVVsihVPL 210
                                       7999*************9987.6889999.******************766...66555...556666666222556 PP

                                       SSSSS-SB-HHHHHCCH CS
                      Shikimate_DH  83 taseepilekeeveeal 99 
                                       t  +++++++e+++ ++
  gi|320101099|ref|YP_004176691.1| 211 TPQTQHLINEEKLRLMK 227
                                       77888888888877554 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 ?   -1.1   0.0       1.8   2.9e+03      16      48 ..      21      50 ..       9      60 .. 0.75
   2 ?   13.6   0.0   4.7e-05     0.076       2      72 ..     148     211 ..     147     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
                                      HHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC- CS
                     F420_oxidored 16 sgllaagaqpheivvansrnpekaeelaeelgv 48
                                      + l a+g    e+vv  ++ ++++++l + + +
  gi|320101099|ref|YP_004176691.1| 21 ETLRANG---FEVVVREEPGEDELASLIKGFHA 50
                                      5677788...89999999999999888776664 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.7e-05
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpe 72 
                                       +gi+GaG++g+++a+ + + g    ++ ++   +p + e+l++e+g  +  vd  ++++e+dvv + v+ +
  gi|320101099|ref|YP_004176691.1| 148 LGIVGAGRIGSTVAR-ICRFG---FNMNII-YYDPYRNEQLEKEVG--ARYVDLDTLLRESDVVSIHVPLT 211
                                       89************9.99999...555545.679********9987..6667799*********9999864 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   6.2e-05       0.1       3      79 ..     148     217 ..     146     234 .. 0.77
   2 ?   -1.9   0.0       3.4   5.6e+03      74      83 ..     297     306 ..     254     315 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                                       EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHH CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheela 79 
                                        +i+GaG+igs  +    + +r+   + ++  d+ r e++ ++ g+  y dl+ ll+  e d+v++ +p + + ++ 
  gi|320101099|ref|YP_004176691.1| 148 LGIVGAGRIGSTVA----RICRFGFNMNIIYYDPYRNEQLEKEVGAR-YVDLDTLLR--ESDVVSIHVPLTPQTQHL 217
                                       69**********99....33344445567788888999999999988.*********..889999999985555554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                                       GHHHHHHHHH CS
                      GFO_IDH_MocA  74 theelakaal 83 
                                        + e+a++++
  gi|320101099|ref|YP_004176691.1| 297 AGIEVAEKIV 306
                                       3333333333 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.41   6.7e+02      27      80 ..       9      58 ..       3     113 .. 0.59
   2 ?   11.0   0.0   0.00023      0.38       2      42 ..     149     185 ..     148     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.41
                                      EEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG CS
                   Sacchrp_dh_NADP 27 itvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi 80
                                      + va+  +ek+ +   +++   fe +      +++ La+l+k+  +++  s p 
  gi|320101099|ref|YP_004176691.1|  9 VLVASHIHEKALE---TLRANGFEVVVREEPGEDE-LASLIKGFHALIVRSKPL 58
                                      5555555555333...3345555555555555555.777777765555444333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00023
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHC CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaa 42 
                                        i+GaG++G+ va+ +   f++  +i+  d+++++  +l +
  gi|320101099|ref|YP_004176691.1| 149 GIVGAGRIGSTVARICRFGFNM--NIIYYDPYRNE--QLEK 185
                                       69***************99999..99999998877..3332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2471.00
//
Query:       gi|320101100|ref|YP_004176692.1|  [L=384]
Description: class V aminotransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-37  128.4   0.0    3.5e-37  128.2   0.0    1.0  1  Aminotran_5    Aminotransferase class-V
    2.8e-05   23.5   0.0    4.5e-05   22.8   0.0    1.2  1  Aminotran_1_2  Aminotransferase class I and II
    0.00086   18.3   0.0     0.0013   17.7   0.0    1.2  1  GDC-P          Glycine cleavage system P-protein


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2   0.0   5.8e-41   3.5e-37       3     371 .]      22     367 ..      20     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 5.8e-41
                                       EBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHH CS
                       Aminotran_5   3 ldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlval 79 
                                       l+ a++   ++eVl+a++ +          +++h++ke ++  +++ +++a+++ a+++  ++  s++t  +++ ++
  gi|320101100|ref|YP_004176692.1|  22 LFTAGPVACFPEVLEAMRIQ----------QLSHRSKEYQELHRDTVKRLADFLLARKATVLLIPSSGTGFMEASIR 88 
                                       67788888888888888888..........99*************************96666666777778999999 PP

                                       HCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-..-TTEEEEEEESBETTTTE CS
                       Aminotran_5  80 slarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll..nektklvaithvsnvtGt 154
                                       ++   + p+ +++vt+++  +n+   +e+ +r g   +v+++  ++ + ++el+++l  n ++++v+it ++++tG+
  gi|320101100|ref|YP_004176692.1|  89 NA---VTPKGKVLVTVIGEFGNR--YREAVERNGRVPVVLEKPLGKPVLPEELDDALrkNRDVEAVTITYNETSTGV 160
                                       99...******************..777776766555577777777788********54478999************ PP

                                       B--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTS.STT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 155 iqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllg.PtGiGvlyvrkellekleplllggem 230
                                       ++p+ e++k++k++g l++vDa++a+g + i v+++g+D++++s++K +g P+G+ +  v++e+ ek++ +   g +
  gi|320101100|ref|YP_004176692.1| 161 LNPLRELAKVVKEHGKLLFVDAVSAMGAADIRVDDWGIDIVFASSQKAFGvPPGLAMAAVSEEVFEKAKSIPERGLY 237
                                       ***********************************************5555************************** PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHH.HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-C CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyl.eeigleaiekhekelaeyllerlkslpgvrlygpdkae 306
                                       ++  ++ e  +++ ++     Tp++++i gl+ al+++ + +g e+     +e ae+++ ++++l+   +++p    
  gi|320101100|ref|YP_004176692.1| 238 FDLLEIREFLVKQWST--P-TTPPIPQIAGLNVALRIVeKMGGRERWLGMYAERAERIRRGVQELGLKLFAEP---G 308
                                       ******8887555444..3.2*****************55567788889999***************999554...6 PP

                                       TCBSEEEEEE..TTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 307 rrasivsfnf..kgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                         + ++++++  +gv+   +   L+++gI++  G   +         ++t+R++ + y t+e++d+l
  gi|320101100|ref|YP_004176692.1| 309 YYSPTITVVYnpPGVKGPVIYEELRKRGIEIAKGYGKV--------KDETFRIGHMGYITSEDIDAL 367
                                       6666777766568*********************9999........89*****************97 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 !   22.8   0.0   7.5e-09   4.5e-05      19     250 ..      30     235 ..      22     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.5e-09
                                       HHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E CS
                     Aminotran_1_2  19 tlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgde 95 
                                        +pev++a++   + ++  +ey+  +   +  ++la+fl      + k+ + ++ +sG+g + + +  +   ++g++
  gi|320101100|ref|YP_004176692.1|  30 CFPEVLEAMRI-QQLSHRSKEYQELH--RDTVKRLADFLL-----ARKATVLLIPSSGTGFMEASIRNAV-TPKGKV 97 
                                       57788888876.88889999999888..888899******.....6677778888999999999999999.688888 PP

                                       EEEEESS-TH.HHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHH CS
                     Aminotran_1_2  96 ilvpdptyas.yknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleele 171
                                        +     +++ y ++++ +g   v  +  ++ +  +  e+l++al+++      +  + ++     tG++ +l el 
  gi|320101100|ref|YP_004176692.1|  98 LVTVIGEFGNrYREAVERNGRVPVVLE--KPLGKPVLPEELDDALRKNR----DVEAVTITYNETSTGVLNPLRELA 168
                                       888888898768999999999888888..89999************954....4689******************** PP

                                       HHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHH CS
                     Aminotran_1_2 172 klldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsr 248
                                       k+   +k+++ llfvD + a ++ +          v++   +++  s  KafG++   +++++++++v + ++++  
  gi|320101100|ref|YP_004176692.1| 169 KV---VKEHGKLLFVDAVSAMGAAD--------IRVDDWGIDIVFASSQKAFGVPP-GLAMAAVSEEVFEKAKSIPE 233
                                       **...***********987777777........344443336***********975.38888889999999998865 PP

                                       HH CS
                     Aminotran_1_2 249 pf 250
                                       ++
  gi|320101100|ref|YP_004176692.1| 234 RG 235
                                       55 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.1e-07    0.0013     192     265 ..     139     214 ..     112     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-07
                                       S-...S-EEEEEEEES-T.TSB----HHHHHHHHHTT-EEEE.EE-TTGGGTB--HHHHT-SEEEEE-TT.TT---G CS
                             GDC-P 192 vtdkekevagvlvqypnt.eGriedlkelvekakkkkslvvv.aadllaLtllkpPgelgaDivvGsaqr.fGvPlg 265
                                       +  k+++v +v + y +t +G +++l+el++ +k++  l+ v a+  +  + ++   ++g Div+ s+q+ fGvP g
  gi|320101100|ref|YP_004176692.1| 139 ALRKNRDVEAVTITYNETsTGVLNPLRELAKVVKEHGKLLFVdAVSAMGAADIRV-DDWGIDIVFASSQKaFGVPPG 214
                                       333799*********9983588999*********998766652667787777775.79**********9779***76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3067.08
//
Query:       gi|320101101|ref|YP_004176693.1|  [L=127]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1082.44
//
Query:       gi|320101102|ref|YP_004176694.1|  [L=69]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 515.66
//
Query:       gi|320101103|ref|YP_004176695.1|  [L=370]
Description: peptidase M24 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-59  200.4   0.1    3.6e-59  200.0   0.1    1.1  1  Peptidase_M24  Metallopeptidase family M24
    3.2e-16   60.2   0.0    5.8e-16   59.4   0.0    1.4  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 !  200.0   0.1     4e-63   3.6e-59       2     208 ..     152     353 ..     151     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 4e-63
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvl 78 
                                       ++r+a +i+ + ++ v +++  gvte+ela ++e++ ++r+g++++af+pi+a+ +n++++h  p+ r+l ++dl+l
  gi|320101103|ref|YP_004176695.1| 152 AVRRAVEITIKGIRVVQDNVADGVTEAELAGVFEER-VRREGVGKYAFEPIIAFKPNNSYPHTLPGRRRLGKRDLIL 227
                                       68********************************77.8999************************************ PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                       +d+g+++ g +sD tr++  G+++pe+r+ +eav+ea+ + i+ + pGv+++++ ++a +vle++gl++ f hglGH
  gi|320101103|ref|YP_004176695.1| 228 VDVGVKHGGRCSDLTRMITWGRPSPEERKSLEAVEEALWESIDHIYPGVKAGDVAETAVKVLEKHGLREKFIHGLGH 304
                                       ***************************************************************************** PP

                                       EESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 156 gvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       g+G  vh+  p++    ++++++e+Gmvft+Epg+yf+ g +gvr e++vlvt
  gi|320101103|ref|YP_004176695.1| 305 GIGVVVHEP-PYLR--IGNSTVIEPGMVFTVEPGVYFN-GAYGVRMEEDVLVT 353
                                       *******88.9986..4679****************75.999**********9 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   6.4e-20   5.8e-16       1     132 []       6     144 ..       6     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 6.4e-20
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.......TTSE CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaees......atvee 70 
                                       Rl +l  lmeekgl  l++ spen++Y tG+ +    +++ l v++ g+ +l+v+ l+y + + +       + v +
  gi|320101103|ref|YP_004176695.1|   6 RLGKLLSLMEEKGLQDLILVSPENIEYYTGV-EAVADAVMMLHVSRGGSiSLYVPLLEYYRYRDSLpgsievKAVTK 81 
                                       899****************************.77888888888******************9999999877655555 PP

                                       EEEEST...HSSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                      Creatinase_N  71 vveydd...pvealadllkellesekrvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                        ++ +d    +++++d++ke + s++rvgv++++  ++++ a+ + lp +++vd+se i++ R++
  gi|320101103|ref|YP_004176695.1|  82 TLKPSDvkaSEKDYPDIVKEIAGSSNRVGVDKSH--PGSLTAVLQSLPAERIVDVSEDIWRHRMI 144
                                       55555589899**********************8..99999999********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2404.55
//
Query:       gi|320101104|ref|YP_004176696.1|  [L=278]
Description: inositol monophosphatase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   58.6   0.0    8.8e-16   58.2   0.0    1.0  1  Inositol_P  Inositol monophosphatase family
    2.5e-08   33.7   0.0    3.9e-08   33.0   0.0    1.3  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   9.9e-20   8.8e-16       4     237 ..       6     238 ..       4     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 9.9e-20
                                       HHHHHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHH.HHHHSTTSEEEHHCHHHHCCCT CS
                        Inositol_P   4 evtkaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilea.laekfpshkilgeetlakgeks 79 
                                       ++ +a+ ++ a++ ++lre++++    ++ ++   + d+  ++d  +ee+++e+  ++ f++ +i +e ++ k    
  gi|320101104|ref|YP_004176696.1|   6 SIVDASRRILAGLKTLLREHYGDAYYGNVVGE-GVSGDVTRRIDLLAEEYVVEEfSRAGFNTWVISEEKGVYKLR-- 79 
                                       5677788889999999*****96666666666.5789*****************667777666666666666666.. PP

                                       .SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEE.......TTEEEEEEEEETTTTEEECEETTTEEEETCEEEEE CS
                        Inositol_P  80 eltedgltwivDPiDGTknFvrgipqvaVsigllv.......egkpvlGviaqPllgqlysaakgkGaflngeklpl 149
                                         +++++++++DP+DG  n++++ip   Vsi++++        ++++ Gv+a+ + +  +  ++gk   +ng++++ 
  gi|320101104|ref|YP_004176696.1|  80 --ERAEYIVLLDPLDGSLNYASQIPFSSVSIAVYKasdppplLHEAIYGVVASIFSDIQVEYVNGK-VLYNGRVFEQ 153
                                       ..7777*****************************88777777999*********99988877555.4589988887 PP

                                       CTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCH.EEEBESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHH CS
                        Inositol_P 150 srappiseallvtlfavssrkdtseasllekvesavsae.gvrsvgssalklaavaeGkadaylefg.rekkWDhAA 224
                                       + ++  +  + v+++ ++s+++ s    l+ +   ++   ++r +gs+al+  + a G +d +++ + r+   D+A 
  gi|320101104|ref|YP_004176696.1| 154 RAGK--NTGFKVASIYFDSVEELSI---LRDMFMNHTGGfKLRVMGSAALEATLAALGLIDYFISLTgRLRNTDVAL 225
                                       7777..6666677899999999998...7777666666688999**********************99********* PP

                                       HHHHHHHTTEEEE CS
                        Inositol_P 225 GeaileeaGGvvt 237
                                       ++a  e  GG+v+
  gi|320101104|ref|YP_004176696.1| 226 AVATAERLGGRVL 238
                                       **********986 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 !   33.0   0.0   4.4e-12   3.9e-08      48     120 ..      31     100 ..      13     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.4e-12
                            FBPase  48 lGlagaeNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSnidtn 120
                                       +G    e v Gd+ +++D+la+e ++e ++  +  + ++SEE+     l   ++++y+v++DPlDGS n   +
  gi|320101104|ref|YP_004176696.1|  31 YGNVVGEGVSGDVTRRIDLLAEEYVVEEFSRAGFNTWVISEEKGVY-KL--RERAEYIVLLDPLDGSLNYASQ 100
                                       5666778899***********************999****998654.44..699*************886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2003.83
//
Query:       gi|320101105|ref|YP_004176697.1|  [L=511]
Description: protein kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3566.57
//
Query:       gi|320101106|ref|YP_004176698.1|  [L=278]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1988.70
//
Query:       gi|320101107|ref|YP_004176699.1|  [L=420]
Description: aspartyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-85  286.2   0.1    3.7e-85  285.8   0.1    1.1  1  tRNA-synt_2   tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.023   14.2   0.2      0.066   12.7   0.1    1.7  2  tRNA-synt_2d  tRNA synthetases class II core domain (F)
      0.061   11.8   0.0       0.16   10.4   0.1    1.6  2  PaRep2b       PaRep2b protein


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 !  285.8   0.1   6.2e-89   3.7e-85       3     312 ..     103     413 ..     102     415 .. 0.93

  Alignments for each domain:
  == domain 1  score: 285.8 bits;  conditional E-value: 6.2e-89
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqsp 79 
                                       ++r+k+r+l +r++  ++++r+rs +++a r+yl++ngf+e++tP ++ +  e+ga+lF v+  e+  e + L qsp
  gi|320101107|ref|YP_004176699.1| 103 DTRIKYRWLLVRNPVEKAIFRVRSAMLAAAREYLSSNGFTEVQTPKIVAAGAEGGATLFRVQYFEN--EAY-LSQSP 176
                                       689**********************************************************44433..555.***** PP

                                       HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHH.HHHHHHHHHHHHHHHHHHCSCCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeed.imqvleelikslvkevlessakdief 155
                                       ql++++l+++ ++rv++i++ FRaE+ +t+rhl+E + i++e  fi+  + ++++le+l+ ++++ v +++a+++e 
  gi|320101107|ref|YP_004176699.1| 177 QLFKQMLMAG-FTRVYEITPYFRAEKYNTTRHLNESWGIDVEQGFINSLEdVLNTLENLVAYIIDYVSRNNAEELE- 251
                                       ********99.************************************9999****************777776665. PP

                                       TTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHH...HS--SEEEEEEEBGGGSTTCBBBSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 156 virrnskdlkkpfkrltykeaieklnei......gkdldkaderalvk...keknepvfvtdfPaelkpFyarkeed 223
                                       v   n +++++pfkrl ++ea+++l+++      ++dl+ + e+ l +   +++++ +f++ fP++ + Fy  +ee+
  gi|320101107|ref|YP_004176699.1| 252 VLGVNLRKPSTPFKRLRFQEAVDILRSEgievsdTEDLSDQAEKKLGEimaEKGHDLYFIVGFPWSSTGFYYMREEN 328
                                       55556679999***************99999999666666666655445559************************9 PP

                                       STTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 224 dkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllg 300
                                           t+++Dl ++g+E+++G +R++++e+l e l++kgl+   +++f++ylea++yG+pphgG+glG++Rl+m +lg
  gi|320101107|ref|YP_004176699.1| 329 -GVYTRKFDLDYRGLEIASGGQREHRYERLVEALREKGLN---PASFDFYLEAFKYGMPPHGGFGLGVERLLMRMLG 401
                                       .8**************************************...********************************** PP

                                       -SSGGGCSSS-X CS
                                       xxxxxxxxxxxx RF
                       tRNA-synt_2 301 sesIrdviaFPk 312
                                       +e++r++i+F +
  gi|320101107|ref|YP_004176699.1| 402 LENVREAILFVR 413
                                       **********87 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.51   3.1e+03      18      43 ..     124     149 ..     113     152 .. 0.77
   2 ?   12.7   0.1   1.1e-05     0.066     213     233 ..     387     407 ..     376     418 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHHHHCTTCEESSTTSE CS
                      tRNA-synt_2d  18 pltkvleeikeiflelgfeevegpev 43 
                                       + + +l   +e++ + gf+ev+ p++
  gi|320101107|ref|YP_004176699.1| 124 VRSAMLAAAREYLSSNGFTEVQTPKI 149
                                       5566778889999999****999987 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.1e-05
                                       EEEEEHHHHHHHHHT-SSGHH CS
                      tRNA-synt_2d 213 afGlGveRlamlkygieDiRe 233
                                       +fGlGveRl m ++g+e++Re
  gi|320101107|ref|YP_004176699.1| 387 GFGLGVERLLMRMLGLENVRE 407
                                       7*******************8 PP

>> PaRep2b  PaRep2b protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   2.7e-05      0.16      23      85 ..     198     262 ..     178     277 .. 0.76
   2 ?   -2.6   0.0      0.23   1.4e+03     209     237 ..     339     367 ..     329     369 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.7e-05
                           PaRep2b  23 dafkvvtreavkrkfgidlaydvrn..esffkkleeivtmvedyvyrnvaverglldtsgklPkv 85 
                                        a k  t   +++ +gid++ +  n  e + + le++v+++ dyv rn a e + l  + + P +
  gi|320101107|ref|YP_004176699.1| 198 RAEKYNTTRHLNESWGIDVEQGFINslEDVLNTLENLVAYIIDYVSRNNAEELEVLGVNLRKPST 262
                                       55555566788999******9998755799******************99999988888777665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.23
                           PaRep2b 209 skkievkyqprseasknaavnaLkarGlk 237
                                       ++ +e+    + e+  +  v+aL+++Gl+
  gi|320101107|ref|YP_004176699.1| 339 YRGLEIASGGQREHRYERLVEALREKGLN 367
                                       56788888888899999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3019.47
//
Query:       gi|320101108|ref|YP_004176700.1|  [L=106]
Description: PadR family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   27.0   0.0    4.8e-06   26.4   0.0    1.3  1  PadR             Transcriptional regulator PadR-like family
    8.5e-05   22.7   0.0    0.00011   22.3   0.0    1.3  1  PaaX             PaaX-like protein
     0.0002   21.7   0.2    0.00031   21.1   0.0    1.4  2  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.029   15.0   0.0      0.047   14.3   0.0    1.4  1  RTP              Replication terminator protein
      0.034   13.9   0.0       0.12   12.1   0.0    1.8  2  CobS_N           Cobaltochelatase CobS subunit N terminal


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 !   26.4   0.0   1.3e-09   4.8e-06       4      74 ..      27      91 ..      23      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.3e-09
                                      HHCC.S-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  4 llee.qpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      ll+e +p+  y+++ +l+e++ g +++ + ++Y++  r++++g++++++e      +  +Y +T++G ++++
  gi|320101108|ref|YP_004176700.1| 27 LLDEgKPLKAYDVKVRLRERF-G-IDPPAVTVYTVIYRMSRDGILARRQEG-----EETVYSVTERGVDAFR 91
                                      457779999***********7.7.8**********************9775.....689********99886 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.2e-08   0.00011      27      70 .]      41      86 ..      23      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.2e-08
                              PaaX 27 irllaelGises..lvRaalsRlakaGwlvrekegrrsfYrLsdkg 70
                                      +rl + +Gi+    +v + + R++++G l+r +eg + +Y+ +++g
  gi|320101108|ref|YP_004176700.1| 41 VRLRERFGIDPPavTVYTVIYRMSRDGILARRQEGEETVYSVTERG 86
                                      899999***965116789*************************996 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.9     1e+04      43      52 ..       8      17 ..       8      18 .. 0.76
   2 !   21.1   0.0   8.6e-08   0.00031       8      73 ..      23      91 ..      20     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.9
                                      HHHHHTTS-E CS
                   Penicillinase_R 43 rrLvkKglls 52
                                      +rLvkK  ++
  gi|320101108|ref|YP_004176700.1|  8 TRLVKKLTVE 17
                                      6899998775 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 8.6e-08
                                      HHHHHHHHS-.EEHHHHHHT--GG..G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXX CS
                   Penicillinase_R  8 vmeilwekge.atvkevveeleee..kelaysTVktllrrLvkKgllsrekegrafiYsplvseeeava 73
                                      + +il ++g+ +++ +v  +l e+   ++   TV t++ r+ + g+l+r++eg +++Ys + +  +a +
  gi|320101108|ref|YP_004176700.1| 23 IVKILLDEGKpLKAYDVKVRLRERfgIDPPAVTVYTVIYRMSRDGILARRQEGEETVYSVTERGVDAFR 91
                                      677888888889999*******9966778999***************************9876666555 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.047      12      89 ..      21      90 ..      10      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                      HHHHHHH..HTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHH CS
                               RTP 12 lylitlv..ekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkek 88
                                      ly+++++  e k+l ++ +  +l+++   +g  P+  ++y  +  ++ dgil rr+e +e        +Ys+t+ G ++
  gi|320101108|ref|YP_004176700.1| 21 LYIVKILldEGKPLKAYDVKVRLRER---FGIDPPAVTVYTVIYRMSRDGILARRQEGEE-------TVYSVTERGVDA 89
                                      77777653244555566666666665...599**********************998763.......457777777776 PP

                                      H CS
                               RTP 89 a 89
                                      +
  gi|320101108|ref|YP_004176700.1| 90 F 90
                                      6 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 ?   12.1   0.0   3.4e-05      0.12       7      20 ..      38      51 ..      34      52 .. 0.93
   2 ?   -1.4   0.0      0.56     2e+03      24      29 ..      87      92 ..      86      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                            CobS_N  7 DtkvsvRevFGIDs 20
                                      D kv  Re FGID+
  gi|320101108|ref|YP_004176700.1| 38 DVKVRLRERFGIDP 51
                                      889**********7 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.56
                            CobS_N 24 VpAFse 29
                                      V+AF++
  gi|320101108|ref|YP_004176700.1| 87 VDAFRK 92
                                      99**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 745.48
//
Query:       gi|320101109|ref|YP_004176701.1|  [L=386]
Description: L-myo-inositol-1-phosphate synthase [Desulfurococcus mucosus DSM 2162]
Scores for 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   67.6   0.0    1.9e-18   66.7   0.0    1.5  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
     0.0062   16.0   0.0       0.01   15.3   0.0    1.3  1  NAD_binding_5   Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
       0.09   12.8   0.1        1.4    9.0   0.1    2.4  1  Med26           TFIIS helical bundle-like domain


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.0   3.2e-22   1.9e-18       1     109 []     211     316 ..     211     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 3.2e-22
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEEEE-GG CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvikYvpy 77 
                                       G+T +   L+e++ er+ kv +i+++Ni+Gn+D+++l+ +er+ +Kk++Ks +v+di++++  +y        Y+++
  gi|320101109|ref|YP_004176701.1| 211 GATPFTADLLEHMYERNRKVIDIAQFNIGGNTDFLALNLPERNIMKKKTKSAIVEDILGYDAPNYI---RPTGYLEP 284
                                       99**********************************************************887662...445***** PP

                                       GTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                    Inos-1-P_synth  78 lgDsKvaldeieseiflggkntielkleceDS 109
                                       lgD+K+  + +e+  f+++k ++ + ++++DS
  gi|320101109|ref|YP_004176701.1| 285 LGDKKFVAMIVEYYSFGEFKDEFYVVMRINDS 316
                                       *******************************8 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-06      0.01     202     269 ..     155     334 ..     129     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
                                       xxxxxxxxxxxxxxxx.....xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..................... RF
                     NAD_binding_5 202 eispstiyavAaileg.....vpyingsPqntl.vpglvelAekkgvfiaGdDfKt..................... 251
                                       ++ +s+ ya+Aa l       v+++n  P+     pg ++l +++++++ GdD  t                     
  gi|320101109|ref|YP_004176701.1| 155 DLTASQTYAYAATLYSakyrpVAFVNAIPSPIAnDPGFIKLCSERRCVVFGDDGSTgatpftadllehmyernrkvi 231
                                       5789999***99886522223789*******9999*******************99888888888888888888888 PP

                                       ............................................................................. RF
                     NAD_binding_5 252 ............................................................................. 251
                                                                                                                    
  gi|320101109|ref|YP_004176701.1| 232 diaqfniggntdflalnlpernimkkktksaivedilgydapnyirptgyleplgdkkfvamiveyysfgefkdefy 308
                                       88888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                                       .........xxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 252 .........lLAaPlilDLvllveLaq 269
                                                 LA  l++DL ++  +a 
  gi|320101109|ref|YP_004176701.1| 309 vvmrindspALAG-LLVDLSRIGRIAL 334
                                       8888666665543.5666666655543 PP

>> Med26  TFIIS helical bundle-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00024       1.4      18      51 ..      56     123 ..      43     124 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00024
                                       HHSHHHHHHHHHH...................................-TTS-HHHHHHHHHHHHHHHH CS
                             Med26  18 stgIGkvVnalrk...................................hkhetaevktlAksLvekWkk 51 
                                       ++++Gk+V  l+k                                   ++ e++ ++   ++Lv++W++
  gi|320101109|ref|YP_004176701.1|  56 ESKVGKTVYELAKrdypgnhipgslkdivvsrgihlnsmkglpfkargRE-EDKGIEAAINELVDEWRS 123
                                       799********984544444444444444444554444445555454332.377777779999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2705.24
//
Query:       gi|320101110|ref|YP_004176702.1|  [L=78]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 597.22
//
Query:       gi|320101111|ref|YP_004176703.1|  [L=94]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 718.91
//
Query:       gi|320101112|ref|YP_004176704.1|  [L=226]
Description: adenylate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-51  173.1   0.0    4.6e-51  172.9   0.0    1.1  1  ADK              Adenylate kinase
    5.7e-24   85.1   0.0    8.8e-24   84.5   0.0    1.2  1  AAA_17           AAA domain
    2.5e-11   43.4   4.7      4e-11   42.7   4.7    1.3  1  ADK_lid          Adenylate kinase, active site lid
    1.1e-08   35.6   0.0    1.9e-08   34.9   0.0    1.3  1  AAA_18           AAA domain
     0.0015   18.9   0.6          2    8.6   0.0    2.7  3  Hydin_ADK        Hydin Adenylate kinase-like domain
  ------ inclusion threshold ------
      0.037   14.3   0.0      0.099   12.9   0.0    1.7  2  AAA_28           AAA domain
      0.071   13.3   0.0       0.15   12.2   0.0    1.5  1  AAA_33           AAA domain
      0.093   12.4   0.0         16    5.1   0.0    2.6  3  Thymidylate_kin  Thymidylate kinase


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.9   0.0   2.1e-54   4.6e-51       1     150 [.       5     186 ..       5     187 .. 0.99

  Alignments for each domain:
  == domain 1  score: 172.9 bits;  conditional E-value: 2.1e-54
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgf 77 
                                       l+GaPgaGKGt a+ + +ky+++h+stGd+lR+e+++g+elG ++k+++++g lvpde+v+++vk +le++d+++gf
  gi|320101112|ref|YP_004176704.1|   5 LIGAPGAGKGTYAQIIRDKYCIPHISTGDILREEIAKGSELGLKVKSYVERGLLVPDEIVIEVVKRRLEQPDAANGF 81 
                                       79*************************************************************************** PP

                                       EEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                               ADK  78 llDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg................................ 122
                                       +lDGfPRt+eqa+al++      +++d+v++l ++eev v+Rl+g                                
  gi|320101112|ref|YP_004176704.1|  82 VLDGFPRTLEQAKALDR-----MTRVDAVIHLVISEEVAVKRLSGrricpvcnrvyniyyepkpredekcdydgaql 153
                                       *****************.....789**************************************************** PP

                                       .....GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 .....DneetvkkRletykkqtkplidyykkkg 150
                                            D+++ v++R ++++++ +p+idyykk+g
  gi|320101112|ref|YP_004176704.1| 154 vrrpdDEPDVVRNRYKVFYETFAPIIDYYKKTG 186
                                       ******************************986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   3.9e-27   8.8e-24       1     122 [.       6     122 ..       6     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 3.9e-27
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       +G PG+GKgt+++ + +ky ++h+s+Gd+lree+++g +l  k +++++++ l++++ + + +++++++ ++ +g++
  gi|320101112|ref|YP_004176704.1|   6 IGAPGAGKGTYAQIIRDKYCIPHISTGDILREEIAKGsELgLKVKSYVERGLLVPDEIVIEVVKRRLEQPDAANGFV 82 
                                       69*******************************999964556889******************************** PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                       +dg+pr+ eqa++ld++++       +da+i l +++e+ ++r+  +
  gi|320101112|ref|YP_004176704.1|  83 LDGFPRTLEQAKALDRMTR-------VDAVIHLVISEEVAVKRLSGR 122
                                       *************999886.......699*********999999776 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 !   42.7   4.7   1.8e-14     4e-11       1      36 []     122     158 ..     122     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.8e-14
                                       EEE-TTT--EEETTTB-.-SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnp.PkveglCDkCGepLvqRsD 36 
                                       Rr+Cp C+r+Y++ + p P+++ +CD +G +Lv+R+D
  gi|320101112|ref|YP_004176704.1| 122 RRICPVCNRVYNIYYEPkPREDEKCDYDGAQLVRRPD 158
                                       9***********778777******************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   8.4e-12   1.9e-08       1     114 [.       3     123 ..       3     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 8.4e-12
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf......gvnlrd.vakenglllevdpealdeskrldedkldklldaleenssa 70 
                                       I+l G+pG+GK t a+ ++++  +      g++lr+ +ak ++l l v  +  +  ++ de + +++ + le+ ++ 
  gi|320101112|ref|YP_004176704.1|   3 IVLIGAPGAGKGTYAQIIRDKY-CiphistGDILREeIAKGSELGLKVKSYVERGLLVPDEIVIEVVKRRLEQPDA- 77 
                                       89****************9994.58977775555541444445555555555566677788888888888888655. PP

                            AAA_18  71 leegknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRg 114
                                          ++  v+dg++  le+++a d+ +     ++L  s+e+  +Rl+ R+
  gi|320101112|ref|YP_004176704.1|  78 ---ANGFVLDGFPRTLEQAKALDRMTrvdavIHLVISEEVAVKRLSGRR 123
                                       ...9999***************************************996 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 !    7.6   0.0    0.0019       4.2       2      44 ..       3      44 ..       2      55 .. 0.89
   2 !    8.6   0.0    0.0009         2     169     197 ..      57      85 ..      51      86 .. 0.93
   3 ?   -1.0   0.0      0.83   1.9e+03      29      54 ..     101     126 ..      96     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgnss 44
                                      i++ GaP +GK + a  +  kY +  ++  +++ e i++g+ +
  gi|320101112|ref|YP_004176704.1|  3 IVLIGAPGAGKGTYAQIIRDKYCIPHISTGDILREEIAKGS-E 44
                                      7889*********************************9875.3 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0009
                         Hydin_ADK 169 cvLPedllveIlsERlqlndCyrGvvfDg 197
                                       ++ P+++++e++  Rl+  d   G v+Dg
  gi|320101112|ref|YP_004176704.1|  57 LLVPDEIVIEVVKRRLEQPDAANGFVLDG 85 
                                       578*************************9 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.83
                         Hydin_ADK  29 tiDsvvleAisdgnssaGlrArelCa 54 
                                        +D v+   is++ +   l  r +C 
  gi|320101112|ref|YP_004176704.1| 101 RVDAVIHLVISEEVAVKRLSGRRICP 126
                                       58999999999999999999999995 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.4e-05     0.099       1      65 [.       2      69 ..       2      90 .. 0.66
   2 ?   -2.0   0.0       1.7   3.7e+03     103     121 ..      96     114 ..      82     120 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
                            AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaervleeqle 65
                                      +iv++G++++GK t ++ + ++  +p++   ++ re + ++++ g +   +ve+ l + ++++ e ++
  gi|320101112|ref|YP_004176704.1|  2 RIVLIGAPGAGKGTYAQIIRDKyCIPHIstGDILREEIAKGSELGLKVKSYVERGLLVPDEIVIEVVK 69
                                      79***************999775677776778888877777777766555556555555544444443 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                            AAA_28 103 aarekrydlvfllppapei 121
                                         r  r d+v++l  ++e+
  gi|320101112|ref|YP_004176704.1|  96 LDRMTRVDAVIHLVISEEV 114
                                       2235567888888877665 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   6.7e-05      0.15       2     118 ..       3     122 ..       3     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllss.dtlrrrlfg...tdqqsktdytr...vldr.lyqilnelarkalsag 70 
                                       ++l+G+pG+GK t+a+ +  k    ++s+ d+lr+ +++    + + k++  r   v d+ +++ ++++++    a+
  gi|320101112|ref|YP_004176704.1|   3 IVLIGAPGAGKGTYAQIIRDKYCIPHISTgDILREEIAKgseLGLKVKSYVERgllVPDEiVIEVVKRRLE-QPDAA 78 
                                       689*************9998888888887355555777666533334444444332333356666666663.46777 PP

                            AAA_33  71 rnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakR 118
                                       ++++ld   ++ ++ ++++++ r     ++++++  +ee++ +Rl  R
  gi|320101112|ref|YP_004176704.1|  79 NGFVLDGFPRTLEQAKALDRMTR----VDAVIHLVISEEVAVKRLSGR 122
                                       88888887777788888888888....568888999999999998888 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0073        16       3      47 ..       7      54 ..       7      72 .. 0.79
   2 ?    4.5   0.0     0.011        25     117     140 ..     101     124 ..      77     134 .. 0.81
   3 ?   -2.0   0.0       1.1   2.5e+03     150     181 ..     169     200 ..     154     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0073
                                      ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelll 47
                                      G  GaGK t a++++++++  +i+   +++    +g+e+G k++++++
  gi|320101112|ref|YP_004176704.1|  7 GAPGAGKGTYAQIIRDKYCIPHIStgdILREEIAKGSELGLKVKSYVE 54
                                      5569**************999888753344444578888888888877 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                                       E-SEEEEEESSHHHHHTSCCTTSS CS
                   Thymidylate_kin 117 kPdltflldvdpevalkRlakrde 140
                                       + d+++ l +++eva+kRl+ r+ 
  gi|320101112|ref|YP_004176704.1| 101 RVDAVIHLVISEEVAVKRLSGRRI 124
                                       6699***************99975 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHTTSTEEEEETTS-HHHH CS
                   Thymidylate_kin 150 dflrkvrerylelakederiliidasksieev 181
                                       +++ ++ +   + +k+++r++ +d ++s++ev
  gi|320101112|ref|YP_004176704.1| 169 KVFYETFAPIIDYYKKTGRLIEVDSNRSVREV 200
                                       55555555566677778899999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 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:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1642.95
//
Query:       gi|320101113|ref|YP_004176705.1|  [L=168]
Description: transcriptional regulator AsnC-type-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   26.6   0.3    6.2e-06   25.7   0.3    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
    4.5e-05   23.2   0.6    7.6e-05   22.5   0.6    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.001   19.0   4.6      0.042   13.8   2.3    2.4  2  KOW            KOW motif
     0.0066   16.2   0.0      0.011   15.6   0.0    1.3  1  HTH_10         HTH DNA binding domain
  ------ inclusion threshold ------
       0.01   15.5   0.1      0.019   14.6   0.1    1.4  1  GntR           Bacterial regulatory proteins, gntR family
      0.013   15.4   0.2      0.034   14.0   0.1    1.7  1  MarR_2         MarR family
       0.02   14.8   0.1      0.057   13.3   0.1    1.7  2  TrmB           Sugar-specific transcriptional regulator TrmB
      0.038   13.9   0.1      0.063   13.2   0.1    1.3  1  MarR           MarR family
      0.046   13.8   0.0      0.079   13.0   0.0    1.4  1  DUF2089        Protein of unknown function (DUF2089)
      0.064   13.2   0.2       0.11   12.5   0.2    1.3  1  HTH_11         HTH domain
      0.098   12.3   0.1       0.16   11.6   0.1    1.3  1  HTH_50         Helix-turn-helix domain
       0.17   12.0   0.0       0.25   11.4   0.0    1.2  1  HTH_Mga        M protein trans-acting positive regulator (MGA
       0.18   11.6   0.1       0.35   10.7   0.1    1.5  1  LexA_DNA_bind  LexA DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.3   4.5e-09   6.2e-06      12      47 ..      12      47 ..      10      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 4.5e-09
                            HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      L +npris+r LA +lg+S  +++ rl++L  +GlI
  gi|320101113|ref|YP_004176705.1| 12 LVENPRISIRRLANELGVSYIALRDRLRKLSHKGLI 47
                                      569***************************999998 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 !   22.5   0.6   5.5e-08   7.6e-05      12      41 ..      12      41 ..       8      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.5e-08
                     HTH_AsnC-type 12 LqedaRisyaeLAervGlSestvlrRvrrL 41
                                      L e++Ris ++LA ++G+S  + + R+r+L
  gi|320101113|ref|YP_004176705.1| 12 LVENPRISIRRLANELGVSYIALRDRLRKL 41
                                      889**************************9 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.016        22      13      30 ..      58      86 ..      57      87 .. 0.80
   2 !   13.8   2.3   3.1e-05     0.042       2      26 ..      94     118 ..      93     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                                      TTCEEEEEEEETTT...........TEEE CS
                               KOW 13 kGktGkVvkvdqhk...........vrVf 30
                                      +G ++ Vv+v  h+           +rV+
  gi|320101113|ref|YP_004176705.1| 58 AGSVAAVVRVHGHRvddmlskasrcNRVI 86
                                      7999**********777777777777765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.1e-05
                                       TSEEEESSSTTTTCEEEEEEEETTT CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhk 26 
                                       G+ V V+ G++kG++  V +v +++
  gi|320101113|ref|YP_004176705.1|  94 GEAVLVIYGRDKGDIVSVIDVLRNN 118
                                       899*******************999 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.7e-06     0.011      23      48 ..      17      42 ..      14      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.7e-06
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkae 48
                                      r++++ LA+elG+s  +l ++Lrk  
  gi|320101113|ref|YP_004176705.1| 17 RISIRRLANELGVSYIALRDRLRKLS 42
                                      799********************966 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.3e-05     0.019      22      55 ..      16      48 ..       8      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                                      SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 22 dkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                       ++ s r La e+gVs   +R  Lr+L+ +gl+ 
  gi|320101113|ref|YP_004176705.1| 16 PRI-SIRRLANELGVSYIALRDRLRKLSHKGLIS 48
                                      577.99**************************85 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.4e-05     0.034      16      52 ..      14      48 ..       9      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                                      CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                       +p+  ++++ la +lg+s  a+  +l++L+ +GL+ 
  gi|320101113|ref|YP_004176705.1| 14 ENPR--ISIRRLANELGVSYIALRDRLRKLSHKGLIS 48
                                      5665..9****************************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 ?   13.3   0.1   4.1e-05     0.057      16      53 ..      11      48 ..      10      55 .. 0.95
   2 ?   -2.1   0.0       2.8   3.8e+03      25      46 ..      58      79 ..      49      87 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-05
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      +L+++ + +++ +a+elgv++    + Lr+L+ kGl+ 
  gi|320101113|ref|YP_004176705.1| 11 KLVENPRISIRRLANELGVSYIALRDRLRKLSHKGLIS 48
                                      699*********************************95 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                                      HCHHCCCTTSSCHCHHHHHHHH CS
                              TrmB 25 adeiaeelgvprskvYevLrsL 46
                                      a  +a  + v   +v ++L++ 
  gi|320101113|ref|YP_004176705.1| 58 AGSVAAVVRVHGHRVDDMLSKA 79
                                      6667777778888888888775 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   4.6e-05     0.063      11      50 ..      11      50 ..       7      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                      HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      +l e++ +s+  La+ lgvs  ++   l++L +kGli+ +
  gi|320101113|ref|YP_004176705.1| 11 KLVENPRISIRRLANELGVSYIALRDRLRKLSHKGLISFT 50
                                      677999*******************************976 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.7e-05     0.079      49      74 ..      17      42 ..       1      50 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                           DUF2089 49 rGnlkevekelgisYpTvrnrldeil 74
                                      r +++++++elg+sY ++r rl ++ 
  gi|320101113|ref|YP_004176705.1| 17 RISIRRLANELGVSYIALRDRLRKLS 42
                                      5689******************9986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   7.7e-05      0.11      14      43 ..      15      45 ..       6      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.7e-05
                            HTH_11 14 gp.isgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      +p is+ +LA eL+vS  + r ++++L+ +g
  gi|320101113|ref|YP_004176705.1| 15 NPrISIRRLANELGVSYIALRDRLRKLSHKG 45
                                      334********************99999888 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00012      0.16      25      46 ..      19      40 ..       9      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                            HTH_50 25 StRklAkrLGvShtaianklrk 46
                                      S+R lA  LGvS  a   +lrk
  gi|320101113|ref|YP_004176705.1| 19 SIRRLANELGVSYIALRDRLRK 40
                                      9************999999997 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.25      14      53 ..      12      48 ..       4      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                           HTH_Mga 14 LteneksltldelakeLglseltlqsdiseLnelFpeels 53
                                      L e ++++++  la+eLg s  +l++++++L    ++ +s
  gi|320101113|ref|YP_004176705.1| 12 LVE-NPRISIRRLANELGVSYIALRDRLRKLS--HKGLIS 48
                                      778.*************************997..555555 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 ?   10.7   0.1   0.00025      0.35      27      58 ..      19      49 ..       9      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyier 58
                                      sir +a++lg++   a   +L++L+ KG+i  
  gi|320101113|ref|YP_004176705.1| 19 SIRRLANELGVS-YIALRDRLRKLSHKGLISF 49
                                      899*******97.99**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1276.86
//
Query:       gi|320101114|ref|YP_004176706.1|  [L=286]
Description: aldo/keto reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-52  176.4   0.1    5.9e-50  170.1   0.1    2.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.1   3.3e-54   5.9e-50       2     290 ..      36     283 ..      35     286 .] 0.93

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 3.3e-54
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       +glGt  + +      e+a+e+  +al +G+n++DtAe+Y +g++ee++G+++k+  + r+ v+i+tK+      ++
  gi|320101114|ref|YP_004176706.1|  36 IGLGTYGIRN-----YEKAFEAFTYALTHGVNLVDTAEMYDTGRAEEFVGRVVKA--VGRDGVFITTKM-----LPN 100
                                       7788887775.....8***************************************..************.....555 PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kkkkk 154
                                       +   +e+i+++ ee l+rLg++yvDl+l+H+p+  lp i  +++ +e l + G+ r+iGvSnf+ ++l++a ++++ 
  gi|320101114|ref|YP_004176706.1| 101 RLEDRESIVKAAEEALRRLGVSYVDLYLIHWPNERLP-ISVQVRNFEVLAERGLTRYIGVSNFEPAMLREAiESTGR 176
                                       666678*******************************.*************************************** PP

                                       --EEEEE-B-BTT.-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHH CS
                      Aldo_ket_red 155 vkivavqveynll.releeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaae 230
                                       ++iv++qv+y++  r+  e++ll++c + ++ l ay+pl +G+                                ++
  gi|320101114|ref|YP_004176706.1| 177 HEIVVNQVHYSVInRHYVEKELLPFCIERKITLQAYTPLERGSVV-----------------------------INS 224
                                       *************9******************************9.............................789 PP

                                       HHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHH CS
                      Aldo_ket_red 231 elselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeld 290
                                       +++++a+++g+++ q+al+y++s   ++++ip+a n+ +++++l++  + +  e++++l+
  gi|320101114|ref|YP_004176706.1| 225 AVKKMAEKYGKTPVQVALNYLIS-HSNVVAIPKAENMVHVKEILGSIGWWMRVEDLEYLR 283
                                       **********************6.566789**************9987766666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2188.00
//
Query:       gi|320101115|ref|YP_004176707.1|  [L=176]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-10   40.0   0.1    7.9e-10   39.3   0.1    1.3  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.1   4.4e-14   7.9e-10       2      84 ..      15     118 ..      14     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 4.4e-14
                          CxxCxxCC   2 CkeCgaCCk.elkvklteedlerlkaaevaeeeeeskkiak..............adgrCvfldeetk..lCkiYee 61 
                                       C + g+CC+   +v lt+ d+ r++++   e    + +++                  rCvfl+ e+    C+iY  
  gi|320101115|ref|YP_004176707.1|  15 CIRSGTCCRsGPNVALTAFDICRIARFLNTEWRGLRGRFIYvviadqipipvlrgISDRCVFLKTENSvpSCSIYPA 91 
                                       9999****9778999*********9999955544444443379************9********999999******* PP

                          CxxCxxCC  62 Rpkicrlfpas....ekeellaraetC 84 
                                       Rp  crlfp+     + ++ +++++ C
  gi|320101115|ref|YP_004176707.1|  92 RPMRCRLFPFIpvspSIRDKMYVSRIC 118
                                       **********98888777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1415.08
//
Query:       gi|320101116|ref|YP_004176708.1|  [L=45]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.019   15.3   0.5      0.025   14.9   0.5    1.2  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> 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 ?   14.9   0.5   1.4e-06     0.025       7      17 .]      34      44 ..      34      44 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-06
                     EndIII_4Fe-2S  7 kCeaCPLaDlC 17
                                      kC +CPL  +C
  gi|320101116|ref|YP_004176708.1| 34 KCSRCPLKGFC 44
                                      8********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 341.17
//
Query:       gi|320101117|ref|YP_004176709.1|  [L=208]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1540.13
//
Query:       gi|320101118|ref|YP_004176710.1|  [L=329]
Description: regulatory protein IclR [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-10   38.1   0.1    1.6e-09   37.2   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.2e-09   37.3   0.0    3.5e-09   36.6   0.0    1.3  1  HTH_20          Helix-turn-helix domain
      6e-09   35.7   0.0    1.6e-08   34.3   0.0    1.6  1  MarR_2          MarR family
    2.4e-08   33.6   0.0    4.4e-08   32.8   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    2.4e-05   24.7   0.1    5.3e-05   23.6   0.1    1.5  1  HTH_27          Winged helix DNA-binding domain
    2.6e-05   24.1   0.0    5.1e-05   23.1   0.0    1.4  1  MarR            MarR family
    0.00014   21.3   0.0    0.00023   20.7   0.0    1.2  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
    0.00029   20.8   0.1    0.00062   19.7   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00075   19.3   0.0     0.0035   17.2   0.0    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0011   19.1   0.0     0.0022   18.2   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain
     0.0011   19.1   0.0      0.028   14.6   0.0    2.5  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0015   18.4   0.4     0.0059   16.5   0.1    2.0  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.003   17.5   0.1      0.014   15.4   0.0    2.0  2  HTH_36          Helix-turn-helix domain
     0.0074   16.2   0.0      0.018   15.0   0.0    1.7  1  HTH_11          HTH domain
     0.0077   15.7   0.1      0.014   14.9   0.1    1.4  1  Sigma70_r4      Sigma-70, region 4
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.036   14.2   0.0    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.032   14.1   0.0      0.062   13.1   0.0    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.042   13.9   0.1      0.072   13.1   0.1    1.4  1  HTH_29          Winged helix-turn helix
       0.11   13.1   2.1        2.5    8.7   0.0    2.7  2  MucBP_2         Mucin binding domain
       0.12   12.4   0.0       0.21   11.7   0.0    1.3  1  HemN_C          HemN C-terminal domain
       0.14   12.2   0.0       0.29   11.1   0.0    1.6  1  HTH_1           Bacterial regulatory helix-turn-helix protein
       0.14   12.5   0.0       0.31   11.4   0.0    1.5  1  Rrf2            Transcriptional regulator
       0.16   12.1   0.1       0.37   11.0   0.1    1.5  1  HTH_28          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 !   37.2   0.1     2e-12   1.6e-09       3      47 ..     255     301 ..     253     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2e-12
                            HTH_24   3 etdrkILelLqk..nprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                          r I+++L +    +++q+e+  r+g ++s v+rr+krLeeeG+I
  gi|320101118|ref|YP_004176710.1| 255 PVSRSIIRILGEagGEGLTQAEITNRTGAPKSSVSRRIKRLEEEGYI 301
                                       56789999**9976666*****************************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 !   36.6   0.0   4.4e-12   3.5e-09       4      61 .]     249     308 ..     246     308 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.4e-12
                                       HHHHS-HHHHHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20   4 aeALahPvRrrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       a++L +Pv r i r L  a++eglt +e+  r + +k+++s++++ Lee g++ v r+g+
  gi|320101118|ref|YP_004176710.1| 249 ADVLNDPVSRSIIRILgeAGGEGLTQAEITNRTGAPKSSVSRRIKRLEEEGYIAVDRTGK 308
                                       789999***************************************************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0     2e-11   1.6e-08       4      52 ..     257     302 ..     254     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2e-11
                                       -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2   4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52 
                                       ++++ r+L++ g ++   lt++e++ r+g +ks+vsr++krL++ G++ 
  gi|320101118|ref|YP_004176710.1| 257 SRSIIRILGEAGGEG---LTQAEITNRTGAPKSSVSRRIKRLEEEGYIA 302
                                       556667777776666...9****************************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 !   32.8   0.0   5.7e-11   4.4e-08       8      51 ..     260     304 ..     258     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 5.7e-11
                                       HHCT-CTTBSS.-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR   8 iLdalaeapqe.ltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       i+++l+ea++e lt +e+ +rtg pkS+v+R ++ L+e+Gy+  d
  gi|320101118|ref|YP_004176710.1| 260 IIRILGEAGGEgLTQAEITNRTGAPKSSVSRRIKRLEEEGYIAVD 304
                                       8999****99966****************************9766 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   6.7e-08   5.3e-05      12      68 .]     264     318 ..     256     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.7e-08
                            HTH_27  12 ir.hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       ++   +++ ++a++  r+   +s++s  +k+L+e G++   + ++ +++  ++lTdkG
  gi|320101118|ref|YP_004176710.1| 264 LGeAGGEGLTQAEITNRTGAPKSSVSRRIKRLEEEGYI---AVDRTGKYNYLKLTDKG 318
                                       44556788999***************************...44456777********9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.5e-08   5.1e-05       7      48 ..     259     302 ..     255     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.5e-08
                                       HHHHHHHHSTT..EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   7 viLrilyeqgp..lsvseLakklgvskstvtrvldrLekkGlie 48 
                                       +i+ril e g+  l+++e+ ++ g  ks+v+r ++rLe++G+i 
  gi|320101118|ref|YP_004176710.1| 259 SIIRILGEAGGegLTQAEITNRTGAPKSSVSRRIKRLEEEGYIA 302
                                       57889999988779999*************************96 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 !   20.7   0.0   2.9e-07   0.00023      93     134 ..     262     303 ..     256     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.9e-07
                                       HHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEE CS
                     RNA_pol_Rpc34  93 siIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiks 134
                                        i  e+G eG  +++i+++++ +ks v + +k Le ++yi+ 
  gi|320101118|ref|YP_004176710.1| 262 RILGEAGGEGLTQAEITNRTGAPKSSVSRRIKRLEEEGYIAV 303
                                       56779***********************************85 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   7.9e-07   0.00062      22      54 ..     272     305 ..     257     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.9e-07
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis.rg 54 
                                       ltq+e+ ++ G+  ++vsr +++L++eg+i   +
  gi|320101118|ref|YP_004176710.1| 272 LTQAEITNRTGAPKSSVSRRIKRLEEEGYIAvDR 305
                                       8*****************************9633 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.6     2e+03       7      19 ..     232     244 ..     228     246 .. 0.84
   2 !   17.2   0.0   4.5e-06    0.0035       4      45 ..     257     301 ..     254     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.6
                                       HHHHHTTSSEEHH CS
                             HTH_5   7 ILklLaegelcvc 19 
                                       IL+l  +++++++
  gi|320101118|ref|YP_004176710.1| 232 ILYLILRRPKSIG 244
                                       9999999*99986 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.5e-06
                                       HHHHHHHHTT..SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   4 RlkILklLae..ge.lcvcelaeelglsqstvShHLkkLreaGLV 45 
                                        + I+++L e  ge l+  e+++ +g ++s vS+  k+L+e+G++
  gi|320101118|ref|YP_004176710.1| 257 SRSIIRILGEagGEgLTQAEITNRTGAPKSSVSRRIKRLEEEGYI 301
                                       5678899988888889***************************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 !   18.2   0.0   2.8e-06    0.0022      13      71 ..     270     324 ..     259     327 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-06
                            HTH_34  13 deadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71 
                                       +  + +e+ + ++a ++  s  +k Le+ gYi vd + k +     l++T++G ea+ k
  gi|320101118|ref|YP_004176710.1| 270 EGLTQAEITNRTGAPKSSVSRRIKRLEEEGYIAVDRTGKYN----YLKLTDKGVEAYRK 324
                                       566788999**************************998777....99********9976 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.47   3.7e+02       3      17 ..     150     164 ..     149     189 .. 0.76
   2 !   14.6   0.0   3.6e-05     0.028      24      54 ..     273     303 ..     263     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.47
                                       -HHHHHHHHHHHHHH CS
                    Fe_dep_repress   3 vestEdYLetIYtls 17 
                                       ++s E+YL  +Y + 
  gi|320101118|ref|YP_004176710.1| 150 SPSVEMYLLGVYNAT 164
                                       6789********986 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.6e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkLekdGyvey 54 
                                       +++++  r +  +ssVs  +k+Le++Gy+ +
  gi|320101118|ref|YP_004176710.1| 273 TQAEITNRTGAPKSSVSRRIKRLEEEGYIAV 303
                                       567888888899****************976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   2.4e+03      17      47 ..      97     127 ..      90     129 .. 0.82
   2 !   16.5   0.1   7.6e-06    0.0059      22      62 ..     271     311 ..     269     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                                       HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHH CS
                              TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLe 47 
                                       L+++   t +    +++v+  + Y ++++L 
  gi|320101118|ref|YP_004176710.1|  97 LVEYNDTTGYASITAVNVSSVTMYFSVSNLT 127
                                       6788888888888899999999999999986 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.6e-06
                                       CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                              TrmB  22 patadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62 
                                        +t  ei +++g p+s+v + +++Le+ G++ + +  ++ Y
  gi|320101118|ref|YP_004176710.1| 271 GLTQAEITNRTGAPKSSVSRRIKRLEEEGYIAVDRTGKYNY 311
                                       67999**************************9998665544 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.1   2.4e+03       4      15 ..     227     238 ..     227     241 .. 0.84
   2 !   15.4   0.0   1.8e-05     0.014      26      55 .]     272     301 ..     257     301 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.1
                            HTH_36   4 spsaklllgsla 15 
                                       s +a++l+++l+
  gi|320101118|ref|YP_004176710.1| 227 SAVAIILYLILR 238
                                       56899****997 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.8e-05
                            HTH_36  26 psqetlakrlglsknTvsraikeLeqlGyi 55 
                                        +q+ + +r+g  k++vsr ik Le+ Gyi
  gi|320101118|ref|YP_004176710.1| 272 LTQAEITNRTGAPKSSVSRRIKRLEEEGYI 301
                                       5899*************************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.3e-05     0.018       3      44 ..     258     301 ..     256     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                            HTH_11   3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg.v 44 
                                       ++i+++L ea g  ++ +e+  +++  ++ v r+Ik+Lee g +
  gi|320101118|ref|YP_004176710.1| 258 RSIIRILGEAGGEgLTQAEITNRTGAPKSSVSRRIKRLEEEGyI 301
                                       789***************************************44 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.8e-05     0.014      18      43 ..     269     294 ..     254     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekr 43 
                                       geglT++EI +r g +++ V++++kr
  gi|320101118|ref|YP_004176710.1| 269 GEGLTQAEITNRTGAPKSSVSRRIKR 294
                                       8**********************998 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 ?   14.2   0.0   4.7e-05     0.036       7      49 ..     260     302 ..     255     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                    B-block_TFIIIC   7 lLelIassRysGitqsdLakeskqdprslfyrlksLekkgLIv 49 
                                       +  +++ ++ +G+tq ++ + ++  ++s+  r+k Le+ g+I 
  gi|320101118|ref|YP_004176710.1| 260 IIRILGEAGGEGLTQAEITNRTGAPKSSVSRRIKRLEEEGYIA 302
                                       5667899999*******************************96 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.9e-05     0.062       2      42 .]     254     296 ..     254     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-05
                     HTH_AsnC-type   2 DeiDrkILeaLqed..aRisyaeLAervGlSestvlrRvrrLe 42 
                                       D + r I+++L e     ++ ae+  r+G   s v rR++rLe
  gi|320101118|ref|YP_004176710.1| 254 DPVSRSIIRILGEAggEGLTQAEITNRTGAPKSSVSRRIKRLE 296
                                       67789999999999877899**********************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 ?   13.1   0.1   9.2e-05     0.072      10      57 ..     266     315 ..     259     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-05
                            HTH_29  10 eGvs...tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrl 57 
                                       e+++   t ++i  ++g  +++v r +kr ee+G  a ++  ++ ++ ++ 
  gi|320101118|ref|YP_004176710.1| 266 EAGGeglTQAEITNRTGAPKSSVSRRIKRLEEEGYIAVDR-TGKYNYLKLT 315
                                       4444447***************************766654.3333443344 PP

>> MucBP_2  Mucin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.15   1.2e+02      37      57 ..      87     107 ..      39     125 .. 0.72
   2 ?    8.7   0.0    0.0032       2.5      12      54 ..     268     309 ..     259     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.15
                           MucBP_2  37 ikaleaqgYvlvssdgfpagt 57 
                                        + ++a+gY lv+ +++++ +
  gi|320101118|ref|YP_004176710.1|  87 YTGYPATGYLLVEYNDTTGYA 107
                                       4799********766665554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0032
                           MucBP_2  12 tnktltddtltGktgetisYstadtikaleaqgYvlvssdgfp 54 
                                       +++ lt+ ++t  tg++ s s +  ik le++gY  v+ +g  
  gi|320101118|ref|YP_004176710.1| 268 GGEGLTQAEITNRTGAPKS-SVSRRIKRLEEEGYIAVDRTGKY 309
                                       6778899999999999999.8899************9766655 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.21      19      65 ..     270     319 ..     269     320 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                            HemN_C  19 eGldlaafeqrfgldleellaaaleklqeqGLLeldg....grlrltprGr 65 
                                       eGl  a+++ r+g +   ++   +++l+e+G++  d     ++l+lt++G+
  gi|320101118|ref|YP_004176710.1| 270 EGLTQAEITNRTGAP-KSSVSRRIKRLEEEGYIAVDRtgkyNYLKLTDKGV 319
                                       7889999*******8.6777788*************999999999999995 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 ?   11.1   0.0   0.00037      0.29      24      59 ..     282     318 ..     278     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                                       TS-HHHHHHHHHHHHHHHTS-SEEESSS.E.EEE-HHH CS
                             HTH_1  24 glsqpavsrqikrLEeelgvpLfeRtgr.g.lrLTeaG 59 
                                       g   ++vsr+ikrLEee g   ++Rtg+ + l+LT+ G
  gi|320101118|ref|YP_004176710.1| 282 GAPKSSVSRRIKRLEEE-GYIAVDRTGKyNyLKLTDKG 318
                                       66789**********98.66667887764368888877 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   0.00039      0.31      17      59 ..     264     305 ..     256     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                                       HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2  17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59 
                                       L +  +e+ ++ +ei +r++ ++s +++ +++L+++g++ + r
  gi|320101118|ref|YP_004176710.1| 264 LGEAGGEG-LTQAEITNRTGAPKSSVSRRIKRLEEEGYIAVDR 305
                                       44455555.9*****************************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 ?   11.0   0.1   0.00047      0.37      11      40 ..     270     299 ..     261     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                            HTH_28  11 aGhsvreaArelgisrrtvyrWikryeegG 40 
                                       +G +++e+ ++ g   ++v+r ikr+ee+G
  gi|320101118|ref|YP_004176710.1| 270 EGLTQAEITNRTGAPKSSVSRRIKRLEEEG 299
                                       3449*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2453.23
//
Query:       gi|320101119|ref|YP_004176711.1|  [L=167]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1274.34
//
Query:       gi|320101120|ref|YP_004176712.1|  [L=375]
Description: DNA primase large subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-29  102.7   0.0    5.8e-29  101.3   0.0    1.6  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 !  101.3   0.0   3.3e-33   5.8e-29       3     208 ..     150     342 ..     148     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 3.3e-33
                                       EEEEHHHHHHHTT-G..........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---H CS
                   DNA_primase_lrg   3 ykvpfedvldlvkrr..........rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikedere 69 
                                       y++p+ +++ +v+ r          + +++ G++y++k++++++l+e+++  +  +       l     ++ e++r+
  gi|320101120|ref|YP_004176712.1| 150 YSLPWAEYAGIVSGRlsqdpsysleNNVVEGGKVYMDKRTVVRVLEEAITGYIVSDASVGIGTLGIDLGFFLEEARK 226
                                       8889999999999666778999999999***********************99886666444444333566666665 PP

                                       HHHHH..HCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--C CS
                   DNA_primase_lrg  70 kleel..lealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsl 144
                                       +l+e+   ++l+              + +  + +++a e fPpC+ +++  ++++g+++he+r++l++Fl +igl++
  gi|320101120|ref|YP_004176712.1| 227 ILSEAgwFKTLR-------------VEQGYGKAGEVAPEKFPPCILRIIGIIESGGNPSHEERFNLAAFLANIGLDV 290
                                       555542223333.............233334467899**************************************** PP

                                       HHHHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-HHH CS
                   DNA_primase_lrg 145 deilelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cpfr 208
                                       d ile++++      ++F++   ry+i+h+ G  g++++y+pysCek+         ++ g Cp+ 
  gi|320101120|ref|YP_004176712.1| 291 DSILEYFRKT-----PDFNEkIARYQIEHISGVRGSGKKYMPYSCEKM---------KSMGiCPVE 342
                                       *********8.....*****8888************************.........888888864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.44
# Mc/sec: 2577.35
//
Query:       gi|320101121|ref|YP_004176713.1|  [L=84]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 633.71
//
Query:       gi|320101122|ref|YP_004176714.1|  [L=132]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1035.80
//
Query:       gi|320101123|ref|YP_004176715.1|  [L=122]
Description: acetyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-22   77.5   0.0    9.7e-22   76.9   0.0    1.2  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    1.2e-05   25.6   0.0    1.8e-05   24.9   0.0    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00047   20.5   0.0    0.00069   20.0   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0067   16.5   0.0      0.029   14.4   0.0    1.9  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.014   14.8   0.0      0.023   14.1   0.0    1.3  1  Acetyltransf_15  Putative acetyl-transferase
      0.032   14.2   0.0       0.05   13.5   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0   3.2e-25   9.7e-22       5      79 ..      18      90 ..      14      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 3.2e-25
                   Acetyltransf_CG  5 tldegeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvptCsyvaaylekhpeyad 79
                                      +l  + ++a+++Y+  ++gv+++  T++p+++rG+GiA++L+++al+ are+++ v p+Csy+  y+ k+p  +d
  gi|320101123|ref|YP_004176715.1| 18 RLP-DGSKAYIKYS-VEGGVMKLISTYTPPQFRGRGIAGRLMEYALKLARENNWLVEPICSYAVYYFMKNPGVRD 90
                                      555.4479*****9.8888****************************************************8877 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   6.2e-09   1.8e-05      52      92 ..      27      67 ..      12      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.2e-09
                                      EEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
                    Acetyltransf_1 52 kipdekggvayieslaVspeyrgkGlGsaLlealeeraree 92
                                      +++  +ggv+ ++s +  p++rg+G++ +L+e++++ are+
  gi|320101123|ref|YP_004176715.1| 27 IKYSVEGGVMKLISTYTPPQFRGRGIAGRLMEYALKLAREN 67
                                      4445678999999**************************99 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.3e-07   0.00069      28      49 ..      39      71 ..      10     111 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                                      EEEEE-GGGTTSSHHHHHHHH...........T CS
                    Acetyltransf_7 28 trlaVdpeyrgkGiGraLlea...........a 49
                                      +  ++ p++rg+Gi+ +L+e+           +
  gi|320101123|ref|YP_004176715.1| 39 ISTYTPPQFRGRGIAGRLMEYalklarennwlV 71
                                      336999**************7455443333330 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   9.8e-06     0.029      78     106 ..      40      68 ..      30      82 .. 0.87
   2 ?   -0.4   0.0      0.37   1.1e+03       2      15 ..      96     109 ..      95     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.8e-06
                                       EEEE-CCGTTS-HHHHHHHHHHHHHHHTT CS
                    Acetyltransf_9  78 gVavapehrgrgvlskLlaraleemreeg 106
                                       ++ + p+ rgrg++ +L+++al+ +re++
  gi|320101123|ref|YP_004176715.1|  40 STYTPPQFRGRGIAGRLMEYALKLARENN 68 
                                       66799******************999986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.37
                                       EEEE-GGGHHHHHH CS
                    Acetyltransf_9   2 irelteedldevle 15 
                                       +r ltee+++ ++e
  gi|320101123|ref|YP_004176715.1|  96 YRGLTEEEWKRFYE 109
                                       89999999999875 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.8e-06     0.023      67     101 ..      30      64 ..       6      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-06
                   Acetyltransf_15  67 lieknvleiYtlyvsekyrgkGlakklLeeslkel 101
                                       ++e  v+++ + y+++++rg+G+a +l+e +lk  
  gi|320101123|ref|YP_004176715.1|  30 SVEGGVMKLISTYTPPQFRGRGIAGRLMEYALKLA 64 
                                       566778899999*****************998865 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.7e-05      0.05      57      83 ..      41      67 ..      11      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                   Acetyltransf_10 57 lfVdpeyrgqGigkaLleaveeeaekd 83
                                       +  p++rg+Gi+ +L+e++++ a+++
  gi|320101123|ref|YP_004176715.1| 41 TYTPPQFRGRGIAGRLMEYALKLAREN 67
                                      57889*****************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 892.96
//
Query:       gi|320101124|ref|YP_004176716.1|  [L=96]
Description: MoaD family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   43.5   0.0    4.4e-11   43.3   0.0    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 !   43.3   0.0   2.4e-15   4.4e-11       1      77 []      11      96 .]      11      96 .] 0.95

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2.4e-15
                                      EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG........TTTTEEEEETTEEEGCCTTTSB--TTCEEE CS
                              ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypela........lerrvavavNgeivprlwldtelkdgDeva 69
                                      v++  +l  ++g  ee++e++++  +++l++ Lger+ +l          e +++v+ N +  ++ + dt+l+d Dev+
  gi|320101124|ref|YP_004176716.1| 11 VKYMLWLESKTGlrEEVVEVGDNCRLRDLVKMLGERHTALSrligellhGESGIIVLHNSRTPEE-GMDTPLRDMDEVV 88
                                      67888999999**************************9999*******97799******998888.************* PP

                                      EEESTTC- CS
                              ThiS 70 ilppVaGG 77
                                      ++ppV+GG
  gi|320101124|ref|YP_004176716.1| 89 LMPPVSGG 96
                                      *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 719.96
//
Query:       gi|320101125|ref|YP_004176717.1|  [L=95]
Description: 50S ribosomal protein L44E [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-28   97.0  13.1    9.3e-28   96.5  13.1    1.2  1  Ribosomal_L44   Ribosomal protein L44
     0.0054   16.4   2.5        1.1    9.0   0.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
       0.02   15.3   0.3      0.034   14.6   0.3    1.4  1  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
      0.021   14.7   4.6       0.11   12.4   0.4    2.3  2  zinc_ribbon_4   zinc-ribbon domain
      0.032   14.1   6.5       0.52   10.2   1.5    2.4  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.069   13.2   2.9       0.73    9.9   0.2    2.1  2  CpXC            CpXC protein
       0.07   13.6   0.4       0.07   13.6   0.4    3.2  1  Ribosomal_L33   Ribosomal protein L33
       0.13   12.4   2.3        1.8    8.7   0.2    2.4  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        0.2   12.2   3.2       0.46   11.0   0.1    2.1  2  DUF1660         Prophage protein (DUF1660)
       0.22   12.3   3.6        1.3    9.9   3.6    1.9  1  zinc_ribbon_15  zinc-ribbon family
       0.22   11.7   4.0        1.8    8.7   4.3    2.0  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.26   11.2   0.2       0.26   11.2   0.2    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.6   10.2   6.3        2.8    8.0   1.3    2.1  2  CxC5            CxC5 like cysteine cluster associated with KD
       0.75   10.0   5.4       0.93    9.7   5.4    1.1  1  Ribosomal_S8e   Ribosomal protein S8e
       0.75    9.4   3.6       0.61    9.7   0.3    2.1  2  RecR            RecR protein


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 !   96.5  13.1   7.8e-31   9.3e-28       1      75 [.      16      90 ..      16      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 7.8e-31
                                      EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EE CS
                     Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfel 75
                                      +Hteh+v+ yk+gk+++la+g+Rry+rk++gyg+++kp +k++aK+tKK+vl+l+C++C+++++++++R+kk el
  gi|320101125|ref|YP_004176717.1| 16 THTEHSVTIYKHGKRRSLAEGERRYARKKKGYGSKRKPEQKRFAKVTKKTVLKLKCQKCGYTIHREGIRLKKAEL 90
                                      6************************************************************************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 !    9.0   0.1   0.00096       1.1      13      22 ..       8      17 ..       2      18 .. 0.85
   2 !    7.3   0.5    0.0032       3.8       1       9 [.      70      78 ..      70      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00096
                     zinc_ribbon_2 13 akFCpyCGtp 22
                                      +++Cp+C+t+
  gi|320101125|ref|YP_004176717.1|  8 VTYCPRCRTH 17
                                      689****996 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0032
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +C +CG+++
  gi|320101125|ref|YP_004176717.1| 70 KCQKCGYTI 78
                                      799999887 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 ?   14.6   0.3   2.8e-05     0.034      23      65 ..      52      95 .]      42      95 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                                      -TT-BBSS---HHHHHHHHHHHT-----GGGEE-TTT.-SBSSE CS
                    Ribosomal_L9_C 23 gedgklFGsVtakdIaealkkklgieidkkkieleep.iktlGe 65
                                      + ++k F +Vt+k + +   +k g++i+++ i+l+++ + ++G+
  gi|320101125|ref|YP_004176717.1| 52 KPEQKRFAKVTKKTVLKLKCQKCGYTIHREGIRLKKAeLAEVGK 95
                                      568899***********999999***********9955999985 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.046        55       4      10 ..      10      16 ..       8      17 .. 0.73
   2 ?   12.4   0.4   9.5e-05      0.11      18      35 ..      60      78 ..      58      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.046
                     zinc_ribbon_4  4 tCpsCka 10
                                       Cp+C +
  gi|320101125|ref|YP_004176717.1| 10 YCPRCRT 16
                                      5888876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.5e-05
                     zinc_ribbon_4 18 klpakgv.kvrCskCghvF 35
                                      k+++k+v k++C kCg ++
  gi|320101125|ref|YP_004176717.1| 60 KVTKKTVlKLKCQKCGYTI 78
                                      77766666********986 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   0.00044      0.52       4      13 ..      11      20 ..      11      23 .. 0.89
   2 ?    6.2   0.2     0.008       9.5       2      16 ..      69      83 ..      68      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00044
                                      -TTT--BBEE CS
                      zf-FPG_IleRS  4 CpRCwryier 13
                                      CpRC++++e+
  gi|320101125|ref|YP_004176717.1| 11 CPRCRTHTEH 20
                                      *******997 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.008
                                      SB-TTT--BBEEEEC CS
                      zf-FPG_IleRS  2 epCpRCwryiervgq 16
                                       +C  C+ +i r+g+
  gi|320101125|ref|YP_004176717.1| 69 LKCQKCGYTIHREGI 83
                                      59**********997 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.053        64       3      14 ..      11      22 ..       8      36 .. 0.64
   2 ?    9.9   0.2   0.00061      0.73      28      48 ..      59      79 ..      47      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.053
                              CpXC  3 CpaCgkefeaei 14
                                      Cp+C++++e  +
  gi|320101125|ref|YP_004176717.1| 11 CPRCRTHTEHSV 22
                                      888877666543 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00061
                              CpXC 28 eklldgslfeatCpkCgatak 48
                                      +k+ ++++++ +C+kCg+t++
  gi|320101125|ref|YP_004176717.1| 59 AKVTKKTVLKLKCQKCGYTIH 79
                                      68999*************986 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   5.8e-05      0.07      33      43 ..      10      20 ..       6      21 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.8e-05
                                      EETTTTEEEEE CS
                     Ribosomal_L33 33 Ycprcrkhtlh 43
                                      Ycprcr ht h
  gi|320101125|ref|YP_004176717.1| 10 YCPRCRTHTEH 20
                                      *********99 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.076        91       2       8 ..       9      15 ..       9      17 .. 0.80
   2 ?    8.7   0.2    0.0015       1.8       3      14 ..      70      81 ..      69      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.076
                            zf-ACC  2 tKCpsCg 8 
                                      t Cp+C 
  gi|320101125|ref|YP_004176717.1|  9 TYCPRCR 15
                                      6799996 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                            zf-ACC  3 KCpsCgemlykk 14
                                      KC +Cg +++++
  gi|320101125|ref|YP_004176717.1| 70 KCQKCGYTIHRE 81
                                      9********996 PP

>> DUF1660  Prophage protein (DUF1660)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00039      0.46      22      57 ..       8      43 ..       2      45 .. 0.72
   2 ?    2.0   0.5      0.26   3.1e+02      15      30 ..      61      77 ..      45      92 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                           DUF1660 22 elyCeRCeivkekvkclekklnrsdLdesenvfpek 57
                                        yC RC +  e+  ++ k+ +r +L e e+++ +k
  gi|320101125|ref|YP_004176717.1|  8 VTYCPRCRTHTEHSVTIYKHGKRRSLAEGERRYARK 43
                                      459****444444455577788999***9*999865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.26
                           DUF1660 15 npaadseelyCeRC.ei 30
                                      +  +++ +l C++C ++
  gi|320101125|ref|YP_004176717.1| 61 VTKKTVLKLKCQKCgYT 77
                                      44455667789999533 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.6    0.0011       1.3      35      77 ..       6      80 ..       1      84 [. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                    zinc_ribbon_15 35 kpylacskCkslleaskelgkeiekkesse................................kkeCknCgkevee 77
                                        + +c +C+++ e+s +  k+ ++++ +e                                k +C++Cg +++ 
  gi|320101125|ref|YP_004176717.1|  6 VIVTYCPRCRTHTEHSVTIYKHGKRRSLAEgerryarkkkgygskrkpeqkrfakvtkktvlKLKCQKCGYTIHR 80
                                      567899999999999998888888877777899999999999999999999*******************99986 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.3    0.0015       1.8       1      28 [.      10      80 ..      10      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                          zf-Mss51  1 lCPvpkhkqt...........................................apkhvdfeCpdCGiptyc 28
                                      +CP + ++ +                                           ++   +++C++CG+ ++ 
  gi|320101125|ref|YP_004176717.1| 10 YCPRCRTHTEhsvtiykhgkrrslaegerryarkkkgygskrkpeqkrfakvtKKTVLKLKCQKCGYTIHR 80
                                      5888865555788888888888888888888888999999999999999999888889**********996 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.9       0.3   3.5e+02      30      39 ..      10      19 ..       8      52 .. 0.77
   2 ?   11.2   0.2   0.00022      0.26      41      59 ..      63      81 ..      40      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.3
                    OrfB_Zn_ribbon 30 tCseCgsknk 39
                                       C++C    +
  gi|320101125|ref|YP_004176717.1| 10 YCPRCRTHTE 19
                                      4666655444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00022
                    OrfB_Zn_ribbon 41 alsgrtfkCpnCgfeadrD 59
                                      +++  ++kC++Cg++++r 
  gi|320101125|ref|YP_004176717.1| 63 KKTVLKLKCQKCGYTIHRE 81
                                      4567789**********96 PP

>> CxC5  CxC5 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.3    0.0024       2.8      46      78 ..       6      40 ..       2      48 .. 0.70
   2 ?    5.2   0.4     0.018        21      43      59 ..      63      79 ..      42      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                              CxC5 46 vlslyCpkCktrYypdyyvhdg..vrtYyggspky 78
                                      v+ +yCp+C t+  ++ ++++    r   +g+ +y
  gi|320101125|ref|YP_004176717.1|  6 VIVTYCPRCRTHTEHSVTIYKHgkRRSLAEGERRY 40
                                      7889*******999999877444444444444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.018
                              CxC5 43 pvwvlslyCpkCktrYy 59
                                      +  vl l+C+kC+ + +
  gi|320101125|ref|YP_004176717.1| 63 KKTVLKLKCQKCGYTIH 79
                                      44799*******97655 PP

>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.4   0.00077      0.93       8      65 ..      28      90 ..      22      94 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00077
                                      CCSEESSTEEXXXSSXXXCCSBXXXXXXXEES...SHEEEEEEETTC..EEEEEEESESEEEE CS
                     Ribosomal_S8e  8 khkrkltGgkakllrkkrkielgrkekatklg...aervkvvrvrgG..krkkralrlkkanv 65
                                       + r+l  g ++  rkk+ +  +rk+++ +++   +++v +++++     +++ ++rlkka++
  gi|320101125|ref|YP_004176717.1| 28 GKRRSLAEGERRYARKKKGYGSKRKPEQKRFAkvtKKTVLKLKCQKCgyTIHREGIRLKKAEL 90
                                      467888888899999999999999999999964445555555555432467779999999986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00051      0.61      16      29 ..       8      21 ..       5      22 .. 0.89
   2 ?    0.2   0.2      0.46   5.5e+02      18      23 ..      70      75 ..      69      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00051
                                      -EE-TTT--EESSS CS
                              RecR 16 vrhCsrCgnlteed 29
                                      v++C+rC++ te+ 
  gi|320101125|ref|YP_004176717.1|  8 VTYCPRCRTHTEHS 21
                                      89*******99975 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.46
                                      E-TTT- CS
                              RecR 18 hCsrCg 23
                                       C++Cg
  gi|320101125|ref|YP_004176717.1| 70 KCQKCG 75
                                      5****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 684.97
//
Query:       gi|320101126|ref|YP_004176718.1|  [L=68]
Description: 30S ribosomal protein S27E [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   62.8   1.2    2.1e-17   62.5   1.2    1.1  1  Ribosomal_S27e  Ribosomal protein S27
      0.001   18.5   0.4     0.0015   18.0   0.4    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0021   17.8   0.6       0.46   10.3   0.1    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0086   16.1   0.2       0.01   15.9   0.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.009   16.1   0.6      0.014   15.5   0.6    1.3  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.015   15.3   0.4      0.021   14.8   0.4    1.3  1  DZR             Double zinc ribbon
      0.032   14.1   0.1        8.6    6.3   0.0    2.1  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
      0.057   13.2   3.0        1.3    8.9   3.4    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.087   12.7   1.7        2.4    8.1   0.1    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.089   11.9   0.0      0.091   11.9   0.0    1.1  1  Aminotran_1_2   Aminotransferase class I and II
      0.095   12.4   3.4       0.51   10.1   3.3    2.1  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.096   12.7   2.3       0.56   10.2   2.3    1.9  1  ADK_lid         Adenylate kinase, active site lid
       0.19   11.5   2.7        1.5    8.6   0.1    2.1  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
          1    9.5   4.1         14    5.8   0.1    2.2  2  zf-BED          BED zinc finger
          1    9.3   4.5        4.2    7.3   0.3    2.2  2  zf-trcl         Probable zinc-ribbon domain


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 !   62.5   1.2   1.8e-20   2.1e-17       1      52 [.      11      62 ..      11      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.8e-20
                                      -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEE CS
                    Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqile 52
                                      prs+F +v C+ C++e vvFsha+    C  Cg+ Lv+PtGGka++ ++  e
  gi|320101126|ref|YP_004176718.1| 11 PRSRFYKVICKVCGAENVVFSHASFPARCKVCGTQLVQPTGGKARILKDKAE 62
                                      89*******************************************9776555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.4   1.2e-06    0.0015       2      29 ..      19      46 ..      18      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                                      EETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                                      +C++Cg +n+v+ +++   +C+ CG+ l
  gi|320101126|ref|YP_004176718.1| 19 ICKVCGAENVVFSHASFPARCKVCGTQL 46
                                      7************************865 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 !   10.3   0.1   0.00038      0.46       4      17 ..      18      31 ..      17      35 .. 0.84
   2 !    6.0   0.0    0.0081       9.7       6      14 ..      39      47 ..      36      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
                     A2L_zn_ribbon  4 kvCsvCggngilns 17
                                      ++C+vCg ++++ s
  gi|320101126|ref|YP_004176718.1| 18 VICKVCGAENVVFS 31
                                      68********9976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0081
                     A2L_zn_ribbon  6 CsvCggngi 14
                                      C+vCg++ +
  gi|320101126|ref|YP_004176718.1| 39 CKVCGTQLV 47
                                      *****9976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   8.5e-06      0.01      69     106 ..      16      56 ..      10      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.5e-06
                                       -EEEETTTS-EEECHHH...HHS-TTTSSS-EEEEESSSEE CS
                              HypA  69 vkvrCreCgkefeleek...alrCpkCgsadveivsGeell 106
                                        kv C++Cg+e  + ++    +rC+ Cg++ v+ ++G+   
  gi|320101126|ref|YP_004176718.1|  16 YKVICKVCGAENVVFSHasfPARCKVCGTQLVQPTGGKARI 56 
                                       5799*****99885442224569**********99998655 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   1.2e-05     0.014       4      36 ..      16      46 ..      15      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                       Zn-ribbon_8  4 YeYrCeeCghefevlqsisdaplta.CPeCgsev 36
                                      Y   C+ Cg e  v+  +s    +a C+ Cg ++
  gi|320101126|ref|YP_004176718.1| 16 YKVICKVCGAENVVFSHAS---FPArCKVCGTQL 46
                                      7778*****8888888766...7777*****955 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4   1.8e-05     0.021      14      40 ..      19      49 ..      10      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                               DZR 14 fCseCgtklkavaa...edrCpsCgek.vdp 40
                                       C+ Cg++    ++   + rC  Cg++ v+p
  gi|320101126|ref|YP_004176718.1| 19 ICKVCGAENVVFSHasfPARCKVCGTQlVQP 49
                                      799***995555556789*******997766 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0084        10       9      20 ..      13      24 ..       7      26 .. 0.82
   2 ?    6.3   0.0    0.0072       8.6       9      21 ..      33      44 ..      29      48 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0084
                         zf-C2H2_3  9 ksfgasqCkeCg 20
                                      + f ++ Ck+Cg
  gi|320101126|ref|YP_004176718.1| 13 SRFYKVICKVCG 24
                                      6788888****9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0072
                         zf-C2H2_3  9 ksfgasqCkeCgM 21
                                       sf a +Ck+Cg 
  gi|320101126|ref|YP_004176718.1| 33 ASFPA-RCKVCGT 44
                                      56665.8****95 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.4    0.0011       1.3       2      23 .]      20      46 ..      19      46 .. 0.88
   2 ?    6.7   0.1     0.005         6       1       9 [.      38      46 ..      38      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                     zinc_ribbon_2  2 CpnCGael.q.dnakF...CpyCGtpl 23
                                      C+ CGae+     a F   C  CGt l
  gi|320101126|ref|YP_004176718.1| 20 CKVCGAENvVfSHASFparCKVCGTQL 46
                                      9*******66999999********986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.005
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +C+ CG++l
  gi|320101126|ref|YP_004176718.1| 38 RCKVCGTQL 46
                                      699999998 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 ?    4.5   0.1     0.028        33      25      35 ..      18      29 ..       8      32 .. 0.69
   2 ?    8.1   0.1     0.002       2.4      25      36 ..      37      48 ..      31      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.028
                    Zn_ribbon_SprT 25 YrCrrCk.gtLr 35
                                       +C+ C+ ++ +
  gi|320101126|ref|YP_004176718.1| 18 VICKVCGaENVV 29
                                      69****955544 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.002
                    Zn_ribbon_SprT 25 YrCrrCkgtLrg 36
                                       rC+ C+ +L++
  gi|320101126|ref|YP_004176718.1| 37 ARCKVCGTQLVQ 48
                                      69****988876 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.6e-05     0.091      92     121 ..       2      31 ..       1      50 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                                       TT-EEEEEESS-THHHHHHHHTTSEEEEEE CS
                     Aminotran_1_2  92 pgdeilvpdptyasyknilrlsggevvryp 121
                                       ++++il+p+p    yk i++ +g+e v ++
  gi|320101126|ref|YP_004176718.1|   2 KKKRILIPAPRSRFYKVICKVCGAENVVFS 31 
                                       7899*********************55555 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.3   0.00043      0.51       2      27 ..      19      46 ..      18      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                                      B-SSS--B----SSS..----SSS---- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgd..piRCkeCGhRi 27
                                      iC  Cgae+ + + +  p RCk CG  +
  gi|320101126|ref|YP_004176718.1| 19 ICKVCGAENVVFSHAsfPARCKVCGTQL 46
                                      7999***999544443489******865 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 ?   10.2   2.3   0.00047      0.56       3      33 ..      19      48 ..      18      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00047
                                      E-TTT--EEETTTB--SSTTB-TTT--.-B- CS
                           ADK_lid  3 vCpkCGrsYhvvfnpPkveglCDkCGepLvq 33
                                      +C+ CG+  +vvf     +  C +CG +Lvq
  gi|320101126|ref|YP_004176718.1| 19 ICKVCGAE-NVVFSHASFPARCKVCGTQLVQ 48
                                      89999997.77777777899**********9 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0012       1.5       2      14 ..      15      27 ..      14      31 .. 0.78
   2 ?    3.1   0.3     0.064        77       7      11 ..      39      43 ..      38      49 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                           zf-RRN7  2 ekgppCgvCgcrs 14
                                      +++ +C vCg+ +
  gi|320101126|ref|YP_004176718.1| 15 FYKVICKVCGAEN 27
                                      78899*****954 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.064
                           zf-RRN7  7 CgvCg 11
                                      C vCg
  gi|320101126|ref|YP_004176718.1| 39 CKVCG 43
                                      66665 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.7     0.017        21      15      24 ..      16      25 ..       9      29 .. 0.87
   2 ?    5.8   0.1     0.012        14      17      27 ..      37      47 ..      27      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                                      S--EETTTTE CS
                            zf-BED 15 qkavCryCgk 24
                                       k++C+ Cg+
  gi|320101126|ref|YP_004176718.1| 16 YKVICKVCGA 25
                                      69******97 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                                      -EETTTTEE-- CS
                            zf-BED 17 avCryCgkils 27
                                      a+C+ Cg +l 
  gi|320101126|ref|YP_004176718.1| 37 ARCKVCGTQLV 47
                                      79*****9986 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0035       4.2       5      15 ..      18      28 ..      16      34 .. 0.80
   2 ?    3.5   0.6     0.057        68      33      39 ..      36      42 ..      30      46 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0035
                           zf-trcl  5 ltCkdCgaefv 15
                                      ++Ck Cgae v
  gi|320101126|ref|YP_004176718.1| 18 VICKVCGAENV 28
                                      68******986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.057
                           zf-trcl 33 pkRCkaC 39
                                      p RCk C
  gi|320101126|ref|YP_004176718.1| 36 PARCKVC 42
                                      7777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 517.42
//
Query:       gi|320101127|ref|YP_004176719.1|  [L=97]
Description: HTH DNA-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   0.7     0.0002   21.4   0.7    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
    0.00077   18.5   0.0    0.00092   18.2   0.0    1.0  1  LMBR1            LMBR1-like membrane protein
  ------ inclusion threshold ------
      0.065   12.9   0.1      0.079   12.6   0.1    1.0  1  DUF4131          Domain of unknown function (DUF4131)
      0.074   11.9   0.0      0.088   11.6   0.0    1.1  1  DUF2254          Predicted membrane protein (DUF2254)
      0.087   12.9   1.2         11    6.0   0.0    2.0  2  T2SSM            Type II secretion system (T2SS), protein M
       0.26   11.6   9.1          9    6.7   9.1    2.0  1  DPM2             Dolichol phosphate-mannose biosynthesis regu


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.7   6.6e-08    0.0002      41     111 ..       7      76 ..       5      77 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.6e-08
                   Phage_holin_3_6  41 gaagvlallalllllvalalala.a.lwlaalivaavllvlagvlalvglkklkkakplpertieelkedvaa 111
                                       ++ g+lal  +++++ a +l+l+   + l  + ++++++ + g+l+++g+  +     +p + iee+++ ++a
  gi|320101127|ref|YP_004176719.1|   7 VGWGLLALSVVVVVVYAYILFLTpYsSLLIQITLMVAVAGVFGILGWIGYTLATT---PPPKPIEEIEKEIEA 76 
                                       5566677777777777777777544555555556677777778888888874444...577889999888765 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.1e-07   0.00092     126     210 ..       5      84 ..       3      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-07
                             LMBR1 126 naiiyllllvivlglliyvliilqklsllsiksllpilislantwGlvllilllGyGlvel.Prslwreiksdldee 201
                                       +++ ++ll++ v+++++y +i++  l+ +s  sll  +  ++ + G++ ++  +Gy l+ + P + + ei+++++ e
  gi|320101127|ref|YP_004176719.1|   5 QLVGWGLLALSVVVVVVYAYILF--LTPYS--SLLIQITLMVAVAGVFGILGWIGYTLATTpPPKPIEEIEKEIEAE 77 
                                       66779999999999999988885..44442..5555555566778****************8667777899999999 PP

                             LMBR1 202 lkklyfeaa 210
                                       lkkl  e+ 
  gi|320101127|ref|YP_004176719.1|  78 LKKL--EEN 84 
                                       9999..433 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.6e-05     0.079       6      78 ..       9      81 ..       5      91 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                           DUF4131  6 alvllalllllllllllllrr.rprrrvllllllllllallgfalrapqpnandlsqllesgqeviveGvvasl 78
                                      + +l ++++++ +++++l++    +  + ++l+++ + +++ + +  ++ ++++ ++ +e+  e ++e+++ +l
  gi|320101127|ref|YP_004176719.1|  9 WGLLALSVVVVVVYAYILFLTpYSSLLIQITLMVAVAGVFGILGWIGYTLATTPPPKPIEE-IEKEIEAELKKL 81
                                      5666666677777777776663333333444444444444455566667777777777774.333444444444 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.9e-05     0.088     118     177 ..      24      88 ..       8      97 .] 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                           DUF2254 118 e......vpqlsvlvalllaivsvllLiyFihhlarsiqvsnviarveeelrkai...learedeeeee 177
                                       +        +l++ ++l++a++ v+ ++ +i  +  +    + i+++e+e+++++   +   e++  ++
  gi|320101127|ref|YP_004176719.1|  24 YilfltpYSSLLIQITLMVAVAGVFGILGWIGYTLATTPPPKPIEEIEKEIEAELkklE---ENTG-KD 88 
                                       23344224569999*****************************************3321...2211.11 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.7     0.017        51      19      40 ..      11      32 ..       3      40 .. 0.88
   2 ?    6.0   0.0    0.0038        11      19      59 ..      42      83 ..      37      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                                      XXXXXXXXXXXXXXXXXXXXXX CS
                             T2SSM 19 laalglvlllallylllwqPls 40
                                      l+al++v++++  y+l+++P s
  gi|320101127|ref|YP_004176719.1| 11 LLALSVVVVVVYAYILFLTPYS 32
                                      88999***************87 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0038
                                      XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             T2SSM 19 laalglv.lllallylllwqPlserieraqaelqklraqlaw 59
                                      +a++g++ +l  + y l  +P+ + ie+ ++e++++ ++l++
  gi|320101127|ref|YP_004176719.1| 42 VAVAGVFgILGWIGYTLATTPPPKPIEEIEKEIEAELKKLEE 83
                                      55555552566789999****************999888876 PP

>> DPM2  Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   9.1     0.003         9       2      29 ..       4      31 ..       3      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.003
                              DPM2  2 dklvGlllllvalllfvYYtiwvillPf 29
                                      d+lvG +ll++++++ v Y   ++l+P+
  gi|320101127|ref|YP_004176719.1|  4 DQLVGWGLLALSVVVVVVYAYILFLTPY 31
                                      9**************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1686  (0.0940376); expected 358.6 (0.02)
Passed bias filter:                     1056  (0.058899); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 777.27
//
Query:       gi|320101128|ref|YP_004176720.1|  [L=319]
Description: DNA methylase N-4/N-6 domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-27   95.0   0.0      3e-14   53.3   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    9.4e-09   35.2   0.1    1.1e-07   31.8   0.1    2.0  1  UPF0020          Putative RNA methylase family UPF0020
    0.00096   19.5   0.0     0.0021   18.4   0.0    1.5  2  baeRF_family3    Bacterial archaeo-eukaryotic release factor 
    0.00098   19.7   0.0        1.4    9.6   0.0    2.8  2  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.026   14.1   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.019   14.6   0.0      0.076   12.6   0.0    2.0  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.028   15.1   0.0        8.1    7.2   0.1    3.1  2  Methyltransf_25  Methyltransferase domain
      0.061   13.1   0.0       0.12   12.1   0.0    1.4  1  Met_10           Met-10+ like-protein
      0.063   12.7   0.0      0.096   12.1   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   1.5e-17     3e-14     145     226 ..      44     120 ..       9     124 .. 0.84
   2 !   39.8   0.0   1.9e-13   3.9e-10       1     113 [.     173     299 ..     173     311 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.5e-17
                                       -B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEES CS
                       N6_N4_Mtase 145 gkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGiei 221
                                        +  ++iW ++++ s + ++       +    P ++++ lI+ +t++g+ivlDp aGSGtT+++a  lgrk+i ++i
  gi|320101128|ref|YP_004176720.1|  44 TDVSTTIWSFPKRGSWATHRGD-----YRGNWPPQMARALILGYTEPGEIVLDPMAGSGTTCIEAVLLGRKCIAVDI 115
                                       4455678*99999999998874.....9************************************************* PP

                                       SHHHH CS
                       N6_N4_Mtase 222 eeeyv 226
                                       + ++v
  gi|320101128|ref|YP_004176720.1| 116 NYNAV 120
                                       97766 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 1.9e-13
                                       EEEEEE--SSSSSCS.......GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT..........HH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy..endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk..........el 65 
                                       vdl+ t pPY++   y  + d ++    + eeyle+l++v+ e++rvLk++    i i+d + +           e+
  gi|320101128|ref|YP_004176720.1| 173 VDLVATHPPYFNIIGYggNVDGDLSNARTLEEYLEWLREVAGEIYRVLKPGRYCGILIGDTRVHGhyvpithyalEV 249
                                       89**********9999999*************************************************766655544 PP

                                       HHHHHHHTT-EEEEEEEEEEES.SSTTTSTCC..S-B--EEEEEEEESSTT CS
                       N6_N4_Mtase  66 kaladeifggffllnvivwkkp.nsmpesnkd..rltsthEyilvfsknkk 113
                                       ++ a  i++   +++  +++k+  ++++  ++  +l   hE ++vf+k++ 
  gi|320101128|ref|YP_004176720.1| 250 FLDAGFILK-EEVIKIQHKMKTtREVWNRLRKrnFLLIYHEKLFVFRKPGV 299
                                       444444444.44444444455452444443334478999*********976 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   5.4e-11   1.1e-07      15     138 ..      73     189 ..      65     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 5.4e-11
                                       HHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHH CS
                           UPF0020  15 tLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqg 91 
                                       ++A+al+ l   +pge  lDPm GsGt  IEa llg+++++  +        + +    ++ + l+ +  ++ ++ g
  gi|320101128|ref|YP_004176720.1|  73 QMARALI-LGYTEPGEIVLDPMAGSGTTCIEAVLLGRKCIAVDI------NYNAVMLTHHRLYYLVNALRKQGALPG 142
                                       6777765.667889**************************5444......223333334466668888888889999 PP

                                       HHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE----------H CS
                           UPF0020  92 areNaekagvgdliefsqadaakLr.lkegevdvivtnpPYGerlgsk 138
                                            e +gv++   f   da+ L   +++ vd+++t pPY + +g  
  gi|320101128|ref|YP_004176720.1| 143 LDAGGEGTGVQGYRVFHG-DARRLDeIRDNTVDLVATHPPYFNIIGYG 189
                                       999999999999888876.9999997666699********98777655 PP

>> baeRF_family3  Bacterial archaeo-eukaryotic release factor family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.1   8.2e+03      95     122 ..      10      37 ..       8      44 .. 0.72
   2 !   18.4   0.0     1e-06    0.0021      12     126 ..     155     279 ..     152     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.1
                     baeRF_family3  95 frevsknpsliegglegnpaelsaeeLr 122
                                       ++ vs+n ++i gg e + +  + + L 
  gi|320101128|ref|YP_004176720.1|  10 LDFVSRNRRIIVGGQEVDLSPIEVRRLE 37 
                                       5668899999999998887766666665 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1e-06
                     baeRF_family3  12 vrLfegtrdsleeveadgfPltleealgeedperqegh..gdkkseyrdedtrrFlreVdkalqevlsesplplvla 86 
                                        r f+g+ ++l+e++++ + l   + + +++     g   gd  ++   e++ + lreV  ++ +vl++ +   +l+
  gi|320101128|ref|YP_004176720.1| 155 YRVFHGDARRLDEIRDNTVDLVA-THPPYFNIIGYGGNvdGDLSNARTLEEYLEWLREVAGEIYRVLKPGRYCGILI 230
                                       689************98899888.5566677777665546777788899**************************** PP

                     baeRF_family3  87 Gveenlslfrevsknp.........sliegglegnpaelsaeeLreaaw 126
                                       G+++++ ++  +++++          l e+ ++++++  +++e++ +++
  gi|320101128|ref|YP_004176720.1| 231 GDTRVHGHYVPITHYAlevfldagfILKEEVIKIQHKMKTTREVWNRLR 279
                                       ******************9999997777778899999999999999876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0051        10       5      66 ..      94     177 ..      90     182 .. 0.64
   2 !    9.6   0.0   0.00071       1.4      72      94 ..     204     226 ..     190     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0051
                                       -TTSHHHHHHHHTTSEEEEEES-HHHH...........HHHHHHCCHHT-..........EEEETTEECCCT.SS-T CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskeml...........klakekaseegl..........kvefvvadaekl.pfed 59 
                                       +G+G  + +    g+++++vD++ +++           ++ ++++  +gl            ++ ++da++l  ++d
  gi|320101128|ref|YP_004176720.1|  94 AGSGTTCIEAVLLGRKCIAVDINYNAVmlthhrlyylvNALRKQGALPGLdaggegtgvqGYRVFHGDARRLdEIRD 170
                                       56666666666667888888888887744444333332222444444433666666666655679*******88*** PP

                                       T-EEEEE CS
                   Methyltransf_11  60 nsfDlvv 66 
                                       n++Dlv 
  gi|320101128|ref|YP_004176720.1| 171 NTVDLVA 177
                                       ****996 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00071
                                       CC-CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLkpgGll 94 
                                       +++e ++++  ei+RvLkpg ++
  gi|320101128|ref|YP_004176720.1| 204 EYLEWLREVAGEIYRVLKPGRYC 226
                                       445667899**********9776 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 ?   14.1   0.0   1.3e-05     0.026       2      41 ..      87     126 ..      86     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhN 41 
                                       +++lD+++G+G  +i+  l ++k ia++in + + +++h 
  gi|320101128|ref|YP_004176720.1|  87 EIVLDPMAGSGTTCIEAVLLGRKCIAVDINYNAVMLTHHR 126
                                       689*********************************9995 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.8e-05     0.076      42      81 ..      86     124 ..      78     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHH CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilk 81 
                                       g+ vLD  aGsG+  +EA+  g +k+++v+ + +av + +
  gi|320101128|ref|YP_004176720.1|  86 GEIVLDPMAGSGTTCIEAVLLG-RKCIAVDINYNAVMLTH 124
                                       6789***************999.89999999999987655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0041       8.1       1      41 [.      89     127 ..      89     187 .. 0.59
   2 ?    3.3   0.0     0.068   1.4e+02      82      96 ..     209     223 ..     189     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0041
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHH CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarera 41 
                                       vLd  +G+G++++++    g  k ++vDi+ +++  +++r+
  gi|320101128|ref|YP_004176720.1|  89 VLDPMAGSGTTCIEAVLL-G-RKCIAVDINYNAVMLTHHRL 127
                                       899999***999999977.5.99999999877776555433 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHHEEEE CS
                   Methyltransf_25  82 lekalkeiarvLkpg 96 
                                       l+++  ei+rvLkpg
  gi|320101128|ref|YP_004176720.1| 209 LREVAGEIYRVLKPG 223
                                       678999********8 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.9e-05      0.12      92     139 ..      77     122 ..      72     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                                       HHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHH CS
                            Met_10  92 erlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvky 139
                                       + +    e+ge+V+d +AG G   i +     +++ +a+d+n ++v +
  gi|320101128|ref|YP_004176720.1|  77 ALILGYTEPGEIVLDPMAGSGTTCIEAVL--LGRKCIAVDINYNAVML 122
                                       55667799*****************9998..566779*****988765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.8e-05     0.096     158     202 ..      82     125 ..      73     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvake 202
                                       + ++ge vlD  +GSG   i a++Lg k  +avDi+  Av  +++
  gi|320101128|ref|YP_004176720.1|  82 YTEPGEIVLDPMAGSGTTCIEAVLLGRK-CIAVDINYNAVMLTHH 125
                                       67899*********************75.78*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2403.28
//
Query:       gi|320101129|ref|YP_004176721.1|  [L=253]
Description: hemerythrin-like metal-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   21.0   0.3    0.00039   21.0   0.3    1.7  2  Hemerythrin  Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.42   7.5e+03      76      90 ..       7      21 ..       7      31 .. 0.80
   2 !   21.0   0.3   2.2e-08   0.00039       6     116 ..     134     229 ..     129     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.42
                                      HHHHHHHHHHHHHHH CS
                       Hemerythrin 76 lereHdeirelleel 90
                                      + re ++i++++ee+
  gi|320101129|ref|YP_004176721.1|  7 MVREDEDIERVMEEI 21
                                      568888899888875 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHHHHH.HHHHHHHHHHHHCCCHCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHHHH CS
                       Hemerythrin   6 ldeeHralralle.rlraladaaaevhgalrklaelldelvdeleaHhaaEEellfPlledrpggravldvlereHd 81 
                                       +d+ Hr +++ l+  ++ +++ +      ++k+ e+++e  d+++  +++EEe++  +      ++  ++++ + H+
  gi|320101129|ref|YP_004176721.1| 134 MDDAHRVMFEKLNgVIEYIVEGK------PDKITEAFKEAYDYILLYFKIEEEYM-ARCG---YDKKKMKEHMKRHR 200
                                       7999*********5555555553......89***********************7.3333...67777899999999 PP

                                       HHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHH CS
                       Hemerythrin  82 eirelleelrellkgleepsaaafaelleeladll 116
                                       e+ e+l++l ++ +  e      f  ++ el++ +
  gi|320101129|ref|YP_004176721.1| 201 EFKEVLDKLTAAGRASE------FVAMFGELYEYM 229
                                       99999999996666655......666555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 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:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1986.10
//
Query:       gi|320101130|ref|YP_004176722.1|  [L=114]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-23   80.7   0.4    6.3e-23   80.5   0.4    1.1  1  Thiamine_BP   Thiamine-binding protein
  ------ inclusion threshold ------
       0.15   12.0   0.0       0.22   11.4   0.0    1.3  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 


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 !   80.5   0.4     7e-27   6.3e-23       3      91 ..       7      96 ..       5      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 7e-27
                                      EEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEESSS CS
                       Thiamine_BP  3 isviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrrdk 80
                                      + v+P+gt ++s+s+yVa+v +v ++ glk+ lt+  T+ie++ ++ev e++k++ ++l  +G+ R+++ + id+r dk
  gi|320101130|ref|YP_004176722.1|  7 LRVTPIGTCTTSLSDYVAEVERVFESLGLKHVLTASATIIEVNnVEEVSEILKAVIDVLTHKGVRRILIDLSIDYRVDK 85
                                      789**************************************************************************** PP

                                      ---HHHHHHHH CS
                       Thiamine_BP 81 eqtleeKvksv 91
                                      + ++e+Kv+sv
  gi|320101130|ref|YP_004176722.1| 86 DLSIEGKVASV 96
                                      *********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 ?   11.4   0.0   2.5e-05      0.22      76     112 ..      15      56 ..       8      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHHHHTT.SC.....EEEEEEGTTSCBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx RF
                      tRNA-synt_2b  76 lddslrdlikaisriferlglef.....raiielmsaksady 112
                                          sl+d++ +++r+fe+lgl+        iie+++ ++++ 
  gi|320101130|ref|YP_004176722.1|  15 CTTSLSDYVAEVERVFESLGLKHvltasATIIEVNNVEEVSE 56 
                                       56789****************964554444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 922.60
//
Query:       gi|320101131|ref|YP_004176723.1|  [L=168]
Description: transcriptional regulator-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   28.3   1.9    2.2e-06   27.3   1.9    1.5  1  DivIC            Septum formation initiator
    1.6e-06   28.4   6.7    2.4e-06   27.9   6.0    1.7  1  ZapB             Cell division protein ZapB
      2e-05   24.7   2.7    2.9e-05   24.2   2.7    1.2  1  ADIP             Afadin- and alpha -actinin-Binding
    4.9e-05   23.3   2.0    0.00012   22.1   2.0    1.6  1  bZIP_1           bZIP transcription factor
    7.2e-05   22.8   3.3    9.3e-05   22.5   2.7    1.4  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    7.4e-05   22.4   2.6     0.0001   21.9   2.6    1.2  1  Leu_zip          Leucine zipper
    9.7e-05   21.7   0.3    9.7e-05   21.7   0.3    1.3  1  HAP1_N           HAP1 N-terminal conserved region
    0.00048   20.5   8.1     0.0026   18.1   1.6    2.5  2  FlaC_arch        Flagella accessory protein C (FlaC)
    0.00048   20.0   1.5    0.00064   19.6   1.5    1.3  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
    0.00062   18.9   0.8    0.00073   18.7   0.8    1.1  1  Atg14            Vacuolar sorting 38 and autophagy-related su
    0.00077   19.5   3.2     0.0011   19.0   3.2    1.3  1  DHR10            Designed helical repeat protein 10 domain
    0.00093   19.5   4.1     0.0023   18.2   4.0    1.7  1  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0011   18.6   3.6     0.0019   17.8   3.6    1.3  1  PspA_IM30        PspA/IM30 family
     0.0013   19.2   3.9      0.061   13.8   2.8    2.7  2  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
     0.0015   19.1   2.3     0.0019   18.7   2.3    1.3  1  APG6_N           Apg6 coiled-coil region
     0.0016   17.4   2.5     0.0019   17.1   2.5    1.1  1  Spc7             Spc7 kinetochore protein
     0.0019   17.9   0.6     0.0027   17.4   0.6    1.2  1  YkyA             Putative cell-wall binding lipoprotein
     0.0021   17.7   2.3     0.0032   17.1   2.3    1.2  1  Filament         Intermediate filament protein
     0.0023   18.0   5.0     0.0023   18.0   5.0    1.8  1  bZIP_2           Basic region leucine zipper
     0.0023   16.6   0.6     0.0026   16.5   0.6    1.1  1  AAA_13           AAA domain
     0.0035   17.3   4.9      0.006   16.5   4.9    1.3  1  Wtap             WTAP/Mum2p family
     0.0038   17.2   1.1     0.0051   16.8   0.6    1.5  1  Sipho_Gp157      Siphovirus Gp157
     0.0044   17.1   2.3     0.0079   16.2   2.3    1.4  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0045   17.2   2.8     0.0077   16.4   2.1    1.8  1  HALZ             Homeobox associated leucine zipper
     0.0045   17.4   0.5     0.0076   16.7   0.5    1.5  1  DUF4140          N-terminal domain of unknown function (DUF41
     0.0047   17.1   0.8      0.011   15.9   0.8    1.5  1  GCN5L1           GCN5-like protein 1 (GCN5L1)
     0.0054   16.6   0.4     0.0072   16.1   0.4    1.2  1  Phage_GP20       Phage minor structural protein GP20
     0.0055   17.2   1.5     0.0089   16.6   1.5    1.5  1  Syntaxin-6_N     Syntaxin 6, N-terminal
     0.0077   14.5   1.4      0.009   14.2   1.4    1.1  1  EzrA             Septation ring formation regulator, EzrA
     0.0077   15.7   0.9      0.011   15.2   0.9    1.3  1  DUF4618          Domain of unknown function (DUF4618)
  ------ inclusion threshold ------
      0.011   14.7   0.5      0.011   14.6   0.5    1.1  1  DUF812           Protein of unknown function (DUF812)
      0.011   16.1   0.4      0.015   15.6   0.4    1.2  1  THOC7            Tho complex subunit 7
      0.012   15.8   1.2      0.023   14.9   1.2    1.5  1  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
      0.014   15.4   0.3       0.02   14.9   0.3    1.4  1  DUF1664          Protein of unknown function (DUF1664)
      0.014   15.2   3.4       0.81    9.6   0.6    3.0  2  Shugoshin_N      Shugoshin N-terminal coiled-coil region
      0.015   15.3   8.5      0.025   14.6   7.5    1.9  1  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
      0.017   14.9   0.0      0.047   13.5   0.0    1.7  1  HTH_23           Homeodomain-like domain
      0.017   13.8   1.5      0.023   13.5   1.5    1.2  1  DUF773           CDK5 regulatory subunit-associated protein 3
      0.018   15.1   0.9      0.028   14.5   0.9    1.3  1  TcpS             Toxin-coregulated pilus protein S
      0.019   15.1   2.1      0.028   14.5   2.1    1.3  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.023   14.8   5.6      0.033   14.3   5.6    1.2  1  Tropomyosin_1    Tropomyosin like
      0.024   15.1   3.2      0.073   13.5   3.2    1.8  1  Snapin_Pallidin  Snapin/Pallidin
      0.024   15.0   1.0       0.39   11.1   0.5    2.4  2  LPP              Lipoprotein leucine-zipper
      0.029   14.6   4.2      0.044   14.0   4.2    1.2  1  ATG16            Autophagy protein 16 (ATG16)
      0.031   14.4   1.6      0.054   13.6   1.6    1.4  1  Herpes_BLRF2     Herpesvirus BLRF2 protein
      0.033   13.5   5.1      0.049   13.0   5.1    1.2  1  GAS              Growth-arrest specific micro-tubule binding
      0.035   13.8   0.7      0.095   12.4   0.0    2.1  1  Sigma70_r4_2     Sigma-70, region 4
      0.038   14.3  10.2       0.91    9.9   0.4    3.6  2  TSC22            TSC-22/dip/bun family
      0.046   13.8   0.3       0.08   13.0   0.3    1.5  1  DUF2730          Protein of unknown function (DUF2730)
      0.049   13.3   2.6      0.073   12.7   2.6    1.3  1  GrpE             GrpE
      0.057   13.3   0.9      0.073   12.9   0.9    1.2  1  DUF724           Protein of unknown function (DUF724)
      0.063   12.5   1.2      0.087   12.1   1.2    1.2  1  TMPIT            TMPIT-like protein
      0.069   12.4   2.4      0.096   12.0   2.4    1.2  1  DUF3450          Protein of unknown function (DUF3450)
       0.07   13.1   7.7        0.3   11.1   7.5    2.0  2  Prefoldin_2      Prefoldin subunit
      0.077   13.2   3.3       0.15   12.3   3.3    1.6  1  Spc24            Spc24 subunit of Ndc80
      0.081   13.5   2.1      0.081   13.5   2.1    2.7  2  M                M protein repeat
      0.085   13.3   0.9       0.26   11.8   1.0    1.8  2  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.087   13.3   3.5       0.16   12.5   3.6    1.4  1  DUF16            Protein of unknown function DUF16
      0.093   13.0   3.5       0.16   12.2   2.7    1.9  1  DUF5082          Domain of unknown function (DUF5082)
       0.11   11.3   1.4       0.13   11.1   1.4    1.1  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
       0.12   13.0   3.2       0.36   11.5   3.2    1.8  1  YabA             Initiation control protein YabA
       0.12   12.5   1.6       0.32   11.2   0.7    1.5  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.13   12.2   3.9       0.19   11.6   1.2    2.1  2  Prefoldin        Prefoldin subunit
       0.13   12.3   4.0       0.31   11.2   4.0    1.6  1  Swi5             Swi5
       0.15   12.3   4.7       0.38   11.0   4.7    1.7  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.27   10.6   4.3        0.3   10.4   2.4    1.9  2  CASP_C           CASP C terminal
       0.31   10.9   4.5       0.94    9.4   1.3    2.6  2  WD40_alt         Alternative WD40 repeat motif
       0.35   11.0   4.2       0.34   11.0   2.8    1.7  1  IFP_35_N         Interferon-induced 35 kDa protein (IFP 35) N
       0.36   11.0   6.7       0.59   10.3   6.7    1.3  1  Cnn_1N           Centrosomin N-terminal motif 1
       0.39   10.8   2.9        0.6   10.2   2.9    1.3  1  ORF6C            ORF6C domain
       0.41   11.3   4.2        1.1   10.0   4.2    1.7  1  SlyX             SlyX
       0.51   10.7   6.9        1.8    9.0   6.6    2.0  2  Csm1_N           Csm1 N-terminal domain
       0.57   10.3   5.3        2.6    8.2   4.7    2.2  1  Med9             RNA polymerase II transcription mediator com
       0.66   10.3   6.2        2.1    8.7   6.2    2.0  1  ABC_tran_CTD     ABC transporter C-terminal domain
        1.4    9.2   5.0        2.5    8.4   5.0    1.4  1  XhlA             Haemolysin XhlA
          7    7.8   5.1         58    4.8   4.6    2.1  1  DUF5320          Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   1.9   9.3e-09   2.2e-06      15      60 ..     114     159 ..     108     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.3e-09
                                       XXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                             DivIC  15 gllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                        + ++ +lk++i+ l++e+++l+++++eLea+v++L+++ + +++r
  gi|320101131|ref|YP_004176723.1| 114 EIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKAR 159
                                       5667889*******************************99999877 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   6.0     1e-08   2.4e-06       5      65 ..     100     163 ..      96     168 .] 0.90

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1e-08
                              ZapB   5 lLeqLEsk...iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                       +L++LEs+   i+  i  +++L+ +i  L+een+el ++++ele++++ql+++ e +++rlk L
  gi|320101131|ref|YP_004176723.1| 100 VLSELESRggyIEVEIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKEL 163
                                       6788888777677788999*******************************************98 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   2.7   1.2e-07   2.9e-05      56     104 ..     119     167 ..     111     168 .] 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-07
                              ADIP  56 eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekkl 104
                                       esl+++i+ le e++ l+++i+ l++q++ql++ ++lv+a++++l+ +l
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       89*******************************************9876 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   2.0   4.9e-07   0.00012      28      63 ..     118     153 ..     116     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.9e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       +e L+ +   Le+eNk+L+++++el+ +v++L++ v
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQELEAQVSQLRNTV 153
                                       799*****************************9876 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 !   22.5   2.7     4e-07   9.3e-05      13      95 ..      84     166 ..      78     168 .] 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4e-07
                    CENP-F_leu_zip  13 KeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekel 89 
                                       ++  r  d +   v +  +ele  +   e  i  +E+ ka++++l+ee +el+++ +ele+++++lr+  e ++  l
  gi|320101131|ref|YP_004176723.1|  84 RRYTRGGDTISKLVSSVLSELESRGGYIEVEIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARL 160
                                       56667778888888889999999999999999******************************************999 PP

                    CENP-F_leu_zip  90 qkkqer 95 
                                       ++ qe+
  gi|320101131|ref|YP_004176723.1| 161 KELQET 166
                                       999987 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   2.6   4.3e-07    0.0001     127     177 ..     117     167 ..     109     168 .] 0.93

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.3e-07
                           Leu_zip 127 gaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkel 177
                                       ++e Lk +i+ L+een+ L++r++elE+q+ ++ +  + +++ lkelq++l
  gi|320101131|ref|YP_004176723.1| 117 SVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       57889****************************99999*********9875 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   4.1e-07   9.7e-05     159     213 ..     112     165 ..      32     168 .] 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.1e-07
                            HAP1_N 159 lqklvqldlLqeklreLeeeNekLreeasqLktetdtlEekEqqLvldcveqlse 213
                                       + ++++++ L+ k++ LeeeN++Lr++ ++L+ + ++l +   +Lv+   ++l+e
  gi|320101131|ref|YP_004176723.1| 112 EVEIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRN-TVELVKARLKELQE 165
                                       567899*************************888777754.45677777777766 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 !   18.1   1.6   1.1e-05    0.0026       5      40 ..     111     149 ..     107     150 .. 0.84
   2 !   12.8   0.6   0.00051      0.12       1      30 [.     138     167 ..     138     168 .] 0.94

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-05
                         FlaC_arch   5 lEnklsklst...eletvkkeneelsksveelkenVkdl 40 
                                       +E +++++++   +++ +++en+el+k ++el+ +V +l
  gi|320101131|ref|YP_004176723.1| 111 IEVEIPSVESlkaKINGLEEENKELRKRIQELEAQVSQL 149
                                       5666666666666*********************99876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00051
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksv 30 
                                       ri+elE ++s+l  ++e vk+ ++el++++
  gi|320101131|ref|YP_004176723.1| 138 RIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       89************************9987 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 !   19.6   1.5   2.7e-06   0.00064      82     130 ..     117     165 ..      73     168 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-06
                          KASH_CCD  82 krarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlk 130
                                       + ++lka+ + le en+ L+++i++L+ +  +l+   + +k +lkeL +
  gi|320101131|ref|YP_004176723.1| 117 SVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       5678899999999999999999999999999999999999999999976 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 !   18.7   0.8   3.1e-06   0.00073      84     130 ..     119     165 ..      87     168 .] 0.55

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.1e-06
                             Atg14  84 qelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrk 130
                                       + lk+k+  l +e++e +k++++l +++++ r + e+++ +l+e ++
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       34444444444444444444444444444444444444444444433 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 !   19.0   3.2   4.6e-06    0.0011      45     100 ..     111     166 ..      91     168 .] 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.6e-06
                             DHR10  45 ieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreq 100
                                       ie+e+ ++e+ k+k++ l+++ +e++++ +ele++ ++l+  +e  + +l  l+e+
  gi|320101131|ref|YP_004176723.1| 111 IEVEIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       8999999*******************************************999986 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 !   18.2   4.0   9.9e-06    0.0023      43      94 ..     118     166 ..     110     168 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.9e-06
                           BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       ++sl++k++ l   +ee +++ ++i+++e+qv++L ++v+ + +  keL++ 
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGL---EEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       44555555555...5588889999********************99999876 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   3.6   8.1e-06    0.0019      99     144 ..     117     162 ..     115     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.1e-06
                         PspA_IM30  99 qaealetqlaqqrsaveqlrkqlealetkieelkakkellkareka 144
                                       ++e l+++ + +++  ++lrk +++le+++++l++ +el+kar+k 
  gi|320101131|ref|YP_004176723.1| 117 SVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKE 162
                                       588999999**********************************985 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 ?    3.8   0.0      0.34        80      58      75 ..      37      54 ..      30      56 .. 0.86
   2 !   13.8   2.8   0.00026     0.061       8      45 ..     116     153 ..     110     168 .] 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.34
                       Cep57_MT_bd 58 eelvkrlEaKadqIykLy 75
                                       +l++++E Ka  I++Ly
  gi|320101131|ref|YP_004176723.1| 37 LQLLSSVEDKAGFIKELY 54
                                      5899*************9 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00026
                       Cep57_MT_bd   8 spkeaLaevlkeLedEfehlklelqelaaqynaldpsl 45 
                                       ++ e+L+  +++Le+E ++l+++ qel+aq  +l   +
  gi|320101131|ref|YP_004176723.1| 116 PSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTV 153
                                       6779999**************************98444 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.3   8.2e-06    0.0019      47      96 ..     116     165 ..      80     168 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.2e-06
                            APG6_N  47 eeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96 
                                        ++e+l+ ++  le+e +el + ++ele++ ++l++ ++  ++ l++l+e
  gi|320101131|ref|YP_004176723.1| 116 PSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       56789999999999999999999999999999999999999999999987 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.5   8.1e-06    0.0019     200     249 ..     117     166 ..      92     168 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.1e-06
                              Spc7 200 eLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleee 249
                                       ++e+l+ +++ l++e +e++k+++el++q+ +l++++e +k++ +el+e 
  gi|320101131|ref|YP_004176723.1| 117 SVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       57999999999999999999999999999999999999999999999986 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.6   1.1e-05    0.0027      50     116 ..      91     159 ..      71     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-05
                              YkyA  50 dkikklsdealenveeReellekekesieeakeefekikeeieei..edeelkkeaeelieameeryea 116
                                       d+i+kl++ +l+ +e R  ++e e  s+e+ k +++ ++ee +e+    +el+ ++++l +++e  ++ 
  gi|320101131|ref|YP_004176723.1|  91 DTISKLVSSVLSELESRGGYIEVEIPSVESLKAKINGLEEENKELrkRIQELEAQVSQLRNTVELVKAR 159
                                       88*******************************************763446666666666665544433 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.3   1.3e-05    0.0032     204     253 ..     118     167 ..     110     168 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-05
                                       XXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 204 aeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerl 253
                                       +e+ +++++  +ee +elr++iq+le+++++l+++ + ++a+l+el+e+l
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       667788899999*********************************99975 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   5.0   9.6e-06    0.0023      24      53 ..     122     151 ..     119     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.6e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  24 kakeeeleervkeLeeeNaqLrqkveqLek 53 
                                       kak ++lee++keL++++++L+++v+qL++
  gi|320101131|ref|YP_004176723.1| 122 KAKINGLEEENKELRKRIQELEAQVSQLRN 151
                                       99**************************86 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   1.1e-05    0.0026     424     469 ..     117     162 ..      88     168 .] 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                            AAA_13 424 aieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                       ++e+l+++++  e+e k+l+++i+eLe+q+++ ++++e +   Lk+
  gi|320101131|ref|YP_004176723.1| 117 SVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKE 162
                                       5778888888888888888888888888888888888888888876 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.9   2.5e-05     0.006      90     142 ..     120     167 ..     116     168 .] 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.5e-05
                              Wtap  90 rLmakcrvLeqENeELgkvleegrvakLeselalqkkfveelkkaleeleell 142
                                       +L ak+  Le+EN+EL       r+++Le +++ ++++ve +k +l+el+e l
  gi|320101131|ref|YP_004176723.1| 120 SLKAKINGLEEENKEL-----RKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       5789************.....66888899999999999999999888888865 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   2.2e-05    0.0051      50      86 ..     118     154 ..      91     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-05
                       Sipho_Gp157  50 iknleaeaeaikeeekrLaerkkslenkaenLKeyle 86 
                                       +++l+a++++++ee k+L +r + le+++ +L++++e
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVE 154
                                       789******************************9976 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 !   16.2   2.3   3.4e-05    0.0079       2      43 ..     124     165 ..     115     168 .] 0.64

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-05
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqq 43 
                                       +++ leee k+l+++++e+ea++++l++ +e  ++++ke q+
  gi|320101131|ref|YP_004176723.1| 124 KINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       455566666666666666666666666666666666666665 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.1   3.3e-05    0.0077      15      42 ..     119     146 ..     117     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-05
                              HALZ  15 daLksdydsLkkenekLkaelqeLkekl 42 
                                       ++Lk++ + L++en++L++ +qeL +++
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQV 146
                                       89**********************9975 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 !   16.7   0.5   3.2e-05    0.0076      63      96 ..     129     161 ..      95     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.2e-05
                           DUF4140  63 eeeelkalraeleeledelaaledelaaaearla 96 
                                       ee e k+lr++++ele++ ++l+++ + ++arl+
  gi|320101131|ref|YP_004176723.1| 129 EE-ENKELRKRIQELEAQVSQLRNTVELVKARLK 161
                                       23.599*************************997 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.8   4.6e-05     0.011      50      88 ..     126     164 ..     116     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.6e-05
                            GCN5L1  50 kklekeakalqanvakfakqtdqWlalvesfnsalkeiG 88 
                                       + le+e k+l++++++++ q++q  ++ve ++ +lke+ 
  gi|320101131|ref|YP_004176723.1| 126 NGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQ 164
                                       679**********************************96 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4     3e-05    0.0072      16      64 ..     119     166 ..      96     168 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3e-05
                        Phage_GP20  16 t..kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqak 64 
                                          kak++ +eee+++l +++++ + q+++L +    +e +++ ++elq++
  gi|320101131|ref|YP_004176723.1| 119 EslKAKINGLEEENKELRKRIQELEAQVSQLRNT---VELVKARLKELQET 166
                                       2579***************************655...9**********997 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 !   16.6   1.5   3.8e-05    0.0089      34      70 ..     123     159 ..      75     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.8e-05
                      Syntaxin-6_N  34 stseeldetrteLrkalrsiewdledLeetvrivekn 70 
                                       ++ + l+e ++eLrk ++++e ++++L++tv+ v++ 
  gi|320101131|ref|YP_004176723.1| 123 AKINGLEEENKELRKRIQELEAQVSQLRNTVELVKAR 159
                                       3677899999999999999999999999999998764 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.4   3.8e-05     0.009     344     394 ..     116     166 ..      91     168 .] 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                                       TTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHH CS
                              EzrA 344 eklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieek 394
                                        ++++l+++++ le++ +el+++++e ++  S+l++ +e ++ +l+e++e 
  gi|320101131|ref|YP_004176723.1| 116 PSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       455555666666666666666666666666666666666666666555554 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.9   4.5e-05     0.011      62     104 ..     118     160 ..      90     168 .] 0.59

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.5e-05
                           DUF4618  62 kkqleqakaeLqeweekeekklekLeqqleqlnakvqklqeel 104
                                        + l++  + L+e ++++ k++++Le q+ ql ++v+ ++  l
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARL 160
                                       4445555555555555555555555555555555555554444 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   4.7e-05     0.011     332     380 ..     118     166 ..      77     168 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.7e-05
                            DUF812 332 leelqeqieeleskieeleeeikklessikqveeeleeekeeneeleke 380
                                       +e+l+ +i+ le++ +el++ i++le++++q+ +++e  k+  +el+++
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       6788999999999999999999999999999999999999888888876 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.4   6.3e-05     0.015       8     105 ..      76     167 ..      70     168 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.3e-05
                             THOC7   8 Llnveerplkrltkrllklltslaesteeeleqlkedllldfaafelsierlqllakanerereryeaekeeiesei 84 
                                       L +  e++++r t+  ++ ++ l++s  +ele+    +++++ + e+  ++++ l++ n++ r+r++    e+e++ 
  gi|320101131|ref|YP_004176723.1|  76 LGI-PEKTVRRYTRGGDT-ISKLVSSVLSELESRGGYIEVEIPSVESLKAKINGLEEENKELRKRIQ----ELEAQV 146
                                       555.67777888877777.444457789999999999999999999999999999999999999998....789999 PP

                             THOC7  85 eavreeieelkaqLeearatr 105
                                       +++r+  e  ka+L+e ++t+
  gi|320101131|ref|YP_004176723.1| 147 SQLRNTVELVKARLKELQETL 167
                                       999999999999999999886 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.2   9.6e-05     0.023      11      84 ..      78     154 ..      71     168 .] 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.6e-05
                            CENP-Q  11 fPpat...qsdggkekeldfeklldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaearerk 84 
                                       +P +t   +++gg+  ++ + ++l+e  +   + + e  s+e L+a i+ +e++ ++  + ++eLe++++ ++++ +
  gi|320101131|ref|YP_004176723.1|  78 IPEKTvrrYTRGGDTISKLVSSVLSELESRGGYIEVEIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVE 154
                                       56655655567777777777778888888888888888888888888888888888888888888888887776633 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   8.6e-05      0.02      69     116 ..     119     166 ..      82     168 .] 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.6e-05
                           DUF1664  69 drvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       +++ +k++  +e  ke+++ ++e++ ++s++++ ve vk+  ++l+++
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       445555555555566666666666666666666666666555555554 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 ?    7.4   0.2     0.017         4      17      34 ..     119     136 ..     117     138 .. 0.88
   2 ?    9.6   0.6    0.0034      0.81      16      35 ..     132     151 ..     132     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.017
                       Shugoshin_N  17 salslkirelekevseLl 34 
                                        +l++ki+ le e+ eL+
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELR 136
                                       5799***********997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0034
                       Shugoshin_N  16 NsalslkirelekevseLls 35 
                                       N+ l+ +i+ele+ vs+L++
  gi|320101131|ref|YP_004176723.1| 132 NKELRKRIQELEAQVSQLRN 151
                                       666888************98 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 ?   14.6   7.5   0.00011     0.025      22      68 ..     119     165 ..     117     168 .] 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.00011
                        TMF_DNA_bd  22 ekLskkelklnntikkLrkknkelekeikelkkkleklekeleelee 68 
                                       e L++k + l++  k+Lrk ++ele ++++l + +e +   l+el+e
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       55666666666666666666666666666666666666666666666 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0    0.0002     0.047       8      37 ..      57      86 ..      53      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0002
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrw 37
                                      +++l +++  +s+  I++eLg+++ Tv+r+
  gi|320101131|ref|YP_004176723.1| 57 ASALSMFRANYSYGLISQELGIPEKTVRRY 86
                                      578999999999999*************97 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.5   9.7e-05     0.023     425     490 ..     101     166 ..      91     168 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-05
                            DUF773 425 LiliktspryvdrlvasLeqklkqeeklkeklkdleekreelqeelselepkleklvkktrelkkl 490
                                       L ++ +   y++  + s e+ +++++ l+e+ k+l+++ +el+ ++s+l+ ++e + ++ +el++ 
  gi|320101131|ref|YP_004176723.1| 101 LSELESRGGYIEVEIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       56677777899999999***********************************************87 PP

>> TcpS  Toxin-coregulated pilus protein S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.9   0.00012     0.028      28      63 ..     112     152 ..      96     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00012
                              TcpS  28 ennyksiesLknkleqL.....eLkkkileveieikeaedk 63 
                                       e ++ s+esLk k++ L     eL+k+i+e+e ++ + ++ 
  gi|320101131|ref|YP_004176723.1| 112 EVEIPSVESLKAKINGLeeenkELRKRIQELEAQVSQLRNT 152
                                       66789*********76633333699********99987754 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 ?   14.5   2.1   0.00012     0.028      21      76 ..     110     166 ..      94     168 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00012
                             Mod_r  21 lvk.tlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkeleke 76 
                                       +++ ++p+v++lk++   l++en++l ++  +le ++ +lr+ ++     lkel+++
  gi|320101131|ref|YP_004176723.1| 110 YIEvEIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       565577999999999999999999999999999999999999999999999999886 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   5.6   0.00014     0.033      16      64 ..     118     166 ..     112     168 .] 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00014
                     Tropomyosin_1  16 aeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakek 64 
                                       +e l++k+  le+en+e  + i++L+ +++ql + ve ++++lke +e+
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       6889999999*********************************999987 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.2   0.00031     0.073      13      51 ..     116     154 ..     109     168 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00031
                   Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                       p+++ l++k++ l+++ +eL++++++l +++ +l+++ e
  gi|320101131|ref|YP_004176723.1| 116 PSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVE 154
                                       899999999999999999999999999999999988776 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.24        58       9      31 ..     118     140 ..     116     141 .. 0.86
   2 ?   11.1   0.5    0.0017      0.39       4      35 ..     134     165 ..     131     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.24
                               LPP   9 VsqLkskvdqlssdvnsakaaaq 31 
                                       V++Lk+k++ l+++ +++++ +q
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQ 140
                                       899**********9999887766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0017
                               LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                       eL + +++L+++v+ql + v+ +ka +++ +e
  gi|320101131|ref|YP_004176723.1| 134 ELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       67788899999999999999888888877765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.2   0.00019     0.044     105     152 ..     119     166 ..     115     168 .] 0.54

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00019
                             ATG16 105 lelneelqkleeklkedeerlaeleaeraaletklkdreeelrekekl 152
                                        +l++++  lee+ ke ++r++elea++++l+  ++  +++l+e++++
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       445555555555555555555555555555555555555555555544 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.6   0.00023     0.054       3      27 ..     117     141 ..     115     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00023
                      Herpes_BLRF2   3 tvEdlaaelakLkvENkaLkkklks 27 
                                       +vE l+a+++ L+ ENk+L+k++++
  gi|320101131|ref|YP_004176723.1| 117 SVESLKAKINGLEEENKELRKRIQE 141
                                       89*******************9954 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 ?   13.0   5.1   0.00021     0.049      29      77 ..     119     167 ..     113     168 .] 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00021
                               GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkql 77 
                                       +slK +i+ l++++++ +k+++e++++ ++l+ +++ +++ ++eL++ l
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       5677777777777777777777777777777777777777777777655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0004     0.095      26      46 ..      66      86 ..      57      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0004
                                      ---HHHHHHHHT--HHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksr 46
                                      ++sy  I+++lgi+e+tV+++
  gi|320101131|ref|YP_004176723.1| 66 NYSYGLISQELGIPEKTVRRY 86
                                      689999*************97 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4    0.0039      0.91      16      34 ..     118     136 ..     116     137 .. 0.90
   2 ?    8.0   4.7     0.015       3.5      18      43 ..     134     159 ..     131     168 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0039
                             TSC22  16 VevLkekIkeLeernsele 34 
                                       Ve Lk kI  Lee+n+el+
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELR 136
                                       99************99996 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.015
                             TSC22  18 vLkekIkeLeernseleeENslLkal 43 
                                       +L+++I+eLe+++s+l++  +l ka 
  gi|320101131|ref|YP_004176723.1| 134 ELRKRIQELEAQVSQLRNTVELVKAR 159
                                       699************99988888865 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   0.00034      0.08      32      67 ..     122     157 ..      91     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00034
                           DUF2730  32 redleklaekveendkrlteletkvenLPtakdlek 67 
                                       +  ++ l+e+ +e +kr++ele++v++L ++++l k
  gi|320101131|ref|YP_004176723.1| 122 KAKINGLEEENKELRKRIQELEAQVSQLRNTVELVK 157
                                       567788999999999999999999999999998854 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.6   0.00031     0.073       8      52 ..     119     163 ..     111     168 .] 0.60

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00031
                                       TTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHH CS
                              GrpE   8 eeeedeeeeleeeleelekevkelkekllrllaefenlrkrteke 52 
                                       e+++++++ leee +el+k+++el+ ++ +l++ +e ++ r+++ 
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKEL 163
                                       345556666666666666666666666666666666666666554 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   0.00031     0.073      77     146 ..     101     167 ..      85     168 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00031
                            DUF724  77 laeLekhGFdVkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerql 146
                                       l+eLe  G     ++  +  + slk + + l+ee k+l k+i+e e++ ++l + ++ ++ + +el++ l
  gi|320101131|ref|YP_004176723.1| 101 LSELESRGG---YIEVEIPSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       666666663...44556777889999999999************99999999999999999999999876 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   0.00037     0.087       4      53 ..     118     167 ..     115     168 .] 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00037
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelkssl 53 
                                       +e+l+ +++ lee++ke++++++el+++ s+++++++  k rlkel+++l
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       7899999***************************************9987 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.4   0.00041     0.096      42      86 ..     121     165 ..     116     168 .] 0.47

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00041
                           DUF3450  42 lddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                       l+ + + l++e ++l++++++le++ +ql++ v+ +++++++l+e
  gi|320101131|ref|YP_004176723.1| 121 LKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       344444445555555555555555555555555555555555544 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       2.3   5.4e+02      61      88 ..      98     125 ..      86     130 .. 0.77
   2 ?   11.1   7.5    0.0013       0.3      65     103 ..     126     164 ..     117     168 .] 0.65

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  61 eevkeeLeerketlekeiktlekqlekl 88 
                                        +v++eLe r  ++e ei ++e+ + k+
  gi|320101131|ref|YP_004176723.1|  98 SSVLSELESRGGYIEVEIPSVESLKAKI 125
                                       6778888888888888888887766554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                                       + Lee+ ++l k+i++le q ++l++++e +k+ l++++
  gi|320101131|ref|YP_004176723.1| 126 NGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQ 164
                                       456677777777777777777777777777777766665 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.3   0.00064      0.15       2      40 ..     128     166 ..     117     168 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00064
                             Spc24   2 ldnekfriakelsdleselesleselaelkeeleeleee 40 
                                       l++e+ ++ k +++le+++++l+++ +  k++l+el+e 
  gi|320101131|ref|YP_004176723.1| 128 LEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       678888999999999999999999999999999999985 PP

>> M  M protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.1   0.00035     0.081       1      20 [.     130     149 ..     130     150 .. 0.93
   2 ?    0.7   0.7       5.1   1.2e+03       6      16 ..     156     166 ..     154     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00035
                                 M   1 eakkeLEaelqeLeeelqaL 20 
                                       e++keL ++ qeLe++  +L
  gi|320101131|ref|YP_004176723.1| 130 EENKELRKRIQELEAQVSQL 149
                                       79**************9988 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 5.1
                                 M   6 LEaelqeLeee 16 
                                       + a+l+eL+e 
  gi|320101131|ref|YP_004176723.1| 156 VKARLKELQET 166
                                       67999999985 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.15        36      29      60 ..     110     141 ..      93     143 .. 0.77
   2 ?   11.8   1.0    0.0011      0.26      20      65 ..     118     160 ..     111     168 .] 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.15
                           NPV_P10  29 dvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                        ++ ++p v+ l++k++++ ++ +el + +++
  gi|320101131|ref|YP_004176723.1| 110 YIEVEIPSVESLKAKINGLEEENKELRKRIQE 141
                                       57778999999999999999999999988876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0011
                           NPV_P10  20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       V++l+++++ ++e+ ++   l ++++++ aq+ +l ++ve ++  L
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKE---LRKRIQELEAQVSQLRNTVELVKARL 160
                                       77888888888887666...77888888888888888887766555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.6   0.00068      0.16      44      89 ..     119     164 ..      91     168 .] 0.48

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00068
                                       H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHH CS
                             DUF16  44 dklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelil 89 
                                       ++l+ +in le++ +++ ++i+el++++ + ++ ++ v+  l+ + 
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQ 164
                                       2333333333333333333333333333333333333333333333 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.7    0.0007      0.16       1      43 [.     121     167 ..     118     168 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0007
                           DUF5082   1 lktkisklqaqiaelrseiaaleekIerLk....eaktklsdekesl 43 
                                       lk+ki+ l+++  elr++i+ le +++ L+     +k +l++ +e+l
  gi|320101131|ref|YP_004176723.1| 121 LKAKINGLEEENKELRKRIQELEAQVSQLRntveLVKARLKELQETL 167
                                       67899999999999999999999999999955555666666666665 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   0.00056      0.13     177     239 ..     105     166 ..      98     168 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00056
                        Fmp27_WPPW 177 eeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkes 239
                                       e+R   +e +i ++e+   +++  +e+ ++el+++i+ele ++++l++ +e++++ l++l+e+
  gi|320101131|ref|YP_004176723.1| 105 ESRGGYIEVEIPSVESLKAKINGLEEE-NKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       566667777777666666666666666.688**************************999986 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.2    0.0015      0.36      22      70 ..     116     164 ..      94     168 .] 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXX CS
                              YabA  22 eeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegk 70 
                                        ++e+lk++++ l een+eL+   ++l  ++++ +++ +  k++l+e +
  gi|320101131|ref|YP_004176723.1| 116 PSVESLKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQ 164
                                       4567778888888888888887777777777555555444444444444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7    0.0014      0.32      76     129 ..      94     150 ..      80     154 .. 0.80
   2 ?   10.7   1.5    0.0019      0.46      26      65 ..     128     167 ..     124     168 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHCCCHHHHHHHCCH...HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  76 dnvikksskeleeeilrlketidaqe...snirvLqnvlesneqkiqkLeqdidqke 129
                                       +++++++ +ele++  +++ +i + e    +i+ L +  ++++++iq+Le +++q++
  gi|320101131|ref|YP_004176723.1|  94 SKLVSSVLSELESRGGYIEVEIPSVEslkAKINGLEEENKELRKRIQELEAQVSQLR 150
                                       567788889999999999998876653356899999999999999999999999986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0019
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdsl 65 
                                       l++ +k+++k++++le ++++++n+ + ++   ke++++l
  gi|320101131|ref|YP_004176723.1| 128 LEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       6777888888888888888888888888888888888765 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.2   0.00082      0.19      86     118 ..     118     150 ..     116     152 .. 0.85
   2 ?   -0.1   0.1       3.4   8.1e+02      78      93 ..     152     167 ..     149     168 .] 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00082
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  86 leelekqlekleeeleklkdqittleanlaqly 118
                                       +e+l++ +  leee ++l+++i++lea+++ql 
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRKRIQELEAQVSQLR 150
                                       688999999999999999999999999999875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekql 93 
                                        +el+k +l+el+++l
  gi|320101131|ref|YP_004176723.1| 152 TVELVKARLKELQETL 167
                                       4667777777777665 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.0    0.0013      0.31       2      45 ..     122     165 ..     121     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                              Swi5   2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklLhe 45 
                                       +a+i+ lee+ +el+k ++el+++  +  +  e vk  +k L+e
  gi|320101131|ref|YP_004176723.1| 122 KAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       7899999*****************999999999*****999997 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 ?   11.0   4.7    0.0016      0.38      46      96 ..     119     166 ..      92     168 .] 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  46 eelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                       e+l+a+ N l +e +++ k    ++el a+v++l + ++ ++a+lkel++ 
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRK---RIQELEAQVSQLRNTVELVKARLKELQET 166
                                       4444444444444444443...24444444444444444444444444444 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       7.5   1.8e+03     202     218 ..      72      88 ..      58      89 .. 0.74
   2 ?   10.4   2.4    0.0013       0.3      97     126 ..     136     165 ..     133     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.5
                            CASP_C 202 aykrLsllerlvlsltr 218
                                         ++L ++e++v + tr
  gi|320101131|ref|YP_004176723.1|  72 ISQELGIPEKTVRRYTR 88 
                                       6789999***9999988 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                            CASP_C  97 rkrnaeLEeelrkqeetvsslraeiaslqk 126
                                       rkr++eLE+++++ ++tv+ ++a +++lq+
  gi|320101131|ref|YP_004176723.1| 136 RKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       9***************************96 PP

>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.3     0.004      0.94      13      32 ..     118     137 ..     115     142 .. 0.90
   2 ?    4.4   1.1      0.14        33      15      31 ..     134     150 ..     133     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.004
                          WD40_alt  13 qeqlkvrvseLeeEVrtLrK 32 
                                       +e+lk ++  LeeE + LrK
  gi|320101131|ref|YP_004176723.1| 118 VESLKAKINGLEEENKELRK 137
                                       79*****************9 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.14
                          WD40_alt  15 qlkvrvseLeeEVrtLr 31 
                                       +l+ r+ eLe  V+ Lr
  gi|320101131|ref|YP_004176723.1| 134 ELRKRIQELEAQVSQLR 150
                                       5899**********999 PP

>> IFP_35_N  Interferon-induced 35 kDa protein (IFP 35) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.8    0.0014      0.34       2      28 ..     125     151 ..     124     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0014
                          IFP_35_N   2 iaeitkeniqLkeeiqkLeaELQettr 28 
                                       i+ +++en++L ++iq Lea   ++  
  gi|320101131|ref|YP_004176723.1| 125 INGLEEENKELRKRIQELEAQVSQLRN 151
                                       56799**************99887765 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 ?   10.3   6.7    0.0025      0.59      18      66 ..     120     167 ..     118     168 .] 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0025
                            Cnn_1N  18 dLKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkll 66 
                                       +LK +i+ Lee+ ++l++  ++el+++  +l+ +ve  +  lke+++ l
  gi|320101131|ref|YP_004176723.1| 120 SLKAKINGLEEENKELRK-RIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       699999999999999999.999999999999999999999999999987 PP

>> ORF6C  ORF6C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.9    0.0025       0.6       6      43 ..     129     166 ..     124     168 .] 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0025
                             ORF6C   6 lealkehdekieeidervkkLeenmpldesekeeiqkk 43 
                                        e++ke+ ++i+e++ +v++L+++  l ++  +e+q+ 
  gi|320101131|ref|YP_004176723.1| 129 EEENKELRKRIQELEAQVSQLRNTVELVKARLKELQET 166
                                       5899*************************999999975 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.2    0.0045       1.1       3      52 ..     123     165 ..     117     168 .] 0.49

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                       ++++ LE++        +eL + + e + q+++l+  ++l++ rlkel+e
  gi|320101131|ref|YP_004176723.1| 123 AKINGLEEEN-------KELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       3444444444.......555555555555555555555555555555554 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.0     0.028       6.6      41      66 ..     116     141 ..      93     144 .. 0.70
   2 ?    9.0   6.6    0.0075       1.8      22      62 ..     125     165 ..     119     168 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.028
                            Csm1_N  41 qeiesLkeqlaeleekvkeleerrkk 66 
                                         +esLk++++ lee++kel +r ++
  gi|320101131|ref|YP_004176723.1| 116 PSVESLKAKINGLEEENKELRKRIQE 141
                                       56888888888888888888877554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0075
                            Csm1_N  22 vsklvhENsvLsqkletkdqeiesLkeqlaeleekvkelee 62 
                                       ++ l +EN  L+++++  + ++++L+++++ +++++kel+e
  gi|320101131|ref|YP_004176723.1| 125 INGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQE 165
                                       56667889999999999999999999999999999988887 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 ?    8.2   4.7     0.011       2.6      21      63 ..     125     164 ..     115     168 .] 0.52

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.011
                              Med9  21 skdletktgelrhkLkkarelirelpgidrsveeqeaeieele 63 
                                       ++ le +  elr+++++  +++++   +  +ve  +a+++el+
  gi|320101131|ref|YP_004176723.1| 125 INGLEEENKELRKRIQELEAQVSQ---LRNTVELVKARLKELQ 164
                                       444555555666666666666666...4444444444444444 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.2    0.0088       2.1      11      57 ..     119     167 ..     101     168 .] 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0088
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleeleaeL 57 
                                       e l a+I+ LEee +el +++++ e   s+  +++  + a+l+el++ L
  gi|320101131|ref|YP_004176723.1| 119 ESLKAKINGLEEENKELRKRIQELEAQvSQLrNTVELVKARLKELQETL 167
                                       6788899999999999999888777443333555666666677666655 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.0     0.011       2.5       2      48 ..     121     167 ..     118     168 .] 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.011
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkklesnq 48 
                                       +k +++ +e++ ++l +r+++le   +  ++ ++ +  +lk+l++++
  gi|320101131|ref|YP_004176723.1| 121 LKAKINGLEEENKELRKRIQELEAQVSQLRNTVELVKARLKELQETL 167
                                       57899999999999999*****************9999***999985 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.6      0.25        58      66      99 .]     130     163 ..     112     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.25
                           DUF5320  66 taeaskeeekelLeeqaeaLeeeleaikkrlkel 99 
                                        ++++ +++++ Le+q + L++ +e +k+rlkel
  gi|320101131|ref|YP_004176723.1| 130 EENKELRKRIQELEAQVSQLRNTVELVKARLKEL 163
                                       4455556667778888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1950  (0.108762); expected 358.6 (0.02)
Passed bias filter:                     1438  (0.0802053); expected 358.6 (0.02)
Passed Vit filter:                       407  (0.0227007); expected 17.9 (0.001)
Passed Fwd filter:                        78  (0.00435049); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              76  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 1223.21
//
Query:       gi|320101132|ref|YP_004176724.1|  [L=332]
Description: peptidase M19 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-71  241.3   0.0    1.6e-71  241.1   0.0    1.0  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
    0.00035   20.5   0.0     0.0029   17.4   0.0    2.1  1  Amidohydro_2   Amidohydrolase


Domain annotation for each model (and alignments):
>> Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.1   0.0   1.8e-75   1.6e-71       7     318 ..       4     328 ..       2     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: 241.1 bits;  conditional E-value: 1.8e-75
                                       .EEEEEE-HHHHHHHCTTTTT.....-TTTHCTSSS-HHHHHHHTEEEEEEEEE--C..........CCCCCCHHHH CS
                     Peptidase_M19   7 iviDghndlplklrqekkesl.....llekdselqtdlerlraggvsavlfaifvpe..........dasyeeavka 68 
                                       +++D h dl++++ + +  +      l  ++   + d++++ a+   + + a+f+            +  +  +++ 
  gi|320101132|ref|YP_004176724.1|   4 PLVDLHEDLAAYILSGSLLNPfplkpLDVDEPYRHADIPKYIASNTRLIVGAVFP-MipwytghgriTYRHYPSLEL 79 
                                       67889999988887777655577887777788899*********99999999993.346899****99999****** PP

                                       HHHHHHHHHHHHHHGTTTEEE-SSHHHHHHHHH..TT-EEEEEEEESCGGGTT-HHHHHHHHHTTEEEEES-SSS-B CS
                     Peptidase_M19  69 tleqidlirrlvrknpeqlklvrtaddierakk..egkiavllgiegaealgddlallrafyalGvrvlgltynrnn 143
                                       + e i+l+r+lv +++e lklv+  d +   ++   +++++++g+ega++l ++ + l+ ++++G+rvlglt+n++n
  gi|320101132|ref|YP_004176724.1|  80 VFEGISLYRNLVTAHRE-LKLVEAKDGLTGLFEgdWNRMGLIIGLEGADPL-RNPEELDLLHSAGLRVLGLTWNYSN 154
                                       ****************9.************9996568**************.99*********************** PP

                                       SSB-BCCGTT.SSSSB-HHHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH-SSE.EECCEEBTTTS--TTSB-HHHH CS
                     Peptidase_M19 144 kfAdgaleekdedgGLsefGkelVrelNrlgiliDlShlsektfldvlelSkaPvvaSHSnaralcdhpRNltDeql 220
                                       k+A++++ +   d+GL++ G elV ++ +lg+++Dl+h+s+kt++dv e++ +Pv++SH+n+++++d pRNl+D+ l
  gi|320101132|ref|YP_004176724.1| 155 KYASSCRAQ--VDNGLTREGVELVGRAVELGVVVDLAHASAKTIRDVYEVTGKPVLVSHANVKTVHDAPRNLDDKSL 229
                                       ********8..****************************************************************** PP

                                       HHHHHTT-EEEE-SSHHHCTTTS--BHHHHHHHHHHHHHHT-GGGEEE---T..TTTSS-BBTBSSGGGHHHHHHHH CS
                     Peptidase_M19 221 kaiaesgGvvgvtfvpaflkekaeatledvvdhidyivelaGidhVGlGsDf..dgggelpegledvsklpnltaeL 295
                                       + iaes+Gvvg++f++ f+++  ++ + ++v+h  yi++ +G+d +++GsD+    ++ l++gle+++k+ nl   L
  gi|320101132|ref|YP_004176724.1| 230 ETIAESKGVVGLVFISPFVSS-GRPGVAELVRHAVYIRDNYGVDVIAIGSDYfgSLDTPLVAGLESIDKIGNLWSSL 305
                                       *******************99.9*****************************664445569**************** PP

                                       HHTTS-HHHHHHHHTHHHHHHHH CS
                     Peptidase_M19 296 lrrgyseadiekilggNflrvle 318
                                        ++g++ +dieki+++N++rvl+
  gi|320101132|ref|YP_004176724.1| 306 VAEGFTPEDIEKIAWRNAVRVLS 328
                                       *********************96 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.2e-07    0.0029     238     289 ..     267     327 ..     133     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.2e-07
                                       HHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH.........SSHHHHHHHHTHHHHHHC CS
                      Amidohydro_2 238 eavgpdrilfGsDyPhptleaepealalldlval.........lsdeerekilggNAarly 289
                                       + +g d i  GsDy+ +  +  ++ l  +d++           +++e+ eki++ NA+r++
  gi|320101132|ref|YP_004176724.1| 267 DNYGVDVIAIGSDYFGSLDTPLVAGLESIDKIGNlwsslvaegFTPEDIEKIAWRNAVRVL 327
                                       5566666667*********************999*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 00:00:00.41
# Mc/sec: 2407.14
//
Query:       gi|320101133|ref|YP_004176725.1|  [L=421]
Description: cysteine desulfurase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-144  480.2   0.0   4.5e-144  480.0   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    1.8e-08   34.1   0.0    2.6e-08   33.6   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.6e-07   29.5   0.0      3e-06   26.0   0.0    2.2  3  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    2.9e-05   23.5   0.0    3.6e-05   23.2   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0098   14.9   0.0      0.016   14.3   0.0    1.2  1  SelA             L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
       0.16   12.4   0.3        0.3   11.5   0.3    1.4  1  FAM195           FAM195 family


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.0   0.0  1.5e-147  4.5e-144       1     371 []      24     395 ..      24     395 .. 1.00

  Alignments for each domain:
  == domain 1  score: 480.0 bits;  conditional E-value: 1.5e-147
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       +y+d+aAttqkp +V++a+++yy+ +nanvhr+ h+l++ea++++eea+ekva++ina s  e++f+s+ttea+n+v
  gi|320101133|ref|YP_004176725.1|  24 VYFDNAATTQKPLQVINAISNYYMYHNANVHRGFHTLSQEASQMYEEAHEKVAKFINAYSWREVVFCSNTTEALNIV 100
                                       7**************************************************************************** PP

                                       HHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTT CS
                       Aminotran_5  78 alslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtG 153
                                       a++++ + l++gdeiv+t+++hh+ ++pw+ +ak +ga+vk++ ++++g l+ +++e+l++ekt++va+  +snv+G
  gi|320101133|ref|YP_004176725.1| 101 AYGWGLWnLREGDEIVLTVMDHHSSMLPWRIIAKLKGARVKYVDITDDGYLRYEQFEELISEKTRVVAFPIASNVLG 177
                                       ***************************************************************************** PP

                                       EB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 154 tiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggem 230
                                       ti++  +i++la+++ga+v++D+aq+v+hip dv++l+vDflafsghK+lgPtGiGvl++r++lle+++p+++gg++
  gi|320101133|ref|YP_004176725.1| 178 TINDARRIARLAHRVGAIVVADGAQSVPHIPTDVRELEVDFLAFSGHKMLGPTGIGVLWGRQDLLESMHPFKVGGDT 254
                                       ***************************************************************************** PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                       +++v+l+++++++ p++feaGTpn+a+ iglg a+eyl +ig++++++hek+l ey+l+r+++l++v+ ygp++   
  gi|320101133|ref|YP_004176725.1| 255 IKDVTLDDIVWHDLPWRFEAGTPNIAEGIGLGVAVEYLTRIGMSNVREHEKTLVEYTLKRMRELEDVEYYGPRNPAD 331
                                       ***************************************************************************** PP

                                       CBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       ++++++fn+kg++++ v+++Ld  gIavr+G hca+pl+ rl+l+gtvRaS yiynt ee+d++
  gi|320101133|ref|YP_004176725.1| 332 KTGVIAFNIKGLNHHTVGSALDLFGIAVRTGMHCAHPLHYRLGLKGTVRASYYIYNTLEEIDYF 395
                                       **************************************************************87 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   8.7e-12   2.6e-08      31     150 ..      77     205 ..      53     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 8.7e-12
                                       HHHHHHT-SEEEEESSHHHHHHHHHHH...TTTTTT-EEEEESSS-THHHHH....HHHTT-EEEEE-B-TTTSSB- CS
                   DegT_DnrJ_EryC1  31 afaaylgvkhaiavssGtaAlhlaLra...lgvgpgdeVIvpsltFvatana....vlelgakpvfvDvdpdtynid 100
                                       +f +    + ++ +s+ t+Al ++       ++ +gde++ + +   +++ +    +   ga++ +vD++ d+  + 
  gi|320101133|ref|YP_004176725.1|  77 KFINAYSWREVVFCSNTTEALNIVAYGwglWNLREGDEIVLTVMDHHSSMLPwriiAKLKGARVKYVDIT-DDGYLR 152
                                       33344446899***********987774545666***************87533324456*********9.88889* PP

                                       GGGCGGG--TTEEEE...EEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 101 paaieaaitertkaI...lpVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                        ++ e++i e+t+ +   ++ +++G ++d  ++ ++a++ g +v+ D A+++ 
  gi|320101133|ref|YP_004176725.1| 153 YEQFEELISEKTRVVafpIASNVLGTINDARRIARLAHRVGAIVVADGAQSVP 205
                                       ************988655789*****************************975 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 ?    0.6   0.0     0.055   1.6e+02     241     270 ..      52      82 ..      26      96 .. 0.81
   2 !   26.0   0.0     1e-09     3e-06      88     200 ..     109     227 ..     100     239 .. 0.86
   3 ?   -3.2   0.0      0.76   2.3e+03     297     329 ..     332     362 ..     327     364 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.055
                                       HHHHHHTTHHHHHHHHHHHHH.HHHHHHHTS CS
                   Cys_Met_Meta_PP 241 lllrGlkTLslRlerhqenAl.kvAefLekh 270
                                        ++rG +TLs   ++  e A  kvA+f+++ 
  gi|320101133|ref|YP_004176725.1|  52 NVHRGFHTLSQEASQMYEEAHeKVAKFINAY 82 
                                       578************99998648****9875 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1e-09
                                       S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHH CS
                   Cys_Met_Meta_PP  88 lkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklvylEtptnpllkvvDieki 159
                                       l++Gdeiv++   + ++    + ++k  g +vk+vd         e++e+ i+e+t++v +   +n l  + D ++i
  gi|320101133|ref|YP_004176725.1| 109 LREGDEIVLTVMDHHSSMLPWRIIAKLKGARVKYVDItddgyLRYEQFEELISEKTRVVAFPIASNVLGTINDARRI 185
                                       578999999999999999999999999*********93333334799****************************** PP

                                       HHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTT CS
                   Cys_Met_Meta_PP 160 aklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKyl 200
                                       a+la+ +g++vv D + + p + +   +l++D    S+ K l
  gi|320101133|ref|YP_004176725.1| 186 ARLAHRVGAIVVADGAQSVPhIPTDVRELEVDFLAFSGHKML 227
                                       ****************99994444555788888888877766 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.76
                                       G-SEEEEEESSHHHHHHHHHHC-SSSEECSS-S CS
                   Cys_Met_Meta_PP 297 aggvlsFelkseeekakkfvdnlklfslaeslG 329
                                       ++gv++F++k+   + +++ ++l lf +a+  G
  gi|320101133|ref|YP_004176725.1| 332 KTGVIAFNIKGL--NHHTVGSALDLFGIAVRTG 362
                                       6789*****998..4678888888888887766 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.2e-08   3.6e-05      48     216 ..      85     249 ..      52     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.2e-08
                                       SEEEEES-HHHHHHHHH....HHH--TTEEEEEETT.-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS- CS
                   Beta_elim_lyase  48 eaalfvpqGtaAnsill....killqrgeevivtep.ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaik 119
                                         ++f+ + t A +i         l+ g+e+++t    h  +   + ia l+g++++ +++ ++G++  e++e++i 
  gi|320101133|ref|YP_004176725.1|  85 REVVFCSNTTEALNIVAygwgLWNLREGDEIVLTVMdHHSSMLPWRIIAKLKGARVKYVDITDDGYLRYEQFEELIS 161
                                       46677777777755555466555667888888776636677777799****************************** PP

                                       -S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEES CS
                   Beta_elim_lyase 120 evgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmsl 196
                                       e      k++++   ++ n+      +++  r++a +a++ g  ++ DgA     + ++  +v+e+   vD + +s+
  gi|320101133|ref|YP_004176725.1| 162 E------KTRVVAFPIASNV----LGTINDARRIARLAHRVGAIVVADGAQS---VPHIPTDVREL--EVDFLAFSG 223
                                       9......699*********8....5578999******************953...44556666665..5******** PP

                                       SSTT--SS-.EEEEE-HH......... CS
                   Beta_elim_lyase 197 kKdllanvG.gvlafrddel......e 216
                                        K  l + G gvl +r+d l      +
  gi|320101133|ref|YP_004176725.1| 224 HKM-LGPTGiGVLWGRQDLLesmhpfK 249
                                       **7.568999*******9555555550 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.2e-06     0.016     201     234 ..     213     246 ..     193     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-06
                                       HTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHH CS
                              SelA 201 aeGvdlvsfsGDkllGgpqaGiivGkkelieklk 234
                                       +  vd ++fsG k+lG    G++ G+++l+e ++
  gi|320101133|ref|YP_004176725.1| 213 ELEVDFLAFSGHKMLGPTGIGVLWGRQDLLESMH 246
                                       3469**************************9986 PP

>> FAM195  FAM195 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3    0.0001       0.3       7      49 ..      47      88 ..      43      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                            FAM195  7 vFhrvngkkslrasstkeseeevitpqheElikyind.sWnevv 49
                                      ++h++n  + +  ++ +++ ++++ ++he + k+in  sW evv
  gi|320101133|ref|YP_004176725.1| 47 MYHNANVHRGF--HTLSQEASQMYEEAHEKVAKFINAySWREVV 88
                                      68999999999..666777789*************9659**998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3108.44
//
Query:       gi|320101134|ref|YP_004176726.1|  [L=55]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 426.83
//
Query:       gi|320101135|ref|YP_004176727.1|  [L=466]
Description: amidohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-63  214.9   0.0    2.3e-63  214.6   0.0    1.1  1  Amidohydro_1  Amidohydrolase family
    9.9e-17   61.5   0.8    1.3e-12   48.0   0.1    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 !  214.6   0.0   2.5e-67   2.3e-63       1     344 []      60     424 ..      60     424 .. 0.95

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 2.5e-67
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       iv+PGlI++HvHl q+llr      +l  wl           +pe+a + ++ ++ +++k Gtt ++++g +  +gi
  gi|320101135|ref|YP_004176727.1|  60 IVMPGLINTHVHLAQGLLRACadylPLIPWLkervwplqgnYKPEEALASAKLVVLEMIKTGTTGFLETGLVGRYGI 136
                                       79**************999989999999999********************************************** PP

                                       HHHHHHHHTSSSEEEEEEESSEGGS...............GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECG CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldr...............gsaetskasreklkagaaetikgkadgvvkvalaphe 125
                                       + + e ++    g+r+ +++ ++d                + ++ts + + +l++      +   dg++ ++++p+ 
  gi|320101135|ref|YP_004176727.1| 137 DNIVEFIHGS--GIRAAIARHVMDLkgyalednilheglvEPGDTSFKDTLRLHSKY----H-GWDGRIWIWFGPRT 206
                                       *********9..****************************77777777788887776....3.4489999******* PP

                                       TCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHH CS
                      Amidohydro_1 126 apafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpte 202
                                       + a+s e+ + ++++a++ ++ v++H++e +++ve++++ fg   +   ++e+a+ +gl ++ +++l+h v+++++e
  gi|320101135|ref|YP_004176727.1| 207 PGAVSVELYRRISEKARELKTGVTMHLAEVREDVEYTSKVFG---KK--PVEFAHWVGLTGP-NTVLVHVVWVSDEE 277
                                       ******************************************...66..*************.************** PP

                                       HHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCH CS
                      Amidohydro_1 203 aellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegg 279
                                       +++l e   ++ v+h p+sn++l+sg ++++++l+  v+v+lgtDg  s+n+ +l++e+++a++lq +    + ++ 
  gi|320101135|ref|YP_004176727.1| 278 IRILGET--GTTVSHNPSSNMKLASGAARIAEMLSHRVNVALGTDGGPSNNTYDLVREMKHAALLQPLRTL-R-ADA 350
                                       *******..******************************************************88885444.4.777 PP

                                       CHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.....CT....CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 280 lslkealrmaTingAkalglddkvGsievGkdADlvvvdl.....di....laafvglkkdgnvkkvivkGklv 344
                                       ++++++l+maT+ngA+al +d+ vGsievGk+AD++vvd+     ++     +++v+ ++   vk+ i++G+lv
  gi|320101135|ref|YP_004176727.1| 351 IRAEQVLEMATLNGARALMIDNMVGSIEVGKRADIIVVDYwsphlHPlnnpVSHLVYAASGSDVKHSIIDGRLV 424
                                       *****************************************8866336777********************997 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0     1e-05     0.094       2      26 ..      53      77 ..      52      86 .. 0.87
   2 !   48.0   0.1   1.4e-16   1.3e-12     352     472 ..     297     424 ..     257     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHlagggv 26
                                      vi+a+  +v+PG++  H Hla g +
  gi|320101135|ref|YP_004176727.1| 53 VINAERDIVMPGLINTHVHLAQGLL 77
                                      899999**************99874 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 1.4e-16
                      Amidohydro_3 352 erargstpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalg 426
                                       + a+g ++++e+l+++v+valg+D  +  +++d   ++ +a  +++ r      +   +  e++l + T ++A+al 
  gi|320101135|ref|YP_004176727.1| 297 KLASGAARIAEMLSHRVNVALGTDggPSNNTYDLVREMKHAALLQPLRTL----RADAIRAEQVLEMATLNGARALM 369
                                       4577789******************99999****************9775....6669******************* PP

                      Amidohydro_3 427 ledrkGtLevGadADlvvld.....adpldvdppelaear....vrltvvdGrvv 472
                                        +   G++evG++AD++v d       pl  + ++l++a     v++ ++dGr v
  gi|320101135|ref|YP_004176727.1| 370 IDNMVGSIEVGKRADIIVVDywsphLHPLNNPVSHLVYAAsgsdVKHSIIDGRLV 424
                                       ***99***************888888888888888888879999********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3572.73
//
Query:       gi|320101136|ref|YP_004176728.1|  [L=606]
Description: adenine deaminase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-60  201.0   0.2    3.6e-59  198.9   0.1    2.0  2  Adenine_deam_C  Adenine deaminase C-terminal domain
    5.9e-27   94.9   0.0    8.9e-26   91.0   0.0    2.1  1  Amidohydro_1    Amidohydrolase family
    1.3e-09   38.0   1.4    0.00094   18.8   0.3    2.4  2  Amidohydro_3    Amidohydrolase family
  ------ inclusion threshold ------
       0.18   12.3   0.0       0.72   10.4   0.0    1.9  2  CRISPR_Cse2     CRISPR-associated protein Cse2 (CRISPR_cse2)


Domain annotation for each model (and alignments):
>> Adenine_deam_C  Adenine deaminase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.28   1.2e+03     108     127 ..     235     254 ..     231     258 .. 0.89
   2 !  198.9   0.1     8e-63   3.6e-59       2     168 ..     427     594 ..     426     595 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.28
                                       TTTBBSS-HHHHHHHHHHHH CS
                    Adenine_deam_C 108 aGlmSdepaeevaekleele 127
                                       aG++Sd++  +  e+le+l+
  gi|320101136|ref|YP_004176728.1| 235 AGILSDHESTSAGEALEKLR 254
                                       9**************99997 PP

  == domain 2  score: 198.9 bits;  conditional E-value: 8e-63
                                       SS-EEEEEEEEEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHHH CS
                    Adenine_deam_C   2 liTkelevelpvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedma 78 
                                        +Tk++++e++v+dg+v++d+ +d+++i v++Rh+++g+ + g++kg+++k gA+A+++ahD+hn+iv+G n++dm+
  gi|320101136|ref|YP_004176728.1| 427 ALTKWRILEMQVSDGEVKPDPGRDIMFISVIDRHRGSGSHSAGLIKGLNFKAGAVAQTIAHDTHNLIVAGWNRRDMV 503
                                       58*************************************************************************** PP

                                       HHHHHHHHTTSEEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHH.HHHHTTS-TTTBSGGGGGSTT-TTSSS CS
                    Adenine_deam_C  79 lAvnrvielgGGivvvedgkvlaelpLpiaGlmSdepaeevaekleele.aalkelgvkledpfmtlsflalpviPe 154
                                       +Av+rv+el+GGivvv+dg+v++e++L +aGlmS ++ eev +++ ++  a++k+ + ++e+ fmtl++++lpviPe
  gi|320101136|ref|YP_004176728.1| 504 TAVKRVVELQGGIVVVNDGEVVSEVELRLAGLMSVKEPEEVFREYLNMVdALKKRFHLDFESFFMTLALVSLPVIPE 580
                                       *********************************************9999677777999******************* PP

                                       EEEETTSEEETTTT CS
                    Adenine_deam_C 155 lkltdkGlvdvkkf 168
                                       l++td+Glvdv k 
  gi|320101136|ref|YP_004176728.1| 581 LRITDRGLVDVAKA 594
                                       ***********985 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0     2e-29   8.9e-26       2     344 .]      83     370 ..      82     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 2e-29
                                       EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEE CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglr 78 
                                        +PG+ID+H+H+e++ll         +p  +++ al++g++t + ++++ v+  g++   g++  +ea++elpl++ 
  gi|320101136|ref|YP_004176728.1|  83 AVPGFIDLHIHIESTLL---------DPVGFSKIALKHGTTTVVADPHEVVNVLGIH---GLKMFIEASRELPLKIL 147
                                       69***********9988.........******************************7...***************** PP

                                       EEEESSEGGS.............GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE..EEEEECGTCCSHHHHHHHHHHH CS
                      Amidohydro_1  79 ilggkvsldr.............gsaetskasreklkagaaetikgkadgvvk..valapheapafsdeelkealke 140
                                        +++++++++             +s                 ++ +++ ++v    ++++   +   d e+   +k+
  gi|320101136|ref|YP_004176728.1| 148 YEVPSCVPATdpsymletfgsllDSR---------------SVEEAMHLEGVAglGEVMDFVSVIRADREVLFKVKA 209
                                       *********87665544443332222...............2333333333322589999999999999******** PP

                                       HHHHTTEEEEEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCE CS
                      Amidohydro_1 141 akkrdlpvaiHa..letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagv 215
                                       a +r + v+ Ha  l+ ++  +++ a++ +++e+++  e +e+          l +g++l +               
  gi|320101136|ref|YP_004176728.1| 210 AWDRRMVVDGHAplLSGEELDAYVAAGILSDHESTSAGEALEK----------LRRGMFLFVR-------------- 262
                                       **************888888899***********999999999..........********77.............. PP

                                       EHHHHHHHHSEHHHHHHHHHHHHTSC..EEEEEECT........TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHH CS
                      Amidohydro_1 216 ahcpfsnsilrsgrealrkaldeGvk..vglgtDga........asgnslnlleelrlalklqrgllyedeegglsl 282
                                             + +   ++ al +++++G    +++++D++        ++++ +     + la+           e+g+++
  gi|320101136|ref|YP_004176728.1| 263 ------EGSAWRDLKALLPVVRSGDCklCAFVSDDVnvydlftkGHMDRI-----INLAV-----------EYGVDP 317
                                       ......33455688888888888554478888886655555555666666.....77777...........99**** PP

                                       HHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 283 kealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                        +al+ aTin+A+ l l+d++Gsi++G+  D+v+             +  ++++vi +G++v
  gi|320101136|ref|YP_004176728.1| 318 VKALQYATINPAIRLHLEDQIGSITPGRLGDIVIT---------RRIEHVEPITVIANGDIV 370
                                       ***********************************.........666668889999999887 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   2.1e-07   0.00094       2      38 ..      75     106 ..      74     127 .. 0.72
   2 !   18.0   0.0   3.5e-07    0.0016     411     473 .]     318     371 ..     188     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-07
                      Amidohydro_3   2 viDakGrlvlPGFvDsHtHlagggvnlrllrlpdarv 38 
                                       viD k r+ +PGF+D H+H+ ++      l++ + ++
  gi|320101136|ref|YP_004176728.1|  75 VIDGKDRYAVPGFIDLHIHIESTL-----LDPVGFSK 106
                                       8******************65554.....65555444 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.5e-07
                      Amidohydro_3 411 eealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaearvrltvvdGrvvy 473
                                        +al+  T +pA +l+led  G++ +G  +D+v+ +  + +v+p          ++ +G +vy
  gi|320101136|ref|YP_004176728.1| 318 VKALQYATINPAIRLHLEDQIGSITPGRLGDIVITR-RIEHVEP--------ITVIANGDIVY 371
                                       589*******************************95.6666664........46666666665 PP

>> CRISPR_Cse2  CRISPR-associated protein Cse2 (CRISPR_cse2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.73   3.3e+03      32      70 ..     223     254 ..     198     260 .. 0.76
   2 ?   10.4   0.0   0.00016      0.72      62     122 ..     502     570 ..     477     583 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHHHHHHHCCHCS-SB-TT-CHHHHHHHHH CS
                       CRISPR_Cse2  32 ekepeeraayavaalyaahqqekehdsgkslgaalgrlr 70 
                                         + ee  ay++a+++  h+++       s g+al +lr
  gi|320101136|ref|YP_004176728.1| 223 LLSGEELDAYVAAGILSDHEST-------SAGEALEKLR 254
                                       5678899999999999999984.......6777777766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHTCT.H........HHHHHHHHHHCT-SSCCCHHHHHHHHHHHHHCTT--B-HHHHHHHH CS
                       CRISPR_Cse2  62 lgaalgrlreases.s........esierRfqalltadtpeelarrLrrlvkllrskevpldyarLaddL 122
                                       + +a++r++e ++           + +e+R++ l++ ++pee++r    +v  l+++  +ld++++   L
  gi|320101136|ref|YP_004176728.1| 502 MVTAVKRVVELQGGiVvvndgevvSEVELRLAGLMSVKEPEEVFREYLNMVDALKKR-FHLDFESFFMTL 570
                                       55666666644444336666777767*****************************76.****99987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 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:                        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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4255.57
//
Query:       gi|320101137|ref|YP_004176729.1|  [L=191]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1494.98
//
Query:       gi|320101138|ref|YP_004176730.1|  [L=240]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   82.7   0.0    4.5e-23   82.3   0.0    1.2  1  ABC_tran      ABC transporter
    2.1e-12   47.5   0.7    3.9e-05   23.6   0.6    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.1e-09   35.4   0.0     0.0025   17.3   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    3.1e-05   23.6   0.1      6e-05   22.7   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
    5.6e-05   23.7   0.0      6e-05   23.6   0.0    1.2  1  AAA_23        AAA domain
     0.0021   17.5   0.0     0.0035   16.8   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0026   17.4   0.1     0.0039   16.8   0.1    1.2  1  AAA_27        AAA domain
     0.0029   17.4   0.0     0.0038   17.0   0.0    1.2  1  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.015   15.2   0.2      0.024   14.6   0.2    1.3  1  RsgA_GTPase   RsgA GTPase
       0.03   14.7   0.0      0.045   14.1   0.0    1.3  1  AAA_16        AAA ATPase domain
      0.034   13.8   0.0      0.044   13.4   0.0    1.2  1  SRP54         SRP54-type protein, GTPase domain
      0.039   14.1   0.5      0.059   13.5   0.5    1.5  1  AAA_33        AAA domain
      0.048   13.4   0.1      0.077   12.7   0.1    1.2  1  AAA_30        AAA domain
      0.057   12.3   0.0      0.078   11.8   0.0    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
      0.057   12.7   0.0      0.094   12.0   0.0    1.3  1  Zeta_toxin    Zeta toxin
      0.059   12.7   0.5      0.093   12.1   0.2    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.066   13.1   0.3       0.17   11.8   0.3    1.6  2  NACHT         NACHT domain
      0.079   12.9   0.1       0.28   11.1   0.0    1.8  2  NTPase_1      NTPase
       0.09   13.0   0.0       0.12   12.6   0.0    1.3  1  AAA_28        AAA domain
       0.15   12.3   0.1       0.27   11.5   0.1    1.4  1  AAA_22        AAA domain
       0.16   10.7   0.5       0.27   10.0   0.5    1.3  1  ABC_ATPase    Predicted ATPase of the ABC class
       0.16   11.5   0.1       0.27   10.8   0.1    1.3  1  AAA_25        AAA domain
       0.27   10.3   0.0       0.39    9.8   0.0    1.1  1  G-alpha       G-protein alpha subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   5.8e-26   4.5e-23       2     136 ..      21     158 ..      20     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 5.8e-26
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       +n+ ++l++g ++++vG nG+GKStLlk++ag lkp +G+++++g ++++ +++ + + +g++ q+  + f e +v+
  gi|320101138|ref|YP_004176730.1|  21 ENIGFTLEPG-LHVLVGANGSGKSTLLKTMAGILKPLKGKVEINGVNIHRVPRRDAARLVGYVWQNpFHGFIEASVE 96 
                                       7899999999.5679***************************************************65566777676 PP

                                       HH.......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++       +  ++  +++ +l +     + +++sp sLSgG+ +rva+a +l  ++++++lDEp+
  gi|320101138|ref|YP_004176730.1|  97 REiafisktTGARQHGEIVYRLVD----PELMDRSPFSLSGGEARRVAIASVLSIDQPVWFLDEPF 158
                                       668555444444444455555554....55566666*****************************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 !   23.6   0.6     5e-08   3.9e-05       1      23 [.      31      53 ..      31      71 .. 0.80
   2 !   21.9   0.0   1.6e-07   0.00013     220     303 .]     114     194 ..      74     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      l vl+G+NgsGKS+LL+++ ++ 
  gi|320101138|ref|YP_004176730.1| 31 LHVLVGANGSGKSTLLKTMAGIL 53
                                      579****************7774 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.6e-07
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                        v+ l+++   ++++++lS G  r  a+++ l  +    ++ ++DEp + L++k  r l++l+++  ++g  +++tT
  gi|320101138|ref|YP_004176730.1| 114 IVYRLVDPELMDRSPFSLSGGEARRVAIASVLSIDQ---PVWFLDEPFSDLDYKGYRVLADLVEYGVKKGKIIVVTT 187
                                       666666666667799*******99967777777766...9****************************66666**** PP

                            AAA_21 297 HSpllld 303
                                       H  +lld
  gi|320101138|ref|YP_004176730.1| 188 HIVSLLD 194
                                       *999886 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   6.7e-06    0.0052      19      44 ..      24      49 ..      17      57 .. 0.85
   2 !   17.3   0.0   3.2e-06    0.0025     136     197 ..     130     187 ..      56     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.7e-06
                                      EEETTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 19 ilpfsksftaivGpNGSGKsnlldAi 44
                                         +++++ ++vG+NGSGKs ll  +
  gi|320101138|ref|YP_004176730.1| 24 GFTLEPGLHVLVGANGSGKSTLLKTM 49
                                      5678999**************99877 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.2e-06
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivisl 197
                                       +LSgGe   va+a +++i     +p+++lDe  + LD k  + +a+l++   k+  +iv++ 
  gi|320101138|ref|YP_004176730.1| 130 SLSGGEARRVAIASVLSID----QPVWFLDEPFSDLDYKGYRVLADLVEYGVKKGKIIVVTT 187
                                       79**************997....6**********************************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 !   22.7   0.1   7.7e-08     6e-05      23      55 ..      30      63 ..      21      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.7e-08
                            AAA_29 23 gatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      g ++l+G++GsGKSTll  ++ +L p k kv+ N
  gi|320101138|ref|YP_004176730.1| 30 GLHVLVGANGSGKSTLLKTMAGILKPLKgKVEIN 63
                                      4689********************9998888777 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   7.7e-08     6e-05      15      43 ..      23      53 ..      17     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.7e-08
                            AAA_23 15 idF..skgltlItGpNGaGKTTildAiklaL 43
                                      i F  ++gl +++G NG+GK+T+l  +  +L
  gi|320101138|ref|YP_004176730.1| 23 IGFtlEPGLHVLVGANGSGKSTLLKTMAGIL 53
                                      55555*******************8776655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.4e-06    0.0035      26      68 ..      33      75 ..      29     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.4e-06
                      Mg_chelatase 26 llvGppGsGKtmlakrlpsllpplseeealevakiasvagkke 68
                                      +lvG+ GsGK+ l k ++++l pl+ +  ++  +i+ v ++++
  gi|320101138|ref|YP_004176730.1| 33 VLVGANGSGKSTLLKTMAGILKPLKGKVEINGVNIHRVPRRDA 75
                                      689************************9999999998877332 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     5e-06    0.0039      24      49 ..      27      52 ..      19      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5e-06
                            AAA_27 24 eeadlhliyGpNEAGKstalrAisdl 49
                                       e++lh+++G+N +GKst+l+ +  +
  gi|320101138|ref|YP_004176730.1| 27 LEPGLHVLVGANGSGKSTLLKTMAGI 52
                                      479*****************998765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.9e-06    0.0038      21      48 ..      27      54 ..      19      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-06
                            AAA_15 21 lseeltvliGkNnsGKSsilealdlFln 48
                                      l++ l vl+G+N+sGKS++l+ +  +l+
  gi|320101138|ref|YP_004176730.1| 27 LEPGLHVLVGANGSGKSTLLKTMAGILK 54
                                      566699**************98876665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2     3e-05     0.024      90     122 ..      20      52 ..       9      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                                       HHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  90 leelkellkdktsvlvGqSGvGKStLinallpe 122
                                       +e++   l+  + vlvG  G GKStL++++++ 
  gi|320101138|ref|YP_004176730.1|  20 VENIGFTLEPGLHVLVGANGSGKSTLLKTMAGI 52 
                                       57788899999*****************99875 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   5.7e-05     0.045      24      69 ..      29      69 ..      23     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy 69
                                      p+l +l+G+ G+GKs+l+++ +  + k     l+gk + ++ +i++
  gi|320101138|ref|YP_004176730.1| 29 PGLHVLVGANGSGKSTLLKTMA-GILKP----LKGKVEINGVNIHR 69
                                      567789************9999.56666....67777666555444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.6e-05     0.044       4      42 ..      32      70 ..      29     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSST CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRa 42
                                       +lvG +G+GK t l  +a +lk  + kv +  + + R+
  gi|320101138|ref|YP_004176730.1| 32 HVLVGANGSGKSTLLKTMAGILKPLKGKVEINGVNIHRV 70
                                      689********************9999999888877775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   7.6e-05     0.059       1      20 [.      31      50 ..      31     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.6e-05
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      l +lvG++GsGKstl++ ++
  gi|320101138|ref|YP_004176730.1| 31 LHVLVGANGSGKSTLLKTMA 50
                                      6799************9986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.8e-05     0.077      20      49 ..      31      60 ..      24      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrv 49
                                      ++vl+G+ G+GK+t+lk+++ +++  +g+v
  gi|320101138|ref|YP_004176730.1| 31 LHVLVGANGSGKSTLLKTMAGILKPLKGKV 60
                                      899****************99998776666 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001     0.078      29      79 ..      33      82 ..      27      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                              DLIC 29 lvlGedgsGkttliaklqGveeekkGrGleylyldvkdedrddltrlnvwi 79
                                      +++G +gsGk+tl+  + G+ ++ kG+ +e   ++++   r d +rl  ++
  gi|320101138|ref|YP_004176730.1| 33 VLVGANGSGKSTLLKTMAGILKPLKGK-VEINGVNIHRVPRRDAARLVGYV 82
                                      578***********************8.89999999999999999987655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012     0.094      15      51 ..      28      64 ..      22      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                        Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvvrldp 51
                                      +P l +l+G+ G+GKs+l++ ++  l++ ++ v++++
  gi|320101138|ref|YP_004176730.1| 28 EPGLHVLVGANGSGKSTLLKTMAGILKPLKGKVEING 64
                                      68899***************99999888888888775 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00012     0.093      43      59 ..      33      49 ..      19      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                      EEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE 43 lvaGatgsGKStalntL 59
                                      +++Ga gsGKSt l+t+
  gi|320101138|ref|YP_004176730.1| 33 VLVGANGSGKSTLLKTM 49
                                      568*************9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00022      0.17       4      23 ..      33      52 ..      31      62 .. 0.86
   2 ?   -2.8   0.0       6.8   5.3e+03      77     127 ..     145     187 ..     132     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                      EEEC-TTTCHHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklala 23
                                      +l G++GsGK+tLl+ +a  
  gi|320101138|ref|YP_004176730.1| 33 VLVGANGSGKSTLLKTMAGI 52
                                      799***********998765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.8
                                       CCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEE CS
                             NACHT  77 lelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltv 127
                                       l++ + +++    lDe  +dl+     +  ++L++l++  + ++  +++t+
  gi|320101138|ref|YP_004176730.1| 145 LSIDQPVWF----LDEPFSDLDY----KGYRVLADLVEYGVKKGKIIVVTT 187
                                       555555555....4666665555....566666666666555555555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00036      0.28       4      41 ..      34      73 ..      32      84 .. 0.78
   2 ?   -1.4   0.0       2.4   1.9e+03     115     145 ..     170     197 ..     166     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                                      EE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE--- CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkss..gvkvgGfyteevreg 41
                                      + G  G+GK+Tl+k ++  lk     v+++G+  ++v ++
  gi|320101138|ref|YP_004176730.1| 34 LVGANGSGKSTLLKTMAGILKPLkgKVEINGVNIHRVPRR 73
                                      6799***********9999985433799999999998743 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                                       HHHHHHHHTTTSEEEEE--SS--SHHHHHHH CS
                          NTPase_1 115 keaveevLksekpvlavihrrkdlalveeir 145
                                       ++ ve  +k++k+++++ h     +l+++++
  gi|320101138|ref|YP_004176730.1| 170 ADLVEYGVKKGKIIVVTTHIV---SLLDSLK 197
                                       566777778888888888877...3555555 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   0.00016      0.12       2      20 ..      32      50 ..      31     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                       v++G+ ++GK+tll+ +a
  gi|320101138|ref|YP_004176730.1| 32 HVLVGANGSGKSTLLKTMA 50
                                      599************9998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00035      0.27       6      26 ..      30      50 ..      27      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                            AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                      g+ v++G  G+GK+tll++++
  gi|320101138|ref|YP_004176730.1| 30 GLHVLVGANGSGKSTLLKTMA 50
                                      6779**************986 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 ?   10.0   0.5   0.00035      0.27     239     264 ..      24      49 ..       9      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00035
                                       EEEE-SSEEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 239 GmgipkGvtlIvGggfhGKsTLLeAl 264
                                       G  +  G+ ++vG +  GKsTLL+ +
  gi|320101138|ref|YP_004176730.1|  24 GFTLEPGLHVLVGANGSGKSTLLKTM 49 
                                       888999*****************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00034      0.27      29      54 ..      25      50 ..      14      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                            AAA_25 29 llpagelallaGapgtGKttlaldla 54
                                      +  + +l++l+Ga g+GK+tl+  +a
  gi|320101138|ref|YP_004176730.1| 25 FTLEPGLHVLVGANGSGKSTLLKTMA 50
                                      5567799**************86665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00049      0.39      27      46 ..      33      52 ..      31      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00049
                                      EEEESTTSSHHHHHHHHHHH CS
                           G-alpha 27 lllGqseSGKsTilkqlkll 46
                                      +l+G+++SGKsT+lk +  +
  gi|320101138|ref|YP_004176730.1| 33 VLVGANGSGKSTLLKTMAGI 52
                                      589*************9844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1784.55
//
Query:       gi|320101139|ref|YP_004176731.1|  [L=161]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-29  101.5  16.6    5.7e-29  101.3  16.6    1.0  1  QueT         QueT transporter
  ------ inclusion threshold ------
       0.22   11.1   0.5       0.37   10.3   0.5    1.4  1  m04gp34like  Immune evasion protein


Domain annotation for each model (and alignments):
>> QueT  QueT transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3  16.6   6.3e-33   5.7e-29       3     138 ..      10     157 ..       8     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 6.3e-33
                              QueT   3 raaviaAlYvvltlvlapisfgaiqvRiseaLtlLpv...ftpaailGltiGcliaNllsplgllDvifGslatlia 76 
                                       r+ +iaA+Y+++t++l  +s+g +q+R+s+a+++Lp+   ++ +a++GltiG ++ Nl+sp+ ++D++fG la+l a
  gi|320101139|ref|YP_004176731.1|  10 RSIIIAAVYTAVTVMLGYLSYGELQFRVSDAMMILPLvrgIGLEAVVGLTIGGFLGNLTSPFIPWDWLFGPLANLAA 86 
                                       6789********************************95445699********************************* PP

                              QueT  77 alltyllkkkr.......llaalppvlvnalivgavl..lelpflltvltvglgelivlyvlGlpllkale 138
                                        ll+yl+ +++       + ++l+ +l+ ++ivg++l  +    +lt ++++++e++v+ v+G ++++ l+
  gi|320101139|ref|YP_004176731.1|  87 SLLVYLVGRTGlntyikvAASTLLAALAISVIVGYELtaIYGLPWLTTVYIFVSEVVVIGVIGGLVYRSLK 157
                                       *******88889997653366699999999999966333333449999*****************999886 PP

>> m04gp34like  Immune evasion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   4.1e-05      0.37     231     265 ..       5      39 ..       1      44 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.1e-05
                                       ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       m04gp34like 231 llvtilsvivvllivvvllvLaylYgpsllrrlss 265
                                        l+ti s+i+++++ +v ++L yl ++ l  r+s+
  gi|320101139|ref|YP_004176731.1|   5 PLFTIRSIIIAAVYTAVTVMLGYLSYGELQFRVSD 39 
                                       589********************877677766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1335.67
//
Query:       gi|320101140|ref|YP_004176732.1|  [L=95]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); 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:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 802.05
//
Query:       gi|320101141|ref|YP_004176733.1|  [L=190]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   17.4   0.2     0.0056   16.5   0.1    1.5  2  DUF1465    Protein of unknown function (DUF1465)
  ------ inclusion threshold ------
       0.11   12.0   2.6       0.35   10.5   2.6    2.0  1  Trimer_CC  Trimerisation motif
       0.13   11.6   1.4       0.21   10.8   1.3    1.5  1  CorA       CorA-like Mg2+ transporter protein
       0.13   12.7   0.9       0.17   12.3   0.3    1.5  2  ZapB       Cell division protein ZapB
       0.17   11.5   4.9        3.6    7.2   0.0    3.3  3  HTH_24     Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.6e-06    0.0056      85     136 ..      30      81 ..      17      94 .. 0.82
   2 ?   -2.8   0.0       1.4   5.1e+03     102     125 ..     138     163 ..     127     171 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-06
                                       S-------..-----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXX CS
                           DUF1465  85 kkrvklaaaeasdaeavaeLpeelqeLierserLyervrrLdrelreeaeaa 136
                                        + ++ ++++  d++++++L+e+l  Li+  ++L er+rrL+++l ++  ++
  gi|320101141|ref|YP_004176733.1|  30 SRSIQGSQSNGADNHGLSNLDEKLDLLIALIRELSERIRRLEETLEKRGVDH 81 
                                       445666666689999*****************************99887665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                                       ----HHHHHHHHHHHH..HHHHHHHH CS
                           DUF1465 102 aeLpeelqeLierser..LyervrrL 125
                                       +e+ ++++ L  rs r  + ervrrL
  gi|320101141|ref|YP_004176733.1| 138 SEIHRRVRGLRGRSSRriVGERVRRL 163
                                       44455555555544332234555554 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.6   9.7e-05      0.35      19      50 ..      44      75 ..      16      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.7e-05
                                      XX--HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Trimer_CC 19 davSRLEEelrkLqatVQelQkRLDrLEetvq 50
                                        +S L E l  L a + el +R+ rLEet +
  gi|320101141|ref|YP_004176733.1| 44 HGLSNLDEKLDLLIALIRELSERIRRLEETLE 75
                                      46899************************975 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.3     6e-05      0.21     116     190 ..      49     125 ..      31     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6e-05
                              CorA 116 ldeivdrlfellekleeeldeledel.edstkkeilrelaqlrrr.lvklrralapnrevlkrllakaddklldded 190
                                       lde +d l++l+++l+e++++le++l ++  ++++++  +++       l r+l   r++++ +++ ++ + ++++ 
  gi|320101141|ref|YP_004176733.1|  49 LDEKLDLLIALIRELSERIRRLEETLeKRGVDHPEVKMALEIASAfSLPLLRSLEIARNAYEVIVRLGEPDPITRAI 125
                                       89999*********************777777777777777664435556666666666665555555555555444 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   4.8e-05      0.17       6      37 ..      46      77 ..      42     107 .. 0.88
   2 ?   -2.9   0.0       2.8     1e+04      55      66 ..     153     164 ..     134     166 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                              ZapB  6 LeqLEskiqkaidtitlLqmeieeLkeeneel 37
                                      L+ L +k + +i  i++L+++i++L+e  e+ 
  gi|320101141|ref|YP_004176733.1| 46 LSNLDEKLDLLIALIRELSERIRRLEETLEKR 77
                                      889************************98876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.8
                              ZapB  55 reawqerlkkLL 66 
                                       r  + er++ L+
  gi|320101141|ref|YP_004176733.1| 153 RRIVGERVRRLI 164
                                       444445555555 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   0.2     0.075   2.7e+02      35      43 ..      64      72 ..      61      73 .. 0.86
   2 ?    7.2   0.0     0.001       3.6       2      26 ..     119     143 ..     118     145 .. 0.89
   3 ?    3.5   0.2     0.015        52      36      47 ..     158     169 ..     156     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.075
                            HTH_24 35 nrrlkrLee 43
                                      ++r++rLee
  gi|320101141|ref|YP_004176733.1| 64 SERIRRLEE 72
                                      789****98 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.001
                            HTH_24   2 detdrkILelLqknprisqreLAer 26 
                                       d ++r+I+e+L + +  s++e+ +r
  gi|320101141|ref|YP_004176733.1| 119 DPITRAIIEALSDCSEASISEIHRR 143
                                       889******************9665 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.015
                            HTH_24  36 rrlkrLeeeGlI 47 
                                       +r++rL++ G++
  gi|320101141|ref|YP_004176733.1| 158 ERVRRLIDRGVL 169
                                       79********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 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:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1592.26
//
Query:       gi|320101142|ref|YP_004176734.1|  [L=161]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0014   19.1   2.9     0.0027   18.2   0.3    2.6  3  HSCB_C       HSCB C-terminal oligomerisation domain
     0.0017   17.9   6.4       0.24   11.0   0.1    2.3  2  DUF2312      Uncharacterized protein conserved in bacteria (D
  ------ inclusion threshold ------
      0.035   14.3   2.9      0.092   12.9   2.9    1.7  1  GreA_GreB_N  Transcription elongation factor, N-terminal
      0.045   14.4   0.9        1.7    9.3   0.1    2.6  2  DUF3502      Domain of unknown function (DUF3502)
       0.14   12.4   0.0        4.2    7.7   0.0    2.1  2  DUF4112      Domain of unknown function (DUF4112)
       0.29   11.6   2.4        1.6    9.3   1.3    2.3  3  PP2C_C       Protein serine/threonine phosphatase 2C, C-termi


Domain annotation for each model (and alignments):
>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.63   1.9e+03      15      40 ..      14      30 ..       8      33 .. 0.43
   2 !   18.2   0.3   8.9e-07    0.0027      12      56 ..      33      76 ..      32      99 .. 0.83
   3 ?   -0.2   0.0      0.48   1.4e+03      38      67 ..      86     116 ..      84     123 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.63
                                      HHHCGGGSSSHHHHHHHHHHHHHHHH CS
                            HSCB_C 15 eleeaeeaadkeeleelkaeveerie 40
                                       +ee+             +e+++ri+
  gi|320101142|ref|YP_004176734.1| 14 VVEEL---------GLRDEELKKRIK 30
                                      33333.........333344444444 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 8.9e-07
                                      HHHHHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HH CS
                            HSCB_C 12 lrEeleeaeeaadkeeleelkaeveerieeleaeleeafekkdle 56
                                      +rE+l+ea+e++d++e++e+ a+v+  i+++ ++l++ + k+ l+
  gi|320101142|ref|YP_004176734.1| 33 IREKLAEAREEGDAAEVREILAAVTPFIDDIFNALRTGL-KDVLD 76
                                      8***********************************999.44333 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHTT.-HHHHHHHHHHHHH CS
                            HSCB_C  38 rieeleaeleeafekk.dleaaadllrrlrY 67 
                                       +i e +a+l +a++ +   ++  ++ ++  Y
  gi|320101142|ref|YP_004176734.1|  86 KIGEDVAQLYQALKSQgLPDEMIREMVKQYY 116
                                       5667777777777444455666666666544 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 !    8.7   2.3   0.00043       1.3      14      48 ..      21      54 ..       9      57 .. 0.82
   2 !   11.0   0.1   8.1e-05      0.24      19      48 ..      84     113 ..      71     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00043
                           DUF2312 14 rleeEkkaiaedikdvyaeaKseGfdtkvlrkivk 48
                                      r ee kk i+++i++  aea+ eG d + +r+i++
  gi|320101142|ref|YP_004176734.1| 21 RDEELKKRIKDKIREKLAEAREEG-DAAEVREILA 54
                                      446669*****************9.8888898876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.1e-05
                           DUF2312  19 kkaiaedikdvyaeaKseGfdtkvlrkivk 48 
                                        k+i ed+ ++y+  Ks+G+   ++r+ vk
  gi|320101142|ref|YP_004176734.1|  84 GKKIGEDVAQLYQALKSQGLPDEMIREMVK 113
                                       589************************998 PP

>> GreA_GreB_N  Transcription elongation factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.9   3.1e-05     0.092      16      45 ..      23      52 ..      12      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                      HHHHHXHHHHHHHHHHHHHHHSSSTSSHHH CS
                       GreA_GreB_N 16 eelktverpeiaeaikeareeGDlsENaeY 45
                                      eelk+    +i e+++eareeGD  E +e 
  gi|320101142|ref|YP_004176734.1| 23 EELKKRIKDKIREKLAEAREEGDAAEVREI 52
                                      78999999***************9997665 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00057       1.7      69     125 ..      45     115 ..      22     118 .. 0.73
   2 ?   -2.0   0.0       1.8   5.3e+03      40      56 ..     136     152 ..     124     160 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00057
                           DUF3502  69 DsspvkteiaalsnvveeykkaletGlvDp.............eetlpkfneklkaaGi.dkviaelqkQl 125
                                       D  +v++ +aa++  ++   +al tGl D+              e ++++ ++lk+ G+ d+ i e+ kQ+
  gi|320101142|ref|YP_004176734.1|  45 DAAEVREILAAVTPFIDDIFNALRTGLKDVldfiqhsydgkkiGEDVAQLYQALKSQGLpDEMIREMVKQY 115
                                       77888888999999999999999999888622222222222223567788888888886578888888886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                           DUF3502  40 legepedkwekvkefne 56 
                                       l ++++ +w++++e + 
  gi|320101142|ref|YP_004176734.1| 136 LVTQSTAEWTQTRETSG 152
                                       44566677777665533 PP

>> DUF4112  Domain of unknown function (DUF4112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0014       4.2      23      86 ..      67     129 ..      52     130 .. 0.82
   2 ?    5.3   0.0    0.0077        23      28      55 ..     117     144 ..     112     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                           DUF4112  23 lrfGldpiigliPvvGdvisallslylvleakkaeglpkslllrmlvnialDlliglvPvvGdl 86 
                                       lr Gl+ ++ +i    d  +++  + ++++a k +glp +++++m+ +   D  + + P  Gd+
  gi|320101142|ref|YP_004176734.1|  67 LRTGLKDVLDFIQHSYDGKKIGEDVAQLYQALKSQGLPDEMIREMVKQ-YYDKRLAALPAWGDI 129
                                       7889999999998888888999999999999999**********9755.578888888888887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0077
                           DUF4112  28 dpiigliPvvGdvisallslylvleakk 55 
                                       d+ ++ +P +Gd+++ l++l+   +a++
  gi|320101142|ref|YP_004176734.1| 117 DKRLAALPAWGDILGRLMQLVTQSTAEW 144
                                       566889************9988777755 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 ?    9.3   1.3   0.00053       1.6      13      52 ..      14      54 ..      11      63 .. 0.78
   2 ?   -0.3   0.0      0.52   1.6e+03      57      64 ..      98     105 ..      65     117 .. 0.58
   3 ?    0.4   0.0      0.31   9.3e+02      25      40 ..     105     119 ..      95     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00053
                            PP2C_C 13 vseeavkkEkeldekleervkeiie.keekkeeldlekvlk 52
                                      v ee   +++el+++++ +++e ++ ++e+++  ++ ++l 
  gi|320101142|ref|YP_004176734.1| 14 VVEELGLRDEELKKRIKDKIREKLAeAREEGDAAEVREILA 54
                                      67788889**************9995556666666666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.52
                            PP2C_C  57 edipnlPp 64 
                                        + ++lP+
  gi|320101142|ref|YP_004176734.1|  98 LKSQGLPD 105
                                       33344443 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.31
                            PP2C_C  25 dekleervkeiiekee 40 
                                       de ++e+vk+ ++ ++
  gi|320101142|ref|YP_004176734.1| 105 DEMIREMVKQYYD-KR 119
                                       6777777777766.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1519  (0.0847231); expected 358.6 (0.02)
Passed bias filter:                      922  (0.0514251); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 1341.10
//
Query:       gi|320101143|ref|YP_004176735.1|  [L=201]
Description: 3-hexulose-6-phosphate isomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-18   64.4   0.0    1.6e-17   63.5   0.0    1.4  1  SIS              SIS domain
      8e-14   51.8   2.6    3.1e-09   37.0   0.7    2.2  2  SIS_2            SIS domain
     0.0036   17.2   1.5        1.3    8.8   0.1    2.2  2  PRMT5            PRMT5 arginine-N-methyltransferase
     0.0062   15.9   0.8       0.33   10.3   0.2    2.2  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.067   12.5   0.2        0.3   10.4   0.2    1.9  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
       0.15   12.2   0.0         26    4.9   0.0    2.6  2  Isochorismatase  Isochorismatase family


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 !   63.5   0.0   5.5e-21   1.6e-17       2     106 ..      40     138 ..      39     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 5.5e-21
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelake 78 
                                       L + ++++++GaG+s+ ++k +a+ l ++g++v++v ++       l+ ++++d+++ is sg+t+ +vaaae a++
  gi|320101143|ref|YP_004176735.1|  40 LKNGRKVFIIGAGRSGLVGKAFAMRLLHLGFNVYVVGETI------LPRASQGDVLVSISGSGRTRLVVAAAEAARS 110
                                       566789********************99998888887665......58899************************** PP

                                       TTSEEEEEESSTTSHHHHHSSEEEEEEE CS
                               SIS  79 rgakiiaITdskgsplareadlalyina 106
                                        g+k+iaIT  ++spl r ad+++ i+ 
  gi|320101143|ref|YP_004176735.1| 111 VGVKVIAITTYPDSPLGRIADIVVKIPG 138
                                       ***********************99986 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.6e-06     0.017      22      59 ..      30      67 ..      15      81 .. 0.86
   2 !   37.0   0.7   1.1e-12   3.1e-09      90     137 ..      74     119 ..      70     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.6e-06
                                      HHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT- CS
                             SIS_2 22 ekaaeliadslenggkvlvfGsGhSaalaeelaaragg 59
                                      ek + ++ d+l+ng+kv++ G+G S +  + +a r+  
  gi|320101143|ref|YP_004176735.1| 30 EKMISTLIDALKNGRKVFIIGAGRSGLVGKAFAMRLLH 67
                                      6788999********************99999999875 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 1.1e-12
                                       THHHHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2  90 gyakqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                       +++++il +  +++gDvL+ iS sG+   vv+aaeaa+++g+kviA+t
  gi|320101143|ref|YP_004176735.1|  74 VVGETILPR--ASQGDVLVSISGSGRTRLVVAAAEAARSVGVKVIAIT 119
                                       566677766..99**********************************9 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00044       1.3      53      85 ..      26      63 ..      15      78 .. 0.71
   2 !    7.6   0.3     0.001       3.1      63      99 ..      85     118 ..      71     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00044
                                      HHCTCCGTCC......-EEEEEEES-TTSHHHHHHHHH CS
                             PRMT5 53 dlkkekkkks.....ekklvilvvGaGRGplvdralka 85
                                      d++kek  ++     ++   ++++GaGR +lv +a+ +
  gi|320101143|ref|YP_004176735.1| 26 DEEKEKMISTlidalKNGRKVFIIGAGRSGLVGKAFAM 63
                                      444444333367766677889***********999865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.001
                                       .-EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEEEE CS
                             PRMT5  63 ekklvilvvGaGRGplvdralkaleetkvtkvkivav 99 
                                       + ++ + + G+GR  lv +a +a+++ +   vk++a+
  gi|320101143|ref|YP_004176735.1|  85 QGDVLVSISGSGRTRLVVAAAEAARSVG---VKVIAI 118
                                       57899******************99999...666666 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   0.2   0.00011      0.33      35      69 ..      42      79 ..      10      91 .. 0.81
   2 !    4.5   0.0    0.0068        20      48      96 ..     101     150 ..      82     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                                      TTSEEEEES-SH...HHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C 35 sgktvGiiGlGr...IGqavakrlkafgmkviaydrsk 69
                                      +g++v iiG+Gr   +G+a+a rl  +g++v+++  + 
  gi|320101143|ref|YP_004176735.1| 42 NGRKVFIIGAGRsglVGKAFAMRLLHLGFNVYVVGETI 79
                                      6899******9877789**************9987765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0068
                                       HHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEE CS
                      2-Hacid_dh_C  48 Gqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivs 96 
                                         a+a+ ++++g+kvia+ +++++   + ++  v+     ++ +e D++s
  gi|320101143|ref|YP_004176735.1| 101 VVAAAEAARSVGVKVIAITTYPDSPLgRIADIVVKIPGRTKMSSEEDYIS 150
                                       456789999************98665666666666666666666666665 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 ?   10.4   0.2    0.0001       0.3      35      88 ..      42      94 ..      31     120 .. 0.76
   2 ?   -0.1   0.0      0.17   5.1e+02      63      94 ..     113     144 ..      99     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                                      TT-EEEEE-..--TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS CS
                     THF_DHG_CYH_C 35 egkkvvvvG..rsnivgkplallLleknatVtvchsktkdlaeitreadivvvavG 88
                                      +g+kv+++G  rs +vgk+ a+ Ll+ +  V v+ +    +    ++ d++v+  G
  gi|320101143|ref|YP_004176735.1| 42 NGRKVFIIGagRSGLVGKAFAMRLLHLGFNVYVVGET---ILPRASQGDVLVSISG 94
                                      7999***9644899*************9999988643...5556677777765443 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                                       EEEE-TTSCCHHHHHCCSSEEEE-SS-TT-B- CS
                     THF_DHG_CYH_C  63 VtvchsktkdlaeitreadivvvavGkpelik 94 
                                       V+v+   t   + + r adivv   G+ ++ +
  gi|320101143|ref|YP_004176735.1| 113 VKVIAITTYPDSPLGRIADIVVKIPGRTKMSS 144
                                       566666666666677889***99999988755 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.014        41     128     146 ..      59      77 ..      35      85 .. 0.81
   2 ?    4.9   0.0    0.0087        26      30      52 ..     101     123 ..      92     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                   Isochorismatase 128 eatardaldlGyevvvvsD 146
                                       +a a+ +l lG++v+vv +
  gi|320101143|ref|YP_004176735.1|  59 KAFAMRLLHLGFNVYVVGE 77 
                                       678999**********975 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0087
                   Isochorismatase  30 inkllkaarkagipviftrdvhe 52 
                                       ++ +++aar  g++vi+++ +++
  gi|320101143|ref|YP_004176735.1| 101 VVAAAEAARSVGVKVIAITTYPD 123
                                       567899**************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 1614.83
//
Query:       gi|320101144|ref|YP_004176736.1|  [L=304]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-13   49.0   0.0      3e-12   47.3   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    1.3e-07   31.7   1.0      0.023   14.4   0.0    2.3  2  DUF1848      Domain of unknown function (DUF1848)
  ------ inclusion threshold ------
      0.014   15.7   0.0       0.32   11.2   0.0    2.6  2  GGDEF_2      GGDEF-like domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   4.9e-16     3e-12       3     158 ..      25     179 ..      23     187 .. 0.73
   2 ?   -0.7   0.0      0.28   1.7e+03      93     131 ..     186     222 ..     180     251 .. 0.55

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 4.9e-16
                                       EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC..C CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla..v 75 
                                       ++ gC++ C +C+ ++  +rr  +++   ++++++ +++  a++g v e+ ++++ p    +  + l r++ +   +
  gi|320101144|ref|YP_004176736.1|  25 PYTGCSHFCLYCYATSYiGRRPSTPKPDFTRRLERDLDK--ARRGsVVELSSSSD-PYPPLESWMGLTRRSLEIlgK 98 
                                       578************964333333333333333333333..33442444444443.55555555555555544499* PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivg 151
                                        g++i v+t    + e+ +++l++++   v +++ ++d e   ++++ + + ++++l+a+++l ++gi++ v   ++
  gi|320101144|ref|YP_004176736.1|  99 HGFKILVTTKSNIV-ERDVDLLARYP-SSVMITITTLDQE-LSRKLEpGAPPPDKRLDAVRRLSDKGIPVGVRLDPI 172
                                       **************.***********.*************.******9999******************76666677 PP

                                       BTTTSHH CS
                                       xxxxxxx RF
                       Radical_SAM 152 lpGende 158
                                       +p  nd+
  gi|320101144|ref|YP_004176736.1| 173 IPFLNDD 179
                                       7777776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.28
                                       HHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  93 klerllelgvdrvslgleaaddekvlklmnrghtfeevl 131
                                        +++++e+g  +v+++   a  +  ++lm     +e  +
  gi|320101144|ref|YP_004176736.1| 186 LIREIKEAGALQVTVSTYKAKWDSLRRLM-S-AFPEISV 222
                                       57788888855555554444444444444.2.4444444 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   3.5   1.4e-05     0.082     240     265 .]      13      38 ..       7      38 .. 0.90
   2 !   14.4   0.0   3.8e-06     0.023      68     131 ..     119     182 ..     101     281 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                           DUF1848 240 keCgCveskDiGayntClhgCvYCYA 265
                                       + C+C     +  y  C+h+C+YCYA
  gi|320101144|ref|YP_004176736.1|  13 PLCTCPFKYSLHPYTGCSHFCLYCYA 38 
                                       5699*9999****************9 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.8e-06
                           DUF1848  68 lkergiklyfqfTltdyeke....lepnvpsleerietfkelseklgkerviwRyDPilltekltvel 131
                                       l   +++  +++T+t+ ++e    lep+ p+ ++r++++++ls+k     v +R DPi+   + + + 
  gi|320101144|ref|YP_004176736.1| 119 LA--RYPSSVMITITTLDQElsrkLEPGAPPPDKRLDAVRRLSDKGI--PVGVRLDPIIPFLNDDPAG 182
                                       33..4777788888876554222389999***************975..5889*****9655544443 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.064   3.8e+02      13      59 ..      55     110 ..      52     113 .. 0.83
   2 ?   11.2   0.0   5.4e-05      0.32      74     111 ..     201     249 ..     127     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.064
                           GGDEF_2  13 rrlgldldgpyvvvvieleedaer.........llraleealralgpdalvavrgd 59 
                                       rrl  dld+ ++  v+el ++++          l r+  e+l ++g ++lv+++++
  gi|320101144|ref|YP_004176736.1|  55 RRLERDLDKARRGSVVELSSSSDPyppleswmgLTRRSLEILGKHGFKILVTTKSN 110
                                       6777899999999999997766666777778889999999999999****999986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.4e-05
                           GGDEF_2  74 e......allerlarrlgg.....lsvriGiGspveglaglrrSyreAr 111
                                       +      + l+rl +++++     +++++G G   +g   l+rSyreA+
  gi|320101144|ref|YP_004176736.1| 201 StykakwDSLRRLMSAFPEisvklRELYVGKGEFIHGYMYLPRSYREAL 249
                                       0444444667888888888999999***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2089.83
//
Query:       gi|320101145|ref|YP_004176737.1|  [L=177]
Description: ZPR1-like zinc finger protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   98.8   0.0    3.3e-28   98.6   0.0    1.0  1  zf-ZPR1         ZPR1 zinc-finger domain
  ------ inclusion threshold ------
      0.021   14.5   2.7        1.9    8.3   0.1    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.12   12.2   0.8        1.3    8.9   0.1    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.13   12.5   0.2       0.13   12.5   0.2    2.3  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase


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 !   98.6   0.0   7.3e-32   3.3e-28       2     158 ..      17     167 ..      16     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 7.3e-32
                           zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatv 78 
                                       +Cp Cg  ++    ++ +iPy++ ++++  eC++Cgyk+++v  +++ e+  +ri ++ve++ d +  +++S  +++
  gi|320101145|ref|YP_004176737.1|  17 KCPVCG-GEMLYAEYVYRIPYYGVILMTVGECRSCGYKHRDVGLLERREP--RRIIYRVEKPGDERALLVRSAGSRL 90 
                                       7****8.6677777888*********************************..************************* PP

                           zf-ZPR1  79 eipeleleippg.tlegrlttvEGlLeqikeelekeegdqaeredeekekieeflekleeliegeepftlildDpag 154
                                        ipel+l+i+pg  ++g++ttvEG++e+++e+ +      +e e ++++++  +l kle++++g  ++t+i++D +g
  gi|320101145|ref|YP_004176737.1|  91 LIPELGLSIEPGpFSQGFITTVEGVIEDFAEKTR---FLCEEGE-AKESECSLILGKLERAMKGLISYTVIIEDETG 163
                                       *********************************5...2222332.36899*************99************ PP

                           zf-ZPR1 155 nSfi 158
                                        S +
  gi|320101145|ref|YP_004176737.1| 164 LSDV 167
                                       9965 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00043       1.9      11      21 ..      12      22 ..       9      23 .. 0.84
   2 ?    6.4   0.3    0.0017       7.5       2      11 ..      46      55 ..      46      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00043
                      Rubredoxin_2 11 akwfGrCpsCg 21
                                      + + G+Cp Cg
  gi|320101145|ref|YP_004176737.1| 12 NEYTGKCPVCG 22
                                      6789******8 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0017
                      Rubredoxin_2  2 vCsqCGfesa 11
                                      +C++CG++++
  gi|320101145|ref|YP_004176737.1| 46 ECRSCGYKHR 55
                                      6******986 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.091   4.1e+02       4      14 ..      18      28 ..      18      31 .. 0.75
   2 ?    8.9   0.1    0.0003       1.3      23      30 ..      46      53 ..      41      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.091
                                      ESTTTSBEEEE CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpk 14
                                      Cp Cg  +l++
  gi|320101145|ref|YP_004176737.1| 18 CPVCGGEMLYA 28
                                      99**8766655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0003
                                      EESSSS-E CS
                    RNA_POL_M_15KD 23 eCrqCgYe 30
                                      eCr+CgY+
  gi|320101145|ref|YP_004176737.1| 46 ECRSCGYK 53
                                      8******7 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     3e-05      0.13       1      12 [.      13      24 ..      13      30 .. 0.89
   2 ?    0.2   0.5      0.21   9.6e+02      28      33 ..      47      51 ..      45      57 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                                      EEEE--TTTT-T CS
                    Prim_Zn_Ribbon  1 gkhspCPvCGGr 12
                                      ++ + CPvCGG+
  gi|320101145|ref|YP_004176737.1| 13 EYTGKCPVCGGE 24
                                      68999******8 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.21
                                      ETTTTB CS
                    Prim_Zn_Ribbon 28 CrqCgg 33
                                      Cr+C g
  gi|320101145|ref|YP_004176737.1| 47 CRSC-G 51
                                      8888.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1270.84
//
Query:       gi|320101146|ref|YP_004176738.1|  [L=369]
Description: peptidase M29 aminopeptidase II [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-105  352.1   0.0   4.1e-105  351.9   0.0    1.0  1  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.9   0.0  2.3e-109  4.1e-105       2     406 .]       3     365 ..       2     365 .. 0.97

  Alignments for each domain:
  == domain 1  score: 351.9 bits;  conditional E-value: 2.3e-109
                                       HHHHHHHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT--- CS
                     Peptidase_M29   2 eeklekyAellvkvglnlqkgqevvinaevealelarlvaeeaykagakkvvvewsdeeltkerlknaseeqleevp 78 
                                       +++++++A+l+v+++++l kg+evvina++e+++l+r++++++++aga +v v++ de +t++++k+as + l++v+
  gi|320101146|ref|YP_004176738.1|   3 DPRISNLARLIVNYCVHLGKGEEVVINATTESIPLVREIVRHVVEAGAYPVFVNIGDESITEAFYKYASPDVLSHVS 79 
                                       57899************************************************************************ PP

                                       HHHHHHHHHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHHHHHHHHHHTTSS-B-BEE---TTTHHHH- CS
                     Peptidase_M29  79 eweaekleelveegaarlsilae.dpkllkgvdpekiaaaqkarskalkeyreriasgklrWcvvavPteawAkkvf 154
                                        +e    +e+v++  a +sila+ ++k l gvdpek++ +++ar++++k++ er a+g+l+W+++ +Pt+a+A+   
  gi|320101146|ref|YP_004176738.1|  80 ILE----KEVVSRIHAQISILAPsHTKPLVGVDPEKLKIRSQARRELSKIFLERSARGELKWVIAPYPTRALAQ--- 149
                                       ***....*******************************************************************... PP

                                       --S-HHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS CS
                     Peptidase_M29 155 pdleaeealeklwdaifkavrldeedpvaaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWigga 231
                                          ea++++++++d++++a+++d++dpv++W+++ ++++k++ +Ln+   ke++y+  pg+dL +++ +g++W++ +
  gi|320101146|ref|YP_004176738.1| 150 ---EAGMSISEYEDFVYHATYADTPDPVSEWSRIGERQSKIVGFLNK--AKEIKYT-GPGIDLYLRV-DGRTWVNDD 219
                                       ...********************************************..*******.77********.********* PP

                                       ---SSS----SBSS---EEE-EEEEEEEEEEE-SS-EEETTEEEBS-EEEEETTEEEEEE-SB-HHHHHHHTTSSSG CS
                     Peptidase_M29 232 ektkkgiefvaNiPteevftaPdkrgvnGvvratkPlsysGnliegirltFedGkvveakAekGeevLkklletDeg 308
                                       ++         N+P +evf+aP +++v+G+v +++P++++G ++eg+rl F+ G+vvea+A++Ge++L+k+letDeg
  gi|320101146|ref|YP_004176738.1| 220 GHY--------NMPGGEVFSAPLEDSVEGYVEFDYPAVWRGVEVEGVRLVFRRGEVVEASARRGEQFLRKMLETDEG 288
                                       **9........****************************************************************** PP

                                       GGSEEEEE---TTSHHHHHT-----HHHHHT..TS-EEEEE---GGGB--..-----SHHHHT----S-EEEEE--- CS
                     Peptidase_M29 309 arrLGEvALvpndspisqsgilfyntLfDen..ascHlAlGaaypecleggeelteeelkaaglNdSlihvDfmigs 383
                                       arr+GE+A++ n+ +i++   +++++LfDe+  +++HlAlG+aype+              +g N S+ih+D mi++
  gi|320101146|ref|YP_004176738.1| 289 ARRVGEIAFGLNY-NITR---FTKEILFDEKigGTIHLALGSAYPET--------------GGRNVSAIHWD-MIKD 346
                                       *************.****...**************************..............9**********.**99 PP

                                       TT-EEEEE-TTS-EEEEEETTEE CS
                     Peptidase_M29 384 edldidgitedgkevpifrnGef 406
                                       ++     i  dg   ++++nG+f
  gi|320101146|ref|YP_004176738.1| 347 MRG--SKIYVDGD--LVYENGRF 365
                                       887..55555665..88888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2776.31
//
Query:       gi|320101147|ref|YP_004176739.1|  [L=161]
Description: ferritin Dps family protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-36  123.5   1.2    7.2e-36  123.2   1.2    1.1  1  Ferritin      Ferritin-like domain
    2.4e-07   31.2   0.4    3.2e-07   30.8   0.4    1.2  1  Rubrerythrin  Rubrerythrin
     0.0052   16.8   0.0      0.018   15.1   0.0    1.8  1  CARD          Caspase recruitment domain
  ------ inclusion threshold ------
      0.083   13.1   0.1        3.6    7.9   0.0    2.4  2  Coat_F        Coat F domain


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 !  123.2   1.2   1.6e-39   7.2e-36       2     141 ..       7     142 ..       6     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 1.6e-39
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS. CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke. 77 
                                       +aLn+ql+ el  ay+yl+ma+y+++ gl g+a+ff+ qa ee eha +++ +i+++G      r+ l++i++pk  
  gi|320101147|ref|YP_004176739.1|   7 EALNKQLNQELRNAYLYLSMAAYLDHKGLAGFANFFRVQAREEVEHALRIYRFINDRGW-----RVVLSDIPSPKAd 78 
                                       89*********************************************************.....************* PP

                                       CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  78 fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekler 141
                                       ++s++e +++ + +ek+ te++  l++la+ +gD a + fl++f++eq+e+e++  +ll ++e+
  gi|320101147|ref|YP_004176739.1|  79 WESILELVKDFYGAEKENTERIWSLMDLARRVGDKACEVFLQWFINEQVEEEKNAMELLSRVEM 142
                                       ***********************************************************98876 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.4   7.1e-11   3.2e-07       1     127 [.       7     126 ..       7     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 7.1e-11
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       e L+k +  E     lY ++a  ++ +g+   a++F+  A+eE eHa +++++++++ +           +   +k+
  gi|320101147|ref|YP_004176739.1|   7 EALNKQLNQELRNAYLYLSMAAYLDhKGLAGFANFFRVQAREEVEHALRIYRFINDRGWRVV------LSDIPSPKA 77 
                                       678899999****************************************************9......578889999 PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEk 127
                                       ++++  + ++    ga++e++e + ++ +la+++g++ a ++f ++   E+
  gi|320101147|ref|YP_004176739.1|  78 DWESILELVK-DFYGAEKENTERIWSLMDLARRVGDK-ACEVFLQWFINEQ 126
                                       **99999999.55688899999999*********999.8888888887776 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.9e-06     0.018      42      75 ..      93     126 ..      84     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-06
                                       SSSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHS CS
                              CARD  42 kttrlskareLldlvqkkgekacqaflealkegq 75 
                                       ++++ ++ + L dl ++ g+kac++fl+++ ++q
  gi|320101147|ref|YP_004176739.1|  93 EKENTERIWSLMDLARRVGDKACEVFLQWFINEQ 126
                                       6778999**********************99987 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.036   1.6e+02      32      48 ..       5      21 ..       3      28 .. 0.73
   2 ?    7.9   0.0    0.0008       3.6      35      59 ..      41      65 ..      38      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.036
                            Coat_F 32 lRqtlkqilneeiemqe 48
                                      l ++l+++ln+e+  ++
  gi|320101147|ref|YP_004176739.1|  5 LLEALNKQLNQELRNAY 21
                                      55678888888877665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0008
                            Coat_F 35 tlkqilneeiemqeelfnlmnqkGw 59
                                      +++ ++ ee e++ +++ ++n +Gw
  gi|320101147|ref|YP_004176739.1| 41 FFRVQAREEVEHALRIYRFINDRGW 65
                                      5667899****************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1250.58
//
Query:       gi|320101148|ref|YP_004176740.1|  [L=314]
Description: triphosphoribosyl-dephospho-CoA protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-58  197.4   0.0    4.7e-58  197.1   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 !  197.1   0.0   2.6e-62   4.7e-58       4     280 ..      10     299 ..       8     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 2.6e-62
                                       XXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH. CS
                              CitG   4 avlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaa. 79 
                                       ++l+l+lE+sa+pKPG+V+r ++   +D+++e Fla  + +++yf++ +  G++      +   iG+l++ ++ +a 
  gi|320101148|ref|YP_004176740.1|  10 FSLSLILEASAWPKPGNVHRLRER--RDLRYEAFLATGVLAYRYFKKGVLRGVR----GWRRIIIGDLIYMTVSKAi 80 
                                       6899********************..***********************99998....466779************* PP

                                       ..------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--......---.. CS
                              CitG  80 ..tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv......eel.. 145
                                            +NT++G   ll++l++ +gr++ ++e+  l+++  ea+++l+e++vedav+  ra+r+a++      + +  
  gi|320101148|ref|YP_004176740.1|  81 ddIPSTNTCLGSSTLLMPLSVGTGRCI-AKEDLGLNCITGEASRLLRETSVEDAVYYyRAVRKASPsylkpsD-Ntg 155
                                       *99*********************998.677999********************************9998762.146 PP

                                       ..........HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHH CS
                              CitG 146 ..........kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallalla 212
                                                  ++l++ +++ l +vle+s+++d +++e+++g++++++    +lr+ ++s+++ n+ +v+a+l+lla
  gi|320101148|ref|YP_004176740.1| 156 shvniwdpdyAEKLAA-RGIRLIDVLEYSSRIDIVADEVVNGYKRSLA-LEGFLRKRVSSHGEWNRGVVEAYLHLLA 230
                                       6677777655555555.9****************************99.666999999999**************** PP

                                       HS--HHHHHHHHHHHHHHHHHHHH..........H-.SHHHHHHHHHHHHHHT---HHHHHHHHHHHHH CS
                              CitG 213 elpDtnilrrgGaegaeevqeeArallaaggvaaea.glealeeldrelvernisPGgsADllaatlfl 280
                                       e  Dt ++ ++G e+ae+v+++A ++l +  +a +  + + + +ld+e+ e++i+PG +AD++aa++ l
  gi|320101148|ref|YP_004176740.1| 231 EAMDTVVVLKHGVEVAEYVRRRATEILPEVLAAGSGdWVKPVMRLDDEFYEHGINPGAIADVTAAGIAL 299
                                       ****************************965555556*****************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2274.59
//
Query:       gi|320101149|ref|YP_004176741.1|  [L=313]
Description: oxidoreductase molybdopterin-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-36  126.0   0.0    1.5e-36  125.6   0.0    1.2  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.0   8.4e-41   1.5e-36       3     172 .]     148     293 ..     146     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 8.4e-41
                                       ----.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHH CS
                    Oxidored_molyb   3 avpkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlr 79 
                                        vp++d++kw+lev glv++pl+l+l+ L +l  ++v  +++C++              +w   +v n+e+tGv+l+
  gi|320101149|ref|YP_004176741.1| 148 GVPSIDVAKWSLEVAGLVDNPLKLTLSSLYELGVKTVRRDFHCVT--------------GW---SVRNVEFTGVPLS 207
                                       68999****************************************..............8*...9************ PP

                                       HHHHHTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBT CS
                    Oxidored_molyb  80 dvLekagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvK 156
                                        ++e +++  ++ ++v +e+ d      +y++ ip+e+++  d+l+A+em+g+pL   hGyP Rlvvp+l+g++s+K
  gi|320101149|ref|YP_004176741.1| 208 RIIELVKPG-ETVKWVFVESVD------GYSTIIPFEELTGGDALVALEMDGRPLDLLHGYPARLVVPHLYGWKSAK 277
                                       ********6.9**********9......5***********88*********************************** PP

                                       TEEEEEEESS---SHH CS
                    Oxidored_molyb 157 wlkrievsdeesegyw 172
                                       wl+ri +++e ++gyw
  gi|320101149|ref|YP_004176741.1| 278 WLSRIVFMNEYRDGYW 293
                                       ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        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 0.22s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2251.72
//
Query:       gi|320101150|ref|YP_004176742.1|  [L=122]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 908.80
//
Query:       gi|320101151|ref|YP_004176743.1|  [L=354]
Description: ornithine carbamoyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-41  139.8   0.0    1.3e-40  139.0   0.0    1.4  1  OTCace           Aspartate/ornithine carbamoyltransferase, As
    5.7e-36  123.8   0.0      1e-35  122.9   0.0    1.4  1  OTCace_N         Aspartate/ornithine carbamoyltransferase, ca
  ------ inclusion threshold ------
      0.071   12.9   0.0       0.42   10.4   0.0    2.1  2  Methyltransf_31  Methyltransferase domain
       0.17   12.0   0.0       0.32   11.1   0.0    1.4  1  Limkain-b1       Limkain b1


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 !  139.0   0.0     3e-44   1.3e-40       1     156 [.     179     348 ..     179     349 .. 0.95

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 3e-44
                                       CC.EEEEES......STTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT CS
                            OTCace   1 kglkiafvG......dkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkg 71 
                                       +g+k+++++       ++++v +++i l+ r+g+dvv++ P+g++ d+e++e+ak+ ak +g+++++t++leeav g
  gi|320101151|ref|YP_004176743.1| 179 QGKKYVIMWayspeiRGWCSVQEDMI-LFPRFGVDVVVARPPGFDLDPELVEKAKQLAKDHGATLEFTDNLEEAVRG 254
                                       58999999999999889999999998.************************************************** PP

                                       -SEEEE--SSETTC........CGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTT.BHH CS
                            OTCace  72 aDvvytdvwvsmge........ekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdspr.svv 139
                                       a+ v++++w+  +         ++e+++ ++k+k+++vt+ l++l++k+ +++H LP++rg+E +d+V+d+ + s++
  gi|320101151|ref|YP_004176743.1| 255 AHAVFPRNWATPQLvklgyskfKDEELKIYEKYKHWKVTRSLMDLMDKHGVLMHVLPIFRGYEADDDVIDDAKkSII 331
                                       **********77779******999999*****************************************988666*** PP

                                       HHHHHHHHHHHHHHHHH CS
                            OTCace 140 feqaeNrlhtikAllvl 156
                                       +eqaeN+l+t++A+l+l
  gi|320101151|ref|YP_004176743.1| 332 YEQAENGLWTKMAVLAL 348
                                       ***************97 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.0   2.3e-39     1e-35       1     148 []      14     173 ..      14     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 2.3e-39
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHT...TT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEEST CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkk...ekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslsea 74 
                                       r+l+s+ d+s+ee+e  l+la+e+ke  +    e  +k+l++k+ ++lF+ +StRTr++fe+A+  lGg++ ++++ 
  gi|320101151|ref|YP_004176743.1|  14 RDLISTLDWSDEELEVALRLAKEFKEIAHYygvEAIPKILERKVFYMLFFATSTRTRAAFESAMVYLGGHAAFIDAT 90 
                                       89***********************998889999*****************************************55 PP

                                       TTSCT..TTGGSTTSSCHHHHHHHHHHHTSEEEEE..........ESSHHHHHHHHHHHSSEEEEEEETSSB-HHHH CS
                          OTCace_N  75 ediql..ssvskgrkEsleDtarvlsryvdaiviR..........hpgaeeleelakyasvpviNagdgdgeHPtQa 139
                                        ++++  ++ +k  +E ++D+a + + y++++ iR            g++ ++e+a+ a++pviN+   d+ HPtQ 
  gi|320101151|ref|YP_004176743.1|  91 -TTRMafGKQEKA-GEAVKDVAAMYDVYGHGLGIRildkaidylyGVGNAYIREMAETANIPVINMA-DDKFHPTQG 164
                                       .455545655444.7********************8888777654226667****************.999****** PP

                                       HHHHHHHHH CS
                          OTCace_N 140 LaDlltire 148
                                       LaD++t+re
  gi|320101151|ref|YP_004176743.1| 165 LADIFTFRE 173
                                       *******97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.28   1.2e+03      18      42 ..      30      54 ..      21      56 .. 0.84
   2 ?   10.4   0.0   9.4e-05      0.42      33      58 ..     220     244 ..     216     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.28
                   Methyltransf_31 18 tfelaeelgpkaevvGiDiseeaie 42
                                      +++la+e  + a+++G++  ++ +e
  gi|320101151|ref|YP_004176743.1| 30 ALRLAKEFKEIAHYYGVEAIPKILE 54
                                      6789999999999999999888777 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.4e-05
                   Methyltransf_31  33 GiDiseeaielArenaqklgldnveF 58 
                                       G+D ++e +e+A++ a+++g + +eF
  gi|320101151|ref|YP_004176743.1| 220 GFDLDPELVEKAKQLAKDHGAT-LEF 244
                                       9*******************87.555 PP

>> Limkain-b1  Limkain b1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.2e-05      0.32      32      75 ..      80     124 ..      64     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.2e-05
                        Limkain-b1  32 cGGkvlsisgksavlrfanqeaaeralkrlen.eDvfGnritvse 75 
                                        GG+   i  ++  + f +qe a  a+k +    Dv+G+ + ++ 
  gi|320101151|ref|YP_004176743.1|  80 LGGHAAFIDATTTRMAFGKQEKAGEAVKDVAAmYDVYGHGLGIRI 124
                                       5999999*********************997637*****998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2774.05
//
Query:       gi|320101152|ref|YP_004176744.1|  [L=539]
Description: family 5 extracellular solute-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-75  253.3   1.2    4.1e-75  253.1   1.2    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.1   1.2   2.3e-79   4.1e-75       1     375 [.      76     452 ..      76     454 .. 0.92

  Alignments for each domain:
  == domain 1  score: 253.1 bits;  conditional E-value: 2.3e-79
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       e++paLA + w+ ++Dg+++ f+LR gvkF+DGtp++A +v+ s er+ d     g+   +  ++ +++v++vd+yt
  gi|320101152|ref|YP_004176744.1|  76 EFKPALAVN-WSSNEDGTEWVFHLRRGVKFHDGTPFNATAVKISVERARDIYRETGRGLGYI-WDAVEEVQVVDEYT 150
                                       689******.799*************************************987777655553.79************ PP

                                       EEEEESSETTTTTTHCHHHHHHHGC..........CHTCTCTTT.TTGTTTSE-BSSSEEEEEEETTTEEEEEE-TT CS
                         SBP_bac_5  78 vrftlkkpnalfltllaavpasiak..........kaaekeddk.dkdtnekpvgtGPYklkefkpgqkivlernpd 143
                                       vrf+l+ p+ l ++  a ++a i++             +++++  ++++  +  gtGPY+++ + p+++i+l+++ +
  gi|320101152|ref|YP_004176744.1| 151 VRFKLSYPQRLDIIAAASYAAYIFSpsalvksgasS--PMDRALeEWFNTGNEAGTGPYMITYYRPDSEIRLRKFNE 225
                                       **********88888888888777788899999752..33333303444445589********************** PP

                                       ST....TTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTST CS
                         SBP_bac_5 144 Yw....gggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkp 216
                                       +w    ++++ ++d+++++++++++++ + l +Geid+++++p ++i+ l ++kg kv  + ++   + ++fN k++
  gi|320101152|ref|YP_004176744.1| 226 WWgwsiVNNPDAPDEVVIRIVTEPQSQYNGLIAGEIDVASSVPRDNIADL-VKKGFKV-FNLTTFHNYIMFFNVKRY 300
                                       *999*999999**************************************7.8888889.8999************** PP

                                       GGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEE CS
                         SBP_bac_5 217 pfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglr 293
                                       p + +++R+A+ + i+ +e v  +++gya+++ +++p+++pg+ +  ++    yd e+A k+L+e G  +       
  gi|320101152|ref|YP_004176744.1| 301 PTNITEFRKAILHMINLDEAVALAMKGYAVKGSGVVPHGFPGHVDGLSY---RYDKEEALKYLNESGVRTPVS---- 370
                                       ************************************************9...5899**************975.... PP

                                       TCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH.....HHHHHHHHCTTESEEEEEEECTTSTTHHH CS
                         SBP_bac_5 294 ekklkltlllasgspaekaiaeliqqqlkkiGikvevktvdwa.....atylervkdgdfdmillgwgadypdpdnf 365
                                            + +l++ +++  k  ae++q+ l++iG+++ +k+ +w+     a+  +++ + ++ +i+ +w+++ p+p+++
  gi|320101152|ref|YP_004176744.1| 371 -----IEILYQVDYEELKIFAEYLQSRLREIGVNLILKPQPWSqlkdtAKGVWENPESTPHIIIADWWPTIPSPYDY 442
                                       .....***********************************9999**99888899*********************** PP

                                       HHHHHSTTCT CS
                         SBP_bac_5 366 lnpflsssga 375
                                       l+++++s ++
  gi|320101152|ref|YP_004176744.1| 443 LYSMFHSDSK 452
                                       *****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3757.89
//
Query:       gi|320101153|ref|YP_004176745.1|  [L=342]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  107.0  15.5    9.5e-31  107.0  15.5    1.6  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.8      0.22   3.9e+03     159     172 ..      16      29 ..       4      34 .. 0.47
   2 !  107.0  15.5   5.3e-35   9.5e-31       1     184 [.     119     341 ..     119     342 .] 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.22
                      BPD_transp_1 159 lalviavlllnlva 172
                                       + ++i  ++l+ ++
  gi|320101153|ref|YP_004176745.1|  16 ILIIIGAIVLSYLV 29 
                                       33333333333333 PP

  == domain 2  score: 107.0 bits;  conditional E-value: 5.3e-35
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       g++lGi++al+r+++ d +++    +l  +P+f+la  ++l+f                                  
  gi|320101153|ref|YP_004176745.1| 119 GVFLGIYSALRRGSRRDSIIQAAGTILANTPTFWLATGFFLAFsifgvslygrvntrlaistgfhpvtgfylidsli 195
                                       89************************************99999********************************** PP

                      BPD_transp_1  44 .....vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitgli 115
                                            v+ ++l   i p+++++++ ++ ++rl+r  + ++l +d++++a a G++r +i+++++l++++p ++  ++
  gi|320101153|ref|YP_004176745.1| 196 qgntaVFVDVLLRIIPPALAISVYPLGVLIRLTRTLMAEALLEDFIRTAVAWGVKRSTIIWRYALKASIPGVLQVAG 272
                                       *****9999******************************************************************** PP

                      BPD_transp_1 116 lafggllggavllef.lgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       l+f+++l +a+++e+ +++  Glg+ll +a+++ d+ +++ g+++++++++l++n+++di+q+l+dprv+
  gi|320101153|ref|YP_004176745.1| 273 LSFAYSLIDAMVVEYtVFGREGLGSLLYDALNYTDFRLAT-GLIIVVTVFYLVVNTLTDIVQALVDPRVK 341
                                       *************96369999*******************.***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2512.85
//
Query:       gi|320101154|ref|YP_004176746.1|  [L=298]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   94.7  10.0    5.4e-27   94.7  10.0    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne
    0.00032   20.6   0.1    0.00032   20.6   0.1    2.5  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 ?   -1.9   0.6      0.26   2.3e+03     176     176 ..      45      45 ..      22     107 .. 0.56
   2 !   94.7  10.0     6e-31   5.4e-27       1     185 []     108     292 ..     108     292 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.26
                      BPD_transp_1 176 q 176
                                       +
  gi|320101154|ref|YP_004176746.1|  45 A 45 
                                       1 PP

  == domain 2  score: 94.7 bits;  conditional E-value: 6e-31
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       g+l+G+ aa +++++l ++l  l+++++s+P +v+a+ + l     ++ g+++  ++ l+++ + +y+r+++  a +
  gi|320101154|ref|YP_004176746.1| 108 GVLVGVSAA-YYRGPLEHVLNYLVELFMSIPAIVIALAVRL----ATGPGFHVV-AVSLVATWWSWYARVTYVYARS 178
                                       899******.999*************************993....366666665.566777789************* PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       ++++d+v +a++ G+s  +i++++vl+na pp++ +++  +g++l +a+ + f+g    lg +l ++++g  + e++
  gi|320101154|ref|YP_004176746.1| 179 IVEMDYVVLAKLSGLSNLKIIYRHVLRNATPPVLVQAVTDMGSVLLEATSINFMG----LGVPLNSPEWGVIMLEGL 251
                                       *******************************************************....999999999999999999 PP

                      BPD_transp_1 155 ..........nggvlalviavlllnlvadilqrlldprvrk 185
                                                 +++ + l++  l ++lv d l + ldpr+r+
  gi|320101154|ref|YP_004176746.1| 252 pvitiapwitMFPGILLLATALGFSLVGDSLREELDPRMRR 292
                                       9999***********************************95 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 !   20.6   0.1   3.6e-08   0.00032      14      42 ..      22      54 ..      13      67 .. 0.75
   2 ?   -2.4   0.1      0.53   4.8e+03      27      38 ..     156     167 ..     138     177 .. 0.65
   3 ?   -2.3   0.1      0.52   4.7e+03      32      39 ..     256     263 ..     253     279 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-08
                            OppC_N 14 klAvvglvilllllliaifaPliaPydp....q 42
                                       +  vgl+++l++++iai+ P+iaPy+      
  gi|320101154|ref|YP_004176746.1| 22 TRFRVGLALVLTVTVIAILSPVIAPYPEdglgY 54
                                      6778*********************97555441 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.53
                            OppC_N  27 lliaifaPliaP 38 
                                       ++++++a +++ 
  gi|320101154|ref|YP_004176746.1| 156 VAVSLVATWWSW 167
                                       445666666654 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.52
                            OppC_N  32 faPliaPy 39 
                                       +aP+i+ +
  gi|320101154|ref|YP_004176746.1| 256 IAPWITMF 263
                                       57777543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2247.91
//
Query:       gi|320101155|ref|YP_004176747.1|  [L=317]
Description: oligopeptide/dipeptide ABC transporter ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   0.0    1.5e-24   87.1   0.0    1.2  1  ABC_tran      ABC transporter
    1.2e-15   57.7   0.0      2e-15   57.0   0.0    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    3.9e-09   36.7   0.2    0.00028   20.8   0.2    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.8e-05   25.0   0.0    6.4e-05   23.3   0.0    1.7  1  AAA_22        AAA domain
      0.001   18.6   0.1      0.011   15.1   0.1    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0057   16.4   0.0       0.01   15.5   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.026   13.8   0.1    1.4  1  AIG1          AIG1 family
      0.022   15.1   0.3      0.085   13.2   0.3    1.9  1  AAA_16        AAA ATPase domain
      0.025   14.5   0.0       0.04   13.8   0.0    1.2  1  RsgA_GTPase   RsgA GTPase
      0.049   13.2   0.0        3.5    7.1   0.0    2.2  2  AAA_25        AAA domain
      0.051   14.0   0.0      0.085   13.2   0.0    1.4  1  RNA_helicase  RNA helicase
      0.077   13.5   0.0       0.12   12.9   0.0    1.2  1  AAA_23        AAA domain
       0.11   12.9   0.0       0.35   11.3   0.0    1.8  2  AAA           ATPase family associated with various cellular 
       0.16   10.6   0.0       0.26    9.9   0.0    1.2  1  AAA_13        AAA domain
       0.22   10.5   0.0        0.3   10.0   0.0    1.1  1  Herpes_UL74   Herpes UL74 glycoproteins


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   1.3e-27   1.5e-24       2     137 .]      26     182 ..      25     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.3e-27
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..pq 69 
                                       + +s+++ ege++ +vGe+G+GKSt  +++ag l     t Ge+ + g+++ +    + + +  + ++++pq+  ++
  gi|320101155|ref|YP_004176747.1|  26 RGISFQVDEGEIYCLVGESGCGKSTTGNAIAGILPShavTRGELYIYGRKVIDddrvDYRGVRGRLVSYIPQNpgTS 102
                                       679******************************988889*****99988887756666667777889******9999 PP

                                       S-TTSBHHHH...........HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxxxxx...........xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  70 lfpeltvren...........esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       l+p  tv+++            +++ +e+a++ l+++e ++++v+++ p++LSgG++qrva+  al++ ++++++DE
  gi|320101155|ref|YP_004176747.1| 103 LNPYETVENQfyyvlnsiygySREKALETARRYLSMVElDPERVLDHYPHELSGGMQQRVAIGIALATGARVVVADE 179
                                       *****99999*********975555577777777777733477778888**************************** PP

                                       TTT CS
                                       xxx RF
                          ABC_tran 135 pta 137
                                       pt+
  gi|320101155|ref|YP_004176747.1| 180 PTS 182
                                       *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 !   57.0   0.0   1.7e-18     2e-15       1      65 []     233     296 ..     233     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 1.7e-18
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E+g+ s l++eplHPYT++L+++vp l  +k  l++i+ge+p +    + C+F++RCp+a ++C
  gi|320101155|ref|YP_004176747.1| 233 IEEGKGSLLLTEPLHPYTQMLVDAVPILGLKKP-LKSIPGEPPRAGGEIRECVFRDRCPQAFDKC 296
                                       799*************************99998.*********99999999************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.8e-05     0.021       2      83 ..      38     124 ..      37     145 .. 0.88
   2 !   20.8   0.2   2.4e-07   0.00028     221     300 ..     138     215 ..     122     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl......drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvry 72 
                                        +l+G  g+GKS+   a+ ++           ++ g++ ++++++++r+++++l +y p  p++   +  ++ ++ +
  gi|320101155|ref|YP_004176747.1|  38 YCLVGESGCGKSTTGNAIAGILPShavtrgELYIYGRKVIDDDRVDYRGVRGRLVSYIPQNPGTSLNP-YETVENQF 113
                                       68****************999999***************************************99999.99888888 PP

                            AAA_21  73 ryglrlersqv 83 
                                        y l+  +   
  gi|320101155|ref|YP_004176747.1| 114 YYVLNSIYGYS 124
                                       88887766555 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.4e-07
                            AAA_21 221 vvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltT 296
                                       +v l++++  +  ++elS G+++  a+  al+  +   ++++ DEp ++L+ +l   l++l+++l++  g  vil T
  gi|320101155|ref|YP_004176747.1| 138 MVELDPERVLDHYPHELSGGMQQRVAIGIALATGA---RVVVADEPTSSLDAHLRLQLIKLIRRLRDeQGLSVILIT 211
                                       666666667777899*********99999999988...*****************999999988888899******* PP

                            AAA_21 297 HSpl 300
                                       H+ +
  gi|320101155|ref|YP_004176747.1| 212 HDLV 215
                                       *975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.3e-08   6.4e-05       5     128 ..      35     210 ..      32     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.3e-08
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsstsskdllrellr 62 
                                         i +++GesG+GK+t+ + ++  l+ +a  +                     r ++v++ ++++++s + ++ + +
  gi|320101155|ref|YP_004176747.1|  35 GEIYCLVGESGCGKSTTGNAIAGILPSHAVTRGelyiygrkvidddrvdyrgVRGRLVSYIPQNPGTSLNPYETVEN 111
                                       57899*********************9988888**************999997777778888888888888888888 PP

                            AAA_22  63 alglelka..............................erlsseellealeqalrarav............iellii 97 
                                       ++   l++                              ++++++  +                         ++++ 
  gi|320101155|ref|YP_004176747.1| 112 QFYYVLNSiygysrekaletarrylsmveldpervldhYPHELSGGM-----------QqrvaigialatgARVVVA 177
                                       88887777888888889999998888866655555444333333333...........233334444566889**** PP

                            AAA_22  98 DEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       DE    l+   + ++++ +r+l +  ++g+++iL+
  gi|320101155|ref|YP_004176747.1| 178 DEPTSsLDahlRLQLIKLIRRLRD--EQGLSVILI 210
                                       **9999988666************..********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 !   15.1   0.1   9.6e-06     0.011      26     211 ..      37     226 ..      28     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.6e-06
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk.skekasvkkaeveitfdnedkklkiekeevs 98 
                                       + ++vG+ G+GKs   +Ai  +L  ++    r e +   +++i   + + + v    v+ + +n++ +    ++  +
  gi|320101155|ref|YP_004176747.1|  37 IYCLVGESGCGKSTTGNAIAGILPSHAV--TRGELYiygRKVIDDdRVDYRGVRGRLVSYIPQNPGTS---LNPYET 108
                                       6689999999999999999999985444..44443223367887744455555555666666777776...556667 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske........lLSgGektLvalaLlfAiqkvkpaplyllDei 167
                                       ++ + +   +s y   ++++  +  ++ l+++++++e        +LSgG ++ va+ + +A+     a +++ De 
  gi|320101155|ref|YP_004176747.1| 109 VENQFYYVLNSIYGYSREKAL-ETARRYLSMVELDPErvldhyphELSGGMQQRVAIGIALATG----ARVVVADEP 180
                                       778888888888888777764.55688899999999999999999***********99999875....56899**** PP

                                       TTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-..SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                             SMC_N 168 daaLDeknvkkvaellkeksknaQfivislreemleka..dklvgv 211
                                        + LD++ + ++ +l+++ +++  + vi +++++++      +vgv
  gi|320101155|ref|YP_004176747.1| 181 TSSLDAHLRLQLIKLIRRLRDEQGLSVILITHDLVSAGriCDVVGV 226
                                       *****************99887555555555544443322555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.6e-06      0.01       7      46 ..      21      59 ..      15      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.6e-06
                            AAA_29  7 vNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      v+W   +g ++++d+ +++ l+G+sG GKST   Ai+ +L
  gi|320101155|ref|YP_004176747.1| 21 VHWA-VRGISFQVDEGEIYCLVGESGCGKSTTGNAIAGIL 59
                                      5553.455678899667**************988888777 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.2e-05     0.026       5      22 ..      40      57 ..      38      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                                      EESSTTSSHHHHHHHHHT CS
                              AIG1  5 lvGktgnGkSaTgNsilg 22
                                      lvG +g+GkS+TgN+i g
  gi|320101155|ref|YP_004176747.1| 40 LVGESGCGKSTTGNAIAG 57
                                      9**************965 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   7.2e-05     0.085      24      59 ..      35      74 ..      29     214 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.2e-05
                            AAA_16 24 pelvllsGesGvGKsslvrellralekd.......ggiflrgk 59
                                      +e+  l+GesG+GKs+  ++++  l  +       +   ++g+
  gi|320101155|ref|YP_004176747.1| 35 GEIYCLVGESGCGKSTTGNAIAGILPSHavtrgelY---IYGR 74
                                      47899************9999965555533332220...3333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-05      0.04      95     121 ..      30      57 ..      17      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                                       HHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  95 ellkd.ktsvlvGqSGvGKStLinallp 121
                                        ++++ ++ +lvG+SG GKSt  na+++
  gi|320101155|ref|YP_004176747.1|  30 FQVDEgEIYCLVGESGCGKSTTGNAIAG 57 
                                       55555599**************999976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0029       3.5      22      49 ..      21      51 ..       6      58 .. 0.80
   2 ?    3.8   0.0     0.032        38     166     188 ..     190     212 ..     170     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0029
                            AAA_25 22 rrwlvkg...llpagelallaGapgtGKttl 49
                                      + w v+g    + +ge+  l+G +g+GK+t 
  gi|320101155|ref|YP_004176747.1| 21 VHWAVRGisfQVDEGEIYCLVGESGCGKSTT 51
                                      56777775444689***************95 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.032
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                        +l++ ++r++++ g  v+l+ H
  gi|320101155|ref|YP_004176747.1| 190 LQLIKLIRRLRDEQGLSVILITH 212
                                       5899******************9 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.1e-05     0.085       2      62 ..      39      99 ..      38     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvk 62
                                      +l+G+sg+GKSt+ + +a  l ++  +  +  +y r++ dd    Y+g    ++  ++q++
  gi|320101155|ref|YP_004176747.1| 39 CLVGESGCGKSTTGNAIAGILPSHAVTRGELYIYGRKVIDDDRVDYRGVRGRLVSYIPQNP 99
                                      799*************999998888777777777777766666666666555555555555 PP

>> AAA_23  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      0.12      17      43 ..      30      59 ..      25      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.7e-05
                            AAA_23 17 F...skgltlItGpNGaGKTTildAiklaL 43
                                      F   +  +++++G+ G+GK+T  +Ai  +L
  gi|320101155|ref|YP_004176747.1| 30 FqvdEGEIYCLVGESGCGKSTTGNAIAGIL 59
                                      555555799****************98877 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.35       2      25 ..      39      62 ..      38      98 .. 0.84
   2 ?   -1.3   0.0       2.3   2.8e+03      86     110 ..     189     212 ..     137     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                                      EEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  2 llyGppGtGKTllakavakelgve 25
                                      +l+G  G+GK+++ +a+a  l ++
  gi|320101155|ref|YP_004176747.1| 39 CLVGESGCGKSTTGNAIAGILPSH 62
                                      89****************987544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHTTTSSSTEEEEEEES CS
                               AAA  86 vnqLlteldgvkkkeskvivigatn 110
                                         qL++ + +++++++ + vi++t+
  gi|320101155|ref|YP_004176747.1| 189 RLQLIKLIRRLRDEQG-LSVILITH 212
                                       4577777777777544.77777776 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   0.00022      0.26     526     571 ..     171     214 ..     166     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnl 571
                                         ++vv D P SSLD+      + li+     +++   +++ TH l
  gi|320101155|ref|YP_004176747.1| 171 GARVVVADEPTSSLDAHLRLQLIKLIRRLR--DEQGLSVILITHDL 214
                                       679************************995..66677799999976 PP

>> Herpes_UL74  Herpes UL74 glycoproteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00025       0.3     124     225 ..      41     144 ..      37     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                       Herpes_UL74 124 tgekgcgnfttfnpmffnvprwnt...klyigsnkvnvdsqtiyflgltalllryaqrnctrsfylvnamsrnlfrv 197
                                        ge gcg+ tt n +   +p        lyi   kv +d + + + g+   l+ y  +n   s+   +++  +++ v
  gi|320101155|ref|YP_004176747.1|  41 VGESGCGKSTTGNAIAGILPSHAVtrgELYIYGRKV-IDDDRVDYRGVRGRLVSYIPQNPGTSLNPYETVENQFYYV 116
                                       59*************9999987532227*******9.677888999************************999999* PP

                       Herpes_UL74 198 pkyingtklkntmrklkrkqalvkeqpq 225
                                        + i g    +++   +r  ++v  +p+
  gi|320101155|ref|YP_004176747.1| 117 LNSIYGYSREKALETARRYLSMVELDPE 144
                                       9999999999998888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2112.79
//
Query:       gi|320101156|ref|YP_004176748.1|  [L=259]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-34  119.4   0.0      2e-34  119.0   0.0    1.2  1  ABC_tran      ABC transporter
    6.8e-09   36.0   3.9    0.00019   21.4   0.2    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0008   19.8   0.1    0.00099   19.5   0.1    1.3  1  AAA_16        AAA ATPase domain
    0.00097   19.4   0.6     0.0036   17.6   0.6    1.9  1  AAA_22        AAA domain
     0.0011   18.7   0.1     0.0019   17.9   0.1    1.3  1  AAA_29        P-loop containing region of AAA domain
     0.0011   18.5   0.3       0.58    9.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0012   18.8   1.6       0.71    9.9   0.1    3.1  3  AAA_5         AAA domain (dynein-related subfamily)
     0.0018   17.9   1.2       0.97    9.0   0.1    2.2  2  AAA_25        AAA domain
     0.0056   16.8   0.1      0.012   15.7   0.1    1.5  1  DUF87         Helicase HerA, central domain
     0.0059   16.1   0.1      0.011   15.2   0.1    1.4  1  Pox_A32       Poxvirus A32 protein
     0.0065   15.9   0.0      0.026   13.9   0.0    1.9  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0078   16.1   0.1      0.015   15.2   0.1    1.5  1  NACHT         NACHT domain
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.032   14.1   0.1    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.023   14.1   0.6        2.3    7.6   0.1    2.3  2  TniB          Bacterial TniB protein
      0.031   14.2   0.2      0.068   13.1   0.1    1.6  2  RsgA_GTPase   RsgA GTPase
      0.033   14.7   0.0      0.058   13.9   0.0    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
      0.033   13.2   0.1      0.067   12.2   0.1    1.4  1  T2SSE         Type II/IV secretion system protein
      0.049   13.3   0.2       0.18   11.5   0.0    1.8  2  AAA_30        AAA domain
      0.051   13.3   0.1      0.072   12.8   0.1    1.2  1  AAA_24        AAA domain
      0.059   13.9   0.1       0.11   13.0   0.1    1.4  1  AAA_23        AAA domain
       0.06   13.0   0.1       0.18   11.5   0.0    1.6  2  AAA_15        AAA ATPase domain
      0.065   12.2   0.0      0.099   11.6   0.0    1.2  1  DUF3987       Protein of unknown function (DUF3987)
      0.068   13.6   0.5        0.9   10.0   0.5    2.2  1  AAA           ATPase family associated with various cellular 
      0.095   11.9   0.0       0.18   11.0   0.0    1.5  1  PIF1          PIF1-like helicase
       0.17   11.5   0.0       0.24   11.0   0.0    1.2  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.19   12.1   0.3       0.34   11.3   0.3    1.7  1  AAA_19        AAA domain
        0.2   11.4   0.3        1.7    8.3   0.3    2.0  1  DEAD          DEAD/DEAH box helicase
       0.22   11.2   0.3       0.68    9.7   0.1    1.8  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.25   11.3   1.0       0.41   10.5   0.2    1.7  2  NTPase_1      NTPase
       0.25    9.9   0.1        4.5    5.8   0.0    2.0  2  AAA_13        AAA domain
       0.27   10.4   0.1       0.41    9.7   0.1    1.2  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 !  119.0   0.0   3.5e-37     2e-34       1     137 []      35     184 ..      35     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 3.5e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfp 72 
                                       lkn+sl ++ ge++ai+Ge+G+GK+tLlk+++gllkp eG++ + gkd+      ++  + +++g++pq+    l+p
  gi|320101156|ref|YP_004176748.1|  35 LKNISLAVRDGERLAIIGESGSGKTTLLKVILGLLKPFEGKVFVAGKDIYAlkwGQRILVLRQVGYVPQDpyRALNP 111
                                       79*************************************************99888888999********9999*** PP

                                       TSBHHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        ++v++            ++ +++++ l+l++l  +v++  ps+LSgG++qrv +ara++ +p++l+lDEpt+
  gi|320101156|ref|YP_004176748.1| 112 SIRVKSIleeplealGIGDRDARVREALRLVQLSSEVLQMYPSELSGGMRQRVLIARAIIHDPEILILDEPTS 184
                                       **999999999999966666777777778888888************************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   1.4e-05    0.0081       3      23 ..      49      69 ..      48     105 .. 0.84
   2 !   21.4   0.2   3.2e-07   0.00019     232     299 ..     151     216 ..      90     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      ++iG  gsGK++LL+ + +l 
  gi|320101156|ref|YP_004176748.1| 49 AIIGESGSGKTTLLKVILGLL 69
                                      79***************9995 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.2e-07
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                         ++elS G+++   ++ a++ ++    +l++DEp + L+ ++++ ++ l+++ +r  g  v+ +TH+ 
  gi|320101156|ref|YP_004176748.1| 151 MYPSELSGGMRQRVLIARAIIHDP---EILILDEPTSALDVSIQAQVVNLINDIHRkLGLAVLTVTHDL 216
                                       457899*****9978888888777...9***********************77777699********96 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   0.1   1.7e-06   0.00099      15      88 ..      37     104 ..      24     210 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-06
                            AAA_16  15 ale.rvrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                        ++ +vr+g  e + ++GesG+GK++l++ +l  l k   g +f++gk          + + q +   + +  + ++
  gi|320101156|ref|YP_004176748.1|  37 NISlAVRDG--ERLAIIGESGSGKTTLLKVILG-LLKPfeGKVFVAGKDIYA------LKWGQRILVLRQVGYVPQD 104
                                       445356666..6799*************99994.555522233344444433......4455555444444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.6   6.3e-06    0.0036       8     117 ..      48     203 ..      42     222 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.3e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.....................erpevv...fvtlpsst.sskdllre 59 
                                       l+++GesG+GKTtll+ +l  l+  ++                        +++++v    + + +++   k++l+e
  gi|320101156|ref|YP_004176748.1|  48 LAIIGESGSGKTTLLKVILGLLK--PFE-GkvfvagkdiyalkwgqrilvlRQVGYVpqdPYRALNPSiRVKSILEE 121
                                       79**************9998883..222.147788888888888877777766666677766666666677777777 PP

                            AAA_22  60 llralglelka....................erlsseellealeqalrarav................ielliiDEa 100
                                        l+alg +  +                    +    +el                             +e+li+DE 
  gi|320101156|ref|YP_004176748.1| 122 PLEALGIGDRDarvrealrlvqlssevlqmyP----SEL------------SggmrqrvliaraiihdPEILILDEP 182
                                       77777776666666655555555444433221....222............12222222233334555777777777 PP

                            AAA_22 101 qh.lr...seealeeLrslln 117
                                          l+   ++++++ + +++ 
  gi|320101156|ref|YP_004176748.1| 183 TSaLDvsiQAQVVNLINDIHR 203
                                       776666433666666655555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   3.3e-06    0.0019      23      48 ..      45      71 ..      35      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.3e-06
                            AAA_29 23 g.atlltGpsGsGKSTllDAiqalLvp 48
                                      g    ++G+sGsGK+Tll  i  lL p
  gi|320101156|ref|YP_004176748.1| 45 GeRLAIIGESGSGKTTLLKVILGLLKP 71
                                      35789*************888888776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0054       3.1      27      45 ..      48      66 ..      35      75 .. 0.85
   2 !    9.5   0.0     0.001      0.58     130     199 ..     149     214 ..     112     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0054
                                      EEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAil 45
                                       ai+G+ GSGK+ ll  il
  gi|320101156|ref|YP_004176748.1| 48 LAIIGESGSGKTTLLKVIL 66
                                      58************99884 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.001
                                       TT-STTCS-HH..HHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 130 agiskelLSgG..ektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                        ++++++LSgG  ++ L+a a++      +   + +lDe  +aLD +  ++v++l++  + +  + v ++++
  gi|320101156|ref|YP_004176748.1| 149 LQMYPSELSGGmrQRVLIARAII------HDPEILILDEPTSALDVSIQAQVVNLINDIHRKLGLAVLTVTH 214
                                       45667799999444456666655......4455889*********************888887666666555 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 ?    2.0   0.0      0.33   1.9e+02      65      98 ..       4      37 ..       1      44 [. 0.89
   2 !    9.9   0.1    0.0012      0.71       3      24 ..      49      71 ..      47      85 .. 0.81
   3 ?    4.8   0.0     0.046        27      59      96 ..     165     205 ..     131     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.33
                                      G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..- CS
                             AAA_5 65 egeilvlDEveraesevlnsLlslleerrlllee 98
                                      +g+i++l+ ++     v   L  ll err+ l +
  gi|320101156|ref|YP_004176748.1|  4 QGDIIRLENITAGYLVVKRGLKGLLKERRIVLKN 37
                                      799********99999999**********98765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                                      EEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.n 24
                                       ++G++G+gK++l + ++ +l  
  gi|320101156|ref|YP_004176748.1| 49 AIIGESGSGKTTLLKVILGLLkP 71
                                      589************99999862 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.046
                                       ------....G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE. CS
                             AAA_5  59 lvraar....egeilvlDEverae.sevlnsLlslleerrlll 96 
                                       l    r     +eil+lDE + a   ++++ + +l+++ ++ l
  gi|320101156|ref|YP_004176748.1| 165 LIA--RaiihDPEILILDEPTSALdVSIQAQVVNLINDIHRKL 205
                                       332..1336799*********99989***********998875 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     0.004       2.3      29      50 ..      41      62 ..      14      67 .. 0.77
   2 !    9.0   0.1    0.0017      0.97      98     188 ..     134     214 ..     114     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.004
                            AAA_25 29 llpagelallaGapgtGKttla 50
                                       ++ ge  +++G +g+GKttl+
  gi|320101156|ref|YP_004176748.1| 41 AVRDGERLAIIGESGSGKTTLL 62
                                      4678999*************97 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                            AAA_25  98 rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalvealer 174
                                       r ++ l++++l + e l+++ ++  g  +++++  +++ai   ++++ +++D  ++al+ + +     +++v+ +++
  gi|320101156|ref|YP_004176748.1| 134 RVREALRLVQLSS-EVLQMYPSELSGGMRQRVL--IARAII--HDPEILILDEPTSALDVSIQ-----AQVVNLIND 200
                                       5666666776654.4677766666666666664..555544..58999999999999999888.....89******* PP

                            AAA_25 175 iarrtgaavllvhH 188
                                       i r++g avl v H
  gi|320101156|ref|YP_004176748.1| 201 IHRKLGLAVLTVTH 214
                                       *************9 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.2e-05     0.012      24      47 ..      46      69 ..      37      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-05
                             DUF87 24 rHlAilgsTGsGKSntvavLleel 47
                                      ++lAi+g++GsGK+++ +v+l  l
  gi|320101156|ref|YP_004176748.1| 46 ERLAIIGESGSGKTTLLKVILGLL 69
                                      579*****************9655 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.9e-05     0.011      14      34 ..      46      66 ..      36      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                           Pox_A32 14 FrlalvGgsGsGktvyLlsLl 34
                                       rla++G+sGsGkt+ L+ +l
  gi|320101156|ref|YP_004176748.1| 46 ERLAIIGESGSGKTTLLKVIL 66
                                      59*************998765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.6e-05     0.026      13      64 ..      36      87 ..      27     120 .. 0.80
   2 ?   -0.7   0.0       1.3   7.7e+02     171     196 ..     142     167 ..     133     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                      Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasva 64
                                      + + +a+  g  l ++G +GsGKt l k + +ll p + +  +  + i++++
  gi|320101156|ref|YP_004176748.1| 36 KNISLAVRDGERLAIIGESGSGKTTLLKVILGLLKPFEGKVFVAGKDIYALK 87
                                      567788889999***********************99988877777777665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                      Mg_chelatase 171 ctcsekeierYlsklsgplldRidlq 196
                                       ++ s++  + Y s lsg +  R+ + 
  gi|320101156|ref|YP_004176748.1| 142 VQLSSEVLQMYPSELSGGMRQRVLIA 167
                                       5667788899***********99775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.6e-05     0.015       3      24 ..      48      69 ..      46      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                      +++ Ge+GsGKTtLl+ +  ++
  gi|320101156|ref|YP_004176748.1| 48 LAIIGESGSGKTTLLKVILGLL 69
                                      789************9987655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.5e-05     0.032       2      25 ..      48      71 ..      47      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-05
                              MobB  2 lgivgksgsGKTtLleklipelka 25
                                      l+i+g sgsGKTtLl+ ++  lk 
  gi|320101156|ref|YP_004176748.1| 48 LAIIGESGSGKTTLLKVILGLLKP 71
                                      789*************99998875 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.03        17      37      53 ..      47      63 ..      35      68 .. 0.87
   2 ?    7.6   0.1    0.0041       2.3     119     160 ..     173     212 ..     155     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.03
                              TniB 37 nlllvGdsnnGKtmive 53
                                       l ++G+s  GKt++++
  gi|320101156|ref|YP_004176748.1| 47 RLAIIGESGSGKTTLLK 63
                                      689***********986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0041
                              TniB 119 kvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       ++++Li+DE  ++l   ++ q +++n++  ++++l +++ +v
  gi|320101156|ref|YP_004176748.1| 173 DPEILILDEPTSAL--DVSIQAQVVNLINDIHRKLGLAVLTV 212
                                       578***********..6777889************9998776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00012     0.068      91     121 ..      36      67 ..      19      77 .. 0.82
   2 ?   -2.8   0.0       8.7     5e+03      65      84 ..     195     214 ..     184     229 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       ++++ +++d +  +++G+SG GK+tL++++l+
  gi|320101156|ref|YP_004176748.1|  36 KNISLAVRDgERLAIIGESGSGKTTLLKVILG 67 
                                       55666666668899*************99986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHTTSEEEE--T CS
                       RsgA_GTPase  65 leelkeelealgyevllvsa 84 
                                       ++ +++  ++lg++vl+v  
  gi|320101156|ref|YP_004176748.1| 195 VNLINDIHRKLGLAVLTVTH 214
                                       55555566666666666644 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 ?   13.9   0.0    0.0001     0.058       1      24 [.     235     258 ..     235     259 .] 0.97

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0001
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrs 24 
                                       vE+g+++ l+++p+  YT+ L++s
  gi|320101156|ref|YP_004176748.1| 235 VEEGDMDSLIKHPRSDYTRILVSS 258
                                       8*********************98 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012     0.067     119     158 ..      35      74 ..      17      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                             T2SSE 119 aevlrkavrerglilvsGgTgsGKttllyallkeinksde 158
                                        + ++ avr    + + G  gsGKttll ++l  ++  + 
  gi|320101156|ref|YP_004176748.1|  35 LKNISLAVRDGERLAIIGESGSGKTTLLKVILGLLKPFEG 74 
                                       56678888888999999***************99987655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.18      17      51 ..      45      78 ..      36      87 .. 0.76
   2 ?   -0.7   0.0       1.7   9.6e+02      82     114 ..     167     200 ..     111     223 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                      g+   ++ G  G+GKtt+lk++  +++  +g+v++
  gi|320101156|ref|YP_004176748.1| 45 GE-RLAIIGESGSGKTTLLKVILGLLKPFEGKVFV 78
                                      44.35688*************98888766666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                            AAA_30  82 grarlepgtllivDE.agmvdtkqlaallkaaek 114
                                       +ra +++ ++li DE ++ +d +  a++++ +++
  gi|320101156|ref|YP_004176748.1| 167 ARAIIHDPEILILDEpTSALDVSIQAQVVNLIND 200
                                       4455566688888883344466666666665554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013     0.072       4      22 ..      47      65 ..      44      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                      +++i+G+sg+GKTtl+k +
  gi|320101156|ref|YP_004176748.1| 47 RLAIIGESGSGKTTLLKVI 65
                                      899************9865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00019      0.11      23      39 ..      49      65 ..      36      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                            AAA_23 23 lItGpNGaGKTTildAi 39
                                      +I+G+ G+GKTT+l  i
  gi|320101156|ref|YP_004176748.1| 49 AIIGESGSGKTTLLKVI 65
                                      69************877 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.18      25      48 ..      47      70 ..      31      90 .. 0.76
   2 ?   -1.5   0.0       2.7   1.5e+03     320     364 ..     170     214 ..     157     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                            AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                                         +iG+ +sGK+++l+++  +l+
  gi|320101156|ref|YP_004176748.1| 47 RLAIIGESGSGKTTLLKVILGLLK 70
                                      5689***************88887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                            AAA_15 320 keeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +  ++ il+++EP   L  + q ++++l+ ++ ++    v+  TH
  gi|320101156|ref|YP_004176748.1| 170 IIHDPEILILDEPTSALDVSIQAQVVNLINDIHRKLGLAVLTVTH 214
                                       566889999***999999999999999998888777667777777 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017     0.099      40      66 ..      49      75 ..      47      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                           DUF3987 40 lvvapsGerKSpvdklvlrpleeieae 66
                                      +++++sG++K++++k++l +l+++e +
  gi|320101156|ref|YP_004176748.1| 49 AIIGESGSGKTTLLKVILGLLKPFEGK 75
                                      79**********************976 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5    0.0016       0.9       3      66 ..      50     181 ..      48     227 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                                       EESSTTSSHHHHHHHHHHHHT.HE..................................................... CS
                               AAA   3 lyGppGtGKTllakavakelg.ve..................................................... 25 
                                       ++G  G GKT+l k +   l+ +e                                                     
  gi|320101156|ref|YP_004176748.1|  50 IIGESGSGKTTLLKVILGLLKpFEgkvfvagkdiyalkwgqrilvlrqvgyvpqdpyralnpsirvksileepleal 126
                                       789*************9998642233333334444444444444444444444444444444444444444444444 PP

                                       ..............EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  26 ..............fleisgsellskyvgesekkirelfkeakeka.kpsilfiDE 66 
                                                     ++++s  e+l++y +e +  +r+ +  a++   +p il++DE
  gi|320101156|ref|YP_004176748.1| 127 gigdrdarvrealrLVQLSS-EVLQMYPSELSGGMRQRVLIARAIIhDPEILILDE 181
                                       44444444444332222222.22223555555555555544444444456666666 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0003      0.18       3      53 ..      28      76 ..      26      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                                      -HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCE CS
                              PIF1  3 neeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkiv 53
                                       +e + v+++i  ++  + g+ + + G +G+gKt l+k +l  l++ + +v
  gi|320101156|ref|YP_004176748.1| 28 LKERRIVLKNI--SLAVRDGERLAIIGESGSGKTTLLKVILGLLKPFEGKV 76
                                      57889999999..8888999***********************99965444 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 ?   11.0   0.0   0.00042      0.24      10      61 ..      41     140 ..      36     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                                       -EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                       ATP-synt_ab  10 pivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg...................................... 48 
                                        +  G+r++i+g++g Gkt++++ ++   +  +  ++v+                                      
  gi|320101156|ref|YP_004176748.1|  41 AVRDGERLAIIGESGSGKTTLLKVILGLLKPFEGKVFVAgkdiyalkwgqrilvlrqvgyvpqdpyralnpsirvks 117
                                       5678******************9988776544555555556666667777777777777777777777777777777 PP

                                       ..........ESEEHHHHHHHHH CS
                                       ..........xxxxxxxxxxxxx RF
                       ATP-synt_ab  49 ..........iGergnevaevle 61 
                                                 iG r   v+e l+
  gi|320101156|ref|YP_004176748.1| 118 ileeplealgIGDRDARVREALR 140
                                       77777777777777766666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00058      0.34      11      36 ..      46      71 ..      38     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00058
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallve 36
                                      + l++++  G+GKT++lk i+ ll+ 
  gi|320101156|ref|YP_004176748.1| 46 ERLAIIGESGSGKTTLLKVILGLLKP 71
                                      6689***************9988875 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3     0.003       1.7      12     150 ..      42     202 ..      31     215 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.003
                                       H.TTCEEEEEESTTSSHHHHHHHHHHHHHHHS.............TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTS CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  12 l.gggdvlvaaeTGsGKTlaflipvlqivyet.............kgktgpkalivePtreLaeqtlnnlkkfkkyi 74 
                                       + +g+ + + +e GsGKT+     v+  +++                k g ++l++       ++ ++ l+ ++   
  gi|320101156|ref|YP_004176748.1|  42 VrDGERLAIIGESGSGKTTLL--KVILGLLKPfegkvfvagkdiyALKWGQRILVLRQVGYVPQDPYRALNPSIRVK 116
                                       347788999999999999873..222223332333455555555444444555555555555555555444444421 PP

                                       T.....SEEEEEET.TSSH.HHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH....CTTEEEEEEETHHHHHHTTTHH CS
                                       x.....xxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  75 d.....lrvlliig.gvaa.rdqlskldngvdivvgtpgrlddllstgkln....lsqvrflVlDEadrlldqgfsd 140
                                       +     l++l  ig  +a+ r+ l+ ++ + +++ + p+ l   ++++ l     +++ ++l+lDE    ld + + 
  gi|320101156|ref|YP_004176748.1| 117 SileepLEAL-GIGdRDARvREALRLVQLSSEVLQMYPSELSGGMRQRVLIaraiIHDPEILILDEPTSALDVSIQA 192
                                       1211222222.233222222333333344466666666666664433332224446666777777777777776666 PP

                                       HHHHHHHHSH CS
                                       xxxxxxxxxx RF
                              DEAD 141 finrilnqlp 150
                                       ++ +++n ++
  gi|320101156|ref|YP_004176748.1| 193 QVVNLINDIH 202
                                       6666666664 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0012      0.68       3      21 ..      47      65 ..      45      71 .. 0.86
   2 ?   -1.5   0.0       3.3   1.9e+03      58      74 ..     186     202 ..     144     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                         PduV-EutP  3 killiGkvgsGKttLtqal 21
                                      ++ +iG++gsGKttL + +
  gi|320101156|ref|YP_004176748.1| 47 RLAIIGESGSGKTTLLKVI 65
                                      6789***********9987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                         PduV-EutP  58 ivtsaeadvialvqdat 74 
                                         +s++a+v+ l+ d++
  gi|320101156|ref|YP_004176748.1| 186 LDVSIQAQVVNLINDIH 202
                                       35688999999998876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00072      0.41       2      24 ..      48      70 ..      47      81 .. 0.86
   2 ?   -1.8   0.0       4.5   2.6e+03     136     156 ..     193     213 ..     164     237 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00072
                                      EEEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellk 24
                                      ++i G++G+GKtTl+k +l llk
  gi|320101156|ref|YP_004176748.1| 48 LAIIGESGSGKTTLLKVILGLLK 70
                                      6799**************99997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                                       --SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1 136 kdlalveeirerkdvkvfevt 156
                                       +  +l+++i+++ +  v++vt
  gi|320101156|ref|YP_004176748.1| 193 QVVNLINDIHRKLGLAVLTVT 213
                                       233333333333333333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.099        57      21      39 ..      50      68 ..      45      95 .. 0.80
   2 ?    5.8   0.0    0.0078       4.5     525     576 ..     172     221 ..     166     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.099
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G  G+GKTtL +++  l
  gi|320101156|ref|YP_004176748.1| 50 IIGESGSGKTTLLKVILGL 68
                                      66999*******9998766 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0078
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffke 576
                                          +i ++D P S LD  ++  v++li++    +k    ++  TH l   ++
  gi|320101156|ref|YP_004176748.1| 172 HDPEILILDEPTSALDVSIQAQVVNLINDIH--RKLGLAVLTVTHDLGVAQY 221
                                       56789***********************997..4556667777887766655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00071      0.41      25      44 ..      47      66 ..      24      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00071
                                      EEEEEESTTSSHHHHHHHHH CS
                           G-alpha 25 kllllGqseSGKsTilkqlk 44
                                      +l ++G+s+SGK+T+lk + 
  gi|320101156|ref|YP_004176748.1| 47 RLAIIGESGSGKTTLLKVIL 66
                                      899*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1772.34
//
Query:       gi|320101157|ref|YP_004176749.1|  [L=514]
Description: phenylalanyl-tRNA synthetase subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-78  262.0   0.0    6.9e-78  261.5   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    3.3e-06   26.4   1.4     0.0033   16.6   0.1    2.8  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.9e-05   24.2   0.0      0.004   16.6   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
  ------ inclusion threshold ------
      0.031   14.2   0.3       0.69    9.9   0.0    2.7  2  HTH_Crp_2        Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.5   0.0   1.5e-81   6.9e-78       2     244 ..     226     489 ..     225     490 .. 0.97

  Alignments for each domain:
  == domain 1  score: 261.5 bits;  conditional E-value: 1.5e-81
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       +d++++ +   ++++hp+++++++++++++++gfeev+gp+ve+ef+nfdaL++ qdhpaR+++dtF+lk++ ka  
  gi|320101157|ref|YP_004176749.1| 226 FDLSIEPPTPGRARKHPFMEFIDDLRDVLVAMGFEEVKGPHVEAEFWNFDALFQAQDHPAREIHDTFFLKTSMKArv 302
                                       57888888888999*******************************************************999999** PP

                                       .......................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEE CS
                      tRNA-synt_2d  77 .......................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqveg 129
                                                               + +l+LR++ttav++rt+ e+ +   ++++i+r fR +++Da+h++eFhq++g
  gi|320101157|ref|YP_004176749.1| 303 dpvlleragriheagwrykwspeRALRLVLRSQTTAVSARTIyERGEGEYRVFTIDRNFRPENLDAKHSMEFHQLDG 379
                                       **********************9889****************9999******************************* PP

                                       EEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-. CS
                      tRNA-synt_2d 130 lvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgid 206
                                       ++v+++v++++l+ +++el  +l g + +v f+p yfpftePs+e  + +   + +w+E++  G++rpev+e +g  
  gi|320101157|ref|YP_004176749.1| 380 VIVGKEVNFKHLLYFFKELSAAL-GVK-EVWFKPGYFPFTEPSVEGYIKH--PQLGWIEVFPGGVFRPEVMEILGA- 451
                                       ***********************.***.*********************9..9***********************. PP

                                       TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 207 eevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                         v+++a+G+Gv+Rlam  +g++DiR l+++dl+ l++
  gi|320101157|ref|YP_004176749.1| 452 PGVRAIAWGIGVDRLAMTVLGLDDIRLLFTRDLDRLEN 489
                                       89*******************************98876 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.18   7.9e+02      28      52 ..     246     270 ..     243     299 .. 0.67
   2 !   16.6   0.1   7.3e-07    0.0033      93     119 ..     353     378 ..     348     398 .. 0.91
   3 !    7.4   0.0   0.00045         2     287     306 ..     459     478 ..     453     511 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHTT-EE----SEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  28 vtkavrkyleengfieietPiLsks 52 
                                        ++ +r++l   gf e++ P +  +
  gi|320101157|ref|YP_004176749.1| 246 FIDDLRDVLVAMGFEEVKGPHVEAE 270
                                       56778999**********9987766 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7.3e-07
                                       EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                       rvf+i r+FR E++++++ + EF q++
  gi|320101157|ref|YP_004176749.1| 353 RVFTIDRNFRPENLDAKHSM-EFHQLD 378
                                       9*******************.****99 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00045
                                       EEEEHHHHHHHHCT-SSGGG CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrd 306
                                       +g+G+dRl m++lg+++Ir 
  gi|320101157|ref|YP_004176749.1| 459 WGIGVDRLAMTVLGLDDIRL 478
                                       79****************95 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 !    5.4   0.0    0.0025        11       8      37 ..     234     262 ..     229     286 .. 0.86
   2 !   16.6   0.0     9e-07     0.004      90     190 ..     345     433 ..     324     458 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0025
                   tRNA_synthFbeta   8 apttegelnkeqklrrklrdllagaGlnEv 37 
                                       +p  ++ +++  ++ + lrd+l+++G+ Ev
  gi|320101157|ref|YP_004176749.1| 234 TPGRAR-KHPFMEFIDDLRDVLVAMGFEEV 262
                                       555555.8899******************9 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9e-07
                   tRNA_synthFbeta  90 largnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefe 165
                                       ++rg+ + r+F i + f+++  + +   e ++l +v++gk+           v+f +l  + ++l ++lg+++v+f+
  gi|320101157|ref|YP_004176749.1| 345 YERGEGEYRVFTIDRNFRPEnLDAKHSMEFHQLDGVIVGKE-----------VNFKHLLYFFKELSAALGVKEVWFK 410
                                       4789999*************76667799*************...........************************* PP

                   tRNA_synthFbeta 166 paehpalhpgrsAeikvdgkevGvl 190
                                       p   p+ +p     ik    ++G++
  gi|320101157|ref|YP_004176749.1| 411 PGYFPFTEPSVEGYIK--HPQLGWI 433
                                       **99999996555554..4555554 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 ?    9.9   0.0   0.00015      0.69      21      59 ..      23      62 ..      11      66 .. 0.84
   2 ?    1.2   0.1     0.084   3.8e+02      42      63 ..     167     189 ..     165     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrr.iri 59
                                      pl  + lA ++G+++e + r ++eL+ ++li+  + r ++i
  gi|320101157|ref|YP_004176749.1| 23 PLELDVLAPLVGSRPEDIMRDIAELEGRKLIKvIK-RvVKI 62
                                      5666889*************************655.33555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.084
                                       HHHHHHTTSEE.ETEEEEES-HH CS
                         HTH_Crp_2  42 lseLkreglis.rgrririldle 63 
                                       l  L+r+ l++ r + +++l +e
  gi|320101157|ref|YP_004176749.1| 167 LDTLRRRRLVEvRDKAVIVLEPE 189
                                       6689999****544446666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3587.27
//
Query:       gi|320101158|ref|YP_004176750.1|  [L=313]
Description: radical SAM domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00081   19.7   0.0     0.0016   18.7   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
     0.0013   18.8   0.0     0.0024   18.0   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
     0.0059   17.0   0.0     0.0084   16.5   0.0    1.4  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.7e-07    0.0016      14     113 ..      31     133 ..      17     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-07
                           Fer4_12  14 gCnlsCkgCfnketw..sfksgkeftkelleeiiedlkk..esiegltllG.GEPllpenaeallelvkevkeekpe 85 
                                        C+l+C  C  +       ++ ++++ + l+ ++e+ ++  e+i+++ l G G+Pll en +++++++k + + +  
  gi|320101158|ref|YP_004176750.1|  31 KCPLNCFHCPLPGDGnvPRTYVTKIDVNHLKAALEEYSEvfERIKKVRLWGfGDPLLIENLPDVAKVIKGFMTDGA- 106
                                       67887777754433311334666777777777777777667999*******************************9. PP

                           Fer4_12  86 kdiwlytgytleelskkekeellkeidv 113
                                         i+ ++g+tl   +k++  e+++ei v
  gi|320101158|ref|YP_004176750.1| 107 -LIVHSSGVTLSRAMKTHLVEMVDEISV 133
                                       .8*************9988888887765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.1e-07    0.0024       7      95 ..      31     120 ..      29     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.1e-07
                           Fer4_14   7 gCnlsCkgCd..nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeype 80 
                                       +C+l+C  C      +   ++ ++ + + l++ l++ ++   +i+++ l G G+PL+ en +++ k++k   + +  
  gi|320101158|ref|YP_004176750.1|  31 KCPLNCFHCPlpGDGNVPRTYVTKIDVNHLKAALEEYSEVFERIKKVRLWGfGDPLLIENLPDVAKVIKGFMTDG-- 105
                                       799******97744446678888888889999999999999999*************************999988.. PP

                           Fer4_14  81 kkiwletngtleiel 95 
                                         i   ++ tl   +
  gi|320101158|ref|YP_004176750.1| 106 ALIVHSSGVTLSRAM 120
                                       666666676666444 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-06    0.0084       4      63 ..      29      91 ..      26     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                                      ESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTH CS
                                      xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxx RF
                       Radical_SAM  4 trgCnlrCsfCarpet.vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdf 63
                                       r C+l+C +C+ p +   ++ ++  ++v  +++ ++e++ +  + +k+ ++g g+pll  ++
  gi|320101158|ref|YP_004176750.1| 29 PRKCPLNCFHCPLPGDgNVPRTYVTKIDVNHLKAALEEYSeVFERiKKVRLWGFGDPLLIENL 91
                                      689**************999********************99999788888899999995443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2384.00
//
Query:       gi|320101159|ref|YP_004176751.1|  [L=299]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-36  124.2   0.0    1.1e-35  123.3   0.0    1.4  1  DUF89     Protein of unknown function DUF89


Domain annotation for each model (and alignments):
>> DUF89  Protein of unknown function DUF89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.3   0.0   5.9e-40   1.1e-35       3     346 ..       5     283 ..       4     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 5.9e-40
                                       HTHHHHHHHHHHHHHHHHTCCHHHHHHHHHHH.HHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHH CS
                             DUF89   3 eerlpciltqviddlekakdekeeelkkiiee.lselkeelqtdkpltpledeeekrswfnapwlfaecylyrrlle 78 
                                       +e+l cilt  ++++e ++ +   ++ +++++ l +l +e+  +++   +                +++++++ l +
  gi|320101159|ref|YP_004176751.1|   5 PECLRCILTTRLREIEYSTLS-PTAKVALAKKlLVKLVDEFTLESTELSM----------------LASRVFEDLVA 64 
                                       578888888888888887777.3333333333033355555444444444................45555555544 PP

                                       HHTHSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHH CS
                             DUF89  79 lfglskelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllateediqkdqeee 155
                                               +  D+++ +K +s++ al+ ve  +k+ e+l d+ e+++ llk+s  GN iD+++ +  +++++  e +
  gi|320101159|ref|YP_004176751.1|  65 EAP-----DIVDYYRLIKARSMRIALSNVEVHRKHAERLGDY-ERLHYLLKLSALGNLIDYGVAE--HVFEEHIEPS 133
                                       444.....699******************************9.*********************9..8999999999 PP

                                       HHHHHHCTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHH CS
                             DUF89 156 arkaleknilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeD 232
                                         +++e  i  dd+++l+e + + +  rv+++lDNaG E v+D llae+++    ++ V+ ++k+ P f +Dvt++D
  gi|320101159|ref|YP_004176751.1| 134 MVEKAEPAI--DDSHRLYELV-ERRGLRVLFLLDNAG-EAVYDSLLAEYMRG--KGSMVIGVAKDEPGFQNDVTLSD 204
                                       999999988..**********.9999***********.*************9..9********************** PP

                                       HHHHHHHHH-TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHHC-SEEEEEHHHHHHHHT CS
                             DUF89 233 fewlleqladsksfelsalgagldellkegklvlrgssfwttglsysempeapelyeelekadLvifKGdlNyrkLt 309
                                       +                  + gld+  + + +++ g +  ++ + ++++  ++++++ l + dL+i+KG++ +++L+
  gi|320101159|ref|YP_004176751.1| 205 LL-----------------ASGLDK--AFDMVITPGCRGVCSSIHLEKT--SEDFRRLLGSVDLIIAKGMAHFEYLY 260
                                       **.................******..9999999999999999999999..*************************9 PP

                                       TSCTTTTTSEHHHHTGTSS--EEEEEE--SHHHHHHH CS
                             DUF89 310 gdrkwppttpfttalgfspvpvlaLrtvKadvvagll 346
                                       +    +p              vl+++t K+++va+ l
  gi|320101159|ref|YP_004176751.1| 261 EAGIGKP--------------VLFILTPKCNPVAAAL 283
                                       9988886..............*************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2218.58
//
Query:       gi|320101160|ref|YP_004176752.1|  [L=335]
Description: molybdopterin-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for 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   57.7   0.2    1.7e-15   56.9   0.2    1.3  1  MoCF_biosynth    Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.089   12.8   0.1       0.57   10.2   0.0    2.3  2  Peptidase_S24    Peptidase S24-like
       0.16   11.9   0.0       0.31   10.9   0.0    1.4  1  HU-CCDC81_bac_1  CCDC81-like prokaryotic HU domain 1


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 !   56.9   0.2   2.8e-19   1.7e-15       2     108 ..     179     289 ..     178     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.8e-19
                                       EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHH CS
                     MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpeal 78 
                                        +++G+e++ g+ +D  +p+++e+l+ + ++   +   +Dde+ei+ea+++ l ++d++++ GG+++ p D tp a+
  gi|320101160|ref|YP_004176752.1| 179 LVITGTEIVDGRKRDLATPVIVEKLRLYELQQGTLVYARDDEKEISEAIKTLLMDHDAVVVAGGMSIDPTDRTPIAI 255
                                       689**********************************************8888899*******************99 PP

                                       HHHHSE....E-HHHHHHHHHHHHHHCCTTSHGG CS
                     MoCF_biosynth  79 aklfek....elegfeeafrrvslkpgkpvgvap 108
                                       a++ ++     ++  + ++ ++++++gkp++ + 
  gi|320101160|ref|YP_004176752.1| 256 AAVADEvvayGVPVKPTTMSMIAYREGKPIVGVS 289
                                       9888862222568889999999999999987654 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.3   1.8e+03      28      33 ..      51      56 ..      31      96 .. 0.55
   2 ?   10.2   0.0   9.5e-05      0.57      17      55 ..     198     239 ..     196     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.3
                                      TSEEEE CS
                     Peptidase_S24 28 Gdivvf 33
                                      G+++v 
  gi|320101160|ref|YP_004176752.1| 51 GHYYVY 56
                                      333333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.5e-05
                                       EEEECTS..---TTSEEEEEETTCE.-EEEEEEEEETTEEEE CS
                     Peptidase_S24  17 ilVdkfs..epkrGdivvfrlpgee.eayiKrviglpgdrvl 55 
                                       ++V+k +  e+++G +v++r++++e    iK + ++++ +v 
  gi|320101160|ref|YP_004176752.1| 198 VIVEKLRlyELQQGTLVYARDDEKEiSEAIKTLLMDHDAVVV 239
                                       899999999****************9999***9999988876 PP

>> HU-CCDC81_bac_1  CCDC81-like prokaryotic HU domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.2e-05      0.31       3      21 ..     222     240 ..     221     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.2e-05
                   HU-CCDC81_bac_1   3 elerhIekLLlehdcVivP 21 
                                       e+++ I++LL++hd V+v 
  gi|320101160|ref|YP_004176752.1| 222 EISEAIKTLLMDHDAVVVA 240
                                       899**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2619.88
//
Query:       gi|320101161|ref|YP_004176753.1|  [L=293]
Description: molybdenum ABC transporter periplasmic molybdate-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  103.6   0.0    1.6e-29  103.3   0.0    1.1  1  SBP_bac_11       Bacterial extracellular solute-binding prote
     0.0033   17.1   0.0     0.0044   16.7   0.0    1.2  1  Phosphonate-bd   ABC transporter, phosphonate, periplasmic su
  ------ inclusion threshold ------
      0.044   13.7   0.0      0.054   13.4   0.0    1.3  1  Intein_splicing  Intein splicing domain
       0.11   11.8   0.0       0.18   11.2   0.0    1.3  1  SBP_bac_6        Bacterial extracellular solute-binding prote


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0   3.5e-33   1.6e-29       1     215 [.      38     249 ..      38     264 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 3.5e-33
                                       .EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEE CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavpl 76 
                                       l v++ +s+++ l+e+a  + +a++ vk+++ +g  g+l+++i  + + D++i a+ +++ ++ ++glv++e+ +++
  gi|320101161|ref|YP_004176753.1|  38 LLVYTPPSIQPLLEEAARSYmQANPRVKINIVGGATGTLLNKISLTGEGDIFITADHEYMVNASRKGLVRNETIRVV 114
                                       679*****************8899*******************9999***********************8888888 PP

                                       EEEEEEEEESTT-TT---SHHHHHHSS--..EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHH CS
                        SBP_bac_11  77 assplviavpkgnpkkikgwadLlkpglk..lavadPttspsGlaalalleaagaqellkalekkvvklgessrqll 151
                                           +++++pkgnp++i+g++dL  +++k  +++a+P+ +p G+ a+all++ g   +++++++k v++g+ ++q++
  gi|320101161|ref|YP_004176753.1| 115 SFLVIALITPKGNPANITGLQDLVSKNIKkgIGIANPQVAPFGRMAVALLQKNG---IYEKVKDKLVVYGD-VGQTA 187
                                       888888889*******************668***********************...**********8876.9**** PP

                                       HHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHT CS
                        SBP_bac_11 152 taveageadagivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafL 215
                                        +v+ g++d+++ +    ++   + +++++ l  +++ + + + +avl+++++ ++A +F +fL
  gi|320101161|ref|YP_004176753.1| 188 MQVALGSVDVAVLPHIVYYW--YRNDTSIIWLNSSQLPKVSCQMVAVLNTTKNYAEAVRFEEFL 249
                                       **************887775..58899999999999875567888899999999*********9 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 !   16.7   0.0   9.8e-07    0.0044      48     192 ..      83     240 ..      52     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.8e-07
                                       TTS-SEEE--HHHHHHHHHHS-E.EEEEEEEETT--SEEEEEEEEETTSS..--SHHHH....GG-EEEE--TT-TT CS
                    Phosphonate-bd  48 agqvDiaflgplayvqardqagv.eplatrvrsdGsasyrsviivradsd..iqsledL....kgktiafvspsSts 117
                                       +g+ Di  +  + y++ + ++g+ +   +rv     + +  ++i++++++  i+ l+dL      k i+++ p  + 
  gi|320101161|ref|YP_004176753.1|  83 TGEGDIFITADHEYMVNASRKGLvRNETIRV----VSFLVIALITPKGNPanITGLQDLvsknIKKGIGIANPQVAP 155
                                       7889999999999988777777423334444....4899999******975689*****998856667777777655 PP

                                       TTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHHH...........TTEE CS
                    Phosphonate-bd 118 GylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsadaledlvaegpedk...........delr 183
                                          +  alL +++g+  +   + v  g+  +++ +v+ g +d+a+++  +++ ++++ ++++           + + 
  gi|320101161|ref|YP_004176753.1| 156 FGRMAVALL-QKNGIYEKVKDKLVVYGDVGQTAMQVALGSVDVAVLPHIVYYWYRNDTSIIWlnssqlpkvscQMVA 231
                                       334444457.8****9997779999999******************9999999997766666666666566667777 PP

                                       EEEEEEEEE CS
                    Phosphonate-bd 184 viassppip 192
                                       v+++++ + 
  gi|320101161|ref|YP_004176753.1| 232 VLNTTKNYA 240
                                       777777665 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05     0.054      48     103 ..      76     174 ..      50     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                       EEEEEEETTS-EEEEETT-EEEECCT.TEEEEEECCC--TT-EEEEE.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.............................. RF
                   Intein_splicing  48 elyeiklesgrkikaTpeHkllvvrd.egivEkradeLkegdliavp.............................. 93 
                                        l +i l+    i +T++H+++v    +g+  +r++++++  +++++                              
  gi|320101161|ref|YP_004176753.1|  76 LLNKISLTGEGDIFITADHEYMVNASrKGL--VRNETIRVVSFLVIAlitpkgnpanitglqdlvsknikkgigian 150
                                       6789********************999999..899999999988877778888888888877777777777777777 PP

                                       ..............HSCEEEEEEE CS
                                       ..............xxxxxxxxxx RF
                   Intein_splicing  94 ..............dadvvwdkvk 103
                                                     +++ +++kvk
  gi|320101161|ref|YP_004176753.1| 151 pqvapfgrmavallQKNGIYEKVK 174
                                       777777777777775555555554 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.1e-05      0.18      76     204 ..     133     253 ..     110     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                         SBP_bac_6  76 sWaDLldPeykgkvalpgnngsdlfealllalykdfg.edgvkkllrnlkanlhpaqmvkaagslesgepavsvvpy 151
                                         +DL++ + k+ +++ ++   ++f  +++al +++g  ++vk++l  + + ++ a+ + a+gs++       v+p+
  gi|320101161|ref|YP_004176753.1| 133 GLQDLVSKNIKKGIGIANPQV-APFGRMAVALLQKNGiYEKVKDKLVVYGDVGQTAM-QVALGSVDVA-----VLPH 202
                                       679*****************9.***********************999999888887.5556665544.....4555 PP

                         SBP_bac_6 152 ffadilpekkkgknlkvvwPedGalvspif.mlvkkg..kkkelakafidfllspe 204
                                         +  ++++     + ++w ++  l  + + m+ + +  k+ ++a +f +fl++  
  gi|320101161|ref|YP_004176753.1| 203 IVYYWYRND-----TSIIWLNSSQLPKVSCqMVAVLNttKNYAEAVRFEEFLVEYA 253
                                       555555555.....477777775554443303333335677777777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2128.43
//
Query:       gi|320101162|ref|YP_004176754.1|  [L=255]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-13   49.3  18.7    4.5e-13   49.3  18.7    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        0.4   11.1   0.1        0.4   11.1   0.1    4.0  4  AtpR          N-ATPase, AtpR subunit


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.6      0.13   1.2e+03      15      64 ..      18      49 ..       3      69 .. 0.41
   2 !   49.3  18.7   5.1e-17   4.5e-13       2     174 ..      64     244 ..      59     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                      BPD_transp_1 15 kldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsa 64
                                      +l   ++    v+l                  s  ghl+ +    l+ls+
  gi|320101162|ref|YP_004176754.1| 18 VLATPIYLSLTVGL------------------SLPGHLVNAFYSSLILSL 49
                                      22222222223333..................444444433333333332 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 5.1e-17
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......vilsilghlilp..viillllsaapyvr 69 
                                       i++G+++   r+ + + ll+p++ +++s+ + ++++ l+++f       v++s +   + p  ++++ ++  +p+ +
  gi|320101162|ref|YP_004176754.1|  64 IPVGYYVS--RRVTRRGLLLPIVMLPSSVSPAAIGLALLVFFvknplgsVVNSMFNIVNDPkgIVVAQFFIGVPIGV 138
                                       56666666..99999************************999*******5555666444443378888888999999 PP

                      BPD_transp_1  70 lirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleail 146
                                         + a ++s+p++++ aa+++G ++ + ++ ++lP+  + i+ g+il+f+++lg++ + + +g++  lg +++ +i 
  gi|320101162|ref|YP_004176754.1| 139 SYFTALFSSIPRSYEDAALTMGFTHTEYLYSILLPMNYREILIGFILVFTRVLGDFGASYVIGGGI-LGKTVTLPIF 214
                                       99*************************************************************666.*********9 PP

                      BPD_transp_1 147 gydyseis..nggvlalviavlllnlvadi 174
                                        + +s+     ++v++l i++l +++++ +
  gi|320101162|ref|YP_004176754.1| 215 LFLVSQFGeiSILVVVLSIYMLSVLALITL 244
                                       887773333325555555555555555444 PP

>> AtpR  N-ATPase, AtpR subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.2     0.027   2.5e+02      63      77 ..       2      16 ..       1      23 [. 0.81
   2 ?   -1.3   0.2      0.33     3e+03      32      32 ..      56      56 ..      21     103 .. 0.64
   3 ?   11.1   0.1   4.5e-05       0.4       3      36 ..     126     159 ..     124     173 .. 0.82
   4 ?   -0.7   1.6      0.23     2e+03      48      79 ..     209     241 ..     197     248 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.027
                              AtpR 63 rlLaallGFllaRll 77
                                      rlLa llGFl+a  +
  gi|320101162|ref|YP_004176754.1|  2 RLLAILLGFLVALDV 16
                                      79********98555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.33
                              AtpR 32 k 32
                                      +
  gi|320101162|ref|YP_004176754.1| 56 S 56
                                      2 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.5e-05
                              AtpR   3 lllalllGlllGaiyFggLwltvrrliaskrpal 36 
                                       +++ +++G+ +G+ yF++L+ ++ r+       +
  gi|320101162|ref|YP_004176754.1| 126 VVAQFFIGVPIGVSYFTALFSSIPRSYEDAALTM 159
                                       6899*****************9998877665555 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.23
                              AtpR  48 ivlagfyl.laagglarlLaallGFllaRllll 79 
                                       ++l  f++ +++ g   +L+++l ++++ +l+l
  gi|320101162|ref|YP_004176754.1| 209 VTLPIFLFlVSQFGEISILVVVLSIYMLSVLAL 241
                                       455555552577777888888887777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1862.23
//
Query:       gi|320101163|ref|YP_004176755.1|  [L=376]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-27   95.4   0.0    5.8e-27   94.9   0.0    1.2  1  ABC_tran    ABC transporter
    2.5e-14   53.8   0.9    3.8e-07   30.2   0.0    2.2  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    0.00034   20.8   0.0     0.0015   18.7   0.0    1.9  1  AAA_33      AAA domain
    0.00065   20.1   0.0    0.00093   19.6   0.0    1.3  1  AAA_16      AAA ATPase domain
     0.0007   18.5   0.0      0.037   12.8   0.0    2.1  2  ABC_ATPase  Predicted ATPase of the ABC class
    0.00088   18.9   0.0     0.0015   18.2   0.0    1.3  1  AAA_27      AAA domain
     0.0032   18.0   0.0     0.0051   17.3   0.0    1.2  1  AAA_23      AAA domain
     0.0033   17.1   0.0      0.007   16.1   0.0    1.5  1  AAA_29      P-loop containing region of AAA domain
     0.0036   17.2   0.0       0.01   15.8   0.0    1.6  2  ATPase_2    ATPase domain predominantly from Archaea
     0.0038   16.5   0.0     0.0054   16.0   0.0    1.2  1  Zeta_toxin  Zeta toxin
     0.0072   16.1   0.0      0.012   15.4   0.0    1.2  1  AAA_15      AAA ATPase domain
     0.0087   15.5   0.0      0.036   13.5   0.0    1.9  1  SMC_N       RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.031   14.3   0.0    1.4  1  AAA_14      AAA domain
       0.04   14.3   0.0       0.32   11.4   0.0    2.2  1  AAA         ATPase family associated with various cellular ac
      0.045   12.8   0.0      0.067   12.2   0.0    1.2  1  T2SSE       Type II/IV secretion system protein
       0.09   13.0   0.0        0.5   10.6   0.0    2.0  2  AAA_22      AAA domain
       0.16   10.8   0.0       0.23   10.3   0.0    1.1  1  DLIC        Dynein light intermediate chain (DLIC)
       0.23   11.2   0.0        0.4   10.4   0.0    1.3  1  AAA_30      AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0   5.8e-30   5.8e-27       3     136 ..      19     170 ..      17     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 5.8e-30
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.........qeleslrkeigvlpqepql 70 
                                       +vs+  ++ge+v++vG+n +GK+tLlk +agl++p+ G il++g+ + e          +++ ++++ig++p e++l
  gi|320101163|ref|YP_004176755.1|  19 DVSFRAEKGEIVVVVGPNASGKTTLLKSIAGLVEPDHGVILVNGDLVYEkkpgmrkarVNKPPYERNIGFVPTEHSL 95 
                                       89**************************************99988888889999999989999************** PP

                                       -TTSBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                        p+lt+r n             + d++i ++l+ +gl+e  d        +LS G kq+ ++aral  +p+llllDE
  gi|320101163|ref|YP_004176755.1|  96 YPHLTLRGNlelplrkrgwsrgDIDRRIRELLEVMGLEEYGDMYP----GQLSNGLKQKASIARALSYNPPLLLLDE 168
                                       ******************999999999999999999999666665....**************************** PP

                                       TT CS
                                       xx RF
                          ABC_tran 135 pt 136
                                       p+
  gi|320101163|ref|YP_004176755.1| 169 PF 170
                                       *7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2     1e-07    0.0001       1      22 [.      29      50 ..      29      65 .. 0.82
   2 !   30.2   0.0   3.8e-10   3.8e-07     220     297 ..     126     201 ..      67     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + v++GpN+sGK++LL+ + +l
  gi|320101163|ref|YP_004176755.1| 29 IVVVVGPNASGKTTLLKSIAGL 50
                                      679****************777 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 3.8e-10
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQv 292
                                        +  +  + +++  + +lS G k+ + ++ al + +   +lll+DEp + ++P    kl +++l+l+   ++ g+ v
  gi|320101163|ref|YP_004176755.1| 126 LLEVMGLEEYGDMYPGQLSNGLKQKASIARALSYNP---PLLLLDEPFSAIDPvtreKLREEFLGLF---RKLGVTV 196
                                       4444555677888999*********66666666666...9*************55555555555555...5559*** PP

                            AAA_21 293 iltTH 297
                                       ++tTH
  gi|320101163|ref|YP_004176755.1| 197 VMTTH 201
                                       ***** PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.5e-06    0.0015       1      99 [.      29     196 ..      29     209 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg.avllssdtlrrrlfgtdqqskt........................... 46 
                                       +v++vG+++sGK+tl++++   +++ + ++l++ d ++++  g  + + +                           
  gi|320101163|ref|YP_004176755.1|  29 IVVVVGPNASGKTTLLKSIaglVEPDHgVILVNGDLVYEKKPGMRKARVNkppyernigfvptehslyphltlrgnl 105
                                       599**************984434443369999999966655553333322233344455555555555555555555 PP

                            AAA_33  47 .................................dytrvldrlyqilnelar..kalsagrn.vildat......nls 81 
                                                                        ++     +l + l++ a   +als + + ++ld +       ++
  gi|320101163|ref|YP_004176755.1| 106 elplrkrgwsrgdidrrirellevmgleeygdmYP----GQLSNGLKQKASiaRALSYNPPlLLLDEPfsaidpVTR 178
                                       55555555555555555666666666664333333....33444444333300344444444555777444443444 PP

                            AAA_33  82 rrerarflklarrlgvpv 99 
                                       ++ r++fl l+r+lgv v
  gi|320101163|ref|YP_004176755.1| 179 EKLREEFLGLFRKLGVTV 196
                                       677788888888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   9.4e-07   0.00093      22      63 ..      25      67 ..      14     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.4e-07
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdg.giflrgkcdql 63
                                        +e+v+++G+ ++GK++l+++++  +e d+ +i+++g+ +  
  gi|320101163|ref|YP_004176755.1| 25 EKGEIVVVVGPNASGKTTLLKSIAGLVEPDHgVILVNGDLVYE 67
                                      3349********************9999996355577776655 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 !   12.8   0.0   3.7e-05     0.037     244     265 ..      26      48 ..      18      55 .. 0.89
   2 ?    3.5   0.0     0.025        25     328     364 ..     148     184 ..     141     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                       SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAle 265
                                       kG ++++vG+++ GK+TLL++++
  gi|320101163|ref|YP_004176755.1|  26 KGeIVVVVGPNASGKTTLLKSIA 48 
                                       6669****************997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHH CS
                        ABC_ATPase 328 sqAanimealeagakllLiDEDtsAtNlmirDermqe 364
                                        q a+i++al  + +llL+DE  sA   + r ++ +e
  gi|320101163|ref|YP_004176755.1| 148 KQKASIARALSYNPPLLLLDEPFSAIDPVTREKLREE 184
                                       5789*********************988877776665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0015      12      49 ..      13      50 ..       9      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                            AAA_27 12 GkftdrsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      G+  +r ++f+ae+ ++ +++GpN +GK+t+l++i  l
  gi|320101163|ref|YP_004176755.1| 13 GRAVNRDVSFRAEKGEIVVVVGPNASGKTTLLKSIAGL 50
                                      6667899**************************99876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.1e-06    0.0051      14      39 ..      19      47 ..       8      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.1e-06
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAi 39
                                      ++ F   +  +++++GpN +GKTT+l  i
  gi|320101163|ref|YP_004176755.1| 19 DVSFraeKGEIVVVVGPNASGKTTLLKSI 47
                                      455666445799**************988 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   7.1e-06     0.007      17      50 ..      22      55 ..      13      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.1e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                      ++ + kg +++++Gp+ sGK+Tll +i+ l  p++
  gi|320101163|ref|YP_004176755.1| 22 FRAE-KGeIVVVVGPNASGKTTLLKSIAGLVEPDH 55
                                      4444.44699**************99999888876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05      0.01      17      43 ..      24      50 ..      20      62 .. 0.84
   2 ?   -2.4   0.0       3.7   3.6e+03     120     151 ..     162     191 ..     148     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkeiien 43
                                       e+ ei+++ Gp  sGKt+Llk i+  
  gi|320101163|ref|YP_004176755.1| 24 AEKGEIVVVVGPNASGKTTLLKSIAGL 50
                                      57889*****************99765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                          ATPase_2 120 iiiiiDelqklidlglngaellvkeLlnlies 151
                                       + +++De + +id   +  e+l +e+l l+ +
  gi|320101163|ref|YP_004176755.1| 162 PLLLLDEPFSAIDPVTR--EKLREEFLGLFRK 191
                                       89999999999977766..8888888887765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.4e-06    0.0054      12      65 ..      23      76 ..      14      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.4e-06
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeil 65
                                      + e+  +++++G  ++GK++l++ ++  +e++ +v+ +++D + e  P  ++++
  gi|320101163|ref|YP_004176755.1| 23 RAEKGEIVVVVGPNASGKTTLLKSIAGLVEPDHGVILVNGDLVYEKKPGMRKAR 76
                                      4577789***********************************999999988755 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.012      23      44 ..      28      48 ..      18      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                            AAA_15 23 eeltvliGkNnsGKSsileald 44
                                      e + v++G+N+sGK+++l+ + 
  gi|320101163|ref|YP_004176755.1| 28 E-IVVVVGPNASGKTTLLKSIA 48
                                      3.89***************996 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   3.7e-05     0.036      24      80 ..      27      78 ..       2     201 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                                      SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeve 80
                                       ++ ++vGpN SGK+ ll +i  +   ++          dl+++  +k+ + ka+v+
  gi|320101163|ref|YP_004176755.1| 27 GEIVVVVGPNASGKTTLLKSIAGLVEPDHG---VILVNGDLVYE--KKPGMRKARVN 78
                                      45789***************9544433333...22333455554..55555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.1e-05     0.031       2      39 ..      27      63 ..      26      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinld 39
                                      ++i+v++G+  +GKTtllk ++     ++  ++ +n d
  gi|320101163|ref|YP_004176755.1| 27 GEIVVVVGPNASGKTTLLKSIAGL-VEPDHGVILVNGD 63
                                      689****************99843.3366666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.32       1      66 [.      30     168 ..      30     207 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                       EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS...................................... CS
                               AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellsk...................................... 37 
                                       v+++Gp   GKT+l k++a  ++    ++ ++g  + +k                                      
  gi|320101163|ref|YP_004176755.1|  30 VVVVGPNASGKTTLLKSIAGLVEpdHGVILVNGDLVYEKkpgmrkarvnkppyernigfvptehslyphltlrgnle 106
                                       5799***************9985323344444444444433333344444444444444444444444444444444 PP

                                       ................................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 ................................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                                       y g+ ++ +++  + a++ + +p  l++DE
  gi|320101163|ref|YP_004176755.1| 107 lplrkrgwsrgdidrrirellevmgleeygdmYPGQLSNGLKQKASIARALSyNPPLLLLDE 168
                                       44444444444444444444444444444444555555555555555555555556666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.8e-05     0.067     130     161 ..      28      59 ..      13      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.8e-05
                             T2SSE 130 glilvsGgTgsGKttllyallkeinksderiv 161
                                        +++v G+  sGKttll ++   ++ ++  i+
  gi|320101163|ref|YP_004176755.1|  28 EIVVVVGPNASGKTTLLKSIAGLVEPDHGVIL 59 
                                       578999**************999998854444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00051       0.5       4      28 ..      26      50 ..      23      76 .. 0.84
   2 ?   -0.4   0.0       1.3   1.3e+03      58      99 ..     124     168 ..     103     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      +  i+vv+G+  +GKTtll+ ++  
  gi|320101163|ref|YP_004176755.1| 26 KGEIVVVVGPNASGKTTLLKSIAGL 50
                                      67899**************998765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                            AAA_22  58 rellralglelka..erlsseellealeqalrarav.ielliiDE 99 
                                       rell+ +gle  +  ++++++  l++ +  +ra +  ++ll++DE
  gi|320101163|ref|YP_004176755.1| 124 RELLEVMGLEEYGdmYPGQLSNGLKQKASIARALSYnPPLLLLDE 168
                                       333333443333366666777777666666666666889999998 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00023      0.23      25      54 ..      27      56 ..      15      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                              DLIC 25 gksvlvlGedgsGkttliaklqGveeekkG 54
                                      g  v+v+G ++sGkttl+  + G+ e+  G
  gi|320101163|ref|YP_004176755.1| 27 GEIVVVVGPNASGKTTLLKSIAGLVEPDHG 56
                                      6679*******************9988777 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    0.0004       0.4      16      45 ..      25      54 ..      20      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa 45
                                      ++  ++v++Gp  +GKtt+lk+++ ++e +
  gi|320101163|ref|YP_004176755.1| 25 EKGEIVVVVGPNASGKTTLLKSIAGLVEPD 54
                                      556799*****************9998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2751.98
//
Query:       gi|320101164|ref|YP_004176756.1|  [L=310]
Description: GTP cyclohydrolase subunit MoaA [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-19   68.4   0.0    1.6e-18   67.6   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    2.2e-15   56.7   0.0    3.2e-15   56.2   0.0    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    2.9e-05   24.2   0.1    9.4e-05   22.5   0.1    1.8  1  Fer4_14      4Fe-4S single cluster domain
    0.00049   20.4   0.0     0.0011   19.2   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 !   67.6   0.0   3.6e-22   1.6e-18       3     152 ..      17     159 ..      15     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 3.6e-22
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       vt  Cn++C+fC+r  +   + r++ ls  +   +++   ++ g+  + l+ggepl+++d+v+ ++++a      + 
  gi|320101164|ref|YP_004176756.1|  17 VTSRCNYQCIFCHREGM-TGGLRSEALSAGDYGFLAEVS-VKLGITSFKLTGGEPLVRDDIVDVVREIASH---TRD 88 
                                       899************96.555555566666666666555.9**************************9998...9** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                       ++++tng l+ +  + rl+e+g+ r++++l++++  +++ ++++   +e+vl++++ + ++g+k+ +   v++
  gi|320101164|ref|YP_004176756.1|  89 VSMTTNGSLL-PGRAGRLAEAGLSRLNVSLHSLNHSVYRFITGGSTMLERVLKGVDEALDHGVKV-KLDFVVM 159
                                       **********.*************************777777788889****************5.5444444 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 !   56.2   0.0   7.1e-19   3.2e-15       2     124 ..     179     299 ..     178     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 7.1e-19
                                       EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--E CS
                       Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakketkgpakrykikdgkgeiglIapvsep.FCasCnR 77 
                                       ++ +IEl p+++  e  ++++ + d ++e +ee+   + +  +  ++++ry +++g   +++++ + +p  Ca+C+R
  gi|320101164|ref|YP_004176756.1| 179 DVNIIELIPLNTPPEAYREQYTPVDPVVEYLEEASVGKTV--RDFQNRPRYIMPSGI-VVEVVRGYGNPaLCARCTR 252
                                       799****************************999877777..568999*****9998.6****************** PP

                                       EEE-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHHT--- CS
                       Mob_synth_C  78 lRltadGklktCLfaeee.idlrdllregaseeeLkelikealarkke 124
                                       lRlt +G++ktCLf ee  +d+ + l+++++ + + e i++a+  +++
  gi|320101164|ref|YP_004176756.1| 253 LRLTPEGWIKTCLFVEEPfVDISSKLKNRDE-DGVVEGIRRAVYLREP 299
                                       *****************************75.5699999999999886 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 !   22.5   0.1   2.1e-08   9.4e-05       5      91 ..      18      97 ..      15     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.1e-08
                           Fer4_14  5 lsgCnlsCkgCdnket...wkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80
                                      +s+Cn +C +C ++      +se+    ++  l ++       +  i    ltGGePL     ++++++v+++  ++  
  gi|320101164|ref|YP_004176756.1| 18 TSRCNYQCIFCHREGMtggLRSEALSAGDYGFLAEVS-----VKLGITSFKLTGGEPLV---RDDIVDVVREIASHT-- 86
                                      89**********6663000344555555555554443.....334456678*******5...499**********99.. PP

                           Fer4_14 81 kkiwletngtl 91
                                       ++ + tng+l
  gi|320101164|ref|YP_004176756.1| 87 RDVSMTTNGSL 97
                                      999999*9986 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 !   19.2   0.0   2.5e-07    0.0011      12      95 ..      18      97 ..       4     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.5e-07
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwl 90
                                      +s+Cn +C +C+ + +    +++  +      + e   k  i+ + l+GGEPl+   +++++++v+e+ ++  + + + 
  gi|320101164|ref|YP_004176756.1| 18 TSRCNYQCIFCHREGMTGGLRSEALSAGDYGFLAEVSVKLGITSFKLTGGEPLV---RDDIVDVVREIASHTRD-VSMT 92
                                      799*********999998888888876666666666667799************...9999*******999985.7888 PP

                           Fer4_12 91 ytgyt 95
                                      ++g+ 
  gi|320101164|ref|YP_004176756.1| 93 TNGSL 97
                                      88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2442.74
//
Query:       gi|320101165|ref|YP_004176757.1|  [L=148]
Description: GTP cyclohydrolase subunit MoaC [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-46  158.3   2.1    1.2e-46  158.2   2.1    1.0  1  MoaC          MoaC family
  ------ inclusion threshold ------
      0.024   15.2   0.1      0.043   14.3   0.1    1.6  2  Ribosomal_S9  Ribosomal protein S9/S16


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 !  158.2   2.1   1.3e-50   1.2e-46       1     136 []       5     145 ..       5     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 1.3e-50
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mvdv+ k+e+ r+A+A+g+++l+++t+e+++++ ++kGdvla++ ia+i+++K+t++++pl+H++p+t+v+v++++ 
  gi|320101165|ref|YP_004176757.1|   5 MVDVTGKDEVYREATATGFIRLKPSTIEAVRKGLVEKGDVLAASTIAAILGVKETPRVLPLTHNIPITHVKVDFTVL 81 
                                       9*************************************************************************987 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEESS CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsgG 136
                                         +e +++++tvkt++ktGvemEAL++v++a+l+++DmvK+++k+       + i++vr+veK++G
  gi|320101165|ref|YP_004176757.1|  82 --DEGIRVHVTVKTTAKTGVEMEALMGVAAALLNIWDMVKKYEKDekgqypdTLITDVRVVEKRKG 145
                                       ..79****************************************999*****************98 PP

>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.42   3.7e+03      64      88 ..       9      33 ..       2      51 .. 0.62
   2 ?   14.3   0.1   4.8e-06     0.043      48     106 ..      81     144 ..      16     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.42
                                      HHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ribosomal_S9 64 sgqaeAirlgiaraLvalekeekke 88
                                      +g+ e  r + a + ++l++++ ++
  gi|320101165|ref|YP_004176757.1|  9 TGKDEVYREATATGFIRLKPSTIEA 33
                                      5666666777777777776633333 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.8e-06
                                       TSSSEEEEEEEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHC.....TCCCTS-B-------- CS
                      Ribosomal_S9  48 llgkfdvfvkvkgGGlsgqaeAirlgiaraLvalekeekkeLk.....kaglltrDpRvvErkK 106
                                       l + + v+v+vk   ++g    + +g+a aL+++ +  kk  k         l  D RvvE++K
  gi|320101165|ref|YP_004176757.1|  81 LDEGIRVHVTVKTTAKTGVEMEALMGVAAALLNIWDMVKKYEKdekgqYPDTLITDVRVVEKRK 144
                                       334689*************99999*********9762233333222225778999*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1187.47
//
Query:       gi|320101166|ref|YP_004176758.1|  [L=78]
Description: sulfur carrier protein ThiS [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-09   37.1   0.0    3.9e-09   37.0   0.0    1.1  1  ThiS             ThiS family
    0.00036   20.3   0.0    0.00043   20.1   0.0    1.2  1  Ub-Mut7C         Mut7-C ubiquitin
    0.00052   20.0   0.2     0.0012   18.9   0.2    1.5  1  TGS              TGS domain
  ------ inclusion threshold ------
      0.064   12.9   0.0       0.11   12.2   0.0    1.3  1  N_formyltrans_C  N-formyltransferase dimerization C-terminal 


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 !   37.0   0.0   8.8e-13   3.9e-09      10      77 .]      14      78 .]       5      78 .] 0.90

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 8.8e-13
                                      HHT.CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS 10 lag.eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      + g e e+ l+ + tv+elle L   y+    e++ +v+vNgei      d +l++gD v i pp++GG
  gi|320101166|ref|YP_004176758.1| 14 FIGgEVEISLDRDITVGELLEYLRGSYGMP-QEPKPVVLVNGEITGL---DRVLRNGDIVYIAPPFSGG 78
                                      5677999****************9888544.55999***********...******************9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   9.7e-08   0.00043      26      77 ..      20      75 ..      11      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.7e-08
                          Ub-Mut7C 26 avafdeaatvkhviE....alGVPhtEVelilvnGesvgfshiledGdrvavypvf 77
                                      +   d+  tv++++E    + G P     ++lvnGe +g++++l++Gd v ++p f
  gi|320101166|ref|YP_004176758.1| 20 EISLDRDITVGELLEylrgSYGMPQEPKPVVLVNGEITGLDRVLRNGDIVYIAPPF 75
                                      56677778888888855556699999999**********************99976 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   2.6e-07    0.0012      37      58 ..      50      71 ..      49      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.6e-07
                                      EEECSEEEETTSBB-SSEEEEE CS
                               TGS 37 AlVnGqrvgldhvLedgdvveI 58
                                       lVnG++ gld+vL++gd+v I
  gi|320101166|ref|YP_004176758.1| 50 VLVNGEITGLDRVLRNGDIVYI 71
                                      68******************87 PP

>> N_formyltrans_C  N-formyltransferase dimerization C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.5e-05      0.11       7      25 ..      20      38 ..      18      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                                      B--TT-EEEHHHHHHHHHH CS
                   N_formyltrans_C  7 eidLdkkvtlrElidlLRA 25
                                      ei Ld+ +t++El+++LR+
  gi|320101166|ref|YP_004176758.1| 20 EISLDRDITVGELLEYLRG 38
                                      89****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 616.05
//
Query:       gi|320101167|ref|YP_004176759.1|  [L=156]
Description: molybdopterin biosynthesis protein MoaE [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-21   76.9   0.0    1.7e-21   76.6   0.0    1.1  1  MoaE      MoaE protein


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   9.3e-26   1.7e-21      10     113 .]      23     126 ..      13     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 9.3e-26
                                       HHHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEETTSEE CS
                              MoaE  10 eiealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelevgeas 86 
                                       ++ +l + + aGA+  F+G+v+ s +g  v+eL y+a + +a+++leeia+++  +++l ++a++HrlG l++g+++
  gi|320101167|ref|YP_004176759.1|  23 KLRSLAKGKGAGAFSAFIGLVKGSVNGVVVDELVYTAINDVALRKLEEIARDICVKYSLDAIAIYHRLGALKPGDTT 99 
                                       4556667889******************************************************************* PP

                                       EEEEEEESSHHHHHHHHHHHHHHHHHH CS
                              MoaE  87 vvvavssahRkeafeaceylidelKkr 113
                                       +++++ +  R++   a++++++++Kk+
  gi|320101167|ref|YP_004176759.1| 100 IYIVALGVSRRNTNPAVSEALERVKKE 126
                                       *************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1170.30
//
Query:       gi|320101168|ref|YP_004176760.1|  [L=376]
Description: FAD dependent oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  176.3   0.2    1.4e-51  176.1   0.2    1.0  1  DAO             FAD dependent oxidoreductase
      9e-07   28.4   3.3     0.0029   16.9   0.1    2.5  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.1e-06   26.3   0.7      0.055   12.7   0.1    2.5  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00017   21.6   1.2      0.013   15.5   0.1    2.5  2  NAD_binding_9   FAD-NAD(P)-binding
    0.00063   18.9   0.3      0.002   17.3   0.1    1.8  2  FAD_binding_2   FAD binding domain
    0.00071   19.8   0.9     0.0014   18.8   0.2    1.9  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0012   17.6   0.3        1.1    7.9   0.1    2.2  2  HI0933_like     HI0933-like protein
     0.0036   16.6   0.3      0.028   13.7   0.2    2.0  2  FAD_binding_3   FAD binding domain
     0.0053   17.3   0.9       0.54   10.9   0.3    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.028   13.7   0.0        4.9    6.3   0.0    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase
      0.058   13.5   0.0       0.16   12.1   0.0    1.7  2  TetR_C_34       Tetracyclin repressor-like, C-terminal domain
       0.21   10.4   0.2       0.32    9.8   0.2    1.3  1  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.1   0.2   9.7e-55   1.4e-51       3     351 ..       6     343 ..       4     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 176.1 bits;  conditional E-value: 9.7e-55
                                       EEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   3 viiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       +i+GGG++Gl+tA  L  +g   +t++ek+  +gsg + r +  +++++ + ++    +  +++a++++  l+e+lg
  gi|320101168|ref|YP_004176760.1|   6 LIVGGGVTGLFTAVSLLDHGyrdITIVEKS-YIGSGGTFRCATGIRASFTSREH----VNIMKRAIDLWPILAEKLG 77 
                                       8****************9999*********.9999************9975553....59****************9 PP

                                       STTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHHHHH CS
                               DAO  77 ididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpakltaa 151
                                         + yrr G+l++ + e++ e +++ ++  ++++++++++ +eev+el p   ++g+l a+++p +g +  + +t  
  gi|320101168|ref|YP_004176760.1|  78 --FKYRRDGYLWVLTREKDVEFFKRVVEFHHSLNVPTRMMGPEEVKELIPSmnTEGVLSAVHDPLAGKASVFNATVN 152
                                       ..89**********988889999887777788999***************87655********************** PP

                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTT.CTTTSEEEEEEEEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgll.keldlpispvrgqvl 225
                                        a+ +++ Gv+i+egt++t++  e+g+     ++t+ g++ +ad+v +aa   +  l++ +  el  pi+ +  +vl
  gi|320101168|ref|YP_004176760.1| 153 AAALLKRSGVKIYEGTQATRITSEGGR-LI--VETNrGRI-EADKVLVAAARDTVdLVKDMgAEL--PIRNLAKHVL 223
                                       *********************666544.34..47777986.5699*****877765663333555..********** PP

                                       EEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCS.HHHHHHHHHHHHHHSGGGCG CS
                               DAO 226 vlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevd.eedidellealrklfPqlgd 301
                                        ++  +        i p+  ++d +++ y+++ + g++++G++  +e+ +d p+v+  + +++      ++fP l++
  gi|320101168|ref|YP_004176760.1| 224 ITEAFKP------VIKPL--IIDWSTSSYILQVLHGNIYIGADI-PEE-YDAPAVNkYAFLEKAAGIWVRYFPWLSE 290
                                       **55433......56666..78999****************986.444.4554555044555577777899999977 PP

                                       ..EEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 302 ..vlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                         vlr w+G+++ +pd+ p++g+ ++++++++a+G+sghG+++apa++++la 
  gi|320101168|ref|YP_004176760.1| 291 vyVLRYWVGYYDmTPDHHPIVGPLEENENVIVAAGFSGHGFMMAPAVAEALAS 343
                                       56889*******55*********77899**********************995 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   7.2e-05      0.11     145     173 ..       5      34 ..       1      43 [. 0.91
   2 !   16.9   0.1     2e-06    0.0029     190     252 ..     154     213 ..     140     220 .. 0.79
   3 ?   -2.9   0.0         2   3.1e+03     101     120 ..     318     338 ..     316     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.2e-05
                                       EEEES-SHHHHHHHHHHHHHT-E.EEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgke.vtlvea 173
                                       +++vGgG++G+ +A  l + g++ +t+ve 
  gi|320101168|ref|YP_004176760.1|   5 LLIVGGGVTGLFTAVSLLDHGYRdITIVEK 34 
                                       68********************98***996 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2e-06
                                       HHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 190 eealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglel 252
                                       ++ l+++Gv+++ gt++++i+++g +l  v+++  +i+ad v+va+ +   + l+ +++g el
  gi|320101168|ref|YP_004176760.1| 154 AALLKRSGVKIYEGTQATRITSEGGRLI-VETNRGRIEADKVLVAAARDTVD-LV-KDMGAEL 213
                                       5668889*****************9555.55555559*********776665.55.7888887 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2
                                       SEEEE---EEE-BC.TCTTC. CS
                                       xxxxxxxxxxxxxx.xxxxxx RF
                       Pyr_redox_2 101 dklvlAtGssprdl.gipGva 120
                                       +++++A G+s + +   p+va
  gi|320101168|ref|YP_004176760.1| 318 ENVIVAAGFSGHGFmMAPAVA 338
                                       578999998777665666664 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   3.7e-05     0.055       1      33 [.       6      38 ..       6      62 .. 0.94
   2 !   11.5   0.0   8.4e-05      0.13      90     132 ..     156     198 ..     144     221 .. 0.90
   3 ?   -3.0   0.0       2.3   3.4e+03     126     135 ..     318     327 ..     314     339 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      +I+G+G  Gl +a+ l ++g  d++i+Ek  ig
  gi|320101168|ref|YP_004176760.1|  6 LIVGGGVTGLFTAVSLLDHGYRDITIVEKSYIG 38
                                      6****************************9887 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.4e-05
                       Pyr_redox_3  90 vaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAt 132
                                       + k+  ++i + ++ +++++e++  +vet+++ +eA+kv++A+
  gi|320101168|ref|YP_004176760.1| 156 LLKRSGVKIYEGTQATRITSEGGRLIVETNRGRIEADKVLVAA 198
                                       67788999*********************************97 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.3
                       Pyr_redox_3 126 kkviiAtGef 135
                                       ++vi+A+G+ 
  gi|320101168|ref|YP_004176760.1| 318 ENVIVAAGFS 327
                                       4666666653 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 !   15.5   0.1   8.4e-06     0.013       2      43 ..       7      44 ..       6      67 .. 0.93
   2 ?    4.6   0.1      0.02        30     114     153 ..     159     198 ..     144     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.4e-06
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwr 43
                                      ivG+G++Gl ++  Ll++       +it++++s +g+g+ +r
  gi|320101168|ref|YP_004176760.1|  7 IVGGGVTGLFTAVSLLDH----GYRDITIVEKSYIGSGGTFR 44
                                      9*****************....588***********999987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                     NAD_binding_9 114 gvtvevh.raevvdleeradgqavlladgaslaadaVvLAl 153
                                       +  v+++  +++++++ ++++  +++++  +++ad+V +A 
  gi|320101168|ref|YP_004176760.1| 159 RSGVKIYeGTQATRITSEGGR-LIVETNRGRIEADKVLVAA 198
                                       345566524599999988776.68899999*******9985 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.4e-06     0.002       2      51 ..       5      55 ..       4      73 .. 0.88
   2 ?   -0.7   0.0      0.38   5.7e+02     151     174 ..     157     180 ..      92     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                                      EEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSGGGG--S-EE-TT.. CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGl.kvavvekeqefggatawsqGgidavlsp 51
                                      ++++G+G+ GL  A+++ ++G  ++++vek    +g t+ +  gi a+ ++
  gi|320101168|ref|YP_004176760.1|  5 LLIVGGGVTGLFTAVSLLDHGYrDITIVEKSYIGSGGTFRCATGIRASFTS 55
                                      59******************************9888999888888887754 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.38
                                       HHTCTEEEEESEEEEEEEECTTEE CS
                     FAD_binding_2 151 arkagvdfqerteadeLivedgrv 174
                                       +++ gv+++e t+a++++ e+gr 
  gi|320101168|ref|YP_004176760.1| 157 LKRSGVKIYEGTQATRITSEGGRL 180
                                       233348888888888888877753 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 !   18.8   0.2   9.4e-07    0.0014       1      28 [.       7      35 ..       7      63 .. 0.84
   2 ?   -3.5   0.0       8.8   1.3e+04      11      22 ..     153     164 ..     152     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.4e-07
                                      EE--SHHHHHHHHHHHCCTE.EEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekr 28
                                      IvG+G++Gl +A  L ++g+ d++++ek+
  gi|320101168|ref|YP_004176760.1|  7 IVGGGVTGLFTAVSLLDHGYrDITIVEKS 35
                                      9*****************9977*****96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.8
                                       HHHHHHCCTEEE CS
                     NAD_binding_8  11 aAylLakagfdv 22 
                                       aA+lL++ g+++
  gi|320101168|ref|YP_004176760.1| 153 AAALLKRSGVKI 164
                                       799999999875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1   0.00074       1.1       3      32 ..       5      35 ..       3      59 .. 0.84
   2 !    7.9   0.0   0.00075       1.1     119     162 ..     157     198 ..     145     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00074
                                      EEEE--SHHHHHHHHHHHHTT--.EEEE-SS CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkr.Vllleka 32
                                      ++++GgG  Gl++A+s+ ++g r ++++ek 
  gi|320101168|ref|YP_004176760.1|  5 LLIVGGGVTGLFTAVSLLDHGYRdITIVEKS 35
                                      579**************87775427777775 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00075
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAt 162
                                       lk++gvk++  t+ +++++ e+g++ v+t +++++eadk+++A 
  gi|320101168|ref|YP_004176760.1| 157 LKRSGVKIYEGTQATRITS-EGGRLIVET-NRGRIEADKVLVAA 198
                                       7899*************66.6666*****.************95 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   1.9e-05     0.028       3      33 ..       4      35 ..       2      65 .. 0.86
   2 ?    0.9   0.0      0.14   2.1e+02      16      77 ..     153     229 ..     149     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                      EEEEE--SHHHHHHHHHHHHTTHH.EEEEESS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvr.vvlvekr 33
                                        lIVG+G +Gl +a  L  +G r  ++vek 
  gi|320101168|ref|YP_004176760.1|  4 GLLIVGGGVTGLFTAVSLLDHGYRdITIVEKS 35
                                      569*******************9967899985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                                       HHHHHHHTTHH...............EEEEESSSSSCCSSS--EEEHH.HHHHHHHTT-HHHHHHHSEECCCCEEEE CS
                     FAD_binding_3  16 lallLseaGvr...............vvlvekrsttvvlpradglnqr.tmellrqlGledrilaegapnelmgeal 76 
                                       +a lL++ Gv+                ++ve  + +++  +  +   r t++l +++G e  i++ + ++ l++ea+
  gi|320101168|ref|YP_004176760.1| 153 AAALLKRSGVKiyegtqatritseggRLIVETNRGRIEADKVLVAAARdTVDLVKDMGAELPIRNLA-KHVLITEAF 228
                                       78999999999999999999999999999999999999999998877669********999999999.888888877 PP

                                       E CS
                     FAD_binding_3  77 y 77 
                                       +
  gi|320101168|ref|YP_004176760.1| 229 K 229
                                       6 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.3   0.00036      0.54       2      30 ..       5      34 ..       4      37 .. 0.91
   2 ?    4.4   0.0     0.038        57      48      72 ..     155     179 ..     147     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                      EEEECSSHHHHHHHHHHHHTT.SEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvver 30
                                      +++vGgG++gl  A  l ++g  ++t+ve 
  gi|320101168|ref|YP_004176760.1|  5 LLIVGGGVTGLFTAVSLLDHGyRDITIVEK 34
                                      68*******************6699**997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.038
                                       HHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  48 eklekngievllntkveeiegsedg 72 
                                         l++ g++++ +t++++i+ ++  
  gi|320101168|ref|YP_004176760.1| 155 ALLKRSGVKIYEGTQATRITSEGGR 179
                                       568899*************977754 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0058       8.7       2      22 ..      13      34 ..      12      36 .. 0.93
   2 ?    6.3   0.0    0.0033       4.9     215     262 ..     155     200 ..     103     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0058
                                      HHHHHHHHHHHTT.EEEEEEES CS
                     Amino_oxidase  2 aGLaaArqLlsaG.fdVtvlEa 22
                                      +GL +A  Ll++G +d+t++E 
  gi|320101168|ref|YP_004176760.1| 13 TGLFTAVSLLDHGyRDITIVEK 34
                                      8********************7 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0033
                                       HHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-H CS
                     Amino_oxidase 215 alaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvpl 262
                                       al  +++g++i  +t  ++i+ eg+   v++  g+ +eaD+V+v++  
  gi|320101168|ref|YP_004176760.1| 155 ALL-KRSGVKIYEGTQATRITSEGGRLIVETNRGR-IEADKVLVAAAR 200
                                       333.599***************9999999987666.5*******9865 PP

>> TetR_C_34  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.1   6.1e+03      30      48 ..     148     166 ..     120     171 .. 0.71
   2 ?   12.1   0.0    0.0001      0.16      47     120 .]     274     347 ..     270     347 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.1
                         TetR_C_34  30 nvsvealvafKrallerle 48 
                                       n +v+a++  Kr+ ++++e
  gi|320101168|ref|YP_004176760.1| 148 NATVNAAALLKRSGVKIYE 166
                                       5566666666666666655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0001
                         TetR_C_34  47 lerlaalleralPelseeqaaallaaalalvaglwplahpsealreayedpelaalrvdFeeelrellaalltG 120
                                       le++a +  r++P+lse  +++  ++ + ++   +p+  p e+++ ++ +++++ + + ++++++e+la  ++G
  gi|320101168|ref|YP_004176760.1| 274 LEKAAGIWVRYFPWLSEVYVLRYWVGYYDMTPDHHPIVGPLEENENVIVAAGFSGHGFMMAPAVAEALASYILG 347
                                       677888999*************************************************************9998 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00022      0.32       2      38 ..       5      39 ..       4      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigt 38
                                      ++ivGGG  G  +A  l  ++    ++t+ve++ ig 
  gi|320101168|ref|YP_004176760.1|  5 LLIVGGGVTGLFTAVSLLDHG--YRDITIVEKSYIGS 39
                                      58************9998888..469*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2597.89
//
Query:       gi|320101169|ref|YP_004176761.1|  [L=93]
Description: BFD (2Fe-2S)-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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    1.7e-12   47.5   0.0    1.0  1  SO_alpha_A3  Sarcosine oxidase A3 domain
    1.7e-10   41.1   1.1    2.3e-10   40.7   1.1    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 !   47.5   0.0   1.9e-16   1.7e-12       6      82 ..      10      86 ..       6      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.9e-16
                       SO_alpha_A3  6 vdlqnDvtvkdielavregfesiehvKRYttlgmgtdQgklsavnaaaivaeltgkevaevgtttlRpPlapvklaa 82
                                      v+  + vt +d+ +a++ g +++e++KR   +gmg+ Qg++  +  a i+ ++tgk+ +e+ + + RpP++pvk+  
  gi|320101169|ref|YP_004176761.1| 10 VCRCENVTLADVLNAIESGIDNLELLKRKLRIGMGQCQGQTCLLIVAGILMKKTGKSFEEIFMPRNRPPISPVKIKY 86
                                      666789*******************************************************************9875 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 !   40.7   1.1   2.5e-14   2.3e-10       1      49 [.       9      59 ..       9      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.5e-14
                          Fer2_BFD  1 iVCrCegvtegeIrdairraglttveevkrrtkagtg.Cgg..CrpaieeiL 49
                                      iVCrCe+vt  ++ +ai + g+ ++e +kr+++ g+g C+g  C   ++ iL
  gi|320101169|ref|YP_004176761.1|  9 IVCRCENVTLADVLNAI-ESGIDNLELLKRKLRIGMGqCQGqtCLLIVAGIL 59
                                      8****************.999***********************98877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 714.57
//
Query:       gi|320101170|ref|YP_004176762.1|  [L=160]
Description: 4Fe-4S ferredoxin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-10   39.6  18.1    6.3e-08   32.1   4.1    2.7  3  Fer4      4Fe-4S binding domain
    1.1e-08   35.5   6.6    2.3e-08   34.5   6.6    1.5  1  Fer4_7    4Fe-4S dicluster domain
    9.5e-08   32.1   8.7    1.6e-07   31.4   8.7    1.4  1  Fer4_9    4Fe-4S dicluster domain
    1.2e-06   28.3  15.1    0.00015   21.6   3.1    2.7  2  Fer4_6    4Fe-4S binding domain
      2e-06   27.8  11.7    3.7e-06   26.9  11.7    1.5  1  Fer4_10   4Fe-4S dicluster domain
      2e-06   27.5  14.4    4.8e-05   23.2   3.4    2.4  2  Fer4_2    4Fe-4S binding domain
    4.9e-06   26.6  10.2    4.5e-05   23.6   0.8    2.4  2  Fer4_4    4Fe-4S binding domain
    8.4e-06   25.8  21.1     0.0005   20.1  11.7    1.8  2  Fer4_21   4Fe-4S dicluster domain
    0.00011   22.5   5.0     0.0017   18.8   0.1    2.3  2  Fer4_8    4Fe-4S dicluster domain
    0.00052   20.7   0.2    0.00052   20.7   0.2    2.7  3  Fer4_15   4Fe-4S single cluster domain
    0.00064   20.6  11.5      0.068   14.1   1.3    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0065   17.0   0.4     0.0065   17.0   0.4    2.6  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.019   15.9  15.3        0.9   10.6   5.7    2.7  2  Fer4_3    4Fe-4S binding domain
      0.058   14.0  11.8      0.087   13.4   2.8    2.4  3  Fer4_17   4Fe-4S dicluster domain
      0.084   12.6   0.3       0.14   11.9   0.3    1.4  1  RPEL      RPEL repeat
       0.12   13.3   1.4       0.12   13.3   1.4    2.0  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 ?   -1.9   0.1       3.1   3.5e+03      16      21 ..      34      39 ..      33      41 .. 0.73
   2 !   16.5   2.1   4.9e-06    0.0055      11      23 ..      42      54 ..      42      55 .. 0.94
   3 !   32.1   4.1   5.7e-11   6.3e-08       2      23 ..      64      85 ..      63      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
                                      HHSTTT CS
                              Fer4 16 evCPvg 21
                                        CP +
  gi|320101170|ref|YP_004176762.1| 34 LECPEE 39
                                      57**76 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.9e-06
                                      -THHHHHSTTTEE CS
                              Fer4 11 CGaCvevCPvgAI 23
                                      C++Cv++CP++A 
  gi|320101170|ref|YP_004176762.1| 42 CNICVSACPFNAV 54
                                      ************7 PP

  == domain 3  score: 32.1 bits;  conditional E-value: 5.7e-11
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      + d+ekCigCG Cv  CP  AI
  gi|320101170|ref|YP_004176762.1| 64 KLDPEKCIGCGVCVAKCPGLAI 85
                                      68****************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 !   34.5   6.6     2e-11   2.3e-08       4      49 ..      41      81 ..      40      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2e-11
                            Fer4_7  4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49
                                       C+ Cv+aCp +a++  +       e +++dpekC+gCg+Cva CP
  gi|320101170|ref|YP_004176762.1| 41 PCNICVSACPFNAVSKSKI-----YEIPKLDPEKCIGCGVCVAKCP 81
                                      6**************9886.....56789****************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 !   31.4   8.7   1.4e-10   1.6e-07       4      49 ..      41      83 ..      35      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.4e-10
                            Fer4_9  4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                       C+ Cv+aCp+++v++++  ++ +l+ +   +CigCg Cv++Cp  
  gi|320101170|ref|YP_004176762.1| 41 PCNICVSACPFNAVSKSKIYEIPKLDPE---KCIGCGVCVAKCPGL 83
                                      5***********************9874...8************75 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   4.4   0.00025      0.28      10      23 ..      40      53 ..      36      54 .. 0.87
   2 !   21.6   3.1   1.4e-07   0.00015       5      20 ..      66      81 ..      62      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                            Fer4_6 10 igCgdCvrvCPega 23
                                      i C+ Cv++CP++a
  gi|320101170|ref|YP_004176762.1| 40 IPCNICVSACPFNA 53
                                      47**********98 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.4e-07
                            Fer4_6  5 dpdkCigCgdCvrvCP 20
                                      dp+kCigCg Cv+ CP
  gi|320101170|ref|YP_004176762.1| 66 DPEKCIGCGVCVAKCP 81
                                      9**************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 !   26.9  11.7   3.3e-09   3.7e-06      10      56 .]      40      81 ..      32      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.3e-09
                           Fer4_10 10 irCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      i C+ Cv+aCP+      +   +s++ ++ k ++ekC+gcg Cv++CP
  gi|320101170|ref|YP_004176762.1| 40 IPCNICVSACPF------NAVSKSKIYEIPKlDPEKCIGCGVCVAKCP 81
                                      78**********......444444444444449**************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 !    9.6   3.3   0.00089         1      10      21 ..      36      50 ..      28      51 .. 0.77
   2 !   23.2   3.4   4.3e-08   4.8e-05       2      21 ..      62      81 ..      61      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00089
                            Fer4_2 10 Cig...CgaCvsaCP 21
                                      C +   C++CvsaCP
  gi|320101170|ref|YP_004176762.1| 36 CPEeipCNICVSACP 50
                                      554555********* PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.3e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                       ++ d+++CigCg Cv  CP
  gi|320101170|ref|YP_004176762.1| 62 IPKLDPEKCIGCGVCVAKCP 81
                                      5899***********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 !    7.3   2.8    0.0068       7.6       7      17 .]      42      52 ..      34      52 .. 0.74
   2 !   23.6   0.8     4e-08   4.5e-05       1      15 [.      67      81 ..      67      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0068
                            Fer4_4  7 CgsCvaaCPqg 17
                                      C  Cv+aCP++
  gi|320101170|ref|YP_004176762.1| 42 CNICVSACPFN 52
                                      556******86 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4e-08
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +e+CigCg+Cva CP
  gi|320101170|ref|YP_004176762.1| 67 PEKCIGCGVCVAKCP 81
                                      69************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 !   20.1  11.7   4.5e-07    0.0005       9      52 ..      40      81 ..      32      87 .. 0.82
   2 !   17.7   1.9   2.6e-06    0.0029       3      26 ..      65      88 ..      63      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.5e-07
                           Fer4_21  9 igCgkCliaCedtshqaieidaktvlkv.vedeCvGCnlCssvCP 52
                                      i C+ C+ aC+    +a+++++   ++    ++C+GC +C++ CP
  gi|320101170|ref|YP_004176762.1| 40 IPCNICVSACP---FNAVSKSKIYEIPKlDPEKCIGCGVCVAKCP 81
                                      89*********...78898776666655168************** PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.6e-06
                           Fer4_21  3 idedkCigCgkCliaCedtshqai 26
                                      +d++kCigCg C+  C+  ++  +
  gi|320101170|ref|YP_004176762.1| 65 LDPEKCIGCGVCVAKCPGLAIFVV 88
                                      688888888888888886665555 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.2     0.019        22       7      22 ..      41      56 ..      35      67 .. 0.76
   2 !   18.8   0.1   1.5e-06    0.0017       3      17 ..      68      87 ..      66     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                            Fer4_8  7 eCgaCqsaCpvlrrtk 22
                                       C  C saCp+   +k
  gi|320101170|ref|YP_004176762.1| 41 PCNICVSACPFNAVSK 56
                                      5999999999766555 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.5e-06
                            Fer4_8  3 ekCieCgaCqsaCp.....v 17
                                      ekCi+Cg C ++Cp     v
  gi|320101170|ref|YP_004176762.1| 68 EKCIGCGVCVAKCPglaifV 87
                                      79***********9555541 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 ?   -1.7   0.0       4.5   5.1e+03      54      62 ..      31      39 ..       8      40 .. 0.66
   2 ?    0.6   0.6      0.89   9.9e+02      11      19 ..      42      50 ..      38      57 .. 0.72
   3 !   20.7   0.2   4.6e-07   0.00052       3      33 ..      65      99 ..      64     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.5
                           Fer4_15 54 eAaraCPvd 62
                                       A+ +CP++
  gi|320101170|ref|YP_004176762.1| 31 VAVLECPEE 39
                                      477788876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.89
                           Fer4_15 11 cglCvaeap 19
                                      c+ Cv ++p
  gi|320101170|ref|YP_004176762.1| 42 CNICVSACP 50
                                      777777776 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 4.6e-07
                           Fer4_15  3 vDrdaCigcglCvaeape....vfeldedglasvl 33
                                      +D ++Cigcg+Cva +p     v+ + + g+a+v+
  gi|320101170|ref|YP_004176762.1| 65 LDPEKCIGCGVCVAKCPGlaifVVDISKPGKAYVT 99
                                      89**************8622213344445777776 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   1.3     6e-05     0.068       5      24 ..      42      61 ..      35      69 .. 0.78
   2 !   11.2   3.3   0.00048      0.54       1      17 [.      69      85 ..      69      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
                           Fer4_16  5 CgkCaevCPtnaikekkeke 24
                                      C+ C+++CP na+++ k +e
  gi|320101170|ref|YP_004176762.1| 42 CNICVSACPFNAVSKSKIYE 61
                                      99999999999999885444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00048
                           Fer4_16  1 rCgtCgkCaevCPtnai 17
                                      +C++Cg C+  CP  ai
  gi|320101170|ref|YP_004176762.1| 69 KCIGCGVCVAKCPGLAI 85
                                      59***********8887 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.4   4.9e+03      47      55 ..      32      40 ..      31      40 .. 0.81
   2 ?    1.2   4.6       0.5   5.7e+02       7      17 ..      40      50 ..      35      52 .. 0.92
   3 !   17.0   0.4   5.8e-06    0.0065       2      17 ..      66      81 ..      65      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.4
                           Fer4_13 47 AadaCPves 55
                                      A+ +CP e+
  gi|320101170|ref|YP_004176762.1| 32 AVLECPEEI 40
                                      7789**986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.5
                           Fer4_13  7 iacgaCvelaP 17
                                      i c++Cv+++P
  gi|320101170|ref|YP_004176762.1| 40 IPCNICVSACP 50
                                      78********9 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 5.8e-06
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D ++Ci+cg+Cv+ +P
  gi|320101170|ref|YP_004176762.1| 66 DPEKCIGCGVCVAKCP 81
                                      889************* PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.1    0.0013       1.4       4      15 .]      42      53 ..      36      53 .. 0.93
   2 ?   10.6   5.7    0.0008       0.9       1      13 [.      70      82 ..      70      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                            Fer4_3  4 CgaCvevCPvgA 15
                                      C+ Cv +CP +A
  gi|320101170|ref|YP_004176762.1| 42 CNICVSACPFNA 53
                                      888******998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0008
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+gCg Cv  CP 
  gi|320101170|ref|YP_004176762.1| 70 CIGCGVCVAKCPG 82
                                      ************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 ?    5.5   1.6     0.022        24       5      17 ..      42      54 ..      35      64 .. 0.74
   2 ?   13.4   2.8   7.8e-05     0.087      44      57 ..      68      81 ..      55      85 .. 0.81
   3 ?   12.0   3.1   0.00022      0.24       2      13 ..      70      81 ..      69      95 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                           Fer4_17  5 CgyClpeCpsyea 17
                                      C  C+ +Cp+++ 
  gi|320101170|ref|YP_004176762.1| 42 CNICVSACPFNAV 54
                                      7777777777665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.8e-05
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++Ci+Cg C++kCP
  gi|320101170|ref|YP_004176762.1| 68 EKCIGCGVCVAKCP 81
                                      67888888888888 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00022
                           Fer4_17  2 CiqCgyClpeCp 13
                                      Ci+Cg C+++Cp
  gi|320101170|ref|YP_004176762.1| 70 CIGCGVCVAKCP 81
                                      555555555555 PP

>> RPEL  RPEL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00013      0.14      11      23 ..      10      22 ..      10      23 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                              RPEL 11 treELvernILpe 23
                                      t+eEL+e++ Lp+
  gi|320101170|ref|YP_004176762.1| 10 TPEELEEKGLLPP 22
                                      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 ?   -0.3   1.4       1.8     2e+03       4      13 ..      41      50 ..      35      56 .. 0.74
   2 ?   13.3   1.4    0.0001      0.12      74      93 ..      62      81 ..      51      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.8
                           Fer4_22  4 sCgaCtlvCp 13
                                       C+ C  +Cp
  gi|320101170|ref|YP_004176762.1| 41 PCNICVSACP 50
                                      5777777776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.0001
                           Fer4_22 74 kekfgesgCvGCgRCieacp 93
                                        k + ++C+GCg C+++cp
  gi|320101170|ref|YP_004176762.1| 62 IPKLDPEKCIGCGVCVAKCP 81
                                      45678899***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        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):              16  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1224.69
//
Query:       gi|320101171|ref|YP_004176763.1|  [L=489]
Description: monooxygenase FAD-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-31  109.9   4.8      2e-31  109.3   4.8    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.3e-22   77.4   0.0    1.4e-21   76.3   0.0    1.6  1  Fer2_4          2Fe-2S iron-sulfur cluster binding domain
    9.1e-14   51.4   0.1    7.8e-08   31.9   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    5.4e-11   42.3   4.2      2e-07   30.6   0.2    2.2  2  FAD_binding_3   FAD binding domain
    2.5e-09   37.2   4.0    8.7e-05   22.7   0.3    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.9e-09   36.5   7.5      5e-07   29.1   1.2    2.7  3  FAD_binding_2   FAD binding domain
    7.8e-09   35.1   1.0    2.7e-06   26.8   0.1    2.3  2  Thi4            Thi4 family
    2.1e-08   33.6   6.2    2.9e-05   23.3   0.1    3.5  4  GIDA            Glucose inhibited division protein A
    6.5e-08   33.0   9.7    2.7e-05   24.7   1.9    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    9.1e-08   31.9   5.3      1e-07   31.7   0.1    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    1.8e-07   31.1   7.9     0.0025   17.4   0.1    3.3  3  DAO             FAD dependent oxidoreductase
    4.6e-06   25.6   2.8    0.00031   19.6   0.2    2.4  2  HI0933_like     HI0933-like protein
    9.6e-06   26.0   1.7      0.098   13.1   0.2    2.4  2  NAD_binding_7   Putative NAD(P)-binding
    1.9e-05   24.3   2.6     0.0044   16.7   0.1    2.4  2  ApbA            Ketopantoate reductase PanE/ApbA
    0.00066   18.8   4.1     0.0051   15.9   0.7    2.2  2  Lycopene_cycl   Lycopene cyclase protein
    0.00081   18.8   1.6       0.18   11.0   0.1    2.7  3  Amino_oxidase   Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
      0.014   15.5   1.3       0.77    9.8   0.1    2.3  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.049   13.4   1.0        7.8    6.1   0.1    2.2  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
      0.065   12.6   2.1        3.1    7.1   0.1    2.4  2  ThiF            ThiF family
      0.072   13.7   1.0        1.3    9.7   0.1    2.9  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.31   10.6   2.6          9    5.8   0.1    2.3  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.65    9.9   7.7        1.1    9.1   0.2    2.7  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.84    9.9   3.2         27    5.1   0.5    2.7  2  TrkA_N          TrkA-N domain
        2.2    8.3   5.7        5.7    6.9   0.1    3.1  3  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 !  109.3   4.8   2.7e-34     2e-31       2     293 ..     120     425 ..     119     426 .. 0.75

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 2.7e-34
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...........HHHHCHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias...........evvkklnqgi 67 
                                       dv+v+G+GpAGl+aal+l+++g++v+lv  ++++ +gg l++++   +++ +               e ++kl   +
  gi|320101171|ref|YP_004176763.1| 120 DVLVVGAGPAGLQAALKLGEKGVDVVLV--TDHFRLGGQLVKQTHKFFGDTRYYGGmrgfkiagklvEALSKLP-TV 193
                                       8***************************..45555555555444444444443333446666665554444444.36 PP

                                       CCCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BC.....TCTTC.TTBEECCSECHHHHHHCC CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  68 elllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssprdl.....gipGvaenvgklvrtldsaealkl 138
                                       ++++++ + ++  +    v ++ ++   +  ++  + v+AtG++ +++     ++pGv  ++g   +tl++  ++k 
  gi|320101171|ref|YP_004176763.1| 194 KTYTRAYAYGFFSEGyMGVAVQGEN-PVNLLVKPRYMVIATGATEKTIlfennDLPGV-MGAGG-AQTLMNEYGVKP 267
                                       7777766666653332444443332.33446677*********8888778999999*9.44444.489999999988 PP

                                       SS-TSEEEEES-SHHHHHHHHHHHHHT-EEE.EEESSSSSSTTS-HHHHHHH..HHHHHHTTEEEEESCEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 139 kllpkrivvvGgGyiGvElAaalaklgkevt.lveardrllraldkelsaal..eealekeGvevklgtsvkeidgn 212
                                              +vvG+G++G+ +A +l ++g++v+ +ve ++++          ++  + +l+++Gv + +g+++++++g+
  gi|320101171|ref|YP_004176763.1| 268 GDDA---LVVGSGNVGLIIAYQLLQAGVRVHsVVELMKEIG--------GWVvhASKLRRHGVPILTGHTIVRAEGR 333
                                       8876...**********************873555555554........444115679999**************** PP

                                       TE...........EEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE...EETTEE..E--TTSBESSTTEEE CS
                                       xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxx RF
                       Pyr_redox_2 213 ge...........klevvledgeeidadlvvvavGvrpstelleeklglel...derggi..vvdeflrtnvpgiya 273
                                       ++           kl  v ++++e+ +dlv++avG++p+ +ll  ++g  +    e+gg+  v    ++t++pg+++
  gi|320101171|ref|YP_004176763.1| 334 ERvekavvaavdeKLNPVQGSEREYSVDLVLLAVGLQPNYALL-SQMGAVMkyiPEAGGLvpVRTVDMETSIPGVFV 409
                                       *99999888776555688889999*******************.899988867778888866677788********* PP

                                       -GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 274 iGDvaggkggpelaqaAvqq 293
                                       +GD +    g+e a++A  +
  gi|320101171|ref|YP_004176763.1| 410 AGDLT----GIEEATTAFIE 425
                                       ***99....99999999765 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 !   76.3   0.0   1.9e-24   1.4e-21       2      79 ..      18      96 ..      17      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1.9e-24
                            Fer2_4  2 rpvtltfDGkevtvpeGdtvasAllangvdvp.rsckygrprgelcaggeCrnClVevegepnvracstpvedGlkvet 79
                                      r+v++t++G  v+++eG+++++ l+a g +v+ rs    rprg +c++g C+ Cl +v+g+pn+r c+ pv+dG++v +
  gi|320101171|ref|YP_004176763.1| 18 RRVSFTYNGSIVEAYEGESILASLYAVGYRVFsRSPDGSRPRGAFCMIGRCSSCLSKVNGVPNTRICIEPVRDGVSVVS 96
                                      789*****************************9*******************************************976 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.2e-06    0.0024       1      29 [.     122     150 ..     114     167 .. 0.84
   2 !   31.9   0.0     1e-10   7.8e-08     126     305 .]     227     411 ..     222     411 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEk 29 
                                       +++GaGPaGl+aa++l ++g++ +l+ + 
  gi|320101171|ref|YP_004176763.1| 122 LVVGAGPAGLQAALKLGEKGVDVVLVTDH 150
                                       699*****************977777665 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1e-10
                       Pyr_redox_3 126 kkviiAtGe......fdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtr. 195
                                       ++ +iAtG       f++ +++++ G+      +  ++e+    g++ +V+G +n +  +A++l ++g +V+ v++ 
  gi|320101171|ref|YP_004176763.1| 227 RYMVIATGAtektilFENNDLPGVMGAGGA---QTLMNEYGVKPGDDALVVGSGNVGLIIAYQLLQAGVRVHSVVEl 300
                                       678888886444444778888888888743...333445555679**************************977662 PP

                       Pyr_redox_3 196 gseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkdd.vvlatGykpdl 271
                                        +ei  +  + s +l+ +  + l     ++ ++++ +++v++     +  k++  +g++ e + d v+la+G +p++
  gi|320101171|ref|YP_004176763.1| 301 MKEIGGWVVHAS-KLRRHGVPILTG---HTIVRAEGRERVEKAVVAAVDEKLNPVQGSEREYSVDlVLLAVGLQPNY 373
                                       567777775555.577777777765...345788888888887777777777766666666655505666******* PP

                       Pyr_redox_3 272 sflkk....slfeldedgrpvlteeteetnvpglflaG 305
                                        +l++    ++   ++ g + + + ++et +pg+f+aG
  gi|320101171|ref|YP_004176763.1| 374 ALLSQmgavMKYIPEAGGLVPVRTVDMETSIPGVFVAG 411
                                       ****97743333346778999****************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 !   30.6   0.2   2.7e-10     2e-07       1      33 [.     118     150 ..     118     153 .. 0.94
   2 !   13.0   0.5   5.9e-05     0.044       3      30 ..     270     297 ..     269     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.7e-10
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       etdVl+VGaGpaGl +al L e+Gv+vvlv+ +
  gi|320101171|ref|YP_004176763.1| 118 ETDVLVVGAGPAGLQAALKLGEKGVDVVLVTDH 150
                                       69***************************9866 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.9e-05
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlv 30 
                                       d l+VG+G +Gl+ a  L +aGvrv+ v
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQLLQAGVRVHSV 297
                                       679*********************7533 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3   1.2e-07   8.7e-05       1      53 [.     123     178 ..     123     189 .. 0.87
   2 !   15.3   0.3   2.3e-05     0.017       1      38 [.     273     311 ..     273     338 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.2e-07
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE...TTCEECTS---EE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev...pgvrvdygahifh 53 
                                       +vGaG +Gl aA  L ++g+dv+l+  + rlGG++   ++   ++ r+  g++ f+
  gi|320101171|ref|YP_004176763.1| 123 VVGAGPAGLQAALKLGEKGVDVVLVTDHFRLGGQLVKQTHkffGDTRYYGGMRGFK 178
                                       8*********************************9988886666688877777775 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.3e-05
                                       EE--SHHHHHHHHHHHCCTEEEE.EE-SSSSSSGGG-EE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvl.llekrdrlGGraasy 38 
                                       +vG+G  Gl +Ay L +ag++v+ ++e    +GG++  +
  gi|320101171|ref|YP_004176763.1| 273 VVGSGNVGLIIAYQLLQAGVRVHsVVELMKEIGGWVVHA 311
                                       8*******************974499*9*****997554 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   1.2   6.7e-10     5e-07       1      39 [.     120     158 ..     120     162 .. 0.96
   2 ?   -0.3   0.0      0.57   4.3e+02     115     204 ..     152     238 ..     150     262 .. 0.74
   3 !   10.3   0.5   0.00035      0.26       1      36 [.     270     306 ..     270     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.7e-10
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                       Dv+V+G+G AGL AAl++ e+G +v++v+  ++ gg+++
  gi|320101171|ref|YP_004176763.1| 120 DVLVVGAGPAGLQAALKLGEKGVDVVLVTDHFRLGGQLV 158
                                       9*********************************99876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.57
                                       E-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEE CS
                     FAD_binding_2 115 elGglsatartlhdaadarretlvtghallarlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevri 190
                                       +lGg+  + +t+   +d r    + g++++  lve++ k++ v+ ++r++a  +    ++  G+ v+  e++ +  +
  gi|320101171|ref|YP_004176763.1| 152 RLGGQLVK-QTHKFFGDTRYYGGMRGFKIAGKLVEALSKLPtVKTYTRAYAYGFFS--EGYMGVAVQ-GENPVNLLV 224
                                       57888888.777778887558888999**********99999*******9999977..677777777.455555566 PP

                                       EESEEEE-----GG CS
                     FAD_binding_2 191 rakavvlatgGfgr 204
                                       + +  v+atg+ ++
  gi|320101171|ref|YP_004176763.1| 225 KPRYMVIATGATEK 238
                                       66678888887776 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00035
                                       SEEEE--SHHHHHHHHHHHHTTT-EE.EEESSSGGGS CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkva.vvekeqefgg 36 
                                       D++V+GsG  GL  A+++ +aG +v  vve ++e gg
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQLLQAGVRVHsVVELMKEIGG 306
                                       89*********************99658999998888 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   3.6e-09   2.7e-06      13      56 ..     114     156 ..     105     164 .. 0.89
   2 !    6.7   0.1    0.0049       3.6      19      55 ..     270     306 ..     257     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.6e-09
                                       HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4  13 lkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56 
                                        +  e+Dv++vGaG++GL aa  l++k ++ v+++  +  +GG 
  gi|320101171|ref|YP_004176763.1| 114 KEVLETDVLVVGAGPAGLQAALKLGEK-GVDVVLVTDHFRLGGQ 156
                                       5688***********************.***********99995 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0049
                                       EEEEE--SHHHHHHHHHHHHCTTS-EE.EEESSSS--T CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkva.ilersvspGG 55 
                                       D ++vG+G  GL  ay l ++ +++v  ++e    +GG
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQLLQA-GVRVHsVVELMKEIGG 306
                                       899****************99.9998537777666666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   3.9e-08   2.9e-05       1      34 [.     120     153 ..     120     190 .. 0.88
   2 ?   -2.6   0.0       2.9   2.1e+03     139     159 ..     224     243 ..     214     261 .. 0.73
   3 !    5.7   0.2    0.0085       6.4       2      40 ..     271     309 ..     270     331 .. 0.89
   4 !    6.1   0.0    0.0064       4.8     349     386 ..     399     435 ..     392     440 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.9e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34 
                                       dv V+G+G AG+ AAl++ ++G++v+L+t ++  
  gi|320101171|ref|YP_004176763.1| 120 DVLVVGAGPAGLQAALKLGEKGVDVVLVTDHFRL 153
                                       79**************************877654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                                       EEECEEEE--TT-BT-EEEET CS
                              GIDA 139 ikakavviatGtflkgkihig 159
                                       +k + +viatG+  + +i + 
  gi|320101171|ref|YP_004176763.1| 224 VKPRYMVIATGA-TEKTILFE 243
                                       677899*****9.55555544 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0085
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SS CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsC 40 
                                         V+G G  G+  A+++ ++G++v  +++ +++i+  + 
  gi|320101171|ref|YP_004176763.1| 271 ALVVGSGNVGLIIAYQLLQAGVRVHSVVELMKEIGGWVV 309
                                       67***********************99999999987665 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0064
                                       TSBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHH CS
                              GIDA 349 tLetkkvkgLflAGqinGteGYeEaaaqGllAGinaar 386
                                       ++et+ ++g+f+AG+++G e  + a   G +A+  +  
  gi|320101171|ref|YP_004176763.1| 399 DMETS-IPGVFVAGDLTGIEEATTAFIEGEIAAYAILE 435
                                       68888.*************9666666699999987765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   0.00016      0.12       2      35 ..     121     154 ..     120     167 .. 0.86
   2 !   24.7   1.9   3.6e-08   2.7e-05       2      75 ..     271     338 ..     270     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       v+vvG+G  gl +A  l e g +V +v  + +l 
  gi|320101171|ref|YP_004176763.1| 121 VLVVGAGPAGLQAALKLGEKGVDVVLVTDHFRLG 154
                                       89*************************9887776 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 3.6e-08
                                       EEEECSSHHHHHHHHHHHHTTSEE.EEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkV.tvversdkllrllDeeaskilqeklekngievllntkveeiegsedgves 75 
                                       ++vvG+G++gl  A  l + g +V +vve ++++          + + kl+++g+ +l+++++++ eg e+ ve+
  gi|320101171|ref|YP_004176763.1| 271 ALVVGSGNVGLIIAYQLLQAGVRVhSVVELMKEIG------GWVVHASKLRRHGVPILTGHTIVRAEGRER-VEK 338
                                       58**********************99999999999......6667799*******************9998.554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   1.4e-10     1e-07       1      46 [.     120     165 ..     120     206 .. 0.82
   2 ?    2.0   1.3      0.14   1.1e+02       1      39 [.     270     309 ..     270     344 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.4e-10
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatd 46 
                                       Dv+VvG+gpaG+ AA+   ++G  v+Lv ++ +lGG+l ++    +
  gi|320101171|ref|YP_004176763.1| 120 DVLVVGAGPAGLQAALKLGEKGVDVVLVTDHFRLGGQLVKQTHKFF 165
                                       9*************************************99986554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakv.lLveergvlGGllt 39 
                                       D +VvG+g  G++ A++  +aG +v  +ve  + +GG + 
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQLLQAGVRVhSVVELMKEIGGWVV 309
                                       679*********************9459999999999765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.4e-06    0.0025       1      38 [.     120     158 ..     120     225 .. 0.84
   2 !   11.7   1.6   0.00019      0.14       1      23 [.     270     295 ..     270     312 .. 0.83
   3 ?    4.5   0.0     0.029        22     153     207 ..     311     376 ..     308     406 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGG CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSg 38 
                                       dv+++G+G +Gl +A+ L ++g  V+l+  + ++g g+  
  gi|320101171|ref|YP_004176763.1| 120 DVLVVGAGPAGLQAALKLGEKGvdVVLVTDHFRLG-GQLV 158
                                       8*****************9999**99999998998.7655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00019
                                       EEEEECTSHHHHHHHHHHHHTT...E CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...V 23 
                                       d +++G+G +Gl +Ay+L ++g    
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQLLQAGvrvH 295
                                       789****************9996651 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.029
                                       HHHHHHTT-EEEESECEEEEEEEE....TCEEEEE...........EECTEEEE..EEEEEEE--GGGHH..HH CS
                               DAO 153 araaealGveilegtevtgleeed....gkvwgve...........rttpgend..aadavVnaaGawsd..ll 207
                                       a++++++Gv il+g+++++ e ++                      +   g+++  ++d v +a G++ +  ll
  gi|320101171|ref|YP_004176763.1| 311 ASKLRRHGVPILTGHTIVRAEGRErvekA-----VvaavdeklnpvQ---GSEReySVDLVLLAVGLQPNyaLL 376
                                       678999********999887544333322.....1233346653221...3332347799******99887544 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   4.2e-07   0.00031       2      35 ..     120     153 ..     119     159 .. 0.86
   2 !    6.0   0.2    0.0055       4.1       2      36 ..     270     305 ..     269     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.2e-07
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       dv+v+G+G+AGl aA++++++g +V+l+    +l
  gi|320101171|ref|YP_004176763.1| 120 DVLVVGAGPAGLQAALKLGEKGVDVVLVTDHFRL 153
                                       89**********************9998665555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0055
                                       SEEEE--SHHHHHHHHHHHHTT--E.EEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrV.lllekakklg 36 
                                       d +v+G G  Gl  A ++ ++g rV  ++e +k++g
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQLLQAGVRVhSVVELMKEIG 305
                                       679**********************45999999988 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00032      0.24       8      40 ..     119     151 ..     115     199 .. 0.85
   2 !   13.1   0.2   0.00013     0.098       9      44 ..     270     304 ..     267     366 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                         vlvvG+G+ +++ + kl e+g +v++v+  +
  gi|320101171|ref|YP_004176763.1| 119 TDVLVVGAGPAGLQAALKLGEKGVDVVLVTDHF 151
                                       679**************************9874 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00013
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeel 44 
                                         lvvG G+v++  +++ll+ag +v+ v + +ke +
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQLLQAGVRVHSVVELMKE-I 304
                                       689**********************988777433.3 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.2    0.0036       2.7       1      29 [.     121     149 ..     121     161 .. 0.92
   2 !   16.7   0.1   5.9e-06    0.0044       2      47 ..     272     318 ..     271     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0036
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilr 29 
                                       ++++GaG  G   a kL ++g dv+l++ 
  gi|320101171|ref|YP_004176763.1| 121 VLVVGAGPAGLQAALKLGEKGVDVVLVTD 149
                                       68************************985 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.9e-06
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg 47 
                                       +++G+G +G ++a++L +ag  v+ ++    ++  ++ + ++l+++g
  gi|320101171|ref|YP_004176763.1| 272 LVVGSGNVGLIIAYQLLQAGVRVHSVVELMkEIGGWVVHASKLRRHG 318
                                       69********************9999877666666666666665555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.7   6.8e-06    0.0051       1      30 [.     120     147 ..     120     158 .. 0.92
   2 ?    4.0   0.1     0.028        21       1      30 [.     270     297 ..     270     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.8e-06
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvli 30 
                                       Dv+v+GaGpAgl+ A +l   ++g+ vvl+
  gi|320101171|ref|YP_004176763.1| 120 DVLVVGAGPAGLQAALKL--GEKGVDVVLV 147
                                       9*****************..********99 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.028
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvli 30 
                                       D +v+G+G  gl +A +l   ++g++v ++
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQL--LQAGVRVHSV 297
                                       779***************..6666666555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1    0.0088       6.6       2      32 ..     129     159 ..     128     177 .. 0.88
   2 !   11.0   0.1   0.00025      0.18       3      32 ..     280     310 ..     280     341 .. 0.81
   3 ?   -1.4   0.0       1.5   1.1e+03     415     451 ..     401     433 ..     379     434 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTTS-E CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirt 32 
                                       aGL aA +L ++G+dV+++    r+GG +  
  gi|320101171|ref|YP_004176763.1| 129 AGLQAALKLGEKGVDVVLVTDHFRLGGQLVK 159
                                       9**************************8765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHTTEEE.EEEESSSSSBTTS-E CS
                     Amino_oxidase   3 GLaaArqLlsaGfdV.tvlEardrvGGRirt 32 
                                       GL+ A+qLl+aG++V +v+E    +GG++  
  gi|320101171|ref|YP_004176763.1| 280 GLIIAYQLLQAGVRVhSVVELMKEIGGWVVH 310
                                       9***********77747***********975 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.5
                                       CHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 415 kpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                       +   +p++f+AG+ t  e       A+  G  aA +i
  gi|320101171|ref|YP_004176763.1| 401 E-TSIPGVFVAGDLTGIEE---ATTAFIEGEIAAYAI 433
                                       3.479********998333...555566666666555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1     0.001      0.77       9      42 ..     115     148 ..     107     163 .. 0.85
   2 ?    4.2   0.1     0.056        42      14      39 ..     270     295 ..     259     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                       ++ e  vl++GaG  + ++a +L +kgv+ v+v+
  gi|320101171|ref|YP_004176763.1| 115 EVLETDVLVVGAGPAGLQAALKLGEKGVDVVLVT 148
                                       455789***********************99886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.056
                                       EEEEES-SHHHHHHHHHHHCCT-CEE CS
                      Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkv 39 
                                        +l++G G+++  +a +Ll++gv+  
  gi|320101171|ref|YP_004176763.1| 270 DALVVGSGNVGLIIAYQLLQAGVRVH 295
                                       689******************99855 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.013        10      21      64 ..     108     150 ..     104     156 .. 0.85
   2 ?    6.1   0.1      0.01       7.8      32      63 ..     268     299 ..     253     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                                       HHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEES CS
                     ELFV_dehydrog  21 mlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDs 64 
                                       + +++k + + ++ v + G G  g  aal+l e+g  vv v D+
  gi|320101171|ref|YP_004176763.1| 108 VSSHVKKE-VLETDVLVVGAGPAGLQAALKLGEKGVDVVLVTDH 150
                                       55565555.77789*************************99996 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                                       TEEEEEE--SHHHHHHHHHHHHCT-EEEEEEE CS
                     ELFV_dehydrog  32 gkrvaisGsGnvgsyaallltelgakvvavsD 63 
                                       g    + GsGnvg   a  l ++g +v +v++
  gi|320101171|ref|YP_004176763.1| 268 GDDALVVGSGNVGLIIAYQLLQAGVRVHSVVE 299
                                       5567899********************99975 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0042       3.1      13      50 ..     113     150 ..     104     151 .. 0.89
   2 ?    4.7   0.3     0.023        17      21      43 ..     271     293 ..     254     301 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0042
                                       HHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  13 qekLrdskvllvGaGglGsellknLalsGvgkltlvDn 50 
                                        +++ ++ vl+vGaG  G  ++  L   Gv  + ++D+
  gi|320101171|ref|YP_004176763.1| 113 KKEVLETDVLVVGAGPAGLQAALKLGEKGVDVVLVTDH 150
                                       56788899**********************99999996 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.023
                                       EEEE--SHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  21 vllvGaGglGsellknLalsGvg 43 
                                        l+vG G +G +++ +L  +Gv+
  gi|320101171|ref|YP_004176763.1| 271 ALVVGSGNVGLIIAYQLLQAGVR 293
                                       59*******************98 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.1     3e+03      62      80 ..     119     137 ..     102     149 .. 0.55
   2 ?    9.7   0.1    0.0017       1.3       4      29 ..     273     298 ..     271     303 .. 0.91
   3 ?    0.3   0.0       1.4     1e+03      24      81 ..     323     379 ..     310     385 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.1
                                       -SEEEE-S-HHHHHHHHHH CS
                     F420_oxidored  62 advvvlavkpedveevlse 80 
                                       +dv+v+   p+ ++++l+ 
  gi|320101171|ref|YP_004176763.1| 119 TDVLVVGAGPAGLQAALKL 137
                                       5555555555444444433 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                                       EETTSHHHHHHHHHHHHTTS-GGCEE CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheiv 29 
                                       ++G+Gn+g  +a +ll+ag++ h++v
  gi|320101171|ref|YP_004176763.1| 273 VVGSGNVGLIIAYQLLQAGVRVHSVV 298
                                       57******************999998 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                                       -GGCEEEEEESSCCCHHHHH.HHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                     F420_oxidored  24 qpheivvansrnpekaeela.eelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81 
                                       + h iv a     e++e++  +++  k+ +v+ +e   + d v+lav  +   ++ls++
  gi|320101171|ref|YP_004176763.1| 323 TGHTIVRA--EGRERVEKAVvAAVDEKLNPVQGSEREYSVDLVLLAVGLQPNYALLSQM 379
                                       44666633..4444444444344444555555555555679999999988888777776 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 ?    5.8   0.1     0.012         9       3      29 ..     121     147 ..     119     151 .. 0.92
   2 ?    4.7   0.3     0.027        20       5      36 ..     273     304 ..     270     344 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                                       EEEE--STTHHHHHHHHHHCTSEEEEE CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigv 29 
                                       + v+G+G  Gl  a+ l e+g++v++v
  gi|320101171|ref|YP_004176763.1| 121 VLVVGAGPAGLQAALKLGEKGVDVVLV 147
                                       789*********************988 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.027
                                       EE--STTHHHHHHHHHHCTSEEEEE-S-HHHH CS
                    UDPG_MGDP_dh_N   5 viGlGYvGlvtaavlaeighevigvDideekv 36 
                                       v+G+G vGl+ a  l ++g+ v  v    + +
  gi|320101171|ref|YP_004176763.1| 273 VVGSGNVGLIIAYQLLQAGVRVHSVVELMKEI 304
                                       9******************9998775555555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.023        17       2      29 ..     121     148 ..     120     163 .. 0.92
   2 ?   -2.7   0.3       6.3   4.7e+03       8      20 ..     249     261 ..     248     265 .. 0.84
   3 ?    9.1   0.2    0.0014       1.1       4      28 ..     273     297 ..     270     367 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE- CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvd 29 
                                       v v+GaG  G + a  + ++g++Vvlv 
  gi|320101171|ref|YP_004176763.1| 121 VLVVGAGPAGLQAALKLGEKGVDVVLVT 148
                                       78***********************985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                                       SCCHHHHHHHHHH CS
                           3HCDH_N   8 GtmGagiaavfas 20 
                                       G+mGag a+ +++
  gi|320101171|ref|YP_004176763.1| 249 GVMGAGGAQTLMN 261
                                       99*****998876 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0014
                                       EE--SCCHHHHHHHHHHTT-EEEEE CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlv 28 
                                       v+G+G +G  ia+++++ag++V+ v
  gi|320101171|ref|YP_004176763.1| 273 VVGSGNVGLIIAYQLLQAGVRVHSV 297
                                       9*********************865 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.05        38       1      29 [.     121     149 ..     121     160 .. 0.89
   2 ?    5.1   0.5     0.036        27       2      48 ..     272     325 ..     271     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.05
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEES CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidk 29 
                                       ++++G+G  G + a +L e+g dvv++ +
  gi|320101171|ref|YP_004176763.1| 121 VLVVGAGPAGLQAALKLGEKGVDVVLVTD 149
                                       68*****************7757999865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.036
                                       EEES-SHHHHHHHHHHHHTT.EEEEEEESSHHH......HHHHHHTTSEEEES- CS
                            TrkA_N   2 iiiGlGrvGrslaeeLsegg.kdvvvidkdeer......veelreeglevvvgd 48 
                                       +++G G+vG  +a +L ++g +  +v++  +e       + +lr++g++++ g+
  gi|320101171|ref|YP_004176763.1| 272 LVVGSGNVGLIIAYQLLQAGvRVHSVVELMKEIggwvvhASKLRRHGVPILTGH 325
                                       79****************554556788877765555555777777777777665 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 ?    6.9   0.1    0.0077       5.7       2      40 ..     123     156 ..     122     163 .. 0.71
   2 ?    1.9   0.3      0.27     2e+02       2      28 ..     273     294 ..     272     319 .. 0.72
   3 ?    0.4   0.1      0.74   5.6e+02     134     154 ..     348     368 ..     325     370 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0077
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlf.dpsepgagr 40 
                                       +vGaGp+Gl ++ +L ++      +++ l+ d   +g g+
  gi|320101171|ref|YP_004176763.1| 123 VVGAGPAGLQAALKLGEKG-----VDVVLVtDHFRLG-GQ 156
                                       8*************99884.....6666552445556.54 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.27
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkksplei 28 
                                       +vG G  Gl ++ +Ll+       +++
  gi|320101171|ref|YP_004176763.1| 273 VVGSGNVGLIIAYQLLQAG-----VRV 294
                                       8***************985.....333 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.74
                     NAD_binding_9 134 qavlladgaslaadaVvLAlG 154
                                          ++ +++++ +d V LA+G
  gi|320101171|ref|YP_004176763.1| 348 LNPVQGSEREYSVDLVLLAVG 368
                                       3446788999**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 3710.90
//
Query:       gi|320101172|ref|YP_004176764.1|  [L=249]
Description: AAA ATPase [Desulfurococcus mucosus DSM 2162]
Scores for 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   78.4   0.0    6.4e-22   78.0   0.0    1.0  1  ATPase       KaiC
    3.9e-09   36.4   0.0    6.6e-09   35.6   0.0    1.4  1  AAA_25       AAA domain
    9.6e-08   31.7   0.0    1.5e-07   31.1   0.0    1.2  1  DnaB_C       DnaB-like helicase C terminal domain
    2.5e-06   27.6   0.0    3.6e-06   27.1   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0001   22.3   0.1       0.18   11.7   0.0    3.0  3  NACHT        NACHT domain
    0.00017   21.2   0.0    0.00026   20.6   0.0    1.4  1  Elong_Iki1   Elongator subunit Iki1
    0.00018   22.0   0.0    0.00035   21.0   0.0    1.7  1  AAA_16       AAA ATPase domain
    0.00061   19.3   0.0     0.0011   18.5   0.0    1.4  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0011   18.6   0.0      0.005   16.5   0.0    1.9  2  SRP54        SRP54-type protein, GTPase domain
     0.0012   18.2   0.0     0.0021   17.4   0.0    1.3  1  Zeta_toxin   Zeta toxin
     0.0012   18.6   0.0     0.0023   17.7   0.0    1.4  1  IstB_IS21    IstB-like ATP binding protein
     0.0013   18.2   0.1     0.0021   17.6   0.1    1.3  1  ParA         NUBPL iron-transfer P-loop NTPase
     0.0046   16.2   0.0     0.0071   15.6   0.0    1.3  1  ArsA_ATPase  Anion-transporting ATPase
     0.0084   16.0   0.1      0.051   13.5   0.0    2.0  2  AAA_31       AAA domain
     0.0092   15.5   0.0      0.025   14.0   0.0    1.7  2  KTI12        Chromatin associated protein KTI12
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.026   14.5   0.0    1.7  1  AAA_5        AAA domain (dynein-related subfamily)
      0.014   15.4   0.0      0.038   14.0   0.0    1.8  1  AAA_14       AAA domain
      0.015   15.2   0.0      0.053   13.4   0.0    1.8  2  ATPase_2     ATPase domain predominantly from Archaea
      0.022   13.9   0.0      0.047   12.8   0.0    1.5  2  PAXNEB       PAXNEB protein
      0.032   13.5   0.0      0.048   13.0   0.0    1.3  1  MipZ         ATPase MipZ
      0.042   12.8   0.0       0.28   10.1   0.0    2.0  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.042   13.0   0.0      0.066   12.4   0.0    1.3  1  DUF815       Protein of unknown function (DUF815)
      0.063   13.2   0.0       0.18   11.7   0.0    1.7  2  APS_kinase   Adenylylsulphate kinase
      0.076   12.9   0.4       0.32   10.9   0.4    2.3  1  NTPase_1     NTPase
      0.092   13.3   0.0       0.14   12.7   0.0    1.3  1  ABC_tran     ABC transporter
      0.093   12.4   0.0       0.12   12.0   0.0    1.3  1  AAA_30       AAA domain
      0.097   12.7   0.1       0.32   11.0   0.1    1.8  1  DUF4192      Domain of unknown function (DUF4192)
      0.099   11.8   0.0       0.17   11.0   0.0    1.3  1  NB-ARC       NB-ARC domain
       0.12   11.8   0.0       0.13   11.7   0.0    1.2  1  ELP6         Elongation complex protein 6
       0.12   12.1   0.0       0.34   10.7   0.0    1.7  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
       0.14   12.5   0.0       0.28   11.4   0.0    1.6  1  AAA_22       AAA domain
       0.14   11.9   0.2          2    8.1   0.0    2.7  3  DUF835       Protein of unknown function (DUF835)
       0.15   12.6   0.0       0.32   11.6   0.0    1.7  1  AAA_18       AAA domain
       0.17   11.7   0.1        0.4   10.5   0.1    1.6  1  AAA_29       P-loop containing region of AAA domain
       0.19   11.5   0.0        2.5    7.8   0.0    2.2  2  AAA_24       AAA domain
        0.2   11.4   0.1       0.72    9.6   0.1    1.8  2  ATP_bind_1   Conserved hypothetical 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 !   78.0   0.0   1.3e-24   6.4e-22      11     225 ..      11     241 ..       2     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1.3e-24
                            ATPase  11 ilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiid 87 
                                       il +Gip+++ v ++G+ G+GK+ ++++ + + +e+ gep+v+v ++ +++ + e+  s+G  +e+  ++ +l+++d
  gi|320101172|ref|YP_004176764.1|  11 ILPEGIPRNSLVILAGKGGSGKSAIVANIAKNIVEN-GEPVVYVGLDDDPVTIVEQLDSFGLKVEEAASSRLLMLVD 86 
                                       4459***********************988888777.**************************************** PP

                            ATPase  88 asesaeesaee.........kdkedleelieelaeaikeika...krvviDsitglayeekeavaReilrqlvrvl. 151
                                        ++  ++  +e          d  +++++++ + +++++++      v+iDs++  + + ++  + e ++ l   + 
  gi|320101172|ref|YP_004176764.1|  87 GFSYLIKGRRErahpavveeVDPRNPDNVASAVLRVLESTGLkgrGLVIIDSLNEAMISLDPTRFIEFVKFLRANVs 163
                                       *99987766667889999998889999999999999999888443579********99**************99998 PP

                            ATPase 152 kklgvTailvsekssseeaaggygveefivdgvivLdlkeiee.....elvRtleivkmRgtkhskkehpfeIteeg 223
                                       k l+v  i +   s++  +   y +e+ +vdg i  ++ e+         vR ++i+k+ g +h+   + ++I++ g
  gi|320101172|ref|YP_004176764.1| 164 KALRVPVIATLHTSTEGFEEYLYTIEH-LVDGLIETQNLEEGLssqlpMQVRQVIIRKIKGVSHRHGWVLYTIDKTG 239
                                       99**********9999999999*****.******9986665558899999*************************99 PP

                            ATPase 224 ik 225
                                       +k
  gi|320101172|ref|YP_004176764.1| 240 VK 241
                                       96 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   1.3e-11   6.6e-09      26     162 ..      12     151 ..      10     180 .. 0.66

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.3e-11
                            AAA_25  26 vkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.... 97 
                                       +++ +p+++l++laG +g+GK++++ ++a  ++  G+           +V+yv ++d+  ++ + l   g ++    
  gi|320101172|ref|YP_004176764.1|  12 LPEGIPRNSLVILAGKGGSGKSAIVANIAKNIVeNGE-----------PVVYVGLDDDPVTIVEQLDSFGLKVeeaa 77 
                                       55668****************************5555...........8*********************9998876 PP

                            AAA_25  98 ..................rddarllvldlagveslpLfakdrggtl.ltadvdaleaaieev..egvrlvviDplsr 153
                                                         r++a+ +v+                +++  + +  a+ +++e++  +g +lv+iD+l++
  gi|320101172|ref|YP_004176764.1|  78 ssrllmlvdgfsylikgrRERAHPAVVE-------------EVDPRnPDNVASAVLRVLESTglKGRGLVIIDSLNE 141
                                       6666664444444444322222222222.............22333234444445555555322669********** PP

                            AAA_25 154 algg.densn 162
                                       a+   d+++ 
  gi|320101172|ref|YP_004176764.1| 142 AMISlDPTRF 151
                                       8876677754 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 !   31.1   0.0   2.9e-10   1.5e-07      14     175 ..      14     173 ..       8     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.9e-10
                                       TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSXHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  14 sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgklkeedwe 90 
                                       +G+ ++ l+i+A++ + Gk+a++ nia+n+++ +  pv+++ l+ +  ++v++l s   ++++ +  +  +  + ++
  gi|320101172|ref|YP_004176764.1|  14 EGIPRNSLVILAGKGGSGKSAIVANIAKNIVE-NGEPVVYVGLDDDPVTIVEQLDSFGLKVEEAASSRLLMLVDGFS 89 
                                       6888999**********************997.5669*****************99999999888777666677899 PP

                                       HHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHH...TTEEEEEEEEGGGTBTSCSSSCCCHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  91 klteaieelseaklfiddtpaltvseirskarrlkke...kglgliviDyLqlmegseekenreqevseisrsLkal 164
                                        l +  +  +  + ++++    ++ ++ s + r+ ++   kg gl++iD L+    s  + +r  e  +  r+  ++
  gi|320101172|ref|YP_004176764.1|  90 YLIKGRR-ERAHPAVVEEVDPRNPDNVASAVLRVLEStglKGRGLVIIDSLNEAMISL-DPTRFIEFVKFLRA--NV 162
                                       9988754.466789999999999****9999887666588889********8665432.45676666666654..78 PP

                                       HHHCTSXEEEE CS
                                       xxxxxxxxxxx RF
                            DnaB_C 165 akelnvpvial 175
                                       +k l+vpvia 
  gi|320101172|ref|YP_004176764.1| 163 SKALRVPVIAT 173
                                       89999999986 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 !   27.1   0.0   7.2e-09   3.6e-06       1      55 [.      21     180 ..      21     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.2e-09
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep................... 54 
                                       ++i ++kGG+GK+ ++an+a+ + ++g  V+ v +D + + + +     +gl+ +++                    
  gi|320101172|ref|YP_004176764.1|  21 LVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLDDD-PVTIVeqldSFGLKVEEAAssrllmlvdgfsylikgrr 96 
                                       5899*****************************99999.88777888988888888889999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|320101172|ref|YP_004176764.1|  97 erahpavveevdprnpdnvasavlrvlestglkgrglviidslneamisldptrfiefvkflranvskalrvpviat 173
                                       99999999999999999999988888888888888888888888888888666666666666665543333333333 PP

                                       ......C CS
                                       ......x RF
                              CbiA  55 ......d 55 
                                             +
  gi|320101172|ref|YP_004176764.1| 174 lhtsteG 180
                                       3333331 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00035      0.18       2      27 ..      21      46 ..      20      53 .. 0.87
   2 ?    1.4   0.0      0.53   2.6e+02      79      95 ..      77      93 ..      61     107 .. 0.75
   3 ?    5.4   0.0      0.03        15      79     141 ..     128     187 ..     106     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                      lvil G+ GsGK++ ++ +a  + e+
  gi|320101172|ref|YP_004176764.1| 21 LVILAGKGGSGKSAIVANIAKNIVEN 46
                                      79******************988765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.53
                                      SCCCEEEEEE-STT-SS CS
                             NACHT 79 lperlLlilDglDelvt 95
                                         rlL+++Dg+ +l +
  gi|320101172|ref|YP_004176764.1| 77 ASSRLLMLVDGFSYLIK 93
                                      5689********99866 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.03
                                       SCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSC CS
                             NACHT  79 lperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqlee 141
                                       l+ r L i+D+l+e+   l++ +  +  + L+  ++k    ++++++t+++++    ee+l +
  gi|320101172|ref|YP_004176764.1| 128 LKGRGLVIIDSLNEAMISLDPTRFIEFVKFLRANVSK--ALRVPVIATLHTSTE-GFEEYLYT 187
                                       578999*********9999998888888888888888..556777777777665.44555544 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.1e-07   0.00026      71     165 ..     112     208 ..      34     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.1e-07
                        Elong_Iki1  71 lkelakeiksalspkssekkkkalviiDsln.plas..likeeslaaflssllssp.svslvavYHtdveyapsplt 143
                                       ++++a+++   l+++    k + lviiDsln +++s   ++  ++++fl+  +s+   v ++a++Ht +e   + l 
  gi|320101172|ref|YP_004176764.1| 112 PDNVASAVLRVLESTGL--KGRGLVIIDSLNeAMISldPTRFIEFVKFLRANVSKAlRVPVIATLHTSTEGFEEYLY 186
                                       55555555555533222..4899********66666664455677777776665437999***************** PP

                        Elong_Iki1 144 lLkylAttiltveslshelark 165
                                       ++++l    +++++l++ l  +
  gi|320101172|ref|YP_004176764.1| 187 TIEHLVDGLIETQNLEEGLSSQ 208
                                       *************999877655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     7e-07   0.00035      24      88 ..      19      78 ..       9     237 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7e-07
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88
                                       +lv+l G  G+GKs++v  +++ + ++g  +++   d+     p ++++++l+  +l  ++++ 
  gi|320101172|ref|YP_004176764.1| 19 NSLVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLDDD----P-VTIVEQLDSFGLKVEEAAS 78
                                      389*************************744444444444....1.2366666555555544444 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 !   18.5   0.0   2.2e-06    0.0011       4      37 ..      23      56 ..      20      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                         Fer4_NifH  4 aiyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                       + GkGG+Gks  ++n+++ ++e+g+ v+ vG D
  gi|320101172|ref|YP_004176764.1| 23 ILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLD 56
                                      577*****************************98 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-05     0.005       3      56 ..      21      74 ..      19      83 .. 0.92
   2 ?   -0.9   0.0       2.1   1.1e+03     121     166 ..     192     238 ..     179     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklg 56
                                      +++l+G  G+GK   +a +a+ + ++g+ v+ v +D   +  veQL  ++ k++
  gi|320101172|ref|YP_004176764.1| 21 LVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLDDDPVTIVEQLDSFGLKVE 74
                                      6899*******************************************9998876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                                       EETTBHTHHHHHHHHHHHHSSCSEEEEESTTS.SSSTTHHHHHHHHH CS
                             SRP54 121 ldattgqeavkqakaFkeavgitgviltklDg.dakgGaalsiaael 166
                                       +d++++ + +++  +++  +++ +vi+ k+ g + + G +l   +++
  gi|320101172|ref|YP_004176764.1| 192 VDGLIETQNLEEGLSSQLPMQVRQVIIRKIKGvSHRHGWVLYTIDKT 238
                                       68888888888888888889999999999998344677777555444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.3e-06    0.0021      15      52 ..      18      56 ..      11      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.3e-06
                        Zeta_toxin 15 rPklillgGqpGAGKselaellkdele.rqgnvvrldpD 52
                                      r  l++l+G  G+GKs++ + +++++  +++ vv +  D
  gi|320101172|ref|YP_004176764.1| 18 RNSLVILAGKGGSGKSAIVANIAKNIVeNGEPVVYVGLD 56
                                      5579**************999999998455556666666 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.5e-06    0.0023      46     122 ..      18      93 ..      13     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-06
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdlli.lDdlgllp 121
                                       ++  ++l G  G GKs + + ++++ v++g  v++v ++d    + + ++ +++  ++++ + ++ll+ +D +++l 
  gi|320101172|ref|YP_004176764.1|  18 RNSLVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLDD--DPVTIVEQLDSFGLKVEEAASSRLLMlVDGFSYLI 92 
                                       677899********************************99..67778888888998888888887765167777775 PP

                         IstB_IS21 122 l 122
                                        
  gi|320101172|ref|YP_004176764.1|  93 K 93 
                                       5 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.2e-06    0.0021       4      37 ..      19      52 ..      17      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.2e-06
                              ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgl 37
                                      + +++l+gKGG GKS + +n+A ++ ++g  v  
  gi|320101172|ref|YP_004176764.1| 19 NSLVILAGKGGSGKSAIVANIAKNIVENGEPVVY 52
                                      6789*********************999987654 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-05    0.0071       3      38 ..      21      56 ..      19      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +++++GKGG GK+++ a +a ++ e+g+ v+ + +D
  gi|320101172|ref|YP_004176764.1| 21 LVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLD 56
                                      6899***************************99886 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0    0.0001     0.051       6      40 ..      23      57 ..      19      96 .. 0.88
   2 ?    0.1   0.0       1.3   6.4e+02     143     169 ..     166     193 ..     149     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                            AAA_31  6 ianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                      i   KGG GK++ + n+a+ + ++g+ v  v lD 
  gi|320101172|ref|YP_004176764.1| 23 ILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLDD 57
                                      6678***************************9985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                            AAA_31 143 viipvqaea.yaleGleqllktieevkk 169
                                       + +pv a+   ++eG+e++l tie++ +
  gi|320101172|ref|YP_004176764.1| 166 LRVPVIATLhTSTEGFEEYLYTIEHLVD 193
                                       557777665489**********998766 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     5e-05     0.025       3      40 ..      21      60 ..      20      87 .. 0.81
   2 ?   -2.5   0.0       5.6   2.8e+03      68      80 ..     128     140 ..     116     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
                                      EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-..THHH CS
                             KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvvid..desl 40
                                      Lv+l G   sGKs +++++ak + e++  vv++   d+ +
  gi|320101172|ref|YP_004176764.1| 21 LVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGldDDPV 60
                                      9******************************986324444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                                       HTT.SEEEE-S-- CS
                             KTI12  68 LskekvVIvDsln 80 
                                       L+   +VI+Dsln
  gi|320101172|ref|YP_004176764.1| 128 LKGRGLVIIDSLN 140
                                       566679*****99 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.3e-05     0.026       2      91 ..      22     125 ..      21     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-05
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.............--------....... CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik....ngttslvdsplvraar....... 64 
                                       v+L G+ G+gKs ++  +a+ +   + +v+yv l +d  + +++ +++      ++ +s +   lv+ +        
  gi|320101172|ref|YP_004176764.1|  22 VILAGKGGSGKSAIVANIAKNIvenGEPVVYVGLDDD--PVTIVEQLDSFglkvEEAASSRLLMLVDGFSylikgrr 96 
                                       89**********************7788888877775..33333333322232455555555555555558888888 PP

                                       .G-SEEEEESGGG--.HHHHHHHHHHHHS CS
                             AAA_5  65 .egeilvlDEverae.sevlnsLlsllee 91 
                                        +++ +v++Ev+  + ++v++++l++le 
  gi|320101172|ref|YP_004176764.1|  97 eRAHPAVVEEVDPRNpDNVASAVLRVLES 125
                                       88888888888877768888888888876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.6e-05     0.038       3      57 ..      20      74 ..      18     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelil 57
                                       ++++ G   +GK+ ++ +++k+   + e ++y+ ldd++ +  ++ +++   + 
  gi|320101172|ref|YP_004176764.1| 20 SLVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLDDDPVTIVEQLDSFGLKVE 74
                                      678999999************9988999**********99876665543333333 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   0.0   0.00011     0.053      21     138 ..      20     149 ..      14     195 .. 0.64
   2 ?   -0.7   0.0       2.2   1.1e+03      78     123 ..     201     245 ..     175     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyy..ialreesiskldefie...eeeekkklekal.......... 82 
                                       + + + G  gsGK+a++ +i++n  + ++ v+y+  ++      ++ld+f +   ee  +++l   +          
  gi|320101172|ref|YP_004176764.1|  20 SLVILAGKGGSGKSAIVANIAKNIVENGEPVVYVglDDDPVTIVEQLDSF-GlkvEEAASSRLLMLVdgfsylikgr 95 
                                       56667799************************983223333344555555.35566666666666669999987666 PP

                          ATPase_2  83 giavpkaeleeilkeksklvfkaielllekikkkgkk..iiiiiDelqklidlglnga 138
                                        ++   a +ee+     ++ ++  +++l+ ++ +g k    +iiD l ++  + l+  
  gi|320101172|ref|YP_004176764.1|  96 RERAHPAVVEEV---DPRNPDNVASAVLRVLESTGLKgrGLVIIDSLNEAM-ISLDPT 149
                                       555555555554...444445555555555555555555677889999998.777733 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiii 123
                                       le+ l++++p  ++ +++ +k+k v      +l  i k+g k++i+
  gi|320101172|ref|YP_004176764.1| 201 LEEGLSSQLPM-QVRQVIIRKIKGVSHRHGWVLYTIDKTGVKPVIL 245
                                       34444444443.2334444667888888888999999999999986 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.8   1.9e+03      65      88 ..      46      69 ..      39      80 .. 0.74
   2 ?   12.8   0.0   9.4e-05     0.047     211     292 ..     134     210 ..     109     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                            PAXNEB 65 qkhevlvlsldddpeewlreLPgp 88
                                      ++  v++++ldddp +++++L + 
  gi|320101172|ref|YP_004176764.1| 46 NGEPVVYVGLDDDPVTIVEQLDSF 69
                                      4568999********999999655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.4e-05
                            PAXNEB 211 ivipsLlspllydyppeeskpedllkFLhsLrallrss.nlvalitlplsliarssslvrkieqlvDtvieLesfag 286
                                       ++i sL   ++      + +p+++++F++ Lra +++  ++ +++tl +s     ++++  ie+lvD++ie + +++
  gi|320101172|ref|YP_004176764.1| 134 VIIDSLNEAMI------SLDPTRFIEFVKFLRANVSKAlRVPVIATLHTSTE-GFEEYLYTIEHLVDGLIETQNLEE 203
                                       67777777777......6689***************7725556667666665.77889999**********999887 PP

                            PAXNEB 287 .sekete 292
                                         +++++
  gi|320101172|ref|YP_004176764.1| 204 gLSSQLP 210
                                       6555554 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.5e-05     0.048       4      40 ..      22      58 ..      19      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.5e-05
                                      EE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ  4 vlgnekGGsGksttavhvavaLlkkGarvaaidldlr 40
                                      v+   kGGsGks++   +a  ++++G  v  + ld  
  gi|320101172|ref|YP_004176764.1| 22 VILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLDDD 58
                                      66678*************************9999965 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00056      0.28      28      66 ..      18      56 ..       6      62 .. 0.86
   2 ?    0.3   0.0      0.57   2.9e+02     195     252 ..     158     215 ..     117     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      r   v l G  G+Gks +v +++ +++++G+ v  + +D
  gi|320101172|ref|YP_004176764.1| 18 RNSLVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLD 56
                                      56677899***********************99988776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.57
                                       HCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                              MeaB 195 leeekekeWrpkvlktsavegeGidelvdaieehrevlkktGllekrrrerakeelre 252
                                       l  + +k  r +v+ t  +  eG +e + +ie+  + l +t +le+    +   ++r+
  gi|320101172|ref|YP_004176764.1| 158 LRANVSKALRVPVIATLHTSTEGFEEYLYTIEHLVDGLIETQNLEEGLSSQLPMQVRQ 215
                                       4444577788899999999999999999999999988888877776666555555555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.066      56     143 ..      22     115 ..      12     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            DUF815  56 vLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpkl...vellr.erperfilfvDDLsFeeeeeeyk 126
                                       v+L G+ G+GKS++v  + +++ e+g  +  + ++ + ++ +++l     +++ +++ r++++vD  s+  + ++ +
  gi|320101172|ref|YP_004176764.1|  22 VILAGKGGSGKSAIVANIAKNIVENGepVVYVGLDDDPVTIVEQLdsfGLKVEeAASSRLLMLVDGFSYLIKGRRER 98 
                                       89*********************999666666667666665555511133444245677888888888777666666 PP

                            DUF815 127 sLksvLeGsleakpenv 143
                                       +  +v+e    ++p+nv
  gi|320101172|ref|YP_004176764.1|  99 AHPAVVEEVDPRNPDNV 115
                                       66666665555555555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00037      0.18       3      40 ..      20      59 ..      18      73 .. 0.82
   2 ?   -1.9   0.0       5.5   2.8e+03      36      67 ..     196     225 ..     176     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEE..EEHHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvyl..LdGdn 40
                                        v l+G  gsGKs+i  +++k++ve+g  v+   Ld d 
  gi|320101172|ref|YP_004176764.1| 20 SLVILAGKGGSGKSAIVANIAKNIVENGEPVVYvgLDDDP 59
                                      57899***********************665431266665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.5
                                       EEHHHHTTTTTTT--SSHHHHHHHHHHHHHHH CS
                        APS_kinase  36 LdGdnvRhgLnkdLgfseedRkenirrvaeva 67 
                                       ++ +n+ +gL+++L+++   R+  ir++  v+
  gi|320101172|ref|YP_004176764.1| 196 IETQNLEEGLSSQLPMQ--VRQVIIRKIKGVS 225
                                       45678888888888765..4677777777666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00064      0.32       2      30 ..      22      50 ..      21     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00064
                                      EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      v++ G+ G+GK+ +v ++++++ ++g +v
  gi|320101172|ref|YP_004176764.1| 22 VILAGKGGSGKSAIVANIAKNIVENGEPV 50
                                      799*******************9998665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00028      0.14       8      37 ..      16      45 ..      13      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00028
                                      EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkp 37
                                      + ++++v + G+ G+GKS +++ +a++   
  gi|320101172|ref|YP_004176764.1| 16 IPRNSLVILAGKGGSGKSAIVANIAKNIVE 45
                                      678899******************998753 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.12      18      55 ..      19      56 ..      16     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrviglApt 55
                                      + +++l G  G+GK+ +++ +++ + ++g++v+ +   
  gi|320101172|ref|YP_004176764.1| 19 NSLVILAGKGGSGKSAIVANIAKNIVENGEPVVYVGLD 56
                                      56899****************99999999999987655 PP

>> DUF4192  Domain of unknown function (DUF4192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00064      0.32      16      87 ..      17     108 ..      16     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00064
                           DUF4192  16 PedSvVlvaldggrg..............rlgpvlRvDlpraeagleavardlaellaregadavvavvvddr.... 74 
                                       P +S+V++a +gg+g                +pv+ v+l++++ ++ + ++++   ++++++ + +++v d+     
  gi|320101172|ref|YP_004176764.1|  17 PRNSLVILAGKGGSGksaivaniakniveNGEPVVYVGLDDDPVTIVEQLDSFGLKVEEAASSRLLMLV-DGFsyli 92 
                                       99*********99999*****************************999999999988666666666555.4445555 PP

                           DUF4192  75 ..gqd..rvrplvdalr 87 
                                         + +  +++++v++++
  gi|320101172|ref|YP_004176764.1|  93 kgR-RerAHPAVVEEVD 108
                                       431.1346666666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.17      21      43 ..      20      42 ..      11      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                      EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnk 43
                                       +v l G+gG+GK+ ++++i ++
  gi|320101172|ref|YP_004176764.1| 20 SLVILAGKGGSGKSAIVANIAKN 42
                                      57899***************987 PP

>> ELP6  Elongation complex protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.13     133     228 ..     124     214 ..      43     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                              ELP6 133 dgeeewkppvllvDdlsvLlslgvsaaavldFihyCratvcsklkgnvvvlvradeeeedeeeelllkslkHqssla 209
                                       +++  ++  ++++D+l+  + ++++++  ++F+++ ra v ++l+  v++ ++++ e  +e     l +++H  +  
  gi|320101172|ref|YP_004176764.1| 124 ESTGLKGRGLVIIDSLNEAM-ISLDPTRFIEFVKFLRANVSKALRVPVIATLHTSTEGFEEY----LYTIEHLVDGL 195
                                       44556777899*****9754.7889****************************988877766....66788888888 PP

                              ELP6 210 lkveGLatGyckdvHGqle 228
                                       ++ + L+ G + ++  q++
  gi|320101172|ref|YP_004176764.1| 196 IETQNLEEGLSSQLPMQVR 214
                                       8888888888877766664 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 ?   10.7   0.0   0.00069      0.34       1      31 [.      26      56 ..      26      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00069
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                      G+  sGKS+++++++ +++++g+ +vyv lD
  gi|320101172|ref|YP_004176764.1| 26 GKGGSGKSAIVANIAKNIVENGEPVVYVGLD 56
                                      6778************************999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00057      0.28       6     102 ..      20     141 ..      17     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00057
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka........... 70 
                                       +++++ G  G+GK+  +++++++ +e       + +vv+v l  +  +  + l  +  ++++ +++           
  gi|320101172|ref|YP_004176764.1|  20 SLVILAGKGGSGKSAIVANIAKNIVEN------GEPVVYVGLDDDPvTIVEQLDSFGLKVEEAASSrllmlvdgfsy 90 
                                       678999*****************9875......77788877777776666666666666666666677777777777 PP

                            AAA_22  71 .................erlsseellealeqalrarav..ielliiDEaqh 102
                                                         + + + + +a+ + l++++   ++l+iiD    
  gi|320101172|ref|YP_004176764.1|  91 likgrrerahpavveevDPRNPDNVASAVLRVLESTGLkgRGLVIIDSLNE 141
                                       777777779999999988888888889999999999888889999997666 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.7   1.8e+03      63      82 ..      34      53 ..      32      56 .. 0.81
   2 ?   -0.2   0.0       1.5   7.5e+02      78      89 ..      79      92 ..      60      95 .. 0.70
   3 ?    8.1   0.0    0.0041         2      54     109 ..     105     163 ..      97     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.7
                            DUF835 63 kltetivkflkeaekgvvli 82
                                      ++ + i k++ e+++ vv++
  gi|320101172|ref|YP_004176764.1| 34 AIVANIAKNIVENGEPVVYV 53
                                      57788899999999999987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.5
                            DUF835 78 g..vvliDgleyLv 89
                                      +  + l+Dg+ yL+
  gi|320101172|ref|YP_004176764.1| 79 SrlLMLVDGFSYLI 92
                                      134899******97 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0041
                            DUF835  54 ntvsPtnlekltetivkflkeaekg...vvliDgleyLvlengFesvlkflltlkDavl 109
                                       ++v+P+n ++    + + l++ + +   +v+iD+l   +++ +  + ++f++ l+ +v 
  gi|320101172|ref|YP_004176764.1| 105 EEVDPRNPDNVASAVLRVLESTGLKgrgLVIIDSLNEAMISLDPTRFIEFVKFLRANVS 163
                                       5788888888888888888876644555*************998888888888887765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00064      0.32       1      44 [.      22      66 ..      22     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00064
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gfgvnlrdvakenglllevdpe 44
                                      ++l+G+ G+GK+ +  +++k   ++g+ +  v  ++++++ v++ 
  gi|320101172|ref|YP_004176764.1| 22 VILAGKGGSGKSAIVANIAKNIvENGEPVVYVGLDDDPVTIVEQL 66
                                      79******************9866666666666666666655555 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 ?   10.5   0.1   0.00081       0.4      23      39 ..      20      36 ..      15      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00081
                            AAA_29 23 gatlltGpsGsGKSTll 39
                                      + ++l+G+ GsGKS+++
  gi|320101172|ref|YP_004176764.1| 20 SLVILAGKGGSGKSAIV 36
                                      46899**********98 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.005       2.5       5      77 ..      22     142 ..      18     148 .. 0.61
   2 ?    1.5   0.0      0.42   2.1e+02     110     138 ..     153     183 ..     150     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.005
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel............... 59 
                                       +++ G+ g+GK+ +++++       g+ ++++ +++       d +  +e+++ f  +v+e                
  gi|320101172|ref|YP_004176764.1|  22 VILAGKGGSGKSAIVANIaknivenGEPVVYVGLDD-------DPVTIVEQLDSFGLKVEEAassrllmlvdgfsyl 91 
                                       6899**************555555444444444444.......3333333333333333333444445555555555 PP

                            AAA_24  60 .................................aaeladyktlviDtidel 77 
                                                                        ++ l++   ++iD+++e+
  gi|320101172|ref|YP_004176764.1|  92 ikgrrerahpavveevdprnpdnvasavlrvleSTGLKGRGLVIIDSLNEA 142
                                       666666666666666666677777777777777777777777777777776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.42
                            AAA_24 110 efrrllkk..lqelrknvifiahektrkded 138
                                       ef+++l++   ++lr  vi++ h+ t+ +e+
  gi|320101172|ref|YP_004176764.1| 153 EFVKFLRAnvSKALRVPVIATLHTSTEGFEE 183
                                       6777777764567788999999999999886 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0014      0.72       2      33 ..      25      56 ..      24      61 .. 0.95
   2 ?   -0.8   0.0       2.1     1e+03     133     170 ..     143     182 ..     115     224 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                      +G  GsGK+ +v ++++ + ++g +v +v LD
  gi|320101172|ref|YP_004176764.1| 25 AGKGGSGKSAIVANIAKNIVENGEPVVYVGLD 56
                                      6999***************************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                        ATP_bind_1 133 qrltdptkfisgl.lsalsamlrlelPhvvvl.nkfDllk 170
                                        ++ dpt fi+ + ++  ++   l++P +  l + +++++
  gi|320101172|ref|YP_004176764.1| 143 MISLDPTRFIEFVkFLRANVSKALRVPVIATLhTSTEGFE 182
                                       4444566666643234445666677777766523334433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 1728.11
//
Query:       gi|320101173|ref|YP_004176765.1|  [L=256]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2029.72
//
Query:       gi|320101174|ref|YP_004176766.1|  [L=391]
Description: L-carnitine dehydratase/bile acid-inducible protein F [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-120  402.0   0.0   2.9e-120  401.8   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 !  401.8   0.0  1.6e-124  2.9e-120       1     368 []       2     365 ..       2     365 .. 0.99

  Alignments for each domain:
  == domain 1  score: 401.8 bits;  conditional E-value: 1.6e-124
                      CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegre 77 
                                       L+GvrVldls+ laGp+a+++LAdlGAeVIkvE+p  gD++R + p+ + ges+y+l++nr+K+s+++Dlk++egre
  gi|320101174|ref|YP_004176766.1|   2 LKGVRVLDLSHTLAGPFASMVLADLGAEVIKVEAP-HGDETRSWAPFVD-GESSYYLSINRGKKSIVVDLKNPEGRE 76 
                                       89*********************************.********99997.*************************** PP

                      CoA_transf_3  78 llkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdg 154
                                       ++ rL++++D+vieNfrpgv e+lg++ye+l +inPr+iyas++g+ q   ++ +p+yDl++q ++Glm+ tge+++
  gi|320101174|ref|YP_004176766.1|  77 IIYRLAERSDIVIENFRPGVPEKLGVDYESLLKINPRIIYASIKGFKQGSRYQYKPAYDLIIQGMTGLMTSTGEEGR 153
                                       ***********************************************999*************************** PP

                      CoA_transf_3 155 pPvkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapy 231
                                       pPv+v+++l D++tgll++v ++  l+a +   +  +i+v +++aa+  + +  ++yl+tg++p+r+gn++p++ py
  gi|320101174|ref|YP_004176766.1| 154 PPVRVSFALFDVITGLLLSVYVVSTLYAGR---RPVKIEVPMYDAAVFSMCYLPMMYLTTGRKPKRMGNAHPSMVPY 227
                                       **************************9999...5689**************************************** PP

                      CoA_transf_3 232 gvyrtkdg.wvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagv 307
                                       +++r kdg w+++aaa+d+ wa++c+algr++la dprf+tna+r++nr+ l   l+e++++ +++ewl+ l++agv
  gi|320101174|ref|YP_004176766.1| 228 QAFRDKDGkWFIVAAANDRLWASMCRALGREDLAGDPRFRTNADRVANRDLLVSMLQEIFETGSRDEWLKKLEEAGV 304
                                       ***************************************************************************** PP

                      CoA_transf_3 308 paapvntleevlddpqlaarglvvevddpdygevpvvglpvrlsetparvkraaPklGedt 368
                                       paapv +l+ev++dp + ++++v ++ +p +ge+p+ + p  +++++   +  +P+lGe+t
  gi|320101174|ref|YP_004176766.1| 305 PAAPVYELDEVFKDPYVVEQEIVYRIHHPVLGEIPQLSEPGYFNGERYSSRMHPPRLGEHT 365
                                       ************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2547.18
//
Query:       gi|320101175|ref|YP_004176767.1|  [L=499]
Description: gamma-glutamyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-78  264.2   0.0      6e-78  262.9   0.0    1.6  1  G_glu_transpept  Gamma-glutamyltranspeptidase
  ------ inclusion threshold ------
      0.025   14.7   0.3       0.13   12.4   0.1    2.2  2  TOBE_2           TOBE domain


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.9   0.0   6.7e-82     6e-78       2     464 ..      26     453 ..      25     492 .. 0.90

  Alignments for each domain:
  == domain 1  score: 262.9 bits;  conditional E-value: 6.7e-82
                                       HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTTTSCBCCHHHHSSG CS
                   G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmfdkegdsklsktga 78 
                                       evL+kGGnA+DAa+A++++l+vv+pq+ G GG+gfll +  ++    a+  ++++P+  +++ f     ++++ +g+
  gi|320101175|ref|YP_004176767.1|  26 EVLEKGGNAFDAAIAVSAVLSVVQPQMGGPGGDGFLLGFIGDDI--VAYASSGRSPSGFDPERF----ITEKPLKGP 96 
                                       8************************************9998776..579***************....9999***** PP

                                       GG-BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE--TTS CS
                   G_glu_transpept  79 lavgVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlkage 155
                                       l v+VPG v  +  + ++yG+l++a+ll+pai la +Gf+   +la+a+++ e++l+   ++ak++    +    g+
  gi|320101175|ref|YP_004176767.1|  97 LTVTVPGLVYLWGVVNEEYGTLDLATLLKPAISLAYNGFHAGYTLAKAVKSVEKDLAGF-KWAKYY----KGIGLGS 168
                                       ******************************************************99988.666666....5699*** PP

                                       EE--HHHHHHHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTCSHH CS
                   G_glu_transpept 156 llkqpalAktLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyepppssgg 232
                                       ++++++ A+tL+++a+ G e+FY+G+lAe++v+elq++g  + ++D+ +++   +epl++++ ++ ++ye pp+++g
  gi|320101175|ref|YP_004176767.1| 169 RVVNKEMARTLRLIASRGWEEFYHGKLAEEIVDELQDQGVGIGLDDMMDHEGYRVEPLKLEV-EDLVLYELPPNTQG 244
                                       **************************************************************.9************* PP

                                       HHHHHHHHHHCTTTGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHHHHTT.BTTB CS
                   G_glu_transpept 233 ivllqiLnilegfdlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeyakeraklIkdka 309
                                       + +lq +  l +  l++l+ +++++++     +   ya R++ylgDpd+++ +   v e+l  + +ke         
  gi|320101175|ref|YP_004176767.1| 245 ASTLQLISALYEEGLDKLEFRDPRRVEAWSRPVEAVYAFRDEYLGDPDHMA-I--DVGEYLTYTRVKE--------- 309
                                       **********999999******88888888888889**************7.4..5777777766655......... PP

                                       ..SGGGCSCGGCSCG.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBSTS..TTSCSTTS CS
                   G_glu_transpept 310 atpsseyykaaeaaeesggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstgvenafgldpsp 386
                                             +y++   ++ +g+Tt++ v D + + V +++++ ++FGsg++    G+  +n++  f+         +   
  gi|320101175|ref|YP_004176767.1| 310 -----MVYRGVGRPSGGGDTTFFIVSDGD-SLVGFIQSLFHPFGSGLMAG--GFPVQNRGIGFA--------RTTGL 370
                                       .....35666667788************9.9*******************..************........99999 PP

                                       TTB--TT----B----EEEEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--EEE.SSSST...EE CS
                   G_glu_transpept 387 anaiePgkRplssmaPtivlkdgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdaprihh.qllpd...kv 459
                                       +n ++P+k pl++++ + v   g+ + ++G  GG+  ++ +l v  n +++g+d+ eav+apr+   +  p+   +v
  gi|320101175|ref|YP_004176767.1| 371 PNSPAPRKLPLHTLSILGVS-GGREKYIIGCVGGDYRPQLHLRVYENLFVYGMDPVEAVNAPRFIYtE--PRgrqEV 444
                                       **************966665.59*****************************************9952..4444588 PP

                                       EEST....T CS
                   G_glu_transpept 460 evEe....g 464
                                        vEe    +
  gi|320101175|ref|YP_004176767.1| 445 VVEEplkpT 453
                                       888844441 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.22   1.9e+03       5      30 ..     291     314 ..     291     316 .. 0.78
   2 ?   12.4   0.1   1.5e-05      0.13      21      53 ..     458     490 ..     443     497 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.22
                            TOBE_2   5 PEklrlaaaggan.glsGtVedveylG 30 
                                       P+++ +  + g +  +  +V++ +y+G
  gi|320101175|ref|YP_004176767.1| 291 PDHMAI--DVG-EyLTYTRVKEMVYRG 314
                                       888999..444.5477899******99 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.5e-05
                            TOBE_2  21 GtVedveylGsstryvvelaggqlvvvrqpnad 53 
                                        tV+ vey+Gs+ +++v++ +g + +++ ++++
  gi|320101175|ref|YP_004176767.1| 458 ITVKLVEYFGSHGHVHVAVYDGVKTLLVNDPRS 490
                                       59*****************99988777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3707.06
//
Query:       gi|320101176|ref|YP_004176768.1|  [L=311]
Description: beta-ribofuranosylaminobenzene 5'-phosphate synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-05   25.8   0.0    2.4e-05   24.6   0.0    1.6  1  GHMP_kinases_C  GHMP kinases C terminal
     0.0026   17.9   1.1     0.0038   17.4   0.1    1.9  2  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.7e-09   2.4e-05       8      80 ..     212     286 ..     202     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.7e-09
                    GHMP_kinases_C   8 gdlellgellnlsqrs....elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralr 80 
                                       +d++++ ++l+ +q+       +++ g+ +    e+++al+++G    ++ ++++Gptv+++++  +eae+++ ++ 
  gi|320101176|ref|YP_004176768.1| 212 RDYSSFTRALTMLQETvgsmFSRYQGGVFSTGSSEAVRALRKAG--VEGVGQSSWGPTVYGVVEGLEEAEKILGRIE 286
                                       78888999999999999999889999******************..**************************98874 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.3e-07    0.0038       2      65 ..      77     136 ..      76     137 .. 0.74
   2 ?   -2.4   0.1      0.68   6.1e+03       8      15 ..     169     176 ..     168     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.3e-07
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyG 65 
                                       +++   +P + GLGS + l++a+++ l+ l+g +++     +e+ r+ ++g+ sg+  +++ +G
  gi|320101176|ref|YP_004176768.1|  77 VNVMECVPRHVGLGSTTQLVLAAAYGLAVLNGSPMD----PVEIARETGLGRYSGVGTYVFKHG 136
                                       6666779************************97754....444445555566666666666555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.68
                                       SHTTSSSC CS
                    GHMP_kinases_N   8 iPvgaGLG 15 
                                       +P+g GLG
  gi|320101176|ref|YP_004176768.1| 169 VPPGQGLG 176
                                       79*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2206.41
//
Query:       gi|320101177|ref|YP_004176769.1|  [L=204]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   0.0    8.2e-21   74.6   0.0    1.0  1  DUF447        Protein of unknown function (DUF447)
    0.00043   20.3   0.0    0.00086   19.3   0.0    1.6  1  Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.048   13.7   0.0      0.083   13.0   0.0    1.3  1  DUF2054       Uncharacterized conserved protein (DUF2054)


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 !   74.6   0.0   1.4e-24   8.2e-21       1     167 [.      10     186 ..      10     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.4e-24
                                       EEEEEEEE-TT-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETT. CS
                            DUF447   1 yEvivtTksekrpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetk. 76 
                                       yE ivt ++ ++p a+P+G  + gd+v+++l+kgsrT + l++ ++ v+nvt+Dp+lf+++a++  ++   +++   
  gi|320101177|ref|YP_004176769.1|  10 YEAIVTLLAGSEPYATPVGFWRLGDEVLIKLYKGSRTHSLLKTVENPVLNVTRDPFLFYRTAFKSESNGLTREDFIi 86 
                                       899***99999****************************************************97665544444332 PP

                                       .TC.TT.EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEET.TB---B-HHHHHHHHHHHHHHCCCC......SH CS
                            DUF447  77 .pa.kiavlksaeawveveveevegdsealelelepvkeeile.ervkpfnRgdaaviEaaVlatRldi......ed 144
                                        +   +a+l++aea++ +++  v + ++   +++ ++++   + + v+p+ R  + +iE+ V at  +       e+
  gi|320101177|ref|YP_004176769.1|  87 dEEkGVAYLRNAEAYILLKLIGVVEYEHYGLFKYGILEAREGAvRCVEPYTRCYSSLIEMIVYATKVKAwrdlagEE 163
                                       2334788****************9999999999999998888757899*******************9999999999 PP

                                       HHHHHHHHHHHHHHHHHH--HHH CS
                            DUF447 145 keklleeieylssvikktggere 167
                                        e  l+ ie+ ++v++kt  +r+
  gi|320101177|ref|YP_004176769.1| 164 LEAALRSIEDSFRVVSKTCRSRD 186
                                       9999**************99887 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.4e-07   0.00086      20      57 ..      17      56 ..       1      77 [. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-07
                                      EETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCC..T-- CS
                      Pyridox_ox_2 20 vddgepvilPvnyvvdgdslyfhgakgsrlaaalr..gap 57
                                        ++ep+++Pv +++ gd++++  +kgsr + +l+  ++p
  gi|320101177|ref|YP_004176769.1| 17 LAGSEPYATPVGFWRLGDEVLIKLYKGSRTHSLLKtvENP 56
                                      34678*****************************944333 PP

>> DUF2054  Uncharacterized conserved protein (DUF2054)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.083      57     121 ..     129     193 ..     120     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                           DUF2054  57 kseCCeeyeyCvsCClepdkkelleevlekaakkrkkvllasvedqfelClakCRtssesvqhen 121
                                       + +C e y  C s  +e    +++ ++ +  a ++ +++l s+ed+f +  ++CR     v  en
  gi|320101177|ref|YP_004176769.1| 129 AVRCVEPYTRCYSSLIEMIVYATKVKAWRDLAGEELEAALRSIEDSFRVVSKTCRSRDYLVLAEN 193
                                       568***************9999999999999*************************999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1560.57
//
Query:       gi|320101178|ref|YP_004176770.1|  [L=400]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-85  284.6   1.0    1.1e-84  284.4   1.0    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 !  284.4   1.0   6.4e-89   1.1e-84       1     326 [.       6     364 ..       6     365 .. 0.92

  Alignments for each domain:
  == domain 1  score: 284.4 bits;  conditional E-value: 6.4e-89
                           DUF1464   1 GiDPGtksydvvvvddlgkvvlekeiptdevekdpsvlvkaieea.radivalpSGyGlPlkriselae.......r 69 
                                       G+DPG+ks d+ ++ d g+v++ek+i t e ++dp ++v+a+ee+ +ad+valpSGyG+ + r s+++         
  gi|320101178|ref|YP_004176770.1|   6 GMDPGSKSIDLCGLCD-GEVCFEKSIDTLEASRDPARVVEAVEEFgEADLVALPSGYGVEVTRLSDVDTailedwyY 81 
                                       89**************.****************************899*******************9988765544 PP

                           DUF1464  70 eillltlaeeseegl....vG......LrellkelaskelnaftiPgVieLptvPewRKvnkiDmGtADKlasavla 136
                                         +l+t +ee e gl    vG      + ++ +el+ + + +++iP+Vi+L+++P +RK+n++DmGtADKla+avl+
  gi|320101178|ref|YP_004176770.1|  82 TFILATTREEVEVGLrkgsVGafiydaMGKITRELKRRGVKGVFIPSVINLESIPVHRKLNRVDMGTADKLAVAVLG 158
                                       445555555555555666666999999999*********************************************** PP

                           DUF1464 137 vadeaeee..eyrelsFilvEvGsgfnaviaVknGkivDGlGgtilpG..flsaGalDgEvAyllgkvakiekslif 209
                                       +++ + e+   y ++++i vE+G+g+naviaV+nG ivDG+Ggt++pG  fl+aGa+D EvA ++g   +++k+++f
  gi|320101178|ref|YP_004176770.1| 159 IHEVSSEHglPYGKVNYIHVEMGFGYNAVIAVRNGLIVDGVGGTLMPGpaFLTAGAMDLEVAQAIG---SLDKNDVF 232
                                       ********999*************************************99****************...******** PP

                           DUF1464 210 sgGvasiagea...elekklsee.....aferlke.vvksvaellsskykleeiivSGrlkrikelgkklesrleev 277
                                       s+G + ++g     +   k+se       f++++e +vk+v ++ + +  + ei++SGr  r   +   le++l ++
  gi|320101178|ref|YP_004176770.1| 233 STGCGPLTGSPtpeDWISKVSEDplagvCFDAMMEsLVKTVYSMIPVVGGAVEILLSGRVSRNPVVVDYLEEKLGDL 309
                                       *******9998666555566666888889*********************************************999 PP

                           DUF1464 278 ......kllelaskaKeaaqGaAiianalaGgryrelvdhleiekssgtvldyvk 326
                                             k l +as  Ke+aqG+A+ia++laGg+++ lv+h+++ +++g+ ldy++
  gi|320101178|ref|YP_004176770.1| 310 apvrrmKGLPGASTVKETAQGYAVIADGLAGGVFHTLVEHVGVVNARGSSLDYIV 364
                                       999966666689999**************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2883.64
//
Query:       gi|320101179|ref|YP_004176771.1|  [L=480]
Description: MATE efflux family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-40  138.6  31.0    1.3e-23   83.4   9.4    2.4  2  MatE             MatE
    2.2e-11   44.0  43.0      3e-10   40.3  15.3    4.3  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
      0.061   13.1   0.1        0.2   11.4   0.1    1.9  1  TOM6p            Mitochondrial import receptor subunit TOM6 h


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 !   83.4   9.4   2.1e-27   1.3e-23       1     161 []      31     192 ..      31     192 .. 0.97
   2 !   61.0  13.6   1.8e-20   1.1e-16       1     161 []     261     422 ..     261     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 2.1e-27
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P++  +l+ ++++++d ++++r+++ a Aa   ++++++l  +++ gl +a  +l +q +Ga+n+ +a++++ + + 
  gi|320101179|ref|YP_004176771.1|  31 PLMAVQLVNVSYNIADAYWLSRYSEIAYAAPRQVMPTFMLWNAVAQGLIAANLALLTQLVGARNYGEARRYISYFVS 107
                                       9999************************************************************************* PP

                              MatE  78 lllllsliiallvllfseqilslf.tqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                       ++l +  +ia+++++++++i++++ ++++++   +++y ri+ l i++ a++l++s+il+++g+t++p+ i+++++l
  gi|320101179|ref|YP_004176771.1| 108 AALMVNSVIAVVYFFLRPFIFRYIvGTPPQLYGDTMTYSRIITLDIVFSAFTLTYSTILQSIGDTRTPATINALAAL 184
                                       *********************876266777*********************************************** PP

                              MatE 154 lniplnyl 161
                                        n++l++l
  gi|320101179|ref|YP_004176771.1| 185 ANVILDPL 192
                                       *****985 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 1.8e-20
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ l+++  sl +++ + l++++g+   Aa++i+l +  l  + l+g+  +++++vgqalGa+ ++ra++++ ++++
  gi|320101179|ref|YP_004176771.1| 261 PVSLMMASNSLAFMLQNNLINQFGEYTAAAAAIGLILMDLADATLWGFTGSVSIMVGQALGAGLTERARRVASKAML 337
                                       999************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.l 153
                                          l  l+ +l+++  ++ ++  ft ++ ++  a+ ++   i+++p++al+++  +i rg g t +p+++ +++l  
  gi|320101179|ref|YP_004176771.1| 338 YIGLSTLVGSLIAFTVRDAFINAFTGNPVIVREARVFVATFIPSLPFFALFFIGVSIGRGSGHTVFPTILGVVRLwA 414
                                       ***************************************************************************** PP

                              MatE 154 lniplnyl 161
                                       ++i+l+y+
  gi|320101179|ref|YP_004176771.1| 415 VRILLGYI 422
                                       ******97 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   2.2    0.0089        53      71     116 ..      80     126 ..      68     134 .. 0.80
   2 !   40.3  15.3   5.1e-14     3e-10       3     133 ..     147     297 ..     145     349 .. 0.85
   3 !   10.8   8.9   6.3e-05      0.38       3      74 ..     376     450 ..     374     459 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0089
                   Polysacc_synt_C  71 vlnlyalrrllgikl..ellrrllkpllaalvmgivvylllllllgll 116
                                       + nl +l +l+g +   e  rr + ++++a++m+  v+++++++l  +
  gi|320101179|ref|YP_004176771.1|  80 AANLALLTQLVGARNygE-ARRYISYFVSAALMVNSVIAVVYFFLRPF 126
                                       457788888888888854.89999***********9999999887655 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 5.1e-14
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli...........plfgivGaaiatvlallv 68 
                                       +i++l i+f++++ ++s+iLq++g +++++ +++++al+++il  l+i           p +g+ Gaa+atvl+ l+
  gi|320101179|ref|YP_004176771.1| 147 RIITLDIVFSAFTLTYSTILQSIGDTRTPATINALAALANVILDPLFIlgvnaggvqllPAMGVAGAAYATVLSRLA 223
                                       688899******************************************8777777777778888************* PP

                   Polysacc_synt_C  69 vavlnlyalrrllgikl.........ellrrllkpllaalvmgivvylllllllgllllaal..alllavlvgalv 133
                                       +++l+l++l+ ++ + +         e++ r +++ + + +m++    l+ +l + l  +++   +++a+++g ++
  gi|320101179|ref|YP_004176771.1| 224 GLLLLLRRLSTKYPYMVpkltlhierEWILRSIRIGAPVSLMMASNS-LAFMLQNNLI-NQFgeYTAAAAAIGLIL 297
                                       ***************99999988877677777787777777777733.2222222222.23445777777777765 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 6.3e-05
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllliplfgi..vGaaiatvlallvvavlnl 74 
                                       a +++s++f++l+ ++ si  g g++ ++++  v+ +  v ++l ++l   +g+  +G+ ia+ l+ +v+ ++++
  gi|320101179|ref|YP_004176771.1| 376 ATFIPSLPFFALFFIGVSIGRGSGHTVFPTILGVVRLWaVRILLGYILSFNLGLgsLGVWIAMSLSNIVSGAVMV 450
                                       56899******************************9855**********8876555*************999986 PP

>> TOM6p  Mitochondrial import receptor subunit TOM6 homolog
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.4e-05       0.2      30      65 ..     408     443 ..     400     451 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                             TOM6p  30 svyrfaadrndfrrnlllnlGlfaaGvwlarnlsdi 65 
                                       +v+r+ a r  +   l  nlGl + Gvw+a  ls+i
  gi|320101179|ref|YP_004176771.1| 408 GVVRLWAVRILLGYILSFNLGLGSLGVWIAMSLSNI 443
                                       555666666666666789****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3414.05
//
Query:       gi|320101180|ref|YP_004176772.1|  [L=518]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3712.99
//
Query:       gi|320101181|ref|YP_004176773.1|  [L=341]
Description: CRISPR-associated protein Cas1 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-60  202.5   0.0    9.1e-60  202.2   0.0    1.1  1  Cas_Cas1  CRISPR associated protein Cas1


Domain annotation for each model (and alignments):
>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.2   0.0   5.1e-64   9.1e-60       1     259 [.       9     281 ..       9     302 .. 0.93

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 5.1e-64
                                       EEEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.S CS
                          Cas_Cas1   1 lyvteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.e 76 
                                       l v+e+ga+l+kk++r+vv+  g+ ++e+ l+ i+++v+ g++s+s+++l+++a  g+ +++ s++g++l+rl+p +
  gi|320101181|ref|YP_004176773.1|   9 LLVDEYGAFLGKKHGRVVVRVGGS-REEYALKLIRDVVVAGRASISSELLKAMAYSGVGLLVTSYTGTPLARLIPaR 84 
                                       6799******************98.9*************************************************** PP

                                       SSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTT....HHHHCHCHHHHHHHHHHHH-.... CS
                          Cas_Cas1  77 esgnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdree....eeleeaieeleellekleka.... 145
                                         g+ + r++Qy+a++d + ++ +a+ +++gk++nq ++++++++ r +    ++l e++  l+ l+++l++     
  gi|320101181|ref|YP_004176773.1|  85 AGGTFRNRVEQYKALEDGR-ACIIARDLITGKVKNQSSNIKYYSKARAQesekKALYEKALLLDGLIKQLSTYtpgt 160
                                       *****************98.999************************44466799999999999999999999**** PP

                                       ....HSHHHHHHHHHHHHHHHHHHHHHHCSCGGS-SS-SSSS.....-SSHHHHHHHHHHHHHHHHHHHHHHTSS-- CS
                          Cas_Cas1 146 ....esleeLrgiEGeaakaYfeafdkllkeefefegRsrrp.....pkDpvNalLsfgYtllysevlsaieavgLd 213
                                           e +e+++ +E++aa++Y++ ++ +l  ++ fe+R + p     + D vN+ L+ +Y +l+ ++++ + + gLd
  gi|320101181|ref|YP_004176773.1| 161 grleECREKVLSVEAQAAEIYWDGMRVVL-GDYGFERRVKIPeaedkQLDTVNTALNIVYNILAGNMWKYVLRFGLD 236
                                       *************************9888.8*********995555559**************************** PP

                                       TT--SSS--TTSS-HHHHHHHHHHHHHHCHHHHHHHHHTTSS-GGG CS
                          Cas_Cas1 214 PyiGfLHedrpgrpsLalDLmEefRpllvDrlvlslinkrqlkekd 259
                                       Py+GfLH++rpgr sL++DL+E+fRp l Drl+ sl++++ l++ +
  gi|320101181|ref|YP_004176773.1| 237 PYAGFLHAERPGRLSLVYDLIEPFRP-LGDRLIASLLRRGVLRPGM 281
                                       **************************.9************999764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2595.02
//
Query:       gi|320101182|ref|YP_004176774.1|  [L=315]
Description: Cas1 family CRISPR-associated protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-68  231.0   0.0    2.6e-68  230.5   0.0    1.1  1  Csa1      CRISPR-associated exonuclease Csa1
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.15   11.8   0.0    1.2  1  Dna2      DNA replication factor Dna2


Domain annotation for each model (and alignments):
>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.5   0.0   2.9e-72   2.6e-68       5     290 ..       6     311 ..       1     313 [. 0.87

  Alignments for each domain:
  == domain 1  score: 230.5 bits;  conditional E-value: 2.9e-72
                              Csa1   5 leevrlL.krlkklsaskeveeElRGWnwnePPvkprsl.vklslsdvvsgyCetkRdvYLkrvlgvrge.eekkll 78 
                                       + evrlL ++l  +++ ++ +e lRGWnw++ Pvkp++  + ls+ +v+ + C+t+Rdv+L+r l  +    +  ++
  gi|320101182|ref|YP_004176774.1|   6 HAEVRLLsQDLLPRVRLNPPDERLRGWNWSQSPVKPYTRdIPLSVWEVAARTCPTNRDVWLRRKLLRKNMpSSLVMV 82 
                                       6789***9****************************99879********************9766554441456678 PP

                              Csa1  79 lGaaiHeavakaleelkkliysgeklds.....slerllvadeivalledvie.........kakelykylasrvsa 141
                                       +G +iH +v+  ++e+++ iy g+  d      ++ r +++de+ +  ++v            + e+ ky+a+ +++
  gi|320101182|ref|YP_004176774.1|  83 KGVVIHRVVQALFKEARRSIYLGQLSDLrerlvEKGRAVTEDELGSFSRQVDTgqladelraLSSEVSKYIATVIES 159
                                       9*******************9887666411111444566677776554444444455555548899*********** PP

                              Csa1 142 elsevrskfekatedsvaarviPvlvefkvdGsllGlsslvrvDafililplvvelkvgsykeehelalaGYalalE 218
                                       +l e+rsk ++ +eds+a+ v P++ e ++dGsllGls ++r+Da  +  +lv ++k+g+ +  h+l +aGYala+E
  gi|320101182|ref|YP_004176774.1| 160 HLLEARSKYPYIDEDSLASLVFPFAIELPIDGSLLGLSPNLRADASWIFGGLVYDIKTGERQWWHRLQIAGYALAIE 236
                                       *********************************************888888************************** PP

                              Csa1 219 sqleiPvDfGvlisvtvn...gevklkaelvaisdslRkefleeRdraidivekesDPGlakkCsskClflevCk 290
                                       s +e PvD+G++i+v      g+++++++ + +sd+lR++fle Rd+++ +++ +++P +a++C+  Clf+e+C 
  gi|320101182|ref|YP_004176774.1| 237 SFYERPVDIGAVIYVNYSsrtGGLRIEKDFFIVSDDLRSRFLEYRDELQMMLAGNKEPPVAEACPRWCLFREHCL 311
                                       ***************655111456**************************************************5 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.7e-05      0.15      70     152 ..      64     155 ..      53     171 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                              Dna2  70 avLqerl.kvsgesskamliGtilHelfqkalleee..ldkekleelldklle......knleelyalglteeeake 137
                                         L+ +l + + +ss  m+ G ++H+++q++++e +  +   +l++l ++l+e      +     ++ +++  ++ +
  gi|320101182|ref|YP_004176774.1|  64 VWLRRKLlRKNMPSSLVMVKGVVIHRVVQALFKEARrsIYLGQLSDLRERLVEkgravtEDELGSFSRQVDTGQLAD 140
                                       55666665777799******************774423444455555555554333321222222334444555555 PP

                              Dna2 138 eikekleeiekwakk 152
                                       e+++  +e++k++ +
  gi|320101182|ref|YP_004176774.1| 141 ELRALSSEVSKYIAT 155
                                       555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2432.02
//
Query:       gi|320101183|ref|YP_004176775.1|  [L=90]
Description: Cas2 family CRISPR-associated protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-19   68.7   0.0    4.1e-19   68.5   0.0    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   2.3e-23   4.1e-19       1      73 [.       1      72 [.       1      75 [. 0.96

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 2.3e-23
                                      EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHH CS
                       CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqf 73
                                      m+vlvvYDi +d+  r+++a++lk++G++r+Q+S F+g+l++++ e+l+++l+++  +e+d+i i++++e+  
  gi|320101183|ref|YP_004176775.1|  1 MMVLVVYDI-ADNGLRTRIAEVLKDHGLTRIQKSAFIGDLTPQERETLAEKLSRLQLDETDRIDIFPICERDL 72
                                      9********.********************************************999999*********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 724.76
//
Query:       gi|320101184|ref|YP_004176776.1|  [L=184]
Description: CRISPR-associated protein Cas4 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   57.0   0.0    2.9e-15   56.8   0.0    1.0  1  Cas_Cas4  Domain of unknown function DUF83
    6.1e-10   39.4   0.7    3.8e-07   30.3   0.0    2.1  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.041   13.9   0.2      0.085   12.9   0.2    1.5  1  DUF1707   Domain of unknown function (DUF1707)


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 !   56.8   0.0   4.8e-19   2.9e-15       5     160 ..      12     179 ..       9     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 4.8e-19
                          Cas_Cas4   5 iqyyliCkrklwlisheitleensetvelGkllhe....esyerek......kevelse.....sikiDvvekekek 66 
                                       ++ y++C+  ++l  +  + +      e+Gk ++     + +   +      +ev l+      ++++D+v + ++ 
  gi|320101184|ref|YP_004176776.1|  12 LEEYFFCPFAFYLSRVAGEARAPGLWSEVGKDVQAelssHVE---SrykvigREVFLESvrlrlRGRVDYVVELHGL 85 
                                       789******************************995655333...1234678777773357778********99999 PP

                          Cas_Cas4  67 lvvvEvKkskkkeeaaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeieeiissekp 142
                                         + EvK+s++ ++ +k+ l +Y++l e k    +k++ l +p  ++  ++e+  e+r+++e+a++ + +i++   +
  gi|320101184|ref|YP_004176776.1|  86 PAPLEVKHSRRLRPWWKYTLVAYAMLAEeKYSKPVKQALLILPGPRE-IRLEVASEDRRRVEEALTAATAILEGRLT 161
                                       ****************************8999999988888888775.689************************** PP

                          Cas_Cas4 143 pkvkkkkiCkkCayaelC 160
                                       p++ +++ C +C y+  C
  gi|320101184|ref|YP_004176776.1| 162 PRPYESRSCINCDYSAAC 179
                                       ****************99 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2   0.00039       2.3       6      25 ..      11      30 ..       9      46 .. 0.82
   2 !   30.3   0.0   6.4e-11   3.8e-07     103     255 .]      47     180 ..      34     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00039
                          PDDEXK_1  6 rletfleCplrfflryllgl 25
                                       le +  Cp++f+l++++g 
  gi|320101184|ref|YP_004176776.1| 11 DLEEYFFCPFAFYLSRVAGE 30
                                      699*************9985 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 6.4e-11
                          PDDEXK_1 103 rlaeeleakrgfrpvalelefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalae 179
                                       +l+   + +  +++++ e+   + ++rL+Gr+D v + +g    ++ K ++    +++    +    l +Y+++++e
  gi|320101184|ref|YP_004176776.1|  47 ELSS--HVESRYKVIGREVFLESVRLRLRGRVDYVVELHGLPAPLEVKHSR----RLRP---WWKYTLVAYAMLAEE 114
                                       4444..44555777777853334679**********************555....5552...344469********9 PP

                          PDDEXK_1 180 geelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskk..CeyCpyksvC 254
                                       +  + +   p+++++l l       +++++     +e+++++++ l   a +il+g+  +rp++   C +C+y++ C
  gi|320101184|ref|YP_004176776.1| 115 K--YSK---PVKQALLIL-----PGPREIRLE-VASEDRRRVEEALTA-ATAILEGRLTPRPYESrsCINCDYSAAC 179
                                       9..442...777777777.....355566655.455566677777766.699***********9999********** PP

                          PDDEXK_1 255 r 255
                                       r
  gi|320101184|ref|YP_004176776.1| 180 R 180
                                       7 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.4e-05     0.085       4      33 ..     138     169 ..     135     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                           DUF1707   4 sdadReravelLreala..eGrLtldEfdeRl 33 
                                         +dR r+ e+L++a a  eGrLt   ++ R+
  gi|320101184|ref|YP_004176776.1| 138 ASEDRRRVEEALTAATAilEGRLTPRPYESRS 169
                                       678**********998888**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1530.96
//
Query:       gi|320101185|ref|YP_004176777.1|  [L=109]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 913.61
//
Query:       gi|320101186|ref|YP_004176778.1|  [L=362]
Description: DevR family CRISPR-associated autoregulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-68  229.3   0.7    5.4e-68  229.0   0.7    1.1  1  DevR      CRISPR-associated negative auto-regulator DevR/Csa2


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 !  229.0   0.7     3e-72   5.4e-68       2     268 ..       7     308 ..       6     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 229.0 bits;  conditional E-value: 3e-72
                                       EEEEE-------------------EEEEEE--T..T--EEEEEE-THHHHHHHHHHHHHHHHTS.TTSSBHHH...H CS
                              DevR   2 sgrvvvnveaLNmdesvGNytehrkvpvvlkee..ykvrtvpaiSgeslkHayfetlvklaken.nlpvcelc...k 72 
                                       ++rv++nveaLNm e++GN+ +hr++p+++ ++  yk+++vpaiSgesl Ha++++lv+ a+   +  v+++    +
  gi|320101186|ref|YP_004176778.1|   7 AARVRANVEALNMTETIGNVSKHRRAPYIISTRegYKLVYVPAISGESLGHAFQANLVDAAQYIyG--VEKKPvplD 81 
                                       68***************************999999************************9997742..333321125 PP

                                       TT------TT--EEEBTTS...................EESS-HHHHHHH-HHHHHH-EEEGGGT..EEE--SEEE- CS
                              DevR  73 rvegdggvikfatekklke...................kelkvekeiikecvveDvfGfLitekeksvkRkspvkfs 130
                                        +++  +++kf+++k+l e                    +  +ek++i+e++v+D++Gf+++ek + v+R+s ++++
  gi|320101186|ref|YP_004176778.1|  82 PYSARYEFVKFSDSKHLPEslkkileesgkkkkegieeLQHLFEKTAIQESIVADIGGFMLAEKMP-VRRTSLFEVG 157
                                       67788*************9*****************988888*******************97775.********** PP

                                       -BEE-TTTTTTT.-----------............------------------HHHHHSSEEEEEEEEEGGGTTS- CS
                              DevR 131 yavpveesekav.vdaqfharydl............lenrarkkgeeeekqnifqvEehsalYalsfvlDldriGkp 194
                                       yavpvee++ ++ ++aq+har +             ++ ++  +g+e+++q++++vE++s++Y++s+ +Dl +iG++
  gi|320101186|ref|YP_004176778.1| 158 YAVPVEEAVSESiIEAQMHARQAVvgleveektsgkKAGEEAGEGKEAKQQMLYYVEVASTVYGMSMCIDLGSIGVT 234
                                       *********999******************999988555556667799***************************** PP

                                       TTS--EE---S-HHHHHHHHHHHHHTHHHHHH--.------------EEEEEEEE--S.SS------TTTTHHHHH CS
                              DevR 195 evkkskieyvleeeerkkRikaalkallnlLsgs.fgakrarllPvfeveslvaavsk.kpfpvfpirledyveee 268
                                       ++   k+e ++ ++e+ +R+k+al al+ ++  +  gakr+r++Pv+ +e++va++sk  p+ ++p++++ y+ee+
  gi|320101186|ref|YP_004176778.1| 235 SM--VKREEAVAKDEKLRRVKSALLALAMTFGLQlYGAKRSRFSPVLSIENMVAVISKpLPIAASPPQVSTYIEET 308
                                       **..99999***********************999***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2639.01
//
Query:       gi|320101187|ref|YP_004176779.1|  [L=270]
Description: Cas5 family CRISPR-associated protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1981.57
//
Query:       gi|320101188|ref|YP_004176780.1|  [L=416]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   17.7   0.0     0.0024   17.1   0.0    1.2  1  Cas_Csx9  CRISPR-associated protein (Cas_Csx9)


Domain annotation for each model (and alignments):
>> Cas_Csx9  CRISPR-associated protein (Cas_Csx9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-07    0.0024      86     163 ..     141     215 ..      91     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-07
                          Cas_Csx9  86 geslstiktdkngtylgiayngeqailpai.ikqpeyyerqsgflspttgqkaqirmdplwfsfmalgfftsfagfi 161
                                        e l +i+ d+   ylg     e a  p + + + e y+    +ls t   k q+++  +w+s++  g++ sf+g++
  gi|320101188|ref|YP_004176780.1| 141 AEELKSIRMDEGDIYLGRD---ESAQYPQLqVFKLEKYKYGKKYLSFT-EFKGQMKISSIWYSILGAGWLLSFSGYL 213
                                       588999**********965...566666542556788999999**975.689************************9 PP

                          Cas_Csx9 162 gg 163
                                       g 
  gi|320101188|ref|YP_004176780.1| 214 GS 215
                                       96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2874.87
//
Query:       gi|320101189|ref|YP_004176781.1|  [L=590]
Description: CRISPR-associated helicase Cas3 [Desulfurococcus mucosus DSM 2162]
Scores for 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   37.8   0.1    5.9e-09   36.2   0.1    1.9  1  Helicase_C  Helicase conserved C-terminal domain
    2.2e-06   27.6   0.1    1.8e-05   24.6   0.0    2.4  2  DEAD        DEAD/DEAH box helicase
    5.3e-05   23.3   0.0    0.00013   22.0   0.0    1.6  1  ResIII      Type III restriction enzyme, res subunit


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 !   36.2   0.1     1e-12   5.9e-09       3     110 ..     248     357 ..     246     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1e-12
                                       HHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSS..EEEESG CS
                        Helicase_C   3 leallellkleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesd..vLiatd 74 
                                       ++++lel+ ++  ++k ++    ++ ++  + ++e++     +v +lhg l+ n+ree+ ++  +++ +   L+at+
  gi|320101189|ref|YP_004176781.1| 248 IDKVLELIASRDATRKLIVLNSPREAIKVYRKIQEQNiegTGEVFMLHGLLSRNDREETTRKLLENKNKpfTLVATQ 324
                                       6678888866666666666666666665479998888997799********************64333336****** PP

                                       GGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  75 vaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       v+e G+d+ +++l+i   +p  ++s++qr+GR+ R 
  gi|320101189|ref|YP_004176781.1| 325 VVEAGLDV-SADLLITDLAP--IQSLVQRMGRVSRW 357
                                       ********.58888876666..899********995 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.9e-09   1.8e-05      18     170 ..      21     184 ..      13     191 .. 0.66
   2 ?   -1.7   0.0      0.36   2.1e+03      78     113 ..     216     257 ..     201     274 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.9e-09
                                       EEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT.........TST.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxx.......... RF
                              DEAD  18 lvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk.........yid.......... 75 
                                       +++ +TG+GKT+ f+  + ++ +   gk + +a++ +P+r+L e+ + +l++++          y++          
  gi|320101189|ref|YP_004176781.1|  21 VLKLPTGYGKTELFMELAKRTCM---GKIA-RAIYASPLRALNEDLYYKLEERGYcvvhqrarqYMErsespffhrk 93 
                                       6788***********99998884...5666.***********************95444444332223344444322 PP

                                       ..SEEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHH CS
                                       ..xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                              DEAD  76 ..lrvlliiggvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinrilnq 148
                                         +++  ++g + ++   ++++ + v+ +v+  +r   ++s  + n+s+  ++ +DE +    + g ++ +  il+ 
  gi|320101189|ref|YP_004176781.1|  94 vvVTTIDTLGFSVYKVPTAEMS-DiVEGYVMKDERTRGHFSIPRANISDS-VVLIDEPHLAFTEsGLERLLLGILQY 168
                                       1111111122222222222332.236666666677777776666666665.7889****998886888888888888 PP

                                       SHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 149 lpqitcdgklqrqvivlSATlp 170
                                       l       k   +vi+ SATl+
  gi|320101189|ref|YP_004176781.1| 169 L----LASK--ATVILASATLT 184
                                       7....3334..45*******98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.36
                                       EEEEETTSSHHHHHHHHH..TTCSEEEEEHHHHHHHH.....H CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx.....x RF
                              DEAD  78 vlliiggvaardqlskld..ngvdivvgtpgrlddll.....s 113
                                       ++++ ++++++++ ++++  ++v++ + t ++l+d +     s
  gi|320101189|ref|YP_004176781.1| 216 ECSF-SSNTRDEEFDQVQakKNVEMEIHTSKQLIDKVleliaS 257
                                       4433.34455555555542266999999999988854344441 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 !   22.0   0.0   2.1e-08   0.00013      27     169 ..      20     183 ..       3     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.1e-08
                                       EEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--....... CS
                            ResIII  27 glikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstn 103
                                       +++k++TG GKT + ++l++r    gk+ +++   p ++l e ++ ++++   + +++    + ++++++      +
  gi|320101189|ref|YP_004176781.1|  20 AVLKLPTGYGKTELFMELAKRTCM-GKIARAIYASPLRALNEDLYYKLEERGYCVVHQRARQYMERSESP----FFH 91 
                                       579******************998.6888************************99999888888888777....789 PP

                                       -SEEEEEHHHHHHTH...................HHHTTT-S.........EEEEETGGGTTS.TTTHHH....HHT CS
                            ResIII 104 kkilvttiqsldadseee...........eeeseellrdrfd.........viiiDEaHrlgakkswrei....lek 156
                                       +k++vtti++l  +  +              +++e  r++f          v++iDE H +  ++  +++    l++
  gi|320101189|ref|YP_004176781.1|  92 RKVVVTTIDTLGFSVYKVptaemsdivegYVMKDERTRGHFSipranisdsVVLIDEPHLAFTESGLERLllgiLQY 168
                                       9**********99995559999999999977777777788878999999**********999988777765565555 PP

                                       -...--SEEEEEESS- CS
                            ResIII 157 f...keavllglTATp 169
                                       +   k+ v+l+ +AT+
  gi|320101189|ref|YP_004176781.1| 169 LlasKATVILA-SATL 183
                                       55524444444.8886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 4496.93
//
Query:       gi|320101190|ref|YP_004176782.1|  [L=277]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   19.1   0.0     0.0017   18.5   0.0    1.3  1  HD_6      HD domain
     0.0024   18.1   0.2      0.022   15.0   0.0    2.2  2  HD        HD domain


Domain annotation for each model (and alignments):
>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-07    0.0017      36     140 ..      37     198 ..      13     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-07
                                       -HHHHHC.TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH...... CS
                              HD_6  36 sllarllrgleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle...... 106
                                       +l ar+l g++ ++lr+ +++  + HD+GK+   F ++  +  ek+++a        +   H+ l+  +l+      
  gi|320101190|ref|YP_004176782.1|  37 ELTARRL-GIDASELREAIIVAEVFHDIGKIF--FHSNL-NVDEKCDNAPN------SYRGHEVLSSFILNtisdqy 103
                                       3366777.9*********************96..44444.55666665422......5779*****99966666667 PP

                                       ......................HHHHHHHHHHHTTTS---HHHHHTSS-HHHHTT...................... CS
                              HD_6 107 ......................evarslaaavggHHGkppkeeeekaekkssaae...................... 139
                                                             + + s+   ++gHH     +++++a++++ +++                      
  gi|320101190|ref|YP_004176782.1| 104 rvfeydtpraregtepeciiqrALKYSVHLSIIGHHEAMGYQRRSHASSREVYEKflwfkkrtgisageavegflsn 180
                                       667777776666767777776677779999******97777666666666655557665555555555555555555 PP

                                       .................H CS
                              HD_6 140 .................d 140
                                                        d
  gi|320101190|ref|YP_004176782.1| 181 vlsgtpinlgtlrydalD 198
                                       555555555555555444 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-06     0.022      11      67 ..      39      96 ..      35     110 .. 0.78
   2 ?    0.4   0.1     0.078     7e+02      66     121 ..     202     249 ..     189     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHH....CTCCHHHHHHHHHHH CS
                                HD 11 larrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeee....fekflaHekvgaeil 67
                                       arrl++d    e re + +a  +HDiGk+ f++  ++  e+     ++ ++He+ +  il
  gi|320101190|ref|YP_004176782.1| 39 TARRLGIDAS--ELREAIIVAEVFHDIGKIFFHS-NLNVDEKcdnaPNSYRGHEVLSSFIL 96
                                      5899999999..9999***************996.44443334556677777888887766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCT.SCHHHHHHHHHHHHHH CS
                                HD  66 ilrevekrlgldledvaklirehheswegkkrprglaerq.lslearivklaDrlaa 121
                                       ++r++++r+   ++ v  +++ h+es+e      +l++ +  ++ + +++ aD+++a
  gi|320101190|ref|YP_004176782.1| 202 LVRRYLERF---VSHVDSVYNLHNESKE------YLYASAiATRVSAVLMMADNFSA 249
                                       567777777...6678888888888888......44444404555677777887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2107.48
//
Query:       gi|320101191|ref|YP_004176783.1|  [L=223]
Description: CRISPR locus-like DNA-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-06   26.5   0.3    1.2e-05   25.1   0.3    1.7  1  TrmB             Sugar-specific transcriptional regulator Trm
      1e-05   25.9   0.2    4.1e-05   24.0   0.0    2.1  3  HTH_27           Winged helix DNA-binding domain
    1.3e-05   24.6   0.2      3e-05   23.5   0.2    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.4e-05   24.0   1.9    4.8e-05   23.1   0.0    2.5  3  HTH_IclR         IclR helix-turn-helix domain
    0.00019   21.3   0.0    0.00041   20.2   0.0    1.6  1  MarR             MarR family
    0.00028   19.8   0.0    0.00038   19.4   0.0    1.1  1  Cas_Cas02710     CRISPR-associated protein (Cas_Cas02710)
    0.00084   19.2   0.1     0.0015   18.4   0.1    1.4  1  MarR_2           MarR family
     0.0017   18.0   0.1     0.0099   15.5   0.0    2.1  2  SMC_ScpB         Segregation and condensation complex subunit
     0.0017   18.6   0.2     0.0082   16.3   0.1    2.1  2  PaaX             PaaX-like protein
      0.002   18.1   0.1     0.0065   16.5   0.1    1.9  2  HTH_20           Helix-turn-helix domain
     0.0037   16.9   0.1     0.0046   16.6   0.1    1.3  1  Cas_DxTHG        CRISPR-associated (Cas) DxTHG family
     0.0056   16.5   0.0      0.078   12.8   0.0    2.5  3  DUF1495          Winged helix DNA-binding domain (DUF1495)
     0.0091   15.8   0.0      0.025   14.4   0.0    1.7  1  RuvB_C           RuvB C-terminal winged helix domain
     0.0098   15.8   0.1      0.048   13.6   0.0    2.1  2  PadR             Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.023   15.1   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
      0.029   14.1   0.1       0.24   11.0   0.0    2.1  2  Cas_NE0113       CRISPR-associated protein NE0113 (Cas_NE0113
      0.033   12.9   0.0      0.039   12.6   0.0    1.1  1  DUF1887          Domain of unknown function (DUF1887)
       0.05   14.0   0.0       0.12   12.7   0.0    1.6  1  Rrf2             Transcriptional regulator
       0.08   12.7   0.0       0.87    9.3   0.0    2.5  3  DUF4364          Domain of unknown function (DUF4364)
       0.12   12.5   0.0       0.17   11.9   0.0    1.3  1  Replic_Relax     Replication-relaxation


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.3   1.3e-08   1.2e-05       6      66 ..     148     209 ..     147     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.3e-08
                                       HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                              TrmB   6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravd 66 
                                       Lse   k+  ++  +g+ + +e+++  + p+++vY+++r+L++ Gl++  k gr  +Yr ++
  gi|320101191|ref|YP_004176783.1| 148 LSELSRKALRVIADRGEISLTELSQSMDKPKPSVYRAVRELLKLGLINEYKrGRASVYRLTP 209
                                       566666788888999********************************999835566998765 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       8.2   7.3e+03      37      46 ..      44      53 ..      36      61 .. 0.74
   2 ?   -2.2   0.0       6.7     6e+03      16      33 ..     128     145 ..     126     154 .. 0.73
   3 !   24.0   0.0   4.6e-08   4.1e-05       8      68 .]     155     211 ..     148     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.2
                            HTH_27 37 yslkkLtekG 46
                                      ++lk+L+e +
  gi|320101191|ref|YP_004176783.1| 44 KVLKALEEID 53
                                      7889988864 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                            HTH_27  16 rrrkkladlcgrlnveds 33 
                                       +++k+ ad++++ ++   
  gi|320101191|ref|YP_004176783.1| 128 EDGKTRADISFVSYIPLR 145
                                       578888999998776655 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 4.6e-08
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                        L++i+  r++ +l++l++ ++  + ++  ++++L + GL+  +++ + +r++ +rlT+kG
  gi|320101191|ref|YP_004176783.1| 155 ALRVIA-DRGEISLTELSQSMDKPKPSVYRAVRELLKLGLI--NEY-KRGRASVYRLTPKG 211
                                       699999.8888888***************************..444.558**********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 !   23.5   0.2   3.3e-08     3e-05       2      47 ..     149     194 ..     148     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.3e-08
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +e+ rk L+++ + + is +eL++  + +++ v r +++L + GlI
  gi|320101191|ref|YP_004176783.1| 149 SELSRKALRVIADRGEISLTELSQSMDKPKPSVYRAVRELLKLGLI 194
                                       68899****************************************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 ?   -2.2   0.1       4.3   3.8e+03       3      13 ..     101     111 ..     101     112 .. 0.87
   2 !   23.1   0.0   5.3e-08   4.8e-05       9      48 ..     156     194 ..     152     196 .. 0.88
   3 ?   -2.1   0.0       3.9   3.5e+03      32      38 ..     201     207 ..     200     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.3
                                       HHHHHHHCT-C CS
                          HTH_IclR   3 dRalaiLdala 13 
                                       +R + iL ++a
  gi|320101191|ref|YP_004176783.1| 101 MRIMGILTLFA 111
                                       79999**9998 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 5.3e-08
                                       HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR   9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                       L+ +a +++  +l+el++  + pk++v+R ++ L +lG++
  gi|320101191|ref|YP_004176783.1| 156 LRVIADRGE-ISLTELSQSMDKPKPSVYRAVRELLKLGLI 194
                                       566666666.8***************************97 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.9
                                       HHHHHHH CS
                          HTH_IclR  32 kStvhRl 38 
                                       +++v+Rl
  gi|320101191|ref|YP_004176783.1| 201 RASVYRL 207
                                       89****9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.6e-07   0.00041       7      50 ..     154     197 ..     148     200 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.6e-07
                                       HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       ++Lr ++++g++s++eL   +   k++v r++++L k Gli+ +
  gi|320101191|ref|YP_004176783.1| 154 KALRVIADRGEISLTELSQSMDKPKPSVYRAVRELLKLGLINEY 197
                                       689**************************************866 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.2e-07   0.00038      14      93 ..      33     115 ..      26     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.2e-07
                                       EEEEEE-TGGGGGH...HHHHHHH-S-...EEEE.E--TT-HHHHHHHHHHHHHHS.TTS-EEEE-SSS-HHHHHHH CS
                      Cas_Cas02710  14 rVvflasekSekkl...eevkealgkklkqevll.dedandllelykkikevlekaleeeevivDlTgGtkeMtagl 86 
                                       ++++  s+kSek+l   ee+ +++ + l+ ev++ ++d +++ +++ ++ +  +   ++ evi+D++gG + M +  
  gi|320101191|ref|YP_004176783.1|  33 FISIVNSDKSEKVLkalEEIDKFVRDYLEAEVETwEIDFSNVDKAFLELCKRFSSL-RNGEVIIDVSGGMRIMGILT 108
                                       5788889999987611156669999999998865388*********9999999998.****************9888 PP

                                       HHHHHHH CS
                      Cas_Cas02710  87 alagill 93 
                                         a+i++
  gi|320101191|ref|YP_004176783.1| 109 LFAAIVT 115
                                       7777765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.7e-06    0.0015       9      53 ..     154     196 ..     147     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                        +L ++++r++  ++ +el + ++ +k++v r++++L + GL+ +
  gi|320101191|ref|YP_004176783.1| 154 KALRVIADRGE--ISLTELSQSMDKPKPSVYRAVRELLKLGLINE 196
                                       58999*****9..******************************54 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 ?   -0.2   0.0      0.75   6.7e+02      25      59 ..      69     103 ..      29     114 .. 0.73
   2 !   15.5   0.0   1.1e-05    0.0099      79     144 ..     146     210 ..     132     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.75
                          SMC_ScpB  25 lskeeveealeeLkeeyeeedrglelvevaggyrl 59 
                                       ++ ++v++a  eL +++++ ++g  ++ v gg r+
  gi|320101191|ref|YP_004176783.1|  69 IDFSNVDKAFLELCKRFSSLRNGEVIIDVSGGMRI 103
                                       44556777777777777777777777777777665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.1e-05
                          SMC_ScpB  79 trLsqaaletLaiIaykqpvtraeieeiRGvn...sdsvvrtLlerglieekgrkeepgrpilYgtTek 144
                                       + Ls+ + + L +Ia +  ++ +e+++  ++    ++++vr+Ll+ gli+e +     gr+ +Y++T k
  gi|320101191|ref|YP_004176783.1| 146 PALSELSRKALRVIADRGEISLTELSQSMDKPkpsVYRAVRELLKLGLINEYK----RGRASVYRLTPK 210
                                       6788888889999*************99987434599****************....89*******975 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.2   1.9e+03       6      23 ..     106     123 ..     105     124 .. 0.87
   2 !   16.3   0.1   9.1e-06    0.0082      25      70 .]     166     211 ..     157     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.2
                              PaaX   6 ivtlygdyveprggaiwl 23 
                                       i+tl+ + v  ++  i++
  gi|320101191|ref|YP_004176783.1| 106 ILTLFAAIVTLEPKDIRI 123
                                       89***9999999998876 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.1e-06
                              PaaX  25 sLirllaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdkg 70 
                                       sL +l ++++    +v  a+  l k G++ + k gr+s+YrL+ kg
  gi|320101191|ref|YP_004176783.1| 166 SLTELSQSMDKPKPSVYRAVRELLKLGLINEYKRGRASVYRLTPKG 211
                                       688999999*9*******************************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 ?   -2.6   0.0       6.7     6e+03      14      30 ..     122     136 ..     108     137 .. 0.62
   2 !   16.5   0.1   7.2e-06    0.0065      16      61 .]     156     201 ..     147     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.7
                                       HHHHHHSTCTTB-HHHH CS
                            HTH_20  14 rilraLaraegltasel 30 
                                       ri+ +   ++g t +++
  gi|320101191|ref|YP_004176783.1| 122 RIYLWT--EDGKTRADI 136
                                       444444..777776655 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.2e-06
                                       HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       lr +a++++ +++el + +d +k ++++ +r+L + gL+   + gr
  gi|320101191|ref|YP_004176783.1| 156 LRVIADRGEISLTELSQSMDKPKPSVYRAVRELLKLGLINEYKRGR 201
                                       6777999********************************9988876 PP

>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.1e-06    0.0046      85     149 ..      34     124 ..       4     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.1e-06
                         Cas_DxTHG  85 veiipgggte....................eelwe........ifekllekleen..deiilDiThGfrylPvlall 131
                                       + i+ + ++e                     e+we         f +l+++  +    e+i+D++ G+r++ +l+l 
  gi|320101191|ref|YP_004176783.1|  34 ISIVNSDKSEkvlkaleeidkfvrdyleaeVETWEidfsnvdkAFLELCKRFSSLrnGEVIIDVSGGMRIMGILTLF 110
                                       55666666666666666666666666666545777888888889999999955544488*************99977 PP

                         Cas_DxTHG 132 alaylrnvknltikgiyY 149
                                       a+ +  + k+++    +Y
  gi|320101191|ref|YP_004176783.1| 111 AAIVTLEPKDIR----IY 124
                                       666666666543....34 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.6   5.9e+03       4      21 ..      35      52 ..      33      74 .. 0.69
   2 ?    0.2   0.0      0.73   6.5e+02      69      88 ..     116     135 ..     109     136 .. 0.81
   3 !   12.8   0.0   8.7e-05     0.078      53      86 ..     182     214 ..     169     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.6
                           DUF1495  4 slnkSkvRkkvllyLysi 21
                                      s+ +S   +kvl  L +i
  gi|320101191|ref|YP_004176783.1| 35 SIVNSDKSEKVLKALEEI 52
                                      666677777777777655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.73
                           DUF1495  69 eeseglklYklteeGieive 88 
                                        e +++++Y  te G++ ++
  gi|320101191|ref|YP_004176783.1| 116 LEPKDIRIYLWTEDGKTRAD 135
                                       567899*********98665 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 8.7e-05
                           DUF1495  53 ynsessLielGLveeeeeseglklYklteeGiei 86 
                                       y + + L++lGL++ e ++    +Y+lt++G  +
  gi|320101191|ref|YP_004176783.1| 182 YRAVRELLKLGLIN-EYKRGRASVYRLTPKGSVM 214
                                       777788*******6.78888899********866 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 !   14.4   0.0   2.8e-05     0.025       4      62 ..     148     202 ..     147     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                                       --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEE CS
                            RuvB_C   4 LdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRi 62 
                                       L+el +k L++++   + g+++l+ l++ ++ +k  +   +   Llk glI+  +rGR 
  gi|320101191|ref|YP_004176783.1| 148 LSELSRKALRVIA---DRGEISLTELSQSMDKPKPSVYRAV-RELLKLGLINEYKRGRA 202
                                       89999*******9...68********************888.78**************5 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.9   2.6e+03      61      72 ..     122     133 ..     115     135 .. 0.82
   2 !   13.6   0.0   5.4e-05     0.048      19      70 ..     167     212 ..     165     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                                       EEEEESHCCCHH CS
                              PadR  61 kyYrlTdaGrre 72 
                                       ++Y  T++G+++
  gi|320101191|ref|YP_004176783.1| 122 RIYLWTEDGKTR 133
                                       79999****986 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.4e-05
                                       HHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCC CS
                              PadR  19 leelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGr 70 
                                       l+els+  ++  + s+Y+a ++L k gl++++++     ++  +YrlT++G 
  gi|320101191|ref|YP_004176783.1| 167 LTELSQS-MDKPKPSVYRAVRELLKLGLINEYKR-----GRASVYRLTPKGS 212
                                       5677666.7788889*****************77.....4789*******96 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.5e-05     0.023       1      63 [.     148     206 ..     148     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                                       ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
                   Penicillinase_R   1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYs 63 
                                       l+el ++ ++++ ++ge++ +e+ + ++++    + +V   +r L+k gl++++k gra +Y+
  gi|320101191|ref|YP_004176783.1| 148 LSELSRKALRVIADRGEISLTELSQSMDKP----KPSVYRAVRELLKLGLINEYKRGRASVYR 206
                                       577888899999999999999999999988....9999999*********************8 PP

>> Cas_NE0113  CRISPR-associated protein NE0113 (Cas_NE0113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.28   2.5e+02      26      49 ..      39      61 ..      22      77 .. 0.76
   2 ?   11.0   0.0   0.00027      0.24      82     137 ..      78     130 ..      64     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.28
                        Cas_NE0113 26 ttkdgkvrealelLleeflkdyga 49
                                      + k++kv++ale + ++f++dy  
  gi|320101191|ref|YP_004176783.1| 39 SDKSEKVLKALEEI-DKFVRDYLE 61
                                      55789999999999.*******86 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00027
                        Cas_NE0113  82 lqlivrlvrelrenegerlhlsiaGGRKtmsillalaaqLygreqDrlyHvlveee 137
                                       +  ++++  +lr+     + + ++GG ++m+il   aa    +++D   ++++e+ 
  gi|320101191|ref|YP_004176783.1|  78 FLELCKRFSSLRNG---EVIIDVSGGMRIMGILTLFAAIVTLEPKDIRIYLWTEDG 130
                                       44567788888888...599*****************9999999999999999865 PP

>> DUF1887  Domain of unknown function (DUF1887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.4e-05     0.039      45     136 ..      45     136 ..      22     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                           DUF1887  45 lekvlkekgidv.eifeled...evdleeleeslkglleelka..aeevvlNvtgGtklmalgayevfRskhkrIfy 115
                                       + k+l+e +  v + +e e    e+d+++++++ ++l +++    + ev++ v+gG++ m   ++ +f    + I+ 
  gi|320101191|ref|YP_004176783.1|  45 VLKALEEIDKFVrDYLEAEVetwEIDFSNVDKAFLELCKRFSSlrNGEVIIDVSGGMRIMG--ILTLF----AAIVT 115
                                       3344443333333666554311268*************998876799**********9885..56677....77888 PP

                           DUF1887 116 vetasdkleflspeGkediev 136
                                        e++  ++     +Gk ++++
  gi|320101191|ref|YP_004176783.1| 116 LEPKDIRIYLWTEDGKTRADI 136
                                       888888888888888888777 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   0.00013      0.12      16      68 ..     158     208 ..     148     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                       HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE.ETTT-TCEEES CS
                              Rrf2  16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvks.vrGkgGGyrLa 68 
                                       ++a + e   +s++e++++++ +++ + + +++L k gl++  +rG+   yrL+
  gi|320101191|ref|YP_004176783.1| 158 VIADRGE---ISLTELSQSMDKPKPSVYRAVRELLKLGLINEyKRGRASVYRLT 208
                                       4444444...9*****************************75379999888886 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.4   1.3e+03      70     102 ..      30      62 ..      18      74 .. 0.70
   2 ?   -0.8   0.0       1.3   1.1e+03      29      47 ..     137     155 ..     120     173 .. 0.76
   3 ?    9.3   0.0   0.00097      0.87      38      70 ..     183     215 ..     180     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                           DUF4364  70 lelfenripksirekideylkenkeelkkesev 102
                                       ++ f + + ++  ek+ ++l+e  + ++   e 
  gi|320101191|ref|YP_004176783.1|  30 INRFISIVNSDKSEKVLKALEEIDKFVRDYLEA 62 
                                       456777888888888888888877777665554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                           DUF4364  29 eytnYfdlqqalseLvesg 47 
                                        +++Y+ l  alseL  + 
  gi|320101191|ref|YP_004176783.1| 137 SFVSYIPLRPALSELSRKA 155
                                       5788999999999996654 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00097
                           DUF4364  38 qalseLvesglieeeekenktlykiTekGketl 70 
                                        a+ eL++ gli+e ++   ++y++T+kG+ ++
  gi|320101191|ref|YP_004176783.1| 183 RAVRELLKLGLINEYKRGRASVYRLTPKGSVMA 215
                                       5889*************************8765 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.17      17      66 ..     172     212 ..     156     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                      Replic_Relax  17 rllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGa 66 
                                       + + + +  +++r+ ++L +lgl++ +++    +++     vY LtpkG 
  gi|320101191|ref|YP_004176783.1| 172 QSMDKPKP-SVYRAVRELLKLGLINEYKRG---RAS-----VYRLTPKGS 212
                                       44444444.5****************7776...445.....********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 1738.26
//
Query:       gi|320101192|ref|YP_004176784.1|  [L=331]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-08   35.4   0.0    2.8e-08   34.3   0.0    1.6  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
    0.00023   21.4   0.1    0.00037   20.8   0.1    1.3  1  Cas6_N       Cas6 N-terminal domain


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   3.2e-12   2.8e-08       4      86 .]     172     299 ..     160     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.2e-12
                                       EEEE-EE.......TEEESS--HHHHHHHHHHHHHHHTSS.............................EECHHHHH CS
                       CRISPR_Cas6   4 ltPtrfk.......krkgllpsprlvfssllrrwnalaglkgk..........................ptveeele 47 
                                       + P+r++       ++++l  sp+l+++s+l  + ++ g+ g+                          +       
  gi|320101192|ref|YP_004176784.1| 172 TMPLRIRrvlhgtlRHFRLSVSPGLLAASILGEIAEYVGVTGEetwriqyltsryfdalieevylklmaE------- 241
                                       56888889999888888888********************999776666666665555554444444332....... PP

                                       H...............EEEEEEEE...--.HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                       CRISPR_Cas6  48 g...............GfvGevky...sg.eleelekllrfaeylgvGkktafGlGkv 86 
                                       +               G+ G++ y   ++   e++ kll++a ++gvG ++ +G+G++
  gi|320101192|ref|YP_004176784.1| 242 TvtieknsagdykvarGVKGQLAYkpvKEtCGEAFVKLLWLATLIGVGDGREVGFGEI 299
                                       0333344455666666********6541157888888*******************85 PP

>> Cas6_N  Cas6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   4.1e-08   0.00037       2     112 ..      20     139 ..      19     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.1e-08
                                       EEEEEEEESS-EE--SSTTHHHHHHHHTSSGGGHHHHH---TT-SEEE..---BS.TTSB--..S----..--EE-S CS
                            Cas6_N   2 katfevtpkrDvilppltSKvskyillslspslsklvesrekyKplri..svlkd.ngrrly..aegkk..kvrlka 71 
                                        +t+++++k+   lp ++S + k +++  ++ ++ l+e+++++   r+    +k  +g++ly  +++++     +k 
  gi|320101192|ref|YP_004176784.1|  20 RLTYSLKTKETLQLPYFSSYLVKNLIET-MDVYRPLIEAQDSHMQGRVifRAIKTsKGTPLYpvHSRNEgcTPYIKP 95 
                                       6799************************.************998877733689999******8644444114469** PP

                                       SSSEEEEEEEESSSC..CTTTTGSEEE.EEETTEEEEEEEEEEE CS
                            Cas6_N  72 gerlsfslsfaledv..veeivekegv.vktvygefsveLkeik 112
                                       ++++s  + + +e++  + eiv+++++ +kt++ge ++eL  ++
  gi|320101192|ref|YP_004176784.1|  96 NKSYSTEIIVISENLgfMDEIVANPYTsFKTPHGEVEFELLGMH 139
                                       ******99999988532677999987537899999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 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:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2588.49
//
Query:       gi|320101193|ref|YP_004176785.1|  [L=315]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-08   34.5   0.1    5.5e-08   33.4   0.1    1.5  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1     3e-12   5.5e-08       2      84 ..     195     308 ..     195     309 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3e-12
                                       EEEEEE-EE..TEEESS--HHHHHHHHHHHHHHHTSS........................EECHHHHHH....... CS
                       CRISPR_Cas6   2 rfltPtrfk..krkgllpsprlvfssllrrwnalaglkgk.....................ptveeeleg....... 48 
                                       +fltP r    +  g+l s++++++s+lrr + +++++                       +               
  gi|320101193|ref|YP_004176785.1| 195 SFLTPYRVVegGVAGPLTSFESLVKSALRRFSVIMPQYMYvnpvrdvgklleearkvglagA-------Dlhrvpiv 264
                                       59********99**************************888877777655544444443330.......03333333 PP

                                       .......EEEEEEEE--.HHHECCCHHHHHHHH-SSSTGGGTTT CS
                       CRISPR_Cas6  49 .......GfvGevkysg.eleelekllrfaeylgvGkktafGlG 84 
                                                vG+ +++g    ++  ll+f e++++Gk++++G G
  gi|320101193|ref|YP_004176785.1| 265 yrgkredYYVGTYEFKGeIGMDVALLLAFSELFHIGKRASYGHG 308
                                       3444444778888886666668999*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2504.42
//
Query:       gi|320101194|ref|YP_004176786.1|  [L=518]
Description: NADH-ubiquinone/plastoquinone (complex I) oxidoreductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-29  101.4  23.0      5e-29  101.4  23.0    2.1  3  Proton_antipo_M  Proton-conducting membrane transporter
    1.1e-05   24.9   7.6    1.1e-05   24.9   7.6    2.6  3  NADHdeh_related  NADH dehydrogenase I, subunit N related prot


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.7      0.28   2.5e+03     120     149 ..      85     114 ..      75     130 .. 0.57
   2 !  101.4  23.0   5.6e-33     5e-29       3     277 ..     134     418 ..     132     436 .. 0.93
   3 ?   -1.6   0.1      0.13   1.2e+03     145     167 ..     420     442 ..     412     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.28
                   Proton_antipo_M 120 l.Aatlvkagvlllirlllllavssneisql 149
                                       + A++ + ++vl+l+ + +ll+ ssn i  +
  gi|320101194|ref|YP_004176786.1|  85 FsASLGLLVAVLGLL-MYPLLHASSNSIGEY 114
                                       336666677777777.455555455555433 PP

  == domain 2  score: 101.4 bits;  conditional E-value: 5.6e-33
                   Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal....... 72 
                                       d++  ++ lE+  ++++ L +  ++  ++++A+l + ll ++  l+ +++ +lly + g l++ +++          
  gi|320101194|ref|YP_004176786.1| 134 DVFNSFVMLEVLTISMLGLLASPGSI-DAYRATLRYGLLAFVTGLVYFFAAALLYFAVGALNMGYIAAWNifpgvvt 209
                                       7888999**************99666.**************************************9988889***** PP

                   Proton_antipo_M  73 .....elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vss 143
                                                 s +ll++lll++ +l++  a++plh+Wlpday +aP +v  llA++  ++g +ll+rl   +  +  
  gi|320101194|ref|YP_004176786.1| 210 gkalyASIPLSETLLFILLLMTWSLIAEEALAPLHFWLPDAYSAAPPAVAGLLAGVGEAVGYYLLLRLYYTVYsTIP 286
                                       *9988888899999*****************************************************9987774777 PP

                   Proton_antipo_M 144 neisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllag 220
                                       + ++ +l +++++++++g+l+ +    + + + yS i   Gy+ ia+++ +  gv a++ ++++ha++k llF ++g
  gi|320101194|ref|YP_004176786.1| 287 WPVALMLRVVGAATIIVGGLGMVYSKRLLKTVSYSVILDTGYIAIAASL-GPAGVPAVLSYIVAHAVVKPLLFTVSG 362
                                       77899999*****************************************.**************************9 PP

                   Proton_antipo_M 221 sviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaava 277
                                        + ++r  ++++++++g +    i++l ++ ++l++ G+Ppt  F +k+++ +++++
  gi|320101194|ref|YP_004176786.1| 363 WAAHAR-GSDSLEDLKGVFRGSTIMQLGFTTGALAVIGVPPTVLFAAKLSLYTGLLN 418
                                       999988.9****************************************998776665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.13
                   Proton_antipo_M 145 eisqlllilaiismllgslvala 167
                                       + s   lil+++++llgs +ala
  gi|320101194|ref|YP_004176786.1| 420 ITSDPTLILSLAAALLGSGLALA 442
                                       55667899************996 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2      0.52   4.7e+03     144     164 ..      47      67 ..      38      97 .. 0.55
   2 !   24.9   7.6   1.2e-09   1.1e-05      74     169 ..     120     214 ..     104     238 .. 0.85
   3 ?   -2.0   0.9      0.22   1.9e+03     134     179 ..     294     340 ..     288     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.52
                   NADHdeh_related 144 astGtlsifelaklagdvlli 164
                                       a t + si   ++ +g +ll+
  gi|320101194|ref|YP_004176786.1|  47 AFTAASSIVVYMEAQGRILLY 67 
                                       444444444444433333332 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.2e-09
                   NADHdeh_related  74 laivcglatlgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtls 150
                                       l +v+gl  lg+v tgdvfn  ++l ++ i+ +G++a+  +  +  a+ +yGl+a+++ l  f +aal+  + G+l 
  gi|320101194|ref|YP_004176786.1| 120 LGLVAGL--LGVVYTGDVFNSFVMLEVLTISMLGLLASPGSIDAYRATLRYGLLAFVTGLVYFFAAALLYFAVGALN 194
                                       4455554..79****************************************************************99 PP

                   NADHdeh_related 151 ifelaklagd.vlliaklll 169
                                       +  +a+ +    ++  k+l+
  gi|320101194|ref|YP_004176786.1| 195 MGYIAAWNIFpGVVTGKALY 214
                                       97777665443455566655 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.22
                   NADHdeh_related 134 plfggaalilastGtlsifelakl.agdvlliaklllvlGvvGetGv 179
                                        + g+a++i++  G +    l k+ +++v+l +  + ++  +G +Gv
  gi|320101194|ref|YP_004176786.1| 294 RVVGAATIIVGGLGMVYSKRLLKTvSYSVILDTGYIAIAASLGPAGV 340
                                       56799999999999887777666536668888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); 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:                         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 0.27s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3797.35
//
Query:       gi|320101195|ref|YP_004176787.1|  [L=338]
Description: NADH dehydrogenase (ubiquinone) 30 kDa subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   0.0    4.7e-26   91.8   0.0    1.5  2  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    4.7e-09   36.2   0.0    8.4e-09   35.3   0.0    1.4  1  Oxidored_q6     NADH ubiquinone oxidoreductase, 20 Kd subunit
  ------ inclusion threshold ------
      0.021   14.7   0.4       0.15   11.9   0.0    2.2  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.031   13.7   0.1      0.073   12.5   0.1    1.5  1  DDE_Tnp_IS66    Transposase IS66 family


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2     1e+04      39      58 ..     154     173 ..     123     200 .. 0.55
   2 !   91.8   0.0   1.1e-29   4.7e-26       2     120 ..     207     324 ..     206     326 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                                       EEEEEEEE--S-.-EEEEEE CS
                    Complex1_30kDa  39 fevvyhllsleknerirvkv 58 
                                       f+ +  l++lek++r+  + 
  gi|320101195|ref|YP_004176787.1| 154 FKKIAELEELEKQWRLQYEE 173
                                       44455555555555544443 PP

  == domain 2  score: 91.8 bits;  conditional E-value: 1.1e-29
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STH CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsleknerirvkvevdeeepevpSvtdlfpga 77 
                                       +v+p++l+ev+  lk+    g+ +l+++  vD++ ++ +ev+y++++ ++  +  vk++v + +pe++Sv+d++p a
  gi|320101195|ref|YP_004176787.1| 207 TVSPARLREVLVELKN---KGYILLVNIDTVDYPeKGVIEVYYIVENPSDASQTWVKTYVGRAAPEIDSVSDIYPIA 280
                                       689*************...89***********998999********99999*********999************** PP

                                       HHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-.TTSTTS---- CS
                    Complex1_30kDa  78 dwyEREayDmfGivfeghpdlrrillpedfegh.PLRkdfplsg 120
                                       ++ ERE+y+++Givf +hp+l++++l+ ++eg  PLRkd++++g
  gi|320101195|ref|YP_004176787.1| 281 KYIEREVYEFMGIVFRNHPELKKWILEGNWEGPpPLRKDVDTAG 324
                                       ******************************99889*****9876 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 !   35.3   0.0   1.9e-12   8.4e-09      34     130 ..      50     132 ..      21     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.9e-12
                                       -HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E CS
                       Oxidored_q6  34 skeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevvpv 110
                                       +         ++ d+ +  G +t+k+ +   +++++++++++v a  +C ++GG++  ++++++    ++l++ v+v
  gi|320101195|ref|YP_004176787.1|  50 P---------RQSDLYIGMGYLTKKTVKLFLNMYRQMPEPRLVLAGCNCTSTGGLY--WDSYATY---KRLDDFVEV 112
                                       3.........388999999*************************************..7744444...5799***** PP

                                       .EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6 111 dinipGCPphpeailetlla 130
                                       +  +pGC p p++ ++++ +
  gi|320101195|ref|YP_004176787.1| 113 EGWVPGCMPMPDDYTAMIEH 132
                                       **************999987 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.4e-05      0.15      10      27 ..      17      34 ..      16      38 .. 0.86
   2 ?    0.2   0.1      0.16   7.1e+02       7      18 ..      82      93 ..      78      97 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                           DUF35_N 10 vgqrCpdCGtvqfPPrav 27
                                      ++ +C++CG+v fPP   
  gi|320101195|ref|YP_004176787.1| 17 MIHYCSACGAVEFPPLVM 34
                                      788************765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                           DUF35_N  7 grLvgqrCpdCG 18
                                        L g+ C+++G
  gi|320101195|ref|YP_004176787.1| 82 LVLAGCNCTSTG 93
                                      345555566666 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.6e-05     0.073     108     216 ..      71     193 ..      59     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                      DDE_Tnp_IS66 108 yspsRggevaealLag....fkGvlvsDgyagYnklae........eqvthalCw..........aHlrRkfvdaee 162
                                           R++  ++ +Lag     +G l  D ya Y++l++        +     +C+           H+rR++     
  gi|320101195|ref|YP_004176787.1|  71 LNMYRQMPEPRLVLAGcnctSTGGLYWDSYATYKRLDDfvevegwvP-----GCMpmpddytamiEHVRRDIAGRGF 142
                                       555688888999999977666699************98887555551.....44322222222228******98777 PP

                      DDE_Tnp_IS66 163 akkksqaaaealarigklyaiereareaeaeerlalrqeesrpllaeleawlee 216
                                       +k  s++  +a ++i++l ++e+++r    +  +++r+e s+pl  ++++   +
  gi|320101195|ref|YP_004176787.1| 143 EKYVSRIKPDAFKKIAELEELEKQWRL---QYEEKMRAEASKPLNYDFKETYPA 193
                                       65558999999999***********73...4789999999****9999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2428.26
//
Query:       gi|320101196|ref|YP_004176788.1|  [L=368]
Description: membrane bound protein complex subunit MbxL [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-68  229.3   0.0    2.3e-52  177.8   0.0    2.1  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
     0.0032   16.4   0.0     0.0059   15.6   0.0    1.4  1  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.8   0.0   2.5e-56   2.3e-52       2     161 ..     122     281 ..     121     292 .. 0.96
   2 !   49.8   0.0   2.7e-17   2.4e-13     198     271 .]     292     368 .]     286     368 .] 0.88

  Alignments for each domain:
  == domain 1  score: 177.8 bits;  conditional E-value: 2.5e-56
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkk 78 
                                       +G  t+ ++a++ Re+il+ + +++G R+ +++  +GGv++ lp++++e++ ++++ +e++++++e  l  n++fk+
  gi|320101196|ref|YP_004176788.1| 122 VGLRTPAYWAVAAREEILKWFARLSGHRVYHNISVPGGVRYPLPDSFVEDTLRVADFVEERVRDVEAALLGNKVFKD 198
                                       7999************************************************************************* PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       Rtkg g l+++ealelg+tGpvlRa+G++yDlR+a+pY  Y ++ fd+p+g++gD+ydR +vr++E+ +Sl+Ii+  
  gi|320101196|ref|YP_004176788.1| 199 RTKGLGKLTAREALELGATGPVLRATGLPYDLRRANPYLNYGKVGFDIPTGSAGDSYDRSMVRFREIYESLRIIRES 275
                                       ***************************************************************************** PP

                                       HHT--. CS
                    Complex1_49kDa 156 leklpe 161
                                       +++++ 
  gi|320101196|ref|YP_004176788.1| 276 VKRIDP 281
                                       ***954 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 2.7e-17
                                       ---SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHT...TTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 198 kvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleell...kgellaDvvailgsldivlgevDR 271
                                       ++p+ge +a+vE+++Ge+++++vs g++kpyr+++r+ s   l ++ e +   ++ ++aD++++l+s+d++++++DR
  gi|320101196|ref|YP_004176788.1| 292 TAPPGEGVARVETARGEYMIHIVSTGGRKPYRVRLRSMSMPLLTTVIEYIvsrEEVTIADFPVLLASMDPCTPDLDR 368
                                       6899************************************99887655442335679*******************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   6.6e-07    0.0059       1      69 [.      46     114 ..      46     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.6e-07
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivh 69 
                                       RG+E+++++r+ +   +l  R+C   +    +a  +a+e+  +++ip+na+++r + a    + +h+ +
  gi|320101196|ref|YP_004176788.1|  46 RGFEKMMENRTWEMNVVLSYRFCVEDPDPLEIAYSMALEKIHRVDIPENAKYLRMIQAEFSRIASHLFW 114
                                       9*******************************************************9999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.40
# Mc/sec: 2767.84
//
Query:       gi|320101197|ref|YP_004176789.1|  [L=156]
Description: NuoI NADH dehydrogenase I subunit I [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-17   60.3   7.6    9.9e-10   37.8   0.7    2.2  2  Fer4      4Fe-4S binding domain
    9.4e-14   51.7  21.8    5.1e-11   43.0  10.0    1.6  2  Fer4_7    4Fe-4S dicluster domain
    1.1e-13   51.0  16.7    1.1e-09   38.3  10.3    1.8  2  Fer4_10   4Fe-4S dicluster domain
    4.8e-10   40.2   3.8     0.0004   21.3   0.9    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    5.5e-10   39.3   7.6    7.9e-10   38.8   7.6    1.2  1  Fer4_9    4Fe-4S dicluster domain
      8e-10   38.7  21.9    2.7e-07   30.6  10.3    2.0  2  Fer4_21   4Fe-4S dicluster domain
    2.5e-09   36.8   9.9    2.7e-05   24.0   0.8    2.2  2  Fer4_6    4Fe-4S binding domain
    1.8e-08   34.0  10.4    6.9e-05   22.7   2.0    2.3  2  Fer4_2    4Fe-4S binding domain
    8.5e-06   26.4  17.5     0.0011   19.7   3.3    2.2  2  Fer4_3    4Fe-4S binding domain
      1e-05   26.1   5.0      0.021   15.5   0.1    2.3  2  Fer4_15   4Fe-4S single cluster domain
    1.9e-05   25.0  12.9     0.0008   19.8  13.6    2.1  3  Fer4_8    4Fe-4S dicluster domain
    1.9e-05   25.1  11.5    0.00038   20.9  11.7    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00014   22.1   9.5      0.024   15.1   0.9    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00023   21.6   6.9      0.072   13.6   0.1    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00045   21.0   3.3      0.095   13.6   0.3    2.2  2  Fer4_22   4Fe-4S dicluster domain
    0.00076   19.7   4.3       0.17   12.1   0.7    2.2  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 !   26.4   1.2   3.6e-09   4.1e-06       2      23 ..      39      60 ..      38      61 .. 0.91
   2 !   37.8   0.7   8.8e-13   9.9e-10       2      23 ..      79     100 ..      78     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.6e-09
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      v d+ kC+gC  C +vCP + I
  gi|320101197|ref|YP_004176789.1| 39 VLDMAKCTGCSMCQQVCPANSI 60
                                      6799***************988 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 8.8e-13
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        id +kC++CG+Cve CP++A+
  gi|320101197|ref|YP_004176789.1|  79 RIDLNKCTFCGLCVEYCPFNAL 100
                                       79*******************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   3.8   3.1e-07   0.00035      31      51 ..      38      58 ..      17      59 .. 0.75
   2 !   43.0  10.0   4.5e-14   5.1e-11       1      52 []      44      99 ..      44      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.1e-07
                            Fer4_7 31 veidpekClgCgaCvavCPtg 51
                                       ++d+ kC+gC +C++vCP++
  gi|320101197|ref|YP_004176789.1| 38 HVLDMAKCTGCSMCQQVCPAN 58
                                      4789***************86 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 4.5e-14
                            Fer4_7  1 rCigCgaCvaaCpvkaield....eeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+gC  C+++Cp++ i++     e+ ++++++ ++id +kC++Cg Cv+ CP++a
  gi|320101197|ref|YP_004176789.1| 44 KCTGCSMCQQVCPANSIDMVvvegEYPQNPRKRFPRIDLNKCTFCGLCVEYCPFNA 99
                                      7*****************99666545555677889*******************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 !   38.3  10.3   9.7e-13   1.1e-09       3      56 .]      39      96 ..      38      96 .. 0.89
   2 !   23.2   0.4   4.9e-08   5.5e-05       3      35 ..      79     115 ..      77     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 9.7e-13
                           Fer4_10  3 vidddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+d  +C++C  C+++CPa+        g ++++ ++   r+++ kCt+cg Cve CP
  gi|320101197|ref|YP_004176789.1| 39 VLDMAKCTGCSMCQQVCPANSidmvVVEGEYPQNPRKRFPRIDLNKCTFCGLCVEYCP 96
                                      67999**************88977777777788888888999***************9 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.9e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadl....tsvgakgeasee 35 
                                       +id ++C+ Cg Cv+ CP+++    t+ g++ +++++
  gi|320101197|ref|YP_004176789.1|  79 RIDLNKCTFCGLCVEYCPFNAlsmtTATGYELFTTDK 115
                                       799****************887776555555555555 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.9   3.5e-07    0.0004      51      67 .]      42      58 ..      26      61 .. 0.88
   2 !   20.0   0.1   8.9e-07     0.001       1      24 [.      84     107 ..      70     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.5e-07
                           Fer4_16 51 qeaitgCdiCqdvCPan 67
                                        ++tgC +Cq+vCPan
  gi|320101197|ref|YP_004176789.1| 42 MAKCTGCSMCQQVCPAN 58
                                      4689***********98 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 8.9e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkeke 24 
                                       +C+ Cg C+e CP na+++++++ 
  gi|320101197|ref|YP_004176789.1|  84 KCTFCGLCVEYCPFNALSMTTATG 107
                                       488888888888888888875554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   7.6   7.1e-13   7.9e-10       1      50 [.      44      99 ..      44     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.1e-13
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase......eaCigCgaCveaCpkga 50
                                      kCtgC  C+++Cpa+ + +  +e++  ++ ++       ++C++Cg Cve Cp +a
  gi|320101197|ref|YP_004176789.1| 44 KCTGCSMCQQVCPANSIDMVVVEGEYPQNPRKRfpridlNKCTFCGLCVEYCPFNA 99
                                      7******************999999999888889*******************876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   3.7   3.6e-07   0.00041      37      59 .]      41      62 ..      31      62 .. 0.83
   2 !   30.6  10.3   2.4e-10   2.7e-07       3      59 .]      40     102 ..      38     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.6e-07
                           Fer4_21 37 vedeCvGCnlCssvCPvedciem 59
                                         +C+GC +C +vCP  + i+m
  gi|320101197|ref|YP_004176789.1| 41 DMAKCTGCSMCQQVCPA-NSIDM 62
                                      4689************5.99987 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.4e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqai......eidaktvlkvv.edeCvGCnlCssvCPvedciem 59 
                                       +d +kC gC  C ++C+ +s++ +        +++++++ +  ++C+ C lC++ CP  ++++m
  gi|320101197|ref|YP_004176789.1|  40 LDMAKCTGCSMCQQVCPANSIDMVvvegeyPQNPRKRFPRIdLNKCTFCGLCVEYCPF-NALSM 102
                                       6899********************44443312233455554279*************7.88776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.7   3.7e-06    0.0041       5      24 .]      41      60 ..      40      60 .. 0.91
   2 !   24.0   0.8   2.4e-08   2.7e-05       1      24 []      77     100 ..      77     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d  kC+gC  C  vCP++ i
  gi|320101197|ref|YP_004176789.1| 41 DMAKCTGCSMCQQVCPANSI 60
                                      778*************9865 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.4e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +++id +kC+ Cg Cv  CP++a+
  gi|320101197|ref|YP_004176789.1|  77 FPRIDLNKCTFCGLCVEYCPFNAL 100
                                       689*******************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 !   22.7   2.0   6.2e-08   6.9e-05       5      22 .]      40      57 ..      37      57 .. 0.92
   2 !   16.1   1.5     8e-06     0.009       3      21 ..      78      96 ..      76      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.2e-08
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                       d ++C+gC+ C+++CPa
  gi|320101197|ref|YP_004176789.1| 40 LDMAKCTGCSMCQQVCPA 57
                                      7899*************8 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      + +d ++C+ Cg Cv  CP
  gi|320101197|ref|YP_004176789.1| 78 PRIDLNKCTFCGLCVEYCP 96
                                      6799*************** PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   6.4    0.0002      0.23       1      13 [.      45      57 ..      45      59 .. 0.91
   2 !   19.7   3.3     1e-06    0.0011       1      15 []      85      99 ..      85      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      CtgC+ C +vCP 
  gi|320101197|ref|YP_004176789.1| 45 CTGCSMCQQVCPA 57
                                      ************6 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct Cg+Cve CP +A
  gi|320101197|ref|YP_004176789.1| 85 CTFCGLCVEYCPFNA 99
                                      ************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 !   12.2   1.3   0.00022      0.24       2      20 ..      39      57 ..      39      65 .. 0.92
   2 !   15.5   0.1   1.9e-05     0.021       3      19 ..      80      96 ..      79     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      v+D  +C+gc +C +++p 
  gi|320101197|ref|YP_004176789.1| 39 VLDMAKCTGCSMCQQVCPA 57
                                      589**************95 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.9e-05
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      +D ++C+ cglCv+ +p
  gi|320101197|ref|YP_004176789.1| 80 IDLNKCTFCGLCVEYCP 96
                                      9***************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   5.2   5.7e-05     0.064      48      64 ..      42      58 ..      24      60 .. 0.84
   2 !   19.8  13.6   7.1e-07    0.0008       2      64 ..      42      98 ..      41      99 .. 0.71
   3 !   14.5   1.5   3.3e-05     0.037       2      63 ..      82      97 ..      81     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                      + +Ct+c +C++vCp +
  gi|320101197|ref|YP_004176789.1| 42 MAKCTGCSMCQQVCPAN 58
                                      67899999999999875 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 7.1e-07
                            Fer4_8  2 lekCieCgaCqsaCp.....vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      + kC++C++Cq+ Cp     ++  +++ ++++r++                l++Ct cg C+e Cp +
  gi|320101197|ref|YP_004176789.1| 42 MAKCTGCSMCQQVCPansidMVVVEGEYPQNPRKRFPR-----------IDLNKCTFCGLCVEYCPFN 98
                                      789************44444444444555555555333...........2489*************76 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.3e-05
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      l+kC+ Cg+C + Cp                                               
  gi|320101197|ref|YP_004176789.1| 82 LNKCTFCGLCVEYCP----------------------------------------------F 97
                                      456666666666665..............................................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 !   13.9   3.4   5.5e-05     0.062      43      59 ..      42      58 ..      26      61 .. 0.80
   2 !   20.9  11.7   3.4e-07   0.00038       1      59 [.      44      98 ..      44     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
                           Fer4_17 43 aslCieCgeCerkCPqg 59
                                      + +C++C +C+++CP++
  gi|320101197|ref|YP_004176789.1| 42 MAKCTGCSMCQQVCPAN 58
                                      67788888888888865 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.4e-07
                           Fer4_17  1 rCiqCgyClpeCpsyea.....ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      +C++C++C ++Cp + +      +++p+++++++              ++C+ Cg+C+++CP +
  gi|320101197|ref|YP_004176789.1| 44 KCTGCSMCQQVCPANSIdmvvvEGEYPQNPRKRFPR---------IDLNKCTFCGLCVEYCPFN 98
                                      6************97776666678889999998544.........36799************65 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   2.1   0.00034      0.38       3      16 ..      44      57 ..      42      64 .. 0.91
   2 !   15.1   0.9   2.2e-05     0.024       2      17 .]      83      98 ..      82     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +C+gC  C  +CP 
  gi|320101197|ref|YP_004176789.1| 44 KCTGCSMCQQVCPA 57
                                      8************6 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.2e-05
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C+ Cg Cv +CP++
  gi|320101197|ref|YP_004176789.1| 83 NKCTFCGLCVEYCPFN 98
                                      89************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 !    9.8   2.9     0.001       1.1       2      18 ..      41      57 ..      40      58 .. 0.91
   2 !   13.6   0.1   6.4e-05     0.072       1      17 [.      80      96 ..      80     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D  +C++c  C +++P 
  gi|320101197|ref|YP_004176789.1| 41 DMAKCTGCSMCQQVCPA 57
                                      7789************6 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.4e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      +D ++C+ cg+Cve +P
  gi|320101197|ref|YP_004176789.1| 80 IDLNKCTFCGLCVEYCP 96
                                      799*************9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.3   8.5e-05     0.095      77      95 ..      40      58 ..      13      59 .. 0.80
   2 !    8.3   0.2    0.0038       4.2      76      94 ..      79      97 ..      68      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.5e-05
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                       ++ +C+GC  C+++cp++
  gi|320101197|ref|YP_004176789.1| 40 LDMAKCTGCSMCQQVCPAN 58
                                      57889**********9975 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0038
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                      +++ ++C+ Cg C+e cp 
  gi|320101197|ref|YP_004176789.1| 79 RIDLNKCTFCGLCVEYCPF 97
                                      56889999*******9986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.7   0.00015      0.17      57      76 ..      41      61 ..      21      67 .. 0.85
   2 !    9.1   0.2    0.0013       1.5      58      73 ..      82      97 ..      70     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                           Fer4_18 57 gagdcidcescvkvcPtg.id 76
                                      ++++c+ c++c +vcP + id
  gi|320101197|ref|YP_004176789.1| 41 DMAKCTGCSMCQQVCPANsID 61
                                      5789************74255 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                           Fer4_18 58 agdcidcescvkvcPt 73
                                       ++c+ c+ cv+ cP 
  gi|320101197|ref|YP_004176789.1| 82 LNKCTFCGLCVEYCPF 97
                                      578************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1296.75
//
Query:       gi|320101198|ref|YP_004176790.1|  [L=97]
Description: multiple resistance and pH regulation protein F [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-08   33.1   8.8    5.5e-08   33.1   8.8    1.9  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M
  ------ inclusion threshold ------
        0.2   11.4   9.4       0.37   10.6   9.4    1.4  1  MASE5      Membrane-associated sensor


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.066   5.9e+02      10      24 ..      14      28 ..      10      35 .. 0.74
   2 !   33.1   8.8   6.1e-12   5.5e-08       1      52 [.      36      87 ..      36      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.066
                         MrpF_PhaF 10 lgtllvallallail 24
                                      ++ l +a+++l++++
  gi|320101198|ref|YP_004176790.1| 14 ITGLFTAAMILYSLR 28
                                      666778888888876 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 6.1e-12
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                      +D v+A+D+l++ lv+ll+l+a+++++p +l  ++ lA +  +  v++ar++
  gi|320101198|ref|YP_004176790.1| 36 PDAVLAVDALSVDLVVLLVLIALYYKSPMLLIGVVPLAAWILLLDVIIARYM 87
                                      799************************************************6 PP

>> MASE5  Membrane-associated sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   9.4   4.1e-05      0.37      99     142 ..      39      83 ..      10      91 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.1e-05
                             MASE5  99 lplvepLl.diLlltaliALYpevrlllafvlPllltslvarvll 142
                                       +  v+ L+ d+ +l +liALY++ ++ll+ v+Pl    l+  v++
  gi|320101198|ref|YP_004176790.1|  39 VLAVDALSvDLVVLLVLIALYYKSPMLLIGVVPLAAWILLLDVII 83 
                                       44455554156678899****************987777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 836.74
//
Query:       gi|320101199|ref|YP_004176791.1|  [L=122]
Description: MnhG/PhaG subunit monovalent cation/proton antiporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-16   60.6   7.5    1.6e-16   60.3   7.5    1.1  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   7.5   8.7e-21   1.6e-16       2      79 .]      14     100 ..      13     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 8.7e-21
                    PhaG_MnhG_YufB   2 lllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaa........slkllliilfllltaPv 69 
                                        + G+++ ++++ig +rl+d+y+Rlhaat+++  G +  l+Gl+l + sl          s+  l+++++++l +P 
  gi|320101199|ref|YP_004176791.1|  14 TITGGVLDIIASIGFFRLKDFYMRLHAATIGSIGGGFYPLIGLALIVlSLDVdiyfkayfSGVCLIAAALIALGTPA 90 
                                       689******************************************88777769************************ PP

                    PhaG_MnhG_YufB  70 aahliaraay 79 
                                       ++h++araay
  gi|320101199|ref|YP_004176791.1|  91 GSHILARAAY 100
                                       *********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1041.82
//
Query:       gi|320101200|ref|YP_004176792.1|  [L=79]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-12   45.3   4.2      7e-12   45.3   4.2    1.3  1  DUF4040   Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
       0.48    9.4   1.0       0.47    9.4   1.0    1.0  1  Pex24p    Integral peroxisomal membrane peroxin


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   4.2   7.8e-16     7e-12       2      64 ..      11      73 ..      10      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 7.8e-16
                           DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrr 64
                                      l++la++a+ + rd+ +a++++g+ + ++a+l  +l APD+ ++++a++ g+  +ll+++l++
  gi|320101200|ref|YP_004176792.1| 11 LALLATIAVFRERDVAKAIVYSGIESAFYAILLSYLLAPDLLIAYIAIGLGVNSLLLIYVLSK 73
                                      7899*********************************************************98 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.0   5.3e-05      0.47     128     183 ..       3      58 ..       1      72 [. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 5.3e-05
                            Pex24p 128 llnpidalekflkelagfkdenlstllfltllltpililllsrlipwrlillvlga 183
                                       l+  i+a+ ++l+++a f ++++ + ++++ + ++++ +lls+l+ + l++  +++
  gi|320101200|ref|YP_004176792.1|   3 LIAAISATLALLATIAVFRERDVAKAIVYSGIESAFYAILLSYLLAPDLLIAYIAI 58 
                                       66778899999************************************988876663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); 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:                         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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 686.26
//
Query:       gi|320101201|ref|YP_004176793.1|  [L=270]
Description: Na+/H+ antiporter MnhB subunit-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-17   61.5  12.2    9.5e-17   61.5  12.2    2.2  2  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter
      0.001   18.6   0.2      0.001   18.6   0.2    1.9  3  DUF2106   Predicted membrane protein (DUF2106)


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.1      0.18   1.6e+03      87      87 ..      34      34 ..       3      96 .. 0.53
   2 !   61.5  12.2   1.1e-20   9.5e-17       1     123 [.     114     254 ..     114     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                              MnhB 87 f 87
                                      f
  gi|320101201|ref|YP_004176793.1| 34 F 34
                                      1 PP

  == domain 2  score: 61.5 bits;  conditional E-value: 1.1e-20
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafglee..lekllrvklaprileglgllla 75 
                                       i+rtv++ +v ++ +vs++++l+Gh++PGGGFqgG i+ +a +l++la g++   +  ++++kl    + +l+++l+
  gi|320101201|ref|YP_004176793.1| 114 IVRTVVKPVVLIVAVVSVSVALHGHLTPGGGFQGGSIFVIAPLLVLLALGISPlyKAGFTPRKLL--GVRALAVTLI 188
                                       79***************************************************877777788855..9********* PP

                              MnhB  76 vltgllglll.....g...fltslflelel.........llgeve.lgtallfdlgVylvVvggll 123
                                       +++g+++l++     g   ++++l+ +++           +g  +  gt++ ++++ +l+V +g++
  gi|320101201|ref|YP_004176793.1| 189 FVLGVIPLAYsivsgGkayLFQNLAKPYSQfsfpalvetPMGPLLlSGTLFWLNFFEFLAVSSGFT 254
                                       **********6666426754444433332257777544322233369**************98875 PP

>> DUF2106  Predicted membrane protein (DUF2106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.2e-07     0.001      91     145 ..      38      91 ..      14      97 .. 0.86
   2 ?   -4.2   0.3       1.2   1.1e+04     130     142 ..     117     129 ..     113     136 .. 0.55
   3 ?   -3.5   0.1      0.75   6.7e+03      15      37 ..     177     198 ..     172     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-07
                           DUF2106  91 yltPlsellaettlylGttivssPGGiideilyytrGldtvlessillvafvias 145
                                        lt l+++  ++  y G    s    ++  +++  rG+dt +e+s+l++a +  s
  gi|320101201|ref|YP_004176793.1|  38 ELTGLAQIYLAHVAYPGSPWTSMSTEVVTSVIWDQRGFDTYFETSVLFLAIAA-S 91 
                                       58899999999999***********************************9753.4 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 1.2
                           DUF2106 130 tvlessillvafv 142
                                       tv+   +l+va v
  gi|320101201|ref|YP_004176793.1| 117 TVVKPVVLIVAVV 129
                                       5555555555544 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.75
                           DUF2106  15 lprlyalllavvlivgllvplsl 37 
                                       l  + al +++++++g+ +pl++
  gi|320101201|ref|YP_004176793.1| 177 LLGVRALAVTLIFVLGV-IPLAY 198
                                       55566777777777775.45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2217.12
//
Query:       gi|320101202|ref|YP_004176794.1|  [L=137]
Description: NADH-ubiquinone oxidoreductase subunit 4L [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.7e-19   67.5   2.2    8.3e-19   67.2   2.2    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   2.2   4.6e-23   8.3e-19       2     103 ..      11     131 ..       8     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 4.6e-23
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............................. CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi...................tnpat 59 
                                       +++++++ ++ +lygv +r +++k+l+ + ++s av++llv +g++ +  +++                     + +
  gi|320101202|ref|YP_004176794.1|  11 IMVTVVFTIAYSLYGVATRPHIVKKLVFITILSDAVYVLLVFMGYRLTASTPPvypggtllnpqlpwnpsevVSFIA 87 
                                       456777777889**********************************99888889****************999999* PP

                                       ..TTSCGGHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  60 efadplpqalvLtaivigaaetavgLallvrlyreygtddvqel 103
                                       +++dp+pq+l+ taivig+a ++++ a+++r+ + +gt +v+ l
  gi|320101202|ref|YP_004176794.1|  88 RSVDPVPQVLIVTAIVIGLAQLIFLSAIALRIVKATGTFNVNRL 131
                                       *****************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1058.19
//
Query:       gi|320101203|ref|YP_004176795.1|  [L=166]
Description: cation antiporter [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-35  119.5   0.9    1.1e-34  119.2   0.9    1.0  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.9   6.4e-39   1.1e-34       2     146 .]      11     164 ..      10     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 6.4e-39
                              MNHE   2 lllflvWllltgs..lgelllGlllallvalllrrll.......lplrrvllrllayllvflweivkanldVakrvl 69 
                                       ll+++++l+ tg   + e ++++  ++lva++++ l        l +rr+ll+l +++ +f +  +ka++ V+k++l
  gi|320101203|ref|YP_004176795.1|  11 LLSAVTYLVYTGVfdILEAMIAVTAGTLVAYVFK-LElvsdagkLTPRRMLLGLYYLFKYFTVIEAKAHWGVVKVIL 86 
                                       7899*****************************4.335889988888999999999999**9888************ PP

                              MNHE  70 rpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvede.eeeareeikgrlErrlle 145
                                       +p++ ++p+iv+vp r++sd+++t++ansit tPGT++vd+d++r+v+yvH+l  +d  +e a +e++ ++E++l+e
  gi|320101203|ref|YP_004176795.1|  87 SPSPLPTPAIVRVPFRVSSDYGVTFVANSITNTPGTIVVDLDQERKVYYVHWLTPTDVsDEGAYREVSAEFEKYLKE 163
                                       *****************************************************885545999*************99 PP

                              MNHE 146 i 146
                                       +
  gi|320101203|ref|YP_004176795.1| 164 V 164
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1314.96
//
Query:       gi|320101204|ref|YP_004176796.1|  [L=112]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 854.00
//
Query:       gi|320101205|ref|YP_004176797.1|  [L=325]
Description: NADH dehydrogenase subunit H [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-59  200.6  18.6    4.1e-59  200.3  18.6    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.3  18.6   2.3e-63   4.1e-59       8     297 ..      18     322 ..      12     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 200.3 bits;  conditional E-value: 2.3e-63
                                       HHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTT CS
                            NADHdh   8 vvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafa 84 
                                       ++++++++l+++l Rkv+Ariq R GP ++G  G+lqplaD+lKl++K+d+++k +     +++p++++ la+ a++
  gi|320101205|ref|YP_004176797.1|  18 FFMIVLIILTQWLARKVTARIQFRRGPVYAGVAGVLQPLADLLKLVVKKDLVNKYS----LKASPLIVISLAIGALV 90 
                                       35666677*******************************************98666....8899999999******* PP

                                       TS-SSS....SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS CS
                            NADHdh  85 viPfge....vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagsl 157
                                       viP ++    +  + +++ +++l+l+ l ++g++  + a  ++Y+ +G  R +a ++s E a++l++l++v+la+  
  gi|320101205|ref|YP_004176797.1|  91 VIPSATplaiQPLHAEYDAIVVLYLLLLIPFGLAYLAAAHPNPYTAIGVGRYIALLLSSEPAYALTILVPVILASRH 167
                                       ***88457445555577*******************************************************98887 PP

                                       .....-HHHHHHCCCTT-C.....CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHH CS
                            NADHdh 158 .....slseiveaqeeiwf.....illqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflae 224
                                            sl       +  w       + + la  + ++ l+  +  +PFD+peaesEL+ G++tE +g ++al f+a+
  gi|320101205|ref|YP_004176797.1| 168 ygagySLYYTSLVSHMLWAisplkTVSMALATAAGFLGLMSMLMVKPFDTPEAESELYWGMFTELGGPRLALGFFAK 244
                                       5555533333222233476778887777999999******************************************* PP

                                       HHHHHHHHHHHHHHCT.SS-HCCS......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHH CS
                            NADHdh 225 yanmvlvsalavllFlgGwllpfs......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanl 295
                                       +a+ +++ ++ +llFlgG  +pf         +++l+K+++++ ++++i+a+lpR++ +q++++ wk+l p ++++l
  gi|320101205|ref|YP_004176797.1| 245 FAERIVYPLIYTLLFLGGA-WPFTvgdwlpASIIILAKTIAVFTVLTVIDAALPRYKPEQAVRFLWKYLYPASIISL 320
                                       *****************94.67777899999999*****************************************99 PP

                                       HH CS
                            NADHdh 296 ll 297
                                        l
  gi|320101205|ref|YP_004176797.1| 321 TL 322
                                       87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2526.78
//
Query:       gi|320101206|ref|YP_004176798.1|  [L=344]
Description: deoxyhypusine synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-89  298.3   0.0    5.8e-89  298.2   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.2   0.0   3.2e-93   5.8e-89       1     286 [.      23     321 ..      23     323 .. 0.96

  Alignments for each domain:
  == domain 1  score: 298.2 bits;  conditional E-value: 3.2e-93
                                DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       ell ++++++fq++slgea+++l +m +de+  +flgl++++ ++G+ +ii++l++e++vdv+v+T++ i+eD+++a
  gi|320101206|ref|YP_004176798.1|  23 ELLLEMGDTAFQGRSLGEAYRVLIDMFSDEDNLVFLGLAGSMSTAGMWRIIKWLIEERYVDVVVSTGAIISEDIYEA 99 
                                       68899************************************************************************ PP

                                DS  78 lgkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeinde..eSi 152
                                       +g k+y+ +  ++deeL + +++R+++++ ++e+y+k+e+ ++e++++l +  +  s++e+++e+G+++n++  +Si
  gi|320101206|ref|YP_004176798.1| 100 MGFKYYKTHPCVNDEELLKYKYDRFYDTVASEEDYRKMERLIQEFIESLPAG-RPYSTAEFLHEFGRYLNERgvDSI 175
                                       *************************************************985.567**************7777*** PP

                                DS 153 lywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanl 229
                                       +++Ay++++pvf+pal+D+ +G++++l++  ++ ++++ld+v+D+++l +i  +a k +ai++GGGvpK+++  +++
  gi|320101206|ref|YP_004176798.1| 176 VAAAYRAGVPVFSPALVDSGYGMAAVLAY--RRGHRVVLDMVRDFHQLVEIGRRAGKLSAIYIGGGVPKDYVNLVTV 250
                                       ***********************666666..89999************************************99998 PP

                                DS 230 m..............rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                       +               + ++y+v+ tt+ +++G+lsgatl+EavSwgk++++ak+  vy DaTi+lPL+++
  gi|320101206|ref|YP_004176798.1| 251 AqtligeyeegrhdyYKSLEYVVQFTTDAPQWGGLSGATLEEAVSWGKVSPRAKKKVVYVDATIALPLIAH 321
                                       8899*******9988468***************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2441.29
//
Query:       gi|320101207|ref|YP_004176799.1|  [L=467]
Description: anion transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-71  242.3  38.4    1.4e-71  242.0  38.4    1.0  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    1.2e-32  113.3  43.8    1.2e-32  113.3  43.8    2.2  3  CitMHS         Citrate transporter
  ------ inclusion threshold ------
      0.061   13.7   6.6      0.096   13.1   3.7    2.9  2  BatA           Aerotolerance regulator N-terminal
        4.4    7.9   6.0       0.84   10.2   0.1    2.6  2  GTA_holin_3TM  Holin of 3TMs, for gene-transfer release


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 !  242.0  38.4   3.1e-75   1.4e-71       5     460 ..       8     457 ..       4     464 .. 0.91

  Alignments for each domain:
  == domain 1  score: 242.0 bits;  conditional E-value: 3.1e-75
                     Na_sulph_symp   5 aklllllvvlliilllPapdgleskawrllaifiaaivglileplplavialialsllavligvlaakalsevlsgf 81 
                                       a  +++l v+  +++lP p+gl+sk + +++i i+a+v + +e +p++ + ++++    +l gv +   l +++s  
  gi|320101207|ref|YP_004176799.1|   8 AVAFATLLVMHAVAMLPPPEGLTSKSMAMIGITIMAVVYWATECVPMPLTGVMIMLAQ-ALYGVFP---LAKAVSYI 80 
                                       55689999******************************************99876655.6777777...79999999 PP

                     Na_sulph_symp  82 ssdttlLvfaalliaaavektgLgkRiAlvlvkivGkrt..liLgyalvladlllapatpsntAraggivfpviksl 156
                                        sd+++Lv+a+l+i+ a+ + g++k i   +++i+G++   l+Lg +l +a l++++ +++++A +++i+f v+k +
  gi|320101207|ref|YP_004176799.1|  81 ASDVNILVLAGLVISLALGVHGIDKYIGIKVLSIMGEKSsrLVLGLMLSTAILSMWIPNTAAAALMAPIAFGVLKLV 157
                                       9************************************998999******************************9876 PP

                     Na_sulph_symp 157 ssafgsepekqserkigaylmltvvqsasitsiaflTamApNllllglinsilgveitwasWflaaiptgvillllv 233
                                        +    e       ++g+ +m+ v+++a+i++i +  ++ p ++++  i ++ gv+i +a W++  +p++++l++++
  gi|320101207|ref|YP_004176799.1| 158 NA----ERT---GGNLGKAMMIGVAYAATIGGIGTPVGTPPVPITIRNIREATGVDIGFATWMSWGVPVSLLLVVVA 227
                                       43....333...3359************************************************************* PP

                     Na_sulph_symp 234 plllyvlyppeikkkeeakavaktelkelGpltarekallilfvlllllWifgesln..idattvaivvlvillllr 308
                                       ++ll  +y pe + +    +v+++el+ +G l++ +++ lilf l+ llW+ +  +   ++  t  +  l+i l + 
  gi|320101207|ref|YP_004176799.1| 228 WWLLMLFYRPEHEVIAGSREVVERELRSMGGLNRVQRKTLILFSLVALLWLLDPVFSrwVSGWTYIVSLLAIALFSF 304
                                       ***************************************************99977666665443333344433222 PP

                     Na_sulph_symp 309 ....vldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSa 381
                                           vl+W Di ++k+ W++l+l +g++al  +l  +g+++ ++ +++ + sgl    ++++i +++ l+ + f+S 
  gi|320101207|ref|YP_004176799.1| 305 pvigVLSWSDI-SEKADWGVLFLIAGGLALGAGLRDTGVVDVIARAVAAHTSGLPEYGVLLVISVVSGLSITVFSSI 380
                                       5566*****87.789*************************************8888888888888889********* PP

                     Na_sulph_symp 382 tAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiigllil 458
                                       tAt ++++p+ + va+a+ g++p+++ +  ++a+ +a fllp +t+pn+i+++ gy+k  +++r+G++l + + l+l
  gi|320101207|ref|YP_004176799.1| 381 TATSSTMVPVAIGVAKAT-GVDPVIAGVVAGIASCYA-FLLPANTPPNAIAYSYGYFKNYEMARIGIVLILASSLLL 455
                                       ******************.******************.*******************************99888877 PP

                     Na_sulph_symp 459 ll 460
                                       l 
  gi|320101207|ref|YP_004176799.1| 456 LP 457
                                       65 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   2.6      0.23     1e+03      13     294 ..       8      43 ..       1      49 [. 0.44
   2 !  113.3  43.8   2.7e-36   1.2e-32       2     294 ..      45     404 ..      42     416 .. 0.83
   3 ?   -1.8   0.2      0.32   1.4e+03     124     168 ..     412     456 ..     401     465 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.23
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  13 vvallvlvllvltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllvlltallsafv 89 
                                       +v                                                                           
  gi|320101207|ref|YP_004176799.1|   8 AV--------------------------------------------------------------------------- 9  
                                       44........................................................................... PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  90 sndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnllllalllvgllplvl 166
                                                                                                                    
  gi|320101207|ref|YP_004176799.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 167 lfmfgvalalpvnapkvkkqkaiieaiarsllpvatilllaykkveWsvlllfaGvfllvgaleqtGilealadllg 243
                                                                                                                    
  gi|320101207|ref|YP_004176799.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxx.xxxxxxx RF
                            CitMHS 244 aggplvalalvlgliallsafisnvavaalmapialgmap........algl.lspspla 294
                                                                a+a+l++  a++m+p        ++ + + + ++a
  gi|320101207|ref|YP_004176799.1|  10 -------------------------AFATLLVMHAVAMLPppegltskSM-AmIGITIMA 43 
                                       .........................4555555555555554444433211.123333333 PP

  == domain 2  score: 113.3 bits;  conditional E-value: 2.7e-36
                                       xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            CitMHS   2 vllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd. 73 
                                       v++++e ++++++ ++++++     v+ + +a+s ias++ +l+l++ +i+ al   G+ ++++ k+l+++g+k   
  gi|320101207|ref|YP_004176799.1|  45 VYWATECVPMPLTGVMIMLAQalygVFPLAKAVSYIASDVNILVLAGLVISLALGVHGIDKYIGIKVLSIMGEKSSr 121
                                       78999999999998888777788*999************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                            CitMHS  74 llvllvlltallsafvsndgvvlimipivlslakrlkklppl.......lliplalaaniggaltpiGtpttraa.. 141
                                       l++ l+l ta+ls+++ n++++++m+pi++ + k   +  +        ++i +a+aa igg+ tp+Gtp+++    
  gi|320101207|ref|YP_004176799.1| 122 LVLGLMLSTAILSMWIPNTAAAALMAPIAFGVLKL-VNAERTggnlgkaMMIGVAYAATIGGIGTPVGTPPVPITir 197
                                       *********************************95.45555569999***********************99999** PP

                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 142 ........arpglslpnllllalllvgllplvllfmfgvalalpvnap.........kvkkqkaiieaiarsllpva 201
                                               ++   +++ + +++ ll ++++ +ll++f ++ + +++           +       +++++r+ l   
  gi|320101207|ref|YP_004176799.1| 198 nireatgvDIGFATWMSWGVPVSLLLVVVAWWLLMLFYRPEHEVIAGSrevverelrS----MGGLNRVQRKTLILF 270
                                       *******988888999999988888889999999988899998888886666643330....333444444444444 PP

                                       xxxxxx.......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 202 tillla.......................................ykkveWsvlllfaGvfllvgaleqtGileala 239
                                       ++++l+                                        +k +W+vl+l+aG + l+++l++tG+++ +a
  gi|320101207|ref|YP_004176799.1| 271 SLVALLwlldpvfsrwvsgwtyivsllaialfsfpvigvlswsdiSEKADWGVLFLIAGGLALGAGLRDTGVVDVIA 347
                                       444333455666666666666666666677888888888899*****************************999999 PP

                                       xxxxx...x.xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 240 dllga...g.gplvalalvlglial.lsafisnvavaalmapialgmapalgllspspla 294
                                        ++ a   g + + +l+++ ++++l +++f s +a+  +m+p+a+g+a+a+g   ++p++
  gi|320101207|ref|YP_004176799.1| 348 RAVAAhtsGlPEYGVLLVISVVSGLsITVFSSITATSSTMVPVAIGVAKATG---VDPVI 404
                                       9995567645666777899******************************999...55544 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.32
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxx RF
                            CitMHS 124 aniggaltpiGtpttraaarpglslpnlll.............lalllvgllplvllf 168
                                       a+    l+p  tp            pn ++             ++++l+++   +ll+
  gi|320101207|ref|YP_004176799.1| 412 ASCYAFLLPANTP------------PNAIAysygyfknyemarIGIVLILA-SSLLLL 456
                                       3333446777777............88888888888888888855544433.222222 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.7   2.1e-05     0.096      13      70 ..     221     278 ..     210     279 .. 0.91
   2 ?   -2.7   0.0       1.8   7.9e+03      60      70 ..     292     302 ..     284     309 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                              BatA  13 llllplpiillyllkrrpqevvfsslrlleevekdeealqrlkknllllLrllalall 70 
                                       lll+++ ++ll+l+ r   ev   s + +e+ ++++  l r +++ l+l  l+al+ l
  gi|320101207|ref|YP_004176799.1| 221 LLLVVVAWWLLMLFYRPEHEVIAGSREVVERELRSMGGLNRVQRKTLILFSLVALLWL 278
                                       6778888***********************************************9866 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.8
                              BatA  60 llLrllalall 70 
                                        ++ lla+al 
  gi|320101207|ref|YP_004176799.1| 292 YIVSLLAIALF 302
                                       55555555554 PP

>> GTA_holin_3TM  Holin of 3TMs, for gene-transfer release
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   2.3       1.2   5.4e+03      74     112 ..      37      61 ..       7     100 .. 0.57
   2 ?   10.2   0.1   0.00019      0.84      45      97 ..     238     287 ..     219     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                     GTA_holin_3TM  74 lgyvtlalllwaivldPllaaaialglalvPepLwwllg 112
                                       +g +++a++ wa               + vP+pL  ++ 
  gi|320101207|ref|YP_004176799.1|  37 IGITIMAVVYWAT--------------ECVPMPLTGVMI 61 
                                       3334444444444..............444444433333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                     GTA_holin_3TM  45 eleqleaqleimkaEaasddgfnrrwRPllgyvtlalllwaivldPllaaaia 97 
                                       e e++++ +e+++ E +s  g+nr  R +l++  l++llw   ldP+ ++ + 
  gi|320101207|ref|YP_004176799.1| 238 EHEVIAGSREVVERELRSMGGLNRVQRKTLILFSLVALLWL--LDPV-FSRWV 287
                                       4567999*********************************8..9998.55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3204.74
//
Query:       gi|320101208|ref|YP_004176800.1|  [L=344]
Description: phosphate uptake regulator PhoU [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-25   90.0  15.1    1.2e-18   67.4   8.2    2.3  2  PhoU            PhoU domain
      3e-09   36.6   0.0    5.9e-09   35.7   0.0    1.5  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.024   14.9   0.0      0.067   13.5   0.0    1.7  1  KORA            TrfB plasmid transcriptional repressor


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   8.2     2e-22   1.2e-18       2      89 .]     145     236 ..     144     236 .. 0.90
   2 !   26.9   0.5   8.4e-10     5e-06       7      89 .]     254     330 ..     248     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2e-22
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HGG-SH.HHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak...rqplae.dlrellsllriard 74 
                                       rr++ iv++m++d+ ++l++ d++ a ++i+rdde+dr++++i r+l  al     + +l+  ++ e+ls++ iar+
  gi|320101208|ref|YP_004176800.1| 145 RRLHLIVNNMMEDVKTLLRTMDENVAYAIIQRDDEADRFHHMIVRELSMALLDvrvQHELGItNVVEALSYRIIARN 221
                                       79********************************************887775455444444499999********** PP

                                       HHHHHHHHHHHHHHH CS
                              PhoU  75 lERigDhavniaerv 89 
                                       lERi+Dh vnia+rv
  gi|320101208|ref|YP_004176800.1| 222 LERIADHNVNIARRV 236
                                       *************86 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 8.4e-10
                                       HHHHHHHHHHHHHHCT-HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   7 iveemlddalealeekdtelarevier.ddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82 
                                        +++ +++a+ al++  +  a+evi+  +  +d++ek i++++++    ++++a        l  i+ ++ Ri++++
  gi|320101208|ref|YP_004176800.1| 254 KASDLFNKAMGALYSLSRRDAEEVIQSsRALVDEIEKTIYEEIINSTLPDNEKAG-------LTLICDSIRRIARYS 323
                                       57899****************9998765999****************99999998.......888************ PP

                                       HHHHHHH CS
                              PhoU  83 vniaerv 89 
                                         iae+v
  gi|320101208|ref|YP_004176800.1| 324 NGIAESV 330
                                       ****975 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 !   35.7   0.0   9.8e-13   5.9e-09       2      42 ..      12      52 ..      11      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 9.8e-13
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCH CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrplk 42
                                      ++++s ++++Pke++++ g++ Gd v +e  gdk++++p++
  gi|320101208|ref|YP_004176800.1| 12 TGSSSFIITLPKEWVDSVGLKSGDYVNVEKYGDKLVIIPPS 52
                                      899************************************87 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.067       6      42 ..     215     252 ..     211     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                              KORA   6 FeeiikgleelaeqtveiargvLV.egkkqadvatelg 42 
                                       +++i   le++a+++v+iar+vL  ++ + +d++ +l 
  gi|320101208|ref|YP_004176800.1| 215 YRIIARNLERIADHNVNIARRVLAmKKTSGSDIVYKLV 252
                                       789999*****************614555678887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2631.58
//
Query:       gi|320101209|ref|YP_004176801.1|  [L=74]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   28.2  13.1    5.6e-06   25.9  12.6    2.0  2  DUF3096          Protein of unknown function (DUF3096)
  ------ inclusion threshold ------
      0.014   15.7   7.0      0.039   14.3   7.0    1.7  1  DUF308           Short repeat of unknown function (DUF308)
      0.075   13.0   1.2       0.11   12.5   1.2    1.2  1  IBV_3A           IBV 3A protein
       0.08   12.5   1.1      0.086   12.4   1.1    1.2  1  SLATT_6          SMODS and SLOG-associating 2TM effector doma
      0.096   12.7   0.3       0.19   11.7   0.3    1.5  1  LisH             LisH
       0.16   11.5   0.1       0.19   11.3   0.1    1.1  1  Cytochrom_B558a  Cytochrome Cytochrome b558 alpha-subunit
       0.53   10.4   4.3       0.77    9.8   4.3    1.1  1  DUF2892          Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> DUF3096  Protein of unknown function (DUF3096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.017        43       5      14 ..      21      30 ..      18      30 .. 0.90
   2 !   25.9  12.6   2.2e-09   5.6e-06       3      32 ..      26      55 ..      24      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                           DUF3096  5 LiaGiLILim 14
                                      L aG+L L++
  gi|320101209|ref|YP_004176801.1| 21 LFAGVLMLVF 30
                                      78******96 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 2.2e-09
                           DUF3096  3 vALiaGiLILimPRLLNyiVAiYLIviGll 32
                                      + L+ G+LIL+ P LLN+++A YLI+ Gll
  gi|320101209|ref|YP_004176801.1| 26 LMLVFGLLILVLPELLNLLIAAYLIIEGLL 55
                                      56899***********************97 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   7.0   1.5e-05     0.039       2      46 ..      23      64 ..      22      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                            DUF308  2 lGillivlGilalllPvaallalvllfGilllvsGivqii.aafaa 46
                                       G+l++v+G+l+l+lP +    l ll++++l++ G++ ii +++++
  gi|320101209|ref|YP_004176801.1| 23 AGVLMLVFGLLILVLPEL----LNLLIAAYLIIEGLLVIIdEYVKS 64
                                      7***************86....778999999999999999445444 PP

>> IBV_3A  IBV 3A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.2   4.3e-05      0.11       5      51 ..      19      67 ..      16      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
                            IBV_3A  5 PtsflivlillWck..lvlscfrefiialqqliqvllqiinsnlqsrlt 51
                                      P  f  vl+l++    lvl  + +++ia   +i  ll ii+  ++sr+t
  gi|320101209|ref|YP_004176801.1| 19 PRLFAGVLMLVFGLliLVLPELLNLLIAAYLIIEGLLVIIDEYVKSRIT 67
                                      666777888887651157778999***********************98 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 ?   12.4   1.1   3.4e-05     0.086      38      73 ..      23      58 ..       7      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                           SLATT_6 38 islislavGilalvieelstkllsalliiigiialy 73
                                       +++ l++G+l lv++el + l++a lii g++ ++
  gi|320101209|ref|YP_004176801.1| 23 AGVLMLVFGLLILVLPELLNLLIAAYLIIEGLLVII 58
                                      578999*************************98765 PP

>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   7.4e-05      0.19       1      16 [.      39      54 ..      39      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.4e-05
                                      HHHHHHHHHHHHHCT- CS
                              LisH  1 eeLNrLIydYLvkeGy 16
                                      e+LN LI  YL+ eG+
  gi|320101209|ref|YP_004176801.1| 39 ELLNLLIAAYLIIEGL 54
                                      68************96 PP

>> Cytochrom_B558a  Cytochrome Cytochrome b558 alpha-subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   7.2e-05      0.19      15      58 ..      23      66 ..      16      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.2e-05
                   Cytochrom_B558a 15 asglillaggivavagqfkkwefaayaiaagvfvclleyprgkr 58
                                      a  l+l+ g ++ v  ++ +  +aay i+ g +v++ ey +++ 
  gi|320101209|ref|YP_004176801.1| 23 AGVLMLVFGLLILVLPELLNLLIAAYLIIEGLLVIIDEYVKSRI 66
                                      444566667788999************************99875 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.3    0.0003      0.77      13      48 ..      20      54 ..      18      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0003
                           DUF2892 13 rivvGlvllllallglsggwgwllglvGavllltgl 48
                                      r+++G+++l+++ll l  +  +l +l++a l+++gl
  gi|320101209|ref|YP_004176801.1| 20 RLFAGVLMLVFGLLILVLP-ELLNLLIAAYLIIEGL 54
                                      99**************654.999**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); 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:                         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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 589.93
//
Query:       gi|320101210|ref|YP_004176802.1|  [L=441]
Description: peptidase U62 modulator of DNA gyrase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.8e-43  147.3   0.0      1e-42  146.9   0.0    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 !  146.9   0.0   5.6e-47     1e-42       1     278 [.      18     302 ..      18     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 5.6e-47
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.. 75 
                                       ea vr++es++t  +++n+e + ++++++ ++g+ ++k+ r+ +a  + ++ +    ++ + +++a +  e + +  
  gi|320101210|ref|YP_004176802.1|  18 EAVVRVVESTRTMAKIANSEPSVVQHWRSLDVGLYLVKDRRIMVAEVKGLDPARTSYTLSQLLSLAGKLRESELYap 94 
                                       689*****************************************665555554666777777777766666666677 PP

                                       ..........GGS-HHHHHHHHHHHHHH.CHCSTTEEEEE.EEEEE......EEE.EEEEEEETTSEEEEEEEEEEE CS
                         PmbA_TldD  76 ..........eevsaeekielleelekalrsadpkiensk.garisgvsaslsaskeeklianSeGldveqtrtrvs 141
                                                 +++  +e i ++e+ ++ ++   + i+  + + ++++v ++++ ++e+ ++a+S+G+++++++t+++
  gi|320101210|ref|YP_004176802.1|  95 lpepgepvgvGNLVDSEVIRYIEDPSSLAE---EVITA-AhEEKVDYVAGMIDLKHEKEYLASSKGFEGTHEYTSME 167
                                       777787778866666666655554442211...12222.235699******************************** PP

                                       EEEEEEE..STCSETEEEEEEEE...SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHH CS
                         PmbA_TldD 142 lslsvia.ddggsgdgmgggsgy...edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavg 214
                                        +l + a ++       g+g ++   ++l +++l e+a+ aa+ a++s   ++++pg y++vlsp+++g+ll  +++
  gi|320101210|ref|YP_004176802.1| 168 SYLRAFAgEE-------GSGQWStcsTRLRRDKLVEMARIAARYAVDSRSRQDIEPGVYDLVLSPMVFGNLLD-YIS 236
                                       *******443.......3345557777777788999**************9*********************9.688 PP

                                       HHTBHHHHHTT--TTTT.-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE-- CS
                         PmbA_TldD 215 haleadavlegrSflkd.klGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkn 278
                                        ++++ ++  g+S++ + k G+kvase+lt++d+p+  + +gs++fD EG  t+ +++Ie+GvL n
  gi|320101210|ref|YP_004176802.1| 237 YMASGFSIMTGMSMFMGnKPGDKVASEKLTLIDNPHEpELPGSRGFDMEGARTSVKPIIERGVLAN 302
                                       9**************8879*****************99**************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3278.29
//
Query:       gi|320101211|ref|YP_004176803.1|  [L=483]
Description: peptidase U62 modulator of DNA gyrase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-47  161.9   0.0    8.1e-47  160.4   0.0    1.6  2  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 !  160.4   0.0   4.5e-51   8.1e-47       1     274 [.      25     328 ..      25     331 .. 0.86
   2 ?   -1.5   0.0       0.1   1.8e+03     269     279 .]     412     422 ..     410     422 .. 0.89

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 4.5e-51
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.. 75 
                                       + e+r++  +++++  +ng v  ++  ++sg+gvrv+++g+lgfa t+++s++++++averav +a+ a+    +  
  gi|320101211|ref|YP_004176803.1|  25 YGEARFHGVSGLNIYTRNGGVVGSGVVSRSGIGVRVLVNGALGFAATPELSRDGVRRAVERAVGLARAASRLMRRpl 101
                                       5699****************************************99999999**************98888777799 PP

                                       ....................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEE.EEEEE......EEE.EEEEEEETTSE CS
                         PmbA_TldD  76 ....................eevsaeekielleelekalrsadpkiensk.garisgvsaslsaskeeklianSeGl 131
                                                           ++++++ek+e+l  l +        ++ s  +ar+   ++++++++eek+i+nS+G 
  gi|320101211|ref|YP_004176803.1| 102 rlddsrlgrarysvepakpfDSLPVDEKVEYLTGLWRS-------VQGSTrEARVPVLTVTYNEWVEEKIIVNSDGG 171
                                       99999999988888888888888888888776666633.......444555889*********************** PP

                                       EEEEEEEEEEEEEEEEE..S.TCS.ET.EEEEEEEE.SSHHH.S..SSHHHHHHHHHHCTTT-B---SEEEEEEE-H CS
                         PmbA_TldD 132 dveqtrtrvslslsvia.dd.ggs.gd.gmgggsgy.edlee.edleeiaeeaaekalasleakplppgkypVvlsp 202
                                       +ve++ +r++++++v++ +   gs ++ ++ ggsg  e l++    e++  e+a+    + +a+p+p+   +V+ ++
  gi|320101211|ref|YP_004176803.1| 172 YVESRIPRITMYYNVVVsSPvKGSlQRwEQLGGSGGvELLDKwRLHEKLPVELARYEEILFKAVPPPTDPVDVIVGS 248
                                       *****************54355556333333333332333334445667777788878888999************* PP

                                       HHHHHHHHGHHHHHTBHHHHH......TT--TTTT.-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEE CS
                         PmbA_TldD 203 eavgsllheavghaleadavl......egrSflkd.klGekvaselltivddpts.gglgsypfDdEGvptqrtvlI 271
                                       e vg+++he++gh+ ead++l      +g+Sf k+ + G +++se+ t++ddpt+ g++g+y +DdE vp+ +++l 
  gi|320101211|ref|YP_004176803.1| 249 EIVGLIVHESCGHPSEADRILgreaaqAGKSFIKPgMTGVRIGSEHATVIDDPTIpGSYGFYLYDDEAVPAGPRYLY 325
                                       ***********************99999*****9988**************************************** PP

                                       ETT CS
                         PmbA_TldD 272 enG 274
                                       ++G
  gi|320101211|ref|YP_004176803.1| 326 KEG 328
                                       *99 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.1
                                       EEEETTEE--- CS
                         PmbA_TldD 269 vlIenGvLkny 279
                                       +++enG Lk y
  gi|320101211|ref|YP_004176803.1| 412 YIVENGELKEY 422
                                       89*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3498.27
//
Query:       gi|320101212|ref|YP_004176804.1|  [L=224]
Description: endonuclease V [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-50  169.8   0.0    6.4e-50  169.6   0.0    1.0  1  Endonuclease_5  Endonuclease V
  ------ inclusion threshold ------
      0.093   12.6   0.0       0.11   12.4   0.0    1.2  1  UvrC_HhH_N      UvrC Helix-hairpin-helix N-terminal


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 !  169.6   0.0   7.1e-54   6.4e-50      15     197 .]      33     208 ..      15     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 169.6 bits;  conditional E-value: 7.1e-54
                                       GG-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS--SEEE CS
                    Endonuclease_5  15 eklklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkqkpdvll 91 
                                       ++++lvaGvD+++       + +++v++d++s + ++ +++v++  +pY+pg+LaFRE+pv++kal+kl ++pd++l
  gi|320101212|ref|YP_004176804.1|  33 SRVRLVAGVDAAY---GGGVQAGCAVLVDYASSTQLAYTCHVREPPIPYVPGLLAFREAPVYIKALRKLPENPDIIL 106
                                       4489*********...4555599****************************************************** PP

                                       EEC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EEEEEEC CS
                    Endonuclease_5  92 vDGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiyvSvGh 168
                                       vDG+G++Hpr lG+A+h+G++l+ ptiGvaK+ l+g+ ++ + +      ++++g + g +l   k v ++yvS+G 
  gi|320101212|ref|YP_004176804.1| 107 VDGHGLTHPRALGIATHIGLVLGKPTIGVAKNPLYGEEKTVNGR----RLITAHGVTAGEILEPVKGV-KLYVSIGY 178
                                       ************************************55444333....344566999******99997.69****** PP

                                       SS-HHHHHHHHHHCS-.T-SS-HHHHHHHH CS
                    Endonuclease_5 169 risletalelvlallk.kyrlPepirqAdl 197
                                        i le+a+++v++l+k + +lP p+ +Ad+
  gi|320101212|ref|YP_004176804.1| 179 LIRLEDAVTVVKHLMKpGLKLPLPLHLADK 208
                                       ***************9789*********95 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 ?   12.4   0.0   1.2e-05      0.11      61     122 ..      13     147 ..       6     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHTTS.................................................................. CS
                                       xxxxxxxxxxxxxx............................................................... RF
                        UvrC_HhH_N  61 revlrRrfkrllke............................................................... 74 
                                       +e+l+Rr+ + +++                                                               
  gi|320101212|ref|YP_004176804.1|  13 QEALSRRVLEEAASfpgldpsrvrlvagvdaaygggvqagcavlvdyasstqlaytchvreppipyvpgllafreap 89 
                                       56666666555555677777777777777777777777777777777777777777777777777777777777777 PP

                                       ..........---SEEEESSSHHHHHHHHHHHHHTT-..---EEEEES.......... CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N  75 ........fsklPdLiliDGGkgqlnaakevleelgl..kipvvglaKdkkrktraka 122
                                                 + Pd+il+DG       a  + +++gl    p +g+aK+    +++++
  gi|320101212|ref|YP_004176804.1|  90 vyikalrkLPENPDIILVDGHGLTHPRALGIATHIGLvlGKPTIGVAKNPLYGEEKTV 147
                                       777777667789********988889999999999998999*******8766555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1671.56
//
Query:       gi|320101213|ref|YP_004176805.1|  [L=184]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-59  198.7   0.1      7e-59  198.5   0.1    1.0  1  DUF2204   Nucleotidyl transferase of unknown function (DUF220


Domain annotation for each model (and alignments):
>> DUF2204  Nucleotidyl transferase of unknown function (DUF2204)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.1   3.9e-63     7e-59       4     181 .]       7     179 ..       4     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 3.9e-63
                           DUF2204   4 alaevlkvLeekgvkfvviGgtvvelalgrkrlekDvDlFiteksqlleedfyreiaeeedwdvgstelgtvkliak 80 
                                       +la+vl++L ++gvkf+viG+tvv+lalgr+ le+D+DlF +e+s+lle+ fyre+a +++w+ ++telgtvkli++
  gi|320101213|ref|YP_004176805.1|   7 ELARVLETLLDEGVKFTVIGDTVVQLALGRETLEGDLDLFTYEPSPLLEAGFYRELAARHGWEASTTELGTVKLIVP 83 
                                       7999************************************************************************* PP

                           DUF2204  81 vekeevevdlleNildlyvpeeiLerakeveiggvevkvislEdyivlKaraareeaeeeldeiarlikelklkldv 157
                                       +++++++v+l+eN++d+++peeiL +a+ v+++ ve  +i +E+y+vlKar+++      ld++a+++k+l+ ++dv
  gi|320101213|ref|YP_004176805.1|  84 LSEDYLNVELYENYMDIEIPEEILGKAEPVRVNSVEAPMIPVEAYLVLKARQGVG-----LDKLAEYVKQLRKTIDV 155
                                       *******************************************************.....***************** PP

                           DUF2204 158 rlvkehveafpeeeaelilkrLre 181
                                       rlv e + ++pe+e e+i+ rLr+
  gi|320101213|ref|YP_004176805.1| 156 RLVDELAAQYPEDEYETIVSRLRS 179
                                       **********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1408.93
//
Query:       gi|320101214|ref|YP_004176806.1|  [L=58]
Description: 50S ribosomal protein L40E [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   32.7   3.4    5.8e-08   32.5   3.4    1.1  1  Ribosomal_L40e  Ribosomal L40e family
    0.00059   19.5   3.1    0.00081   19.0   3.1    1.2  1  zinc_ribbon_2   zinc-ribbon domain
     0.0017   18.3   0.8      0.002   18.1   0.8    1.2  1  DZR             Double zinc ribbon
     0.0018   18.3   0.7      0.022   14.8   0.0    2.0  2  CpXC            CpXC protein
     0.0034   16.6   3.5      0.014   14.7   3.3    2.0  2  zf-RanBP        Zn-finger in Ran binding protein and others
  ------ inclusion threshold ------
       0.01   15.2   3.0      0.014   14.8   3.0    1.2  1  zf-ribbon_3     zinc-ribbon domain
      0.023   15.0   1.1      0.028   14.7   1.1    1.1  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
      0.042   13.6   1.3      0.094   12.5   1.3    1.6  1  Rubredoxin_2    Rubredoxin metal binding domain
      0.071   13.1   0.4      0.085   12.9   0.4    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.56   10.1   9.3        2.8    7.8   2.2    2.2  2  zf-CCHC_2       Zinc knuckle
        6.5    6.3  10.5        8.6    5.9   2.3    2.4  2  DUF2688         Protein of unknown function (DUF2688)


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 !   32.5   3.4   3.5e-11   5.8e-08       3      50 .]       6      51 ..       4      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.5e-11
                    Ribosomal_L40e  3 psLrqLAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKkl 50
                                      p L+++      +K +Cr+C A  pp At+Cr  +C     lrpKK +
  gi|320101214|ref|YP_004176806.1|  6 PELQKIVFNRVLNKTVCRRCGALNPPGATKCR--RCKAKGTLRPKKAV 51
                                      778888888889********************..9***********75 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   3.1     5e-07   0.00081       2      21 ..      22      41 ..      21      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5e-07
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      C +CGa ++++a+ C +C +
  gi|320101214|ref|YP_004176806.1| 22 CRRCGALNPPGATKCRRCKA 41
                                      ******************55 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.8   1.3e-06     0.002       1      21 [.      22      42 ..      15      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                               DZR  1 CpqCgeelppdarfCseCgtk 21
                                      C +Cg+ +pp+a  C +C++k
  gi|320101214|ref|YP_004176806.1| 22 CRRCGALNPPGATKCRRCKAK 42
                                      899999999999999999987 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.4e-05     0.022      22      48 ..       4      30 ..       1      34 [. 0.89
   2 ?    2.7   0.1     0.077   1.2e+02      39      51 ..      35      47 ..      32      57 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                              CpXC 22 edpelkeklldgslfeatCpkCgatak 48
                                      ++pel++ +++  l++++C +Cga + 
  gi|320101214|ref|YP_004176806.1|  4 NNPELQKIVFNRVLNKTVCRRCGALNP 30
                                      79*********************9875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.077
                              CpXC 39 tCpkCgataklea 51
                                      +C +C a+++l  
  gi|320101214|ref|YP_004176806.1| 35 KCRRCKAKGTLRP 47
                                      6777777776654 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 !    8.5   0.1   0.00076       1.2      18      30 .]      19      31 ..      17      31 .. 0.86
   2 !   14.7   3.3   8.4e-06     0.014       7      27 ..      22      42 ..      21      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00076
                                      SSB-TTT--BTSC CS
                          zf-RanBP 18 stkCvaCqapkpd 30
                                      +t+C +C+a++p+
  gi|320101214|ref|YP_004176806.1| 19 KTVCRRCGALNPP 31
                                      79*******9985 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.4e-06
                                      -SSS--EEESSSSB-TTT--B CS
                          zf-RanBP  7 CskClvqNfawstkCvaCqap 27
                                      C  C++ N++ +tkC +C+a+
  gi|320101214|ref|YP_004176806.1| 22 CRRCGALNPPGATKCRRCKAK 42
                                      999****************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 ?   14.8   3.0   8.4e-06     0.014       3      24 ..      20      41 ..      18      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.4e-06
                       zf-ribbon_3  3 vrCPnCGa.plssddnvCpyCGt 24
                                      + C +CGa +  +++++C  C +
  gi|320101214|ref|YP_004176806.1| 20 TVCRRCGAlN-PPGATKCRRCKA 41
                                      67999***99.**********87 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 ?   14.7   1.1   1.7e-05     0.028      39      70 ..      13      44 ..       6      56 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                      -SSTCCCTB-TTT--B--CTTTEEEEEE-SSS CS
                              Rpr2 39 lppsvkrtvCkkCgsvlipgvtcsvrvenksk 70
                                       ++ +++tvC++Cg++  pg t   r + k +
  gi|320101214|ref|YP_004176806.1| 13 FNRVLNKTVCRRCGALNPPGATKCRRCKAKGT 44
                                      567789****************9999975332 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.3   5.7e-05     0.094       2      28 .]      21      47 ..      21      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                      Rubredoxin_2  2 vCsqCGfesakwfGrCpsCgsWntlke 28
                                      vC++CG+  +    +C+ C++ +tl++
  gi|320101214|ref|YP_004176806.1| 21 VCRRCGALNPPGATKCRRCKAKGTLRP 47
                                      7********************999987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   5.2e-05     0.085      61      96 ..      10      43 ..       3      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                      EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 61 eLeieevpvkvrCreCgkefeleekalrCpkCgsad 96
                                      ++ +++v  k+ Cr+Cg+       a++C +C++++
  gi|320101214|ref|YP_004176806.1| 10 KIVFNRVLNKTVCRRCGALNPPG--ATKCRRCKAKG 43
                                      66788899999******666655..569****9875 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.7     0.004       6.6       5      10 ..      21      26 ..      21      27 .. 0.89
   2 ?    7.8   2.2    0.0017       2.8       5      13 ..      35      43 ..      35      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.004
                         zf-CCHC_2  5 vChiCg 10
                                      vC++Cg
  gi|320101214|ref|YP_004176806.1| 21 VCRRCG 26
                                      8****9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0017
                         zf-CCHC_2  5 vChiCgkkG 13
                                      +C++C++kG
  gi|320101214|ref|YP_004176806.1| 35 KCRRCKAKG 43
                                      7*******9 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.3    0.0053       8.6       8      14 ..      20      26 ..      10      28 .. 0.88
   2 ?    5.5   1.0    0.0071        12       7      13 ..      33      39 ..      32      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0053
                           DUF2688  8 TqCrRCG 14
                                      T CrRCG
  gi|320101214|ref|YP_004176806.1| 20 TVCRRCG 26
                                      99***** PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0071
                           DUF2688  7 tTqCrRC 13
                                      +T+CrRC
  gi|320101214|ref|YP_004176806.1| 33 ATKCRRC 39
                                      59***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 470.92
//
Query:       gi|320101215|ref|YP_004176807.1|  [L=321]
Description: integral membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-17   64.1  30.5    1.9e-17   63.7  30.1    1.4  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 !   63.7  30.1   1.1e-21   1.9e-17       2     274 ..      11     284 ..      10     302 .. 0.71

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.1e-21
                   LPG_synthase_TM   2 llglals.alllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrsl..garislrrllrayl 75 
                                       ++++al+ +++l++ + +  l+al  +l++ +    +++ +l++l ++++a+r +lll+s   ++r++l++++++ l
  gi|320101215|ref|YP_004176807.1|  11 VAAVALAtVVILVYSVVTSSLGALPGLLSADT----AFSAALITLGWVVSAVRLKLLLESYggRVRLPLLDAVAIRL 83 
                                       67788886566666667778888888888777....9999999******************77778899******** PP

                   LPG_synthase_TM  76 iglfvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllala 152
                                       ig +v n+tP+++gGe++ray+++r++g+  +++ a v+ e  +d++a+ l+g+++ +  +         l + +l+
  gi|320101215|ref|YP_004176807.1|  84 IGGLVANITPSSIGGEPARAYYVSRRTGLGMAESYALVIYEVYYDVIAVNLAGVFLSIQAL--------PLSTPVLL 152
                                       *****************************************************87776333........67778888 PP

                   LPG_synthase_TM 153 llllavlalllllllrrrlarlarvlkrlarllarfarklasakr.......................klvlasprr 206
                                       +++++++ +l +++   +  r     ++l r+ + f r++    +                         ++    +
  gi|320101215|ref|YP_004176807.1| 153 VAVFMSTSWLYASFKVSKTGRSVGDGSSLPRWVPGFLRSRF---NalyarylefarsyssvsssiplrVKAA----A 222
                                       88888888877777777777777666666666555553322...1235667666655655444333211111....2 PP

                   LPG_synthase_TM 207 lllafllslliwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllal 274
                                       ++l++ ++++     a++ +   +al +++  +++   ++++  ++   p+PgG+G++E++l lll +
  gi|320101215|ref|YP_004176807.1| 223 WALTLVYHTIW--GLAVVPFTGSAALPLAARAVEA---YFLMQSFS-SLPTPGGSGAAEYGLSLLLDP 284
                                       33333333333..2233333333444444444333...44444444.458**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2263.73
//
Query:       gi|320101216|ref|YP_004176808.1|  [L=361]
Description: peptide chain release factor subunit 1 (aeRF-1) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-41  142.2   0.0    1.8e-41  141.6   0.0    1.3  1  eRF1_2          eRF1 domain 2
      3e-20   72.8   0.2      1e-18   67.9   0.0    2.9  2  eRF1_3          eRF1 domain 3
    6.5e-19   68.5   0.0    1.2e-17   64.5   0.0    2.5  3  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    3.9e-12   46.6   0.1    1.3e-11   45.0   0.0    1.9  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    0.00023   21.2   0.0    0.00037   20.5   0.0    1.3  1  eRF1_1          eRF1 domain 1
  ------ inclusion threshold ------
      0.037   13.9   0.0       0.18   11.7   0.0    2.1  3  DUF86           Protein of unknown function DUF86
      0.094   12.8   0.3       0.31   11.1   0.0    1.9  2  DUF496          Protein of unknown function (DUF496)
       0.11   12.0   0.0       0.24   10.8   0.0    1.5  1  DUF5321         Family of unknown function (DUF5321)
       0.39   11.0   3.4       0.46   10.8   0.0    2.8  4  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b


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 !  141.6   0.0   9.1e-45   1.8e-41       2     133 .]     132     265 ..     131     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 9.1e-45
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.HCHTTTE CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafl.lvdkdkl 77 
                                       vgl++++++ Atigllkg+r +v++++e  +P+Kh++Ggqs+rr++R++e+++e f+k+v+e++nkafl l++++kl
  gi|320101216|ref|YP_004176808.1| 132 VGLLIVERDAATIGLLKGNRLQVVEELEDYIPGKHQKGGQSQRRYDRIIEQMVEDFYKRVGEHVNKAFLpLLEQGKL 208
                                       799************************************************************************** PP

                                       SEEEEEESSTHHHHHHHHHHHHHHHHTCCEE.EEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  78 kgiilagpgfvkeefldkdlldaelkkkvik.lvdvsyggesglnevlekaaevlkd 133
                                       k+i+++gp+++k +f++kd++d++lkk v+   +dv+y+ge gl+e++ ka ++lk+
  gi|320101216|ref|YP_004176808.1| 209 KAILVGGPAYAKYDFMEKDYMDYRLKKIVLPeFIDVAYQGEPGLREMILKAGDALKE 265
                                       ****************************99889*****************9999985 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.2   2.4e+03      43      78 ..     154     187 ..     119     196 .. 0.64
   2 !   67.9   0.0     5e-22     1e-18       2     110 ..     269     356 ..     268     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                                       EEHCHHTSSSH.HHHHS-HHH-HHHHHH.HHHHHHHHH CS
                            eRF1_3  43 vseelersrdt.lkekvketgeelelve.lieelvenv 78 
                                       v+eele++  +    k+++ g+ +++ + +ie++ve+ 
  gi|320101216|ref|YP_004176808.1| 154 VVEELEDY--IpG--KHQKGGQSQRRYDrIIEQMVEDF 187
                                       44555444..212..22466677776667777777654 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 5e-22
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHH CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenv 78 
                                       ++  k+leef  +lakd+g++vYG eev++alemg vetLL+ e+ e+                      ee+++ +
  gi|320101216|ref|YP_004176808.1| 269 AETLKALEEFKYHLAKDDGMIVYGDEEVRNALEMGLVETLLIGESREDV---------------------EEWLDLA 324
                                       567799**************************************98875.....................799**** PP

                                       HHTT-EEEEE-TTSHHHHHHHHHTTTEEEEES CS
                            eRF1_3  79 eesgakveiisseseeGeqlvkafgGiaaiLR 110
                                       ++ gak  ++s++ +eGe+++k+f+G+a+iLR
  gi|320101216|ref|YP_004176808.1| 325 RKRGAKPLVLSDDIPEGEWFTKTFNGLAGILR 356
                                       *******************************9 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   4.3e+03     102     124 ..      49      71 ..      35      87 .. 0.69
   2 !   64.5   0.0   5.9e-21   1.2e-17       3     121 ..     132     256 ..     130     265 .. 0.87
   3 ?    0.9   0.0      0.26   5.1e+02      68     108 ..     280     322 ..     263     333 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                           acVLRF1 102 areelldvpdprravLedavrra 124
                                          +l ++ ++++++L  a++r 
  gi|320101216|ref|YP_004176808.1|  49 DNIKLKKTRNAVERALSVAIERV 71 
                                       44456677777777777777765 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 5.9e-21
                           acVLRF1   3 lgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae... 76 
                                       +g+l+v r++ ++g+++g++l+ +++ + ++ g++++GG+Sq+R++R +e+ +++ +++v e++++ + +  ++   
  gi|320101216|ref|YP_004176808.1| 132 VGLLIVERDAATIGLLKGNRLQVVEELEDYIPGKHQKGGQSQRRYDRIIEQMVEDFYKRVGEHVNKAFLPLLEQgkl 208
                                       799*****************************************************************665555566 PP

                           acVLRF1  77 ..vvlgGdrslvaevledar.laplatlareelldvpdprravLedav 121
                                         +++gG+  +  +++e+   + +l++ + +e++dv+   +  L++++
  gi|320101216|ref|YP_004176808.1| 209 kaILVGGPAYAKYDFMEKDYmDYRLKKIVLPEFIDVAYQGEPGLREMI 256
                                       77***************9553667888888888888877777776665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.26
                           acVLRF1  68 rllaeesaevvlgGdrslvaevledarlaplatlare...elld 108
                                        +l ++++ +++ Gd++++++++     + l +  re   e+ld
  gi|320101216|ref|YP_004176808.1| 280 YHL-AKDDGMIVYGDEEVRNALEMGLVETLLIGESREdveEWLD 322
                                       333.4444599999**9999999886655554444442334444 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 !   45.0   0.0   6.3e-15   1.3e-11       6     104 ..     122     223 ..     118     245 .. 0.87
   2 ?   -2.0   0.0       1.9   3.8e+03      90     105 ..     286     301 ..     260     308 .. 0.63

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 6.3e-15
                    baeRF_family10   6 LlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellak 82 
                                       L + + e   +g+++v+r+ a +    + +l+ vee+e+ +pg++++gg+ sq+r+ r  e+++e ++k+v+e+++k
  gi|320101216|ref|YP_004176808.1| 122 LEDMVSESNMVGLLIVERDAATIGLLKGNRLQVVEELEDYIPGKHQKGGQ-SQRRYDRIIEQMVEDFYKRVGEHVNK 197
                                       6678889999****************************************.************************** PP

                    baeRF_family10  83 ll....eergverlvlgGdeeetaal 104
                                       ++    e+ +++++++gG++ ++  +
  gi|320101216|ref|YP_004176808.1| 198 AFlpllEQGKLKAILVGGPAYAKYDF 223
                                       7622225666********97665555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                    baeRF_family10  90 erlvlgGdeeetaall 105
                                       +  ++ Gdee+++al+
  gi|320101216|ref|YP_004176808.1| 286 DGMIVYGDEEVRNALE 301
                                       4578899999998887 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.9e-07   0.00037       7     128 ..      15     125 ..       8     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                                       CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT...SSE CS
                            eRF1_1   7 dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd...agv 80 
                                       + + + + +++L++++   ++++ nl++++ sv+ +++ k +r         + v+ +L + +e+v   ++   +g+
  gi|320101216|ref|YP_004176808.1|  15 KWKAHATILLSLYIPPGRPISDVLNLLRQELSVADNIKLKKTR---------NAVERALSVAIERVSKIPKvpdKGL 82 
                                       4556778899******************************999.........78999999999999887777779** PP

                                       EEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  81 lrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                       + ++G++ +  e       +t+ l +++++ ++ ++ ++ f++e L+++
  gi|320101216|ref|YP_004176808.1|  83 VLFTGENPDTGE------SITVMLIPPEDVPVFFYRtDKVFHTEFLEDM 125
                                       *****9988777......8999999999999999998888999999987 PP

>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     9e-05      0.18      12      47 ..      34      77 ..       7      92 .. 0.73
   2 ?   -2.0   0.0       1.5     3e+03      17      40 ..     171     194 ..     152     198 .. 0.51
   3 ?   -3.7   0.0       5.4   1.1e+04      72      85 ..     265     278 ..     259     286 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9e-05
                                      H...........TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF86 12 t........eeldeeeflsdeleydavernlqvigEaaidiakh 47
                                               +el+ ++ ++ +++++aver+l v++E + +i+k 
  gi|320101216|ref|YP_004176808.1| 34 IsdvlnllrQELSVADNIKLKKTRNAVERALSVAIERVSKIPKV 77
                                      055555555788877777899*********************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                       STSCCGSHHHHHHHHHHHHHHHHH CS
                             DUF86  17 eeeflsdeleydavernlqvigEa 40 
                                       + +   d++    ve ++  +gE 
  gi|320101216|ref|YP_004176808.1| 171 QSQRRYDRIIEQMVEDFYKRVGEH 194
                                       333333555566666666666665 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.4
                                       -HHHHHHHHHHHCC CS
                             DUF86  72 aeepeepwrkmigl 85 
                                       ++e++e+++++  +
  gi|320101216|ref|YP_004176808.1| 265 EQEYAETLKALEEF 278
                                       45555555555444 PP

>> DUF496  Protein of unknown function (DUF496)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       3.4   6.8e+03       4      21 ..      47      64 ..      45      71 .. 0.70
   2 ?   11.1   0.0   0.00015      0.31      33      75 ..     150     197 ..     147     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                            DUF496  4 vlelvrlarrknklkrei 21
                                      v + ++l++ +n ++r +
  gi|320101216|ref|YP_004176808.1| 47 VADNIKLKKTRNAVERAL 64
                                      556677777888877766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                            DUF496  33 krvlllenlleyi.....kedmsieeikaiienmkddyedrvddyiik 75 
                                        r++++e+l++yi     k   s++    iie+m +d+ +rv +++ k
  gi|320101216|ref|YP_004176808.1| 150 NRLQVVEELEDYIpgkhqKGGQSQRRYDRIIEQMVEDFYKRVGEHVNK 197
                                       5889999999*99554333456889999****************9865 PP

>> DUF5321  Family of unknown function (DUF5321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.24      83     123 ..     237     277 ..     220     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                           DUF5321  83 lLreviekvqrGEevdveklLGtGdeekEreWeevLkeiee 123
                                       +L e i+   +GE    e +L +Gd+ kE+e++e Lk +ee
  gi|320101216|ref|YP_004176808.1| 237 VLPEFIDVAYQGEPGLREMILKAGDALKEQEYAETLKALEE 277
                                       78899999999999999*********************997 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 ?   -2.1   0.1       2.4   4.7e+03      30      41 ..       4      15 ..       2      20 .. 0.80
   2 ?   -2.7   0.0       3.7   7.4e+03       5      14 ..      57      66 ..      44      74 .. 0.67
   3 ?   -1.7   0.0       1.9   3.8e+03      15      42 ..     248     275 ..     242     285 .. 0.57
   4 ?   10.8   0.0   0.00023      0.46       1      47 [.     289     332 ..     289     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                     SpoU_sub_bind 30 krleellklakk 41
                                      +rl+e+lk++kk
  gi|320101216|ref|YP_004176808.1|  4 QRLREILKELKK 15
                                      788999999987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                     SpoU_sub_bind  5 lhaVleaLks 14
                                      ++aV+ aL  
  gi|320101216|ref|YP_004176808.1| 57 RNAVERALSV 66
                                      4667776654 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.9
                     SpoU_sub_bind  15 grr.iekllvtegradkrleellklakkr 42 
                                       g++ +++++++ g+a k+ +e  + +k++
  gi|320101216|ref|YP_004176808.1| 248 GEPgLREMILKAGDALKE-QEYAETLKAL 275
                                       344488999999955544.3444444433 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00023
                     SpoU_sub_bind   1 liyGlhaVleaLksgrriekllvtegradkrleellklakkrgikve 47 
                                       ++yG   V+ aL+ g  +e+ll+ e+r+d +  e+l+la+krg k  
  gi|320101216|ref|YP_004176808.1| 289 IVYGDEEVRNALEMGL-VETLLIGESREDVE--EWLDLARKRGAKPL 332
                                       69999*********95.*********66655..*********98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2682.85
//
Query:       gi|320101217|ref|YP_004176809.1|  [L=85]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   13.1   0.0      0.071   13.1   0.0    1.1  1  GerD      Spore germination GerD central core domain


Domain annotation for each model (and alignments):
>> GerD  Spore germination GerD central core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.9e-06     0.071      54      87 ..       1      34 [.       1      59 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-06
                              GerD 54 mkDpeYqkmlleilkdpemekqllellkskeyrk 87
                                      m Dp+Y+++ll+++ +  +e+ ++e l+++ +++
  gi|320101217|ref|YP_004176809.1|  1 MMDPSYRRELLSLIVNAGLEEDFIEWLRTQGVKH 34
                                      89***************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 654.46
//
Query:       gi|320101218|ref|YP_004176810.1|  [L=279]
Description: glutamine amidotransferase-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   33.4   0.0    2.9e-08   33.0   0.0    1.1  1  GATase_4  Glutamine amidotransferases class-II
    0.00013   22.2   0.0     0.0002   21.6   0.0    1.3  1  GATase_6  Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   3.2e-12   2.9e-08      26     140 ..      39     162 ..      29     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 3.2e-12
                          GATase_4  26 ggltdahadGwGiafye.....gkaarvfkdpepsaes.plaelv.reyp.iksknvvaHiRkatqGevk.lenthp 93 
                                        g++ +h dGwG+a            + +++p  s +s ++  lv r+        v+ H Rk ++ e   ++ thp
  gi|320101218|ref|YP_004176810.1|  39 SGKSREHDDGWGVAAVGyggnpSVVYQRMLEPIYSENSlRILDLVaRRLRrYSEVYVLIHARKSSRNEPYgQDYTHP 115
                                       577899*******9765556444455778899988888434455523333244567889******998761566*** PP

                          GATase_4  94 FvRelwgrewifAHnGdl.keykpklegrfePvGsTDsElafCellee 140
                                       F+R + +    fAHnG   ke   ++ g++ P  + DsEl    ++  
  gi|320101218|ref|YP_004176810.1| 116 FMRLMDNGALWFAHNGGAdKEALARVLGVY-PWVRVDSELLGYFIMGL 162
                                       ****************99555555666665.66689999876666655 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.2e-08    0.0002      14      81 ..      94     159 ..      76     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-08
                          GATase_6  14 valaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall 81 
                                        +l H+R ++++++  +   +Pf     +g l+++hNG  ++  +l++ l          r+D+e+l   +
  gi|320101218|ref|YP_004176810.1|  94 YVLIHARKSSRNEPYGQDYtHPFmrLMDNGALWFAHNGGADKE-ALARVLGV----YPWVRVDSELLGYFI 159
                                       799***********999999***988999**********9998.46666665....44558****998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2189.87
//
Query:       gi|320101219|ref|YP_004176811.1|  [L=378]
Description: ATP-NAD/AcoX kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-53  181.1   0.2      3e-53  180.9   0.2    1.0  1  NAD_kinase  ATP-NAD kinase
    0.00081   19.0   0.4      0.002   17.8   0.1    1.9  2  DAGK_cat    Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.024   14.0   0.0    1.3  1  PFK         Phosphofructokinase
      0.034   14.1   0.0       0.14   12.1   0.0    2.0  2  DeoRC       DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.2   6.6e-57     3e-53       1     291 [.       9     373 ..       9     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 6.6e-57
                                       .EEEEESSC.....................GGTCSHHHHHHHHHHHCT.-..EEEEECCGG.CCSSSTT--....HH CS
                        NAD_kinase   1 kvgivvnpi.....................kkeaieraeevarwLlda.lsrvlevtveek.lgeslaeaa....ef 50 
                                       kvg++vnpi                     +++a+ ++ ++a   l++ +s+ +e++ + + +g ++++++      
  gi|320101219|ref|YP_004176811.1|   9 KVGFIVNPIagmggrvglkgtdgeayktalERGAEPVSPRRAVEFLNHvSSKCFEIYSAPGiMGADEVSESvhrdRL 85 
                                       79****************************99999999888777777735577777665441343333333000055 PP

                                       HHTTTT--.......EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE..EGGGHH CS
                        NAD_kinase  51 rsevisvlkkvkttddtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef..epeaaa 125
                                        + v s++k ++tt+  +  +  + ++ vd++++vGGDGTa+d+ ++++  e Pvlgv+ Gvk+++++f  +p+aaa
  gi|320101219|ref|YP_004176811.1|  86 AMIVGSTRKGASTTREDTVRIAGEMKRLVDILVFVGGDGTARDIHEAVDG-ELPVLGVPSGVKMYSSVFavNPRAAA 161
                                       5677788888888886666666666************************8.************************** PP

                                       HHHHHHHHT-SEEEEEEEEE...............................EEEEETTE..........EEEEEEES CS
                        NAD_kinase 126 ellekllegeirvekrevld...............................avimrskgee....diadiviensvl 167
                                       ell ++++ge  +e+rev+d                                +++ +  ee    +ia+++ e +  
  gi|320101219|ref|YP_004176811.1| 162 ELLVRFINGETVIEEREVVDvdehafrldrvslriygyvktpvyhgllqssKSVYAGMDEElnkeAIAEYIVETM-E 237
                                       ********************************************977777755555555557888******7776.9 PP

                                       SEEEEEESSSSS-EE..EEEEETTEEEEEEEESEE.......................EEE-TGGGGTHHHHTT--E CS
                        NAD_kinase 168 nevviirgpgstlie..lelyvdtelleadqldgl.......................ivstPtGstayslsaGgpl 219
                                        +  +i+gpgst++    +l+v+ +ll++d++ ++                       +v+tP+G++++++++G+++
  gi|320101219|ref|YP_004176811.1| 238 HGTPYILGPGSTVKAvcSKLGVSCTLLGVDVVLNGgvvvkdawekhlleildtygtakLVVTPIGGQGFLFGRGNQQ 314
                                       *****************************9998888***************************************** PP

                                       E-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                        NAD_kinase 220 isPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfklir 291
                                       +sP+vl         ++ +s +iVv+++sk+r     + + ll+++G+++++  ++++++v++++  +++++
  gi|320101219|ref|YP_004176811.1| 315 LSPRVLS--------LIGRSNVIVVATESKIR-----QLKELLIDTGDPAVDKMLEGYYKVVVGYGRYRVVK 373
                                       *******........****************9.....********************************997 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2   5.2e+03       2      13 ..      10      21 ..       9      24 .. 0.80
   2 !   17.8   0.1   4.4e-07     0.002      40      91 ..      99     145 ..      75     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                      EEEEE-TTCTTT CS
                          DAGK_cat  2 llvivNpksGkg 13
                                      + +ivNp +G g
  gi|320101219|ref|YP_004176811.1| 10 VGFIVNPIAGMG 21
                                      679*****9954 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.4e-07
                                       STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-S CS
                          DAGK_cat  40 epgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlG 91 
                                        ++d  ++a e+k+  vd++v +GGDGt++ + +++ +    ++p+  +P G
  gi|320101219|ref|YP_004176811.1|  99 TREDTVRIAGEMKR-LVDILVFVGGDGTARDIHEAVDG----ELPVLGVPSG 145
                                       46778889999999.79******************999....5555556666 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.4e-06     0.024      50     128 ..      71     144 ..      29     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-06
                                       E-SGGGTT..-TT--S-TT-----GGGGSHHHHHHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T....--EE CS
                               PFK  50 ltledvsg..ilsegGtiLgsaRskefkeregrkkaaenlkklgidaLvviGGdgslkganklseerkglleelkiv 124
                                       ++ ++vs+     +   i gs+R+    +re++ ++a ++k+  +d Lv +GGdg+ + +   +e+ +g   el++ 
  gi|320101219|ref|YP_004176811.1|  71 MGADEVSEsvHRDRLAMIVGSTRKGASTTREDTVRIAGEMKR-LVDILVFVGGDGTARDI---HEAVDG---ELPVL 140
                                       4455555511455568899*****999999999999999976.59**********97655...555555...59999 PP

                                       EEEE CS
                               PFK 125 giPk 128
                                       g+P+
  gi|320101219|ref|YP_004176811.1| 141 GVPS 144
                                       9997 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.1e-05      0.14       5      49 ..     224     271 ..     220     295 .. 0.80
   2 ?   -1.6   0.0      0.52   2.3e+03     129     141 ..     327     339 ..     324     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                             DeoRC   5 eKrrIAkaAaeliedgdtifldaGtTtlelaraLaekk...nltvvTn 49 
                                       +K++IA++ +e  e g   +l+ G+T+ +++++L  +     + vv n
  gi|320101219|ref|YP_004176811.1| 224 NKEAIAEYIVETMEHGTPYILGPGSTVKAVCSKLGVSCtllGVDVVLN 271
                                       7********************************988754445555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.52
                             DeoRC 129 rvillaDssKfgk 141
                                       +vi++a +sK+++
  gi|320101219|ref|YP_004176811.1| 327 NVIVVATESKIRQ 339
                                       699*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2823.57
//
Query:       gi|320101220|ref|YP_004176812.1|  [L=306]
Description: phosphoprotein phosphatase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-21   76.2   0.0    6.6e-21   75.7   0.0    1.1  1  Metallophos  Calcineurin-like phosphoesterase


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 !   75.7   0.0   3.7e-25   6.6e-21       3     201 ..      55     253 ..      54     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 3.7e-25
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHH.TTESEEEEESTSSSSS..HHHHHHHHHHHHHHHHTSEEEEEC-TTS. CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllre.ekpdlvllaGDlvdrg..dlekellellaalvkypipvylllGNHe. 75 
                                       i++igD+H     g++++l+++l+++l++  +   v+++GD+ drg  +le+ l+  l  +  yp +v+ll+GNHe 
  gi|320101220|ref|YP_004176812.1|  55 ITFIGDIH-----GDFYSLIAVLENTLPRiAGGGTVVFLGDYADRGyaQLES-LALVLLLKKYYPERVVLLRGNHEp 125
                                       789*****.....**********9995555455555555*******776666.4444555555589**********5 PP

                                       .....CHHHHHHHHHHHHHHH............HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEE.......T CS
                       Metallophos  76 .....gfeeellnkygylgif............sepwrsdaevfnnlplaslgsgslkvlllhGgspel.......l 128
                                                     y+  +              ++++   + +fn+lpl+++  g   ++ +hGg+p l       l
  gi|320101220|ref|YP_004176812.1| 126 pewlkP--------YP--HDLpsvlaerfsgdaARLYGLLTRFFNHLPLIGFRRG--GFIAVHGGPP-LksirssrL 189
                                       544431........22..2222133222222334444444999************..********33.336664555 PP

                                       HHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                       Metallophos 129 vsldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                       ++  ++gs ++  e+ e    +++d       ++ + +  +p +rg+gyl+g+  +++ l   +   +++GH+
  gi|320101220|ref|YP_004176812.1| 190 EEAFEIGSPEFSAETLE--SVLWSD-------PTELGVEAVPSPRGAGYLYGPGFTAKALSLVDGGFIVRGHE 253
                                       66666666666666666..9*****.......888888888888*************998888889******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2249.42
//
Query:       gi|320101221|ref|YP_004176813.1|  [L=108]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   13.9   0.7       0.14   13.2   0.7    1.4  1  DUF4834   Domain of unknown function (DUF4834)


Domain annotation for each model (and alignments):
>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   7.6e-06      0.14      82      97 ..      26      41 ..       2      43 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.6e-06
                           DUF4834 82 kkiFekdeGEYVdFEE 97
                                       k ++++ +EYV++EE
  gi|320101221|ref|YP_004176813.1| 26 EKYYSDKVDEYVEYEE 41
                                      399************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 843.09
//
Query:       gi|320101222|ref|YP_004176814.1|  [L=274]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.032   14.3   0.4      0.054   13.5   0.4    1.3  1  DZR             Double zinc ribbon
       0.17   11.6   2.0        1.8    8.3   0.3    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.41   10.4   3.3       0.85    9.4   3.3    1.5  1  zinc_ribbon_2   zinc-ribbon domain
       0.41   10.1   4.4          2    7.9   4.3    2.0  2  zf-ribbon_3     zinc-ribbon domain
        0.7    9.8   2.5        1.1    9.2   2.5    1.3  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   1.5e-05     0.054       1      24 [.     171     194 ..     169     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                               DZR   1 CpqCgeelppdarfCseCgtklka 24 
                                       Cp+Cg +  + + +C  Cg+++++
  gi|320101222|ref|YP_004176814.1| 171 CPKCGFNSVSPDYTCIVCGSPVPE 194
                                       999999999999999999999974 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 ?    8.3   0.3    0.0005       1.8      17      27 ..     168     178 ..     164     179 .. 0.83
   2 ?    2.4   0.1     0.035   1.2e+02       1      11 [.     183     193 ..     183     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0005
                                       ----SSS---- CS
                    DNA_RNApol_7kD  17 piRCkeCGhRi 27 
                                        +RC +CG+ +
  gi|320101222|ref|YP_004176814.1| 168 MVRCPKCGFNS 178
                                       79******965 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.035
                                       -B-SSS--B-- CS
                    DNA_RNApol_7kD   1 YiCgeCgaevs 11 
                                       Y+C  Cg++v 
  gi|320101222|ref|YP_004176814.1| 183 YTCIVCGSPVP 193
                                       99******996 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.3   0.00024      0.85       1      22 [.     170     191 ..     170     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00024
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtp 22 
                                       +Cp+CG      +  C  CG+p
  gi|320101222|ref|YP_004176814.1| 170 RCPKCGFNSVSPDYTCIVCGSP 191
                                       6*******************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 ?    7.9   4.3   0.00056         2       2      15 ..     168     182 ..     167     191 .. 0.80
   2 ?    0.1   0.3      0.17     6e+02       4      12 ..     184     192 ..     182     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00056
                       zf-ribbon_3   2 tvrCPnCGa.plssd 15 
                                       +vrCP+CG   +s+d
  gi|320101222|ref|YP_004176814.1| 168 MVRCPKCGFnSVSPD 182
                                       89******9668887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                       zf-ribbon_3   4 rCPnCGapl 12 
                                       +C  CG+p+
  gi|320101222|ref|YP_004176814.1| 184 TCIVCGSPV 192
                                       677899975 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 ?    9.2   2.5   0.00031       1.1      13      34 ..     170     191 ..     168     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00031
                           DUF35_N  13 rCpdCGtvqfPPravCphCgsd 34 
                                       rCp+CG   + P   C  Cgs 
  gi|320101222|ref|YP_004176814.1| 170 RCPKCGFNSVSPDYTCIVCGSP 191
                                       9*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1981.41
//
Query:       gi|320101223|ref|YP_004176815.1|  [L=116]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 916.22
//
Query:       gi|320101224|ref|YP_004176816.1|  [L=221]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.007   15.0   0.0     0.0071   15.0   0.0    1.1  1  DUF2339   Predicted membrane protein (DUF2339)
  ------ inclusion threshold ------
      0.035   13.5   5.0      0.035   13.5   5.0    2.0  2  SKG6      Transmembrane alpha-helix domain
       0.82    9.7   4.9        1.4    8.9   4.9    1.4  1  DUF2771   Protein of unknown function (DUF2771)


Domain annotation for each model (and alignments):
>> DUF2339  Predicted membrane protein (DUF2339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-06    0.0071     202     275 ..      52     209 ..       3     220 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-06
                           DUF2339 202 y............................................................................ 202
                                       y                                                                            
  gi|320101224|ref|YP_004176816.1|  52 Yvevknadypyvkytagiektegdekvcgsvygwlilglsfssatpvnveenppgrggfftnpsftgdvdltgvegr 128
                                       05555555555555555555555555555555555555555566666666666666666666666666666555555 PP

                           DUF2339 203 ..............lalalllallfvaarra...vdatlvfgaplvalvlqyalladl.eygwalaalalaalylal 261
                                                     l +++++++       +   vd+++ f+ p  + +l  +l+++  + ++a+a++++a+++++l
  gi|320101224|ref|YP_004176816.1| 129 atyvngvlksaeikLETPIVASV-------SisvVDSSIQFVKPSPLNALTSFLTQHSvPAAIAVAVVVVAVVIAVL 198
                                       55555555555555233333333.......02239**********************96777777777777777766 PP

                           DUF2339 262 aawlarrkrekara 275
                                       +   +rr+r++  a
  gi|320101224|ref|YP_004176816.1| 199 T---WRRQRHTVAA 209
                                       6...4444444333 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   2.2       1.4   8.3e+03      24      29 ..       9      14 ..       6      17 .. 0.45
   2 ?   13.5   5.0   5.8e-06     0.035       6      27 ..     178     198 ..     176     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.4
                              SKG6 24 iivLla 29
                                      +i+L+a
  gi|320101224|ref|YP_004176816.1|  9 LIILIA 14
                                      344443 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.8e-06
                              SKG6   6 nsntvaIavaVaVPVaViiivL 27 
                                       +s  +aIavaV+V VaV+i+vL
  gi|320101224|ref|YP_004176816.1| 178 HSVPAAIAVAVVV-VAVVIAVL 198
                                       7777999999999.88888887 PP

>> DUF2771  Protein of unknown function (DUF2771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.9   0.00024       1.4       3      35 ..     182     216 ..     180     221 .] 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00024
                           DUF2771   3 alvavvvvvvaavvavqvwalaree..aepedpei 35 
                                       a++av+vvvva+v+av +w+ +r+   a+p  ++ 
  gi|320101224|ref|YP_004176816.1| 182 AAIAVAVVVVAVVIAVLTWRRQRHTvaAQPAPVAS 216
                                       88999999************999954344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1607.54
//
Query:       gi|320101225|ref|YP_004176817.1|  [L=551]
Description: thermosome subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-181  603.1  14.8   4.1e-181  602.9  14.8    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 !  602.9  14.8  2.3e-185  4.1e-181       1     490 [.      34     528 ..      34     529 .. 0.97

  Alignments for each domain:
  == domain 1  score: 602.9 bits;  conditional E-value: 2.3e-185
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       la++++t+lGP+G+dKmlv+++g+v+vTnDGati+ke+e++hPaakllve+a++qd evGDGTt++v+Lag+Ll +a
  gi|320101225|ref|YP_004176817.1|  34 LAEVLRTSLGPRGLDKMLVDSFGDVTVTNDGATIVKEMEVQHPAAKLLVEVAKAQDAEVGDGTTSAVVLAGTLLAKA 110
                                       799************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXST..HHHHHHHHHHHHHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltske..aeelsklvvdAvkl 152
                                       e+l+++++hp+ iiegy ka+++al+aL+ei  +++++ kd++ L+++++t++ssk++  +  +++++++++dA ++
  gi|320101225|ref|YP_004176817.1| 111 EELLDQNIHPSIIIEGYTKAMKEALKALDEI--AVKVNPKDKDVLRRIVNTTISSKYIGGDviSKKITEIAIDAALA 185
                                       *******************************..7777788****************6654323689*********77 PP

                                       HCCCS....EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCC CS
                        Cpn60_TCP1 153 ieene....keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvls 225
                                       + e +    +++ ++ +k++k++gg++ d++lv G+vldk+v++p mp+++enak++lld  Leiek+e++++++++
  gi|320101225|ref|YP_004176817.1| 186 VAEPKpdgtYDFRVDDVKIEKKKGGNVLDTQLVYGIVLDKEVVHPGMPRRVENAKIALLDAALEIEKPEITAKINIT 262
                                       7766679999******************************************************************* PP

                                       SCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGG CS
                        Cpn60_TCP1 226 daeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssle 302
                                       ++e +++++++e ++l+e+++ki++ g+nvvvcqkgid++a+hflak+gila+rr+k++dle+l +atG+++vss+ 
  gi|320101225|ref|YP_004176817.1| 263 SPELIKAFLDKEAEMLKEMVDKIASVGANVVVCQKGIDEVAQHFLAKKGILAVRRAKRSDLEKLERATGGRIVSSVR 339
                                       ***************************************************************************** PP

                                       GGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCH CS
                        Cpn60_TCP1 303 dltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGat 379
                                       dl+pe+lG+a  vee+++g++k+++ie++k++k++til+rga+d+v+deier+i+dAlnv++n+++++k+vpGGGa+
  gi|320101225|ref|YP_004176817.1| 340 DLKPEDLGYAALVEERRVGNDKMVFIEGCKNPKAVTILVRGASDMVMDEIERSIKDALNVLRNVMRSPKIVPGGGAV 416
                                       ***************************************************************************** PP

                                       HHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTC.EEECC CS
                        Cpn60_TCP1 380 elelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesge.iidlv 455
                                       e+ela +l+eyak++ g+eqlaieafa+ALe+ip +Lae +G +p ++l klr+ h++g+k +g+++ +ge i+d+ 
  gi|320101225|ref|YP_004176817.1| 417 EIELAMRLREYAKKIGGKEQLAIEAFASALEEIPLILAETSGREPLDTLMKLRQLHSEGKKYAGVNAVTGEiIEDMA 493
                                       ***********************************************************************6678** PP

                                       CCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 456 eagvvDplkvkrqalksAteaastiLrideiikak 490
                                       +++v++pl vk++++k+A eaa tiL+id++i a 
  gi|320101225|ref|YP_004176817.1| 494 ASNVIEPLLVKESMIKTAGEAAVTILKIDDVIAAS 528
                                       ********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3813.50
//
Query:       gi|320101226|ref|YP_004176818.1|  [L=106]
Description: DNA-directed RNA polymerase subunit omega [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-11   43.6   0.0    2.8e-11   43.2   0.0    1.2  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 !   43.2   0.0   1.5e-15   2.8e-11       4      48 ..      14      65 ..      11      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.5e-15
                                      TSS--HHHHHHHHHHHHHHH....HT...........SS-SSSSTTCHHHHTT-S- CS
                      RNA_pol_Rpb6  4 skvltrYelvriaakRArQieegesl...........etqkpvviAlrEiaegkip 48
                                      sk +tr+e +r++++RA+Q+    s+             ++pv iA++E+  g++p
  gi|320101226|ref|YP_004176818.1| 14 SKRMTRFEVARVVGARALQL----SMgappvidvsslPVKDPVYIAIKEVLTGLLP 65
                                      7999****************....8888877777775256**********999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 829.08
//
Query:       gi|320101227|ref|YP_004176819.1|  [L=366]
Description: peptidase M50 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   42.0  10.1    1.7e-07   30.8  10.1    2.7  1  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
       0.64    9.6   7.8      0.097   12.3   1.3    2.6  3  PRA1           PRA1 family protein


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 !   30.8  10.1   1.9e-11   1.7e-07       3     248 ..     118     306 ..     116     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.9e-11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp.LGGyVkmageepeeelseeeaka 78 
                                        l++ ++++ HE+GH+++ +++gv+++   ++  p +          ++ +l  +G+++ m++  p+++        
  gi|320101227|ref|YP_004176819.1| 118 TLIFALVLLTHEFGHIYISRRSGVRIDGPILLPAPPI----------QLGFLGtFGAVIYMRTLPPSRR-------- 176
                                       57899999******************88555555666..........6666656***********9988........ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...-EEECECTTTSCEE-SEEEC-XXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilailvfvv...pkkskeseeekrgviGvspkpvkkegllealkegvektlkvvvl 152
                                              + +   ++Gpl++fi a +v vv   +            vi v+++        e + +g  +   v+ l
  gi|320101227|ref|YP_004176819.1| 177 -------ELAKLGVSGPLTGFIAATIVGVVglyM----------SPVIPVEQAA-------EMMGKGELTPTPVSSL 229
                                       .......888999*************99994331..........2344444444.......7777777777778888 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 153 tvkalgklitgklslktlggpisiaqlaseaaeaglssflqllalisvnLgilNLlPipvLDGghllfalleairrk 229
                                       +++++  l  g       gg+i +             ++l ++a+i   +++lNLlPi +LDGgh+++++ +  +++
  gi|320101227|ref|YP_004176819.1| 230 MLQVITLLRPG------NGGVIVM-------------HPLLFIAYIMYLITFLNLLPIGQLDGGHVVRSFTNSETHR 287
                                       88888888877......6777755.............7889*****************************9988877 PP

                                       XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 230 plserkeevanlvglalll 248
                                        l   +  ++  vg +l l
  gi|320101227|ref|YP_004176819.1| 288 RLGSLTVMMLLAVGTLLFL 306
                                       7777666666666666655 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.23     2e+03      79     113 ..      58      93 ..      48     109 .. 0.70
   2 ?   -0.5   0.7     0.097   8.7e+02      79     106 ..      94     124 ..      71     135 .. 0.45
   3 ?   12.3   1.3   1.1e-05     0.097      53     128 ..     244     328 ..     241     343 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.23
                              PRA1  79 seplvl.fgrelsdrvvlivllvvsvlllfltgavl 113
                                       ++p+v+ ++    ++ + ++l ++s++ + ltg +l
  gi|320101227|ref|YP_004176819.1|  58 EKPVVRlIEADAGRSRFKLALTMASLITIGLTGYGL 93 
                                       566665466666777888888888888888887554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.097
                              PRA1  79 seplvlfgrelsdrvvliv...llvvsvlll 106
                                       se++  +g +++d v l+v     ++ ++l+
  gi|320101227|ref|YP_004176819.1|  94 SESFLSLGGRVADTVALAVntlAYTLIFALV 124
                                       5555556666665544433111222223333 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 1.1e-05
                              PRA1  53 slltnplslivllllvlawlflyflr...seplvl.fgrelsdr.....vvlivllvvsvlllfltgavlvllwall 120
                                       +++++pl  i+ ++ ++  l l  +      ++v+ f ++ ++r     +v+++l+v ++l+l+ ++a++ +l+  +
  gi|320101227|ref|YP_004176819.1| 244 VIVMHPLLFIAYIMYLITFLNLLPIGqldGGHVVRsFTNSETHRrlgslTVMMLLAVGTLLFLLGSSAYSFYLSLGA 320
                                       57788877777766666655555533455777776444444333599867777777777777777777777777777 PP

                              PRA1 121 iglllvll 128
                                       +++ll l+
  gi|320101227|ref|YP_004176819.1| 321 VAALLYLV 328
                                       77777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2491.65
//
Query:       gi|320101228|ref|YP_004176820.1|  [L=691]
Description: DNA topoisomerase I [Desulfurococcus mucosus DSM 2162]
Scores for 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-109  366.4   0.0   2.4e-109  366.1   0.0    1.1  1  Topoisom_bac  DNA topoisomerase
    1.6e-14   53.9   0.0    4.3e-14   52.6   0.0    1.8  1  Toprim        Toprim domain


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 !  366.1   0.0  2.7e-113  2.4e-109       2     412 ..     169     580 ..     168     581 .. 0.93

  Alignments for each domain:
  == domain 1  score: 366.1 bits;  conditional E-value: 2.7e-113
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltk....klkg.kkvlsaGRVqtptLaliveRereienFvpeeyweveatl 73 
                                       ++ ++++a+ +R+elDwl+Gin+sr+l+k    ++ g   vlsaGRVqtptL+ +ve++ e++ F+p + ++v++t 
  gi|320101228|ref|YP_004176820.1| 169 LDYEMIEAGLCRHELDWLWGINVSRALMKavedAT-GrRIVLSAGRVQTPTLKYVVEKTVERNLFIPLPQYRVTVTA 244
                                       67899************************665322.258999**********************************8 PP

                      Topoisom_bac  74 kkekkekekkkkkkkerikdkeeaeaileklkkk.eakvesvekkekkkppplpfdtttLqkeasrklglsakktls 149
                                       +++++e     + + + ++++ ea++i+e+++ +  + ve+ve k+   +pp pf++ +Lq+ea+r++g+s++kt+ 
  gi|320101228|ref|YP_004176820.1| 245 ERNGEEV--VLEYAGNPVEKHGEARSIVERVRRQgYLIVEEVEGKTYVLKPPPPFNLGDLQEEAARIYGFSPAKTQA 319
                                       6666555..6999******************99889***********997777************************ PP

                      Topoisom_bac 150 iaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkks..vvknkkveaHeAIrPte 224
                                       ia++LY +  li+YpRT+s++l+++ + + il++la+  gk y++ +++ll++t++    v ++k++ aH+AI+Pt+
  gi|320101228|ref|YP_004176820.1| 320 IAEQLYLD-ALISYPRTNSQKLPPTLNYRGILDNLAS-IGK-YSGLVASLLSETRGVLkpVEGEKEDPAHPAIYPTG 393
                                       *******7.****************669********9.576.***********99988877777777*********8 PP

                      Topoisom_bac 225 elpklkelsddekklYelIvrrflaslmkdakyeettvklev..eeeefkasgktilekGfkkvykeekkeeeeeel 299
                                         p    l+d+++ +Y+lIvrrfla ++++a+ ++ tvk     ++  fkas +++ e+G++k+y  +  + +  + 
  gi|320101228|ref|YP_004176820.1| 394 MKP--GGLTDEQWAVYDLIVRRFLAVFAQPARLTHYTVKAVTpsRDAVFKASWQRVEEQGWMKYYGFHTYKSS--RA 466
                                       877..79********************************96656999******************88777766..59 PP

                      Topoisom_bac 300 pelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalv 376
                                       p l +g+++ v +v+++e  Tkppkr+++ +++++me+ +iGt+aTra+iiekl+er+Y+  ++k + +++lG+ +v
  gi|320101228|ref|YP_004176820.1| 467 PGLVKGDKLGVVKVSMRESYTKPPKRLSKIDVLRWMESVEIGTEATRAQIIEKLFERKYLFLESKGIGVSDLGFGVV 543
                                       **************************************************************99************* PP

                      Topoisom_bac 377 ellekf.kdlvspelTaeleekLdeIaegkadakevl 412
                                       e++e+f +dl s elT+++e+++d+I++g +++ +vl
  gi|320101228|ref|YP_004176820.1| 544 EVVERFfPDLLSIELTRRFEKEMDAIRRGLRSRGQVL 580
                                       ***9999***********************9999998 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   4.8e-18   4.3e-14       1     102 [.      22     153 ..      22     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 4.8e-18
                                       EEEEESSHHHHHHHHHTHT...................STEEEEEEESSSSEEEHS..........TTEEEEE...E CS
                            Toprim   1 elvivEgpsdaktiakalg...................sgfqavtaslGhildlet..........efkpvye...e 45 
                                       +lvi+E+p++a++ia+al+                   ++   v +s+Gh+++l t          e+ p       
  gi|320101228|ref|YP_004176820.1|  22 VLVIAEKPKAARKIAEALSpgyvtrrigsipvyeinayGSMILVASSVGHLYELNTgvkgypvysyEWVPSHLvnpG 98 
                                       69******************************************************998888777766666669999 PP

                                       CTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                            Toprim  46 iedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                       ++ ++++l++lk+l + +d+ + a+D D eG+ i+++++++ +  +e+k  r++fs+
  gi|320101228|ref|YP_004176820.1|  99 KRHAREYLEVLKKLCRGVDYYVNACDYDIEGSVIGYLIIKFNG--DEEKALRAKFSS 153
                                       9999***********************************7655..666679999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 4861.65
//
Query:       gi|320101229|ref|YP_004176821.1|  [L=155]
Description: peptidase S26B, signal peptidase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-10   38.9   0.5    9.7e-10   38.3   0.5    1.4  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
       0.51    9.8   2.3       0.76    9.3   0.1    2.0  2  E1-E2_ATPase   E1-E2 ATPase


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 !   38.3   0.5   1.1e-13   9.7e-10       2      60 ..      46     108 ..      45     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.1e-13
                                       XXSSTTCCTXXTTXEEEEECTS..---TTSEEEEEETTCE-EEEEEEE....EETTEEEEE.SST CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs..epkrGdivvfrlpgeeeayiKrvi....glpgdrvllasnn 60 
                                       v+G SM ptl++Gd++l +k++  ++k+Gdiv+    +   ++i+rvi    +++   + ++ +n
  gi|320101229|ref|YP_004176821.1|  46 VKGYSMLPTLREGDVVLLEKTPpdSIKPGDIVIYSAGDR--LIIHRVIdvevRDGRYYYVTKGDN 108
                                       99*******************999**********98888..*******77655555555555555 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3     0.055     5e+02     122     143 ..      18      39 ..      10      55 .. 0.53
   2 ?    9.3   0.1   8.5e-05      0.76      16      37 ..      64      85 ..      50      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHS-STTTSS CS
                      E1-E2_ATPase 122 lvpvvlliallvflialllgks 143
                                       l ++ l++a++v+l++++l ++
  gi|320101229|ref|YP_004176821.1|  18 LLATTLALAFIVLLVLPMLLNG 39 
                                       4445555555555555554443 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 8.5e-05
                                      EEEEGGG--TTSEEEEETT-B- CS
                      E1-E2_ATPase 16 eeidakelvpGDivllkagdrv 37
                                      e+ + + ++pGDiv+  agdr 
  gi|320101229|ref|YP_004176821.1| 64 EKTPPDSIKPGDIVIYSAGDRL 85
                                      5678899************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1205.85
//
Query:       gi|320101230|ref|YP_004176822.1|  [L=100]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00061   19.6   2.4       0.14   12.0   0.3    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
     0.0019   18.1   4.7        0.2   11.6   0.2    2.6  2  zinc_ribbon_4    zinc-ribbon domain
     0.0029   17.7   0.8       0.93    9.7   0.1    2.3  2  Zn-ribbon_8      Zinc ribbon domain
     0.0029   17.6   0.2        1.5    8.8   0.1    2.2  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0037   17.6   0.5     0.0075   16.6   0.5    1.5  1  zf-IS66          zinc-finger binding domain of transposase IS
     0.0047   16.6   4.3      0.062   13.0   0.5    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
  ------ inclusion threshold ------
      0.011   15.1   1.9       0.27   10.7   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.019   14.8   4.7        1.1    9.2   0.2    2.4  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.024   14.1   0.9       0.37   10.3   0.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.025   13.7   0.6      0.029   13.5   0.6    1.1  1  GcpE             GcpE protein
      0.038   14.0   3.3       0.12   12.3   3.0    1.9  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.046   13.8   0.1        0.1   12.7   0.1    1.5  1  Elf1             Transcription elongation factor Elf1 like
      0.048   13.4   0.7      0.048   13.4   0.7    2.2  2  Zn_Tnp_IS1       InsA N-terminal domain
      0.056   13.4   0.4          3    7.9   0.1    2.1  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.08   13.3   1.6       0.57   10.6   0.1    2.2  2  DUF4379          Probable Zinc-ribbon domain
       0.08   12.7   0.7         16    5.3   0.0    2.3  2  zinc_ribbon_5    zinc-ribbon domain
      0.083   13.0   3.6        1.4    9.1   0.1    2.2  2  UPF0547          Uncharacterised protein family UPF0547
      0.086   12.5   4.5          3    7.6   0.0    2.4  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.12   12.2   2.5        2.3    8.1   0.1    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.12   11.8   0.1       0.12   11.8   0.1    2.1  2  Mu-like_Com      Mu-like prophage protein Com
       0.15   12.1   0.0       0.23   11.5   0.0    1.3  1  CpXC             CpXC protein
       0.17   12.4   2.3        3.8    8.1   0.7    2.2  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.18   11.7   0.7        9.2    6.3   0.1    2.2  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.52   10.5   3.3        3.2    8.0   0.2    2.2  2  zf-Dof           Dof domain, zinc finger
        1.1    8.9   4.7         11    5.8   0.4    2.2  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
        1.1    9.3   3.8        2.5    8.3   0.5    2.3  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        3.3    7.7   9.2        1.1    9.2   0.3    3.2  3  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
        5.2    6.9   7.7         16    5.3   0.8    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0053       3.4       2      11 ..       7      16 ..       6      22 .. 0.89
   2 !   12.0   0.3   0.00022      0.14      29      39 .]      43      53 ..      40      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0053
                           TFIIS_C  2 kCpkCgsrea 11
                                      kCp+Cgs e+
  gi|320101230|ref|YP_004176822.1|  7 KCPRCGSSEV 16
                                      8*****9986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
                           TFIIS_C 29 ykCtkCghrWr 39
                                      ++C +CghrWr
  gi|320101230|ref|YP_004176822.1| 43 MRCRSCGHRWR 53
                                      68********8 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.6    0.0045       2.9      24      32 ..       4      12 ..       2      14 .. 0.78
   2 !   11.6   0.2   0.00032       0.2      25      36 .]      42      53 ..      31      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0045
                     zinc_ribbon_4 24 vkvrCskCg 32
                                      + v+C++Cg
  gi|320101230|ref|YP_004176822.1|  4 RQVKCPRCG 12
                                      679999998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00032
                     zinc_ribbon_4 25 kvrCskCghvFr 36
                                       +rC  Cgh +r
  gi|320101230|ref|YP_004176822.1| 42 VMRCRSCGHRWR 53
                                      68*********7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0015      0.93      26      36 ..       5      16 ..       1      19 [. 0.76
   2 ?    6.5   0.0     0.014       8.9       7      14 ..      44      51 ..      42      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                       Zn-ribbon_8 26 ltaCPeCgs.ev 36
                                      +++CP+Cgs ev
  gi|320101230|ref|YP_004176822.1|  5 QVKCPRCGSsEV 16
                                      566*****9776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                       Zn-ribbon_8  7 rCeeCghe 14
                                      rC++Cgh+
  gi|320101230|ref|YP_004176822.1| 44 RCRSCGHR 51
                                      9*****98 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0024       1.5      86     102 ..       5      21 ..       1      26 [. 0.80
   2 !    7.3   0.0    0.0073       4.7      66      81 ..      38      53 ..      30      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                                       HHS-TTTSSS-EEEEES CS
                              HypA  86 alrCpkCgsadveivsG 102
                                       +++Cp+Cgs++v++ + 
  gi|320101230|ref|YP_004176822.1|   5 QVKCPRCGSSEVDVEKT 21 
                                       579*********99875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0073
                                      EE--EEEETTTS-EEE CS
                              HypA 66 evpvkvrCreCgkefe 81
                                      +v  ++rCr+Cg++++
  gi|320101230|ref|YP_004176822.1| 38 TVMGVMRCRSCGHRWR 53
                                      567789*******997 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 !   16.6   0.5   1.2e-05    0.0075       3      46 .]       7      49 ..       6      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                           zf-IS66  3 tCpcCGgllkpigedrvreeldipPakfrViehirpkyaCpcCe 46
                                      +Cp CG+  + ++++ ++ +  +p  + r++ ++  + +C++C+
  gi|320101230|ref|YP_004176822.1|  7 KCPRCGSSEVDVEKT-WQLVSPFPDSQGRITVTVMGVMRCRSCG 49
                                      5******55899999.99999999*******************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 ?    5.0   0.3     0.031        20      17      25 ..       5      13 ..       2      14 .. 0.84
   2 !   13.0   0.5   9.7e-05     0.062      17      26 ..      42      51 ..      34      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.031
                                      ----SSS-- CS
                    DNA_RNApol_7kD 17 piRCkeCGh 25
                                      +++C  CG+
  gi|320101230|ref|YP_004176822.1|  5 QVKCPRCGS 13
                                      69*****96 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.7e-05
                                      ----SSS--- CS
                    DNA_RNApol_7kD 17 piRCkeCGhR 26
                                      + RC+ CGhR
  gi|320101230|ref|YP_004176822.1| 42 VMRCRSCGHR 51
                                      68*******9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00042      0.27       3      11 ..       6      14 ..       2      20 .. 0.70
   2 ?    3.9   0.2     0.058        37      19      24 ..      45      50 ..      41      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                       zf-ribbon_3  3 vrCPnCGap 11
                                      v+CP+CG+ 
  gi|320101230|ref|YP_004176822.1|  6 VKCPRCGSS 14
                                      678888875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.058
                       zf-ribbon_3 19 CpyCGt 24
                                      C +CG+
  gi|320101230|ref|YP_004176822.1| 45 CRSCGH 50
                                      999997 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 ?    9.2   0.2    0.0017       1.1      25      36 ..       5      16 ..       3      17 .. 0.81
   2 ?    7.2   0.6    0.0074       4.8      12      19 ..      43      50 ..      42      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                           DUF35_N 25 ravCphCgsddl 36
                                      +  Cp+Cgs+++
  gi|320101230|ref|YP_004176822.1|  5 QVKCPRCGSSEV 16
                                      578******987 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0074
                           DUF35_N 12 qrCpdCGt 19
                                      +rC++CG+
  gi|320101230|ref|YP_004176822.1| 43 MRCRSCGH 50
                                      7******8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00058      0.37       2      12 ..       7      18 ..       6      23 .. 0.79
   2 ?    2.1   0.1      0.21   1.3e+02      20      26 ..      43      49 ..      40      52 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00058
                                      EETTTTCEE.CH CS
                      TF_Zn_Ribbon  2 kCPnCgstn.lv 12
                                      kCP Cgs++ +v
  gi|320101230|ref|YP_004176822.1|  7 KCPRCGSSEvDV 18
                                      9******97444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.21
                                      EEESSSS CS
                      TF_Zn_Ribbon 20 lvCtdCG 26
                                      ++C +CG
  gi|320101230|ref|YP_004176822.1| 43 MRCRSCG 49
                                      5677777 PP

>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   4.5e-05     0.029     264     302 ..       5      42 ..       1      49 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-05
                                       EEE----TTS-CHHHHHHHHHHHHCCCHHCG-EEEEESS CS
                              GcpE 264 lisCPsCgRtlfdlqelveeveealehlkkglkiavmGC 302
                                        + CP+Cg  ++d++++ + v+   ++    ++++vmG 
  gi|320101230|ref|YP_004176822.1|   5 QVKCPRCGSSEVDVEKTWQLVSPFPDSQ-GRITVTVMGV 42 
                                       689****************999888777.99******95 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.0   0.00019      0.12      19      45 ..       6      50 ..       2      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                     Zn_Tnp_IS1595 19 fvCPhCgsr..kayrikt................rglfqCkeCrk 45
                                      + CP+Cgs+   + ++++                 g+ +C++C++
  gi|320101230|ref|YP_004176822.1|  6 VKCPRCGSSevDVEKTWQlvspfpdsqgritvtvMGVMRCRSCGH 50
                                      45*******775555555888**********************98 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00016       0.1      21      62 ..       5      59 ..       2      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                              Elf1 21 kFdCpfCnheksvevkldkkek................iaevsCkvCgesfetkvnal 62
                                      + +Cp+C+++   ev+++k+ +                +++++C++Cg + +  v++l
  gi|320101230|ref|YP_004176822.1|  5 QVKCPRCGSS---EVDVEKTWQlvspfpdsqgritvtvMGVMRCRSCGHRWRGPVSKL 59
                                      679******9...7888888778899**********************9988777766 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 ?   13.4   0.7   7.6e-05     0.048       1      16 [.       1      16 [.       1      18 [. 0.92
   2 ?    1.5   0.6       0.4   2.6e+02      30      34 ..      44      48 ..      42      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                        Zn_Tnp_IS1  1 MAsVsihCPrCsstdV 16
                                      M s  + CPrC s +V
  gi|320101230|ref|YP_004176822.1|  1 MSSRQVKCPRCGSSEV 16
                                      88999********998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.4
                        Zn_Tnp_IS1 30 rCrdC 34
                                      rCr+C
  gi|320101230|ref|YP_004176822.1| 44 RCRSC 48
                                      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 ?    7.9   0.1    0.0047         3       4      12 ..       7      15 ..       1      21 [. 0.88
   2 ?    4.0   0.0     0.077        49      19      29 ..      42      52 ..      39      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0047
                    PhnA_Zn_Ribbon  4 kCplCaSey 12
                                      kCp C+S++
  gi|320101230|ref|YP_004176822.1|  7 KCPRCGSSE 15
                                      9******86 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.077
                    PhnA_Zn_Ribbon 19 llvCpeCahEw 29
                                      ++ C  C+h w
  gi|320101230|ref|YP_004176822.1| 42 VMRCRSCGHRW 52
                                      799******99 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.44   2.8e+02      31      56 .]       7      11 ..       1      23 [. 0.67
   2 ?   10.6   0.1   0.00088      0.57      31      45 ..      44      58 ..      42      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.44
                           DUF4379 31 kCakCgheWeasvsnrtkgsskCpkC 56
                                      k                     Cp C
  gi|320101230|ref|YP_004176822.1|  7 K---------------------CPRC 11
                                      4.....................5555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00088
                           DUF4379 31 kCakCgheWeasvsn 45
                                      +C+ Cgh W+  vs+
  gi|320101230|ref|YP_004176822.1| 44 RCRSCGHRWRGPVSK 58
                                      8*********99886 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.4     0.027        17      26      33 ..       6      13 ..       2      14 .. 0.61
   2 ?    5.3   0.0     0.025        16       3      23 ..      43      63 ..      42      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                     zinc_ribbon_5 26 VrCakCae 33
                                      V+C +C++
  gi|320101230|ref|YP_004176822.1|  6 VKCPRCGS 13
                                      66666654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.025
                     zinc_ribbon_5  3 irCpdCdtkFklvdsklKksg 23
                                       rC  C+   +   sklK+ g
  gi|320101230|ref|YP_004176822.1| 43 MRCRSCGHRWRGPVSKLKVGG 63
                                      69******9999999999977 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.5     0.051        33       2       7 ..       7      12 ..       6      14 .. 0.66
   2 ?    9.1   0.1    0.0022       1.4      16      24 ..      44      52 ..      42      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.051
                           UPF0547  2 vCPeCe 7 
                                      +CP+C 
  gi|320101230|ref|YP_004176822.1|  7 KCPRCG 12
                                      577774 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                           UPF0547 16 fCphCGyvF 24
                                      +C+ CG+++
  gi|320101230|ref|YP_004176822.1| 44 RCRSCGHRW 52
                                      7*9*****9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0046         3       6      20 ..       8      22 ..       8      25 .. 0.74
   2 ?    5.0   1.7     0.029        19      22      30 ..      43      51 ..      42      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0046
                     zf-NADH-PPase  6 CgrCGaptepaeggw 20
                                      C+rCG+  + +e  w
  gi|320101230|ref|YP_004176822.1|  8 CPRCGSSEVDVEKTW 22
                                      *****9776666666 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                     zf-NADH-PPase 22 rvCpaCgle 30
                                      ++C +Cg++
  gi|320101230|ref|YP_004176822.1| 43 MRCRSCGHR 51
                                      9*******7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0036       2.3       1       6 [.       7      12 ..       2      14 .. 0.60
   2 ?    4.0   0.2     0.065        42       2       7 ..      45      50 ..      41      51 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0036
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +Cp+CG
  gi|320101230|ref|YP_004176822.1|  7 KCPRCG 12
                                      455555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.065
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C +CG+
  gi|320101230|ref|YP_004176822.1| 45 CRSCGH 50
                                      666664 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 ?   11.8   0.1   0.00019      0.12      24      32 ..       5      13 ..       2      16 .. 0.90
   2 ?   -2.1   0.8       4.1   2.6e+03       6      31 ..      44      49 ..      42      53 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                       Mu-like_Com 24 tiKCPRCGt 32
                                      ++KCPRCG 
  gi|320101230|ref|YP_004176822.1|  5 QVKCPRCGS 13
                                      89******6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                       Mu-like_Com  6 RCGeCaRLLaKaeAlDeltiKCPRCG 31
                                      RC  C                    G
  gi|320101230|ref|YP_004176822.1| 44 RCRSC--------------------G 49
                                      55444....................3 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00036      0.23       1      47 [.       6      52 ..       6      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                              CpXC  1 ltCpaCgkefe..aeiwtsidadedpelkeklldgslfeatCpkCgata 47
                                      ++Cp+Cg++     ++w+++ +   p+ + ++    +  ++C +Cg++ 
  gi|320101230|ref|YP_004176822.1|  6 VKCPRCGSSEVdvEKTWQLVSPF--PDSQGRITVTVMGVMRCRSCGHRW 52
                                      79****98643114577777766..99999****************975 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        72       6      14 ..       6      14 ..       3      22 .. 0.88
   2 ?    8.1   0.7     0.006       3.8       4      17 ..      41      54 ..      40      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                   Zn_ribbon_recom  6 lrCgeCGsp 14
                                      ++C +CGs+
  gi|320101230|ref|YP_004176822.1|  6 VKCPRCGSS 14
                                      79*****95 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.006
                   Zn_ribbon_recom  4 GllrCgeCGspmtr 17
                                      G++rC  CG++ ++
  gi|320101230|ref|YP_004176822.1| 41 GVMRCRSCGHRWRG 54
                                      89*********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 ?    6.3   0.1     0.014       9.2      44      54 ..       3      13 ..       1      24 [. 0.68
   2 ?    4.1   0.1     0.068        44      46      56 ..      42      52 ..      32      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                    OrfB_Zn_ribbon 44 grtfkCpnCgf 54
                                      +r++kCp+Cg 
  gi|320101230|ref|YP_004176822.1|  3 SRQVKCPRCGS 13
                                      56677777764 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.068
                    OrfB_Zn_ribbon 46 tfkCpnCgfea 56
                                      +++C++Cg+++
  gi|320101230|ref|YP_004176822.1| 42 VMRCRSCGHRW 52
                                      78899999876 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2     0.005       3.2       3      13 ..       5      15 ..       3      19 .. 0.84
   2 ?    3.3   0.4      0.15        94      30      51 ..      44      63 ..      42      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.005
                            zf-Dof  3 alkCprCestn 13
                                      ++kCprC s++
  gi|320101230|ref|YP_004176822.1|  5 QVKCPRCGSSE 15
                                      689*****987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                            zf-Dof 30 fCkaCrryWtkgGklRnvpvgg 51
                                       C++C + W   G + ++ vgg
  gi|320101230|ref|YP_004176822.1| 44 RCRSCGHRWR--GPVSKLKVGG 63
                                      5********5..5555555555 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4     0.017        11      12      17 ..       7      12 ..       4      14 .. 0.88
   2 ?    5.0   0.4      0.03        19       6      17 ..      38      49 ..      35      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                           zf-tcix 12 kCpkCG 17
                                      kCp+CG
  gi|320101230|ref|YP_004176822.1|  7 KCPRCG 12
                                      8***** PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.03
                           zf-tcix  6 tlRGvrkCpkCG 17
                                      t+ Gv +C +CG
  gi|320101230|ref|YP_004176822.1| 38 TVMGVMRCRSCG 49
                                      899********9 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.5    0.0039       2.5       2       9 ..       6      13 ..       6      14 .. 0.88
   2 ?    1.7   0.1      0.43   2.7e+02       3       8 ..      44      49 ..      43      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0039
                            zf-ACC  2 tKCpsCge 9 
                                      +KCp+Cg+
  gi|320101230|ref|YP_004176822.1|  6 VKCPRCGS 13
                                      7*****97 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.43
                            zf-ACC  3 KCpsCg 8 
                                      +C sCg
  gi|320101230|ref|YP_004176822.1| 44 RCRSCG 49
                                      799**9 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 ?    9.2   0.3    0.0018       1.1       3      14 ..       7      18 ..       7      21 .. 0.80
   2 ?   -1.4   2.7       3.5   2.2e+03       3       9 ..      44      50 ..      44      51 .. 0.83
   3 ?    2.0   0.0      0.31     2e+02       9      22 ..      54      67 ..      52      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                                      B-TTT--BBEEE CS
                      zf-FPG_IleRS  3 pCpRCwryierv 14
                                      +CpRC+   ++v
  gi|320101230|ref|YP_004176822.1|  7 KCPRCGSSEVDV 18
                                      8*****877776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                                      B-TTT-- CS
                      zf-FPG_IleRS  3 pCpRCwr 9 
                                      +C+ C++
  gi|320101230|ref|YP_004176822.1| 44 RCRSCGH 50
                                      5999*98 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.31
                                      -BBEEEECTTEEEE CS
                      zf-FPG_IleRS  9 ryiervgqagrsty 22
                                      +++++ +++grs +
  gi|320101230|ref|YP_004176822.1| 54 GPVSKLKVGGRSLE 67
                                      688999*****986 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.8     0.026        16      16      23 ..       7      14 ..       7      15 .. 0.83
   2 ?    5.1   1.0      0.03        19       2       8 ..      44      50 ..      44      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.026
                      Rubredoxin_2 16 rCpsCgsW 23
                                      +Cp Cgs 
  gi|320101230|ref|YP_004176822.1|  7 KCPRCGSS 14
                                      7****985 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.03
                      Rubredoxin_2  2 vCsqCGf 8 
                                      +C++CG+
  gi|320101230|ref|YP_004176822.1| 44 RCRSCGH 50
                                      6888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 800.54
//
Query:       gi|320101231|ref|YP_004176823.1|  [L=104]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 865.78
//
Query:       gi|320101232|ref|YP_004176824.1|  [L=435]
Description: enolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.1e-114  382.7   0.0   1.4e-114  382.4   0.0    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    3.8e-51  172.7   0.1    7.7e-51  171.7   0.1    1.5  1  Enolase_N  Enolase, N-terminal domain
    7.2e-10   38.8   0.0    1.1e-09   38.2   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
    8.5e-05   21.8   0.0    0.00015   21.0   0.0    1.3  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 !  382.4   0.0  3.1e-118  1.4e-114       3     290 ..     148     428 ..     146     433 .. 0.97

  Alignments for each domain:
  == domain 1  score: 382.4 bits;  conditional E-value: 3.1e-118
                                       EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSH CS
                         Enolase_C   3 vlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsn 79 
                                       +lPvP+ln+inGG hagnkl++qefmi+P+g ssf++al+  +evyh+lk ++k+kyg +a nvGdeGG+aP l++ 
  gi|320101232|ref|YP_004176824.1| 148 TLPVPLLNIINGGVHAGNKLDFQEFMIVPAGFSSFHDALKAAVEVYHELKTIIKNKYGPTAVNVGDEGGYAPPLEKV 224
                                       79*************************************************************************** PP

                                       HHHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEE CS
                         Enolase_C  80 kealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsi 154
                                       ++aldl+veai+ aGy++  ++ ia+d+ass+fy+e+++ y ++++e        +t +++  ly++lv++yP+vsi
  gi|320101232|ref|YP_004176824.1| 225 RDALDLLVEAIKGAGYEPggQIAIAIDAASSQFYREDKGAYIVEGRE--------MTRDDMLLLYEKLVEDYPVVSI 293
                                       *****************988*********************999988........99******************** PP

                                       ES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EE CS
                         Enolase_C 155 edpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygv 231
                                       edpl e+d+e+++++  +lg ++ ivGddl+ tnp rl+++ie +a+na+l+kvnq+G+l+e+++ vk+a+e+gy +
  gi|320101232|ref|YP_004176824.1| 294 EDPLHEEDFEGFAEMRRRLGGRILIVGDDLFTTNPARLSKGIETGAGNAVLVKVNQVGTLSETIDVVKMAHENGYRA 370
                                       ***************************************************************************** PP

                                       EEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GG CS
                         Enolase_C 232 vvshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelgekakyaGk 290
                                       ++shrsGetedt iad++vgls+G iktGapar er akyn+ll i eel  k +y G 
  gi|320101232|ref|YP_004176824.1| 371 IISHRSGETEDTSIADIVVGLSTGLIKTGAPARGERTAKYNRLLEIAEELE-KPRYPGF 428
                                       *************************************************95.5666665 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.1   1.7e-54   7.7e-51       1     131 []      12     141 ..      12     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 1.7e-54
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       Ik+vkar++ldSrGnpTv+v+v+te   +g a +psGaStg++ea+elrDg  + ++gkgv++avenvn+ iapal+
  gi|320101232|ref|YP_004176824.1|  12 IKDVKARTVLDSRGNPTVQVRVVTEGLGVGVANAPSGASTGRHEAVELRDG-GRDFKGKGVSRAVENVNKLIAPALV 87 
                                       89**********************98889*********************9.899********************** PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       gl+ ++q e+D+ lie+Dgt+nk++lG+Nai+a+SlAvakaa++++++p+y yl
  gi|320101232|ref|YP_004176824.1|  88 GLSSRRQYEVDSKLIEIDGTPNKARLGGNAIVATSLAVAKAASSTMGVPFYYYL 141
                                       ***************************************************997 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 !   38.2   0.0   2.5e-13   1.1e-09      43     155 ..     242     373 ..     186     393 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.5e-13
                                       TTSTSEEEEE-TTTS................BHHHHHHHHHHH.GGGTESEEESSSSTTTHHHHHHHHHHHH..SSE CS
                          MR_MLE_C  43 pgddvdlmvDanqaw................dlatAirvarel.eeldllwlEEPvppeddleglaelrara..sip 100
                                       pg ++ +++Da  +                 ++++ + + ++l e++ +  +E+P++  +d eg ae r+r   +i 
  gi|320101232|ref|YP_004176824.1| 242 PGGQIAIAIDAASSQfyredkgayivegremTRDDMLLLYEKLvEDYPVVSIEDPLHE-EDFEGFAEMRRRLggRIL 317
                                       4556777777777734566666677777777777777777777477***********9.57********73367788 PP

                                       EEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEB CS
                          MR_MLE_C 101 iaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapH 155
                                       i+++   ++ +a++ + +e+ga  +v ++v++vg ++e+++v+++a+++g++ ++ 
  gi|320101232|ref|YP_004176824.1| 318 IVGDDLFTTnPARLSKGIETGAGNAVLVKVNQVGTLSETIDVVKMAHENGYRAIIS 373
                                       8888888778*****************************************97654 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 !   21.0   0.0   3.3e-08   0.00015     108     217 ..     291     394 ..     267     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.3e-08
                            MAAL_C 108 lliegPldagskeeqierlaelreklkekgikvelvaDeWcnt.ledirefvdaeaadlvqiktPDlGginntieav 183
                                       + ie+Pl +    e+ e +ae+r++l   g ++ +v D+   t    + + ++++a+++v +k+  +G++++ti+ v
  gi|320101232|ref|YP_004176824.1| 291 VSIEDPLHE----EDFEGFAEMRRRL---GGRILIVGDDLFTTnPARLSKGIETGAGNAVLVKVNQVGTLSETIDVV 360
                                       357777654....4566677777655...77899999986555167899**************************** PP

                            MAAL_C 184 lyckekgvgaylGGscnetdvsarvsvhvalatr 217
                                        +++e+g +a +   + et+ ++ + + v+l+t+
  gi|320101232|ref|YP_004176824.1| 361 KMAHENGYRAIISHRSGETEDTSIADIVVGLSTG 394
                                       ********************99999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3461.90
//
Query:       gi|320101233|ref|YP_004176825.1|  [L=81]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   1.9       0.18   11.8   1.4    1.4  2  DUF1198   Protein of unknown function (DUF1198)
       0.18   11.6   5.6       0.21   11.4   5.6    1.2  1  DUF443    Protein of unknown function (DUF443)
       0.66   10.1   5.3        3.2    7.9   1.4    2.1  2  CrgA      Cell division protein CrgA
        3.1    7.8   5.0       0.42   10.6   1.0    1.6  2  LRR19-TM  Leucine-rich repeat family 19 TM domain
        3.8    6.8   6.4        4.1    6.7   6.4    1.1  1  TMEM43    Transmembrane protein 43


Domain annotation for each model (and alignments):
>> DUF1198  Protein of unknown function (DUF1198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.8   9.9e+03      42      53 ..      10      21 ..       8      22 .. 0.75
   2 ?   11.8   1.4   5.1e-05      0.18       2      33 ..      25      56 ..      24      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.8
                                      HHHHHHTS-HHH CS
                           DUF1198 42 veslldemGkta 53
                                      v++l++ +Gk  
  gi|320101233|ref|YP_004176825.1| 10 VNALVSALGKVS 21
                                      778888898875 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.1e-05
                                      XXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHH CS
                           DUF1198  2 iWlilatlvvvfivGfrvltsdtrraikrlse 33
                                      +Wl la +v+ +++Gf +  +   ra k+l +
  gi|320101233|ref|YP_004176825.1| 25 TWLFLAGFVILLVIGFSMALTLLIRALKELPN 56
                                      6***************9988888888876643 PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.6   5.9e-05      0.21      65     111 ..      34      80 ..      27      81 .] 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                            DUF443  65 gllalGsavllgnllrklidvfniqlsklvnliillivlllvlvlri 111
                                        ll++G++++l+ l+r+l ++ n  +s+++ l ++  + l+++ l+i
  gi|320101233|ref|YP_004176825.1|  34 ILLVIGFSMALTLLIRALKELPNLTVSQFLKLTVITAIALMIIGLVI 80 
                                       5789***************************9999999999998876 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.4   0.00089       3.2      60      84 ..      18      43 ..       1      46 [. 0.75
   2 ?    4.5   0.1      0.01        36      33      47 ..      65      79 ..      50      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00089
                              CrgA 60 pfmaelgawNlliGfgl.iivGllmt 84
                                        ++++g+w +l Gf + +++G+ m+
  gi|320101233|ref|YP_004176825.1| 18 GKVSGVGTWLFLAGFVIlLVIGFSMA 43
                                      347799*********962578**997 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                              CrgA 33 wyvpvmlglmllGll 47
                                      + v++ ++lm++Gl+
  gi|320101233|ref|YP_004176825.1| 65 LTVITAIALMIIGLV 79
                                      567788888888886 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 ?   10.6   1.0   0.00012      0.42      13      38 ..      24      50 ..      12      60 .. 0.79
   2 ?   -1.3   0.2      0.61   2.2e+03      19      30 ..      64      75 ..      53      80 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                          LRR19-TM 13 ksWaylvgvvv.lalvtsllillaikc 38
                                       +W +l+g+v+ l+++ s+ ++l i++
  gi|320101233|ref|YP_004176825.1| 24 GTWLFLAGFVIlLVIGFSMALTLLIRA 50
                                      59******8762688999999998885 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.61
                          LRR19-TM 19 vgvvvlalvtsl 30
                                         v++a+ + +
  gi|320101233|ref|YP_004176825.1| 64 KLTVITAIALMI 75
                                      444555544433 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.4    0.0011       4.1     184     244 ..      23      78 ..       4      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0011
                            TMEM43 184 lltwllRllGfllmflglllllsplsvlvslipllgelvglgla.lvalllslslsllvial 244
                                       + twl+ ++ ++l+++g++++l++l   ++ +p       l+++ +++l++ ++++l++i+l
  gi|320101233|ref|YP_004176825.1|  23 VGTWLFLAGFVILLVIGFSMALTLLIRALKELPN------LTVSqFLKLTVITAIALMIIGL 78 
                                       569999999999*********9997666665555......3333377777778888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1252  (0.069831); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 615.57
//
Query:       gi|320101234|ref|YP_004176826.1|  [L=266]
Description: isopentenyl phosphate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-27   94.8   0.0    7.4e-27   94.5   0.0    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 !   94.5   0.0   4.2e-31   7.4e-27       5     241 .]      14     242 ..      11     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 4.2e-31
                                       EEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHH CS
                         AA_kinase   5 vKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeage 75 
                                       vKlGGs +t ke+      ++l+++a+ +++    +  l++  Gggsf++  +++ + +++  +             
  gi|320101234|ref|YP_004176826.1|  14 VKLGGSFITVKEKpvtlrkDALDAVAAVLKQV-HGEVGLILGNGGGSFAHYAVKK-YCVNDPVQC-----------V 77 
                                       8********66566******************.7778888888889*********.999999886...........7 PP

                                       HHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETT CS
                         AA_kinase  76 vatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldee 152
                                       v  +++   l++ +v++l+a g+pa +l+ +a+ +        s+g  ++v  + + ++l+ g +pv+ g  +++ e
  gi|320101234|ref|YP_004176826.1|  78 VKCHQSTRLLNRMVVDHLVALGVPASSLQTSAIVSA-------SPGGGYRVFPDPVYNYLSLGLIPVVYGE-CIPSE 146
                                       8889***************************99976.......45669**********************6.58999 PP

                                       TEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.......CSSS.TTTHHHHC CS
                         AA_kinase 153 gelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.......saselatgGmkvk 222
                                        +  ++s++ +  llAe +++ +++++tdV GVy+++p  +++ +l+++i+   +ee       +++ +atg+++ k
  gi|320101234|ref|YP_004176826.1| 147 RGYSVVSTEKVFELLAESIKPLRIVLVTDVKGVYTCNPYTCENPELIRRINSGNMEEvlellsrEEGRDATGSIYGK 223
                                       8888**********************************************9999999999***************** PP

                                       HHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 223 hpaalaaarrggipvvItn 241
                                       ++++ a+ rr g++v+I++
  gi|320101234|ref|YP_004176826.1| 224 VKSMSALSRRIGVKVIIVS 242
                                       **********88****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2067.46
//
Query:       gi|320101235|ref|YP_004176827.1|  [L=454]
Description: GPI mannosyltransferase 1 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   40.2  26.3    3.1e-10   40.2  26.3    2.8  3  GT87        Glycosyltransferase family 87
  ------ inclusion threshold ------
      0.024   14.4   1.5       0.75    9.6   0.4    3.0  2  Sensor_TM1  Sensor N-terminal transmembrane domain


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.3     0.067     6e+02      37      67 ..       8      38 ..       5      57 .. 0.59
   2 !   40.2  26.3   3.4e-14   3.1e-10       3     235 ..      76     307 ..      75     313 .. 0.78
   3 ?   -5.2   5.5         2   1.8e+04      50      92 ..     338     377 ..     302     438 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.067
                              GT87 37 alrlllrrlgralasavalalllaalalepv 67
                                      a+r+ll+r+ ++ ++ + ++l+ a+++l +v
  gi|320101235|ref|YP_004176827.1|  8 AMRRLLNRVPSTVRREWRIILANALALLLAV 38
                                      5566666665555555555554444444444 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 3.4e-14
                              GT87   3 YPPfaallfaplallp......yglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlgf 73 
                                       YPP+a+++f++ +l+         ++++l+  + l+a++ +++l+lrr            +  ++l+   v+  ++ 
  gi|320101235|ref|YP_004176827.1|  76 YPPLAVYIFIVPHLIAtslpysSIALVRLIDKAPLIAAFNMVYLILRRRY-------GHTAGNLWLLNYMVYGVIAD 145
                                       *************9988875666666666666779999999999999943.......33333345556677888999 PP

                              GT87  74 GqinllllllvlldllllrrrrpllaGlliGlaaaiKltPalfllylll....rrrwralaaaaatalvltalplll 146
                                        q++l+ ++ +l+++ +l +r+  +a ++i l a++K++ a+f++++l+    +r++r++a   ++ l+++ + ++ 
  gi|320101235|ref|YP_004176827.1| 146 YQFDLVAVVFLLMGFIYLTERKYTAASVMITLSALVKQLLAVFMVFPLIelfkARDYRGMARVLLVSLGVASVFIAP 222
                                       9*************99999888889**************************************88888888776666 PP

                              GT87 147 lppssleyfle.tlfdtseriaedvgnqsllslagllaralalglsavtllwlvlvllv.valaavaawrlr.rrer 220
                                       ++    + f + +l  + +  +++ +n+sl +l+ +l++   ++  a+   wl+ v++  ++la+++++ ++ r+ +
  gi|320101235|ref|YP_004176827.1| 223 FMLRNPYGFIGkVLLFH-G--ERYPQNYSLWALPVHLSW---YNI-ASLPSWLTWVWIMpFTLALLILYLYFyRDTP 292
                                       66666888888788888.5..699*****999****999...666.4556899999999988888888888855555 PP

                              GT87 221 llalaaallvall...al 235
                                       +   +   l + +   +l
  gi|320101235|ref|YP_004176827.1| 293 VGHDS---LLGYFalaSL 307
                                       55444...3333212233 PP

  == domain 3  score: -5.2 bits;  conditional E-value: 2
                              GT87  50 asavalalllaalalepvlstlgfGqinllllllvlldllllr 92 
                                       ++ + l++   ++ + p+l  l  G+   +++++v+ d l+++
  gi|320101235|ref|YP_004176827.1| 338 RTPRRLIS---LYIFIPLLIGLIAGFLIEFTAAVVGDDILMVE 377
                                       33333333...45555555555555555555555555555544 PP

>> Sensor_TM1  Sensor N-terminal transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.014   1.3e+02      15      31 ..      25      41 ..      10      45 .. 0.84
   2 ?    9.6   0.4   8.3e-05      0.75      19      37 ..     148     166 ..     146     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.014
                        Sensor_TM1 15 kIillnLlaLvvLvaGi 31
                                      +Iil n laL+  v+G 
  gi|320101235|ref|YP_004176827.1| 25 RIILANALALLLAVSGW 41
                                      8***********99996 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 8.3e-05
                        Sensor_TM1  19 lnLlaLvvLvaGiLYlnqf 37 
                                       ++L+a v+L++G++Yl++ 
  gi|320101235|ref|YP_004176827.1| 148 FDLVAVVFLLMGFIYLTER 166
                                       89**************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3231.64
//
Query:       gi|320101236|ref|YP_004176828.1|  [L=504]
Description: nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-121  403.5   0.0   1.1e-120  403.3   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
    0.00023   20.3   0.0     0.0028   16.7   0.0    2.0  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.3   0.0  1.2e-124  1.1e-120       2     462 .]      30     491 ..      29     491 .. 0.95

  Alignments for each domain:
  == domain 1  score: 403.3 bits;  conditional E-value: 1.2e-124
                                       ET-SSSEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH.HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHH CS
                            Aldedh   2 vesesetievinPatgeviakvpaataedvdaavaaAkeafk.awaklpaeeRaeiLrkaadlleerkeelaeletl 77 
                                       +++ +e ++v  P++g+ +a+v++   e vd+a+++     + + +++p  +R eiL ++a+llee++ ++++++ l
  gi|320101236|ref|YP_004176828.1|  30 IDT-GEYLDVATPIDGSLVARVSKTPWELVDSALESIYVEGRwSVRNTPGWRRLEILGRLAELLEEHRRDMVNALIL 105
                                       544.35699***************************998777699******************************** PP

                                       HH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.....TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHH CS
                            Aldedh  78 etGkplaearaeveeaidvlryyaelaeklegevlpss.....egklalvrrePlGvvgaItPWNfPlllaawklap 149
                                       + Gk+ ++a++ev+ +i+ ++  +  a+k+ ge +p +      +++a+vrreP+Gvv+aI+P+N+Pl+ ++ k+a 
  gi|320101236|ref|YP_004176828.1| 106 NSGKTRKQAEGEVNASIERVKASVFDARKIFGEYMPGDwdsttIETEAVVRREPYGVVLAIIPFNYPLFDTVSKIAY 182
                                       **********************************99976777778899***************************** PP

                                       HHHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHH CS
                            Aldedh 150 alaaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaa 226
                                         + GN+vv+KP +  pl +llla+l+eeag+P++ l v + +g+e g+ lv+++++ +vsftGs+e+gr+i+ +a+
  gi|320101236|ref|YP_004176828.1| 183 SFVSGNAVVVKPPSADPLPVLLLARLLEEAGFPRDGLAVAMVPGRESGR-LVADRRISVVSFTGSSETGRRILGSAG 258
                                       ***********************************99999999999996.77889********************** PP

                                       CTTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTS CS
                            Aldedh 227 knlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpld 303
                                         +k++++ElGG +p+ivl+daDl++a+e+i +g++++aGQ+C a++ +lv  + y e+  ++ve++++++vgdp++
  gi|320101236|ref|YP_004176828.1| 259 --IKQFIMELGGGDPAIVLPDADLEDAAEKISTGIYSYAGQRCDAIRLILVSADAYHELAGRIVERLSRVRVGDPRR 333
                                       ..9************************************************************************** PP

                                       TT-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEE....ES-TTTSHHHHS---SSEEE CS
                            Aldedh 304 edtdvGPliseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvl....anvtpdmriaqeEiFGPVls 376
                                       ed+d+GPli+ea+++++++ ve+a+++g ++l+Gg     ++  g++vePt++     +  +d +++qeE+F+PV+ 
  gi|320101236|ref|YP_004176828.1| 334 EDVDMGPLIDEAAVDTMMEAVEDAVKKGGRILYGG-----RRLGGNYVEPTLIgfedNKRIKDVKLYQEEVFAPVAL 405
                                       ***********************************.....45789*******83322223368899*********** PP

                                       EEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHH CS
                            Aldedh 377 vikfkdeeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegl 453
                                       ++++++++ea+e+aN  +yGL a+vf+ d+e ++r+++ le+G +yiNd+ ++ +   p+gG k+Sg+Greg  +++
  gi|320101236|ref|YP_004176828.1| 406 ITSYRSLDEAVELANGRRYGLDAAVFGHDIEDIRRLVRLLEFGAIYINDMPRHGIGYYPYGGRKDSGIGREGIGYSV 482
                                       ***************************************************************************** PP

                                       HHTEEEEEE CS
                            Aldedh 454 eeytevktv 462
                                       e +t +kt+
  gi|320101236|ref|YP_004176828.1| 483 EYVTAYKTI 491
                                       *****9986 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.2e-07    0.0028      83     268 ..     153     327 ..     142     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.2e-07
                              LuxC  83 syekaqprglvlhvlsgNvpllpvms.ilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyfks 158
                                          ++ p g+vl +++ N pl   +s i+ + +++n+ ++k++s dp  +  l++ l +     +   +++ v+ ++
  gi|320101236|ref|YP_004176828.1| 153 AVVRREPYGVVLAIIPFNYPLFDTVSkIAYSFVSGNAVVVKPPSADPLPVLLLARLLEEAGFP-RDGLAVAMVPGRE 228
                                       567889***************9755449*******************8887777777776664.2233455565555 PP

                              LuxC 159 gdtkleeeivqnaDvvvawGgeeaikaiseklkpgkqlikfGakvSfavvdkealeeealdkaaeraAkDiivfdQq 235
                                       +   +++       vv+  G++e+ + i + +  +  +++ G     a+v ++a    +l++aae++ + i ++  q
  gi|320101236|ref|YP_004176828.1| 229 SGRLVADR---RISVVSFTGSSETGRRILGSAGIKQFIMELGGGD-PAIVLPDA----DLEDAAEKISTGIYSYAGQ 297
                                       55555554...4789999************999988888888765.46677778....8****************** PP

                              LuxC 236 AClspqvvfvekddkieidefaeaLaaaLekra 268
                                        C + + ++v +d   +++e+a ++ + L +  
  gi|320101236|ref|YP_004176828.1| 298 RCDAIRLILVSAD---AYHELAGRIVERLSRVR 327
                                       ***********88...99999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 3784.97
//
Query:       gi|320101237|ref|YP_004176829.1|  [L=135]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   18.4   0.3     0.0027   17.7   0.3    1.4  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 !   17.7   0.3   1.5e-07    0.0027       4      62 .]      70     124 ..      67     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-07
                                       XXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   4 vGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                        G+ ++V++ +++ + g+g+   + g  ++v +++  +G +V ++It+v+  ++ Ge+l
  gi|320101237|ref|YP_004176829.1|  70 PGRILTVEIGDVD-KHGNGVVNYK-GTRIIVYNAS--LGSKVRIRITRVNGDTAYGEIL 124
                                       6888899999998.6677766666.7777777754..6******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 978.07
//
Query:       gi|320101238|ref|YP_004176830.1|  [L=111]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.7   0.0       0.24   11.1   0.0    1.4  1  Chlam_vir  Pgp3 C-terminal domain


Domain annotation for each model (and alignments):
>> Chlam_vir  Pgp3 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.4e-05      0.24      49      91 ..      62     104 ..      44     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.4e-05
                         Chlam_vir  49 adiiasrmegtvvlalvkegdskpcaisygyssgvpnvislrt 91 
                                         +ia  ++g+ v+ l k+gds+ c +s   s    n+  l +
  gi|320101238|ref|YP_004176830.1|  62 CYVIAMEIDGGYVFYLAKKGDSSLCWMSSSGSEVSKNIRRLEA 104
                                       5699***********************9998888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 784.28
//
Query:       gi|320101239|ref|YP_004176831.1|  [L=162]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-74  246.4   0.1    1.1e-73  246.2   0.1    1.0  1  Adenosine_kin  Adenosine specific kinase


Domain annotation for each model (and alignments):
>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.2   0.1   5.9e-78   1.1e-73       1     154 []       8     161 ..       8     161 .. 1.00

  Alignments for each domain:
  == domain 1  score: 246.2 bits;  conditional E-value: 5.9e-78
                                       EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEE CS
                     Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvf 77 
                                       v++e+pe++n+i+g+shfiktved+ye+lvtsvpg++fglaf+EasgkrLvr+egndeelv++av++al+ig+gh+f
  gi|320101239|ref|YP_004176831.1|   8 VDVEIPEGANIIIGRSHFIKTVEDIYEVLVTSVPGVRFGLAFNEASGKRLVRYEGNDEELVNAAVNAALKIGSGHTF 84 
                                       799************************************************************************** PP

                                       EEEEEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                     Adenosine_kin  78 villknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                       +++++na+Pin+ln++k+v+evv++++At np++v+vaet+qgr+++gvvDG+ p+gve  +d++erke+lr+igYk
  gi|320101239|ref|YP_004176831.1|  85 ILYIRNAYPINILNQLKNVQEVVSLYVATGNPVQVLVAETNQGRTIIGVVDGYPPLGVEGAADREERKEFLRRIGYK 161
                                       ****************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 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:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1165.80
//
Query:       gi|320101240|ref|YP_004176832.1|  [L=126]
Description: methylated-DNA--protein-cysteine methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-22   76.9   0.0    1.2e-21   76.6   0.0    1.1  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   6.8e-26   1.2e-21       4      81 .]      23      99 ..      20      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 6.8e-26
                                      HHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTT.TTCHHHHHHHHHHTTS CS
                     DNA_binding_1  4 qrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggy.agglerkralLeaEgv 81
                                      ++V+ l+  Ip G+ ttY+ iA+ lg   ++r V+++l  n+ +ilvPcHRVv ++g lggy  gg+  kr+lLe Egv
  gi|320101240|ref|YP_004176832.1| 23 EAVYMLTMIIPVGSATTYSSIARVLG--VHPRIVARCLSLNRDPILVPCHRVVYSNGGLGGYtPGGVGVKRRLLEVEGV 99
                                      68************************..**********************************999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 977.77
//
Query:       gi|320101241|ref|YP_004176833.1|  [L=164]
Description: molybdopterin-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-27   93.9   0.0    8.2e-27   93.6   0.0    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.22   11.4   0.0    1.3  1  M60-like_N     N-terminal domain of M60-like peptidases


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 !   93.6   0.0   9.2e-31   8.2e-27       2     140 ..      11     147 ..      10     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 9.2e-31
                                       EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHH CS
                     MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpeal 78 
                                       +++v+d+++ g+  D +g   +e+l+++g++vs  tvv+  + +i++ l+++  +++vi+++GGtGp+p+D+t+++l
  gi|320101241|ref|YP_004176833.1|  11 IVVVSDRIAGGESIDVSGEKAVEYLASRGFKVSGKTVVGNSYRDIVRVLRES--KSRVILFIGGTGPSPRDITVDVL 85 
                                       89***********************************************777..449******************** PP

                                       HHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE......TTEEEEE-SSHHHHHHHHHHHHHG CS
                     MoCF_biosynth  79 aklfekelegfeeafrrvslkpgkpvgvapgailsrav......gktiigLPGspkavkealeeillp 140
                                       + l  +el+gf+eafrr+s        +++ ailsra       g+  ++LPGs +a +++l +++ +
  gi|320101241|ref|YP_004176833.1|  86 ESLAWRELPGFGEAFRRLSSST-----IGHRAILSRAGlyilpdGRITVALPGSTQALEVGLSILV-D 147
                                       *********************7.....*********99*****555588************99988.5 PP

>> M60-like_N  N-terminal domain of M60-like peptidases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.4e-05      0.22      14      50 ..     106     144 ..      76     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                        M60-like_N  14 kpysrysswqsTGlYlppgetvtievpdnag..kanlkv 50 
                                       +++ ++  +  +GlY+ p+  +t+++p++++  +++l++
  gi|320101241|ref|YP_004176833.1| 106 STIGHRAILSRAGLYILPDGRITVALPGSTQalEVGLSI 144
                                       45578888889*****************99945444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1319.66
//
Query:       gi|320101242|ref|YP_004176834.1|  [L=241]
Description: haloacid dehalogenase domain-containing protein hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   51.6   0.0      3e-13   50.3   0.0    1.7  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.2e-06   28.9   0.0    5.1e-06   26.9   0.0    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
    2.7e-05   24.1   0.0    5.3e-05   23.2   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   4.9e-17     3e-13       3     172 ..       9     198 ..       7     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 4.9e-17
                             HAD_2   3 FDlDgTlldteeliiqafnelleeyglselseeelrkliglslr.ellrklgeseeeee.................. 60 
                                       FD+ gTl+d  +++ +  + + ++ gl    ee  r ++g +++   lr+l+++ +  e                  
  gi|320101242|ref|YP_004176834.1|   9 FDVWGTLVDLDKTLDHLSEVASRRLGL--TGEEARRAVYGSHDDaRRLRRLTPNLHPAElisrakemlaarlstetr 83 
                                       677777777777666666666655544..555555555555443145666666665555666666666666665444 PP

                             HAD_2  61 .kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivtsedvek 133
                                            l++ + + k   e  +y++v+ +L eL+eag  +g++ +     ++ +   le++g+ +yF++ v s++v+ 
  gi|320101242|ref|YP_004176834.1|  84 vVDSILFEAFTTVK--PEAILYPDVEPALSELEEAGCYMGVIGNVlfwPSSYTVTVLERIGLSRYFKTLVFSDTVGY 158
                                       22222233333333..35889***********************966679999************************ PP

                             HAD_2 134 kKPdpeviekaleklklkkeeviyvGDsp.tDieaakkag 172
                                       +KPd  +++++ e  ++++ ++i vGD++  D+ +a   g
  gi|320101242|ref|YP_004176834.1| 159 SKPDRGIFLEFAEASGFEPGRIIHVGDNTlEDVGGALSSG 198
                                       *********************************9998776 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   8.5e-10   5.1e-06       3     202 ..       6     190 ..       4     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8.5e-10
                                       EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlta 79 
                                       +v fD+ GTL++  + +  + + a             + +g    +a  a+ g+ ++ ++      + +  p +  a
  gi|320101242|ref|YP_004176834.1|   6 AVSFDVWGTLVDLDKTLDHLSEVA------------SRRLGLTGEEARRAVYGSHDDARR------LRRLTPNLHPA 64 
                                       788999999998775555555555............222222223333333333333333......33333333333 PP

                                       HHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEH..HHHH.HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxx RF
                         Hydrolase  80 ldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnp..etae.raan 153
                                       + i+   ++    + ++ r v        a  t++ +  ++p+++ a+ +L +ag+ ++++ +     + +   +++
  gi|320101242|ref|YP_004176834.1|  65 ELISRAKEMLAARLSTETRVVDSI--LFEAFTTVKPEAILYPDVEPALSELEEAGCYMGVIGNVLFwpSSYTvTVLE 139
                                       355555555555667777777766..6778888888888*****************877777554344555558999 PP

                                       HTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.H CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                         Hydrolase 154 qlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.D 202
                                       ++G  +yf+  + sd+++ +kp+  ++++ ++  + +p ++++VGD+   D
  gi|320101242|ref|YP_004176834.1| 140 RIGlSRYFKTLVFSDTVGYSKPDRGIFLEFAEASGFEPGRIIHVGDNTLeD 190
                                       999*******************************************96555 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   8.8e-09   5.3e-05       2      52 ..     158     208 ..     157     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.8e-09
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSS CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGv 52 
                                       ++KP ++++ + +e+ g +p++++ +GD+   D+ gA   G  +vL+ +  
  gi|320101242|ref|YP_004176834.1| 158 YSKPDRGIFLEFAEASGFEPGRIIHVGDNTLEDVGGALSSGFIGVLINRRT 208
                                       68***************************************9999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1801.50
//
Query:       gi|320101243|ref|YP_004176835.1|  [L=520]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3705.06
//
Query:       gi|320101244|ref|YP_004176836.1|  [L=178]
Description: inorganic diphosphatase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-57  193.6   0.0    2.1e-57  193.4   0.0    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.4   0.0   1.2e-61   2.1e-57       1     158 [.      19     172 ..      19     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 1.2e-61
                                       EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEE CS
                   Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkv 77 
                                       vv+Eip +s +Kye+dke+g l++drvl+ts+ yp+nYGfip Tle+     DgDP+Dvlv+++epl+pg+v+++++
  gi|320101244|ref|YP_004176836.1|  19 VVIEIPVNSGVKYELDKETGLLFVDRVLYTSMVYPFNYGFIPGTLEE-----DGDPVDVLVVSSEPLVPGSVIKARP 90 
                                       79*********************************************.....************************* PP

                                       EEEEEEEETTEEEEEEEEEETT..SGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHH CS
                   Pyrophosphatase  78 lGvlamiDegetDdKiiavpvk..dprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvi 152
                                       +Gvl+ +De+++D+Kiiavp++  dpr++ ++di d+p+ ++++i+hfFe+yk+le ++k+vk  +w+++eeA+k i
  gi|320101244|ref|YP_004176836.1|  91 VGVLETEDEKGRDAKIIAVPADkvDPRYSGVRDIGDIPEPVKQRIKHFFEHYKELE-PGKWVKTIGWRNREEALKRI 166
                                       ********************************************************.789***************** PP

                                       HHHHHH CS
                   Pyrophosphatase 153 eeaher 158
                                       ++a+er
  gi|320101244|ref|YP_004176836.1| 167 RAAIER 172
                                       **9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1353.20
//
Query:       gi|320101245|ref|YP_004176837.1|  [L=137]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00073   19.4   2.2      0.001   18.9   2.2    1.2  1  DUF1351          Protein of unknown function (DUF1351)
     0.0019   18.1   2.5       0.59   10.1   0.1    2.4  2  Prefoldin        Prefoldin subunit
  ------ inclusion threshold ------
      0.013   15.4   0.9      0.013   15.4   0.9    1.9  2  Sec5             Exocyst complex component Sec5
      0.014   16.2   0.9      0.072   13.9   0.4    2.0  2  Rho_Binding      Rho Binding
      0.018   14.9   0.3      0.086   12.7   0.1    2.1  2  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
      0.021   15.0   2.0      0.025   14.8   0.8    1.7  2  CREPT            Cell-cycle alteration and expression-elevate
      0.024   14.6   1.2      0.074   13.0   1.1    1.9  1  SOAR             STIM1 Orai1-activating region
      0.033   14.4   0.9      0.039   14.2   0.1    1.5  2  FliJ             Flagellar FliJ protein
      0.047   14.1   2.5          8    6.9   0.9    2.2  2  Syntaxin_2       Syntaxin-like protein
       0.22   11.8   4.7        4.9    7.5   1.0    2.5  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.32   11.5   2.8        1.3    9.5   0.2    2.2  2  DUF4094          Domain of unknown function (DUF4094)
          2    9.0   6.8    1.1e+02    3.3   7.0    2.3  1  NPV_P10          Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> DUF1351  Protein of unknown function (DUF1351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.2   6.7e-07     0.001      71     155 ..       8      98 ..       2     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.7e-07
                           DUF1351  71 ideFeakikelekkikeaidkideqikefeeke.keekkkevkaliselaeeae.veleeieiqek..wln..ktvs 141
                                       +++F + +k ++++i +  ++++e++k++e+++ ++e +k++++ +++l+ +   v+ +ei++++     n    + 
  gi|320101245|ref|YP_004176837.1|   8 VSSFRDVVKMIDDTITSLKQQLAENLKKLEDARvRAEQVKKLRETFKNLLGDEVlVSGREIDLKDAkiLINpdPLTE 84 
                                       578999************************9875899************988878******7777644334655566 PP

                           DUF1351 142 lkkieeeieaakae 155
                                       lk iee ie++ ++
  gi|320101245|ref|YP_004176837.1|  85 LKVIEEAIEKINTT 98 
                                       77777777555444 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.4    0.0017       2.6      79     111 ..      15      47 ..       6      72 .. 0.67
   2 !   10.1   0.1   0.00039      0.59      10      45 ..      83     117 ..      82     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittle 111
                                       ++ +++ +++l++ql +  ++le+++ +++++ 
  gi|320101245|ref|YP_004176837.1|  15 VKMIDDTITSLKQQLAENLKKLEDARVRAEQVK 47 
                                       566666666666666666666666666555543 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEE CS
                         Prefoldin  10 aelaqlkeaieelektletlktlkkedegkevlvpl 45 
                                       +el+ ++eaie++++t+ tl++lkk   +  ++v++
  gi|320101245|ref|YP_004176837.1|  83 TELKVIEEAIEKINTTILTLQNLKK-SLEPWTTVEV 117
                                       578999*******************.5555555554 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.9   8.5e-06     0.013     128     174 ..       5      57 ..       2      62 .. 0.88
   2 ?    1.3   0.3      0.17   2.5e+02     127     150 ..      81     104 ..      47     114 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.5e-06
                              Sec5 128 kkqvkvfkkvwsevekiieeyrkklwekLleld......esqeeflkliskLl 174
                                       +k+v+ f++v + ++++i +++++l e+L++l+      e++++  +++++Ll
  gi|320101245|ref|YP_004176837.1|   5 IKEVSSFRDVVKMIDDTITSLKQQLAENLKKLEdarvraEQVKKLRETFKNLL 57 
                                       57999****************************99988877777777777776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                              Sec5 127 dkkqvkvfkkvwsevekiieeyrk 150
                                         +++kv+++  ++++++i ++++
  gi|320101245|ref|YP_004176837.1|  81 PLTELKVIEEAIEKINTTILTLQN 104
                                       455677777777777777766654 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   4.8e-05     0.072       9      52 ..      19      62 ..      12      64 .. 0.88
   2 ?    0.4   0.0      0.78   1.2e+03      18      46 ..      84     108 ..      79     114 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                       Rho_Binding  9 akekeelnkklkkleeelekakeeeeeieklkasyekqLktErl 52
                                      +   + l+++l +  ++le a+  +e+++kl++++++ L  E l
  gi|320101245|ref|YP_004176837.1| 19 DDTITSLKQQLAENLKKLEDARVRAEQVKKLRETFKNLLGDEVL 62
                                      56678899**************99***************99986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.78
                       Rho_Binding  18 klkkleeelekakeeeeeieklkasyekq 46 
                                       +lk +ee++ek +++   +++lk    k+
  gi|320101245|ref|YP_004176837.1|  84 ELKVIEEAIEKINTTILTLQNLK----KS 108
                                       56777888888877777777777....44 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.8e-05     0.086       6      36 ..       2      32 ..       1      36 [. 0.91
   2 ?   -0.6   0.0      0.82   1.2e+03      16      29 ..      89     102 ..      85     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-05
                   HU-CCDC81_bac_2  6 siaeaegisyeeAlqkiekeveelkqeLeee 36
                                      s++ +e  s+++++++i++ +++lkq+L e+
  gi|320101245|ref|YP_004176837.1|  2 SVMIKEVSSFRDVVKMIDDTITSLKQQLAEN 32
                                      57888999********************987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.82
                   HU-CCDC81_bac_2  16 eeAlqkiekeveel 29 
                                       eeA +ki++ + +l
  gi|320101245|ref|YP_004176837.1|  89 EEAIEKINTTILTL 102
                                       56666666655433 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 ?   14.8   0.8   1.7e-05     0.025      68     118 ..       5      55 ..       1      59 [. 0.90
   2 ?   -1.3   0.0       1.5   2.2e+03      47      67 ..      89     109 ..      80     116 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                             CREPT  68 eaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelks 118
                                        +e++  + + km++d ++++k++la++ +kle+ + ++e+vk+ r++ k+
  gi|320101245|ref|YP_004176837.1|   5 IKEVSSFRDVVKMIDDTITSLKQQLAENLKKLEDARVRAEQVKKLRETFKN 55 
                                       578888899***********************************9998776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                             CREPT  47 ekllkqveealellaeYnkrL 67 
                                       e+ ++++++ +  l++  k+L
  gi|320101245|ref|YP_004176837.1|  89 EEAIEKINTTILTLQNLKKSL 109
                                       333444444444444444444 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.1     5e-05     0.074      22      73 ..      25      79 ..      19     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5e-05
                              SOAR 22 lnkkkqeaekqlqeAke...eveklkkkrssllgslrlahssslddvdkkileak 73
                                      l+++ +e+ k+l+ A+    +v+kl+   ++llg   l+ ++++d  d+kil   
  gi|320101245|ref|YP_004176837.1| 25 LKQQLAENLKKLEDARVraeQVKKLRETFKNLLGDEVLVSGREIDLKDAKILINP 79
                                      6777788999*****97222555555566789******************98655 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.6e-05     0.039      44     111 ..       5      72 ..       1      76 [. 0.81
   2 ?   -2.0   0.0       2.7     4e+03      58      69 ..      89     100 ..      83     110 .. 0.43

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                              FliJ  44 aaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeqkeenrrE 111
                                       + e   ++   + +d++i+++kq+la   k++e ar +  + ++ r++++ L   e     +e++ ++
  gi|320101245|ref|YP_004176837.1|   5 IKEVSSFRDVVKMIDDTITSLKQQLAENLKKLEDARVRAEQVKKLRETFKNLLGDEVLVSGREIDLKD 72 
                                       56677788889999999****************99999999999999999998776665555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                              FliJ  58 deaiaqqkqela 69 
                                       +eai+++  ++ 
  gi|320101245|ref|YP_004176837.1|  89 EEAIEKINTTIL 100
                                       333333333332 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9    0.0054         8      31      83 ..      11      57 ..       4      59 .. 0.71
   2 ?    6.8   0.0    0.0058       8.7       1      23 [.      88     110 ..      88     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0054
                        Syntaxin_2 31 lreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkeal 83
                                      +r+ ++ + + i+ l ++  e+lkkl+      +      q  kL++ fk++l
  gi|320101245|ref|YP_004176837.1| 11 FRDVVKMIDDTITSLKQQLAENLKKLEDARVRAE------QVKKLRETFKNLL 57
                                      5566666666777777777788888777776665......8999999999887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0058
                        Syntaxin_2   1 issnlqkinsnvstleklvkqLg 23 
                                       i++ + kin+ + tl++l k+L+
  gi|320101245|ref|YP_004176837.1|  88 IEEAIEKINTTILTLQNLKKSLE 110
                                       6889***************9986 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.0    0.0033       4.9      33      81 ..       5      53 ..       2      59 .. 0.63
   2 ?    5.4   0.1     0.015        22      64      92 ..      82     110 ..      69     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0033
                           BLOC1_2 33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81
                                      ++++ + +dv++ + +++  l+++ +e  ++l+      +qv++L e+ 
  gi|320101245|ref|YP_004176837.1|  5 IKEVSSFRDVVKMIDDTITSLKQQLAENLKKLEDARVRAEQVKKLRETF 53
                                      6677777788888888888888844444444444444456777776665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                           BLOC1_2  64 lqqidqiekqvteLeeavseLDeyskeLE 92 
                                       l++++ ie+ ++++ +++  L +  k+LE
  gi|320101245|ref|YP_004176837.1|  82 LTELKVIEEAIEKINTTILTLQNLKKSLE 110
                                       56788888888888888888888888887 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00086       1.3      57      84 ..       4      31 ..       2      35 .. 0.91
   2 ?    2.3   0.2      0.15   2.3e+02      56      79 ..      80     103 ..      40     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00086
                           DUF4094 57 ilgevskthkaiqtLdktissLemeLaa 84
                                      +++evs  +++++ +d ti sL ++La 
  gi|320101245|ref|YP_004176837.1|  4 MIKEVSSFRDVVKMIDDTITSLKQQLAE 31
                                      678***********************95 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                           DUF4094  56 dilgevskthkaiqtLdktissLe 79 
                                       d l e +  ++ai++++ ti +L+
  gi|320101245|ref|YP_004176837.1|  80 DPLTELKVIEEAIEKINTTILTLQ 103
                                       566677777899999999999997 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   7.0     0.075   1.1e+02      10      54 ..      12      56 ..       4     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.075
                           NPV_P10 10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLael 54
                                      r+ +k +dd +++l+qq+++  ++l+d     e++ ++ ++ ++l
  gi|320101245|ref|YP_004176837.1| 12 RDVVKMIDDTITSLKQQLAENLKKLEDARVRAEQVKKLRETFKNL 56
                                      788999999999999999887777888776667776666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      981  (0.0547158); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 988.07
//
Query:       gi|320101246|ref|YP_004176838.1|  [L=292]
Description: succinyl-CoA synthetase subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   93.3   0.8    2.5e-26   92.2   0.3    1.8  2  CoA_binding    CoA binding domain
    5.3e-14   52.3   0.0    8.3e-14   51.7   0.0    1.3  1  Ligase_CoA     CoA-ligase
    1.7e-13   50.6   0.0    1.3e-12   47.6   0.0    2.0  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.5e-07   31.9   0.1    3.1e-06   27.6   0.0    2.2  2  CoA_binding_2  CoA binding domain


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 !   92.2   0.3   5.6e-30   2.5e-26       2      96 .]       7     100 ..       6     100 .. 0.97
   2 ?   -2.2   0.0       1.5   6.9e+03       5      39 ..     148     182 ..     144     194 .. 0.61

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 5.6e-30
                                       TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCT.TTEEEEES-HHHHHH CS
                       CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekte.vdvavitvPaesaqe 77 
                                       + t+v+v+G++g+  +g +h+k +l+yg+++v+g++p+k+g+ v+g+pvy+s+ e++ + + vd+++++vPa++a +
  gi|320101246|ref|YP_004176838.1|   7 SATRVVVQGVTGR--EGSFHTKLMLEYGTRIVAGTSPGKGGSYVHGVPVYNSIWEAVREQGaVDASIVFVPARFAGD 81 
                                       689**********..********************************************966*************** PP

                                       HHHHHHHTT-SEEEEESST CS
                       CoA_binding  78 avdelveagikgiviiteg 96 
                                       av e+v++g++++v+iteg
  gi|320101246|ref|YP_004176838.1|  82 AVYEAVDNGVRTVVVITEG 100
                                       *****************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                       EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TT CS
                       CoA_binding   5 kviviGagglgiaglyhfkeklkygikavfgvnpr 39 
                                       +v+++  +g+ + +  +  +k +yg++ v g +++
  gi|320101246|ref|YP_004176838.1| 148 RVGIVSRSGTLTYEIARELSKHGYGVSTVLGLGGD 182
                                       55555555555555544445567777777776655 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   1.9e-17   8.3e-14       1     150 [.     152     271 ..     152     273 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.9e-17
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++++GtL+ye +  ++++              g + +++++lG+d  t         + ++i+a k + ad+ ++++
  gi|320101246|ref|YP_004176838.1| 152 VSRSGTLTYEIARELSKH--------------GYGVSTVLGLGGDPVT---------GLDFIDAAKLFFADSGTDAL 205
                                       689***************..............****************.........******************** PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraa 150
                                       ++ +++G g +e+  a++ + + e k      pvva+vaG +a+p++++++a+a+ + g+  ++sk   l+ a
  gi|320101246|ref|YP_004176838.1| 206 VVVGEIG-GDAEERFAGFYAGLAERK------PVVAYVAGRTAPPGKRMGHAGAIISMGMGDYASKRRSLEEA 271
                                       *******.***********9999998......*********************************99888776 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 ?    0.5   0.0      0.11   4.9e+02      50      77 ..      86     115 ..      81     123 .. 0.80
   2 !   47.6   0.0     3e-16   1.3e-12       1     128 [.     146     279 ..     146     285 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                      Succ_CoA_lig  50 aedpetkvillylEsi..rdgrkflsaarr 77 
                                       a d+ ++++++  E+i  +d  +f++ ar+
  gi|320101246|ref|YP_004176838.1|  86 AVDNGVRTVVVITEGIplHDELRFVNYARS 115
                                       5689999*******9833578889988886 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 3e-16
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsird.grkflsa 74 
                                       pG+++++s SG+l  ++++ ++++g g+s+v+ lG    + +d+ d  + + +d+ t++++++ E  +d  ++f+  
  gi|320101246|ref|YP_004176838.1| 146 PGRVGIVSRSGTLTYEIARELSKHGYGVSTVLGLGGdpVTGLDFIDAAKLFFADSGTDALVVVGEIGGDaEERFAGF 222
                                       79*********************************9556889***********************9999569***** PP

                      Succ_CoA_lig  75 arraarkkpvvvlksGrseagaraaashtgal....agsdavvdaafrqaGvlrvdsl 128
                                          +a++kpvv++ +Gr++   +  + h ga+    +g++a  +  +++aG+ ++++ 
  gi|320101246|ref|YP_004176838.1| 223 YAGLAERKPVVAYVAGRTAPPGKR-MGHAGAIismgMGDYASKRRSLEEAGIPVAETP 279
                                       *****************8654443.356666522235677777777777777777765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0     7e-10   3.1e-06      37     114 ..      43     129 ..      10     130 .. 0.84
   2 ?    1.8   0.0     0.075   3.4e+02       6      33 ..     149     176 ..     149     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 7e-10
                                       -..SEETTEES----T.......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHTT-E CS
                     CoA_binding_2  37 e..eeilgekvyaslaed...pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeeagir 104
                                       +  + ++g++vy s+ e+   +++vd+  vf+p+  + + v ea++ g+++v++  +      +  ++++a+++g+ 
  gi|320101246|ref|YP_004176838.1|  43 KggSYVHGVPVYNSIWEAvreQGAVDASIVFVPARFAGDAVYEAVDNGVRTVVVITEgiplHDELRFVNYARSRGVV 119
                                       344779*********9844899*****************************9999998988888899********** PP

                                       EE.ES-HHHH CS
                     CoA_binding_2 105 vvgdrCilve 114
                                       vvg++ ++v+
  gi|320101246|ref|YP_004176838.1| 120 VVGPNTPGVM 129
                                       *******997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.075
                                       ET--S-TTSHHHHHHHHHHHHT--EEEE CS
                     CoA_binding_2   6 vGasdnpgkfgykvlryllehglpvvpV 33 
                                       vG  +++g   y ++r l +hg+ v  V
  gi|320101246|ref|YP_004176838.1| 149 VGIVSRSGTLTYEIARELSKHGYGVSTV 176
                                       78999999999***********988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2255.26
//
Query:       gi|320101247|ref|YP_004176839.1|  [L=379]
Description: succinyl-CoA synthetase subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-59  198.9   0.1    4.1e-58  196.3   0.0    2.0  2  ATP-grasp_2     ATP-grasp domain
    2.6e-20   72.8   0.5    4.3e-20   72.1   0.5    1.4  1  Ligase_CoA      CoA-ligase
    4.2e-11   42.7   0.1    2.5e-10   40.2   0.1    2.2  1  ATP-grasp_5     ATP-grasp domain
    7.9e-05   22.5   0.1    0.00015   21.6   0.1    1.4  1  GARS_A          Phosphoribosylglycinamide synthetase, ATP-gra
    0.00087   19.1   0.9     0.0026   17.6   0.1    2.0  2  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
     0.0065   16.4   1.2      0.011   15.6   0.3    1.8  2  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.045   13.3   0.0      0.079   12.5   0.0    1.4  1  ATP-grasp       ATP-grasp domain


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 !  196.3   0.0   1.6e-61   4.1e-58       1     201 [.       2     195 ..       2     196 .. 0.99
   2 ?    0.3   0.0      0.17   4.4e+02     143     187 ..     333     375 ..     294     378 .. 0.68

  Alignments for each domain:
  == domain 1  score: 196.3 bits;  conditional E-value: 1.6e-61
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellg 77 
                                       +l+Ey++kei ++ygv+vp+g +a+s ee++ea ++lg++++v+KaQvl+GGRG agGvk + s eea ++a el++
  gi|320101247|ref|YP_004176839.1|   2 KLYEYEGKEIARRYGVDVPRGLLASSVEEVAEAYRRLGSQVVVLKAQVLVGGRGLAGGVKKAGSLEEAVAKAGELFS 78 
                                       69*************************************************************************** PP

                                       SEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB- CS
                       ATP-grasp_2  78 kelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl 154
                                       ++++       G++v k+lveea+ i++ElY+s+++Dras+++v ++S +GGv+iEe+a ++P+k+ ++++dp +g+
  gi|320101247|ref|YP_004176839.1|  79 TSIR-------GERVGKLLVEEAVCISRELYVSLTVDRASRRLVYLVSGMGGVEIEELARRHPDKVLRIPVDPFNGF 148
                                       ***9.......****************************************************************** PP

                                       -HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                       ATP-grasp_2 155 keeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                       ++++ar+ +  lgl+ +++  + +++ ++y+++v++da+lvE NPL+
  gi|320101247|ref|YP_004176839.1| 149 SSYMARQALGFLGLPWDKLGVLENVMRAMYRIMVDYDAELVEFNPLA 195
                                       *********************************************97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                                       EEEEEEBTTTB--HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHH CS
                       ATP-grasp_2 143 iikvaidpakglkeeqareiakklglekelvkkaakiikklyklf 187
                                       ++k ++    g +ee+ r+i+++ g+++  ++++ +++ k+++l 
  gi|320101247|ref|YP_004176839.1| 333 VAKPVVVRMLGTNEEEGRRILREHGINA--YTEMDEAVLKVVQLA 375
                                       4556666778888999999999999885..555666666665554 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.5   1.7e-23   4.3e-20       1     148 [.     254     369 ..     254     374 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1.7e-23
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++nG++L++++md+i +               g+ +++++d+G++a+           +++ ea k+++  p+vk++
  gi|320101247|ref|YP_004176839.1| 254 ISNGAGLTMATMDAILHY--------------GGRPANFLDIGGGAT----------RERVREAAKIVLTHPRVKAV 306
                                       689***************..............***************..........8******************* PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalr 148
                                       l++i++G+ +++++aa++++a+kea      +pvv+r+ Gt+++     e++++l+e g++ ++  ++a+ 
  gi|320101247|ref|YP_004176839.1| 307 LVNIFGGITRCDEVAAGVVEALKEAG---VAKPVVVRMLGTNEE-----EGRRILREHGINAYTEMDEAVL 369
                                       *************************7...***************.....***********99999888876 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.1   9.8e-14   2.5e-10      10     222 .]       3     211 ..       1     211 [. 0.80

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 9.8e-14
                       ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeile 86 
                                       L+e+e ke+ + yg++v++  lass+ee++ea +++g +vv+  +   +  +  +gGv+   + +e+v++a e + +
  gi|320101247|ref|YP_004176839.1|   3 LYEYEGKEIARRYGVDVPRGLLASSVEEVAEAYRRLGSQVVVLKAQVLVGGRGLAGGVKKAGSLEEAVAKAGELFST 79 
                                       99************************************96554444568899999***9988888888888888888 PP

                       ATP-grasp_5  87 rvkekspeariegvlVqemakrggrElivgvteDpvFGpvi..lfGlGGtavevlkdvavalpplnstlareliert 161
                                       +++     +r+ ++lV+e +   +rEl v++t D     ++  + G+GG+++e l+ ++ + +     +  +  ++ 
  gi|320101247|ref|YP_004176839.1|  80 SIRG----ERVGKLLVEEAVC-ISRELYVSLTVDRASRRLVylVSGMGGVEIEELARRHPDKVLRIPVDPFNGFSS- 150
                                       8855....8999*******88.89***********9999872256**********999544333222222233333. PP

                       ATP-grasp_5 162 kaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeeg.vvalDarirl 222
                                        +++ + g+ g +  +l  le+++  + +++vd+   + ++ nPl  + +g ++alDa++ +
  gi|320101247|ref|YP_004176839.1| 151 YMARQALGFLGLPWDKLGVLENVMRAMYRIMVDYD-AELVEFNPLAYTCSGgLTALDAKVIV 211
                                       44455568889956889999999999999999965.578899**99988666*****99976 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   5.9e-08   0.00015       7      89 ..       9      95 ..       5     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.9e-08
                                      HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-....EEEESSHHHHHHHHHHHCTS-TTCCCCS CS
                            GARS_A  7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKg....vivakseeealkavkeilekkkfGeage 81
                                      k++ +++g+  ++    +++ee+ e  ++++++++V+Ka+ l +g+g    v+ a s eea++ + e++++   Ge   
  gi|320101247|ref|YP_004176839.1|  9 KEIARRYGVDVPRGLLASSVEEVAEAYRRLGSQVVVLKAQVLVGGRGlaggVKKAGSLEEAVAKAGELFSTSIRGERVG 87
                                      788999***************************************9633336777999********************* PP

                                      SEEEEE-- CS
                            GARS_A 82 kvviEell 89
                                      k+++Ee +
  gi|320101247|ref|YP_004176839.1| 88 KLLVEEAV 95
                                      *****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 ?   -0.5   0.1      0.39   9.9e+02      74      97 ..      31      55 ..      25      91 .. 0.60
   2 !   17.6   0.1     1e-06    0.0026       2     102 ..     249     356 ..     248     373 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.39
                      Succ_CoA_lig 74 aarraark.kpvvvlksGrseagar 97
                                      +a++ +r   +vvvlk+     g+ 
  gi|320101247|ref|YP_004176839.1| 31 VAEAYRRLgSQVVVLKAQVLVGGRG 55
                                      5555555568899999876433333 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1e-06
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn.eadvdvadlleylaedpetkvillyl.Esird....grkfl 72 
                                       G+i++is   +l +a +d+  + g + ++++ +G  ++   v +  + + ++p++k++l+ +  +i +    ++  +
  gi|320101247|ref|YP_004176839.1| 249 GDIGVISNGAGLTMATMDAILHYGGRPANFLDIGGgATRERVREAAKIVLTHPRVKAVLVNIfGGITRcdevAAGVV 325
                                       99*******************************995666789****************9976366777667788999 PP

                      Succ_CoA_lig  73 saarraarkkpvvvlksGrsea.garaaash 102
                                       +a+++a  +kpvvv   G++e+ g+r  + h
  gi|320101247|ref|YP_004176839.1| 326 EALKEAGVAKPVVVRMLGTNEEeGRRILREH 356
                                       ******************9665055555555 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 ?   -1.9   0.0         1   2.6e+03      54      63 ..      66      75 ..      23     113 .. 0.62
   2 !   15.6   0.3   4.3e-06     0.011      60     121 ..     302     362 ..     284     375 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                                      HHHHHTT-SE CS
                    NAD_binding_10 54 laealkgada 63
                                      l+ea++ a  
  gi|320101247|ref|YP_004176839.1| 66 LEEAVAKAGE 75
                                      3333333333 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.3e-06
                                       T-SEEEES---TCC.HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHH CS
                    NAD_binding_10  60 gadaVvsalggggk.deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkayl 121
                                        + aV++++ gg +  +e+a+ +v+a+keagv + v+v  +g+++e  ++   + ++ ++ay 
  gi|320101247|ref|YP_004176839.1| 302 RVKAVLVNIFGGITrCDEVAAGVVEALKEAGVAKPVVVRMLGTNEEEGRRI--LREHGINAYT 362
                                       5679999997766668899************************97655443..3334455544 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05     0.079       3      80 ..      14     103 ..      12     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                                       TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEE.EECTCCGHHCHHHHC...........GTTCEE CS
                         ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqs.vvrseedleqaleal...........keekvi 67 
                                       + g+ vpr l+++s ee+ ea ++lg  vvv ++++   G+G    v+++ +le+a++ +           + +k++
  gi|320101247|ref|YP_004176839.1|  14 RYGVDVPRGLLASSVEEVAEAYRRLGSQVVVLKAQVLVGGRGLAgGVKKAGSLEEAVAKAgelfstsirgeRVGKLL 90 
                                       57899*********************999887799999****7636999999**9999999999****9988899** PP

                                       EEE----SEEEEE CS
                         ATP-grasp  68 vEefvpfekElsv 80 
                                       vEe v  ++El v
  gi|320101247|ref|YP_004176839.1|  91 VEEAVCISRELYV 103
                                       ******9999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2844.39
//
Query:       gi|320101248|ref|YP_004176840.1|  [L=307]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2417.81
//
Query:       gi|320101249|ref|YP_004176841.1|  [L=273]
Description: methylthioadenosine phosphorylase [Desulfurococcus mucosus DSM 2162]
Scores for 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-48  164.7   0.0    2.3e-48  164.5   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.5   0.0   1.3e-52   2.3e-48       2     233 ..      11     250 ..      10     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 1.3e-52
                                       EEEEESSH....HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC- CS
                         PNP_UDP_1   2 iaiivgsp....gevellaespleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefg 69 
                                       +a+i+gs+    +++++++e     tp+g +  + ++++G+l+g+++ ++ ++G    i ++ ++++a+i++lk+ g
  gi|320101249|ref|YP_004176841.1|  11 VAVIGGSGvyslPGLANVREY-KVYTPYGAP--SDNIIVGELNGRTIaFLPRHGrghrIPPHRVNYRANIWALKSIG 84 
                                       89*******999999999999.*********..*********8888879**************************** PP

                                       -SEEEEEEEEEESSTTT-TT-EEEEEEEEE.SSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTT.TTEE CS
                         PNP_UDP_1  70 vkaiiriGtaGglnpdlkvGDvvipddain.fdgrsplygpkeegqyfpdsydapadpelrallkeaaealg.ikvh 144
                                       vk +i+++++G+l++d+++GD+v+pd++i+ + g ++ ++++ +++ ++ ++d+ +++ lr+++ eaa ++  i+vh
  gi|320101249|ref|YP_004176841.1|  85 VKWVIAVSAVGSLREDYRPGDFVVPDQFIDmTKGVRAFTFFEGGSVAHVSVADP-FCECLRKKILEAAGRHSdIRVH 160
                                       ******************************645555555555558999999999.***********77777789999 PP

                                       E.EEEEEESESS-CHHHHHH.HHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHH CS
                         PNP_UDP_1 145 r.Gvvatadgfyaeteaelr.llrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaq 219
                                         G++++ +g++++t+ae+r +   + ad+v+M+ ++++ lA e+++++a+i++v+d ++ +a+++ t eev ++++
  gi|320101249|ref|YP_004176841.1| 161 GkGTYICIEGPRFSTRAESRvWRDVFKADIVGMTLVPEVNLACEAQLCYATIAMVTD-YDVWAEKPVTAEEVVATMR 236
                                       99******************6666666******************************.899**************** PP

                                       HHHHHHHHHHHHHH CS
                         PNP_UDP_1 220 eaaknaaalllall 233
                                       ++ +++++ll  ++
  gi|320101249|ref|YP_004176841.1| 237 RNTEKIQKLLPDII 250
                                       *********97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1963.65
//
Query:       gi|320101250|ref|YP_004176842.1|  [L=227]
Description: phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-16   58.2   0.0    9.9e-16   57.7   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   5.5e-20   9.9e-16      16     150 ..      18     149 ..      11     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 5.5e-20
                                       EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-.EE-EEEEEE-TTT--EE........EE----TTSEEE CS
                      Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeLevp.layvrkvkyrpdgseeaargssdesrlledpagkkVl 91 
                                        r +a++++e +++pd+vv++ rgG+++a  + d L+v+ la ++++   +  + +    ++ +     d  g  Vl
  gi|320101250|ref|YP_004176842.1|  18 SRNLARLVRESGFRPDLVVAVSRGGFVPARLVCDFLGVEnLASIQSQHWTEAAKAGERAILKYP--YRLDASGLNVL 92 
                                       57899999999*************************9998888888776666666665545444..899******** PP

                                       EE-SEESSSHHHHHHHHHHH.CC-BSEEEEEEEE.E-HHHHHHHHHH-TTS.....EEEEE CS
                      Pribosyltran  92 iVDDildtGgTllaalelLk.ekgpeevriavlv.dkpateeevdknakrvfslspdnfva 150
                                       +VDDi+dtG Tl+ a + ++ + gp ev++a+l    p  + ++d+++ +v+    ++ ++
  gi|320101250|ref|YP_004176842.1|  93 VVDDIVDTGETLRLARDYVRdNWGPREVKTAALQwISPVAKYRPDYYYLEVK----EWVWF 149
                                       *****************776367*********97777777777778888887....55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1732.81
//
Query:       gi|320101251|ref|YP_004176843.1|  [L=183]
Description: flavin reductase domain-containing FMN-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-28   99.4   0.0    2.2e-28   99.2   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.0   1.2e-32   2.2e-28       4     143 ..      14     162 ..      12     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 1.2e-32
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...S CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgp 80 
                                       +++pv++v++   +++ + + +s++ ++s +P l+a+s+ + s t++ + e+gef++n+l e++ + a   ++ sg 
  gi|320101251|ref|YP_004176843.1|  14 HPRPVYLVVSRSRGGRLNVMSASWVSPISDEPFLIAVSIWRGSLTHEYVSETGEFTVNVLGEEHLETAFKAGSVSG- 89 
                                       699*******99999999********************************************99997777777799. PP

                                       CCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTT.........B CS
                     Flavin_Reduct  81 rtddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadee.........p 143
                                       r++dk+ + gl++ +s  + +p ++gal+ leC v ++v++g ++lfi+ V av+v+ d  +          +
  gi|320101251|ref|YP_004176843.1|  90 REVDKWGLLGLKPYPSrHVSVPGVEGALGILECVVENRVPVGESTLFIAGVKAVRVNRDLYGRygwnlgkarI 162
                                       ****************99999************************************9976545555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1493.78
//
Query:       gi|320101252|ref|YP_004176844.1|  [L=119]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.015   14.2   2.1      0.017   14.0   2.1    1.1  1  Arabinose_trans  Mycobacterial cell wall arabinan synthesis p
      0.019   14.2   4.8      0.023   13.9   4.8    1.1  1  LtrA             Bacterial low temperature requirement A prot
      0.023   15.0   0.6      0.023   15.0   0.6    2.2  2  DUF2568          Protein of unknown function (DUF2568)
        6.1    7.4  10.3        2.8    8.4   0.9    2.2  2  DUF202           Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> Arabinose_trans  Mycobacterial cell wall arabinan synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.1   3.7e-06     0.017     200     266 ..      21      91 ..       7     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-06
                   Arabinose_trans 200 PaavavvvAaltlaaaPtGliavaallaalrpllrilvkrakel....gllallapllAagtlvllvvfad 266
                                        ++v +  A++t + +PtG+ a  +llaa+   + + ++r  +     +ll ll+p++Aag l+  ++   
  gi|320101252|ref|YP_004176844.1|  21 GLGVFAGSATATYSSTPTGVAAGLVLLAASMLYFYMYIERYGSRrealSLLYLLTPVVAAGSLLGALLSGP 91 
                                       55566667999999***************98877766665433323338************9887666555 PP

>> LtrA  Bacterial low temperature requirement A protein (LtrA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.8   5.2e-06     0.023      72     156 ..      19     100 ..      16     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-06
                              LtrA  72 maavlvlalsipeafeerglvfalayvvmrlvlvlqylraaradpklsarrlarvyaagllisavlwlagallpgsa 148
                                       +a++ v+a s +++ +++++ +a++ v++ + ++++y+++ r  +   +r+++++  + + ++a++ l+gall g+ 
  gi|320101252|ref|YP_004176844.1|  19 LAGLGVFAGSATATYSSTPTGVAAGLVLLAASMLYFYMYIERYGS---RREALSLLYLLTPVVAAGSLLGALLSGPS 92 
                                       58999**********************************888877...57777776677778888999999999995 PP

                              LtrA 149 rlvlwlva 156
                                       + + +++a
  gi|320101252|ref|YP_004176844.1|  93 PAAGFTAA 100
                                       55555544 PP

>> DUF2568  Protein of unknown function (DUF2568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   5.2e-06     0.023      49      91 ..       6      48 ..       4      49 .. 0.93
   2 ?   -0.6   1.2      0.37   1.7e+03      74      78 ..      96     100 ..      62     114 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.2e-06
                           DUF2568 49 Pkarvrlpgpvrlllellvfalaalalavaghptlalvfaava 91
                                      P +rv  +g +r+l  l vfa+ a a++++  + +a++++++a
  gi|320101252|ref|YP_004176844.1|  6 PVSRVLYSGKARYLAGLGVFAGSATATYSSTPTGVAAGLVLLA 48
                                      7789999********************************9987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.37
                           DUF2568  74 alava 78 
                                        + +a
  gi|320101252|ref|YP_004176844.1|  96 GFTAA 100
                                       22233 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   0.9   0.00063       2.8      21      66 ..      20      65 ..      16      67 .. 0.71
   2 ?    3.7   2.7     0.019        84      33      59 ..      88     111 ..      68     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00063
                            DUF202 21 ialglallrffltgepsalgkilglilivlgiltllvglvrylrrq 66
                                      ++lg++      t + +++g+++gl+l+++++l + + + ry +r+
  gi|320101252|ref|YP_004176844.1| 20 AGLGVFAGSATATYSSTPTGVAAGLVLLAASMLYFYMYIERYGSRR 65
                                      34444444443467777789*************9999888887665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                            DUF202  33 tgepsalgkilglilivlgiltllvgl 59 
                                        ++ps+   ++g++++++++++l+++l
  gi|320101252|ref|YP_004176844.1|  88 LSGPSP---AAGFTAAGVSVASLILVL 111
                                       445555...788999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1022.54
//
Query:       gi|320101253|ref|YP_004176845.1|  [L=296]
Description: 30S ribosomal protein S6 modification protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-21   77.0   0.0    1.8e-21   76.6   0.0    1.1  1  RimK             RimK-like ATP-grasp domain
    5.5e-10   38.9   0.0      8e-10   38.4   0.0    1.1  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    6.5e-07   29.5   0.0      2e-06   27.9   0.0    1.7  1  ATP-grasp_3      ATP-grasp domain
    1.8e-06   27.6   0.0      0.021   14.3   0.0    2.2  2  Ins134_P3_kin    Inositol 1,3,4-trisphosphate 5/6-kinase ATP-
      5e-06   26.0   0.0      0.063   12.5   0.0    2.3  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    0.00047   20.2   0.3    0.00086   19.4   0.3    1.3  1  R2K_3            ATP-grasp domain, R2K clade family 3
      0.002   17.4   0.0       0.67    9.2   0.0    2.2  2  ATPgrasp_YheCD   YheC/D like ATP-grasp
  ------ inclusion threshold ------
      0.087   12.3   0.0       0.14   11.7   0.0    1.2  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
       0.18   12.1   0.0         17    5.8   0.0    2.4  2  DUF2999          Protein of unknown function (DUF2999)


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   8.8e-25   1.8e-21       1     187 [.     101     289 ..     101     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 8.8e-25
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--. CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeai. 76 
                                       ardK+++l  L  ++++vp+t +++++  a +++ + +    vv K ++gs G++  l ++++ + +v  +l +   
  gi|320101253|ref|YP_004176845.1| 101 ARDKWRCLLHLHLKGLPVPETLVTENPFTAMRYVREKQ---LVVYKPLMGSLGLGSTLIHDPDLAFNVTRGLMNIGq 174
                                       79******************************999875...699************************999544223 PP

                                       ..EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-..EEEE----HHHHHHHHHHHHHCT-SEEEE CS
                              RimK  77 ..lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGg..vaeklqlseeekelAikaakamelvvaGv 149
                                           q ++++  + d Rv+vv++ v++a++rv +   +++n+ +G+  va k + ++e  el +ka +a++l++aGv
  gi|320101253|ref|YP_004176845.1| 175 psYYQVFLDK-PGYDYRVFVVGGRVIGAMKRV-NPYSWKTNVAQGAggVAVKESEEPEVYELGLKAVEALGLDYAGV 249
                                       5588888875.679******************.777******997611556666667788***************** PP

                                       EEE..EETTEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
                              RimK 150 Dll..rakrgllvlEvnsspglekiektlgidiakkliea 187
                                       D+   +a  g+++lEvn+ p+ e++   +g++   +++e+
  gi|320101253|ref|YP_004176845.1| 250 DVAydKATGGYYILEVNAFPQWEGLRSATGVNPPDHIVEY 289
                                       *762234468**********************99999887 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0     4e-13     8e-10      12     155 ..     118     255 ..     108     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4e-13
                                       S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EEEE CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeikeGDkRi 88 
                                       +p+tlv+++  + +++++e++ v+ KPl g+ G g   +++ d  +++   l+   g+ p   q +l++    D R+
  gi|320101253|ref|YP_004176845.1| 118 VPETLVTENPFTAMRYVREKQLVVYKPLMGSLGLGSTLIHDPDLAFNVTRGLMN-IGQ-PSYYQVFLDKPGY-DYRV 191
                                       69*************************************999999988766654.444.7889****99776.**** PP

                                       EEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETTE CS
                         GSH-S_ATP  89 llvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigdk 155
                                       ++v G+ ig a++Rv      ++n+a g+ ++a++ + ++ e+ e   +++++ Gl ++G+Dv  dk
  gi|320101253|ref|YP_004176845.1| 192 FVVGGRVIG-AMKRVNP-YSWKTNVAQGAGGVAVKES-EEPEVYELGLKAVEALGLDYAGVDVAYDK 255
                                       *********.****975.5799******999998855.5667777777789999*********8665 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0     1e-09     2e-06       1     156 [.     101     267 ..     101     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1e-09
                                       HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-------B--SS--TTE.............E CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve......l 65 
                                       a dK+++   L+ +g++vP      +  +a++  +e++ +v Kp  G+ g + +++++ + a++    +        
  gi|320101253|ref|YP_004176845.1| 101 ARDKWRCLLHLHLKGLPVPetlvteNPFTAMRYVREKQLVVYKPLMGSLGLGSTLIHDPDLAFNVTRGLMnigqpsY 177
                                       57*****************99998888999999999**************999999988666544443335666778 PP

                                       EEE---..SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEE.ES----HHHHHHHHHHHHHTTSTT--EEEE CS
                       ATP-grasp_3  66 vqefie..GkplSvsllsdgekvlvlavnrqliekaekefvyaGnv.tpietelkeevvelaeevvekleglaGyvG 139
                                        q f++  G ++ v +++      +  vn+  +++    +v +G   + ++ +++ ev+el  ++ve+l gl  y+G
  gi|320101253|ref|YP_004176845.1| 178 YQVFLDkpGYDYRVFVVGGRVIGAMKRVNPYSWKT----NVAQGAGgVAVKESEEPEVYELGLKAVEAL-GL-DYAG 248
                                       88898544888888888866555555667766655....55555431445557799*************.76.6*** PP

                                       EEEEESS...SEEEEEEES CS
                       ATP-grasp_3 140 vDlvlkd..eepyviEvNP 156
                                       vD+ + +  ++ y++EvN+
  gi|320101253|ref|YP_004176845.1| 249 VDVAYDKatGGYYILEVNA 267
                                       ****999999********7 PP

>> Ins134_P3_kin  Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00011      0.21      35      90 ..     140     199 ..     113     221 .. 0.75
   2 !   14.3   0.0     1e-05     0.021     145     189 ..     232     275 ..     221     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                       EEEEESB-S...ST.TTTEEEEE-S.GGGGTT--SSEEEEE----TTEEEEEEEETTEEE CS
                     Ins134_P3_kin  35 liakplvad...Gtakshelslvyd.qeglkklkpPlvlqefvnhggvlfkvyvvGesvk 90 
                                       ++ kpl      G++  h+  l+++  +gl  +  P   q f++  g  ++v+vvG  v 
  gi|320101253|ref|YP_004176845.1| 140 VVYKPLMGSlglGSTLIHDPDLAFNvTRGLMNIGQPSYYQVFLDKPGYDYRVFVVGGRVI 199
                                       45566554333388889999999984579**************************97653 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHH---EEEEEEEE-TTT.--EEEEEEEES---TT-T CS
                     Ins134_P3_kin 145 eelakalrralGlrLfnldiirdaktkdrylvidinyfPGyakmp 189
                                        el+ +  +alGl   ++d+  d+ t + y+++++n+fP ++++ 
  gi|320101253|ref|YP_004176845.1| 232 YELGLKAVEALGLDYAGVDVAYDKAT-GGYYILEVNAFPQWEGLR 275
                                       566767779*************9998.89**********999875 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 !   11.4   0.0   6.9e-05      0.14       5      80 ..      87     157 ..      83     169 .. 0.79
   2 !   12.5   0.0   3.1e-05     0.063     227     268 ..     230     271 ..     201     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                       ATPgrasp_ST   5 rlirkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleeg.vviKpakgsgGkGilvit 80 
                                       +li+ +N+ +   +  dK  +   ++ +gl+vp++l++   ++ ++++  +v+e   + vv Kp  gs+G G + i 
  gi|320101253|ref|YP_004176845.1|  87 SLIPVVNDPSRSLVARDKWRCLLHLHLKGLPVPETLVT---ENPFTAM-RYVREK--QlVVYKPLMGSLGLGSTLIH 157
                                       78999*****************************5544...3333333.344444..449************98885 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.1e-05
                       ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivlde.ekgplllElNarpgl 268
                                       ev el  ka e  +gl y G+D++ d+ ++g ++lE+Na p  
  gi|320101253|ref|YP_004176845.1| 230 EVYELGLKAVE-ALGLDYAGVDVAYDKaTGGYYILEVNAFPQW 271
                                       789999*****.9*************8357899*****98765 PP

>> R2K_3  ATP-grasp domain, R2K clade family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.3   4.3e-07   0.00086     118     184 ..     188     268 ..     176     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.3e-07
                             R2K_3 118 EwRvFvvdGevvaa....srYr....kanddpdl.........epdlaafa.eavralvgappfyvlDvavtad.Gr 175
                                        +RvFvv+G+v++a     +Y      a++   +         ep++ ++  +av+al+  +    +Dva+++  G 
  gi|320101253|ref|YP_004176845.1| 188 DYRVFVVGGRVIGAmkrvNPYSwktnVAQG---AggvavkeseEPEVYELGlKAVEALG--LDYAGVDVAYDKAtGG 259
                                       79**********982222455565553344...14458888554555554337777888..***********97799 PP

                             R2K_3 176 wkVVEvndg 184
                                       +++ Evn++
  gi|320101253|ref|YP_004176845.1| 260 YYILEVNAF 268
                                       *******86 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00033      0.67      11      67 ..     103     156 ..      98     176 .. 0.84
   2 !    6.2   0.0    0.0026       5.2     207     235 ..     247     276 ..     206     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00033
                    ATPgrasp_YheCD  11 nKwevyelLskdpelrpyLPetellesledleemlekyksvylKpanGskGkgilri 67 
                                       +Kw++  +L+ +      +Pet   e++ +  +++++ + v+ Kp  Gs+G g   i
  gi|320101253|ref|YP_004176845.1| 103 DKWRCLLHLHLKG---LPVPETLVTENPFTAMRYVREKQLVVYKPLMGSLGLGSTLI 156
                                       6777666666655...458********************************886555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0026
                    ATPgrasp_YheCD 207 lGlDlgidk.egkvWllEvNskpgrsifke 235
                                        G+D++ dk +g +++lEvN+ p+ +  + 
  gi|320101253|ref|YP_004176845.1| 247 AGVDVAYDKaTGGYYILEVNAFPQWEGLRS 276
                                       499*****84589********999776665 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     7e-05      0.14     128     176 ..     221     269 ..     204     274 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7e-05
                                       ----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEEEESS- CS
                   Dala_Dala_lig_C 128 aklekeveekiqelalkaykaldlrGlaRvDffl.teegeivlnEvNtlP 176
                                       +++++++e ++ el lka +al+l + a vD+ + +++g  ++ EvN  P
  gi|320101253|ref|YP_004176845.1| 221 VAVKESEEPEVYELGLKAVEALGL-DYAGVDVAYdKATGGYYILEVNAFP 269
                                       578899999*************98.7999*****7789**********99 PP

>> DUF2999  Protein of unknown function (DUF2999)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.032        64      25      38 ..     123     136 ..     118     165 .. 0.81
   2 ?    5.8   0.0    0.0083        17      62      80 ..     237     255 ..     227     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.032
                           DUF2999  25 ltenPlaamaliqq 38 
                                       +tenP+ am  + +
  gi|320101253|ref|YP_004176845.1| 123 VTENPFTAMRYVRE 136
                                       69*******99865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0083
                           DUF2999  62 eaveelgldfskveaakak 80 
                                       +ave lgld++ v+ a +k
  gi|320101253|ref|YP_004176845.1| 237 KAVEALGLDYAGVDVAYDK 255
                                       79************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2481.12
//
Query:       gi|320101254|ref|YP_004176846.1|  [L=372]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   11.8   0.1       0.13   11.8   0.1    1.4  2  DUF4795   Domain of unknown function (DUF4795)


Domain annotation for each model (and alignments):
>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.5e-06      0.13     112     170 ..     248     308 ..     244     312 .. 0.84
   2 ?   -3.7   0.1      0.41   7.3e+03      12      27 ..     341     356 ..     330     363 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.5e-06
                           DUF4795 112 kkaldtLqeelkekldrlelepLkeqleerlkelqkelqeamekedk..edeaaglrkkLl 170
                                       +k+  +L++elk ++++ e++++++ + e  ke+q + +e+ e e+   +  +a+   kL+
  gi|320101254|ref|YP_004176846.1| 248 DKLPVELRSELKARIEKGEVKSIRDVVGEVRKEIQLRAEERREREYRqvASIMAAALAKLS 308
                                       55666899***************************99999988888788667777777775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.41
                           DUF4795  12 lqeaieklqeelekle 27 
                                       lq  +++lq +l++l+
  gi|320101254|ref|YP_004176846.1| 341 LQLSLQELQGKLSNLN 356
                                       4444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3088.94
//
Query:       gi|320101255|ref|YP_004176847.1|  [L=376]
Description: radical SAM protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-14   52.5   0.0    1.5e-13   51.4   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    7.1e-05   23.1   0.0    0.00013   22.3   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.022   14.9   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   2.6e-17   1.5e-13       2     166 ..     160     317 ..     159     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.6e-17
                                       EEESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       v++ gCn++C++C+++e  +  + r+ ++     l+++++    +g++++  +ggep+ + +f  +le l++l+  +
  gi|320101255|ref|YP_004176847.1| 160 VFYGGCNFKCVYCQNWEIsQ-VHARSGERVAPGRLAIIQRWLRLNGARNINHVGGEPTPHLPF--ILESLKHLD-VN 232
                                       7899*************953.3333333333333333333322334*************8877..788888885.8* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpG 154
                                       +     +n ++  +e +++l +  vd    +l+ +++e+  +l + ++ +e   +++++++++ ++ +++r+++lpG
  gi|320101255|ref|YP_004176847.1| 233 VPQLWNSNMYMS-WESMRLLID-IVDIWLPDLKYGSNECAWRLSKVRNYWEVATRNIKAAHDS-GD-IIIRHLVLPG 305
                                       ***********8.*********.55*************666777788****************.67.9********* PP

                                       TSHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 155 endeeleellel 166
                                         +   + +le+
  gi|320101255|ref|YP_004176847.1| 306 HVECCTRRVLEW 317
                                       987666666665 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.1e-08   0.00013       9      95 ..     159     243 ..     149     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.1e-08
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfk..sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeek 83 
                                       ++f +gCn++C +C n e+ +++  sg+ +    l+ i + l  +  + +  +GGEP    + + +le +k++  + 
  gi|320101255|ref|YP_004176847.1| 159 TVFYGGCNFKCVYCQNWEISQVHarSGERVAPGRLAIIQRWLRLNGARNINHVGGEPTP--HLPFILESLKHLDVNV 233
                                       79****************99776447888876666666666777999************..9999999999999999 PP

                           Fer4_12  84 pekdiwlytgyt 95 
                                       p  + w ++ y+
  gi|320101255|ref|YP_004176847.1| 234 P--QLWNSNMYM 243
                                       9..589888876 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.7e-06     0.022       2      77 ..     161     232 ..     160     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-06
                           Fer4_14   2 fvrlsgCnlsCkgCdnke..twkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlke 76 
                                       f   +gCn++C+ C n e  + + ++g+  +   l +i++     + +++ +  +GGeP  +   + +l+ +k+l  
  gi|320101255|ref|YP_004176847.1| 161 FY--GGCNFKCVYCQNWEisQVHARSGERVAPGRL-AIIQRWLRLNGARN-INHVGGEPTPH--LPFILESLKHLDV 231
                                       44..9**********76511455578888888888.78877777777566.999*****855..6777776666665 PP

                           Fer4_14  77 e 77 
                                       +
  gi|320101255|ref|YP_004176847.1| 232 N 232
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2987.22
//
Query:       gi|320101256|ref|YP_004176848.1|  [L=131]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 951.85
//
Query:       gi|320101257|ref|YP_004176849.1|  [L=815]
Description: valyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  370.3   0.0   3.7e-109  365.7   0.0    2.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.9e-29  102.6   0.3    3.5e-29  101.7   0.3    1.4  1  Anticodon_1    Anticodon-binding domain of tRNA
      2e-28   99.3   1.0    2.7e-14   52.7   0.0    4.2  3  tRNA-synt_1g   tRNA synthetases class I (M)
      2e-05   24.2   0.0     0.0023   17.5   0.0    2.3  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    0.00079   19.6   0.5        3.7    7.6   0.3    4.1  2  Mut7-C         Mut7-C RNAse domain
  ------ inclusion threshold ------
      0.028   13.7   2.1        5.8    6.3   0.0    3.5  3  zf-TFIIB       Transcription factor zinc-finger
       0.03   13.2   0.0        1.5    7.6   0.0    2.4  2  tRNA-synt_1f   tRNA synthetases class I (K)
      0.085   12.9   0.7        9.5    6.3   0.1    3.0  3  DZR            Double zinc ribbon
       0.11   11.8   0.0        4.8    6.4   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
          4    7.6   6.8      1e+02    3.1   0.1    4.3  4  zf-ACC         Acetyl-coA carboxylase zinc finger 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 !  365.7   0.0  2.1e-112  3.7e-109       2     601 ..      22     583 ..      21     584 .. 0.94

  Alignments for each domain:
  == domain 1  score: 365.7 bits;  conditional E-value: 2.1e-112
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       l++kWe e++++ + +  + ++   +  +PPy+ G+ H+G a + +  d+v ry rmkG++vl  +  D  Gl++e 
  gi|320101257|ref|YP_004176849.1|  22 LLDKWEGEGIHEFKADPGDPREIIAIDTPPPYASGKWHVGGAAHYAQIDMVARYFRMKGYNVLVPFYADRNGLPVEV 98 
                                       6899******9999888888999****************************************************** PP

                       tRNA-synt_1  79 kvekklgakekk.erkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                       +vek +  + +k + +  gre+f + +re+ ++   +i + ++rlG s+ + ++  T ++e+   ++ +f +l++kg
  gi|320101257|ref|YP_004176849.1|  99 QVEKAYKVNPHKlSSTPEGREHFLKLCREFLDKAERDIVSVWRRLGCSFQYWKN-GTDSEEYRRITQATFIELYKKG 174
                                       *****9877655266778********************************9876.5889****************** PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitke 231
                                       liy+++++vnw+++++t+l+++E ey +++ +l++++f++++  e +lv+aTT+Pe l + +a++ +p         
  gi|320101257|ref|YP_004176849.1| 175 LIYEAERPVNWCPRCRTSLADAELEYVEEDTYLYYIRFQVKETGE-HLVVATTRPELLRSCKALVYHPG-------- 242
                                       *******************************************99.***********************........ PP

                       tRNA-synt_1 232 klilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                                              der+++ +g ++ +p+ + ++pi++ + vd   GtG+V +  + d+ D ++ ++
  gi|320101257|ref|YP_004176849.1| 243 -----------------------DERYSKYKGMHAVNPVYGHEMPILEYEEVDPGYGTGLVMVCSYGDQADVKMFRD 296
                                       .......................9***************************************************** PP

                       tRNA-synt_1 309 ynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvk 385
                                        +le+++i+ +dg lteea+  +glk ++ar k+ e l+ kgll+k+e+i+hs+p+c+r k+pi    ++ Wf ++ 
  gi|320101257|ref|YP_004176849.1| 297 LGLEPLVIVSKDGYLTEEAGPIAGLKPEEARVKIAEILESKGLLVKKERIRHSIPVCWRCKTPIQIVNSKEWFLKQL 373
                                       ***************************************************************************** PP

                       tRNA-synt_1 386 eladaalkavekvqfvpkskekryaswleni.qdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeae 461
                                       e++da+lk +e++ f+p  ++++  +w++ +  dW iS++r++ + ipl++ ++ + +   e   ++        + 
  gi|320101257|ref|YP_004176849.1| 374 EFKDALLKLIEQIDFKPPLHKRKLVDWVNSVsTDWPISKDRYYATEIPLWRCSRCGSILLPEPGRYYR-----PWRD 445
                                       *****************************9836***********************888833322222.....2333 PP

                       tRNA-synt_1 462 kkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlills 538
                                        + ++k  +   +  +++l  ++ v+D+WF+S+ +   + +y  +    ++k+f   +  +G Diir W++ ++l  
  gi|320101257|ref|YP_004176849.1| 446 PAPWDKCPV--CGAPRESLVGESKVFDTWFDSSISVLYVTHYMRN-PALFEKAFKHTLRPQGQDIIRTWLYYSLLRV 519
                                       333343333..4889**************************9988.899**************************** PP

                       tRNA-synt_1 539 laltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                        +ltg+  fk v ++g+ +de+G  m Ks+gNvidp+  i+kygada R++ + +++ g d ++
  gi|320101257|ref|YP_004176849.1| 520 YQLTGKPAFKWVRITGMGLDEKGEAMHKSKGNVIDPDPFIEKYGADAFRYWAAaSAKLGYDYRF 583
                                       ****************************************************988888888776 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 !  101.7   0.3   1.9e-32   3.5e-29       1     150 [.     620     767 ..     620     770 .. 0.89

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 1.9e-32
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk...ra.aqevllevletl 73 
                                       d+  l+ l +++++v++ay e++ ++ +++ly+f+wn ++++y+el+k+r y+++++ +   ++ a ++l++ l+++
  gi|320101257|ref|YP_004176849.1| 620 DKATLAYLGRVLEKVDKAYSELDVYEPVNELYQFTWNYFASHYIELTKSRAYNREGKYSeleQKaAWYTLHYTLKAV 696
                                       7888999*************************************************999**966699********** PP

                       Anticodon_1  74 lrllaPfmPfitEelwqreeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselk 149
                                       lr laP+mPfit+ ++    +e  + +s++ + +pe  ee+ ++ +    v+++ ++ +ai  +++++++k s +lk
  gi|320101257|ref|YP_004176849.1| 697 LRALAPIMPFITDAIY----RE-LYGRSVHTERFPEPLEEHlKQPH--DLVDRVMNADSAIWGYKKKKGLKLSDPLK 766
                                       ****************....55.46678*******85545534444..689998888999999**********9977 PP

                       Anticodon_1 150 v 150
                                        
  gi|320101257|ref|YP_004176849.1| 767 T 767
                                       5 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 !   52.7   0.0   1.5e-17   2.7e-14       2     136 ..      46     199 ..      45     203 .. 0.83
   2 !   16.4   0.1   1.6e-06    0.0029     167     238 ..     351     421 ..     319     428 .. 0.88
   3 !   23.2   0.0   1.4e-08   2.5e-05     241     371 ..     465     588 ..     455     594 .. 0.74

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.5e-17
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HH............. CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpe............. 64 
                                        + t+ pYa+gk H+G ++++ + D++aRy r++g++vl     D  G p+e++ ek+ +v+p+             
  gi|320101257|ref|YP_004176849.1|  46 AIDTPPPYASGKWHVGGAAHYAQIDMVARYFRMKGYNVLVPFYADRNGLPVEVQVEKAyKVNPHklsstpegrehfl 122
                                       578999**********************************************9988753556541111111222222 PP

                                       ....HHHHHHHHHHHHHHHHTT---SEEEE.TTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                      tRNA-synt_1g  65 ....elvekvheeikelfkklnisfdkygr.ttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                           e+ +k+++ i +++++l+ sf ++++ t+see ++++q+ f +l++kgliye e  + +cp++ + l+d ++e
  gi|320101257|ref|YP_004176849.1| 123 klcrEFLDKAERDIVSVWRRLGCSFQYWKNgTDSEEYRRITQATFIELYKKGLIYEAERPVNWCPRCRTSLADAELE 199
                                       22225567888889999***********8747889999***********************************8765 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.6e-06
                                       ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       p++  +++  ++ +++++f+k  +f+++l + ie+ +  ++   k+++ +w+++  +d+ is+d  ++ ++P
  gi|320101257|ref|YP_004176849.1| 351 PVCWRCKTPIQIVNSKEWFLKQLEFKDALLKLIEQID-FKPPLHKRKLVDWVNSVSTDWPISKDRYYATEIP 421
                                       88999999999999*******************4444.57788888889********************999 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.4e-08
                                       CCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH...TT----S- CS
                      tRNA-synt_1g 241 ekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg...aelklpkk 314
                                       e+kv+  W+d  i  + +t+++     ++  +++ + k    +     g+dii+  t ++ ++l     ++  + k 
  gi|320101257|ref|YP_004176849.1| 465 ESKVFDTWFDSSISVLYVTHYMR----NPALFEKAF-K----HTLRPQGQDIIR--TWLYYSLLRVyqlTGKPAFKW 530
                                       56788888888888888887765....566777777.2....345556888886..333333333322333345555 PP

                                       EEEE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHH CS
                      tRNA-synt_1g 315 vvahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedf 371
                                       v  +++ l  +g+ + kS+g+v++++ ++e++ ad++RY+ aa+a+   D  fs++++
  gi|320101257|ref|YP_004176849.1| 531 VRITGMgLDEKGEAMHKSKGNVIDPDPFIEKYGADAFRYWAAASAKLGYDYRFSEQTL 588
                                       66666547789******************************************99876 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 ?    4.3   0.0     0.014        25      11      39 ..     209     237 ..     208     249 .. 0.87
   2 !   17.5   0.0   1.3e-06    0.0023      85     143 ..     250     308 ..     243     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                     tRNA-synt_1_2  11 eiefkveeseeklevfttrpdtlfGvtfv 39 
                                        i+f+v+e+ e+l v ttrp+ l + + +
  gi|320101257|ref|YP_004176849.1| 209 YIRFQVKETGEHLVVATTRPELLRSCKAL 237
                                       599******99**********99877655 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.3e-06
                     tRNA-synt_1_2  85 tglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpe 143
                                       +g++a++P+ g+++pi   + v  +ygtg vm +   dq D +  +  +l+   +++++
  gi|320101257|ref|YP_004176849.1| 250 KGMHAVNPVYGHEMPILEYEEVDPGYGTGLVMVCSYGDQADVKMFRDLGLEPLVIVSKD 308
                                       799******************************************99999988887754 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.3    0.0021       3.7       9     111 ..      69     204 ..      66     223 .. 0.58
   2 !    5.7   0.0     0.008        14      28     110 ..     287     370 ..     274     432 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0021
                            Mut7-C   9 lgklakyLRllGydalyasdv................edeellalaakekrillTrdreLlkraklkkgvl...... 63 
                                       +  +a+y+R+ Gy++l+   +                                    ++L +  + ++++l      
  gi|320101257|ref|YP_004176849.1|  69 IDMVARYFRMKGYNVLVPFYAdrnglpvevqvekaykV-----------------NPHKLSSTPEGREHFLklcref 128
                                       6789**********997775411233333333333330.................3444444444443333344444 PP

                            Mut7-C  64 .............................ltsrdveeqlreviarlglklslkpelsrCvaCngeleevekeevker 111
                                                                      +r +++ ++e+  + gl +++++ ++ C +C + l+ +e e v+e+
  gi|320101257|ref|YP_004176849.1| 129 ldkaerdivsvwrrlgcsfqywkngtdseEYRRITQATFIELY-KKGLIYEAERPVNWCPRCRTSLADAELEYVEED 204
                                       4555555555556666666666666655445666677777884.445666666668888888888888877777665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.008
                            Mut7-C  28 dvedeellalaakekrillTrdreLlkraklkkgvlltsrdveeqlreviarlglkl...slkpelsrCvaCngele 101
                                       d++d ++ +    e  +++++d  L ++a   +   l+ ++ + +++e+++  gl +   ++++ +  C +C ++++
  gi|320101257|ref|YP_004176849.1| 287 DQADVKMFRDLGLEPLVIVSKDGYLTEEAGPIA--GLKPEEARVKIAEILESKGLLVkkeRIRHSIPVCWRCKTPIQ 361
                                       667777888888888899999999999888774..445566666777777777765511245556667888888888 PP

                            Mut7-C 102 evekeevke 110
                                        v+++e   
  gi|320101257|ref|YP_004176849.1| 362 IVNSKEWFL 370
                                       887776543 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0032       5.8       2      17 ..     186     201 ..     185     205 .. 0.84
   2 ?    3.0   0.0     0.036        64      15      26 ..     418     429 ..     413     435 .. 0.86
   3 ?    1.5   0.1      0.11   1.9e+02       1       8 [.     451     458 ..     451     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0032
                          zf-TFIIB   2 CPkCqdeleeserggv 17 
                                       CP+C+++l ++e+  v
  gi|320101257|ref|YP_004176849.1| 186 CPRCRTSLADAELEYV 201
                                       ********99998665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.036
                          zf-TFIIB  15 ggveidyCpqCr 26 
                                        ++++++C +C+
  gi|320101257|ref|YP_004176849.1| 418 TEIPLWRCSRCG 429
                                       589********8 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.11
                          zf-TFIIB   1 kCPkCqde 8  
                                       kCP+C+++
  gi|320101257|ref|YP_004176849.1| 451 KCPVCGAP 458
                                       8****986 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 ?    2.8   0.0     0.026        46      33      64 ..      54      85 ..      49     151 .. 0.87
   2 ?    7.6   0.0   0.00086       1.5     275     310 ..     538     573 ..     525     586 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.026
                      tRNA-synt_1f 33 pSGliHiGnlrevltadlvaralrkrgeevrl 64
                                      +SG+ H+G +   ++ d+var +r +g +v +
  gi|320101257|ref|YP_004176849.1| 54 ASGKWHVGGAAHYAQIDMVARYFRMKGYNVLV 85
                                      59**********************99988754 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00086
                      tRNA-synt_1f 275 llkggekmssSkGnvltledwlevaepevlrflilr 310
                                       l+++ge+m++SkGnv+ ++  +e +  +  r+  + 
  gi|320101257|ref|YP_004176849.1| 538 LDEKGEAMHKSKGNVIDPDPFIEKYGADAFRYWAAA 573
                                       578899***************999999999998765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.1   1.8e+02      14      23 ..     185     194 ..     175     211 .. 0.79
   2 ?    0.1   0.0      0.47   8.4e+02      30      38 ..     352     360 ..     341     369 .. 0.66
   3 ?    6.3   0.1    0.0053       9.5      15      37 ..     425     458 ..     420     462 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.1
                               DZR  14 fCseCgtklk 23 
                                        C++C+t+l 
  gi|320101257|ref|YP_004176849.1| 185 WCPRCRTSLA 194
                                       5777777775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                               DZR  30 rCpsCgekv 38 
                                       +C++C++++
  gi|320101257|ref|YP_004176849.1| 352 VCWRCKTPI 360
                                       455555543 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0053
                               DZR  15 CseCgtklkavaa...........edrCpsCgek 37 
                                       Cs+Cg+ l +++             d+Cp Cg++
  gi|320101257|ref|YP_004176849.1| 425 CSRCGSILLPEPGryyrpwrdpapWDKCPVCGAP 458
                                       999**998877778999999999999*****987 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0027       4.8      22      48 ..      57      83 ..      49      89 .. 0.91
   2 ?    2.7   0.0     0.038        68     250     295 ..     541     587 ..     523     591 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0027
                                      --BHHHHHHHHHHHHHHHHHHHTT-EE CS
                      tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdv 48
                                      + h+G a  +  +D+++r+++++gY+v
  gi|320101257|ref|YP_004176849.1| 57 KWHVGGAAHYAQIDMVARYFRMKGYNV 83
                                      68************************9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.038
                                       TTBE--TTTT---BHHHHHTTS-HHHHHHHH.HSS-TTS-EEE-HHH CS
                      tRNA-synt_1e 250 egekmsksLknfitikdvlkkfdprqlRlll.lsahyrsqldfkeel 295
                                       +ge m ks +n+i    +++k+ + ++R+   +sa+      f+e++
  gi|320101257|ref|YP_004176849.1| 541 KGEAMHKSKGNVIDPDPFIEKYGADAFRYWAaASAKLGYDYRFSEQT 587
                                       6899************************9651455555566666665 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.056     1e+02       4      17 ..     186     199 ..     185     200 .. 0.94
   2 ?   -0.9   0.0      0.99   1.8e+03       6      13 ..     233     240 ..     232     241 .. 0.89
   3 ?    2.6   0.0     0.082   1.5e+02       2      11 ..     423     432 ..     423     434 .. 0.87
   4 ?    1.6   0.8      0.17   3.1e+02       1       9 [.     449     457 ..     449     458 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.056
                            zf-ACC   4 CpsCgemlykkeLe 17 
                                       Cp+C ++l   eLe
  gi|320101257|ref|YP_004176849.1| 186 CPRCRTSLADAELE 199
                                       ********999998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.99
                            zf-ACC   6 sCgemlyk 13 
                                       sC++++y 
  gi|320101257|ref|YP_004176849.1| 233 SCKALVYH 240
                                       8*****95 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.082
                            zf-ACC   2 tKCpsCgeml 11 
                                       ++C +Cg++l
  gi|320101257|ref|YP_004176849.1| 423 WRCSRCGSIL 432
                                       58******98 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.17
                            zf-ACC   1 WtKCpsCge 9  
                                       W KCp Cg+
  gi|320101257|ref|YP_004176849.1| 449 WDKCPVCGA 457
                                       77*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (815 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); 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:                        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: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 4851.78
//
Query:       gi|320101258|ref|YP_004176850.1|  [L=230]
Description: PHP domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-17   61.0   0.1    1.3e-16   60.1   0.1    1.5  1  PHP_C     PHP-associated
    4.2e-06   27.2   0.0    5.2e-06   26.9   0.0    1.4  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1   1.4e-20   1.3e-16       3      54 ..     143     195 ..     141     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.4e-20
                             PHP_C   3 aNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepia.tpdelleaireg 54 
                                       aNr+A ++A+ lg+pg+++SDAH++e +G+ayT +  ++a ++ ++leair+g
  gi|320101258|ref|YP_004176850.1| 143 ANRKAMEAARLLGKPGLASSDAHVPEHIGSAYTYILLDNAsSIVDVLEAIRKG 195
                                       8**********************************77777366*********9 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   5.8e-10   5.2e-06       1      84 [.       5      82 ..       5     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.8e-10
                                      EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHH...HTTTTSEEEEEEE.......... CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakk...kykagikpiiGleayvaddseke 75
                                      dlHvH++ys +  +     e+++ a+ +g   iaiTDh+ + g +e y+  ++     + g+ ++ G+e        ++
  gi|320101258|ref|YP_004176850.1|  5 DLHVHSSYSdGR-AGP--REILRYAALKGVGVIAITDHDTFRGGLEGYRLSREaagTGSPGVLVVPGIE-------LRS 73
                                      89*******444.555..9***********************999988877663334447788888888.......333 PP

                                      ........E CS
                                      xxxxxxxxx RF
                               PHP 76 rpshltlla 84
                                          +++++
  gi|320101258|ref|YP_004176850.1| 74 SGGDILVYC 82
                                      344455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1661.17
//
Query:       gi|320101259|ref|YP_004176851.1|  [L=61]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-13   48.1  12.6    5.7e-07   29.1   0.6    2.1  2  Fer4          4Fe-4S binding domain
    5.9e-10   38.8  11.8    2.4e-05   24.2   0.7    2.1  2  Fer4_6        4Fe-4S binding domain
    1.5e-09   37.3  11.8    8.4e-05   22.4   1.0    2.1  2  Fer4_2        4Fe-4S binding domain
    7.6e-09   35.5  21.7    7.7e-07   29.1  11.3    1.9  2  Fer4_10       4Fe-4S dicluster domain
    1.9e-08   34.8  11.9    3.6e-08   33.9  12.0    1.4  1  Fer4_7        4Fe-4S dicluster domain
    6.3e-08   32.7   8.6      1e-07   32.0   8.6    1.3  1  Fer4_9        4Fe-4S dicluster domain
    1.1e-06   28.6  11.8     0.0057   17.1   1.3    2.1  2  Fer4_4        4Fe-4S binding domain
      7e-06   26.4   9.0      0.011   16.2   1.1    2.1  2  Fer4_8        4Fe-4S dicluster domain
    4.5e-05   24.3   9.7      0.027   15.4   0.5    2.1  2  Fer4_16       4Fe-4S double cluster binding domain
    5.8e-05   23.7   7.7     0.0017   19.1   0.5    2.1  2  Fer4_15       4Fe-4S single cluster domain
    6.8e-05   22.9  13.1      0.024   14.8   2.6    2.0  2  Fer4_21       4Fe-4S dicluster domain
    0.00014   22.4   8.4     0.0061   17.1   0.3    2.1  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    0.00035   21.0  13.9      0.029   14.9   2.8    2.1  2  Fer4_17       4Fe-4S dicluster domain
    0.00058   20.6  19.1      0.055   14.4   5.0    2.2  2  Fer4_3        4Fe-4S binding domain
  ------ inclusion threshold ------
      0.018   15.3   8.5       0.27   11.4   8.7    1.9  2  Fer4_18       4Fe-4S dicluster domain
      0.043   13.6   2.4      0.043   13.6   2.4    2.0  2  Fer4_20       Dihydroprymidine dehydrogenase domain II, 4Fe-4
      0.093   12.9   4.9       0.17   12.0   4.9    1.7  1  ETF_QO        Electron transfer flavoprotein-ubiquinone oxido
        6.8    5.4   7.6        7.5    5.2   7.6    1.0  1  Dynactin_p62  Dynactin p62 family


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 !   29.1   0.6   5.7e-10   5.7e-07       3      20 ..       6      23 ..       4      27 .. 0.90
   2 !   23.9   5.6   2.4e-08   2.4e-05       1      23 [.      33      55 ..      33      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5.7e-10
                                      EETTTSSS-THHHHHSTT CS
                              Fer4  3 ideekCigCGaCvevCPv 20
                                       de+kC+ C++Cve CP 
  gi|320101259|ref|YP_004176851.1|  6 LDESKCTLCMLCVEYCPA 23
                                      69***************6 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.4e-08
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +v+  e+C+ C aC+  CP gA 
  gi|320101259|ref|YP_004176851.1| 33 IVVEAERCVECYACEPLCPAGAV 55
                                      68999*****************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 !   24.2   0.7   2.4e-08   2.4e-05       5      21 ..       7      23 ..       6      26 .. 0.93
   2 !   19.4   4.5   7.7e-07   0.00076       2      23 ..      33      54 ..      32      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.4e-08
                            Fer4_6  5 dpdkCigCgdCvrvCPe 21
                                      d++kC+ C+ Cv  CP+
  gi|320101259|ref|YP_004176851.1|  7 DESKCTLCMLCVEYCPA 23
                                      89**************8 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7.7e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      +++ +++C+ C++C+  CP+ga
  gi|320101259|ref|YP_004176851.1| 33 IVVEAERCVECYACEPLCPAGA 54
                                      7899****************99 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.0   8.4e-08   8.4e-05       2      22 .]       3      23 ..       2      23 .. 0.93
   2 !   20.2   3.9   4.5e-07   0.00044       2      22 .]      32      52 ..      31      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.4e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++  d+ +C+ C  Cv  CPa
  gi|320101259|ref|YP_004176851.1|  3 RILLDESKCTLCMLCVEYCPA 23
                                      5789****************8 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.5e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++vv+++rC++C aC   CPa
  gi|320101259|ref|YP_004176851.1| 32 RIVVEAERCVECYACEPLCPA 52
                                      789*****************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 !   29.1  11.3   7.7e-10   7.7e-07       2      56 .]       4      51 ..       3      51 .. 0.96
   2 !   17.3   2.7   3.8e-06    0.0038       2      23 ..      33      54 ..      32      61 .] 0.81

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.7e-10
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + +d+++C+ C  Cv+ CPa         ++ +e+++ +  e+C +c aC   CP
  gi|320101259|ref|YP_004176851.1|  4 ILLDESKCTLCMLCVEYCPA-------FVFTLREGRIVVEAERCVECYACEPLCP 51
                                      6789****************.......9**************************9 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.8e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      +v+++++C++C +C   CPa +
  gi|320101259|ref|YP_004176851.1| 33 IVVEAERCVECYACEPLCPAGA 54
                                      78999***************44 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9  12.0   3.6e-11   3.6e-08       1      52 []      10      54 ..      10      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.6e-11
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+ C  Cv++Cp+ +++l+e        ++++++e+C+ C+aC+  CP+ga
  gi|320101259|ref|YP_004176851.1| 10 KCTLCMLCVEYCPAFVFTLRE-------GRIVVEAERCVECYACEPLCPAGA 54
                                      7******************77.......479*******************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 !   32.0   8.6     1e-10     1e-07       1      50 [.      10      54 ..      10      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      kCt C  Cve Cpa v++ ++++  ++ +     +C++C aC+  Cp ga
  gi|320101259|ref|YP_004176851.1| 10 KCTLCMLCVEYCPAFVFTLREGRIVVEAE-----RCVECYACEPLCPAGA 54
                                      7**********************999985.....6************997 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.3   5.7e-06    0.0057       2      15 ..       9      22 ..       8      30 .. 0.91
   2 !   16.9   3.4   6.6e-06    0.0066       2      17 .]      38      53 ..      37      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.7e-06
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++C+ C+ Cv +CP
  gi|320101259|ref|YP_004176851.1|  9 SKCTLCMLCVEYCP 22
                                      58************ PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.6e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      erC++C +C+  CP g
  gi|320101259|ref|YP_004176851.1| 38 ERCVECYACEPLCPAG 53
                                      9*************75 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.1   1.1e-05     0.011      50      63 ..      10      23 ..       7      29 .. 0.80
   2 !   15.0   1.5   2.5e-05     0.025       2      17 ..      37      52 ..      36      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            Fer4_8 50 sCttcgaCtevCpv 63
                                      +Ct c+ C+e Cp 
  gi|320101259|ref|YP_004176851.1| 10 KCTLCMLCVEYCPA 23
                                      68888888888886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.5e-05
                            Fer4_8  2 lekCieCgaCqsaCpv 17
                                      +e+C+eC aC+  Cp+
  gi|320101259|ref|YP_004176851.1| 37 AERCVECYACEPLCPA 52
                                      7899999999999996 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.5   2.7e-05     0.027       1      20 [.      10      29 ..      10      39 .. 0.78
   2 !   13.6   3.2   9.6e-05     0.096       1      19 [.      39      57 ..      39      61 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C+ C  C+e CP+ +++ +
  gi|320101259|ref|YP_004176851.1| 10 KCTLCMLCVEYCPAFVFTLR 29
                                      5************9988876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.6e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                      rC++C +C   CP++a+k 
  gi|320101259|ref|YP_004176851.1| 39 RCVECYACEPLCPAGAVKV 57
                                      6***************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 !   19.1   0.5   1.7e-06    0.0017       1      22 [.       4      25 ..       4      32 .. 0.84
   2 !    8.7   1.5    0.0028       2.8       1      20 [.      33      52 ..      33      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-06
                           Fer4_15  1 VvvDrdaCigcglCvaeapevf 22
                                      + +D+++C+ c lCv+ +p ++
  gi|320101259|ref|YP_004176851.1|  4 ILLDESKCTLCMLCVEYCPAFV 25
                                      679***************9764 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                           Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                      +vv+ ++C  c +C  ++p 
  gi|320101259|ref|YP_004176851.1| 33 IVVEAERCVECYACEPLCPA 52
                                      79*************99995 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.6   2.4e-05     0.024      36      52 ..       6      22 ..       1      28 [. 0.84
   2 !   14.4   2.8   3.1e-05     0.031      34      58 ..      33      56 ..      25      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                           Fer4_21 36 vvedeCvGCnlCssvCP 52
                                      + e++C+ C lC++ CP
  gi|320101259|ref|YP_004176851.1|  6 LDESKCTLCMLCVEYCP 22
                                      5689************* PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.1e-05
                           Fer4_21 34 lkvvedeCvGCnlCssvCPvedcie 58
                                      + v +++Cv C  C   CP  ++++
  gi|320101259|ref|YP_004176851.1| 33 IVVEAERCVECYACEPLCPA-GAVK 56
                                      56778999999999999995.7775 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   6.1e-06    0.0061       2      19 ..       7      24 ..       6      34 .. 0.87
   2 !    9.1   2.8    0.0019       1.9       1      18 [.      35      52 ..      35      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.1e-06
                           Fer4_13  2 DrdtCiacgaCvelaPdv 19
                                      D+++C+ c++Cve +P +
  gi|320101259|ref|YP_004176851.1|  7 DESKCTLCMLCVEYCPAF 24
                                      899*************84 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0019
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      V+ ++C++c aC  l+P 
  gi|320101259|ref|YP_004176851.1| 35 VEAERCVECYACEPLCPA 52
                                      7899*************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 !   12.1   3.3   0.00022      0.22      44      58 ..       9      23 ..       7      26 .. 0.85
   2 !   14.9   2.8   2.9e-05     0.029      42      59 ..      36      53 ..      26      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      s+C+ C +C+++CP+
  gi|320101259|ref|YP_004176851.1|  9 SKCTLCMLCVEYCPA 23
                                      579999999999996 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.9e-05
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                      +a++C+eC  Ce  CP+g
  gi|320101259|ref|YP_004176851.1| 36 EAERCVECYACEPLCPAG 53
                                      6899************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   5.0   5.5e-05     0.055       1      12 [.      11      22 ..      11      24 .. 0.97
   2 !   12.3   6.2   0.00027      0.27       1      15 []      40      54 ..      40      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-05
                            Fer4_3  1 CtgCgaCvevCP 12
                                      Ct C++Cve CP
  gi|320101259|ref|YP_004176851.1| 11 CTLCMLCVEYCP 22
                                      ***********9 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00027
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C+aC+  CP gA
  gi|320101259|ref|YP_004176851.1| 40 CVECYACEPLCPAGA 54
                                      ************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 ?   11.4   8.7   0.00027      0.27      58      92 ..       8      47 ..       3      51 .. 0.71
   2 ?    8.2   1.4    0.0027       2.6      54      74 ..      33      53 ..      25      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                           Fer4_18 58 agdcidcescvkvcPtgi.dirkGlql.e...ciscllci 92
                                      +++c+ c  cv+ cP  +  +r+G  + e   c++c  c 
  gi|320101259|ref|YP_004176851.1|  8 ESKCTLCMLCVEYCPAFVfTLREGRIVvEaerCVECYACE 47
                                      679************987479**96432511255555554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
                           Fer4_18 54 kekgagdcidcescvkvcPtg 74
                                         +a  c++c +c  +cP g
  gi|320101259|ref|YP_004176851.1| 33 IVVEAERCVECYACEPLCPAG 53
                                      5567788************87 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.8     0.054        54      21      38 ..       8      23 ..       2      28 .. 0.82
   2 ?   13.6   2.4   4.4e-05     0.043      13      39 ..      29      53 ..      24      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.054
                                      HTT----TT-HHHHCSTT CS
                           Fer4_20 21 AsRClqCkkapcvkgCPv 38
                                       s+C  C    cv+ CP+
  gi|320101259|ref|YP_004176851.1|  8 ESKCTLC--MLCVEYCPA 23
                                      5789999..89******7 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.4e-05
                                      -HHHHHHHHTT----TT-HHHHCSTT- CS
                           Fer4_20 13 teeealeeAsRClqCkkapcvkgCPve 39
                                      +e +++ eA+RC++C    c+  CP+ 
  gi|320101259|ref|YP_004176851.1| 29 REGRIVVEAERCVEC--YACEPLCPAG 53
                                      5567899********..789999*985 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   4.9   0.00017      0.17      46      90 ..      17      55 ..       2      61 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                      HHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--E CS
                            ETF_QO 46 eqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqni 90
                                      +  yCPa v+ + e       +++++a+ Cv C +C+   p   +
  gi|320101259|ref|YP_004176851.1| 17 CVEYCPAFVFTLRE------GRIVVEAERCVECYACEPLCPAGAV 55
                                      678******98874......469*************977776665 PP

>> Dynactin_p62  Dynactin p62 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   7.6    0.0075       7.5      16      60 ..      11      52 ..       6      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0075
                      Dynactin_p62 16 CpRCvteeivtyyCPnCLFevpssnvkseGnRCtRsCfqC.PiCis 60
                                      C  C+       yCP  +F      +  e +RC  +C+ C P+C +
  gi|320101259|ref|YP_004176851.1| 11 CTLCM---LCVEYCPAFVFTLREGRIVVEAERCV-ECYACePLCPA 52
                                      44444...4667*********************8.7****999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 453.90
//
Query:       gi|320101260|ref|YP_004176852.1|  [L=79]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   17.6   5.3       0.19   11.8   2.9    2.2  2  DZR             Double zinc ribbon
      0.003   17.6   3.1      0.037   14.1   0.1    2.2  2  Zn-ribbon_8     Zinc ribbon domain
      0.005   16.7  11.2         17    5.4   9.4    3.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
  ------ inclusion threshold ------
      0.015   15.4   5.3        1.2    9.3   5.3    2.5  1  DUF1272         Protein of unknown function (DUF1272)
      0.016   15.1   2.3       0.89    9.5   0.6    2.3  2  Prok-RING_1     Prokaryotic RING finger family 1
      0.026   13.9   5.2        2.2    7.7   1.4    2.5  2  zf-TFIIB        Transcription factor zinc-finger
      0.028   14.3   5.7       0.32   10.9   5.7    2.2  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.028   14.7   3.2      0.028   14.7   3.2    2.6  2  zf-C6H2         zf-MYND-like zinc finger, mRNA-binding
      0.056   13.0   8.5       0.58    9.7   1.6    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.13   12.1   8.9       0.93    9.4   0.4    3.5  4  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
       0.13   11.7   9.3        2.3    7.8   0.3    3.4  3  zf-ribbon_3     zinc-ribbon domain
       0.22   11.7   3.7       0.56   10.4   1.0    2.1  2  zf-piccolo      Piccolo Zn-finger
       0.32   10.9   5.1       0.68    9.9   3.1    2.1  2  PyrI_C          Aspartate carbamoyltransferase regulatory cha
       0.33   11.3   5.1        1.4    9.3   3.5    2.2  1  DnaJ_CXXCXGXG   DnaJ central domain
       0.49   10.0   4.2       0.17   11.5   2.1    1.3  1  DpnI            Dam-replacing family
       0.52   10.3   9.4       0.68   10.0   5.3    2.6  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.56   10.3   6.5         16    5.6   0.1    3.1  2  Rubredoxin      Rubredoxin
       0.59   10.1   4.0        4.3    7.4   0.1    2.2  2  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
       0.63   10.4  11.5       0.26   11.6   2.1    2.4  2  C1_2            C1 domain
       0.73    9.8   6.1         13    5.7   6.1    2.2  1  C1_1            Phorbol esters/diacylglycerol binding domain 
        1.4    8.9   6.2       0.24   11.3   1.5    2.0  2  DUF4428         Domain of unknown function (DUF4428)
        3.5    7.8   9.3        1.8    8.7   1.3    3.0  2  zf-C3H2C3       Zinc-finger
        3.7    7.6   6.9         18    5.4   2.2    2.6  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        4.9    7.5   9.6        2.2    8.6   0.6    3.0  3  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        5.9    6.7  10.4          2    8.2   0.9    2.6  2  A2L_zn_ribbon   A2L zinc ribbon domain
        9.4    6.1  10.6         14    5.5   1.4    2.4  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   2.1   0.00072       0.5      14      45 ..      21      56 ..      14      58 .. 0.77
   2 !   11.8   2.9   0.00027      0.19       1      40 [.      43      76 ..      37      79 .] 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00072
                               DZR 14 fCseCgtklkavaa.....edrCpsCgek.vdpearfC 45
                                       C  Cgt+l+ v+       + Cp+C ++ +  +a fC
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTTLDFVSGyeaknIYYCPRCVSQgL--KAYFC 56
                                      5999****88666688899999****88733..33455 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00027
                               DZR  1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdp 40
                                      Cp+C ++   +a fCs+    l     +++Cp C+ +++p
  gi|320101260|ref|YP_004176852.1| 43 CPRCVSQ-GLKAYFCSADARVL-----HYKCPYCKGELKP 76
                                      4455444.44455555555555.....7******988776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   5.4e-05     0.037       7      34 ..      21      48 ..      21      55 .. 0.82
   2 ?    3.9   0.7     0.086        59      28      36 ..      65      74 ..      54      76 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgs 34
                                      +C  Cg++ + ++s  +a+++  CP+C s
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTTLD-FVSGYEAKNIYyCPRCVS 48
                                      7*****9999.555569999999****76 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.086
                       Zn-ribbon_8 28 a.CPeCgsev 36
                                        CP C++e+
  gi|320101260|ref|YP_004176852.1| 65 YkCPYCKGEL 74
                                      4488887765 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 ?    4.7   0.0     0.041        29      23      37 ..      20      32 ..      18      33 .. 0.84
   2 ?    5.4   9.4     0.024        17       5      35 ..      41      75 ..      37      76 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.041
                    Zn_ribbon_SprT 23 hnYrCrrCkgtLrgk 37
                                      ++  C +C+ tL ++
  gi|320101260|ref|YP_004176852.1| 20 EK--CAICGTTLDFV 32
                                      66..********986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                    Zn_ribbon_SprT  5 YrCtgCgreythhlsirrhn............YrCrrCkgtLr 35
                                      Y+C++C         ++  +            Y C++Ckg+L+
  gi|320101260|ref|YP_004176852.1| 41 YYCPRCV--------SQGLKayfcsadarvlhYKCPYCKGELK 75
                                      7888887........33333344444667888*********97 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.3    0.0018       1.2      31      52 ..      55      75 ..      18      77 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                           DUF1272 31 FCaeCaeevlenvCPncgGelv 52
                                      FC++   +vl+  CP c Gel 
  gi|320101260|ref|YP_004176852.1| 55 FCSAD-ARVLHYKCPYCKGELK 75
                                      56554.456799********96 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.6    0.0013      0.89       4      27 ..      19      47 ..      17      54 .. 0.79
   2 ?    5.1   0.0     0.032        22       5      15 ..      65      75 ..      61      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                       Prok-RING_1  4 gkkCpvCgkelkee.....dDiVvCpeCg 27
                                       +kC +Cg +l+       + i  Cp C 
  gi|320101260|ref|YP_004176852.1| 19 TEKCAICGTTLDFVsgyeaKNIYYCPRCV 47
                                      689******987433355599******95 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.032
                       Prok-RING_1  5 kkCpvCgkelk 15
                                       kCp C+ elk
  gi|320101260|ref|YP_004176852.1| 65 YKCPYCKGELK 75
                                      79*****9997 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.4    0.0032       2.2       1      25 [.      21      46 ..      21      50 .. 0.78
   2 ?    7.4   0.1     0.004       2.8       1      12 [.      66      77 ..      66      79 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                          zf-TFIIB  1 kCPkCqdele.eserggveidyCpqC 25
                                      kC  C+++l   s      i+yCp+C
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTTLDfVSGYEAKNIYYCPRC 46
                                      68888888886444455679****** PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                          zf-TFIIB  1 kCPkCqdelees 12
                                      kCP C+ el+++
  gi|320101260|ref|YP_004176852.1| 66 KCPYCKGELKPY 77
                                      8********986 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.7   0.00046      0.32       3      46 ..      20      73 ..      18      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                                      SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH..........TT-B-TTT--B CS
                        zf-C3HC4_3  3 eeCviClerprnvvllpCgHlvlCeeCaekllk..........rkkkCpiCrrp 46
                                      e+C iC ++   v  ++ + +++C +C+++ lk           + kCp+C+ +
  gi|320101260|ref|YP_004176852.1| 20 EKCAICGTTLDFVSGYEAKNIYYCPRCVSQGLKayfcsadarvLHYKCPYCKGE 73
                                      78******999999999999999999998888888888888888*******987 PP

>> zf-C6H2  zf-MYND-like zinc finger, mRNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.2   4.1e-05     0.028      10      32 ..      37      59 ..      12      60 .. 0.88
   2 ?    2.3   0.3      0.32   2.2e+02      14      19 ..      66      71 ..      59      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-05
                           zf-C6H2 10 ass.LqCptClklgikesfFCsqe 32
                                      a++   Cp C+++g+k ++FCs +
  gi|320101260|ref|YP_004176852.1| 37 AKNiYYCPRCVSQGLK-AYFCSAD 59
                                      545568**********.****975 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.32
                           zf-C6H2 14 qCptCl 19
                                      +Cp C 
  gi|320101260|ref|YP_004176852.1| 66 KCPYCK 71
                                      8****4 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.6   0.00084      0.58       2      25 ..      21      46 ..      20      48 .. 0.89
   2 ?    7.3   0.8    0.0048       3.3       1       9 [.      65      73 ..      65      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00084
                                      EETTTTCEE.CHEETSTTCE.EESSS CS
                      TF_Zn_Ribbon  2 kCPnCgstn.lveDpergel.vCtdC 25
                                      kC +Cg+t  +v  +e  ++ +C++C
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTTLdFVSGYEAKNIyYCPRC 46
                                      8*******9889998888888***** PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0048
                                      EEETTTTCE CS
                      TF_Zn_Ribbon  1 ykCPnCgst 9 
                                      ykCP+C+++
  gi|320101260|ref|YP_004176852.1| 65 YKCPYCKGE 73
                                      8*****986 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.016        11       2      11 ..      20      29 ..      20      30 .. 0.90
   2 ?    9.4   0.4    0.0013      0.93      22      28 ..      41      47 ..      38      49 .. 0.89
   3 ?   -1.8   0.0       4.4     3e+03      21      24 ..      53      56 ..      52      60 .. 0.81
   4 ?   -0.1   0.3       1.3   8.8e+02       3       9 ..      66      72 ..      66      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                                      SB-TTT--BB CS
                      zf-FPG_IleRS  2 epCpRCwryi 11
                                      e+C  C++++
  gi|320101260|ref|YP_004176852.1| 20 EKCAICGTTL 29
                                      8*******85 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                                      EE-TTTT CS
                      zf-FPG_IleRS 22 yfCprCq 28
                                      y+CprC 
  gi|320101260|ref|YP_004176852.1| 41 YYCPRCV 47
                                      8*****7 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.4
                                      EEE- CS
                      zf-FPG_IleRS 21 tyfC 24
                                       yfC
  gi|320101260|ref|YP_004176852.1| 53 AYFC 56
                                      6999 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.3
                                      B-TTT-- CS
                      zf-FPG_IleRS  3 pCpRCwr 9 
                                      +Cp C++
  gi|320101260|ref|YP_004176852.1| 66 KCPYCKG 72
                                      8999986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.023        16      18      24 ..      21      27 ..      18      29 .. 0.79
   2 ?    3.2   0.6     0.088        61       3       8 ..      41      46 ..      40      49 .. 0.91
   3 ?    7.8   0.3    0.0033       2.3       4      23 ..      66      71 ..      63      75 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.023
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C+ CGt
  gi|320101260|ref|YP_004176852.1| 21 KCAICGT 27
                                      7999998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.088
                       zf-ribbon_3  3 vrCPnC 8 
                                      ++CP+C
  gi|320101260|ref|YP_004176852.1| 41 YYCPRC 46
                                      69***9 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0033
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCG 23
                                      +              CpyC 
  gi|320101260|ref|YP_004176852.1| 66 K--------------CPYCK 71
                                      4..............55555 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0   0.00081      0.56       2      29 ..      21      49 ..      20      58 .. 0.91
   2 ?    2.0   0.1      0.34   2.3e+02       2      11 ..      66      75 ..      65      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00081
                        zf-piccolo  2 lCplCktelnvgs.keppnyntCteCkkq 29
                                       C +C t l ++s  e+ n   C  C +q
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTTLDFVSgYEAKNIYYCPRCVSQ 49
                                      6***********98999*********765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.34
                        zf-piccolo  2 lCplCkteln 11
                                       Cp Ck el+
  gi|320101260|ref|YP_004176852.1| 66 KCPYCKGELK 75
                                      5*****9986 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 ?    0.7   0.0      0.72     5e+02      33      44 ..      19      30 ..      11      32 .. 0.80
   2 ?    9.9   3.1   0.00098      0.68      11      42 ..      44      73 ..      36      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.72
                                      EEEETTT--EEE CS
                            PyrI_C 33 klkCkYCekeis 44
                                      + kC  C+++++
  gi|320101260|ref|YP_004176852.1| 19 TEKCAICGTTLD 30
                                      569****99876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00098
                                      TTBGGGTTS-.-EEEEEETTTTEEEETTT--E CS
                            PyrI_C 11 pnCItnnepveskFkvedkekvklkCkYCeke 42
                                      p+C+++   +++ F   d   +++kC YC  e
  gi|320101260|ref|YP_004176852.1| 44 PRCVSQ--GLKAYFCSADARVLHYKCPYCKGE 73
                                      689987..56899**9*************765 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.5    0.0021       1.4       9      50 ..      35      73 ..      22      77 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                     DnaJ_CXXCXGXG  9 akkgkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGt 50
                                       ++++   C++C  +G +    +      +  + +Cp C+G+
  gi|320101260|ref|YP_004176852.1| 35 YEAKNIYYCPRCVSQGLKAYFCS-A--DARVLHYKCPYCKGE 73
                                      44455777999999994333322.2..223346789999997 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.1   0.00025      0.17      29      62 ..      38      73 ..      27      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                      HHH---TTT--SS-EE-..-------EEE-TTT--E CS
                              DpnI 29 aknlyCpkCgskklsef..ennkpvaDfyCesckee 62
                                      ++  yCp C s+ l+++  +++ +v  + C  ck e
  gi|320101260|ref|YP_004176852.1| 38 KNIYYCPRCVSQGLKAYfcSADARVLHYKCPYCKGE 73
                                      44579***********95568899*********976 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   2.5      0.33   2.3e+02      21      43 ..      22      46 ..      15      46 .. 0.63
   2 ?   10.0   5.3   0.00099      0.68      20      44 ..      42      71 ..      34      73 .. 0.90
   3 ?    7.0   0.4    0.0082       5.7      20      30 ..      66      77 ..      59      79 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.33
                     Zn_Tnp_IS1595 21 CPhCgsr..kayriktrglfqCkeC 43
                                      C  Cg +   +  +++   + C +C
  gi|320101260|ref|YP_004176852.1| 22 CAICGTTldFVSGYEAKNIYYCPRC 46
                                      7778865544444444778888887 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00099
                     Zn_Tnp_IS1595 20 vCPhCgsr..kayrikt...rglfqCkeCr 44
                                       CP+C s+  kay+ ++      ++C  C+
  gi|320101260|ref|YP_004176852.1| 42 YCPRCVSQglKAYFCSAdarVLHYKCPYCK 71
                                      4****************998899****998 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0082
                     Zn_Tnp_IS1595 20 vCPhCgsr.kay 30
                                       CP+C+++ k+y
  gi|320101260|ref|YP_004176852.1| 66 KCPYCKGElKPY 77
                                      6*****999887 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   2.2      0.09        62       3      22 ..      21      40 ..      19      55 .. 0.75
   2 ?    5.6   0.1     0.023        16      34      43 ..      64      73 ..      63      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.09
                                      EETTT-BEEETTTBBGGGTB CS
                        Rubredoxin  3 eCkvCgyvYdpakGdpdegi 22
                                      +C +Cg+  d  +G + ++i
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTTLDFVSGYEAKNI 40
                                      68888888777777777665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.023
                                      T-BBTTTB-B CS
                        Rubredoxin 34 dWvCPdCgve 43
                                      +++CP C+ e
  gi|320101260|ref|YP_004176852.1| 64 HYKCPYCKGE 73
                                      689****876 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 ?    7.4   0.1    0.0062       4.3      11      41 ..      20      51 ..      18      65 .. 0.81
   2 ?    4.7   2.9     0.044        30      13      39 ..      43      73 ..      42      75 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0062
                                      EE-TTTTTTSEETTE.......E-TTTTTSSE CS
                         Anti-TRAP 11 tkCdaCngsGkiepe.eprasleCPkCsGkgl 41
                                      +kC  C  + +  +  e +    CP+C  +gl
  gi|320101260|ref|YP_004176852.1| 20 EKCAICGTTLDFVSGyEAKNIYYCPRCVSQGL 51
                                      6899999999987776999999*****87765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                                      -TTTTTTSEET...TE.......E-TTTTTS CS
                         Anti-TRAP 13 CdaCngsGkie...peepra.sleCPkCsGk 39
                                      C+ C   G  +   +++ r    +CP C+G+
  gi|320101260|ref|YP_004176852.1| 43 CPRCVSQGLKAyfcSADARVlHYKCPYCKGE 73
                                      788888876652224455542579****995 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.1   0.00038      0.26      17      38 ..      18      46 ..       6      51 .. 0.81
   2 ?    4.7   1.6     0.054        37      33      46 ..      54      67 ..      47      74 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                              C1_2 17 esfnCsaCgrk...idgff....YsCseC 38
                                       + +C +Cg++   ++g++    Y+C++C
  gi|320101260|ref|YP_004176852.1| 18 TTEKCAICGTTldfVSGYEakniYYCPRC 46
                                      5689*******888556557899****99 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.054
                              C1_2 33 YsCseCdfslhvrC 46
                                      Y Cs    +lh +C
  gi|320101260|ref|YP_004176852.1| 54 YFCSADARVLHYKC 67
                                      55555555555555 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 ?    5.7   6.1     0.019        13      11      34 ..      19      46 ..      13      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                                      --B-TTT-SB-...-S.SSS-EEEETTT CS
                              C1_1 11 ptfCkhCgefl...wg.kekqglkCswC 34
                                      + +C+ Cg  l   +g ++k ++ C  C
  gi|320101260|ref|YP_004176852.1| 19 TEKCAICGTTLdfvSGyEAKNIYYCPRC 46
                                      689*****99999988888888888888 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   0.00035      0.24       1      29 [.      21      49 ..      21      60 .. 0.92
   2 ?   -0.6   0.2       1.9   1.3e+03      23      30 ..      67      74 ..      65      78 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                           DUF4428  1 iCaiCgkKigllkrlkleDgyvCkdClkK 29
                                      +CaiCg+ +   +    ++ y C+ C ++
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTTLDFVSGYEAKNIYYCPRCVSQ 49
                                      7***********99************987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                           DUF4428 23 CkdClkKl 30
                                      C+ C ++l
  gi|320101260|ref|YP_004176852.1| 67 CPYCKGEL 74
                                      55555554 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.3    0.0026       1.8       1      22 [.      22      42 ..      22      49 .. 0.79
   2 ?    2.1   1.5      0.31   2.1e+02      14      34 ..      64      70 ..      53      71 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0026
                         zf-C3H2C3  1 CdnCglkLdypfvaysCkHlvH 22
                                      C +Cg+ Ld+ ++ y  k ++ 
  gi|320101260|ref|YP_004176852.1| 22 CAICGTTLDF-VSGYEAKNIYY 42
                                      99*******8.78888887775 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.31
                         zf-C3H2C3 14 aysCkHlvHakCadeevCPkC 34
                                      +y+              CP C
  gi|320101260|ref|YP_004176852.1| 64 HYK--------------CPYC 70
                                      333..............6666 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.2     0.026        18      14      28 ..      35      49 ..      21      49 .. 0.88
   2 ?    4.2   0.2      0.06        42       4      11 ..      66      73 ..      64      75 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                    PhnA_Zn_Ribbon 14 YedgallvCpeCahE 28
                                      Ye + ++ Cp C ++
  gi|320101260|ref|YP_004176852.1| 35 YEAKNIYYCPRCVSQ 49
                                      788999******987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.06
                    PhnA_Zn_Ribbon  4 kCplCaSe 11
                                      kCp C+ e
  gi|320101260|ref|YP_004176852.1| 66 KCPYCKGE 73
                                      67777665 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.5      0.37   2.6e+02      33      40 ..      21      28 ..       3      53 .. 0.64
   2 ?    1.1   0.6      0.71   4.9e+02       3      11 ..      41      49 ..      39      58 .. 0.65
   3 ?    8.6   0.6    0.0032       2.2       3      11 ..      65      73 ..      63      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.37
                           zf-Di19 33 vCPvCaek 40
                                       C +C ++
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTT 28
                                      56666543 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.71
                           zf-Di19  3 ftCPyCgke 11
                                      + CP C  +
  gi|320101260|ref|YP_004176852.1| 41 YYCPRCVSQ 49
                                      668888763 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0032
                           zf-Di19  3 ftCPyCgke 11
                                      ++CPyC+ e
  gi|320101260|ref|YP_004176852.1| 65 YKCPYCKGE 73
                                      89****976 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.9     0.003         2       5      27 ..      21      46 ..      19      48 .. 0.90
   2 ?    4.9   0.5     0.031        22       4      12 ..      65      73 ..      64      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.003
                     A2L_zn_ribbon  5 vCsvCggngiln...seqgylvCieC 27
                                      +C  Cg+  ++     ++++++C+ C
  gi|320101260|ref|YP_004176852.1| 21 KCAICGTTLDFVsgyEAKNIYYCPRC 46
                                      7999999999988889*********9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.031
                     A2L_zn_ribbon  4 kvCsvCggn 12
                                      ++C +C+g+
  gi|320101260|ref|YP_004176852.1| 65 YKCPYCKGE 73
                                      89*****98 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 ?    5.4   2.1     0.021        15      25      51 ..      22      47 ..      21      50 .. 0.72
   2 ?    5.5   1.4     0.021        14      39      51 ..      59      71 ..      48      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.021
                    zinc_ribbon_10 25 CskChshnGlapkeeleevkyrCpkCg 51
                                      C  C ++   ++  e+ +  y+Cp C 
  gi|320101260|ref|YP_004176852.1| 22 CAICGTTLDFVSGYEA-KNIYYCPRCV 47
                                      7778888888855554.45699****6 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                    zinc_ribbon_10 39 eleevkyrCpkCg 51
                                      +++ + y+Cp+C+
  gi|320101260|ref|YP_004176852.1| 59 DARVLHYKCPYCK 71
                                      455569******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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):              26  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 525.93
//
Query:       gi|320101261|ref|YP_004176853.1|  [L=231]
Description: metallophosphoesterase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-14   53.4   0.0    6.1e-14   53.0   0.0    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    1.6e-09   38.1   0.2    3.5e-08   33.8   0.0    2.0  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   6.8e-18   6.1e-14       3     203 ..       4     202 ..       2     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 6.8e-18
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH..TSEEEEEC-TTS.. CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky..pipvylllGNHe.. 75 
                                       +   +D+H    + +l+ ++k+l++ +++  pd+++laGD+v+r+++ + + + l+ l  +  ++p++++ GN e  
  gi|320101261|ref|YP_004176853.1|   4 VCASSDIH---SPRHLELFKKALEESRCD--PDVFVLAGDVVERNNIAE-YGRVLSLLKTRhpGTPIVAVFGNEEyr 74 
                                       66679***...999999999999999888..**************9999.9999999999999************** PP

                                       CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEE.THHHHHHHHHHHSCHHHHCC.HHH CS
                       Metallophos  76 gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspel.lvsldklgslnleleapepg.dew 150
                                       gfe+e+ +ky++    ++ +r     ++ l +++  +  l+  +       +  ++l  l ++  el+a   +  e+
  gi|320101261|ref|YP_004176853.1|  75 GFEKEYMEKYRDVVFLNDSYRILEARGSRLVVVGPRGA-LDKPTK------WqEKNLPGLARYYSELPA---RlSEL 141
                                       *********99888776666666555555555551111.111222......122444444444444444...25999 PP

                                       HHHHHHHTTCSEEEEEESSESS........CSSSCSCCHHHHHHHHHHTT..ESEEEEESSSS CS
                       Metallophos 151 lkdlekrekadwvivlgHsply........rgsgylfgdealedllkkyg..vdlvisGHtHv 203
                                       l+d  + + + ++++++H +++           +++ ++ ++e++  ++   +++vi+GH H 
  gi|320101261|ref|YP_004176853.1| 142 LSD--ASSTHLPILLVTHYGVThrnligenPAVYPYLASVRMEEVIARHSglLKAVIHGHAHN 202
                                       999..*****************999999988888888888888885555569*********96 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 !   33.8   0.0   3.9e-12   3.5e-08       3     133 ..       4     167 ..       3     174 .. 0.83
   2 ?    1.9   0.5     0.026   2.3e+02     110     141 ..     183     216 ..     172     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.9e-12
                     Metallophos_2   3 laiiSDlH..snldaleavlealkevgvdaiihaGDl.eeeepevleellela.......pvlaVrGNnDeev.vee 68 
                                       +++ SD+H  ++l++ +++le+ +++++d  ++aGD+ e  +     ++l+l+       p++aV+GN + +  +e+
  gi|320101261|ref|YP_004176853.1|   4 VCASSDIHspRHLELFKKALEE-SRCDPDVFVLAGDVvERNNIAEYGRVLSLLktrhpgtPIVAVFGNEE-YRgFEK 78 
                                       5678****999***********.8899*********987777776777777667889*************.445777 PP

                     Metallophos_2  69 dvlreaaelgtdlpeeaelelagekvlliHgdpl.....................gvkdalaellkeaeegsd.... 120
                                       + +++  ++     +++ le++g ++ ++                          +++++l+ell++a++++     
  gi|320101261|ref|YP_004176853.1|  79 EYMEKYRDVVFLNDSYRILEARGSRLVVVGPR-GaldkptkwqeknlpglaryysELPARLSELLSDASSTHLpill 154
                                       77777777766667999999777765555433.25789999**************************9999989999 PP

                     Metallophos_2 121 vvvcGHtHvpeve 133
                                       v  +G+tH+  + 
  gi|320101261|ref|YP_004176853.1| 155 VTHYGVTHRNLIG 167
                                       999*****98765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.026
                     Metallophos_2 110 ellkeaeegsdvvvcGHtHvpeveke..ggvlvv 141
                                       e++ +++   + v++GH H   ve    ggv v 
  gi|320101261|ref|YP_004176853.1| 183 EVIARHSGLLKAVIHGHAHNGAVESVevGGVKVY 216
                                       5555545555689******997776633466555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1775.83
//
Query:       gi|320101262|ref|YP_004176854.1|  [L=288]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2051.69
//
Query:       gi|320101263|ref|YP_004176855.1|  [L=205]
Description: metal dependent phosphohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-12   46.1   0.3    1.2e-11   44.9   0.1    1.7  2  HD        HD domain
  ------ inclusion threshold ------
       0.14   11.9   0.0        0.2   11.5   0.0    1.2  1  RMI1_C    Recq-mediated genome instability protein 1, C-termi
       0.17   12.0   0.0       0.28   11.3   0.0    1.3  1  HTH_54    ParA helix turn helix 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 !   44.9   0.1     2e-15   1.2e-11       4     121 ..      25     124 ..      22     125 .. 0.94
   2 ?   -2.3   0.0      0.81   4.8e+03       7      30 ..     132     158 ..     131     162 .. 0.63

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH... CS
                                HD   4 HsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld... 77 
                                       H  +V+ ++ ++a++ g   d+ell+la  lHD+G +  +               H+ ++a  ++e++  lgl+   
  gi|320101263|ref|YP_004176855.1|  25 HVERVLGYSLKIAREGGVVVDEELLKLAVFLHDLGRMIGE--------------PHAYYSALAAEELLVELGLPrdr 87 
                                       9999**********9999********************55..............4****************999*** PP

                                       HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  78 ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       +e+v+++i++h++s ++        +   s +++i+++aD+l+a
  gi|320101263|ref|YP_004176855.1|  88 VEAVVDAIKAHSFSFNR-------SGASGSTLSMILSDADKLDA 124
                                       ***************95.......589***************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.81
                                       HHHHHHHHHHHHHHH...HHHHHHHHH CS
                                HD   7 eVaklarrlaedlge...eedrellll 30 
                                       +V  +++r +++l+e     d+ +l+l
  gi|320101263|ref|YP_004176855.1| 132 RVFLYGERHGRSLEEslkHFDEKILRL 158
                                       667777777777776666666666665 PP

>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.3e-05       0.2      89     119 ..     139     169 ..     106     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.3e-05
                            RMI1_C  89 kkrqklkealkeaqekLidleclmeielnpa 119
                                        + ++l+e lk++ ek+ +le+lm +e+++ 
  gi|320101263|ref|YP_004176855.1| 139 RHGRSLEESLKHFDEKILRLEGLMRLEYSRR 169
                                       67899**********************9987 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 ?   11.3   0.0   4.7e-05      0.28      22      68 ..      66     111 ..      59     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.7e-05
                            HTH_54  22 deyyqtyskaalaklpklsrrkvdkavsemeaeGyefekkeagstek 68 
                                       + yy   +  +l  + +l r  v++ v++++a+ ++f++  a   + 
  gi|320101263|ref|YP_004176855.1|  66 HAYYSALAAEELLVELGLPRDRVEAVVDAIKAHSFSFNRSGAS-GST 111
                                       67************************************99543.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1482.84
//
Query:       gi|320101264|ref|YP_004176856.1|  [L=282]
Description: N-glycosylase/DNA lyase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-38  131.8   0.0    3.3e-38  131.4   0.0    1.1  1  AGOG       N-glycosylase/DNA lyase
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.26   11.3   0.0    1.6  1  EF-hand_6  EF-hand domain


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 !  131.4   0.0   3.7e-42   3.3e-38      12     231 ..      22     242 ..      16     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 3.7e-42
                                       HHHHHCCTSHHHHHHHHHHCCC-H.HHHHHHHHHHHHT-SS-TT-HHHHHHHHHHHHCTS--SSHHHHHHHHHHH-T CS
                              AGOG  12 vlkleekvDpQykaveelveklgedelfvklvilNaLvSYqLsgrGEewWkefskyfsekeiknileefikfleksk 88 
                                       v++l ++ DpQ+kav +l+e+ g+    + lvi+N+LvSYqL +rGEe+W  fs+yf++ + + + ee+++f++++ 
  gi|320101264|ref|YP_004176856.1|  22 VITLLKHGDPQFKAVVNLLEARGA-GEAAVLVIANSLVSYQLNTRGEEYWYRFSEYFRDASRSVTPEELLAFMSSTG 97 
                                       67888899****************.667799********************************************** PP

                                       TS-TTHHHHHHHHHHHCCHHHTTTHH...HHHHHHHTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHHTS-- CS
                              AGOG  89 gnrrlreakikRiekivefledlele...elksylenleelleelakilgskkesKTvvFavKmlyYalrialgeei 162
                                        n rl+e+k +R++ +   +++l+ +   +   y  +l+ l +el   l     sKTv+FavKm+ Y +   ++  +
  gi|320101264|ref|YP_004176856.1|  98 LNTRLLEQKKRRLSAFF--ASSLSRRlntDGLVYCGDLRGLYDELTG-LYGGGYSKTVAFAVKMYWYLCE--ASGLK 169
                                       ***************94..4444432000222233559999999986.5667899**************9..56669 PP

                                       ---TTS-----HHHHHHHHHTTS-SS-HHHHHHTHCCHC...S.HHHHHHHHHHHHT--HHHHHHHHH.HHCC CS
                              AGOG 163 plpfeipiPvDvRiakltktsglielknekklarkelvq...eevieaWkevsreseiPplhlDsllW.vlgk 231
                                       p++  +p P+D R + l  +s+++e   + + +++ +++    e+++a + + + s++  l+lD l+W ++g 
  gi|320101264|ref|YP_004176856.1| 170 PVAKGVPPPLDLRNSLLLCSSCIAEGYGSLEDCVEAVMSrnrREALKALQVMCECSGLDCLELDVLTWlIVGV 242
                                       *******************************99999999888899999999*****************44443 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.9e-05      0.26       3      29 ..      70      95 ..      68      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                         EF-hand_6  3 reaFklfDkdgdGkidaeElrkalrka 29
                                      ++ F ++ +d + ++++eEl ++++ +
  gi|320101264|ref|YP_004176856.1| 70 WYRFSEYFRDASRSVTPEELLAFMS-S 95
                                      678*********************9.6 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:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2163.35
//
Query:       gi|320101265|ref|YP_004176857.1|  [L=95]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-07   31.7   0.0    2.5e-07   31.0   0.0    1.3  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
      0.051   13.4   0.1         11    6.0   0.1    2.3  2  SH3_4          Bacterial SH3 domain


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 !   31.0   0.0   2.7e-11   2.5e-07       8      93 ..      15      92 ..      10      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.7e-11
                                      TCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBH CS
                     Nitro_FeMo-Co  8 hFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykgaggtv 86
                                       F  a+ +++y+veeg  + v+        ++   ++ l+++++e ++ v+++++i ++ ++ +e+agi+++++++g+v
  gi|320101265|ref|YP_004176857.1| 15 SFEAAEKLLVYDVEEG--RPVKSL------GRPVTPDLLEDVVEEYDAWVLFTRGITRENREPVEEAGIKIVETRAGSV 85
                                      6999**********66..567777......566889******************************************* PP

                                      HHHHHHH CS
                     Nitro_FeMo-Co 87 eealkev 93
                                       +++ke+
  gi|320101265|ref|YP_004176857.1| 86 VDVVKEF 92
                                      *****98 PP

>> SH3_4  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0021        19      22      40 ..      41      59 ..      39      62 .. 0.86
   2 ?    6.0   0.1    0.0012        11      10      36 ..      68      95 .]      66      95 .] 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0021
                             SH3_4 22 eaGvpvrvvackgnWcrvr 40
                                       ++++  vv++++ W+ ++
  gi|320101265|ref|YP_004176857.1| 41 TPDLLEDVVEEYDAWVLFT 59
                                      6889999********9775 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0012
                             SH3_4 10 gPskkaavi.ayleaGvpvrvvackgnW 36
                                      +P ++a +  ++ +aG +v vv++   W
  gi|320101265|ref|YP_004176857.1| 68 EPVEEAGIKiVETRAGSVVDVVKEFFTW 95
                                      7888888988**************9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 788.66
//
Query:       gi|320101266|ref|YP_004176858.1|  [L=117]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 829.97
//
Query:       gi|320101267|ref|YP_004176859.1|  [L=73]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   0.8    4.2e-12   46.1   0.8    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 !   46.1   0.8   2.3e-16   4.2e-12       2      49 .]      16      65 ..      15      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 2.3e-16
                           DUF2283  2 itYDpeaDalYIylsegpveeseev...dddiilDfDedGrlvGIEiLnAS 49
                                      ++YD++ D+lYIy+++++ e+ ee+   d+d+ +++ ++Gr+++I+++n+S
  gi|320101267|ref|YP_004176859.1| 16 FEYDQQSDILYIYFTDEEQEADEEIlgeDGDTAFRV-KQGRILSIMVMNFS 65
                                      69************9999899999899899******.************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 576.72
//
Query:       gi|320101268|ref|YP_004176860.1|  [L=105]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   13.1   0.1        0.1   12.8   0.1    1.1  1  SMODS     Second Messenger Oligonucleotide or Dinucleotide Sy


Domain annotation for each model (and alignments):
>> 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 ?   12.8   0.1   5.6e-06       0.1      63     134 ..       5      78 ..       3      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-06
                             SMODS  63 pvsdkdmlfeldvdllvvvnevegdepsdlleklkkal...kktyksseirqdrqvvvvel...neikidvvPaven 133
                                       ++sdk    eld  l+ + +++  de ++ ++++ +++   +k  +  ++r + + +++ +    + k+d++P++++
  gi|320101268|ref|YP_004176860.1|   5 RISDK----ELDEALMEKQEKKPADEKQRWINRIMRSAkqyHKICPYYDKRTKMCFLLMGTkceRDGKFDICPVFKS 77 
                                       56777....9****************************65555556778888888877666558899********97 PP

                             SMODS 134 k 134
                                        
  gi|320101268|ref|YP_004176860.1|  78 F 78 
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 772.43
//
Query:       gi|320101269|ref|YP_004176861.1|  [L=380]
Description: Fmu (Sun) domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  135.2   0.0    2.9e-39  134.8   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    3.5e-08   33.3   0.0    6.8e-08   32.4   0.0    1.5  1  PUA              PUA domain
     0.0016   18.2   0.0     0.0034   17.2   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
     0.0036   17.9   0.0       0.14   12.8   0.0    2.3  2  Methyltransf_11  Methyltransferase domain
     0.0054   17.4   0.0        1.3    9.8   0.0    2.3  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.027   14.6   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
      0.069   12.8   0.0       0.15   11.7   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.16   11.7   0.0       0.24   11.1   0.0    1.3  1  Met_10           Met-10+ like-protein


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 !  134.8   0.0   1.3e-42   2.9e-39       3     200 .]     180     376 ..     178     376 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 1.3e-42
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlgg. 77 
                                       +L p+++e ++D+ a+PGgKT+hi +l + ++ vvA d++  ++++++e+l+ Lg++ n+i + +D r+ + +    
  gi|320101269|ref|YP_004176861.1| 180 ILGPEPGELVVDMNASPGGKTSHIVQLTRGRALVVAFDRSPGKVEKLKETLTNLGLNlNVIAVPYDSRYAHLDFKLa 256
                                       799*****************************************************989999*****9876544322 PP

                                       ..EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHH CS
                   Methyltr_RsmB-F  78 elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaL 154
                                        + Dr+L+D PCs +gv  r  d    r  +d+a+l++ q++ l+aa+ ++k+gG++vYsTC++++eEnee i +a 
  gi|320101269|ref|YP_004176861.1| 257 GKADRVLVDPPCSNLGVRPRLVDD---RGVRDVASLSSYQRQFLKAAARVVKPGGYIVYSTCTLTLEENEENIVYAV 330
                                       58***************8777665...8889********************************************** PP

                                       HH-..TTEEEESSBSTTSTTSSECEECTSEEE-TTTTSS-SEEEEEEE CS
                   Methyltr_RsmB-F 155 kkr..edvelvetelsepkglklgeeagtlrllPhtenkdgffiaklk 200
                                       ++   e vel++ + ++ k +  g+     r+ P + ++ g fia l+
  gi|320101269|ref|YP_004176861.1| 331 EELglESVELESSPPFSEKTSYRGVVG--YRYTPLSGDMPGHFIALLR 376
                                       985336788887777766666666555..89*************9985 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   3.1e-11   6.8e-08       2      67 ..      79     143 ..      78     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3.1e-11
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggks 67 
                                       rvvvd+  +  l+ ga+L+ pGvv+    f++gd    v++ g++va+  a +ss  l ++++g +
  gi|320101269|ref|YP_004176861.1|  79 RVVVDEKTAVSLMLGANLYRPGVVKSSS-FRKGDRLLAVTRHGTPVACLEATVSSRSLHRAEKGLV 143
                                       8***********************9987.*********************************9976 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.5e-06    0.0034       9     121 ..     191     325 ..     184     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                   Methyltransf_31   9 DlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.lekl.led.ekfDlilsn. 81 
                                       D  +  G +t  + ++ + +a vv +D+s+  +e+ +e + +lgl n+++ + +  +    l ++   k D +l + 
  gi|320101269|ref|YP_004176861.1| 191 DMNASPGGKTSHIVQLTRGRALVVAFDRSPGKVEKLKETLTNLGL-NLNVIAVPYDSrYAHLdFKLaGKADRVLVDp 266
                                       5555566677777778888999***********************.6777776666655555566678999999998 PP

                   Methyltransf_31  82 ..................evlnaladpdkileeiervlkpggilliedpr.llaelpak 121
                                                         +v  + + + ++l+ + rv+kpgg+++ +++  +l+e+ ++
  gi|320101269|ref|YP_004176861.1| 267 pcsnlgvrprlvddrgvrDVASLSSYQRQFLKAAARVVKPGGYIVYSTCTlTLEENEEN 325
                                       888888888777777777777999999**********************9766666533 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.09     2e+02      12      47 ..     204     239 ..     192     265 .. 0.74
   2 !   12.8   0.0   6.4e-05      0.14      76      95 ..     292     311 ..     270     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.09
                                       HHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEE CS
                   Methyltransf_11  12 ealakrg.arvvgvDlskemlklakekaseeglkvef 47 
                                        +l+ rg a vv++D s+  ++  ke   + gl++++
  gi|320101269|ref|YP_004176861.1| 204 VQLT-RGrALVVAFDRSPGKVEKLKETLTNLGLNLNV 239
                                       4444.45699**************9999998864333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.4e-05
                                       CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                        ++++lk +aRv+kpgG++v
  gi|320101269|ref|YP_004176861.1| 292 YQRQFLKAAARVVKPGGYIV 311
                                       6799**************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00056       1.3       1      52 [.     189     241 ..     189     272 .. 0.79
   2 ?    5.4   0.0     0.014        31      82      97 .]     293     308 ..     283     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeeglnvefvq 52 
                                       v+d+ + +G  t ++ +   g+a v+++D s++ +e+ +e + + gln++++ 
  gi|320101269|ref|YP_004176861.1| 189 VVDMNASPGGKTSHIVQLTrGRALVVAFDRSPGKVEKLKETLTNLGLNLNVIA 241
                                       7788889999999999998779********************99999766654 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHEEEEE CS
                   Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                       ++++lk +arv+kpgG
  gi|320101269|ref|YP_004176861.1| 293 QRQFLKAAARVVKPGG 308
                                       689************9 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-05     0.027      21     158 ..     185     341 ..     173     356 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHH.TTEEEECS-CCCSSHHHHHCHCHHH....SSEE CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...apl.pgvttiqgditdpetiekikealse....rkvd 89 
                                       pg+ vvD  a+PGg +  ++q +  ++ vva+D  p+   + l + +t +  + +  ++    + a  +     k+d
  gi|320101269|ref|YP_004176861.1| 185 PGELVVDMNASPGGKTSHIVQLTRGRALVVAFDRSPGkveK-LkETLTNLGLNLNVIAVPYDSRYAHLDfklaGKAD 260
                                       7889******************9778********9996643.33666666444443333332221111123346899 PP

                                       EEEE--S-..........SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCH...CCCHHHHHHHHH.CCE CS
                              FtsJ  90 lvvsDgap..........dvsgvhdldeylqsqLllaalelalkllkpggtfvlkifr...geeteallkqlk.kfF 152
                                        v+ D             d  gv+d+ ++ +    ++ l+ a +++kpgg +v  +++   +e+ e+++++++  + 
  gi|320101269|ref|YP_004176861.1| 261 RVLVDPPCsnlgvrprlvDDRGVRDVASLSS--YQRQFLKAAARVVKPGGYIVYSTCTltlEENEENIVYAVEeLGL 335
                                       9999964345555565444444444444444..57788888889999999999888888777777788888543777 PP

                                       EEEEEE CS
                              FtsJ 153 ekvsvv 158
                                       e+v++ 
  gi|320101269|ref|YP_004176861.1| 336 ESVELE 341
                                       777665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.9e-05      0.15      60     123 ..     206     268 ..     186     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                                       HHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SS CS
                     Cons_hypoth95  60 lSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPPy 123
                                       l Rg + +v++++++  v+ lke l +l+l+ ++ ++  d+  a l   k +++ d v +DPP 
  gi|320101269|ref|YP_004176861.1| 206 LTRGRALVVAFDRSPGKVEKLKETLTNLGLNLNVIAVPYDSRYAHLDF-KLAGKADRVLVDPPC 268
                                       78999**************************96666555555555554.466788********6 PP

>> Met_10  Met-10+ like-protein
   #    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      99     197 ..     184     310 ..     178     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                       -TT-EEEETT-TTTCCHHHCCHHTTSS.EEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---....TT-EE CS
                            Met_10  99 eegevVvdvfAGiGpfaipiakyskak.rvlaidlnPesvkylkeniklNkvekvvkpileDgrevir....eqlad 170
                                       e+ge+Vvd+ A  G  +  i ++++++  v+a d  P  v+ lke ++   ++  v ++  D+r          +ad
  gi|320101269|ref|YP_004176861.1| 184 EPGELVVDMNASPGGKTSHIVQLTRGRaLVVAFDRSPGKVEKLKETLTNLGLNLNVIAVPYDSRYAHLdfklAGKAD 260
                                       79*********99987777777777652699***************9999999999999999996544222266667 PP

                                       .......................EEEE--TTTGGGGHHHHHHHEEEEEEE CS
                            Met_10 171 .......................rvvmnlpksaieFldkvlaalkdggvi 197
                                                              r v  l ++  +Fl+++ +++k gg i
  gi|320101269|ref|YP_004176861.1| 261 rvlvdppcsnlgvrprlvddrgvRDVASLSSYQRQFLKAAARVVKPGGYI 310
                                       67777777777777777777666666666666677777766666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2568.12
//
Query:       gi|320101270|ref|YP_004176862.1|  [L=173]
Description: nucleotide-binding protein, PINc [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-13   50.2   0.1    3.6e-13   49.8   0.1    1.2  1  PIN_6           PIN domain of ribonuclease
    7.6e-06   25.2   3.2    1.2e-05   24.5   3.2    1.3  1  zf-ribbon_3     zinc-ribbon domain
     0.0019   18.2   0.4     0.0032   17.4   0.4    1.3  1  DZR             Double zinc ribbon
     0.0077   16.4   2.8       0.16   12.2   0.2    2.4  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
  ------ inclusion threshold ------
      0.086   12.6   1.6          1    9.2   0.1    2.2  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
      0.092   12.6   0.2      0.092   12.6   0.2    2.3  2  Rad50_zn_hook   Rad50 zinc hook motif
      0.092   12.7   0.1       0.16   11.9   0.1    1.4  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
      0.098   12.4   7.5       0.58    9.9   7.5    2.0  1  zinc_ribbon_2   zinc-ribbon domain
       0.14   12.1   3.3        2.7    8.0   0.2    2.3  2  Nudix_N_2       Nudix N-terminal
       0.25   11.5   4.5        2.1    8.5   0.7    2.3  2  Zn-ribbon_8     Zinc ribbon domain
       0.42   10.8   0.1       0.42   10.8   0.1    1.9  2  DUF2256         Uncharacterized protein conserved in bacteria
        0.5   10.4   0.1        0.5   10.4   0.1    2.7  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.54   10.4   5.1        9.4    6.4   0.7    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.63    9.8   5.1          2    8.1   0.8    2.4  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.1   2.8e-16   3.6e-13       1      89 []       7      97 ..       7      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 2.8e-16
                             PIN_6  1 lVlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellpl..elevrePspesvkkvtefakktGDlsvLSk 77
                                      ++lD+g l+++ +  l ++  ++ytt+    E+ d+++++ l+ + +   lev +P+++s+++v e a+++G++s LS+
  gi|320101270|ref|YP_004176862.1|  7 VILDTGGLLAKYYRLLPHHLYRVYTTRLAAGEVVDEENKAALTDALEagLLEVLDPDESSYSRVLEEARRIGEVSRLSE 85
                                      69**************************************9999885469***************************** PP

                             PIN_6 78 tDievlALtyeL 89
                                      tD+++ +L+++L
  gi|320101270|ref|YP_004176862.1| 86 TDLSIASLAVML 97
                                      *********987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   3.2   9.6e-09   1.2e-05       4      26 .]     140     163 ..     138     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.6e-09
                       zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGtkl 26 
                                       +CP CG  p++++ ++Cp CGt+l
  gi|320101270|ref|YP_004176862.1| 140 YCPTCGYvPAKPGEKTCPLCGTPL 163
                                       8******99*************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   2.5e-06    0.0032       1      22 [.     141     163 ..     130     170 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.5e-06
                               DZR   1 CpqCgee.lppdarfCseCgtkl 22 
                                       Cp+Cg    +p+ ++C+ Cgt+l
  gi|320101270|ref|YP_004176862.1| 141 CPTCGYVpAKPGEKTCPLCGTPL 163
                                       45554322445555555555544 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   0.2     0.043        55      16      22 ..     139     145 ..     137     149 .. 0.74
   2 !   12.2   0.2   0.00012      0.16      16      29 ..     154     167 ..     153     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.043
                     Auto_anti-p27  16 etCpvCg 22 
                                       e+Cp+Cg
  gi|320101270|ref|YP_004176862.1| 139 EYCPTCG 145
                                       6899995 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                     Auto_anti-p27  16 etCpvCgvPLmrdr 29 
                                       +tCp Cg+PL r r
  gi|320101270|ref|YP_004176862.1| 154 KTCPLCGTPLTRRR 167
                                       79*********977 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.097   1.2e+02       2       8 ..     139     145 ..     138     147 .. 0.88
   2 ?    9.2   0.1    0.0008         1       2      15 ..     154     167 ..     153     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.097
                                       EE-SSS- CS
                    zf-C4_Topoisom   2 ekCPkCg 8  
                                       e CP Cg
  gi|320101270|ref|YP_004176862.1| 139 EYCPTCG 145
                                       68****9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0008
                                       EE-SSS--EEEEEE CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkr 15 
                                       ++CP Cg +L ++r
  gi|320101270|ref|YP_004176862.1| 154 KTCPLCGTPLTRRR 167
                                       69*********998 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.1       1.5   1.9e+03      22      26 ..     141     145 ..     139     146 .. 0.90
   2 ?   12.6   0.2   7.2e-05     0.092      20      33 ..     153     167 ..     149     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                                       -TTT- CS
                     Rad50_zn_hook  22 CPlCg 26 
                                       CP Cg
  gi|320101270|ref|YP_004176862.1| 141 CPTCG 145
                                       ****8 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.2e-05
                                       E.E-TTT--EE-HHH CS
                     Rad50_zn_hook  20 g.cCPlCgReldeeh 33 
                                       +  CPlCg +l++ +
  gi|320101270|ref|YP_004176862.1| 153 EkTCPLCGTPLTRRR 167
                                       339********9876 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00013      0.16      16      53 ..     137     172 ..     135     173 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                          zf-C2HC5  16 aapnClnCGkiiCakeglskpCsfCgspllsseerqel 53 
                                       ++  C +CG +  ak g  k+C+ Cg+pl  + + +++
  gi|320101270|ref|YP_004176862.1| 137 YLEYCPTCGYVP-AKPGE-KTCPLCGTPLTRRRASSAM 172
                                       667899***996.44454.8*********988776665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.5   0.00046      0.58       1      23 []     140     163 ..     140     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00046
                     zinc_ribbon_2   1 fCpnCGael.qdnakFCpyCGtpl 23 
                                       +Cp CG+   ++++k Cp CGtpl
  gi|320101270|ref|YP_004176862.1| 140 YCPTCGYVPaKPGEKTCPLCGTPL 163
                                       8*****987568***********8 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.025        33       2      30 ..     140     146 ..     139     148 .. 0.59
   2 ?    8.0   0.2    0.0021       2.7       3      14 ..     156     167 ..     154     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                                       B-TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2   2 FCsqCGtpvelripdgDnreRlvCpaCgt 30 
                                       +                      Cp Cg+
  gi|320101270|ref|YP_004176862.1| 140 Y----------------------CPTCGY 146
                                       4......................666665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                                       -TTT--B-EEE- CS
                         Nudix_N_2   3 CsqCGtpvelri 14 
                                       C+ CGtp+++r 
  gi|320101270|ref|YP_004176862.1| 156 CPLCGTPLTRRR 167
                                       *******99985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.026        34      26      34 ..     138     146 ..     123     150 .. 0.77
   2 ?    8.5   0.7    0.0016       2.1      24      38 ..     151     165 ..     147     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.026
                       Zn-ribbon_8  26 ltaCPeCgs 34 
                                       l+ CP+Cg 
  gi|320101270|ref|YP_004176862.1| 138 LEYCPTCGY 146
                                       567****95 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                       Zn-ribbon_8  24 apltaCPeCgsevrr 38 
                                       + +++CP Cg +++r
  gi|320101270|ref|YP_004176862.1| 151 PGEKTCPLCGTPLTR 165
                                       45778******7777 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 ?   -0.8   0.2       1.4   1.8e+03       9      14 ..     140     145 ..     139     147 .. 0.85
   2 ?   10.8   0.1   0.00033      0.42       7      21 ..     153     167 ..     149     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                           DUF2256   9 iCavCg 14 
                                        C++Cg
  gi|320101270|ref|YP_004176862.1| 140 YCPTCG 145
                                       5****8 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00033
                           DUF2256   7 sKiCavCgrpftwRk 21 
                                       +K+C+ Cg p+t R+
  gi|320101270|ref|YP_004176862.1| 153 EKTCPLCGTPLTRRR 167
                                       7***********998 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.7   4.7e+03       8      17 ..      38      47 ..      37      48 .. 0.81
   2 ?    2.1   0.4      0.16     2e+02       2       6 ..     141     145 ..     140     146 .. 0.90
   3 ?   10.4   0.1   0.00039       0.5       1      11 [.     155     165 ..     155     173 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.7
                    DNA_ligase_ZBD  8 avvReegeai 17
                                      +vv ee+ a+
  gi|320101270|ref|YP_004176862.1| 38 EVVDEENKAA 47
                                      6899999997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                    DNA_ligase_ZBD   2 CPvCG 6  
                                       CP CG
  gi|320101270|ref|YP_004176862.1| 141 CPTCG 145
                                       ****9 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00039
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP CG+++ R
  gi|320101270|ref|YP_004176862.1| 155 TCPLCGTPLTR 165
                                       7********97 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.7    0.0074       9.4      17      23 ..     141     147 ..     138     147 .. 0.88
   2 ?    5.9   0.3     0.011        13       1      22 [.     154     161 ..     154     163 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0074
                           UPF0547  17 CphCGyv 23 
                                       Cp CGyv
  gi|320101270|ref|YP_004176862.1| 141 CPTCGYV 147
                                       ******8 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                           UPF0547   1 KvCPeCeakvPvaaqfCphCGy 22 
                                       K               Cp+CG+
  gi|320101270|ref|YP_004176862.1| 154 K--------------TCPLCGT 161
                                       4..............4666665 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.051        66       5      10 ..     140     145 ..     139     146 .. 0.90
   2 ?    8.1   0.8    0.0016         2       6      23 ..     156     173 .]     156     173 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.051
                     zf-NADH-PPase   5 FCgrCG 10 
                                       +C++CG
  gi|320101270|ref|YP_004176862.1| 140 YCPTCG 145
                                       899999 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                     zf-NADH-PPase   6 CgrCGaptepaeggwarv 23 
                                       C+ CG+p  + ++  a++
  gi|320101270|ref|YP_004176862.1| 156 CPLCGTPLTRRRASSAMR 173
                                       ********9999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1244.90
//
Query:       gi|320101271|ref|YP_004176863.1|  [L=275]
Description: ATP-NAD/AcoX kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-11   43.6   0.1    4.1e-11   42.6   0.1    1.5  1  NAD_kinase  ATP-NAD kinase
     0.0014   18.3   0.0     0.0024   17.5   0.0    1.3  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 !   42.6   0.1   4.5e-15   4.1e-11      66     291 ..      38     256 ..       9     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 4.5e-15
                                       EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHH..CT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEE CS
                        NAD_kinase  66 dtrkaleafadagvdliivvGGDGTaldvarllqk..aeiPvlgvnaGvkgfltefepeaaaellekllegeirvek 140
                                        t +++ +    + dl++ vGGDGT+l+++ +lq    ++ +l  + G+ +   + +++ a  + ek+l+g++ v++
  gi|320101271|ref|YP_004176863.1|  38 STVDDASTRSVVDKDLVLSVGGDGTILRISLMLQGesTTPLILPHPCGRRNTFYDEDIPSASLIVEKVLKGDFMVQL 114
                                       555666666667789*******************964456699*****99988888*******************99 PP

                                       EEEEEEEEEETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEE...EEEESEEEEE-TGGGGTHHHH CS
                        NAD_kinase 141 revldavimrskgeediadiviensvlnevviirgpgstlielelyvdtelle...adqldglivstPtGstaysls 214
                                         + ++ ++++             + lne  +       +i + + v  + +    ++  dg ivst++Gs +y ls
  gi|320101271|ref|YP_004176863.1| 115 YPRGRVCVRDRCV-----------YFLNEAAVLNMDMGRVIGFTVTVRSAGVYsryDFEGDGFIVSTAPGSAGYNLS 180
                                       9988866655544...........457888888888888888777776665531115689999************** PP

                                       TT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                        NAD_kinase 215 aGgplisPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfklir 291
                                       a gpl+    ++++++ ++P  l    i ++   ++  + asr  ++l +dG++   l  ++ vr+t +    kl+r
  gi|320101271|ref|YP_004176863.1| 181 ARGPLVAGWGDELVLTHLNPMQLGIPSITLPAYVSVV-EAASRGYTVLYVDGEKMRLLDRREPVRITGGVGFLKLVR 256
                                       ***********************99999999887554.44499999999***9999999999999988877666665 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.6e-07    0.0024      18      96 ..      20      90 ..       9      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-07
                                      HHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS--HH CS
                          DAGK_cat 18 llrkvrelleeagvelelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtgNdl 96
                                      +++k+ +l++ +gv++e+ +++     ++ ++++ ++  dl++ +GGDGt+  +   l + ++t+p +   P+G  N +
  gi|320101271|ref|YP_004176863.1| 20 IAKKYSDLFKGRGVSVEVSTVD-----DASTRSVVDK--DLVLSVGGDGTILRISLMLQG-ESTTPLILPHPCGRRNTF 90
                                      5578888888888888888887.....3345666676..***************999999.999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1981.12
//
Query:       gi|320101272|ref|YP_004176864.1|  [L=349]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  138.2   0.0    3.9e-40  137.7   0.0    1.1  1  Met_10           Met-10+ like-protein
    1.7e-06   27.8   0.0    3.9e-06   26.6   0.0    1.6  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    0.00021   20.8   0.0    0.00031   20.3   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0075   15.5   0.0      0.012   14.8   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
  ------ inclusion threshold ------
      0.024   14.0   0.0      0.034   13.5   0.0    1.1  1  DNA_methylase    C-5 cytosine-specific DNA methylase
       0.16   11.6   0.0       0.21   11.3   0.0    1.2  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


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 !  137.7   0.0   1.3e-43   3.9e-40       2     198 ..      98     299 ..      97     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 1.3e-43
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +++ iG v+i++ +      + ++ +v+  ++  +++++ k+++v  ++Rt+ l++l G+   e+ +kE+g +fk+ 
  gi|320101272|ref|YP_004176864.1|  98 SYDLIGGVAIVRDNVLGYMGEAELIQVLRSIHpGLRAIYVKEETV-DKYRTPVLRLLWGEPVEEVLVKEYGLSFKVS 173
                                       689999999997776655667888899999999***********6.68*************9*************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT..-TTC CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNk..vekv 152
                                       + + y++++l++E++r+a+lv++gevVvd+f GiG f++ ia   +   v+a+dlnPe++++l+eni+lN+  ++ +
  gi|320101272|ref|YP_004176864.1| 174 LGRAYYNPRLSEEHHRVASLVRDGEVVVDLFTGIGGFPVHIAS-LRTALVIANDLNPEAYRLLCENIALNHrrLKGT 249
                                       ******************************************8.77888*********************64489** PP

                                       EEEEES-GGG---....TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEE CS
                            Met_10 153 vkpileDgrevir....eqladrvvmnlpksaieFldkvlaalkdggvih 198
                                       + p++ D+rev         adrv+ nlpk ++eF d   a l+ ggv h
  gi|320101272|ref|YP_004176864.1| 250 IIPLNLDAREVEGyvkvAGRADRVIANLPKWSVEFTDVYDALLRPGGVLH 299
                                       ***********9887777889****************9999999999988 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 !   26.6   0.0   1.3e-09   3.9e-06       1      42 [.      25      66 ..      25      70 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.3e-09
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S- CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkee 42
                                      c+ V+k  +E v k+L + +l d+++ +++++d ++IPvk+ 
  gi|320101272|ref|YP_004176864.1| 25 CVSVEKHLAEAVLKRLGSRSLVDPDHLVTRSGDSILIPVKDA 66
                                      9***************************************96 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     1e-07   0.00031     157     256 ..     192     298 ..     188     316 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1e-07
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev...alseellk.....ee 225
                                       +lv+ ge v+D+ tG G   +  a L ++ v+a D+++ A +   eN++lN+ + k ++   +l ++ ++     ++
  gi|320101272|ref|YP_004176864.1| 192 SLVRDGEVVVDLFTGIGGFPVHIASLRTALVIANDLNPEAYRLLCENIALNHRRLKGTIiplNLDAREVEgyvkvAG 268
                                       67999**********************************************98875444222444333324445689 PP

                              PrmA 226 kadvivaNILaevlielaedikklvkeggll 256
                                       +ad ++aN L +  +e+++   +l+++gg+l
  gi|320101272|ref|YP_004176864.1| 269 RADRVIAN-LPKWSVEFTDVYDALLRPGGVL 298
                                       9*******.7888889999999999999876 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     4e-06     0.012      76     221 ..     151     292 ..     140     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-06
                   Methyltrans_SAM  76 evlvgeldespvvvesglkyqldigrnq.nfglfldmrlgrdwvqenakdknvlnlfaytcgfsvaaiaggaskvvn 151
                                        +l+ge+ e+  v+e gl +++ +gr   n  l  +     + v++   +  v++lf+   gf v   +  +  v+ 
  gi|320101272|ref|YP_004176864.1| 151 RLLWGEPVEEVLVKEYGLSFKVSLGRAYyNPRLSEEHHRVASLVRD---GEVVVDLFTGIGGFPVHIASLRTALVIA 224
                                       589***********************85266666666666677776...56799***********988889999999 PP

                   Methyltrans_SAM 152 vdmargslnkgrdnhrlnghdlr.rvsflgydifkswgkikksgpydlviidppsfqkgsfaltkdykkil 221
                                        d+   +     +n  ln   l+  +  l  d     g +k +g+ d vi + p     s  +t  y  +l
  gi|320101272|ref|YP_004176864.1| 225 NDLNPEAYRLLCENIALNHRRLKgTIIPLNLDAREVEGYVKVAGRADRVIANLPK---WSVEFTDVYDALL 292
                                       9*****************999972566799999999999*99***9999998874...4555555555555 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 ?   13.5   0.0   1.1e-05     0.034       3      43 ..     200     240 ..     199     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-. CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk 43 
                                       ++dLf GiGGf +  ++  +  v+a++ +++a  +++ n+ 
  gi|320101272|ref|YP_004176864.1| 200 VVDLFTGIGGFPVHIASLRTALVIANDLNPEAYRLLCENIA 240
                                       79*********************************999985 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.9e-05      0.21      20      67 ..     196     244 ..     184     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.9e-05
                                       --SEEEETT-TTSCCHHCS....SSCEEEEES-HHHHHHHHHHCCHSHH CS
                   MethyltransfD12  20 kgktfvepFaGggaVffeakk.qgkkvlinDinedlinlykaliknnve 67 
                                       +g+++v++F+G g + +++ + +   v++nD+n++ + l    i+ n +
  gi|320101272|ref|YP_004176864.1| 196 DGEVVVDLFTGIGGFPVHIASlRTALVIANDLNPEAYRLLCENIALNHR 244
                                       7899*******999999999999*************9987666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2678.48
//
Query:       gi|320101273|ref|YP_004176865.1|  [L=165]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-46  155.7   0.0      7e-46  155.5   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 !  155.5   0.0   3.9e-50     7e-46       1     132 [.       4     136 ..       4     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 3.9e-50
                                       EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE-- CS
                            DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGs 77 
                                       i+arGH+ ++a+h+sT+e+t++++lt+rgdCIigv+adk+++d+s ++keal+++++++ v+++vg+ +d i ++Gs
  gi|320101273|ref|YP_004176865.1|   4 IHARGHPSIRATHASTIEVTREEHLTERGDCIIGVAADKSPRDFSGSFKEALRRDDSILIVVFKVGDFSDFILAQGS 80 
                                       79*************************************************************************** PP

                                       TT-----SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHT.T-EEEEEEEE CS
                            DUF371  78 pkltlenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkk.gaeltvelev 132
                                       ++l ++++ +l++R+S +v+++T+ ++a+kaa+d+dr lv+aL++ g+ l+v+l v
  gi|320101273|ref|YP_004176865.1|  81 SRLVVDDPVKLIIRRSLFVEPATVGIRANKAARDIDRGLVNALRNpGSLLEVRLYV 136
                                       *********************************************99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1363.64
//
Query:       gi|320101274|ref|YP_004176866.1|  [L=226]
Description: protein-L-isoaspartate O-methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-66  222.4   0.0    6.4e-66  222.1   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    7.4e-08   32.3   0.0    9.3e-08   32.0   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    9.4e-06   26.3   0.0    1.3e-05   25.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    3.6e-05   24.7   0.0    5.3e-05   24.2   0.0    1.3  1  Methyltransf_24  Methyltransferase domain
    0.00016   21.5   0.0    0.00023   20.9   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00093   19.8   0.0     0.0015   19.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0024   17.0   0.0     0.0037   16.4   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0066   16.5   0.0     0.0096   15.9   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.085   12.0   0.0       0.12   11.5   0.0    1.1  1  Fibrillarin      Fibrillarin
      0.093   12.0   0.0       0.12   11.7   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
       0.11   11.6   0.0       0.17   11.0   0.0    1.2  1  Methyltransf_3   O-methyltransferase
       0.16   11.8   0.0       0.18   11.7   0.0    1.3  1  Methyltransf_23  Methyltransferase domain


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 !  222.1   0.0   4.3e-69   6.4e-66       5     208 ..      10     218 ..       6     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: 222.1 bits;  conditional E-value: 4.3e-69
                                       HHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES CS
                              PCMT   5 alieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevG 81 
                                        ++e l++ g+i+s+k a al+ v+Re f+p +++e+aY d+pl+igy++tiSa+hmva++++ l+ ++g++vLevG
  gi|320101274|ref|YP_004176866.1|  10 LVVEGLRSLGYIRSEKTARALLRVPREAFLPPQLREYAYYDTPLPIGYGQTISAIHMVAIMTDELDPEPGDKVLEVG 86 
                                       57899************************************************************************ PP

                                       -TTSHHHHHHHHHH.....CTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-SEEEEEESSBB CS
                              PCMT  82 sGsGyltavlarlv.....gekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaPYdaihvgaaa 152
                                       +GsGy++avla++v     g+kg+v s+eri+el+e a+ +l++ ++  +v+vvvgDG+ G + +aP+++++v+aa+
  gi|320101274|ref|YP_004176866.1|  87 TGSGYQAAVLAEIVarsdpGRKGHVYSVERIPELAEYARTRLREAGYGdDVTVVVGDGTLGLPGEAPFNRVIVTAAT 163
                                       **************544444678***********************9769*************************** PP

                                       SS--HHHHHTEEEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCC CS
                              PCMT 153 peiPealidQLkeGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdk 208
                                       p +P +lidQL++GGrlv+Pvg++ +Q+l  v+kk+ g+++ ++ +e++fvpl ++
  gi|320101274|ref|YP_004176866.1| 164 PAVPPPLIDQLADGGRLVAPVGDRFSQRLVIVEKKG-GSITKRYGMECVFVPLIGR 218
                                       ************************************.****************876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   6.2e-11   9.3e-08       3      80 ..      78     159 ..      76     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 6.2e-11
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelae.....elgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklled 72 
                                        g +vl++G+G+G+ + +lae       g k++v+++++ +e  e+Ar+++++ g+   v++ +gd +  l+    +
  gi|320101274|ref|YP_004176866.1|  78 PGDKVLEVGTGSGYQAAVLAEivarsDPGRKGHVYSVERIPELAEYARTRLREAGYGdDVTVVVGDGTLgLPG---E 151
                                       6789****************9988655555999***********************99********9999993...3 PP

                   Methyltransf_31  73 ekfDlils 80 
                                       ++f+ ++ 
  gi|320101274|ref|YP_004176866.1| 152 APFNRVIV 159
                                       78887665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   8.9e-09   1.3e-05       1      84 [.      82     173 ..      82     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 8.9e-09
                                       EEEET-TTSHHHHHHHCTS.....T.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BSSSTTTEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.....g.kakvtgvDiseemleaareraeeegl..nvefvqgdaed.lpfedgsfDlv 68 
                                       vL++G+G+G  ++ la+ +     g k++v+ v+  +e+ e+ar+r++e+g+  +v++v+gd +  lp  ++ f+ v
  gi|320101274|ref|YP_004176866.1|  82 VLEVGTGSGYQAAVLAEIVarsdpGrKGHVYSVERIPELAEYARTRLREAGYgdDVTVVVGDGTLgLPG-EAPFNRV 157
                                       9***********999999887776479**********************99999*********653775.5699999 PP

                                       EEESTGGGSSHHHHHH CS
                   Methyltransf_25  69 vssgalhhlsdedlek 84 
                                       +++ a   ++++ +++
  gi|320101274|ref|YP_004176866.1| 158 IVTAATPAVPPPLIDQ 173
                                       9976677777665554 PP

>> Methyltransf_24  Methyltransferase 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   5.3e-05       1      58 [.      83     144 ..      83     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.5e-08
                   Methyltransf_24   1 vEiGvysGvstlwllralrrnga...grlvavdhdpg.aeeaaalareaglddrvrlikads 58 
                                       +E+G+ sG+ +++l++ + r +    g++++v+  p+ ae a+  +reag+ d v+++++d 
  gi|320101274|ref|YP_004176866.1|  83 LEVGTGSGYQAAVLAEIVARSDPgrkGHVYSVERIPElAEYARTRLREAGYGDDVTVVVGDG 144
                                       7*******************999999**********544445555556**********9986 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.5e-07   0.00023      29     100 ..      67     143 ..      55     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.5e-07
                             GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartva...P..tGhlftfefheqraekareefrehelsqlvtvthrD 100
                                       +++++ +L+ +pG +v+e GtGsg  +  +a  va   P  +Gh++++e   + ae ar  +re +  + vtv + D
  gi|320101274|ref|YP_004176866.1|  67 VAIMTDELDPEPGDKVLEVGTGSGYQAAVLAEIVArsdPgrKGHVYSVERIPELAEYARTRLREAGYGDDVTVVVGD 143
                                       67778899999************9877766666653332348************************99999987655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.7e-07    0.0015       1      59 [.      83     150 ..      83     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.7e-07
                                       EEET-TTSHHHHHHH......HTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-T CS
                   Methyltransf_11   1 LdvGcGtGrlaeala......krg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfed 59 
                                       L+vG+G+G+ a+ la      + g  ++v+ v+  +e+ ++a+++ +e+g    v++vv+d + l ++ 
  gi|320101274|ref|YP_004176866.1|  83 LEVGTGSGYQAAVLAeivarsDPGrkGHVYSVERIPELAEYARTRLREAGYgdDVTVVVGDGT-LGLPG 150
                                       89*************777665444889**************************99******98.55544 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.4e-06    0.0037      23      84 ..      71     143 ..      58     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                                       HHHH-GGTTSEEEEES-TTTCCHHHHHCC-........SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S- CS
                            RrnaAD  23 ldklnleekltvleigpGkGilTeeLakra........kqvvvlElderLakllqkkls...kdeklkvvhqD 84 
                                        d+l++e+ ++vle+g+G G + + La+++         +v ++E  ++La+  +++l+    +  ++vv  D
  gi|320101274|ref|YP_004176866.1|  71 TDELDPEPGDKVLEVGTGSGYQAAVLAEIVarsdpgrkGHVYSVERIPELAEYARTRLReagYGDDVTVVVGD 143
                                       4789999*********************998777776335668899999999988888866666667776666 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.4e-06    0.0096      10      75 ..      64     132 ..      58     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.4e-06
                   Methyltransf_32  10 aelvakllkelakesgaltvvDvGaGkgYLsfvlal...kek.eyklkvvgidakeelvekaekraeklg 75 
                                       +++va +++e  + ++  +v++vG G gY + vla    ++    k +v++++   el+e a++r ++ g
  gi|320101274|ref|YP_004176866.1|  64 IHMVAIMTDE-LDPEPGDKVLEVGTGSGYQAAVLAEivaRSDpGRKGHVYSVERIPELAEYARTRLREAG 132
                                       5677777777.5888899*****************9986333369******************9988876 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     8e-05      0.12      65     106 ..      73     119 ..      61     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8e-05
                                       --S--TTSEEEEESTTTSHHHHHHHHHH.....TTTSEEEEEESSHH CS
                       Fibrillarin  65 elpikkgskvLYlGaasGttvsHvsDiv.....geegvvyavefspr 106
                                       el  ++g+kvL +G++sG  ++ +++iv     g++g vy+ve  p 
  gi|320101274|ref|YP_004176866.1|  73 ELDPEPGDKVLEVGTGSGYQAAVLAEIVarsdpGRKGHVYSVERIPE 119
                                       556689**********************55544568*******8875 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.9e-05      0.12      52     118 ..      68     141 ..      61     166 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.9e-05
                                       HHHHTTTT--TT-EEEEES-TTSH...HHHHHHHHH--....EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEE CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGs...lvrraverydv....kvvglTlSkeqaklakkrvdeldlerkvevkl 118
                                        ++ + l+ +pG+++L++G+G G+   ++ + v+r d     +v ++    e a++a+ r+ e++  ++v+v +
  gi|320101274|ref|YP_004176866.1|  68 AIMTDELDPEPGDKVLEVGTGSGYqaaVLAEIVARSDPgrkgHVYSVERIPELAEYARTRLREAGYGDDVTVVV 141
                                       567899999*************9722234555666665111134444444455677778888887777777765 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.17      50     109 ..      81     145 ..      73     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                       EEEEE--TTSHHHHHHHTTS....-.TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HH CS
                    Methyltransf_3  50 rvleiGvftGyslLatalal....P.eDGkilaididreayeialkfiqkagvaekieliegdal 109
                                       +vle+G+  Gy +  +a  +    P   G++ +++  +e +e a+  ++ ag+++ + + +gd++
  gi|320101274|ref|YP_004176866.1|  81 KVLEVGTGSGYQAAVLAEIVarsdPgRKGHVYSVERIPELAEYARTRLREAGYGDDVTVVVGDGT 145
                                       89*********9887776552222334699*******************************9986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.18      21      58 ..      77     122 ..      29     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengf........svtgvDlspeave 58 
                                       ++g +vL++G+G+G+ + vl+e ++        +v+ v+  pe+ e
  gi|320101274|ref|YP_004176866.1|  77 EPGDKVLEVGTGSGYQAAVLAEIVArsdpgrkgHVYSVERIPELAE 122
                                       67789**********9999988543222222345666665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 1652.53
//
Query:       gi|320101275|ref|YP_004176867.1|  [L=356]
Description: flap endonuclease 1 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-28   96.5   0.0    1.4e-27   95.9   0.0    1.3  1  XPG_I       XPG I-region
    3.7e-22   78.7   0.0    6.9e-22   77.8   0.0    1.5  1  XPG_N       XPG N-terminal domain
    0.00055   20.5   0.2     0.0018   18.8   0.0    2.0  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.045   14.4   0.1       0.26   11.9   0.0    2.3  2  HHH_5       Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   3.1e-31   1.4e-27       2      94 .]     145     240 ..     144     240 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 3.1e-31
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       +mgip+v+Ap E+EAq+ay+++kg+++a +s+D+D+llFG+p+++rnl+ ++++k    +e++++k+evi+l+k+l+
  gi|320101275|ref|YP_004176867.1| 145 AMGIPWVQAPAEGEAQAAYMARKGDAYASASQDYDSLLFGSPRLVRNLTiSGRRKLPrrEEYVEVKPEVIELDKLLS 221
                                       79***********************************************6555554488999*************** PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                       +lg+t e+l+d+ illg+D
  gi|320101275|ref|YP_004176867.1| 222 KLGVTYENLVDIGILLGTD 240
                                       ******************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   1.5e-25   6.9e-22       2     100 ..       2     104 ..       1     105 [. 0.93

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.5e-25
                                       --TTHHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTE CS
                             XPG_N   2 GikgLlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgi 73 
                                       G+  L +l+ + a i   ++++l g+++aiD++  ly+fl a+r+++g+ l+      tshl glf+r++ +++ gi
  gi|320101275|ref|YP_004176867.1|   2 GVD-LRELIPDDAKIIIEDLRTLRGRVIAIDGYNALYQFLAAIRQPDGTPLMDgsgriTSHLSGLFYRTINIVEAGI 77 
                                       553.778888888888999*********************************99*********************** PP

                                       EEEEEE--S--GGGHHHHHHHHHHHHH CS
                             XPG_N  74 kPifVFdgkapdlkkeelekrserrqe 100
                                       kP++VFdgk+p+lk++e+e+r+  r+e
  gi|320101275|ref|YP_004176867.1|  78 KPVYVFDGKPPELKAKEIERRRVVREE 104
                                       *********************998887 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   6.3e+03      53      74 ..     111     132 ..      96     145 .. 0.68
   2 !   18.8   0.0   4.1e-07    0.0018       5      48 ..     229     271 ..     225     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                        5_3_exonuc  53 ekklkekLeenkeearlskkLa 74 
                                       e  ++  Le ++ +a++s +L+
  gi|320101275|ref|YP_004176867.1| 111 EAVQAGDLESARRYAMMSARLT 132
                                       3344566888888888888886 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.1e-07
                        5_3_exonuc   5 qiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenl 48 
                                       +++d+  L G    n  G +giG+k+A +L+k ygs+e+i + l
  gi|320101275|ref|YP_004176867.1| 229 NLVDIGILLGTDY-NPDGFEGIGPKKALQLVKVYGSVEKIPKPL 271
                                       5666666666543.6789**********************8855 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.94   4.2e+03      13      24 ..     137     149 ..     136     158 .. 0.82
   2 ?   11.9   0.0   5.9e-05      0.26       8      29 ..     247     267 ..     244     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.94
                                       HHHHHHHTT.T-- CS
                             HHH_5  13 ktAlallsa.Gie 24 
                                       ++A+all+a Gi 
  gi|320101275|ref|YP_004176867.1| 137 RDAKALLDAmGIP 149
                                       6899999998875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.9e-05
                                       TT--HHHHHHHHTTT--SHHHH CS
                             HHH_5   8 sGiGpktAlallsaGiesvedl 29 
                                       +GiGpk Al l++  ++sve++
  gi|320101275|ref|YP_004176867.1| 247 EGIGPKKALQLVKV-YGSVEKI 267
                                       8*************.****988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2664.87
//
Query:       gi|320101276|ref|YP_004176868.1|  [L=86]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   19.1   0.0     0.0013   18.8   0.0    1.1  1  HTH_20        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.039   13.9   0.1      0.053   13.5   0.1    1.3  1  PadR          Transcriptional regulator PadR-like family
      0.075   13.3   0.0      0.093   13.0   0.0    1.1  1  DNAJ_related  DNA-J related protein


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 !   18.8   0.0   2.1e-07    0.0013      10      61 .]      13      71 ..      11      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-07
                                      HHHHHHHHHH.STCTTB-HHHHHHHHT......S-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 10 PvRrrilraL.araegltaselaerld......lskntlsyHLrvLeeagLvevvregr 61
                                      P  r+il  L + +eg+  s+l ++l         k++l++ L  Le  gL+ v+ +gr
  gi|320101276|ref|YP_004176868.1| 13 PLFRAILEILvSKPEGMPESDLEDALKkkyelvFNKSELYHTLIRLELSGLIQVESVGR 71
                                      8889**********************6678899*************99******99886 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.8e-06     0.053      14      51 ..      33      68 ..      18      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.8e-06
                                      HHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEE CS
                              PadR 14 eiikeleelsegllelseGslYpaLkrLekeglvesew 51
                                      ++ ++l++ +e  l +++++lY +L rLe +gl++ e 
  gi|320101276|ref|YP_004176868.1| 33 DLEDALKKKYE--LVFNKSELYHTLIRLELSGLIQVES 68
                                      67788888864..7899*****************8765 PP

>> DNAJ_related  DNA-J related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.6e-05     0.093       2      40 ..      13      51 ..      12      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                      DNAJ_related  2 eLleallellkeapegikeyeLikeLkereaelfeklal 40
                                      +L++a+le+l ++peg+ e +L ++Lk++   +f+k++l
  gi|320101276|ref|YP_004176868.1| 13 PLFRAILEILVSKPEGMPESDLEDALKKKYELVFNKSEL 51
                                      7999*************************8889998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 674.14
//
Query:       gi|320101277|ref|YP_004176869.1|  [L=730]
Description: AAA ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-99  327.9   0.0    2.3e-49  167.2   0.0    2.7  2  AAA              ATPase family associated with various cellul
    1.2e-34  117.8   0.0    7.2e-17   60.9   0.0    2.6  2  AAA_lid_3        AAA+ lid domain
    1.8e-19   69.7   0.1    6.3e-19   67.9   0.1    2.0  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.4e-15   57.4   0.0    3.5e-07   30.1   0.0    3.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.3e-15   55.6   0.2    3.5e-06   27.5   0.0    4.0  2  AAA_16           AAA ATPase domain
    5.6e-14   52.6   0.0    7.4e-08   32.7   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    9.7e-13   48.3   0.9    5.8e-06   26.3   0.1    3.5  2  AAA_5            AAA domain (dynein-related subfamily)
    7.2e-11   41.9   0.0    0.00028   20.2   0.0    2.5  2  TIP49            TIP49 P-loop domain
    9.6e-11   42.1   0.9    0.00028   21.1   0.1    3.9  2  AAA_22           AAA domain
    2.2e-10   40.9   0.0    9.1e-05   22.6   0.0    2.5  2  AAA_33           AAA domain
    5.3e-10   39.4   0.0    0.00053   20.0   0.0    2.3  2  AAA_14           AAA domain
    2.8e-08   34.1   0.0     0.0041   17.5   0.0    2.5  2  RNA_helicase     RNA helicase
    2.8e-08   34.4   0.0     0.0046   17.5   0.0    2.6  2  AAA_18           AAA domain
    9.9e-08   32.4   0.1     0.0051   17.1   0.0    2.7  2  AAA_28           AAA domain
      1e-07   31.9   0.0     0.0083   15.9   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
      2e-07   30.6   0.4      0.017   14.5   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.7e-07   30.3   0.4    5.3e-07   29.3   0.4    1.6  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    3.1e-07   30.3   0.0     0.0038   17.0   0.0    2.7  2  AAA_24           AAA domain
    3.7e-07   29.6   0.0      0.034   13.3   0.0    2.7  2  DUF815           Protein of unknown function (DUF815)
      8e-07   29.2   2.4       0.19   11.6   0.3    3.8  3  ATPase_2         ATPase domain predominantly from Archaea
      3e-06   27.2   0.0      0.078   13.0   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    5.1e-06   26.4   0.0      0.072   12.9   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    5.5e-06   26.9   0.0       0.17   12.4   0.0    2.4  2  ABC_tran         ABC transporter
      6e-06   25.7   0.1      0.068   12.4   0.0    2.6  2  Zeta_toxin       Zeta toxin
    7.2e-06   25.8   0.1      0.093   12.4   0.0    3.1  2  Sigma54_activat  Sigma-54 interaction domain
    1.2e-05   24.7   0.4       0.27   10.5   0.0    3.4  3  ATPase           KaiC
    1.5e-05   24.6   0.0      0.041   13.4   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
      2e-05   23.8   0.2      0.024   13.7   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    2.5e-05   24.3   0.0       0.12   12.3   0.0    3.1  3  Rad17            Rad17 P-loop domain
    3.4e-05   23.8   0.0      0.022   14.6   0.0    2.7  2  Bac_DnaA         Bacterial dnaA  protein
    3.5e-05   23.8   0.3       0.35   10.8   0.1    3.0  3  NACHT            NACHT domain
    0.00035   20.1   0.4       0.76    9.2   0.0    2.3  2  PhoH             PhoH-like protein
    0.00043   20.7   0.0        1.7    9.1   0.0    2.7  2  AAA_17           AAA domain
    0.00057   19.2   0.0      0.048   12.9   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00063   19.4   6.4       0.44   10.1   0.1    3.7  3  AAA_25           AAA domain
    0.00082   19.2   0.0       0.63    9.8   0.0    2.2  2  AAA_11           AAA domain
    0.00091   18.5   0.0        1.1    8.4   0.0    2.3  2  NB-ARC           NB-ARC domain
     0.0021   17.8   0.0       0.71    9.6   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0023   17.4   0.0     0.0041   16.6   0.0    1.4  1  UFD1             Ubiquitin fusion degradation protein UFD1
     0.0033   17.2   0.0        2.8    7.7   0.0    2.9  3  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0038   17.3   0.0        4.3    7.4   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0069   16.5   0.0        3.7    7.7   0.0    2.4  2  SKI              Shikimate kinase
  ------ inclusion threshold ------
      0.011   14.7   0.4        1.5    7.7   0.1    2.4  2  AFG1_ATPase      AFG1-like ATPase
      0.012   15.6   1.0         12    5.8   0.0    3.6  3  NTPase_1         NTPase
      0.021   14.6   1.2        1.7    8.4   0.0    2.9  2  AAA_30           AAA domain
      0.023   15.1   4.0          5    7.4   0.1    3.3  3  AAA_19           AAA domain
      0.025   14.3   0.1        3.2    7.4   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
      0.026   13.6   0.0       0.29   10.2   0.0    2.2  2  T2SSE            Type II/IV secretion system protein
      0.047   12.9   0.0          4    6.5   0.0    2.2  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.047   13.4   0.1         29    4.3   0.0    3.8  4  Guanylate_kin    Guanylate kinase
      0.061   13.3   0.0        3.7    7.6   0.0    2.7  2  Vps4_C           Vps4 C terminal oligomerisation domain
      0.067   12.8   0.0        9.6    5.8   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.077   12.4   0.1        9.3    5.6   0.0    2.3  2  IPT              Isopentenyl transferase
      0.078   12.2   0.1         29    3.8   0.1    3.0  3  KAP_NTPase       KAP family P-loop domain
      0.083   12.3   0.0         15    5.0   0.0    2.5  2  SRPRB            Signal recognition particle receptor beta su
        0.1   12.7   0.0        8.6    6.4   0.0    2.5  2  Cytidylate_kin2  Cytidylate kinase-like family
       0.13   12.3   0.0        7.9    6.5   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
       0.22   11.3   0.0         27    4.6   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
        0.3   10.0   0.1        1.3    7.9   0.0    1.9  2  AAA_6            Hydrolytic ATP binding site of dynein motor 


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 !  167.2   0.0   7.6e-52   2.3e-49       1     131 [.     212     344 ..     212     345 .. 0.97
   2 !  157.9   0.0   5.6e-49   1.7e-46       1     131 [.     492     622 ..     492     623 .. 0.97

  Alignments for each domain:
  == domain 1  score: 167.2 bits;  conditional E-value: 7.6e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidalaksrs 75 
                                       +llyGppGtGKTllaka+a+e++++f++i+g+e++sky gese+++re+fk a++k+  +p i+fiDEida+a++r+
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNAYFITINGPEIMSKYYGESEQRLREIFKLARKKSkkNPAIIFIDEIDAIAPKRD 288
                                       69***************************************************99999889***************9 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +   e+e+rvv+qLl+ +dg++++ ++vivi+atnrp+ ldpal+r gRfdr+iei+
  gi|320101277|ref|YP_004176869.1| 289 EVIGEVERRVVAQLLALMDGLESR-GNVIVIAATNRPNALDPALRRpGRFDREIEIP 344
                                       9**********************7.66****************************97 PP

  == domain 2  score: 157.9 bits;  conditional E-value: 5.6e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       vllyGppG+GKTllakava+e+g++f+ ++g+e+lsk+vgesek +re+f++a+  a p+++f+DEida+a+ r  +
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGANFIAVKGPEVLSKWVGESEKAVREIFRKARLYA-PVVVFFDEIDAIASLRgID 567
                                       79*****************************************************99.****************888 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++s+++ervv qL+te+dgv+k e+ v+v++atnrpd ldpallr gRfd+ i+++
  gi|320101277|ref|YP_004176869.1| 568 TDSGVSERVVTQLVTEMDGVQKLEN-VVVLAATNRPDLLDPALLRpGRFDKLIYVP 622
                                       89********************865.***************************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 !   54.3   0.0   2.7e-17   8.2e-15       1      34 [.     371     404 ..     371     431 .. 0.81
   2 !   60.9   0.0   2.4e-19   7.2e-17       1      44 [.     645     690 ..     645     691 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.7e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrg 34 
                                       dvdl+++Ae T+Gy+GADlaal++eA+l+A+rr 
  gi|320101277|ref|YP_004176869.1| 371 DVDLAKIAEITHGYTGADLAALVKEAVLHAIRRQ 404
                                       9********************************4 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 2.4e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrg..ikeitmedfe 44 
                                       dvdl+eLA+ TeGySGADl+a++reA++lAlr++  i+ ++ ++f+
  gi|320101277|ref|YP_004176869.1| 645 DVDLAELARSTEGYSGADLEAVVREAVMLALRESpfIERVGRKHFI 690
                                       9********************************8757779999995 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 !   67.9   0.1   2.1e-21   6.3e-19       2      84 ..       6      88 ..       5      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 2.1e-21
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      L+V +a+ +d g+gi+r+dpe+me++g+  gd + ieg+ +++a++ ++ p+d+g+g++r+d ++R+na++ iG +VtV
  gi|320101277|ref|YP_004176869.1|  6 LKVLDAERRDYGKGIARLDPEVMEKYGIMDGDLLVIEGEAEAAALAGTGGPQDKGRGVVRLDPLLRANARAEIGASVTV 84
                                      89***************************************************************************** PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      +k+e
  gi|320101277|ref|YP_004176869.1| 85 EKVE 88
                                      **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 !   30.1   0.0   1.1e-09   3.5e-07      34     104 ..     210     291 ..     182     334 .. 0.76
   2 !   23.4   0.0   1.3e-07   4.1e-05      35      70 ..     491     526 ..     465     564 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.1e-09
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl.........ekagdlaalltnl..eekdvlfideihrlsra 99 
                                         +llyGpPG Gkt lak +a+e+++ + +  gP +         ++ +++  l  +   ++  ++fidei  ++++
  gi|320101277|ref|YP_004176869.1| 210 KGILLYGPPGTGKTLLAKALANEVNAYFITINGPEImskyygeseQRLREIFKLARKKskKNPAIIFIDEIDAIAPK 286
                                       469*******************************984444432222334444444333114456***********99 PP

                            RuvB_N 100 veevl 104
                                        +ev+
  gi|320101277|ref|YP_004176869.1| 287 RDEVI 291
                                       99987 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.3e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                                        vllyGpPG Gkt lak +a+e g+++ +  gP + 
  gi|320101277|ref|YP_004176869.1| 491 GVLLYGPPGCGKTLLAKAVATESGANFIAVKGPEVL 526
                                       69******************************9653 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.2e-08   3.5e-06      24     139 ..     209     317 ..     197     318 .. 0.84
   2 !   21.5   0.1   8.1e-07   0.00024      24      63 ..     489     525 ..     480     681 .. 0.58

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.2e-08
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p  +ll+G++G+GK+ l+++l+++++   ++f++ +  +  ++  y    q l r e+++    +++++ +  + ++
  gi|320101277|ref|YP_004176869.1| 209 PKGILLYGPPGTGKTLLAKALANEVN---AYFITINGPEI-MSKYYGESEQRL-R-EIFKLARKKSKKNPAIIFIDE 279
                                       489*******************8777...78999999999.555555588888.7.999999999999999999999 PP

                            AAA_16 101 leealaavpelagaeasrllellkrllallsrderplvl 139
                                       +++ +   +e+ g+ ++r+ ++l +l++ l++++  +++
  gi|320101277|ref|YP_004176869.1| 280 IDAIAPKRDEVIGEVERRVVAQLLALMDGLESRGN-VIV 317
                                       9999999999999999***********99998676.433 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 8.1e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       p  vll+G++G+GK+ l+++++++  ++   f++ k  + 
  gi|320101277|ref|YP_004176869.1| 489 PKGVLLYGPPGCGKTLLAKAVATESGAN---FIAVKGPEV 525
                                       579*******************877777...444444444 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   2.4e-10   7.4e-08       6     105 ..     212     308 ..     207     323 .. 0.81
   2 !   17.3   0.0   1.4e-05    0.0041       6      95 ..     492     577 ..     487     588 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.4e-10
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                       ill gp g+Gkt+lakala+  ++     +i+++  e++     e+e+ + r+i +    +++++  i+++DEid i
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNA----YFITINGPEIMSkyYGESEQRL-REIFKLARKKSKKNPAIIFIDEIDAI 283
                                       8999******************96....9*****9999996533444444.5666777777888889********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk ++   +v r  V+  LL +++g
  gi|320101277|ref|YP_004176869.1| 284 APKrDEVIGEVERR-VVAQLLALMDG 308
                                       **977777777775.77778899987 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.4e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a    +    ++i +   e+l     e+e+ v +   ++  y  +    +v++DEid i
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGA----NFIAVKGPEVLSkwVGESEKAVREIFRKARLYAPV----VVFFDEIDAI 560
                                       6899****************9995....99999999998845566777777777777777654....********** PP

                                       ---..---------HHH CS
                             AAA_2  81 hpk..essgadvSregV 95 
                                       ++     + + vS+  V
  gi|320101277|ref|YP_004176869.1| 561 ASLrgIDTDSGVSERVV 577
                                       *9843333344555444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   1.9e-08   5.8e-06       2     136 ..     212     333 ..     211     334 .. 0.74
   2 !   18.2   0.1   6.1e-06    0.0018       1     134 [.     491     609 ..     491     612 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-08
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       +lL GppGtgK+ la+ la  +n+ + ++++++ +++     + ++    ++  + + +++ ++++i+++DE++ + 
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNAYFITINGPEIMSKYYGESEQRL----REIFKLARKKSKKNPAIIFIDEIDAIA 284
                                       89*******************************9987543333333....4444445555667***********887 PP

                                       ...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  79 ...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                          +ev++++ +    + l l++g e  +         + via++n+++     l+palr+
  gi|320101277|ref|YP_004176869.1| 285 pkrDEVIGEVERRVVAQLLALMDGLESRGN--------VIVIAATNRPN----ALDPALRR 333
                                       333467777766666666665555555533........99999999998....88888886 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 6.1e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppG+gK+ la+ +a   ++++  v +++      ++ ++    g+ +    ++ r+ar   + ++++DE++
  gi|320101277|ref|YP_004176869.1| 491 GVLLYGPPGCGKTLLAKAVATESGANFIAVKGPE------VLSKWV---GESEKAVREIFRKARlyAPVVVFFDEID 558
                                       59*******************9999999999998......444555...3444444455555555688888888888 PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                        + s       s  +er +   ++ ++++  +   le++ v+a++n++d     l+pal
  gi|320101277|ref|YP_004176869.1| 559 AIASLRGIDTDSGVSERVVT--QLVTEMDGVQ--KLENVVVLAATNRPD----LLDPAL 609
                                       55533222233333444333..2333332222..233377778877777....666666 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   9.2e-07   0.00028      51     101 ..     210     258 ..     202     323 .. 0.84
   2 !   19.1   0.0     2e-06   0.00061      51     106 ..     490     544 ..     485     549 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.2e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltq 101
                                       +++Ll Gp+gtGkt la a+++e++    f++++g e+ s     +e  ++
  gi|320101277|ref|YP_004176869.1| 210 KGILLYGPPGTGKTLLAKALANEVN--AYFITINGPEIMSKYYGESEQRLR 258
                                       89**********************9..79**********998887775443 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       ++vLl Gp+g Gkt la a++ e g    f+a++g ev s  v  +e ++ + +rk+
  gi|320101277|ref|YP_004176869.1| 490 KGVLLYGPPGCGKTLLAKAVATESG--ANFIAVKGPEVLSKWVGESEkAVREIFRKA 544
                                       89********************988..78**************99984677889987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   9.3e-07   0.00028       8      87 ..     212     269 ..     207     323 .. 0.61
   2 !   14.0   0.1   0.00015     0.047       8      29 ..     492     513 ..     487     543 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.3e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                       ++++G++GtGKT+l++ l+++  ++++++ ++pe++ +++  s+                       +++e++++ +
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEV-NAYFITINGPEIMsKYYGESEQ----------------------RLREIFKLAR 265
                                       89******************97.3333333344444333333333......................3333444444 PP

                            AAA_22  84 qalr 87 
                                       + ++
  gi|320101277|ref|YP_004176869.1| 266 KKSK 269
                                       4444 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00015
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++++G++G+GKT+l++ ++ + 
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATES 513
                                       689**************99876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     3e-07   9.1e-05       2      80 ..     212     323 ..     212     342 .. 0.77
   2 !   15.7   0.0   4.1e-05     0.012       2      42 ..     492     534 ..     492     620 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.............................. 46 
                                       +ll G+pG+GK+ la+ l+++    +++++ ++++++++g+ +q+++                              
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNayFITINGPEIMSKYYGESEQRLReifklarkkskknpaiifideidaiapkrd 288
                                       6789***************999999999************9888888777777777777888888888888877655 PP

                            AAA_33  47 .dytrvldrlyqilnelarkalsagrnvildatnl 80 
                                           +v+ r+ ++l +l +   s+g+ +++ atn+
  gi|320101277|ref|YP_004176869.1| 289 eVIGEVERRVVAQLLALMDGLESRGNVIVIAATNR 323
                                       32223566666677777776666666666777765 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdq 42 
                                       vll G+pG+GK+ la+ ++ + g  ++ +  ++++++ +g+ +
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGanFIAVKGPEVLSKWVGESE 534
                                       7899*******************88788888887777666444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.7e-06   0.00053       5      77 ..     212     284 ..     209     323 .. 0.73
   2 !   16.9   0.0   1.6e-05    0.0049       5      78 ..     492     562 ..     489     593 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke...ekktylflDEiqevp 77 
                                       +++ G+  +GKT l+k l++e       ++ in  +   k + ++e+ l++i++++++   ++  ++f+DEi  + 
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVN---AYFITINGPEIMSKYYGESEQRLREIFKLARKkskKNPAIIFIDEIDAIA 284
                                       7899***************8877...9999999999888777766655555555422224468899******9883 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.6e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek..lkeekktylflDEiqevpe 78 
                                       +++ G+  +GKT l+k ++ e+     +++ ++  +   k   ++ek  ++i++k  l+     ++f+DEi  + +
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESG---ANFIAVKGPEVLSKWVGESEKAVREIFRKarLY--APVVVFFDEIDAIAS 562
                                       7899***************9999...999999998888877777665555555553433..5799******98865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.4e-05    0.0041       1      34 [.     212     245 ..     212     282 .. 0.81
   2 !   14.2   0.0   0.00014     0.044       1      24 [.     492     515 ..     492     558 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsv 34 
                                       i+lyGp+g+GK++lak La+++   + +++ +++
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNAYFITINGPEI 245
                                       789*****************99977644444444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00014
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallk 24 
                                       ++lyGp+g+GK++lak +a++   
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGA 515
                                       689**************8887654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.5e-05    0.0046       1      25 [.     212     242 ..     212     321 .. 0.75
   2 !   14.3   0.0   0.00015     0.045       1      44 [.     492     553 ..     492     598 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.....g 25 
                                       Ill G+pG+GKt lak+L+++  ++     g
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVnAYfitinG 242
                                       99****************9996333554441 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00015
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe 44 
                                       +ll G+pG+GKt lak+++ +  ++                    +r+++++ +l+ +v  +
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESgANfiavkgpevlskwvgesEKAVREIFRKARLYAPVVVF 553
                                       799***************87753335888888888888888878888888888888777666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-05    0.0051       2      41 ..     212     256 ..     211     275 .. 0.75
   2 !   12.4   0.0   0.00045      0.14       2      34 ..     492     529 ..     491     553 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklak 41 
                                       i + G+++tGKT l++aLa++    + ++  pE++ +++ e  ++
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEvnaYFITIngPEIMSKYYGESEQR 256
                                       7899***************87754344445777777777555444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00045
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaarei 34 
                                       + + G++++GKT l++a a + g + +    pE+  + 
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATEsGANFIavkgPEVLSKW 529
                                       6799***************7665554411355554444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-05    0.0083      48      70 ..     210     232 ..     200     280 .. 0.91
   2 !   13.1   0.0    0.0002      0.06      48      71 ..     490     513 ..     478     525 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                       ++i+l Gp+G+GK+ la al+ e
  gi|320101277|ref|YP_004176869.1| 210 KGILLYGPPGTGKTLLAKALANE 232
                                       689*****************986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0002
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       ++++l Gp+G GK+ la a+++e 
  gi|320101277|ref|YP_004176869.1| 490 KGVLLYGPPGCGKTLLAKAVATES 513
                                       6899****************9876 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   5.7e-05     0.017      25      43 ..     212     230 ..     208     236 .. 0.91
   2 !   13.6   0.1   0.00011     0.033      25      43 ..     492     510 ..     489     512 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+l+
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALA 230
                                       89**************996 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVA 510
                                       79*************9875 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 !   29.3   0.4   1.7e-09   5.3e-07       5      62 ..     109     166 ..     105     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.7e-09
                                       CCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTC CS
                           CDC48_2   5 demaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpv 62 
                                         ++ +++++ g+pv +   + ++    +++++Vvs++P gp++it++Te+ + ++pv
  gi|320101277|ref|YP_004176869.1| 109 HVLESIRNKLIGHPVMEDNEIHVTIVDIPVPFRVVSVKPRGPAIITDETEVYVFEEPV 166
                                       556799*********************************************9888887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.3e-05    0.0038       5      77 ..     212     283 ..     209     322 .. 0.77
   2 !   10.6   0.0    0.0012      0.35       5      22 ..     492     509 ..     489     570 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvel.aaeladyktlviDtidel 77 
                                       il+yGp+g+GKT lak l  + ++ fi +++   ++  + +   es + +++ ++   ++ +++  +++iD id +
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALanEVNAYFITING--PEIMSKYYG--ESEQRLREIFKLArKKSKKNPAIIFIDEIDAI 283
                                       89****************9888888888777..233333332..36677777777765555666678888888876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0012
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+yGp+g GKT lak  
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAV 509
                                       89*************987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00011     0.034      52     116 ..     208     280 ..     160     333 .. 0.67
   2 !   13.2   0.0   0.00012     0.038      22     116 ..     449     557 ..     430     609 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evek....edlkelpklvellrerper..filfvDDL 116
                                       p + +LL+G  GtGK  l kal ne+++  + +   e+      e+ + l ++++l r+++++   i+f+D +
  gi|320101277|ref|YP_004176869.1| 208 PPKGILLYGPPGTGKTLLAKALANEVNAYFITINgpEIMSkyygESEQRLREIFKLARKKSKKnpAIIFIDEI 280
                                       66789**********************9986553225544111155677888888888665543379999976 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
                            DUF815  22 vdevklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeegLrl..iev 87 
                                       v  v+++d+ g+++ k++l en+e  l++         +p + vLL+G  G+GK  l ka+ +e  ++ +++   ev
  gi|320101277|ref|YP_004176869.1| 449 VPDVRWSDIGGLEEVKRSLRENVELPLKHpeiyekygiKPPKGVLLYGPPGCGKTLLAKAVATESGANFIAVkgPEV 525
                                       5678999999999999999999987665433333333368899*******************999888755411466 PP

                            DUF815  88 ekedlkelpklvellrerp...erfilfvDDL 116
                                         + + e +k v+++ +++     +++f D +
  gi|320101277|ref|YP_004176869.1| 526 LSKWVGESEKAVREIFRKArlyAPVVVFFDEI 557
                                       66666666665555543321113456666654 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 !   11.6   0.3   0.00062      0.19      19     118 ..     208     314 ..     198     320 .. 0.54
   2 !   11.2   0.0   0.00085      0.26      19      44 ..     488     513 ..     478     521 .. 0.80
   3 ?   -1.2   0.0       5.3   1.6e+03     109     133 ..     536     563 ..     515     599 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00062
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal............. 82 
                                       p + +++YGp g GKt L k ++++ +      +  i+  e+ ++++ e+   e+  +++ k +             
  gi|320101277|ref|YP_004176869.1| 208 PPKGILLYGPPGTGKTLLAKALANEVNA----YFITINGPEIMSKYYGES---EQRLREIFKLArkkskknpaiifi 277
                                       5566899*********999999999843....223455556666666666...333333333332223333334455 PP

                          ATPase_2  83 .giavpkaeleeilkeksklvfkaielllekikkkgk 118
                                         i+    + +e++ e  + v +++ +l++ ++ +g 
  gi|320101277|ref|YP_004176869.1| 278 dEIDAIAPKRDEVIGEVERRVVAQLLALMDGLESRGN 314
                                       5333333333444455555555555555555555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00085
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienl 44 
                                       p + +++YGp g+GKt L k +++++
  gi|320101277|ref|YP_004176869.1| 488 PPKGVLLYGPPGCGKTLLAKAVATES 513
                                       5666899***********99988765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.3
                          ATPase_2 109 llekikkkgkk...iiiiiDelqklidl 133
                                       + ++i +k++    +++++De+  + +l
  gi|320101277|ref|YP_004176869.1| 536 AVREIFRKARLyapVVVFFDEIDAIASL 563
                                       3444444444466699999999888743 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   0.00026     0.078      19      59 ..     209     249 ..     185     265 .. 0.74
   2 !   11.3   0.0   0.00084      0.26      21      51 ..     491     523 ..     461     525 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00026
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                        + ilL+G+ G+GKT l+++la++++    +++ P   ++++Y
  gi|320101277|ref|YP_004176869.1| 209 PKGILLYGPPGTGKTLLAKALANEVNAYfiTINGP--EIMSKY 249
                                       4459*******************998765666666..455555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00084
                                       EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        +lL+G+ G+GKT l++++a + g +  +vk P
  gi|320101277|ref|YP_004176869.1| 491 GVLLYGPPGCGKTLLAKAVATESGANfiAVKGP 523
                                       49*******************999987778776 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00024     0.072       2      77 ..     212     286 ..     211     325 .. 0.68
   2 !   10.8   0.0    0.0011      0.33       2     112 ..     492     602 ..     491     606 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00024
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke.kefefkkGpvfanllladeinrappk 77 
                                       +ll g PG++ktll+kala+ +++ f  i   p+++     G +  + +e  ++  kk      +++ dei+  +pk
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNAYFITIN-GPEIMSK-YYGESEQRLREiFKLARKKSKKNPAIIFIDEIDAIAPK 286
                                       7999*******************9998886.4666643.33433332222244444444455556666666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanl.lladeinrapp. 76 
                                       vll g PG +ktll+ka+a+  +++f  ++  p++l    +G +   ek+ +  f+k  ++a + ++ dei+  ++ 
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGANFIAVK-GPEVLSK-WVGES---EKAVREIFRKARLYAPVvVFFDEIDAIASl 563
                                       7999*********************99887.5666644.44543...233334466777777651456888764432 PP

                             AAA_3  77 ...ktqsalleameerqvtvegethklpepflvlatqnP 112
                                           t+s + e +  + vt  +  +kl++  ++ at+ P
  gi|320101277|ref|YP_004176869.1| 564 rgiDTDSGVSERVVTQLVTEMDGVQKLENVVVLAATNRP 602
                                       222577888888888888888888888877777777665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00055      0.17       8      60 ..     206     260 ..     202     318 .. 0.69
   2 !   12.2   0.0   0.00066       0.2       8      68 ..     486     544 ..     483     599 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00055
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrke 60 
                                       + + + + + G+ G+GK+ L+k+la++++     i+++g ++ +    +++++lr+ 
  gi|320101277|ref|YP_004176869.1| 206 VDPPKGILLYGPPGTGKTLLAKALANEVNAY--FITINGPEIMSkyygESEQRLREI 260
                                       566677889******************9864..455566666554454344444433 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00066
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqep 68 
                                       +k+ + v + G+ G+GK+ L+k++a ++   +  i ++g ++ ++   +++k ++ ++ ++
  gi|320101277|ref|YP_004176869.1| 486 IKPPKGVLLYGPPGCGKTLLAKAVATESG--ANFIAVKGPEVLSKWVGESEKAVREIFRKA 544
                                       67778899****************99875..455666666666666666666666666555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00093      0.28      14      51 ..     207     242 ..     198     255 .. 0.87
   2 !   12.4   0.0   0.00022     0.068      14      50 ..     487     521 ..     479     525 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00093
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       + Pk ill G pG GK+ la++l++e+  +  ++++++
  gi|320101277|ref|YP_004176869.1| 207 DPPKGILLYGPPGTGKTLLAKALANEV--NAYFITING 242
                                       56999*********************9..777777765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00022
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       + Pk +ll G pG+GK+ la+++++e   + n++ ++
  gi|320101277|ref|YP_004176869.1| 487 KPPKGVLLYGPPGCGKTLLAKAVATES--GANFIAVK 521
                                       56999*********************8..78888775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00031     0.093      23      63 ..     210     247 ..     197     333 .. 0.63
   2 !    9.0   0.0    0.0036       1.1      23      47 ..     490     514 ..     479     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00031
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-T CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipe 63 
                                         +l+ G  GtGK+lla+a+ ++ +   + f+++n  +i +
  gi|320101277|ref|YP_004176869.1| 210 KGILLYGPPGTGKTLLAKALANEVN---AYFITINGPEIMS 247
                                       569****************987665...7899999877643 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0036
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                         vl+ G  G+GK+lla+a+ ++s 
  gi|320101277|ref|YP_004176869.1| 490 KGVLLYGPPGCGKTLLAKAVATESG 514
                                       679****************987765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0031      0.94      20      38 ..     210     228 ..     199     244 .. 0.84
   2 ?    0.9   0.1      0.78   2.4e+02     110     154 ..     262     309 ..     238     322 .. 0.69
   3 !   10.5   0.0   0.00089      0.27      13      42 ..     483     512 ..     459     542 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0031
                            ATPase  20 rvvlitGepGtGKtifalq 38 
                                       + +l++G pGtGKt++a+ 
  gi|320101277|ref|YP_004176869.1| 210 KGILLYGPPGTGKTLLAKA 228
                                       5689************975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.78
                            ATPase 110 elaeaikeikakrvviDsitglayeeke...avaReilrqlvrvlkkl 154
                                       +la+  ++++   + iD i+++a + +e   +v R+ + ql+  + +l
  gi|320101277|ref|YP_004176869.1| 262 KLARKKSKKNPAIIFIDEIDAIAPKRDEvigEVERRVVAQLLALMDGL 309
                                       455555667778899999999944444412245688888888888665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00089
                            ATPase  13 kgGipegrvvlitGepGtGKtifalqFlik 42 
                                       k Gi   + vl++G pG+GKt++a+  + +
  gi|320101277|ref|YP_004176869.1| 483 KYGIKPPKGVLLYGPPGCGKTLLAKAVATE 512
                                       568888899**************9876655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00013     0.041      30      64 ..     206     239 ..     196     290 .. 0.67
   2 !    8.5   0.0    0.0044       1.3      33      56 ..     489     512 ..     482     521 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekyls 64 
                                       ++  k +ll+Gp GtGKt+++k l ++++   +++
  gi|320101277|ref|YP_004176869.1| 206 VDPPKGILLYGPPGTGKTLLAKALANEVN-AYFIT 239
                                       5566889******************9999.33333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0044
                             AAA_7  33 kkpvllvGptGtGKtviikdllkk 56 
                                        k vll+Gp G+GKt+++k + ++
  gi|320101277|ref|YP_004176869.1| 489 PKGVLLYGPPGCGKTLLAKAVATE 512
                                       5789*************9986655 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 !   13.7   0.0     8e-05     0.024     117     141 ..     212     236 ..     208     242 .. 0.91
   2 !    7.9   0.0    0.0048       1.5     117     136 ..     492     511 ..     486     516 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8e-05
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                       +++yGp+ tGkt la+a+a+ v  y
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNAY 236
                                       899*****************99877 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0048
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ +Gkt la+a a+
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVAT 511
                                       89***************987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.061        18      48      70 ..     212     234 ..     202     243 .. 0.81
   2 ?    2.9   0.0      0.29        88     140     178 ..     244     283 ..     234     289 .. 0.84
   3 !   12.3   0.0    0.0004      0.12      48     112 ..     492     557 ..     482     568 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.061
                             Rad17  48 LLisGPsGCgkstvvkvLskelg 70 
                                       +L+ GP+G gk+   k L+ e  
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVN 234
                                       6889**************99865 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.29
                             Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                                       ++ +k+y++s ++lre+ + + + s+  p i+ i ei+ +
  gi|320101277|ref|YP_004176869.1| 244 EIMSKYYGESeQRLREIFKLARKKSKKNPAIIFIDEIDAI 283
                                       677999*99989*******999999999********9875 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0004
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslke.pdnqksdfkgltekesrflsqiesfkel 112
                                       +L+ GP+GCgk+   k ++ e g +++    p  l +     ++ ++ ++ k   + + +  f e+
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGANFIAVKGPEVLSKwVGESEKAVREIFRKARLYAPVVVFFDEI 557
                                       6899********************999988886664414446666777777777777777777666 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   7.4e-05     0.022      37     176 ..     212     356 ..     206     375 .. 0.77
   2 ?    6.1   0.0     0.028       8.5      37      62 ..     492     517 ..     483     650 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.4e-05
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-H CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLliDDiqflagke 113
                                       +++yg+ G Gkt L ka++nev + +       + ++++  e  + lr+  + + k++ ++  ++ iD+i  +a k 
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNAYFITINGPEIMSKYYG-ESEQRLREIFKLARKKSKKNPAIIFIDEIDAIAPKR 287
                                       79********************999998888888876654.55677888777888888899999*********9985 PP

                                       .........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
                          Bac_DnaA 114 .........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                                                ++  +l+ +++ l   g+ +v+++   P++l+    r   rf++   ++i  pd++ rl+ilk
  gi|320101277|ref|YP_004176869.1| 288 devigeverRVVAQLLALMDGLESRGNVIVIAATNRPNALDPAL-RRPGRFDR--EIEIPMPDKKGRLEILK 356
                                       22222111134456777777778889999********9887644.33567776..56777899999999987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.028
                                       EEEE-SSSSSHHHHHHHHHHHHHHHS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlena 62 
                                       +++yg+ G Gkt L ka++ e  +n+
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGANF 517
                                       79****************98876665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0029      0.87       3      24 ..     212     233 ..     210     236 .. 0.89
   2 ?   -1.4   0.0       6.3   1.9e+03      82     123 ..     272     316 ..     246     342 .. 0.62
   3 !   10.8   0.1    0.0012      0.35       3      23 ..     492     512 ..     490     516 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0029
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       ++l G++G GKT L++ la + 
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEV 233
                                       7899**************9875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.3
                                       CEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EE CS
                             NACHT  82 rlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasl 123
                                        + + +D +D ++ + ++   + +++v   L  l+ +   +++ +
  gi|320101277|ref|YP_004176869.1| 272 PAIIFIDEIDAIAPKRDEvigEVERRVVAQLLALMDGLESRGNVI 316
                                       445566777777766666666333333333446666644444444 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0012
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G+GKT L++ +a++
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATE 512
                                       799*************99976 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    0.0025      0.76      23      41 ..     213     231 ..     206     236 .. 0.86
   2 !    8.5   0.1    0.0039       1.2      22      42 ..     492     512 ..     485     519 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                                       EEE--TTSSTTHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalav 41 
                                          Gp GtGKt+la ala 
  gi|320101277|ref|YP_004176869.1| 213 LLYGPPGTGKTLLAKALAN 231
                                       568***********99985 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0039
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp G+GKt+la a+a e
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATE 512
                                       6789*************9976 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    0.0056       1.7       1      25 [.     215     239 ..     215     302 .. 0.66
   2 !    9.0   0.0     0.006       1.8       1      24 [.     495     518 ..     495     552 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0056
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG GK+ +++ l+ +++  +++
  gi|320101277|ref|YP_004176869.1| 215 YGPPGTGKTLLAKALANEVNAYFIT 239
                                       7****************99655443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.006
                                       EE-TTSSHHHHHHHHHHHHTEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                       +G+PG+GK+ +++ ++ + g  ++
  gi|320101277|ref|YP_004176869.1| 495 YGPPGCGKTLLAKAVATESGANFI 518
                                       7***********999998865554 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00016     0.048       4      66 ..     212     267 ..     209     292 .. 0.70
   2 ?    4.3   0.0     0.066        20       4      25 ..     492     513 ..     489     543 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeafek 66 
                                       +l  G +GtGKt+++ +l++e+       +a +++ N+p+++ +++ + +++  ++ +k a +k
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEV-------NAYFITINGPEIMsKYYGESEQRL-REIFKLARKK 267
                                       6789*****************9.......788888888887635555554444.3333333333 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.066
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl  G +G GKt+++ ++++e 
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATES 513
                                       6789***********9999886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1    0.0014      0.44      36      55 ..     212     231 ..     208     235 .. 0.88
   2 ?   -0.0   0.0       1.8   5.6e+02     131     176 ..     261     306 ..     234     322 .. 0.69
   3 !    9.0   0.7     0.003      0.92      36      54 ..     492     510 ..     485     595 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +ll+G+pgtGKt la  la 
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALAN 231
                                       69*************99885 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.8
                            AAA_25 131 daleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                        +l+++  + ++++ + iD ++++ +   +   +v +++v++l  + 
  gi|320101277|ref|YP_004176869.1| 261 FKLARKKSK-KNPAIIFIDEIDAIAPKRDEVIGEVeRRVVAQLLALM 306
                                       355665555.6799999999999999955555555588888876664 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.003
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pg+GKt la  +a
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVA 510
                                       69**********9986555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0021      0.63      20      43 ..     212     245 ..     202     275 .. 0.67
   2 ?    7.1   0.0     0.013         4      19      70 ..     491     540 ..     463     548 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0021
                            AAA_11  20 tliqGPPGtgKTktivellsqll..........s 43 
                                        l+ GPPGtgKT    +l ++++           
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNayfitingpeI 245
                                       5899********9999999888744444444430 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                            AAA_11  19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriLv..CapSNaAvDel 70 
                                        +l+ GPPG+gKT    ++  +       +  + ++p++L    ++S++Av e+
  gi|320101277|ref|YP_004176869.1| 491 GVLLYGPPGCGKTLLAKAVATES----GANFIAVKGPEVLSkwVGESEKAVREI 540
                                       5799*********7777776666....334455666666532266666666666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0072       2.2       8      43 ..     200     232 ..     196     239 .. 0.76
   2 !    8.4   0.0    0.0035       1.1      23      43 ..     492     512 ..     487     519 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0072
                                       HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC   8 viekLlekdelqslvvalvGmgGvGKttlakqilnk 43 
                                       v  kL   d ++   + l+G +G GKt lak   n+
  gi|320101277|ref|YP_004176869.1| 200 VFRKLG-VDPPK--GILLYGPPGTGKTLLAKALANE 232
                                       555555.44444..5889************998887 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0035
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l+G +G+GKt lak +  +
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATE 512
                                       679*************99876 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.027       8.2       4      71 ..     215     280 ..     212     285 .. 0.70
   2 !    9.6   0.0    0.0023      0.71       5      71 ..     496     557 ..     492     569 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.027
                   Viral_helicase1   4 hGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + l+++   + +t+n p  e+ ++   +++++  + ++ + ++ +k  +  i+++DE+
  gi|320101277|ref|YP_004176869.1| 215 YGPPGTGKTLLAKALANEVnaYFITINGP--EIMSKYYGESEQRLREIFKLARKKSKK--NPAIIFIDEI 280
                                       588***************88555555555..666666656666655555555555444..5899999997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0023
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pGcGK+ l + ++ +s  ++ +++   e+l++++ ++++   + ++++   + +     ++++DE+
  gi|320101277|ref|YP_004176869.1| 496 GPPGCGKTLLAKAVATESgANFIAVKG-PEVLSKWVGESEKAVREIFRKARLYA-PV----VVFFDEI 557
                                       78*************999*88877777.89*****9777776555555554433.33....6777776 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.4e-05    0.0041      69     173 .]      62     165 ..      58     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-05
                              UFD1  69 gtvylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpk.avLekaLrnfatLtkgdvieikyndk 144
                                       g v l   +  n + e g  v++e+v+   +++vkl p + +  +i+d+  + + ++L  + ++  ++ i+++  d 
  gi|320101277|ref|YP_004176869.1|  62 GVVRLDPLLRANARAEIGASVTVEKVERRYARVVKLAPTNYH-ASIDDHVlESIRNKLIGHPVME-DNEIHVTIVDI 136
                                       66777777888999999*********************9665.56777642678899****9986.56799****** PP

                              UFD1 145 vyelkvlevkpes.avsiietdlevdfaeP 173
                                        + ++v+ vkp+  a+ + et++ v f+eP
  gi|320101277|ref|YP_004176869.1| 137 PVPFRVVSVKPRGpAIITDETEVYV-FEEP 165
                                       ***********988********998.6665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0092       2.8       2      28 ..     210     236 ..     209     241 .. 0.87
   2 ?   -1.6   0.0       6.7     2e+03      40      58 ..     406     424 ..     400     429 .. 0.71
   3 ?    5.9   0.0     0.033        10       2      24 ..     490     512 ..     489     515 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0092
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkY 28 
                                       k ill G+ g+GKt L++al +e   Y
  gi|320101277|ref|YP_004176869.1| 210 KGILLYGPPGTGKTLLAKALANEVNAY 236
                                       6699*****************997777 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.7
                         PduV-EutP  40 viDtPGeylenrklysali 58 
                                        +DtPGe+     l s+++
  gi|320101277|ref|YP_004176869.1| 406 RLDTPGEWPPPDDLLSSIK 424
                                       48*****976666666665 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.033
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k +ll G+ g+GKt L++a+  e
  gi|320101277|ref|YP_004176869.1| 490 KGVLLYGPPGCGKTLLAKAVATE 512
                                       5699**************98765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.017       5.1      24      44 ..     212     232 ..     207     287 .. 0.86
   2 ?    7.4   0.0     0.014       4.3      24      48 ..     492     516 ..     487     562 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.017
                                       EEEEEETT--HHHHHHCC--T CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhkn 44 
                                       ++l G++G+gk+l A++L+++
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANE 232
                                       799***************986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.014
                                       EEEEEETT--HHHHHHCC--TTS-E CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                       v+l G++G+gk+l A++ + +sg +
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGAN 516
                                       9****************99988764 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.012       3.7       1      23 [.     218     240 ..     218     268 .. 0.81
   2 ?    6.5   0.0     0.028       8.5       1      22 [.     498     519 ..     498     544 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.012
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k+lA++++  fi +
  gi|320101277|ref|YP_004176869.1| 218 PGTGKTLLAKALANEVNAYFITI 240
                                       69******************986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.028
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ ++k++A + g +fi 
  gi|320101277|ref|YP_004176869.1| 498 PGCGKTLLAKAVATESGANFIA 519
                                       6******************985 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0048       1.5      48      79 ..     197     226 ..     183     235 .. 0.81
   2 ?    4.4   0.0     0.049        15      59      79 ..     486     506 ..     470     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                       AFG1_ATPase  48 lgklfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                       ++k+f+ k   v p++g+ l+G+ G GKt l 
  gi|320101277|ref|YP_004176869.1| 197 YRKVFR-KL-GVDPPKGILLYGPPGTGKTLLA 226
                                       456665.43.689****************985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.049
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                                        +p++g+ l+G+ G GKt l 
  gi|320101277|ref|YP_004176869.1| 486 IKPPKGVLLYGPPGCGKTLLA 506
                                       579***************985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.039        12       2      32 ..     212     242 ..     211     256 .. 0.84
   2 ?    1.6   0.1      0.73   2.2e+02      81     116 ..     257     292 ..     236     327 .. 0.69
   3 ?    4.4   0.0      0.11        32       2      23 ..     492     513 ..     491     528 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.039
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       +++ GppG+GKt l k ++++++   ++++G
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNAYFITING 242
                                       6788************999999776666655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHH CS
                          NTPase_1  81 feelalealrkalseadviviDEiGkmElkskkfke 116
                                       + e++  a +k+ +++ +i iDEi  +  k  +++ 
  gi|320101277|ref|YP_004176869.1| 257 LREIFKLARKKSKKNPAIIFIDEIDAIAPKRDEVIG 292
                                       444433344444467779999999666555555554 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.11
                                       EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                       v++ GppG GKt l k v+ + 
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATES 513
                                       6788********9999998765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0054       1.7      21      42 ..     212     233 ..     198     243 .. 0.80
   2 ?    3.8   0.1      0.13        41      21      39 ..     492     510 ..     487     522 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0054
                            AAA_30  21 avltGpAGtGKttalkalreaw 42 
                                        +l Gp+GtGKt + kal++ +
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEV 233
                                       5789************998765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                            AAA_30  21 avltGpAGtGKttalkalr 39 
                                       ++l Gp+G GKt + ka++
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVA 510
                                       5789*********999986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.017         5      12      32 ..     211     231 ..     206     259 .. 0.85
   2 ?    1.1   0.0       1.5   4.5e+02      94     133 ..     263     303 ..     246     308 .. 0.70
   3 ?    5.4   0.1     0.071        21      11      30 ..     490     509 ..     486     519 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.017
                            AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                        +l+ ++pGtGKT + k+  +
  gi|320101277|ref|YP_004176869.1| 211 GILLYGPPGTGKTLLAKALAN 231
                                       5899*********98777665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.5
                            AAA_19  94 aeeekklqeeellivDEfqdvdelqyrLlkallgek.kkll 133
                                        +++k  ++ +++++DE+  + +   +++ ++  +  ++ll
  gi|320101277|ref|YP_004176869.1| 263 LARKKSKKNPAIIFIDEIDAIAPKRDEVIGEVERRVvAQLL 303
                                       344444446679*********99999998888765555555 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.071
                            AAA_19  11 kvllvtaGpGtGKTrvlkhi 30 
                                       k +l+ ++pG+GKT + k++
  gi|320101277|ref|YP_004176869.1| 490 KGVLLYGPPGCGKTLLAKAV 509
                                       56899*********877665 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.011       3.2       3      27 ..     214     238 ..     212     242 .. 0.89
   2 ?    4.3   0.1     0.098        30       4      27 ..     495     518 ..     492     521 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+ala+++++ ++
  gi|320101277|ref|YP_004176869.1| 214 LYGPPGTGKTLLAKALANEVNAYFI 238
                                       67******************99886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.098
                                       E-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                        GP g GK  +a+a+a++ g++++
  gi|320101277|ref|YP_004176869.1| 495 YGPPGCGKTLLAKAVATESGANFI 518
                                       6*****************999987 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 ?   10.2   0.0   0.00094      0.29     129     163 ..     209     240 ..     170     253 .. 0.83
   2 ?    0.5   0.0      0.81   2.5e+02     131     152 ..     491     512 ..     481     520 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00094
                             T2SSE 129 rglilvsGgTgsGKttllyallkeinksderivtv 163
                                        + il+ G+ g+GKt l+ al +e+n++   ++t+
  gi|320101277|ref|YP_004176869.1| 209 PKGILLYGPPGTGKTLLAKALANEVNAY---FITI 240
                                       4679**********************98...6666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.81
                             T2SSE 131 lilvsGgTgsGKttllyallke 152
                                        +l+ G+ g GKt l+ a+ +e
  gi|320101277|ref|YP_004176869.1| 491 GVLLYGPPGCGKTLLAKAVATE 512
                                       58999**********9998765 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.08        24      24      56 ..     210     241 ..     199     254 .. 0.77
   2 ?    6.5   0.0     0.013         4      21      60 ..     487     525 ..     471     547 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.08
                                       -EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEE CS
                              DAP3  24 krlvltGekgsGKSvlLlqalayAlekgwvvlh 56 
                                       k ++l+G +g+GK++ L++ala  +++ ++ ++
  gi|320101277|ref|YP_004176869.1| 210 KGILLYGPPGTGKTL-LAKALANEVNAYFITIN 241
                                       5679*********85.67777776666666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                                       S---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-G CS
                              DAP3  21 kkvkrlvltGekgsGKSvlLlqalayAlekgwvvlhvpea 60 
                                       k+ k ++l+G +g+GK++ L++a+a    ++++ ++ pe+
  gi|320101277|ref|YP_004176869.1| 487 KPPKGVLLYGPPGCGKTL-LAKAVATESGANFIAVKGPEV 525
                                       6677799*********86.677766655556666665554 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.096        29       4      30 ..     211     237 ..     209     245 .. 0.87
   2 ?    1.9   0.0      0.52   1.6e+02      75      95 ..     246     266 ..     239     287 .. 0.81
   3 ?    1.5   0.0      0.66     2e+02       4      30 ..     491     517 ..     489     525 .. 0.86
   4 ?   -0.9   0.0       3.8   1.2e+03      77     109 ..     528     564 ..     522     570 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.096
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        + l gp g+Gk  l kaL +e + +f
  gi|320101277|ref|YP_004176869.1| 211 GILLYGPPGTGKTLLAKALANEVNAYF 237
                                       6899***************99998888 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.52
                                       TTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                        +++yg+s +  +e+++ +++
  gi|320101277|ref|YP_004176869.1| 246 MSKYYGESEQRLREIFKLARK 266
                                       689**************9986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.66
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        v l gp g Gk  l ka+ +e   +f
  gi|320101277|ref|YP_004176869.1| 491 GVLLYGPPGCGKTLLAKAVATESGANF 517
                                       6889**************999988877 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.8
                                       EEEEEEHHHHHHHHHTTSE.....EEEE--.CHHHHHHH CS
                     Guanylate_kin  77 nlygtsveaieevlekgki.....viLDvd.iqavkqlr 109
                                       +  g+s +a++e++ k++      v    d i+a+++lr
  gi|320101277|ref|YP_004176869.1| 528 KWVGESEKAVREIFRKARLyapvvV--FFDeIDAIASLR 564
                                       56799**********9998777433..333366666555 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.49   1.5e+02      21      44 ..     416     440 ..     412     440 .. 0.79
   2 ?    7.6   0.0     0.012       3.7      29      56 ..     684     711 ..     680     715 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.49
                            Vps4_C  21 sdklleP.pvtlkDflkalkkarpt 44 
                                       +d+ll   +vt++Dfl a ++  p+
  gi|320101277|ref|YP_004176869.1| 416 PDDLLSSiKVTFEDFLFAYRSIVPS 440
                                       56666666********998887775 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                            Vps4_C  29 vtlkDflkalkkarptVskeDLekheeF 56 
                                       v +k+f+ al+ ++p+++++ ++ + e+
  gi|320101277|ref|YP_004176869.1| 684 VGRKHFIGALELVKPSINEALVKFYLEW 711
                                       6789****************99999999 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.078        24      18      49 ..     213     291 ..     210     330 .. 0.60
   2 ?    5.8   0.0     0.032       9.6      18      78 ..     493     599 ..     489     605 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.078
                                       EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.............................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg.............................................. 48 
                                       l+ g  g+Gkt ++++l+++ n+   i + g                                              
  gi|320101277|ref|YP_004176869.1| 213 LLYGPPGTGKTLLAKALANEVNAY-FITINGpeimskyygeseqrlreifklarkkskknpaiifideidaiapkrd 288
                                       678999**************8766.3333335666666555555555555555555555555555555555555555 PP

                                       ..E CS
                                       ..x RF
                       ATP-synt_ab  49 ..i 49 
                                         i
  gi|320101277|ref|YP_004176869.1| 289 evI 291
                                       555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                                       EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.............................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg.............................................. 48 
                                       l+ g  g+Gkt ++++++ +s ++   i v                                               
  gi|320101277|ref|YP_004176869.1| 493 LLYGPPGCGKTLLAKAVATESGAN--FIAVKgpevlskwvgesekavreifrkarlyapvvvffdeidaiaslrgid 567
                                       678999**************8666..444445888888877777777777777777777777777777777777777 PP

                                       ..ESEEHHHHHHHHHHCHHSSGGGGEEEEEEE CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  49 ..iGergnevaevleefpegtimkrtvlvant 78 
                                          G  ++ v+++++e+   + ++++v++a+t
  gi|320101277|ref|YP_004176869.1| 568 tdSGVSERVVTQLVTEMDGVQKLENVVVLAAT 599
                                       77777777777777777777777777777666 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.079        24       5      28 ..     213     236 ..     210     241 .. 0.86
   2 ?    5.6   0.0     0.031       9.3       5      32 ..     493     520 ..     490     543 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.079
                               IPT   5 lifGatttGKtaeaiklaketgap 28 
                                       l++G+ +tGKt  a +la+e  a 
  gi|320101277|ref|YP_004176869.1| 213 LLYGPPGTGKTLLAKALANEVNAY 236
                                       89****************997765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.031
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l++G+ + GKt  a ++a e ga  i++
  gi|320101277|ref|YP_004176869.1| 493 LLYGPPGCGKTLLAKAVATESGANFIAV 520
                                       89*********************99985 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 ?    3.0   0.0      0.17        51      20      45 ..     209     234 ..     195     241 .. 0.87
   2 ?    3.8   0.1     0.094        29     160     196 ..     256     294 ..     239     322 .. 0.78
   3 ?    1.3   0.0      0.53   1.6e+02      19      42 ..     488     511 ..     475     562 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.17
                        KAP_NTPase  20 pivvgLygkWGsGKssllnkledelk 45 
                                       p  + Lyg+ G+GK+ l + l +e +
  gi|320101277|ref|YP_004176869.1| 209 PKGILLYGPPGTGKTLLAKALANEVN 234
                                       55689****************99987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.094
                        KAP_NTPase 160 lladmektLda..lqkrlVvviDdLDrceteevlqllea 196
                                        l +++k  ++  ++ + +++iD++D + +++   + e+
  gi|320101277|ref|YP_004176869.1| 256 RLREIFKLARKksKKNPAIIFIDEIDAIAPKRDEVIGEV 294
                                       45555555555678999*********9999886666665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.53
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkled 42 
                                       +p  v Lyg+ G+GK+ l + +  
  gi|320101277|ref|YP_004176869.1| 488 PPKGVLLYGPPGCGKTLLAKAVAT 511
                                       666799**********99887655 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 ?    5.0   0.0      0.05        15       6      43 ..     212     249 ..     209     286 .. 0.79
   2 ?    4.6   0.0     0.063        19       5      28 ..     491     514 ..     488     538 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.05
                                       EEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG CS
                             SRPRB   6 vllvGlsdsGKTslftrLttdsvkktvtSqessaalkv 43 
                                       +ll G+  +GKT+l + L ++      t   +++  k+
  gi|320101277|ref|YP_004176869.1| 212 ILLYGPPGTGKTLLAKALANEVNAYFITINGPEIMSKY 249
                                       89************999988755444444466666666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.063
                                       EEEEE-STTSSHHHHHHHHHHSS- CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsv 28 
                                        vll G+  +GKT+l + + t+s 
  gi|320101277|ref|YP_004176869.1| 491 GVLLYGPPGCGKTLLAKAVATESG 514
                                       599************998888764 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.23        69       8      52 ..     218     262 ..     212     317 .. 0.72
   2 ?    6.4   0.0     0.028       8.6       8      55 ..     498     545 ..     494     596 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.23
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde 52 
                                        G+g++ +++aLA++ +  f+  + +e ++k  g se+ ++e+ +
  gi|320101277|ref|YP_004176869.1| 218 PGTGKTLLAKALANEVNAYFITINGPEIMSKYYGESEQRLREIFK 262
                                       69*****************99999999999999999888866555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.028
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevdersr 55 
                                        G+g++ +++a+A++ g +f+  + +e ++k  g se+ v+e+  ++r
  gi|320101277|ref|YP_004176869.1| 498 PGCGKTLLAKAVATESGANFIAVKGPEVLSKWVGESEKAVREIFRKAR 545
                                       59**************************99999999999966555444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.026       7.9      21      49 ..     193     234 ..     181     289 .. 0.73
   2 ?    3.0   0.0       0.3        91      22      46 ..     487     511 ..     459     543 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.026
                                       ...............TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  21 s.............krdkrglikmaTGtGKTlvaaklierll 49 
                                       +             +  k +l+  + GtGKTl+a +l+ ++ 
  gi|320101277|ref|YP_004176869.1| 193 IplkyrkvfrklgvDPPKGILLYGPPGTGKTLLAKALANEVN 234
                                       45555555555665777889999**********998888765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.3
                                       .TTSEEEEEESTTSTHHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklie 46 
                                       k  k +l+  + G+GKTl+a +++ 
  gi|320101277|ref|YP_004176869.1| 487 KPPKGVLLYGPPGCGKTLLAKAVAT 511
                                       778899999*********9955544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.088        27      21      39 ..     209     226 ..     199     231 .. 0.76
   2 ?    4.0   0.0      0.14        42      21      42 ..     489     509 ..     481     511 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.088
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|320101277|ref|YP_004176869.1| 209 PKG-ILLYGPPGTGKTLLA 226
                                       356.9**********8765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.14
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       +kg +ll Gp G GK+ l  A+
  gi|320101277|ref|YP_004176869.1| 489 PKG-VLLYGPPGCGKTLLAKAV 509
                                       456.9**********8776555 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 ?    7.9   0.0    0.0044       1.3      37      69 ..     214     246 ..     205     252 .. 0.88
   2 ?   -1.1   0.1       2.3   7.1e+02      35      62 ..     492     519 ..     485     527 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0044
                             AAA_6  37 paGpagtGKtEtvkdLakalakqvvvfncsdql 69 
                                       ++Gp gtGKt   k La+++  +++ +n  + +
  gi|320101277|ref|YP_004176869.1| 214 LYGPPGTGKTLLAKALANEVNAYFITINGPEIM 246
                                       78***********************99976655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                             AAA_6  35 gapaGpagtGKtEtvkdLakalakqvvv 62 
                                         ++Gp g GKt   k +a + +  ++ 
  gi|320101277|ref|YP_004176869.1| 492 VLLYGPPGCGKTLLAKAVATESGANFIA 519
                                       5578999999999999998887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        59  (0.00329076); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              59  [number of targets reported over threshold]
# CPU time: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.43
# Mc/sec: 5084.92
//
Query:       gi|320101278|ref|YP_004176870.1|  [L=93]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.7e-05   23.9   0.1    0.00012   23.1   0.0    1.4  1  DUF5320      Family of unknown function (DUF5320)
  ------ inclusion threshold ------
       0.05   13.0   0.0      0.057   12.8   0.0    1.0  1  Helo_like_N  Fungal N-terminal domain of STAND proteins
       0.12   12.3   0.1       0.15   12.0   0.1    1.0  1  Prefoldin_2  Prefoldin subunit


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 !   23.1   0.0   1.9e-08   0.00012      43      99 .]      30      88 ..      14      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.9e-08
                           DUF5320 43 grglgrgfgrrrraggarla..aaetaeaskeeekelLeeqaeaLeeeleaikkrlkel 99
                                       +g  r++g+  +++g+ ++  aa +++a  e +k+++e+ ++aL+eel  i++rlkel
  gi|320101278|ref|YP_004176870.1| 30 LFGSYRWYGGYVFPPGYYWGaqAADSERAWLEYRKAMIENTIRALNEELSYIDRRLKEL 88
                                      589999999999999999997777788888999************************97 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 ?   12.8   0.0   9.6e-06     0.057     143     177 ..      55      89 ..      50      93 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-06
                       Helo_like_N 143 vtaevleeykeliedttsdLeehLedideklealt 177
                                        ++  le  k +ie+t   L+e L+ id++l++l 
  gi|320101278|ref|YP_004176870.1|  55 SERAWLEYRKAMIENTIRALNEELSYIDRRLKELG 89 
                                       56677887799********************9986 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.5e-05      0.15      65      95 ..      58      88 ..      51      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2 65 eeLeerketlekeiktlekqleklekeleel 95
                                      + Le rk+ +e  i++l+++l+++ ++l+el
  gi|320101278|ref|YP_004176870.1| 58 AWLEYRKAMIENTIRALNEELSYIDRRLKEL 88
                                      56999***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 715.67
//
Query:       gi|320101279|ref|YP_004176871.1|  [L=108]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   76.7   0.0    1.8e-21   76.5   0.0    1.1  1  DUF134        Protein of unknown function  DUF134
    2.2e-05   23.9   0.0    3.2e-05   23.3   0.0    1.3  1  Sigma70_r4    Sigma-70, region 4
    0.00074   19.1   0.0      0.001   18.7   0.0    1.3  1  Sigma70_r4_2  Sigma-70, region 4
     0.0043   16.8   3.9      0.011   15.5   0.0    2.6  3  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.021   14.7   0.1    1.1  1  Sigma70_ECF   ECF sigma factor
       0.02   14.8   0.0      0.026   14.5   0.0    1.1  1  HTH_1         Bacterial regulatory helix-turn-helix protein, 
      0.023   15.0   1.3      0.028   14.8   1.3    1.4  1  HTH_31        Helix-turn-helix domain
      0.082   13.1   0.0      0.082   13.1   0.0    2.8  3  HTH_28        Helix-turn-helix domain
       0.18   11.8   2.4        0.2   11.7   0.5    2.0  2  HTH_29        Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   8.9e-25   1.8e-21       5      96 ..      14     105 ..       6     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 8.9e-25
                            DUF134   5 grprklrdileePkvrifkPeaveetgkvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiaka 81 
                                       grp k+ ++   P  r+f+Pe  ++ g   ++l elea+rlvd e  + +eaa+ m is+  +wrl+t ar k+a a
  gi|320101279|ref|YP_004176871.1|  14 GRPPKPIHVALPPVKRVFNPE-PPGVGEEYLTLPELEALRLVDLEGRSLDEAAASMNISRGYVWRLVTGARAKVARA 89 
                                       577777777777999******.8888889************************************************ PP

                            DUF134  82 lveGr.aiilkGGeyk 96 
                                       l+eG  +i+  GGe +
  gi|320101279|ref|YP_004176871.1|  90 LIEGMrIIVEPGGEVE 105
                                       ****846666699876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.6e-08   3.2e-05       9      48 ..      47      86 ..      43      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.6e-08
                                      HHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  9 erevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48
                                      e e l+l+ +eg++l E ++ ++iSr+ V ++ + A+ k+
  gi|320101279|ref|YP_004176871.1| 47 ELEALRLVDLEGRSLDEAAASMNISRGYVWRLVTGARAKV 86
                                      568899***********************99999998886 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   0.0   5.1e-07     0.001      17      53 ..      49      85 ..      41      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.1e-07
                                      HHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2 17 eifllryleglsykEIAellgisegtVksrlsRArkk 53
                                      e++ l +leg s +E+A+ ++is g V + +  Ar+k
  gi|320101279|ref|YP_004176871.1| 49 EALRLVDLEGRSLDEAAASMNISRGYVWRLVTGARAK 85
                                      899**************************99999988 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.19   3.7e+02      36      43 ..       5      12 ..       3      18 .. 0.77
   2 !   15.5   0.0   5.6e-06     0.011       8      38 ..      48      79 ..      47      81 .. 0.91
   3 ?   -0.7   0.0      0.66   1.3e+03       7      19 ..      83      95 ..      81      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                            HTH_23 36 rwlkryre 43
                                       w++r+r 
  gi|320101279|ref|YP_004176871.1|  5 CWRRRWRG 12
                                      6*****74 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 5.6e-06
                            HTH_23  8 lrilllla.eGlsvreIAreLgvsrrTvyrwl 38
                                      l++l+l++ eG s  e+A+ +++sr  v+r +
  gi|320101279|ref|YP_004176871.1| 48 LEALRLVDlEGRSLDEAAASMNISRGYVWRLV 79
                                      6899****55*******************975 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.66
                            HTH_23  7 RlrillllaeGls 19
                                      R++++++l eG++
  gi|320101279|ref|YP_004176871.1| 83 RAKVARALIEGMR 95
                                      8999999999876 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.1e-05     0.021     141     183 ..      48      90 ..      41      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                       Sigma70_ECF 141 arlvelrkleGlsveEiAeklgvskrtverrlalaRawlerel 183
                                       ++ + l  leG s +E+A+ +++s+  v r    aRa+++r+l
  gi|320101279|ref|YP_004176871.1|  48 LEALRLVDLEGRSLDEAAASMNISRGYVWRLVTGARAKVARAL 90 
                                       566778889*****************************99986 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.026       4      47 ..      48      92 ..      45     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEE CS
                             HTH_1  4 lrlfvavaeeg.sftrAAeeLglsqpavsrqikrLEeelgvpLfe 47
                                      l+++  v  eg s+ +AA  +++s   v+r +   ++ +   L+e
  gi|320101279|ref|YP_004176871.1| 48 LEALRLVDLEGrSLDEAAASMNISRGYVWRLVTGARAKVARALIE 92
                                      788888888888*********************999999999987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.3   1.4e-05     0.028      12      46 ..      56      90 ..       6      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                            HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrgrpspav 46
                                       +G s++e+A+  ++s+ ++ rl +G+r  + +a 
  gi|320101279|ref|YP_004176871.1| 56 LEGRSLDEAAASMNISRGYVWRLVTGARAKVARAL 90
                                      4599***********************98776665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.5       0.6   1.2e+03      32      38 ..       6      12 ..       4      18 .. 0.83
   2 ?   13.1   0.0   4.1e-05     0.082       3      29 ..      48      75 ..      48      79 .. 0.90
   3 ?    0.8   0.3      0.27   5.4e+02       2      15 ..      83      96 ..      82      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.6
                            HTH_28 32 Wikryee 38
                                      W++r++ 
  gi|320101279|ref|YP_004176871.1|  6 WRRRWRG 12
                                      9999997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.1e-05
                            HTH_28  3 leiiklla.aGhsvreaArelgisrrtv 29
                                      le+++l+  +G+s +eaA+ ++isr  v
  gi|320101279|ref|YP_004176871.1| 48 LEALRLVDlEGRSLDEAAASMNISRGYV 75
                                      799999999****************866 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.27
                            HTH_28  2 RleiikllaaGhsv 15
                                      R+++ ++l++G+++
  gi|320101279|ref|YP_004176871.1| 83 RAKVARALIEGMRI 96
                                      99*********975 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.8   1.6e+03      30      40 ..       4      14 ..       3      22 .. 0.78
   2 ?   11.7   0.5    0.0001       0.2       4      45 ..      50      91 ..      48      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.8
                            HTH_29 30 yrwlkrfeegG 40
                                      ++w++r++  G
  gi|320101279|ref|YP_004176871.1|  4 RCWRRRWRGVG 14
                                      67999998666 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0001
                            HTH_29  4 alllla.eGvstvsqiAkllglsrrtvyrwlkrfeegGlaall 45
                                      al+l++ eG s   ++A+ +++sr +v r +   +++ ++al+
  gi|320101279|ref|YP_004176871.1| 50 ALRLVDlEGRS-LDEAAASMNISRGYVWRLVTGARAKVARALI 91
                                      55666526665.***************9998877777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 783.05
//
Query:       gi|320101280|ref|YP_004176872.1|  [L=95]
Description: PadR family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-05   23.2   0.1    6.7e-05   22.8   0.1    1.2  1  HTH_45    Winged helix-turn-helix
     0.0029   17.5   0.3     0.0076   16.2   0.3    1.7  1  PadR      Transcriptional regulator PadR-like family
     0.0097   14.3   0.0     0.0097   14.3   0.0    1.0  1  DUF505    Protein of unknown function (DUF505)
  ------ inclusion threshold ------
      0.024   14.6   0.1      0.042   13.8   0.1    1.3  1  HTH_12    Ribonuclease R winged-helix domain
      0.035   14.2   0.4       0.17   12.0   0.4    2.0  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.9e-08   6.7e-05      40      72 ..      48      80 ..      33      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.9e-08
                            HTH_45 40 LdmLvekglikkskekYvlTekGlelleklkel 72
                                      L  L + gl++ks+++Y+lT kG++l e l  +
  gi|320101280|ref|YP_004176872.1| 48 LILLEKAGLVRKSGNEYRLTSKGRKLAEALYGF 80
                                      77899*********************9988755 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.1e-06    0.0076      29      72 ..      39      73 ..      31      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-06
                                      TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      l +G++Y +L  Lek glv ++ +e         YrlT +Gr+ 
  gi|320101280|ref|YP_004176872.1| 39 LGAGTIYYNLILLEKAGLVRKSGNE---------YRLTSKGRKL 73
                                      568*****************99765.........9999999975 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.7e-06    0.0097      37      70 ..      48      80 ..      19      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-06
                            DUF505 37 lleLelagLvrleepekielTyaGkklaelldel 70
                                      l+ Le agLvr +++++++lT  G+klae+l   
  gi|320101280|ref|YP_004176872.1| 48 LILLEKAGLVR-KSGNEYRLTSKGRKLAEALYGF 80
                                      67799******.*****************99765 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.2e-05     0.042      30      64 ..      39      72 ..      35      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                            HTH_12 30 igeravRyrLrkleergltrrvgyagreltEkGle 64
                                      +g+ ++ y L  le+ gl+r+ g+   +lt kG +
  gi|320101280|ref|YP_004176872.1| 39 LGAGTIYYNLILLEKAGLVRKSGNE-YRLTSKGRK 72
                                      5777899****************99.99****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 ?   12.0   0.4   4.6e-05      0.17       5      56 ..      12      59 ..       7      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                                      HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++L+ P+R+ +l +L  ++ + +  + +   l   t++y+L  Le+agLv+ 
  gi|320101280|ref|YP_004176872.1| 12 RLLTAPSRMLVLMHL--GARRKVDFIRAG--LGAGTIYYNLILLEKAGLVRK 59
                                      678888888888888..555555555555..6899***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 699.89
//
Query:       gi|320101281|ref|YP_004176873.1|  [L=382]
Description: carbohydrate ABC transporter ATP-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-34  117.7   0.0    8.3e-34  117.0   0.0    1.3  1  ABC_tran  ABC transporter
    6.2e-10   39.2   1.2      2e-09   37.6   1.2    1.9  1  TOBE      TOBE domain
    2.1e-06   27.7   0.1      0.047   13.5   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    4.1e-06   26.9   1.5    1.3e-05   25.2   1.3    2.1  2  TOBE_2    TOBE domain
  ------ inclusion threshold ------
      0.012   15.1   0.0       0.32   10.4   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.024   15.0   0.0      0.053   13.9   0.0    1.5  1  AAA_16    AAA ATPase domain
      0.027   14.8   0.1      0.062   13.6   0.1    1.8  1  AAA_22    AAA domain
      0.036   14.0   0.0      0.065   13.2   0.0    1.3  1  Rad17     Rad17 P-loop domain
      0.054   13.9   0.0       0.12   12.8   0.0    1.6  1  AAA       ATPase family associated with various cellular acti
        0.1   12.9   0.0       0.27   11.4   0.0    1.7  1  AAA_28    AAA domain
       0.13   12.0   0.0       0.27   11.0   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
       0.14   12.6   0.0       0.26   11.8   0.0    1.3  1  AAA_23    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.0   5.6e-37   8.3e-34       2     136 ..      20     165 ..      19     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 5.6e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++v+l+++ ge  a++G++G+GK+t l+l+agl+ p+eG+i + ++d+++  l+  ++ +++++q+  l p++tv e
  gi|320101281|ref|YP_004176873.1|  20 DHVTLSINDGEFFALLGPSGCGKTTTLRLIAGLEYPDEGSIYIGDRDVTR--LHPRNRDVAMVFQNYALYPHMTVFE 94 
                                       789***********************************************..99*********************** PP

                                       H.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n                 + ++ + + ++ lg+++l d++      +LSgGq+qrvalaral++kpk++llDEp 
  gi|320101281|ref|YP_004176873.1|  95 NiafplevrrrelgltrdDIRRMVVETARFLGIDHLLDRRP----GQLSGGQQQRVALARALVRKPKVWLLDEPL 165
                                       ******98888888764433333777777778888777777....*****************************7 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   1.2   1.3e-12     2e-09       7      63 ..     320     371 ..     319     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.3e-12
                              TOBE   7 lpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvh 63 
                                       ++g+V+vvep+g e+ V+v lg++  + A+v+++++++     G++V++++ ++k+ 
  gi|320101281|ref|YP_004176873.1| 320 VEGEVLVVEPTGTESIVTVKLGDEV-VRAVVPGDARVQ----MGSTVRLRFEWSKTL 371
                                       68***********************.************....***********9975 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   7.1e-05      0.11       1      22 [.      31      52 ..      31      97 .. 0.75
   2 !   13.5   0.0   3.2e-05     0.047     219     298 ..     116     197 ..      87     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + +l Gp g+GK++ L+++ +l
  gi|320101281|ref|YP_004176873.1| 31 FFALLGPSGCGKTTTLRLIAGL 52
                                      679****************999 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.2e-05
                            AAA_21 219 r....gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsr.ng 289
                                       r    + +fl  ++  ++ + +lS G+++  al+ al r +   ++ l+DEp ++L+   lr l+   lk+l++  g
  gi|320101281|ref|YP_004176873.1| 116 RmvveTARFLGIDHLLDRRPGQLSGGQQQRVALARALVRKP---KVWLLDEPLSNLDA-KLRLLMrAELKRLQKtLG 188
                                       1455578888899999999***********9*******988...9*************.556666556677777789 PP

                            AAA_21 290 aQviltTHS 298
                                       +  + +TH+
  gi|320101281|ref|YP_004176873.1| 189 ITTVYVTHD 197
                                       999999998 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.9   8.8e+03      31      41 ..     269     279 ..     269     282 .. 0.83
   2 !   25.2   1.3     9e-09   1.3e-05       1      76 []     302     373 ..     302     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.9
                            TOBE_2  31 sstryvvelag 41 
                                       s tryv+el+g
  gi|320101281|ref|YP_004176873.1| 269 SKTRYVLELPG 279
                                       579******98 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 9e-09
                            TOBE_2   1 laiRPEklrla.aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       la+RP ++ +  ++g+   ++G+V  ve  G+++ ++v+l+++   ++++p  +   +++ G+tV+l+++  +++++
  gi|320101281|ref|YP_004176873.1| 302 LAVRPQQVGVVfGDGA-WDVEGEVLVVEPTGTESIVTVKLGDEVV-RAVVPGDA---RVQMGSTVRLRFEWSKTLLF 373
                                       79********755554.49***********************955.66677776...9***********98777776 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 ?    2.6   0.0     0.053        80      24      40 ..      29      45 ..      15      50 .. 0.80
   2 ?   10.4   0.0   0.00021      0.32     135     214 ..      89     211 ..      57     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.053
                                      SSEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnl 40
                                       +f a++Gp G+GK+  
  gi|320101281|ref|YP_004176873.1| 29 GEFFALLGPSGCGKTTT 45
                                      46899*********975 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00021
                                       T...............................................CS-HHHHHHHHHHHHHHHHCCS--SEEEE CS
                                       x...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e...............................................lLSgGektLvalaLlfAiqkvkpaplyll 164
                                       +                                               +LSgG+++ vala       v++  ++ll
  gi|320101281|ref|YP_004176873.1|  89 HmtvfeniafplevrrrelgltrddirrmvvetarflgidhlldrrpgQLSGGQQQRVALARA----LVRKPKVWLL 161
                                       4555555555555555555555555555555566666666666666669******99988754....45666799** PP

                                       CTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 165 DeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkv 214
                                       De  ++LD+k +  +   lk+ +k+  +  + +++++ e +    ++   
  gi|320101281|ref|YP_004176873.1| 162 DEPLSNLDAKLRLLMRAELKRLQKTLGITTVYVTHDQAEAMTMADRIAVM 211
                                       ***********************998887777777777777666555554 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   3.6e-05     0.053      21      45 ..      26      50 ..      17      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrell 45
                                       +++e   l G+sG+GK++ +r ++
  gi|320101281|ref|YP_004176873.1| 26 INDGEFFALLGPSGCGKTTTLRLIA 50
                                      45668899*************9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.1e-05     0.062       6      28 ..      30      52 ..      26     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleq 28
                                       + ++ G+sG+GKTt+lr ++  
  gi|320101281|ref|YP_004176873.1| 30 EFFALLGPSGCGKTTTLRLIAGL 52
                                      678999***********988765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.065      48      66 ..      32      50 ..      17      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                             Rad17 48 LLisGPsGCgkstvvkvLs 66
                                        + GPsGCgk+t+++ ++
  gi|320101281|ref|YP_004176873.1| 32 FALLGPSGCGKTTTLRLIA 50
                                      5688***********9876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     8e-05      0.12       3      20 ..      34      51 ..      32      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8e-05
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      l Gp G+GKT++ + +a 
  gi|320101281|ref|YP_004176873.1| 34 LLGPSGCGKTTTLRLIAG 51
                                      89*************995 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.27       2      24 ..      32      54 ..      31      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                            AAA_28  2 ivitGgestGKTtlleaLaargy 24
                                      ++++G++++GKTt+l+ +a  +y
  gi|320101281|ref|YP_004176873.1| 32 FALLGPSGCGKTTTLRLIAGLEY 54
                                      689*************9986544 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   0.00018      0.27      13      39 ..      20      46 ..      17      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      d+ t++i+  +++ l GpsG GK+T l
  gi|320101281|ref|YP_004176873.1| 20 DHVTLSINDGEFFALLGPSGCGKTTTL 46
                                      567888885559************976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.26      19      39 ..      29      49 ..      11      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                            AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                        ++++ Gp G+GKTT l+ i
  gi|320101281|ref|YP_004176873.1| 29 GEFFALLGPSGCGKTTTLRLI 49
                                      36899************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2717.57
//
Query:       gi|320101282|ref|YP_004176874.1|  [L=165]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0086   16.1   0.0      0.016   15.3   0.0    1.5  1  KH_5       NusA-like KH domain
  ------ inclusion threshold ------
      0.094   12.4   0.1       0.19   11.4   0.1    1.5  1  Pox_VLTF3  Poxvirus Late Transcription Factor VLTF3 like
       0.17   11.9   0.1         23    5.1   0.0    2.6  3  EFP        Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.6e-06     0.016      32      68 ..      83     118 ..      71     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-06
                              KH_5  32 avsseLkgekidvvewseDlaefianalsPaevlsVk 68 
                                       ++s+ L +++++v+ ++   +++i+++l+Pa ++ V+
  gi|320101282|ref|YP_004176874.1|  83 ELSRRL-DTRVKVIVETGEQKRLIERLLAPASLIGVN 118
                                       345556.**************************9997 PP

>> Pox_VLTF3  Poxvirus Late Transcription Factor VLTF3 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.2e-05      0.19      48      98 ..      37      88 ..      16     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                         Pox_VLTF3 48 ikevtkakvlkiLKelgl.kklyedvklIleiltgkrpdklssleeklikdi 98
                                       + ++ ++ lk+LK+ ++ k ++   +l+ ++  g +++++s+lee+l   +
  gi|320101282|ref|YP_004176874.1| 37 KALIDLEDELKFLKKGEYvKSYRMSSQLVVMVRDGFEQEEISRLEEELSRRL 88
                                      6778888889*******846666778899999999***********987773 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 ?    4.1   0.1    0.0081        48      30      44 ..      41      55 ..      31      57 .. 0.75
   2 ?    5.1   0.0    0.0038        23       6      27 ..      57      78 ..      54      82 .. 0.92
   3 ?   -2.2   0.0      0.73   4.4e+03      26      44 ..     110     128 ..     106     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0081
                                      HHTTGCGG--TT-EE CS
                               EFP 30 qlgdaakfLkEgmev 44
                                      +l+d++kfLk g+ v
  gi|320101282|ref|YP_004176874.1| 41 DLEDELKFLKKGEYV 55
                                      5789******99876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0038
                                      EEEETTEEEEEETTT--EEEEE CS
                               EFP  6 lYkdgdeyvFMdnetYeqielp 27
                                      +Y+  +++v+M  + +eq e++
  gi|320101282|ref|YP_004176874.1| 57 SYRMSSQLVVMVRDGFEQEEIS 78
                                      79999*************9997 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.73
                                       EEHHHHTTGCGG--TT-EE CS
                               EFP  26 lpkeqlgdaakfLkEgmev 44 
                                        p++ +g ++ +L  g ev
  gi|320101282|ref|YP_004176874.1| 110 APASLIGVNQVWLPGGIEV 128
                                       6889999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      807  (0.0450109); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1237.60
//
Query:       gi|320101283|ref|YP_004176875.1|  [L=368]
Description: tRNA pseudouridine synthase D TruD [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-47  160.1   0.0    8.6e-39  133.5   0.0    3.0  2  TruD      tRNA pseudouridine synthase D (TruD)
  ------ inclusion threshold ------
       0.24   11.3   1.7       0.62   10.0   1.1    2.0  2  DUF1514   Protein of unknown function (DUF1514)


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 !  133.5   0.0   9.6e-43   8.6e-39       6     282 ..      19     279 ..      15     293 .. 0.80
   2 !   19.2   0.0   4.7e-08   0.00043     351     416 .]     302     360 ..     290     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 9.6e-43
                              TruD   6 lyvtdtegigGrlrespeDFiVeEieef...sgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGt 79 
                                        y+     +g+  r sp+ F+V+Ei ++   + ++   ++ y+vlrv kr++dt +++r l+r+lgi   ++ f G+
  gi|320101283|ref|YP_004176875.1|  19 KYCLTDLKVGCWYRVSPDTFRVREIVDAegfTHQAPRGRDGYIVLRVVKRGVDTFEALRLLSRRLGIPVGNIYFHGL 95 
                                       477777889****************99954222234445668*********************************** PP

                              TruD  80 KDkrAvTtQlisirk.vepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeileel 154
                                       KD++A Tt ++ +++ +  e++  le k+v+ e +g +r k + G  +GN+Fe++v +v     ++++++ +i+  +
  gi|320101283|ref|YP_004176875.1|  96 KDRNATTTSYFYVKRlLVDETVFPLEEKGVSYEIAGYTRSKPHPGLFKGNEFEVVVDGVnR---SQQESLIRITGLI 169
                                       *************88555556777999*******************************833...3467999****** PP

                              TruD 155 eekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeee..sedtreareavaetgdleealeelpk 229
                                       e +g +P y+G+QRFG rr +thl+Gk  +k   + ++++++ + ++ e  +   +++r+++               
  gi|320101283|ref|YP_004176875.1| 170 EMHG-LPSYYGYQRFGVRRHNTHLLGKFFLKHYEDLFAKHLLETVYPFEdfEAVLKRVRRNY--------------V 231
                                       *988.*************************99888888888876554430044444454444..............3 PP

                              TruD 230 slryErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRler 282
                                        l+yE     +L  +++   + l+ + + L+ + v+Ay  yl+N +l++ +e+
  gi|320101283|ref|YP_004176875.1| 232 GLHYE-----NLYAETRYSGRGLSMVVEALHGIIVDAYAGYLYNLLLNKVVEE 279
                                       34444.....3444344456677777778888888888888888888777765 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.7e-08
                              TruD 351 revleeegleledFklpklpelsskGtrRaillrvedlelsaeedeltleFsLpkGsYATvvlrEi 416
                                       +++++ e++++++ k  +lp ++ +G ++++ +rv+      ++ ++ l FsL +G YATvvlrE+
  gi|320101283|ref|YP_004176875.1| 302 SDIFKAEDVDPAEAK--RLPCFHRRGLFKPLNTRVSC-----SGGSCRLVFSLGPGLYATVVLREL 360
                                       677788888887765..45568888888888888775.....45789*****************96 PP

>> DUF1514  Protein of unknown function (DUF1514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.4   1.2e+04      36      51 ..      60      74 ..      55      78 .. 0.63
   2 ?   10.0   1.1   6.9e-05      0.62      32      52 ..     267     287 ..     260     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.4
                           DUF1514 36 YLldelvktkGveGLe 51
                                      Y++ ++vk +Gv+  e
  gi|320101283|ref|YP_004176875.1| 60 YIVLRVVK-RGVDTFE 74
                                      56666666.4666555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 6.9e-05
                           DUF1514  32 YmndYLldelvktkGveGLed 52 
                                       Y+ + Ll+++v +kG++GL++
  gi|320101283|ref|YP_004176875.1| 267 YLYNLLLNKVVEEKGYKGLDE 287
                                       88899**************64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2801.12
//
Query:       gi|320101284|ref|YP_004176876.1|  [L=115]
Description: peptidyl-tRNA hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  135.1   0.0    1.5e-39  134.9   0.0    1.0  1  PTH2             Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.016   15.1   0.0    1.1  1  NAD_binding_10   NAD(P)H-binding
       0.13   12.7   0.0       0.28   11.6   0.0    1.6  1  Acylphosphatase  Acylphosphatase


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 !  134.9   0.0   2.4e-43   1.5e-39       1     117 []       1     115 []       1     115 [] 0.96

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 2.4e-43
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-S CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglp 77 
                                       +k+v++vr+DL+mskGkiaaq+ahA+v+++ ++  + ++ e+++eW ++gqkkiv+k e eeeL + + +a ++glp
  gi|320101284|ref|YP_004176876.1|   1 MKQVIMVRSDLGMSKGKIAAQVAHASVMAAFEAYFK-HR-EWFEEWWRSGQKKIVVKLEGEEELVKRYMEAVSQGLP 75 
                                       69************************9988777776.56.8************************************ PP

                                       EEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                              PTH2  78 aalirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                       a+++rDag t+++pgt+T+ aigPap++ vdk+tg+L+ll
  gi|320101284|ref|YP_004176876.1|  76 ASIVRDAGLTELPPGTVTAAAIGPAPDERVDKLTGDLRLL 115
                                       **************************************97 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.7e-06     0.016      87     159 ..      19      97 ..      15     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
                                       HCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHH......SSSEEEEEEE-CEE-ST--SEEEE CS
                    NAD_binding_10  87 eagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellra......sgldwTivrpggLtdepttkyrvv 157
                                       +a+v +  ++ a+ ++ ++ + f+ew+++  k+++ + +  eel+++       gl   ivr +gLt+ p++++ ++
  gi|320101284|ref|YP_004176876.1|  19 AAQVAHASVMAAFEAYFKHREWFEEWWRSGQKKIVVKLEGEEELVKRymeavsQGLPASIVRDAGLTELPPGTVTAA 95 
                                       68899999*********99**********9999988777777777777777977**************998887766 PP

                                       ET CS
                    NAD_binding_10 158 ek 159
                                       + 
  gi|320101284|ref|YP_004176876.1|  96 AI 97 
                                       54 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.7e-05      0.28      36      74 ..      49      87 ..      44      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                   Acylphosphatase 36 dgsVeivaegeeekvekfleelksgppkarvdeveveel 74
                                      + ++ + +egeee v++++e++++g p++ v++   +el
  gi|320101284|ref|YP_004176876.1| 49 QKKIVVKLEGEEELVKRYMEAVSQGLPASIVRDAGLTEL 87
                                      567999***********************9999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 843.61
//
Query:       gi|320101285|ref|YP_004176877.1|  [L=73]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-08   32.8  15.1    6.2e-07   29.3   2.8    2.7  2  DUF1610         Domain of unknown function (DUF1610)
    0.00014   21.8  11.7     0.0021   18.1  12.0    2.3  2  DZR             Double zinc ribbon
     0.0011   19.4   7.8     0.0019   18.7   7.8    1.5  1  zf-CHY          CHY zinc finger
     0.0017   18.5  13.6       0.95    9.7   0.1    3.8  3  zf-RING_7       C4-type zinc ribbon domain
     0.0046   17.0   7.6      0.023   14.7   0.2    2.1  2  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0053   16.7   8.2      0.018   14.9   0.2    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0063   16.1   1.8     0.0063   16.1   1.8    1.5  1  DUF2321         Uncharacterized protein conserved in bacteria
     0.0069   16.5  11.2       0.11   12.6   2.0    2.9  2  DUF1272         Protein of unknown function (DUF1272)
  ------ inclusion threshold ------
      0.011   15.8   0.3      0.019   15.0   0.3    1.4  1  His_Me_b4a2     His-Me finger endonuclease beta4-alpha2 domai
      0.024   13.6   1.8      0.029   13.3   1.8    1.3  1  tRNA-synt_1f    tRNA synthetases class I (K)
      0.045   13.2  17.9       0.12   11.8   3.9    3.4  3  zf-ribbon_3     zinc-ribbon domain
       0.05   13.7   1.6        8.3    6.6   0.3    2.2  2  DUF2752         Protein of unknown function (DUF2752)
      0.058   11.3   2.6      0.058   11.3   2.6    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
      0.059   13.5   5.7       0.91    9.7   0.8    2.3  2  Acetone_carb_G  Acetone carboxylase gamma subunit
      0.073   13.0   2.9      0.073   13.0   2.9    3.2  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.076   13.3   0.1      0.076   13.3   0.1    1.7  2  PSCyt3          Protein of unknown function (DUF1588)
      0.093   12.8   9.0        1.6    8.9   1.1    2.3  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.094   12.2   4.3        0.1   12.0   4.3    1.2  1  DUF1258         Protein of unknown function (DUF1258)
       0.11   12.5  10.9          5    7.1   0.0    4.2  4  zinc_ribbon_4   zinc-ribbon domain
       0.17   11.5   4.2       0.19   11.3   4.2    1.2  1  DpnI            Dam-replacing family
       0.18   11.4   3.3        9.3    5.9   0.3    2.5  2  zf_C2H2_10      C2H2 type zinc-finger
       0.27   11.4  17.5        5.1    7.3   0.2    3.7  2  Zn-ribbon_8     Zinc ribbon domain
       0.31   11.1   9.9        1.1    9.3   2.2    2.9  3  Nop10p          Nucleolar RNA-binding protein, Nop10p family
       0.35   10.9  10.2         10    6.2   2.9    3.5  2  ADK_lid         Adenylate kinase, active site lid
       0.35   11.1   9.7       0.21   11.8   2.2    2.2  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.36   10.8  12.6        4.8    7.2   1.3    3.9  4  Nudix_N_2       Nudix N-terminal
       0.68   10.2  14.7         37    4.7   7.5    3.7  3  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.81   10.1  11.6       0.85   10.0   2.5    2.1  2  C1_2            C1 domain
       0.88    9.4  19.7        3.6    7.4   7.2    3.5  3  zinc_ribbon_2   zinc-ribbon domain
       0.91    9.5  15.7        0.2   11.6   5.3    2.7  2  zf-HIT          HIT zinc finger
        1.2    8.7   9.4        1.2    8.6   3.5    2.8  2  Mu-like_Com     Mu-like prophage protein Com
        1.2    9.3  12.8       0.32   11.2   1.3    3.1  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        1.3    8.7   0.1        1.3    8.7   0.1    3.8  4  Sgf11           Sgf11 (transcriptional regulation protein)
        1.9    8.1   9.5        6.3    6.4   3.2    2.1  2  TackOD1         Thaumarchaeal output domain 1
        2.1    8.5  10.5        5.6    7.1   0.5    2.5  3  zf-MYND         MYND finger
        2.3    7.9  13.6        7.1    6.3   0.2    3.8  4  zf_UBZ          Ubiquitin-Binding Zinc Finger
        2.6    7.8  11.6        1.8    8.2   4.0    2.3  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
          3    7.6  16.5        6.9    6.5   3.9    3.5  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
        3.9    7.7  13.6        2.1    8.6   6.6    2.6  2  zf-B_box        B-box zinc finger
        4.1    7.7   9.4        1.5    9.1   2.8    2.1  2  DUF2072         Zn-ribbon containing protein
        4.2    7.7  10.9    2.8e+02    1.9  10.9    3.1  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
        4.4    6.0   8.1        3.2    6.4   7.2    1.3  1  Dynactin_p62    Dynactin p62 family
        5.3    6.7  19.3        1.8    8.2   4.1    3.5  3  TF_Zn_Ribbon    TFIIB zinc-binding
        5.3    7.3  13.4        6.1    7.1   2.9    2.9  3  zf-AN1          AN1-like Zinc finger
        6.1    6.3  15.9       0.61    9.5   1.7    3.1  3  zf_Rg           Reverse gyrase zinc finger


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 !   29.3   2.8   1.5e-09   6.2e-07       1      24 []      24      47 ..      24      47 .. 0.96
   2 !   12.1   0.9   0.00036      0.14      15      23 ..      61      69 ..      60      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.5e-09
                           DUF1610  1 CtSCGaelaprEravvFpCPNCGE 24
                                      C SC +   p+E +v+F+CPNCG+
  gi|320101285|ref|YP_004176877.1| 24 CDSCHRLMEPGEYGVEFYCPNCGK 47
                                      88*********************8 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00036
                           DUF1610 15 vvFpCPNCG 23
                                      v++ CPNCG
  gi|320101285|ref|YP_004176877.1| 61 VEYTCPNCG 69
                                      7899****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.3   0.00042      0.17      26      49 .]      19      46 ..       3      46 .. 0.73
   2 !   18.1  12.0   5.2e-06    0.0021       1      49 []      24      69 ..      24      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00042
                               DZR 26 aaedrCpsCgekvdpearf....CpeCG 49
                                      a++ +C+sC++ ++p++      Cp+CG
  gi|320101285|ref|YP_004176877.1| 19 ATPPVCDSCHRLMEPGEYGvefyCPNCG 46
                                      33889*******99997545556****9 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.2e-06
                               DZR  1 CpqCgeelppdar....fCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                      C +C++ ++p+      +C++Cg+ l      +rC sC + v +   +Cp+CG
  gi|320101285|ref|YP_004176877.1| 24 CDSCHRLMEPGEYgvefYCPNCGKVLI-----KRCKSCRKLVVEY--TCPNCG 69
                                      99********9988888*********9.....9*******98776..799998 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   7.8   4.7e-06    0.0019      21      73 ..      23      69 ..       6      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.7e-06
                            zf-CHY 21 aCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCk 73
                                       C++CH+     e  ++ v+ + c +C ++    + Ck+C+k + ey+Cp+C 
  gi|320101285|ref|YP_004176877.1| 23 VCDSCHR---LMEPGEYGVE-FYCPNCGKV--LIKRCKSCRKLVVEYTCPNCG 69
                                      6*****9...3344566666.88*****97..8899****************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 !    9.0   0.0    0.0041       1.6      14      32 ..      12      30 ..       8      31 .. 0.68
   2 !    9.7   0.1    0.0024      0.95      23      31 ..      39      47 ..      34      49 .. 0.78
   3 ?    2.2   6.6      0.52   2.1e+02      24      30 ..      63      69 ..      50      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0041
                                      HHHHCCSTB-EE-TTT--E CS
                         zf-RING_7 14 lselragdevvtCpeCGRI 32
                                      + ++  +   + C++C+R+
  gi|320101285|ref|YP_004176877.1| 12 EVKIGEAATPPVCDSCHRL 30
                                      555555555789******8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0024
                                      -EE-TTT-- CS
                         zf-RING_7 23 vvtCpeCGR 31
                                       ++Cp+CG 
  gi|320101285|ref|YP_004176877.1| 39 EFYCPNCGK 47
                                      589****96 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.52
                                      EE-TTT- CS
                         zf-RING_7 24 vtCpeCG 30
                                       tCp+CG
  gi|320101285|ref|YP_004176877.1| 63 YTCPNCG 69
                                      79****9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   5.9e-05     0.023      58      95 ..       9      48 ..       1      52 [. 0.77
   2 ?    5.9   2.8     0.032        13      72      93 ..      52      69 ..      47      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.9e-05
                                      TT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS CS
                              HypA 58 egaeLeieevpvkvrCreCgkefeleek..alrCpkCgsa 95
                                      ++ e++i e      C++C++ +e  e+  ++ Cp+Cg+ 
  gi|320101285|ref|YP_004176877.1|  9 AEVEVKIGEAATPPVCDSCHRLMEPGEYgvEFYCPNCGKV 48
                                      346667778888889*********77745799*****985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.032
                                      EETTTS-EEECHHHHHS-TTTS CS
                              HypA 72 rCreCgkefeleekalrCpkCg 93
                                      rC++C+k +     +++Cp+Cg
  gi|320101285|ref|YP_004176877.1| 52 RCKSCRKLVV----EYTCPNCG 69
                                      8999996665....358****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 !   14.9   0.2   4.6e-05     0.018      21      55 ..      14      48 ..       4      52 .. 0.87
   2 ?    5.1   3.0     0.056        22      30      55 ..      52      71 ..      50      72 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-05
                    OrfB_Zn_ribbon 21 evnpayTSktCseCgsknkealsgrtfkCpnCgfe 55
                                      ++ +a T   C  C + +++   g +f+CpnCg +
  gi|320101285|ref|YP_004176877.1| 14 KIGEAATPPVCDSCHRLMEPGEYGVEFYCPNCGKV 48
                                      678899999***********9************87 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.056
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                      +C  C + + e      ++CpnCgf+
  gi|320101285|ref|YP_004176877.1| 52 RCKSCRKLVVE------YTCPNCGFR 71
                                      56666666666......999999985 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.8   1.6e-05    0.0063       7      45 ..      23      58 ..      17      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                           DUF2321  7 iClnGHvitdsvnkkeelveeyCekcGektitkcpkCst 45
                                      +C + H+  +     e+ ve yC +cG+ +i++c++C+ 
  gi|320101285|ref|YP_004176877.1| 23 VCDSCHRLME---PGEYGVEFYCPNCGKVLIKRCKSCRK 58
                                      6666666544...44578899****************86 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.1     0.014       5.5      40      54 ..      38      52 ..      22      52 .. 0.72
   2 !   12.6   2.0   0.00027      0.11      32      48 ..      53      69 ..      53      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
                           DUF1272 40 lenvCPncgGelvkR 54
                                      +e  CPncg  l+kR
  gi|320101285|ref|YP_004176877.1| 38 VEFYCPNCGKVLIKR 52
                                      4668*****999988 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00027
                           DUF1272 32 CaeCaeevlenvCPncg 48
                                      C++C + v+e +CPncg
  gi|320101285|ref|YP_004176877.1| 53 CKSCRKLVVEYTCPNCG 69
                                      9***************8 PP

>> His_Me_b4a2  His-Me finger endonuclease beta4-alpha2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   4.8e-05     0.019       4      48 ..      14      58 ..      12      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-05
                       His_Me_b4a2  4 KtGkgfdkKiCNiCHiLkktedFeiNqtdakgrkvtRPSCreCRk 48
                                      K G++ +  +C  CH L +  ++ +     +  kv    C+ CRk
  gi|320101285|ref|YP_004176877.1| 14 KIGEAATPPVCDSCHRLMEPGEYGVEFYCPNCGKVLIKRCKSCRK 58
                                      789999999***********************************9 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.8   7.3e-05     0.029     172     208 ..      37      71 ..      18      73 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.3e-05
                      tRNA-synt_1f 172 pylpvcekcgrvdttevvevdaeeeeieYkceecGee 208
                                        ++ +c++cg+v+  + +++   +  +eY+c +cG++
  gi|320101285|ref|YP_004176877.1|  37 GVEFYCPNCGKVLIKRCKSCR--KLVVEYTCPNCGFR 71 
                                       5789****************9..9***********97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.9       2.4   9.4e+02      18      22 ..      23      27 ..      21      28 .. 0.72
   2 ?   11.8   3.9   0.00031      0.12       2      13 ..      39      51 ..      38      58 .. 0.73
   3 ?   10.1   0.4     0.001      0.41       3       9 ..      63      69 ..      61      71 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.4
                       zf-ribbon_3 18 vCpyC 22
                                      vC +C
  gi|320101285|ref|YP_004176877.1| 23 VCDSC 27
                                      67777 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00031
                       zf-ribbon_3  2 tvrCPnCGa.pls 13
                                      + +CPnCG+ +++
  gi|320101285|ref|YP_004176877.1| 39 EFYCPNCGKvLIK 51
                                      579******4444 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.001
                       zf-ribbon_3  3 vrCPnCG 9 
                                      ++CPnCG
  gi|320101285|ref|YP_004176877.1| 63 YTCPNCG 69
                                      6677776 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3     0.021       8.3       8      15 ..      39      46 ..      37      48 .. 0.89
   2 ?    6.3   0.0     0.025        10       5      16 ..      59      70 ..      57      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.021
                           DUF2752  8 GipCPGCG 15
                                       ++CP CG
  gi|320101285|ref|YP_004176877.1| 39 EFYCPNCG 46
                                      58*****9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                           DUF2752  5 altGipCPGCGl 16
                                       +  + CP CG 
  gi|320101285|ref|YP_004176877.1| 59 LVVEYTCPNCGF 70
                                      567899*****5 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 ?   11.3   2.6   0.00015     0.058     625     662 ..      34      69 ..       4      72 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                          PolC_DP2 625 gketlearCeeCgekteeklvCkkceeeveeekcekce 662
                                       g+ ++e+ C++Cg+   +  +Ck+c++ v e +c++c+
  gi|320101285|ref|YP_004176877.1|  34 GEYGVEFYCPNCGKVLIK--RCKSCRKLVVEYTCPNCG 69 
                                       466788888888887777..788888877777888886 PP

>> Acetone_carb_G  Acetone carboxylase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8    0.0023      0.91      76      86 ..      38      48 ..       7      54 .. 0.82
   2 ?    6.8   0.5     0.018       7.3      75      84 ..      60      69 ..      50      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0023
                                      EEEE-TTT--E CS
                    Acetone_carb_G 76 rEyycPecgtl 86
                                      +E+ycP+cg++
  gi|320101285|ref|YP_004176877.1| 38 VEFYCPNCGKV 48
                                      6********86 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.018
                                      EEEEE-TTT- CS
                    Acetone_carb_G 75 irEyycPecg 84
                                      ++Ey cP+cg
  gi|320101285|ref|YP_004176877.1| 60 VVEYTCPNCG 69
                                      78*******9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4       1.8   7.4e+02      26      32 ..      22      28 ..      19      31 .. 0.69
   2 ?    6.0   0.5     0.027        11      13      20 ..      41      48 ..      41      49 .. 0.76
   3 ?   13.0   2.9   0.00018     0.073       7      32 ..      46      69 ..      46      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.8
                           DUF35_N 26 avCphCg 32
                                      +vC  C+
  gi|320101285|ref|YP_004176877.1| 22 PVCDSCH 28
                                      6677776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.027
                           DUF35_N 13 rCpdCGtv 20
                                      +Cp+CG+v
  gi|320101285|ref|YP_004176877.1| 41 YCPNCGKV 48
                                      68888887 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00018
                           DUF35_N  7 grLvgqrCpdCGtvqfPPravCphCg 32
                                      g++++ rC++C ++++  +  Cp+Cg
  gi|320101285|ref|YP_004176877.1| 46 GKVLIKRCKSCRKLVV--EYTCPNCG 69
                                      7899**********97..*******6 PP

>> PSCyt3  Protein of unknown function (DUF1588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00019     0.076      65      88 ..      18      41 ..       5      51 .. 0.81
   2 ?   -0.9   0.1       5.1     2e+03      69      77 ..      51      59 ..      46      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00019
                            PSCyt3 65 hrsaeaCasCHelidplGfalenf 88
                                        + + C sCH+l++p  ++ e +
  gi|320101285|ref|YP_004176877.1| 18 AATPPVCDSCHRLMEPGEYGVEFY 41
                                      556788**********98888877 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 5.1
                            PSCyt3 69 eaCasCHel 77
                                      ++C+sC +l
  gi|320101285|ref|YP_004176877.1| 51 KRCKSCRKL 59
                                      569999775 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1     0.004       1.6       2      24 ..      24      47 ..      21      51 .. 0.66
   2 ?    8.4   1.5    0.0057       2.3      12      24 ..      58      70 ..      51      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.004
                          zf-Mss51  2 CPvpkhkqt....apkhvdfeCpdCGi 24
                                      C  ++         +  v+f Cp+CG 
  gi|320101285|ref|YP_004176877.1| 24 CDSCH---RlmepGEYGVEFYCPNCGK 47
                                      44453...3333445569********5 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0057
                          zf-Mss51 12 pkhvdfeCpdCGi 24
                                      +  v+++Cp+CG+
  gi|320101285|ref|YP_004176877.1| 58 KLVVEYTCPNCGF 70
                                      45699*******7 PP

>> DUF1258  Protein of unknown function (DUF1258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.3   0.00026       0.1      11      43 ..      34      64 ..      23      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                           DUF1258 11 knfsthkfcnkcGkvvaksekcelcggkvakfv 43
                                       ++ + ++c +cGkv+   ++c+ c + v++++
  gi|320101285|ref|YP_004176877.1| 34 GEYGVEFYCPNCGKVL--IKRCKSCRKLVVEYT 64
                                      6799**********76..689*****9999986 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       1.2   4.9e+02       5       9 ..      24      28 ..      23      31 .. 0.78
   2 ?    7.1   0.0     0.013         5      26      34 ..      40      48 ..      34      50 .. 0.63
   3 ?    2.6   0.8      0.32   1.3e+02      27      33 ..      52      58 ..      51      60 .. 0.70
   4 ?    6.2   0.1     0.025        10       4      10 ..      64      70 ..      62      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.2
                     zinc_ribbon_4  5 CpsCk 9 
                                      C sC+
  gi|320101285|ref|YP_004176877.1| 24 CDSCH 28
                                      88887 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                     zinc_ribbon_4 26 vrCskCghv 34
                                        C++Cg+v
  gi|320101285|ref|YP_004176877.1| 40 FYCPNCGKV 48
                                      556666654 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.32
                     zinc_ribbon_4 27 rCskCgh 33
                                      rC+ C++
  gi|320101285|ref|YP_004176877.1| 52 RCKSCRK 58
                                      6777764 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.025
                     zinc_ribbon_4  4 tCpsCka 10
                                      tCp+C++
  gi|320101285|ref|YP_004176877.1| 64 TCPNCGF 70
                                      7999986 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.2   0.00048      0.19      31      59 ..      39      68 ..      23      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00048
                                      H---TTT--SS-EE------.--EEE-TTT CS
                              DpnI 31 nlyCpkCgskklsefennkp.vaDfyCesc 59
                                      ++yCp+Cg+  +++ ++ ++ v+++ C +c
  gi|320101285|ref|YP_004176877.1| 39 EFYCPNCGKVLIKRCKSCRKlVVEYTCPNC 68
                                      69************998765489******9 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 ?    5.9   0.3     0.023       9.3       2      12 ..      39      49 ..      39      49 .. 0.84
   2 ?    5.7   0.2     0.027        11       2      11 ..      62      71 ..      62      73 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                        zf_C2H2_10  2 efsCPKCqekl 12
                                      ef CP C+ +l
  gi|320101285|ref|YP_004176877.1| 39 EFYCPNCGKVL 49
                                      699****9875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                        zf_C2H2_10  2 efsCPKCqek 11
                                      e+ CP C+  
  gi|320101285|ref|YP_004176877.1| 62 EYTCPNCGFR 71
                                      689****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 ?    7.3   0.2     0.013       5.1      16      34 ..      10      29 ..       7      32 .. 0.79
   2 ?    4.2  12.4      0.12        47       5      33 ..      39      69 ..      39      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.013
                       Zn-ribbon_8 16 evlqsisdaplta.CPeCgs 34
                                      ev ++i +a+ ++ C +C+ 
  gi|320101285|ref|YP_004176877.1| 10 EVEVKIGEAATPPvCDSCHR 29
                                      77889998887777****86 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.12
                       Zn-ribbon_8  5 eYrCeeCghefevlqsis.daplta.CPeCg 33
                                      e+ C +Cg++  +++++  +   +  CP+Cg
  gi|320101285|ref|YP_004176877.1| 39 EFYCPNCGKVLIKRCKSCrKLVVEYtCPNCG 69
                                      899*********99998855556666****9 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 ?    0.2   0.0         2   8.1e+02      14      18 ..       4       9 ..       2      22 .. 0.65
   2 ?    7.0   0.4     0.014       5.8       8      27 ..      24      49 ..      20      51 .. 0.79
   3 ?    9.3   2.2    0.0029       1.1       3      24 ..      48      69 ..      47      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2
                                      EESS.S CS
                            Nop10p 14 YTLk.k 18
                                      YTLk  
  gi|320101285|ref|YP_004176877.1|  4 YTLKpA 9 
                                      999953 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                                      -TTT-......-EESSSB-TTT-SB- CS
                            Nop10p  8 cgkcr......vYTLkkvcpecggpt 27
                                      c +c+      +Y  +  cp+cg+ +
  gi|320101285|ref|YP_004176877.1| 24 CDSCHrlmepgEYGVEFYCPNCGKVL 49
                                      6666666677799999*******975 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0029
                                      ---EE-TTT--EESSSB-TTT- CS
                            Nop10p  3 sylrkcgkcrvYTLkkvcpecg 24
                                      + +++c++cr+   +++cp+cg
  gi|320101285|ref|YP_004176877.1| 48 VLIKRCKSCRKLVVEYTCPNCG 69
                                      689******************9 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 ?    6.2   2.9     0.026        10      20      34 ..      38      52 ..       4      53 .. 0.76
   2 ?    4.1   0.1      0.12        46       3       8 ..      64      69 ..      63      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.026
                                      STTB-TTT--.-B-- CS
                           ADK_lid 20 veglCDkCGepLvqR 34
                                      ve  C +CG  L++R
  gi|320101285|ref|YP_004176877.1| 38 VEFYCPNCGKVLIKR 52
                                      666788888888887 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.12
                                      E-TTT- CS
                           ADK_lid  3 vCpkCG 8 
                                      +Cp+CG
  gi|320101285|ref|YP_004176877.1| 64 TCPNCG 69
                                      8****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 ?   11.8   2.2   0.00052      0.21      11      38 ..      24      54 ..      22      55 .. 0.81
   2 ?    5.9   3.0     0.036        14       8      30 ..      50      69 ..      47      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00052
                      NOB1_Zn_bind 11 ChaCfkvtkd...mtkkFCpkCGnktLkrva 38
                                      C +C+++++        +Cp+CG+  +kr++
  gi|320101285|ref|YP_004176877.1| 24 CDSCHRLMEPgeyGVEFYCPNCGKVLIKRCK 54
                                      999999995433377889*******999986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.036
                      NOB1_Zn_bind  8 vlrChaCfkvtkdmtkkFCpkCG 30
                                      + rC +C k++ + t   Cp+CG
  gi|320101285|ref|YP_004176877.1| 50 IKRCKSCRKLVVEYT---CPNCG 69
                                      78*******998876...****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 ?    5.1   0.1     0.054        21      17      30 ..      16      29 ..       7      31 .. 0.68
   2 ?    7.2   1.3     0.012       4.8       2      10 ..      41      49 ..      40      55 .. 0.77
   3 ?    0.4   0.2       1.6   6.3e+02      24      29 ..      52      57 ..      50      60 .. 0.79
   4 ?    4.6   0.2     0.078        31      24      30 ..      64      70 ..      61      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.054
                                      T-SS-EEEETTTTE CS
                         Nudix_N_2 17 gDnreRlvCpaCgt 30
                                      g+  +  vC++C+ 
  gi|320101285|ref|YP_004176877.1| 16 GEAATPPVCDSCHR 29
                                      55555569****85 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                                      B-TTT--B- CS
                         Nudix_N_2  2 FCsqCGtpv 10
                                      +C++CG+ +
  gi|320101285|ref|YP_004176877.1| 41 YCPNCGKVL 49
                                      899999866 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.6
                                      EETTTT CS
                         Nudix_N_2 24 vCpaCg 29
                                      +C++C 
  gi|320101285|ref|YP_004176877.1| 52 RCKSCR 57
                                      699996 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.078
                                      EETTTTE CS
                         Nudix_N_2 24 vCpaCgt 30
                                      +Cp+Cg+
  gi|320101285|ref|YP_004176877.1| 64 TCPNCGF 70
                                      7888885 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 ?    0.9   0.3       1.4   5.4e+02       6      13 ..      22      29 ..      17      34 .. 0.64
   2 ?    4.7   7.5     0.092        37      55      67 ..      38      50 ..      22      64 .. 0.86
   3 ?    2.4   4.6      0.48   1.9e+02      55      63 ..      61      69 ..      53      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.4
                     zf-LITAF-like  6 vdCpaCqq 13
                                        C +C++
  gi|320101285|ref|YP_004176877.1| 22 PVCDSCHR 29
                                      56666665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.092
                     zf-LITAF-like 55 vehyCpnCgallg 67
                                      ve yCpnCg++l 
  gi|320101285|ref|YP_004176877.1| 38 VEFYCPNCGKVLI 50
                                      7889999999885 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.48
                     zf-LITAF-like 55 vehyCpnCg 63
                                      ve++CpnCg
  gi|320101285|ref|YP_004176877.1| 61 VEYTCPNCG 69
                                      789999997 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.1      0.05        20      20      46 ..      23      53 ..      16      53 .. 0.79
   2 ?   10.0   2.5    0.0021      0.85      19      40 ..      51      70 ..      48      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.05
                              C1_2 20 nCsaCgrk.idgff....YsCseCdfslhvrC 46
                                       C+ C r    + +    ++C+ C  +l +rC
  gi|320101285|ref|YP_004176877.1| 23 VCDSCHRLmE-PGEygveFYCPNCGKVLIKRC 53
                                      6*******62.3333678******98888888 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0021
                              C1_2 19 fnCsaCgrkidgffYsCseCdf 40
                                      ++C+ C++ +   +Y+C+ C f
  gi|320101285|ref|YP_004176877.1| 51 KRCKSCRKLV--VEYTCPNCGF 70
                                      79*******6..67******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 ?    0.1   0.1       1.9   7.5e+02       2      11 ..      24      33 ..      23      35 .. 0.70
   2 ?    7.4   7.2    0.0091       3.6       1      17 [.      41      57 ..      41      58 .. 0.85
   3 ?    1.9   7.9      0.51     2e+02      16      21 ..      65      70 ..      52      72 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.9
                     zinc_ribbon_2  2 CpnCGaelqd 11
                                      C +C++  ++
  gi|320101285|ref|YP_004176877.1| 24 CDSCHRLMEP 33
                                      8899876655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0091
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCp 17
                                      +CpnCG+ l ++ k C 
  gi|320101285|ref|YP_004176877.1| 41 YCPNCGKVLIKRCKSCR 57
                                      8******9988888885 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.51
                     zinc_ribbon_2 16 CpyCGt 21
                                      Cp+CG+
  gi|320101285|ref|YP_004176877.1| 65 CPNCGF 70
                                      788876 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.7      0.32   1.3e+02       4      20 ..      23      46 ..      20      49 .. 0.63
   2 ?   11.6   5.3   0.00049       0.2       3      21 ..      51      70 ..      51      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.32
                                      B-TTT-S...B-SEE....-TTT- CS
                            zf-HIT  4 lCgvCgf...pakYk....CpkCn 20
                                      +C  C+    p+ Y     Cp+C+
  gi|320101285|ref|YP_004176877.1| 23 VCDSCHRlmePGEYGvefyCPNCG 46
                                      566666666666663333399998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00049
                                      -B-TTT-S.B-SEE-TTT-- CS
                            zf-HIT  3 klCgvCgf.pakYkCpkCnt 21
                                      k C  C +    Y+Cp+C+ 
  gi|320101285|ref|YP_004176877.1| 51 KRCKSCRKlVVEYTCPNCGF 70
                                      57****************96 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   3.5    0.0031       1.2       7      33 ..      24      48 ..      23      58 .. 0.83
   2 ?   -1.0   4.2       3.1   1.2e+03      24      31 ..      62      69 ..      50      71 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0031
                       Mu-like_Com  7 CGeCaRLLaKaeAlDeltiKCPRCGtL 33
                                      C  C+RL+  +e +  ++  CP CG +
  gi|320101285|ref|YP_004176877.1| 24 CDSCHRLMEPGE-YG-VEFYCPNCGKV 48
                                      999****99888.55.899******75 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                       Mu-like_Com 24 tiKCPRCG 31
                                      +  CP CG
  gi|320101285|ref|YP_004176877.1| 62 EYTCPNCG 69
                                      34588887 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.3   0.00081      0.32      19      40 .]      22      46 ..      18      46 .. 0.76
   2 ?    4.8   0.6      0.08        32      16      22 ..      63      69 ..      60      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00081
                     Auto_anti-p27 19 pvC..gvPLmrdr..kggkvyCvaCd 40
                                      pvC     Lm+ +  +g++ yC++C+
  gi|320101285|ref|YP_004176877.1| 22 PVCdsCHRLME-PgeYGVEFYCPNCG 46
                                      55654457888.55889********6 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.08
                     Auto_anti-p27 16 etCpvCg 22
                                       tCp+Cg
  gi|320101285|ref|YP_004176877.1| 63 YTCPNCG 69
                                      5899997 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.35   1.4e+02       6      13 ..      23      30 ..      22      34 .. 0.85
   2 ?    8.7   0.1    0.0032       1.3       4      12 ..      39      47 ..      37      49 .. 0.86
   3 ?   -0.2   0.6       1.9   7.4e+02       6      12 ..      52      58 ..      50      62 .. 0.75
   4 ?    6.8   1.0     0.012       4.8       4      11 ..      62      69 ..      59      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.35
                                      E-TTTSSE CS
                             Sgf11  6 tCpnCgRq 13
                                      +C+ C R 
  gi|320101285|ref|YP_004176877.1| 23 VCDSCHRL 30
                                      6*****96 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0032
                                      EEE-TTTSS CS
                             Sgf11  4 yvtCpnCgR 12
                                       + CpnCg+
  gi|320101285|ref|YP_004176877.1| 39 EFYCPNCGK 47
                                      699****97 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.9
                                      E-TTTSS CS
                             Sgf11  6 tCpnCgR 12
                                      +C+ C +
  gi|320101285|ref|YP_004176877.1| 52 RCKSCRK 58
                                      5999976 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.012
                                      EEE-TTTS CS
                             Sgf11  4 yvtCpnCg 11
                                       +tCpnCg
  gi|320101285|ref|YP_004176877.1| 62 EYTCPNCG 69
                                      68*****7 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.4     0.018       7.2     148     170 ..      23      47 ..      12      51 .. 0.67
   2 ?    6.4   3.2     0.016       6.3      74      94 ..      51      69 ..      47      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                           TackOD1 148 kCnsCkslfs..epevkarClsCek 170
                                       +C+sC++l+   e  v++ C +C+k
  gi|320101285|ref|YP_004176877.1|  23 VCDSCHRLMEpgEYGVEFYCPNCGK 47 
                                       5777777765224456677777765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.016
                           TackOD1 74 rlCpsCksghlnvrevCpkCk 94
                                      + C+sC+  +l v ++Cp+C+
  gi|320101285|ref|YP_004176877.1| 51 KRCKSCR--KLVVEYTCPNCG 69
                                      5788886..799999*****6 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.16        65      12      22 ..      23      42 ..      14      43 .. 0.53
   2 ?    7.1   0.5     0.014       5.6       1      19 [.      24      48 ..      24      49 .. 0.75
   3 ?    4.6   8.3     0.088        35       1      19 [.      42      59 ..      42      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                                      E-TTTS-S.........EES CS
                           zf-MYND 12 kCagCksv.........fYC 22
                                       C  C++          fYC
  gi|320101285|ref|YP_004176877.1| 23 VCDSCHRLmepgeygveFYC 42
                                      78888544333333334666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                                      -TTT--.......B-SC.E-TTTS-S CS
                           zf-MYND  1 CavCgk......aealk.kCagCksv 19
                                      C +C++        + +  C++C +v
  gi|320101285|ref|YP_004176877.1| 24 CDSCHRlmepgeYGV-EfYCPNCGKV 48
                                      99****987764344.26*****887 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.088
                                      -TTT--.B-SCE-TTTS-S CS
                           zf-MYND  1 CavCgkaealkkCagCksv 19
                                      C +Cgk    k+C+ C++ 
  gi|320101285|ref|YP_004176877.1| 42 CPNCGK-VLIKRCKSCRKL 59
                                      999***.8899*****753 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.12        50       4      15 ..      23      34 ..      22      37 .. 0.83
   2 ?    6.3   0.2     0.018       7.1       3      12 ..      40      49 ..      38      52 .. 0.85
   3 ?    0.0   0.3       1.7   6.7e+02       4      12 ..      52      60 ..      50      62 .. 0.76
   4 ?    6.0   0.5     0.023         9       3      10 ..      63      70 ..      61      73 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.12
                            zf_UBZ  4 lCerCgkeipes 15
                                      +C+ C++ +++ 
  gi|320101285|ref|YP_004176877.1| 23 VCDSCHRLMEPG 34
                                      7*****999875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                            zf_UBZ  3 ylCerCgkei 12
                                      + C+ Cgk +
  gi|320101285|ref|YP_004176877.1| 40 FYCPNCGKVL 49
                                      88*****975 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.7
                            zf_UBZ  4 lCerCgkei 12
                                       C+ C k +
  gi|320101285|ref|YP_004176877.1| 52 RCKSCRKLV 60
                                      599998865 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.023
                            zf_UBZ  3 ylCerCgk 10
                                      y+C+ Cg 
  gi|320101285|ref|YP_004176877.1| 63 YTCPNCGF 70
                                      9*****96 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.0    0.0046       1.8      13      28 ..      42      57 ..      41      59 .. 0.96
   2 ?    4.1   0.9     0.091        36      13      17 ..      65      69 ..      63      73 .] 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0046
                           zf-tcix 13 CpkCGtyNGtRglsCk 28
                                      Cp+CG    +R++sC+
  gi|320101285|ref|YP_004176877.1| 42 CPNCGKVLIKRCKSCR 57
                                      ***************8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.091
                           zf-tcix 13 CpkCG 17
                                      Cp+CG
  gi|320101285|ref|YP_004176877.1| 65 CPNCG 69
                                      ***** 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 ?    6.5   3.9     0.017       6.9      42      52 ..      37      47 ..      16      49 .. 0.72
   2 ?    4.0   4.8       0.1        41      43      52 ..      61      70 ..      53      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.017
                    zinc_ribbon_10 42 evkyrCpkCga 52
                                       v+++Cp+Cg 
  gi|320101285|ref|YP_004176877.1| 37 GVEFYCPNCGK 47
                                      479******97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                    zinc_ribbon_10 43 vkyrCpkCga 52
                                      v+y Cp+Cg+
  gi|320101285|ref|YP_004176877.1| 61 VEYTCPNCGF 70
                                      69******96 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6      0.52   2.1e+02      24      29 ..      22      27 ..      20      33 .. 0.67
   2 ?    8.6   6.6    0.0053       2.1       4      29 ..      40      68 ..      37      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.52
                          zf-B_box 24 plCeeC 29
                                      p+C++C
  gi|320101285|ref|YP_004176877.1| 22 PVCDSC 27
                                      577777 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0053
                          zf-B_box  4 tkCpeHknkpatlfCedCqqpl....CeeC 29
                                       +Cp+++ k ++  C++C++++    C++C
  gi|320101285|ref|YP_004176877.1| 40 FYCPNCG-KVLIKRCKSCRKLVveytCPNC 68
                                      58*****.**********997534447776 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.8    0.0037       1.5       2      27 ..      22      47 ..      21      55 .. 0.92
   2 ?    2.1   1.6      0.54   2.2e+02      17      27 ..      60      70 ..      50      72 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0037
                           DUF2072  2 HkCtkCekvfedgskeilkGCpsCGg 27
                                        C +C++++e g+  +   Cp+CG 
  gi|320101285|ref|YP_004176877.1| 22 PVCDSCHRLMEPGEYGVEFYCPNCGK 47
                                      57***********************5 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.54
                           DUF2072 17 eilkGCpsCGg 27
                                      ++   Cp+CG 
  gi|320101285|ref|YP_004176877.1| 60 VVEYTCPNCGF 70
                                      45668*****7 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9  10.9      0.71   2.8e+02      37      90 .]      13      69 ..       7      69 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.71
                                      ---SSTCCCTB-TTT--B--CTTTEEEEE........E-SSS-E.........EEEEETTTT CS
                              Rpr2 37 lrlppsvkrtvCkkCgsvlipgvtcsvrv........enkskkkkkkkkkadvlvvtClaCg 90
                                      +++ ++    vC +C+ ++ pg                     k+ k+ ++ v+ +tC +Cg
  gi|320101285|ref|YP_004176877.1| 13 VKIGEAATPPVCDSCHRLMEPGEYGVEFYcpncgkvlI-----KRCKSCRKLVVEYTCPNCG 69
                                      56666667779999999999996544443333332221.....1222333478889999996 PP

>> Dynactin_p62  Dynactin p62 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   7.2    0.0081       3.2       6      36 ..      40      72 ..      33      73 .] 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0081
                      Dynactin_p62  6 lyCedChqirCpRC..vteeivtyyCPnCLFev 36
                                       yC +C ++  +RC      +v y CPnC F  
  gi|320101285|ref|YP_004176877.1| 40 FYCPNCGKVLIKRCksCRKLVVEYTCPNCGFRG 72
                                      5*******988888334578999******9975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.1    0.0045       1.8      18      29 ..      38      49 ..      22      52 .. 0.69
   2 ?    2.0   0.3      0.39   1.5e+02      21      31 ..      52      63 ..      50      64 .. 0.78
   3 ?    6.4   1.5     0.016       6.4       1       7 [.      63      69 ..      63      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0045
                                      TCEEESSSSBEE CS
                      TF_Zn_Ribbon 18 gelvCtdCGlVl 29
                                       e++C++CG Vl
  gi|320101285|ref|YP_004176877.1| 38 VEFYCPNCGKVL 49
                                      599999999997 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.39
                                      EESSS.SBEEEE CS
                      TF_Zn_Ribbon 21 vCtdC.GlVled 31
                                      +C++C  lV+e+
  gi|320101285|ref|YP_004176877.1| 52 RCKSCrKLVVEY 63
                                      599998888875 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.016
                                      EEETTTT CS
                      TF_Zn_Ribbon  1 ykCPnCg 7 
                                      y+CPnCg
  gi|320101285|ref|YP_004176877.1| 63 YTCPNCG 69
                                      7899998 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.43   1.7e+02      12      21 ..      20      29 ..      15      33 .. 0.80
   2 ?    3.7   3.3      0.17        69       1      22 [.      24      48 ..      24      49 .. 0.74
   3 ?    7.1   2.9     0.015       6.1       1      20 [.      53      69 ..      50      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.43
                            zf-AN1 12 lpfkCryCgk 21
                                      +p  C++C++
  gi|320101285|ref|YP_004176877.1| 20 TPPVCDSCHR 29
                                      5678999986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.17
                            zf-AN1  1 CsfksCkkkd.....flpfkCryCgkv 22
                                      C+  sC+++       + f C++Cgkv
  gi|320101285|ref|YP_004176877.1| 24 CD--SCHRLMepgeyGVEFYCPNCGKV 48
                                      55..78888866665556******986 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.015
                            zf-AN1  1 CsfksCkkkdflpfkCryCg 20
                                      C+  sC+k++   ++C++Cg
  gi|320101285|ref|YP_004176877.1| 53 CK--SCRKLVV-EYTCPNCG 69
                                      44..6777775.7******8 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1         2   8.1e+02      36      43 ..      24      31 ..      20      35 .. 0.69
   2 ?    1.4   5.7      0.52   2.1e+02       9      14 ..      41      46 ..      38      57 .. 0.80
   3 ?    9.5   1.7    0.0015      0.61       3      14 ..      58      69 ..      56      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2
                             zf_Rg 36 gdvckaLk 43
                                       d+c+ L 
  gi|320101285|ref|YP_004176877.1| 24 CDSCHRLM 31
                                      57787775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.52
                             zf_Rg  9 lCPNCg 14
                                       CPNCg
  gi|320101285|ref|YP_004176877.1| 41 YCPNCG 46
                                      6****7 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0015
                             zf_Rg  3 kavfeklCPNCg 14
                                      k+v+e  CPNCg
  gi|320101285|ref|YP_004176877.1| 58 KLVVEYTCPNCG 69
                                      689********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        65  (0.00362541); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 481.18
//
Query:       gi|320101286|ref|YP_004176878.1|  [L=90]
Description: translation elongation factor 1B (aEF-1B) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-19   69.7   0.1    1.9e-19   69.6   0.1    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.1   1.1e-23   1.9e-19       2      90 .]       6      89 ..       5      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.1e-23
                                      EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEES.SS-GGGGHHHHHHTTS-S..... CS
                           EF1_GNE  2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvie.ddkvstdeleekieeiegeledl 78
                                      v+++v Ped+et leel +++ + +l++ ++++  +++epiafGlk+L++ +v++ +++++t++le+ +++++g     
  gi|320101286|ref|YP_004176878.1|  6 VIVKVLPEDVETPLEELRERISD-SLPQgYELK-MWDEEPIAFGLKALRLAIVMPeETEGGTEALENLLSQVQG----- 77
                                      899********************.88888****.5*******************978899**************..... PP

                                      SEEEEEEEEEE- CS
                           EF1_GNE 79 Vqsveivsfnkl 90
                                      V++ve++ +n+l
  gi|320101286|ref|YP_004176878.1| 78 VSQVEVEYVNRL 89
                                      **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 662.27
//
Query:       gi|320101287|ref|YP_004176879.1|  [L=218]
Description: TrkA-N domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-16   59.3   0.7    7.4e-16   58.5   0.4    1.6  1  TrkA_N         TrkA-N domain
    6.4e-05   23.3   0.4    0.00026   21.4   0.1    1.9  2  NAD_binding_7  Putative NAD(P)-binding
     0.0016   18.2   3.2     0.0018   18.1   0.5    2.3  2  TrkA_C         TrkA-C domain
  ------ inclusion threshold ------
      0.044   14.4   0.1        0.5   11.0   0.0    2.6  3  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


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 !   58.5   0.4   1.6e-19   7.4e-16       1     109 [.       6     116 ..       6     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.6e-19
                                       EEEES-SHHHHHHHHHHHHTT..EEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLsegg..kdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgdde 74 
                                       i++iG G+v+++l   ++ ++  ++vvv+dkd++r + +++ g + v+ gdatd  +  e++++++ av+a+t++de
  gi|320101287|ref|YP_004176879.1|   6 ILVIGGGKVAEHLFTIFNVHEeaDEVVVVDKDPRRRAVFERIGdILVLDGDATDVGLYNEINMKEITAVLALTNSDE 82 
                                       79*************9988444867***************999999******************************* PP

                                       HHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHT CS
                            TrkA_N  75 anilavllakelnpkkkiiaraqdpehaellkklg 109
                                       +n++++++ak+ ++ +  i r  +p+ ael+++lg
  gi|320101287|ref|YP_004176879.1|  83 VNLMVLAIAKT-FGVPVRIGRFTEPKIAELVSSLG 116
                                       **********8.55588999999999999999877 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 !   21.4   0.1   5.8e-08   0.00026       8      91 ..       4     100 ..       1     107 [. 0.70
   2 ?   -0.2   0.0      0.29   1.3e+03      50      72 ..     138     160 ..     100     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.8e-08
                     NAD_binding_7   8 kkvlvvGgGevAarkvr..klleagakvtvvapev.keele.......elvklaeee..l....ekdlegadlviaa 68 
                                        ++lv+GgG+vA++ +   ++ e+  +v+vv+++              +++ l  +   +    e +++++  v+a 
  gi|320101287|ref|YP_004176879.1|   4 PRILVIGGGKVAEHLFTifNVHEEADEVVVVDKDPrR---RavferigDILVLDGDAtdVglynEINMKEITAVLAL 77 
                                       589*********986551156677789******9530...22343443333333222222334445589999***** PP

                     NAD_binding_7  69 tddrelneriaeaakarrilvnv 91 
                                       t+ +e+n  + + ak+ +++v +
  gi|320101287|ref|YP_004176879.1|  78 TNSDEVNLMVLAIAKTFGVPVRI 100
                                       ***************99999975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.29
                     NAD_binding_7  50 laeeelekdlegadlviaatddr 72 
                                       +++ ++ +++ + ++v+aa++d+
  gi|320101287|ref|YP_004176879.1| 138 ISSGKVLGEIGEEKIVMAAISDA 160
                                       44555566777778888888886 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.29   1.3e+03      50      62 ..      48      60 ..      46      66 .. 0.82
   2 !   18.1   0.5   3.9e-07    0.0018       2      63 ..     153     213 ..     152     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.29
                                      T-EEEEEEEHHHH CS
                            TrkA_C 50 GDvllvvgspsdl 62
                                      GD+l++ g+  d+
  gi|320101287|ref|YP_004176879.1| 48 GDILVLDGDATDV 60
                                      9*******98887 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.9e-07
                                       EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdla 63 
                                       v+ +++   p+vG t++e+ l +    ++ +  g ++ +p +++v ++G +l++++ ++++ 
  gi|320101287|ref|YP_004176879.1| 153 VMAAISDADPVVGNTIGEISLGD-EGKIILLFDGLRFKVPEPSDVVKPGNILIILARSEEVL 213
                                       567888999**************.88888888999***********************9974 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   0.0   0.00011       0.5       1      54 [.       5      56 ..       5      90 .. 0.81
   2 ?   -1.1   0.0      0.66     3e+03      69      91 ..     122     144 ..     105     147 .. 0.86
   3 ?   -0.6   0.0      0.44     2e+03      24      43 ..     198     217 ..     193     218 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECEC CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavd 54
                                      +i +iG+G+++e l   +  +  ++ e+vv+ +++p +++ +++   + v  +d
  gi|320101287|ref|YP_004176879.1|  5 RILVIGGGKVAEHLFTIFNVHE-EADEVVVV-DKDPRRRAVFERIGDILVLDGD 56
                                      5889************998887.99999988.9999999888776665555444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.66
                                       S-HHHHHHHHHHCGHHHHTTSEE CS
                     F420_oxidored  69 vkpedveevlselakdalkgklv 91 
                                       v+p +v+++++++  + ++gk++
  gi|320101287|ref|YP_004176879.1| 122 VQPVVVANIIAQILTSISSGKVL 144
                                       78888999999999999988875 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.44
                                       -GGCEEEEEESSCCCHHHHH CS
                     F420_oxidored  24 qpheivvansrnpekaeela 43 
                                       +p +i+++  r++e +++l+
  gi|320101287|ref|YP_004176879.1| 198 KPGNILIILARSEEVLRKLK 217
                                       5679999999**99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1667.11
//
Query:       gi|320101288|ref|YP_004176880.1|  [L=267]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0075   15.8   5.8      0.011   15.3   5.8    1.2  1  DUF1624     Protein of unknown function (DUF1624)
  ------ inclusion threshold ------
        1.7    8.4   5.3        4.8    7.0   5.3    1.7  1  Sarcolipin  Sarcolipin


Domain annotation for each model (and alignments):
>> DUF1624  Protein of unknown function (DUF1624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   5.8   1.2e-06     0.011      67     147 ..      41     116 ..       8     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                           DUF1624  67 slrwrkflkRglkilaaallitaatylllpdsfivFGiLhlialalllallflrlpkalllllallilalglllrea 143
                                       s+  r+++ R++ ++++ ++i++a ++++p+++   G+L ++ +  l++++fl +p  + ++  l+++ +g+ +r++
  gi|320101288|ref|YP_004176880.1|  41 SITLRDAAIRVIDVTLIVMAISVAVLVFIPQYW---GVLTVFVILGLIGVFFLIYPLSSYMA--LAVIQVGVPVRGK 112
                                       3445999************************65...*******************9999988..4455556667776 PP

                           DUF1624 144 ifdl 147
                                       +f++
  gi|320101288|ref|YP_004176880.1| 113 FFEI 116
                                       6665 PP

>> Sarcolipin  Sarcolipin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.3   0.00053       4.8      12      22 ..      13      23 ..      12      27 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00053
                        Sarcolipin 12 FTvVLITViLm 22
                                      FTvV+IT+iL+
  gi|320101288|ref|YP_004176880.1| 13 FTVVIITIILI 23
                                      9*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2113.89
//
Query:       gi|320101289|ref|YP_004176881.1|  [L=428]
Description: MiaB family RNA modification protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-23   82.3   0.2    4.4e-22   79.2   0.1    2.2  2  Radical_SAM  Radical SAM superfamily
    7.8e-22   77.2   0.0    1.7e-21   76.1   0.0    1.6  1  UPF0004      Uncharacterized protein family UPF0004
    6.7e-06   26.0   0.0    1.8e-05   24.6   0.0    1.7  1  TRAM         TRAM domain
  ------ inclusion threshold ------
      0.048   14.0   0.1        2.5    8.5   0.0    2.9  3  Rep_fac-A_3  Replication factor A protein 3


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.1   9.7e-26   4.4e-22       1     166 [.     139     314 ..     139     315 .. 0.85
   2 ?    0.5   0.0      0.16   7.1e+02     127     151 ..     348     371 ..     317     375 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 9.7e-26
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.......TTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.......pdfvellerl 70 
                                       ++v++gC  +CsfC+ ++    +++  s s++ +++ v ++ +++g+ ev l+g++   y       +++ +l++r+
  gi|320101289|ref|YP_004176881.1| 139 IPVQEGCLSNCSFCISRH---ARRVLVSHSIDAVVKAVGKA-VRDGAVEVQLTGMDLGTYgmdlyraRRLPDLIRRI 211
                                       6899*************9...8*******************.9**********999888877777775555555555 PP

                                       HHTCCCTEEEEEEECSSCHG....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  71 aklavpgiritvetngtlpd....eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreag 141
                                       +++   ++ ++v    + +     e+ ++  ++++     ++++l++++++ vlklm+r++t+ee+le +++ +++ 
  gi|320101289|ref|YP_004176881.1| 212 VENVRGNYMLRVGMINPEHLrhilEDLVKVVADAEnvYKFLHIPLQSGSNR-VLKLMRRNYTVEEYLEMVDRVKSS- 286
                                       55544455555544444444468888888888888****************.************************. PP

                                       SET...EEEEEEEBTTTSHHHHHHHHHH CS
                                       xxx...xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 142 ikr...vvdrivglpGendeeleellel 166
                                       i++    +d+ivg+p e++e++ e+l+ 
  gi|320101289|ref|YP_004176881.1| 287 IPEvsiATDIIVGHPMESEEDFAETLRV 314
                                       *************************985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivg 151
                                        e+vl+al+   ++g++ v  r+vg
  gi|320101289|ref|YP_004176881.1| 348 KERVLKALRVVEKVGMR-VRARYVG 371
                                       599************99.8888876 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   3.8e-25   1.7e-21       1      92 [.       2      94 ..       2      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 3.8e-25
                                      XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTS.T.--EEEEEEHH CS
                           UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalk.kpekkvvvlGCm 78
                                      kv+iet+GC  N++d   + ++++ +g+ lv+d+ +Ad++++nTC+vr ++e ++++++rel +l+ + +kk++v+GCm
  gi|320101289|ref|YP_004176881.1|  2 KVYIETYGCALNRSDEALMRESITGKGHVLVNDPGDADAIIINTCTVRLDTEYHMVKRIRELYKLSmEAGKKLIVAGCM 80
                                      89****************************************************************8899********* PP

                                      HHS-HHHHHHH-TT CS
                           UPF0004 79 aqrekeellkeepe 92
                                      a +++ ++ + +p 
  gi|320101289|ref|YP_004176881.1| 81 ARAQPYTVSRIAPG 94
                                      **999888777665 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     4e-09   1.8e-05       2      61 ..     368     427 ..     367     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4e-09
                                       XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT-.....-T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM   2 syvGstqeVlveglsksegegiGrtdngkvvfvpgd.....lpgIGdfVeVkItkvkrqyLrGel 61 
                                       +yvG+ ++  +++ +   g+++ r+ n+ +v+++g+         G++VeV +++++++ LrG+l
  gi|320101289|ref|YP_004176881.1| 368 RYVGTSVRCFITEHT---GTWVCRLTNYIPVVIRGGagstlDY--GKWVEVLVEEATFFDLRGRL 427
                                       678888888888877...******************9977555..******************86 PP

>> Rep_fac-A_3  Replication factor A protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.56   2.5e+03      57      97 ..     165     207 ..     162     213 .. 0.73
   2 ?    8.5   0.0   0.00057       2.5       7      78 ..     225     296 ..     223     311 .. 0.81
   3 ?    1.5   0.0     0.083   3.7e+02      41      66 ..     390     415 ..     359     424 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.56
                                       ---SEEEEEEEE-TTS-E.EEEEEEE---.---HHHHHHHHHH CS
                       Rep_fac-A_3  57 eiskwvEvvGkvsddlgi.rldsvvefge.dlDldlynklvql 97 
                                       +i+ +v  vGk+  d ++ + ++ +++g+  +Dl  +  l +l
  gi|320101289|ref|YP_004176881.1| 165 SIDAVVKAVGKAVRDGAVeVQLTGMDLGTyGMDLYRARRLPDL 207
                                       6788999999999999997777777777767776666655555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00057
                                       EE-GGGGGGGTTSEEEEEEEEEEETTSSEEEEE-TTS-EEEEEESS--SS---SEEEEEEEE-T...TS-EEEEE CS
                       Rep_fac-A_3   7 rvnpsmLsqfvgrtvrivgkvesvpsgktlilqstdggsvtvrlsedstleiskwvEvvGkvsd...dlgirlds 78 
                                       ++np++L+ + + +v +v+ +e+v +   + lqs+  ++  ++l++  +  +++++E v +v++   + +i++d 
  gi|320101289|ref|YP_004176881.1| 225 MINPEHLRHILEDLVKVVADAENVYKFLHIPLQSG--SNRVLKLMR-RNYTVEEYLEMVDRVKSsipEVSIATDI 296
                                       69**********************55566666666..888888888.59999**********9877766666654 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.083
                                       TTS-EEEEEESS--SS---SEEEEEE CS
                       Rep_fac-A_3  41 tdggsvtvrlsedstleiskwvEvvG 66 
                                       t+   v +r    stl+ +kwvEv  
  gi|320101289|ref|YP_004176881.1| 390 TNYIPVVIRGGAGSTLDYGKWVEVLV 415
                                       44445888999999*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3360.40
//
Query:       gi|320101290|ref|YP_004176882.1|  [L=141]
Description: translation initiation factor 2 subunit beta (aeIF-2b) [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  111.9   0.0    1.8e-32  111.6   0.0    1.0  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.014   15.4   0.3      0.021   14.8   0.3    1.3  1  Elf1             Transcription elongation factor Elf1 like
      0.022   14.8   0.4      0.034   14.2   0.4    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.027   13.9   0.4        2.6    7.6   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.041   13.9   0.3      0.069   13.1   0.3    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.049   13.6   1.5      0.087   12.8   1.5    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.065   13.4   1.1        0.2   11.8   1.1    1.9  1  Zn-ribbon_8      Zinc ribbon domain
      0.087   13.0   1.7        7.7    6.7   0.1    2.2  2  DUF678           Protein of unknown function (DUF678)
       0.19   11.5   1.9         10    6.0   0.1    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.21   12.0   0.7        8.3    6.9   0.0    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.29   11.1   3.9          6    6.8   0.1    2.3  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.63   10.0   2.3         12    5.8   1.7    2.2  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        1.7    8.7   5.2         12    5.9   0.6    2.3  2  zinc_ribbon_4    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.0   1.3e-35   1.8e-32       9     116 ..      28     134 ..      22     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 1.3e-35
                                       S--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHH CS
                      eIF-5_eIF-2B   9 erykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyie 85 
                                       e ++mp+++v v g  kt+i+Nf++ia+ Lnrd+e + +y++kel++ +si+e g+l l+gkf+ + +++ll +++e
  gi|320101290|ref|YP_004176882.1|  28 EVFEMPQASVLVIGG-KTIIQNFRQIANILNRDEELLKRYFMKELNVPSSINEAGQLELKGKFNPSAVNQLLVRFVE 103
                                       6799**********9.************************************************************* PP

                                       HHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  86 eyVlCkeCkspetelekeerllvlkCkaCga 116
                                       +yV C++C+s +t+l+k+++++vl+C+aCga
  gi|320101290|ref|YP_004176882.1| 104 RYVKCSTCGSVHTRLTKKGKVFVLRCDACGA 134
                                       ******************************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 ?   14.8   0.3   1.5e-05     0.021      18      57 ..     102     138 ..      86     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                              Elf1  18 lptkFdCpfCnheksvevkldkkekiaevsCkvCgesfet 57 
                                       ++++ +C  C+   sv+ +l+kk k+ +++C  Cg+++++
  gi|320101290|ref|YP_004176882.1| 102 VERYVKCSTCG---SVHTRLTKKGKVFVLRCDACGAETTL 138
                                       55666777776...66*******************98875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   2.4e-05     0.034      58      96 ..      93     136 ..      51     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                       TT-EEEEEEE--EEEETTTS-EEE.CHHH....HHS-TTTSSS- CS
                              HypA  58 egaeLeieevpvkvrCreCgkefe.leek....alrCpkCgsad 96 
                                       +  +L ++ v+  v+C++Cg+  + l++k     lrC +Cg++ 
  gi|320101290|ref|YP_004176882.1|  93 AVNQLLVRFVERYVKCSTCGSVHTrLTKKgkvfVLRCDACGAET 136
                                       456788999***********877755543324455******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 ?    7.6   0.1    0.0019       2.6       2      11 ..     105     115 ..     104     118 .. 0.80
   2 ?    4.4   0.0     0.019        27       4      10 ..     128     134 ..     126     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                       zf-ribbon_3   2 tvrCPnCGa.p 11 
                                       +v+C+ CG+ +
  gi|320101290|ref|YP_004176882.1| 105 YVKCSTCGSvH 115
                                       589*****944 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                       zf-ribbon_3   4 rCPnCGa 10 
                                       rC +CGa
  gi|320101290|ref|YP_004176882.1| 128 RCDACGA 134
                                       7999997 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 ?   13.1   0.3     5e-05     0.069      14      45 ..     100     134 ..      97     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                     Zn_Tnp_IS1595  14 rWpng.fvCPhCgsrkayrikt..rglfqCkeCrk 45 
                                       r+ ++ + C  Cgs + + +k+   ++++C +C++
  gi|320101290|ref|YP_004176882.1| 100 RFVERyVKCSTCGSVHTRLTKKgkVFVLRCDACGA 134
                                       67777455*****87666665588*********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 ?   12.8   1.5   6.3e-05     0.087      30      55 ..     107     135 ..     102     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                    OrfB_Zn_ribbon  30 tCseCgsknke...alsgrtfkCpnCgfe 55 
                                       +Cs Cgs++++   + +  +++C++Cg+e
  gi|320101290|ref|YP_004176882.1| 107 KCSTCGSVHTRltkKGKVFVLRCDACGAE 135
                                       8**********95444555568*****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 ?   11.8   1.1   0.00015       0.2       7      36 ..     107     136 ..     104     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgsev 36 
                                       +C  Cg+++++l +  +     C +Cg+e+
  gi|320101290|ref|YP_004176882.1| 107 KCSTCGSVHTRLTKKGKVFVLRCDACGAET 136
                                       7***********9877554555*****964 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0056       7.7      54      71 ..     101     118 ..      88     121 .. 0.76
   2 ?    6.1   0.2     0.009        12      55      67 ..     123     135 ..     116     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0056
                            DUF678  54 gkgntlrCaACgSsLtlL 71 
                                       + +  ++C+ CgS+ t L
  gi|320101290|ref|YP_004176882.1| 101 FVERYVKCSTCGSVHTRL 118
                                       5667789*****998877 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.009
                            DUF678  55 kgntlrCaACgSs 67 
                                       k  +lrC ACg +
  gi|320101290|ref|YP_004176882.1| 123 KVFVLRCDACGAE 135
                                       55689******87 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.015        20       3      12 ..     108     117 ..     107     119 .. 0.83
   2 ?    6.0   0.1    0.0073        10       2      10 ..     128     136 ..     128     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.015
                      Rubredoxin_2   3 CsqCGfesak 12 
                                       Cs CG+++ +
  gi|320101290|ref|YP_004176882.1| 108 CSTCGSVHTR 117
                                       9****99876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0073
                      Rubredoxin_2   2 vCsqCGfes 10 
                                       +C++CG+e+
  gi|320101290|ref|YP_004176882.1| 128 RCDACGAET 136
                                       799999987 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 ?    6.9   0.0     0.006       8.3      27      40 ..      96     117 ..      59     125 .. 0.72
   2 ?    3.5   0.1     0.067        92       4      15 ..     127     138 ..     124     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.006
                   Lar_restr_allev  27 q........cvyCadCgastpw 40 
                                       q        +v C  Cg +++ 
  gi|320101290|ref|YP_004176882.1|  96 QllvrfverYVKCSTCGSVHTR 117
                                       155555556********95444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.067
                   Lar_restr_allev   4 kpCPfCggravl 15 
                                       + C+ Cg + +l
  gi|320101290|ref|YP_004176882.1| 127 LRCDACGAETTL 138
                                       568888888776 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.6     0.017        24      13      21 ..     107     115 ..     104     115 .. 0.84
   2 ?    6.8   0.1    0.0044         6       6      19 ..     121     134 ..     119     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                           DUF35_N  13 rCpdCGtvq 21 
                                       +C+ CG+v+
  gi|320101290|ref|YP_004176882.1| 107 KCSTCGSVH 115
                                       8*****996 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0044
                           DUF35_N   6 egrLvgqrCpdCGt 19 
                                        g++ + rC++CG+
  gi|320101290|ref|YP_004176882.1| 121 KGKVFVLRCDACGA 134
                                       5888999******7 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 ?    4.9   0.4     0.017        23      21      30 ..     105     114 ..      99     115 .. 0.79
   2 ?    5.8   1.7     0.009        12       4      30 ..     108     135 ..     108     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                                       EEEESSSS-E CS
                    RNA_POL_M_15KD  21 nfeCrqCgYe 30 
                                       ++ C++Cg++
  gi|320101290|ref|YP_004176882.1| 105 YVKCSTCGSV 114
                                       488****986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.009
                                       ESTTTSBEEEEECSCCCE.EEESSSS-E CS
                    RNA_POL_M_15KD   4 CpkCgNlLlpkedkegkn.feCrqCgYe 30 
                                       C++Cg+     ++k ++  + C+ Cg+e
  gi|320101290|ref|YP_004176882.1| 108 CSTCGSVHTRLTKKGKVFvLRCDACGAE 135
                                       888888766666666655899****998 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.6    0.0089        12      25      34 ..     105     114 ..      94     116 .. 0.86
   2 ?    4.8   0.4      0.02        28      24      33 ..     125     134 ..     116     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0089
                     zinc_ribbon_4  25 kvrCskCghv 34 
                                        v+Cs Cg v
  gi|320101290|ref|YP_004176882.1| 105 YVKCSTCGSV 114
                                       59*****976 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                     zinc_ribbon_4  24 vkvrCskCgh 33 
                                         +rC +Cg+
  gi|320101290|ref|YP_004176882.1| 125 FVLRCDACGA 134
                                       4799999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1107.76
//
Query:       gi|320101291|ref|YP_004176883.1|  [L=100]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-21   75.7   0.0      3e-21   75.5   0.0    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   1.7e-25     3e-21       2      91 ..       9      99 ..       8     100 .] 0.94

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.7e-25
                                      EETTE.EEEEEEEGGGTT-EEEETT..EEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG- CS
                            DUF424  2 rtddllklvavcdkellgktfkege..lllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsV 78
                                      +++++  ++a+cd+++lg +++++e  ++ +v++ fy+gel++ eea+++L +at  Nivge +v+la+++Glv+p++V
  gi|320101291|ref|YP_004176883.1|  9 SVGNE-LIIAACDENILGLRLVDEErkANFYVDPFFYKGELVDPEEAVNTLSSATMGNIVGEVIVKLAIERGLVHPEAV 86
                                      56777.99**************999778999************************************************ PP

                                      EEETTEEEEEEEE CS
                            DUF424 79 lvidgvphaqigk 91
                                      l+i+gvp a  ++
  gi|320101291|ref|YP_004176883.1| 87 LWIKGVPIAMFVR 99
                                      *******999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 829.54
//
Query:       gi|320101292|ref|YP_004176884.1|  [L=355]
Description: NMD3 family protein [Desulfurococcus mucosus DSM 2162]
Scores for 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   0.1    2.5e-42  145.1   0.1    1.1  1  NMD3           NMD3 family
  ------ inclusion threshold ------
      0.029   14.4   3.3       0.47   10.5   1.9    2.6  2  DZR            Double zinc ribbon
      0.037   13.7   6.6      0.045   13.4   0.1    2.7  3  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
      0.064   13.1   3.2        5.2    6.9   0.1    2.5  2  CxC4           CxC4 like cysteine cluster associated with KDZ
       0.29   10.9   4.7        9.6    6.1   0.0    2.8  3  zinc_ribbon_2  zinc-ribbon domain
       0.62   10.0   0.1       0.62   10.0   0.1    2.6  3  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
        1.9    8.0   6.0        3.5    7.2   0.1    2.9  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 !  145.1   0.1   9.6e-46   2.5e-42       1     243 []       7     240 ..       7     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 9.6e-46
                              NMD3   1 CcrCGkei..eelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkv 75 
                                       C+rCG+e+  eelinglC dC+lk++ +++ +++++v vC++Cg+++ kg W +  l+ +e +++ l +++ + L  
  gi|320101292|ref|YP_004176884.1|   7 CVRCGRETkpEELINGLCIDCYLKHHGVFKEKPRVKVVVCPKCGSWYFKGVWHQP-LDLREVIRRELLSELYRFLY- 81 
                                       ********8877999********************************999**554.78888888877777788887. PP

                              NMD3  76 seeveevkvel.vdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQv 151
                                        +e++  +v++  d ++i       +  v+  ++ ev g  +++ + +  v v++++++C++C+r+++g+++a+vQv
  gi|320101292|ref|YP_004176884.1|  82 -SEIRVLEVDVaSDIRKIS----AGEHGVEAVFTLEVAG--KHVARIRGLVAVETEYKVCDKCMRRTTGSHKALVQV 151
                                       .344444444103444344....4445567777777755..456788999999************************ PP

                              NMD3 152 RqkrelteeehkrtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedk 228
                                       R +     ee  ++ + +  l+ +   +++i++++e+++G+D++f +  aAr+ v+ l +++g++++es k v+ d 
  gi|320101292|ref|YP_004176884.1| 152 RFD---PPEETGELYREVSALLHSMGLENSIVEVEERRDGMDVKFDDVIAARRYVDVLARKYGARTSESFKSVKYDF 225
                                       ***...44555555555555556666889************************************************ PP

                              NMD3 229 ksgkevyrltysvrl 243
                                       + gk++  +t+svr+
  gi|320101292|ref|YP_004176884.1| 226 QAGKWSGVVTISVRI 240
                                       **************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.9   0.00018      0.47      11      35 ..       3      50 ..       1      53 [. 0.74
   2 ?    1.9   0.0     0.091   2.3e+02      10      20 ..     129     139 ..     118     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                               DZR 11 darfCseCgtklkavaa.......................edrCpsCg 35
                                      + rfC +Cg + k+++                          +Cp+Cg
  gi|320101292|ref|YP_004176884.1|  3 STRFCVRCGRETKPEELinglcidcylkhhgvfkekprvkVVVCPKCG 50
                                      568999999998855548777777777777777788888888888887 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.091
                               DZR  10 pdarfCseCgt 20 
                                        + ++C++C  
  gi|320101292|ref|YP_004176884.1| 129 TEYKVCDKCMR 139
                                       45556666654 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.8e-05     0.045       1      17 [.       2      18 ..       2      19 .. 0.91
   2 ?    3.7   0.1     0.019        48      23      29 ..      45      51 ..      43      54 .. 0.64
   3 ?   -3.1   0.5       2.6   6.6e+03      22      27 ..     132     137 ..     132     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                     zf-NADH-PPase  1 rthrFCgrCGaptepae 17
                                      +++rFC rCG +t+p+e
  gi|320101292|ref|YP_004176884.1|  2 DSTRFCVRCGRETKPEE 18
                                      589***********975 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                     zf-NADH-PPase 23 vCpaCgl 29
                                      vCp Cg 
  gi|320101292|ref|YP_004176884.1| 45 VCPKCGS 51
                                      5666664 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.6
                     zf-NADH-PPase  22 rvCpaC 27 
                                       +vC+ C
  gi|320101292|ref|YP_004176884.1| 132 KVCDKC 137
                                       69**99 PP

>> CxC4  CxC4 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.7     0.004        10      14      56 ..       4      50 ..       1      67 [. 0.70
   2 ?    6.9   0.1     0.002       5.2      35      64 ..     117     144 ..     107     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.004
                              CxC4 14 earC.rCgtsldpsrptlek..ectvytl.tgalevrielqrCpaCa 56
                                      +  C rCg++++p++ +     +c + ++     + r++++ Cp+C 
  gi|320101292|ref|YP_004176884.1|  4 TRFCvRCGRETKPEELINGLciDCYLKHHgVFKEKPRVKVVVCPKCG 50
                                      5679999999955555443355999977745667789*********3 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.002
                              CxC4  35 tvytltgalevrielqrCpaCahtrrfiGp 64 
                                       +v  ++g ++v++e++ C +C   rr +G 
  gi|320101292|ref|YP_004176884.1| 117 HVARIRGLVAVETEYKVCDKCM--RRTTGS 144
                                       677888999************4..777776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0037       9.6       1       8 [.       6      13 ..       2      20 .. 0.68
   2 ?    5.9   0.2    0.0041        11      15      20 ..      45      50 ..      42      51 .. 0.62
   3 ?   -2.4   0.1       1.8   4.6e+03      14      19 ..     132     137 ..     127     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0037
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      fC +CG+e
  gi|320101292|ref|YP_004176884.1|  6 FCVRCGRE 13
                                      56666666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0041
                     zinc_ribbon_2 15 FCpyCG 20
                                       Cp+CG
  gi|320101292|ref|YP_004176884.1| 45 VCPKCG 50
                                      466666 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                     zinc_ribbon_2  14 kFCpyC 19 
                                       k C +C
  gi|320101292|ref|YP_004176884.1| 132 KVCDKC 137
                                       668888 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 ?   -0.2   0.2      0.38   9.9e+02      26      33 ..       5      12 ..       4      15 .. 0.74
   2 ?   10.0   0.1   0.00024      0.62       8      22 ..      40      54 ..      37      54 .. 0.85
   3 ?   -2.1   0.2       1.5   3.9e+03      13      19 ..     133     139 ..     130     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.38
                           DUF35_N 26 avCphCgs 33
                                      ++C +Cg+
  gi|320101292|ref|YP_004176884.1|  5 RFCVRCGR 12
                                      68999986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00024
                           DUF35_N  8 rLvgqrCpdCGtvqf 22
                                      r+ +  Cp+CG+++f
  gi|320101292|ref|YP_004176884.1| 40 RVKVVVCPKCGSWYF 54
                                      777789*******99 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.5
                           DUF35_N  13 rCpdCGt 19 
                                        C++C +
  gi|320101292|ref|YP_004176884.1| 133 VCDKCMR 139
                                       7999977 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.03        77       1       9 [.       3      11 ..       3      18 .. 0.85
   2 ?    7.2   0.1    0.0014       3.5      17      23 ..      44      50 ..      37      51 .. 0.67
   3 ?   -1.4   0.2      0.68   1.7e+03      17      22 ..     132     137 ..     127     137 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                       zf-ribbon_3  1 stvrCPnCG 9 
                                      st++C +CG
  gi|320101292|ref|YP_004176884.1|  3 STRFCVRCG 11
                                      6899****9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
                       zf-ribbon_3 17 nvCpyCG 23
                                      +vCp+CG
  gi|320101292|ref|YP_004176884.1| 44 VVCPKCG 50
                                      5666666 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.68
                       zf-ribbon_3  17 nvCpyC 22 
                                       +vC +C
  gi|320101292|ref|YP_004176884.1| 132 KVCDKC 137
                                       456666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2592.78
//
Query:       gi|320101293|ref|YP_004176885.1|  [L=116]
Description: translation initiation factor 1A (aeIF-1A) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-17   62.0   0.2    4.4e-17   61.7   0.2    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.2   2.4e-21   4.4e-17       2      64 .]      28      89 ..      27      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.4e-21
                                      EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      ++i+ Vi+ lg++    ++ d g+ +  +ipgk+R+++wi +Gd++lV l++++ +kG++vy+
  gi|320101293|ref|YP_004176885.1| 28 TIICGVIRHLGGDFLVAKCLD-GVDRKIRIPGKLRRRVWISEGDIILVGLWDFSSDKGEVVYK 89
                                      6799***************96.***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 913.86
//
Query:       gi|320101294|ref|YP_004176886.1|  [L=271]
Description: Non-specific serine/threonine protein kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-60  203.9   0.0    2.1e-60  203.5   0.0    1.1  1  RIO1            RIO1 family
    9.8e-09   35.5   0.2    2.6e-05   24.3   0.0    2.8  2  APH             Phosphotransferase enzyme family
    0.00029   20.3   0.0     0.0044   16.4   0.0    2.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0028   16.5   0.0     0.0042   15.9   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.018   14.4   0.0      0.039   13.3   0.0    1.5  2  Pkinase         Protein kinase domain
       0.13   12.5   0.0       0.22   11.7   0.0    1.3  1  DUF3993         Protein of unknown function (DUF3993)


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 !  203.5   0.0   7.1e-64   2.1e-60       2     180 ..      62     244 ..      61     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 203.5 bits;  conditional E-value: 7.1e-64
                                       EEEEEETTTEEEEEEEE-S---SS-H.HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkk.rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       Vy a   +g+ +a+Kiy ts +eF+k + ky+ g++rf++ +   ++r+l+ +w++kE+rnLkr+++agv+vP+p++
  gi|320101294|ref|YP_004176886.1|  62 VYLASGYRGEYLAVKIYLTSSAEFRKgIYKYIAGDPRFENIR-VRDTRDLIYAWTRKEYRNLKRMHAAGVKVPRPVA 137
                                       9*************************9************995.899******************************* PP

                                       EETTEEEEE--EETTEEGGBHHHCG.-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GT CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdve.e..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvs 150
                                       ++++vlvmef+ge+gv++p l ++  e   ee+++ly+ +lee+ k+y +a+lvH+DLSeyNv+v+ + +v iIDvs
  gi|320101294|ref|YP_004176886.1| 138 FMNNVLVMEFLGENGVRYPLLVEAYrEldAEELRNLYRLILEEVVKIYCKARLVHGDLSEYNVMVTPGpDVAIIDVS 214
                                       *********************9998667899********************************************** PP

                                       TEEETTSTTHHHHHHHHHHHHHHHHHTTC- CS
                              RIO1 151 QaveldhpnalefLerDveniikfFrrkgv 180
                                       Qav+l+hpna efL rD++ni++fFr ++ 
  gi|320101294|ref|YP_004176886.1| 215 QAVDLSHPNADEFLARDLRNINRFFREEAG 244
                                       *************************98754 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0012       3.6      33      60 ..     111     138 ..      52     149 .. 0.59
   2 !   24.3   0.0   8.6e-09   2.6e-05     141     193 ..     162     213 ..     149     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                                       -HHHHHHHHHHHHHHHHTT-B--B-CTT CS
                               APH  33 aaeeirrevallrlLakagvpvPevlag 60 
                                        ++ +r+e++ l+ +++agv+vP+++a+
  gi|320101294|ref|YP_004176886.1| 111 IYAWTRKEYRNLKRMHAAGVKVPRPVAF 138
                                       34456778889***************96 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 8.6e-09
                                       TCC.HHHHHHHHHHHHHHHH--S.SS-EEEE-SS-SGGGEEEC..TTEEEEE--- CS
                               APH 141 lld.lleeleeqvlaalaallpg.elptvllHgDlhpgNllvdpddgrvtGviDf 193
                                       +++ ++eel+  +++ +++++ +   +++l+HgDl+  N++v+  +g+ +++iD 
  gi|320101294|ref|YP_004176886.1| 162 YRElDAEELRN-LYRLILEEVVKiYCKARLVHGDLSEYNVMVT--PGPDVAIIDV 213
                                       33455677777.888888888889*******************..666668***6 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-06    0.0044      58      83 ..     115     140 ..     103     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                               Kdo  58 avrEfrllkrLeeagvavpkpvaaga 83 
                                        ++E+r+lkr+++agv+vp+pva+  
  gi|320101294|ref|YP_004176886.1| 115 TRKEYRNLKRMHAAGVKVPRPVAFMN 140
                                       679********************965 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.4e-06    0.0042     322     368 ..     184     225 ..     173     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-06
                    Pkinase_fungal 322 LflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddsse 368
                                        + ka+++H D Se+N+++t     +++   +iD+  a++ls+++++
  gi|320101294|ref|YP_004176886.1| 184 IYCKARLVHGDLSEYNVMVT-----PGPDVAIIDVSQAVDLSHPNAD 225
                                       57799***************.....9***************998765 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.98   2.9e+03       7      37 ..      54      83 ..      50      92 .. 0.80
   2 ?   13.3   0.0   1.3e-05     0.039      73     151 ..     141     222 ..     102     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.98
                                      EEEESSEEEEEEEETTTTEEEEEEEEECHCH CS
                           Pkinase  7 lGeGsfGkVykaveketgkivAvKkikkeka 37
                                      +  G+ ++Vy a    +g+  AvK+  +++a
  gi|320101294|ref|YP_004176886.1| 54 ISAGKEARVYLAS-GYRGEYLAVKIYLTSSA 83
                                      5579999999998.68999999999877665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.3e-05
                                       EEEEEE--TTEB..HHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEEEE-SGTTSE CS
                           Pkinase  73 lylvleyvegge..ladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgelKitDFGlak 146
                                        +lv+e++ ++   +  l+e+ + l+ ee++++ + ile +  ++ +++++H Dl   N+++    ++ i+D   a 
  gi|320101294|ref|YP_004176886.1| 141 NVLVMEFLGENGvrYPLLVEAYRELDAEELRNLYRLILEEVVKIYcKARLVHGDLSEYNVMVTPGPDVAIIDVSQAV 217
                                       568999886555333333345567*********************6677**************9999****988777 PP

                                       ESSSS CS
                           Pkinase 147 eless 151
                                        l++ 
  gi|320101294|ref|YP_004176886.1| 218 DLSHP 222
                                       77665 PP

>> DUF3993  Protein of unknown function (DUF3993)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.3e-05      0.22      20      91 ..      12      84 ..       5      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.3e-05
                           DUF3993 20 geeaevdRkevletlqsayeaqfslsekersleemievLePYftd.afasvfveenaseekagniiyGtdage 91
                                      ++e+    k+++et+++++++ + ++  e++  ++i  L+  +     a v++    + e  +  iy t  +e
  gi|320101294|ref|YP_004176886.1| 12 RNEPRRKDKDLFETVEEVFDTATVMTIVELTRRKVIRKLSGVISAgKEARVYLASGYRGEYLAVKIYLTSSAE 84
                                      5677777899****************************99887642567777777777777777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 1948.48
//
Query:       gi|320101295|ref|YP_004176887.1|  [L=205]
Description: KH domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-09   37.3   0.2     0.0011   18.8   0.0    2.4  2  KH_1      KH domain
     0.0094   15.8   0.9       0.27   11.1   0.1    2.4  2  KH_2      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 !   18.8   0.0   1.2e-07    0.0011       6      40 ..      20      53 ..      16      68 .. 0.86
   2 !   16.3   0.1   7.3e-07    0.0066      10      64 ..     118     164 ..     112     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-07
                                      EGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT CS
                              KH_1  6 vPsslvgriIGkgGsnIkeIreetgakIkvpksed 40
                                      +P + vg +IG +G++ keI+e+t +  +++ se 
  gi|320101295|ref|YP_004176887.1| 20 LPLERVGVLIGDNGRVKKEIEERTRTTLTID-SET 53
                                      68889************************87.554 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.3e-07
                                       HHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                              KH_1  10 lvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                         gr+IG  G+  + ++e tg++I +   e+       + i+G+ e+ + A+ ++
  gi|320101295|ref|YP_004176887.1| 118 VLGRVIGEEGRARRVLEEATGTYISIY--EP------YIAIIGDYESANIARTAV 164
                                       469**********************64..33......59999*999999998766 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1     3e-05      0.27      35      58 ..      24      47 ..      22      59 .. 0.88
   2 ?    2.8   0.1     0.012   1.1e+02      37      58 ..     120     141 ..     116     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3e-05
                                      CHHHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2 35 qpgivIGkgGsnikkigkelrkdi 58
                                      + g++IG +G+  k+i++  r  +
  gi|320101295|ref|YP_004176887.1| 24 RVGVLIGDNGRVKKEIEERTRTTL 47
                                      89****************999877 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.012
                                       HHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2  37 givIGkgGsnikkigkelrkdi 58 
                                       g+vIG +G+  + ++++ +  i
  gi|320101295|ref|YP_004176887.1| 120 GRVIGEEGRARRVLEEATGTYI 141
                                       99******99999988887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1624.62
//
Query:       gi|320101296|ref|YP_004176888.1|  [L=139]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for 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   76.6  16.1    2.4e-21   76.4  16.1    1.0  1  EamA          EamA-like transporter family
  ------ inclusion threshold ------
       0.02   14.3   5.5      0.043   13.2   5.2    1.4  1  TPT           Triose-phosphate Transporter family
      0.052   12.1   0.7      0.073   11.7   0.7    1.2  1  AMP-binding   AMP-binding enzyme
      0.078   11.9   7.2        0.1   11.5   7.2    1.3  1  CRT-like      CRT-like, chloroquine-resistance transporter-li
       0.19   11.8   4.6       0.43   10.6   4.6    1.7  1  TMEM234       Putative transmembrane family 234
          2    7.6  11.4        2.7    7.2  11.4    1.2  1  Peptidase_U4  Sporulation factor SpoIIGA
        6.3    7.0  10.0          1    9.6   0.5    2.4  2  Pox_A14       Poxvirus virion envelope protein A14


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 !   76.4  16.1   9.3e-25   2.4e-21       3     136 ..       4     138 ..       3     139 .] 0.92

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 9.3e-25
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtvl 77 
                                       ++++all al  a++++l+k++l++v+++t+t++r+++  ++ + i+l+++g    + +++ ++l+++l g +++ l
  gi|320101296|ref|YP_004176888.1|   4 WVVYALLDALAAALATILAKMGLQRVDSVTATALRSIVMMFFAVGIMLYFRGVEhvKGITQVEYLFIVLSG-VAGGL 79 
                                       6789*********************************8777777666666666669**********88888.6999* PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        ++++f+al+k++as +++i + + +f+++lsvl+l+e lt+k+ ++++li ++++l++
  gi|320101296|ref|YP_004176888.1|  80 SWIFYFIALQKGDASSVAMIDRSSILFIILLSVLILHEELTWKKAVSAILIAAALYLLV 138
                                       ********************************************************986 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.2   1.7e-05     0.043      19     129 ..      20     131 ..      13     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                               TPT  19 ilnKkilnvfpyPltvsavqllvgsvlilvlwal.glkkrpkisseflkailplalvktlghvlavvslskvaVSft 94 
                                       il K+ l+ +   + +++ ++++    + +++ + g+++ + i++  +  i+  +++  l+ ++  ++l+k   S  
  gi|320101296|ref|YP_004176888.1|  20 ILAKMGLQRVDSVTATALRSIVMMFFAVGIMLYFrGVEHVKGITQVEYLFIVLSGVAGGLSWIFYFIALQKGDASSV 96 
                                       5566666666544444444444444444455554499999999999999999999*999*************99999 PP

                               TPT  95 htvKasePiFtvilsrlllgeklsllvylsLlpiv 129
                                        ++  s  +F ++ls l+l e+l+ ++ +s + i 
  gi|320101296|ref|YP_004176888.1|  97 AMIDRSSILFIILLSVLILHEELTWKKAVSAILIA 131
                                       99999999*************99999999988886 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   2.8e-05     0.073      21      68 ..       3      50 ..       1      53 [. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                                      EEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHH CS
                       AMP-binding 21 qtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallail 68
                                      q++ Y+ ld+ + +lA  L ++G+++ d V   + +s+ +++ +++i+
  gi|320101296|ref|YP_004176888.1|  3 QWVVYALLDALAAALATILAKMGLQRVDSVTATALRSIVMMFFAVGIM 50
                                      8999****************************************9997 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 ?   11.5   7.2     4e-05       0.1      40     136 ..      39     135 ..       4     139 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                          CRT-like  40 vyvpiffavvlykllltndipketrsfpkrkFaimgaL.DavsgilvvigavstsGslqvllnqaiipitllaslll 115
                                         v +ffav + +l++         +  ++ F++++ +  ++s i+ +i+  +   s   ++  ++i +++l+s+l+
  gi|320101296|ref|YP_004176888.1|  39 SIVMMFFAVGI-MLYFRGVEHVKGITQVEYLFIVLSGVaGGLSWIFYFIALQKGDASSVAMIDRSSILFIILLSVLI 114
                                       45778888666.777766655555666788899986551789*********************************** PP

                          CRT-like 116 lkerysliqylGAlviilgvv 136
                                       l+e   + + + A++i++++ 
  gi|320101296|ref|YP_004176888.1| 115 LHEELTWKKAVSAILIAAALY 135
                                       **************9998876 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.6   0.00017      0.43      42     115 ..      62     137 ..       8     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                           TMEM234  42 llrlkyliplllNqsgS...vlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       +++++yl+ +l  + g    +++f++l+k d s + +i  s +++f +l + l+  + l++k+ +  +l+ ++++l+
  gi|320101296|ref|YP_004176888.1|  62 ITQVEYLFIVLSGVAGGlswIFYFIALQKGDASSVAMIDRS-SILFIILLSVLILHEELTWKKAVSAILIAAALYLL 137
                                       5566666666666665422379**********998888777.55666666666666667778888889999998886 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  11.4     0.001       2.7      37     129 ..      13     114 ..       4     138 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                      Peptidase_U4  37 laAllGalyvvlvlflpklesillsillkilvsllmvlia...fgpkslkeflkalllfylvsfllgGilfalsyll 110
                                       laA+l+++++ +   l++  s+ ++ l  i++ ++ v i+    g + +k + ++  lf+++s ++gG+  ++++  
  gi|320101296|ref|YP_004176888.1|  13 LAAALATILAKM--GLQRVDSVTATALRSIVMMFFAVGIMlyfRGVEHVKGITQVEYLFIVLSGVAGGLSWIFYFIA 87 
                                       344444444333..223444455555555555555554442215677788999999999999999999999888855 PP

                      Peptidase_U4 111 lkskn.............llvlllgalvayll 129
                                       l+  +             +   l+++l+ +l+
  gi|320101296|ref|YP_004176888.1|  88 LQ--KgdassvamidrssI---LFIILLSVLI 114
                                       54..335777777775442...2222222222 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 ?    9.6   0.5   0.00039         1      23      58 ..      16      51 ..       4      56 .. 0.88
   2 ?    2.5   1.8     0.061   1.6e+02      14      59 ..      70     114 ..      60     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00039
                           Pox_A14 23 ilacifafvdfskststtdkawralsivsFilgivi 58
                                      +la i+a + + ++ s t +a+r++ ++ F +gi++
  gi|320101296|ref|YP_004176888.1| 16 ALATILAKMGLQRVDSVTATALRSIVMMFFAVGIML 51
                                      5799*****************************987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.061
                           Pox_A14  14 vliaGiiLLilacifafvdfskststtdkawralsivsFilgivil 59 
                                       +++ G++   l+ if f+ + k   ++  +    si+  il  v++
  gi|320101296|ref|YP_004176888.1|  70 IVLSGVAG-GLSWIFYFIALQKGDASSVAMIDRSSILFIILLSVLI 114
                                       55555543.4789*********999665444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 978.50
//
Query:       gi|320101297|ref|YP_004176889.1|  [L=483]
Description: cation transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-45  156.0  22.5    1.6e-25   89.6   8.8    2.1  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 !   71.5   6.6   2.7e-24   4.8e-20      33     248 ..      69     267 ..      62     293 .. 0.84
   2 !   89.6   8.8   8.8e-30   1.6e-25     313     490 ..     295     469 ..     285     478 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 2.7e-24
                              TrkH  33 kddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvv 109
                                        +++ +  ++++++ v ++++l   +  ++f+da fe+vsg+t tgl+v   +++l +s+ ++ra +q++G+lg+vv
  gi|320101297|ref|YP_004176889.1|  69 TEAYFVSTVSWLIIPVLAAIPLH-MEIGVPFIDAFFESVSGFTGTGLTVLSGLDHLKKSINWWRALMQWSGELGFVV 144
                                       56677777889999999999986.7889999********************************************** PP

                              TrkH 110 laylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsp 186
                                       +a +++p + r ++ ly  e          + +l+ +++ ++ +y++++++++vll         y ++v      +
  gi|320101297|ref|YP_004176889.1| 145 FAMVMIPFFWRFGYTLYGVER-----PVRVMYTLRRTARRITEVYILVTLMGVVLL---------YYSGV------S 201
                                       ***************998765.....455788999999******************.........99999......* PP

                              TrkH 187 lwwaffhsmSafnnlGfsltp.nSlasfnknivillvaiifiilGnigF...pillrviiaikkki 248
                                       l++a+ h+m+a+ ++G+s ++ n  a ++ +++  +++i++++lG+++F   ++ll++ ++  ++ 
  gi|320101297|ref|YP_004176889.1| 202 LYDAVIHTMTAVATGGMSNYDaNYEAIYRYAPLSIFPTILVMVLGGMNFlnlSLLLDFRAREAFRS 267
                                       *********************888899**********************44445555544444444 PP

  == domain 2  score: 89.6 bits;  conditional E-value: 8.8e-30
                              TrkH 313 gsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvye.efslgkyeieqekepk 387
                                       +s+++ ++F  vs+ t+ GF++   +  +  +k +lvl+m+igg++ Stagg++  ++ + +++lg y +++   ++
  gi|320101297|ref|YP_004176889.1| 295 ASSIVLGVFNTVSAMTTtGFNIGVVGGFPVGVKEILVLAMFIGGMSFSTAGGVKVYRLVVlLRKLGTYGASTLLRER 371
                                       6788999******99999***************************************87725789999999999999 PP

                              TrkH 388 avskksidgkhlerqllvdlws.lflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaq 463
                                          k+s+dgk l+++ +  +   +++  +i+l++    l +v+ p  +f+d+Lfe++Sa   vGLS+G    ++sa 
  gi|320101297|ref|YP_004176889.1| 372 VSLKVSMDGKNLDEDEVSGVLLvVVIHAFIVLLAA--SLIKVAMPHVDFLDALFESTSAASCVGLSTG----ITSAS 442
                                       889*********98765555441555556655555..8999999************************....9999* PP

                              TrkH 464 lttisklvlialmirGrlrglpvlldr 490
                                        + + kl lia m +Gr + lp+++++
  gi|320101297|ref|YP_004176889.1| 443 SPLLVKLALIAGMYLGRIEYLPLIVAA 469
                                       ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3358.93
//
Query:       gi|320101298|ref|YP_004176890.1|  [L=908]
Description: alanyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-92  310.0   0.0    3.4e-91  306.4   0.0    2.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
    2.3e-12   46.8   0.1    5.1e-12   45.7   0.1    1.7  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    8.7e-05   21.9   0.0    0.00015   21.2   0.0    1.3  1  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
    0.00015   22.2   0.5    0.00033   21.1   0.5    1.7  1  DHHA1         DHHA1 domain
     0.0072   16.1   0.1      0.012   15.3   0.1    1.3  1  Laminin_I     Laminin Domain I


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 !  306.4   0.0   9.5e-95   3.4e-91       1     551 [.      62     591 ..      62     592 .. 0.89

  Alignments for each domain:
  == domain 1  score: 306.4 bits;  conditional E-value: 9.5e-95
                                       HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVG 77 
                                       e+rekF+ f ++kgH vv  ++v+++++++l++++A++  f+p ++ +  +p+++++v++Q++iR++    D++nVG
  gi|320101298|ref|YP_004176890.1|  62 EVREKFIGFLRSKGHGVVDPYPVLARWRNDLYLTIASIIVFQPAVTEGIVDPPYNPLVIIQPSIRLS----DIDNVG 134
                                       89*****************************************************************....****** PP

                                       TS.SS--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGG CS
                      tRNA-synt_2c  78 kt.arHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeer 146
                                        t +rH+T FeM G ++f+     +Y+ e +   + e+++ke+g+d ++l++++ ++++  +a+++ e lv + e +
  gi|320101298|ref|YP_004176890.1| 135 LTfGRHLTSFEMGGMHAFNkpgrfIYWVEGILDNTIEFFNKEIGIDLDDLVFKEGWWEGggNAGPAPEVLVDGMELA 211
                                       *978******************************************************999**************** PP

                                       EEEE-HHHHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEE CS
                      tRNA-synt_2c 147 ilrfgekdnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksid 223
                                       +l+    + ++ +  ++ + p  +++ ++g e+ ++  +++++   +++  ++n  +   ++e +  +  L+k    
  gi|320101298|ref|YP_004176890.1| 212 TLVH---MMYKVVDGKYVENPVLVVDCGYGIERIAWFTQKTPTGFHAIYGRLINEYKDVLGVE-EPPYDVLKKAV-- 282
                                       ***9...9***********************************************99999999.56666666554.. PP

                                       EEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHH CS
                      tRNA-synt_2c 224 tGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYv 300
                                         m   r ++ ++e +   +++ f   i++  ++              l+ + DH+r+++ +l+dGvvpsn+g+gY+
  gi|320101298|ref|YP_004176890.1| 283 -YMLSDREIEGIREYERALREHGFGDHIDEFVKVIY------------LYSVLDHARTMSLMLSDGVVPSNTGEGYL 346
                                       .4999********99999999888776665555544............8999************************* PP

                                       HHHHHHHHHHHHHHTT-SSTHHHHHHH....HHHHHHTT..TGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHH CS
                      tRNA-synt_2c 301 lRrllRravrhakkLglkekflaklva....vvvevlgd..vypelkekeekveeiieeEeerFakTlerGlkllee 371
                                       +R+++Rr +r + +Lg++ + l+++v+     +++  ++  +y ++++++++++++   E+++F   ++rG +++++
  gi|320101298|ref|YP_004176890.1| 347 ARLVIRRLLRNLVRLGVEPARLTDVVQelldRQIKYWKNdyIYGKFEAHRDYIMDVAAVETAKFIDAVSRGIDIVDK 423
                                       ******************987666665111155666665336789******************************** PP

                                       HHHHCCCCSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSH CS
                      tRNA-synt_2c 372 likklkkkkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkel 448
                                       l+kk   +k l ++d++++yd++G+P++ ++e a+e+g++v i+g ++++ +qr++s     ++k   ++      +
  gi|320101298|ref|YP_004176890.1| 424 LLKK---RKSLGLDDLITIYDSHGIPPEFVAERAREHGVEVSIPGDFYSKIAQRHSSPGVLVKEK---EHEFPSDVV 494
                                       **97...789**********************************************954333333...222222233 PP

                                       CHHCCTSTTTXXXXXXTSXXXXX.XSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEET CS
                      tRNA-synt_2c 449 kkteeflgyeeleaeakvlallk.dkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkak 524
                                       + ++ f g  +      v ++    ++ +++v  +++ ++vLdrT++Y+  GGq+ D+G+ie  g + +v+ v k++
  gi|320101298|ref|YP_004176890.1| 495 EWASRFPGTVR------VFHMDPyLTSVEARVLGVRDRYLVLDRTVMYPWAGGQDHDTGFIEVAGRRYAVEYVGKVG 565
                                       33344444444......33333214677889999******************************************* PP

                                       TEEEEEXSS.XSXXXTTSEEEEEEXHH CS
                      tRNA-synt_2c 525 gvvlhkgkleegklkvgdkvkaevdee 551
                                       +v++h+ k    ++ +g+ v+ ++d+ 
  gi|320101298|ref|YP_004176890.1| 566 NVIIHVLKEP-VEIAEGTVVNVSIDWY 591
                                       ********97.9*************85 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.1   1.4e-15   5.1e-12       1      44 []     691     734 ..     691     734 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.4e-15
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +r+v+i  ++ ++C GtHv+nT+eIg +ki++ e+i++g+ R++
  gi|320101298|ref|YP_004176890.1| 691 LRIVEIPGWDAQACFGTHVHNTSEIGGVKIVNAERIQDGVVRLE 734
                                       69****66**********************************86 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.1e-08   0.00015      96     251 ..     176     329 ..     167     357 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.1e-08
                                       HCT--CCCS-EEEEEEEEEEGGGTEEEEEEEEEETTCEEEEEEEE..EEETTEE-.SS.--EEEEEEHHHHHHHHCT CS
                      tRNA-synt_2e  96 algidlkehdirfveDdWesptlGawGlGwevwldGmeitqftYf..qqvgglel.kp.vsveityGleRlamylqe 168
                                       ++gidl  +d+ f e  We    G  G   ev +dGme++ + ++  + v g  + +p + v+  yG+eR+a + q+
  gi|320101298|ref|YP_004176890.1| 176 EIGIDL--DDLVFKEGWWEG--GGNAGPAPEVLVDGMELATLVHMmyKVVDGKYVeNPvLVVDCGYGIERIAWFTQK 248
                                       566665..699999999986..6999*************987654215565544413415789************** PP

                                       -SSGGG-ECCT.TEEHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHCCT-HHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_2e 169 vdnvydlewne.kvtygdvflqneveqsaynfeeadvelllklfeeyekeakrllekklvlpaydlvlkashtfnll 244
                                       + + +   + +   +y+dv   +e     y++ +  v +l +   e  +e +r l+++      d  +k+ +++ +l
  gi|320101298|ref|YP_004176890.1| 249 TPTGFHAIYGRlINEYKDVLGVEE---PPYDVLKKAVYMLSDREIEGIREYERALREHGFGDHIDEFVKVIYLYSVL 322
                                       *****9999883568999987666...45666666666666666666666666666666666666666666666666 PP

                                       HHTT--- CS
                      tRNA-synt_2e 245 dargais 251
                                       d  +++s
  gi|320101298|ref|YP_004176890.1| 323 DHARTMS 329
                                       6555554 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.5   9.3e-08   0.00033       1     134 [.     770     901 ..     770     905 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.3e-08
                                       HHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEE CS
                             DHHA1   1 leslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvak 77 
                                       ++++  e++e+ k lee++  la+ + ++ ++  + ++gv v ++e+ +  d + l+++ ++l    k+ + +++ +
  gi|320101298|ref|YP_004176890.1| 770 VRKMSREHAEVSKLLEEYRARLADTLVSQGVAGKTSICGVDVTYVEL-PVRDEKLLRQVLEELSL--KQGILTVIDA 843
                                       578999***************************99999*********.*****************..8899998888 PP

                                       EECTEEEEEEEESSH...SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHH CS
                             DHHA1  78 eegdkvkvsarskkd...gvdagelakeaaaklgggGGGH.dlAaGagipaekleealeal 134
                                        e  +  + ++  k+   ++d+++ a +  ++ g +GGG+ d  a  +++a + e+++++l
  gi|320101298|ref|YP_004176890.1| 844 GE--TLEIAVKPEKAsekNIDLRKTAAR-LSAKGAKGGGKpDHVALRKTSALSREDVISEL 901
                                       65..89999999988999**********.9999*******766555444555556665555 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.4e-06     0.012      84     137 ..     738     790 ..     722     798 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.4e-06
                         Laminin_I  84 akeLaekikkladnikeilekvatlneneealpssklseelaeaqrlLeelrsR 137
                                       ++ L++ i+ l+ +i e+l+ + +  + + a +++k+s+e+ae+++lLee r+R
  gi|320101298|ref|YP_004176890.1| 738 STRLVDHIRSLEGEIDEALAVMGARQG-DLASAVRKMSREHAEVSKLLEEYRAR 790
                                       6789******************88877.99**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (908 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 5893.77
//
Query:       gi|320101299|ref|YP_004176891.1|  [L=106]
Description: 50S ribosomal protein L12 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   61.2  17.0    1.3e-16   61.0  17.0    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
     0.0079   16.2   7.0        0.5   10.4   0.1    2.2  2  PepSY_2        Peptidase propeptide and YPEB domain
  ------ inclusion threshold ------
      0.022   14.8   0.6      0.028   14.4   0.6    1.2  1  Ribonuc_L-PSP  Endoribonuclease L-PSP
      0.069   13.5   0.1       0.23   11.8   0.0    1.7  2  EF-hand_14     EF-hand domain
       0.19   11.5   0.4       0.24   11.2   0.4    1.1  1  Adenine_glyco  Methyladenine glycosylase


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 !   61.0  17.0   3.6e-20   1.3e-16       1      88 []      16     105 ..      16     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.6e-20
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX. CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaa.aaaaaaaaaaaaaeekkkeeeee 76 
                                       e+++en+kkvl+aagv v+++rvk lv+a+++ di+++l+++ a+  ++aaa+ +aa a a aa++++e+kkeee +
  gi|320101299|ref|YP_004176891.1|  16 EISEENVKKVLEAAGVAVDEVRVKSLVAAIKNIDIAKVLEQAIAA--PVAAAPvQAAPATAPAAEEKKEEKKEEESK 90 
                                       69****************************************988..444444133333344444444444444444 PP

                                       XX--S..S--.STTT CS
                     Ribosomal_60s  77 Eeedd..dmG.fgLF 88 
                                       E +++   +G  +LF
  gi|320101299|ref|YP_004176891.1|  91 ELSEEalSEGfSALF 105
                                       766665788956676 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00014       0.5      27      52 ..      14      39 ..      11      45 .. 0.90
   2 !    7.9   2.9   0.00086       3.1       3      43 ..      60     100 ..      56     104 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                           PepSY_2 27 adwlpreklvakleaqGykvkkievd 52
                                       +++++e++++ lea+G  v++++v+
  gi|320101299|ref|YP_004176891.1| 14 GKEISEENVKKVLEAAGVAVDEVRVK 39
                                      57899******************995 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00086
                           PepSY_2   3 alalalallaaaAlA.....grrdtdspkadwlpreklvakleaqG 43 
                                       a ++a+ + aa+A A           ++++++   ++l++ +  +G
  gi|320101299|ref|YP_004176891.1|  60 APVAAAPVQAAPATApaaeeK-----KEEKKEEESKELSEEALSEG 100
                                       445666677777777532222.....22222223444444444444 PP

>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.6   7.8e-06     0.028      48     101 ..      18      70 ..      10      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-06
                                       HHHHHHHHHHHTT--GGGEEEEEEEESSGGGHHHHHHHHHHHSSSST.S--EEEE CS
                     Ribonuc_L-PSP  48 alenlkavLaaagaslsdvVkvtvFladiedfaevnevyaeafdelk.eaParsa 101
                                       + en+k+vL+aag+++++ V+v+ ++a i++  ++ +v+++a++++   aP+++a
  gi|320101299|ref|YP_004176891.1|  18 SEENVKKVLEAAGVAVDE-VRVKSLVAAIKN-IDIAKVLEQAIAAPVaAAPVQAA 70 
                                       568**********99988.6***********.89***********9655666554 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.4e-05      0.23      13      52 ..      13      52 ..       2      63 .. 0.83
   2 ?   -0.9   0.2       0.6   2.1e+03      51      66 ..      80      95 ..      73     101 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.4e-05
                        EF-hand_14 13 etdklsvakllkaLaetGirkdDpRLkellkklkkvekek 52
                                        +++s ++  k+L+++G+  d  R+k+l+ ++k+++  k
  gi|320101299|ref|YP_004176891.1| 13 AGKEISEENVKKVLEAAGVAVDEVRVKSLVAAIKNIDIAK 52
                                      457899999*************************998665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.6
                        EF-hand_14 51 ekseaeesetleldre 66
                                      +k+e++e e++el+ e
  gi|320101299|ref|YP_004176891.1| 80 KKEEKKEEESKELSEE 95
                                      3334555555666555 PP

>> Adenine_glyco  Methyladenine glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   6.7e-05      0.24      65     150 ..      16     102 ..      10     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.7e-05
                     Adenine_glyco  65 kydeekveelladegiirnrlKieavis...nAravlalqeefgsfseylwsfvdgkpiveelksaeevpattelse 138
                                       +++ee+v+++l+ +g+  ++ ++++ ++   n  ++  l++     +      v+  p + + +++++ ++++e+s+
  gi|320101299|ref|YP_004176891.1|  16 EISEENVKKVLEAAGVAVDEVRVKSLVAaikNIDIAKVLEQA--IAAPVAAAPVQAAPATAPAAEEKKEEKKEEESK 90 
                                       6789****************9999766500044444433333..334444556678888889899999999****** PP

                     Adenine_glyco 139 alskdLkkrGfk 150
                                       +ls++   +Gf+
  gi|320101299|ref|YP_004176891.1|  91 ELSEEALSEGFS 102
                                       *****9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1444  (0.0805399); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 758.75
//
Query:       gi|320101300|ref|YP_004176892.1|  [L=335]
Description: 50S ribosomal protein L10 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-20   71.9   2.5    6.4e-20   71.2   0.0    2.4  3  Ribosomal_L10   Ribosomal protein L10
    2.8e-16   59.3   0.1      1e-15   57.5   0.1    2.0  1  RL10P_insert    Insertion domain in 60S ribosomal protein L10
  ------ inclusion threshold ------
        0.5    9.2   1.7        0.7    8.7   1.7    1.1  1  Cytochrom_C552  Cytochrome c552


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 !   71.2   0.0   1.1e-23   6.4e-20       3      98 ..       9     104 ..       7     105 .. 0.95
   2 ?   -2.3   0.0      0.83   4.9e+03      45      59 ..     147     161 ..     140     166 .. 0.69
   3 ?   -1.0   0.5      0.33     2e+03       2      16 ..     310     324 ..     309     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.1e-23
                                       CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S.SCGCCSSS CS
                     Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek.lkellkgp 78 
                                       + +K+e+v+el ell  +++++++d +g++++ +q lRkkl ++ a lk vK +l+ +Ale++g++ + +ke+l+g+
  gi|320101300|ref|YP_004176892.1|   9 PRWKAEIVEELVELLRRHRVFALIDTTGIPANHIQMLRKKLHGK-AVLKAVKPRLLGIALEKAGINPElFKEHLTGQ 84 
                                       68*****************************************9.********************85479******* PP

                                       EEEEEESS-TCHHHHCCCCC CS
                     Ribosomal_L10  79 valvftnedpvalakvleef 98 
                                       v+ vft+++p++la +++++
  gi|320101300|ref|YP_004176892.1|  85 VVAVFTDMNPFELAMLMDKY 104
                                       **************998876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.83
                                       HHGCEEEEESCCCCC CS
                     Ribosomal_L10  45 engaelkvvKntlmr 59 
                                        +g+ + v+K t++ 
  gi|320101300|ref|YP_004176892.1| 147 VQGNVIYVAKDTVVA 161
                                       345678888888876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.33
                                       SCCCHCCCCCCCCCC CS
                     Ribosomal_L10   2 tkekKeelvkelkel 16 
                                       + ekKee  kel+e 
  gi|320101300|ref|YP_004176892.1| 310 KEEKKEEESKELSEE 324
                                       7899*******9985 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 !   57.5   0.1   1.7e-19     1e-15       2      70 ..     111     179 ..     111     180 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.7e-19
                      RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLg 70 
                                       ++G++ +++++ip+g+++  Pg++ + + +l+++tk++  +i + +d++v+k G++++s+ a+lL++Lg
  gi|320101300|ref|YP_004176892.1| 111 KPGEKTDKEIVIPEGNTGIPPGPMLSVFGRLKIQTKVQGNVIYVAKDTVVAKPGDVVSSDLASLLQKLG 179
                                       79******************************************************************8 PP

>> Cytochrom_C552  Cytochrome c552
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.7   0.00012       0.7     355     424 ..     254     323 ..     235     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00012
                                       HHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-TS---.---SSHHHHHHHTT--HHHHHHHHHHHH CS
                    Cytochrom_C552 355 agfHaPeealrvlasavdkaakarlklakllakagvkdevaipdistlekakkalkvdveklkaekekfl 424
                                       agf  Pe a  vl  av+ka+   +++ak + + g++++  + ++++ +k+k+  k + +k++++ke  +
  gi|320101300|ref|YP_004176892.1| 254 AGFITPETAEAVLLAAVAKANALAAEVAKHAPELGLEVKQPVQQVQQEAKGKEGEKKEEKKEEESKELSE 323
                                       57889*****************99*************988888888888888877777777666665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1654  (0.0922528); expected 358.6 (0.02)
Passed bias filter:                      999  (0.0557198); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 2340.65
//
Query:       gi|320101301|ref|YP_004176893.1|  [L=213]
Description: 50S ribosomal protein L1P [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-37  128.1   0.0    4.2e-37  127.9   0.0    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   0.0   2.4e-41   4.2e-37       7     204 .]      23     209 ..      13     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 2.4e-41
                                       SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT- CS
                      Ribosomal_L1   7 kkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyks 83 
                                       ++f++sve+++ l+++++k +  ++++ ++Lp++ gke ++c++++++ a+   +a+eag  + v++ ++l+   k 
  gi|320101301|ref|YP_004176893.1|  23 RRFKQSVEMIIVLRDVDVKGQAGKIREFVTLPKGRGKERSVCVVADGDLAA---KAREAG-AKLVLTSQDLQGINK- 94 
                                       579************************************************...9*****.788889999999885. PP

                                       HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEE CS
                      Ribosomal_L1  84 feakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvk 160
                                        ++ +k++ ++d++l+  ++m   +++LG+ +g+r+k P+p      +++d++  ++++ + tvv r++++  ++v+
  gi|320101301|ref|YP_004176893.1|  95 -KQAKKIAGQCDWILVRTDLMAVTGRVLGPALGPRGKAPVPL--P--ASADIQGLIKRYAN-TVVARVKDQPQIMVA 165
                                       .7****************************************..4..368***********.*************** PP

                                       EEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 161 vGklsftaeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                       +G+ ++++e+la+N+ av++a+++k+p++  ni +i+ kttm++
  gi|320101301|ref|YP_004176893.1| 166 IGTEDMKPEDLADNALAVLSAIESKLPSGMGNIGKIVFKTTMGM 209
                                       ******************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 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:                        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 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1643.31
//
Query:       gi|320101302|ref|YP_004176894.1|  [L=170]
Description: 50S ribosomal protein L11 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   81.8   1.1    4.3e-23   80.9   1.1    1.5  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    1.3e-19   70.5   1.8    2.1e-19   69.8   1.8    1.3  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 !   80.9   1.1   4.8e-27   4.3e-23       4      62 ..       2      61 ..       1      64 [. 0.93

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 4.8e-27
                   Ribosomal_L11_N  4 vvkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitv.yqd 62
                                      v+k++k++v++GkAtp+PplGp+L+p+ +ni++++k++n+aTkd++gl +pV+i +  ++
  gi|320101302|ref|YP_004176894.1|  2 VKKTIKVMVEGGKATPGPPLGPTLSPYKVNIPQVVKAINDATKDFEGLSVPVEIVIdTDT 61
                                      579*****************************************************4444 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 !   69.8   1.8   2.3e-23   2.1e-19       2      70 .]      70     137 ..      69     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 2.3e-23
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                        P+t++lL+k+ag+++ +g p ++++G++s++qv+++A  Kk++l+a+ +l+aavk+ilgtAr +Gi+V
  gi|320101302|ref|YP_004176894.1|  70 IPTTTALLMKEAGAKQPTGDPAHQKIGNISFEQVVKVALLKKESLSAK-TLKAAVKTILGTARAIGITV 137
                                       59****************************************999999.******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1374.81
//
Query:       gi|320101303|ref|YP_004176895.1|  [L=163]
Description: 50S ribosomal protein L24 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-17   61.6   0.6    6.9e-17   61.1   0.6    1.3  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    1.9e-08   33.9   0.3      2e-07   30.7   0.2    2.3  2  KOW       KOW motif
  ------ inclusion threshold ------
      0.071   13.6   0.1       0.11   13.0   0.1    1.3  1  NusG      Transcription termination factor nusG


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.6   1.2e-20   6.9e-17       1      84 []      13      97 ..      13      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.2e-20
                          Spt5-NGN  1 siwavkctagqErevalslmkkilelakken.leIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpik 78
                                      +i+avk+t g+E +va+ ++ +++e+ +k + + ++S++ p+++kGy+++E ++ + + r++++i++v+++ + ++ ++
  gi|320101303|ref|YP_004176895.1| 13 RIYAVKTTVGRELDVAFIISMRVEEKKAKGEeTSVRSIIIPPDIKGYVFLEVEKLSELYRVVSDIRYVKAGRPMKIAYE 91
                                      69********************98874443359********************************************** PP

                          Spt5-NGN 79 Evedll 84
                                      E+e+ll
  gi|320101303|ref|YP_004176895.1| 92 ELEKLL 97
                                      ***997 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.2   3.3e-11     2e-07       1      31 [.     108     138 ..     108     141 .. 0.91
   2 ?    0.6   0.0       0.1     6e+02       1       9 [.     152     160 ..     152     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.3e-11
                                       TTSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfv 31 
                                       +Gd+V++++Gp+kG  +k++ vd++k+  +v
  gi|320101303|ref|YP_004176895.1| 108 VGDIVEITRGPFKGMRAKITGVDRNKNMLTV 138
                                       7*************************76555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.1
                                       TTSEEEESS CS
                               KOW   1 pGdhVkVvs 9  
                                       pGd+Vk +s
  gi|320101303|ref|YP_004176895.1| 152 PGDYVKKMS 160
                                       8****9775 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.9e-05      0.11      24      94 ..      25      96 ..       7      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                                      CT-EEE-SCEEEEEEETTEEE........CSSTTEEEEEE---CHHHHHHHCSTTEEEE-EETTSSCC-EB-HHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              NusG 24 eglevivPaeekveirqgkkk........klfpgyifikadmndkllmairktpgVtgfvrvggeskpvplseeevqni 94
                                       ++ +i+ ++ ++++ +g+++        + ++gy+f++++  ++l +++  +    ++v+ g    p+ +  ee++++
  gi|320101303|ref|YP_004176895.1| 25 LDVAFIISMRVEEKKAKGEETsvrsiiipPDIKGYVFLEVEKLSELYRVVSDI----RYVKAGR---PMKIAYEELEKL 96
                                      455666677555554477777899*****************998999999888....8887766...999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1240.84
//
Query:       gi|320101304|ref|YP_004176896.1|  [L=59]
Description: protein translocase subunit secE/sec61 gamma [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       361  (0.020135); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 452.56
//
Query:       gi|320101305|ref|YP_004176897.1|  [L=296]
Description: signal recognition particle-docking protein FtsY [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-68  230.4   0.0    2.7e-68  229.5   0.0    1.5  2  SRP54            SRP54-type protein, GTPase domain
    1.4e-06   28.5   1.9    1.4e-06   28.5   1.9    1.7  2  SRP54_N          SRP54-type protein, helical bundle domain
    0.00016   21.7   0.0    0.00068   19.7   0.0    2.1  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00041   20.1   0.1    0.00073   19.3   0.1    1.4  1  AAA_30           AAA domain
     0.0026   16.8   1.6      0.061   12.3   1.6    2.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0039   17.1   0.1      0.014   15.3   0.0    1.9  2  AAA_31           AAA domain
      0.009   15.7   0.0      0.017   14.8   0.0    1.6  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.015   15.3   2.4        0.6   10.0   1.4    2.5  1  NTPase_1         NTPase
      0.019   15.0   1.1      0.096   12.8   0.4    2.3  2  MMR_HSR1         50S ribosome-binding GTPase
      0.028   14.0   0.4      0.083   12.5   0.4    1.7  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.038   13.3   0.2       0.08   12.2   0.0    1.7  2  Zeta_toxin       Zeta toxin
      0.045   13.2   0.2       0.11   12.0   0.0    1.7  2  Arf              ADP-ribosylation factor family
      0.046   12.9   0.7       0.14   11.3   0.1    2.0  2  ArsA_ATPase      Anion-transporting ATPase
       0.08   13.3   0.0       0.18   12.1   0.0    1.6  2  AAA_19           AAA domain
        0.1   12.3   0.4        1.2    8.8   0.0    2.5  3  Thymidylate_kin  Thymidylate kinase
       0.15   12.3   0.3        0.3   11.3   0.0    1.7  2  AAA_28           AAA domain
       0.16   11.7   1.1        1.1    9.0   0.1    2.4  3  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.19   12.2   0.9       0.49   10.8   0.1    2.1  2  AAA              ATPase family associated with various cellul
       0.22   11.8   0.3         26    5.1   0.1    3.0  3  AAA_22           AAA domain
       0.45   10.9   1.9          1    9.8   0.1    2.3  3  AAA_17           AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.4     4e+03      29      49 ..      32      52 ..      20      71 .. 0.64
   2 !  229.5   0.0     3e-71   2.7e-68       2     195 ..      99     292 ..      98     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.4
                                      TS-EEEEEESTSSTTHHHHHH CS
                             SRP54 29 gkkvllvaaDtfRaaAveQLk 49
                                      + k+ lva D+   aA +  +
  gi|320101305|ref|YP_004176897.1| 32 EFKLNLVASDVAYEAAEDIAA 52
                                      567777777777777755333 PP

  == domain 2  score: 229.5 bits;  conditional E-value: 3e-71
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                         i+++G++G+GKTtt+aK+a +++ +g k+l+vaaDtfRa+A+eQLk++ e++g+pv++ + + dpaa+a++av+ 
  gi|320101305|ref|YP_004176897.1|  99 FKIVFLGVNGVGKTTTIAKIAVYMRGNGFKPLMVAADTFRAGAQEQLKIHSERTGIPVFTGRYGWDPAALAYDAVQY 175
                                       5799************************************************************************* PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                          +++dv l+DTaGr++ d +l++elkk+ +vvkp+ ++lv+da+tg++av+qa+ F+eavg++gv++tk+D+  +
  gi|320101305|ref|YP_004176897.1| 176 GVGRGFDVFLIDTAGRMHVDVDLVNELKKVVRVVKPNVKILVVDALTGNDAVEQARFFNEAVGVDGVVVTKVDAYEE 252
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       gG  ls+a+ l++Pi f+gvG+ ++dl++f+p ++v+r+l
  gi|320101305|ref|YP_004176897.1| 253 GGVPLSLAYVLGKPILFVGVGQDYKDLKPFNPIEYVDRVL 292
                                       *************************************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 !   28.5   1.9   1.5e-09   1.4e-06       3      75 .]       3      77 ..       1      77 [. 0.78
   2 ?   -2.4   0.2       6.5   5.8e+03      41      51 ..     196     206 ..     193     223 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.5e-09
                                      HHHHHHHHHHCCSS.CG..HHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHHH CS
                           SRP54_N  3 kklnsalkklsgks.ki..deedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkdeL 75
                                      +kl++a++++ +   +i  + e l ea++e +  L+ +DV++++++++ +++ + +v+e ++k+++++++++++ L
  gi|320101305|ref|YP_004176897.1|  3 RKLKEAFARFIDTAsSIltSREKLLEAIEEFKLNLVASDVAYEAAEDIAAQLSR-RVEEGRVKRREDLVEALREIL 77
                                      566667755444331334545556666*************************77.***899***********9976 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.5
                                       HHHHHHHHHHH CS
                           SRP54_N  41 vkvvkklienv 51 
                                       v++v +l + v
  gi|320101305|ref|YP_004176897.1| 196 VDLVNELKKVV 206
                                       55555555544 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 ?   -2.3   0.0       4.7   4.2e+03      76      99 ..      30      53 ..       9      75 .. 0.45
   2 !   19.7   0.0   7.6e-07   0.00068       9      85 ..     108     248 ..     101     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.7
                                      EEEEEEEEESS...-TTCHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA 76 iagvvlnrvdgeneetllkealee 99
                                      i  + ln v ++ ++++ ++  ++
  gi|320101305|ref|YP_004176897.1| 30 IEEFKLNLVASDVAYEAAEDIAAQ 53
                                      444444444444333333333333 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 7.6e-07
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       GvGKTt+ a++a+++  +g++ l+v aD+ +  +   e+l++  e+                               
  gi|320101305|ref|YP_004176897.1| 108 GVGKTTTIAKIAVYMRGNGFKPLMVAADTFRAGAQ--EQLKIHSERtgipvftgrygwdpaalaydavqygvgrgfd 182
                                       9***************************9966655..4444444447888999999999999999999999999999 PP

                                       ..........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEES CS
                                       ..........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..........................................dlkrllellealgkkkalllkiagvvlnrvd 85 
                                                                                 d+    +++++        + + gvv+++vd
  gi|320101305|ref|YP_004176897.1| 183 vflidtagrmhvdvdlvnelkkvvrvvkpnvkilvvdaltgnDAVEQARFFNEA-------VGVDGVVVTKVD 248
                                       999999999988888777777777777777777777555555333334444333.......334688888877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   8.1e-07   0.00073      22     140 ..     102     236 ..      88     248 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.1e-07
                            AAA_30  22 vltGpAGtGKttalkalreaweaag.grviglAptgkaAkv..La...eelgieastiakllkrlk..........g 82 
                                       v  G+ G GKtt++++++  ++ +g ++++++A t +a ++  L+   e +gi+      ++ r++           
  gi|320101305|ref|YP_004176897.1| 102 VFLGVNGVGKTTTIAKIAVYMRGNGfKPLMVAADTFRAGAQeqLKihsERTGIPV-----FTGRYGwdpaalaydaV 173
                                       5679******************998577888888888866512333333444444.....44443366677999996 PP

                            AAA_30  83 rarlepg.tllivDEagmv..dtkqlaallkaaeka..gakvilvGDerQlasVeaGgvlrdl 140
                                       +  + +g +++++D ag +  d + +++l k ++    ++k+++v      ++Ve+ + +++ 
  gi|320101305|ref|YP_004176897.1| 174 QYGVGRGfDVFLIDTAGRMhvDVDLVNELKKVVRVVkpNVKILVVDALTGNDAVEQARFFNEA 236
                                       67899999*********8867666655555554442117888888767777777777776665 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 !   12.3   1.6   6.8e-05     0.061      30     150 ..      99     209 ..      87     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                                       EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-----HH.H CS
                              MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslpsrGalG.G 105
                                        ++ + Gv G+Gk t++ ++++ +r +G +  ++a D   +f  G+   ++l++++  +   vf      +G+ G  
  gi|320101305|ref|YP_004176897.1|  99 FKIVFLGVNGVGKTTTIAKIAVYMRGNGFKPLMVAAD---TFRAGA--QEQLKIHSERTGIPVF------TGRYGwD 164
                                       567789*****************************99...566666..3455554444444444......4666624 PP

                                       HHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEE CS
                              MeaB 106 laaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvll 150
                                        aa + ++v+   + GfDv li+t G    +vd+++  + +v ++
  gi|320101305|ref|YP_004176897.1| 165 PAALAYDAVQYGVGRGFDVFLIDTAGRMHVDVDLVNELKKVVRVV 209
                                       577788999999999999999999999999999888888777766 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05     0.014      12      41 ..     108     137 ..     101     157 .. 0.86
   2 ?   -1.9   0.0       3.1   2.8e+03      28      37 ..     210     219 ..     179     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQ 41 
                                       GvGKTTt  ++a+ +  +g k L+v +D+ 
  gi|320101305|ref|YP_004176897.1| 108 GVGKTTTIAKIAVYMRGNGFKPLMVAADTF 137
                                       9**************************975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                            AAA_31  28 klgkkvLlvD 37 
                                       k + k+L+vD
  gi|320101305|ref|YP_004176897.1| 210 KPNVKILVVD 219
                                       3344555555 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   1.9e-05     0.017       3      77 ..      99     192 ..      97     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfi..dtek.Glksldadkfpdie..........swedfldevvel 59 
                                        ki+  G +g+GKTt+++++       g kpl++  dt++ G+   +  k+ + +          +w+    +++++
  gi|320101305|ref|YP_004176897.1|  99 FKIVFLGVNGVGKTTTIAKIavymrgnGFKPLMVaaDTFRaGA--QEQLKIHSERtgipvftgryGWDPAALAYDAV 173
                                       699*****************99999997788887334444333..33333333336455555555555555555555 PP

                            AAA_24  60 .aaeladyktlviDtidel 77 
                                        +   +++++  iDt++ +
  gi|320101305|ref|YP_004176897.1| 174 qYGVGRGFDVFLIDTAGRM 192
                                       8888999999999998766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.4   0.00067       0.6       3      29 ..     102     128 ..     100     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00067
                                       EEE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvk 29 
                                       +  G  GvGKtT + k++  ++ +g+k
  gi|320101305|ref|YP_004176897.1| 102 VFLGVNGVGKTTTIAKIAVYMRGNGFK 128
                                       556899************999888765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.6   2.3e+03      50      86 ..      12      43 ..       4      75 .. 0.49
   2 ?   12.8   0.4   0.00011     0.096       1      87 [.     100     224 ..     100     244 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.6
                                      EEECGGCSSHHHHHHHHHHHHHH.HHCTSEEEEEEETT CS
                          MMR_HSR1 50 lvDtpGliegaseekglgkafla.leeadlillvvdas 86
                                      ++Dt+  i         ++++l+ +ee +l l+  d++
  gi|320101305|ref|YP_004176897.1| 12 FIDTASSIL------TSREKLLEaIEEFKLNLVASDVA 43
                                      667776432......11222222022234444444433 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                                       EEEEEESTTSSHHHHHHHHH.....T..STEEESSSTTSSSSEEEEEEEETTEE....................... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinalt.....g..ekaivsdkpgtTrdinegrvklkgke....................... 47 
                                       +++++G   vGK+t i ++      +  +   v++  +     ++ +++ +  +                       
  gi|320101305|ref|YP_004176897.1| 100 KIVFLGVNGVGKTTTIAKIAvymrgNgfKPLMVAADTFRAGAQEQLKIHSE--Rtgipvftgrygwdpaalaydavq 174
                                       5899999***********985555313324466666666655555555522..124555666666666667777777 PP

                                       ........EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETT..T CS
                          MMR_HSR1  48 ........ielvDtpGliegaseekglgkaflalee...adlillvvdas..e 87 
                                               + l+Dt+G +   + + +l ++++++ +    ++ +lvvda   +
  gi|320101305|ref|YP_004176897.1| 175 ygvgrgfdVFLIDTAGRM---HVDVDLVNELKKVVRvvkPNVKILVVDALtgN 224
                                       77777777********44...4666666666665553216999****965332 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 ?   12.5   0.4   9.3e-05     0.083       3     155 ..     101     252 ..      99     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.3e-05
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleale 77 
                                       +v+ G  G GKTt + ++    + +g k   +  +    +  ++l  +++   + + +G      +  +  +++  +
  gi|320101305|ref|YP_004176897.1| 101 IVFLGVNGVGKTTTIAKIAvyMRGNGFKPLMVAADTFRAGAQEQLKIHSERTGIPVFTGRYGWDPAALAYDAVQYGV 177
                                       57789999999999999998877788888888888888888888877777778889999998886666666666666 PP

                                       HHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHH CS
                              cobW  78 ereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDll 153
                                        r   +dv li t G +     ++ + +++ + ++ ++++ vvDa    ++   ++  + ++    d +v++K+D  
  gi|320101305|ref|YP_004176897.1| 178 GRG--FDVFLIDTAGrMHVDVDLVNELKKVVRVVKPNVKILVVDALTG-NDA-VEQARFFNEAVGVDGVVVTKVDAY 250
                                       666..**********544445555668999999************443.344.444455555666799*******87 PP

                                       CH CS
                              cobW 154 de 155
                                       +e
  gi|320101305|ref|YP_004176897.1| 251 EE 252
                                       75 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.8   2.5e+03     161     189 ..      21      49 ..       3      68 .. 0.57
   2 ?   12.2   0.0   8.9e-05      0.08      12      56 ..      94     139 ..      87     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                        Zeta_toxin 161 eafeglresvealeeekqldrvkikdrdg 189
                                        + e+l e++e+++ +  +++v +   ++
  gi|320101305|ref|YP_004176897.1|  21 TSREKLLEAIEEFKLNLVASDVAYEAAED 49 
                                       44455666666666655555555554444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.9e-05
                        Zeta_toxin  12 sqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                       ++++P  i+  G  G GK++++++++ +++ ++ + + + +D++R+
  gi|320101305|ref|YP_004176897.1|  94 RSRKPFKIVFLGVNGVGKTTTIAKIAVYMRgNGFKPLMVAADTFRA 139
                                       568999999999*****************977778999****9996 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.11       7      35 ..      91     119 ..      86     129 .. 0.86
   2 ?   -2.7   0.1       3.8   3.4e+03      86     110 ..     183     208 ..     183     227 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       GGTT.TTEEEEEEEESTTSSHHHHHHHHH CS
                               Arf   7 klklkkkelrilllGLDnaGKtTilkklk 35 
                                       +l  ++k ++i++lG  + GKtT + k+ 
  gi|320101305|ref|YP_004176897.1|  91 SLARSRKPFKIVFLGVNGVGKTTTIAKIA 119
                                       56677999***************998875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                                       EEEEETT-CTTHH.HHHHHHHHHCTS CS
                               Arf  86 ifvvDsadreRle.eakeeLkallee 110
                                       +f++D+a r+ ++ +  +eLk++++ 
  gi|320101305|ref|YP_004176897.1| 183 VFLIDTAGRMHVDvDLVNELKKVVRV 208
                                       57777777666652344566665543 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00016      0.14       4      38 ..     101     135 ..      99     139 .. 0.90
   2 ?   -1.4   0.0       1.1     1e+03     118     134 ..     174     190 ..     162     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                       i++ G  GVGKtt  a +av++  +g k l+++ D
  gi|320101305|ref|YP_004176897.1| 101 IVFLGVNGVGKTTTIAKIAVYMRGNGFKPLMVAAD 135
                                       5677889***********************99988 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                       HHHHCSSSSEEEEESBS CS
                       ArsA_ATPase 118 kyvkeeeydvvvlDtaP 134
                                       +y  ++ +dv ++Dta 
  gi|320101305|ref|YP_004176897.1| 174 QYGVGRGFDVFLIDTAG 190
                                       55667778888888884 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       8.1   7.3e+03     103     127 ..       8      32 ..       3      39 .. 0.70
   2 ?   12.1   0.0    0.0002      0.18      13      69 ..     101     167 ..      91     244 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.1
                            AAA_19 103 eellivDEfqdvdelqyrLlkallg 127
                                       +++ ++D ++ +     +Ll+a+ +
  gi|320101305|ref|YP_004176897.1|   8 AFARFIDTASSILTSREKLLEAIEE 32 
                                       4466788888888888899988874 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...........a 69 
                                       ++ ++  G GKT+++ +i a++ + +g kp  +++ +f   A ++l+   +  g +           a
  gi|320101305|ref|YP_004176897.1| 101 IVFLGVNGVGKTTTIAKI-AVYMRGNGFKPLMVAADTFRAGAQEQLKIHSERTGIPvftgrygwdpaA 167
                                       5567889********865.6666666676677777777777777776555444555444545444440 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.59   5.3e+02      56      79 ..      31      56 ..       9      70 .. 0.68
   2 ?    8.8   0.0    0.0013       1.2       3      26 ..     105     128 ..     103     136 .. 0.88
   3 ?   -1.4   0.0       1.8   1.6e+03     101     125 ..     193     218 ..     189     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.59
                                      H..HHHHHHHHHHHTTHHHHHHHHHT CS
                   Thymidylate_kin 56 t..eallfaadriehleekikpalkq 79
                                          ++l a d++++++e i ++l++
  gi|320101305|ref|YP_004176897.1| 31 EefKLNLVASDVAYEAAEDIAAQLSR 56
                                      23367788888888888888887765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                                       ESTTSSHHHHHHHHHHHHHHTTE. CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik 26 
                                       G++G+GKtt +++++ +++ +g k
  gi|320101305|ref|YP_004176897.1| 105 GVNGVGKTTTIAKIAVYMRGNGFK 128
                                       9****************9999976 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                                       TTTCHHHHHHGGGTTS.E-SEEEEEE CS
                   Thymidylate_kin 101 gvdldlvlslnedvll.kPdltflld 125
                                       +vd+dlv +l++ v   kP + +l+ 
  gi|320101305|ref|YP_004176897.1| 193 HVDVDLVNELKKVVRVvKPNVKILVV 218
                                       58899999999888778999888764 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       6.6   5.9e+03      32      41 ..      48      57 ..      25      77 .. 0.50
   2 ?   11.3   0.0   0.00034       0.3       1      37 [.     100     143 ..     100     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.6
                            AAA_28 32 reileeklak 41
                                       +i  +++++
  gi|320101305|ref|YP_004176897.1| 48 EDIAAQLSRR 57
                                      3333333322 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00034
                            AAA_28   1 kivitGgestGKTtlleaLa..ar..gyp...vvpEaareilee 37 
                                       kiv++G  + GKTt+++++a   r  g++   v ++++r   +e
  gi|320101305|ref|YP_004176897.1| 100 KIVFLGVNGVGKTTTIAKIAvyMRgnGFKplmVAADTFRAGAQE 143
                                       79****************99542245544442336666655555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.1   2.8e+03     199     216 ..      21      38 ..       6      60 .. 0.59
   2 ?    9.0   0.1    0.0012       1.1       2      33 ..     104     135 ..     103     143 .. 0.91
   3 ?    0.5   0.0      0.47   4.2e+02      92     144 ..     182     235 ..     169     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                        ATP_bind_1 199 klaeaiaelleefalvlr 216
                                       ++ e++ e++eef+l+l+
  gi|320101305|ref|YP_004176897.1|  21 TSREKLLEAIEEFKLNLV 38 
                                       445566666666666633 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                       +G+ G+GKtt + +++ +++ +g ++ +v  D
  gi|320101305|ref|YP_004176897.1| 104 LGVNGVGKTTTIAKIAVYMRGNGFKPLMVAAD 135
                                       799********************999999766 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.47
                        ATP_bind_1  92 dyllfDtPGQiel.fthseslakiveeLesefalvvvyLvDsqrltdptkfisg 144
                                       d +l+Dt G + + + ++++l+k+v+  + ++++ vv  +  + + + + f+++
  gi|320101305|ref|YP_004176897.1| 182 DVFLIDTAGRMHVdVDLVNELKKVVRVVKPNVKILVVDALTGNDAVEQARFFNE 235
                                       678999999999845799999999999999888888877666666666667665 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 ?   -1.5   0.0       3.6   3.2e+03      63      98 ..      12      35 ..       8      74 .. 0.63
   2 ?   10.8   0.1   0.00055      0.49       2      35 ..     102     138 ..     101     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.6
                                      EEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA 63 fiDEidalaksrsgseseeeervvnqLlteldgvkk 98
                                      fiD + ++ +sr            ++Ll++++++k 
  gi|320101305|ref|YP_004176897.1| 12 FIDTASSILTSR------------EKLLEAIEEFKL 35
                                      556666666666............666666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00055
                                       EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCS CS
                               AAA   2 llyGppGtGKTllakavakel...gvefleisgsell 35 
                                       ++ G  G+GKT+++  +a  +   g++ l + + +++
  gi|320101305|ref|YP_004176897.1| 102 VFLGVNGVGKTTTIAKIAVYMrgnGFKPLMVAADTFR 138
                                       789***************9985444666666666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.19   1.7e+02      53      91 ..      47      82 ..      15      92 .. 0.80
   2 ?    5.1   0.1     0.029        26       8      25 ..     101     118 ..      93     120 .. 0.86
   3 ?    0.3   0.0      0.86   7.7e+02      83     124 ..     174     214 ..     143     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.19
                            AAA_22 53 skdllrellralglelkaerlsseellealeqalrarav 91
                                       +d++ +l r +++++ +   ++e+l+eal++ l  +++
  gi|320101305|ref|YP_004176897.1| 47 AEDIAAQLSRRVEEGRVK---RREDLVEALREILLGYFT 82
                                      678888888888888888...***********9999887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.029
                            AAA_22   8 lvvtGesGtGKTtllrrl 25 
                                       +v  G  G+GKTt+++++
  gi|320101305|ref|YP_004176897.1| 101 IVFLGVNGVGKTTTIAKI 118
                                       5677999*******9876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.86
                            AAA_22  83 eqalraravielliiDEaqhlr.seealeeLrsllnlsrkgvq 124
                                       +  + +     +++iD a ++    ++++eL++ + + + +v+
  gi|320101305|ref|YP_004176897.1| 174 QYGVGRG-F-DVFLIDTAGRMHvDVDLVNELKKVVRVVKPNVK 214
                                       3334444.4.5999****9995459999999888776444454 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.8   2.5e+03      83     129 ..      20      64 ..       6      73 .. 0.51
   2 ?    9.8   0.1    0.0011         1       1      36 [.     104     143 ..     104     159 .. 0.76
   3 ?   -1.3   0.0         3   2.7e+03      73     108 ..     183     217 ..     166     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.8
                                       EETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS CS
                            AAA_17  83 keqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdd 129
                                        ++++ l +  +e++ +l  + + + ea +e+i +++ ++ ++gr  
  gi|320101305|ref|YP_004176897.1|  20 LTSREKLLEAIEEFKLNLVASDVAY-EA-AEDIAAQLSRRVEEGRVK 64 
                                       4444444333344444443333333.33.334666666665555544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                                       EE-TTSSHHHHHHHHHHHH...TEE.EEEHHHHHHHHHHT CS
                            AAA_17   1 lGgPGsGKgtqceklveky...gft.hlsaGdllreeakr 36 
                                       lG+ G+GK+t ++k++  +   gf+  + a d +r+ a++
  gi|320101305|ref|YP_004176897.1| 104 LGVNGVGKTTTIAKIAVYMrgnGFKpLMVAADTFRAGAQE 143
                                       79*************9655555776345677777776655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3
                                       EEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                            AAA_17  73 gvlvdghprikeqagfldglpkevleelkpdaiill 108
                                        +l+d+  r+  + +++ +l+k v++ +kp++ il+
  gi|320101305|ref|YP_004176897.1| 183 VFLIDTAGRMHVDVDLVNELKK-VVRVVKPNVKILV 217
                                       6899999999888888888875.8899999654443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2105.64
//
Query:       gi|320101306|ref|YP_004176898.1|  [L=153]
Description: prefoldin subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-17   61.0   0.1    1.6e-16   60.3   0.0    1.4  1  Prefoldin       Prefoldin subunit
    8.2e-07   28.9   0.6      0.046   13.7   0.0    2.1  2  Prefoldin_2     Prefoldin subunit
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.017   14.4   0.1    1.3  1  EAP30           EAP30/Vps36 family
      0.012   15.7   1.5       0.72   10.0   0.2    2.2  2  TolA_bind_tri   TolA binding protein trimerisation
      0.016   15.1   0.0      0.021   14.7   0.0    1.2  1  STAT_alpha      STAT protein, all-alpha domain
      0.018   15.5   1.4        3.2    8.3   0.1    2.2  2  ZapB            Cell division protein ZapB
       0.04   14.0   0.7      0.073   13.2   0.2    1.6  2  Gon7            Gon7 family
      0.041   13.8   0.0        0.1   12.5   0.0    1.7  1  Holin_BhlA      BhlA holin family
      0.052   12.9   0.0      0.078   12.3   0.0    1.3  1  ADPrib_exo_Tox  ADP-ribosyltransferase exoenzyme
      0.081   11.2   0.0      0.088   11.1   0.0    1.1  1  SpecificRecomb  Site-specific recombinase
      0.083   12.3   0.1        1.8    7.9   0.0    2.0  2  FAM92           FAM92 protein
       0.09   11.9   0.2        5.3    6.1   0.0    2.0  2  phiKZ_IP        phiKZ-like phage internal head proteins
      0.095   12.8   2.7        2.1    8.4   0.1    2.1  2  ADIP            Afadin- and alpha -actinin-Binding
       0.22   11.7   3.8        5.6    7.2   0.2    2.2  2  JIP_LZII        JNK-interacting protein  leucine zipper II


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 !   60.3   0.0   1.3e-19   1.6e-16       2     118 ..      26     144 ..      25     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.3e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE-..-STTEEEEEEETTEEEEEEHH CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaev..kdtdkvlvdlGagyyveksle 76 
                                       +e+++ l+++++++ ++++el+ +letlk+l +++ +  ++v+  +++ ++a+v  +  ++vlv+lG gyy++ + +
  gi|320101306|ref|YP_004176898.1|  26 REYANILASTINNYLTQQRELQLALETLKSLPENGGEGFIVVDRLSTAMIPATVdkEWSKRVLVHLGLGYYLKTDRD 102
                                       57788899*************************999999***************5223566**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  77 eAiellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                        A++++ ++ ++le+ + +le++      +++ l+++l++ y
  gi|320101306|ref|YP_004176898.1| 103 RAVDIVSRRSASLERLINELEKKYSAVVGEMNRLRNILETTY 144
                                       *********************************999999877 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.3   3.9e-05     0.051       2      44 ..      17      59 ..      16      62 .. 0.95
   2 !   13.7   0.0   3.6e-05     0.046      56     100 ..      97     141 ..      94     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT CS
                       Prefoldin_2  2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelellded 44
                                      el+++ ++l++    la+ i+++ tq +el+l+le+l++l+e+
  gi|320101306|ref|YP_004176898.1| 17 ELVARINELREYANILASTINNYLTQQRELQLALETLKSLPEN 59
                                      789999**********************************996 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.6e-05
                                       EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  56 vkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelq 100
                                       +k+d++ + + +  r ++le  i++lek+++ +  e++ l++ l 
  gi|320101306|ref|YP_004176898.1|  97 LKTDRDRAVDIVSRRSASLERLINELEKKYSAVVGEMNRLRNILE 141
                                       799*************************************98875 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.3e-05     0.017     112     177 ..       8      86 ..       2     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                             EAP30 112 engglisleelyalvnrarggva.........lvspdDllraiekllvlg....sglsvlqvggkkvvrSvptelnt 175
                                       ++g  +sleel+a++n  r+ ++         l  + +l+ a+e+l+ l+     g+ v+   ++ ++  +  +  +
  gi|320101306|ref|YP_004176898.1|   8 QSGRSVSLEELVARINELREYANilastinnyLTQQRELQLALETLKSLPenggEGFIVVDRLSTAMIPATVDKEWS 84 
                                       56789************9966658999999999999**********99999999******98899999888877776 PP

                             EAP30 176 dq 177
                                       + 
  gi|320101306|ref|YP_004176898.1|  85 KR 86 
                                       66 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00056      0.72      27      73 ..      15      61 ..      12      63 .. 0.90
   2 ?    5.0   0.1      0.02        26      10      49 ..     109     148 ..     102     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                     TolA_bind_tri 27 lealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkleagg 73
                                      le+l + ++eLR     l+  +++ +++Qr+l l l+++ +  e+gg
  gi|320101306|ref|YP_004176898.1| 15 LEELVARINELREYANILASTINNYLTQQRELQLALETLKSLPENGG 61
                                      7899999*****************************99988777765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                     TolA_bind_tri  10 ErilearsqlllelqqqlealqqelreLRGqiEelqyqle 49 
                                        r +++ ++l+ el ++ +a   e+++LR  +E    +++
  gi|320101306|ref|YP_004176898.1| 109 SRRSASLERLINELEKKYSAVVGEMNRLRNILETTYSRVQ 148
                                       5666667788889999999999999999999987665555 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 ?   14.7   0.0   1.7e-05     0.021       3      94 ..      17     148 ..      15     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl..................................... 42 
                                       e+ +r++elr+  + + ++i++   +q e+++  ++l++l                                     
  gi|320101306|ref|YP_004176898.1|  17 ELVARINELREYANILASTINNYLTQQRELQLALETLKSLpenggegfivvdrlstamipatvdkewskrvlvhlgl 93 
                                       78899999**************999**************9************************************* PP

                        STAT_alpha  43 ....eqeraesekkelkkqkellqqmlnaLdqkRkelvdklkellnlleslqekll 94 
                                           +++r +  +  ++++ ++l++++n+L +k  ++v ++++l n le+  +++ 
  gi|320101306|ref|YP_004176898.1|  94 gyylKTDRDRAVDI-VSRRSASLERLINELEKKYSAVVGEMNRLRNILETTYSRVQ 148
                                       *9965555555555.9*********************************9998875 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   0.1    0.0093        12      14      56 ..      16      58 ..      14      87 .. 0.81
   2 ?    8.3   0.1    0.0025       3.2       6      29 ..     119     142 ..     114     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0093
                              ZapB 14 qkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeere 56
                                      ++++ +i +L++    L    +++  ++rel+  +e lk  +e
  gi|320101306|ref|YP_004176898.1| 16 EELVARINELREYANILASTINNYLTQQRELQLALETLKSLPE 58
                                      4678888888888888888888888888888877777775554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0025
                              ZapB   6 LeqLEskiqkaidtitlLqmeiee 29 
                                        ++LE+k+++ + ++ +L++ +e 
  gi|320101306|ref|YP_004176898.1| 119 INELEKKYSAVVGEMNRLRNILET 142
                                       689****************97665 PP

>> Gon7  Gon7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   5.7e-05     0.073      58      87 ..      17      46 ..       5      56 .. 0.84
   2 ?   -2.0   0.0       2.9   3.8e+03      58      70 ..     128     140 ..      99     146 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-05
                              Gon7 58 aelteLseLRaqltgLQddiNefLTermee 87
                                      + +++++eLR     L + iN++LT++ e+
  gi|320101306|ref|YP_004176898.1| 17 ELVARINELREYANILASTINNYLTQQREL 46
                                      457899********************9775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.9
                              Gon7  58 aelteLseLRaql 70 
                                       a + e+++LR+ l
  gi|320101306|ref|YP_004176898.1| 128 AVVGEMNRLRNIL 140
                                       3445566666655 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.2e-05       0.1      18      63 ..      88     135 ..      83     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.2e-05
                        Holin_BhlA  18 LfvvllvYilkkqekre.ekqeerekkyqeiikkltekfeiv.eeikk 63 
                                       L  + l+Y lk+ + r  +    r  +++ +i++l +k+  v  e+++
  gi|320101306|ref|YP_004176898.1|  88 LVHLGLGYYLKTDRDRAvDIVSRRSASLERLINELEKKYSAVvGEMNR 135
                                       5555699******99972456688889************877566654 PP

>> ADPrib_exo_Tox  ADP-ribosyltransferase exoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.1e-05     0.078      22      64 ..      23      73 ..      14      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-05
                                      HHHHHHCCTTHHHHHHHHHCTTTSGGGS-S.CHHHHH.......HHHHHHH CS
                    ADPrib_exo_Tox 22 eaireYtgsgysdINnyLrqnkgerndldk.selekk.......iknldsa 64
                                      +++reY +  +s+INnyL q+++ +  l++ + l ++       +++l+ a
  gi|320101306|ref|YP_004176898.1| 23 NELREYANILASTINNYLTQQRELQLALETlKSLPENggegfivVDRLSTA 73
                                      789***************999977777776666666566666666666655 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.9e-05     0.088      25     128 ..      11     119 ..       2     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.9e-05
                    SpecificRecomb  25 aaerlraLlellernpelrealrellrallseadqlslftda..GllsrsgffselaerleekllPeapdeedlsdl 99 
                                       +  +l++L+  +++ +e+++ l++++++ l+++++l+l  ++   l+++ g    +++rl+  ++P+++d+e  + +
  gi|320101306|ref|YP_004176898.1|  11 RSVSLEELVARINELREYANILASTINNYLTQQRELQLALETlkSLPENGGEGFIVVDRLSTAMIPATVDKEWSKRV 87 
                                       677899******************************99988744677887888889***************999999 PP

                    SpecificRecomb 100 lsll...fpkeeDaewlealddetlarLlell 128
                                       l +l   +  ++D +   ++ +++ a+L +l+
  gi|320101306|ref|YP_004176898.1|  88 LVHLglgYYLKTDRDRAVDIVSRRSASLERLI 119
                                       87763334445555554444444444444444 PP

>> FAM92  FAM92 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.07        89      42      78 ..      19      55 ..      12      62 .. 0.73
   2 ?    7.9   0.0    0.0014       1.8      12      53 ..     100     141 ..      91     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.07
                             FAM92 42 vrktaklrdkadelvkevkayadd.eeineklcqGlks 78
                                      v ++  lr+ a+ l+  ++ y  +  e ++ l + lks
  gi|320101306|ref|YP_004176898.1| 19 VARINELREYANILASTINNYLTQqRELQLAL-ETLKS 55
                                      56778899999999999999975414566666.66666 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0014
                             FAM92  12 tkddrvkilneavsivekhlgelcsifalvvrktaklrdkad 53 
                                       ++d  v i+  + +  e+ + el + +++vv  + +lr+ ++
  gi|320101306|ref|YP_004176898.1| 100 DRDRAVDIVSRRSASLERLINELEKKYSAVVGEMNRLRNILE 141
                                       477789999999**************************8765 PP

>> phiKZ_IP  phiKZ-like phage internal head proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0041       5.3      68     111 ..      16      59 ..      12      66 .. 0.87
   2 ?    4.0   0.1     0.017        22      58     105 ..     103     150 ..     101     153 .] 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0041
                          phiKZ_IP  68 elikkiietlkdaavritsgierlskridkLeerlkslkkedek 111
                                       e + + i++l+++a+ + s+i +  +++ +L+ +l+ lk  +e+
  gi|320101306|ref|YP_004176898.1|  16 EELVARINELREYANILASTINNYLTQQRELQLALETLKSLPEN 59 
                                       55667799*****************************9887775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                          phiKZ_IP  58 klkeagkkakelikkiietlkdaavritsgierlskridkLeerlksl 105
                                       ++++++ +   +++++i++l   ++ + + + rl+  +++  +r++++
  gi|320101306|ref|YP_004176898.1| 103 RAVDIVSRRSASLERLINELEKKYSAVVGEMNRLRNILETTYSRVQEA 150
                                       6778888888999***********************999999999987 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.024        31      68     109 ..      14      55 ..       7      60 .. 0.89
   2 ?    8.4   0.1    0.0017       2.1      86     127 ..     101     142 ..      98     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.024
                              ADIP  68 eierlqskierlktqleqlerelalvqakerqlekklktleq 109
                                       ++e l ++i+ l +    l++ +  +  ++r+l+ +l+tl++
  gi|320101306|ref|YP_004176898.1|  14 SLEELVARINELREYANILASTINNYLTQQRELQLALETLKS 55 
                                       67899999****************9********999999986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
                              ADIP  86 lerelalvqakerqlekklktleqklknekeelqrlknalqq 127
                                        +r ++ v ++ ++le+ + +le+k      e++rl+n+l++
  gi|320101306|ref|YP_004176898.1| 101 RDRAVDIVSRRSASLERLINELEKKYSAVVGEMNRLRNILET 142
                                       6789999*******************************9987 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 ?    5.6   0.5     0.014        18      29      63 ..      16      50 ..      12      55 .. 0.82
   2 ?    7.2   0.2    0.0044       5.6      35      66 ..     119     150 ..     104     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
                          JIP_LZII 29 ddLIarvdeLtsereiLreEleslqkakerlesri 63
                                      ++L+ar+ eL +  +iL + +++  +++++l+  +
  gi|320101306|ref|YP_004176898.1| 16 EELVARINELREYANILASTINNYLTQQRELQLAL 50
                                      57999999999999999999999988888887665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0044
                          JIP_LZII  35 vdeLtsereiLreEleslqkakerlesrikel 66 
                                       + eL + ++++  E+++l++++e+ +sr++e+
  gi|320101306|ref|YP_004176898.1| 119 INELEKKYSAVVGEMNRLRNILETTYSRVQEA 150
                                       789**************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      935  (0.0521501); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1118.43
//
Query:       gi|320101307|ref|YP_004176899.1|  [L=86]
Description: 50S ribosomal protein LX [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-13   49.4   0.3      7e-13   48.7   0.3    1.3  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.3   3.9e-17     7e-13      66     121 .]       3      62 ..       1      62 [. 0.86

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.9e-17
                                       .................TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                    Ribosomal_L18A  66 vkny...g.iwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                       vk+y   g +++  d + ++++f+ke+r + e++a+e+vYs lgs+h++kr++I++e+ve
  gi|320101307|ref|YP_004176899.1|   3 VKTYrvtGyMLISHDRYPTWQKFTKEVRGVDEKDALEKVYSILGSNHKLKRYHIRVESVE 62 
                                       56662221147889999****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 650.80
//
Query:       gi|320101308|ref|YP_004176900.1|  [L=229]
Description: translation initiation factor 6 (aeIF-6) [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-58  195.6   1.2    6.5e-58  195.4   1.2    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 !  195.4   1.2   3.6e-62   6.5e-58       1     197 []       5     207 ..       5     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 3.6e-62
                                       .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-E.EEE--BTTBS-HHHH-EE-SSEEEEETT--HHHH CS
                             eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkve.vvettiagsrlvGslvvgNsngllvpstvtdeel 76 
                                       r+s++g+s+iGv+a+++ k++++p+g++++ v+++ e+L+ve vve+++ag+ l G++++gN+n++++p+ +  +el
  gi|320101308|ref|YP_004176900.1|   5 RMSFFGNSNIGVYAYVNGKVLILPPGISSHDVRELTEVLGVEaVVEARVAGTVLNGVFTAGNDNAIILPRVIFADEL 81 
                                       789**************************************99********************************** PP

                                       HHHHHHHH...---..EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE- CS
                             eIF-6  77 eklkeslk...lev..erleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvt 148
                                       e +k++l+   +++  ++  +++tAlGN++ +N+k+++ +p l+ke+ve+++ vLgve+ ++++ ++ + Gs++vv+
  gi|320101308|ref|YP_004176900.1|  82 EYIKKQLDsrgIDIrlHVSGSRYTALGNLLSCNNKGCIASPLLEKEEVEELRGVLGVEILQTRLVNLDIPGSVLVVN 158
                                       *******9988666768889********************************************************* PP

                                       SSEEEE-TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 149 nkgllvhpkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       ++g++ hp+++e++l+++e +l+v+ve +TvN G+++v+sgl+aN++g+
  gi|320101308|ref|YP_004176900.1| 159 DHGGVAHPDVSEDDLKTVEGVLRVRVERATVNAGVPFVKSGLLANNHGI 207
                                       **********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1676.89
//
Query:       gi|320101309|ref|YP_004176901.1|  [L=93]
Description: 50S ribosomal protein L31 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-10   41.1   0.4    1.9e-10   40.8   0.4    1.1  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.4   1.1e-14   1.9e-10      14      78 ..      18      83 ..       7      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.1e-14
                    Ribosomal_L31e 14 rihgvgfkkraprAlkeikkfamkemg.tpdvridtrLnkavwakgirnvpyrirvrlsrkrnedE 78
                                      r++  ++ +ra rA++ +kk+++++++  +   +d+ Lnk++w++g +++p+r+ v++   ++ +E
  gi|320101309|ref|YP_004176901.1| 18 RVYFGRRMNRADRAVRLVKKYVARHFKdAEKIIVDPLLNKYIWSRGREKPPRRVVVEVRFDKESKE 83
                                      5555677899*****************566669*********************999887665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 708.90
//
Query:       gi|320101310|ref|YP_004176902.1|  [L=52]
Description: 50S ribosomal protein L39E [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   59.9   7.5    1.6e-16   59.7   7.5    1.1  1  Ribosomal_L39  Ribosomal L39 protein
  ------ inclusion threshold ------
      0.062   13.2   0.3      0.072   13.0   0.3    1.2  1  DUF4224        Domain of unknown function (DUF4224)


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 !   59.7   7.5   1.7e-20   1.6e-16       1      42 []       9      50 ..       9      50 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.7e-20
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                      +KlrLa alk+Nr++P+Wv +kt+ +vr+ +  R+WRr+kLk
  gi|320101310|ref|YP_004176902.1|  9 RKLRLAAALKSNRAIPIWVSAKTRLRVRRGFALRNWRRSKLK 50
                                      7****************************************8 PP

>> DUF4224  Domain of unknown function (DUF4224)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   8.1e-06     0.072      15      42 ..       9      37 ..       2      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.1e-06
                           DUF4224 15 rrsaQakwLran.GipfvvradGrpiVlR 42
                                      r+ + a++L++n  ip++v a+ r++V R
  gi|320101310|ref|YP_004176902.1|  9 RKLRLAAALKSNrAIPIWVSAKTRLRVRR 37
                                      6778899*****9**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 397.87
//
Query:       gi|320101311|ref|YP_004176903.1|  [L=115]
Description: DNA-binding TFAR19-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-22   78.1   9.8    1.3e-21   76.9   9.8    1.5  1  dsDNA_bind      Double-stranded DNA-binding domain
    0.00049   19.5   4.5     0.0006   19.2   4.5    1.0  1  Radial_spoke_3  Radial spoke protein 3
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.015   15.2   0.1    1.3  1  LPD16           Large polyvalent protein-associated domain 16


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 !   76.9   9.8   2.2e-25   1.3e-21       2     111 .]      20     115 .]      13     115 .] 0.85

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2.2e-25
                                       XXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH- CS
                        dsDNA_bind   2 rkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqs 78 
                                       r+++l+elq++ +               +e++++ +  ++L++iL+peAreRL+++rlvkpe ae +e++Li laqs
  gi|320101311|ref|YP_004176903.1|  20 RRRKLEELQRRIE---------------EEKQKRLMIDTALRRILTPEARERLNNLRLVKPELAEILEQQLIALAQS 81 
                                       4555555555332...............1222568999*************************************** PP

                                       -SS-----HHHHHHHHHHHS-.--XXXXX..XXX CS
                        dsDNA_bind  79 GqlrskvteeqLkeLLeqvae.kkketkivisrr 111
                                       G+++  +t+e Lk+LL+++ e ++ke +i+++r+
  gi|320101311|ref|YP_004176903.1|  82 GRVKIPITDEFLKRLLSEIYEqTHKEPRIEFKRK 115
                                       *********************777779***9996 PP

>> Radial_spoke_3  Radial spoke protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   4.5     1e-07    0.0006     172     265 ..      17     107 ..      11     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-07
                    Radial_spoke_3 172 elaevqrLeeqekrlreekerrlkqqke.alkkeketaekiaaralakqylaellpsvlesLedsgyfydpverdve 247
                                       e  + ++Lee ++r +eek++rl  +++ +     e++e++ + +l+k  lae+l++ l  L +sg ++ p+    +
  gi|320101311|ref|YP_004176903.1|  17 EALRRRKLEELQRRIEEEKQKRLMIDTAlRRILTPEARERLNNLRLVKPELAEILEQQLIALAQSGRVKIPI----T 89 
                                       6677899************9998766551666899*******************************655555....5 PP

                    Radial_spoke_3 248 teflpwLmeeveeelekr 265
                                       +efl  L++e+ e+++k+
  gi|320101311|ref|YP_004176903.1|  90 DEFLKRLLSEIYEQTHKE 107
                                       556666655555555544 PP

>> LPD16  Large polyvalent protein-associated domain 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.6e-06     0.015      21      72 ..       3      65 ..       1      80 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                             LPD16 21 ceeGydytlYdkdyreldgGqld..........npdltieeaadeilade...dlkgkkaekvdl 72
                                      +e+Gy+ + Yd+++++l    l+          +  l+i +a++ il++e   +  +++++ v  
  gi|320101311|ref|YP_004176903.1|  3 SETGYGNEGYDEELEALRRRKLEelqrrieeekQKRLMIDTALRRILTPEareR--LNNLRLVKP 65
                                      699*****************************9999**************7442..333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1314  (0.0732891); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 825.19
//
Query:       gi|320101312|ref|YP_004176904.1|  [L=159]
Description: 30S ribosomal protein S19 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-51  171.4   0.0    8.6e-51  171.2   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
      3e-05   23.9   1.5    0.00032   20.6   1.5    2.2  1  HTH_12          Ribonuclease R winged-helix domain
     0.0019   18.0   0.1      0.011   15.6   0.1    2.1  2  RuvB_C          RuvB C-terminal winged helix domain
  ------ inclusion threshold ------
      0.058   13.2   0.0          2    8.3   0.0    2.3  2  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.0   1.9e-54   8.6e-51       2     135 ..       4     138 ..       3     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 1.9e-54
                                       SSSHHHHHHHHHS--S--.-S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGG.GGS----SS-SS CS
                    Ribosomal_S19e   2 vkdVpaeelikalaeeLk.ksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrg.pvGverlrkvYG 76 
                                       + +Vpa++li++lae+Lk +  ++++Pew  +vKt+s+ke++p++++W+y+RaAsilRk+y  g pvG+++lr++YG
  gi|320101312|ref|YP_004176904.1|   4 ALEVPADKLINRLAEYLKeNVPEVKPPEWSIFVKTSSHKERPPSNPEWWYYRAASILRKLYKAGrPVGLSELRREYG 80 
                                       568***************7789****************************************988************ PP

                                       S-------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXX CS
                    Ribosomal_S19e  77 gkkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeeva 135
                                       g+k+rgvrp+++ +a g  irkilqqLe+++lv++++ +gr+lt++G+++ldr++ e++
  gi|320101312|ref|YP_004176904.1|  81 GRKNRGVRPERTIRAPGGAIRKILQQLEQAQLVRRTR-RGRVLTPQGKSMLDRLSFEIL 138
                                       *********************************8885.5***************99885 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 !   20.6   1.5   7.2e-08   0.00032       3      66 .]      59     130 ..      57     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.2e-08
                            HTH_12   3 ILkilaesdkpigakeiaeeLkkr.gydig.er.......avRyrLrkleergltrrvgyagreltEkGleeL 66 
                                       IL+ l ++ +p+g  e+  e   r +  ++ er       a+R  L+ le+ +l+rr +++ r lt +G ++L
  gi|320101312|ref|YP_004176904.1|  59 ILRKLYKAGRPVGLSELRREYGGRkNRGVRpERtirapggAIRKILQQLEQAQLVRRTRRG-RVLTPQGKSML 130
                                       89999999999999999999855543333313322233447999**************998.*******9997 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 ?   -0.5   0.0      0.27   1.2e+03      11      29 ..      59      75 ..      56      83 .. 0.73
   2 !   15.6   0.1   2.4e-06     0.011      50      71 ..     109     130 ..     101     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.27
                                      HHHHHHHT.TT--B-HHHH CS
                            RuvB_C 11 yLkllkekfkggpvglktl 29
                                      +L+ l++   g+pvgl+ l
  gi|320101312|ref|YP_004176904.1| 59 ILRKLYK--AGRPVGLSEL 75
                                      5666665..5889999877 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.4e-06
                                       HTTSEEEETTEEEE-HHHHHHH CS
                            RuvB_C  50 keglIertsrGRilTkkglkyl 71 
                                       + +l++rt+rGR lT++g+++l
  gi|320101312|ref|YP_004176904.1| 109 QAQLVRRTRRGRVLTPQGKSML 130
                                       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 ?    8.3   0.0   0.00045         2       4      27 ..      55      78 ..      54      81 .. 0.92
   2 ?    2.5   0.0     0.029   1.3e+02      34      50 ..      99     115 ..      93     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00045
                                      HHHHHHCT-CTTBSS-BHHHHHHH CS
                          HTH_IclR  4 RalaiLdalaeapqeltlselArr 27
                                      Ra++iL+ l +a+++++lsel r+
  gi|320101312|ref|YP_004176904.1| 55 RAASILRKLYKAGRPVGLSELRRE 78
                                      9*******************9776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHTTSEE. CS
                          HTH_IclR  34 tvhRlLqtLvelGyveq 50 
                                       + + +Lq L++  +v++
  gi|320101312|ref|YP_004176904.1|  99 AIRKILQQLEQAQLVRR 115
                                       56789**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1122.17
//
Query:       gi|320101313|ref|YP_004176905.1|  [L=105]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   0.1    1.9e-10   40.8   0.1    1.1  1  CRS1_YhbY        CRS1 / YhbY (CRM) domain
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.42   10.3   0.0    1.8  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus


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 !   40.8   0.1   2.1e-14   1.9e-10      14      82 ..      20      92 ..       8      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.1e-14
                         CRS1_YhbY 14 irlkpkvkiGkaGvtkevvdeiheklkteelvkvkc....egppalnmkrmaeiLeektgglviqrsgtsivL 82
                                      i  k  +++Gk+G+t++++de++ +l+++ +vk+++    +   + + +++ae ++  +gg v +++g +i+L
  gi|320101313|ref|YP_004176905.1| 20 IAGKTDLQLGKNGLTQGFIDEVKLRLEKHGVVKIRVlksfRSNYTGDLEELAERIAGLSGGRVYEVRGFTITL 92
                                      5568899*******************************996677778*********************99987 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 ?   10.3   0.0   4.7e-05      0.42      17      34 ..      29      49 ..      14      53 .. 0.86
   2 ?   -1.1   0.0      0.17   1.5e+03       3      14 ..      64      75 ..      62      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.7e-05
                   Cation_ATPase_N 17 lenGLtq...aeaaerlkkyG 34
                                       +nGLtq   +e++ rl+k+G
  gi|320101313|ref|YP_004176905.1| 29 GKNGLTQgfiDEVKLRLEKHG 49
                                      39******************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.17
                   Cation_ATPase_N  3 alsleevlekLe 14
                                      +++lee++e++ 
  gi|320101313|ref|YP_004176905.1| 64 TGDLEELAERIA 75
                                      678999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 791.84
//
Query:       gi|320101314|ref|YP_004176906.1|  [L=112]
Description: RNAse P, Rpr2/Rpp21 subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   56.1   0.0    4.2e-15   55.8   0.0    1.1  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
       0.07   13.1   4.5        4.4    7.3   0.2    2.5  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.087   12.9   0.1       0.13   12.4   0.1    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 !   55.8   0.0     7e-19   4.2e-15       1      90 []      14      95 ..      14      95 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7e-19
                                      HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E....... CS
                              Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka 79
                                      r+  Ly+ +  + ++    l+r++++ + +++ ka +r p+ ++r +C++C++ lipg+t svr++ + k+        
  gi|320101314|ref|YP_004176906.1| 14 RMMLLYKYSLEEARRGDLGLARRYIEIMLRIAGKAGVRPPKYIRRGYCRRCHTPLIPGLTLSVRIRGRGKG-------- 84
                                      788999999999999999***********************************************865554........ PP

                                      ..EEEEETTTT CS
                              Rpr2 80 dvlvvtClaCg 90
                                       ++v++Cl+Cg
  gi|320101314|ref|YP_004176906.1| 85 SRVVYRCLECG 95
                                      3489******7 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.7   0.00095       5.6      26      35 ..      60      69 ..      50      70 .. 0.80
   2 ?    7.3   0.2   0.00074       4.4       4      18 ..      88     100 ..      86     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00095
                    Zn_ribbon_SprT 26 rCrrCkgtLr 35
                                      +CrrC+  L 
  gi|320101314|ref|YP_004176906.1| 60 YCRRCHTPLI 69
                                      6*****9885 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00074
                    Zn_ribbon_SprT   4 vYrCtgCgreythhl 18 
                                       vYrC  Cg   t+++
  gi|320101314|ref|YP_004176906.1|  88 VYRCLECG--WTRRF 100
                                       7*******..67776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.1e-05      0.13      13      35 ..      59      95 ..      51      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                               DZR 13 rfCseCgtklkavaa..............edrCpsCg 35
                                       +C +C t+l +  +               +rC +Cg
  gi|320101314|ref|YP_004176906.1| 59 GYCRRCHTPLIPGLTlsvrirgrgkgsrvVYRCLECG 95
                                      49********9766699*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 872.31
//
Query:       gi|320101315|ref|YP_004176907.1|  [L=229]
Description: suppressor Mra1 family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-51  174.0   0.0      3e-51  173.9   0.0    1.0  1  EMG1      EMG1/NEP1 methyltransferase


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.9   0.0   1.7e-55     3e-51       1     194 []       7     222 ..       7     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 1.7e-55
                                       EEEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT CS
                              EMG1   1 ivLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkag 61 
                                       i+L easLe+v+ +                k++  LL+ + h++++k+l  ++k++RpDIvH +Ll +l+spLnkag
  gi|320101315|ref|YP_004176907.1|   7 IILLEASLETVPASiaahpavvksaarrgkKPTDILLDVSIHYHAMKRLPLKHKRGRPDIVHVSLLEALESPLNKAG 83 
                                       89*************************************************************************** PP

                                       .EEEEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC...SEEEEE-TT CS
                              EMG1  62 llqvyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp..gskiillses 136
                                       ++++y+ht +++ I +np+tRiPr+++rF gLm+qL+k++si++ + + +Ll+v  +p++++l++     +ill e 
  gi|320101315|ref|YP_004176907.1|  84 MMEIYVHTLNGHAILINPSTRIPRNYNRFTGLMEQLFKEGSIPPGSAN-PLLRVETMPLERLLEAagARGLILLREA 159
                                       *********************************************999.***************9866678888888 PP

                                       SEE-.................EEEE-SSSS....---HH.......EEESSSS---HHHHHHHHHHHCH CS
                              EMG1 137 aekklvdleefv....vkpvvfvigamskgsvkidykee.......eisisnypLsaavvcskiltafE 194
                                       +e++  ++e+++    ++ +++ +g++++g    d++ee        +si ++pL +++v+s++++  E
  gi|320101315|ref|YP_004176907.1| 160 CEPH--RVEDVArealEEGLAVGVGGFPHG----DFEEEtlrhasrCYSIHREPLATWIVVSRVIAGAE 222
                                       8855..466666666699************....666666666777******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1692.94
//
Query:       gi|320101316|ref|YP_004176908.1|  [L=631]
Description: anaerobic ribonucleoside-triphosphate reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.3e-146  489.7   0.0   1.5e-146  489.5   0.0    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
     0.0022   17.7   0.0     0.0037   17.0   0.0    1.3  1  TackOD1         Thaumarchaeal output domain 1
     0.0034   17.4   0.1     0.0071   16.4   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.024   14.9   0.3      0.064   13.5   0.3    1.6  1  Ribosomal_L32p  Ribosomal L32p protein family
      0.044   13.2   1.5       0.08   12.4   1.5    1.4  1  zf-ribbon_3     zinc-ribbon domain
      0.097   12.7   0.2        0.2   11.7   0.2    1.4  1  DZR             Double zinc ribbon
        0.1   12.7   0.6       0.23   11.6   0.6    1.5  1  DUF1272         Protein of unknown function (DUF1272)
       0.22   11.0   0.0       0.36   10.3   0.0    1.3  1  GFP             Green fluorescent protein
       0.49   10.6   3.3         11    6.2   4.1    2.3  2  Zn-ribbon_8     Zinc ribbon domain
        3.2    7.7   5.6        8.4    6.4   5.1    2.0  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.5   0.0  8.3e-150  1.5e-146       1     561 []      27     629 ..      26     629 .. 0.92

  Alignments for each domain:
  == domain 1  score: 489.5 bits;  conditional E-value: 8.3e-150
                                       .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SS CS
                              NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgng 77 
                                       enan     +  + ++l +e++k+  l  llp ++ +ah++g i+iH+l + +l+++yC g++l++lle+Glkt   
  gi|320101316|ref|YP_004176908.1|  27 ENANR-YIGPGSFFSYLLEEYMKRDLL-GLLPGHILRAHRDGLIYIHKLPH-SLYIPYCTGHSLARLLEKGLKTPTV 100
                                       78888.88899999***********99.6********************88.688*******************999 PP

                                       S-B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTTS-S..S CS
                              NRDD  78 vsrppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynlntlpsrr 154
                                       +srp++h++t++++++n+l+tlq+ ++G+qa+ss+++y+ pf+r d      + ++++++q++q+++ynln +p+r 
  gi|320101316|ref|YP_004176908.1| 101 ISRPARHLDTFVDHVANYLITLQHYFTGAQAFSSVEWYAGPFIRGD------GADYRAVRQNIQRLLYNLN-YPTRI 170
                                       9*********************************************......*******************.***** PP

                                       SSS---EEEEEE.-HH................................HHHHHTTTTS-HCH----SEEEEEEEEET CS
                              NRDD 155 GaQvpFtninlgldtp.................tegrfee..kliikallevmleGdgnkgtpftFPilifklkedf 212
                                       G Q+pFtn+++ +d                   + g +e+  k +  al+e +++Gd   g+pftFPi++++ + ++
  gi|320101316|ref|YP_004176908.1| 171 GLQTPFTNFTIIMDAArkalegdyavydgrktePLGAYEKeaKTFLLALFENYMNGDSV-GQPFTFPIPTLMTTAKM 246
                                       *********************************7788877789****************.***************** PP

                                       ETTH.....HHHHHHHHHHTTT--EEE........EEES--GGGTT--------....................... CS
                              NRDD 213 nleeedpnydlfklalevtakrgfpyffnlle.dlepedekevasmgCRlrldege..................... 267
                                        +e+     ++ +++++++akrg+ y+ n+   d  p+    + +m+CRl ++++e                     
  gi|320101316|ref|YP_004176908.1| 247 LWED----PEIHEAVFKTAAKRGSFYWLNTRVvD--PD---ASYAMCCRLSIQKNEllyaykntgfslsslrkdaea 314
                                       ****....9******************9996423..44...478*********522344454566667777777777 PP

                                       ............S---.......EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              NRDD 268 ............rlgg.......rgslgvvtiNlprlaleakgdeekffelLdellelakealeerrkilekllakg 325
                                                   r+gg       +gs++vv +Nlprlale++gd+++f+el+de l l++ea++  r++  ++l ++
  gi|320101316|ref|YP_004176908.1| 315 lreeywgkmerqRFGGlwampdiTGSVNVVDVNLPRLALESRGDDDRFWELYDEALGLVREAVNWFRNRYVRMLREH 391
                                       7776666666655555************************************************9999999999988 PP

                                       ..-HHH.HTTSS-GE.............EEEEEEE-HHHHHHHT........TEEEE..-HHHHHHHHHHHHHHHHH CS
                              NRDD 326 ..lpflmgkgylksrkkkdeveevlkngtltiGfiGlaEalkal........tgkkigeseeakefalkvlkhmrek 392
                                         + + m  +y+          e+  ++++tiG+iGl Ea+++l        +g +  ++ +a e++ ++++h  e+
  gi|320101316|ref|YP_004176908.1| 392 pgFYY-MITEYMP---------EFPGTHFNTIGLIGLPEAAAILmqepklwlDGGRS-DWLRAGELMRRIVEHATET 457
                                       64444.5666775.........699**************************766565.9****************** PP

                                       HHHHHHHHSS-EEEEE---TTHHHHHHHHH..HH................HHG-SSSS-TTSSB-HHHHHHHHHHHT CS
                              NRDD 393 adelkeetglnfsleatPaEslsgrfakldkkkfgeipgvdke......pyYtNsfhvpvdekislfekikleaefq 463
                                       a+++++e+g+ +++e++PaEs+s r+a++d k+  e+ +          p+Y++s+ +++ ++++l e+i++ea +q
  gi|320101316|ref|YP_004176908.1| 458 ARRWMREEGTPWNVEEVPAESASPRMAEIDLKRHPELAE---YlpdpsnPVYSTSIAPYYASEMELPERIEVEAMVQ 531
                                       **********************************55555...3355789**************************** PP

                                       GGGTT-S-EEEEBSS--SSHHHHHHHHHHHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--BE.EEEEEESS CS
                              NRDD 464 klttGGailyieldeekknpealeklvkiakktgigYfsinpkidvCnecgy..kgeiekCpkCgseeevevirRit 538
                                       k++tGG++++i+l ee ++peal+kl k +++t+i+Y+s++p +++C++c++  +g++  Cp+Cgsee vev++Ri+
  gi|320101316|ref|YP_004176908.1| 532 KYFTGGVMMHIFLAEE-PEPEALAKLAKRIMETDIVYWSFTPALTYCPRCNKtyTGLHRACPRCGSEE-VEVWSRII 606
                                       *************877.9**********77888******************999***********877.******** PP

                                       SSEEEHHHHHHHHHHHSGG---B CS
                              NRDD 539 GYlrpvsswnkgkkaElkdRvkh 561
                                       GY+rp ++wn+ +++E+++R+++
  gi|320101316|ref|YP_004176908.1| 607 GYYRPLKNWNPQRRKEFWTRHHY 629
                                       ********************987 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.1e-06    0.0037      46     100 ..     547     601 ..     516     608 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                           TackOD1  46 skekeeseelleelvkrglleeelvdrirlCpsCksghlnvrevCpkCkSidiee 100
                                       + e e   +l++++ + +++  ++   +  Cp+C+     ++ +Cp C+S ++e 
  gi|320101316|ref|YP_004176908.1| 547 EPEPEALAKLAKRIMETDIVYWSFTPALTYCPRCNKTYTGLHRACPRCGSEEVEV 601
                                       44555778889999999*********************************99886 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     4e-06    0.0071      64      99 ..     568     601 ..     541     604 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4e-06
                                       EEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                              HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsadvei 99 
                                        + +p+ ++C +C+k+++  ++   Cp+Cgs++ve+
  gi|320101316|ref|YP_004176908.1| 568 WSFTPALTYCPRCNKTYTGLHR--ACPRCGSEEVEV 601
                                       5678999**********95534..7********997 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   3.5e-05     0.064      23      47 ..     571     596 ..     568     602 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                                       ---EEEETTTC.CEECTTC-BTTTTB CS
                    Ribosomal_L32p  23 apnlvecpncg.elklpHrvcpscGy 47 
                                       +p+l+ cp c+  ++  Hr+cp cG 
  gi|320101316|ref|YP_004176908.1| 571 TPALTYCPRCNkTYTGLHRACPRCGS 596
                                       58999*****98999*********95 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.5   4.5e-05      0.08       3      24 ..     575     596 ..     573     597 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGt 24 
                                       ++CP+C++   +   ++Cp CG+
  gi|320101316|ref|YP_004176908.1| 575 TYCPRCNKtY-TGLHRACPRCGS 596
                                       79******77.***********7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00011       0.2      29      49 .]     575     595 ..     552     600 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                               DZR  29 drCpsCgekvdpearfCpeCG 49 
                                       + Cp+C++  +  +r Cp CG
  gi|320101316|ref|YP_004176908.1| 575 TYCPRCNKTYTGLHRACPRCG 595
                                       557777777666667777776 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00013      0.23      30      50 ..     575     597 ..     561     601 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                           DUF1272  30 tFCaeCaeev..lenvCPncgGe 50 
                                       t+C +C ++   l+  CP cg e
  gi|320101316|ref|YP_004176908.1| 575 TYCPRCNKTYtgLHRACPRCGSE 597
                                       9*****9876448*******987 PP

>> GFP  Green fluorescent protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002      0.36      48     126 ..     228     305 ..     191     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                                       .-SS-GGGGTTT-----GGG-B--GGGG-HHHHTTTT-EEE.EEEEEETTS-EEEEEEEE.EEETTEEEEEEEEEEE CS
                               GFP  48 hlpvsfdllvttlkyGlkqfakypddmkdffkaaveeGglswertisleddGgyktvvevskleddtlvyrielkGi 124
                                       ++  +f   ++tl   +k++   p+  +  fk+a + G   w  t +++ d +y        ++++ l y  +  G 
  gi|320101316|ref|YP_004176908.1| 228 SVGQPFTFPIPTLMTTAKMLWEDPEIHEAVFKTAAKRGSFYWLNTRVVDPDASYAMCCRL-SIQKNELLYAYKNTGF 303
                                       4444555556888888999999********************************999999.6788888887777776 PP

                                       S- CS
                               GFP 125 dl 126
                                        l
  gi|320101316|ref|YP_004176908.1| 304 SL 305
                                       54 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.017        30      23      35 ..     571     583 ..     563     587 .. 0.79
   2 ?    6.2   4.1    0.0062        11       8      37 ..     577     600 ..     576     601 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.017
                       Zn-ribbon_8  23 dapltaCPeCgse 35 
                                        ++lt CP+C+++
  gi|320101316|ref|YP_004176908.1| 571 TPALTYCPRCNKT 583
                                       677888****975 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0062
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.evr 37 
                                       C +C+++++ l++       aCP+Cgs ev+
  gi|320101316|ref|YP_004176908.1| 577 CPRCNKTYTGLHR-------ACPRCGSeEVE 600
                                       9999999999974.......5******8775 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 ?    2.0   0.6      0.11     2e+02      20      31 ..     568     580 ..     568     583 .. 0.78
   2 ?    6.4   5.1    0.0047       8.4      11      37 .]     574     600 ..     573     600 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                           DUF35_N  20 vqfPPr.avCphC 31 
                                       + f P   +Cp+C
  gi|320101316|ref|YP_004176908.1| 568 WSFTPAlTYCPRC 580
                                       6677777999999 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0047
                           DUF35_N  11 gqrCpdCGtvqfPPravCphCgsddle 37 
                                       +++Cp C + +    ++Cp+Cgs ++e
  gi|320101316|ref|YP_004176908.1| 574 LTYCPRCNKTYTGLHRACPRCGSEEVE 600
                                       689*******99999********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4494.28
//
Query:       gi|320101317|ref|YP_004176909.1|  [L=274]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2096.85
//
Query:       gi|320101318|ref|YP_004176910.1|  [L=215]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-11   42.6   0.4    6.8e-11   42.6   0.4    2.2  2  DUF996    Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.4   3.8e-15   6.8e-11       2     118 ..      33     147 ..      32     153 .. 0.80
   2 ?    1.5   0.9     0.019   3.4e+02      31      57 ..     167     195 ..     153     207 .. 0.60

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 3.8e-15
                            DUF996   2 sivGliLvlvalkeiskavndekifsnaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvli 78 
                                       ++vGl Lvl +l e++ka+++e+ ++ a+ a+ +++++++v++++ l +++  at  e    +      ++  ++l+
  gi|320101318|ref|YP_004176910.1|  33 AFVGLLLVLEGLREVAKAYGEESAYKWAVKAVAVEVVGFAVFAALGLYAAYLEATLCEWWFCSP--TPRVFGRAALL 107
                                       689**************************************96665555555555444432222..23344444444 PP

                            DUF996  79 iayvlliisavflkksyellgkrtgvklFetagllyfiGa 118
                                       +++  +++ a++++k++++l+++tg+klF+ ag  ++ G+
  gi|320101318|ref|YP_004176910.1| 108 VLAASQLAGATLFRKAFDALASKTGEKLFKAAGVAMVAGT 147
                                       556789*****************************99985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.019
                            DUF996  31 iafilsiialvva..ilalllvlgalata 57 
                                        +++ ++ia+v++  ++ l +++ a++++
  gi|320101318|ref|YP_004176910.1| 167 LSIVPGVIAFVIIayVAPLTAWVPAAFAF 195
                                       45666666666664444445555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1463.68
//
Query:       gi|320101319|ref|YP_004176911.1|  [L=248]
Description: anaerobic ribonucleoside-triphosphate reductase activating protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-20   73.0   0.0    7.7e-20   71.9   0.0    1.5  2  Radical_SAM  Radical SAM superfamily
      1e-10   42.1   0.0    1.5e-10   41.5   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    3.6e-07   30.3   0.0    5.9e-07   29.6   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   1.3e-23   7.7e-20       6     165 ..      28     182 ..      24     184 .. 0.94
   2 ?   -2.8   0.0       1.2   7.4e+03     129     143 ..     226     240 ..     213     244 .. 0.56

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.3e-23
                                       EESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiri 80 
                                       gCnl+C+fC++++   +++++ r l+v+++l ev++ k   g +++++++ggepll+++    l+r++k+   g+ +
  gi|320101319|ref|YP_004176911.1|  28 GCNLKCPFCHNWRLaTGDREVCRPLDVDRLLSEVDSSK---GfIDYLHVTGGEPLLQYRGLAGLFRRVKE--IGVPV 99 
                                       9***********99888889999999999999998886...77***************************..7**** PP

                                       EEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                       +v tn tl   + l++l+e g +d+v+ +l+++  e +  ++     f+ ++++l++  e+ i+    ri++ +G +
  gi|320101319|ref|YP_004176911.1| 100 SVNTNLTL--YKPLKTLVEEGlIDHVATDLKTPFAELTGTPLSSSTLFKLYVDSLRLVVENEIP-LELRIPVAKGLT 173
                                       ********..7*************************8888888999******************.************ PP

                                       HHHHHHHHH CS
                                       xxxxxxxxx RF
                       Radical_SAM 157 deeleelle 165
                                          +ee +e
  gi|320101319|ref|YP_004176911.1| 174 AGSIEEAVE 182
                                       *99999887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 129 evlealeklreagik 143
                                       ev  + e++r++g+k
  gi|320101319|ref|YP_004176911.1| 226 EVETVAEAFRRRGFK 240
                                       344445555566666 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 !   41.5   0.0   2.6e-14   1.5e-10       6     101 ..      20     113 ..      14     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.6e-14
                           Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi..egltllGGEPllpenaeallelvkevk 80 
                                       v ++l++ gCnl+C++C+n  +   +++   + ++ ++++ +++ ++   + l ++GGEPll  +++ l+ l+++vk
  gi|320101319|ref|YP_004176911.1|  20 VTFTLWLCGCNLKCPFCHNWRLATGDREVCRPLDV-DRLLSEVDSSKGfiDYLHVTGGEPLL--QYRGLAGLFRRVK 93 
                                       6789**************99888888877776554.7777777654434499**********..************* PP

                           Fer4_12  81 eekpekdiwlytgytleelsk 101
                                       e ++ ++ + ++ + ++ l++
  gi|320101319|ref|YP_004176911.1|  94 EIGV-PVSVNTNLTLYKPLKT 113
                                       *999.6888888888877764 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   9.9e-11   5.9e-07       5      95 ..      26     111 ..      23     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9.9e-11
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       l gCnl+C++C n    +    ++    ++++ l++++ s+  i+ l +tGGePL   + + l  l +r+ke +  +
  gi|320101319|ref|YP_004176911.1|  26 LCGCNLKCPFCHNWR-LATGDREVCRPLDVDRLLSEVDSSKGFIDYLHVTGGEPL--LQYRGLAGLFRRVKEIG--V 97 
                                       479********9765.333333344444555666666666666899*********..7799***********99..* PP

                           Fer4_14  82 kiwletngtleiel 95 
                                       ++ ++tn tl + l
  gi|320101319|ref|YP_004176911.1|  98 PVSVNTNLTLYKPL 111
                                       *******9987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1640.41
//
Query:       gi|320101320|ref|YP_004176912.1|  [L=310]
Description: thymidylate synthase (FAD) [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  192.2   0.0    8.9e-57  191.9   0.0    1.1  1  Thy1      Thymidylate synthase complementing protein


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.9   0.0     5e-61   8.9e-57       1     188 []       9     241 ..       9     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 5e-61
                                       EEEEEE.CHHHHHHHHHHHHHTTCSSHHHH...S.GCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT CS
                              Thy1   1 kLldyt.dpeklvaaaarvcygsseeaeele..e.eekkeklikkllkhghgsplehasftfeiegvSravlrqlvr 73 
                                       +L++y+ d+ +++a+a +++  s+++++++   +  e++e+++++l+k+ghgspleh+ f fe+  +Sra+++qlvr
  gi|320101320|ref|YP_004176912.1|   9 RLVAYLhDSPRIIASASKLTL-SPKDFTSISegMsGERAEEWVRELVKRGHGSPLEHSLFVFEVV-CSRACSHQLVR 83 
                                       699******************.666777777664457788*************************.*********** PP

                                       -TTSEEEE--TTTSGCCCTC............................................BS--GGGCC.HHH CS
                              Thy1  74 HRiasfsqqSqRYvesskea............................................fvippeieqkeel 106
                                       HR+asfsq SqRY+++  +                                             f++pp + +  + 
  gi|320101320|ref|YP_004176912.1|  84 HRHASFSQLSQRYSDKYLRGmikkaceltgipyaedygaflrvlgslsasspgfhdlldvvaeaFIVPPRVVE--AE 158
                                       ****************99778*************************************************995..55 PP

                                       HHHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEEEEEEHHHHHH.HHHHHSSTTS-HHHHHHHHHHHHHH CS
                              Thy1 107 eelyeeamekaleaykelleagvarEdaryvLPlatktklvvtmNlrsLlh.flelracsrAqwEirelaeemleel 182
                                       ++ + ea+ + +e+y++++++g++ Edary+LP+a+kt+l+v+mN+r+Ll+ f+ lr+csrAqwE+r++a++ml el
  gi|320101320|ref|YP_004176912.1| 159 DKGFLEALLRGVESYYRAVASGISFEDARYLLPQAVKTRLLVSMNARELLEvFIPLRTCSRAQWEVRNVAWQMLMEL 235
                                       68899************************************************************************ PP

                                       HHHSHH CS
                              Thy1 183 kkvaPe 188
                                       ++vaPe
  gi|320101320|ref|YP_004176912.1| 236 RRVAPE 241
                                       *****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2231.58
//
Query:       gi|320101321|ref|YP_004176913.1|  [L=1035]
Description: DEAD/DEAH box helicase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   71.1   0.0    3.7e-19   69.2   0.0    2.0  2  DEAD        DEAD/DEAH box helicase
    4.8e-18   65.5   0.1    1.9e-17   63.6   0.1    2.0  2  Helicase_C  Helicase conserved C-terminal domain
      1e-05   25.6   0.0    2.5e-05   24.3   0.0    1.6  1  ResIII      Type III restriction enzyme, res subunit
     0.0085   15.8   0.0      0.026   14.2   0.0    1.9  1  AAA_30      AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.0       0.12   12.3   0.0    2.5  2  FERM_N      FERM N-terminal domain
      0.018   15.4   0.0       0.05   13.9   0.0    1.8  1  AAA_19      AAA domain
      0.039   13.9   0.0        7.1    6.6   0.0    2.5  2  Flavi_DEAD  Flavivirus DEAD 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 !   69.2   0.0   1.4e-22   3.7e-19       2     172 ..      52     230 ..      51     234 .. 0.75
   2 ?   -2.1   0.0       1.1   2.9e+03      50     102 ..     341     396 ..     327     402 .. 0.57

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.4e-22
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid... 75 
                                       + Q +a++++ +g++v+++a TGsGKT+a+++ vl++++   + ++ ++l + Pt +La++++++++++++  +   
  gi|320101321|ref|YP_004176913.1|  52 AHQYRAFQALREGRNVILKAGTGSGKTEAWMLYVLDELS---KGHRIRVLALYPTLALANDQVKRMNRYLSLFGdep 125
                                       6799**********************************5...69999************************766455 PP

                                       SEEEEEET.TSSHHHHHHHH..H.TTCSEEEEEHHHHHHHH.......HCTSSH..CTTEEEEEEETHHHHHHTTTH CS
                                       xxxxxxxx.xxxxxxxxxxx..x.xxxxxxxxxxxxxxxxx.......xxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 lrvlliig.gvaardqlskl..d.ngvdivvgtpgrlddll.......stgkln..lsqvrflVlDEadrlldqgfs 139
                                        ++ ++   +   r+  s++  + +++ +vv++p  +++ l       +t  l   ++++ +lV+DE+d ++     
  gi|320101321|ref|YP_004176913.1| 126 FQIDSVKRgEYVSRHGGSAMrlRaRSASVVVSNPAFILHDLkkylvrkQTALLAslYENIDLLVIDEIDFYSPR-SI 201
                                       334333221222233333332232449*******988886658887754444548899*************998.55 PP

                                       HHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 140 dfinrilnqlpqitcdgklqrqvivlSATlpkd 172
                                         + ++   l++ +++ +   qv vl+ATl+ +
  gi|320101321|ref|YP_004176913.1| 202 ALLLAMTDVLSTVSEK-PP--QVAVLTATLS-N 230
                                       6666666666444444.44..5********8.3 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                       EEEEESSHHHHHHHHHHHHHHTTT.STSEEEEEETTSSHHHHHHHH.HTT.CSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxx.xxxxx RF
                              DEAD  50 alivePtreLaeqtlnnlkkfkky.idlrvlliiggvaardqlskl.dng.vdivv 102
                                       +++ + + + ae++l++l+++  + i + ++  + ++++r+++++  ++g ++i++
  gi|320101321|ref|YP_004176913.1| 341 TIVFTRSISTAEEILRELRNRYGEnIPVATHHHLVSKKKREEVEEAaRSGrIKILI 396
                                       55555566667777777776666445555553333344444444441333566665 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         4     1e+04      14      49 ..     216     252 ..     204     260 .. 0.66
   2 !   63.6   0.1   7.3e-21   1.9e-17      14     110 ..     336     435 ..     326     436 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4
                                       TTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT CS
                        Helicase_C  14 eeggkilifvntidrlek.vklllekkgikvavlhge 49 
                                       e+  ++ + + t ++ ++   +l+ek g ++ v++g+
  gi|320101321|ref|YP_004176913.1| 216 EKPPQVAVLTATLSNPDDlGAFLKEKTGREYSVIDGK 252
                                       5566666666666644443467788889999999996 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 7.3e-21
                                       TTTSEEEEEESSHHHHHH.HHHHHHHT.....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                        Helicase_C  14 eeggkilifvntidrlek.vklllekk.....gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                       e+++ +++f+++i+++e+ ++ l   +     +i va++h   ++++ree+ e+ ++g++++Li+ + +++Gidi +
  gi|320101321|ref|YP_004176913.1| 336 EDEYLTIVFTRSISTAEEiLREL---RnrygeNIPVATHHHLVSKKKREEVEEAARSGRIKILISPRTLSQGIDIGE 409
                                       678899**********9444444...3356889******************************************** PP

                                       ESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  85 vnlVinfdlprnvtsyiqriGRtgRa 110
                                       +  Vi+++lp++v++++qr GR gR 
  gi|320101321|ref|YP_004176913.1| 410 AARVIHLGLPDDVREFHQREGRKGRR 435
                                       ************************95 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   9.8e-09   2.5e-05       4     141 ..      50     193 ..      47     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9.8e-09
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80 
                                       l+ +Q +a ++l+      + +++++k+ TG+GKT   +  +   l+kg++ ++l l p+++l +   ++++++ls 
  gi|320101321|ref|YP_004176913.1|  50 LYAHQYRAFQALR------EGRNVILKAGTGSGKTEAWMLYVLDELSKGHRIRVLALYPTLALANDQVKRMNRYLSL 120
                                       6667777777775......456799**********99988877777788999***********99888666444443 PP

                                       ............GEEEESSS-B--.......-SEEEEEHHHHHHTH............HHHTTT-SEEEEETG CS
                            ResIII  81 ayke........igkkvsgdkkkakekdstnkkilvttiqsldadseee....eeeseellrdrfdviiiDEa 141
                                         +e         g+ vs  + +a + ++ +++++v++   +  d+++     + +    l +++d+++iDE 
  gi|320101321|ref|YP_004176913.1| 121 FGDEpfqidsvkRGEYVSRHGGSAMRLRARSASVVVSNPAFILHDLKKYlvrkQTALLASLYENIDLLVIDEI 193
                                       222233334444444455555555889999****************77799877777778889999*****96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     1e-05     0.026       2     108 ..      50     204 ..      49     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                            AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKtta..lkalreaweaaggrviglAptgkaAkv.La............ 63 
                                       l a Q +a++al ++++  ++l+++ G+GKt a  l +l e+ + +  rv++l pt + A++ ++            
  gi|320101321|ref|YP_004176913.1|  50 LYAHQYRAFQALREGRN--VILKAGTGSGKTEAwmLYVLDELSKGHRIRVLALYPTLALANDqVKrmnrylslfgde 124
                                       7899*****99888886..9***********8622666788888777888876677666654344333555555553 PP

                            AAA_30  64 ....eelgieastiakllkrlk....................................grarlepg.tllivDEagm 99 
                                           +     +    ++++r++                                      a+l ++ +ll++DE+  
  gi|320101321|ref|YP_004176913.1| 125 pfqiD-----SVKRGEYVSRHGgsamrlrarsasvvvsnpafilhdlkkylvrkqtalL-ASLYENiDLLVIDEIDF 195
                                       33330.....3333333333334444444444444444555555555577778777741.34555668888888777 PP

                            AAA_30 100 vdtkqlaal 108
                                        + +++a l
  gi|320101321|ref|YP_004176913.1| 196 YSPRSIALL 204
                                       666666555 PP

>> FERM_N  FERM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.39   9.9e+02      22      34 ..     524     536 ..     522     552 .. 0.83
   2 ?   12.3   0.0   4.7e-05      0.12      30      62 ..     750     784 ..     741     787 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.39
                                       HHHHHHHHHT-S- CS
                            FERM_N  22 lLdtVcariglte 34 
                                       +LdtV++r++  e
  gi|320101321|ref|YP_004176913.1| 524 MLDTVFERLNFYE 536
                                       9*******99655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.7e-05
                                       HT-S-GGGEEEEE--SSS..-SXEEE-SSS-CGGG CS
                            FERM_N  30 igltehdyFgLvfmeekk..degnWLdhsktLreq 62 
                                       +++ e +yF+L + e  +  + +nWLd  kt++e+
  gi|320101321|ref|YP_004176913.1| 750 VKIGEYKYFSLHEPEAAGliNTFNWLDVRKTVEEY 784
                                       7899*********5555599************997 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.9e-05      0.05       3     126 ..      56     208 ..      54     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                            AAA_19   3 eave.alkekvllvtaGpGtGKTrvlk.hivallvelggvkpeeil.lvaftgrAakelrerlaalgae........ 68 
                                       +a +   + +++++ aG G+GKT+  +  ++ +l + +++ +  ++  +a+++  +k+++  l+ +g e        
  gi|320101321|ref|YP_004176913.1|  56 RAFQaLREGRNVILKAGTGSGKTEAWMlYVLDELSKGHRIRVLALYpTLALANDQVKRMNRYLSLFGDEpfqidsvk 132
                                       66665678899************975515667777777765533332567778888899988855555599989988 PP

                            AAA_19  69 ...........................atTiHrlalldfddlltealelleeaeeekklqeee.llivDEfqdvdel 117
                                                                  a  +H l     + l+ ++ +ll        l e+  ll++DE+   ++ 
  gi|320101321|ref|YP_004176913.1| 133 rgeyvsrhggsamrlrarsasvvvsnpAFILHDL--K--KYLVRKQTALLA------SLYENIdLLVIDEIDFYSPR 199
                                       8888777777766666666655555555555555..2..222222333333......344444599****9999999 PP

                            AAA_19 118 qyrLlkall 126
                                         +Ll a++
  gi|320101321|ref|YP_004176913.1| 200 SIALLLAMT 208
                                       999988876 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.012        30       3      48 ..      63     109 ..      61     126 .. 0.82
   2 ?    6.6   0.0    0.0028       7.1      87     115 ..     176     204 ..     146     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                                       X--EEEEE--TTS-TTTTHHHHHHHHHHH.TT--EEEEESSHHHHHH CS
                        Flavi_DEAD   3 kkkltvldlhPGaGktrkvlpelvkeaie.rrlrtlvLaPtrvvlae 48 
                                       +++  +l++  G+Gkt   +  +++e  + +r+r l L Pt   +++
  gi|320101321|ref|YP_004176913.1|  63 EGRNVILKAGTGSGKTEAWMLYVLDELSKgHRIRVLALYPTLALAND 109
                                       66778899999********99999987653899********877665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0028
                                       HHHT------SEEEEETTT--SHHHHHHH CS
                        Flavi_DEAD  87 llspvrkknyeliimDeahflDPasiaar 115
                                        l     +n +l+++De  f  P sia  
  gi|320101321|ref|YP_004176913.1| 176 ALLASLYENIDLLVIDEIDFYSPRSIALL 204
                                       566677899*****************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1035 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 6883.31
//
Query:       gi|320101322|ref|YP_004176914.1|  [L=119]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.071   12.8   3.6       0.12   12.1   3.6    1.4  1  DUF2244    Integral membrane protein (DUF2244)
        1.2    8.8   5.7       0.84    9.3   4.0    1.6  2  Kinocilin  Kinocilin protein


Domain annotation for each model (and alignments):
>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.6   1.3e-05      0.12      11      73 ..       6      70 ..       2      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
                           DUF2244 11 gflllllalalvslvialafl..laGawpvlpFaglevlalalafrvsarhardrEeitltdeel 73
                                      +++ ++ +la++++++ la+   +    +v +F+    +al++  +     ++++E+i + + ++
  gi|320101322|ref|YP_004176914.1|  6 QAVYVYSMLAGLLIIVLLAVSslFELKGIVKIFFTASSIALIVLHYTALYMMARYERIAVYPFTI 70
                                      77888888888888888877653666678999***************************998776 PP

>> Kinocilin  Kinocilin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.0   9.4e-05      0.84      12      66 ..       3      60 ..       1      72 [. 0.73
   2 ?   -0.9   0.0      0.14   1.2e+03      35      60 ..      72      97 ..      63     114 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 9.4e-05
                         Kinocilin 12 clqlacvalsllagsiiig.vsvskaaa..avggifigaaglgllllaypflkarfnl 66
                                      +l+ a    s+lag +ii+ ++vs+      +  if  a+++ l++l y  l      
  gi|320101322|ref|YP_004176914.1|  3 MLDQAVYVYSMLAGLLIIVlLAVSSLFElkGIVKIFFTASSIALIVLHYTALYMMARY 60
                                      577788899*****877652677776541155578**************976544444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.14
                         Kinocilin 35 kaaaavggifigaaglgllllaypfl 60
                                      + aaa g i      + +l+l + + 
  gi|320101322|ref|YP_004176914.1| 72 EEAAAGGSISPDVGQITILVLLFTWR 97
                                      45666677766666677777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 889.22
//
Query:       gi|320101323|ref|YP_004176915.1|  [L=212]
Description: excisionase family DNA-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-26   91.8   0.6    5.9e-26   91.3   0.6    1.2  1  Resolvase     Resolvase, N terminal domain
    2.8e-14   53.0   0.2    7.1e-14   51.7   0.2    1.7  1  HTH_17        Helix-turn-helix domain
    5.4e-07   29.3   0.8    1.2e-06   28.2   0.4    1.8  2  MerR          MerR family regulatory protein
    8.1e-06   25.8   0.1    2.1e-05   24.5   0.1    1.7  1  MerR_1        MerR HTH family regulatory protein
      8e-05   22.3   0.1    0.00025   20.8   0.1    1.8  1  HTH_23        Homeodomain-like domain
    0.00033   20.7   0.1     0.0024   18.0   0.1    2.3  2  HTH_28        Helix-turn-helix domain
    0.00088   19.3   0.0      0.002   18.1   0.0    1.6  1  HTH_29        Winged helix-turn helix
     0.0024   18.1   0.0     0.0054   17.0   0.0    1.6  1  HTH_Tnp_1     Transposase
  ------ inclusion threshold ------
      0.065   12.7   0.0       0.25   10.8   0.0    2.0  2  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.088   12.6   0.1       0.28   11.0   0.0    1.9  2  HTH_8         Bacterial regulatory protein, Fis family


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.6   3.3e-29   5.9e-26       1     136 [.      64     195 ..      64     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 3.3e-29
                                       EEEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC- CS
                         Resolvase   1 aigYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLa 77 
                                       a++YaRvS+++q+++lerQ++ l +y++ +g+++v++ +D  +SG ++eR+ l+rl ++++++ +dv+vv   dRL+
  gi|320101323|ref|YP_004176915.1|  64 AVIYARVSSADQRNDLERQTQYLFQYCATKGYRVVEILTDI-ASGLNTERRVLRRLFDLVTNRSVDVVVVAYKDRLT 139
                                       69***************************************.*********************************** PP

                                       S...S-HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHHHHHHHCT-TTH CS
                         Resolvase  78 Rsvrdlltlleelrekgvslvsldegidtstpmgrlllqilaalaeferelirertkeg 136
                                       R  +++l++   +r+ gv++ ++    +++++m++l+ +++a++a f  +l  +r+++ 
  gi|320101323|ref|YP_004176915.1| 140 RFGFEYLEY--FFRKFGVRIEVAFG-EEPKDAMQELVEDMIAIIASFAGKLYGMRSHKK 195
                                       *********..89***********5.89************************9999875 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.2     4e-17   7.1e-14       1      47 [.       6      53 ..       6      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 4e-17
                            HTH_17  1 lltveEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsdleewl 47
                                      ll ++E +++Lgvs st++r+i++g ++a + +G+++rip s++e+ l
  gi|320101323|ref|YP_004176915.1|  6 LLRPSETCRILGVSYSTLRRWISEGHIKAIRtVGGKYRIPYSEVERLL 53
                                      6899**************************99*************987 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.4   6.5e-10   1.2e-06       3      35 ..      10      41 ..       8      44 .. 0.88
   2 ?   -3.0   0.0       3.7   6.7e+03       4      13 ..      48      57 ..      47      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 6.5e-10
                                      HHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSS CS
                              MerR  3 gevAeltGvsprtLRyYEreGLipppeRtegGy 35
                                      +e ++++Gvs +tLR++ +eG i +++Rt gG 
  gi|320101323|ref|YP_004176915.1| 10 SETCRILGVSYSTLRRWISEGHI-KAIRTVGGK 41
                                      67799******************.******885 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.7
                                      HHHHHHTTTH CS
                              MerR  4 evAeltGvsp 13
                                      ev +l+G+ p
  gi|320101323|ref|YP_004176915.1| 48 EVERLLGLKP 57
                                      8889999876 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 !   24.5   0.1   1.2e-08   2.1e-05       3      46 ..       9      52 ..       7      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.2e-08
                                      HHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHH CS
                            MerR_1  3 igevakilgvtthtlrywekegllkpkrteggrryYtdedierL 46
                                       +e ++ilgv+++tlr w  eg +k  rt gg ++   +++erL
  gi|320101323|ref|YP_004176915.1|  9 PSETCRILGVSYSTLRRWISEGHIKAIRTVGGKYRIPYSEVERL 52
                                      5899************************9988888777778777 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.4e-07   0.00025      17      39 ..       6      28 ..       2      29 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlk 39
                                       l+++e +r+Lgvs++T++rw++
  gi|320101323|ref|YP_004176915.1|  6 LLRPSETCRILGVSYSTLRRWIS 28
                                      57899****************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 !   18.0   0.1   1.3e-06    0.0024      15      34 ..       9      28 ..       2      29 .. 0.90
   2 ?   -0.6   0.0      0.82   1.5e+03       6      36 ..     101     134 ..      98     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-06
                            HTH_28 15 vreaArelgisrrtvyrWik 34
                                       +e++r+lg+s++t++rWi+
  gi|320101323|ref|YP_004176915.1|  9 PSETCRILGVSYSTLRRWIS 28
                                      689***************96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.82
                            HTH_28   6 ikllaaGh..svreaArelgi.srrtvyrWikry 36 
                                       +  +a+G    +r + r++ + + r+v + + +y
  gi|320101323|ref|YP_004176915.1| 101 LTDIASGLntERRVLRRLFDLvTNRSVDVVVVAY 134
                                       5556666335677788888888999998887766 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06     0.002      13      33 ..       7      27 ..       1      35 [. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                            HTH_29 13 stvsqiAkllglsrrtvyrwl 33
                                       ++s+ +++lg+s++t +rw+
  gi|320101323|ref|YP_004176915.1|  7 LRPSETCRILGVSYSTLRRWI 27
                                      3899****************9 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     3e-06    0.0054      27      72 ..      10      64 ..       3      66 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                         HTH_Tnp_1 27 sevArrhgvspnqLykWrrqyr.egeeaspae........feltaleeenrelkr 72
                                      se++r +gvs+++L++W+++   + +     +         +l+ l++e++e ++
  gi|320101323|ref|YP_004176915.1| 10 SETCRILGVSYSTLRRWISEGHiKAIRTVGGKyripysevERLLGLKPEVKEVRA 64
                                      89****************9866633333333334444455566666666666665 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 ?   10.8   0.0   0.00014      0.25      32      49 ..      11      28 ..      10      31 .. 0.88
   2 ?   -2.2   0.0       1.6   2.9e+03      30      47 ..      35      52 ..      32      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                      HTH_Tnp_ISL3 32 avArqlgvSwtTVwrild 49
                                      + +r+lgvS +T++r++ 
  gi|320101323|ref|YP_004176915.1| 11 ETCRILGVSYSTLRRWIS 28
                                      689*************86 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                      HTH_Tnp_ISL3 30 vkavArqlgvSwtTVwri 47
                                      +++v   +++  + V+r 
  gi|320101323|ref|YP_004176915.1| 35 IRTVGGKYRIPYSEVERL 52
                                      678888899999999996 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 ?   11.0   0.0   0.00015      0.28      22      37 ..      10      25 ..       9      29 .. 0.92
   2 ?   -3.5   0.1       5.2   9.3e+03      31      37 ..     111     117 ..     105     117 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                      HHHHHHHTS-HHHHHH CS
                             HTH_8 22 skAArlLGisRrtLyr 37
                                      s+++r+LG+s +tL+r
  gi|320101323|ref|YP_004176915.1| 10 SETCRILGVSYSTLRR 25
                                      789***********98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.2
                                       -HHHHHH CS
                             HTH_8  31 sRrtLyr 37 
                                        Rr L+r
  gi|320101323|ref|YP_004176915.1| 111 ERRVLRR 117
                                       5777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1552.34
//
Query:       gi|320101324|ref|YP_004176916.1|  [L=415]
Description: transposase, IS605 OrfB family [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-18   65.2   0.0      9e-18   64.0   0.0    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.042   14.0   1.2      0.089   13.0   1.2    1.6  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.092   12.2   1.4        0.2   11.1   1.4    1.5  1  zf_Rg           Reverse gyrase zinc finger
       0.16   12.2   0.2        4.7    7.6   0.0    2.9  2  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b
       0.58   10.5   2.6       0.91    9.8   0.2    2.2  2  zinc_ribbon_9   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 !   64.0   0.0   2.5e-21     9e-18       1      69 []     298     366 ..     298     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 2.5e-21
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       fr++ + + +ka+e+Gi+v++vnp+ TS+tC++Cg ++ + +++r + C +Cg e  rD+ A++Ni +r
  gi|320101324|ref|YP_004176916.1| 298 FRSMVREIVQKAREKGIPVIKVNPRGTSSTCPQCGGRLVRGNAPRSLLCLHCGWEGGRDIAAVMNIERR 366
                                       889999************************************************************775 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   2.5e-05     0.089      15      40 .]     325     350 ..     324     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                     Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCvaCd 40 
                                       ++tCp+Cg  L+r      ++C  C+
  gi|320101324|ref|YP_004176916.1| 325 SSTCPQCGGRLVRGNAPRSLLCLHCG 350
                                       789**********9878899*****6 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   5.6e-05       0.2       8      31 ..     326     349 ..     324     362 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.6e-05
                             zf_Rg   8 klCPNCgGdisdeRlekGLpCkrC 31 
                                       + CP CgG +    + + L+C +C
  gi|320101324|ref|YP_004176916.1| 326 STCPQCGGRLVRGNAPRSLLCLHC 349
                                       78********************99 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 ?    0.9   0.0      0.15   5.5e+02      18      56 ..     210     244 ..     205     247 .. 0.81
   2 ?    7.6   0.0    0.0013       4.7      32      51 ..     302     321 ..     290     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                     SpoU_sub_bind  18 iekllvtegradkrleellklakkrgikvelvdkekLdk 56 
                                       i+k+ v  +  ++r  e+l+  k ++     v +++++k
  gi|320101324|ref|YP_004176916.1| 210 IRKITVGYH--NRR--EILQSTKGNRYASRMVKRNEFNK 244
                                       556666666..677..9*****************99997 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0013
                     SpoU_sub_bind  32 leellklakkrgikvelvdk 51 
                                       ++e++++a+++gi+v++v++
  gi|320101324|ref|YP_004176916.1| 302 VREIVQKAREKGIPVIKVNP 321
                                       68****************97 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00025      0.91      13      32 ..     318     336 ..     315     338 .. 0.80
   2 ?    0.4   0.1      0.23   8.3e+02      22      28 ..     344     350 ..     334     354 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                     zinc_ribbon_9  13 svspdedsdvlCPhCgggFV 32 
                                        v p+ +s + CP+Cgg  V
  gi|320101324|ref|YP_004176916.1| 318 KVNPRGTSST-CPQCGGRLV 336
                                       6778888888.*****9765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.23
                     zinc_ribbon_9  22 vlCPhCg 28 
                                        lC hCg
  gi|320101324|ref|YP_004176916.1| 344 LLCLHCG 350
                                       37****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2882.06
//
Query:       gi|320101325|ref|YP_004176917.1|  [L=334]
Description: zinc-binding alcohol dehydrogenase family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-35  121.1   2.5    3.4e-35  120.2   2.5    1.4  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    7.8e-07   30.2   0.2    1.7e-06   29.2   0.1    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    1.9e-06   27.8   0.0    1.5e-05   25.0   0.0    2.3  2  ADH_zinc_N    Zinc-binding dehydrogenase
  ------ inclusion threshold ------
       0.16   11.3   0.0       0.29   10.5   0.0    1.4  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
        0.2   10.9   0.0       0.28   10.5   0.0    1.2  1  BKACE         beta-keto acid cleavage enzyme
       0.53   10.4   3.8       0.47   10.6   1.1    2.1  2  NADH_4Fe-4S   NADH-ubiquinone oxidoreductase-F iron-sulfur bi


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   2.5   1.1e-38   3.4e-35       2     108 ..      30     136 ..      29     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 1.1e-38
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE.-SSSHHHHTT- CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvveplis.cgeCaaCkege 77 
                                       gevli+v+ +g+C++Dlhi++g +  +vklp+i+GH +vG+veevg++v++++ G+rV v++l+  cgeC++C++g 
  gi|320101325|ref|YP_004176917.1|  30 GEVLIRVHKCGVCRTDLHIVEG-ELKPVKLPVIPGHQVVGVVEEVGEGVEGVSPGERVGVPWLYYsCGECRYCRRGL 105
                                       79********************.8************************************998766*********** PP

                                       GGG-TTBEETTTSS-SSSBSEEEECGGGEEE CS
                             ADH_N  78 enlCeeakllgvsldGgfaeyvvvpekklvk 108
                                       enlCe+a ++g+s+dGg+aey+v+++ ++++
  gi|320101325|ref|YP_004176917.1| 106 ENLCENALFTGYSVDGGYAEYMVAKAGFIHR 136
                                       ************************9988765 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   5.5e-10   1.7e-06      23     133 .]     228     331 ..     214     331 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.5e-10
                                       EEEEEES-H.HHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHHHHH CS
                      ADH_zinc_N_2  23 vDvvldtvg.gealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaalie 98 
                                        D+++  +  ++ ++ea++kv +g Gr+v     +++ + l+ ++ + +r vk +  +      ++d  +e ++  e
  gi|320101325|ref|YP_004176917.1| 228 LDAAIVYAPvSQVFIEALRKVDKG-GRVVLAEIYMTPVERLDYSLLWYEREVKSVANV-----TRRD-VREFLEIAE 297
                                       555555555667787777765555.998754432234444444444444444444444.....4788.********* PP

                                       HHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  99 eGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                       ++ ++p v  +++l+ea+eA++ l++g + G iVl
  gi|320101325|ref|YP_004176917.1| 298 KHGVKPEVK-TYGLKEANEALEELKKGGHLGQIVL 331
                                       ********7.9***********************8 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.9e-09   1.5e-05       4     125 ..     183     293 ..     181     298 .. 0.75
   2 ?   -0.0   0.0      0.27     8e+02      27      56 ..     293     324 ..     280     333 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.9e-09
                                       HHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                        ADH_zinc_N   4 laavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                       ++++q+A+ lG +v++  ss+ k+e+a ++Ga+ +  ++e            ++++d+++ ++ + +++ +al+ ++
  gi|320101325|ref|YP_004176917.1| 183 HLVLQVARRLGLRVYVFTSSRWKIEKALENGAEWAGGTSE---------EP-PRKLDAAIVYAPVSQVFIEALRKVD 249
                                       6799*******************************99944.........44.56777777888888*********** PP

                                       EEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHHHH CS
                        ADH_zinc_N  81 pgGrlvvvGggkgeee.fdlrnlllkeksilGsllgslreefkeal 125
                                       +gGr+v+  + + + e +d + l++ e+ ++ +   + r++++e+l
  gi|320101325|ref|YP_004176917.1| 250 KGGRVVLAEIYMTPVErLDYSLLWY-EREVKSVANVT-RRDVREFL 293
                                       *******998444443366665553.34444444444.45555555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.27
                                       HHHHHHTTESEEEETTTC.HHHHHHHHHTT.T CS
                        ADH_zinc_N  27 lelakklGadevinykea.dlverikeltg.g 56 
                                       le+a+k G++  + +    + +e+++el + g
  gi|320101325|ref|YP_004176917.1| 293 LEIAEKHGVKPEVKTYGLkEANEALEELKKgG 324
                                       78889999888887745555777777777523 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 ?   10.5   0.0   9.7e-05      0.29      35      82 ..     169     216 ..     157     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.7e-05
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEE CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvel 82 
                                       s+  +G++G+G+ ++ v ++++ +g++v+++  s+ k e++ e+g+e+
  gi|320101325|ref|YP_004176917.1| 169 SDAVLGLFGYGAAAHLVLQVARRLGLRVYVFTSSRWKIEKALENGAEW 216
                                       56789***************************9999888777777765 PP

>> BKACE  beta-keto acid cleavage enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.2e-05      0.28     118     162 ..     279     323 ..     235     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.2e-05
                                       GCEE---HHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHHHHTT CS
                             BKACE 118 dlvfentpedieellrrmaeagvkpeievfdvghlrnvkrlieeG 162
                                       + v + t +d++e+l+  +++gvkpe++ + +++ +++ + +++G
  gi|320101325|ref|YP_004176917.1| 279 KSVANVTRRDVREFLEIAEKHGVKPEVKTYGLKEANEALEELKKG 323
                                       6788899**************************998887777776 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.74   2.2e+03      16      23 ..      37      44 ..      36      53 .. 0.82
   2 ?   10.6   1.1   0.00016      0.47      14      30 ..      94     110 ..      92     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.74
                                      S--HHHHI CS
                       NADH_4Fe-4S 16 GkCtpCre 23
                                      +kC+ Cr 
  gi|320101325|ref|YP_004176917.1| 37 HKCGVCRT 44
                                      59999996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                                       --S--HHHHIIIIHHHH CS
                       NADH_4Fe-4S  14 sCGkCtpCreGtkrlle 30 
                                       sCG+C  Cr G++ l e
  gi|320101325|ref|YP_004176917.1|  94 SCGECRYCRRGLENLCE 110
                                       9***********98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 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:                        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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2387.87
//
Query:       gi|320101326|ref|YP_004176918.1|  [L=451]
Description: PMT multi-domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3369.59
//
Query:       gi|320101327|ref|YP_004176919.1|  [L=184]
Description: dCTP deaminase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   58.6   0.0    7.4e-16   58.0   0.0    1.2  1  dUTPase   dUTPase
     0.0066   15.3   0.0      0.018   13.8   0.0    1.7  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   8.2e-20   7.4e-16      24     126 ..      71     169 ..      67     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 8.2e-20
                                       EEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEE CS
                           dUTPase  24 ltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLi 100
                                       ++v p e+vl +t  +++ p++l +l++ RS +a+ gl ++p+vid+ ++G++ + l+ +t  +v++  g+R+++Li
  gi|320101327|ref|YP_004176919.1|  71 FVVNPLEHVLTTTLEYVEFPNDLIGLVNLRSTFARYGLYIPPTVIDAGFKGNITIELVGSTI-PVRVYPGQRFLHLI 146
                                       78999**********************************************99999999999.************** PP

                                       EEEBECGEEEEESSTTTESSBTTXTT CS
                           dUTPase 101 fariltaeleevetlkatergeggfg 126
                                       +ar+       ++  + +++g++g++
  gi|320101327|ref|YP_004176919.1| 147 LARTSS---PVYKPYSGKYQGQRGVT 169
                                       **9999...45555589999999985 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 !   13.8   0.0     2e-06     0.018       4     165 ..       2     152 ..       1     169 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-06
                               DCD   4 ilpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaeklee.lklheldLtegavle 79 
                                       il+d +i+  +e++ +   +pl e+ +  + +DLr g++  r r        +++++ +++ l++ ++   eg v++
  gi|320101327|ref|YP_004176919.1|   2 ILSDWDIRVYLEKKLL-VIDPLFEDTVRENGVDLRFGEEFCRFRRGAR--VVDTLRDGVDDvLECSRVG-GEGFVVN 74 
                                       5666677766666655.5567778888888888888888877774422..2334444444413333333.5677777 PP

                               DCD  80 kgcvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleisprsFsilvrkGsrLs 156
                                            +   le ++ p+dl + +n +s+  R  +++            ++ag+kG++ +e++  + +++v +G+r  
  gi|320101327|ref|YP_004176919.1|  75 PLEHVLTTTLEYVEFPNDLIGLVNLRSTFARYGLYIPP--------TVIDAGFKGNITIELVGSTIPVRVYPGQRFL 143
                                       76666777788899999999999999998888887542........35899************************99 PP

                               DCD 157 qirfrrgea 165
                                        + + r+++
  gi|320101327|ref|YP_004176919.1| 144 HLILARTSS 152
                                       998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       173  (0.00964917); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1306.47
//
Query:       gi|320101328|ref|YP_004176920.1|  [L=231]
Description: nucleotidyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-36  124.8   0.0    4.8e-36  124.6   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    9.8e-13   48.8   0.0      2e-12   47.7   0.0    1.5  2  NTP_transf_3     MobA-like NTP transferase domain
     0.0025   17.6   0.0     0.0031   17.3   0.0    1.2  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 !  124.6   0.0     8e-40   4.8e-36       2     245 ..       3     226 ..       2     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 8e-40
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       avILaGG+G+RL+P t +++k++vpv++  ++++ +++ l + g++e  v l  ++++ + e++++gs++gv+v+++
  gi|320101328|ref|YP_004176920.1|   3 AVILAGGYGKRLRPFTEDTPKPMVPVGDR-PILEWQIEWLKRYGFNE-FVLLVGYKKEKIIEHIGSGSRLGVRVTYV 77 
                                       8****************************.*****************.8888889999999**************** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                       +e+e+ gt +Av+ a+ +l +++    +lv++gD++++ +  ++++k ++++     + +i     ++ yGv e+++
  gi|320101328|ref|YP_004176920.1|  78 VEDEPLGTGGAVKNAEHVLSRDNA---FLVVNGDIITNLNPLRLFEKLEKAGY----LGVIASIPLPSPYGVLEIEG 147
                                       ********************9996...***********999999999888887....788888899*********** PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEX CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDv 232
                                       +++v+ f+EKP+  +  +++++G+Y  ++++l++        +++ d  + ++p++ +eg+    +  ++   W+ +
  gi|320101328|ref|YP_004176920.1| 148 DDKVKGFIEKPQLSD--YWINAGVYALTPDALKYF-------PERGDLEKTAFPAMAREGRLG-TVRYTGV-FWKAI 213
                                       *************99..**************9998.......445555566777777776544.4555554.68888 PP

                                       SSHHHHHHHHHHH CS
                   NTP_transferase 233 Gtldslleanekl 245
                                        t++ l ea++++
  gi|320101328|ref|YP_004176920.1| 214 DTFKELEEASKAI 226
                                       8888888888776 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 !   47.7   0.0   3.4e-16     2e-12       1      97 [.       3     110 ..       3     134 .. 0.79
   2 ?   -2.4   0.0      0.91   5.4e+03      98     127 ..     171     199 ..     165     227 .. 0.55

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.4e-16
                                       EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCT..S-EEE- CS
                      NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlg..vrvved 65 
                                       aviLAGG ++R+    +  +K+++p+g++p+le++++ l++ g++e v+ +g+  e++ +++    rlg  v++v++
  gi|320101328|ref|YP_004176920.1|   3 AVILAGGYGKRLRpftEdtPKPMVPVGDRPILEWQIEWLKRYGFNEFVLLVGYkkEKIIEHIgsgSRLGvrVTYVVE 79 
                                       79**********6443145**************************99999999554555554333455622555555 PP

                                       TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-T CS
                      NTP_transf_3  66 edpgkgplaslaaalraaadadavlvlacDmP 97 
                                       + +  g++++++ a + ++++ a+lv+ +D++
  gi|320101328|ref|YP_004176920.1|  80 D-EPLGTGGAVKNAEHVLSRDNAFLVVNGDII 110
                                       5.469*************9***********85 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.91
                                       T--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3  98 lltpelverllaaaaasgadvvvptyeger 127
                                        ltp++++++ ++ + ++ +  + ++e +r
  gi|320101328|ref|YP_004176920.1| 171 ALTPDALKYFPERGDLEKTAFPAMARE-GR 199
                                       578888888888876444433333333.33 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 !   17.3   0.0   5.2e-07    0.0031       1      99 [.       1     107 [.       1     160 [. 0.71

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-07
                                       EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.....CCEE CS
                              IspD   1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.....ksiq 69 
                                       + +vi A G GkR++   +++pK  + + ++++le+ ++ l  ++  + +++v  +++ + +e++ +      + ++
  gi|320101328|ref|YP_004176920.1|   1 MLAVILAGGYGKRLRpftEDTPKPMVPVGDRPILEWQIEWLKRYGFNEFVLLVGYKKE-KIIEHIGSGsrlgvR-VT 75 
                                       579**********854448**************************9999999999988.788887766555533.33 PP

                                       EEE--S..SHHHHHHHHHHTTSSTTSEEEE-- CS
                              IspD  70 lvaGGd..eRaesVlnglkalegeakfVLvHD 99 
                                        v+  +      +V+n+ ++l+ +++f +v  
  gi|320101328|ref|YP_004176920.1|  76 YVVEDEplGTGGAVKNAEHVLSRDNAFLVVNG 107
                                       33322211233456666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1779.84
//
Query:       gi|320101329|ref|YP_004176921.1|  [L=185]
Description: peptidase zinc-dependent [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-30  104.9   0.0    5.6e-30  104.8   0.0    1.1  1  Peptidase_M54  Peptidase family M54
    3.5e-05   23.7   0.1    3.6e-05   23.7   0.1    1.4  1  Peptidase_M10  Matrixin
  ------ inclusion threshold ------
       0.15   10.6   0.2       0.22   10.1   0.2    1.2  1  Metallopep     Putative peptidase family
       0.15   11.9   0.1       0.23   11.4   0.1    1.2  1  Peptidase_M43  Pregnancy-associated plasma protein-A
       0.18   12.3   0.0       0.26   11.8   0.0    1.4  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
       0.21   10.8   0.0       0.33   10.1   0.0    1.2  1  DUF4953        Met-zincin
       0.26   10.9   0.0       0.37   10.4   0.0    1.2  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.0   2.2e-33   5.6e-30      58     193 ..      49     184 ..       1     185 [] 0.85

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 2.2e-33
                                       GGGEETTTTEEEHHHHHHHHHT--S--..SEE........EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T..--. CS
                     Peptidase_M54  58 egavkmyrleavveallgkLkemkddvndDsitkifgittlplgsrdqyidiykkvlGievsiGnyavlals..ike 132
                                       ++ ++++r ++ ++ l++ L++  +    ++ t       l+lg  d y +++++v+G ++     a+++ +  ++e
  gi|320101329|ref|YP_004176921.1|  49 IKCFNWERKQYRAQCLIEYLRSTLQLSGVERST-----PVLGLGFLDGYEEGLNFVFGEAMPNLSAAIVFSKrlRQE 120
                                       6789****************9987555455553.....45789999***************988999998888999* PP

                                       ......SHHHHHHHHHHHHHHHHHHHTT----S-.TSTTS--SSHHHHHHS-SS--HHHHHHHH CS
                     Peptidase_M54 133 fyte..dkeLflervvkevlhelGhlyGLshCke.dCvmnfsndlkdvDrkapkyCksCleklk 193
                                       fy    d +L+ er vke +helGh++GL hC+  +Cvmnfsn++ +vD k+  +C++C ++lk
  gi|320101329|ref|YP_004176921.1| 121 FYGSppDFNLYFERLVKEAVHELGHVLGLDHCRSpGCVMNFSNSIVEVDAKTRYFCNECSRRLK 184
                                       **977799*****************************************************997 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.4e-08   3.6e-05     110     134 ..     136     160 ..      18     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHHTTBESXSSTTSTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 110 flVaaHEiGHalGLeHssdkdalmy 134
                                       +  a+HE+GH+lGL+H ++++ +m 
  gi|320101329|ref|YP_004176921.1| 136 VKEAVHELGHVLGLDHCRSPGCVMN 160
                                       5558*******************97 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   8.6e-05      0.22     319     336 ..     140     159 ..     138     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.6e-05
                        Metallopep 319 lHEiGHllglpHqed..Gvm 336
                                       +HE+GH+lgl H+ +   vm
  gi|320101329|ref|YP_004176921.1| 140 VHELGHVLGLDHCRSpgCVM 159
                                       7***********99864455 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     9e-05      0.23      72      96 ..     139     163 ..     127     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-05
                     Peptidase_M43  72 LthelGhfLgLihtfeggCerGegD 96 
                                         helGh LgL h    gC    ++
  gi|320101329|ref|YP_004176921.1| 139 AVHELGHVLGLDHCRSPGCVMNFSN 163
                                       57**************999766555 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.26     106     123 ..     134     151 ..      75     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                      Reprolysin_3 106 vgadtvaHEiGHnfganH 123
                                         ++ + HE+GH +g++H
  gi|320101329|ref|YP_004176921.1| 134 RLVKEAVHELGHVLGLDH 151
                                       3347899*********** PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00013      0.33      11      29 ..     133     151 ..     124     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                           DUF4953  11 allrfvvaHEvGhtLGLrh 29 
                                       ++l   + HE Gh+LGL+h
  gi|320101329|ref|YP_004176921.1| 133 ERLVKEAVHELGHVLGLDH 151
                                       66777789**********9 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00014      0.37     141     158 ..     141     158 ..     135     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                      Reprolysin_4 141 HEiGHtfGaaHdlsdege 158
                                       HE GH +G++H  s ++ 
  gi|320101329|ref|YP_004176921.1| 141 HELGHVLGLDHCRSPGCV 158
                                       ***********9887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1335.74
//
Query:       gi|320101330|ref|YP_004176922.1|  [L=154]
Description: archease family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-35  122.8   0.0    1.3e-35  122.6   0.0    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 !  122.6   0.0   7.3e-40   1.3e-35       1     138 []      12     154 .]      12     154 .] 0.95

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 7.3e-40
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       + +l+ht D+ ++a+G ++ e+fe+a+lalf++mt+++ v+   e+++ ve+ dle+lL+++L+ell+l+++e++++
  gi|320101330|ref|YP_004176922.1|  12 FDFLEHTGDIYVRAYGGNILELFENAGLALFDSMTNIDGVNCVVERDLLVEGFDLENLLYRWLEELLVLYYSERLMC 88 
                                       789************************************************************************** PP

                                       ---EE.....EE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                          Archease  78 kevkv.....deeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                         ++v     +++ +   ++l+a++  e+fd+++he + evK  Ty+ +ri +++d+w ay+v+Di
  gi|320101330|ref|YP_004176922.1|  89 GWIRVdavsvERHGDGFTYRLKARVSCEEFDPSRHEARVEVKSPTYSLMRILKDEDKWIAYFVLDI 154
                                       ***997766533345558******************99***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1127.72
//
Query:       gi|320101331|ref|YP_004176923.1|  [L=445]
Description: ribulose 1,5-bisphosphate carboxylase large subunit [Desulfurococcus mucosus DSM 2162]
Scores for 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-95  318.5   0.0    4.7e-95  318.2   0.0    1.1  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
      9e-46  154.9   0.0    1.6e-45  154.2   0.0    1.4  1  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai
  ------ inclusion threshold ------
      0.054   13.2   0.0       0.11   12.2   0.0    1.4  1  DUF697           Domain of unknown function (DUF697)
       0.15   12.0   0.0       0.58   10.1   0.0    2.0  2  Vps23_core       Vps23 core domain
       0.19   11.9   0.0       0.69   10.1   0.0    1.9  2  LigA             Aromatic-ring-opening dioxygenase LigAB, Lig


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 !  318.2   0.0   1.3e-98   4.7e-95       2     299 .]     144     439 ..     143     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 318.2 bits;  conditional E-value: 1.3e-98
                                       HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHH CS
                     RuBisCO_large   2 iaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqde 78 
                                       +a+ +e+ ++++rpi+Gt+ KPk G sp+++++++ ell+gglD++KdDEnl+s+ f+r++ r++a++++i++ ++e
  gi|320101331|ref|YP_004176923.1| 144 VAGVKEIFKVSDRPIVGTVPKPKEGYSPDEVEKLAFELLSGGLDYVKDDENLTSPSFCRFEARAKAIMRVIDKVEKE 220
                                       6778899999******************************************************************* PP

                                       HSS--EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--SE CS
                     RuBisCO_large  79 tGekklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskhG 155
                                       tGe+k + +nit +d++em++r  +v++ g   v+vdv+ +G++a+t++r  +++ +l++H Hra+h+a+tr++ hG
  gi|320101331|ref|YP_004176923.1| 221 TGERKAWFANIT-SDIREMEKRLRLVADYGNPYVMVDVVITGWSALTYIRDIAEEYGLAIHGHRAMHAAFTRNPYHG 296
                                       ************.899************************************************************* PP

                                       E-HHHHHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS--T CS
                     RuBisCO_large 156 isfrvlakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGiha 232
                                       is+ vlakl R++G+d+lh+gt+g gkleg +  v  +   lre++ + d+ +  ++eq+++++k+++pv sgG+h 
  gi|320101331|ref|YP_004176923.1| 297 ISMYVLAKLYRIIGIDQLHIGTAGAGKLEGGKIDVIRYARILRENHFKPDQDDQFHLEQPMHHIKPAMPVSSGGLHP 373
                                       ********************************9999***************************************** PP

                                       TTHHHHHHHHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                     RuBisCO_large 233 gqlpellenlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                       g+++ ++e+lg+ +++lq GGG++gHpdg+ aGa a+rqalea+ +G++l ey k+h+eLarA+e+w
  gi|320101331|ref|YP_004176923.1| 374 GNIQPVIEALGS-NIVLQIGGGVIGHPDGPRAGALAVRQALEAISKGIPLDEYMKTHRELARAIEKW 439
                                       ***********9.*****************************************************9 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   0.0   4.3e-49   1.6e-45       1     120 []      12     133 ..      12     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 4.3e-49
                   RuBisCO_large_N   1 dyvdedyepk.etdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkd.ellkklkakvyeieeveeekelv 75 
                                       +yv+ dy+p+ ++d++a+frv+Pa+g+++e+aa+ vAaeSStgtwt++++++d +++++l++k+y ++++ +++++v
  gi|320101331|ref|YP_004176923.1|  12 EYVNRDYNPDpDNDVVAVFRVKPAPGFTIEDAAGGVAAESSTGTWTSLYSWYDvTRVRRLSGKAYFFRDLGDGSWIV 88 
                                       69********99*****************************************99********************** PP

                   RuBisCO_large_N  76 kiAYplelFeegsipqllssiaGnifgmkavkalrleDirlPkay 120
                                       +iAYp+elFeeg+ip ll+siaGnifgmk+v+alrleDi+lP+++
  gi|320101331|ref|YP_004176923.1|  89 RIAYPVELFEEGNIPGLLASIAGNIFGMKRVEALRLEDIYLPRKF 133
                                       ******************************************986 PP

>> DUF697  Domain of unknown function (DUF697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.1e-05      0.11      40      74 ..     250     284 ..     247     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                            DUF697  40 sPlalvDllavaavnlrlirelaelYgielgyega 74 
                                       +P  +vD++++ +  l+ ir++ae Yg+ +  ++a
  gi|320101331|ref|YP_004176923.1| 250 NPYVMVDVVITGWSALTYIRDIAEEYGLAIHGHRA 284
                                       8**************************99877666 PP

>> Vps23_core  Vps23 core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.7     6e+03      33      49 ..     323     339 ..     322     340 .. 0.83
   2 ?   10.1   0.0   0.00016      0.58      32      53 ..     411     434 ..     407     436 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
                        Vps23_core  33 aldrgkidldtflKqvR 49 
                                       +l+ gkid+  + +  R
  gi|320101331|ref|YP_004176923.1| 323 KLEGGKIDVIRYARILR 339
                                       57899***999999877 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00016
                        Vps23_core  32 kald..rgkidldtflKqvReLar 53 
                                       +al+  ++ i+ld+++K+ ReLar
  gi|320101331|ref|YP_004176923.1| 411 QALEaiSKGIPLDEYMKTHRELAR 434
                                       5665557789*************9 PP

>> LigA  Aromatic-ring-opening dioxygenase LigAB, LigA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00019      0.69      49      75 ..     295     321 ..     269     325 .. 0.76
   2 ?   -2.2   0.0       1.3   4.7e+03      68      85 ..     411     428 ..     409     430 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                                       HT--HHHHHHHHHHTT--HHHHHHHHT CS
                              LigA  49 lGgniyyLaKlaavlglsmqeigaamt 75 
                                       +G ++y+LaKl +++g++ ++ig a  
  gi|320101331|ref|YP_004176923.1| 295 HGISMYVLAKLYRIIGIDQLHIGTAGA 321
                                       699*******************98765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                       HHHHHHHTTS-HHHHHTT CS
                              LigA  68 qeigaamtGmsleeFqat 85 
                                       q + a  +G+ l+e+++t
  gi|320101331|ref|YP_004176923.1| 411 QALEAISKGIPLDEYMKT 428
                                       56678889*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3336.67
//
Query:       gi|320101332|ref|YP_004176924.1|  [L=409]
Description: peptidase S8 and S53 subtilisin kexin sedolisin [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-52  177.8   8.0    3.8e-52  177.4   8.0    1.1  1  Peptidase_S8    Subtilase family
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.053   13.5   0.0    1.5  1  CspB_prodomain  Csp protease B prodomain


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 !  177.4   8.0   4.3e-56   3.8e-52       1     284 [.     134     382 ..     134     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 4.3e-56
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g gv+vavlDtG+d+shpdl         + + i++    +++ +++ t  +   d+ng    HGthvAGi+aa+  
  gi|320101332|ref|YP_004176924.1| 134 GYGVVVAVLDTGIDYSHPDLYGR------VAYCINT----IGTTTYKGTTLSRCYDGNG----HGTHVAGIIAAT-I 195
                                       569******************33......3334555....8888999999999999999....************.9 PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkk 154
                                       ++ ++ gvap++++++vkvld+sg+     ++++++i+ea++ ++++++mslg s+ +++  r+    a  +a  ++
  gi|320101332|ref|YP_004176924.1| 196 NNRGVAGVAPNVTLIAVKVLDNSGSGT--VSDIAEGITEAVKAGAKILSMSLG-SSADSSILRD----ASYWAY-QQ 264
                                       999********************9875..49**********************.9999999998....445666.89 PP

                                       T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 155 gvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrq 231
                                       g + v++aGN+g +g+  +++ +v++p+ +  vi+v+a++  g++ ++Ss Gp++      d++apG++i+st++  
  gi|320101332|ref|YP_004176924.1| 265 GAIQVVAAGNSG-DGD--PSTNNVNYPAKYSWVIAVAAVDYYGDVPYWSSDGPEV------DVAAPGVDILSTYPGG 332
                                       ************.666..8**********************************98......6*************** PP

                                       CHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHH.HHTT....--HHHHHHHHHCCS-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx....xxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 232 snnsaglssyqsmsGTSmAsPnaagaaAllls.alpk....ltpetvraallntAqdl 284
                                       +        y + sGTSmA+P+++g++A++   +l +    l   ++ ++l  tA dl
  gi|320101332|ref|YP_004176924.1| 333 K--------YAYLSGTSMATPHVTGVVAVVEAiRLAAgkswLGFSSIYKVLTYTAYDL 382
                                       *........********************99866666666566667888888888666 PP

>> CspB_prodomain  Csp protease B prodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.9e-06     0.053      33      87 ..      34      92 ..      23      93 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-06
                    CspB_prodomain 33 ntwelivkysgdleele..eelgie.veeLln.gYAivtipeskieelaalpeieYiEk 87
                                      +++ +++ y++d ++ +  ++lg++ +++L   +  +v ipes i+++ +lp + Y+Ek
  gi|320101332|ref|YP_004176924.1| 34 QKVRVVIGYRDDASKQSilKSLGVTpLKDLRDiKAMVVVIPESLIQRVKSLPGVRYVEK 92
                                      566777777777777774433333224444431345899*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 3360.00
//
Query:       gi|320101333|ref|YP_004176925.1|  [L=187]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-68  230.2   0.0    1.3e-68  230.0   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.0   0.0   7.1e-73   1.3e-68       2     168 ..       9     177 ..       8     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 230.0 bits;  conditional E-value: 7.1e-73
                                       -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEE CS
                   dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevld 78 
                                       ++i++++l+ep v++D+RGff+e ++++ f ++g++ +fvq n+s s+kgv+RGlH+q +p +q+klv+v+rG+++d
  gi|320101333|ref|YP_004176925.1|   9 LSIPDLMLVEPFVHQDRRGFFTELYKRTVFLSEGIPYSFVQVNMSESRKGVVRGLHYQLKPMEQGKLVTVLRGRIYD 85 
                                       689************************************************************************** PP

                                       EEEE-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---..S CS
                   dTDP_sugar_isom  79 vaVDlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw..e 153
                                       vaVD+RkgSp fg++ gveLs++nk  l+ip+gfahGf++l+d+++vlY+vt+ y+pe+er+i++ Dp++gi+w  e
  gi|320101333|ref|YP_004176925.1|  86 VAVDIRKGSPWFGRYLGVELSEHNKYLLWIPPGFAHGFQALEDNTVVLYMVTKEYSPEHERCISYRDPDIGIEWplE 162
                                       ****************************************************99**********************9 PP

                                       S.B--HHHHT-B-HH CS
                   dTDP_sugar_isom 154 elilSekDkaapsla 168
                                       ++ lSekD++ p l+
  gi|320101333|ref|YP_004176925.1| 163 TIFLSEKDEKCPPLK 177
                                       9**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1596.71
//
Query:       gi|320101334|ref|YP_004176926.1|  [L=298]
Description: dTDP-4-dehydrorhamnose reductase [Desulfurococcus mucosus DSM 2162]
Scores for 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-74  251.2   0.0    1.2e-74  251.1   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    1.9e-22   79.9   0.0    1.5e-21   76.9   0.0    1.9  2  Epimerase        NAD dependent epimerase/dehydratase family
    4.1e-14   52.7   0.2    1.2e-13   51.2   0.2    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.6e-10   38.6   1.2    7.1e-09   35.2   0.4    2.8  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.2e-08   34.4   1.1      2e-06   27.2   0.0    2.9  2  NAD_binding_4    Male sterility protein
    3.2e-06   26.4   0.0      5e-06   25.7   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.016   14.8   0.0    1.3  1  NmrA             NmrA-like family
      0.011   15.6   0.0      0.018   14.9   0.0    1.5  1  NAD_binding_10   NAD(P)H-binding
      0.098   12.5   0.0       0.15   11.8   0.0    1.3  1  DFP              DNA / pantothenate metabolism flavoprotein
        0.1   12.7   0.3       0.23   11.5   0.3    1.6  1  baeRF_family2    Bacterial archaeo-eukaryotic release factor 
       0.22   11.4   3.0        0.7    9.8   0.5    2.6  2  KR               KR domain


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.1   0.0   7.1e-78   1.2e-74       1     285 [.       1     292 [.       1     294 [. 0.97

  Alignments for each domain:
  == domain 1  score: 251.1 bits;  conditional E-value: 7.1e-78
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHHHHH--SEEEE------HH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaellkeakpdvvvnaAAytavD 65 
                                       m+ilvtG++G+lG  ++k + e+g+ev+a + e            +++l+d ++va+++k +kpd+++++AA+t+vD
  gi|320101334|ref|YP_004176926.1|   1 MRILVTGGTGLLGLWVTKVFLERGYEVYASHHErkpvgldgvtweQMNLEDFKSVADTVKRVKPDAIIHTAAFTDVD 77 
                                       99****************************77778****************************************** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SS CS
                     RmlD_sub_bind  66 kaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkk 142
                                        +E+++e+ay+vn  a++ +Ae a++ +a L+++StDyVFdGe+ + Y+e d+++P+n+YG tKl+GE av+   ++
  gi|320101334|ref|YP_004176926.1|  78 GCEEKKELAYRVNYLATRIIAETARELNAYLVYISTDYVFDGERGM-YREFDAPAPVNYYGLTKLLGEVAVNTLAPR 153
                                       *******************************************766.****************************** PP

                                       EEEEEE-SEESS...SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS CS
                     RmlD_sub_bind 143 alivRtswvyge...kgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlaneg 216
                                        livR+s +yg     ++nf  + l+++ ++e+++ ++Dq+ sPT++r lAe +++++++++      gv H+a+e+
  gi|320101334|ref|YP_004176926.1| 154 SLIVRVSGLYGFsptGKRNFGLVALEKLMNNEQVDAFHDQYLSPTYVRPLAERIADMVKREVV-----GVIHVAGER 225
                                       **********97666899*******************************************95.....*******98 PP

                                       -EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHHH CS
                     RmlD_sub_bind 217 etswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlkel 285
                                        +s++efA + ++++g+ +  vk +s +++  +A+RP++S+Ldt ++++  g+++++  e +k++++++
  gi|320101334|ref|YP_004176926.1| 226 -ASRYEFASKLAEALGVPRDLVKKTSIKNAGLRARRPRDSSLDTGRAASM-GLSIPPMNECIKSFINDY 292
                                       .9********************************************9988.9999999**999999986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0   9.4e-25   1.5e-21       1     174 [.       3     164 ..       3     178 .. 0.89
   2 ?    0.6   0.0       0.2   3.3e+02     144     169 ..     178     202 ..     175     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 9.4e-25
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       ilVtG+tG++G  ++k +le+gyev +  ++   ++   l+ +++ +++l d +++++ +k+++pda+ih Aa  +v
  gi|320101334|ref|YP_004176926.1|   3 ILVTGGTGLLGLWVTKVFLERGYEVYASHHE---RKPVGLDGVTWEQMNLEDFKSVADTVKRVKPDAIIHTAAFTDV 76 
                                       8******************************...555556778********************************** PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       +   e+++  ++ n   t+ ++e ar+ ++  l+++s++ v+     +   e       +p + Y+++Kl+ge  v 
  gi|320101334|ref|YP_004176926.1|  77 DGCEEKKELAYRVNYLATRIIAETARELNA-YLVYISTDYVFDGERGM-YREFD---APAPVNYYGLTKLLGEVAVN 148
                                       ******************************.***********988875.66666...789***************99 PP

                                       HHHHHHT-EEEEEEESEEES CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyG 174
                                        +a       +i+r++ lyG
  gi|320101334|ref|YP_004176926.1| 149 TLAPRS----LIVRVSGLYG 164
                                       987766....5666666666 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHT-EEEEEEE CS
                         Epimerase 144 aaKlageklveayaaqyglnaiilrl 169
                                       + Kl+  ++v a+++qy l+ + +r+
  gi|320101334|ref|YP_004176926.1| 178 LEKLMNNEQVDAFHDQY-LSPTYVRP 202
                                       67999999999999999.89998887 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 !   51.2   0.2   7.1e-17   1.2e-13       1     165 [.       4     148 ..       4     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 7.1e-17
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG++G  G ++++ +le+gyev+   +  + +                 + +++ +++l+D +s+ + +++v+pd
  gi|320101334|ref|YP_004176926.1|   4 LVTGGTGLLGLWVTKVFLERGYEVYASHHERKPVG---------------LDGVTWEQMNLEDFKSVADTVKRVKPD 65 
                                       9***********************87433333222...............23467899******************* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       ++++ AA   Vd   ek e  ++vn l+t  + e +r+l+      ++ +St+ v+ + ++  ++E     P + Y+
  gi|320101334|ref|YP_004176926.1|  66 AIIHTAAFTDVDGCEEKKELAYRVNYLATRIIAETARELNA----YLVYISTDYVF-DGERGMYREFDAPAPVNYYG 137
                                       **************************************975....699********.4455799************* PP

                                       HHHHHHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivv 165
                                        +Kl  +  v 
  gi|320101334|ref|YP_004176926.1| 138 LTKLLGEVAVN 148
                                       ****9998876 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.4   4.3e-12   7.1e-09       1     153 [.       3     151 ..       3     160 .. 0.79
   2 ?   -2.0   0.0      0.92   1.5e+03     229     265 ..     221     257 ..     206     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 4.3e-12
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +lvtG++G +G  +++ +l++  +  +  +++E k   ++  +      +++         +++d ++++++++++k
  gi|320101334|ref|YP_004176926.1|   3 ILVTGGTGLLGLWVTKVFLERGYE--VYASHHERKPVGLDGVT---W--EQM---------NLEDFKSVADTVKRVK 63 
                                       678888888888888877777665..45677777777777654...2..223.........467899999******* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG.............GGSS--SHHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD.............KAvnPtnvmGat 141
                                       +d+++h+AA+  V  +ee+   a + N l+t+ ++e+a e +   +v+iStD              A  P+n +G+t
  gi|320101334|ref|YP_004176926.1|  64 PDAIIHTAAFTDVDGCEEKKELAYRVNYLATRIIAETARELNA-YLVYISTDyvfdgergmyrefDAPAPVNYYGLT 139
                                       ****************************************996.79******44444444443333678******** PP

                                       HHHHHHHHHHGG CS
                   Polysacc_synt_2 142 Krlaekllqala 153
                                       K+l e  + +la
  gi|320101334|ref|YP_004176926.1| 140 KLLGEVAVNTLA 151
                                       ***999988776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.92
                                       --.-EEEHHHHHHHH..........SSSS-EEE---- CS
                   Polysacc_synt_2 229 dmGepvkivdlakalielsgleekkeedieikitGlR 265
                                        +Ge  + ++ a++l e  g+  +  ++++ik  GlR
  gi|320101334|ref|YP_004176926.1| 221 VAGERASRYEFASKLAEALGVPRDLVKKTSIKNAGLR 257
                                       4677778888999999999998888899999999998 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4     0.014        23       1      27 [.       5      29 ..       5      37 .. 0.80
   2 !   27.2   0.0   1.2e-09     2e-06      88     214 ..      64     170 ..      46     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.014
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyl 27
                                      +TG+TG LG  + +  L++    ++y+
  gi|320101334|ref|YP_004176926.1|  5 VTGGTGLLGLWVTKVFLERGY--EVYA 29
                                      7*********99999998876..5555 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 1.2e-09
                                       --EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HH CS
                     NAD_binding_4  88 vdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekl 161
                                        d+iih aA +++d+  ++   ++rvN ++tr + e a++l++   l+++ST yv + ++g                
  gi|320101334|ref|YP_004176926.1|  64 PDAIIHTAAFTDVDGCEEKkelAYRVNYLATRIIAETARELNA--YLVYISTDYVFDGERGMY-------------- 124
                                       389*********99854444569****************9855..5******88777777532.............. PP

                                       H--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST- CS
                     NAD_binding_4 162 dederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGw 214
                                           + +     n Y  +K l+E  v++ + r     +ivR+s ++g s tG 
  gi|320101334|ref|YP_004176926.1| 125 ---REFDAPAPVNYYGLTKLLGEVAVNTLAPR----SLIVRVSGLYGFSPTGK 170
                                       ...23344556799****************55....579*****999999986 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 !   25.7   0.0   3.1e-09     5e-06       1     122 [.       4     118 ..       4     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.1e-09
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlas 75 
                                       +vtGg+G lG  + k +++++   ev +   + +p  l+ ++        +  + d +++ + ++ v  d++ih+a+
  gi|320101334|ref|YP_004176926.1|   4 LVTGGTGLLGLWVTKVFLERG--YEVYASHHERKPVGLDGVT------WEQMNLEDFKSVADTVKRVkpDAIIHTAA 72 
                                       69*****************99..4777766666665544443......44556777777777777663379****** PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgp 122
                                        +dv g + +++  ++vn+  Tr + e++++ +  +lvY S+ + v++
  gi|320101334|ref|YP_004176926.1|  73 FTDVDGcEEKKELAYRVNYLATRIIAETARELN-AYLVYIST-DYVFD 118
                                       ******88888999***************9998.69****98.55555 PP

>> NmrA  NmrA-like family
   #    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       1      53 [.       3      50 ..       3      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.8e-06
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdld 53
                                      Ilv+G+TG +G  v++++l++g++v a  ++ k   +      Gv+  + +l+
  gi|320101334|ref|YP_004176926.1|  3 ILVTGGTGLLGLWVTKVFLERGYEVYASHHERKPVGL-----DGVTWEQMNLE 50
                                      9**************************8887743332.....34444444444 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 ?   14.9   0.0   1.1e-05     0.018       1     117 [.       7     132 ..       7     191 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-..SEEEES---TCC.. CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkga..daVvsalggggk.. 73 
                                       G+tG  G  ++k  l+rg +ev a   + + +      +g++  +++++d +++a+++k +  da++ +++ ++   
  gi|320101334|ref|YP_004176926.1|   7 GGTGLLGLWVTKVFLERG-YEVYASHHERKPVG----LDGVTWEQMNLEDFKSVADTVKRVkpDAIIHTAAFTDVdg 78 
                                       9****************5.**987766655555....47********************77557**99997766655 PP

                                       ...HHHH.........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCC CS
                    NAD_binding_10  74 ...deeg.........aknivdaakeagvkRfvlvsaigvgdevpgefgewnkell 117
                                          +            a +i++   ++    +v++s+  v d   g   e++  + 
  gi|320101334|ref|YP_004176926.1|  79 ceeK--KelayrvnylATRIIAETARELNAYLVYISTDYVFDGERGMYREFDAPAP 132
                                       5432..13456667775555554444444466777776666655555555555544 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.4e-05      0.15      21      99 ..       2      80 ..       1      91 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                                      EEEEE----HHHHHHHHHHHHTT-EEEEEE-S-.SS---TT-..EEEE--SHHHHHHHHHHHHTT-SEEEE---S--EE CS
                               DFP 21 RfisNrSSGkmGyalAeaaaarGaeVtlvsgpv.sletpegv..evvkvesaeemleaveealkeadivimaAAvaDyr 96
                                      R++    +G  G+ + + +++rG eV   + +   +   +gv  e ++ e+ ++ +++v++   + d++i++AA  D  
  gi|320101334|ref|YP_004176926.1|  2 RILVTGGTGLLGLWVTKVFLERGYEVYASHHERkPVGL-DGVtwEQMNLEDFKSVADTVKRV--KPDAIIHTAAFTDVD 77
                                      77777889*******************99888413333.24323788899999999999887..56***********87 PP

                                      ES- CS
                               DFP 97 pke 99
                                        e
  gi|320101334|ref|YP_004176926.1| 78 GCE 80
                                      655 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00014      0.23      62      99 ..     202     239 ..     199     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                     baeRF_family2  62 avAeevdrlvresgaelVvlaGDvrarsllrdeLperv 99 
                                         Ae+++++v+++ + ++ +aG+  +r   +++L e++
  gi|320101334|ref|YP_004176926.1| 202 PLAERIADMVKREVVGVIHVAGERASRYEFASKLAEAL 239
                                       57******************************999876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00043       0.7       4      26 ..       4      26 ..       2      84 .. 0.89
   2 ?    1.0   0.1      0.21   3.4e+02      71      91 ..     203     224 ..     175     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00043
                                      EEETTTSHHHHHHHHHHHHHHS- CS
                                KR  4 litGGlGgLGlelarwlaekgar 26
                                      l+tGG+G LGl +++  +e+g +
  gi|320101334|ref|YP_004176926.1|  4 LVTGGTGLLGLWVTKVFLERGYE 26
                                      9******************9965 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.21
                                       HHHHHHHHS.S---EEEE---- CS
                                KR  71 lleeikaee.ppikGvihaAgv 91 
                                       l e+i +   +++ Gvih Ag 
  gi|320101334|ref|YP_004176926.1| 203 LAERIADMVkREVVGVIHVAGE 224
                                       5555544445889******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.25s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 2373.85
//
Query:       gi|320101335|ref|YP_004176927.1|  [L=336]
Description: dTDP-glucose 4,6-dehydratase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-73  246.1   0.0    1.5e-72  244.8   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.2e-64  218.1   0.0    1.4e-64  217.8   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.1e-18   65.2   0.0    5.6e-18   65.1   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
      3e-14   52.7   0.0    3.8e-14   52.4   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      1e-12   47.8   0.0      2e-11   43.6   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.2e-11   42.5   0.0    2.1e-10   40.2   0.0    2.1  1  NAD_binding_4    Male sterility protein
    0.00011   22.4   0.0    0.00017   21.9   0.0    1.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00093   18.8   0.0      0.007   15.9   0.0    1.9  2  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.025   14.5   0.0    1.2  1  KR               KR domain
      0.027   14.9   0.0      0.045   14.2   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
       0.04   13.4   0.0        6.1    6.2   0.0    2.2  2  adh_short        short chain dehydrogenase
      0.042   13.7   0.0      0.073   13.0   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding


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 !  244.8   0.0     1e-75   1.5e-72       2     332 .]       5     304 ..       5     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: 244.8 bits;  conditional E-value: 1e-75
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       + G+aGfiGs+++++L +     + ++ +++++++gr e++a+      ++++ +++gD+ +++ l ++lae +pd 
  gi|320101335|ref|YP_004176927.1|   5 VLGGAGFIGSNFVRYLASHR--SMDLMVYDKLTYAGRYENIADLV---EKGRVLFVRGDIANEELLSHALAEFKPDF 76 
                                       67***************974..45567789999*******99765...368************************** PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-.SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkv.qevpqtEttpfyPrsPYa 154
                                       ++n+AA+ hVd+s+++P  ++++nvlG++++Le+ +++       ++++St+EvYG++  +   +E+ p++P sPY+
  gi|320101335|ref|YP_004176927.1|  77 IVNFAAETHVDRSINDPSPFIKTNVLGVYTVLEVLKKTD----SIYIHISTDEVYGDLwGDGEASEDWPLNPSSPYS 149
                                       ***********************************9975....4799***********56899************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       a+K++ d ++++y ++yg+   + +  n+++p++    ++++i+r++ r ++gk + +++G+++++Rdw hv+D+++
  gi|320101335|ref|YP_004176927.1| 150 ASKAAGDLLIKSYGRTYGIRYRILRPCNNYGPYQ---HPEKLIPRTIIRLLNGK-PAVIYGDGSQVRDWIHVEDTCR 222
                                       *********************************7...689*************9.67779***************** PP

                                       HHHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 232 amwlmlqq.dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       a+ +++q+ + +e y+i+ ++  s+re+v l + +lg++                    +  + + + rpge+++++
  gi|320101335|ref|YP_004176927.1| 223 AIEMVMQRgGDSEVYNICANQYASIREIVSLLVSHLGRD-------------------PLRDIVYGRPRPGEDRRYA 280
                                       *******95567899*********************985...................4556778899********* PP

                                       B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvrem 332
                                       + ++k+k  LgW+p++++ e+++++
  gi|320101335|ref|YP_004176927.1| 281 MKCDKIK-GLGWSPTIGIGEGLKKT 304
                                       ******9.9************9986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.8   0.0   9.5e-68   1.4e-64       1     241 []       3     240 ..       3     240 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 9.5e-68
                                       EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavih 70 
                                       i V+G++GfiGs++v++l+++   ++++ d+l++a++ ++++dl       +v++d+ +++ l  +++e++pd +++
  gi|320101335|ref|YP_004176927.1|   3 IAVLGGAGFIGSNFVRYLASHRsMDLMVYDKLTYAGRYENIADLvekgrvLFVRGDIANEELLSHALAEFKPDFIVN 79 
                                       68*******************9778**************************************************** PP

                                       --S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHH CS
                         Epimerase  71 lAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKl 147
                                       +Aa+ +v++s++dp+ fi++n+ g++++le+++k++   ++++s++evYG+     + e +++ pl+p+spY+a+K+
  gi|320101335|ref|YP_004176927.1|  80 FAAETHVDRSINDPSPFIKTNVLGVYTVLEVLKKTDS-IYIHISTDEVYGDLWG--DGEASEDWPLNPSSPYSASKA 153
                                       ***********************************99.9**************9..88888889************* PP

                                       HHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHH CS
                         Epimerase 148 ageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaill 224
                                       ag+ l+++y ++yg+++ ilr++n+yGp+   ++++++ip+ i ++l+gk + +++gdg+++Rd+++veD ++ai +
  gi|320101335|ref|YP_004176927.1| 154 AGDLLIKSYGRTYGIRYRILRPCNNYGPY---QHPEKLIPRTIIRLLNGK-PAVIYGDGSQVRDWIHVEDTCRAIEM 226
                                       *****************************...99****************.************************** PP

                                       HHHHHTT-STTEEEEES CS
                         Epimerase 225 vlehvdagdkgeiyniG 241
                                       v+++   g + e+yni+
  gi|320101335|ref|YP_004176927.1| 227 VMQR---GGDSEVYNIC 240
                                       ****...9999****96 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   3.7e-21   5.6e-18       1     169 [.       1     199 [.       1     291 [. 0.81

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 3.7e-21
                                       EEEEEESTTSHHHHHHHHHCTT.TSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEE CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae.eglevlaltre.....................eldltdaeavaellkeakpdvv 55 
                                       m+i v+G+ G +Gs+ ++ la+ + ++++  ++                      + d++++e + ++l+e+kpd++
  gi|320101335|ref|YP_004176927.1|   1 MRIAVLGGAGFIGSNFVRYLAShRSMDLMVYDKLtyagryeniadlvekgrvlfvRGDIANEELLSHALAEFKPDFI 77 
                                       89*************9998876588999999887999**************************************** PP

                                       EE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-.TTS-B-TTS----SSHHHHHHHH CS
                     RmlD_sub_bind  56 vnaAAytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGe.kkrpYeeddetsPlnvYGrtKla 131
                                       vn AA t vD+  +++    + n+ +v ++ e+ +++++  ih+StD V+     + + +ed + +P + Y ++K+a
  gi|320101335|ref|YP_004176927.1|  78 VNFAAETHVDRSINDPSPFIKTNVLGVYTVLEVLKKTDSIYIHISTDEVYGDLwGDGEASEDWPLNPSSPYSASKAA 154
                                       **************************************************6445666789999************** PP

                                       HHHHHHH....H-SSEEEEEE-SEESS...SSS-HHHHHHHHHHH CS
                     RmlD_sub_bind 132 GEqavla....agkkalivRtswvyge...kgknfvktmlrlake 169
                                       G   +++    +g ++ i+R    yg     +k   +t++rl++ 
  gi|320101335|ref|YP_004176927.1| 155 GDLLIKSygrtYGIRYRILRPCNNYGPyqhPEKLIPRTIIRLLNG 199
                                       *****9944444557788888888876321233455666666654 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 !   52.4   0.0   2.5e-17   3.8e-14       1     225 [.       4     224 ..       4     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.5e-17
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkleealegv..dvvih 72 
                                       +v+GgaGF+G++ v+ L +  +  ++ v+D+ +     e++  +  k    ++ gD+ +++ l++al +   d ++ 
  gi|320101335|ref|YP_004176927.1|   4 AVLGGAGFIGSNFVRYLASHRS-MDLMVYDKLTYAGRYENIADLVEKGrvlFVRGDIANEELLSHALAEFkpDFIVN 79 
                                       59***************99996.9******655544444444333333344*****************973368999 PP

                         3Beta_HSD  73 laslvdvagklte.deimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaype 148
                                        a+ + v   +++   + k nv G  +vle  +k++  + ++ S+ ev g+        +g+ ++  + +++++y+ 
  gi|320101335|ref|YP_004176927.1|  80 FAAETHVDRSINDpSPFIKTNVLGVYTVLEVLKKTD-SIYIHISTDEVYGD-----LWGDGEASEDWPLNPSSPYSA 150
                                       999999988665416699************988877.7889*******999.....56678888888999******* PP

                         3Beta_HSD 149 sKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvp.llkqlaklglalfkigdeevlsdrvYvgNva 222
                                       sKa a +l++k+ grt    g +    LRp   yG++++  +l p ++ +l+ +g+  + +gd +++ d++ v+   
  gi|320101335|ref|YP_004176927.1| 151 SKA-AGDLLIKSYGRT---YG-IRYRILRPCNNYGPYQHpeKLIPrTIIRLL-NGKPAVIYGDGSQVRDWIHVEDTC 221
                                       *98.667888899933...32.44557*********9852234440444444.5668899*************9877 PP

                         3Beta_HSD 223 wah 225
                                        a+
  gi|320101335|ref|YP_004176927.1| 222 RAI 224
                                       765 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   1.4e-14     2e-11       1     130 [.       3     125 ..       3     130 .. 0.85
   2 ?    2.2   0.0     0.054        81     129     268 ..     139     275 ..     135     283 .. 0.69

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.4e-14
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH.......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeieke.leeelkkkklkveivpvigdvrdkerlekaleel 76 
                                       + v G++G iGs++vr +++++   ++++++  ++    + e + + ++k +    ++ v gd++++e l++al e+
  gi|320101335|ref|YP_004176927.1|   3 IAVLGGAGFIGSNFVRYLASHRSMDLMVYDKLTYAG---RYEnIADLVEKGR----VLFVRGDIANEELLSHALAEF 72 
                                       5689*************************9876653...2331222334433....44579**************** PP

                                       T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGG CS
                   Polysacc_synt_2  77 kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDK 130
                                       k+d++++ AA  hV    + p   iktNvlg  +v+e+ ++++ +  + iStD 
  gi|320101335|ref|YP_004176927.1|  73 KPDFIVNFAAETHVDRSINDPSPFIKTNVLGVYTVLEVLKKTD-SIYIHISTDE 125
                                       *************************************988877.6789999996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.054
                                       GGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT...TSSHHHHHHHHHTTSSEEE.S-TT-EE CS
                   Polysacc_synt_2 129 DKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgSr...GSviplFkkqikeggpvtv.TdpemtR 201
                                       D   nP + + a+K++ ++l+ ++ ++      ++ + R  N  g       +ip    ++ +g+p  +  d + +R
  gi|320101335|ref|YP_004176927.1| 139 DWPLNPSSPYSASKAAGDLLIKSYGRTY---GIRYRILRPCNNYGPYqhpEKLIPRTIIRLLNGKPAVIyGDGSQVR 212
                                       5566777777777777777777777766...5666666655555543111456777777777776655426778889 PP

                                       EEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE----TT- CS
                   Polysacc_synt_2 202 yfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlRpGE 268
                                        ++ +e++++ + + ++++ ++e++   + +  +i+++++ l++  g ++ +    +i +   RpGE
  gi|320101335|ref|YP_004176927.1| 213 DWIHVEDTCRAIEMVMQRGGDSEVYNICANQYASIREIVSLLVSHLGRDPLR----DIVYGRPRPGE 275
                                       9999999999999999999999999888888899999999888877755443....45555556665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.4e-13   2.1e-10      39     208 ..      32     180 ..       5     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.4e-13
                                       HHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHH CS
                     NAD_binding_4  39 eRleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaAtvnfdepyke...llrvNv 112
                                       ++l+ + +  ++ + +    + r+ +v GD+++++  L +++l e   + d i++ aA +++d+++++   ++++Nv
  gi|320101335|ref|YP_004176927.1|  32 DKLTYAGRYENIADLVE---KGRVLFVRGDIANEE--LLSHALAEF--KPDFIVNFAAETHVDRSINDpspFIKTNV 101
                                       44555555566666665...999***********9..566777777..89**************99987779***** PP

                                       HHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHH CS
                     NAD_binding_4 113 eGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvre 189
                                       +G+  vle  kk+ +   ++h+ST  v+g+  g               + e +++   + +  Y+ sKa+++ l+++
  gi|320101335|ref|YP_004176927.1| 102 LGVYTVLEVLKKTDSI--YIHISTDEVYGDLWG---------------DGEASEDWPLNPSSPYSASKAAGDLLIKS 161
                                       ***********88665..******888888886...............56778888889999*************** PP

                                       HHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 190 arrrsglpvvivRpsiitg 208
                                       ++r  g++  i+Rp + +g
  gi|320101335|ref|YP_004176927.1| 162 YGRTYGIRYRILRPCNNYG 180
                                       **************87665 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 !   21.9   0.0   1.1e-07   0.00017       2      80 ..       4      84 ..       3      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-07
                                      EEE--.SHHHHHHHHHHHCTCCT-G....EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS..SEE CS
                   Sacchrp_dh_NADP  2 liiGa.GsvGqavaellarhfdvda....eitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg..dlv 73
                                       ++G+ G++G+ ++++la h ++d     ++t a+r+++ ++ +     + r+ ++  d++n+e  L+ +l+e   d++
  gi|320101335|ref|YP_004176927.1|  4 AVLGGaGFIGSNFVRYLASHRSMDLmvydKLTYAGRYENIADLV----EKGRVLFVRGDIANEEL-LSHALAEFkpDFI 77
                                      678777*****************766777777777777664444....79**************9.************* PP

                                      EE-SSGG CS
                   Sacchrp_dh_NADP 74 vnlsppi 80
                                      vn +  +
  gi|320101335|ref|YP_004176927.1| 78 VNFAAET 84
                                      **98765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.7e-06     0.007       1      72 [.       3      79 ..       3      91 .. 0.81
   2 ?    0.5   0.0      0.24   3.7e+02     125     227 ..     159     260 ..     142     270 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.7e-06
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S.....-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEEEE-- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt.....kselakslkeaGvelv.kgdlddkeslvealkgvdvvfsvt 72
                                      I+v+G++G +G+ +vr+l+++  +   +v d      + e+++ l e+G +l   gd+ ++e+l++al + +  f+v 
  gi|320101335|ref|YP_004176927.1|  3 IAVLGGAGFIGSNFVRYLASHR-SMDLMVYDKltyagRYENIADLVEKGRVLFvRGDIANEELLSHALAEFKPDFIVN 79
                                      89***************99854.44556666667888999*********88766*************99877666655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.24
                                       HHHHHHHCTS-EEEEE.E-EEGGG-BS.SS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHH CS
                              NmrA 125 ieeyvralgipytfvy.agffmenfls.llaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprk 199
                                       i+ y r  gi+y +++ ++ +  +  + +l + ++  + +++  +++ g+g+     + ++eD+ +++  ++++  +
  gi|320101335|ref|YP_004176927.1| 159 IKSYGRTYGIRYRILRpCNNYGPYQHPeKLIPRTIIRLLNGK-PAVIYGDGSQVRDWI-HVEDTCRAIEMVMQRGGD 233
                                       555556666666666424555555554234454444444443.677888888555555.889999888877777666 PP

                                       HTTEEEEE-SEEE-HHHHHHHHHHHHTS CS
                              NmrA 200 lkgkriklagntlsgneivelfekkigk 227
                                        + ++   a+++ s  eiv+l+   +g+
  gi|320101335|ref|YP_004176927.1| 234 SE-VYNICANQYASIREIVSLLVSHLGR 260
                                       54.4555799999999999999888887 PP

>> KR  KR 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     0.025       5      78 ..       5      75 ..       2      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                      EETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR  5 itGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78
                                      + GG+G +G  ++r la++    l++  +   + +   ++ia l ++g +v +v+ D+++++ ++++l+e+k +
  gi|320101335|ref|YP_004176927.1|  5 VLGGAGFIGSNFVRYLASHRSMDLMVYDKL--TYAGRYENIADLVEKG-RVLFVRGDIANEELLSHALAEFKPD 75
                                      89*************************999..55666678****9988.899****************999865 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     3e-05     0.045       1      29 [.       2      30 ..       2      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEE CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvv 29
                                      ++a++G+ G +G++++r+L++h +++l+v
  gi|320101335|ref|YP_004176927.1|  2 RIAVLGGAGFIGSNFVRYLASHRSMDLMV 30
                                      69*********************999876 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.011        16       3      71 ..       3      72 ..       2     113 .. 0.68
   2 ?    6.2   0.0    0.0041       6.1     146     167 ..     145     166 ..     137     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                                      EEEESTTSHHHHHHHHHHHHT.T-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelake.Gakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealveka 71
                                      + v G+++ IG ++++ la+   ++++v+d+     +  ++++ ++  + ++l++++D++++e ++ ++++ 
  gi|320101335|ref|YP_004176927.1|  3 IAVLGGAGFIGSNFVRYLASHrSMDLMVYDKLTY--AGRYENIADLveKGRVLFVRGDIANEELLSHALAEF 72
                                      679999999*********9861455666665543..335555555554789*********887777666655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0041
                                       BHHHHHHHHHHHHHHHHHHHHH CS
                         adh_short 146 vaaYsAsKaavagltrslakel 167
                                        ++YsAsKaa + l++s  + +
  gi|320101335|ref|YP_004176927.1| 145 SSPYSASKAAGDLLIKSYGRTY 166
                                       689***********99987665 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 ?   13.0   0.0   4.9e-05     0.073       1     143 [.       7     175 ..       7     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.......HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S...EEEES CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.......peklaeleaeeglevvegdvtdvedlaealkgad...aVvsa 67 
                                       G+ G +G+  v+ l++++  +  ++v +        e +a+l ++ ++  v gd+ ++e l +al+      +V +a
  gi|320101335|ref|YP_004176927.1|   7 GGAGFIGSNFVRYLASHR--SMDLMVYDkltyagrYENIADLVEKGRVLFVRGDIANEELLSHALAEFKpdfIVNFA 81 
                                       899*********999997..4445555522332224777788899*********************87544566677 PP

                                       ---TCCHHHH.............HHHHHHHHHHCT--EEEEEEETTTTSGCGCH...HHHHHHHCCHHHHHHHHHHH CS
                    NAD_binding_10  68 lggggkdeeg.............aknivdaakeagvkRfvlvsaigvgdevpge...fgewnkellkaylaakraae 128
                                       + ++ + + +             + ++++++k+++   ++ +s+  v+ + +g+    ++w  +  ++y a k+a +
  gi|320101335|ref|YP_004176927.1|  82 AETHVD-RSIndpspfiktnvlgVYTVLEVLKKTDS-IYIHISTDEVYGDLWGDgeaSEDWPLNPSSPYSASKAAGD 156
                                       755444.22334456677777889999999999875.6999999999998777633355676677777777777777 PP

                                       HHHHH....SSSEEEEEEE CS
                    NAD_binding_10 129 ellra....sgldwTivrp 143
                                        l+++     g+ + i+rp
  gi|320101335|ref|YP_004176927.1| 157 LLIKSygrtYGIRYRILRP 175
                                       7776655546899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2359.94
//
Query:       gi|320101336|ref|YP_004176928.1|  [L=357]
Description: glucose-1-phosphate thymidylyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-44  149.8   0.0    1.2e-43  149.5   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    5.1e-10   39.9   0.0    6.6e-10   39.6   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0098   15.7   0.0      0.015   15.0   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.019   15.3   0.3      0.035   14.4   0.3    1.5  1  Bactofilin       Polymer-forming cytoskeletal
      0.048   12.6   0.0      0.072   12.0   0.0    1.1  1  Lyase_8_N        Polysaccharide lyase family 8, N terminal al
       0.11   12.4   0.1       0.32   10.9   0.0    1.7  2  CTP_transf_3     Cytidylyltransferase
       0.24   10.4   0.0       0.34    9.9   0.0    1.1  1  PhoD             PhoD-like phosphatase


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 !  149.5   0.0   4.6e-47   1.2e-43       2     241 ..       6     235 ..       5     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 4.6e-47
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       +vI + G+G+RL+PLt t++k+l+pvlgk +li + ++rl+++g+ +  +++  +   ++ e l++gs +gv++ ++
  gi|320101336|ref|YP_004176928.1|   6 GVIPVAGEGSRLRPLTFTIPKPLIPVLGK-PLIVHSITRLLEAGVSKFTLIVG-HLGYMFSETLGDGSPYGVSIRYV 80 
                                       688899***********************.*****************666655.9999******************* PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                       +++ + g+A+A++ a+e   d+     ++v  gD ++++ +++++++++e +   +v +++++ +++t++G++ + +
  gi|320101336|ref|YP_004176928.1|  81 TQERRLGIAHAIYRAVENGVDNP----FVVHLGDNIFEEGVSRFIREFAEGDY--EVFIVLTRARDPTRFGCALIRD 151
                                       **************999888888....789899999999***********999..9*******************99 PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEE.ETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvf.nsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                        grv r+vEKPke++  +++++G Y f +++++ ++ +dl++++rge e+td+++  +++g++  +++ +++  W+D
  gi|320101336|ref|YP_004176928.1| 152 -GRVVRLVEKPKEPPPGSYVVTGFYAFrDPDMVGKAFRDLKPSQRGEYEVTDLIQWFIDRGYNVGYAVTNGW--WKD 225
                                       .8*************************55899999999*********************************6..*** PP

                                       XSSHHHHHHH CS
                   NTP_transferase 232 vGtldsllea 241
                                        Gt+++ll+ 
  gi|320101336|ref|YP_004176928.1| 226 MGTPSDLLDL 235
                                       *******986 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   2.6e-13   6.6e-10       2     127 ..       7     140 ..       6     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.6e-13
                                       EEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.....CHHHHHHTTCTS-E..EE-T CS
                      NTP_transf_3   2 viLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd.....eevlaalarlgvrv..vede 66 
                                       vi  +G++sR+       +K+l+p+ gkpl+ +++ +l +agv++ ++++g+     +e l +  ++gv++  v++e
  gi|320101336|ref|YP_004176928.1|   7 VIPVAGEGSRLRPltftiPKPLIPVLGKPLIVHSITRLLEAGVSKFTLIVGHlgymfSETLGDGSPYGVSIryVTQE 83 
                                       66679******9444669*******************************9997666657777788888776214444 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                           g++++++ a+++ + + +++v ++D ++  +e v r+++++a+ +++v+++ ++ + 
  gi|320101336|ref|YP_004176928.1|  84 -RRLGIAHAIYRAVEN-GVDNPFVVHLGDNIF--EEGVSRFIREFAEGDYEVFIVLTRARD 140
                                       .479**********98.4799*********99..999*********999999988887765 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 !   15.0   0.0   5.9e-06     0.015       4      50 ..       7      56 ..       4      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.9e-06
                                      EEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEE CS
                              IspD  4 vipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvv 50
                                      vip AG+G+R++      pK ++ + g++l+ h+++ ll+ ++ +  ++v
  gi|320101336|ref|YP_004176928.1|  7 VIPVAGEGSRLRpltFTIPKPLIPVLGKPLIVHSITRLLEAGVSKFTLIV 56
                                      9*********86222689********************996655544444 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   1.4e-05     0.035      19      53 ..     245     277 ..     240     319 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                        Bactofilin  19 lridGkveGdieakgklvvgeggkvegnikaeevv 53 
                                        ri+G+v G++  kg++++++++ veg+++    +
  gi|320101336|ref|YP_004176928.1| 245 ARIEGDVVGEV--KGRVIIEKDALVEGSVTGPAYI 277
                                       44455555554..6678888888888887765444 PP

>> Lyase_8_N  Polysaccharide lyase family 8, N terminal alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.8e-05     0.072      89     140 ..     200     250 ..     197     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHTSSTT....SSHHHHHTHHHHHHHHHHHHCCCSSSHHHHHH CS
                         Lyase_8_N  89 iveglaflsetkynvskeekgNWWdweigtpralndiLillhdelkeeeitk 140
                                       +++ ++++ ++ ynv+ + ++ WW+ ++gtp +l d+L ll d++ + ++  
  gi|320101336|ref|YP_004176928.1| 200 VTDLIQWFIDRGYNVGYAVTNGWWK-DMGTPSDLLDLLYLLLDKVDARIEGD 250
                                       677799**********777777887.9****************998776655 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.32      16      39 ..      26      49 ..      24      56 .. 0.89
   2 ?   -2.2   0.0       1.2   3.1e+03     179     200 ..     172     194 ..     168     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                      GGGSEETTEEHHHHHHHHHHHTTT CS
                      CTP_transf_3 16 Knlldlggkpliayvleaalkska 39
                                      K+l++ +gkpli + + ++l++++
  gi|320101336|ref|YP_004176928.1| 26 KPLIPVLGKPLIVHSITRLLEAGV 49
                                      9********************987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                       EEEEEEEHH.HHHHHHHHSHHHH CS
                      CTP_transf_3 179 agiytfrke.qplkelvidtpts 200
                                        g+y+fr+  ++ k + +++p++
  gi|320101336|ref|YP_004176928.1| 172 TGFYAFRDPdMVGKAFRDLKPSQ 194
                                       58999**9999999999999988 PP

>> PhoD  PhoD-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00013      0.34      15      43 ..      91     119 ..      82     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                              PhoD  15 nayrelaeeedlDlvlhlGDyiYeygpge 43 
                                       ++yr++ +  d  +v+hlGD i+e+g ++
  gi|320101336|ref|YP_004176928.1|  91 AIYRAVENGVDNPFVVHLGDNIFEEGVSR 119
                                       5788888887999***********98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2649.93
//
Query:       gi|320101337|ref|YP_004176929.1|  [L=373]
Description: family 2 glycosyl transferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-19   68.7   0.0    9.5e-19   67.8   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
      8e-16   58.6   0.0    1.4e-14   54.5   0.0    2.1  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    9.6e-05   22.4   0.1    0.00016   21.6   0.1    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0086   15.6   0.0       0.03   13.8   0.0    1.8  2  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   2.1e-22   9.5e-19       1     166 [.       7     185 ..       7     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 2.1e-22
                                       EEEEEESS-TTTHHHHHHHHHHH....GGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq....dpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagal 71 
                                       s++   yN    + ++l+sl +     +p+ ++e+i+vD+gS+D++ e ++++++     rv+ +r+e+n G+ g++
  gi|320101337|ref|YP_004176929.1|   7 SIIWLNYNSMGVIDRVLASLQSVfdldYPPNRYELIIVDNGSSDGSFEAVKKFVEgkDTSRVKMVRLERNLGFTGGV 83 
                                       67777899977777777777777777******************************999****************** PP

                                       HHHHHH--SS..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS......EEEECCHC CS
                   Glycos_transf_2  72 naglraatgd..yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv......generlyf 140
                                       n g+++ +    y+++l+ D + + + l++lve++e  +  +++++++  + ++       ++              
  gi|320101337|ref|YP_004176929.1|  84 NLGFSMRNRGfnYVALLNNDAVATSNSLRELVEFAESYRSVAAVQGVVLDSRGRVDTAG-GFMtedfemMPYLWKEP 159
                                       *****988778**************************7665554444444443333333.23345544333333333 PP

                                       CCCHCCCCCCSTTCSTCCCEEEEHHH CS
                   Glycos_transf_2 141 kerkrslkgnlsfeigsaallrreal 166
                                         +  s+   +++  gs+al+r e++
  gi|320101337|ref|YP_004176929.1| 160 AGKAPSKAFAVTYADGSYALYRIEYI 185
                                       34444555556666666666666665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   3.2e-18   1.4e-14      15     218 ..      20     235 ..       4     246 .. 0.79
   2 ?    2.2   0.0     0.032   1.4e+02     165     226 ..     276     365 ..     245     369 .. 0.69

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 3.2e-18
                   Glyco_tranf_2_3  15 dvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksd 89 
                                       d++++ l s+   +yp+  +e+++v+++s+++  e ++ +++  ++ rv+ v+ +rnlg+tg ++ l   +r+  + 
  gi|320101337|ref|YP_004176929.1|  20 DRVLASLQSVFDLDYPPnrYELIIVDNGSSDGSFEAVKKFVEGKDTSRVKMVRLERNLGFTGGVN-LGFSMRNRGFN 95 
                                       3556667777777896668*****************************************99866.555555666** PP

                   Glyco_tranf_2_3  90 lvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs..tlvsalgalefaerhlrflaar.........ra 154
                                       +v+l++ D+v   ++l+ l+ f+  +++v+av++ v+  +++  t+       +++e++ +++ ++         +a
  gi|320101337|ref|YP_004176929.1|  96 YVALLNNDAVATSNSLRELVEFAeSYRSVAAVQGVVLDSRGRvdTAGG-----FMTEDFEMMPYLWkepagkapsKA 167
                                       ***********************9999******999666555334433.....333444444444455555565577 PP

                   Glyco_tranf_2_3 155 lgvltlnGsgslirrevlkele.gldp...lflltdDyelglrlrragfrtayvpgaavrevfpsslk 218
                                       + v++  Gs  l+r e+ +++  g+++    f  +dD++lgl+l++ g+ ++  p ++ +++++s++ 
  gi|320101337|ref|YP_004176929.1| 168 FAVTYADGSYALYRIEYIERCVgGHMFiweMFAYGDDNILGLMLWNCGYASVSIPVVVAEHERGSTFR 235
                                       7777777**************9735555556******************************9988754 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.032
                   Glyco_tranf_2_3 165 slirrevlkelegldplflltdDyelglrlrragfrtayvpgaa..............................vre 211
                                        +i r+  + +  + +  +l+d+ +lg+rl   g++++++  ++                              +++
  gi|320101337|ref|YP_004176929.1| 276 AVIGRHSTRYI--PVAVRSLVDGRILGRRLAGKGIHIDIYRAPVitvkpleevlglympgrlirkkitervsrfIER 350
                                       55555555555..23357899999**************977776446666666666666666666665555555555 PP

                   Glyco_tranf_2_3 212 vfpsslkayikqrnR 226
                                        + +++++ ++++ R
  gi|320101337|ref|YP_004176929.1| 351 FSMEDFEKCWREKCR 365
                                       555666666666655 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 !   21.6   0.1   3.6e-08   0.00016       1     132 [.      96     236 ..      96     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.6e-08
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelas.pevaivqgpvlv.mnvanwleelaalff.aedhgkdilvrealgrvvpsv. 73 
                                       +++ll  D v + ++lre++++ +s + va+vqg vl  +++ +    + +  f    ++   + ++a+++ + ++ 
  gi|320101337|ref|YP_004176929.1|  96 YVALLNNDAVATSNSLRELVEFAESyRSVAAVQGVVLDsRGRVDTAGGFMTEDFeMMPYLWKEPAGKAPSKAFAVTy 172
                                       6899********************779**********8345556665555555422222333456666666444334 PP

                   Glyco_trans_2_3  74 ..Gsgaflrrsalqevg.....gwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlra 132
                                         Gs+a+ r++ +++ +      w+   ++ ++D  +gl l+  Gy  + +p ++   +  +t+r 
  gi|320101337|ref|YP_004176929.1| 173 adGSYALYRIEYIERCVgghmfIWE--MFAYGDDNILGLMLWNCGYASVSIPVVVAEHERGSTFRS 236
                                       49************88878988999..9************************99666666667664 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 !   13.8   0.0   6.6e-06      0.03      27     109 ..      36     121 ..       8     136 .. 0.76
   2 ?   -1.7   0.0      0.34   1.5e+03     167     194 ..     333     357 ..     306     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-06
                   Glyco_tranf_2_2  27 deeielivvddgSsekfleevssiidlnllvylkded.dkayslaaarNrGaskaes..dlvlFlDaDcfissDkfe 100
                                        +  eli+vd+gSs+   e v+++++ +    +k    ++  + +   N+G+s  +   ++v  l+ D   +s+ + 
  gi|320101337|ref|YP_004176929.1|  36 PNRYELIIVDNGSSDGSFEAVKKFVEGKDTSRVKMVRlERNLGFTGGVNLGFSMRNRgfNYVALLNNDAVATSNSLR 112
                                       3578*********************99988765655414599999999****98664349**************999 PP

                   Glyco_tranf_2_2 101 kilklitik 109
                                        +++++++ 
  gi|320101337|ref|YP_004176929.1| 113 ELVEFAESY 121
                                       999887765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.34
                   Glyco_tranf_2_2 167 silinrraflevGGyDErfrGhgaEDfd 194
                                         li+++   +v  + Erf   + EDf+
  gi|320101337|ref|YP_004176929.1| 333 GRLIRKKITERVSRFIERF---SMEDFE 357
                                       5699999999999999**9...999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2762.45
//
Query:       gi|320101338|ref|YP_004176930.1|  [L=193]
Description: 16S rRNA m(2)G 1207 methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-32  111.2   0.0      4e-32  111.1   0.0    1.0  1  MTS              Methyltransferase small domain
    5.9e-12   45.6   0.0      7e-12   45.3   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.8e-09   37.5   0.0    3.4e-09   36.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
      3e-08   33.7   0.0    5.4e-08   32.9   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
    4.2e-08   33.2   0.0    4.8e-08   33.0   0.0    1.1  1  Met_10           Met-10+ like-protein
    1.4e-07   32.2   0.0    2.2e-07   31.5   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      1e-05   25.4   0.1    1.5e-05   24.8   0.1    1.2  1  Methyltransf_16  Lysine methyltransferase
      2e-05   25.2   0.0    2.7e-05   24.8   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    0.00042   20.9   0.0     0.0006   20.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
      0.001   18.9   0.1     0.0013   18.6   0.1    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0016   18.3   0.0     0.0019   18.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0029   17.2   0.0     0.0037   16.9   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0056   16.4   0.0       0.01   15.6   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
     0.0086   15.7   0.0      0.011   15.4   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.031   13.6   0.1      0.063   12.6   0.1    1.5  1  GidB             rRNA small subunit methyltransferase G
      0.036   13.4   0.0      0.056   12.7   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
       0.12   11.2   0.0       0.16   10.8   0.0    1.1  1  Adeno_hexon      Hexon, adenovirus major coat protein, N-term
       0.15   11.2   0.0       0.19   10.9   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera


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 !  111.1   0.0     4e-35     4e-32       3     159 ..      26     178 ..      24     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 4e-35
                                       EEEEETTSTTTTS--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTT CS
                               MTS   3 tlktlpgvFskdklDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleank 79 
                                       ++++    Fs  ++D G++lLle++   ++g vlD+GcG+Gv+g+++a+ +p+++v ++dv+  A++ a+ n+++n+
  gi|320101338|ref|YP_004176930.1|  26 EFLSYTSLFSGSSIDEGTRLLLENIVIPEEGVVLDIGCGYGVIGIVVARLNPRLKVYMTDVNPLAVKTARFNARRNG 102
                                       6888899********************************************************************** PP

                                       GC..EEEEE-STTTTSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHHS CS
                               MTS  80 le..vevvasdvleeveekkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyeslleelfg 154
                                       +   v vv+ d++  ve   f++i sNPP+ ag      v+ee++  Ake+L+e+G  ++V  r    ++l e++ g
  gi|320101338|ref|YP_004176930.1| 103 VGdrVVVVEGDGYRPVEGLVFNAIYSNPPLAAGMR----VVEEIVLGAKEHLAEEGFAQFVLARG--GSHLAEKAKG 173
                                       *9999*****************************9....*****************999998764..3333344444 PP

                                       --EEE CS
                               MTS 155 nvevv 159
                                       +++vv
  gi|320101338|ref|YP_004176930.1| 174 KYRVV 178
                                       44444 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0     7e-15     7e-12     154     234 ..      46     125 ..      42     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 7e-15
                              PrmA 154 aleklvkege.evlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelNkveaklevalseellkeekad 228
                                       +le++v ++e  vlD+G+G G++ i++a+L+ + kv+ +D++++Avk a+ Na++N+v +++ v ++++  +  +++
  gi|320101338|ref|YP_004176930.1|  46 LLENIVIPEEgVVLDIGCGYGVIGIVVARLNPRlKVYMTDVNPLAVKTARFNARRNGVGDRV-VVVEGDGYR--PVE 119
                                       58888888875789****************98659**************************9.557888775..444 PP

                              PrmA 229 vivaNI 234
                                        +v N 
  gi|320101338|ref|YP_004176930.1| 120 GLVFNA 125
                                       444443 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   3.4e-12   3.4e-09       6      81 ..      57     129 ..      53     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3.4e-12
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlils 80 
                                       +vlD+GCG G ++++ a +l+p+ +v+  D ++ a++ Ar na+++g+  +v + +gd     e       f+ i s
  gi|320101338|ref|YP_004176930.1|  57 VVLDIGCGYGVIGIVVA-RLNPRLKVYMTDVNPLAVKTARFNARRNGVGdRVVVVEGDGYRpVE----GLVFNAIYS 128
                                       79***************.******************************8899988888666333....345555555 PP

                   Methyltransf_31  81 n 81 
                                       n
  gi|320101338|ref|YP_004176930.1| 129 N 129
                                       5 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   5.5e-11   5.4e-08      10      79 ..      50     119 ..      42     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.5e-11
                   Methyltransf_18  10 slvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk 79 
                                        +++++ +v+DiG+  g++ i +++ +   kv+++D+n+ ++++a+ n++++g+ d++ v+ +dG  +++
  gi|320101338|ref|YP_004176930.1|  50 IVIPEEGVVLDIGCGYGVIGIVVARLNPRLKVYMTDVNPLAVKTARFNARRNGVGDRVVVVEGDGYRPVE 119
                                       5789999**********************************************************98875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   4.8e-11   4.8e-08      71     166 ..      22     120 ..      11     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.8e-11
                                       TEEEEEETTTS---GGGHHHHHHHH..TT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHH CS
                            Met_10  71 gcrfklDvskvyfsskleaErerla..kl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeni 144
                                       g +f++     +fs   ++E +rl   ++ + e  vV+d+  G G   i++a++    +v+  d+nP +vk  + n 
  gi|320101338|ref|YP_004176930.1|  22 GQSFEFLSYTSLFSGSSIDEGTRLLleNIvIPEEGVVLDIGCGYGVIGIVVARLNPRLKVYMTDVNPLAVKTARFNA 98 
                                       66677766777888888888888752244355666999*****************99******************** PP

                                       HHTT-TTCEEEEES-GGG---T CS
                            Met_10 145 klNkvekvvkpileDgrevire 166
                                       ++N v ++v ++++Dg   ++ 
  gi|320101338|ref|YP_004176930.1|  99 RRNGVGDRVVVVEGDGYRPVEG 120
                                       ***************9765544 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   2.2e-10   2.2e-07       1      70 [.      58     128 ..      58     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.2e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvs 70 
                                       vLd+GcG G + + +a+  ++ kv+++D+++ ++++ar +a+++g+  +v +v+gd  + p e   f++++s
  gi|320101338|ref|YP_004176930.1|  58 VLDIGCGYGVIGIVVARLNPRLKVYMTDVNPLAVKTARFNARRNGVgdRVVVVEGDGYR-PVEGLVFNAIYS 128
                                       9***************99779*************************9999999998755.445556777766 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   1.5e-08   1.5e-05      49      91 ..      57     100 ..      48     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.5e-08
                   Methyltransf_16  49 svlELGsGtGlvGlavaellpeakviltDlee.llellkkniel 91 
                                        vl++G G G++G++va+l p++kv++tD++  +++  + n   
  gi|320101338|ref|YP_004176930.1|  57 VVLDIGCGYGVIGIVVARLNPRLKVYMTDVNPlAVKTARFNARR 100
                                       59***************************998556666666555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.7e-08   2.7e-05       1      57 [.      59     113 ..      59     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.7e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnveleald 57 
                                       L+iGcG G +  ++++ +p+++++ +D++p a+  + +++++r+n   ++v + + d
  gi|320101338|ref|YP_004176930.1|  59 LDIGCGYGVIGIVVARLNPRLKVYMTDVNPLAV--KTARFNARRNGVGDRVVVVEGD 113
                                       8********************************..6666666666666666665555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     6e-07    0.0006       1      68 [.      59     129 ..      59     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6e-07
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvss 68 
                                       Ld+GcG G +   +a+     +v+ +D+++ ++k+a+ +a+++g+  +v +v++d  + p+e   f +++s+
  gi|320101338|ref|YP_004176930.1|  59 LDIGCGYGVIGIVVARLNprLKVYMTDVNPLAVKTARFNARRNGVgdRVVVVEGDGYR-PVEGLVFNAIYSN 129
                                       8*******9999999777889***********************9999999**99997.8887777777765 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.3e-06    0.0013      66     139 ..      47     120 ..      29     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGG CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyee 139
                                       le + + +   vL++G+G G    v+arl +++ +v   +  +  v++a+ n +++++  +v+vv+gDG+  +e 
  gi|320101338|ref|YP_004176930.1|  47 LENIVIPEEGVVLDIGCGYGVIGIVVARL-NPRLKVYMTDVNPLAVKTARFNARRNGVGdRVVVVEGDGYRPVEG 120
                                       55555777788****************97.666778889999999999********99769********987654 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.9e-06    0.0019      20      62 ..      52     117 ..      35     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                   Methyltransf_23  20 lraggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae.....................k 62 
                                        ++ g vLdiGcG+G i   v+r n+  +v++ D +p av+ a+                      
  gi|320101338|ref|YP_004176930.1|  52 IPEEGVVLDIGCGYGvIGIVVARLNPRlKVYMTDVNPLAVKTARfnarrngvgdrvvvvegdgyrP 117
                                       67889**********7777777999555*********99999887666666655555555554440 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.7e-06    0.0037       3      70 ..      57     126 ..      55     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkleki 70 
                                       v+lD+ +G G   i  a+     kv+  ++n+  ++ a  Na+  gv d++ +v gd    ++ l +++i
  gi|320101338|ref|YP_004176930.1|  57 VVLDIGCGYGVIGIVVARLnpRLKVYMTDVNPLAVKTARFNARRNGVGDRVVVVEGDGYRPVEGLVFNAI 126
                                       79********88888887744568*********************************9998888777776 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05      0.01      72     130 ..      74     131 ..      62     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                                       HHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE--- CS
                           UPF0020  72 earaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpP 130
                                       + +++lk+y  D ++ +v++ar Na++ gvgd++ +++ d      +   +++i +npP
  gi|320101338|ref|YP_004176930.1|  74 RLNPRLKVYMTDVNPLAVKTARFNARRNGVGDRVVVVEGDGYRPV-EGLVFNAIYSNPP 131
                                       5678999*******************************9976433.3447899999999 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05     0.011      42     147 ..      55     155 ..      46     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                       C-EEEETT-TTSHHHHHHHHTT-..SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRga..kkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                       +  vLD+ +G G++g+  + R     k+++ + ++ avk+ + n ++ ++ +++ ++  d ++ ++ l     +f+ 
  gi|320101338|ref|YP_004176930.1|  55 EGVVLDIGCGYGVIGIV-VARLNprLKVYMTDVNPLAVKTARFNARRNGVGDRVVVVEGDGYRPVEGL-----VFNA 125
                                       56799999******995.56644115899***********************9999999999999888.....8*** PP

                                       EEE--SSSTTCH.HHHHHHHHHTT-EEEEEE CS
                     Cons_hypoth95 117 vflDPPyakellieevlelleekkllkenal 147
                                       ++ +PP a+++ + e + l  +k++l+e+++
  gi|320101338|ref|YP_004176930.1| 126 IYSNPPLAAGMRVVEEIVL-GAKEHLAEEGF 155
                                       **********875555544.44677777766 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.3e-05     0.063      51      79 ..      57      85 ..      44      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                                      .EEEETSTTTTTHHHHHHH-TTSEEEEEE CS
                              GidB 51 kviDvGsGaGlPGipLaiarpelkltLle 79
                                       v+D+G G G+ Gi++a ++p lk+++ +
  gi|320101338|ref|YP_004176930.1| 57 VVLDIGCGYGVIGIVVARLNPRLKVYMTD 85
                                      49**********************99876 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.6e-05     0.056      63     121 ..      55     115 ..      28     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                                       -SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS.-----TTEEEEES-TT CS
                    Methyltransf_2  63 lkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehl.sageeervefvgGdff 121
                                         +++D+G G G++   ++++ P +kv + D+ p  v++A+      g  +rv +v+Gd +
  gi|320101338|ref|YP_004176930.1|  55 EGVVLDIGCGYGVIGIVVARLNPRLKVYMTDVnPLAVKTARFNArRNGVGDRVVVVEGDGY 115
                                       56789**************************95667888887766788899999***9966 PP

>> Adeno_hexon  Hexon, adenovirus major coat protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.16      46     101 ..      55     110 ..      48     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                       TT----TTS--EEE--B---.-S--B-SSS-SS--SS-S---------------SS- CS
                       Adeno_hexon  46 dsrvldlGstyfdikGvvdr.GpsfkpygGtaynplapksavfnavvestgeatsvl 101
                                       ++ vld+G+ y  i  vv r  p +k y  t  npla k a fna  +  g++  v+
  gi|320101338|ref|YP_004176930.1|  55 EGVVLDIGCGYGVIGIVVARlNPRLKVYM-TDVNPLAVKTARFNARRNGVGDRVVVV 110
                                       689***********999999679*****6.899***********9877777666665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.19      61     109 ..      66     113 ..      48     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                                       SHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S- CS
                               TRM  61 GlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvinedd 109
                                       G+ +i  a  ++   +v++ D+++ Av++ + N++ n v ++vv+ e+d
  gi|320101338|ref|YP_004176930.1|  66 GVIGIVVAR-LNPRLKVYMTDVNPLAVKTARFNARRNGVGDRVVVVEGD 113
                                       555555554.477889*************************88887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1377.49
//
Query:       gi|320101339|ref|YP_004176931.1|  [L=96]
Description: 50S ribosomal protein L14 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00011   22.0   1.4    0.00026   20.8   1.4    1.7  1  KOW             KOW motif
     0.0014   19.1   0.0      0.002   18.6   0.0    1.3  1  Ribosomal_L14e  Ribosomal protein L14


Domain annotation for each model (and alignments):
>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   1.4     3e-08   0.00026       2      31 ..       7      35 ..       6      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3e-08
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                      G+++  v+G+ +G++++Vv++++++ +V+v
  gi|320101339|ref|YP_004176931.1|  7 GRICVKVAGREAGRKCVVVDIIDDN-FVLV 35
                                      889999*******************.4444 PP

>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.3e-07     0.002       1      39 [.      45      83 ..      45      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-07
                    Ribosomal_L14e  1 pRqaiplkrlkLtkivlklprgartgavkkawekadvee 39
                                      +R ++++k+++ t+  +k++rga+ + v ka+ ++++++
  gi|320101339|ref|YP_004176931.1| 45 KRRKVNIKHIEPTDKSIKISRGASDEEVLKAIGESGLTD 83
                                      6999****************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.28s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 711.97
//
Query:       gi|320101340|ref|YP_004176932.1|  [L=181]
Description: cytidylate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-16   61.6   0.0    1.3e-16   61.2   0.0    1.3  1  AAA_17           AAA domain
    1.5e-16   61.0   0.1    4.4e-14   53.0   0.1    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    8.4e-13   49.0   0.0    1.4e-12   48.3   0.0    1.4  1  AAA_18           AAA domain
    2.9e-08   33.7   0.4    2.4e-05   24.2   0.1    2.1  2  Cytidylate_kin   Cytidylate kinase
    1.1e-06   28.8   0.0    1.9e-06   28.1   0.0    1.5  1  ADK              Adenylate kinase
    9.4e-06   26.0   0.0    4.4e-05   23.8   0.0    1.9  2  AAA_28           AAA domain
    3.1e-05   24.4   0.0    4.9e-05   23.8   0.0    1.4  1  AAA              ATPase family associated with various cellul
    0.00039   20.6   0.1    0.00088   19.5   0.1    1.8  1  AAA_33           AAA domain
    0.00051   19.8   0.1       0.12   12.1   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.032   14.2   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.022   15.1   0.0      0.042   14.1   0.0    1.6  1  AAA_22           AAA domain
      0.031   14.4   0.0       0.73    9.9   0.0    2.1  2  SKI              Shikimate kinase
       0.04   13.8   0.0      0.089   12.7   0.0    1.6  1  NTPase_1         NTPase
      0.044   13.5   0.1      0.077   12.7   0.1    1.4  1  AAA_24           AAA domain
      0.052   12.9   0.0      0.094   12.1   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.057   13.8   0.0      0.071   13.5   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.064   12.7   0.0      0.094   12.2   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
      0.072   13.4   0.0       0.11   12.8   0.0    1.3  1  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.082   12.6   0.0       0.56    9.9   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
      0.091   12.6   0.0       0.36   10.7   0.0    1.9  2  dNK              Deoxynucleoside kinase
        0.1   12.6   0.1       0.86    9.6   0.0    2.2  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.15   12.2   0.0        0.3   11.2   0.0    1.5  1  EFG_II           Elongation Factor G, domain II


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   1.6e-19   1.3e-16       2      87 ..       8      91 ..       7     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.6e-19
                                      E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
                            AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdgh 79
                                      G+PGsGK+tq+++++e ygf+++saG ++re akr++l  ++ ++++ ++ +++ e++++  e+++   ++++++vdgh
  gi|320101340|ref|YP_004176932.1|  8 GPPGSGKTTQAKRVAEYYGFKYFSAGAVFREYAKRRNLtLEELSRIAMEDPSIDIEIDRLTLETVR---GSDNIVVDGH 83
                                      9************************************97788899999999999999999999998...589******* PP

                                      SEEEETTE CS
                            AAA_17 80 prikeqag 87
                                         +  ++
  gi|320101340|ref|YP_004176932.1| 84 LAAWIVSD 91
                                      98765555 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.1   5.4e-17   4.4e-14       2     178 ..       4     157 ..       3     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 5.4e-17
                   Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekl 77 
                                       I +s+  Gsg++t ++++Ae +g+++++  ++++e ak+ +l+ ee+ ++               +       d ++
  gi|320101340|ref|YP_004176932.1|   4 IVFSGPPGSGKTTQAKRVAEYYGFKYFSAgAVFREYAKRRNLTLEELSRIAM-------------E-------DPSI 60 
                                       5578889**********************9****************955554.............2.......5667 PP

                   Cytidylate_kin2  78 ddelfeaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrra 154
                                       d e+ +    +++++  ++++V+ G  a+ i+ d+   lr+++tapl  r+ rva r ++  + a ++   ++  ++
  gi|320101340|ref|YP_004176932.1|  61 DIEIDRL---TLETVRGSDNIVVDGHLAAWIVSDIV-DLRIYVTAPLSLRILRVAGRDNIPLNRALTETLVREYSQR 133
                                       7775554...455555557***************99.9**********************87777777777777777 PP

                   Cytidylate_kin2 155 kyykkytgqdwgdaenYdlvlnts 178
                                        ++ +y+g d+ d++ +d+++nt+
  gi|320101340|ref|YP_004176932.1| 134 RRFMEYYGLDIYDTSIFDVTINTK 157
                                       788999****************95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   1.7e-15   1.4e-12       1     115 [.       4     115 ..       4     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.7e-15
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I+ +G+pG+GKtt ak++++  gf     g + r++ak ++l le+      e   +d++ +   l++++++     
  gi|320101340|ref|YP_004176932.1|   4 IVFSGPPGSGKTTQAKRVAEYYGFkyfsaGAVFREYAKRRNLTLEELSRIAMEDPSIDIEIDRLTLETVRGS----- 75 
                                       8999****************988899********************99955666666666666777777775..... PP

                            AAA_18  73 egknlvidghlaeleseaakdikkvvLtaspeelleRlekRgy 115
                                         +n+v+dghla ++  + +d+  +++ta+ + ++ R++ R++
  gi|320101340|ref|YP_004176932.1|  76 --DNIVVDGHLAAWIVSDIVDLR-IYVTAPLSLRILRVAGRDN 115
                                       ..89*******************.*****************86 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   2.9e-08   2.4e-05       3      37 ..       6      40 ..       4      61 .. 0.90
   2 !    8.6   0.0    0.0017       1.4     103     170 ..      65     133 ..      42     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.9e-08
                                      EE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                    Cytidylate_kin  3 iDGPagsGKssvaralaeklglkyldtgalYRala 37
                                        GP gsGK + a+++ae  g+ky+++ga++R +a
  gi|320101340|ref|YP_004176932.1|  6 FSGPPGSGKTTQAKRVAEYYGFKYFSAGAVFREYA 40
                                      67******************************987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0017
                                       HHHHHTT-B.SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHH CS
                    Cytidylate_kin 103 vkklrelvk.karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeR 170
                                        ++  e v+ ++++vv+G   +  v    +l+i+++A    R+ R +   +   +    e+l++e  +R
  gi|320101340|ref|YP_004176932.1|  65 DRLTLETVRgSDNIVVDGHLAAWIVSDIVDLRIYVTAPLSLRILRVAGRDNIPLNRALTETLVREYSQR 133
                                       555555555599******98888888889**************99776656555556667777776666 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.3e-09   1.9e-06       2      39 ..       7      44 ..       6      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.3e-09
                                      EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevksgt 39
                                       G+Pg+GK tqa+++++ yg++  s+G ++R+  k+  
  gi|320101340|ref|YP_004176932.1|  7 SGPPGSGKTTQAKRVAEYYGFKYFSAGAVFREYAKRRN 44
                                      69*****************************9887654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.4e-08   4.4e-05       1      63 [.       3      63 ..       3      91 .. 0.65
   2 ?   -0.1   0.0       1.2   9.6e+02      55      86 ..     118     153 ..     104     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.4e-08
                            AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaervleeq 63
                                      kiv++G++++GKTt +++ a+  g++++    ++re+ + +  + e+ +     ++a+++  ++ +
  gi|320101340|ref|YP_004176932.1|  3 KIVFSGPPGSGKTTQAKRVAEYyGFKYFsaGAVFREYAKRRNLTLEELS-----RIAMEDPSIDIE 63
                                      79*******************8888877667888888877665444422.....233333333333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                            AAA_28  55 faervleeqleeeaaa....aankvlfcDrglldtl 86 
                                       +++++ e  ++e+ ++    +  ++ ++D++++d++
  gi|320101340|ref|YP_004176932.1| 118 LNRALTETLVREYSQRrrfmEYYGLDIYDTSIFDVT 153
                                       555544444444444344557788899999999986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   6.1e-08   4.9e-05       1      50 [.       4      51 ..       4      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.1e-08
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelf 50
                                      ++++GppG GKT+ ak va+  g+++++  +  ++ +y + ++  ++el 
  gi|320101340|ref|YP_004176932.1|  4 IVFSGPPGSGKTTQAKRVAEYYGFKYFS--AGAVFREYAKRRNLTLEELS 51
                                      5799*****************8877664..55555566666655555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.1e-06   0.00088       2      39 ..       4      41 ..       4     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg 39
                                      +++ G+pGsGK+t a+r+++  g+   s  +++r +++
  gi|320101340|ref|YP_004176932.1|  4 IVFSGPPGSGKTTQAKRVAEYYGFKYFSAGAVFREYAK 41
                                      6899**************99888665555555555554 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 !   12.1   0.0   0.00015      0.12      35      59 ..       3      27 ..       1      40 [. 0.83
   2 ?    5.9   0.1     0.012       9.9      93     119 ..      40      66 ..      31      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            RuvB_N 35 hvllyGpPGlGkttlakiiakelgv 59
                                       ++++GpPG Gktt ak +a+  g 
  gi|320101340|ref|YP_004176932.1|  3 KIVFSGPPGSGKTTQAKRVAEYYGF 27
                                      5899*************99987665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                            RuvB_N  93 ihrlsraveevlysamedfrldivigk 119
                                         r + ++ee+   amed ++di i++
  gi|320101340|ref|YP_004176932.1|  40 AKRRNLTLEELSRIAMEDPSIDIEIDR 66 
                                       56788899***************9975 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.9e-05     0.032       3      28 ..       5      30 ..       3      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                                      EEE--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnreve 28
                                      +  GppG+gK++ a+r+a+ ++ +++
  gi|320101340|ref|YP_004176932.1|  5 VFSGPPGSGKTTQAKRVAEYYGFKYF 30
                                      678*****************966655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.2e-05     0.042       8      29 ..       4      25 ..       3      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                      +v  G++G+GKTt ++r++e +
  gi|320101340|ref|YP_004176932.1|  4 IVFSGPPGSGKTTQAKRVAEYY 25
                                      5788*************99866 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0009      0.73       1      30 [.      10      39 ..      10      51 .. 0.85
   2 ?    2.6   0.0      0.17   1.4e+02      89     143 ..      97     149 ..      83     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0009
                                      TTSSHHHHHHHHHHHHTSEEEEHHHHHHHH CS
                               SKI  1 mGaGKstvGkllAkklglefiDlDeliekr 30
                                      +G+GK+t +k++A+ +g++++ +  ++ + 
  gi|320101340|ref|YP_004176932.1| 10 PGSGKTTQAKRVAEYYGFKYFSAGAVFREY 39
                                      69*****************99877766655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
                                       EEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTS CS
                               SKI  89 iyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaadvvvdese 143
                                       iy+ ++l   + r++ +++ Pl ++ ++   l +e+ +r++++e +   + d+s 
  gi|320101340|ref|YP_004176932.1|  97 IYVTAPLSLRILRVAGRDNIPLNRALTE--TLVREYSQRRRFMEYYGLDIYDTSI 149
                                       99999***99*****9999777777776..5556666688888777655555554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.089       1      23 [.       3      25 ..       3      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                      EEEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlell 23
                                      k++ +GppG+GKtT  k+v+e  
  gi|320101340|ref|YP_004176932.1|  3 KIVFSGPPGSGKTTQAKRVAEYY 25
                                      57899**************9975 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.4e-05     0.077       3      22 ..       2      21 ..       1      31 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.4e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      +ki+  Gp+g+GKTt+ak+ 
  gi|320101340|ref|YP_004176932.1|  2 VKIVFSGPPGSGKTTQAKRV 21
                                      58999************987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012     0.094      25      43 ..       4      22 ..       2      25 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                      Mg_chelatase 25 lllvGppGsGKtmlakrlp 43
                                      +++ GppGsGKt  akr++
  gi|320101340|ref|YP_004176932.1|  4 IVFSGPPGSGKTTQAKRVA 22
                                      899*************986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.7e-05     0.071      27      63 ..       4      39 ..       3     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.7e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      +++sG++G+GK++ ++++++++  +  +f + + ++++
  gi|320101340|ref|YP_004176932.1|  4 IVFSGPPGSGKTTQAKRVAEYYGFK--YFsAGAVFREY 39
                                      5799***************988777..44333333333 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012     0.094       2      24 ..       2      24 ..       1      65 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                      .EEEEE--TTSSHHHHHHHHHHH CS
                             KTI12  2 pLvvltGlPssGKstrakeLaka 24
                                        +v++G P sGK+t ak++a++
  gi|320101340|ref|YP_004176932.1|  2 VKIVFSGPPGSGKTTQAKRVAEY 24
                                      569***************99987 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.11       2      33 ..       4      35 ..       3      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsv 33
                                      i+  G+P sGKt+ a  +a +Y+  +++   v
  gi|320101340|ref|YP_004176932.1|  4 IVFSGPPGSGKTTQAKRVAEYYGFKYFSAGAV 35
                                      7889******************9988876555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00068      0.56       3      20 ..       8      25 ..       6      58 .. 0.90
   2 ?    0.5   0.0       0.5   4.1e+02     119     163 ..      94     140 ..      76     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00068
                                      ESTTSSHHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerl 20
                                      G  G+GKttqa+ ++e++
  gi|320101340|ref|YP_004176932.1|  8 GPPGSGKTTQAKRVAEYY 25
                                      788************987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.5
                                       SEEEEEESSHHHHHTSCCTTSS..TTTSHHHHHHHHHHHHHHHHHHH CS
                   Thymidylate_kin 119 dltflldvdpevalkRlakrde..ldeeeeeqldflrkvrerylela 163
                                       dl +++  + + ++ R+a rd   l+++  e l    + r+r++e +
  gi|320101340|ref|YP_004176932.1|  94 DLRIYVTAPLSLRILRVAGRDNipLNRALTETLVREYSQRRRFMEYY 140
                                       88899999999999999999998866665555555555555555544 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00044      0.36       1      28 [.       4      31 ..       4      60 .. 0.86
   2 ?   -0.4   0.1       1.1   8.9e+02     124     165 ..      94     132 ..      79     178 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                                      EEEEESTTSSHHHHHHHHHCCSTCEEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvfe 28
                                      iv +G+ g+GK+t +k+ ++ +g+k f+
  gi|320101340|ref|YP_004176932.1|  4 IVFSGPPGSGKTTQAKRVAEYYGFKYFS 31
                                      7889********************9987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHH CS
                               dNK 124 dlliYLkasletclerikkRgreeekkieldYlekLhekyee 165
                                       dl iY+ a+l     r+  R++    + +++  e+L ++y++
  gi|320101340|ref|YP_004176932.1|  94 DLRIYVTAPLSLRILRVAGRDN---IPLNRALTETLVREYSQ 132
                                       6666666666555555444443...23444444444444444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0011      0.86      22      46 ..       4      28 ..       1      72 [. 0.83
   2 ?    0.6   0.1      0.65   5.3e+02      54      75 ..     125     148 ..     120     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                      EEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 22 ilLeGdLGaGKTtlvrglakalgve 46
                                      i+++G+ G+GKTt ++ +a+ +g++
  gi|320101340|ref|YP_004176932.1|  4 IVFSGPPGSGKTTQAKRVAEYYGFK 28
                                      899****************999886 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.65
                                       TSEEEEEE..SS...EEEEE-TT-S CS
                              TsaE  54 tlveeYelekeg...lyHfDlYRle 75 
                                       tlv+eY++++ +    y +D+Y  +
  gi|320101340|ref|YP_004176932.1| 125 TLVREYSQRR-RfmeYYGLDIYDTS 148
                                       8999997654.34888889999753 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 ?   11.2   0.0   0.00037       0.3      23      47 ..      48      72 ..      36      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                            EFG_II 23 kaLarlleEDptlrverdeeTketi 47
                                      + L+r++ EDp++++e d+ T et+
  gi|320101340|ref|YP_004176932.1| 48 EELSRIAMEDPSIDIEIDRLTLETV 72
                                      5799***************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1360.45
//
Query:       gi|320101341|ref|YP_004176933.1|  [L=90]
Description: 50S ribosomal protein L34 [Desulfurococcus mucosus DSM 2162]
Scores for 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-27   96.3   0.7    1.1e-27   96.2   0.7    1.0  1  Ribosomal_L34e  Ribosomal protein L34e
     0.0058   16.5   0.0        1.1    9.2   0.0    2.2  2  zf-C4_ClpX      ClpX C4-type zinc finger
  ------ inclusion threshold ------
      0.025   14.5   1.3        3.5    7.6   0.0    2.2  2  DUF4428         Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.7   1.8e-31   1.1e-27      10      92 ..       3      85 ..       1      87 [. 0.94

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.8e-31
                    Ribosomal_L34e 10 rlsYntrsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRaYGgslcakcvker 88
                                      r+  + rs ++ vv+tpgg+++++y+k+++++++C+ c+k L+G+palrp e++ l+kt+k+++R+YGg++c++c+ + 
  gi|320101341|ref|YP_004176933.1|  3 RPMHRNRSWRRIVVRTPGGEVRVHYEKRRPSQARCAICGKPLNGVPALRPVEMRGLAKTEKRPERPYGGYICHECLARG 81
                                      788999*********************************************************************9877 PP

                    Ribosomal_L34e 89 ivra 92
                                      + +a
  gi|320101341|ref|YP_004176933.1| 82 LREA 85
                                      6655 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0     0.003        18       2      10 ..      36      44 ..      35      50 .. 0.81
   2 !    9.2   0.0   0.00019       1.1      22      31 ..      70      79 ..      65      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.003
                        zf-C4_ClpX  2 rCSFCgkse 10
                                      rC  Cgk+ 
  gi|320101341|ref|YP_004176933.1| 36 RCAICGKPL 44
                                      8******95 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
                        zf-C4_ClpX 22 gvyICdeCve 31
                                      g yIC eC +
  gi|320101341|ref|YP_004176933.1| 70 GGYICHECLA 79
                                      56******76 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3     0.002        12       1       9 [.      36      44 ..      36      47 .. 0.86
   2 ?    7.6   0.0   0.00059       3.5      20      29 ..      71      80 ..      69      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.002
                           DUF4428  1 iCaiCgkKi 9 
                                      +CaiCgk +
  gi|320101341|ref|YP_004176933.1| 36 RCAICGKPL 44
                                      5*****976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00059
                           DUF4428 20 gyvCkdClkK 29
                                      gy+C++Cl +
  gi|320101341|ref|YP_004176933.1| 71 GYICHECLAR 80
                                      8******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 731.03
//
Query:       gi|320101342|ref|YP_004176934.1|  [L=151]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   20.1   1.9    0.00085   19.5   0.0    2.0  2  DUF3270   Protein of unknown function (DUF3270)
  ------ inclusion threshold ------
      0.061   12.6   0.2      0.061   12.6   0.2    1.7  2  S_4TM     SMODS-associating 4TM effector domain
       0.19   11.2   2.9       0.99    8.9   0.0    2.3  2  DUF3087   Protein of unknown function (DUF3087)


Domain annotation for each model (and alignments):
>> DUF3270  Protein of unknown function (DUF3270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.5       0.2   1.2e+03      64      80 ..       5      21 ..       1      27 [. 0.59
   2 !   19.5   0.0   1.4e-07   0.00085       5      74 ..      37     107 ..      33     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                           DUF3270 64 latllAfllAilislai 80
                                      l  l+++  Ailis +i
  gi|320101342|ref|YP_004176934.1|  5 LVLLVSISSAILISILI 21
                                      34456666666666655 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.4e-07
                           DUF3270   5 lkdfeeveeeeekeqtpkfqdfqelnensaklkeLlFFariAvFsvitvlvsf.illalklatllAfllAi 74 
                                       ++ +e  e  ++k +  +++++ +l +++++   LlF + i++Fs++ vl+ f + l+ + + ++ ++++i
  gi|320101342|ref|YP_004176934.1|  37 YQLVEIPETPRSKGDIRRLRKYRALYKSAKRRLTLLFITHISLFSLVYVLMIFtVSLVSRSSEVVNIPVSI 107
                                       5556666677777778889999999999999999*******************566888899999999887 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3      0.33     2e+03     172     188 ..       5      21 ..       1      33 [. 0.53
   2 ?   12.6   0.2     1e-05     0.061       2      61 ..      41     104 ..      40     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.33
                             S_4TM 172 falvlwillvlvvglik 188
                                       ++l++ i + ++++++ 
  gi|320101342|ref|YP_004176934.1|   5 LVLLVSISSAILISILI 21 
                                       34444444444444433 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1e-05
                             S_4TM   2 eIrerQneeenlellaAqrqlYsrakrlqalrvilsvvlaivlsvlavlvps....lktylall 61 
                                       eI+e   ++  +++l+ +r+lY+ akr   l +i  + l  ++ vl ++  s    +++++++ 
  gi|320101342|ref|YP_004176934.1|  41 EIPETPRSKGDIRRLRKYRALYKSAKRRLTLLFITHISLFSLVYVLMIFTVSlvsrSSEVVNIP 104
                                       68888899999**********************9988776655555554443333344444443 PP

>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00016      0.99      57      85 ..      11      39 ..       3      44 .. 0.80
   2 ?    2.0   1.0     0.021   1.3e+02       9      36 ..      60      87 ..      54     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
                           DUF3087 57 vlalvltaailrklktkpfmaevvYvWrL 85
                                      + +++l+++++  +k++p++ae++  ++L
  gi|320101342|ref|YP_004176934.1| 11 ISSAILISILIDAVKKHPYFAEAIRTYQL 39
                                      5567777888888**********988887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.021
                           DUF3087  9 erYrkklnrvivalvallavlsllfstl 36
                                      + Y++  +r ++ +++ + ++sl++  +
  gi|320101342|ref|YP_004176934.1| 60 ALYKSAKRRLTLLFITHISLFSLVYVLM 87
                                      679999**********999999987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1226.93
//
Query:       gi|320101343|ref|YP_004176935.1|  [L=475]
Description: protein translocase subunit secY/sec61 alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-59  201.0  17.3    3.6e-59  200.5  17.3    1.2  1  SecY             SecY translocase
    6.2e-11   41.9   0.3    6.2e-11   41.9   0.3    2.4  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 !  200.5  17.3     4e-63   3.6e-59       1     306 []      72     454 ..      72     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 4e-63
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC........... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg........... 65 
                                       ++++LGI+P++ta++i+q+l ++   kl  l+ +++e+rk ++  ++ l+v+la+++a++++ls++           
  gi|320101343|ref|YP_004176935.1|  72 TLMELGIGPIVTAGLIMQILvGA---KLIDLDLTDPENRKIFTASQKTLAVILAAFEAAMYVLSCRywmplgnpvts 145
                                       89******************999...777777669*************************998877999******** PP

                                       .....HH.HHHHHHHHHHHHHHHHHHHHHHH.HSSTTHHHHHHHHHHHHHHC.CHSS-.HHHH............SS CS
                              SecY  66 .....lalllivlqltagtvllmwLgEqite.kGiGnGisllifagivarlp.kalsg.liel............al 122
                                             + l + lql+++++l++ L+E+i++ +GiG+G+sl+i+ g++++++ +++s+ ++++              
  gi|320101343|ref|YP_004176935.1| 146 csaawHVRLAVWLQLFIASYLVIVLDEMIQKgWGIGSGVSLFILSGVATTIFwNTFSTvTYRNevigfipfmiqqL- 221
                                       ****966899******************************************999997555556666666655541. PP

                                       ..............THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHHHHHHHH CS
                              SecY 123 e............gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagviPiIfassl 187
                                       +            g    l+ +++t+ ++ll++y+ +++++ipv++ +    ++ ++++Pl+++y  +iPi+f   l
  gi|320101343|ref|YP_004176935.1| 222 SsgrgldavlirpG-GRDLVGFAATIGIMLLLIYLSNMKVEIPVTSPRL---QSIKTRIPLQFLYVTNIPILFIGIL 294
                                       14555554445542.499***************************9966...578*********************9 PP

                                       HH................HHHCCCCS........................TCCCS.......THHHHHHHHHHHHHH CS
                              SecY 188 la................lpstiaqfl.......................lalls.......psvlyvvlyvlliif 218
                                        a                +ps+i+ +l                       l           + ++y vl ++l ++
  gi|320101343|ref|YP_004176935.1| 295 YAnilvfatlfrtylastVPSSIVDLLakydpntgrligglayylaspngL---YgalgdpvHLLVYSVLVFVLAVL 368
                                       997777777766666666577776666888888888888776655554440...04452332223455666666666 PP

                                       HHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHH CS
                              SecY 219 Fayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggt 293
                                       F  +++e++ +np+  ae+l  sg  +pg r + k ++++L+k++  +t++++l++a+i+v++d+lga  +g  +gt
  gi|320101343|ref|YP_004176935.1| 369 FGLMWVEVAgLNPSAQAEQLVSSGFEVPGLRsNPKILERMLAKYIYPLTILSSLIVAAISVFADVLGA--YG--TGT 441
                                       ********************************99**********************************..66..9** PP

                                       HHHHHHHHHHHHH CS
                              SecY 294 slLivVgvaletv 306
                                       ++L++Vg+  +++
  gi|320101343|ref|YP_004176935.1| 442 GILLAVGILQQYY 454
                                       ********98876 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.3   6.9e-15   6.2e-11       1      35 []      38      71 ..      38      71 .. 0.98
   2 ?   -1.1   0.2       0.2   1.8e+03       7      32 ..     284     311 ..     280     312 .. 0.61

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6.9e-15
                                      HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      ++Y++++++PLyGis ++++ ++ + ++ifAsnrG
  gi|320101343|ref|YP_004176935.1| 38 VVYMIMANTPLYGIS-TAGPEQILLIQIIFASNRG 71
                                      79************9.99****************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.2
                                       CCSB-..TT--SSS-TCCHTTTCCCCTS CS
                   Plug_translocon   7 sqiPL..yGissssssDpfywlRaifAs 32 
                                       ++iP+   Gi ++++  +  ++R+ +As
  gi|320101343|ref|YP_004176935.1| 284 TNIPIlfIGILYANILVFATLFRTYLAS 311
                                       5666522355556666666778888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3736.21
//
Query:       gi|320101344|ref|YP_004176936.1|  [L=155]
Description: 50S ribosomal protein L15 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-18   67.1   0.3    4.2e-18   66.3   0.3    1.4  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
    0.00016   21.1   0.1    0.00025   20.5   0.1    1.4  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   4.6e-22   4.2e-18       2     127 ..      31     144 ..      30     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 4.6e-22
                                       GGGTSSTTTTTTTTT-...S--.......S--.........---GGG..---EEEEHHHHHHTTTTGTTS.--...- CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsg...vkkkpg.feGGqmplyrrlpkrGfknskfkkeykvvnlkdLdelideerle.la...d 70 
                                       G++gG G  G +k+++   +k++p+ +  G++         Gf+ + +  e+++vn+++L+el+ +++le  a   d
  gi|320101344|ref|YP_004176936.1|  31 GSRGGFGAVGFHKHKYiwiIKHAPNwY--GKH---------GFRPRGRIPERRTVNVGELNELAGRLVLEgRAvieD 96 
                                       99**************99544466659..***.........***65656899*****************97778878 PP

                                       ---EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  71 eaeeidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       +  ++d   +          gv Kvlg g++t+ +k+ a++++ +A+ kIe+aGGkv+
  gi|320101344|ref|YP_004176936.1|  97 GLIVVDTVGM----------GVdKVLGFGKVTRRMKIVAREVTDEARRKIEEAGGKVI 144
                                       8888888888..........************************************97 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.8e-08   0.00025      95     128 ..     119     152 ..      92     155 .] 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.8e-08
                     Ribosomal_L18  95 PklsvaALrftetararilkaGGeiltlDqLalr 128
                                        +++++A ++t++ar++i++aGG+++ +++ al+
  gi|320101344|ref|YP_004176936.1| 119 RRMKIVAREVTDEARRKIEEAGGKVILVEEQALK 152
                                       469***********************99988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1180.40
//
Query:       gi|320101345|ref|YP_004176937.1|  [L=162]
Description: 50S ribosomal protein L30 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-12   44.8   0.0    1.6e-11   43.9   0.0    1.5  1  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   8.9e-16   1.6e-11       1      51 []       5      56 ..       5      56 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 8.9e-16
                                      EEEEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhlV 51
                                      ++++r+r+ ++vpp+v  +L+lL+L+k    t ++ + p + GmL k k++V
  gi|320101345|ref|YP_004176937.1|  5 YAIIRVRGQADVPPDVEHVLKLLRLHKKYhLTLYPADLPGLEGMLEKAKDWV 56
                                      57*************************999*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1178.38
//
Query:       gi|320101346|ref|YP_004176938.1|  [L=214]
Description: 30S ribosomal protein S5 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-23   81.6   0.3    4.7e-23   80.4   0.0    1.7  2  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    4.8e-22   77.7   1.3    4.8e-22   77.7   1.3    2.1  3  Ribosomal_S5    Ribosomal protein S5, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.27   2.4e+03      50      62 ..      99     111 ..      92     116 .. 0.72
   2 !   80.4   0.0   5.3e-27   4.7e-23       2      65 ..     141     205 ..     140     211 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHT CS
                    Ribosomal_S5_C  50 nvvkAtfeALkkl 62 
                                         v A  +AL++ 
  gi|320101346|ref|YP_004176938.1|  99 QYVDALAKALRNA 111
                                       6778888888775 PP

  == domain 2  score: 80.4 bits;  conditional E-value: 5.3e-27
                                       EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT CS
                    Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrsp 65 
                                       gk g+v+v lkpaprGtG++ag++++ vl+laGi+D ++ s g +r+++n++kA+ +AL +++ +
  gi|320101346|ref|YP_004176938.1| 141 GKSGSVEVVLKPAPRGTGLVAGDVAKVVLRLAGIRDAWTESFGeTRTTLNFAKAVANALHNTYRF 205
                                       9*************************************************************987 PP

>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.93   8.3e+03       8      23 ..      17      32 ..      12      33 .. 0.73
   2 !   77.7   1.3   5.3e-26   4.8e-22       2      65 .]      56     119 ..      55     119 .. 0.96
   3 ?   -1.9   0.0      0.37   3.3e+03      51      61 ..     192     202 ..     189     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.93
                                      EEEEEEEETTEEEEEE CS
                      Ribosomal_S5  8 ikrvqkvtkgGrrtsf 23
                                        rv +++  G+ ts 
  gi|320101346|ref|YP_004176938.1| 17 RTRVGRMVLEGKLTSL 32
                                      5688899999998875 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 5.3e-26
                                       EEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                      Ribosomal_S5   2 kekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                       k + +++k vqk+t++Grrt+f ++vvvG+++G vG+G+gkak+  +A+ kA ++Ak+n++pv+
  gi|320101346|ref|YP_004176938.1|  56 KYERIDTKIVQKMTDAGRRTKFLVVVVVGNEDGFVGVGTGKAKQYVDALAKALRNAKLNITPVR 119
                                       678899********************************************************96 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.37
                                       HHHHHHHHHTE CS
                      Ribosomal_S5  51 rkAiekAkknl 61 
                                        kA+ +A +n 
  gi|320101346|ref|YP_004176938.1| 192 AKAVANALHNT 202
                                       46667776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1564.90
//
Query:       gi|320101347|ref|YP_004176939.1|  [L=198]
Description: 50S ribosomal protein L18 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-30  104.2   1.2    3.8e-22   79.0   0.5    2.3  2  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    2.7e-06   27.7   0.0    1.2e-05   25.7   0.0    1.8  2  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 
    5.2e-05   24.1   0.0     0.0001   23.2   0.0    1.4  1  Ribosomal_L18_c  Ribosomal L18 C-terminal region


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 !   79.0   0.5   6.3e-26   3.8e-22       2      99 ..       6      97 ..       5     103 .. 0.95
   2 !   24.3   0.0   4.2e-09   2.5e-05     130     161 ..     101     132 ..      96     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 6.3e-26
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelp.kygvkvgl 79
                                      r++v  rrrregkt+Yy+r r++   +        R+v+r t + i +q+++a+ egd+v+aaa+s+el+ k+g k+g 
  gi|320101347|ref|YP_004176939.1|  6 RYKVPRRRRREGKTNYYKRYRMVLSGH-------PRFVIRKTLNYIWVQVVEARPEGDVVIAAAHSNELRkKFGWKAGT 77
                                      9**********************9765.......59*********************************769******* PP

                     Ribosomal_L5e 80 tnyaaaYatglllarrllkk 99
                                       n  aaY+tgll + r+l+k
  gi|320101347|ref|YP_004176939.1| 78 CNTPAAYLTGLLASLRALEK 97
                                      ****************9987 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 4.2e-09
                     Ribosomal_L5e 130 kaiLdvGLartttgakvfgalkgavdgglsip 161
                                        a+ d+GL+r  +ga vf+a+k+a d+gl++p
  gi|320101347|ref|YP_004176939.1| 101 YAVPDIGLHRPVKGALVFAAMKAANDAGLKVP 132
                                       5777***************************9 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 !   25.7   0.0   1.9e-09   1.2e-05       3     114 ..      14     129 ..      10     131 .. 0.68
   2 ?   -0.6   0.0      0.27   1.6e+03     101     114 ..     148     161 ..     144     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.9e-09
                                       CCHHHCHHHHHHTTT--TTSSS-EEEEEE-SS-EEEEEE-TT..T--EEEEECS-SCCCT...S-SSSCHHHHHHHH CS
                    Ribosomal_L18p   3 kkearkrRhkRirkklsgtaerprlvvfrsnrhiyaQviddv..kgktlasastlekelk...lkstknkeaakkvg 74 
                                       ++e ++   kR r  lsg+    r v+ ++ ++i++Qv++     + ++a+a + e + k   +  t n+ aa   g
  gi|320101347|ref|YP_004176939.1|  14 RREGKTNYYKRYRMVLSGHP---RFVIRKTLNYIWVQVVEARpeGDVVIAAAHSNELRKKfgwKAGTCNTPAAYLTG 87 
                                       55666667788888888875...****************97521456777776655444454555566666666667 PP

                                       HHHHHHHCHHCHTC-EE--TTSS.S-CH.HHHHHHHHHCTSS CS
                    Ribosomal_L18p  75 eliAerakekgiekvvfDrggyk.YhGr.vaalAdaaReaGl 114
                                        l   ra+ekg++ +v D g ++  +G  v a  +aa +aGl
  gi|320101347|ref|YP_004176939.1|  88 LLASLRALEKGVSYAVPDIGLHRpVKGAlVFAAMKAANDAGL 129
                                       77777***********99886652344314444455666666 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHCTSS CS
                    Ribosomal_L18p 101 rvaalAdaaReaGl 114
                                       ++a+ A+ +Re+Gl
  gi|320101347|ref|YP_004176939.1| 148 HIASYAKILRENGL 161
                                       58999********8 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.7e-08    0.0001       5      58 ..     141     192 ..     139     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.7e-08
                   Ribosomal_L18_c   5 rkrIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIre 58 
                                       ++rI g+h+a Y + L+e+     +k+Fs+y+++g++++dl   ++++ ++I +
  gi|320101347|ref|YP_004176939.1| 141 EERIRGEHIASYAKILRENGL--LEKRFSRYLASGLQPEDLPAHFEEVKNNILK 192
                                       579**************9865..99************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.29s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1431.62
//
Query:       gi|320101348|ref|YP_004176940.1|  [L=152]
Description: 50S ribosomal protein L19 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-52  178.1   5.8    1.1e-52  177.9   5.8    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
      0.009   15.7   0.7      0.099   12.4   0.0    2.8  3  S4              S4 domain
  ------ inclusion threshold ------
       0.14   11.2   0.0       0.18   10.9   0.0    1.1  1  GcpE            GcpE protein


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 !  177.9   5.8   1.9e-56   1.1e-52       1     143 [.       3     145 ..       3     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.9 bits;  conditional E-value: 1.9e-56
                                       -THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGG CS
                    Ribosomal_L19e   1 dlklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsG 77 
                                       dl+ qkrla+++l+vG++r+++dp+++e++++Aitre+++kli+dg+I+++p++g + +  r r++++ kgrrrg+G
  gi|320101348|ref|YP_004176940.1|   3 DLSFQKRLASEILGVGVSRIRIDPKRIEDVEAAITREEVKKLIRDGAIWVEPVHGIAGYSSRVRHAQRVKGRRRGHG 79 
                                       5889************************************************************************* PP

                                       G--S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                    Ribosomal_L19e  78 krkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                       krkGtkeaRl++kelW+ riR++Rr+L+ lr+kk id +tYr+lY+ akGg+f++ ++Lk y++++
  gi|320101348|ref|YP_004176940.1|  80 KRKGTKEARLDSKELWMGRIRKIRRYLRYLRDKKLIDARTYRRLYMLAKGGYFNSLSSLKLYLREN 145
                                       *************************************************************99876 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.13   7.7e+02      27      38 ..      21      32 ..      20      34 .. 0.87
   2 !   12.4   0.0   1.7e-05     0.099      13      30 ..      35      52 ..      31      55 .. 0.92
   3 ?   -1.0   0.1      0.26   1.5e+03      10      21 ..      59      70 ..      58      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                                      TEEETTEEE--T CS
                                S4 27 rVlVNGkvvkdp 38
                                      r++++ k++ d 
  gi|320101348|ref|YP_004176940.1| 21 RIRIDPKRIEDV 32
                                      79******9985 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.7e-05
                                      SSSHHHHHHHHHTTTEEE CS
                                S4 13 assrreArqlIehGrVlV 30
                                      a++r e+++lI++G ++V
  gi|320101348|ref|YP_004176940.1| 35 AITREEVKKLIRDGAIWV 52
                                      89**************98 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.26
                                      TTSSSSHHHHHH CS
                                S4 10 lglassrreArq 21
                                      +g+ s  r+A++
  gi|320101348|ref|YP_004176940.1| 59 AGYSSRVRHAQR 70
                                      699999999998 PP

>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     3e-05      0.18      79     121 ..       2      46 ..       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3e-05
                                       EEE-SSCHHHHHHHHCC-SEEEE-TTTSSSTTHH..HHHHHHHHH CS
                              GcpE  79 aDihfnpklaleaaeagvdkvRiNPGnigdgkkk..eekvkelve 121
                                       +D+ f+++la e++ +gv+++Ri P  i d +    +e+vk+l++
  gi|320101348|ref|YP_004176940.1|   2 SDLSFQKRLASEILGVGVSRIRIDPKRIEDVEAAitREEVKKLIR 46 
                                       799*************************99766566888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1180.98
//
Query:       gi|320101349|ref|YP_004176941.1|  [L=137]
Description: 50S ribosomal protein L32 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-31  109.1   0.0    1.7e-31  108.8   0.0    1.1  1  Ribosomal_L32e  Ribosomal protein L32
  ------ inclusion threshold ------
      0.071   13.7   0.1       0.28   11.8   0.1    1.8  2  DUF5499         Family of unknown function (DUF5499)


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 !  108.8   0.0   1.9e-35   1.7e-31       2     108 .]      20     126 ..      19     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 1.9e-35
                                       -----TTTTT-TTS-S..S------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTT CS
                    Ribosomal_L32e   2 kkFirhqsdryvklke..swrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmen 76 
                                       + F rh ++++ k+++  +wrkp+Gidn++++++kg+++++k+GY+ p+ +rgl+psG++ v+V+++ eL+ l++++
  gi|320101349|ref|YP_004176941.1|  20 PMFLRHLWWKKAKFRNdpKWRKPKGIDNKMKHQLKGYPPIVKVGYRGPSMVRGLHPSGLEPVVVNSTGELDGLDPAR 96 
                                       78*************888**********************************************************9 PP

                                       E..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  77 ksyaaeiahsVsskkrkeiverAaelgikVtN 108
                                       +  +++i++ V+ +k +ei + A   g+kV+N
  gi|320101349|ref|YP_004176941.1|  97 H--IVYIGSRVGLRKSIEIYKLATGKGFKVAN 126
                                       9..***************************99 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.1e-05      0.28      21      57 ..      17      54 ..       7      57 .. 0.85
   2 ?   -0.9   0.0      0.28   2.5e+03      83      95 ..     103     115 ..      97     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                           DUF5499 21 rkapdgvshkdmvenifrsd.kwrrmkgidsevkdeln 57
                                      rk p  + h    +  fr+d kwr+ kgid+++k +l+
  gi|320101349|ref|YP_004176941.1| 17 RKRPMFLRHLWWKKAKFRNDpKWRKPKGIDNKMKHQLK 54
                                      6777777777778889999889***********99875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.28
                           DUF5499  83 qrvakrksnecyr 95 
                                        rv  rks e y+
  gi|320101349|ref|YP_004176941.1| 103 SRVGLRKSIEIYK 115
                                       6899999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 955.44
//
Query:       gi|320101350|ref|YP_004176942.1|  [L=184]
Description: 50S ribosomal protein L6 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-27   95.1  11.6      1e-17   64.6   2.1    2.1  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.019   14.5   0.1    1.3  1  Oxygenase-NA  Oxygenase, catalysing oxidative methylation of 
      0.044   13.8   0.9       0.23   11.5   0.4    2.3  2  DUF1521       Domain of Unknown Function (DUF1521)


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 !   64.6   2.1   1.7e-21     1e-17       1      76 []      13      86 ..      13      86 .. 0.98
   2 !   36.1   2.3   1.3e-12   7.6e-09       1      76 []      98     174 ..      98     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1.7e-21
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      +P+gv+v+++g   v+v+Gpkg+++r+++++  v +  e++ v v++   +++ k+ l+g+v ++i+nmi+GVt+g
  gi|320101350|ref|YP_004176942.1| 13 VPEGVTVEVEG-SKVTVKGPKGTVSRDFSHARGVFIRLEDGAVIVETYVADRERKA-LVGSVAAHIRNMITGVTKG 86
                                      7*********8.********************************************.*****************98 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 1.3e-12
                                       CSTTEEEEEET..TTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikg..gqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....Aligtvrslinnmik 71 
                                       +P+ v v  k+  ++++++ G+k  + ++i+ +v+v+v+     +++ivv+g d+e v    A i+ ++++ + + +
  gi|320101350|ref|YP_004176942.1|  98 FPISVVVDEKNrvVRIRNFMGEKSDRIAKIHGNVKVKVS-----GEDIVVEGVDIEEVgltaASIERATRVTDRDRR 169
                                       89***********************************99.....********************************* PP

                                       HHHTC CS
                      Ribosomal_L6  72 GVteg 76 
                                       ++++g
  gi|320101350|ref|YP_004176942.1| 170 VFMDG 174
                                       **998 PP

>> Oxygenase-NA  Oxygenase, catalysing oxidative methylation of damaged DNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.2e-06     0.019     116     170 ..      41      96 ..      32      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-06
                      Oxygenase-NA 116 qsraevvkleqGdalifa.treRpvkgkrgvyrvnlrhgvsrvrsGeRltlglifH 170
                                        +r+  ++le G +++ + +++R  k+  g  ++++r  ++ v++G R+ l +if 
  gi|320101350|ref|YP_004176942.1|  41 HARGVFIRLEDGAVIVETyVADRERKALVGSVAAHIRNMITGVTKGYRYKLKIIFS 96 
                                       5788899999**9999764899********************************95 PP

>> DUF1521  Domain of Unknown Function (DUF1521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.17   9.9e+02      53      74 ..      34      55 ..      15      74 .. 0.67
   2 ?   11.5   0.4   3.8e-05      0.23      19      54 ..     101     139 ..      97     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                           DUF1521 53 dgkadfdfkkdmtfqlddGtki 74
                                          df   +++  +l+dG+ i
  gi|320101350|ref|YP_004176942.1| 34 TVSRDFSHARGVFIRLEDGAVI 55
                                      3345666666777777777644 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.8e-05
                           DUF1521  19 titldekdgtilirn...ektgevtrikGdPhvdanGdg 54 
                                       ++ +dek+  + irn   ek++++++i+G+  v + G+ 
  gi|320101350|ref|YP_004176942.1| 101 SVVVDEKNRVVRIRNfmgEKSDRIAKIHGNVKVKVSGED 139
                                       6889**********9888899****************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1468.92
//
Query:       gi|320101351|ref|YP_004176943.1|  [L=133]
Description: 30S ribosomal protein S8 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   92.2   0.0      3e-26   91.9   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 !   91.9   0.0   1.7e-30     3e-26       1     127 []       5     133 .]       5     133 .] 0.88

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.7e-30
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEE CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklk 73 
                                       D++a++l++i Nae++ k+ev v paskl+ ++lkvL++eGyi +fe+  + +  k  i++ +++nk   +vik   
  gi|320101351|ref|YP_004176943.1|   5 DTLANALSAIYNAEMRAKKEVVVwPASKLTLNVLKVLQREGYIGEFEYIdDGRWGKikIQLLGRINK--VGVIKPRY 79 
                                       89********************99************************8555555522555566666..9****999 PP

                                       E-SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  74 rvskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                        v+ + ++ + +  +      ++G++ivsT++Gv+++keA +k++GG +lay +
  gi|320101351|ref|YP_004176943.1|  80 PVKYSELEEFPEWLKRYLPAYNIGVVIVSTPHGVLSHKEAVAKHTGGVLLAYCY 133
                                       9999999988887666666778*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1077.51
//
Query:       gi|320101352|ref|YP_004176944.1|  [L=54]
Description: 30S ribosomal protein S14 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-12   47.4   1.6    1.4e-12   47.1   1.6    1.0  1  Ribosomal_S14    Ribosomal protein S14p/S29e
     0.0072   16.2   2.1      0.012   15.5   2.1    1.4  1  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
      0.008   16.4   4.1      0.051   13.9   0.8    2.1  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
  ------ inclusion threshold ------
      0.015   15.3   0.4      0.016   15.2   0.4    1.1  1  Zn_Tnp_IS91      Transposase zinc-binding domain
      0.016   15.2   2.4       0.02   14.9   2.4    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.016   15.3   0.8      0.018   15.1   0.8    1.1  1  Ribosomal_L37ae  Ribosomal L37ae protein family
      0.025   14.6   0.2       0.03   14.3   0.2    1.2  1  DZR              Double zinc ribbon
      0.048   13.3   0.2      0.064   12.9   0.2    1.2  1  zf-P11           P-11 zinc finger
      0.049   13.7   0.2      0.051   13.6   0.2    1.1  1  DUF1451          Zinc-ribbon containing domain
       0.12   12.7   2.4       0.17   12.3   2.5    1.3  1  DUF2039          Uncharacterized conserved protein (DUF2039)
          5    7.0   8.3        2.4    8.1   0.3    2.5  3  zf-CCHC_2        Zinc knuckle


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 !   47.1   1.6   8.7e-16   1.4e-12       4      53 ..       5      53 ..       4      54 .] 0.97

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 8.7e-16
                                      ----SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE- CS
                     Ribosomal_S14  4 klprnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKa 53
                                      k p+ ++ +r+ + Cr +G + +vi+ +gL  +R+cfRe A     +G+kK+
  gi|320101352|ref|YP_004176944.1|  5 KQPKTYKYGRGTQVCRRCGSRDAVIQAYGLylCRQCFREVAAV---IGFKKY 53
                                      679****************************************...*****8 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.1   7.1e-06     0.012       2      27 ..      17      40 ..      13      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.1e-06
                                      SB-TTT--BBEEEECTTEEEEE-TTT CS
                      zf-FPG_IleRS  2 epCpRCwryiervgqagrstyfCprC 27
                                      ++C+RC+  ++ +    ++ y+C +C
  gi|320101352|ref|YP_004176944.1| 17 QVCRRCGSRDAVIQA--YGLYLCRQC 40
                                      79*************..********* PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.8   3.1e-05     0.051      20      34 ..      11      25 ..       8      29 .. 0.78
   2 ?    4.5   0.1     0.027        44      24      31 ..      33      40 ..      25      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                                      ....S-EEETTTTBX CS
                    Prim_Zn_Ribbon 20 kdgrGtwfCrqCggg 34
                                      k grGt +Cr Cg+ 
  gi|320101352|ref|YP_004176944.1| 11 KYGRGTQVCRRCGSR 25
                                      5699********544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.027
                                      S-EEETTT CS
                    Prim_Zn_Ribbon 24 GtwfCrqC 31
                                      G + CrqC
  gi|320101352|ref|YP_004176944.1| 33 GLYLCRQC 40
                                      7799**** 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 ?   15.2   0.4     1e-05     0.016      25      65 ..       2      42 ..       1      49 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                       Zn_Tnp_IS91 25 ekilrCrtaalGfaryeCeeCghekivyfsCksrhCpsCqk 65
                                       ki + +t ++G  +  C+ Cg++  v +  +   C +C +
  gi|320101352|ref|YP_004176944.1|  2 AKIKQPKTYKYGRGTQVCRRCGSRDAVIQAYGLYLCRQCFR 42
                                      6899999********************************65 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.4   1.2e-05      0.02      18      44 ..      16      41 ..       3      43 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCr 44
                                      ++vC +Cgsr a  i++ gl+ C+ C 
  gi|320101352|ref|YP_004176944.1| 16 TQVCRRCGSRDAV-IQAYGLYLCRQCF 41
                                      499*****99654.44458*******5 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.8   1.1e-05     0.018      31      63 ..      14      46 ..       1      48 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                      HS-BEESSSSSSEEEEEETTEEEETTTTEEEE- CS
                   Ribosomal_L37ae 31 hakytCpfcgktkvkRkavgiwkCkkcgktvaG 63
                                      + ++ C +cg+++   +a g++ C++c ++va+
  gi|320101352|ref|YP_004176944.1| 14 RGTQVCRRCGSRDAVIQAYGLYLCRQCFREVAA 46
                                      44567***********************99996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.8e-05      0.03      11      38 ..      15      44 ..       9      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                               DZR 11 darfCseCgtk..lkavaaedrCpsCgekv 38
                                      + ++C +Cg++  + ++   + C +C ++v
  gi|320101352|ref|YP_004176944.1| 15 GTQVCRRCGSRdaVIQAYGLYLCRQCFREV 44
                                      6799*******66555666*******8876 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.9e-05     0.064       1      29 [.      15      42 ..      15      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                      -SSSBTTTSS--SSEEE-SSSEEEHHHHH CS
                            zf-P11  1 GplsCksCWfkdksLveCsdHYLClrClq 29
                                      G + C+ C    +++++    YLC++C++
  gi|320101352|ref|YP_004176944.1| 15 GTQVCRRCGS-RDAVIQAYGLYLCRQCFR 42
                                      7899999975.5789************85 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.1e-05     0.051     111     139 ..      13      41 ..       2      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                           DUF1451 111 glGtlvCekCgkelalkkteeippCpkCg 139
                                       g Gt vC++Cg + a+ ++  +  C +C 
  gi|320101352|ref|YP_004176944.1|  13 GRGTQVCRRCGSRDAVIQAYGLYLCRQCF 41 
                                       78**************************5 PP

>> DUF2039  Uncharacterized conserved protein (DUF2039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.5    0.0001      0.17      46      80 ..       8      44 ..       2      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                           DUF2039 46 kkYkaltkkkkCvkCeek.tvkkaYh.kiCkkCakek 80
                                      k Yk  + ++ C +C  + +v +aY   +C++C +e 
  gi|320101352|ref|YP_004176944.1|  8 KTYKYGRGTQVCRRCGSRdAVIQAYGlYLCRQCFREV 44
                                      67999999*******8774799***6369****8775 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.9   4.7e+03       1       5 [.       7      11 ..       7      11 .. 0.84
   2 ?    8.1   0.3    0.0015       2.4       5      11 ..      18      24 ..      18      26 .. 0.87
   3 ?    3.9   0.6     0.029        47       4      11 ..      35      42 ..      35      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.9
                         zf-CCHC_2  1 PpgYv 5 
                                      P +Y+
  gi|320101352|ref|YP_004176944.1|  7 PKTYK 11
                                      89996 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                         zf-CCHC_2  5 vChiCgk 11
                                      vC++Cg+
  gi|320101352|ref|YP_004176944.1| 18 VCRRCGS 24
                                      8****97 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.029
                         zf-CCHC_2  4 YvChiCgk 11
                                      Y+C+ C+ 
  gi|320101352|ref|YP_004176944.1| 35 YLCRQCFR 42
                                      9*****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 400.88
//
Query:       gi|320101353|ref|YP_004176945.1|  [L=187]
Description: 50S ribosomal protein L5 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   83.9   0.0    1.3e-23   82.9   0.0    1.5  2  Ribosomal_L5_C  ribosomal L5P family C-terminus
    4.8e-19   68.4   0.1    9.4e-19   67.5   0.1    1.5  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.79     7e+03      79      91 ..      58      70 ..      31      72 .. 0.54
   2 !   82.9   0.0   1.5e-27   1.3e-23       1      82 [.      76     164 ..      76     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.79
                    Ribosomal_L5_C 79 tdeearallkelg 91
                                      + ++a++ +k++g
  gi|320101353|ref|YP_004176945.1| 58 APRRAKKTIKDFG 70
                                      4444444555544 PP

  == domain 2  score: 82.9 bits;  conditional E-value: 1.5e-27
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       +i++ vtLrgek++efl+k++e v +r++      +ssfd+ Gnvs+Gike+i +p+++yd+++g+fGmd++i++++
  gi|320101353|ref|YP_004176945.1|  76 KIAAVVTLRGEKAHEFLRKVFETVGYRVK------ASSFDDYGNVSIGIKEHIHMPGVRYDPEIGVFGMDVAITIER 146
                                       6999*************************......****************************************** PP

                    Ribosomal_L5_C  78 k...tde..........e 82 
                                       +   + +          +
  gi|320101353|ref|YP_004176945.1| 147 PgyrVMRrrrmrsrvprR 164
                                       977633334455555543 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.1   1.1e-22   9.4e-19       1      57 []      19      72 ..      19      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.1e-22
                                      SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      N+M +P + K+++n+gvG  +e+   l ka+k+L+e+tGQ+P  ++akk+i++F+i+
  gi|320101353|ref|YP_004176945.1| 19 NPMLKPYIAKVTVNIGVGADSER---LPKAMKVLEELTGQQPAPRRAKKTIKDFGIK 72
                                      9**********************...*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1440.92
//
Query:       gi|320101354|ref|YP_004176946.1|  [L=252]
Description: 30S ribosomal protein S4 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-22   78.3   0.0    4.9e-22   77.6   0.0    1.3  1  Ribosomal_S4e  Ribosomal family S4e
    1.4e-16   60.3   0.7    2.4e-16   59.6   0.7    1.4  1  RS4NT          RS4NT (NUC023) domain
    8.2e-15   54.3   1.3    1.6e-14   53.4   0.1    2.1  2  S4             S4 domain
    0.00044   19.8   0.0    0.00082   19.0   0.0    1.5  1  40S_S4_C       40S ribosomal protein S4 C-terminus
  ------ inclusion threshold ------
      0.025   14.5   2.8      0.025   14.5   2.8    2.1  2  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 !   77.6   0.0   1.4e-25   4.9e-22       1      73 [.      96     176 ..      96     178 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 1.4e-25
                                       TTEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES.........STT-STTEEEEE CS
                     Ribosomal_S4e   1 tgenyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp.........dpdikvnDtvki 68 
                                       tge yr+++ +++ + l+kI  eea++KLc+i++k tvk+g++ql++hdGr+++++         d  +++   vk+
  gi|320101354|ref|YP_004176946.1|  96 TGELYRVIPVPTRVLGLVKIPREEASFKLCRIENKVTVKGGHIQLNLHDGRNLLVRvndarnpveD-VYETLGAVKL 171
                                       89***************************************************9999999999955.5********* PP

                                       ETTTT CS
                     Ribosomal_S4e  69 dleen 73 
                                       +++ +
  gi|320101354|ref|YP_004176946.1| 172 SIPVQ 176
                                       *9977 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.7   6.6e-20   2.4e-16       2      37 .]       5      40 ..       4      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 6.6e-20
                                      S----EETTTS-TTS---SSSSSEE----SSSS-TT CS
                             RS4NT  2 GpkkHLKrlaAPkhWpldkkegvfavkPspGPHklr 37
                                      G+++HL+ l+AP++Wp+ +ke++++vkPspGPH+++
  gi|320101354|ref|YP_004176946.1|  5 GGSRHLNALNAPRYWPILRKEYKWVVKPSPGPHAIE 40
                                      99*******************************985 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   4.3e-18   1.6e-14       3      48 .]      45      91 ..      43      91 .. 0.92
   2 ?   -2.0   0.1      0.84     3e+03      23      31 ..     133     141 ..     131     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 4.3e-18
                                      HHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4  3 Ldkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      L +++   lg+a++ reAr+lI +G+++V+Gkv+kd++++V+ +Dvi
  gi|320101354|ref|YP_004176946.1| 45 LLVLVrNVLGYAETAREARRLIAGGHFKVDGKVRKDYKFPVGLMDVI 91
                                      666667669************************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.84
                                       HHTTTEEET CS
                                S4  23 IehGrVlVN 31 
                                       +++G++++N
  gi|320101354|ref|YP_004176946.1| 133 VKGGHIQLN 141
                                       799***998 PP

>> 40S_S4_C  40S ribosomal protein S4 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.3e-07   0.00082       1      30 [.     222     250 ..     222     251 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.3e-07
                                       -SSS-EEEEEGGGEEE--STTS-SS---SS CS
                          40S_S4_C   1 DaaGntFATRlsNvFvIGkgnkpwvsLPkg 30 
                                       D +Gn+F T l ++F IG  +kp+++LP+g
  gi|320101354|ref|YP_004176946.1| 222 DRSGNRFQTSLDYIFPIGL-EKPLITLPEG 250
                                       899***************5.9*******98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.8   6.3e+03       3      11 ..     129     137 ..     129     137 .. 0.75
   2 ?   14.5   2.8   6.9e-06     0.025       6      31 ..     191     220 ..     187     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                                       SEEEESSST CS
                               KOW   3 dhVkVvsGp 11 
                                       + V V +G+
  gi|320101354|ref|YP_004176946.1| 129 NKVTVKGGH 137
                                       678898885 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.9e-06
                                       EESSSTTTTCEEEEEEEETTT....TEEEE CS
                               KOW   6 kVvsGphkGktGkVvkvdqhk....vrVfv 31 
                                       +V +G++ G++GkVv++ +       +V++
  gi|320101354|ref|YP_004176946.1| 191 IVSGGRNVGRVGKVVSIHRGMkryrSIVTI 220
                                       799**************9987666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1771.76
//
Query:       gi|320101355|ref|YP_004176947.1|  [L=133]
Description: 50S ribosomal protein L24 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-29  102.7   0.3    1.4e-29  102.4   0.3    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    1.1e-10   41.0   2.0    2.5e-10   39.9   2.0    1.6  1  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   0.3   1.6e-33   1.4e-29       1      82 []       6     120 ..       6     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.6e-33
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xx RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gv 45 
                                       s ++ kqrK + ++p+h r+kl++apLs+eLrek gv++lp+r                                gv
  gi|320101355|ref|YP_004176947.1|   6 SAKPGKQRKHLAEMPLHLRHKLFNAPLSDELREKLGVKRLPVRqgdtvrimrgefkghegkvvevdlkrvrlfveGV 82 
                                       7899************************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                     Ribosomal_L26  46 trekangttvpvgihpSkvvItklkl.DkdrkkiLerk 82 
                                       +r+ka+g++v+v+ihpSkv+I+k ++ Dk+r +i+er+
  gi|320101355|ref|YP_004176947.1|  83 QRKKADGSPVYVPIHPSKVMIIKADVsDKRRLDIVERR 120
                                       ************************************98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   2.0   2.8e-14   2.5e-10       2      32 .]      50      80 ..      49      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.8e-14
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                      Gd+V++++G +kG +GkVv+vd ++vr fv+
  gi|320101355|ref|YP_004176947.1| 50 GDTVRIMRGEFKGHEGKVVEVDLKRVRLFVE 80
                                      9****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 967.99
//
Query:       gi|320101356|ref|YP_004176948.1|  [L=142]
Description: 50S ribosomal protein L14 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-37  127.2   0.0    4.5e-37  126.9   0.0    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.0   2.5e-41   4.5e-37       3     122 .]      23     142 .]      22     142 .] 0.95

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 2.5e-41
                                       CSS-EEE--SSSSBSEEEEEEETT-.--....-EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS- CS
                     Ribosomal_L14   3 qlktrlkvaDNsgakevecikvlggkkr....kaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGs 75 
                                       q+ ++ k aDNsgakev++i v g+++r    + a vGd +vvsvkk++p   +++++v+ka++vr++++++r+dG+
  gi|320101356|ref|YP_004176948.1|  23 QVMSIAKAADNSGAKEVMIIGVPGYHSRlrrvPPAGVGDLVVVSVKKGIP---EMRKKVFKAIIVRQRRPYKRPDGT 96 
                                       788999*****************99944455699****************...89********************** PP

                                       EEEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                     Ribosomal_L14  76 virfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                       +i f+dna+V+l+ +g+p+Gt+i gp+are++e+ +++i++lA++++
  gi|320101356|ref|YP_004176948.1|  97 WIAFEDNAVVILTPEGTPKGTEIRGPIAREAAER-WPQIANLASMII 142
                                       *********************************9.********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1055.73
//
Query:       gi|320101357|ref|YP_004176949.1|  [L=116]
Description: 30S ribosomal protein S17 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-27   95.3   4.0    2.3e-27   94.9   4.0    1.2  1  Ribosomal_S17    Ribosomal protein S17
  ------ inclusion threshold ------
      0.038   14.4   0.8      0.057   13.8   0.1    1.7  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 !   94.9   4.0   2.6e-31   2.3e-27       1      67 [.      41     108 ..      41     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 2.6e-31
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvv 67 
                                       GvVv++km++TvvVr+e+l++ +ky +y+kr+++++ah ++++ vk+GD+V i+e+rPl+kt+ fvv+
  gi|320101357|ref|YP_004176949.1|  41 GVVVKKKMQRTVVVRHEYLHYVRKYMRYEKRHRNIHAHLPPCIeVKEGDVVVIGETRPLAKTVAFVVL 108
                                       9*****************************************************************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.4e-06     0.057      52      69 .]      22      39 ..       4      39 .. 0.79
   2 ?   -2.1   0.1      0.59   5.3e+03      11      17 ..      51      57 ..      44      76 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-06
                                      --TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 52 iDkKCPFtGnvsirGriL 69
                                       D KCP+ G+ ++rG +L
  gi|320101357|ref|YP_004176949.1| 22 EDPKCPWHGHLKVRGVVL 39
                                      499************987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.59
                                      S------ CS
                   Ribosomal_S17_N 11 tvflnkk 17
                                      tv+++++
  gi|320101357|ref|YP_004176949.1| 51 TVVVRHE 57
                                      4433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 839.61
//
Query:       gi|320101358|ref|YP_004176950.1|  [L=92]
Description: ribonuclease P protein subunit Rpp29 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-17   63.7   0.0    1.3e-17   63.5   0.0    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0     7e-22   1.3e-17       2      83 ..       7      88 ..       6      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 7e-22
                                      HHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHH CS
                           UPF0086  2 kLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpad 80
                                      ++++++++G++ ++++  ++ l+g++G+Vv+Et +tl ++ ++ r  +v K++ vFef++ +  +v ++Gs ++ rp d
  gi|320101358|ref|YP_004176950.1|  7 NITSHEIIGLKTRILQYPDRGLIGLEGRVVDETLKTLLVELSNGRRIRVFKSNGVFEFTLPSGETVVIKGSDIIGRPWD 85
                                      799**************************************9******************88889************** PP

                                      HHC CS
                           UPF0086 81 Rae 83
                                      R +
  gi|320101358|ref|YP_004176950.1| 86 RLK 88
                                      *87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 681.81
//
Query:       gi|320101359|ref|YP_004176951.1|  [L=73]
Description: 50S ribosomal protein L29 [Desulfurococcus mucosus DSM 2162]
Scores for 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   72.5   6.8    2.5e-20   72.2   6.8    1.1  1  Ribosomal_L29  Ribosomal L29 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   6.8   1.4e-24   2.5e-20       2      56 ..       5      59 ..       4      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.4e-24
                                      HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdIARikTvlre 56
                                      e+r+++ ee   kl+el+ eL +Lr+q +tg+l+n++rir+v++dIARi+Tv++e
  gi|320101359|ref|YP_004176951.1|  5 EIRKMTPEERLRKLNELRLELVKLRLQSRTGTLTNTARIRNVKRDIARILTVMKE 59
                                      9****************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 537.23
//
Query:       gi|320101360|ref|YP_004176952.1|  [L=222]
Description: 30S ribosomal protein S3 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-22   80.3   0.8    1.8e-22   79.6   0.8    1.4  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    2.2e-13   49.8   0.0    4.3e-13   48.9   0.0    1.5  1  KH_2            KH domain
     0.0018   18.1   0.4     0.0044   16.8   0.1    1.9  2  KH_1            KH domain
     0.0038   17.1   0.1      0.013   15.3   0.0    2.0  2  KH_4            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.8   4.1e-26   1.8e-22       1      83 []     102     185 ..     102     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 4.1e-26
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       i ++lek ++fRr+++++++r+m+aga G++i+vsG+L+ +e+a  ek+k+G+v++  ++++  +d+ava+a +k G
  gi|320101360|ref|YP_004176952.1| 102 IVRALEKEIPFRRVIMYMLKRVMDAGAVGAEIIVSGKLR-GERATYEKLKAGKVYKagEPVEYVVDRAVAKALLKPG 177
                                       7799***********************************.9************************************ PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                       i+Gv+V I
  gi|320101360|ref|YP_004176952.1| 178 IFGVEVVI 185
                                       ******98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   9.6e-17   4.3e-13       2      71 ..      20      86 ..      19      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 9.6e-17
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEE CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklniv 71
                                      i+e+la+ +k+ag+++ve+ rt+ + ++vi+++ pg++IG+gGs ikk+ + l+ +++ l   +V++ i 
  gi|320101360|ref|YP_004176952.1| 20 IDEFLAHYFKDAGYADVELYRTPTGYRVVIHAEYPGRLIGRGGSVIKKLSTILQTRFG-LD--NVNVTIS 86
                                      789****99************************************************7.55..5555555 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   9.7e-07    0.0044       3      27 ..      46      70 ..      44      86 .. 0.89
   2 ?   -2.3   0.0       0.9     4e+03      44      59 ..     192     208 ..     179     210 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.7e-07
                                      EEEEGGGHHHHHHTGGGHHHHHHHH CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIre 27
                                      r+ +++++ gr+IG+gGs+Ik++  
  gi|320101360|ref|YP_004176952.1| 46 RVVIHAEYPGRLIGRGGSVIKKLST 70
                                      789999999*************975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.9
                                       T.-EEEEEE.SHHHHHH CS
                              KH_1  44 derevtisG.speavek 59 
                                        ++ v+++  +pe +e+
  gi|320101360|ref|YP_004176952.1| 192 LPDHVEVKAlKPEEIEQ 208
                                       45677777777777765 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     3e-06     0.013       7      59 ..      23      73 ..      17      85 .. 0.78
   2 ?   -2.2   0.1      0.89     4e+03       7      23 ..     185     201 ..     184     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-06
                              KH_4  7 ilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvs 59
                                      +l   ++d+   +v++   ++ + +++ ++ e  Gr+IG+ G +++ l ++++
  gi|320101360|ref|YP_004176952.1| 23 FLAHYFKDAGYADVELY--RTPTGYRVVIHAEYPGRLIGRGGSVIKKLSTILQ 73
                                      55555555555566665..66788999999***************98888876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.89
                              KH_4   7 ilkalvddpeevevtee 23 
                                       i+k+ ++ p+ vev++ 
  gi|320101360|ref|YP_004176952.1| 185 IVKPNIKLPDHVEVKAL 201
                                       67777888999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1597.10
//
Query:       gi|320101361|ref|YP_004176953.1|  [L=157]
Description: 50S ribosomal protein L22 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   96.5   0.1    1.1e-27   96.2   0.1    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.1   6.2e-32   1.1e-27       3     102 ..      21     153 ..      19     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 6.2e-32
                                       EEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST...............................THHHHHHH CS
                     Ribosomal_L22   3 gsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk...............................aakfvlkl 46 
                                       + +++vs+k +re+a +++gm +++A+++L++  + k+                                ak+ l++
  gi|320101361|ref|YP_004176953.1|  21 RYDIPVSVKYMREIAYTLKGMRLSDAIRFLEDviKMKQavpfrryngklshkrgladrfkwpigrypvkGAKYALEV 97 
                                       6789****************************9766669************************************** PP

                                       HHHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  47 LknaeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                       L+n+eanae+kgl +++lvI++i ++kg +lkr+++rA Gr++p  ++++++evv+
  gi|320101361|ref|YP_004176953.1|  98 LRNVEANAEEKGLSKERLVIVHIAAHKGITLKRYMPRAFGRATPKFRRMSNLEVVV 153
                                       ******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1124.57
//
Query:       gi|320101362|ref|YP_004176954.1|  [L=144]
Description: 30S ribosomal protein S19 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-34  117.0   0.3    3.2e-34  116.7   0.3    1.2  1  Ribosomal_S19  Ribosomal protein S19
  ------ inclusion threshold ------
      0.013   16.1   0.6      0.022   15.3   0.6    1.4  1  bZIP_Maf       bZIP Maf transcription factor
      0.041   12.9   0.0      0.041   12.9   0.0    1.1  1  DUF913         Domain of Unknown Function (DUF913)


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 !  116.7   0.3   5.3e-38   3.2e-34       1      81 []      43     127 ..      43     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 5.3e-38
                                       .HHHSS.TTCCCHHHHHHHHHHTS-...----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT CS
                     Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaek...kkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFs 73 
                                       rslk+g ++ q +ll+k+r+  + +   kk+vikth+Rd+++lPemvglt++VynGk+fvpv+i++em+Gh+LgEFs
  gi|320101362|ref|YP_004176954.1|  43 RSLKRGlTKAQIKLLAKIRRIARDPelaKKTVIKTHVRDMVVLPEMVGLTIAVYNGKEFVPVKISPEMIGHYLGEFS 119
                                       89****999**********888444567************************************************* PP

                                       -SS----S CS
                     Ribosomal_S19  74 pTrkpvkh 81 
                                       pT k v+h
  gi|320101362|ref|YP_004176954.1| 120 PTTKKVTH 127
                                       ******99 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.6   3.7e-06     0.022       4      44 ..      23      72 ..      21      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-06
                          bZIP_Maf  4 eellslsvrEfnrfl.........rglteeeverLKqrRRrlKNrgyaks 44
                                      eell++s+++++  l         rglt+ +++ L ++RR+ +    ak+
  gi|320101362|ref|YP_004176954.1| 23 EELLNMSMDDLVVLLparqrrslkRGLTKAQIKLLAKIRRIARDPELAKK 72
                                      89*********888888888888*****************9987666665 PP

>> DUF913  Domain of Unknown Function (DUF913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-06     0.041     219     261 ..      25      74 ..      13     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-06
                            DUF913 219 nlGssfdELv.....RhhpsLktaiikavikmlarvvelgkeka..akll 261
                                        l  s+d+Lv     R+++sLk  ++ka ik+la+++ ++++++   k +
  gi|320101362|ref|YP_004176954.1|  25 LLNMSMDDLVvllpaRQRRSLKRGLTKAQIKLLAKIRRIARDPElaKKTV 74 
                                       566677777444444*****************************642222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1048.82
//
Query:       gi|320101363|ref|YP_004176955.1|  [L=635]
Description: VWA containing CoxE family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   46.7   0.3    4.8e-12   45.7   0.3    1.4  1  VWA_CoxE       VWA domain containing CoxE-like protein
    2.2e-05   25.0   0.1     0.0001   22.9   0.1    2.0  1  VWA_2          von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.017   15.6   0.1      0.043   14.3   0.1    1.7  1  CoA_binding_2  CoA binding domain
       0.17   11.3   0.0        0.3   10.5   0.0    1.4  1  PALP           Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> 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 !   45.7   0.3   1.1e-15   4.8e-12      18     189 ..     434     595 ..     420     616 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.1e-15
                          VWA_CoxE  18 rrkrrrrgrriDlrrtlranlrhggelvelvrrkprerkprelvllvDvSgSmaaysaiflallhAllqqlp.rtev 93 
                                       rr++++ ++r+ +r tl + +r   e    v+++ rer + +++ +vDvSgSma+++++ +  ++A+    p  +++
  gi|320101363|ref|YP_004176955.1| 434 RRRKTSVRGRLEVRGTLYKWVRLDNEA---VFKR-RERVQ-RVIGVVDVSGSMARFAVWSMLSIAAVF---PvVSHI 502
                                       5578899999*******9999999875...5666.88888.9*************9999888888875...546799 PP

                          VWA_CoxE  94 faFdtrlvdlTralrerDpaeaLarv..saavedlgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdree 168
                                       ++F+ +     + +++ ++  +Lar   +   e+ +G T+i++al+ + el +r +     +++++sD+ ++ +  e
  gi|320101363|ref|YP_004176955.1| 503 VLFSEKPHVYRSPFKKTSL--VLARFleKLYTEGFKGYTNISEALRRAGELASRAD---SKTILVFSDLKQTVPDTE 574
                                       9999999888899995544..4555543444778*******************888...7889*********99999 PP

                          VWA_CoxE 169 llaelarlvrrarrlvwlnpl 189
                                            + lv+++ r++++ p+
  gi|320101363|ref|YP_004176955.1| 575 PWLVARWLVEKGLRVILVVPR 595
                                       9999999***********998 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 !   22.9   0.1   2.3e-08    0.0001       4     105 ..     474     565 ..     471     568 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.3e-08
                             VWA_2   4 vlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevl.ipltkdkakilnalrnleak..gggtn 77 
                                       v+D+SgSm++          a   + ++ + +p     +v fs++p+v  +p++k    + ++l++l ++  +g tn
  gi|320101363|ref|YP_004176955.1| 474 VVDVSGSMARF---------AVWSMLSIAAVFPV-VSHIVLFSEKPHVYrSPFKKTSLVLARFLEKLYTEgfKGYTN 540
                                       89999999886.........44445555555552.2358899999987736889**************99******* PP

                             VWA_2  78 laaaLqlarkalkkrrkgekrvivlitD 105
                                       + +aL+ a ++ ++     +++i++++D
  gi|320101363|ref|YP_004176955.1| 541 ISEALRRAGELASRAD---SKTILVFSD 565
                                       ***********99776...9*******9 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   9.6e-06     0.043      18      74 ..     577     627 ..     568     635 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.6e-06
                                       HHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHH CS
                     CoA_binding_2  18 kvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivke 74 
                                        v+r+l+e+gl+v+ V p+++e   ++ y+        +d+v v+ +pe++p+i+k 
  gi|320101363|ref|YP_004176955.1| 577 LVARWLVEKGLRVILVVPRGTESATVERYRGAG-----CDIV-VVENPEDIPNILKR 627
                                       59********************99999998888.....5655.66889999999986 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.7e-05       0.3      72     114 ..     580     621 ..     577     634 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.7e-05
                                       HHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHH CS
                              PALP  72 aaaallGlkvtivvpadaspekvallrllGaevvevggdydea 114
                                             Gl+v++vvp+++ ++ v+++r  G ++v+v++ +++ 
  gi|320101363|ref|YP_004176955.1| 580 RWLVEKGLRVILVVPRGTESATVERYRGAGCDIVVVEN-PEDI 621
                                       555678******************************44.5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4338.41
//
Query:       gi|320101364|ref|YP_004176956.1|  [L=307]
Description: ATPase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-15   55.8   0.0    7.4e-15   55.2   0.0    1.3  1  AAA_5            AAA domain (dynein-related subfamily)
    4.7e-05   23.3   0.0    0.00035   20.4   0.0    2.1  1  AAA_3            ATPase family associated with various cellul
     0.0041   16.9   0.0      0.056   13.2   0.0    2.1  2  AAA_30           AAA domain
     0.0059   16.3   0.0        2.9    7.6   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.012   16.0   0.1      0.062   13.7   0.1    2.2  1  AAA              ATPase family associated with various cellul
      0.043   13.9   0.0       0.07   13.2   0.0    1.3  1  vWA-TerF-like    vWA found in TerF C terminus
      0.051   13.9   0.0        1.2    9.5   0.0    2.2  2  AAA_19           AAA domain
      0.069   12.5   0.0        4.2    6.7   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.082   12.6   0.0          1    9.1   0.0    2.1  2  AAA_24           AAA domain
      0.083   13.4   0.0       0.37   11.3   0.0    2.0  2  AAA_18           AAA domain
        0.1   12.1   0.0       0.36   10.3   0.0    1.8  2  AAA_7            P-loop containing dynein motor region


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 !   55.2   0.0   4.5e-18   7.4e-15       2     137 ..      63     201 ..      62     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 4.5e-18
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--...............--------G-SEEEE CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik......ngttslvdsplvraaregeilvl 71 
                                       vl  GppGtgK+e+ e ++ +  +++ ++  +++++ e  ++g  +++        ++s+ + pl         +++
  gi|320101364|ref|YP_004176956.1|  63 VLYEGPPGTGKTEIGEAILYLWsGKKPFILPCSENYDEYRVIGDFHPAmamakgFNEESFIPRPLLAGLIMETGVLV 139
                                       6778*******************************************99999877899********77777777889 PP

                                       ESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  72 DEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                       DE+ r + e +n Ll ++++rr+ ++e++++ + +  +    f+v++t+npld  + els a+++R
  gi|320101364|ref|YP_004176956.1| 140 DEIRRSSEEFQNLLLDVIDKRRIIIPELKKVYRQRGAG----FQVVFTSNPLDIAQGELSDAFLRR 201
                                       ********************************999987....***********888899****999 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 !   20.4   0.0   2.2e-07   0.00035      33     116 ..     104     190 ..      62     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                             AAA_3  33 tpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsalleameerqvtveget...hklpepflv 106
                                         d+ P+  + + + ee+     + +G ++   +l+dei r++   q  ll++++ r++ + + +   ++    f v
  gi|320101364|ref|YP_004176956.1| 104 IGDFHPAMAMAKGFNEESFIPRPLLAGLIMETGVLVDEIRRSSEEFQNLLLDVIDKRRIIIPELKkvyRQRGAGFQV 180
                                       555555554444444444455556789999999**************************986544111556678*** PP

                             AAA_3 107 latqnPieqe 116
                                       + t nP++  
  gi|320101364|ref|YP_004176956.1| 181 VFTSNPLDIA 190
                                       ******9964 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   3.4e-05     0.056      20      65 ..      62     120 ..      53     158 .. 0.67
   2 ?    1.5   0.0      0.13   2.1e+02     138     160 ..     154     176 ..     144     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                            AAA_30  20 vavltGpAGtGKttalkalreaweaag............grvig.lAptgkaAkvLaee 65 
                                        ++ +Gp+GtGKt + +a+  +w  ++            +rvig + p  ++Ak  +ee
  gi|320101364|ref|YP_004176956.1|  62 PVLYEGPPGTGKTEIGEAILYLWSGKKpfilpcsenydeYRVIGdFHPAMAMAKGFNEE 120
                                       57899******************988756666666666655554344444445444444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                            AAA_30 138 rdlveaagigtaeLtevvRqkes 160
                                        d++++++i   eL++v+Rq+ +
  gi|320101364|ref|YP_004176956.1| 154 LDVIDKRRIIIPELKKVYRQRGA 176
                                       566678899999********854 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0036       5.8      21      53 ..      59      90 ..      47     100 .. 0.77
   2 !    7.6   0.0    0.0018       2.9      97     122 ..     137     162 ..     130     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0036
                                      SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                   Sigma54_activat 21 tdlsvlitGesGtGKellaraiheaskrkekpf 53
                                      ++ +vl +G  GtGK+ + +ai    +  +kpf
  gi|320101364|ref|YP_004176956.1| 59 NNRPVLYEGPPGTGKTEIGEAILYLWS-GKKPF 90
                                      5689***************99976544.34455 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                                       EEEETGGGS-HHHHHHHHHHHHHSEE CS
                   Sigma54_activat  97 lfLDeigelplelQekLlrvlqegev 122
                                       +++Dei + + e+Q+ Ll v++++++
  gi|320101364|ref|YP_004176956.1| 137 VLVDEIRRSSEEFQNLLLDVIDKRRI 162
                                       468********************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 ?   13.7   0.1   3.8e-05     0.062       1      37 [.      63     100 ..      63     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                                       EEEESSTTSSHHHHHHHHHHHH.THEEEEEETTTCSSS CS
                               AAA   1 vllyGppGtGKTllakavakel.gvefleisgsellsk 37 
                                       vl  GppGtGKT + +a+   + g + + + +se  ++
  gi|320101364|ref|YP_004176956.1|  63 VLYEGPPGTGKTEIGEAILYLWsGKKPFILPCSENYDE 100
                                       5778*************998763355666666666655 PP

>> vWA-TerF-like  vWA found in TerF C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05      0.07     143     192 ..     213     263 ..     200     267 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                     vWA-TerF-like 143 kseygvLe.klDdlegRvvDNagFfavddidkvsdaeLYdrLlsefpeWlk 192
                                       ++ey++Le kl dl++R  DN  F a++ + ++ ++  Y+  +s+  +Wl+
  gi|320101364|ref|YP_004176956.1| 213 QEEYEILElKLGDLARRLSDNLVFKAIEVVGALREKAVYKPGVSDTVTWLT 263
                                       678****989******************************99999999986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00071       1.2       8      31 ..      58      81 ..      52      90 .. 0.81
   2 ?    2.0   0.0      0.15   2.4e+02     104     129 ..     135     160 ..     107     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00071
                            AAA_19  8 lkekvllvtaGpGtGKTrvlkhiv 31
                                      ++++++l  ++pGtGKT++ ++i+
  gi|320101364|ref|YP_004176956.1| 58 INNRPVLYEGPPGTGKTEIGEAIL 81
                                      789999***********9877665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                            AAA_19 104 ellivDEfqdvdelqyrLlkallgek 129
                                       + ++vDE+   +e  ++Ll  + +++
  gi|320101364|ref|YP_004176956.1| 135 TGVLVDEIRRSSEEFQNLLLDVIDKR 160
                                       5699********88888877777333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0026       4.2      24      45 ..      62      83 ..      50      89 .. 0.82
   2 ?    3.4   0.0     0.027        44     107     162 ..     135     190 ..     124     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0026
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsl 45
                                       +l  GppG+GKt + +++  l
  gi|320101364|ref|YP_004176956.1| 62 PVLYEGPPGTGKTEIGEAILYL 83
                                      58999********999887665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                      Mg_chelatase 107 nGvLfLDElpefkrkvlevLRePledgevtisrakakv.efparfqlvaamNpcpcg 162
                                       +GvL +DE+   +++  + L + ++++++ i   k+   +  a fq+v + Np   +
  gi|320101364|ref|YP_004176956.1| 135 TGVL-VDEIRRSSEEFQNLLLDVIDKRRIIIPELKKVYrQRGAGFQVVFTSNPLDIA 190
                                       5666.6*************************9988876356899********97654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00062         1       8      88 ..      66     170 ..      59     180 .. 0.76
   2 ?    1.3   0.0      0.15   2.4e+02      61      98 ..     246     281 ..     205     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00062
                            AAA_24   8 yGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdieswedfldevvel.................... 59 
                                        Gp+g+GKT +   +     g+kp+++ + + +++  ++  +  +++++ + + +e                     
  gi|320101364|ref|YP_004176956.1|  66 EGPPGTGKTEIGEAIlylwsGKKPFILPCSENYDEYRVIG-DFHPAMAMAKGFNEESfiprpllaglimetgvlvde 141
                                       5***********99999**********9999776666555.333466666666666588888888888888888888 PP

                            AAA_24  60 .aaeladyktlviDtideleelclaevirq 88 
                                        ++  ++++ l +D id+  ++++ e+++ 
  gi|320101364|ref|YP_004176956.1| 142 iRRSSEEFQNLLLDVIDKR-RIIIPELKKV 170
                                       8888999999999999886.6666666655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                            AAA_24  61 aeladyktlviDtideleelclaevirqnekaeskedk 98 
                                       +e+a yk  v Dt+++l   +l   i+ +eka++  d+
  gi|320101364|ref|YP_004176956.1| 246 REKAVYKPGVSDTVTWLTLTALLSDIKGKEKADE--DD 281
                                       67888999999*****966555555555555333..33 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   0.00023      0.37       4      44 ..      66     120 ..      63     187 .. 0.60
   2 ?   -0.6   0.0       1.1   1.8e+03      15      69 ..     227     294 ..     218     306 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                            AAA_18   4 tGtpGvGKttlakeL.....skrlgf..........gvnlrdvakenglllevdpe 44 
                                        G+pG+GKt++++++      k+  f           ++++d ++   +  ++++e
  gi|320101364|ref|YP_004176956.1|  66 EGPPGTGKTEIGEAIlylwsGKK-PFilpcsenydeYRVIGDFHPAMAMAKGFNEE 120
                                       6************9966665222.22344444456644444444444444444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                            AAA_18  15 akeLskrlgf......gvnlrdvakenglllevdpe.......aldeskrldedkldklldaleenss 69 
                                       a++Ls+ l f      g    + +++ g +++v++        +++ ++++ded l ++ +a+   + 
  gi|320101364|ref|YP_004176956.1| 227 ARRLSDNLVFkaievvGALREKAVYKPGVSDTVTWLtltallsDIKGKEKADEDDLREAGRAVLYKNP 294
                                       44555544335556666666666666677777766677777777777888888888888888777665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00022      0.36      28      52 ..      55      79 ..      48      94 .. 0.81
   2 ?   -1.7   0.0       1.1   1.8e+03      73      90 ..     144     161 ..     141     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                             AAA_7 28 lllknkkpvllvGptGtGKtviikd 52
                                        + n++pvl+ Gp GtGKt i + 
  gi|320101364|ref|YP_004176956.1| 55 SAFINNRPVLYEGPPGTGKTEIGEA 79
                                      556689**************98766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                             AAA_7  73 tsanqlqdiiesklekrr 90 
                                        s++++q+++ + ++krr
  gi|320101364|ref|YP_004176956.1| 144 RSSEEFQNLLLDVIDKRR 161
                                       68999**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2069.03
//
Query:       gi|320101365|ref|YP_004176957.1|  [L=239]
Description: 50S ribosomal protein L2 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-43  147.0   2.7      5e-43  146.3   2.7    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    4.5e-11   42.6   0.0    1.2e-10   41.2   0.0    1.8  1  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.3   2.7   5.5e-47     5e-43       2     118 ..      91     218 ..      90     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 5.5e-47
                                       SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT CS
                    Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehke 78 
                                       +Gn+lp+++ipeGt+v nie++pg+ggk++r++Gtya +v+++g k++v+lpSg++ +v+ ++rA+iGv+++g++ e
  gi|320101365|ref|YP_004176957.1|  91 NGNILPIGMIPEGTQVANIEKRPGDGGKFVRASGTYAIIVGRSGGKTQVQLPSGKIIEVPDNARAMIGVIGGGGRLE 167
                                       69*************************************************************************** PP

                                       ----STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SS CS
                    Ribosomal_L2_C  79 kklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksr 118
                                       k+l+kAg+++++     +++pkvrGvamn++ HphGGG+    G+  t++r
  gi|320101365|ref|YP_004176957.1| 168 KPLLKAGASYYKwsaksHVWPKVRGVAMNAAFHPHGGGShqhvGRpsTVAR 218
                                       ************9**************************656555444444 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 !   41.2   0.0   1.3e-14   1.2e-10       1      76 [.      11      82 ..      11      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.3e-14
                                      TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                      G++++ ++ + + +     ++y+l+d     +++k++V+++ +DpgR  p+A   +e+g  +y+ a+eg+ vG++v+
  gi|320101365|ref|YP_004176957.1| 11 GKASPvFKTPDHIHVA--PARYPLLDP---SKTYKAVVEDLVHDPGRWVPLAEMRLENGLVFYVPAVEGMYVGQVVE 82
                                      8999999999999999..99*******...66899****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1813.82
//
Query:       gi|320101366|ref|YP_004176958.1|  [L=91]
Description: 50S ribosomal protein L23 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   67.9   3.9    4.7e-18   65.3   3.9    1.9  1  Ribosomal_L23  Ribosomal protein L23
  ------ inclusion threshold ------
      0.027   14.6   0.1      0.031   14.4   0.1    1.1  1  ASL_C          Adenylosuccinate lyase C-terminal
       0.14   12.4   0.0       0.15   12.3   0.0    1.0  1  FliJ           Flagellar FliJ protein


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 !   65.3   3.9   7.9e-22   4.7e-18       1      75 [.      10      72 ..      10      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 7.9e-22
                                      SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEE CS
                     Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkai 75
                                      +vi++Pv++Ek+ +l +k n+++F V+ da+K+e+k+ave+lF+VkVe+V+tl+  + +k+             a+
  gi|320101366|ref|YP_004176958.1| 10 KVIIRPVQSEKALSLIDKqNTLTFIVDIDASKTEVKRAVEELFNVKVEEVRTLITARGEKK-------------AY 72
                                      69**************99789*********************************9886555.............33 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.2e-06     0.031      14      76 ..      14      76 ..      10      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-06
                                      TTCHHHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-TTHHHHHH CS
                             ASL_C 14 RnlgvalahslialksllkglsklevneealaedLdenwevlaEaiqtvlrregiekpYeklk 76
                                      R + +  a sli  +++l+ +  ++++++++++ ++e  +v  E ++t++   g +k+Y kl 
  gi|320101366|ref|YP_004176958.1| 14 RPVQSEKALSLIDKQNTLTFIVDIDASKTEVKRAVEELFNVKVEEVRTLITARGEKKAYVKLA 76
                                      666677789999***********************************************9986 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.15      40      99 ..      20      79 ..       6      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                              FliJ 40 qglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkere 99
                                      ++ls  + +n+  fi  +d   ++ k++++ + ++  +  + ++ ar e+k++ kL  + 
  gi|320101366|ref|YP_004176958.1| 20 KALSLIDKQNTLTFIVDIDASKTEVKRAVEELFNVKVEEVRTLITARGEKKAYVKLAPEF 79
                                      36888999**********************************************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 742.25
//
Query:       gi|320101367|ref|YP_004176959.1|  [L=272]
Description: 50S ribosomal protein L4P [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-35  121.6   0.0    3.8e-35  121.3   0.0    1.1  1  Ribosomal_L4   Ribosomal protein L4/L1 family
  ------ inclusion threshold ------
      0.062   13.4   0.2       0.75   10.1   0.1    2.9  2  Cm_res_leader  Chloramphenicol resistance gene leader peptide


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 !  121.3   0.0   4.3e-39   3.8e-35       1     190 [.      30     264 ..      30     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 4.3e-39
                                       EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT......STTSTT- CS
                      Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir......spiargG 70 
                                       veL p+vF++pir dl++ra+ +  +   q++++++ a++++++  + ++   G G ARv+++       +  +r+G
  gi|320101367|ref|YP_004176959.1|  30 VEL-PEVFNVPIRVDLVRRAFHSAFTGMLQPKGRDPlAGKRTTA--KYWGV--GYGIARVPRLPngtarfVVSTRKG 101
                                       789.****************************************..68888..***********9999999999*** PP

                                       --SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES--.-.-S.............S--HHHHHHHHHHTT CS
                      Ribosomal_L4  71 gvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvdnl.eple.............esktkelvellkklg 133
                                       + a++p+p++++++++n+K+r +A+ saL+a+ + + ++ ++++ + +e             +sk+++++e l+k+g
  gi|320101367|ref|YP_004176959.1| 102 HAAFPPTPWERIREEVNRKERVMAIVSALAATSRVDMVRRRGHVfS-VErlpvvvsddvesaISKASQAREYLEKIG 177
                                       ******************************************5533.445557888888899*************99 PP

                                       -..........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EE CS
                      Ribosomal_L4 134 l..........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vv 180
                                       l                          +++s+L+v+s++++ l++a+rnlpgv+v +  +l+v++l+++      +v
  gi|320101367|ref|YP_004176959.1| 178 LwsdversregtgiragrgkmrgrayvEPRSILFVLSSYESPLARAVRNLPGVDVSTPGNLSVLHLAPGGVpgrlMV 254
                                       999999999999999999999999999999*****************************************9**9** PP

                                       EEHHHHHHHH CS
                      Ribosomal_L4 181 itksavekle 190
                                       i++ a+e+++
  gi|320101367|ref|YP_004176959.1| 255 ISRRALEEVA 264
                                       ******9986 PP

>> Cm_res_leader  Chloramphenicol resistance gene leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.82   7.3e+03       5      10 ..     235     240 ..     233     242 .. 0.83
   2 ?   10.1   0.1   8.4e-05      0.75       3      15 ..     247     259 ..     246     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.82
                     Cm_res_leader   5 PGALAv 10 
                                       PG L v
  gi|320101367|ref|YP_004176959.1| 235 PGNLSV 240
                                       9***98 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 8.4e-05
                     Cm_res_leader   3 GvPGALAvvtRRt 15 
                                       GvPG L v+ RR 
  gi|320101367|ref|YP_004176959.1| 247 GVPGRLMVISRRA 259
                                       9***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1965.62
//
Query:       gi|320101368|ref|YP_004176960.1|  [L=396]
Description: 50S ribosomal protein L3P [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-64  217.6   3.7    5.7e-44  150.6   0.0    3.0  2  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 !   63.2   2.2   1.1e-21     2e-17       1      98 [.       1     115 [.       1     133 [. 0.80
   2 !  150.6   0.0   3.2e-48   5.7e-44     153     350 ..     193     376 ..     169     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.1e-21
                                       XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSB.............TTTTT....XBSEEEEEEEEEEEEEEEC CS
                      Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkdd.............tskpv....kltaflGyKaGmthiVrev 60 
                                       m hrk +aprhgslG++prkRae+  ++v+ +P+               +s+ +     l +f  yKaGmth V + 
  gi|320101368|ref|YP_004176960.1|   1 MGHRKLHAPRHGSLGVRPRKRAEELTPRVRRWPEKSwfdivverlgseaASRGIaakpVLLGFPVYKAGMTHAVVVE 77 
                                       99*******************************86422222222221112222211114678999************ PP

                                       HHTTSCCCCCEEEEEEEEEEC--EEEEEEEEEEEETTE CS
                      Ribosomal_L3  61 dkpgskldkkevveavtvvetppmvivgvvgyvetprG 98 
                                       d+p++++ +kev  +vt+++ pp+v++gv++yv  + G
  gi|320101368|ref|YP_004176960.1|  78 DRPNTPVSGKEVFTPVTILDAPPIVVLGVRTYVVGEDG 115
                                       ********************************987776 PP

  == domain 2  score: 150.6 bits;  conditional E-value: 3.2e-48
                                       HHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EE CS
                      Ribosomal_L3 153 ikkeasvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGf 229
                                        + e + vrvia t      ++ +Kk++++E++++gG+i e+l + ++ l   v+ a+vF +g++iDvigvtkGkGf
  gi|320101368|ref|YP_004176960.1| 193 FSGEVADVRVIASTIPV-FSGIGKKKPEIVELKIGGGSIDERLRYGESILGGYVKAADVFMEGQFIDVIGVTKGKGF 268
                                       45677889****99775.667******************************************************** PP

                                       E-HHHHCT----ST..TTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.S CS
                      Ribosomal_L3 230 eGvvkRWgvkklpr..kthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdlt 304
                                       +GvvkR+gvk+lpr  k+ +g Rk++a +++     +s  ++aGq+G+h+Rte+nk+i rig               
  gi|320101368|ref|YP_004176960.1| 269 QGVVKRFGVKELPRwhKHRKGSRKIGARSPGFG--TMSEPPQAGQMGFHRRTEYNKRILRIGL-------------N 330
                                       *************94455566999877766654..356679*********************9.............4 PP

                                       S..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGS CS
                      Ribosomal_L3 305 ekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqts 350
                                       + e t  GGf hyG v ++++++kG+v Gp kr++ lr+ ++++ +
  gi|320101368|ref|YP_004176960.1| 331 GLEATVEGGFLHYGLVYGPYLMLKGTVFGPAKRMLILRHPVRPHLE 376
                                       5678899********************************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2790.17
//
Query:       gi|320101369|ref|YP_004176961.1|  [L=274]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-34  119.2   0.0    5.1e-34  118.1   0.0    1.5  1  Methyltrn_RNA_3  Putative RNA methyltransferase
     0.0072   16.4   0.0      0.013   15.6   0.0    1.4  1  Peptidase_M60_C  Peptidase M60 C-terminal domain


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 !  118.1   0.0   5.7e-38   5.1e-34       2     284 ..       3     262 ..       2     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 5.7e-38
                   Methyltrn_RNA_3   2 vsiaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFp 78 
                                       vsi++Pssi+s  ++l +k+  + q+AR  +iF V+e+v +++  + + +   + ++++  ++Y+ tPpYLr++l p
  gi|320101369|ref|YP_004176961.1|   3 VSIVLPSSILSVESTLLLKSLRIHQVARWTSIFGVSEVVFYREYGTPHGEYMGHRQLIELHWRYFFTPPYLRRRLVP 79 
                                       8********************************************99998888************************ PP

                   Methyltrn_RNA_3  79 lhkelkyaglLppldaphhl.rsse.egeyreGvvvekskekkskkklVniGlkkevklelkqevpeg.tRVtVkls 152
                                         + l+y+g Lpp++++ +  + +  +ge r G + +++    +   +V    +++   +l +e ++g t+V V   
  gi|320101369|ref|YP_004176961.1|  80 RSPLLRYVGALPPIRLLDFDvKGKPvKGEERVGFAARERG--GV---VVYLDNEEKY-TPL-NECRPGfTKVRVVD- 148
                                       *******************856666899999999988855..44...6777744444.555.35544415555443. PP

                   Methyltrn_RNA_3 153 seesveakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtserge.kveeklaelekkkefkhll 228
                                            ++++V+  +     ++y+G s  + +sl +++t     +g  ++++t + g+ + + +l++l     + ++ 
  gi|320101369|ref|YP_004176961.1| 149 ----TDGRLVECLDV----EYYMGPSLSFKESLMEALTSV---EGDVFKVATDKAGApPAQRELESLG---RAGRIA 211
                                       ....69*****9999....7******************98...6999**********66666666663...4799** PP

                   Methyltrn_RNA_3 229 ivfGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLa 284
                                       + fGg  rgl ++ ea+      g +  +++d ++nt+p+q+  +irtEEavl++L 
  gi|320101369|ref|YP_004176961.1| 212 LFFGGpRRGLFEISEAE------GFNLLDYVDVVWNTIPGQRVVSIRTEEAVLATLG 262
                                       *****9********888......99******************************96 PP

>> Peptidase_M60_C  Peptidase M60 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.5e-06     0.013      14      63 ..     106     153 ..      99     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                                       EC.TCCCEEEEEETTTTEEEEEECCCEEE--TCS..TTEEEEEEECTTEE CS
                   Peptidase_M60_C  14 knGeeAVaFevrknngnklvyfsnrftFtvpssvslagaklyaVqaDGkr 63 
                                       k Gee V+F  r+ +g  +vy  n  ++t  ++     +k+ +V +DG  
  gi|320101369|ref|YP_004176961.1| 106 K-GEERVGFAARERGG-VVVYLDNEEKYTPLNECRPGFTKVRVVDTDGRL 153
                                       4.9************9.*******************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2111.62
//
Query:       gi|320101370|ref|YP_004176962.1|  [L=670]
Description: phosphoadenosine phosphosulfate reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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    1.3e-44  152.3   0.0    1.9  2  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
  ------ inclusion threshold ------
       0.15   11.6   0.9       0.68    9.4   0.0    2.1  2  QueC         Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.0   1.5e-48   1.3e-44       2     173 ..     228     400 ..     227     401 .. 0.97
   2 ?   -0.1   0.0     0.094   8.4e+02     154     172 ..     557     575 ..     542     577 .. 0.76

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 1.5e-48
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssly 78 
                                       + vs+sgGkdslV l+La ka  + ++vf dtg e peti+ v e++eryg++l+v++  + +++++n ++ + ++y
  gi|320101370|ref|YP_004176962.1| 228 VSVSYSGGKDSLVALDLAYKAYGELEMVFNDTGLELPETIRNVHEVSERYGVKLHVASAGDIFWRAVNVFGPPGKDY 304
                                       579************************************************************************** PP

                                       HCHHHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT- CS
                       PAPS_reduct  79 eeaaeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilreni 153
                                       ++ ++++aK++p+ +  + l  +  + ++G+R+ es  rak p  ++++++++ l   P+ +W++ + w yi r+n+
  gi|320101370|ref|YP_004176962.1| 305 RW-CCKVAKLVPIARLTRALwpNGALNIVGQRAFESLDRAKSPKTWRNKWIPHLLSTSPIQDWSQLECWLYIFRHNL 380
                                       **.**********99777767777899************************************************** PP

                                       -B-CCCCTT-SS--BCTTB- CS
                       PAPS_reduct 154 pynpLydqgfrsiGcvpctg 173
                                       pyn+Ly++gf+++Gc+ c++
  gi|320101370|ref|YP_004176962.1| 381 PYNKLYEKGFDRLGCFLCPS 400
                                       *****************986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.094
                                       -B-CCCCTT-SS--BCTTB CS
                       PAPS_reduct 154 pynpLydqgfrsiGcvpct 172
                                       +++ L +  +rs Gcv+c 
  gi|320101370|ref|YP_004176962.1| 557 DLVDLLKVTYRSYGCVKCG 575
                                       57899999*********96 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   7.5e-05      0.68       5      57 ..     231     282 ..     228     289 .. 0.89
   2 ?   -0.2   0.2     0.065   5.8e+02     190     201 ..     568     579 ..     563     581 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7.5e-05
                                       E--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EE CS
                              QueC   5 llSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehk 57 
                                         SGG DS ++l la k++ e+e++  d g    ++++ ++++++++gv + +
  gi|320101370|ref|YP_004176962.1| 231 SYSGGKDSLVALDLAYKAYGELEMVFNDTGLELPETIRNVHEVSERYGV-KLH 282
                                       57**************************9999999999999*9999999.444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.065
                                       TTTTSSSHHHHH CS
                              QueC 190 gkaCgeCdaCal 201
                                       +++C +C +C+l
  gi|320101370|ref|YP_004176962.1| 568 SYGCVKCGSCIL 579
                                       689*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 4994.67
//
Query:       gi|320101371|ref|YP_004176963.1|  [L=929]
Description: DEAD/DEAH box helicase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-28   98.1   0.0      4e-26   91.9   0.0    2.3  2  DEAD            DEAD/DEAH box helicase
    5.7e-21   74.9   0.0    1.6e-19   70.3   0.0    2.4  2  Helicase_C      Helicase conserved C-terminal domain
    9.3e-09   35.4   0.0    2.5e-08   33.9   0.0    1.7  1  DEAD_assoc      DEAD/H associated
    1.3e-05   25.3   0.0      4e-05   23.7   0.0    1.8  2  ResIII          Type III restriction enzyme, res subunit
     0.0013   19.1   0.0     0.0039   17.5   0.0    1.8  1  AAA_19          AAA domain
  ------ inclusion threshold ------
      0.016   15.2   0.0       0.05   13.6   0.0    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.056   12.5   0.0        0.1   11.6   0.0    1.3  1  T2SSE           Type II/IV secretion system protein
       0.11   12.2   0.3       0.33   10.7   0.3    1.7  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.15   12.4   0.1         20    5.5   0.0    3.3  3  AAA_22          AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0     2e-29     4e-26       1     170 [.      17     185 ..      17     189 .. 0.85
   2 ?    3.8   0.0     0.022        43      47     106 ..     246     311 ..     232     326 .. 0.76

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 2e-29
                                       -HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                       t+ Q+e++  +  ++++vlv a+TGsGKT+a+++pv+ +++  +g +   a++++P+r+L +++ +++k++ +  +l
  gi|320101371|ref|YP_004176963.1|  17 TALQKEVFRKVAyENKSVLVTAPTGSGKTEAAVFPVFYRIIV-DGLKPISAIYITPLRALNRDIESRIKRIASCFGL 92 
                                       6789999998886999*********************99987.9999****************************** PP

                                       EEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHH.HCTSSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliiggvaardqlskldng.vdivvgtpgrlddll.stgkln.lsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       rv +  +g++ +  +++l  + +d++++tp+ ++ +l +++ l  + + r+l++DE +++ +++++  + ++l+ l+
  gi|320101371|ref|YP_004176963.1|  93 RVAVR-HGDTPDAARRELAVHpPDVLITTPESFMYILvNEKLLPsVLNARYLIIDEFHEMVESKRGLLLFTVLHLLE 168
                                       **855.5566666677776556*************77354444468889**********************999995 PP

                                       HHCTTST.TTSEEEEEESSBS CS
                                       xxxxxxx.xxxxxxxxxxxxx RF
                              DEAD 151 qitcdgk.lqrqvivlSATlp 170
                                       + ++  k l    i+lSAT++
  gi|320101371|ref|YP_004176963.1| 169 K-YHGFKpL---KIALSATVS 185
                                       4.4544525...6******97 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
                                       S-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHH....HTT.CSEEEEEHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx....xxx.xxxxxxxxx RF
                              DEAD  47 gpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskl....dng.vdivvgtpg 106
                                          +l+ + tr+Lae   + lk++  + + +v+ ++ +g+  r+ ++++    ++g v+i+v+t +
  gi|320101371|ref|YP_004176963.1| 246 YRAVLVFTNTRSLAEILGSLLKTLAGKQGRSVViAVHHGSLSRSHREEVeagfKKGnVNILVATSS 311
                                       456899999**************9999775555466778777888888833333448******975 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.17   3.3e+02      32      58 ..      83     109 ..      63     121 .. 0.78
   2 !   70.3   0.0   7.8e-23   1.6e-19       6     108 ..     236     344 ..     232     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.17
                                       HHHHHHHTTSTEEEESTTSTHHHHHHH CS
                        Helicase_C  32 vklllekkgikvavlhgelpqnereei 58 
                                       +k + + +g++vav hg++p   r+e 
  gi|320101371|ref|YP_004176963.1|  83 IKRIASCFGLRVAVRHGDTPDAARREL 109
                                       45666778**************99986 PP

  == domain 2  score: 70.3 bits;  conditional E-value: 7.8e-23
                                       HHHHHHHTTTTSEEEEEESSHHHHHH....HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek....vklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                       ll++l   e  + +l+f+nt++ +e     +k l  k+  ++ +av+hg+l+ ++ree+ + f+kg++++L+at+ +
  gi|320101371|ref|YP_004176963.1| 236 LLYILRAGEAYRAVLVFTNTRSLAEIlgslLKTLAGKQgrSVVIAVHHGSLSRSHREEVEAGFKKGNVNILVATSSM 312
                                       66777777888999********887654555555444466899********************************** PP

                                       TSSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                       e Gidi  v++V+++  pr v+++iqr+GR g
  gi|320101371|ref|YP_004176963.1| 313 ELGIDIGHVDFVVQYLSPRRVSRLIQRVGRSG 344
                                       ******************************87 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.3e-11   2.5e-08      19     182 ..     602     757 ..     591     761 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.3e-11
                        DEAD_assoc  19 wrlvvhspfGrrvnealalllaarlsrrfg.idvqvaanDdgivlll....pleerlpllldellellspdeleedl 90 
                                       ++++++  +G++vn  l  +l++ l+r+f+ +d+++  +++ +++ +     ++e l +  + l+el +    e+ l
  gi|320101371|ref|YP_004176963.1| 602 RTVFINVNWGSKVNSLLRDVLEHVLKREFPlVDFEAYSSPYVVIVRVkgyvYPAELLRAVKTCLVELYKYIGDEAFL 678
                                       47999************************8469************88776633344443344566777777888999 PP

                        DEAD_assoc  91 eaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDlerlae 167
                                       ++ + +s  f +r  +vA+r+++++ ++ +           ++ +l++++   d+++ +ea++ev  +++Dle++ +
  gi|320101371|ref|YP_004176963.1| 679 RDVVRGSRAFYWRIYQVAQRFGAISPGETK----------VTKPMLEALA---DTVIGDEAFKEVTVKDYDLESALR 742
                                       9***********************988766..........88999*****...************************ PP

                        DEAD_assoc 168 llrriaageirvvev 182
                                       l + +a+gei v+ +
  gi|320101371|ref|YP_004176963.1| 743 LASLLARGEIAVHVR 757
                                       **********99874 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0     2e-08     4e-05       7     169 ..      19     184 ..      14     186 .. 0.82
   2 ?   -3.2   0.0       3.6   7.2e+03     112     141 ..     697     726 ..     695     728 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2e-08
                                       HHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee.kflflvprkslleqtleefkkflsea 81 
                                        Q+e+ ++++     +++k +l+ ++TG+GKT  a + + +r+   g +   ++ + p ++l    ++++k+++s+ 
  gi|320101371|ref|YP_004176963.1|  19 LQKEVFRKVA-----YENKSVLVTAPTGSGKTEAAvFPVFYRIIVDGLKPiSAIYITPLRALNRDIESRIKRIASCF 90 
                                       5666666665.....8899****************88899999888766699********************99986 PP

                                       ...GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T......TT CS
                            ResIII  82 ykeigkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk......sw 150
                                             + +gd+ +a  +e + +  ++l+tt +s+  ++    +e+   +  +  ++iiDE H + ++k      ++
  gi|320101371|ref|YP_004176963.1|  91 GL-RVAVRHGDTPDAarRELAVHPPDVLITTPESFMYIL---VNEKLLPSVLNARYLIIDEFHEMVESKrglllfTV 163
                                       54.6666777777776667888999**************...8899999999999************8677777666 PP

                                       HHHHHT---..SEEEEEESS- CS
                            ResIII 151 reilekfke..avllglTATp 169
                                        ++lek+     ++++l+AT 
  gi|320101371|ref|YP_004176963.1| 164 LHLLEKYHGfkPLKIALSATV 184
                                       666666533338899999997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.6
                                       HHHHHTH........HHHTTT-SEEEEETG CS
                            ResIII 112 qsldadseeeeeeseellrdrfdviiiDEa 141
                                       q++ a+s+ e++ ++ +l+   d +i DEa
  gi|320101371|ref|YP_004176963.1| 697 QRFGAISPGETKVTKPMLEALADTVIGDEA 726
                                       777888888899999999999********8 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     2e-06    0.0039       6     122 ..      26     159 ..      20     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                            AAA_19   6 e.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiH.rlal... 77 
                                       + a ++k +lvta+ G+GKT+  +  v + + + g+kp + + +++ +   + ++ r+   ++ a+ +  r+a+   
  gi|320101371|ref|YP_004176963.1|  26 KvAYENKSVLVTAPTGSGKTEAAVFPVFYRIIVDGLKPISAIYITPLRALNRDIESRI---KRIASCFGlRVAVrhg 99 
                                       357899****************************************999999999999...3334443333333566 PP

                            AAA_19  78 ................ldfddlltealelle...eaeeekklqeeellivDEfqdvdelqyrLl 122
                                                       +    l+t++ +++    +++    + ++ +li+DEf ++ e    Ll
  gi|320101371|ref|YP_004176963.1| 100 dtpdaarrelavhppdV----LITTPESFMYilvNEKLLPSVLNARYLIIDEFHEMVESKRGLL 159
                                       66666666666544441....3333444433444334444455888*******98876666665 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   0.0   2.5e-05      0.05      66     105 ..     795     840 ..     773     845 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                                       EE--EEEETTTS-EEECHHHHH......S-TTTSSS-EEEEESSSE CS
                              HypA  66 evpvkvrCreCgkefeleekal......rCpkCgsadveivsGeel 105
                                       e ++++ C +Cg+  + + ++l      +Cp+Cg a+++iv+G+ l
  gi|320101371|ref|YP_004176963.1| 795 ERELTLICINCGYMKHGKVRELielgkySCPRCGLASLSIVKGDAL 840
                                       5678899*****7766443222334555***************987 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 ?   11.6   0.0   5.2e-05       0.1     112     144 ..      14      46 ..       7      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                             T2SSE 112 ealkekiaevlrkavrerglilvsGgTgsGKtt 144
                                       +++++ ++ev rk   e++++lv+ +TgsGKt 
  gi|320101371|ref|YP_004176963.1|  14 GDFTALQKEVFRKVAYENKSVLVTAPTGSGKTE 46 
                                       5678889999999999***************95 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 ?   10.7   0.3   0.00017      0.33      20      51 ..     797     828 ..     787     830 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                    zinc_ribbon_10  20 ryalICskCh.shnGlapkeeleevkyrCpkCg 51 
                                        + lIC +C  ++ G + +e  e  ky Cp Cg
  gi|320101371|ref|YP_004176963.1| 797 ELTLICINCGyMKHGKV-RELIELGKYSCPRCG 828
                                       578******65899*99.9999999*******8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0099        20       5      21 ..      31      47 ..      27      50 .. 0.86
   2 ?    1.9   0.0      0.13   2.5e+02      93     106 ..     141     161 ..     117     184 .. 0.66
   3 ?   -0.4   0.0      0.64   1.3e+03      37      64 ..     590     625 ..     570     632 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0099
                            AAA_22  5 agilvvtGesGtGKTtl 21
                                       ++++vt+++G+GKT  
  gi|320101371|ref|YP_004176963.1| 31 NKSVLVTAPTGSGKTEA 47
                                      67899**********76 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                            AAA_22  93 elliiDEaqhlr.s......e 106
                                       + liiDE++ +  s       
  gi|320101371|ref|YP_004176963.1| 141 RYLIIDEFHEMVeSkrglllF 161
                                       679*******87633433322 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.64
                            AAA_22  37 e........erpevvfvtlpsstsskdllrellral 64 
                                                e++++vf++++ +++  +llr++l+ +
  gi|320101371|ref|YP_004176963.1| 590 GsevhvdyvEDVRTVFINVNWGSKVNSLLRDVLEHV 625
                                       155555667899*******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (929 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 6412.57
//
Query:       gi|320101372|ref|YP_004176964.1|  [L=113]
Description: YL1 domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 870.85
//
Query:       gi|320101373|ref|YP_004176965.1|  [L=124]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 893.22
//
Query:       gi|320101374|ref|YP_004176966.1|  [L=88]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 652.95
//
Query:       gi|320101375|ref|YP_004176967.1|  [L=253]
Description: DNA polymerase sliding clamp subunit B [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-07   29.1   0.0      1e-05   24.8   0.0    2.0  2  Hus1      Hus1-like protein
    1.1e-06   28.4   0.0    2.7e-06   27.1   0.0    1.6  1  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    3.5e-06   27.2   0.0     0.0022   18.1   0.0    2.9  3  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma


Domain annotation for each model (and alignments):
>> Hus1  Hus1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.7e-09     1e-05       2     102 ..       3      97 ..       2     138 .. 0.91
   2 ?    2.3   0.0     0.012        72      14      51 ..     147     184 ..     137     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-09
                              Hus1   2 kFkaqltdaetlkkvlqslsklgkecilrltpeklrfiiiteaddgvqvwaqlqvdaiFeeyeieSndeneInlevd 78 
                                       kF++   +a+++k ++q+++k+  e  +++tpe++ + + + +d+ +  +++++++  Fee+e e+ +    +++v+
  gi|320101375|ref|YP_004176967.1|   3 KFRVVYPNASKMKYITQAIAKVTDEAPIYVTPEAVEVKVLS-PDKSMLTIVRIPAT-AFEEFEAEGEE----SFMVA 73 
                                       9************************************9996.************98.8*********9....9**** PP

                              Hus1  79 laaLlraLksaeaaksvqlrLtkk 102
                                       + +L r+++   ++  ++++L ++
  gi|320101375|ref|YP_004176967.1|  74 STDLNRVMRRGGRNDVLEMKLDRE 97 
                                       *********************998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.012
                              Hus1  14 kkvlqslsklgkecilrltpeklrfiiiteaddgvqvw 51 
                                       + ++   +++g e++l +++ kl + +++++++ v v+
  gi|320101375|ref|YP_004176967.1| 147 RGIVGDAKSIGEEVVLSFEDGKLTVYSSEQQKEYVGVF 184
                                       56788899*******************99877776665 PP

>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   4.5e-10   2.7e-06       7     117 ..       9     119 ..       3     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.5e-10
                                       SSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTST CS
                            PCNA_N   7 eqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcan 83 
                                        +as +k + +ai  + +ea + +  + +++++l   +  L  +++ + +fe++  + + ++ v  + l+++++ ++
  gi|320101375|ref|YP_004176967.1|   9 PNASKMKYITQAIAKVTDEAPIYVTPEAVEVKVLSPDKSMLTIVRIPATAFEEFEAEGEESFMVASTDLNRVMRRGG 85 
                                       68999************************************************************************ PP

                                       TTSEEEEEEETTSSEEEEEEEECTSSEEEEEEEE CS
                            PCNA_N  84 nedsvtlkaedeadtlalvfesekkdkiaeydlk 117
                                        +d++ +k + e+ +l  vf++ k+     ++++
  gi|320101375|ref|YP_004176967.1|  86 RNDVLEMKLDREHGVLEAVFRDRKTGVERVFQVE 119
                                       *********************9998877777666 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.51     3e+03      15      42 ..      11      38 ..       6      41 .. 0.79
   2 !    5.6   0.0    0.0028        17       6      36 ..     134     164 ..     128     175 .. 0.87
   3 !   18.1   0.0   3.7e-07    0.0022      79     127 ..     202     250 ..     185     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.51
                                      HHHHHHHHHHHTTT-SEEEEEEETTEEE CS
                            PCNA_C 15 ssefaricrdlsqlsdsvvisvtkegvk 42
                                      +s  + i++ ++++ d+  i vt e+v 
  gi|320101375|ref|YP_004176967.1| 11 ASKMKYITQAIAKVTDEAPIYVTPEAVE 38
                                      6677789999999999999999988886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0028
                                       S-SEEEEEEHHHHHHHHHHHTTT-SEEEEEE CS
                            PCNA_C   6 eydavvklpssefaricrdlsqlsdsvvisv 36 
                                       e   vvk+ s ++  i+ d  +++++vv+s 
  gi|320101375|ref|YP_004176967.1| 134 ELGVVVKMLSEDYRGIVGDAKSIGEEVVLSF 164
                                       56689**********************9986 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 3.7e-07
                                       EEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  79 ltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                         ++++ l + +k  s s++vt+s+  + P+++ey++  +g l y++ +
  gi|320101375|ref|YP_004176967.1| 202 ASYSVDLLSATVKPVSASKQVTVSFDTDKPAKIEYELIGGGQLIYWVVP 250
                                       46889999*********************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1962.66
//
Query:       gi|320101376|ref|YP_004176968.1|  [L=192]
Description: pyruvate/ketoisovalerate oxidoreductase subunit gamma [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-38  133.2   0.6    1.2e-38  132.9   0.6    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.6   6.7e-43   1.2e-38       1     176 [.      11     183 ..      11     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 6.7e-43
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH.HHGGG. CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls.ehldg. 75 
                                       GGqG+vta++il +aa+ +G++ q+++++g+e+rG+++++  risd+pi ++    ead++v+ld+ +l+  ++++ 
  gi|320101376|ref|YP_004176968.1|  11 GGQGAVTAANILVEAAMMEGKHGQGFPFFGAERRGAPVTAFARISDKPILRHGMFSEADIIVVLDPGLLDlGVVKRg 87 
                                       9********************************************************************98555556 PP

                                       .EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC....CCHHHHHHHHHHHHHHT.S-H CS
                               POR  76 .lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggn...eraaNtvmlGalaallg.lpl 147
                                        l+++g++++n+e++    +++  +       r ++r+y vdat+ia+e+g      +++Nt mlGala+++g +++
  gi|320101376|ref|YP_004176968.1|  88 vLRENGVVVVNTEKDH---IPPGSLNH-----RGRARIYRVDATRIARELGLViagWPVVNTSMLGALAKATGlIGV 156
                                       7***********6543...33333322.....23579***********99988888********************* PP

                                       HHHHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 148 ealeeaikkrfpkkkeviekNlkafragy 176
                                       e++e+ai + f++k  + e+N+ a++++y
  gi|320101376|ref|YP_004176968.1| 157 ESVEKAIGDYFGGK--AGELNKLAAERAY 183
                                       ************96..9***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1401.03
//
Query:       gi|320101377|ref|YP_004176969.1|  [L=93]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase subunit delta [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-17   61.2  17.4    8.1e-10   38.1   6.2    2.2  2  Fer4      4Fe-4S binding domain
    2.1e-11   44.2  25.4    3.2e-09   37.3  13.8    1.6  2  Fer4_7    4Fe-4S dicluster domain
    3.3e-11   42.7  17.3    1.2e-05   25.1   5.7    2.2  2  Fer4_6    4Fe-4S binding domain
    4.7e-10   39.4  10.2      6e-10   39.1  10.2    1.1  1  Fer4_21   4Fe-4S dicluster domain
    5.8e-10   39.1  22.1    1.2e-06   28.5  12.7    2.1  2  Fer4_10   4Fe-4S dicluster domain
    2.3e-09   38.1   9.3    2.3e-05   25.2   1.4    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    5.5e-08   32.5  14.6     0.0002   21.2   3.3    2.2  2  Fer4_2    4Fe-4S binding domain
    9.1e-08   32.0  16.5    0.00099   19.4   4.8    2.2  2  Fer4_4    4Fe-4S binding domain
    1.1e-07   31.9  11.2    1.6e-07   31.4  11.2    1.2  1  Fer4_9    4Fe-4S dicluster domain
    1.1e-06   28.9   6.3      0.011   16.2   0.7    2.1  2  Fer4_8    4Fe-4S dicluster domain
    8.5e-06   26.2   6.8      0.018   15.6   0.4    2.1  2  Fer4_17   4Fe-4S dicluster domain
      0.002   18.9  19.5       0.11   13.5   7.5    2.3  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.11   13.2  17.0       0.25   12.1   3.6    3.4  3  Fer4_15   4Fe-4S single cluster domain
       0.12   13.0  13.0       0.55   10.8   2.4    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.56   11.1  13.3       0.33   11.8   2.5    2.1  2  Fer4_22   4Fe-4S dicluster domain
          2    8.6  11.7         17    5.6  11.7    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 !   29.2   3.4   4.7e-10   5.2e-07       1      24 []      34      57 ..      34      57 .. 0.95
   2 !   38.1   6.2   7.3e-13   8.1e-10       2      24 .]      65      87 ..      64      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.7e-10
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +v+d+ +C++C +C+  CPv++I+
  gi|320101377|ref|YP_004176969.1| 34 PVVDQGRCTRCYQCEIYCPVNVIR 57
                                      69********************96 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 7.3e-13
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      vid+e C gCG C++vCPv+AI+
  gi|320101377|ref|YP_004176969.1| 65 VIDYEYCKGCGVCADVCPVNAIS 87
                                      8*********************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 !   18.6   3.7   1.9e-06    0.0021      27      52 .]      30      55 ..      16      55 .. 0.85
   2 !   37.3  13.8   2.8e-12   3.2e-09       1      52 []      40      85 ..      40      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                            Fer4_7 27 gtekveidpekClgCgaCvavCPtga 52
                                      +tek+++d+ +C+ C++C+  CP+++
  gi|320101377|ref|YP_004176969.1| 30 RTEKPVVDQGRCTRCYQCEIYCPVNV 55
                                      458899*****************986 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 2.8e-12
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      rC+ C +C+ +Cpv++i++++e    g   ++id+e+C gCg+C++vCP++a
  gi|320101377|ref|YP_004176969.1| 40 RCTRCYQCEIYCPVNVIRVEPE---TG---AVIDYEYCKGCGVCADVCPVNA 85
                                      8******************997...45...89******************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 !   23.7   3.7   3.1e-08   3.5e-05       1      24 []      33      56 ..      33      56 .. 0.96
   2 !   25.1   5.7   1.1e-08   1.2e-05       2      24 .]      64      86 ..      64      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.1e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++++d+ +C+ C+ C++ CP ++i
  gi|320101377|ref|YP_004176969.1| 33 KPVVDQGRCTRCYQCEIYCPVNVI 56
                                      69*******************997 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.1e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      ++id++ C gCg C++vCP +ai
  gi|320101377|ref|YP_004176969.1| 64 AVIDYEYCKGCGVCADVCPVNAI 86
                                      68*******************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 !   39.1  10.2   5.4e-13     6e-10       2      58 ..      35      87 ..      34      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5.4e-13
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      ++d+ +C  C +C i C+   ++ i+++++t + +  + C GC +C++vCPv ++i+
  gi|320101377|ref|YP_004176969.1| 35 VVDQGRCTRCYQCEIYCP---VNVIRVEPETGAVIDYEYCKGCGVCADVCPV-NAIS 87
                                      6899**************...8*****************************9.8886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5  12.7   1.1e-09   1.2e-06       2      56 .]      34      82 ..      33      82 .. 0.86
   2 !   21.9   1.8   1.3e-07   0.00014       2      23 ..      64      85 ..      63      93 .] 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-09
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      +v+d+ +C+rC +C   CP+       + ++ e e+  + ++e C gcg C+++CP
  gi|320101377|ref|YP_004176969.1| 34 PVVDQGRCTRCYQCEIYCPV-------NVIRVEPETGAViDYEYCKGCGVCADVCP 82
                                      68999***************.......666666666666689*************9 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.3e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      +vid + C +Cg C ++CP+++
  gi|320101377|ref|YP_004176969.1| 64 AVIDYEYCKGCGVCADVCPVNA 85
                                      589****************954 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 !   17.6   1.3   4.9e-06    0.0055       1      22 [.      40      61 ..      40      69 .. 0.84
   2 !   25.2   1.4   2.1e-08   2.3e-05       2      20 ..      71      89 ..      70      93 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                                      rC++C +C   CP+n+i+ + e
  gi|320101377|ref|YP_004176969.1| 40 RCTRCYQCEIYCPVNVIRVEPE 61
                                      6****************98744 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 2.1e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg Ca+vCP+nai+  
  gi|320101377|ref|YP_004176969.1| 71 CKGCGVCADVCPVNAISLV 89
                                      ****************976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.6     4e-06    0.0045       1      21 [.      32      52 ..      32      53 .. 0.92
   2 !   21.2   3.3   1.8e-07    0.0002       4      21 ..      65      82 ..      63      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4e-06
                            Fer4_2  1 apvvvdtdrCigCgaCvsaCP 21
                                      +++vvd  rC++C  C   CP
  gi|320101377|ref|YP_004176969.1| 32 EKPVVDQGRCTRCYQCEIYCP 52
                                      579*************999** PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.8e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v+d + C gCg C ++CP
  gi|320101377|ref|YP_004176969.1| 65 VIDYEYCKGCGVCADVCP 82
                                      7999************** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   4.8   8.8e-07   0.00099       1      17 []      38      54 ..      38      54 .. 0.90
   2 !   18.4   3.8     2e-06    0.0022       2      17 .]      69      84 ..      68      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.8e-07
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      q rC++C +C+++CP++
  gi|320101377|ref|YP_004176969.1| 38 QGRCTRCYQCEIYCPVN 54
                                      569************85 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      e C gCg+C ++CP++
  gi|320101377|ref|YP_004176969.1| 69 EYCKGCGVCADVCPVN 84
                                      89************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  11.2   1.4e-10   1.6e-07       1      51 []      40      86 ..      40      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.4e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +Ct+C +C+  Cp +v++ +  ++ +   ++    C gCg C+++Cp +ai
  gi|320101377|ref|YP_004176969.1| 40 RCTRCYQCEIYCPVNVIRVEPETGAVIDYEY----CKGCGVCADVCPVNAI 86
                                      6*****************9999999998765....*************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 !   16.1   0.5     1e-05     0.012      49      65 .]      39      55 ..      14      55 .. 0.80
   2 !   16.2   0.7   9.5e-06     0.011      49      64 ..      69      84 ..      61      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                            Fer4_8 49 wsCttcgaCtevCpvgi 65
                                      ++Ct c +C+  Cpv++
  gi|320101377|ref|YP_004176969.1| 39 GRCTRCYQCEIYCPVNV 55
                                      68************986 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 9.5e-06
                            Fer4_8 49 wsCttcgaCtevCpvg 64
                                      ++C +cg C++vCpv+
  gi|320101377|ref|YP_004176969.1| 69 EYCKGCGVCADVCPVN 84
                                      5677777777777765 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   1.6e-05     0.018      44      60 ..      39      55 ..      20      56 .. 0.84
   2 !   14.1   1.1   4.7e-05     0.053       2      17 ..      71      86 ..      70      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                           Fer4_17 44 slCieCgeCerkCPqgl 60
                                      ++C+ C +Ce +CP ++
  gi|320101377|ref|YP_004176969.1| 39 GRCTRCYQCEIYCPVNV 55
                                      68************875 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.7e-05
                           Fer4_17  2 CiqCgyClpeCpsyea 17
                                      C +Cg C+++Cp +++
  gi|320101377|ref|YP_004176969.1| 71 CKGCGVCADVCPVNAI 86
                                      99*********98765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   4.1   0.00045      0.51       1      14 [.      41      54 ..      41      55 .. 0.95
   2 !   13.5   7.5   9.8e-05      0.11       1      15 []      71      85 ..      71      85 .. 0.98

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      Ct C++C+  CPv+
  gi|320101377|ref|YP_004176969.1| 41 CTRCYQCEIYCPVN 54
                                      ************98 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.8e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gCg C +vCPv+A
  gi|320101377|ref|YP_004176969.1| 71 CKGCGVCADVCPVNA 85
                                      9*************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 ?    4.6   4.8      0.05        56       2      19 ..      35      52 ..      35      58 .. 0.87
   2 ?   12.1   3.6   0.00022      0.25       2      19 ..      65      82 ..      64      84 .. 0.94
   3 ?    6.4   0.1     0.014        16      56      65 ..      78      87 ..      78      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.05
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      vvD+ +C+ c +C   +p
  gi|320101377|ref|YP_004176969.1| 35 VVDQGRCTRCYQCEIYCP 52
                                      69***********87776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00022
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      v+D + C gcg+C++++p
  gi|320101377|ref|YP_004176969.1| 65 VIDYEYCKGCGVCADVCP 82
                                      69**************98 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.014
                           Fer4_15 56 araCPvdAIr 65
                                      a++CPv AI+
  gi|320101377|ref|YP_004176969.1| 78 ADVCPVNAIS 87
                                      89*******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 ?    7.3   3.1    0.0064       7.1       1      17 [.      36      52 ..      36      65 .. 0.86
   2 ?   10.8   2.4   0.00049      0.55       1      17 [.      66      82 ..      66      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0064
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD+ +C+ c +C   +P
  gi|320101377|ref|YP_004176969.1| 36 VDQGRCTRCYQCEIYCP 52
                                      89**************9 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00049
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      +D + C +cg+C++++P
  gi|320101377|ref|YP_004176969.1| 66 IDYEYCKGCGVCADVCP 82
                                      78999***********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 ?    4.4   3.2     0.062        69       1      14 [.      40      53 ..      40      59 .. 0.86
   2 ?   11.8   2.5   0.00029      0.33      77      95 ..      66      84 ..      56      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.062
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      rC +C +C + Cp 
  gi|320101377|ref|YP_004176969.1| 40 RCTRCYQCEIYCPV 53
                                      79999999999995 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00029
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      ++ + C GCg C ++cpv+
  gi|320101377|ref|YP_004176969.1| 66 IDYEYCKGCGVCADVCPVN 84
                                      57789***********986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  11.7     0.015        17      52      95 ..      32      81 ..      17      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                           Fer4_18 52 erkekgagdcidcescvkvcPtgi...dirkGlqle...ciscllcidac 95
                                      e+   ++g c+ c +c   cP+++   +   G  ++   c  c+ c d c
  gi|320101377|ref|YP_004176969.1| 32 EKPVVDQGRCTRCYQCEIYCPVNVirvEPETGAVIDyeyCKGCGVCADVC 81
                                      445667899************986221445677665557999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 673.44
//
Query:       gi|320101378|ref|YP_004176970.1|  [L=393]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-68  228.8   1.2      9e-68  228.5   1.2    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.3e-24   86.4   0.0    2.8e-24   85.4   0.0    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.035   14.0   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.5   1.2   1.5e-71     9e-68       2     230 ..      16     239 ..      15     240 .. 0.98

  Alignments for each domain:
  == domain 1  score: 228.5 bits;  conditional E-value: 1.5e-71
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a++ a++dviaaYPITP+++i+e+l+e++++ge+ d++++++esE++a +a+ GAa+aGar++TaTS+qGll+m+e 
  gi|320101378|ref|YP_004176970.1|  16 AVKLAKPDVIAAYPITPQTSIVEKLSEMIESGEL-DATMIRVESEHSALAACFGAAIAGARVFTATSSQGLLYMHEI 91 
                                       67899****************************9.9***************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       +++a+ +++P+v+++v R+++++ ++i++d+sD+m  rd g+++ ++ ++qea dl+++Af+++e+  v +Pv+v +
  gi|320101378|ref|YP_004176970.1|  92 VHWASRTRTPMVMAIVSRTINAP-WNIWPDHSDFMDQRDAGWVMSYAMDNQEALDLTIQAFKISEDpsVYLPVMVGI 167
                                       ***********************.***************************************************** PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveeve 230
                                       +gf+l h+  +v++p+e     +++e l ++ + +  +d ++pia g+ ++p+    + +  +ea+++a+kv++ev+
  gi|320101378|ref|YP_004176970.1| 168 EGFILGHTTMPVDIPEEH----AVREWLGPRTQGY-VIDGDSPIALGGLTMPEDTEDMFYGIQEAMNEAKKVIREVN 239
                                       ***************999....9999999998877.*************************************9986 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 !   85.4   0.0   4.7e-28   2.8e-24       1     102 []     262     366 ..     262     366 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 4.7e-28
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A++v v mG+++g++ +av++lR eg+ vG +r+r++rPFP e++ e++++vk ++v+dr+isfgs G+++++    
  gi|320101378|ref|YP_004176970.1| 262 AKYVAVSMGAWSGDLIEAVEKLRSEGYPVGAVRIRYYRPFPVEDIWEVARGVKGILVYDRSISFGSYGPIYTDLVGG 338
                                       89************************************************************************877 PP

                                       TGGG...TSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkks...kvkvvnfvaglgGrditvedi 102
                                       l  +    + v n+vag++G  itv+d+
  gi|320101378|ref|YP_004176970.1| 339 LATYtrtLPYVSNIVAGIAGVNITVDDF 366
                                       776665778899*************985 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-06     0.035      15      77 ..     267     329 ..     258     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                                       EEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C  15 vayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       v++G+     +eA+e+L++eg+ +  v +r  +p+  e+i e+++  + ++v +    +g+ g
  gi|320101378|ref|YP_004176970.1| 267 VSMGAWSGDLIEAVEKLRSEGYPVGAVRIRYYRPFPVEDIWEVARGVKGILVYDRSISFGSYG 329
                                       89999***********************************98888777777766666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2744.22
//
Query:       gi|320101379|ref|YP_004176971.1|  [L=301]
Description: thiamine pyrophosphate TPP-binding domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-25   89.8   0.3    2.1e-25   89.3   0.3    1.2  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
     0.0014   17.9   0.1      0.002   17.4   0.1    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 !   89.3   0.3   2.4e-29   2.1e-25      12     152 ..      61     208 ..      51     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 2.4e-29
                                       HHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHH.....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE CS
                      TPP_enzyme_C  12 llkvkrprsylt.sgglgtmGyglpaAiGakla.....kpdrevvaivGDGgflmi.lqelatavrrnlpitvvvln 81 
                                       +     p + l+ s +++ +  + ++A+G++ a      +d +v+a +GDGg+++i +  l+ a++rn +i++++++
  gi|320101379|ref|YP_004176971.1|  61 Y-----PFHSLKtSIVHVPFASAAAVASGVAEAlerrgIRDVQVIAWAGDGGTADIgMASLSGAAERNNNIIYIMYD 132
                                       3.....4444444889***************95444322378*********************************** PP

                                       -SBCCCHHHH...HHHHTCCTTTTSBB..BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  82 Negygmtggq...qepfggkrksgpagk.dlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                       Ne+y++tg q   ++p g++++++p +  ++ ++d+ak++ a+G++ +a+ ++a++ ++ ++l++a+  kg+ +i+
  gi|320101379|ref|YP_004176971.1| 133 NEAYMNTGIQrssSTPLGAWTTTTPIKGkTEAKKDVAKIMIAHGVPyVATASVAYPHDFYNKLQKARGIKGFRFIH 208
                                       **********************998655479999************99999***********************98 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 !   17.4   0.1   2.3e-07     0.002     116     180 ..      78     142 ..      66     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-07
                    DXP_synthase_N 116 sisaalGlavardlkg.ekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknvG 180
                                       + ++a G+a+a + +g ++ +v+a  GDg+ t+ + + +l  ++e +++++ i+ dNe  +++ + 
  gi|320101379|ref|YP_004176971.1|  78 AAAVASGVAEALERRGiRDVQVIAWAGDGG-TADIGMASLSGAAERNNNIIYIMYDNEAYMNTGIQ 142
                                       457899********998899*********9.77788889******************988776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2193.51
//
Query:       gi|320101380|ref|YP_004176972.1|  [L=58]
Description: Sec61_beta domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.4e-14   51.2   0.9    1.1e-13   51.0   0.9    1.1  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.9   5.9e-18   1.1e-13       1      40 [.      16      55 ..      16      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5.9e-18
                                      XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                        Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                      S+aGL+ryyee + g+k++P+v ++l vaf ++Vi+L  +
  gi|320101380|ref|YP_004176972.1| 16 SAAGLVRYYEESDVGVKLKPHVLVALMVAFTVAVIVLSKV 55
                                      89***********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 415.65
//
Query:       gi|320101381|ref|YP_004176973.1|  [L=85]
Description: MazG nucleotide pyrophosphohydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-11   44.8   0.3    1.6e-11   44.2   0.3    1.2  1  MazG          MazG nucleotide pyrophosphohydrolase domain
     0.0012   19.3   0.5     0.0013   19.1   0.5    1.1  1  PRA-PH        Phosphoribosyl-ATP pyrophosphohydrolase
     0.0024   18.1   0.0     0.0037   17.5   0.0    1.2  1  MazG-like     MazG-like family
  ------ inclusion threshold ------
      0.053   13.7   0.0      0.088   13.0   0.0    1.4  1  PG_binding_1  Putative peptidoglycan binding domain


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 !   44.2   0.3   3.7e-15   1.6e-11       7      61 ..      27      77 ..      22      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.7e-15
                                      HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH CS
                              MazG  7 laylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaet 61
                                        + +eEvgE+aea+ + dr  leeEL+Dv+ ++l++an+     ++dle+++++
  gi|320101381|ref|YP_004176973.1| 27 FTWFAEEVGELAEALLHMDRGMLEEELADVFAWLLSIANL----VNVDLEEAFKK 77
                                      67899**********************************9....9******9975 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5   2.9e-07    0.0013      27      77 ..      26      76 ..       3      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.9e-07
                                      HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHHHHH CS
                            PRA-PH 27 raaligEEavElleaasegdlaeladelaDllYvtygllvllGidldavfe 77
                                        ++++EE+ El ea    d+  l +elaD++  ++  + l ++dl++ f+
  gi|320101381|ref|YP_004176973.1| 26 TFTWFAEEVGELAEALLHMDRGMLEEELADVFAWLLSIANLVNVDLEEAFK 76
                                      57899******************************************9997 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.2e-07    0.0037      18      62 ..      33      78 ..      29      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.2e-07
                         MazG-like 18 sveelfkallkgseeeildeLAdviiylylLAdrlGidfee.idek 62
                                      +v+el +all+ ++ ++ +eLAdv++ l+  A+ +++d+ee  ++k
  gi|320101381|ref|YP_004176973.1| 33 EVGELAEALLHMDRGMLEEELADVFAWLLSIANLVNVDLEEaFKKK 78
                                      7899***********************************9966655 PP

>> PG_binding_1  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05     0.088       4      30 ..       2      28 ..       1      31 [. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                      HHHHHHHHHHHTT--.SSSSSB--HHH CS
                      PG_binding_1  4 dvkelqryLsrlGylsgpadgtfgpat 30
                                      d++e+q+  +rl+y +++a g+f ++t
  gi|320101381|ref|YP_004176973.1|  2 DIREAQEHIKRLYYERDSARGVFATFT 28
                                      799***********9********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 641.54
//
Query:       gi|320101382|ref|YP_004176974.1|  [L=253]
Description: geranylgeranylglyceryl diphosphate synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-47  161.0   0.0    3.6e-47  160.7   0.0    1.0  1  PcrB          PcrB family
    1.7e-05   24.4   0.0    2.7e-05   23.7   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.055   12.9   0.1        0.1   12.0   0.1    1.4  1  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.11   11.5   0.1       0.23   10.4   0.1    1.6  2  IMPDH         IMP dehydrogenase / GMP reductase domain


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 !  160.7   0.0   8.1e-51   3.6e-47       6     223 ..      17     241 ..      12     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 8.1e-51
                                       TS.EEEEE-TTS....S-CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSE CS
                              PcrB   6 er.hltklDPee....enpdEiveiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvryaDa 77 
                                       e+ h t++DP++    ++ +E ++ +++ g+D  +igGs+svt +++  +    ++++lP+v++p+n++ +++ aDa
  gi|320101382|ref|YP_004176974.1|  17 EKlHFTLVDPDKagnlDKLEELADLAASAGSDLFLIGGSTSVTPEEAGIVADTLKKTGLPVVIFPGNINCLTPRADA 93 
                                       445*******9944445778999999*************************************************** PP

                                       EEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT CS
                              PcrB  78 lFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllg 153
                                       + +m l+n  ++++++ ++ l++  ++k+   +e ++ gY+v + d++v+ v+ +  ++  k+++a ++ laa+++g
  gi|320101382|ref|YP_004176974.1|  94 VLFMVLMNTLEPYYLMQVQVLAAPLIRKYG--LETIPTGYIVFNMDTAVGHVGRVYpIPYSKPELALAYGLAAEMMG 168
                                       ******************************..********************************************* PP

                                       -SEEEEE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHHHH CS
                              PcrB 154 lrliYlEa.sGaledv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekderkidail 223
                                       ++l+YlEa sGa+ ++     ++ k+ ++ + +vGGGirs+E   e ++a AD+iv+G+v+e ++ + ++ ++
  gi|320101382|ref|YP_004176974.1| 169 FKLLYLEAgSGAPSPIpPVFPQVIKRNTGLITMVGGGIRSPEAVVELLKAgADIIVTGTVMERDPVKGVEVVK 241
                                       ****************888899****************************************99955554444 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   6.1e-09   2.7e-05      68     115 ..     192     239 ..     168     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.1e-09
                                       HHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                      His_biosynth  68 iaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                       i +++ +  +vGGGIrs e+v ell+agad ++ gt++ ++p    e+
  gi|320101382|ref|YP_004176974.1| 192 IKRNTGLITMVGGGIRSPEAVVELLKAGADIIVTGTVMERDPVKGVEV 239
                                       5566777889***************************98888554444 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 ?   12.0   0.1   2.3e-05       0.1     124     168 ..     181     226 ..     179     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                                       SGGG.HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 124 Pglv.pkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                       P+ + p + + ik+++ +  + GG i++ e v e+lkaGa+ + t+
  gi|320101382|ref|YP_004176974.1| 181 PSPIpPVFPQVIKRNTGLITMVGGGIRSPEAVVELLKAGADIIVTG 226
                                       6677444455567778889999999*****************9997 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.57   2.6e+03     229     247 ..      46      64 ..      31      88 .. 0.56
   2 ?   10.4   0.1   5.1e-05      0.23     139     237 ..     192     227 ..     176     252 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.57
                                       T-SEEEESCCCTTBTTSSS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             IMPDH 229 GadavmlGsllagteEspg 247
                                       G+d  ++G   + t E  g
  gi|320101382|ref|YP_004176974.1|  46 GSDLFLIGGSTSVTPEEAG 64 
                                       4444444444443333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.1e-05
                                       HHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 139 ikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGG 215
                                       ik+++  +++++                                                               GG
  gi|320101382|ref|YP_004176974.1| 192 IKRNTGLITMVG---------------------------------------------------------------GG 205
                                       444444455555...............................................................55 PP

                                       --SHHHHHHHHHTT-SEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 216 ikysgdivkAlaaGadavmlGs 237
                                       i++ + +v  l aGad+++ G 
  gi|320101382|ref|YP_004176974.1| 206 IRSPEAVVELLKAGADIIVTGT 227
                                       5555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1754.09
//
Query:       gi|320101383|ref|YP_004176975.1|  [L=112]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-20   71.8   0.2    4.7e-20   71.4   0.2    1.2  1  Elf1             Transcription elongation factor Elf1 like
     0.0014   18.1   2.2      0.011   15.2   2.2    2.2  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0014   18.9   3.0     0.0045   17.2   0.2    2.1  2  Ribosomal_L32p   Ribosomal L32p protein family
  ------ inclusion threshold ------
       0.01   15.2   2.0       0.24   10.9   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.022   15.2   0.1      0.041   14.3   0.1    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.025   14.5   0.2      0.037   13.9   0.2    1.3  1  FdhE             Protein involved in formate dehydrogenase fo
      0.042   13.8   1.2       0.13   12.3   1.3    1.8  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.12   12.3   1.1       0.12   12.3   1.1    1.9  2  DUF1610          Domain of unknown function (DUF1610)
       0.13   12.1   0.9        1.9    8.4   0.1    2.2  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
       0.15   12.0   1.2         13    5.8   0.1    2.4  2  zinc_ribbon_4    zinc-ribbon domain
       0.15   12.3   1.1       0.58   10.5   1.1    1.7  1  zf-LITAF-like    LITAF-like zinc ribbon domain
       0.19   12.0   2.9        1.3    9.2   0.4    2.4  2  zf-RING_7        C4-type zinc ribbon domain
       0.29   11.2   2.4       0.97    9.5   0.0    2.2  2  Rubredoxin       Rubredoxin
       0.42   10.4   3.5        2.2    8.1   0.4    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.43   10.7   2.9        1.5    9.0   0.1    2.3  2  Zn-ribbon_8      Zinc ribbon domain
        1.4    9.4   5.7        9.3    6.7   0.0    3.1  3  zf-IS66          zinc-finger binding domain of transposase IS


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.2   4.2e-23   4.7e-20       2      78 .]       3      79 ..       2      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 4.2e-23
                              Elf1  2 kRkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkek..iaevsCkvCgesfe.tkvnalsepvDvYskwiDace 77
                                      +R+kk+k  + kk+ k+pt F+Cp+C+++ +++v + k e+  +a+vsC+ Cg+++e  +v++++++vDvY+k+iD++e
  gi|320101383|ref|YP_004176975.1|  3 RRRKKRK--IIKKAVKIPTLFQCPNCGSN-TLSVVFAKGESgrKAIVSCSRCGLYYEyGNVPSIYQAVDVYNKFIDLFE 78
                                      5565664..6777888************9.********99889**************557****************998 PP

                              Elf1 78 e 78
                                      e
  gi|320101383|ref|YP_004176975.1| 79 E 79
                                      6 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.2   9.9e-06     0.011       1      31 [.      21      57 ..      21      64 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.9e-06
                                      EEETTTTCEEC.....HEETSTTCE.EESSSSBEEEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstnl.....veDpergel.vCtdCGlVled 31
                                      ++CPnCgs +l       +  r  +  C++CGl  e+
  gi|320101383|ref|YP_004176975.1| 21 FQCPNCGSNTLsvvfaKGESGRKAIvSCSRCGLYYEY 57
                                      79******9885544333355555559****997776 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2     4e-06    0.0045      11      37 ..       3      31 ..       1      44 [. 0.81
   2 ?    2.5   0.2      0.16   1.8e+02      25      33 ..      44      52 ..      34      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                                      HHHHHGGGT..------EEEETTTCCEEC CS
                    Ribosomal_L32p 11 rrrkRrahw..klkapnlvecpncgelkl 37
                                      rrrk+r     ++k p+l +cpncg+ +l
  gi|320101383|ref|YP_004176975.1|  3 RRRKKRKIIkkAVKIPTLFQCPNCGSNTL 31
                                      7777777633599999*********8776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                                      -EEEETTTC CS
                    Ribosomal_L32p 25 nlvecpncg 33
                                      ++v c+ cg
  gi|320101383|ref|YP_004176975.1| 44 AIVSCSRCG 52
                                      567777776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00021      0.24       4      11 ..      22      29 ..      20      33 .. 0.79
   2 ?    3.9   0.1     0.032        36       3       9 ..      46      52 ..      45      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                       zf-ribbon_3  4 rCPnCGap 11
                                      +CPnCG++
  gi|320101383|ref|YP_004176975.1| 22 QCPNCGSN 29
                                      79999996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.032
                       zf-ribbon_3  3 vrCPnCG 9 
                                      v+C++CG
  gi|320101383|ref|YP_004176975.1| 46 VSCSRCG 52
                                      68****9 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.7e-05     0.041       3      37 ..      20      56 ..      18      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-05
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga..s 37
                                      L  CP Cg+    +   ++ +++   v+C  Cg    
  gi|320101383|ref|YP_004176975.1| 20 LFQCPNCGSNTLSVVFAKGESGRKAIVSCSRCGLyyE 56
                                      668******9987777777777777********9442 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.3e-05     0.037     169     204 ..      21      55 ..       4      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                                       SS-TTT---EEEEEEE-------EEEEEETTT--EE CS
                              FdhE 169 glCPvCgsaPvasvvriggeaeglRylhCslCeteW 204
                                         CP Cgs    svv  +ge+ +   ++Cs C   +
  gi|320101383|ref|YP_004176975.1|  21 FQCPNCGSNT-LSVVFAKGESGRKAIVSCSRCGLYY 55 
                                       57******86.6888888878889999*****8766 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.3   0.00011      0.13      19      44 ..      21      52 ..      12      54 .. 0.82
   2 ?    2.3   0.1      0.15   1.7e+02      19      25 ..      46      52 ..      32      60 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                     Zn_Tnp_IS1595 19 fvCPhCgsr..kayrikt....rglfqCkeCr 44
                                      f CP+Cgs   ++ + k+         C++C+
  gi|320101383|ref|YP_004176975.1| 21 FQCPNCGSNtlSVVFAKGesgrKAIVSCSRCG 52
                                      89*******88888888899966678999996 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                     Zn_Tnp_IS1595 19 fvCPhCg 25
                                      + C +Cg
  gi|320101383|ref|YP_004176975.1| 46 VSCSRCG 52
                                      4499998 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.1   0.00011      0.12      16      23 ..      20      27 ..      18      28 .. 0.88
   2 ?   -2.9   0.5       6.1   6.9e+03       1       5 [.      48      52 ..      48      53 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                           DUF1610 16 vFpCPNCG 23
                                       F CPNCG
  gi|320101383|ref|YP_004176975.1| 20 LFQCPNCG 27
                                      69*****9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.1
                           DUF1610  1 CtSCG 5 
                                      C+ CG
  gi|320101383|ref|YP_004176975.1| 48 CSRCG 52
                                      77777 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 ?    2.4   0.1      0.12   1.4e+02      15      20 ..      22      27 ..      11      28 .. 0.76
   2 ?    8.4   0.1    0.0017       1.9      14      27 ..      46      59 ..      35      61 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                         zf-C2H2_3 15 qCkeCg 20
                                      qC++Cg
  gi|320101383|ref|YP_004176975.1| 22 QCPNCG 27
                                      6****8 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
                         zf-C2H2_3 14 sqCkeCgMvYnpgs 27
                                      + C+ Cg+ Y  g+
  gi|320101383|ref|YP_004176975.1| 46 VSCSRCGLYYEYGN 59
                                      45********7775 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.012        13       4       9 ..      22      27 ..       7      29 .. 0.75
   2 ?    5.0   0.1     0.021        24      25      32 ..      45      52 ..      39      56 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                     zinc_ribbon_4  4 tCpsCk 9 
                                      +Cp+C+
  gi|320101383|ref|YP_004176975.1| 22 QCPNCG 27
                                      555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.021
                     zinc_ribbon_4 25 kvrCskCg 32
                                       v Cs+Cg
  gi|320101383|ref|YP_004176975.1| 45 IVSCSRCG 52
                                      56677776 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   0.00052      0.58       3      28 ..      18      43 ..      16      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00052
                     zf-LITAF-like  3 ptqvdCpaCqqrvvTsveyksgkltw 28
                                      pt ++Cp+C+ ++ ++v  k +++  
  gi|320101383|ref|YP_004176975.1| 18 PTLFQCPNCGSNTLSVVFAKGESGRK 43
                                      8999**********999777665554 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 ?    9.2   0.4    0.0012       1.3      22      30 ..      19      27 ..       4      28 .. 0.77
   2 ?    3.0   0.1       0.1   1.2e+02      22      30 ..      39      52 ..      28      52 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                                      B-EE-TTT- CS
                         zf-RING_7 22 evvtCpeCG 30
                                       +++Cp+CG
  gi|320101383|ref|YP_004176975.1| 19 TLFQCPNCG 27
                                      489*****9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.1
                                      B.....-EE-TTT- CS
                         zf-RING_7 22 e.....vvtCpeCG 30
                                      e     +v C  CG
  gi|320101383|ref|YP_004176975.1| 39 EsgrkaIVSCSRCG 52
                                      4444559******8 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00087      0.97      30      42 ..      16      28 ..      13      32 .. 0.88
   2 ?    0.8   0.7      0.45   5.1e+02       3      12 ..      47      56 ..      46      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00087
                                      GS-TT-BBTTTB- CS
                        Rubredoxin 30 dlPddWvCPdCgv 42
                                      ++P  ++CP+Cg 
  gi|320101383|ref|YP_004176975.1| 16 KIPTLFQCPNCGS 28
                                      59*********96 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.45
                                      EETTT-BEEE CS
                        Rubredoxin  3 eCkvCgyvYd 12
                                       C+ Cg  Y+
  gi|320101383|ref|YP_004176975.1| 47 SCSRCGLYYE 56
                                      6999*99886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4     0.002       2.2      16      21 ..      23      28 ..      20      30 .. 0.69
   2 ?    2.8   0.2     0.089     1e+02      16      20 ..      48      52 ..      46      53 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.002
                     zinc_ribbon_2 16 CpyCGt 21
                                      Cp+CG+
  gi|320101383|ref|YP_004176975.1| 23 CPNCGS 28
                                      666665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.089
                     zinc_ribbon_2 16 CpyCG 20
                                      C++CG
  gi|320101383|ref|YP_004176975.1| 48 CSRCG 52
                                      55555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0013       1.5      26      35 ..      20      30 ..       8      35 .. 0.72
   2 ?    6.4   3.2    0.0086       9.6       6      33 ..      21      52 ..      21      57 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                       Zn-ribbon_8 26 ltaCPeCgs.e 35
                                      l +CP+Cgs +
  gi|320101383|ref|YP_004176975.1| 20 LFQCPNCGSnT 30
                                      556*****944 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0086
                       Zn-ribbon_8  6 YrCeeCghefe..vlqsis.daplta.CPeCg 33
                                      ++C +Cg+     v+++    ++ ++ C +Cg
  gi|320101383|ref|YP_004176975.1| 21 FQCPNCGSNTLsvVFAKGEsGRKAIVsCSRCG 52
                                      67777776555444444444344566677776 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 ?    6.7   0.0    0.0083       9.3       3      12 ..      22      32 ..      22      37 .. 0.80
   2 ?    0.6   0.1      0.68   7.6e+02      41      46 .]      47      52 ..      42      53 .. 0.71
   3 ?    3.0   0.3      0.12   1.4e+02      11      24 ..      92     104 ..      88     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0083
                           zf-IS66  3 tCpcCGg.llk 12
                                      +Cp+CG+ +l+
  gi|320101383|ref|YP_004176975.1| 22 QCPNCGSnTLS 32
                                      7*****96675 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.68
                           zf-IS66 41 aCpcCe 46
                                      +C++C+
  gi|320101383|ref|YP_004176975.1| 47 SCSRCG 52
                                      677775 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.12
                           zf-IS66  11 lkpigedrvreeld 24 
                                       l +++e+ v+eel+
  gi|320101383|ref|YP_004176975.1|  92 LEELAEE-VSEELE 104
                                       578999*.****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 825.86
//
Query:       gi|320101384|ref|YP_004176976.1|  [L=130]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0025   17.5   0.0     0.0046   16.6   0.0    1.5  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.6e-07    0.0046       6      36 ..      51      89 ..      45      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-07
                              SWIM  6 dder..vrlnkatCsCpefqk......ngipCkHalAvl 36
                                      ++er  v +  ++CsC +f +        ++CkH+l++ 
  gi|320101384|ref|YP_004176976.1| 51 GPERdyVAIPGTYCSCMDFAIrvvsrgETPYCKHLLGLE 89
                                      45557777789*************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1024.05
//
Query:       gi|320101385|ref|YP_004176977.1|  [L=358]
Description: translation initiation factor, aIF-2BI family [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-79  267.2   0.0    1.7e-79  267.0   0.0    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.0   0.0   9.6e-84   1.7e-79       1     282 []      54     345 ..      54     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: 267.0 bits;  conditional E-value: 9.6e-84
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHH..HHHCCTTTSSHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllk..eiselksssdvkea 75 
                                       ++rG+pai++aa+ ++  + ++++     ++ke++++aid+L  +rPta +l+ a++rl +  e + +    +    
  gi|320101385|ref|YP_004176977.1|  54 EIRGAPAIGVAAALAVGAYSTRISGLPLGDFKERVEEAIDTLWRTRPTAYNLFYALKRLRRvlE-EGVAGGVEPPVL 129
                                       58***********************************************************432.345666666778 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTT CS
                             IF-2B  76 kksliekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPr 144
                                       + +++e++ e++ e++e++  ig+++aeli dg tilT+cn+++        + +v+r a+ ++k+++Vi++E+rP 
  gi|320101385|ref|YP_004176977.1| 130 SRRILEEALEVMWEDVESNIMIGEHGAELIPDGATILTHCNAGAlatsafgtAEAVMRVAWYKGKRIRVIATETRPM 206
                                       999************************************************************************** PP

                                       THH.HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXG CS
                             IF-2B 145 lqG.rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaes 219
                                       lqG rlt++eLv++gipvtlitd++++yv+++  v++vivGAdr++++G ++nkiGT+++A++Ak++ +p++v+a++
  gi|320101385|ref|YP_004176977.1| 207 LQGaRLTVWELVKEGIPVTLITDNMAGYVIRKgLVNAVIVGADRVTREGYVVNKIGTYMIALAAKRHGVPFYVAAPT 283
                                       ***************************************************************************** PP

                                       GGBESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 220 lkfservqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       ++++   ++ +d++ieer+p e++ + g+ i+ ee + +n+afD+t p+l+t+iITe+Gv+ p
  gi|320101385|ref|YP_004176977.1| 284 STIDLS-STVNDVVIEERNPWEVKHVLGRPITLEEADALNYAFDITDPDLVTAIITEKGVVYP 345
                                       *****9.66666888*********************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); 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 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2563.08
//
Query:       gi|320101386|ref|YP_004176978.1|  [L=173]
Description: tRNA intron endonuclease, catalytic domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-10   38.5   0.1    1.4e-09   37.8   0.1    1.3  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    4.6e-05   23.0   0.0    0.00011   21.8   0.0    1.7  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.19   12.0   0.0    1.3  1  Sen15            Sen15 protein


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.1   2.4e-13   1.4e-09       1      85 []      86     164 ..      86     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.4e-13
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                       f+ ++ vy+dLr++G  vr   +  + F+v     +++ +  lV+v++e++ +++ +++++++ a+  + +l+laiv
  gi|320101386|ref|YP_004176978.1|  86 FWPQLLVYKDLRDRGRRVRVVDQ--GRFLVK----DKSGGLRLVYVLEEKKLISIDSIVKEAENARDNSLQLVLAIV 156
                                       8999*****************99..9****8....7777888*********************************** PP

                                       TTTSCEEE CS
                     tRNA_int_endo  78 daegdvty 85 
                                       + +gd+ty
  gi|320101386|ref|YP_004176978.1| 157 SLQGDITY 164
                                       ******99 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 !   21.8   0.0   1.9e-08   0.00011      20      55 ..      27      61 ..      11      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-08
                                      HHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE CS
                   tRNA_int_endo_N 20 rlyekgfYGkplidepLqLslvEAlYLlekGklevv 55
                                       ++e++++G+ +   +L+L+lvE +YL+  +k  v+
  gi|320101386|ref|YP_004176978.1| 27 GILEEKWFGR-RSRGDLVLDLVEVAYLILEKKAVVE 61
                                      4799******.****************987765555 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05      0.19      52      90 ..     130     167 ..     119     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                             Sen15  52 slekldkvfkelkeekserkkrivLaivddDsTvvYYkv 90 
                                       +l ++d+++ke ++ + +++ ++vLaiv+  + + YY+ 
  gi|320101386|ref|YP_004176978.1| 130 KLISIDSIVKEAENAR-DNSLQLVLAIVSLQGDITYYEA 167
                                       5678999999988776.68******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1258.92
//
Query:       gi|320101387|ref|YP_004176979.1|  [L=434]
Description: histidyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-47  162.2   0.1    2.1e-47  161.9   0.1    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    8.9e-12   45.3   0.0    2.2e-11   44.0   0.0    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.3e-06   28.5   0.0    2.7e-06   27.5   0.0    1.5  1  HGTP_anticodon  Anticodon binding domain
     0.0036   16.8   0.0      0.012   15.1   0.0    1.9  3  tRNA-synt_2d    tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.049   12.7   2.3       0.57    9.2   1.3    2.6  3  tRNA-synt_2     tRNA synthetases class II (D, K and N)
        0.2   11.5   0.0       0.42   10.4   0.0    1.5  1  Soyouz_module   N-terminal region of Paramyxovirinae phosphop


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 !  161.9   0.1     7e-51   2.1e-47       1     310 []      12     323 ..      12     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 7e-51
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd+   eae  e l+  + ++++++G++++++P++Ey   ++ ++ge+ + +++ + D+ gr+l+lR+++T++v+
  gi|320101387|ref|YP_004176979.1|  12 GMRDIVGVEAELHEYLADVFRETARRHGFKPIITPTVEYFKLFEMKSGEEIKrSMYVFQDKAGRTLALRPEVTASVV 88 
                                       899***********************************************88579999999**************** PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlg 152
                                       R++ + ++  ++p Rl+Y ++++r ++ + +r re+ Q G E+iG  +++ad+ v   + + le a+gvk+  + +g
  gi|320101387|ref|YP_004176979.1|  89 RAYLKEMRaLPKPVRLYYVAQCFRYEEPQKARYREFWQGGLEVIGDPDINADASVAFAASSFLE-AVGVKHYYV-VG 163
                                       *****9988******************************************************7.****99888.** PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC......HCCHCCCHHHHCHCCHCTHH CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalarkdlaelkelaaeaglkealrellkal...elygdaevleealealaaap 226
                                       +v+ +r l++++g++ ++++ +l+++++  + +  ++++   ++  ++el+++l    l + a  + ++ + l ++ 
  gi|320101387|ref|YP_004176979.1| 164 NVSTYRVLMDKMGVPGETQDLILHLIDKDRVGDALKVLGG-VVTGGHVELFNKLlnsGLDE-APGILREFRLL-GEG 237
                                       ****************999999999999998887777776.58888899999987633444.44455555645.555 PP

                                       HHHHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEE.TT-SS-SEEEEEECTTTGGG.T---EEE CS
                     tRNA-synt_His 227 alqaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaaya.egvgqaiarGGrYdelgaaf.grarpAt 301
                                       + +++ +el+++ + ++ l++ + +  + + ++rg++Yy+Gl+F+  + eg +  i++GGrYd+l +++ g+ + +t
  gi|320101387|ref|YP_004176979.1| 238 EQTTLEAELARTREFIDLLNQMGFHAVYEPRLVRGLAYYSGLIFEYKTsEGLTVSIGGGGRYDGLTRVYgGEYEYST 314
                                       55788889999999999888889**********************865378899***************99****** PP

                                       EEEEEHHHH CS
                     tRNA-synt_His 302 Gfsldleal 310
                                       G++l l+++
  gi|320101387|ref|YP_004176979.1| 315 GLALGLDRI 323
                                       ******986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   7.5e-15   2.2e-11       1     106 [.      67     166 ..      67     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 7.5e-15
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld 77 
                                       Y ++d+ +r ++L+P+ ++ +v+++ +e +r    P++ly++  ++R+E++ ++   R+reF q + +v++ ++   
  gi|320101387|ref|YP_004176979.1|  67 YVFQDKAGRTLALRPEVTASVVRAYLKE-MRALPKPVRLYYVAQCFRYEEP-QKA--RYREFWQGGLEVIGDPD--I 137
                                       8899************************.887445****************.**9..*****************..9 PP

                                       HHHHHHHHHHHHHHHHTT.SCEEEEEEGT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  78 dslrdlikaisriferlglefraiielms 106
                                       + ++ +  a+s ++e++g++ + +++  s
  gi|320101387|ref|YP_004176979.1| 138 NADASVAFAASSFLEAVGVKHYYVVGNVS 166
                                       9999***************9988887754 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   8.9e-10   2.7e-06      19      90 ..     353     423 ..     339     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 8.9e-10
                                       HHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHH CS
                    HGTP_anticodon  19 kklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelvek 90 
                                        +l +++   g+ +++ ++++++ k++  a+++g   +v++G +ele+g+vtv+d++t++q +++  +  + 
  gi|320101387|ref|YP_004176979.1| 353 YELVKRITSGGL-AVIPYRARTVSKALGFANKQGADAVVILGRRELESGVVTVKDMHTGMQSTIEAGDTDAL 423
                                       578888999998.88889*******************************************99987776554 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 !   15.1   0.0   3.9e-06     0.012      27     132 ..      32     132 ..      12     160 .. 0.68
   2 ?   -3.7   0.0       2.2   6.6e+03      24      41 ..     250     267 ..     243     273 .. 0.79
   3 ?   -3.1   0.0       1.5   4.4e+03     213     224 ..     315     326 ..     303     328 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-06
                                       HHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH....TTS- CS
                      tRNA-synt_2d  27 keiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl....ekkk 99 
                                       +e+ ++ gf+ +  p v      f+  ++++ +   +++ + y+ +++    ++l LR   ta  +r+     ++  
  gi|320101387|ref|YP_004176979.1|  32 RETARRHGFKPIITPTV----EYFKLFEMKSGE---EIKRSMYVFQDKA--GRTLALRPEVTASVVRAYlkemRALP 99 
                                       44444444544444444....445555555444...5556666656666..789********999997555546667 PP

                                       SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEE CS
                      tRNA-synt_2d 100 ppikiisigrvfRrdavDathlaeFhqveglvv 132
                                       +p+++  + ++fR ++  + +  eF q    v+
  gi|320101387|ref|YP_004176979.1| 100 KPVRLYYVAQCFRYEEPQKARYREFWQGGLEVI 132
                                       9************************99665444 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.2
                                       HHHHHHHHCTTCEESSTT CS
                      tRNA-synt_2d  24 eeikeiflelgfeevegp 41 
                                       +e+ +++ ++gf++v +p
  gi|320101387|ref|YP_004176979.1| 250 REFIDLLNQMGFHAVYEP 267
                                       578899999999988766 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                                       EEEEEHHHHHHH CS
                      tRNA-synt_2d 213 afGlGveRlaml 224
                                       ++ lG++R+a+l
  gi|320101387|ref|YP_004176979.1| 315 GLALGLDRIALL 326
                                       4457889**998 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.3   0.00019      0.57      83     121 ..      93     130 ..      20     132 .. 0.60
   2 ?   -3.0   0.0      0.97   2.9e+03      19      50 ..     239     270 ..     231     273 .. 0.78
   3 ?    1.1   0.0     0.056   1.7e+02     285     303 ..     314     332 ..     302     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00019
                                       HHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  83 lellivagidrvfqiaraFRaEdsrtdrhlaEFtqieae 121
                                       +e+ +  +  r + +a++FR E+ ++ r   EF+q  +e
  gi|320101387|ref|YP_004176979.1|  93 KEMRALPKPVRLYYVAQCFRYEEPQKARYR-EFWQGGLE 130
                                       555566667799****************99.**996665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.97
                                       HHHHHHHHHHHHHHHHHHHHTT-EE----SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  19 skvlrlrstvtkavrkyleengfieietPiLs 50 
                                       + +l++    t+ + + l++ gf  +  P L+
  gi|320101387|ref|YP_004176979.1| 239 QTTLEAELARTREFIDLLNQMGFHAVYEPRLV 270
                                       56666777778888999999999999999887 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.056
                                       EEEEEEHHHHHHHHCT-SS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 285 gGlglGldRlvmlllgses 303
                                        Gl+lGldR+  ll  ++ 
  gi|320101387|ref|YP_004176979.1| 314 TGLALGLDRIALLLSPEKA 332
                                       7*********999977665 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 ?   10.4   0.0   0.00014      0.42      36      55 ..     412     431 ..     402     433 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                     Soyouz_module  36 kSaIpkGkTkaltkawEkea 55 
                                        S+I  G+T al+k+ Ek++
  gi|320101387|ref|YP_004176979.1| 412 QSTIEAGDTDALIKLLEKHG 431
                                       69****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3197.59
//
Query:       gi|320101388|ref|YP_004176980.1|  [L=482]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-165  549.7   0.0   5.4e-165  549.5   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  549.5   0.0    3e-169  5.4e-165       1     412 []      48     482 .]      48     482 .] 0.99

  Alignments for each domain:
  == domain 1  score: 549.5 bits;  conditional E-value: 3e-169
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       q++nva+lpgi  ++++mPD H+G+g+piG+V+ ++   gvi+P++VG+DI CGvr+l+t+l+ ++++++lkelv++
  gi|320101388|ref|YP_004176980.1|  48 QAANVACLPGIKLYSYVMPDGHQGYGFPIGGVAGFDveeGVISPGGVGYDInCGVRVLRTELDVDDVKPRLKELVDA 124
                                       89*************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       l+++vp+g+gs+++++l  +el+evl++g++wave g+g+++d+e+iee+g++k+ad+ kvsk ak+r+++qlGtlG
  gi|320101388|ref|YP_004176980.1| 125 LFRNVPSGVGSTGHLRLGFNELDEVLNRGVEWAVEAGFGWKRDIEHIEERGRMKTADAGKVSKVAKQRGHEQLGTLG 201
                                       ***************************************************************************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT-.-TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgl.eegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpags 226
                                       +GNHF+E+q+v+ei+d eaak++g+ + gqv++m+H+GSRglGhq+a+dyl ++++a++k+gi++pdr+La+lp++s
  gi|320101388|ref|YP_004176980.1| 202 AGNHFLEIQVVDEIYDPEAAKTMGItRIGQVTLMIHTGSRGLGHQVASDYLMVMERAMRKYGIQVPDRELAALPFQS 278
                                       *************************667************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxx RF
                              RtcB 227 eegqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGA 299
                                       +e+q+Y+kam+aaan+A+aNRq+it+++re++++v+k++ e+l++e+++d+aHNiak Eeh+ +   ++v+VhRKGA
  gi|320101388|ref|YP_004176980.1| 279 PEAQDYFKAMSAAANFAWANRQIITHWTRESFKQVFKRDPEELGIEIIYDIAHNIAKIEEHTvNgekHRVVVHRKGA 355
                                       **************************************************************9457899******** PP

                                       EE-.............TT--EEEE--STTS-EEEEE--HHHH.SSSEE---S-----------------TTTTTCCC CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 300 trA.............kvgqpviipGsmgtkSyivkGkgnae.sfgStsHGAGRlmsRakakkkfkleevkkdleeq 362
                                       trA             ++gqpv+ipGsmgt+Syi+ G+ n   ++ S+ HGAGR +sR +a ++++ e+v ++l ++
  gi|320101388|ref|YP_004176980.1| 356 TRAfppghpdipgdyqSIGQPVLIPGSMGTASYILLGTANGArTWFSAPHGAGRWLSRGDAIRSYSPEKVVDELGRK 432
                                       ***************************************9888********************************** PP

                                       T-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 363 gigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       g++++a++++++ eEap+aYKd+d+Vv ++++ g+++ v+r++p++vvkg
  gi|320101388|ref|YP_004176980.1| 433 GVVLKAATRRVISEEAPGAYKDVDRVVMVAHKVGIARPVVRMRPIGVVKG 482
                                       *************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3451.17
//
Query:       gi|320101389|ref|YP_004176981.1|  [L=529]
Description: DNA topoisomerase VI subunit B [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  207.2   0.0      2e-61  206.4   0.0    1.4  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    3.7e-12   46.2   0.0    6.4e-12   45.5   0.0    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    7.6e-12   45.7   0.0    1.8e-11   44.5   0.0    1.6  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    0.00022   20.1   0.2    0.00091   18.1   0.0    1.8  2  FbpA            Fibronectin-binding protein A N-terminus (Fbp
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.045   14.2   0.0    1.8  1  Ribosomal_S13   Ribosomal protein S13/S18
      0.037   14.2   0.2      0.066   13.4   0.2    1.3  1  DUF3585         Bivalent Mical/EHBP Rab binding domain
       0.11   12.3   0.0       0.36   10.7   0.0    1.8  2  Sec23_helical   Sec23/Sec24 helical 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 !  206.4   0.0   7.9e-65     2e-61       1     158 [.     309     468 ..     309     469 .. 0.97

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 7.9e-65
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGele..keekaeilRfaNrvPLlyde 75 
                                       Pst+++sp+g+e+ie+glk++++pef+ av+r+p++y+ghpf+vE+g+ayGG+++  +++k+ ilR+aN++PLlyde
  gi|320101389|ref|YP_004176981.1| 309 PSTKAISPLGSEIIEAGLKHVFQPEFTYAVSRRPQAYQGHPFVVEAGVAYGGKTPlsENDKPIILRYANKIPLLYDE 385
                                       99***************************************************998788899*************** PP

                    Topo-VIb_trans  76 gadvitkavk.sinwkrYkleqpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskke 151
                                       g+dv+t +vk +i w++Y ++ p+ p+++lvhv+stk+Pfk++gKe+iadv+e+++eiklal++v r+L+kylskk+
  gi|320101389|ref|YP_004176981.1| 386 GSDVTTLVVKeDIGWDNYMITFPA-PIAILVHVCSTKIPFKGVGKESIADVPEVRREIKLALMDVLRELRKYLSKKA 461
                                       *********559*********999.**************************************************** PP

                    Topo-VIb_trans 152 kekeeke 158
                                       +e+e k+
  gi|320101389|ref|YP_004176981.1| 462 REEELKK 468
                                       **99887 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 !   45.5   0.0   2.5e-15   6.4e-12       6     115 ..      36     155 ..      31     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.5e-15
                       HATPase_c_3   6 AlaelvdNsldAdaen.....vkievnknr..gktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkG 74 
                                        + elv+N+ldA   +     vki++++ +  ++  +i++eD+G G++++ + +a+ r+  ssk+    ++++G +G
  gi|320101389|ref|YP_004176981.1|  36 TVRELVENALDATDAHgilpdVKISIKRVDeiQEFYRITVEDNGIGIPPDVVPDAFgRVLFSSKYV--LRQTRGMYG 110
                                       688********988888****888888655336669******************8869*******5..79******* PP

                       HATPase_c_3  75 iGlklAsl....slgkkltvitkkegesstltldvdkidkenekv 115
                                       +G+k+A+l      g+ ++vit+k+g +  + ++++   ++ne v
  gi|320101389|ref|YP_004176981.1| 111 LGVKMAVLygqmTTGRPVEVITSKSGFKRIYYFKLRIDVNKNEPV 155
                                       ******96333379***********99996666655444444444 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 !   44.5   0.0     7e-15   1.8e-11       4      94 ..      31     130 ..      29     178 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 7e-15
                                       HHHHHHHHHHHHHHHHHHSTTT....EEEEEEEE.EE..TEEEEEEEESSSSSTTHHHTGTCS..TTCHHCSTCHTS CS
                         HATPase_c   4 krLrqiisnlvdNavkfatkag....eieveika.se..ddlvisveDnGiGipkedlkklfe..kfsqddstkrgg 71 
                                       + ++q +++lv+Na+++ t+a+    +++++ik+ +e  + ++i+veDnGiGip++ ++  f+   fs+ ++  r++
  gi|320101389|ref|YP_004176981.1|  31 RAIYQTVRELVENALDA-TDAHgilpDVKISIKRvDEiqEFYRITVEDNGIGIPPDVVPDAFGrvLFSS-KYVLRQT 105
                                       5789************9.54442444668888876335679******************9999877777.5555554 PP

                                       .TSSSHHHHHHHHHHH.HTTTEEEE CS
                         HATPase_c  72 .ggtGlGlsivkklve.lmgGeiwv 94 
                                        g  GlG++++  + + + g  ++v
  gi|320101389|ref|YP_004176981.1| 106 rGMYGLGVKMAVLYGQmTTGRPVEV 130
                                       4777777777644333223334444 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 !   18.1   0.0   3.5e-07   0.00091     161     238 ..     226     303 ..     222     342 .. 0.88
   2 ?   -1.0   0.1      0.22   5.5e+02     321     346 ..     452     477 ..     432     487 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.5e-07
                                       SXXXSXBXTTSXXH.HHHHHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHH CS
                              FbpA 161 PpsqdklnPleaeeleefkellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealq 236
                                       Pp   k+ P  ++  e +k+++s  +  ++++ L+k fq +++++a+ +l++ag+d++++  +l+e++l +l ++l+
  gi|320101389|ref|YP_004176981.1| 226 PPVEVKPHPHGVDL-ELLKQIISShNYSSVEELLIKGFQSIGEATARLILQQAGVDPAKPPVDLTENELLSLVNTLR 301
                                       77777788887776.8899999988999********************************************99999 PP

                                       HH CS
                              FbpA 237 el 238
                                       ++
  gi|320101389|ref|YP_004176981.1| 302 SM 303
                                       86 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.22
                                       HHHHHHHCCGGHHHHHCCHH------ CS
                              FbpA 321 klekelekaekaenyrligelltayl 346
                                       +l+k l+k + +e++++ +e l  y+
  gi|320101389|ref|YP_004176981.1| 452 ELRKYLSKKAREEELKKRAEHLAKYI 477
                                       44444444444444444444444444 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-05     0.045      20      67 ..     262     309 ..     252     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                     Ribosomal_S13  20 ikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykip 67 
                                        + iG+ +a+ il++a+vd  k   +lte+e+  +++++  +++ ++p
  gi|320101389|ref|YP_004176981.1| 262 FQSIGEATARLILQQAGVDPAKPPVDLTENELLSLVNTLRSMKDIRAP 309
                                       567**********************************99987776665 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 ?   13.4   0.2   2.6e-05     0.066      60     116 ..     455     511 ..     447     516 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                           DUF3585  60 seLmilareqeLedeqadleqelrelmakeekeKteedkereeelleelvevVeqRd 116
                                       + L   are+eL+++ ++l + + e+        +  dke+e +ll++lv++V +R 
  gi|320101389|ref|YP_004176981.1| 455 KYLSKKAREEELKKRAEHLAKYIPEVARSLALITSGGDKEAEALLLRRLVSIVSKRT 511
                                       56777899***********************************************97 PP

>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   5.1e+03      33      73 ..     296     342 ..     268     346 .. 0.62
   2 ?   10.7   0.0   0.00014      0.36      21      79 ..     434     491 ..     411     506 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                       HHHHHHHHHHH----....---------GGGTTH..HHHHHHHHTST CS
                     Sec23_helical  33 lvdllsayrkvgasg....sspsqlqlpeslklL..PlyilallKsp 73 
                                       lv+ l++ ++  a++    s+ ++ ++ + lk+   P +++a+ + p
  gi|320101389|ref|YP_004176981.1| 296 LVNTLRSMKDIRAPStkaiSPLGSEIIEAGLKHVfqPEFTYAVSRRP 342
                                       45555555555554444444445555555555543367777777765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                                       -HHHHHHHHHHHHHHHHHHHHHH-------------GGGTTHHHHHHHHHTSTTTS-.-T CS
                     Sec23_helical  21 gladarealdtslvdllsayrkvgasgsspsqlqlpeslklLPlyilallKspafrg.gn 79 
                                       ++ ++r+++   l d+l+ +rk+ ++  ++ + +l +  ++L  yi  + +s a++  g 
  gi|320101389|ref|YP_004176981.1| 434 DVPEVRREIKLALMDVLRELRKYLSK--KAREEELKKRAEHLAKYIPEVARSLALITsGG 491
                                       4456********************88..77789**********************98554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3718.17
//
Query:       gi|320101390|ref|YP_004176982.1|  [L=434]
Description: DNA topoisomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-22   78.5   0.2    4.9e-22   77.7   0.2    1.4  1  TP6A_N      Type IIB DNA topoisomerase
     0.0049   16.8   0.0      0.012   15.5   0.0    1.6  1  DUF2399     Protein of unknown function C-terminus (DUF2399)
  ------ inclusion threshold ------
      0.084   12.5   0.1       0.25   11.0   0.1    1.7  1  Vac_Fusion  Chordopoxvirus multifunctional envelope protein A


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 !   77.7   0.2   8.2e-26   4.9e-22       1      62 []      73     149 ..      73     149 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 8.2e-26
                                       HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH...............GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                            TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr...............dvelFksQaesdrliddievllgvsReeLnv 62 
                                       rkf+q+++++++i++ l++++++T+Rd+YYr               +++++++Q+esd++i+d+ev l+v+ReeL +
  gi|320101390|ref|YP_004176982.1|  73 RKFMQTVLMASIIYDSLVNNEYPTIRDLYYRgkhsisyrsssgrevHENTWDEQKESDSVIRDLEVFLNVLREELLI 149
                                       79*******************************************99****************************87 PP

>> DUF2399  Protein of unknown function C-terminus (DUF2399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.1e-06     0.012      18      83 ..     195     263 ..     182     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-06
                           DUF2399  18 egravyVvENpavlaaaadr..lgakaaplvctsGqpsaaalelldkl.aaagarlrYhGDfDwpGlai 83 
                                        +++v VvE  av++ + +     +++a l+  +Gqp +a+ ++l++l  + +  ++   D D+ G  i
  gi|320101390|ref|YP_004176982.1| 195 DAEYVLVVEKDAVFQQLHRYgfWKKNKAILITSAGQPDRATRRFLRRLsDEYNLPVYILTDSDPYGFYI 263
                                       5667************999865556888899999**************445689999999999988766 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 ?   11.0   0.1   4.1e-05      0.25      15      49 ..     118     152 ..     108     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXX CS
                        Vac_Fusion  15 dfqlvikcckrvnealkRlEnHleTlRkamlaLak 49 
                                        ++++ +++k+++ +++ lE  l+ lR  +l+L+k
  gi|320101390|ref|YP_004176982.1| 118 VHENTWDEQKESDSVIRDLEVFLNVLREELLILSK 152
                                       689999***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3304.54
//
Query:       gi|320101391|ref|YP_004176983.1|  [L=244]
Description: 5-formyltetrahydrofolate cyclo-ligase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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    1.3e-29  103.3   0.0    1.0  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0   7.5e-34   1.3e-29       3     187 .]       7     203 ..       6     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 7.5e-34
                                       HHHHHHHH.HHHTS-HHHHHHHHHHHHHHHHTSHHHHH-.SEE........EE----TTS---HHHHHHHHHTTEEE CS
                    5-FTHF_cyc-lig   3 elRkqlla.alralseeevaaesealsqrieslkesqea.krv........alyvsvkgeidtkelikklleegkev 69 
                                       +lR+ +++ ++r+++e +va  + ++ +ri+++k+++ea +r+        a +v v++++++ +l++ lle+g  v
  gi|320101391|ref|YP_004176983.1|   7 QLRQAVREsVWRKIEELGVADFPLPARGRIPNFKGAEEAaRRLislpeaasARVVFVNPDSPQAPLRRMLLEKGVLV 83 
                                       678777776******************************9999*******999************************ PP

                                       EEEEECSSCTEECEEEEEECCCCCCCCCHCTSSCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTHHHHHH CS
                    5-FTHF_cyc-lig  70 llPrvrlesgslkvvrlttlkeedslesgkyglkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGyyDrfl 146
                                       ++ ++r +sg++ ++   +++  +  +s+  g+ +  e+   ++al ++d+ + ++vA+++ GaRlGkG+Gy + ++
  gi|320101391|ref|YP_004176983.1|  84 VVSTPRISSGFILLDPRRIPRGLYHWASTIKGMVKLGEKVH-PSALPRIDMFIAGSVAVNRMGARLGKGEGYSELEY 159
                                       *********************99999998777666555555.45566****************************** PP

                                       HHHTS.T-SS--EEEEE--GGGEES..-----ST----SEEE-S CS
                    5-FTHF_cyc-lig 147 arlkg.gagdkpltvglaldeqlve..rlPleehDvpvdevvte 187
                                         l     +++++++++++++ +v   ++Pl ++D  vd+v t+
  gi|320101391|ref|YP_004176983.1| 160 GILTHyERLNEKTPIATTVHDIQVVdvDIPLKPWDFTVDIVATP 203
                                       *****9**************98887799*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1818.85
//
Query:       gi|320101392|ref|YP_004176984.1|  [L=174]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1234.49
//
Query:       gi|320101393|ref|YP_004176985.1|  [L=208]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   52.8   0.0    7.5e-14   52.2   0.0    1.2  1  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   4.2e-18   7.5e-14       7     106 ..      17     108 ..      10     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4.2e-18
                                       HHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCHHHHHH CS
                              ASCH   7 laslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.sleewrevh 82 
                                       +a +++sG+K+a+ir +  + p++    +++   +  g++++++++++v++++++++t+e+a +eg+ + +e++e++
  gi|320101393|ref|YP_004176985.1|  17 YAGKLLSGEKKATIRLGIVK-PRY---KEVI--VHAGGKPIAKARIRRVYYRRMRDLTDEEARLEGFkNRDELVEEL 87 
                                       999***************99.554...4555..5799**************************************** PP

                                       HCCHHHHHCCEEEEEEEEEEEEEE CS
                              ASCH  83 eefyeeeseeyedelvvveefelv 106
                                       +++y++ s+   d +++v e+e+v
  gi|320101393|ref|YP_004176985.1|  88 RRLYGDISG---DQYLTVLELEVV 108
                                       *******99...999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1506.32
//
Query:       gi|320101394|ref|YP_004176986.1|  [L=51]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0014   18.6   0.2     0.0016   18.3   0.2    1.1  1  Ogr_Delta       Ogr/Delta-like zinc finger
     0.0047   17.1   1.1     0.0072   16.5   1.1    1.4  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
     0.0078   16.5   2.4      0.017   15.4   2.4    1.5  1  zf-LITAF-like   LITAF-like zinc ribbon domain
  ------ inclusion threshold ------
      0.018   15.2   2.8       0.05   13.8   0.2    2.1  2  Ribosomal_L37e  Ribosomal protein L37e
      0.019   15.1   0.7       0.04   14.0   0.7    1.6  1  Zn-ribbon_8     Zinc ribbon domain
      0.021   14.5   1.6        3.8    7.2   0.2    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.023   14.3   1.8       0.28   10.9   0.1    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.028   14.4   0.1      0.035   14.1   0.1    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.029   13.8   1.5       0.28   10.7   0.1    2.1  2  zf-ribbon_3     zinc-ribbon domain
       0.06   13.3   0.0      0.064   13.2   0.0    1.1  1  RL              RL domain
       0.87    9.4   6.6        1.5    8.6   1.7    2.1  2  zinc_ribbon_2   zinc-ribbon domain
          1    9.3   5.6        4.9    7.1   0.8    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)


Domain annotation for each model (and alignments):
>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   1.1e-06    0.0016       1      36 [.       7      40 ..       7      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                         Ogr_Delta  1 rCPhCgapaaartsrnlskdvreryyqCsnfeCgat 36
                                      rC +Cg + +   s +l k  +++y+ Csn  Cg +
  gi|320101394|ref|YP_004176986.1|  7 RCRECGLEWRLLVSFPLKKEFKQLYHYCSN--CGKN 40
                                      799***************************..9976 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 !   16.5   1.1   4.9e-06    0.0072       7      37 ..       4      45 ..       1      51 [] 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.9e-06
                      NOB1_Zn_bind  7 wvlrChaCfk.........vtkd..mtkkFCpkCGnktLkrv 37
                                      wvlrC+ C           + k+  +  ++C++CG+++ + +
  gi|320101394|ref|YP_004176986.1|  4 WVLRCRECGLewrllvsfpLKKEfkQLYHYCSNCGKNSFHEI 45
                                      ********9867776655422433366789******998766 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 !   15.4   2.4   1.1e-05     0.017      46      64 ..      22      39 ..       2      43 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                     zf-LITAF-like 46 PfcvdslkdvehyCpnCga 64
                                      P + +++k+ +hyC+nCg+
  gi|320101394|ref|YP_004176986.1| 22 P-LKKEFKQLYHYCSNCGK 39
                                      3.5589***********97 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.16   2.3e+02      18      23 ..       7      12 ..       4      16 .. 0.80
   2 ?   13.8   0.2   3.3e-05      0.05      12      28 ..      27      43 ..      20      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                    Ribosomal_L37e 18 lCrrCg 23
                                      +Cr Cg
  gi|320101394|ref|YP_004176986.1|  7 RCRECG 12
                                      688888 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.3e-05
                    Ribosomal_L37e 12 kkktHilCrrCgkrsyh 28
                                       k+ +  C  Cgk+s+h
  gi|320101394|ref|YP_004176986.1| 27 FKQLYHYCSNCGKNSFH 43
                                      5668999********** 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   0.7   2.7e-05      0.04       6      35 ..       6      41 ..       1      46 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsis.dap...lta.CPeCgs.e 35
                                       rC+eCg e   l+s+  +++   l + C +Cg+  
  gi|320101394|ref|YP_004176986.1|  6 LRCRECGLEWRLLVSFPlKKEfkqLYHyCSNCGKnS 41
                                      69*********99999977778888888*****955 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0026       3.8      18      30 ..       2      14 ..       2      14 .. 0.90
   2 ?    6.6   0.1    0.0042       6.3       5      11 ..      33      39 ..      30      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0026
                     zf-NADH-PPase 18 ggwarvCpaCgle 30
                                      g w ++C  Cgle
  gi|320101394|ref|YP_004176986.1|  2 GYWVLRCRECGLE 14
                                      67*********97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0042
                     zf-NADH-PPase  5 FCgrCGa 11
                                      +C+ CG 
  gi|320101394|ref|YP_004176986.1| 33 YCSNCGK 39
                                      8999995 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00019      0.28      17      25 ..       5      13 ..       4      18 .. 0.87
   2 ?    3.1   0.2     0.051        76      20      25 ..      34      39 ..      32      43 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                                      ----SSS-- CS
                    DNA_RNApol_7kD 17 piRCkeCGh 25
                                      ++RC+eCG 
  gi|320101394|ref|YP_004176986.1|  5 VLRCRECGL 13
                                      58******5 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.051
                                      -SSS-- CS
                    DNA_RNApol_7kD 20 CkeCGh 25
                                      C +CG 
  gi|320101394|ref|YP_004176986.1| 34 CSNCGK 39
                                      666664 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   2.3e-05     0.035      70      98 ..       5      43 ..       3      49 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                      EEEETTTS-EEECHHHHH...........S-TTTSSS-EE CS
                              HypA 70 kvrCreCgkefeleekal...........rCpkCgsadve 98
                                      ++rCreCg e++l  + +            C +Cg+++++
  gi|320101394|ref|YP_004176986.1|  5 VLRCRECGLEWRLLVS-FplkkefkqlyhYCSNCGKNSFH 43
                                      579*********6543.223456789999******99876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.069     1e+02      19      24 ..       8      13 ..       7      14 .. 0.81
   2 ?   10.7   0.1   0.00019      0.28       4      11 ..      33      40 ..      31      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.069
                       zf-ribbon_3 19 CpyCGt 24
                                      C  CG 
  gi|320101394|ref|YP_004176986.1|  8 CRECGL 13
                                      999996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                       zf-ribbon_3  4 rCPnCGap 11
                                      +C+nCG++
  gi|320101394|ref|YP_004176986.1| 33 YCSNCGKN 40
                                      8*****97 PP

>> RL  RL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.064      16      39 ..      16      39 ..       4      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                RL 16 svLiscpskisekkllkylsqhGk 39
                                       +L+s p k+  k+l++y+s+ Gk
  gi|320101394|ref|YP_004176986.1| 16 RLLVSFPLKKEFKQLYHYCSNCGK 39
                                      58********************98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.041        61       1       6 [.       7      12 ..       7      14 .. 0.75
   2 ?    8.6   1.7     0.001       1.5       1       7 [.      33      39 ..      32      40 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.041
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +C +CG
  gi|320101394|ref|YP_004176986.1|  7 RCRECG 12
                                      588888 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.001
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +C+nCG+
  gi|320101394|ref|YP_004176986.1| 33 YCSNCGK 39
                                      5666665 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 ?    7.1   0.8    0.0033       4.9      30      39 .]       7      16 ..       4      16 .. 0.89
   2 ?    5.0   0.3     0.015        23      28      36 ..      31      39 ..      26      42 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0033
                           TFIIS_C 30 kCtkCghrWr 39
                                      +C +Cg +Wr
  gi|320101394|ref|YP_004176986.1|  7 RCRECGLEWR 16
                                      8********8 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.015
                           TFIIS_C 28 fykCtkCgh 36
                                      ++ C +Cg+
  gi|320101394|ref|YP_004176986.1| 31 YHYCSNCGK 39
                                      667888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 387.47
//
Query:       gi|320101395|ref|YP_004176987.1|  [L=611]
Description: threonyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-47  160.9   0.0      7e-47  158.9   0.0    1.9  2  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    2.3e-25   88.5   0.2    6.1e-25   87.2   0.2    1.8  1  HGTP_anticodon  Anticodon binding domain
      2e-14   53.9   0.3      5e-14   52.7   0.2    1.7  2  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 !  158.9   0.0   1.2e-50     7e-47       1     137 []       1     136 [.       1     136 [. 0.98
   2 ?   -1.2   0.0      0.32   1.9e+03      46      77 ..     341     372 ..     336     375 .. 0.83

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 1.2e-50
                                       -EEEEEEEEEEEEEEEEESSSS-...SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEE CS
                       tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae..eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvv 75 
                                       mrlLliha++++ye++k+a++e+e   e+  +g++e++lvvF++vEk+D+e   +vv  av+ei +v+++vka+++v
  gi|320101395|ref|YP_004176987.1|   1 MRLLLIHARRFSYEVVKPAVEEPEplGEAGGSGAFENTLVVFTSVEKGDDE---SVVPGAVSEILSVFNQVKASSIV 74 
                                       9***********************88889999*******************...9********************** PP

                                       EEE-STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                       tRNA-Thr_ED  76 lypyaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                       +ypyaHLs++la+p  a++il +l+++lke+g+e ++aPFGwyk+f+++c+GhpL+elsr++
  gi|320101395|ref|YP_004176987.1|  75 VYPYAHLSQDLAPPFEAVKILGRLYAALKEAGVEAYKAPFGWYKAFTLECYGHPLSELSRSV 136
                                       ************************************************************85 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.32
                                       T--H...HHHHHHHHHHHHHHHHHT-SEEEEE CS
                       tRNA-Thr_ED  46 eDeeekekvvekavkeikkvakkvkakkvvly 77 
                                       +D +e+ +v  ++ ++i++ a kv+ + v ly
  gi|320101395|ref|YP_004176987.1| 341 RDINEAIEVSMRVQSKIHEEAGKVGRSYVALY 372
                                       67777788999999999999999999999999 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.2     1e-28   6.1e-25       1      92 [.     496     584 ..     496     586 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 1e-28
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       q+ vip+++   e+ e a k+a eL   g+rv++dd++e++gkkir+a + ++p+++v+Ge+e+ +gt++vr r + 
  gi|320101395|ref|YP_004176987.1| 496 QARVIPVSR---EFNEHAFKVAGELASRGFRVDVDDRDETLGKKIRDAGREWVPYIIVIGEREVATGTLNVRVRRSN 569
                                       789******...9**************************************************************** PP

                                       EEEEEETTHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklk 92 
                                       +q  + l+e+++ l 
  gi|320101395|ref|YP_004176987.1| 570 DQKVMRLEEFIDLLN 584
                                       ***********9986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.1   6.4e+03      86     106 ..     230     250 ..     217     264 .. 0.64
   2 !   52.7   0.2   8.4e-18     5e-14       2     177 ..     271     474 ..     270     476 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHTT.SCEEEEEEGT CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  86 aisriferlglefraiielms 106
                                           + ++lg++++++++++ 
  gi|320101395|ref|YP_004176987.1| 230 YSWMVAQSLGIPVFKVMGSNM 250
                                       333456889999999999965 PP

  == domain 2  score: 52.7 bits;  conditional E-value: 8.4e-18
                                       EEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   2 kledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeasld 77 
                                        ++ + +++++L+  +++   ++ rd+v+  k++P+  +++   yR E++ ++   +R+r+F + d ++   +  ++
  gi|320101395|ref|YP_004176987.1| 271 EVQLD-EDRFVLRYAACHQQFAMLRDWVISYKEMPFGAFEVADSYRLEQRgELALCFRLRKFYMPDLHILTRD--IN 344
                                       55545.489******************888899*****************7888779************9874..46 PP

                                       HHHHHHHHHHHHHHHHT...T.SCEEEEEEGTTSCBTTSEEEEEEEEETT..........................T CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................x RF
                      tRNA-synt_2b  78 dslrdlikaisriferl...glefraiielmsaksadykdkkefeavses..........................l 125
                                       + ++  +++ s+i e+    g ++ a+ ++++++  +y dk++  +  e+                          l
  gi|320101395|ref|YP_004176987.1| 345 EAIEVSMRVQSKIHEEAgkvGRSYVALYNITDEFLEKYRDKLVEFVKREKypvllavipsgiyywvlnveyhivdnL 421
                                       7777778888888887722245556666667766666666666555555588888888888888888888888888* PP

                                       SEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxx RF
                      tRNA-synt_2b 126 tkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaile 177
                                       ++ +ei+t q +  +   r+++t++de+++++++++i+ a +g veR + ++l+
  gi|320101395|ref|YP_004176987.1| 422 NRPREIATFQID-VGNGARFNITYVDEKGEKHHPVIIHTAiLGgVERYIYMVLD 474
                                       ************.999************************9999*****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4470.41
//
Query:       gi|320101396|ref|YP_004176988.1|  [L=329]
Description: DNA repair and recombination protein RadA [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-96  321.7   0.0    3.4e-96  321.4   0.0    1.1  1  Rad51       Rad51
    7.3e-18   65.0   0.0    9.6e-18   64.6   0.0    1.1  1  RecA        recA bacterial DNA recombination protein
    5.1e-11   42.4   0.0      8e-11   41.7   0.0    1.4  1  ATPase      KaiC
    1.1e-09   38.2   0.0      4e-09   36.3   0.0    1.8  2  AAA_25      AAA domain
    0.00044   20.8   0.1     0.0015   19.1   0.1    2.0  1  HHH_5       Helix-hairpin-helix domain
      0.002   18.2   0.2      0.087   12.9   0.1    2.5  2  Sigma70_r3  Sigma-70 region 3
     0.0026   18.0   0.3       0.26   11.7   0.0    3.2  3  HTH_31      Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.035   13.8   0.0    1.7  1  AAA_24      AAA domain
      0.029   14.7   0.0       0.12   12.8   0.0    2.1  1  IMS_HHH     IMS family HHH motif
      0.054   13.7   0.0       0.11   12.8   0.0    1.4  1  Cdd1        Pathogenicity locus
      0.056   14.0   0.0       0.15   12.6   0.0    1.8  1  AAA_18      AAA domain
      0.058   13.5   0.1         28    4.9   0.0    3.7  3  HTH_3       Helix-turn-helix
      0.093   13.0   0.0        0.2   11.9   0.0    1.6  1  AAA_22      AAA domain
       0.11   13.0   0.0       0.38   11.3   0.0    1.8  2  ABC_tran    ABC transporter
       0.12   12.2   0.0       0.83    9.5   0.0    2.3  2  IF2_N       Translation initiation factor IF-2, N-terminal re
       0.16   12.2   0.1         16    5.8   0.1    2.4  2  LPD22       Large polyvalent protein associated domain 22


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 !  321.4   0.0   3.1e-99   3.4e-96       2     254 ..      77     325 ..      76     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 321.4 bits;  conditional E-value: 3.1e-99
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                       +f +a e+ ++r ++ ++ttGs++lDelLgGG+et++ite +Ge++sGktqlch+l+v vqlple+gG eg+avyid
  gi|320101396|ref|YP_004176988.1|  77 TFKTAREVKQERLNIRKITTGSRSLDELLGGGVETKTITEFYGEYGSGKTQLCHQLSVNVQLPLEKGGLEGRAVYID 153
                                       6899************************************************************************* PP

                                       SSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------T CS
                             Rad51  79 tegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgel 155
                                       tegtfr er+ ++a   +ld+++v++n+ y Ray+++hq ++++++ + + +++++l++vDsvt+++R+++ gr+ l
  gi|320101396|ref|YP_004176988.1| 154 TEGTFRWERIEAMARALGLDPDKVMDNIYYMRAYNSDHQISIVDELFTFIPKNNVKLVVVDSVTSHFRAEYPGRDHL 230
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEE CS
                             Rad51 156 akRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkv 232
                                       a+Rqqkl+ +l++L +la+ ++vavv+tnqv+a++d     f +dp++ +gG+vlah+  +R++l+k kg++Ri++v
  gi|320101396|ref|YP_004176988.1| 231 AERQQKLNSHLHQLVRLAEAYNVAVVVTNQVMARPDI----FYGDPTIAVGGHVLAHTPGVRVQLKKSKGNKRIARV 303
                                       ************************************9....************************************ PP

                                       ES-SSS-S-EEEEEEETTEEE- CS
                             Rad51 233 vdsPnlpeleavfaigeeGied 254
                                       vd+P+lpe eavf+i eeGi d
  gi|320101396|ref|YP_004176988.1| 304 VDAPHLPEGEAVFVILEEGIRD 325
                                       ********************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 !   64.6   0.0   8.6e-21   9.6e-18      25     227 ..      85     299 ..      62     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 8.6e-21
                                       --.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...HTT...--EEEEESS----. CS
                              RecA  25 ekeklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...kkg...gvaafidaehald. 94 
                                       ++e+l++  i++Gs +ld  lG GG+    i+e yG   sGkt l+ ++ +++q   +kg   g a++id+e ++  
  gi|320101396|ref|YP_004176988.1|  85 KQERLNIRKITTGSRSLDELLG-GGVETKTITEFYGEYGSGKTQLCHQLSVNVQlplEKGgleGRAVYIDTEGTFRw 160
                                       566899****************.**********************999988888555455133679******99862 PP

                                       ...HHHHHHTT--....GGG-EEE--SSHHHHHHHHHHH...HTTT--SEEEEE-TTT---STT-----------HH CS
                              RecA  95 ...pkyakklGvd....idellvsqpdtGeqaleiadal...vrsgaidlivvdsvaalvpkaeieGemgdskvglq 161
                                           + a++lG+d    +d+++  +  + ++ + i+d l   +  + + l+vvdsv++   +ae  G   d+    q
  gi|320101396|ref|YP_004176988.1| 161 eriEAMARALGLDpdkvMDNIYYMRAYNSDHQISIVDELftfIPKNNVKLVVVDSVTSH-FRAEYPG--RDHLAERQ 234
                                       2224689*****9555556778899999*********873336789**********986.5999999..47778888 PP

                                       HHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES---- CS
                              RecA 162 arlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieeike 227
                                        +l s+ l +l    +  n++v+  nq+  +  + +g+p ++ GG+ l     vr+++++++  k+
  gi|320101396|ref|YP_004176988.1| 235 QKLNSH-LHQLVRLAEAYNVAVVVTNQVMARPDIFYGDPTIAVGGHVLAHTPGVRVQLKKSKGNKR 299
                                       888876.89999999********************************************9876655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   7.2e-14     8e-11       2     178 ..      95     283 ..      94     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 7.2e-14
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikg...aekyge..pgvfvtveepa..edlrenakslG 71 
                                        tg   lDe+l gG+  ++++  +Ge+G+GKt ++ q  ++    +ek g   + v++ +e +   e +   a++lG
  gi|320101396|ref|YP_004176988.1|  95 TTGSRSLDELLGGGVETKTITEFYGEYGSGKTQLCHQLSVNVqlpLEKGGLegRAVYIDTEGTFrwERIEAMARALG 171
                                       699999********************************99962223444431156999999988889********** PP

                            ATPase  72 wdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.aye........ekeav 139
                                        d +k+ ++  ++++ a++s+++           ++++el + i + ++k vv+Ds+t++   e        e++++
  gi|320101396|ref|YP_004176988.1| 172 LDPDKVMDN--IYYMRAYNSDHQ----------ISIVDELFTFIPKNNVKLVVVDSVTSHfRAEypgrdhlaERQQK 236
                                       *********..999999999766..........46788888899999***********9953222222222256788 PP

                            ATPase 140 aReilrqlvrvlkklgvTailvsekss........seeaaggygvee 178
                                       + + l+qlvr  + ++v  + ++++             a+gg+ +++
  gi|320101396|ref|YP_004176988.1| 237 LNSHLHQLVRLAEAYNVAVVVTNQVMArpdifygdPTIAVGGHVLAH 283
                                       88999999999999999999999976655555543334445555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2   1.3e+03     164     186 ..      41      63 ..      37      66 .. 0.85
   2 !   36.3   0.0   3.6e-12     4e-09       3     188 ..      82     260 ..      80     263 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                            AAA_25 164 dvgalvealeriarrtgaavllv 186
                                       +++ +v++ e++a++tg  vl v
  gi|320101396|ref|YP_004176988.1|  41 AWSIVVARPEELAEKTGLPVLTV 63 
                                       5678899999********99988 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 3.6e-12
                            AAA_25   3 eplelsavsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsa 79 
                                       ++++ + + ++++ +  ++++ l++g +  ++++ ++G  g+GKt l+ +l++ v +  +         g+ +y+++
  gi|320101396|ref|YP_004176988.1|  82 REVKQERLNIRKITTGSRSLDELLGGGVETKTITEFYGEYGSGKTQLCHQLSVNVQLPLEKG----GLEGRAVYIDT 154
                                       556666677888999999999****999****************************644322....368******** PP

                            AAA_25  80 EdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralg 156
                                       E++  ++ +R++a+ +al +d +    ++     ++ +   +++++  + vd+l   i + ++v+lvv+D++++ ++
  gi|320101396|ref|YP_004176988.1| 155 EGTF-RW-ERIEAMARALGLDPDKVMDNI---YYMRAY--NSDHQI--SIVDELFTFIPK-NNVKLVVVDSVTSHFR 221
                                       ***9.44.689999999944444333332...222323..234444..567889999999.89***********998 PP

                            AAA_25 157 g.....densnsd..vgalvealeriarrtgaavllvhH 188
                                       +     d  ++++   ++ + +l r+a+++++av+++ +
  gi|320101396|ref|YP_004176988.1| 222 AeypgrDHLAERQqkLNSHLHQLVRLAEAYNVAVVVTNQ 260
                                       8766565555555445999****************9866 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.4e-06    0.0015       2      57 .]      17      72 ..      16      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                                      HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                        + s++G+G ++A +l  aG+ s   ++ a +eeLa+ +G+   t++++i+++++
  gi|320101396|ref|YP_004176988.1| 17 ITVRSLPGVGSAIADKLEAAGYVSAWSIVVARPEELAEKTGLPVLTVQKVIEAARK 72
                                      56779*************************************************97 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   7.8e-05     0.087      21      48 ..      47      74 ..      46      87 .. 0.91
   2 ?    2.6   0.0      0.13   1.4e+02      24      49 ..     164     189 ..     162     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.8e-05
                                      XXHHHHHHHHTXXHHHHHHHHHHHXXXE CS
                        Sigma70_r3 21 PtpeEiAeeLglseekVrevleaarepv 48
                                      + peE+Ae++gl++  V++v+eaar+++
  gi|320101396|ref|YP_004176988.1| 47 ARPEELAEKTGLPVLTVQKVIEAARKAL 74
                                      679*********************9875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                                       HHHHHHHTXXHHHHHHHHHHHXXXEE CS
                        Sigma70_r3  24 eEiAeeLglseekVrevleaarepvS 49 
                                       e  A +Lgl+++kV + +   r ++S
  gi|320101396|ref|YP_004176988.1| 164 EAMARALGLDPDKVMDNIYYMRAYNS 189
                                       6689**********987777777666 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.7   3.1e+03      16      34 ..      48      66 ..      47      73 .. 0.73
   2 !   11.7   0.0   0.00023      0.26      41      60 ..     157     176 ..     147     178 .. 0.88
   3 ?    2.4   0.0      0.18   2.1e+02      44      60 ..     241     257 ..     229     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.7
                            HTH_31 16 sqeevAerlgvsestlsrl 34
                                      + ee+Ae +g+ + t+ ++
  gi|320101396|ref|YP_004176988.1| 48 RPEELAEKTGLPVLTVQKV 66
                                      5689999999877666665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00023
                            HTH_31  41 rpspavlealaralgldpae 60 
                                         +++ +ea+aralgldp+ 
  gi|320101396|ref|YP_004176988.1| 157 TFRWERIEAMARALGLDPDK 176
                                       479**************996 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.18
                            HTH_31  44 pavlealaralgldpae 60 
                                       +++l +la+a+++ +  
  gi|320101396|ref|YP_004176988.1| 241 LHQLVRLAEAYNVAVVV 257
                                       6899********98765 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   3.1e-05     0.035       8      78 ..     118     220 ..     112     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                            AAA_24   8 yGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvel....... 59 
                                       yG+ g+GKT l+ +l             + ++++idte+ + + + ++            ++++d + +        
  gi|320101396|ref|YP_004176988.1| 118 YGEYGSGKTQLCHQLsvnvqlplekgglEGRAVYIDTEGTF-RWERIEAM--AralglDPDKVMDNIYYMraynsdh 191
                                       9**************99999999999999999999999854.33333322..2456775566666666666666666 PP

                            AAA_24  60 ..........aaeladyktlviDtidele 78 
                                                    +++ k +v+D+++   
  gi|320101396|ref|YP_004176988.1| 192 qisivdelftFIPKNNVKLVVVDSVTSHF 220
                                       66666666764455557888888888654 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011      0.12      13      31 ..      19      37 ..      15      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                           IMS_HHH 13 itkipGiGgklgekLeklG 31
                                      ++++pG+G+  ++kLe+ G
  gi|320101396|ref|YP_004176988.1| 19 VRSLPGVGSAIADKLEAAG 37
                                      89**************998 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.5e-05      0.11       4      44 ..      15      55 ..      12      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-05
                              Cdd1  4 alkelqdiPniGkalaedlvelGirsveelkgedpeelyek 44
                                      ++ + +++P++G a+a++l + G+ s   +    peel ek
  gi|320101396|ref|YP_004176988.1| 15 EFITVRSLPGVGSAIADKLEAAGYVSAWSIVVARPEELAEK 55
                                      5567789*****************************99887 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   0.00014      0.15       5      91 ..     119     225 ..     116     258 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                            AAA_18   5 GtpGvGKttlakeLskrlgf.......gvnlrdvakenglllevdpealdeskrldedkldklldaleenss..... 69 
                                       G  G+GKt+l++ Ls   ++         +   + +e+  ++e+ ++   + + ld dk++ ++  +++ +s     
  gi|320101396|ref|YP_004176988.1| 119 GEYGSGKTQLCHQLSVNVQLplekgglEGRAVYIDTEGTFRWERIEA-MARALGLDPDKVMDNIYYMRAYNSdhqis 194
                                       667***********776555777774433333344444444444444.45555555555444444444444444444 PP

                            AAA_18  70 .........aleegknlvidghlaeleseaa 91 
                                                   + k +v+d++ ++++ e+ 
  gi|320101396|ref|YP_004176988.1| 195 ivdelftfiPKNNVKLVVVDSVTSHFRAEYP 225
                                       577777777556778889****999998875 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.025        28      13      31 ..      50      68 ..      48      79 .. 0.84
   2 ?    3.1   0.0     0.092     1e+02      39      54 ..     161     176 ..     161     177 .. 0.88
   3 ?    0.1   0.0      0.78   8.8e+02      41      50 ..     244     253 ..     240     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                                      HHHHHHHTSSHHHHHHHHT CS
                             HTH_3 13 eeLAeklGvsrstisriEn 31
                                      eeLAek+G+++ t+++ + 
  gi|320101396|ref|YP_004176988.1| 50 EELAEKTGLPVLTVQKVIE 68
                                      89*******9999998765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHTSEHHH CS
                             HTH_3  39 etlkklakaLgvslde 54 
                                       e+++++a+aLg+++d 
  gi|320101396|ref|YP_004176988.1| 161 ERIEAMARALGLDPDK 176
                                       6899********9986 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.78
                                       HHHHHHHHTS CS
                             HTH_3  41 lkklakaLgv 50 
                                       l++la+a++v
  gi|320101396|ref|YP_004176988.1| 244 LVRLAEAYNV 253
                                       899******9 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   0.00018       0.2       4     101 ..     111     217 ..     109     260 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka......... 70 
                                       t++i+  +Ge G+GKT l+ +l  + +  +  +   + + v+++  +   ++ + ++++ralgl+ ++         
  gi|320101396|ref|YP_004176988.1| 111 TKTITEFYGEYGSGKTQLCHQLSVNVQL-PLEKGgLEGRAVYIDTEGTFRWERI-EAMARALGLDPDKvmdniyymr 185
                                       7889999***************998743.3333369999999999999988888.9999999999888777777775 PP

                            AAA_22  71 ..erlsseell.ealeqalraravielliiDEaq 101
                                         +  + +  + + l   + +  v +l+++D + 
  gi|320101396|ref|YP_004176988.1| 186 ayN-SDHQISIvDELFTFIPKNNV-KLVVVDSVT 217
                                       532.22222222334344444444.566666554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   2.3e+03      80     107 ..      62      92 ..       4     105 .. 0.64
   2 ?   11.3   0.0   0.00034      0.38       8     120 ..     109     248 ..     101     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                                       HHHTCHHHHHHHSTTGGTTCBGESTTS...G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                          ABC_tran  80 esdeeiekalsklglkelkdtvvkssp...s 107
                                       + ++ ie+a++ lg++ ++++ vk++    +
  gi|320101396|ref|YP_004176988.1|  62 TVQKVIEAARKALGITFKTAREVKQERlniR 92 
                                       4455588888888888888887776654445 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00034
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren.. 79 
                                       ++  +++ + Ge G+GK+ L+  l+ +++   ++G +  +g+ +   +e ++  ++i+ +     l+p++ v +n  
  gi|320101396|ref|YP_004176988.1| 109 VETKTITEFYGEYGSGKTQLCHQLSVNVQLplEKGGL--EGRAVYIdTEGTFRWERIEAMARALGLDPDK-VMDNiy 182
                                       77889999*****************999985555555..7777766446666668888999999999999.888888 PP

                                       ......................HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHH CS
                                       ......................xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ......................esdee...iekalsklglkelkdtvvksspssLSgGqkqrvala 120
                                                             + +++   ++ + s+++ ++   +++ +++++L     q v la
  gi|320101396|ref|YP_004176988.1| 183 ymraynsdhqisivdelftfipKNNVKlvvVDSVTSHFRAEYPGRDHLAERQQKLNSHLHQLVRLA 248
                                       888875555555555555555422222444666666666666666666555566655555555555 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 ?    9.5   0.0   0.00074      0.83       6      35 ..      49      81 ..      47      84 .. 0.91
   2 ?   -1.0   0.0       1.4   1.6e+03       5      21 ..     162     178 ..     162     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00074
                             IF2_N  6 VyeLAkeLg...vkskevikkLfkelGievksh 35
                                        eLA++ g   +++++vi+ + k lGi+ k++
  gi|320101396|ref|YP_004176988.1| 49 PEELAEKTGlpvLTVQKVIEAARKALGITFKTA 81
                                      579******9999****************9997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                             IF2_N   5 rVyeLAkeLgvkskevi 21 
                                       r+   A+ Lg+++ +v+
  gi|320101396|ref|YP_004176988.1| 162 RIEAMARALGLDPDKVM 178
                                       677889*******9998 PP

>> LPD22  Large polyvalent protein associated domain 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.014        16      18      46 ..      46      74 ..      45      91 .. 0.83
   2 ?    3.9   0.0     0.056        63      20      42 ..     162     184 ..     161     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                             LPD22 18 aAralrlaeelGlppdvvernleaferaa 46
                                      +Ar ++lae++Glp   v++ +ea+++a 
  gi|320101396|ref|YP_004176988.1| 46 VARPEELAEKTGLPVLTVQKVIEAARKAL 74
                                      6999**************99998887765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.056
                             LPD22  20 ralrlaeelGlppdvvernleaf 42 
                                       r++++a++lGl+pd v +n+  +
  gi|320101396|ref|YP_004176988.1| 162 RIEAMARALGLDPDKVMDNIYYM 184
                                       67899************997544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2383.01
//
Query:       gi|320101397|ref|YP_004176989.1|  [L=309]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-24   84.7   0.0    1.1e-23   84.3   0.0    1.2  1  ABC_tran     ABC transporter
    2.9e-15   56.9   0.0    6.3e-10   39.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.7e-09   37.5   0.1     0.0004   19.9   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00014   21.6   0.0    0.00027   20.6   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00056   19.7   0.0      0.015   15.1   0.0    2.3  2  IstB_IS21    IstB-like ATP binding protein
    0.00066   19.5   0.0       0.36   10.5   0.0    2.1  2  AAA_15       AAA ATPase domain
     0.0016   18.8   0.1     0.0042   17.5   0.1    1.7  1  AAA_16       AAA ATPase domain
     0.0076   16.2   0.0      0.014   15.3   0.0    1.3  1  ATPase_2     ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.011   15.5   0.2      0.091   12.5   0.0    2.1  3  AAA_30       AAA domain
      0.014   15.9   0.0      0.022   15.2   0.0    1.2  1  AAA_23       AAA domain
       0.02   15.2   0.1      0.036   14.4   0.1    1.6  1  AAA_22       AAA domain
       0.02   15.1   0.1      0.045   13.9   0.1    1.6  1  AAA_33       AAA domain
      0.023   14.6   0.0      0.045   13.7   0.0    1.5  1  NACHT        NACHT domain
      0.033   14.1   0.0       0.11   12.5   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
      0.038   13.1   0.0      0.056   12.5   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
      0.044   13.2   0.1       0.26   10.7   0.0    2.0  3  PhoH         PhoH-like protein
      0.047   13.3   0.0      0.076   12.6   0.0    1.3  1  AAA_27       AAA domain
      0.056   12.6   0.4       0.14   11.4   0.0    1.7  3  NB-ARC       NB-ARC domain
      0.064   12.8   0.0       0.46   10.0   0.0    2.1  2  AAA_25       AAA domain
      0.085   11.6   0.1       0.19   10.5   0.0    1.5  2  Adeno_IVa2   Adenovirus IVa2 protein
      0.094   12.3   0.0       0.15   11.6   0.0    1.3  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.13   11.1   0.0       0.19   10.5   0.0    1.1  1  DLIC         Dynein light intermediate chain (DLIC)
       0.14   12.1   0.0       0.26   11.3   0.0    1.4  1  AAA_14       AAA domain
       0.23   11.5   0.3       0.62   10.2   0.2    1.7  2  MMR_HSR1     50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   1.4e-26   1.1e-23       1     137 []      25     165 ..      25     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.4e-26
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ vsl++++ e+va++G+nG+GKStLl+ ++gl+kp +G ++l g++ ++     +  +i++lp+ ++l p +t  
  gi|320101397|ref|YP_004176989.1|  25 LRGVSLSIEKREVVAVMGPNGSGKSTLLRSVIGLEKPSKGFVRLLGTEPQD-----ALGKIAYLPEADCLAPYMTGL 96 
                                       678****************************************99999999.....99*****************99 PP

                                       HH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en             + +++  ++++lgl+ l+ +++    +++S G+k+ +a+  +l+ +++l+++DEpta
  gi|320101397|ref|YP_004176989.1|  97 ENavflagltglgrGYLDKAVSVAEELGLSRLDLKRL---VKKYSMGMKRLLAISLLLAMDRELYIMDEPTA 165
                                       999********99988888999999999999766665...6*****************************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 !   15.5   0.0   1.5e-05     0.011       3      21 ..      39      57 ..      37      86 .. 0.81
   2 !   39.4   0.0   8.4e-13   6.3e-10     236     297 ..     136     194 ..     110     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldl 21
                                      ++ GpNgsGKS+LL+   +
  gi|320101397|ref|YP_004176989.1| 39 AVMGPNGSGKSTLLRSVIG 57
                                      678***********97744 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 8.4e-13
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       + S+G+krlla+ ++l+ ++    l++ DEp +gL+P   +++le + ++++nga v++tTH
  gi|320101397|ref|YP_004176989.1| 136 KYSMGMKRLLAISLLLAMDR---ELYIMDEPTAGLDPVKRPSVLEAFHAAKSNGATVVFTTH 194
                                       45*******99999999999...9***********************777778********* 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   0.0   1.1e-05    0.0082      24      44 ..      35      55 ..      23      63 .. 0.84
   2 !   19.9   0.0   5.4e-07    0.0004     137     210 ..     137     207 ..     113     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                      +++ a++GpNGSGKs ll ++
  gi|320101397|ref|YP_004176989.1| 35 REVVAVMGPNGSGKSTLLRSV 55
                                      56899************9887 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.4e-07
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvg 210
                                        S G k L+a++Ll+A+ +     ly++De  a LD  ++  v e ++++++n a ++ +++     ekadk+v 
  gi|320101397|ref|YP_004176989.1| 137 YSMGMKRLLAISLLLAMDR----ELYIMDEPTAGLDPVKRPSVLEAFHAAKSNgATVVFTTHIGVDAEKADKVVF 207
                                       589*************976....5************************777774777778888888899988875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.6e-07   0.00027      14      42 ..      27      55 ..      23      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-07
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAi 42
                                      g +++i+ ++++ ++Gp+GsGKSTll ++
  gi|320101397|ref|YP_004176989.1| 27 GVSLSIEKREVVAVMGPNGSGKSTLLRSV 55
                                      6778899999***************9655 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 !   15.1   0.0     2e-05     0.015      24      64 ..      11      52 ..       1      66 [. 0.82
   2 ?    2.5   0.0      0.14   1.1e+02      48      70 ..      98     120 ..      90     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                         IstB_IS21 24 fraarsldkrkvkeLatlsf.iekkenivllGpsGvGKshla 64
                                      + + r+l+ + v++L++ s  iek+e ++++Gp G GKs l 
  gi|320101397|ref|YP_004176989.1| 11 WVEYRGLHDKPVQALRGVSLsIEKREVVAVMGPNGSGKSTLL 52
                                      667899999*******999669****************9874 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                       +++ l G +G G+ +l  a++v+
  gi|320101397|ref|YP_004176989.1|  98 NAVFLAGLTGLGRGYLDKAVSVA 120
                                       567899**********9998754 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   0.00048      0.36      17      41 ..      28      53 ..      23      66 .. 0.82
   2 !    7.0   0.0    0.0057       4.2     294     364 ..     134     194 ..     116     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsile 41
                                      v++++++  +  + G+N+sGKS++l+
  gi|320101397|ref|YP_004176989.1| 28 VSLSIEKReVVAVMGPNGSGKSTLLR 53
                                      55666665699*************97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0057
                            AAA_15 294 lnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++k + G++rll ++ll+++ ++         +++++EP a L p    ++ +++  + +++   v++tTH
  gi|320101397|ref|YP_004176989.1| 134 VKKYSMGMKRLLAISLLLAMDRE---------LYIMDEPTAGLDPVKRPSVLEAFHAAKSNGA-TVVFTTH 194
                                       678899*********99876555.........5******************999987766665.9*****9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.7e-06    0.0042      25      63 ..      36      75 ..      19     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.7e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekd.ggif.lrgkcdql 63
                                      e+v + G+ G+GKs+l+r++   lek  +g++ l g+  q 
  gi|320101397|ref|YP_004176989.1| 36 EVVAVMGPNGSGKSTLLRSVIG-LEKPsKGFVrLLGTEPQD 75
                                      89*****************994.555524666666666666 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 !   15.3   0.0   1.8e-05     0.014      17      44 ..      32      59 ..      23      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienl 44
                                       e++e++ + Gp gsGK++Ll+ +i   
  gi|320101397|ref|YP_004176989.1| 32 IEKREVVAVMGPNGSGKSTLLRSVIGLE 59
                                      57899******************99765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.091      16      45 ..      33      62 ..      21      81 .. 0.79
   2 ?   -1.1   0.0       1.7   1.3e+03      61     121 ..     118     191 ..     111     196 .. 0.59
   3 ?   -0.3   0.0         1   7.7e+02      51      81 ..     180     210 ..     171     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa 45
                                      +++ v+++ Gp G+GK+t+l+++  + + +
  gi|320101397|ref|YP_004176989.1| 33 EKREVVAVMGPNGSGKSTLLRSVIGLEKPS 62
                                      56789****************997766655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                            AAA_30  61 vLaeelgieastiakllkrlk.........grarlepgtllivDEagmv....dtkqlaallkaaekagakvil 121
                                        +aeelg+    +++l+k++          +     +++l+i DE           ++ + + aa+++ga+v++
  gi|320101397|ref|YP_004176989.1| 118 SVAEELGLSRLDLKRLVKKYSmgmkrllaiSLLLAMDRELYIMDEPTAGldpvKRPSVLEAFHAAKSNGATVVF 191
                                       56666666666666666666666777776633333455888888844322222555555556666666666665 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1
                            AAA_30  51 glAptgkaAkvLaeelgieastiakllkrlk 81 
                                        +A ++ a  v ++++g++a+  +k++  + 
  gi|320101397|ref|YP_004176989.1| 180 HAAKSNGATVVFTTHIGVDAEKADKVVFMHS 210
                                       5788888999999999999999999998877 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     3e-05     0.022      19      37 ..      35      53 ..      20      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                            AAA_23 19 kgltlItGpNGaGKTTild 37
                                      + ++++ GpNG+GK+T+l+
  gi|320101397|ref|YP_004176989.1| 35 REVVAVMGPNGSGKSTLLR 53
                                      4688999**********97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.8e-05     0.036       4      28 ..      34      58 ..      31     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      ++ +++v+G+ G+GK+tllr +   
  gi|320101397|ref|YP_004176989.1| 34 KREVVAVMGPNGSGKSTLLRSVIGL 58
                                      67889***************98755 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.1e-05     0.045       1      20 [.      37      56 ..      37      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      +v + G++GsGKstl+++++
  gi|320101397|ref|YP_004176989.1| 37 VVAVMGPNGSGKSTLLRSVI 56
                                      7899*************985 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   6.1e-05     0.045       2      21 ..      37      56 ..      36      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      +v++ G++GsGK+tLl++++
  gi|320101397|ref|YP_004176989.1| 37 VVAVMGPNGSGKSTLLRSVI 56
                                      799**************987 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   0.00014      0.11      96     121 ..      31      57 ..       8      67 .. 0.80
   2 ?   -1.9   0.0       3.6   2.7e+03     100     118 ..      98     116 ..      85     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                       HCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallp 121
                                        +++ ++++++G+ G GKStL+ ++++
  gi|320101397|ref|YP_004176989.1|  31 SIEKrEVVAVMGPNGSGKSTLLRSVIG 57 
                                       55555899**************99876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                                       SEEEEECSTTSSHHHHHHH CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLina 118
                                       + ++l+G +G G+  L +a
  gi|320101397|ref|YP_004176989.1|  98 NAVFLAGLTGLGRGYLDKA 116
                                       5667788888887655444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.5e-05     0.056     120     151 ..      26      57 ..       3      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-05
                             T2SSE 120 evlrkavrerglilvsGgTgsGKttllyallk 151
                                       + ++ ++++r ++ v G+ gsGK+tll +++ 
  gi|320101397|ref|YP_004176989.1|  26 RGVSLSIEKREVVAVMGPNGSGKSTLLRSVIG 57 
                                       55678999*******************98875 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00035      0.26      15      83 ..      31      96 ..      21     103 .. 0.71
   2 ?   -0.1   0.0      0.73   5.5e+02      20      41 ..      98     119 ..      87     134 .. 0.78
   3 ?   -1.0   0.0       1.3     1e+03      58      82 ..     116     140 ..     112     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                                      HHHH-SEEEEE--TTSST.THHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHH CS
                              PhoH 15 alkkndivfaiGpaGtGK.tylavalavealkkkkvkriiltrpaveageelGflpgdleekvdpylrpl 83
                                      +++k ++v ++Gp G+GK t+l  ++++e  +k+ v r++ t p+   g ++ +lp   ++ ++py+  l
  gi|320101397|ref|YP_004176989.1| 31 SIEKREVVAVMGPNGSGKsTLLRSVIGLEKPSKGFV-RLLGTEPQDALG-KIAYLPE--ADCLAPYMTGL 96
                                      68899*************567778888887766654.666666665544.4666665..56666666655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.73
                                       SEEEEE--TTSSTTHHHHHHHH CS
                              PhoH  20 divfaiGpaGtGKtylavalav 41 
                                       + vf +G +G G+ yl  a+ v
  gi|320101397|ref|YP_004176989.1|  98 NAVFLAGLTGLGRGYLDKAVSV 119
                                       6799999999999999766655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.3
                                       S--TT----SS---------TTTHH CS
                              PhoH  58 aveageelGflpgdleekvdpylrp 82 
                                       av++ eelG    dl+  v+ y   
  gi|320101397|ref|YP_004176989.1| 116 AVSVAEELGLSRLDLKRLVKKYSMG 140
                                       78999***********999999765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.076      20      47 ..      29      56 ..      24      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            AAA_27 20 dfsaeeadlhliyGpNEAGKstalrAis 47
                                      ++s e++++  ++GpN +GKst+lr++ 
  gi|320101397|ref|YP_004176989.1| 29 SLSIEKREVVAVMGPNGSGKSTLLRSVI 56
                                      56667899999*************9975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.14      17      41 ..      34      56 ..      19      64 .. 0.83
   2 ?   -3.4   0.0       5.9   4.4e+03      22      40 ..      99     117 ..      96     135 .. 0.81
   3 ?   -2.3   0.0       2.7     2e+03     122     138 ..     177     193 ..     116     210 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      TSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqil 41
                                      +    vva++G  G+GK+tl+++++
  gi|320101397|ref|YP_004176989.1| 34 KR--EVVAVMGPNGSGKSTLLRSVI 56
                                      34..49***************9985 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.9
                                       EEEEEESTTSSHHHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqi 40 
                                        v+l G  G+G+  l k +
  gi|320101397|ref|YP_004176989.1|  99 AVFLAGLTGLGRGYLDKAV 117
                                       5899999999998876655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.7
                                       ..HHHHCHTTSEEEEEE CS
                            NB-ARC 122 gvvlparenrlrvllTT 138
                                        +   a++n+  v++TT
  gi|320101397|ref|YP_004176989.1| 177 EAFHAAKSNGATVVFTT 193
                                       33344566777777777 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00061      0.46      30      50 ..      32      52 ..       5      56 .. 0.87
   2 ?   -0.0   0.0      0.75   5.6e+02     175     193 ..     181     199 ..     169     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00061
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + + e+++++G+ g+GK+tl+
  gi|320101397|ref|YP_004176989.1| 32 IEKREVVAVMGPNGSGKSTLL 52
                                      67899**************98 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.75
                            AAA_25 175 iarrtgaavllvhHvgKes 193
                                        a+  ga+v+++ H g ++
  gi|320101397|ref|YP_004176989.1| 181 AAKSNGATVVFTTHIGVDA 199
                                       468889********99875 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.19      80     109 ..      29      57 ..      13      63 .. 0.85
   2 ?   -2.7   0.0       2.5   1.9e+03     274     294 ..     128     148 ..     125     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                        Adeno_IVa2  80 slnyglqPviGviyGPtGsGksqllrnlis 109
                                       sl ++++ v+ v  GP GsGks llr++i 
  gi|320101397|ref|YP_004176989.1|  29 SLSIEKREVVAV-MGPNGSGKSTLLRSVIG 57 
                                       777888888876.6************9985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                        Adeno_IVa2 274 fqlarfvntyakglskdlavl 294
                                         l+r+v+ y+ g+ + la+ 
  gi|320101397|ref|YP_004176989.1| 128 LDLKRLVKKYSMGMKRLLAIS 148
                                       5799**********9877542 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021      0.15       2      22 ..      37      59 ..      36      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                      EEEEEESTTCCHHHHHHHHH..C CS
                              cobW  2 vtvltGflGsGKTtLlnhll..e 22
                                      v+ + G+ GsGK+tLl++++  e
  gi|320101397|ref|YP_004176989.1| 37 VVAVMGPNGSGKSTLLRSVIglE 59
                                      67899*************99532 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.19      27      54 ..      37      64 ..      25      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                              DLIC 27 svlvlGedgsGkttliaklqGveeekkG 54
                                       v v+G +gsGk+tl+  + G+e++ kG
  gi|320101397|ref|YP_004176989.1| 37 VVAVMGPNGSGKSTLLRSVIGLEKPSKG 64
                                      5789**********************99 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00035      0.26       2      29 ..      35      61 ..      34      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvk 29
                                      r++++++G+  +GK+tll+ +i  +  +
  gi|320101397|ref|YP_004176989.1| 35 REVVAVMGPNGSGKSTLLRSVIGLEK-P 61
                                      6899***************9986554.4 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00083      0.62       2      21 ..      38      57 ..      37      71 .. 0.87
   2 ?   -1.9   0.0       4.7   3.5e+03      47      75 ..     156     184 ..     133     222 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00083
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      va++G   +GKStL+++ +g
  gi|320101397|ref|YP_004176989.1| 38 VAVMGPNGSGKSTLLRSVIG 57
                                      89**************9987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.7
                                       EEEEEE..CGGCSSHHHHHHHHHHHHHHHHC CS
                          MMR_HSR1  47 eielvD..tpGliegaseekglgkaflalee 75 
                                       e++++D  t+G ++   ++ ++ +af+a ++
  gi|320101397|ref|YP_004176989.1| 156 ELYIMDepTAG-LD-PVKRPSVLEAFHAAKS 184
                                       45555533444.22.1112245555554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2150.69
//
Query:       gi|320101398|ref|YP_004176990.1|  [L=263]
Description: ABC transporter [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00063   19.0  10.6    0.00089   18.5  10.6    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.026   14.5   1.6       0.94    9.5   1.3    2.7  2  DUF543           Domain of unknown function (DUF543)
       0.31   11.6   3.7        0.2   12.2   1.5    1.8  2  UreF             UreF
        1.5    6.9   3.7        1.8    6.6   3.7    1.1  1  UPF0182          Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5  10.6     2e-07   0.00089     166     312 ..      62     210 ..      51     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-07
                   ABC2_membrane_3 166 liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafgl...gipfgn 237
                                       ++++ +++i+++ +  si+ ++ +++ el++    s+l+ + +++ g+ l + + ++++l+  +a+g    g+++ +
  gi|320101398|ref|YP_004176990.1|  62 MVAFSAMSIGMATLPGSILADRVRGLFELLFPLRHSKLAEVAGRLMGLTLYSTIAAAVVLAtgVALGArytGVTIQE 138
                                       788999**************************************************999996667777777899999 PP

                   ABC2_membrane_3 238 lglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglg 312
                                        +++ l++ll +la+  +g+ l  + + s +a i + +v++  sg+f++ f   +l++ lk +++  P ++  ++
  gi|320101398|ref|YP_004176990.1| 139 ALSASLFILLILLASCGVGLILVPMGRASIAAGISLAVVTSAVSGVFTPYF---ALSENLKAFSRTWPVSSNLHV 210
                                       99999********************99987776655555554777777777...566888888887777776655 PP

>> DUF543  Domain of unknown function (DUF543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.048   2.2e+02      15      47 ..      50      81 ..      40      87 .. 0.80
   2 ?    9.5   1.3   0.00021      0.94      30      67 ..      95     132 ..      90     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.048
                            DUF543 15 sdldekwDaclsnllvkvglgllvGvvasvllf 47
                                      +  ++kw a l+ ++  ++++++++++ + +l+
  gi|320101398|ref|YP_004176990.1| 50 YAAEAKWGATLQ-MVAFSAMSIGMATLPGSILA 81
                                      778999*99996.78889999999999988876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00021
                            DUF543  30 vkvglgllvGvvasvllfrrRaapvalGaGvGiGaAYt 67 
                                       +++ l  ++G ++++ l  + aa v+l++Gv +Ga Yt
  gi|320101398|ref|YP_004176990.1|  95 RHSKLAEVAGRLMGLTLYSTIAAAVVLATGVALGARYT 132
                                       666777899**************************998 PP

>> UreF  UreF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.65   2.9e+03      76      98 ..      20      51 ..       1      74 [. 0.58
   2 ?   12.2   1.5   4.5e-05       0.2      40     117 ..      82     159 ..      58     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.65
                                      -..........-HHHHHHHHHHHHT--HHHHH CS
                              UreF 76 l...t......hypvafglaaaalgipleeal 98
                                      +   t       +p ++ l+a+ + +p+   +
  gi|320101398|ref|YP_004176990.1| 20 IrdpTnlfwtlGWPAIWTLIANTAFVPEGPYA 51
                                      24431333344588888888877776665544 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHH-.-HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHHH CS
                              UreF  40 aalrelddwllatretaelrlaseqmGrsllrllrklthypvafglaaaalgipleeallaylfswaenlvsAavkl 116
                                       +++r l ++l  +r ++ +  a + mG  l  ++++++ +++ ++l a+ +g++ +eal a lf  +  l+s++v l
  gi|320101398|ref|YP_004176990.1|  82 DRVRGLFELLFPLRHSKLAEVAGRLMGLTLYSTIAAAVVLATGVALGARYTGVTIQEALSASLFILLILLASCGVGL 158
                                       588888899999999999999***********9999977*************************9999999888765 PP

                                       T CS
                              UreF 117 v 117
                                       +
  gi|320101398|ref|YP_004176990.1| 159 I 159
                                       4 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.7   0.00041       1.8     206     279 ..     114     188 ..      54     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00041
                           UPF0182 206 dryellyskrgvvtGagYtdvnavlpaktilavialvvavlllvai.vlkklklplialallvllaillgvvlpa 279
                                            ++  +gv+ Ga Yt v+++  +   l+++++++a + +  i v      +++++ l v+++ + gv++p 
  gi|320101398|ref|YP_004176990.1| 114 TIAAAVVLATGVALGARYTGVTIQEALSASLFILLILLASCGVGLIlVPMGRASIAAGISLAVVTSAVSGVFTPY 188
                                       333333335689************999988888877777666555545555556788888888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1842.95
//
Query:       gi|320101399|ref|YP_004176991.1|  [L=264]
Description: peptidase A24A prepilin type IV [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-20   73.9   0.1    1.1e-20   73.9   0.1    1.6  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
      5e-07   30.1   5.6      5e-07   30.1   5.6    1.8  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 ?   -4.6   1.3         2   1.8e+04      74      87 ..     115     128 ..     114     131 .. 0.47
   2 !   73.9   0.1   1.3e-24   1.1e-20       2      91 ..     155     249 ..     154     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 2
                       Arc_PepC_II  74 PflipitaGfiial 87 
                                       P lipi++   +++
  gi|320101399|ref|YP_004176991.1| 115 PPLIPIVLYSTVSV 128
                                       55666654333333 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 1.3e-24
                       Arc_PepC_II   2 kllymligyrvkvkell.kkflflleefeekdgk...ikrkfisvekeldeelrkelkkykkkglieet..vWvtyg 72 
                                       +l+y +i+++++v ++  ++f+++l+ +e  dg+   ++r ++sve e+   +r+ ++k++++g+i+ +  +Wv+yg
  gi|320101399|ref|YP_004176991.1| 155 RLIYPFIARPMRVADFIeTRFYYPLTLIEAGDGEtvtVYRLHYSVE-EDPGVYRELFRKLVEAGTISADtvIWVSYG 230
                                       699************998************9999999999999999.899*****************999******* PP

                       Arc_PepC_II  73 vPflipitaGfiialvlGD 91 
                                       vP++ip+t+G+  +l++GD
  gi|320101399|ref|YP_004176991.1| 231 VPYIIPLTIGVAAFLIIGD 249
                                       ******************9 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 !   30.1   5.6   5.6e-11     5e-07       3      95 ..      19     121 ..      17     143 .. 0.70
   2 ?   -3.1   0.1       1.2     1e+04      84      84 ..     243     243 ..     223     261 .. 0.54

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.6e-11
                     Peptidase_A24   3 lltillvlsviDldtrtlpdeltlpllllgvlfa..qllllglpnlaqavlgalvgalvlllislvdeqamGgGDvk 77 
                                        l++l v s++D ++r+++d+l++ ++  + +f   + l l+     ++v++a+v + ++l   l++ + mG GDv 
  gi|320101399|ref|YP_004176991.1|  19 TLVFLGVFSLQDYRSREISDRLVYLFTGGSAVFLaaT-LMLHGFDPVYMVFSAVVPLTFTL---LYYTGLMGEGDVY 91 
                                       6899**********************99999998432.33355555556666666655555...5************ PP

                     Peptidase_A24  78 laavlgaflgwerl............llav 95 
                                       ++a l ++ + +              + +v
  gi|320101399|ref|YP_004176991.1|  92 VVASLFMLYPSPPRagflprsllpplIPIV 121
                                       ****99999854443444445555553333 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                     Peptidase_A24  84 a 84 
                                       a
  gi|320101399|ref|YP_004176991.1| 243 A 243
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1997.61
//
Query:       gi|320101400|ref|YP_004176992.1|  [L=178]
Description: histidine triad (HIT) protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   50.4   0.1    3.9e-13   49.9   0.1    1.2  1  HIT       HIT domain
    1.6e-07   31.8   0.0    2.4e-07   31.2   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    3.6e-06   26.8   0.1    5.8e-06   26.2   0.1    1.4  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.1   6.6e-17   3.9e-13      12      95 ..      45     129 ..      35     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 6.6e-17
                                       -SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSS.S CS
                               HIT  12 ddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsva.h 87 
                                         +++++l+  p   gh+ v p +h+  l+dl++eel +++++vk  +++++k f+ +g+++ +n g+ ag  v+ h
  gi|320101400|ref|YP_004176992.1|  45 GRHSFIVLNAYPYNSGHVMVAPYRHVGSLEDLSDEELLEIMQLVKLSMRVIRKAFNPDGFNIGVNIGRVAGAGVPgH 121
                                       56899*********************************************************************88* PP

                                       -EEEEEEC CS
                               HIT  88 lHiHvipr 95 
                                       +H+Hv+pr
  gi|320101400|ref|YP_004176992.1| 122 VHVHVVPR 129
                                       ******98 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0     4e-11   2.4e-07       1     100 [.      25     127 ..      25     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4e-11
                                       T-HHHHHHTTSS-B-EEEE-.SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                            DcpS_C   1 kwvfnilakgkepervvyed.ekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                       +++f++l    ++e+++++   +  ++  ++p ++ h++v p+r++ sl+dL++e+l  + ++++    vi++ +  
  gi|320101400|ref|YP_004176992.1|  25 ECLFCRLKTAVDEEALILHRgRHSFIVLNAYPYNSGHVMVAPYRHVGSLEDLSDEELLEIMQLVKLSMRVIRKAF-- 99 
                                       599*****9999999988777666666779**************************9999***********9988.. PP

                                       -EEEEE--SCCCT-.....-S-S--EEEE CS
                            DcpS_C  77 vdaeelrvgvhyqP.....svyhlHlHvi 100
                                        +++ +++gv++          h+H+Hv+
  gi|320101400|ref|YP_004176992.1| 100 -NPDGFNIGVNIGRvagagVPGHVHVHVV 127
                                       .689999999988877666668*****98 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   9.7e-10   5.8e-06       9      76 ..      21      89 ..      14     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.7e-10
                                      HHHHH-S--.--SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHH CS
                          CwfJ_C_1  9 asldsClfC.lsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrk 76
                                      +++++ClfC l+ +  e++li+  g++ ++ l   p +sgHv++ p  H+ +l  l++e+l ei +  k
  gi|320101400|ref|YP_004176992.1| 21 EKSGECLFCrLKTAVDEEALILHRGRHSFIVLNAYPYNSGHVMVAPYRHVGSLEDLSDEELLEIMQLVK 89
                                      5789*****77778888999*********************************9999988888766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1273.97
//
Query:       gi|320101401|ref|YP_004176993.1|  [L=73]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 534.60
//
Query:       gi|320101402|ref|YP_004176994.1|  [L=60]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 470.69
//
Query:       gi|320101403|ref|YP_004176995.1|  [L=81]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0011   19.1   0.1     0.0017   18.5   0.1    1.3  1  Ribosomal_L24e  Ribosomal protein L24e
     0.0027   17.8   0.1     0.0028   17.7   0.1    1.2  1  FYVE            FYVE zinc finger
  ------ inclusion threshold ------
      0.039   14.0   0.0      0.062   13.3   0.0    1.3  1  zf-C2H2_6       C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.8e-07    0.0017       4      42 ..       7      44 ..       4      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.8e-07
                                      -B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHT CS
                    Ribosomal_L24e  4 ekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkq 42
                                      ++C  +g+    G+G++ v +Dg +++F ss+c++ f++
  gi|320101403|ref|YP_004176995.1|  7 HRCVVCGRVFPEGQGIVVV-KDGLTLEFHSSRCASKFLR 44
                                      68*************9977.6*************99986 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.7e-07    0.0028      23      47 ..       4      46 ..       1      80 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-07
                                      S--EE-TTT--EE-..................STTS-EEE.EE CS
                              FYVE 23 rrrhhCrlCGkvvC..................ekCssklvall 47
                                      +rrh C +CG+v+                   ++C sk++++l
  gi|320101403|ref|YP_004176995.1|  4 SRRHRCVVCGRVFPegqgivvvkdgltlefhsSRCASKFLRAL 46
                                      7************999999999999999999888888887776 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 ?   13.3   0.0     1e-05     0.062       1      15 [.       6      20 ..       6      21 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                         zf-C2H2_6  1 vheCsvCsksFpslq 15
                                      +h+C vC+++Fp +q
  gi|320101403|ref|YP_004176995.1|  6 RHRCVVCGRVFPEGQ 20
                                      6***********887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 615.29
//
Query:       gi|320101404|ref|YP_004176996.1|  [L=241]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-63  212.5   9.3      7e-63  212.3   9.3    1.0  1  DUF2208   Predicted membrane protein (DUF2208)
  ------ inclusion threshold ------
       0.82    9.9   9.7         11    6.3   0.2    3.0  3  DUF3784   Domain of unknown function (DUF3784)
        1.3    7.9   5.9        2.4    7.0   5.8    1.4  1  Pex24p    Integral peroxisomal membrane peroxin


Domain annotation for each model (and alignments):
>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.3   9.3   1.2e-66     7e-63       2     229 ..      10     230 ..       9     232 .. 0.98

  Alignments for each domain:
  == domain 1  score: 212.3 bits;  conditional E-value: 1.2e-66
                           DUF2208   2 milisqvsiilfalvlaflpqylflviilYiivimvimsvltsrsllrerkkleevesgktLfeEknalkliekDee 78 
                                       +il+++vsi+lfalv+a++pqy+f++++lY+iv+mv++++ t rs    +k ++++e g+++f+E na +++ +D+ 
  gi|320101404|ref|YP_004176996.1|  10 TILVQAVSILLFALVSAVVPQYAFVIFLLYFIVFMVLAMKATARS----MKVPPRSELGSPIFKEPNAVQAMLTDKM 82 
                                       69******************************************9....**************************** PP

                           DUF2208  79 lqkelkeqlkasmitllllliviilffllyryiiplassllgevleeklarflaflalFealflismflrllarrvl 155
                                       lq+e+ +q+k ++++l ++++v+il++++ +yi+p++++ +g ++++ l +f+++l ++ +++++++++r+l++r +
  gi|320101404|ref|YP_004176996.1|  83 LQAEMGRQMKLMFLNLSMVFLVFILLPVYSEYIWPFIAERTGLTESNLLDNFVRYLGMYMFFIGVMQGSRYLLMRGQ 159
                                       *************************************************************************9999 PP

                           DUF2208 156 kklvmlimatsykvtekGivlkkrtgikfplkenieiklneerkfVElrstkqklktriRLYtkdpeklyeile 229
                                       ++ + +  a+s++v++kG+vl++r++i+f+ +  ++++ ++erkfVElr+ k+ + t +RLYt ++ +l e+l+
  gi|320101404|ref|YP_004176996.1| 160 QPVQPVFSARSFAVYRKGVVLDERQFIQFTQD--VCFNAEQERKFVELRNSKS-KATLTRLYTLEVGRLVEKLR 230
                                       9999999999**********************..****************999.779**************996 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.4    0.0022        13      50      87 ..      11      48 ..       3      54 .. 0.73
   2 ?    6.3   0.2    0.0019        11      35      65 ..      80     110 ..      72     121 .. 0.78
   3 ?    0.9   0.0     0.091   5.4e+02      44      63 ..     136     155 ..     132     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0022
                           DUF3784 50 llligilflllgllsaiesealliialiviiiiviyli 87
                                      +l+ ++ +ll++l+sa+  ++ ++i+l+ +i+++++++
  gi|320101404|ref|YP_004176996.1| 11 ILVQAVSILLFALVSAVVPQYAFVIFLLYFIVFMVLAM 48
                                      44455667788888888999999998888888888765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0019
                           DUF3784  35 ekydekklsrfmgivllligilflllgllsa 65 
                                       +k+ ++ + r+m  ++l ++++fl++ ll+ 
  gi|320101404|ref|YP_004176996.1|  80 DKMLQAEMGRQMKLMFLNLSMVFLVFILLPV 110
                                       6788899*************99999999933 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.091
                           DUF3784  44 rfmgivllligilflllgll 63 
                                       r  g+++++ig++    +ll
  gi|320101404|ref|YP_004176996.1| 136 RYLGMYMFFIGVMQGSRYLL 155
                                       77899999999876666665 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.8   0.00041       2.4      45     160 ..      16     140 ..      13     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00041
                            Pex24p  45 lsfllvytficlvpylelvvlplllllfvvmvpaylyrh..plrksslik...keesknestsegptldea....sk 112
                                       +s+ll+++++++vp + +v++ l +++f+v+ +++ +r    +++s+l +   ke ++ + + + + l+ +     k
  gi|320101404|ref|YP_004176996.1|  16 VSILLFALVSAVVPQYAFVIFLLYFIVFMVLAMKATARSmkVPPRSELGSpifKEPNAVQAMLTDKMLQAEmgrqMK 92 
                                       89*****************9999999999999999998765556666655666333333333333333322555333 PP

                            Pex24p 113 eivlnLrdlqnkmedllnpidalekflkelagfkdenlstllfltlll 160
                                         +lnL  +   + +l    + +  f++e +g+++ nl   +++ l +
  gi|320101404|ref|YP_004176996.1|  93 LMFLNLSMVFLVFILLPVYSEYIWPFIAERTGLTESNLLDNFVRYLGM 140
                                       566777666666655555555555667777776666655555444444 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:                      513  (0.0286129); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1847.84
//
Query:       gi|320101405|ref|YP_004176997.1|  [L=163]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1375.07
//
Query:       gi|320101406|ref|YP_004176998.1|  [L=253]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-31  108.0   0.0    9.4e-31  107.6   0.0    1.0  1  DUF72         Protein of unknown function DUF72
  ------ inclusion threshold ------
       0.21   11.0   0.0        0.9    8.9   0.0    2.1  2  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 !  107.6   0.0     1e-34   9.4e-31      13     212 ..      15     238 ..      12     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 1e-34
                                       HHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS..................G...-.SCHHH CS
                             DUF72  13 yYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraithe..............r...n...e.daeea 68 
                                        Y++++++VE+++tFY lps+e +++ + + p++F+ +vKa++ +th               +   n     +++e 
  gi|320101406|ref|YP_004176998.1|  15 RYVEELSVVELQNTFYDLPSREWCRSLRGSLPSGFEITVKAWQVVTHPstsptwrkmksklkGdpaNygfLkHTREN 91 
                                       79*********************************************444455555555554155523443479999 PP

                                       HHHHHHH.CHHHC.T-EEEEEEE--TT--S.HHHHHHHHHHTTTS-......S.EEEE--BGGGH..HHHHHHHHTT CS
                             DUF72  69 lerflesalepLg.eklgpllfQlppsfkfdeenlerLeaflaalp......l.lavEvRhrswf..ellellrehg 135
                                       +e+f+e  ++  +   + ++++Q pps+ +++ +le  e fl+++         + +E R +     e++ell ++g
  gi|320101406|ref|YP_004176998.1|  92 VEAFMEV-VDRARiLGARIIVLQTPPSMPCTPLSLESAEGFLKEVLgnigegImIGWEPRGECSErkEVVELLGKYG 167
                                       9999996.88874355566***********998********998777999*956*******9887855********* PP

                                       -EEEEE--SSC--------SSTEEEEEE--S...HHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHH CS
                             DUF72 136 vavvldepkkpklpledvttadfvyvRlhgr...eeryayrYseeelaewaerikawaaegrevyvffnndaegqap 209
                                       +++v+d p  ++ p    t + ++y+Rlhgr   e +y+y+Ys+ +l+e+ + i+ + +   e+yv+fnn +     
  gi|320101406|ref|YP_004176998.1| 168 LIHVVD-P-FKRKP--ASTPNGVAYLRLHGRgagETNYRYKYSDSDLEELYAIIEGIGS--SETYVLFNNVYM---F 235
                                       *****9.3.22222..2333489*********97589*******************987..79*******654...4 PP

                                       HHH CS
                             DUF72 210 lna 212
                                       ++a
  gi|320101406|ref|YP_004176998.1| 236 DDA 238
                                       444 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 ?    8.9   0.0    0.0001       0.9      60      91 ..      87     114 ..      48     166 .. 0.77
   2 ?   -0.6   0.0     0.083   7.5e+02      29      52 ..     155     177 ..     140     219 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0001
                                       HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEB CS
                      AP_endonuc_2  60 erearreesvdalkraielaaaLGapllvlhp 91 
                                       +  ++    v+a+ + +++a+ LGa+++vl++
  gi|320101406|ref|YP_004176998.1|  87 HTREN----VEAFMEVVDRARILGARIIVLQT 114
                                       45556....*********************94 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.083
                                       HHHHHHHHHHHTTSEEEEEEECCC CS
                      AP_endonuc_2  29 elrelrkaldelglriaslslftr 52 
                                       e +e+ ++l ++gl  +++ +f r
  gi|320101406|ref|YP_004176998.1| 155 ERKEVVELLGKYGLI-HVVDPFKR 177
                                       556666666666665.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2150.36
//
Query:       gi|320101407|ref|YP_004176999.1|  [L=138]
Description: AbrB family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-05   25.3   0.1    3.9e-05   24.2   0.0    1.6  2  ACT_4           ACT domain
    2.4e-05   24.1   0.4      5e-05   23.1   0.1    1.7  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    7.2e-05   22.5   0.0    0.00015   21.4   0.0    1.7  1  ACT             ACT domain
     0.0012   18.7   0.0      0.002   18.1   0.0    1.4  1  ACT_6           ACT domain
  ------ inclusion threshold ------
       0.04   13.9   0.0       0.07   13.1   0.0    1.4  1  MraZ            MraZ protein, putative antitoxin-like


Domain annotation for each model (and alignments):
>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.6   1.6e+04      45      57 ..      12      24 ..       7      26 .. 0.53
   2 !   24.2   0.0   1.1e-08   3.9e-05       7      78 ..      58     131 ..      56     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.6
                             ACT_4 45 dglaeikitveVk 57
                                      d+  +i+i + V+
  gi|320101407|ref|YP_004176999.1| 12 DQKGRITIPIAVR 24
                                      4444555555555 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.1e-08
                             ACT_4   7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdv..ehLsrviakLraipgVisV 78 
                                       ++l++ +edr+g+La++t+ i+  +++ivs + +  k+++l e+++ v ++ +  ++ s ++  Lr+++ V++V
  gi|320101407|ref|YP_004176999.1|  58 AKLKLLVEDRTGVLAELTRFIAGYNVDIVSTKCVVLKREELGECEMIVDISKTgwADPSVIVGELRKLEPVKNV 131
                                       789*********************************9999*999999999876224556666666666666666 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 !   23.1   0.1   1.4e-08     5e-05       1      41 [.       9      51 ..       9      55 .. 0.91
   2 ?   -2.5   0.0       1.5   5.5e+03      24      35 ..     120     132 ..     119     135 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.4e-08
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTT..CCCCCCC CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgd..kiilrpl 41
                                      +kv+ +g+++iP +vr+  +ireG  + ++ d++   i l+pl
  gi|320101407|ref|YP_004176999.1|  9 VKVDQKGRITIPIAVRELFDIREGMYLLMIADKEarEIKLVPL 51
                                      69**********************9999999999888888776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                                       TCEEEEEECTT.C CS
                    MazE_antitoxin  24 Gdevelevdgd.k 35 
                                       G    le++++  
  gi|320101407|ref|YP_004176999.1| 120 GELRKLEPVKNvE 132
                                       6667788887744 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.2e-08   0.00015       4      30 ..      61      87 ..      58     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.2e-08
                                      EEEEESSTTHHHHHHHHHHHTTSEEEE CS
                               ACT  4 rvgvpDrPGlLarvfgaladrgiNids 30
                                       ++v+Dr G+La++++ +a +++ i+s
  gi|320101407|ref|YP_004176999.1| 61 KLLVEDRTGVLAELTRFIAGYNVDIVS 87
                                      5789*********************87 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.5e-07     0.002      10      41 ..      65      96 ..      60     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.5e-07
                             ACT_6 10 pdrpGltasLtsvlaefgvnilDieqavihgr 41
                                      +dr+G++a+Lt+ +a ++v+i+  + +v+ ++
  gi|320101407|ref|YP_004176999.1| 65 EDRTGVLAELTRFIAGYNVDIVSTKCVVLKRE 96
                                      7************************9999875 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05      0.07       6      28 ..       7      29 ..       4      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                                      EEEEB-TTSEEE--CHHHHHTTS CS
                              MraZ  6 tevelDakGRlllPaklreeakl 28
                                       +v++D+kGR+++P   re +  
  gi|320101407|ref|YP_004176999.1|  7 ETVKVDQKGRITIPIAVRELFDI 29
                                      5799**********988886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1078.08
//
Query:       gi|320101408|ref|YP_004177000.1|  [L=279]
Description: phosphoribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   35.6   0.1    1.2e-08   34.6   0.1    1.5  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.017   15.1   0.1      0.051   13.6   0.1    1.8  1  HTH_3         Helix-turn-helix


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 !   34.6   0.1   1.4e-12   1.2e-08      26     128 ..     150     258 ..     133     278 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.4e-12
                                       --GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE................EE----TTSEEEEE- CS
                      Pribosyltran  26 yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes........rlledpagkkVliVD 94 
                                        + +   +++ a   +p+a+ l+ e+++p+  v +++y  +g +  ++++++++            + +  kVl+  
  gi|320101408|ref|YP_004177000.1| 150 TGKEVSKIIATAEAVLPLATMLSLEFNAPIILVKRKSY--PGVQYYSTSFMKSPkdvetlylDRDLLSRRDKVLVLS 224
                                       344444899******************88776666666..5555555568887788999**96666677779***** PP

                                       SEESSSHHHHHHHHHHHCC-BSEEEEEEEE..E-HH CS
                      Pribosyltran  95 DildtGgTllaalelLkekgpeevriavlv..dkpa 128
                                       D++ +G+Tl+a+lelL + ++e+  i+v++     +
  gi|320101408|ref|YP_004177000.1| 225 DVVYSGRTLEAVLELLSKSRAEITDIIVVLglG--D 258
                                       **********************99999998443..3 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.7e-06     0.051       6      53 ..      61     109 ..      57     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-06
                                       H.HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3   6 k.qlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53 
                                       + +  ls ++L e +G++ s + r+ +G  +Ps e +  ++    +s+d
  gi|320101408|ref|YP_004177000.1|  61 LlKPSLSYRDLYEITGIPESVLCRYARGSIIPSFEQAAQILSRIALSID 109
                                       446779********************************99988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2215.99
//
Query:       gi|320101409|ref|YP_004177001.1|  [L=134]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1041.24
//
Query:       gi|320101410|ref|YP_004177002.1|  [L=561]
Description: DNA repair helicase RAD25 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-27   93.7   0.0    1.9e-26   92.8   0.0    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    2.9e-20   73.0   0.0    7.4e-20   71.6   0.0    1.7  2  ResIII         Type III restriction enzyme, res subunit
      1e-19   70.9   0.1    3.1e-19   69.3   0.0    1.9  2  Helicase_C     Helicase conserved C-terminal domain
    9.3e-07   28.8   0.0    3.6e-06   26.9   0.0    2.0  1  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.047   13.4   0.0        0.3   10.8   0.0    2.1  2  IstB_IS21      IstB-like ATP binding protein
      0.082   13.2   0.1       0.71   10.2   0.1    2.6  2  AAA_22         AAA domain
       0.24   11.2   0.7         15    5.3   0.0    2.8  3  AAA_11         AAA domain


Domain annotation for each model (and alignments):
>> 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 !   92.8   0.0   7.3e-30   1.9e-26      29     183 ..     401     548 ..     387     554 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 7.3e-30
                     ERCC3_RAD25_C  29 kakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknp 105
                                       + +s+ +++l+   ++  +a+e + +   ++g kiivf+  v   +e++++l+  +++Ge++++er++il++fk+++
  gi|320101410|ref|YP_004177002.1| 401 RVHSQMRSILARAKAKIDKAVE-IARSELEKGGKIIVFTQYVDQAREISERLNAYLLTGEIPTEERKRILEEFKNTD 476
                                       5555566655555544444444.56677799*******************************************998 PP

                     ERCC3_RAD25_C 106 kvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrq 182
                                       k   +++  vgD+ +D+P+anv i +s  +gsrrq  qrlGr+Lr+k +    +++a  Y ++ + t+e + ++kr+
  gi|320101410|ref|YP_004177002.1| 477 KG-ILVVTTVGDEGLDIPDANVGIMVSG-TGSRRQFIQRLGRLLRPKPG----GKEAVLYEIILEKTSEEYQARKRK 547
                                       75.77899****************9986.79*****************9....899********************8 PP

                     ERCC3_RAD25_C 183 q 183
                                       +
  gi|320101410|ref|YP_004177002.1| 548 N 548
                                       6 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   2.9e-23   7.4e-20       2     170 ..     175     316 ..     174     317 .. 0.88
   2 ?   -2.5   0.0       1.7   4.4e+03      91      91 ..     463     463 ..     382     486 .. 0.60

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 2.9e-23
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkf 77 
                                       ++lr+yQ ea+ +++     ++++rg+i+++TG+GKTl+  a+l+e   +       l++v +k+ + q+++++ k+
  gi|320101410|ref|YP_004177002.1| 175 VDLRDYQREALGKWV-----ENKHRGVIALPTGSGKTLIGvAALVETGVR------SLIVVYTKEQMMQWRDAILKY 240
                                       579***********9.....7899***************96666666665......5*****************999 PP

                                       TGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHH CS
                            ResIII  78 lseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreil 154
                                       ++ + + ig + s ++k++       + +++tt+qs  +++          l+ +fd++iiDE+H+l a +++r+i+
  gi|320101410|ref|YP_004177002.1| 241 TNIEPSMIGLIHS-EEKRP-------APVTITTYQSGFRQI--------NTLSPFFDMLIIDEVHHLPA-EKFRHIA 300
                                       9988764555555.55555.......5**************........8999****************.******9 PP

                                       HT---SEEEEEESS-S CS
                            ResIII 155 ekfkeavllglTATpe 170
                                        +  + +++gl+ATp 
  gi|320101410|ref|YP_004177002.1| 301 VHSIARYRMGLSATPF 316
                                       99999**********7 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                       S CS
                            ResIII  91 g 91 
                                       +
  gi|320101410|ref|YP_004177002.1| 463 E 463
                                       1 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.7   9.4e+03      13      34 ..     214     237 ..     207     257 .. 0.59
   2 !   69.3   0.0   1.2e-22   3.1e-19       4     109 ..     418     519 ..     415     521 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.7
                                       TTTTSEEEEEESSHHHHHH..HHH CS
                        Helicase_C  13 eeeggkilifvntidrlek..vkl 34 
                                        e g ++li+v t++++ +    +
  gi|320101410|ref|YP_004177002.1| 214 VETGVRSLIVVYTKEQMMQwrDAI 237
                                       466778888888888553344233 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 1.2e-22
                                       HHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                        Helicase_C   4 eallell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerG 79 
                                       ++ +e+  ++ e+ggki++f++++d++   + +  ++ +++  l+ge+p++er++ile+f++ +  +L+ t+v+ +G
  gi|320101410|ref|YP_004177002.1| 418 DKAVEIArSELEKGGKIIVFTQYVDQA---REI--SERLNAYLLTGEIPTEERKRILEEFKNTDKGILVVTTVGDEG 489
                                       555555556679***************...777..6779*********************998888*********** PP

                                       STSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       +dip++n+ i+++   + +++iqr GR  R
  gi|320101410|ref|YP_004177002.1| 490 LDIPDANVGIMVSGTGSRRQFIQRLGRLLR 519
                                       ***************************999 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.4e-09   3.6e-06       2     170 ..     179     316 ..     178     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.4e-09
                                       HHHHHHHHHHHTTC.EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilggg.dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       d+Q+ea+   ++++   ++a +TGsGKTl+ + +++        +tg + liv+ t+e + q  + + k+++ i+  
  gi|320101410|ref|YP_004177002.1| 179 DYQREALGKWVENKhRGVIALPTGSGKTLIGVAALV--------ETGVRSLIVVYTKEQMMQWRDAILKYTN-IEP- 245
                                       789999999996543899************999998........899***********99999999988888.332. PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                         ++ig         + ++ + ++++t +  ++ ++t +     + +l++DE++ l  ++f+    + +++      
  gi|320101410|ref|YP_004177002.1| 246 --SMIGLIHS-----EEKRPAPVTITTYQSGFRQINTLS---PFFDMLIIDEVHHLPAEKFRHIAVHSIARY----- 307
                                       ..34453222.....222347899999999998776433...5569***************99998888887..... PP

                                       TSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlp 170
                                               + lSAT+ 
  gi|320101410|ref|YP_004177002.1| 308 -------RMGLSATPF 316
                                       .......788888876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012       0.3      28      82 ..     173     227 ..     157     236 .. 0.80
   2 ?   -0.6   0.0      0.38   9.7e+02     109     127 ..     280     298 ..     266     314 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                         IstB_IS21  28 rsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvr 82 
                                       r++d r  ++ a ++++e+k+  v+  p+G GK+ + +a  ve+  + l v++++
  gi|320101410|ref|YP_004177002.1| 173 RNVDLRDYQREALGKWVENKHRGVIALPTGSGKTLIGVAALVETGVRSLIVVYTK 227
                                       67788888888999**********************9886666655566677766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                         IstB_IS21 109 vdllilDdlgllpldqaea 127
                                       +d+li+D++  lp ++   
  gi|320101410|ref|YP_004177002.1| 280 FDMLIIDEVHHLPAEKFRH 298
                                       49*******9999887655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00028      0.71      13     112 ..     200     299 ..     190     317 .. 0.61
   2 ?   -2.1   0.0       1.7   4.4e+03      46      80 ..     500     531 ..     493     553 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                            AAA_22  13 esGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka......erlsseell.ea 81 
                                       ++G+GKT+     l +           ++++ v+ ++++  ++d    +l+ ++ e +       e+++   +  ++
  gi|320101410|ref|YP_004177002.1| 200 PTGSGKTLIGVAALVETG--------VRSLIVVYTKEQMmQWRDA---ILKYTNIEPSMiglihsEEKRPAPVTiTT 265
                                       678888877544444442........3333333333333355554...33333333333334444466666666666 PP

                            AAA_22  82 leqalrarav....ielliiDEaqhlrseealeeL 112
                                        +  +r+  +      +liiDE++hl ++e ++++
  gi|320101410|ref|YP_004177002.1| 266 YQSGFRQINTlspfFDMLIIDEVHHL-PAEKFRHI 299
                                       6666666666777889**********.99988887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                            AAA_22  46 tlpsstsskdllrellralglelkaerlsseelle 80 
                                        +++ +s++++ ++l r l  +  +   ++  l+e
  gi|320101410|ref|YP_004177002.1| 500 MVSGTGSRRQFIQRLGRLLRPKPGG---KEAVLYE 531
                                       5566678888888888888855544...3333333 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0057        15       2      35 ..     177     210 ..     176     235 .. 0.81
   2 ?    2.7   0.0     0.035        89     202     225 ..     264     287 ..     227     289 .. 0.84
   3 ?   -1.1   0.3      0.53   1.4e+03     122     148 ..     403     429 ..     351     478 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0057
                            AAA_11   2 lndsqreaiksalseseitliqGPPGtgKTktiv 35 
                                       l d qrea+ + +++++  +i  P G+gKT   v
  gi|320101410|ref|YP_004177002.1| 177 LRDYQREALGKWVENKHRGVIALPTGSGKTLIGV 210
                                       6789**************************4333 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.035
                            AAA_11 202 TlsgagsklleklakkfdvviIDE 225
                                       T   +g +++++l   fd++iIDE
  gi|320101410|ref|YP_004177002.1| 264 TTYQSGFRQINTLSPFFDMLIIDE 287
                                       4456778889999889******** PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.53
                            AAA_11 122 kaqlakeiskeleklakelrafeeeee 148
                                       + q+ + ++++++k++k+++   +e e
  gi|320101410|ref|YP_004177002.1| 403 HSQMRSILARAKAKIDKAVEIARSELE 429
                                       222222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); 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:                         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 0.23s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4151.29
//
Query:       gi|320101411|ref|YP_004177003.1|  [L=220]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1636.11
//
Query:       gi|320101412|ref|YP_004177004.1|  [L=96]
Description: nucleoid protein Alba [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-21   73.5   1.2    1.2e-20   73.1   1.2    1.2  1  Alba      Alba
  ------ inclusion threshold ------
      0.033   14.1   0.3      0.047   13.6   0.2    1.5  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 !   73.1   1.2   1.3e-24   1.2e-20       1      66 [.       8      71 ..       8      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.3e-24
                                      CEEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                              Alba  1 neiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                      n++ V++ +p+m+yv ++l+l  +++ +eV +ka+GraIskAv+++ei+k+rf++g++ v +++++
  gi|320101412|ref|YP_004177004.1|  8 NTVLVGK-KPVMNYVIAVLTLV-HQGVKEVYIKARGRAISKAVDTVEIVKNRFLPGKVDVDEIKIG 71
                                      7999***.**************.*************************************999986 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 ?   13.6   0.2   5.3e-06     0.047      60      79 ..      31      50 ..      26      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-06
                             Rpp20 60 kkeeVfvkatGrAiekalsv 79
                                        +eV++ka GrAi ka+  
  gi|320101412|ref|YP_004177004.1| 31 GVKEVYIKARGRAISKAVDT 50
                                      579**************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 732.08
//
Query:       gi|320101413|ref|YP_004177005.1|  [L=1211]
Description: reverse gyrase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-67  227.6   0.0    7.4e-67  226.1   0.0    1.7  1  Topoisom_bac    DNA topoisomerase
    2.8e-22   78.9   0.0    8.2e-22   77.4   0.0    1.9  1  Toprim          Toprim domain
    2.9e-12   46.7   0.0    8.8e-12   45.1   0.0    1.8  1  DEAD            DEAD/DEAH box helicase
    5.3e-06   26.5   0.0    1.2e-05   25.4   0.0    1.5  1  ResIII          Type III restriction enzyme, res subunit
    0.00042   20.6   0.0      0.039   14.3   0.0    2.7  2  Helicase_C      Helicase conserved C-terminal domain
    0.00068   19.4   0.0     0.0034   17.1   0.0    2.1  2  AAA_30          AAA domain
    0.00081   19.8   0.2     0.0044   17.4   0.0    2.4  2  Toprim_4        Toprim domain
     0.0013   18.4   0.1      0.032   13.8   0.0    2.5  2  AAA_25          AAA domain
     0.0016   18.2   0.2     0.0041   16.9   0.0    1.7  2  IstB_IS21       IstB-like ATP binding protein
     0.0064   16.5   5.0       0.52   10.4   0.7    2.3  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.018   15.0   0.7        8.9    6.4   0.0    2.8  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.02   14.3   2.0      0.025   14.0   0.3    1.9  2  zf_Rg           Reverse gyrase zinc finger
      0.034   14.4   0.1       0.12   12.6   0.1    1.9  1  AAA_22          AAA domain
      0.037   14.4   0.0      0.087   13.2   0.0    1.6  1  AAA_16          AAA ATPase domain
      0.043   13.8   3.8       0.95    9.5   0.6    2.5  2  HypA            Hydrogenase/urease nickel incorporation, meta
        0.1   12.6   2.0       0.66   10.0   0.2    2.3  2  zinc-ribbons_6  zinc-ribbons
       0.19   11.7   0.0       0.38   10.7   0.0    1.4  1  Flavi_DEAD      Flavivirus DEAD domain
        0.2   12.0   0.1       0.45   10.8   0.1    1.7  1  AAA_19          AAA domain
        1.5    8.8   7.1        4.1    7.5   0.6    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        3.1    8.0   9.7       0.67   10.1   1.8    2.7  2  Zn-ribbon_8     Zinc ribbon domain
        4.9    6.8   6.3       0.68    9.5   0.6    2.3  2  RecR            RecR protein


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 !  226.1   0.0   8.7e-70   7.4e-67       3     412 ..     796    1189 ..     794    1190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 226.1 bits;  conditional E-value: 8.7e-70
                      Topoisom_bac    3 nenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRerei.enFvpeeyweveatlkke 76  
                                        n+ lv+    Rr+lD+liG++ls+ l+  ++g ++l aGRVqtp+L+l++eR+r   +n  ++  +++ a l+  
  gi|320101413|ref|YP_004177005.1|  796 NTLLVEGEVYRRVLDRLIGFKLSQELQS-MHGLRFLGAGRVQTPVLGLVIERYRSFlRNRCKRVSFKLGAPLN-- 867 
                                        6778888999**************9986.67789******************986424555555666666542.. PP

                      Topoisom_bac   77 kkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsia 151 
                                         + +     +k +++ +k + +++l+ +       ++ +++   +p+p p++t++L+ +a+r lgl a  +++ia
  gi|320101413|ref|YP_004177005.1|  868 -TVF-TILVDKGSELPSKLKDARVLKLV-------RTRREEVVVSPKP-PYTTDELLADAAR-LGLPAGTAMMIA 931 
                                        .222.23455666666665555555555.......2334444455777.**********999.7*********** PP

                      Topoisom_bac  152 qkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteel 226 
                                        q+L+e  glitY+RTds ++s++  ++ +++++++k g  +++    +   + ++    +++ + HeAIrP+   
  gi|320101413|ref|YP_004177005.1|  932 QQLFEA-GLITYHRTDSHYVSNTG-ISVAVKYMEEK-G--FSR----VAR-PSHW----GSQ-GTHEAIRPVHPY 991 
                                        *****5.*****************.9********95.2..333....232.2234....678.9********998 PP

                      Topoisom_bac  227 p.klkels..............ddekklYelIvrrflaslmkdakyeettvkleveeeef..kasgktilekGfk 284 
                                        + + + l+              + + +lY++I++rf+ s+mk+ k  + t  +  ++ ++      ++i+e+Gf+
  gi|320101413|ref|YP_004177005.1|  992 DvD-DLLKaiaeglvnvvipltGLHLRLYDMIFKRFISSQMKPFKSVKSTFAVYYDGLKLgeVELLTRIVEDGFN 1065
                                        853.33446788999******977777**************************774433311334678999**99 PP

                      Topoisom_bac  285 kvykeekkeeeeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYv 359 
                                         ++k +  +e    l +++  +  +v++  +     +  + yte++L+++m++ g+G+p+T+++iie++ ++gYv
  gi|320101413|ref|YP_004177005.1| 1066 LFEKVKVHSE----LDDVESLDV-SVED--VVIADSSRIPLYTEGELVSLMKQLGLGRPSTYSKIIENVRRHGYV 1133
                                        9986544432....333333222.3333..5556679999*********************************** PP

                      Topoisom_bac  360 erkk..kslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkadakevl 412 
                                          +k   +l+pt+ G++++e l ++++dlvs+e+T++lee++d+I +g+ da+++l
  gi|320101413|ref|YP_004177005.1| 1134 IASKkrLKLIPTKRGMEVYEYLvSRYPDLVSVETTRRLEESIDRIGKGEVDARTLL 1189
                                        998524569*************9999************************998876 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   9.6e-25   8.2e-22       2     103 .]     621     780 ..     620     780 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 9.6e-25
                                       EEEESSHHHHHHHHHTHT......................STEEEEEEESSSSEEEHS.............TTEEEE CS
                            Toprim   2 lvivEgpsdaktiakalg......................sgfqavtaslGhildlet.............efkpvy 43 
                                       lv+vE+p++aktia+++g                        ++++++++Ghi+dl+t              ++pvy
  gi|320101413|ref|YP_004177005.1| 621 LVVVESPTKAKTIARFFGkpvarrlgdvsvyeipvklgdeIVHLNIMPTRGHIFDLTTdnegyygvlinegGVSPVY 697
                                       89*************************************999*****************************999999 PP

                                       E........................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEE CS
                            Toprim  44 e........................eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkig 96 
                                       e                        +  d k+v++al+++a ++de+++atDpD eGe+ia++++ ++k ++e+ i 
  gi|320101413|ref|YP_004177005.1| 698 EsikrcrlcgtqftsgetcprcgsrVFTDSKTVVAALRKIAGEVDEVYIATDPDIEGEKIAYDVYLAVKYYNEK-IW 773
                                       99999999999999***************************************************988855555.** PP

                                       EEEESSS CS
                            Toprim  97 rvefsei 103
                                       r+e +ei
  gi|320101413|ref|YP_004177005.1| 774 RIELHEI 780
                                       ****997 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0     1e-14   8.8e-12       6     139 ..      73     204 ..      69     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1e-14
                                       HHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST......S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                              DEAD   6 eaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid......l 76 
                                          + +++g++ ++ a+TG+GKT+  ++  l   y    ++g+++++++Ptr L  q+++++    + i+      l
  gi|320101413|ref|YP_004177005.1|  73 IWSKRLVSGENTVLIAPTGMGKTTLLIVYSL---YA--ARRGKRVVYIAPTRVLLTQVYRRILDAASRIGladsmiL 144
                                       55567889****************9777776...43..58999************************9995555544 PP

                                       EEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliiggvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfs 139
                                        + +  g++++++ l+++++g ++i+v t + l +  +t  l   +  +++ D +d +  +  +
  gi|320101413|ref|YP_004177005.1| 145 MYDSSAGKKKREEALARIKQGdYRILVVTNSFLSR--KTDLLLPVKPDVVIADDVDSIVRS--E 204
                                       4455577899999999999889********99988..666655666788888888888766..3 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.4e-08   1.2e-05      25     140 ..      82     196 ..      66     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.4e-08
                                       SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG..........GGGTGG....GEEEESS CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef..........kkflseaykeigkkvsg 91 
                                       ++ ++ ++TG+GKT +++    + ++  + ++++ ++p++ ll q ++++           +++  +++++gkk+++
  gi|320101413|ref|YP_004177005.1|  82 ENTVLIAPTGMGKTTLLIVYSLYAAR--RGKRVVYIAPTRVLLTQVYRRIldaasriglaDSMILMYDSSAGKKKRE 156
                                       5678999*******987665555555..556****************888555555555444444443335555555 PP

                                       S-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEET CS
                            ResIII  92 dkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDE 140
                                       +   +  +++ + +ilv+t + l+++        + ll+ + dv+i D 
  gi|320101413|ref|YP_004177005.1| 157 EALAR--IKQGDYRILVVTNSFLSRKT-------DLLLPVKPDVVIADD 196
                                       55555..9***********99999888.......677777777777775 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 !   14.3   0.0   4.6e-05     0.039       5      74 ..      99     174 ..      95     183 .. 0.79
   2 ?    3.2   0.0      0.13   1.1e+02      96     110 ..     535     549 ..     519     550 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHTTTTSEEEEEESSHHHHHH..HHHHHHHT......TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C   5 allellkleeeggkilifvntidrlek..vklllekk......gikvavlhgelpqnereeileqfnkgesdvLiat 73 
                                       +++ l+   ++g++++ +++t+  l +   ++l          +  +++++++  +++ree+l++ ++g++++L+ t
  gi|320101413|ref|YP_004177005.1|  99 IVYSLY-AARRGKRVVYIAPTRVLLTQvyRRILDA-AsriglaDSMILMYDSSAGKKKREEALARIKQGDYRILVVT 173
                                       455554.7788999999999999665554444422.2366777899*****************************99 PP

                                       G CS
                        Helicase_C  74 d 74 
                                       +
  gi|320101413|ref|YP_004177005.1| 174 N 174
                                       8 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                       SHHHHHHHHTTSSST CS
                        Helicase_C  96 nvtsyiqriGRtgRa 110
                                       +v +yiq++GRt R 
  gi|320101413|ref|YP_004177005.1| 535 DVMTYIQASGRTSRL 549
                                       6889********996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.9e-06    0.0034       6      57 ..      71     120 ..      68     140 .. 0.83
   2 ?   -1.9   0.0       2.8   2.4e+03      21      92 ..     438     523 ..     432     526 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.9e-06
                            AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgk 57 
                                       Q+   ++l+++++  +vl +p G GKtt+l ++   ++++g+rv+ +Apt  
  gi|320101413|ref|YP_004177005.1|  71 QRIWSKRLVSGEN--TVLIAPTGMGKTTLLIVYSLYAARRGKRVVYIAPTRV 120
                                       5566667777775..99****************9999999*********976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                            AAA_30  21 avltGpAGt.GKttalkalreaweaaggrviglAptgkaAkv.Laeelgi..........eastiakllkrlk..gr 83 
                                       a l G +G+ GK   l+ l+ ++   + r++ lA +gk  ++ L+ +  +           a+t+ak+ + l+  + 
  gi|320101413|ref|YP_004177005.1| 438 ANLAGDPGArGKAADLRRLVYTLSPGELRLVKLALSGKIPEEtLSSSERLssrypeiknyYAETLAKVKSILDerHV 514
                                       56788899889999999999999999999999999999988767754332222333333377777777666664433 PP

                            AAA_30  84 arlepgtll 92 
                                       +++ + tl+
  gi|320101413|ref|YP_004177005.1| 515 VEMGSITLV 523
                                       444444555 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         7   5.9e+03      55      86 ..     140     170 ..     120     173 .. 0.72
   2 !   17.4   0.0   5.2e-06    0.0044      50      88 ..     737     775 ..     723     776 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7
                          Toprim_4  55 kevilaldgDaeGeataerlaellleegvkvt 86 
                                       + +il++d++ +G++  e+++ ++++++ ++ 
  gi|320101413|ref|YP_004177005.1| 140 DSMILMYDSS-AGKKKREEALARIKQGDYRIL 170
                                       6678888876.688888888776766666665 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 5.2e-06
                          Toprim_4  50 aekkvkevilaldgDaeGeataerlaellleegvkvtrl 88 
                                         ++v+ev++a+d+D eGe+ a  ++ +++  ++k++r+
  gi|320101413|ref|YP_004177005.1| 737 IAGEVDEVYIATDPDIEGEKIAYDVYLAVKYYNEKIWRI 775
                                       45789******************9999887889999887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.8e-05     0.032      26      65 ..      74     114 ..      69     172 .. 0.85
   2 ?    1.7   0.0       0.2   1.7e+02      58     120 ..     824     886 ..     815     903 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                            AAA_25  26 vkgllpagelallaGapgtGKttlaldlalava.tGkpwlg 65 
                                       +   l+ ge ++l++++g GKttl++  +l  a +Gk +  
  gi|320101413|ref|YP_004177005.1|  74 WSKRLVSGENTVLIAPTGMGKTTLLIVYSLYAArRGKRVVY 114
                                       56677899**********************99988886543 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.2
                            AAA_25  58 atGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagv.eslpLfakd 120
                                       + G  +lg     q +Vl ++ E  ++ lr+R ++v  +l ++ +  ++ l+++  +lp   kd
  gi|320101413|ref|YP_004177005.1| 824 MHGLRFLG-AGRVQTPVLGLVIERYRSFLRNRCKRVSFKLGAPLNTVFTILVDKgSELPSKLKD 886
                                       57999999.4458************************999888888888888887777765444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.8e-06    0.0041      46      87 ..      80     121 ..      69     154 .. 0.85
   2 ?   -3.3   0.0       7.6   6.5e+03     107     134 ..     187     214 ..     178     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-06
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLv 87 
                                       + en vl+ p+G+GK+ l i  +  a+r+g++v+++  ++++
  gi|320101413|ref|YP_004177005.1|  80 SGENTVLIAPTGMGKTTLLIVYSLYAARRGKRVVYIAPTRVL 121
                                       579********************************9866643 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.6
                         IstB_IS21 107 lkvdllilDdlgllpldqaeaellfevi 134
                                       +k+d++i Dd+     ++++   l++++
  gi|320101413|ref|YP_004177005.1| 187 VKPDVVIADDVDSIVRSEKNIVRLLRIL 214
                                       6899******999988888888888876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.3     0.004       3.4      14      37 ..      12      37 ..       4      42 .. 0.81
   2 !   10.4   0.7    0.0006      0.52      12      39 ..     700     724 ..     694     730 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.004
                               DZR 14 fCseCgtklkavaa...edrCpsCgek 37
                                      fC+ Cg +++a  +      C +C+++
  gi|320101413|ref|YP_004177005.1| 12 FCPVCGGDVSAS-ElelYGSCKKCSRS 37
                                      9********854.359999*****987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0006
                               DZR  12 arfCseCgtklkavaaedrCpsCgekvd 39 
                                        + C  Cgt+     + ++Cp+Cg+ v 
  gi|320101413|ref|YP_004177005.1| 700 IKRCRLCGTQFT---SGETCPRCGSRVF 724
                                       577999999997...4999999999865 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.013        11       2      10 ..      13      21 ..      12      29 .. 0.84
   2 ?    6.4   0.0      0.01       8.9       1       9 [.     715     723 ..     715     742 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                    DNA_ligase_ZBD  2 CPvCGsavv 10
                                      CPvCG  v 
  gi|320101413|ref|YP_004177005.1| 13 CPVCGGDVS 21
                                      *****9885 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                    DNA_ligase_ZBD   1 hCPvCGsav 9  
                                       +CP CGs v
  gi|320101413|ref|YP_004177005.1| 715 TCPRCGSRV 723
                                       7******98 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.9e-05     0.025       4      31 ..       7      34 ..       4      49 .. 0.90
   2 ?   -2.3   0.1       3.4   2.9e+03       9      15 ..     715     721 ..     713     726 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                             zf_Rg  4 avfeklCPNCgGdisdeRlekGLpCkrC 31
                                       +++  CP CgGd+s+  le    Ck+C
  gi|320101413|ref|YP_004177005.1|  7 PLYKGFCPVCGGDVSASELELYGSCKKC 34
                                      57999***************9999*999 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                             zf_Rg   9 lCPNCgG 15 
                                        CP Cg 
  gi|320101413|ref|YP_004177005.1| 715 TCPRCGS 721
                                       7****96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00014      0.12       7     115 ..      83     214 ..      78     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............. 70 
                                        +v+++++G+GKTtll  +   + +      ++++vv++ ++    +++++r++l a  + + a             
  gi|320101413|ref|YP_004177005.1|  83 NTVLIAPTGMGKTTLLIVYSLYAAR------RGKRVVYIAPTRVL-LTQVYRRILDAASRIGLAdsmilmydssagk 152
                                       589************9888887754......48999988888888.9999999999988888888899999999985 PP

                            AAA_22  71 .......erlsseellealeqalrarav................ielliiDEaqhlr.s.eealeeLrsl 115
                                              +        +  +   r   v                + ++i D+++ +  s +++++ Lr+l
  gi|320101413|ref|YP_004177005.1| 153 kkreealA--------RIKQGDYRILVVtnsflsrktdlllpvkPDVVIADDVDSIVrSeKNIVRLLRIL 214
                                       55555552........333333333333444444444678888889999999999655436666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.087      20     149 ..      79     202 ..      71     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                            AAA_16  20 rsgrpelvllsGesGvGKsslv..rellralekd..ggiflrgkcdqlesaipysalaqalareellrqlldeaesa 92 
                                        sg  e+++l+ + G+GK++l+       ++ ++  ++++++ + + l      +++ ++l++ + +   +++    
  gi|320101413|ref|YP_004177005.1|  79 VSG--ENTVLIAPTGMGKTTLLivY--SLYAARRgkRVVYIAPTRVLL--T---QVYRRILDAASRIGLADSMILMY 146
                                       455..7999*************544..444444411444444444444..1...22555555556666666666667 PP

                            AAA_16  93 eleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade 149
                                       + +a ++k eeala +++ +  +    +  l+r  +ll +  +p v++ Dd++ +  
  gi|320101413|ref|YP_004177005.1| 147 DSSAGKKKREEALARIKQGDYRILVVTNSFLSRKTDLLLP-VKPDVVIADDVDSIVR 202
                                       8888999999999988888888888888888888877787.7889999999996655 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.041        35      70      98 ..      10      40 ..       3      44 .. 0.80
   2 ?    9.5   0.6    0.0011      0.95      72      96 ..     702     723 ..     695     733 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.041
                                      EEEETTTS-EEECHH.H.HHS-TTTSSS-EE CS
                              HypA 70 kvrCreCgkefelee.k.alrCpkCgsadve 98
                                      k  C +Cg +++ +e +   +C+kC++++++
  gi|320101413|ref|YP_004177005.1| 10 KGFCPVCGGDVSASElElYGSCKKCSRSSLT 40
                                      568*******99776444559****998775 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                                       EETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  72 rCreCgkefeleekalrCpkCgsad 96 
                                       rCr Cg++f++    ++Cp+Cgs+ 
  gi|320101413|ref|YP_004177005.1| 702 RCRLCGTQFTSG---ETCPRCGSRV 723
                                       8********977...36*****975 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.34   2.9e+02       3      24 ..      13      36 ..      10      43 .. 0.68
   2 ?   10.0   0.2   0.00078      0.66      17      39 ..     701     723 ..     690     728 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.34
                                      -SSS-S--EE-S..SEEE-TTT-- CS
                    zinc-ribbons_6  3 CpeCqqelekrg..eqyhCeaCqe 24
                                      Cp C   ++ ++     +C++C++
  gi|320101413|ref|YP_004177005.1| 13 CPVCGGDVSASEleLYGSCKKCSR 36
                                      888888888555224447888876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00078
                                       EE-TTT--EEEEEEE-SSS-S-- CS
                    zinc-ribbons_6  17 yhCeaCqedlkkealCpeCeqel 39 
                                        +C+ C ++++   +Cp+C++++
  gi|320101413|ref|YP_004177005.1| 701 KRCRLCGTQFTSGETCPRCGSRV 723
                                       68*****************9976 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00045      0.38       5      53 ..      82     129 ..      78     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                                       -EEEEE--TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHT CS
                        Flavi_DEAD   5 kltvldlhPGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeeal 53 
                                       + tvl +  G Gkt  +++  +  a++r +r + +aPtrv l+ +++ +
  gi|320101413|ref|YP_004177005.1|  82 ENTVLIAPTGMGKTTLLIVYSLY-AARRGKRVVYIAPTRVLLTQVYRRI 129
                                       667888888*****999998886.568999************9998655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00053      0.45       8      62 ..      79     129 ..      71     271 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                       ++ ++ +++a+ G+GKT++l     ++ ++g    ++++ +a+t+    ++  r+
  gi|320101413|ref|YP_004177005.1|  79 VSGENTVLIAPTGMGKTTLLIVYSLYAARRG----KRVVYIAPTRVLLTQVYRRI 129
                                       5678899***********9977766666666....78999999997666666655 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.0     0.051        44      19      45 ..      12      36 ..       9      37 .. 0.83
   2 ?    7.5   0.6    0.0048       4.1      14      33 ..     709     728 ..     702     736 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.051
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayriktrglfqCkeCrk 45
                                      f CP Cg++ +a +++   +  Ck+C++
  gi|320101413|ref|YP_004177005.1| 12 F-CPVCGGDvSASELEL--YGSCKKCSR 36
                                      4.*******98888886..778999987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0048
                     Zn_Tnp_IS1595  14 rWpngfvCPhCgsrkayrik 33 
                                        + +g +CP+Cgsr ++  k
  gi|320101413|ref|YP_004177005.1| 709 QFTSGETCPRCGSRVFTDSK 728
                                       5678899*****99766555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.23     2e+02      29      36 ..      13      20 ..       3      23 .. 0.79
   2 ?   10.1   1.8   0.00079      0.67       7      36 ..     702     723 ..     695     724 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.23
                       Zn-ribbon_8 29 CPeCgsev 36
                                      CP Cg++v
  gi|320101413|ref|YP_004177005.1| 13 CPVCGGDV 20
                                      *****987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00079
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgsev 36 
                                       rC+ Cg++f+     s    ++CP+Cgs+v
  gi|320101413|ref|YP_004177005.1| 702 RCRLCGTQFT-----S---GETCPRCGSRV 723
                                       6********9.....2...568*****965 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.6       1.6   1.4e+03      18      24 ..      12      18 ..      11      38 .. 0.58
   2 ?    9.5   0.6    0.0008      0.68      13      35 ..     697     720 ..     694     722 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                                      E-TTT-- CS
                              RecR 18 hCsrCgn 24
                                      +C++Cg 
  gi|320101413|ref|YP_004177005.1| 12 FCPVCGG 18
                                      7999985 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0008
                                       HHH-EE-TTT--E.ESSSS-CCCC CS
                              RecR  13 kekvrhCsrCgnl.teedlCaICs 35 
                                        e++++C+ Cg+  t  + C+ C 
  gi|320101413|ref|YP_004177005.1| 697 YESIKRCRLCGTQfTSGETCPRCG 720
                                       689********966*********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); 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):              21  [number of targets reported over threshold]
# CPU time: 0.90u 0.30s 00:00:01.20 Elapsed: 00:00:00.46
# Mc/sec: 7945.87
//
Query:       gi|320101414|ref|YP_004177006.1|  [L=87]
Description: nucleoid protein Alba [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-08   32.3   0.3    8.3e-08   31.9   0.1    1.4  2  Alba      Alba


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   4.6e-12   8.3e-08       4      63 ..       8      64 ..       5      68 .. 0.87
   2 ?   -3.3   0.0      0.45   8.1e+03      48      54 ..      70      76 ..      69      85 .. 0.57

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 4.6e-12
                                      EE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEE CS
                              Alba  4 yVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvl 63
                                       V++ +++ +y+ +++ ++ +++ e Vvlk++G  Is+Av++++ l +r+g++ +++ ++
  gi|320101414|ref|YP_004177006.1|  8 NVGR-KSLDDYIVEVILMF-QEGSERVVLKGVGPYISRAVDLYNALVSRMGDS-VELVKV 64
                                      6888.99************.******************************863.655555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.45
                                      HHHHHTC CS
                              Alba 48 ilkrrfg 54
                                       +k r++
  gi|320101414|ref|YP_004177006.1| 70 RIKGRMK 76
                                      5666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); 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: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 749.25
//
Query:       gi|320101415|ref|YP_004177007.1|  [L=173]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-37  127.4   0.0      3e-37  127.2   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   0.0   1.7e-41     3e-37       1     125 [.      42     165 ..      42     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 1.7e-41
                                       EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHH CS
                     Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaal 77 
                                       +vl+p+++++l p  r++v ++gi vvd+sW+rl+  +f+ ++   + +LP L+ +NpvnYgkp+ Ls++EA+aa+l
  gi|320101415|ref|YP_004177007.1|  42 VVLNPYSQEYLGPWLRDTVLQQGILVVDASWRRLSPSRFTGIR-GLHVKLPPLLPGNPVNYGKPCILSSIEAVAASL 117
                                       89**************************************995.68899**************************** PP

                                       HHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHH CS
                     Ribo_biogen_C  78 yilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqke 125
                                       yi+g++ee ++ll  +kw+++F elnkell++Y+k k+  e++++ +e
  gi|320101415|ref|YP_004177007.1| 118 YITGFHEEYSRLLGLYKWMKTFHELNKELLDAYSKSKTPGELESAISE 165
                                       **************************************9999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1280.98
//
Query:       gi|320101416|ref|YP_004177008.1|  [L=87]
Description: AsnC family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   56.1   0.8      3e-15   55.9   0.8    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.061   13.3   0.0      0.069   13.1   0.0    1.3  1  GYD             GYD domain
      0.063   13.7   0.6        0.1   13.1   0.6    1.3  1  HMA             Heavy-metal-associated 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 !   55.9   0.8     5e-19     3e-15       1      75 []      12      83 ..      12      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 5e-19
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75
                                      +l+++e g+     ++ ++l ++peV+e+y+v G yd++lk+ ++ le +++++ +k+++ p+++ t t+i+ e+
  gi|320101416|ref|YP_004177008.1| 12 ILIQTEIGA---EAKVLDELFKIPEVKEAYVVYGTYDIVLKIEAEALEKIREIVTNKIRKYPDIRTTVTMIIVEE 83
                                      678999999...99*********************************************************9985 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.069      36      86 ..      33      84 ..      15      87 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                               GYD 36 kleslyatlGeyDvvvivEapDdetaaalsl.alaasGtvrtetlrafteee 86
                                      ++++ y++ G yD+v  +Ea+  e++  +   +++++  +rt+++  + ee+
  gi|320101416|ref|YP_004177008.1| 33 EVKEAYVVYGTYDIVLKIEAEALEKIREIVTnKIRKYPDIRTTVTMIIVEEK 84
                                      6899****************99888877654257777777776655555555 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   1.7e-05       0.1      13      58 ..      21      64 ..      19      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                               HMA 13 aakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiek 58
                                      +akv + L ++p+V+++ v ++t   + + +ae+  l+ki+e + +
  gi|320101416|ref|YP_004177008.1| 21 EAKVLDELFKIPEVKEAYVVYGTYDIVLKIEAEA--LEKIREIVTN 64
                                      789***************************9999..4666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 671.68
//
Query:       gi|320101417|ref|YP_004177009.1|  [L=361]
Description: tyrosyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-49  167.1   0.0    1.1e-47  162.8   0.0    2.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
       0.16   10.2   0.0       0.26    9.6   0.0    1.3  1  DUF2309       Uncharacterized protein conserved in bacteria (


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 !  162.8   0.0   1.2e-51   1.1e-47       5     292 ..      32     334 ..      28     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: 162.8 bits;  conditional E-value: 1.2e-51
                                       --EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCH CS
                      tRNA-synt_1b   5 plrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgld 81 
                                       + r y G++P+g +H+G+lv + k+++l kag++  +l a +hA+i+d+   +++ +rk+++++  +   + a+g++
  gi|320101417|ref|YP_004177009.1|  32 RPRGYIGFEPSGLVHVGWLVWMFKVRDLVKAGVDFHILEATWHAYINDKLGGDMELIRKAARYTRIV---LDAIGVP 105
                                       6788**********************************************99***************...88999** PP

                                       TTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEG CS
                      tRNA-synt_1b  82 pekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGs 158
                                        + ++++   e  + ++++  l + +k++sl+r+ ++ +++ r   + +  ++ ++Ypl+q  Di++l+ d+ +gG+
  gi|320101417|ref|YP_004177009.1| 106 ESSVKYIDAEELASDKDYWATLLRAAKHTSLARVRRALTIMGRRMDEGETDFSKLIYPLMQVTDIFYLDLDIALGGM 182
                                       *9*************************************66555553589*************************** PP

                                       GGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTS...............SSBTTCETTCGC-BTTCCHHHHHH CS
                      tRNA-synt_1b 159 DQkqnielgrdlarrfnkkevfkkpegltvplltgldG...............ekKmSKSagnsaIfLddekesvkk 220
                                       DQ++   l+rd+a+r++++    kp+++ +p++tgl+G                 KmSKS++++a+f  d++e v++
  gi|320101417|ref|YP_004177009.1| 183 DQRKAHMLTRDIAERLGRR----KPVAIHTPIITGLQGpgermgggeydevaaSVKMSKSKPETAVFVHDSPEAVEA 255
                                       *******************....99999999666666544444444444333356********************** PP

                                       HHHHCHCSTTC.......SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 221 kiqkavtdsde.......evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealne 290
                                       ki ka++ ++        e+ k+l  + e ++ ++er e+++g+   + + +l++ +v++++h+ dlkka+a+aln+
  gi|320101417|ref|YP_004177009.1| 256 KILKAYCPPRTvefnpivEINKYLLFQQEGFKLVVERPEKYGGTIIVENYADLEKMYVNGEIHPLDLKKATANALNK 332
                                       *********999899999999999999999999************999***************************** PP

                                       HH CS
                      tRNA-synt_1b 291 ll 292
                                       ll
  gi|320101417|ref|YP_004177009.1| 333 LL 334
                                       98 PP

>> DUF2309  Uncharacterized protein conserved in bacteria (DUF2309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   2.9e-05      0.26      17      87 ..     272     354 ..     262     361 .] 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 2.9e-05
                           DUF2309  17 fvahNplhgledlpfeeavaelaklfgarlylseeeyrealaegrideedLeaaeeel............eeeetla 81 
                                       +v  N +  ++++ f+ +v++ +k  g+ ++ + +++++ + +g+i++ dL++a+++             e++++ +
  gi|320101417|ref|YP_004177009.1| 272 IVEINKYLLFQQEGFKLVVERPEKYGGTIIVENYADLEKMYVNGEIHPLDLKKATANAlnklldpirrriESDPEAR 348
                                       6899**************************************************42222333333333334444555 PP

                           DUF2309  82 elldal 87 
                                        +l++l
  gi|320101417|ref|YP_004177009.1| 349 GVLEEL 354
                                       555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2577.29
//
Query:       gi|320101418|ref|YP_004177010.1|  [L=228]
Description: metal-dependent hydrolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-25   87.3   0.2    1.3e-24   86.8   0.2    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.1e-24   87.2   0.1    1.4e-24   86.8   0.1    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.3e-11   44.9   3.5    1.9e-11   44.3   3.5    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.2   2.2e-28   1.3e-24       2     201 .]      25     191 ..      24     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 2.2e-28
                                       EEEES--TTHHHHHTCGGS--S...SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCG CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPve...lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfv 75 
                                       +iLiD++ +     +++  Pv+    rd+  +id V++th+H DH+ ++  l++ ++  ++l++  +++ + e++  
  gi|320101418|ref|YP_004177010.1|  25 NILIDPWVE-----NPLS-PVKvgdYRDR--RIDYVIVTHDHGDHMGNAIELAKATG--ATLIGIYETALYAEER-- 89 
                                       9********.....4554.4443345555..***********************544..7899999999998888.. PP

                                       HHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH.HH CS
                     Lactamase_B_2  76 ylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee.ig 151
                                               +v+++  ++g+ +++   ++e+ +tpa h+s r      g   G+++ g + +vy++gDtg ++e+ + 
  gi|320101418|ref|YP_004177010.1|  90 --------GVKAVGGNIGGALKIS--DVEVVLTPATHSSTR------GSPTGVIVHGRDLTVYHAGDTGLFSEMaLI 150
                                       ........56789999*******9..689************......*************************66444 PP

                                       HHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 152 erlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                        +l+ +d+++l+i+         +++++ ++eav+a++ +++k+++++H+
  gi|320101418|ref|YP_004177010.1| 151 GELYRPDVAMLPIG---------GHFTMGIREAVKAVELIKPKIAIPMHY 191
                                       58888*********.........8899999*******************7 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.1   2.4e-28   1.4e-24       2     163 .]       4     190 ..       3     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 2.4e-28
                     Lactamase_B_3   2 ltwlghnsflleta...g..arilvDPf.....ka.nlgyeppaeeaDlvlisqaledHahle.tlkql........ 58 
                                       +++lgh+ f ++     g  ++il+DP+     ++ ++g +   +++D v++++++ dH+  + +l+++        
  gi|320101418|ref|YP_004177010.1|   4 IKYLGHSFFEITLTgldGavKNILIDPWvenplSPvKVGDY-RDRRIDYVIVTHDHGDHMGNAiELAKAtgatligi 79 
                                       89*******9997413256789******8777633356655.4599*************854413444356677766 PP

                     Lactamase_B_3  59 ........aenvkvlee..geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelke 125
                                               ++ vk + +  g++l++ ++e+  +++ h ++ gs+    +g +++ ++lt+yh G+++   +++ + e
  gi|320101418|ref|YP_004177010.1|  80 yetalyaeERGVKAVGGniGGALKISDVEVVLTPATHSSTRGSP----TGVIVHGRDLTVYHAGDTGLFSEMALIGE 152
                                       66666544444444444778999999999999999997665555....5579999**************9******* PP

                     Lactamase_B_3 126 lgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                       l r+Dv ++P+gg++t+g +ea+++++++kpk+ +Pmh
  gi|320101418|ref|YP_004177010.1| 153 LYRPDVAMLPIGGHFTMGIREAVKAVELIKPKIAIPMH 190
                                       *************************************9 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   3.5   3.2e-15   1.9e-11      17     169 ..      25     168 ..      19     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.2e-15
                                       EEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHH CS
                       Lactamase_B  17 viLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasr 93 
                                       +iLiD+ ++++ +  +      ++ ++++d+vi+TH H DH+G++ +l++at++  +  +e+a + +++++      
  gi|320101418|ref|YP_004177010.1|  25 NILIDPWVENPLSPVK----VGDYRDRRIDYVIVTHDHGDHMGNAIELAKATGATLIGIYETALYAEERGV------ 91 
                                       6777777777777764....578899*********************************************...... PP

                                       CCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTS.CCEEEEEETTCCEEEECTTTSSHHCCCCCC....... CS
                       Lactamase_B  94 kglllagvsadkpdvdeeeldgnaggrralyvtggpghg.hghgvveygggkvlftGDallagetgridl....... 162
                                                +   ++    l + + +++++++t+  + g +++++v+ ++ +v  +GD++l  e ++i++       
  gi|320101418|ref|YP_004177010.1|  92 ---------KAVGGNIGGALKISDVEVVLTPATHSSTRGsPTGVIVHGRDLTVYHAGDTGLFSEMALIGElyrpdva 159
                                       .........4467788999999999999999999998661556666669**************99999997766665 PP

                                       ...TTCEEE CS
                       Lactamase_B 163 ..tlrgaev 169
                                         +++g+++
  gi|320101418|ref|YP_004177010.1| 160 mlPIGGHFT 168
                                       554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1640.36
//
Query:       gi|320101419|ref|YP_004177011.1|  [L=296]
Description: methionine aminopeptidase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-40  138.1   0.0    3.9e-40  137.8   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8   0.0   2.2e-44   3.9e-40       2     208 ..       9     287 ..       8     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 2.2e-44
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegd 75 
                                       ++++a+ ia+ ++e++++ +kpg++  e+a+ +e +  +r+ ++++afp  v +g+n+ ++hytp   ++  + +g 
  gi|320101419|ref|YP_004177011.1|   9 KLKRAGWIARVVREEAAKLVKPGMSLLEVAERVEGR--IRELGGEPAFP--VNIGVNHVAAHYTPppgDSSIIPDGS 81 
                                       6899******************************88..778889*****..************9977556669**** PP

                                       EEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSC CS
                     Peptidase_M24  76 lvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphg 152
                                       +v+id+g+++dgy++D++ Tv++   +p+++ l+ea ++a+e++++ vkpGv++sei+++++e+++s+g+  +++++
  gi|320101419|ref|YP_004177011.1|  82 IVKIDLGVHVDGYIADTATTVSF---NPAYEGLVEASQRALERVVEFVKPGVKASEIGRIIEETIKSRGF-NPVRNL 154
                                       ***********************...899999**************************************.999*** PP

                                       SEEEESS.SSSEEEEEESSSTT...CSSB--TTBEEEEEE...............EEEEETTT.............. CS
                     Peptidase_M24 153 lGHgvGl.evhdegpsvsresn...dgrkleeGmvftiEp...............giyfapge.............. 196
                                        GH++ +  +h +  s+++ +n    g +l +G v+++Ep                                     
  gi|320101419|ref|YP_004177011.1| 155 SGHSIDQyVIHSG-LSIPN-YNdffAGWRLGPG-VYAVEPfastgvglvsegrsvT------Iyslkrkkarlppgv 222
                                       ******98***88.55554.2223467777777.7778887777653333333332......033333455555555 PP

                                       ....................................................E.EEEEBEEEEEE CS
                     Peptidase_M24 197 ....................................................g.gvriedtvlvt 208
                                                                                           g + ++e+t++vt
  gi|320101419|ref|YP_004177011.1| 223 vevyekvfnerrtlpfaerwllkytgnpqmavrfmakagvlheypvlversgGlVSQFEHTFIVT 287
                                       6666666666677777777799999999***********************988**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2233.39
//
Query:       gi|320101420|ref|YP_004177012.1|  [L=364]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-148  492.3   7.3   8.1e-148  492.2   7.3    1.0  1  DUF1512   Protein of unknown function (DUF1512)


Domain annotation for each model (and alignments):
>> DUF1512  Protein of unknown function (DUF1512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.2   7.3  4.5e-152  8.1e-148       2     356 .]       9     363 ..       8     363 .. 1.00

  Alignments for each domain:
  == domain 1  score: 492.2 bits;  conditional E-value: 4.5e-152
                           DUF1512   2 isliifllllillllglnqklqlavllrdiekklakleklaeeakkkvvellkklgkedpkklverlleffviePvd 78 
                                       i+++i+l+l++l+++glnqk+q++++++di+ kl  +++++ee+k++++++l++lg ++p+ lv+r++eff+iePv+
  gi|320101420|ref|YP_004177012.1|   9 IIQVIWLILFFLIVTGLNQKIQMKIWITDIRMKLGLISSIVEEDKQRAKNMLRNLGLQTPEVLVDRVIEFFTIEPVE 85 
                                       89*************************************************************************** PP

                           DUF1512  79 lePtgivkrlehllrtsedklkklvekllpeadeversnvetaleiasalnliykvvrHylllakktknlvlllqlq 155
                                       +eP +i+kr++hl+rt++++++k+ve++lp++ ++ers vet+l+i+  l++iykvvrHyll+++k++n++l++qlq
  gi|320101420|ref|YP_004177012.1|  86 VEPIDIIKRMDHLIRTTDTTVRKMVESSLPHVGKYERSLVETTLSIVGVLHMIYKVVRHYLLTGEKENNWILIMQLQ 162
                                       ***************************************************************************** PP

                           DUF1512 156 mllplllklaeayekalkaflkgkPvGDgaGplvaakllekkekksleaakdtviaevelegrkvivvkaeGpgstv 232
                                       +++p++lk++++y++al+af++gkP+GDg+Gplva++l+e+++k s+++ +dt+i+e ++++r+++vvkaeGpgs+v
  gi|320101420|ref|YP_004177012.1| 163 LQMPQILKYVNTYHEALDAFTTGKPIGDGVGPLVAYRLIESGKKVSTRVLEDTSITELWYKDRRIFVVKAEGPGSNV 239
                                       ***************************************************************************** PP

                           DUF1512 233 GrlgeavekiveklkekvdliitvDAalkLEGEetgsvaeGvGvaiGdpGvekikiErvatkygipldaviikmsle 309
                                       G++g++++++v++l++ vdliitvDAalkLEGE+tgs+aeGvG+aiGdpG+eki+iEr+a+k+gipl+a+i+km+l+
  gi|320101420|ref|YP_004177012.1| 240 GHPGAVISRLVDELNGGVDLIITVDAALKLEGESTGSIAEGVGAAIGDPGPEKIAIERAASKHGIPLRALIVKMDLR 316
                                       ***************************************************************************** PP

                           DUF1512 310 eAitaMtkeiaeavdkavervkeiikektkegetvivvGvGNtvGva 356
                                       eAit M+kei+e+++++++++++i++e+tk+ +t+iv+G+GNt+G++
  gi|320101420|ref|YP_004177012.1| 317 EAITVMRKEIFESAETTLKYLEKIMEEHTKPYSTIIVAGIGNTMGIP 363
                                       **********************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2415.30
//
Query:       gi|320101421|ref|YP_004177013.1|  [L=94]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00064   19.2   0.8       0.58    9.7   0.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0014   18.7   0.2     0.0025   17.9   0.2    1.4  1  Zn-ribbon_8      Zinc ribbon domain
     0.0056   16.7   0.1     0.0071   16.3   0.1    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0077   16.1   1.5       0.12   12.4   0.0    2.4  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0078   16.1   0.6        2.2    8.3   0.0    2.3  2  Nudix_N_2        Nudix N-terminal
  ------ inclusion threshold ------
       0.02   14.9   0.8        1.3    9.0   0.0    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.024   14.7   0.0       0.59   10.2   0.0    2.0  2  DUF2089          Protein of unknown function (DUF2089)
      0.071   13.5   2.2        1.9    8.9   0.1    2.2  2  zf-IS66          zinc-finger binding domain of transposase IS
       0.08   13.3   0.1        4.8    7.6   0.1    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.099   12.3   3.0       0.44   10.3   0.3    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.13   12.2   2.8        5.6    7.0   0.0    2.2  2  YhfH             YhfH-like protein
       0.14   12.2   0.9        4.5    7.3   0.1    2.0  2  DUF1451          Zinc-ribbon containing domain
       0.15   11.9   2.7        6.7    6.7   0.1    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.16   12.4   0.1        0.3   11.6   0.0    1.6  2  zf-C2HE          C2HE / C2H2 / C2HC zinc-binding finger
       0.17   11.6   4.0        1.3    8.7   1.3    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.38   10.5   7.2        2.5    7.9   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.44   10.0   6.4        4.7    6.8   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.48   10.6   5.0        7.9    6.7   1.3    2.4  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.48   10.1   5.5         10    5.8   0.1    2.2  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.58   10.1   4.4        5.3    7.1   0.1    2.7  3  zinc_ribbon_4    zinc-ribbon domain
       0.69    9.9   6.3        6.6    6.8   0.3    2.5  2  DUF1610          Domain of unknown function (DUF1610)
        3.6    7.5   6.0        1.8    8.5   0.1    2.2  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


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 !    9.7   0.1   0.00071      0.58       2      21 ..      45      63 ..      44      63 .. 0.86
   2 !    8.0   0.1    0.0025         2       2      10 ..      69      77 ..      68      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00071
                                      EETTTTCEECHEETSTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelv 21
                                      kC  Cg +++++D+e g+++
  gi|320101421|ref|YP_004177013.1| 45 KCTSCG-YRIERDFEAGDFI 63
                                      899999.559*******996 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      kCP+Cg+ +
  gi|320101421|ref|YP_004177013.1| 69 KCPKCGGAT 77
                                      9*****965 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   3.1e-06    0.0025       7      36 ..      45      77 ..      37      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.1e-06
                       Zn-ribbon_8  7 rCeeCghefe.vlqsis.daplta.CPeCgsev 36
                                      +C++Cg + e  + + +    ++  CP+Cg+++
  gi|320101421|ref|YP_004177013.1| 45 KCTSCGYRIErDFEAGDfIGLEKGkCPKCGGAT 77
                                      7*********744444454556667*****955 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.7e-06    0.0071      68      96 ..      41      77 ..      30      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.7e-06
                                      --EEEETTTS-EEECHHHHH.........S-TTTSSS- CS
                              HypA 68 pvkvrCreCgkefeleekal.........rCpkCgsad 96
                                      +v ++C++Cg+++e + + +         +CpkCg+a 
  gi|320101421|ref|YP_004177013.1| 41 RVLLKCTSCGYRIERDFE-AgdfiglekgKCPKCGGAT 77
                                      57789********97743.2355899999******963 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 ?   -3.0   0.0       8.8   7.2e+03      59      67 ..       4      12 ..       2      13 .. 0.81
   2 !   12.4   0.0   0.00014      0.12      42      62 ..      39      59 ..      30      60 .. 0.82
   3 ?    2.6   0.1      0.16   1.3e+02      30      36 ..      69      75 ..      66      85 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.8
                    OrfB_Zn_ribbon 59 DvnAaiNil 67
                                      D n  +Nil
  gi|320101421|ref|YP_004177013.1|  4 DPNTLYNIL 12
                                      778899997 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00014
                    OrfB_Zn_ribbon 42 lsgrtfkCpnCgfeadrDvnA 62
                                      +++ ++kC++Cg+++ rD+ A
  gi|320101421|ref|YP_004177013.1| 39 VTRVLLKCTSCGYRIERDFEA 59
                                      566789************977 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.16
                    OrfB_Zn_ribbon 30 tCseCgs 36
                                      +C++Cg 
  gi|320101421|ref|YP_004177013.1| 69 KCPKCGG 75
                                      4555554 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0027       2.2       3      18 ..      46      61 ..      46      62 .. 0.95
   2 ?    5.9   0.1     0.015        12       3      11 ..      70      78 ..      70      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0027
                                      -TTT--B-EEE--TT- CS
                         Nudix_N_2  3 CsqCGtpvelripdgD 18
                                      C++CG ++e+  ++gD
  gi|320101421|ref|YP_004177013.1| 46 CTSCGYRIERDFEAGD 61
                                      ************9999 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                                      -TTT--B-E CS
                         Nudix_N_2  3 CsqCGtpve 11
                                      C++CG++++
  gi|320101421|ref|YP_004177013.1| 70 CPKCGGATK 78
                                      9****9986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.043        35      34      45 ..      40      51 ..      27      52 .. 0.79
   2 ?    9.0   0.0    0.0016       1.3      20      32 ..      69      82 ..      65      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.043
                     Zn_Tnp_IS1595 34 trglfqCkeCrk 45
                                      tr l++C +C++
  gi|320101421|ref|YP_004177013.1| 40 TRVLLKCTSCGY 51
                                      378999****98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0016
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayri 32
                                       CP+Cg++ k++ i
  gi|320101421|ref|YP_004177013.1| 69 KCPKCGGAtKITGI 82
                                      6*****88766554 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00072      0.59      11      36 ..      42      67 ..      33      69 .. 0.81
   2 ?    2.4   0.0      0.18   1.5e+02       1      16 [.      70      85 ..      70      94 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00072
                           DUF2089 11 trlkcescettiegeFelsefarLsk 36
                                        lkc+sc+ +ie +Fe+ +f  L+k
  gi|320101421|ref|YP_004177013.1| 42 VLLKCTSCGYRIERDFEAGDFIGLEK 67
                                      458******************99986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.18
                           DUF2089  1 CPvcgeelvvtrlkce 16
                                      CP cg+  ++t +   
  gi|320101421|ref|YP_004177013.1| 70 CPKCGGATKITGIYAV 85
                                      9999999999887654 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.062        51      25      46 .]      28      50 ..      25      50 .. 0.81
   2 ?    8.9   0.1    0.0024       1.9       3      14 ..      69      79 ..      67      93 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.062
                           zf-IS66 25 ipPakfrViehirp.kyaCpcCe 46
                                        P k+   e++    ++C +C+
  gi|320101421|ref|YP_004177013.1| 28 SRPRKPQREEYVTRvLLKCTSCG 50
                                      56999999999976589****97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0024
                           zf-IS66  3 tCpcCGgllkpi 14
                                      +Cp+CGg+  +i
  gi|320101421|ref|YP_004177013.1| 69 KCPKCGGAT-KI 79
                                      7******73.33 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.08        65      27      37 ..      38      53 ..      22      64 .. 0.65
   2 ?    7.6   0.1    0.0059       4.8       5      15 ..      69      79 ..      66      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.08
                   Lar_restr_allev 27 q....cvyCadCga.s 37
                                      +       C+ Cg+  
  gi|320101421|ref|YP_004177013.1| 38 YvtrvLLKCTSCGYrI 53
                                      24445789999*9932 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0059
                   Lar_restr_allev  5 pCPfCggravl 15
                                       CP Cgg+ ++
  gi|320101421|ref|YP_004177013.1| 69 KCPKCGGATKI 79
                                      6******9876 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00055      0.44      18      27 ..      44      53 ..      40      53 .. 0.91
   2 ?    2.3   0.2      0.17   1.4e+02      19      24 ..      69      74 ..      61      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
                                      ---SSS---- CS
                    DNA_RNApol_7kD 18 iRCkeCGhRi 27
                                      ++C+ CG+Ri
  gi|320101421|ref|YP_004177013.1| 44 LKCTSCGYRI 53
                                      69*******8 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.17
                                      --SSS- CS
                    DNA_RNApol_7kD 19 RCkeCG 24
                                      +C +CG
  gi|320101421|ref|YP_004177013.1| 69 KCPKCG 74
                                      799998 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0068       5.6      15      25 ..      45      55 ..      44      59 .. 0.83
   2 ?    5.1   0.8     0.028        23      11      20 ..      65      74 ..      62      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0068
                              YhfH 15 kCteCGkeieE 25
                                      kCt+CG  ie 
  gi|320101421|ref|YP_004177013.1| 45 KCTSCGYRIER 55
                                      7******9986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.028
                              YhfH 11 LPkKkCteCG 20
                                      L+k kC++CG
  gi|320101421|ref|YP_004177013.1| 65 LEKGKCPKCG 74
                                      67789***** PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.8    0.0093       7.6     106     139 ..      35      74 ..      26      75 .. 0.61
   2 ?    7.3   0.1    0.0055       4.5     103     128 ..      56      81 ..      52      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0093
                           DUF1451 106 sGevvglGtlvCekCgkela..lkkteei....ppCpkCg 139
                                         e v+   l C++Cg +++  ++  + i     +CpkCg
  gi|320101421|ref|YP_004177013.1|  35 REEYVTRVLLKCTSCGYRIErdFEAGDFIglekGKCPKCG 74 
                                       5677788888899998877522444444422223677776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0055
                           DUF1451 103 vyqsGevvglGtlvCekCgkelalkk 128
                                        +++G+++gl +  C kCg  ++++ 
  gi|320101421|ref|YP_004177013.1|  56 DFEAGDFIGLEKGKCPKCGGATKITG 81 
                                       6899***************9999875 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 ?    6.7   0.1    0.0082       6.7      27      37 ..      42      52 ..      39      54 .. 0.84
   2 ?    5.6   0.4     0.018        15       2       9 ..      69      76 ..      68      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0082
                           TFIIS_C 27 vfykCtkCghr 37
                                      v  kCt+Cg+r
  gi|320101421|ref|YP_004177013.1| 42 VLLKCTSCGYR 52
                                      6789*****97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                           TFIIS_C  2 kCpkCgsr 9 
                                      kCpkCg+ 
  gi|320101421|ref|YP_004177013.1| 69 KCPKCGGA 76
                                      7****975 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00036       0.3      22      51 ..      28      57 ..       4      59 .. 0.84
   2 ?   -2.4   0.2       8.2   6.7e+03      39      44 ..      69      74 ..      68      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                           zf-C2HE 22 eslseeqskelilktpLkCtrCganfgnkf 51
                                      +++ ++q +e++ +  LkCt+Cg +  + f
  gi|320101421|ref|YP_004177013.1| 28 SRPRKPQREEYVTRVLLKCTSCGYRIERDF 57
                                      4566789999*9***********8877776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.2
                           zf-C2HE 39 kCtrCg 44
                                      kC +Cg
  gi|320101421|ref|YP_004177013.1| 69 KCPKCG 74
                                      799998 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.068        56      23      30 ..      45      52 ..      44      53 .. 0.85
   2 ?    8.7   1.3    0.0016       1.3       6      15 ..      70      79 ..      70      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.068
                     zf-NADH-PPase 23 vCpaCgle 30
                                       C +Cg++
  gi|320101421|ref|YP_004177013.1| 45 KCTSCGYR 52
                                      6*****98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                     zf-NADH-PPase  6 CgrCGaptep 15
                                      C++CG++t+ 
  gi|320101421|ref|YP_004177013.1| 70 CPKCGGATKI 79
                                      ********85 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0031       2.5       1      10 [.      45      54 ..      45      57 .. 0.84
   2 ?    4.5   3.1     0.037        30       1       6 [.      69      74 ..      69      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0031
                     zinc_ribbon_2  1 fCpnCGaelq 10
                                      +C++CG+ ++
  gi|320101421|ref|YP_004177013.1| 45 KCTSCGYRIE 54
                                      7*****9875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.037
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +Cp+CG
  gi|320101421|ref|YP_004177013.1| 69 KCPKCG 74
                                      688888 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0058       4.7      18      26 .]      45      53 ..      44      53 .. 0.89
   2 ?    5.7   1.7     0.013        10      19      23 ..      70      74 ..      67      76 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0058
                       zf-ribbon_3 18 vCpyCGtkl 26
                                      +C++CG+++
  gi|320101421|ref|YP_004177013.1| 45 KCTSCGYRI 53
                                      6*****987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                       zf-ribbon_3 19 CpyCG 23
                                      Cp+CG
  gi|320101421|ref|YP_004177013.1| 70 CPKCG 74
                                      66666 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.029        24       3       8 ..      45      50 ..      44      53 .. 0.92
   2 ?    6.7   1.3    0.0097       7.9       3      10 ..      69      76 ..      69      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.029
                            zf-ACC  3 KCpsCg 8 
                                      KC+sCg
  gi|320101421|ref|YP_004177013.1| 45 KCTSCG 50
                                      9****8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0097
                            zf-ACC  3 KCpsCgem 10
                                      KCp+Cg  
  gi|320101421|ref|YP_004177013.1| 69 KCPKCGGA 76
                                      9****975 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.013        10       8      17 ..      41      50 ..      35      52 .. 0.83
   2 ?    5.7   1.8     0.014        11      12      17 ..      69      74 ..      67      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                           zf-tcix  8 RGvrkCpkCG 17
                                      R + kC++CG
  gi|320101421|ref|YP_004177013.1| 41 RVLLKCTSCG 50
                                      6677****** PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                           zf-tcix 12 kCpkCG 17
                                      kCpkCG
  gi|320101421|ref|YP_004177013.1| 69 KCPKCG 74
                                      9****9 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0065       5.3      23      35 ..      41      53 ..      39      54 .. 0.82
   2 ?    4.0   0.4     0.059        48      27      32 ..      69      74 ..      66      76 .. 0.80
   3 ?   -2.0   0.0       4.5   3.7e+03      12      19 ..      83      90 ..      82      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0065
                     zinc_ribbon_4 23 gvkvrCskCghvF 35
                                      +v ++C+ Cg  +
  gi|320101421|ref|YP_004177013.1| 41 RVLLKCTSCGYRI 53
                                      6789*****9865 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.059
                     zinc_ribbon_4 27 rCskCg 32
                                      +C+kCg
  gi|320101421|ref|YP_004177013.1| 69 KCPKCG 74
                                      788887 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.5
                     zinc_ribbon_4 12 yeiddekl 19
                                      y+++ +k+
  gi|320101421|ref|YP_004177013.1| 83 YAVEKSKV 90
                                      99999996 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3     0.008       6.6       1       8 [.      46      53 ..      46      54 .. 0.84
   2 ?    5.4   1.4     0.022        18      19      23 ..      70      74 ..      65      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.008
                           DUF1610  1 CtSCGael 8 
                                      CtSCG  +
  gi|320101421|ref|YP_004177013.1| 46 CTSCGYRI 53
                                      *****765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                           DUF1610 19 CPNCG 23
                                      CP+CG
  gi|320101421|ref|YP_004177013.1| 70 CPKCG 74
                                      ****9 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0022       1.8      18      33 ..      38      55 ..      33      58 .. 0.72
   2 ?    0.8   1.7      0.55   4.5e+02       4       8 ..      70      74 ..      70      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0022
                                      CCCE..EEESSSS-EEES CS
                    RNA_POL_M_15KD 18 egkn..feCrqCgYeepa 33
                                       +++  + C +CgY  + 
  gi|320101421|ref|YP_004177013.1| 38 YVTRvlLKCTSCGYRIER 55
                                      45555899******8775 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.55
                                      ESTTT CS
                    RNA_POL_M_15KD  4 CpkCg 8 
                                      CpkCg
  gi|320101421|ref|YP_004177013.1| 70 CPKCG 74
                                      ****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      872  (0.0486363); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 664.60
//
Query:       gi|320101422|ref|YP_004177014.1|  [L=101]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for 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   1.6      9e-17   61.2   1.6    1.4  2  DUF1805   Domain of unknown function (DUF1805)


Domain annotation for each model (and alignments):
>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.67   1.2e+04      16      30 ..       9      19 ..       5      22 .. 0.54
   2 !   61.2   1.6     5e-21     9e-17       1      63 []      43     101 .]      43     101 .] 0.99

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.67
                                      -EEE-....-S--SH CS
                           DUF1805 16 laarvivagsGVrtl 30
                                      ++ +v    +G +tl
  gi|320101422|ref|YP_004177014.1|  9 VKKIV----VGGKTL 19
                                      33334....666665 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 5e-21
                                       E-TT--HHHHHHTT--EEE-....-S--SHHHHHHSB-SEE-HHHHHTT--TT-BHHHHGGGG CS
                           DUF1805   1 mCGaLdvealeklgdlaarvivagsGVrtledllaapvesvteaAeelGikeGmtgkeaLekl 63 
                                       mCG Ld++a+e+lg +a++v    sGVr++ed+l +++ ++t +A+e G+ +G+++ e+++kl
  gi|320101422|ref|YP_004177014.1|  43 MCGLLDIQAAERLGVAAVKV----SGVRSVEDMLGKEISDATVKAREQGLLKGVKLVEVVDKL 101
                                       9*******************....************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 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:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 753.36
//
Query:       gi|320101423|ref|YP_004177015.1|  [L=469]
Description: pyruvate kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-83  278.4   0.0    8.1e-83  278.2   0.0    1.1  1  PK         Pyruvate kinase, barrel domain
    2.8e-09   37.2   0.1    4.4e-08   33.4   0.0    2.8  4  PK_C       Pyruvate kinase, alpha/beta domain
  ------ inclusion threshold ------
        2.8    8.3   4.1        4.6    7.6   0.2    2.6  2  HTH_Tnp_1  Transposase


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.2   0.0   1.4e-86   8.1e-83       3     344 ..       3     336 ..       1     340 [. 0.98

  Alignments for each domain:
  == domain 1  score: 278.2 bits;  conditional E-value: 1.4e-86
                                       -SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTT CS
                                PK   3 rtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkd 79 
                                       ++ki++tlGP+s++ + ++k++++G+  +r+n +hG+  +  e ++ vre+  +l + + ++lDt Gp++r g +++
  gi|320101423|ref|YP_004177015.1|   3 KVKIIATLGPSSRDHDVVKKMVREGAAGFRINCAHGDEADWLEYVKIVREVSSELDQAIPLILDTPGPQVRSGDFQE 79 
                                       89*************************************************************************99 PP

                                       CSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE CS
                                PK  80 gkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvl 156
                                           +++++gdk+ +s+d + ke    + i++  ++  +  ++G+til  DG +s++v ev e   +e  + n+gv+
  gi|320101423|ref|YP_004177015.1|  80 ----FKVVRGDKVLFSMDPDAKE---GKHIVVPAREFYSAASIGDTILYGDGEVSFRVSEVGEGF-VEALALNEGVV 148
                                       ....89**************997...599*********************************999.*********** PP

                                       -SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHTH CS
                                PK 157 gskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegvenl 233
                                       + +k v + g + d+   se D++  +f+ + +  ++a+s+vr+  Dv+ +r++l ++g    +iakie + g +n+
  gi|320101423|ref|YP_004177015.1| 149 KPRKKVVVEGKEYDVLFPSETDRRVFKFSSEVKASFVALSYVRRQRDVEVARDILAKHGWVPGLIAKIETRSGFNNM 225
                                       ***************999*********************************************************** PP

                                       HHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-S CS
                                PK 234 deileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtD 310
                                        ei++  Dg+mvarGDlG+  p e+++l+q ++++ + ++g++vi+at++lesmi+nPrp r++v D  n+v D  D
  gi|320101423|ref|YP_004177015.1| 226 GEIIRLVDGVMVARGDLGLHFPLEELPLIQERIVREAVRQGRVVIVATEVLESMIENPRPSRSDVVDLYNSVKDLVD 302
                                       ***************************************************************************** PP

                                       EEEESHHHHTSS-HHHHHHHHHHHHHHHHHTS-H CS
                                PK 311 avmLsgetakGkyPveavkamaevaleaekalke 344
                                       av+   eta GkyPve vk   ++   ae++l++
  gi|320101423|ref|YP_004177015.1| 303 AVLFTNETAVGKYPVEVVKWARKIIDAAESSLST 336
                                       *****************************99876 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.23   1.3e+03      82      99 ..     139     156 ..     123     162 .. 0.80
   2 ?   -2.1   0.0      0.76   4.5e+03      47      75 ..     195     223 ..     166     273 .. 0.59
   3 ?   -3.3   0.0       1.7     1e+04      17      38 ..     324     345 ..     322     347 .. 0.79
   4 !   33.4   0.0   7.3e-12   4.4e-08      17     104 ..     368     456 ..     355     463 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.23
                                       HHHHHHTTSS-STSEEEE CS
                              PK_C  82 vkvakeaglvkkgdevvv 99 
                                        + a+++g+vk+ ++vvv
  gi|320101423|ref|YP_004177015.1| 139 EALALNEGVVKPRKKVVV 156
                                       567899**********98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHCTTEEHHH.HHHHH...TT CS
                              PK_C  47 neltarqlalyrGvypvlvekaktaestd 75 
                                       + ++ar +   +G +p l++k +t + ++
  gi|320101423|ref|YP_004177015.1| 195 DVEVARDILAKHGWVPGLIAKIETRSGFN 223
                                       44446666666666666655555533333 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.7
                                       SEEEEE-SSSHHHHHHHHT-TS CS
                              PK_C  17 kaIvvltesGetArliskyrpk 38 
                                       ++I+ + es  +  l+s+yr++
  gi|320101423|ref|YP_004177015.1| 324 RKIIDAAESSLSTALVSEYRSS 345
                                       6788888888888999999986 PP

  == domain 4  score: 33.4 bits;  conditional E-value: 7.3e-12
                                       SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH......TTSHHHHHHHHHHHTTS CS
                              PK_C  17 kaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekakt...aestdellreavkvakeagl 90 
                                         Iv +++sG+ + l+skyrp++ i++   ++l a +l+l  G   v + +      +++ +  +r+++++++ +g+
  gi|320101423|ref|YP_004177015.1| 368 GVIVGYSRSGRMPTLLSKYRPQIRIYVGVGDKLLAEKLSLRYGLNIVDMSR--LisgEDEYERGVRKLLETLVGKGH 442
                                       579****************************************99997654..323445555578888999999*** PP

                                       S-STSEEEEEE-SS CS
                              PK_C  91 vkkgdevvvtaGtp 104
                                       v++gd vv t   p
  gi|320101423|ref|YP_004177015.1| 443 VRPGDIVVETYAKP 456
                                       ********886655 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2   0.00076       4.6       6      32 ..     175     201 ..     171     207 .. 0.92
   2 ?    0.6   0.4      0.12   7.1e+02      13      27 ..     256     270 ..     254     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00076
                         HTH_Tnp_1   6 rwsdefKariVreslepgksvsevArr 32 
                                       ++s e+Ka++V++s+    + +evAr+
  gi|320101423|ref|YP_004177015.1| 175 KFSSEVKASFVALSYVRRQRDVEVARD 201
                                       8***************99999****96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                         HTH_Tnp_1  13 ariVreslepgksvs 27 
                                       +riVre++ +g+ v 
  gi|320101423|ref|YP_004177015.1| 256 ERIVREAVRQGRVVI 270
                                       79*****88887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3317.43
//
Query:       gi|320101424|ref|YP_004177016.1|  [L=230]
Description: triosephosphate isomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-15   56.9   0.0    1.7e-14   53.8   0.0    1.9  2  TIM           Triosephosphate isomerase
    1.2e-06   28.0   0.9    1.6e-06   27.6   0.9    1.2  1  ThiG          Thiazole biosynthesis protein ThiG
    0.00029   20.1   0.1    0.00043   19.5   0.1    1.2  1  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.011   14.8   0.7       0.03   13.4   0.2    1.8  2  FMN_dh        FMN-dependent dehydrogenase
      0.016   14.4   0.2       0.02   14.1   0.2    1.2  1  DHO_dh        Dihydroorotate dehydrogenase
      0.021   14.3   0.2       0.14   11.5   0.1    2.1  2  His_biosynth  Histidine biosynthesis protein
      0.069   13.2   0.2       0.74    9.9   0.1    2.2  2  B12-binding   B12 binding domain
      0.081   12.4   0.2       0.12   11.8   0.2    1.3  1  CutC          CutC family


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 !   53.8   0.0   7.6e-18   1.7e-14       2     123 ..       5     125 ..       4     135 .. 0.80
   2 ?    1.1   0.0     0.097   2.2e+02     159     189 ..     141     174 ..     128     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 7.6e-18
                                       EEEEE-TBTS-HHHHHHHHHH...HHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--B CS
                               TIM   2 liagNwKmnktleeakellkk...lkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevs 75 
                                       ++a N+K +  ++   +  +    +    +e+ vev++appf++l+++ ++++++++k++aq ++  + Ga TG + 
  gi|320101424|ref|YP_004177016.1|   5 ILAVNFKAYYPHSFGGNAYRIaldAVRVWRETGVEVILAPPFTELRRILEAVSGTEVKVYAQHADPVEPGAVTGFIP 81 
                                       677788888866543332222111222334479******************************************** PP

                                       HHHHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE CS
                               TIM  76 aemlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCv 123
                                        e lkd+g++ vi+ HsE +  ++E + lv    k+a++ glk+++C 
  gi|320101424|ref|YP_004177016.1|  82 LEGLKDAGIHGVILNHSEHKLRVSEVNYLV----KKAKSLGLKTLVCA 125
                                       *********************999987765....55677788888885 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.097
                                       EEEE--GGGSSSS--...--HHHHHHHHHHHHHH CS
                               TIM 159 viAYePvWAiGtgkt...atpeqaqevhaairke 189
                                       ++A eP   iGtg +   a+pe + + +++ir++
  gi|320101424|ref|YP_004177016.1| 141 MVAVEPPELIGTGVSvsrAKPEVVTNSVNMIRRV 174
                                       689999999***9771114566666666666654 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.9   7.3e-10   1.6e-06     166     222 ..     167     224 ..     136     230 .] 0.81

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 7.3e-10
                                       HHHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHH CS
                              ThiG 166 alkiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafkl 222
                                        +++i++   kv v+  AGi + +da +a++lG+ +vl+++ + +akdp ++ + ++ 
  gi|320101424|ref|YP_004177016.1| 167 SVNMIRRVNeKVTVLTGAGISNGEDAYMAVKLGTMGVLVASGIVKAKDPYQVMKDMAE 224
                                       45666654469**************************************986665554 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.9e-07   0.00043     144     253 ..     104     221 ..      95     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-07
                                       HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CH........HHHHHCHCC-TTSEE CS
                              IGPS 144 deeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdln........tteeLaklvpkdvll 212
                                        +e++ l++ akslgl+ Lv   + e+ +++  l+ +++ v   +L    v++         ++ +++  v+++v++
  gi|320101424|ref|YP_004177016.1| 104 VSEVNYLVKKAKSLGLKTLVCADTPETGAAVAVLEPDMVAVEPPELIGTGVSVSrakpevvtNSVNMIRRVNEKVTV 180
                                       5678899*************9988888888889*************8887776511111111455677777788*** PP

                                       EEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                              IGPS 213 vaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                        +  Gi++ ed+ +  + g  ++Lv + +++++d  + +++
  gi|320101424|ref|YP_004177016.1| 181 LTGAGISNGEDAYMAVKLGTMGVLVASGIVKAKDPYQVMKD 221
                                       **********************************9988775 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.32   7.2e+02     125     150 ..     107     131 ..     100     143 .. 0.82
   2 ?   13.4   0.2   1.3e-05      0.03     265     303 ..     171     209 ..     153     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHCTESEEEEESSTSS-- CS
                            FMN_dh 125 teellkraeaagykalvltvDtpvlg 150
                                       ++ l+k+a+++g+k+lv   Dtp +g
  gi|320101424|ref|YP_004177016.1| 107 VNYLVKKAKSLGLKTLVC-ADTPETG 131
                                       56799*********9986.5777655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.3e-05
                                       HHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 265 veavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                        ++v+++++vl   Gi++G+D+  A+ lG  +vl++  +
  gi|320101424|ref|YP_004177016.1| 171 IRRVNEKVTVLTGAGISNGEDAYMAVKLGTMGVLVASGI 209
                                       567899***************************998665 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   8.7e-06      0.02     185     279 ..     114     212 ..     102     230 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.7e-06
                                       HHHHTECEEEE...BSEE--CTTCCGCCCCTT....SSEEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHH CS
                            DHO_dh 185 llelkldgiivtNttvqrlaidlkseknvkan....ktGGlsGkalkdialkvirelykrlkkeipiIgvGGiesge 257
                                       ++ l+l+ ++ + t   + a+ + + + v  +     + G+s    k+  + +  ++ +r+++++ ++   Gi+ ge
  gi|320101424|ref|YP_004177016.1| 114 AKSLGLKTLVCADTPETGAAVAVLEPDMVAVEppelIGTGVSVSRAKPEVVTNSVNMIRRVNEKVTVLTGAGISNGE 190
                                       5566666666666666665554444333222224553446************************************* PP

                                       HHHHHHHHTECEEEESHHHHHH CS
                            DHO_dh 258 DalekieaGAslvqvytalvfe 279
                                       Da+  ++ G   v v +++v++
  gi|320101424|ref|YP_004177016.1| 191 DAYMAVKLGTMGVLVASGIVKA 212
                                       *********9999998888754 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.2   4.6e+02     146     171 ..     104     129 ..      85     134 .. 0.75
   2 ?   11.5   0.1   6.5e-05      0.14      60     110 ..     166     214 ..     158     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.2
                                       EEEHHHHHHHHHHTT-SEEEEEETTT CS
                      His_biosynth 146 gldavelakkleelgageilltdidr 171
                                         ++  l+kk+++lg++++++ d  +
  gi|320101424|ref|YP_004177016.1| 104 VSEVNYLVKKAKSLGLKTLVCADTPE 129
                                       45677899**********99988655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.5e-05
                                       HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-TH CS
                      His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpe 110
                                       +  ++++++ e+  ++v  G GI++ ed+  ++++g   v +++  vk ++
  gi|320101424|ref|YP_004177016.1| 166 NSVNMIRRVNEK--VTVLTGAGISNGEDAYMAVKLGTMGVLVASGIVKAKD 214
                                       567889999999..99999*********************99999887665 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       8      53 ..      18      62 ..      15      68 .. 0.74
   2 ?    9.9   0.1   0.00033      0.74      36     101 ..     123     196 ..      85     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.17
                       B12-binding  8 vggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpd 53
                                      +gg+++ ++l+++  + r+ g+eV+l    +e  +i++a+  +++ 
  gi|320101424|ref|YP_004177016.1| 18 FGGNAYRIALDAVR-VWRETGVEVILAPPFTELRRILEAVSGTEVK 62
                                      56666667777765.456669***9999999999999998877665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00033
                       B12-binding  36 anvenedivaairaekpdvvgl..........SalltsqleavkelvellkrirprvkvvvGGahpsldpeetlea 101
                                       ++++++++ aa++ ++pd+v++          S+ + ++ e v++ v++++r++++v v++G a+ s  ++ +++ 
  gi|320101424|ref|YP_004177016.1| 123 VCADTPETGAAVAVLEPDMVAVeppeligtgvSV-SRAKPEVVTNSVNMIRRVNEKVTVLTG-AGISNGEDAYMAV 196
                                       456668999999999*****99999999999888.999999***************877766.4556666665555 PP

>> CutC  CutC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   5.5e-05      0.12      81     195 ..      85     202 ..      81     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                              CutC  81 arelgldgvvlGaltadgeiDlkaleklieaaegLgvtfHrAfDvvad..peeale.qlielgvervLtsGqk..ss 152
                                       ++++g++gv+l    ++ ++ ++ ++ l+++a++Lg+      D+ ++      le +++++    ++  G    + 
  gi|320101424|ref|YP_004177016.1|  85 LKDAGIHGVILNH--SEHKLRVSEVNYLVKKAKSLGLKTLVCADTPETgaAVAVLEpDMVAVEPPELIGTGVSvsRA 159
                                       6788999998865..45678889999999****99999988889876643556677579999999999999883233 PP

                              CutC 153 alegleklaeLveqaaerieimagaGvnaenvaelakktGvae 195
                                       + e + +  +++++ +e++++++gaG++ +  a +a k G+  
  gi|320101424|ref|YP_004177016.1| 160 KPEVVTNSVNMIRRVNEKVTVLTGAGISNGEDAYMAVKLGTMG 202
                                       4567788899******************999999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1704.53
//
Query:       gi|320101425|ref|YP_004177017.1|  [L=382]
Description: fructose-bisphosphate aldolase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-185  615.1   0.0   4.8e-185  614.9   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 !  614.9   0.0  2.7e-189  4.8e-185       1     360 [.       4     363 ..       4     364 .. 1.00

  Alignments for each domain:
  == domain 1  score: 614.9 bits;  conditional E-value: 2.7e-189
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       kvtlsvikaD+Gs+aGh+ +h++ l+ ++++l+eak+kgl+idfyvt+vGDDi+li+th+kg d+ ++h+lawdafk
  gi|320101425|ref|YP_004177017.1|   4 KVTLSVIKADLGSIAGHHMPHPDQLAVATKILAEAKQKGLIIDFYVTHVGDDIQLIITHNKGPDHPDIHGLAWDAFK 80 
                                       89*************************************************************************** PP

                          FBPase_3  78 eatevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGl 154
                                       +at+va+elkly+aGqDlL++afsGnvkGlGPgvaele+eeR++epvv+f aDktepgafnlpl++ifadpfntaGl
  gi|320101425|ref|YP_004177017.1|  81 AATKVARELKLYAAGQDLLSEAFSGNVKGLGPGVAELEMEEREAEPVVTFHADKTEPGAFNLPLFRIFADPFNTAGL 157
                                       ***************************************************************************** PP

                          FBPase_3 155 vidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvyskkdeeiaavvsterlsliaGkYvGkD 231
                                       vidpk+h+Gf fev+Dv e +++ll++pee+yd+lal+g+++ry+++rvy+k+d+  aavvs+erl+liaGkYvGkD
  gi|320101425|ref|YP_004177017.1| 158 VIDPKMHDGFVFEVYDVFEGRSVLLKSPEEMYDILALIGTPGRYIVRRVYRKSDNLLAAVVSVERLNLIAGKYVGKD 234
                                       ***************************************************************************** PP

                          FBPase_3 232 DPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvgpvDl 308
                                       DPvaivRaq+glPavge+le+f++phlvaGwmrGshngplmPv+++ a++trfdgpprv+alg+++++g+l+gp+Dl
  gi|320101425|ref|YP_004177017.1| 235 DPVAIVRAQHGLPAVGEILEAFSFPHLVAGWMRGSHNGPLMPVPMRYARVTRFDGPPRVIALGWNISNGRLIGPADL 311
                                       ***************************************************************************** PP

                          FBPase_3 309 fddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerf 360
                                       fdd afde+R+ a++ia+++Rr+Gpf+phrl +ee+eYttlp+vleklk+rf
  gi|320101425|ref|YP_004177017.1| 312 FDDVAFDETRRLAQNIAEYMRRHGPFMPHRLGPEEMEYTTLPAVLEKLKDRF 363
                                       ***************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3055.56
//
Query:       gi|320101426|ref|YP_004177018.1|  [L=602]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-39  136.0   0.0    7.5e-21   75.1   0.0    2.4  2  ABC_tran         ABC transporter
    2.4e-14   53.9   7.4     0.0038   17.1   0.0    4.2  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.4e-12   46.8   2.1    0.00013   21.5   0.2    3.8  3  SMC_N            RecF/RecN/SMC N terminal domain
    1.3e-11   44.1   4.5    2.7e-11   43.1   4.5    1.6  1  RLI              Possible Fer4-like domain in RNase L inhibit
    2.2e-08   33.6   9.7    2.9e-08   33.2   4.5    2.5  2  Fer4             4Fe-4S binding domain
    4.3e-07   29.7  13.4    1.3e-05   25.0   3.8    2.4  2  Fer4_6           4Fe-4S binding domain
    8.4e-07   29.5   0.0      0.046   14.1   0.0    3.0  3  AAA_16           AAA ATPase domain
    9.4e-07   29.2   0.4      0.036   14.3   0.0    3.1  3  AAA_22           AAA domain
    2.5e-06   27.5  19.5    6.8e-05   22.9   1.1    2.3  2  Fer4_10          4Fe-4S dicluster domain
    2.8e-05   24.2   7.4    5.4e-05   23.2   7.4    1.5  1  Fer4_21          4Fe-4S dicluster domain
    3.6e-05   24.0   0.2       0.33   11.1   0.0    4.1  3  AAA_33           AAA domain
    3.7e-05   24.2   5.2    7.9e-05   23.2   5.2    1.6  1  Fer4_7           4Fe-4S dicluster domain
    6.1e-05   23.0   0.0       0.86    9.5   0.0    3.3  3  RsgA_GTPase      RsgA GTPase
    0.00012   22.6   0.0       0.29   11.7   0.0    2.9  2  AAA_18           AAA domain
    0.00013   22.0   0.0       0.21   11.5   0.0    2.3  2  Rad17            Rad17 P-loop domain
    0.00013   21.8   1.8    0.00013   21.8   1.8    2.4  2  Fer4_2           4Fe-4S binding domain
    0.00037   20.9   0.1       0.86   10.0   0.0    3.2  3  AAA              ATPase family associated with various cellul
    0.00042   20.4   7.2    0.00083   19.5   7.2    1.5  1  Fer4_9           4Fe-4S dicluster domain
    0.00074   19.3   0.2        1.9    8.1   0.0    3.1  3  AAA_15           AAA ATPase domain
    0.00087   19.1   0.2       0.38   10.4   0.0    2.5  2  AAA_30           AAA domain
      0.001   19.2   0.1        1.6    9.0   0.0    3.3  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0012   19.4   1.6        0.3   11.6   0.1    2.4  2  AAA_23           AAA domain
     0.0013   18.5   0.4        1.4    8.7   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
     0.0016   18.4   0.1       0.24   11.4   0.0    3.6  4  AAA_14           AAA domain
     0.0038   17.0   0.2       0.17   11.6   0.0    2.4  2  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.011   16.1   0.0        5.8    7.3   0.0    2.5  2  RNA_helicase     RNA helicase
      0.013   15.2   0.0        6.5    6.4   0.0    3.1  3  Thymidylate_kin  Thymidylate kinase
      0.013   15.1   0.2        5.8    6.5   0.1    2.3  2  SRP54            SRP54-type protein, GTPase domain
      0.015   15.4   2.1        1.9    8.6   0.3    2.9  3  MMR_HSR1         50S ribosome-binding GTPase
      0.016   14.4   0.0        1.4    8.1   0.0    2.4  2  NB-ARC           NB-ARC domain
      0.022   14.0   0.0        1.6    7.9   0.0    2.3  2  KAP_NTPase       KAP family P-loop domain
      0.022   14.4   0.7       0.26   10.9   0.2    2.3  2  DUF359           Protein of unknown function (DUF359)
      0.023   14.9   0.3        5.3    7.3   0.1    3.1  2  AAA_28           AAA domain
      0.026   13.2   0.0       0.46    9.1   0.0    2.1  2  AAA_13           AAA domain
      0.031   15.2   7.6      0.076   14.0   2.4    2.4  2  Fer4_16          4Fe-4S double cluster binding domain
      0.042   13.6   0.3        7.1    6.3   0.0    3.5  4  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.052   14.1   1.7      0.052   14.1   1.7    2.3  2  Fer4_4           4Fe-4S binding domain
      0.057   13.5   1.1         13    5.8   0.0    2.6  2  DUF87            Helicase HerA, central domain
      0.066   13.2   0.0         17    5.4   0.0    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.085   12.8   0.5        1.6    8.7   0.0    2.5  2  NACHT            NACHT domain
       0.09   11.7   0.3        3.1    6.7   0.0    2.2  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.15   12.7   6.7      0.078   13.5   1.6    2.0  2  Fer4_17          4Fe-4S dicluster domain
       0.16   11.8   0.1        8.5    6.2   0.0    2.3  2  dNK              Deoxynucleoside kinase
       0.21   11.2   0.4        1.4    8.5   0.0    2.2  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.78   10.2   7.6      0.097   13.1   1.7    2.0  2  Fer4_8           4Fe-4S dicluster domain
       0.82   10.4   6.1       0.13   13.0   1.4    2.2  1  Fer4_15          4Fe-4S single cluster domain
          2    9.6  15.2       0.33   12.0   4.6    2.3  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 !   58.4   0.0   2.7e-18     1e-15      10     136 ..      99     241 ..      97     242 .. 0.78
   2 !   75.1   0.0     2e-23   7.5e-21       9     137 .]     370     494 ..     367     494 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 2.7e-18
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG..B-HHHCCHCEEEE-SS....-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx..xxxxxxxxxxxxxxxx....xx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke..qeleslrkeigvlpqe....pq 69 
                                        g+++++vG+nGaGKSt +k+lag+lkp+ G+             ++g++l+   ++l s + +  v pq      +
  gi|320101426|ref|YP_004177018.1|  99 TGSILGVVGRNGAGKSTSIKILAGQLKPNLGNYssppdwdtvikYFRGTELQAyfTKLASGEVKAVVKPQYieaaRR 175
                                       699*****************************988888888887777888888553333333333444444222123 PP

                                       S-TTSBHHHH..HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxx..xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  70 lfpeltvren..esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       + +++ vre    +de+    +++++l+l++l +++v     +LSgG+ q+  +a++l+k+ + +++DEp+
  gi|320101426|ref|YP_004177018.1| 176 ILKGT-VRELmvRADERglWREVVDELNLSHLLERRV----DELSGGELQKFLVAAVLVKNGNAYFFDEPC 241
                                       33333.555598555556799****************....*****************************7 PP

  == domain 2  score: 75.1 bits;  conditional E-value: 2e-23
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx.... RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren.... 79 
                                       + ge+++i+G+nG GK+t+lkll ++ +p eG +l+            + ++i+v pqe  p++f+e tv  n    
  gi|320101426|ref|YP_004177018.1| 370 YTGEVLGILGPNGVGKTTFLKLLNREAEPLEGAVLI------------SAEKISVKPQElsPRVFSEETVMANlksa 434
                                       679*******************************55............56777777777777777777777777776 PP

                                       ......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              s+   +++++klgl+ + +++v     +LSgG+ q++a+a al+++++l++lDEp+a
  gi|320101426|ref|YP_004177018.1| 435 spatldPSSWIYHELVRKLGLNRMLERRV----DELSGGELQKLAVAVALARDADLYFLDEPSA 494
                                       66777666666999***************....*****************************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 !    9.8   0.5    0.0016      0.62       3      22 ..     104     123 ..     102     148 .. 0.72
   2 !   13.7   0.0    0.0001     0.039     226     287 ..     203     261 ..     172     271 .. 0.81
   3 !   14.4   0.4   6.7e-05     0.026       3      19 ..     376     392 ..     374     405 .. 0.86
   4 !   17.1   0.0   9.8e-06    0.0038     231     283 ..     460     513 ..     395     523 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                            AAA_21   3 vliGpNgsGKSnLLdaldll 22 
                                       +++G+Ng+GKS+ +++l + 
  gi|320101426|ref|YP_004177018.1| 104 GVVGRNGAGKSTSIKILAGQ 123
                                       79**************9653 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.0001
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                        ++  e+ ++elS G ++  +l++a+l  ++    +++DEp + L+ +   r++ +++e s+
  gi|320101426|ref|YP_004177018.1| 203 LSHLLERRVDELSGGELQK-FLVAAVLVKNG--NAYFFDEPCSYLDIRERIRVANVIREFSD 261
                                       4566788899*********.99999998888..57************998888888877765 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 6.7e-05
                            AAA_21   3 vliGpNgsGKSnLLdal 19 
                                       ++ GpNg+GK+++L++l
  gi|320101426|ref|YP_004177018.1| 376 GILGPNGVGKTTFLKLL 392
                                       799************99 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 9.8e-06
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHP.......kllrrllellk 283
                                       e+ ++elS G ++ la+++al+r++   +l+++DEp + L+        k   ++ ++++
  gi|320101426|ref|YP_004177018.1| 460 ERRVDELSGGELQKLAVAVALARDA---DLYFLDEPSAYLDVeerisvaK---TIRRIVE 513
                                       677899*******************...9************977774444...4444443 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   3.3e-07   0.00013      23     202 ..      99     275 ..      86     293 .. 0.69
   2 ?    4.2   0.0     0.068        26      26      41 ..     374     389 ..     363     393 .. 0.84
   3 !   17.6   0.0   5.4e-06    0.0021     134     186 ..     463     511 ..     403     539 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.3e-07
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       + s+  +vG+NG+GKs  +  +   L  +  +     + + +i++   +    +a+ + + + e k ++++ + ++ 
  gi|320101426|ref|YP_004177018.1|  99 TGSILGVVGRNGAGKSTSIKILAGQLKPNLGNYSSPPDWDTVIKY--FRGTELQAYFTKLASGEVK-AVVKPQYIEA 172
                                       5667789*********98877765555544444456788999999..3333344555544333333.4677777888 PP

                                       EEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-ST...TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtk.kevsellesagisk...elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                        rr+ ++   e ++   e    +ev + l+ +++ +   ++LSgGe +     +l+A   vk    y++De  + LD
  gi|320101426|ref|YP_004177018.1| 173 ARRILKGTVRELMVRADERGLwREVVDELNLSHLLErrvDELSGGELQ----KFLVAAVLVKNGNAYFFDEPCSYLD 245
                                       88888888878777655544448888888877765412279****976....45556666888999*********** PP

                                       HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkeksknaQfivislreeml 202
                                        +++ +va++++e s+ a   v+ ++++++
  gi|320101426|ref|YP_004177018.1| 246 IRERIRVANVIREFSDYARNYVVVVEHDLM 275
                                       **************9998777766666554 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.068
                                       EEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnll 41 
                                       +  i+GpNG GK+ +l
  gi|320101426|ref|YP_004177018.1| 374 VLGILGPNGVGKTTFL 389
                                       5679*********987 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 5.4e-06
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                        ++LSgGe + +a+a+ +A    + a ly+lDe  a LD +++  va+ +++ 
  gi|320101426|ref|YP_004177018.1| 463 VDELSGGELQKLAVAVALA----RDADLYFLDEPSAYLDVEERISVAKTIRRI 511
                                       459*****88777776665....7899**********************9964 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 !   43.1   4.5   7.1e-14   2.7e-11       1      31 [.       2      29 ..       2      33 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 7.1e-14
                                      --EEEES---------TTHHHHHTTSEEEES CS
                               RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvr 31
                                      +r+A+vd++ C+P+KC+  +c+rfcpv  +r
  gi|320101426|ref|YP_004177018.1|  2 VRVAVVDRNYCKPDKCSL-ECIRFCPV--NR 29
                                      69****************.********..88 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2      0.29   1.1e+02      13      21 ..      20      28 ..      19      28 .. 0.90
   2 !   33.2   4.5   7.6e-11   2.9e-08       1      24 []      45      68 ..      45      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.29
                                      HHHHHSTTT CS
                              Fer4 13 aCvevCPvg 21
                                      +C+  CPv+
  gi|320101426|ref|YP_004177018.1| 20 ECIRFCPVN 28
                                      6******98 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 7.6e-11
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      vvi e+ CigCG+Cv+ CP+ AI+
  gi|320101426|ref|YP_004177018.1| 45 VVISEDACIGCGICVKKCPFHAIS 68
                                      699*******************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 !   10.0   2.1    0.0019      0.72       1      22 [.       4      28 ..       4      36 .. 0.86
   2 !   25.0   3.8   3.4e-08   1.3e-05       2      24 .]      45      67 ..      44      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0019
                            Fer4_6  1 vveidpdkCi..gC.gdCvrvCPeg 22
                                      v+++d++ C    C  +C+r CP +
  gi|320101426|ref|YP_004177018.1|  4 VAVVDRNYCKpdKCsLECIRFCPVN 28
                                      689******9778*666******86 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 3.4e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      v+i +d+CigCg Cv+ CP+ ai
  gi|320101426|ref|YP_004177018.1| 45 VVISEDACIGCGICVKKCPFHAI 67
                                      899*****************998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00055      0.21      21     141 ..      96     270 ..      86     284 .. 0.65
   2 ?   -1.3   0.0       6.4   2.4e+03      25      35 ..     283     293 ..     272     293 .. 0.84
   3 !   14.1   0.0   0.00012     0.046      22      88 ..     370     434 ..     360     567 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00055
                            AAA_16  21 sgrp.elvllsGesGvGKsslvrellralekd.................ggiflrgkcdqlesa.......ipysal 72 
                                       ++r+ +++ ++G  G GKs+ ++ l+ +l+ +                 +g  l++ +++l s+         y+  
  gi|320101426|ref|YP_004177018.1|  96 APRTgSILGVVGRNGAGKSTSIKILAGQLKPNlgnyssppdwdtvikyfRGTELQAYFTKLASGevkavvkPQYIEA 172
                                       444448999***********************999999998888777663333666666664444444443444445 PP

                            AAA_16  73 aqalareellrqlldeaesaeleawrekleeala....................................avpelag 113
                                       a+ + + + +r+l    +++e++ wre  +e                                       +++ l+ 
  gi|320101426|ref|YP_004177018.1| 173 ARRILK-GTVRELM--VRADERGLWREVVDELNLshllerrvdelsggelqkflvaavlvkngnayffdePCSYLDI 246
                                       555545.4444443..3356777888765555548888886666666666666666666666666666666666666 PP

                            AAA_16 114 aeasrllellkrllallsrderplvlvl 141
                                        e+ r++++++++ +++++     v+v+
  gi|320101426|ref|YP_004177018.1| 247 RERIRVANVIREFSDYARN----YVVVV 270
                                       6668888888888877777....44444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.4
                            AAA_16  25 elvllsGesGv 35 
                                       ++v+++Ge+Gv
  gi|320101426|ref|YP_004177018.1| 283 NIVVVYGEPGV 293
                                       89********7 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 0.00012
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggif......lrgkcdqlesaipysalaqalareellrqllde 88 
                                        ++e++ + G+ GvGK++ ++ l r++e  +g +      ++ k ++l          +++++e++++ l+++
  gi|320101426|ref|YP_004177018.1| 370 YTGEVLGILGPNGVGKTTFLKLLNREAEPLEGAVlisaekISVKPQEL--------SPRVFSEETVMANLKSA 434
                                       45588899*****************99988755543333333333333........55666666666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1    0.0008      0.31       4      30 ..      99     125 ..      97     225 .. 0.82
   2 ?   -1.7   0.0       8.5   3.3e+03       4      16 ..     281     293 ..     279     293 .. 0.87
   3 !   14.3   0.0   9.4e-05     0.036       7     115 ..     374     511 ..     369     526 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0008
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqld 30 
                                       t +il v+G  G+GK+t+++ l+ ql+
  gi|320101426|ref|YP_004177018.1|  99 TGSILGVVGRNGAGKSTSIKILAGQLK 125
                                       678999***************999984 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8.5
                            AAA_22   4 tagilvvtGesGt 16 
                                       +++i+vv+Ge+G+
  gi|320101426|ref|YP_004177018.1| 281 SDNIVVVYGEPGV 293
                                       57899*******7 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 9.4e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee....................erpevvfvtlpsst.....sskdllr 58 
                                       +l + G+ G+GKTt l+ l ++++  +                         + e+v  +l+s +      s+ +++
  gi|320101426|ref|YP_004177018.1| 374 VLGILGPNGVGKTTFLKLLNREAEPLE---GavlisaekisvkpqelsprvFSEETVMANLKSASpatldPSSWIYH 447
                                       56689*****************96444...24558888999999998888877777766666666666734555588 PP

                            AAA_22  59 ellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsl 115
                                       el+r+lgl++   + + +el    l++ + a a      l  +DE    l+   +  + +++r++
  gi|320101426|ref|YP_004177018.1| 448 ELVRKLGLNRML-ERRVDELSgGELQKLAVAVALardADLYFLDEPSAyLDveeRISVAKTIRRI 511
                                       888888875555.4444444444444444444444444677777755546554335555555555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0  11.4   6.1e-06    0.0023       3      56 .]       6      63 ..       4      63 .. 0.84
   2 !   22.9   1.1   1.8e-07   6.8e-05       2      24 ..      45      73 ..      44      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.1e-06
                           Fer4_10  3 vidddtC..irCg.kCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+d++ C   +C  +C ++CP++  ++++a++   +++ v +  ++C+gcg Cv++CP
  gi|320101426|ref|YP_004177018.1|  6 VVDRNYCkpDKCSlECIRFCPVNRgRRKKAIELSGDNKYVVISEDACIGCGICVKKCP 63
                                      67889995448889********87777778888888888888999************9 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.8e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl......t 24
                                      vvi +d Ci+Cg Cvk CP+++       
  gi|320101426|ref|YP_004177018.1| 45 VVISEDACIGCGICVKKCPFHAisivnlP 73
                                      7899****************885444430 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   7.4   1.4e-07   5.4e-05       2      57 ..       6      67 ..       5      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.4e-07
                           Fer4_21  2 ridedkCi..gCg.kCliaCedt...shqaieidaktvlkvv.edeCvGCnlCssvCPvedci 57
                                      ++d++ C   +C  +C+  C+ +     +aie+++++++ v+ ed C+GC +C++ CP   +i
  gi|320101426|ref|YP_004177018.1|  6 VVDRNYCKpdKCSlECIRFCPVNrgrRKKAIELSGDNKYVVIsEDACIGCGICVKKCPF-HAI 67
                                      66666664336763599999876222589***9988777775499*************7.666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1      0.02       7.8       4      32 ..     105     136 ..     102     277 .. 0.64
   2 ?    0.6   0.0       1.6   5.9e+02      26      46 ..     320     340 ..     309     358 .. 0.74
   3 !   11.1   0.0   0.00087      0.33       4      33 ..     377     417 ..     374     522 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.02
                            AAA_33   4 lvGlpGsGKstlaerllkklg...avllssdt 32 
                                       +vG +G+GKst ++ l+ +l+   +   s ++
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKILAGQLKpnlGNYSSPPD 136
                                       799***********999999865533333444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.6
                            AAA_33  26 vllssdtlrrrlfgtdqqskt 46 
                                        ++++d+lr+r+ +++++++t
  gi|320101426|ref|YP_004177018.1| 320 MRIREDELRFRIQVQERKTET 340
                                       689999999999998888776 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00087
                            AAA_33   4 lvGlpGsGKstlaerllkklg....avllssdt.......l 33 
                                       + G++G+GK+t+++ l ++      avl+s  +       l
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLNREAEplegAVLISAEKisvkpqeL 417
                                       57************996665566699999988755555551 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   5.2   2.1e-07   7.9e-05       5      52 .]      17      66 ..      11      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.1e-07
                            Fer4_7  5 Cg.aCvaaCpvkaieldeeenekgt.ekveidpekClgCgaCvavCPtga 52
                                      C   C + Cpv+  + +++ + +g  ++v+i+++ C+gCg Cv+ CP+ a
  gi|320101426|ref|YP_004177018.1| 17 CSlECIRFCPVNRGRRKKAIELSGDnKYVVISEDACIGCGICVKKCPFHA 66
                                      6558******99999999987777636667899**************976 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0044       1.7      99     131 ..     100     132 ..      69     136 .. 0.84
   2 !    9.5   0.0    0.0023      0.86      98     124 ..     371     397 ..     333     411 .. 0.84
   3 ?    0.3   0.0       1.5   5.7e+02      93     110 ..     528     545 ..     494     548 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0044
                                       TSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +++  +vG  G+GKSt i+ l+++l+ + g+ s
  gi|320101426|ref|YP_004177018.1| 100 GSILGVVGRNGAGKSTSIKILAGQLKPNLGNYS 132
                                       5677789****************9998887776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                                       TTSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpele 124
                                       ++++  ++G+ GvGK+t+++ l+ e+e
  gi|320101426|ref|YP_004177018.1| 371 TGEVLGILGPNGVGKTTFLKLLNREAE 397
                                       6678889*************9998765 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.5
                                       HHHHCTTSEEEEECSTTS CS
                       RsgA_GTPase  93 lkellkdktsvlvGqSGv 110
                                       ++++++d+++v++G+ Gv
  gi|320101426|ref|YP_004177018.1| 528 VQNYISDRVMVFLGKPGV 545
                                       688999*********998 PP

>> AAA_18  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       4.2       3      91 ..     105     210 ..     103     230 .. 0.70
   2 !   11.7   0.0   0.00077      0.29       3      22 ..     377     396 ..     375     431 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.011
                            AAA_18   3 ltGtpGvGKttlakeLskrl.gf.........gvnlrdvakenglllevdpealdeskrlded.kldklldaleens 68 
                                       + G  G+GK+t  k L+  l  +         ++ ++++++  +l  ++++ a  e k ++++ + +++ ++l++  
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKILAGQLkPNlgnyssppdWDTVIKYFRGTELQAYFTKLASGEVKAVVKPqYIEAARRILKGTV 181
                                       78999***********7665433566799999999999999999999999995555555555404555666666666 PP

                            AAA_18  69 s.....aleegknl..vidghlaeleseaa 91 
                                       +     a +e + +  v+d +   ++ e++
  gi|320101426|ref|YP_004177018.1| 182 RelmvrA-DERGLWreVVDELNLSHLLERR 210
                                       6777531.2222224577776666666665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00077
                            AAA_18   3 ltGtpGvGKttlakeLskrl 22 
                                       + G+ GvGKtt+ k L+++ 
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLNREA 396
                                       89**************8874 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00054      0.21      45      79 ..     100     134 ..      85     162 .. 0.83
   2 !    8.0   0.0    0.0066       2.5      47      69 ..     374     396 ..     366     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00054
                             Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                         iL + G  G gkst +k+L+ +l ++l +++ p
  gi|320101426|ref|YP_004177018.1| 100 GSILGVVGRNGAGKSTSIKILAGQLKPNLGNYSSP 134
                                       34999********************9999988877 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0066
                             Rad17  47 iLLisGPsGCgkstvvkvLskel 69 
                                       +L i GP G gk+t +k L +e 
  gi|320101426|ref|YP_004177018.1| 374 VLGILGPNGVGKTTFLKLLNREA 396
                                       7889***************9875 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   2.3       3.5   1.3e+03       6      21 ..       8      26 ..       3      27 .. 0.60
   2 !   21.8   1.8   3.5e-07   0.00013       2      21 ..      44      63 ..      43      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.5
                            Fer4_2  6 dtdrCi.g.Cg.aCvsaCP 21
                                      d++ C    C+  C+  CP
  gi|320101426|ref|YP_004177018.1|  8 DRNYCKpDkCSlECIRFCP 26
                                      5555532336557889998 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.5e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      +vv+ +d+CigCg+Cv+ CP
  gi|320101426|ref|YP_004177018.1| 44 YVVISEDACIGCGICVKKCP 63
                                      57899*************** 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 ?   -1.3   0.0       7.2   2.7e+03     103     128 ..      64      88 ..      58      90 .. 0.82
   2 ?    6.9   0.0     0.021       7.9       3      31 ..     105     133 ..     103     181 .. 0.78
   3 !   10.0   0.0    0.0023      0.86       3      23 ..     377     397 ..     375     434 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 7.2
                                       EEEEEEESSGGGSTHHHHSTTSSEEE CS
                               AAA 103 vivigatnrpdkldpallrgRfdrki 128
                                       +  i + n pd+l++ l+ +R  + +
  gi|320101426|ref|YP_004177018.1|  64 FHAISIVNLPDELEKTLV-HRYGENM 88 
                                       7789999**********9.8987665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.021
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEET CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisg 31 
                                       ++G  G GK++ +k +a +l+ ++ + s 
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKILAGQLKPNLGNYSS 133
                                       689****************9877655554 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0023
                                       EESSTTSSHHHHHHHHHHHHT CS
                               AAA   3 lyGppGtGKTllakavakelg 23 
                                       + Gp G+GKT++ k + +e++
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLNREAE 397
                                       57**************99974 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   7.2   2.2e-06   0.00083       4      51 .]      16      67 ..      11      67 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.2e-06
                            Fer4_9  4 gCg.aCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkgai 51
                                      +C  +C++ Cp +  ++++a +    ++  +     +aCigCg Cv++Cp +ai
  gi|320101426|ref|YP_004177018.1| 16 KCSlECIRFCPVNRGRRKKAIELSGDNK--YvviseDACIGCGICVKKCPFHAI 67
                                      5764699999777665555444333222..12345589************9987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1      0.03        11      28      43 ..     105     120 ..      99     142 .. 0.92
   2 !    8.1   0.0    0.0049       1.9      28      44 ..     377     393 ..     370     418 .. 0.84
   3 ?    1.5   0.0      0.49   1.9e+02     323     356 ..     483     516 ..     475     525 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.03
                            AAA_15  28 liGkNnsGKSsileal 43 
                                       ++G+N++GKS+ +++l
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKIL 120
                                       79*********99998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0049
                            AAA_15  28 liGkNnsGKSsileald 44 
                                       + G+N++GK+++l++l+
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLN 393
                                       77************995 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.49
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       + ++++++EP a+L  +   +++k+++++++++ 
  gi|320101426|ref|YP_004177018.1| 483 DADLYFLDEPSAYLDVEERISVAKTIRRIVEEKG 516
                                       5689*************************99875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.019       7.4      20      40 ..     102     122 ..      96     133 .. 0.83
   2 !   10.4   0.0     0.001      0.38      20      55 ..     374     409 ..     368     522 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
                            AAA_30  20 vavltGpAGtGKttalkalre 40 
                                       +  ++G+ G+GK+t++k l+ 
  gi|320101426|ref|YP_004177018.1| 102 ILGVVGRNGAGKSTSIKILAG 122
                                       56799***********99875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglApt 55 
                                       v  + Gp G GKtt lk l++ +e  +g v++ A +
  gi|320101426|ref|YP_004177018.1| 374 VLGILGPNGVGKTTFLKLLNREAEPLEGAVLISAEK 409
                                       77899**************99888887788888765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.033        13      23      46 ..     204     227 ..     189     257 .. 0.84
   2 !    9.0   0.0    0.0041       1.6      21      48 ..     454     481 ..     439     510 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.033
                           SbcCD_C  23 ekelsrssgtlSGGekqflaylal 46 
                                       +  l+r++ +lSGGe q+++  a+
  gi|320101426|ref|YP_004177018.1| 204 SHLLERRVDELSGGELQKFLVAAV 227
                                       44589**********998876665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0041
                           SbcCD_C  21 gkekelsrssgtlSGGekqflaylalaa 48 
                                       g ++ l+r++ +lSGGe q+la  + +a
  gi|320101426|ref|YP_004177018.1| 454 GLNRMLERRVDELSGGELQKLAVAVALA 481
                                       5566799***********8876444332 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.026        10      24      36 ..     105     117 ..      96     124 .. 0.85
   2 !   11.6   0.1   0.00079       0.3      23      38 ..     376     391 ..     360     393 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.026
                            AAA_23  24 ItGpNGaGKTTil 36 
                                       ++G NGaGK+T +
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSI 117
                                       79*********66 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00079
                            AAA_23  23 lItGpNGaGKTTildA 38 
                                        I GpNG GKTT+l  
  gi|320101426|ref|YP_004177018.1| 376 GILGPNGVGKTTFLKL 391
                                       69***********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 !    8.7   0.0    0.0037       1.4      22      39 ..      99     117 ..      86     126 .. 0.80
   2 !    7.4   0.1    0.0094       3.6      25      39 ..     375     389 ..     368     392 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0037
                            AAA_29  22 kg.atlltGpsGsGKSTll 39 
                                        g +  ++G++G+GKST +
  gi|320101426|ref|YP_004177018.1|  99 TGsILGVVGRNGAGKSTSI 117
                                       55566699*********65 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0094
                            AAA_29  25 tlltGpsGsGKSTll 39 
                                         + Gp+G+GK+T+l
  gi|320101426|ref|YP_004177018.1| 375 LGILGPNGVGKTTFL 389
                                       5599*********97 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.6   2.3e+02       3      27 ..     101     125 ..      99     162 .. 0.85
   2 ?   -0.4   0.0       2.8   1.1e+03      51      96 ..     218     269 ..     167     271 .. 0.65
   3 !   11.4   0.0   0.00063      0.24       3      47 ..     373     416 ..     371     440 .. 0.76
   4 ?   -1.5   0.0       6.3   2.4e+03      64      89 ..     483     514 ..     443     522 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.6
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell 27 
                                        il ++G   +GK+t +k l+ +l 
  gi|320101426|ref|YP_004177018.1| 101 SILGVVGRNGAGKSTSIKILAGQLK 125
                                       688999999*******998886654 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.8
                            AAA_14  51 kllelilek.lkeekktylflDEiqev......pewekalkslvdegknldvi 96 
                                       +l +++ +  l  ++ +  f+DE   +       ++ ++++++ d  +n+ v+
  gi|320101426|ref|YP_004177018.1| 218 ELQKFLVAAvLV-KNGNAYFFDEPCSYldirerIRVANVIREFSDYARNYVVV 269
                                       344445554322.3667789999666645554466777777777777666555 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00063
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47 
                                       ++l i G+  vGKTt+lk l +e   + e  + i+ ++ + k ++
  gi|320101426|ref|YP_004177018.1| 373 EVLGILGPNGVGKTTFLKLLNREAE-PLEGAVLISAEKISVKPQE 416
                                       7899*************99988887.7788888888887775444 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 6.3
                            AAA_14  64 kktylflDEiqev......pewekalkslvde 89 
                                       +  + flDE + +       ++ k+++++v+e
  gi|320101426|ref|YP_004177018.1| 483 DADLYFLDEPSAYldveerISVAKTIRRIVEE 514
                                       45678899988874444445555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.18        67       6      22 ..     104     120 ..      99     128 .. 0.82
   2 !   11.6   0.0   0.00045      0.17       5      23 ..     375     399 ..     371     431 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.18
                            AAA_24   6 liyGpsgiGKTtlakel 22 
                                        ++G +g+GK+t++k l
  gi|320101426|ref|YP_004177018.1| 104 GVVGRNGAGKSTSIKIL 120
                                       689**********9977 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00045
                            AAA_24   5 iliyGpsgiGKTtlakel......g 23 
                                       + i Gp+g+GKTt++k l       
  gi|320101426|ref|YP_004177018.1| 375 LGILGPNGVGKTTFLKLLnreaepL 399
                                       679*************996644443 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.036        14       3      26 ..     105     128 ..     103     150 .. 0.82
   2 ?    7.3   0.0     0.015       5.8       3      22 ..     377     396 ..     375     416 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.036
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkkl 26 
                                       ++G++g GKSt +k La +l  +l
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKILAGQLKPNL 128
                                       78*************999887544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.015
                      RNA_helicase   3 lyGpsgeGKStlakeLakal 22 
                                       + Gp+g+GK+t+ k L ++ 
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLNREA 396
                                       68************987765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.017       6.5       3      36 ..     107     139 ..     105     156 .. 0.81
   2 ?    5.3   0.0     0.038        14       3      32 ..     379     408 ..     377     462 .. 0.88
   3 ?   -2.4   0.0       8.7   3.3e+03      33      59 ..     500     525 ..     492     533 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTS CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggt 36 
                                       G +GaGK+t +++l+  lk +  + + ++++ +t
  gi|320101426|ref|YP_004177018.1| 107 GRNGAGKSTSIKILAGQLKPNLGN-YSSPPDWDT 139
                                       779****************99976.666665555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.038
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESS CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltre 32 
                                       G +G+GKtt+++ll +  +    +v+++ e
  gi|320101426|ref|YP_004177018.1| 379 GPNGVGKTTFLKLLNREAEPLEGAVLISAE 408
                                       899***********9887766655666655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.7
                                       STTSHHHHHHHHHHHTCS---HHHHHH CS
                   Thymidylate_kin  33 pggteiGekirelllkeeeleeqteal 59 
                                       ++  +++++ir++++++ + +   e+ 
  gi|320101426|ref|YP_004177018.1| 500 ER-ISVAKTIRRIVEEKGKTALVVEHD 525
                                       44.678889999888777666555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.015       5.8       6      27 ..     105     126 ..     101     132 .. 0.84
   2 ?    6.2   0.0     0.018       6.9       5      23 ..     376     394 ..     373     409 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                                       EEESTTSSHHHHHHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLaallkk 27 
                                       +vG +GaGK t++  La +lk 
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKILAGQLKP 126
                                       89************99988875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.018
                                       EEEESTTSSHHHHHHHHHH CS
                             SRP54   5 llvGlqGaGKTttlaKLaa 23 
                                        ++G++G+GKTt l  L +
  gi|320101426|ref|YP_004177018.1| 376 GILGPNGVGKTTFLKLLNR 394
                                       589*********9865554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3    0.0049       1.9       3      25 ..     104     127 ..     102     134 .. 0.82
   2 ?    5.1   0.0     0.062        24       3      22 ..     376     395 ..     374     414 .. 0.84
   3 ?   -1.8   0.0       8.2   3.1e+03      67      83 ..     505     522 ..     468     570 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0049
                                       EEEESTTSSHHHHHHHHHTS.TEE CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge.kai 25 
                                       ++vGr  +GKSt i+ l g+ k  
  gi|320101426|ref|YP_004177018.1| 104 GVVGRNGAGKSTSIKILAGQlKPN 127
                                       89**************99985555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.062
                                       EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                       +i+G   vGK+t+++ l +e
  gi|320101426|ref|YP_004177018.1| 376 GILGPNGVGKTTFLKLLNRE 395
                                       89************988654 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 8.2
                                       HHHHHHHHC.TSEEEEEE CS
                          MMR_HSR1  67 gkaflalee.adlillvv 83 
                                       +k+++++ e     +lvv
  gi|320101426|ref|YP_004177018.1| 505 AKTIRRIVEeKGKTALVV 522
                                       444444333111122222 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.069        27      21      38 ..     101     118 ..      91     183 .. 0.83
   2 ?    8.1   0.0    0.0036       1.4      22      49 ..     374     401 ..     366     462 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.069
                                       EEEEEEESTTSSHHHHHH CS
                            NB-ARC  21 lvvalvGmgGvGKttlak 38 
                                        ++++vG+ G GK+t +k
  gi|320101426|ref|YP_004177018.1| 101 SILGVVGRNGAGKSTSIK 118
                                       589***********9665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0036
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg 49 
                                       v+++ G  GvGKtt +k  +++ + +eg
  gi|320101426|ref|YP_004177018.1| 374 VLGILGPNGVGKTTFLKLLNREAEPLEG 401
                                       89**************999998776666 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 ?    4.0   0.0     0.063        24       6      47 ..      86     127 ..      82     286 .. 0.88
   2 ?    7.9   0.0    0.0042       1.6      19      44 ..     371     396 ..     363     449 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.063
                        KAP_NTPase   6 saladilseptlatpivvgLygkWGsGKssllnkledelkef 47 
                                       +++ ++ + p+++t++++g+ g  G+GKs+ ++ l  +lk +
  gi|320101426|ref|YP_004177018.1|  86 ENMFKLYNLPAPRTGSILGVVGRNGAGKSTSIKILAGQLKPN 127
                                       5666677778999*******************9999888765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0042
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledel 44 
                                       t+ v+g+ g+ G+GK+++l++l +e 
  gi|320101426|ref|YP_004177018.1| 371 TGEVLGILGPNGVGKTTFLKLLNREA 396
                                       6679999***************9986 PP

>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00067      0.26      59     109 ..     254     299 ..     249     312 .. 0.78
   2 ?    1.1   0.0      0.74   2.8e+02      57     102 ..     504     544 ..     499     567 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                            DUF359  59 eaikealeseekvlilVdGEEDLavlpaillapegsvvvYGqpdeGvvlvk 109
                                       ++i+e  +  ++ +++V  E DL+vl    +++++ vvvYG p+ + v+ k
  gi|320101426|ref|YP_004177018.1| 254 NVIREFSDYARNYVVVV--EHDLMVL---DYMSDNIVVVYGEPGVYGVVSK 299
                                       56666666667777777..8999887...5899***********9988765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.74
                            DUF359  57 lieaikealeseekvlilVdGEEDLavlpaillapegsvvvYGqpd 102
                                       + ++i++++e++ k++++V  E DL+v     ++++  +v+ G p+
  gi|320101426|ref|YP_004177018.1| 504 VAKTIRRIVEEKGKTALVV--EHDLLVQ---NYISDRVMVFLGKPG 544
                                       678999**********999..8999874...456677777777776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.11        42       5      77 ..     106     194 ..     104     274 .. 0.58
   2 ?    7.3   0.1     0.014       5.3       4      23 ..     377     401 ..     375     525 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                            AAA_28   5 tGgestGKTtlleaLaar............gypvvpEaareileekl....akgedalpwv.edllafaervleeql 64 
                                       +G  ++GK+t ++ La +            ++ +v  ++r    + +    a+ge ++  v  + ++ a+r+l+  +
  gi|320101426|ref|YP_004177018.1| 106 VGRNGAGKSTSIKILAGQlkpnlgnyssppDWDTVIKYFRGTELQAYftklASGEVKA-VVkPQYIEAARRILKGTV 181
                                       68889***********443444443444555556666666554444422112222222.223466777777777776 PP

                            AAA_28  65 eeeaaaaankvlf 77 
                                       +e+  +a+++ l+
  gi|320101426|ref|YP_004177018.1| 182 RELMVRADERGLW 194
                                       6666666555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.014
                            AAA_28   4 itGgestGKTtlleaLaar.....g 23 
                                       i+G+ + GKTt l+ L+++     g
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLNREaepleG 401
                                       89**************955334442 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.23        89      23      39 ..     107     123 ..     104     134 .. 0.81
   2 ?    9.1   0.0    0.0012      0.46      21      76 ..     377     432 ..     375     441 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.23
                            AAA_13  23 GwNGaGKTtLSrllrsl 39 
                                       G+NGaGK+t  ++l+ +
  gi|320101426|ref|YP_004177018.1| 107 GRNGAGKSTSIKILAGQ 123
                                       9********88888764 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                            AAA_13  21 iYGwNGaGKTtLSrllrslelgetepkfang.sieitngeeldirVfNrdFveenls 76 
                                       i G NG GKTt+ +ll+   +      + ++ +i++ + +el  rVf+++ v +nl+
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLNREAEPLEGAVLISAeKISV-KPQELSPRVFSEETVMANLK 432
                                       679*************98432222222222213333.5589*************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 ?    6.9   8.4     0.032        12      50      66 ..      48      64 ..      12      65 .. 0.61
   2 ?   14.0   2.4    0.0002     0.076       2      18 ..      52      68 ..      51      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.032
                           Fer4_16 50 kqeaitgCdiCqdvCPa 66
                                      ++ a++gC+iC++ CP+
  gi|320101426|ref|YP_004177018.1| 48 SEDACIGCGICVKKCPF 64
                                      346788*********98 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.0002
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C++Cg C++ CP +ai+
  gi|320101426|ref|YP_004177018.1| 52 CIGCGICVKKCPFHAIS 68
                                      9*************997 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.49   1.9e+02       1      16 [.     105     120 ..     105     127 .. 0.86
   2 ?   -0.8   0.0       2.7     1e+03      45      78 ..     244     278 ..     241     293 .. 0.74
   3 ?    6.3   0.0     0.019       7.1       1      17 [.     377     393 ..     377     403 .. 0.86
   4 ?   -0.2   0.0       1.8     7e+02      44      79 ..     495     531 ..     492     548 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.49
                        ATP_bind_1   1 vvGpaGsGKttfvgal 16 
                                       vvG  G+GK+t ++ l
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKIL 120
                                       89*********98765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.7
                        ATP_bind_1  45 vdirelitledvmed.lglgpngalvvaleflres 78 
                                       +dire i +++v  +  ++  n  +vv  ++++  
  gi|320101426|ref|YP_004177018.1| 244 LDIRERIRVANVIREfSDYARNYVVVVEHDLMVLD 278
                                       69*********999999999998888877766544 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.019
                        ATP_bind_1   1 vvGpaGsGKttfvgals 17 
                                       ++Gp G+GKttf + l+
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLN 393
                                       68**********99876 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.8
                        ATP_bind_1  44 avdirelitledvmed.lglgpngalvvaleflresl 79 
                                        +d++e i++++   +  + + ++alvv  ++l+++ 
  gi|320101426|ref|YP_004177018.1| 495 YLDVEERISVAKTIRRiVEEKGKTALVVEHDLLVQNY 531
                                       689********9999989999999**99999999886 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.6         1   3.9e+02       9      17 .]      20      28 ..      10      28 .. 0.77
   2 ?   14.1   1.7   0.00014     0.052       2      16 ..      50      64 ..      49      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 1
                            Fer4_4  9 sCvaaCPqg 17
                                       C+++CP++
  gi|320101426|ref|YP_004177018.1| 20 ECIRFCPVN 28
                                      5******75 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00014
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + CigCg Cv  CP+
  gi|320101426|ref|YP_004177018.1| 50 DACIGCGICVKKCPF 64
                                      79************5 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3     0.038        14      26      47 ..     103     124 ..     101     132 .. 0.88
   2 ?    5.8   0.0     0.035        13      26      47 ..     375     396 ..     369     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.038
                             DUF87  26 lAilgsTGsGKSntvavLleel 47 
                                       l+++g+ G+GKS+ +++L  +l
  gi|320101426|ref|YP_004177018.1| 103 LGVVGRNGAGKSTSIKILAGQL 124
                                       68**************998776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.035
                             DUF87  26 lAilgsTGsGKSntvavLleel 47 
                                       l+ilg  G+GK+++ ++L +e+
  gi|320101426|ref|YP_004177018.1| 375 LGILGPNGVGKTTFLKLLNREA 396
                                       69****************8886 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.074        28      19      51 ..     100     134 ..      77     149 .. 0.76
   2 ?    5.4   0.0     0.045        17      19      42 ..     372     395 ..     356     403 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.074
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       g+++   G  GaGK+t ++ la +l+ +  + +SP
  gi|320101426|ref|YP_004177018.1| 100 GSILGVVGRNGAGKSTSIKILAGQLKPNlgNYSSP 134
                                       5678889999*************998877778887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.045
                                       TEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglaka 42 
                                       g+v+ + G+ G+GKTt+ + l ++
  gi|320101426|ref|YP_004177018.1| 372 GEVLGILGPNGVGKTTFLKLLNRE 395
                                       5677888999********998776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.65   2.5e+02       5      24 ..     105     124 ..     101     129 .. 0.81
   2 ?    8.7   0.0    0.0041       1.6       3      21 ..     375     393 ..     373     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.65
                                       EEC-TTTCHHHHHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklalaw 24 
                                       + G++G GK+t ++ la ++
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKILAGQL 124
                                       89*********888777665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0041
                                       EEEEC-TTTCHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                       + + G++G+GKTt+l+ l 
  gi|320101426|ref|YP_004177018.1| 375 LGILGPNGVGKTTFLKLLN 393
                                       5689***********9775 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0081       3.1      30      53 ..     101     124 ..      79     129 .. 0.83
   2 ?    2.8   0.0      0.12        47      29      50 ..     372     393 ..     361     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0081
                                       EEEEEEE-TTSSHHHHHHHHHHHH CS
                              MeaB  30 qvvGltGvPGaGkstlvealglel 53 
                                         +G+ G  GaGkst ++ l+ +l
  gi|320101426|ref|YP_004177018.1| 101 SILGVVGRNGAGKSTSIKILAGQL 124
                                       579**************9988776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                                       SEEEEEEE-TTSSHHHHHHHHH CS
                              MeaB  29 aqvvGltGvPGaGkstlvealg 50 
                                        +v+G+ G  G+Gk t+++ l 
  gi|320101426|ref|YP_004177018.1| 372 GEVLGILGPNGVGKTTFLKLLN 393
                                       479*************998765 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   7.3    0.0036       1.4       5      59 ..      17      65 ..      11      67 .. 0.58
   2 ?   13.5   1.6   0.00021     0.078       2      17 ..      52      67 ..      51      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0036
                           Fer4_17  5 Cgy.ClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      C+  C++ Cp ++ ++++  +l  +     ++++      + Ci+Cg C++kCP +
  gi|320101426|ref|YP_004177018.1| 17 CSLeCIRFCPVNRGRRKKAIELSGD-----NKYV--VISEDACIGCGICVKKCPFH 65
                                      4444666666655555533333333.....2222..23447899999999999976 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00021
                           Fer4_17  2 CiqCgyClpeCpsyea 17
                                      Ci+Cg C+++Cp++++
  gi|320101426|ref|YP_004177018.1| 52 CIGCGICVKKCPFHAI 67
                                      8888888888888765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.19        74       3      23 ..     105     125 ..     103     146 .. 0.87
   2 ?    6.2   0.0     0.022       8.5       3      23 ..     377     397 ..     375     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.19
                                       EEESTTSSHHHHHHHHHCCST CS
                               dNK   3 veGnIgaGKstlvklLskklg 23 
                                       v G  gaGKst +k+L+ +l+
  gi|320101426|ref|YP_004177018.1| 105 VVGRNGAGKSTSIKILAGQLK 125
                                       56888***********98875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.022
                                       EEESTTSSHHHHHHHHHCCST CS
                               dNK   3 veGnIgaGKstlvklLskklg 23 
                                       + G+ g+GK+t++klL+++++
  gi|320101426|ref|YP_004177018.1| 377 ILGPNGVGKTTFLKLLNREAE 397
                                       66899***********99875 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 ?    0.2   0.2       1.3   4.8e+02       3      20 ..     103     120 ..     101     128 .. 0.81
   2 ?    8.5   0.0    0.0036       1.4       2      33 ..     374     405 ..     373     419 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.3
                                       EEEEESTTCCHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhl 20 
                                       ++++G  G+GK+t ++ l
  gi|320101426|ref|YP_004177018.1| 103 LGVVGRNGAGKSTSIKIL 120
                                       6899*********88755 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0036
                                       EEEEEESTTCCHHHHHHHHHCT--SS-EEEEE CS
                              cobW   2 vtvltGflGsGKTtLlnhllenraglklaviv 33 
                                       v+++ G+ G GKTt+l+ l ++++ l+ av++
  gi|320101426|ref|YP_004177018.1| 374 VLGILGPNGVGKTTFLKLLNREAEPLEGAVLI 405
                                       67899************999999999999986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.9     0.035        14      13      63 ..      23      64 ..      10      66 .. 0.54
   2 ?   13.1   1.7   0.00025     0.097       3      18 ..      50      65 ..      48      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.035
                            Fer4_8 13 saCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                        Cpv r ++k   +  g+++  v+ ++         +C +cg C+++Cp 
  gi|320101426|ref|YP_004177018.1| 23 RFCPVNRGRRKKAIELSGDNKY-VVISED--------ACIGCGICVKKCPF 64
                                      5556666555444444444333.333322........46666666666665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00025
                            Fer4_8  3 ekCieCgaCqsaCpvl 18
                                      ++Ci+Cg C ++Cp+ 
  gi|320101426|ref|YP_004177018.1| 50 DACIGCGICVKKCPFH 65
                                      58***********953 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 ?   13.0   1.4   0.00035      0.13       1      19 [.      45      63 ..      45      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00035
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      Vv+ +daCigcg Cv+ +p
  gi|320101426|ref|YP_004177018.1| 45 VVISEDACIGCGICVKKCP 63
                                      78999***********998 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.9      0.62   2.4e+02       3      14 ..      16      28 ..      12      28 .. 0.82
   2 ?   12.0   4.6   0.00087      0.33       1      15 []      52      66 ..      52      66 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.62
                            Fer4_3  3 gCg.aCvevCPvg 14
                                       C+  C + CPv+
  gi|320101426|ref|YP_004177018.1| 16 KCSlECIRFCPVN 28
                                      69856******97 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00087
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv+ CP +A
  gi|320101426|ref|YP_004177018.1| 52 CIGCGICVKKCPFHA 66
                                      ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.41
# Mc/sec: 4446.94
//
Query:       gi|320101427|ref|YP_004177019.1|  [L=96]
Description: DNA-directed RNA polymerase subunit M [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-06   25.8   0.4    1.4e-05   24.8   0.4    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    1.4e-05   24.6   1.1      5e-05   22.9   1.1    1.8  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
    0.00059   19.1   2.1     0.0011   18.2   2.1    1.5  1  zf-TFIIB         Transcription factor zinc-finger
    0.00076   19.1   3.5       0.12   12.2   0.7    2.4  2  zinc_ribbon_2    zinc-ribbon domain
    0.00089   19.1   1.5      0.083   12.8   0.1    2.4  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
    0.00093   19.2   0.5     0.0016   18.4   0.5    1.3  1  DZR              Double zinc ribbon
     0.0042   17.0   3.0      0.036   14.0   3.3    2.2  2  Nudix_N_2        Nudix N-terminal
     0.0043   16.9   1.0     0.0086   16.0   0.6    1.7  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0051   17.2   1.4     0.0083   16.5   1.4    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.011   15.7   2.6      0.011   15.7   2.6    1.9  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.026   14.0   2.1       0.04   13.4   2.1    1.3  1  Sigma70_r4       Sigma-70, region 4
      0.026   14.5   0.4      0.047   13.7   0.4    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.033   14.3   0.1        0.7   10.0   0.1    2.2  1  RuvA_N           RuvA N terminal domain
      0.036   13.9   0.8      0.091   12.6   0.2    1.8  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
       0.04   14.3   3.0       0.77   10.2   2.9    2.5  1  zf-IS66          zinc-finger binding domain of transposase IS
       0.05   13.8   0.5      0.096   12.8   0.5    1.5  1  DUF2387          Probable metal-binding protein (DUF2387)
      0.072   12.8   0.2        0.1   12.3   0.2    1.3  1  DUF3945          Protein of unknown function (DUF3945)
      0.096   12.7   0.6        1.2    9.2   0.6    2.1  1  PriA_CRR         PriA DNA helicase Cys-rich region (CRR) doma
       0.13   12.1   3.4       0.57   10.0   0.2    2.2  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.13   11.7   3.9        1.2    8.7   0.8    2.4  2  zf-ribbon_3      zinc-ribbon domain
       0.41   10.2   5.8        1.5    8.4   0.2    3.0  3  zn-ribbon_14     Zinc-ribbon
       0.43   10.1   6.2        1.2    8.7   0.1    2.3  2  Mu-like_Com      Mu-like prophage protein Com
       0.66   10.1   4.0         14    5.9   0.9    2.2  2  UPF0547          Uncharacterised protein family UPF0547
       0.69   10.0   3.5        4.9    7.2   0.2    2.7  3  HypA             Hydrogenase/urease nickel incorporation, met
        0.8    9.9   3.4        1.2    9.4   3.4    1.3  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
        1.3    9.2   4.6        8.1    6.7   0.4    2.3  1  Zn-ribbon_8      Zinc ribbon domain
          2    8.8   4.5         15    6.0   1.1    2.5  2  zinc_ribbon_9    zinc-ribbon
        2.4    7.7   5.8         17    4.9   0.3    2.9  3  DUF2688          Protein of unknown function (DUF2688)


Domain annotation for each model (and alignments):
>> 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 !   24.8   0.4   2.2e-08   1.4e-05       1      31 [.       2      32 ..       2      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.2e-08
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYee 31
                                      +kFCp Cg  L p +++  +++ C  CgYe 
  gi|320101427|ref|YP_004177019.1|  2 VKFCPRCGGPLVPVKKDDEVVLKCNRCGYEA 32
                                      59******9999877777767********96 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.1   7.8e-08     5e-05       4      30 ..       3      31 ..       3      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.8e-08
                     zf-NADH-PPase  4 rFCgrCGaptepaeg..gwarvCpaCgle 30
                                      +FC+rCG+p +p++   +  + C  Cg+e
  gi|320101427|ref|YP_004177019.1|  3 KFCPRCGGPLVPVKKddEVVLKCNRCGYE 31
                                      5*********9987666**********97 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.1   1.7e-06    0.0011       2      26 ..       5      29 ..       4      29 .. 0.98

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                          zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                      CP+C+ +l+++++++  + +C++C+
  gi|320101427|ref|YP_004177019.1|  5 CPRCGGPLVPVKKDDEVVLKCNRCG 29
                                      ************************7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.7   0.00018      0.12      13      23 .]       2      12 ..       2      12 .. 0.86
   2 !    7.5   0.1    0.0055       3.5       1      10 [.      24      33 ..      18      37 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                     zinc_ribbon_2 13 akFCpyCGtpl 23
                                      +kFCp+CG pl
  gi|320101427|ref|YP_004177019.1|  2 VKFCPRCGGPL 12
                                      59******886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0055
                     zinc_ribbon_2  1 fCpnCGaelq 10
                                      +C +CG+e +
  gi|320101427|ref|YP_004177019.1| 24 KCNRCGYEAK 33
                                      6888888765 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 !   12.8   0.1   0.00013     0.083       3      17 ..       4      18 ..       3      21 .. 0.85
   2 ?    5.4   0.1     0.026        17       3       8 ..      24      29 ..      23      42 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                      B-TTT--BBEEEECT CS
                      zf-FPG_IleRS  3 pCpRCwryiervgqa 17
                                       CpRC+++++ v+++
  gi|320101427|ref|YP_004177019.1|  4 FCPRCGGPLVPVKKD 18
                                      6********999875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.026
                                      B-TTT- CS
                      zf-FPG_IleRS  3 pCpRCw 8 
                                      +C RC+
  gi|320101427|ref|YP_004177019.1| 24 KCNRCG 29
                                      9****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.5   2.5e-06    0.0016      13      41 ..       3      35 ..       2      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-06
                               DZR 13 rfCseCgtklkavaa....edrCpsCgekvdpe 41
                                      +fC++Cg +l +v++      +C +Cg++++ +
  gi|320101427|ref|YP_004177019.1|  3 KFCPRCGGPLVPVKKddevVLKCNRCGYEAKTD 35
                                      8*********999999*999********98765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.3   5.7e-05     0.036       1      30 [.       3      30 ..       3      30 .. 0.77
   2 ?    2.6   0.2       0.2   1.3e+02       3      14 ..      25      36 ..      24      40 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-05
                                      -B-TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgt 30
                                      kFC+ CG+p+       D++  l C++Cg+
  gi|320101427|ref|YP_004177019.1|  3 KFCPRCGGPLVPVK--KDDEVVLKCNRCGY 30
                                      9********87654..46666688988886 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.2
                                      -TTT--B-EEE- CS
                         Nudix_N_2  3 CsqCGtpvelri 14
                                      C+ CG + ++ +
  gi|320101427|ref|YP_004177019.1| 25 CNRCGYEAKTDV 36
                                      888887776655 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 !   16.0   0.6   1.3e-05    0.0086      30      60 ..       4      36 ..       3      39 .. 0.91
   2 ?   -1.2   0.0       3.2     2e+03      12      20 ..      38      46 ..      36      70 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke..alsgrtfkCpnCgfeadrDv 60
                                       C++Cg  + +  ++++ ++kC++Cg+ea  Dv
  gi|320101427|ref|YP_004177019.1|  4 FCPRCGGPLVPvkKDDEVVLKCNRCGYEAKTDV 36
                                      5********9998899999**********9998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.2
                    OrfB_Zn_ribbon 12 akeyGikve 20
                                       ++yG+k++
  gi|320101427|ref|YP_004177019.1| 38 KERYGVKYQ 46
                                      567777765 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 !   16.5   1.4   1.3e-05    0.0083       4      37 ..       3      36 ..       1      67 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga.....s 37
                                      k CP Cgg+ v ++  + v     +  C  Cg+     +
  gi|320101427|ref|YP_004177019.1|  3 KFCPRCGGPLVPVKKDDEV-----VLKCNRCGYeaktdV 36
                                      67*************9999.....89*******533331 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 ?   15.7   2.6   1.8e-05     0.011       2      22 ..       5      27 ..       4      29 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                    DNA_ligase_ZBD  2 CPvCGsavv..ReegeaiyRCtn 22
                                      CP CG ++v  ++++e+++ C +
  gi|320101427|ref|YP_004177019.1|  5 CPRCGGPLVpvKKDDEVVLKCNR 27
                                      *********98899*******65 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   2.1   6.2e-05      0.04       3      25 ..      64      89 ..      64      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                                      HHS-HHHHHHHHHHH...TTT--HHH CS
                        Sigma70_r4  3 asLpererevlelrf...geglTleE 25
                                      a+L+++ere+l+ ++   +e+l +eE
  gi|320101427|ref|YP_004177019.1| 64 AKLSPEEREILREYYevlLEELEQEE 89
                                      68********************9998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   7.4e-05     0.047      21      45 ..       5      30 ..       2      31 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.4e-05
                     Zn_Tnp_IS1595 21 CPhCgsr.kayriktrglfqCkeCrk 45
                                      CP+Cg+   + +  +  +++C++C++
  gi|320101427|ref|YP_004177019.1|  5 CPRCGGPlVPVKKDDEVVLKCNRCGY 30
                                      *****9999999999*********98 PP

>> RuvA_N  RuvA N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0011       0.7      12      31 ..      16      35 ..       9      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                                      ESSCEEEEEETTEEEEEEE- CS
                            RuvA_N 12 kepdsivvevggvGYevfvp 31
                                      k++d++v+ ++  GYe ++ 
  gi|320101427|ref|YP_004177019.1| 16 KKDDEVVLKCNRCGYEAKTD 35
                                      56778**********98876 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00014     0.091      90     116 ..       5      30 ..       3      31 .. 0.94
   2 ?   -0.8   0.0       2.1   1.3e+03      54      73 ..      42      61 ..      33      79 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       TSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  90 CkeCkspetelekeerllvlkCkaCga 116
                                       C+ C+ p + ++k+++++ lkC+ Cg 
  gi|320101427|ref|YP_004177019.1|   5 CPRCGGPLVPVKKDDEVV-LKCNRCGY 30 
                                       *****************9.******96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                                      TSEEEESETTEEEESSSSSC CS
                      eIF-5_eIF-2B 54 gtqgsidengrlilngkfea 73
                                      g++ ++d+++r++  ++ ea
  gi|320101427|ref|YP_004177019.1| 42 GVKYQVDASKRVVTAQATEA 61
                                      55556666666555555444 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 ?   10.2   2.9    0.0012      0.77       3      18 ..       4      19 ..       3      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                           zf-IS66  3 tCpcCGgllkpigedr 18
                                       Cp CGg+l+p+++d+
  gi|320101427|ref|YP_004177019.1|  4 FCPRCGGPLVPVKKDD 19
                                      6******999***995 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   0.00015     0.096      11      65 ..       5      61 ..       3      68 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                           DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsek....gqsvakelktrvnkdeekea 65
                                      CPrC     ++  ++d++ +  C  Cg+  + + k    g + +++ ++rv +++++ea
  gi|320101427|ref|YP_004177019.1|  5 CPRCGGP--LVPVKKDDEVVLKCNRCGYEAKTDVKkeryGVKYQVDASKRVVTAQATEA 61
                                      9999975..8888999999*********8776665111134556666677666655433 PP

>> DUF3945  Protein of unknown function (DUF3945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00016       0.1      28      55 ..      59      86 ..      46      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                           DUF3945 28 deikgvkLteeqkqdLreGkavllegmt 55
                                       e k+ kL++e+++ Lre  +vlle++ 
  gi|320101427|ref|YP_004177019.1| 59 TEAKEAKLSPEEREILREYYEVLLEELE 86
                                      699*********************9986 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6    0.0019       1.2       1      26 [.       5      32 ..       5      33 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                          PriA_CRR  1 CpnCdvsltyHksrnr..LrCHyCgyte 26
                                      Cp+C  +l+  k++ +  L+C  Cgy+ 
  gi|320101427|ref|YP_004177019.1|  5 CPRCGGPLVPVKKDDEvvLKCNRCGYEA 32
                                      77777777777766643399******86 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 ?   10.0   0.2    0.0009      0.57       4      14 ..       5      15 ..       2      20 .. 0.82
   2 ?    3.1   0.3      0.13        81       3      21 ..      24      45 ..      22      46 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0009
                                      -SSS--EEEEE CS
                    zf-C4_Topoisom  4 CPkCggdLvlk 14
                                      CP Cgg+Lv  
  gi|320101427|ref|YP_004177019.1|  5 CPRCGGPLVPV 15
                                      ********965 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
                                      E-SSS-..-EEEEEE-SSS.EE CS
                    zf-C4_Topoisom  3 kCPkCg..gdLvlkrgkkG.kF 21
                                      kC  Cg  ++  +k+ ++G k+
  gi|320101427|ref|YP_004177019.1| 24 KCNRCGyeAKTDVKKERYGvKY 45
                                      8*****8778888888888665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.8    0.0018       1.2      17      26 .]       3      12 ..       1      12 [. 0.64
   2 ?    3.6   0.1     0.074        48       4       9 ..      24      29 ..      22      38 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                       zf-ribbon_3 17 nvCpyCGtkl 26
                                      ++Cp CG++l
  gi|320101427|ref|YP_004177019.1|  3 KFCPRCGGPL 12
                                      5677777665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.074
                       zf-ribbon_3  4 rCPnCG 9 
                                      +C++CG
  gi|320101427|ref|YP_004177019.1| 24 KCNRCG 29
                                      688888 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   0.3      0.29   1.9e+02       2       7 ..       4       9 ..       3      11 .. 0.87
   2 ?    8.4   0.2    0.0023       1.5       2       8 ..      24      30 ..      23      36 .. 0.84
   3 ?    2.0   0.0      0.24   1.5e+02      19      28 ..      80      89 ..      80      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.29
                      zn-ribbon_14 2 kCerCG 7
                                     +C rCG
  gi|320101427|ref|YP_004177019.1| 4 FCPRCG 9
                                     7****9 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0023
                      zn-ribbon_14  2 kCerCGy 8 
                                      kC+rCGy
  gi|320101427|ref|YP_004177019.1| 24 KCNRCGY 30
                                      8****** PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.24
                      zn-ribbon_14 19 vLLegLnkgr 28
                                      vLLe+L++  
  gi|320101427|ref|YP_004177019.1| 80 VLLEELEQEE 89
                                      7*****9876 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 ?    3.4   2.0     0.083        53      27      31 ..       5       9 ..       1      16 [. 0.86
   2 ?    8.7   0.1    0.0018       1.2      21      31 ..      19      29 ..      15      34 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.083
                       Mu-like_Com 27 CPRCG 31
                                      CPRCG
  gi|320101427|ref|YP_004177019.1|  5 CPRCG 9 
                                      ****9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                       Mu-like_Com 21 DeltiKCPRCG 31
                                      De+ +KC RCG
  gi|320101427|ref|YP_004177019.1| 19 DEVVLKCNRCG 29
                                      99********9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.9     0.021        14      14      21 ..       2       9 ..       2       9 .. 0.82
   2 ?    4.9   0.1     0.045        29      16      23 ..      24      31 ..      22      31 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                           UPF0547 14 aqfCphCG 21
                                      ++fCp CG
  gi|320101427|ref|YP_004177019.1|  2 VKFCPRCG 9 
                                      58999998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.045
                           UPF0547 16 fCphCGyv 23
                                      +C  CGy+
  gi|320101427|ref|YP_004177019.1| 24 KCNRCGYE 31
                                      8*99***7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.056        36      89     107 ..       5      23 ..       2      24 .. 0.87
   2 ?    7.2   0.2    0.0076       4.9      67      84 ..      19      36 ..      15      50 .. 0.81
   3 ?    0.8   0.0      0.73   4.7e+02      35      54 ..      65      84 ..      43      94 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.056
                                       -TTTSSS-EEEEESSSEEE CS
                              HypA  89 CpkCgsadveivsGeellv 107
                                       Cp+Cg+  v +++ +e+ +
  gi|320101427|ref|YP_004177019.1|   5 CPRCGGPLVPVKKDDEVVL 23 
                                       *********9999999876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0076
                                      E--EEEETTTS-EEECHH CS
                              HypA 67 vpvkvrCreCgkefelee 84
                                       +v+++C++Cg+e +++ 
  gi|320101427|ref|YP_004177019.1| 19 DEVVLKCNRCGYEAKTDV 36
                                      67899******9998764 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.73
                                      TTCT--HHHHHHHHHHHHCC CS
                              HypA 35 elsgvepeaLefafellaeg 54
                                      +ls  e e+L+ ++e+l e+
  gi|320101427|ref|YP_004177019.1| 65 KLSPEEREILREYYEVLLEE 84
                                      45555667777777776655 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 ?    9.4   3.4    0.0019       1.2      17      40 .]       4      29 ..       1      29 [. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                     Auto_anti-p27 17 tCpvCgvPLmrdr..kggkvyCvaCd 40
                                       Cp+Cg PL+  +  +++ + C +C+
  gi|320101427|ref|YP_004177019.1|  4 FCPRCGGPLVPVKkdDEVVLKCNRCG 29
                                      5**********997667777788885 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4     0.013       8.1      28      36 ..       3      12 ..       1      15 [. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                       Zn-ribbon_8 28 a.CPeCgsev 36
                                      + CP+Cg+++
  gi|320101427|ref|YP_004177019.1|  3 KfCPRCGGPL 12
                                      55*****965 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.1     0.023        15      23      30 ..       4      11 ..       1      14 [. 0.81
   2 ?    4.0   0.1     0.097        62      18      28 ..      17      29 ..      11      31 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                     zinc_ribbon_9 23 lCPhCggg 30
                                      +CP+Cgg 
  gi|320101427|ref|YP_004177019.1|  4 FCPRCGGP 11
                                      7*****97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.097
                     zinc_ribbon_9 18 edsdv..lCPhCg 28
                                      +d++v   C++Cg
  gi|320101427|ref|YP_004177019.1| 17 KDDEVvlKCNRCG 29
                                      45553368****8 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.03        19      10      21 ..       5      16 ..       2      18 .. 0.84
   2 ?    4.9   0.3     0.027        17       6      17 ..      21      32 ..      16      44 .. 0.75
   3 ?   -1.0   0.1         2   1.3e+03      42      48 ..      66      72 ..      63      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.03
                           DUF2688 10 CrRCGkslstls 21
                                      C RCG +l+ ++
  gi|320101427|ref|YP_004177019.1|  5 CPRCGGPLVPVK 16
                                      99*****99765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.027
                           DUF2688  6 VtTqCrRCGksl 17
                                      V  +C RCG   
  gi|320101427|ref|YP_004177019.1| 21 VVLKCNRCGYEA 32
                                      5679*****765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2
                           DUF2688 42 lipEEla 48
                                      l+pEE++
  gi|320101427|ref|YP_004177019.1| 66 LSPEERE 72
                                      8999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1701  (0.0948742); expected 358.6 (0.02)
Passed bias filter:                      836  (0.0466284); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 738.53
//
Query:       gi|320101428|ref|YP_004177020.1|  [L=170]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1301.63
//
Query:       gi|320101429|ref|YP_004177021.1|  [L=71]
Description: 30S ribosomal protein S17 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-19   68.3   1.2    6.1e-19   68.1   1.2    1.0  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.085   13.3   0.1       0.09   13.2   0.1    1.2  1  Sld5            GINS complex protein


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 !   68.1   1.2   6.8e-23   6.1e-19       1      59 [.       1      59 [.       1      69 [. 0.93

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 6.8e-23
                                      XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHH CS
                    Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmk 59
                                      mg+vr ++vK++ar+++eky + +t+dF++nk v+++    +skk+rn iaGyvthl+ 
  gi|320101429|ref|YP_004177021.1|  1 MGKVRIRVVKRTARELLEKYPELFTRDFQHNKTVVSKLVETRSKKIRNLIAGYVTHLVA 59
                                      9********************************************************85 PP

>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     1e-05      0.09      52      88 ..      15      52 ..       6      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                                      HHHHHHHHHH.T.HCHHHHHHHHHHHHHHHHHHHTHCH CS
                              Sld5 52 elavkllela.rdldelkrllrdllevRlakirkfaen 88
                                      el +k+ el+ rd +  k ++ +l+e+R++kir++   
  gi|320101429|ref|YP_004177021.1| 15 ELLEKYPELFtRDFQHNKTVVSKLVETRSKKIRNLIAG 52
                                      566777777733366669****************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 557.90
//
Query:       gi|320101430|ref|YP_004177022.1|  [L=176]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   16.6   0.1       0.33   10.9   0.1    2.3  2  MarR_2    MarR family
  ------ inclusion threshold ------
      0.046   13.6   0.0       0.43   10.5   0.0    2.1  2  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   0.0     0.009        81      13      53 ..      33      71 ..      28      75 .. 0.86
   2 !   10.9   0.1   3.6e-05      0.33      11      43 ..     131     163 ..     128     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.009
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                       ++ + g   t  +l   +gl  + v r+l  L + G ve+
  gi|320101430|ref|YP_004177022.1| 33 LIYSSQG--ATLDDLRSMTGLRTQLVKRALWWLLKSGVVEE 71
                                      5777888..899*****************999999999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.6e-05
                                       HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHH CS
                            MarR_2  11 LaaLgrrpgrdltvgelarrlglsksavsrilk 43 
                                       L++L r+ g  +t +e+ ++l ++ ++++r+++
  gi|320101430|ref|YP_004177022.1| 131 LLELERNAGASFTGREVSQALSIDVGTATRLVR 163
                                       89*****************************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 ?   10.5   0.0   4.9e-05      0.43      15      61 ..      31      78 ..      29      81 .. 0.91
   2 ?    0.5   0.0     0.065   5.9e+02      22      41 ..     141     160 ..     126     166 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.9e-05
                                      HHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTE CS
                              TrmB 15 laLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpkl 61
                                      ++L+ +++ at d++ +++g+  + v ++L  L++ G+Ve   gr+++
  gi|320101430|ref|YP_004177022.1| 31 IYLIySSQGATLDDLRSMTGLRTQLVKRALWWLLKSGVVEEAGGRYYV 78
                                      567768899********************************9999876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.065
                                       CCHHCHHCCCTTSSCHCHHH CS
                              TrmB  22 patadeiaeelgvprskvYe 41 
                                       + t +e++++l ++  ++ +
  gi|320101430|ref|YP_004177022.1| 141 SFTGREVSQALSIDVGTATR 160
                                       56899999999998777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1326.47
//
Query:       gi|320101431|ref|YP_004177023.1|  [L=198]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-29  100.8   0.0    1.5e-28  100.0   0.0    1.4  1  Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX
  ------ inclusion threshold ------
      0.021   14.9   0.1        1.8    8.6   0.3    2.2  2  NLPC_P60       NlpC/P60 family


Domain annotation for each model (and alignments):
>> Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.0   1.7e-32   1.5e-28       2     167 .]      42     194 ..      41     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.7e-32
                     Peptidase_C92   2 lekGdiifqtsraslseainpatasefkHvgivvgeeg..derlvveaaakegvrvtpLseflarrssiavyrlkea 76 
                                       +++Gdi+  +s  +l+ +++p   ++++Hvg+vv+      +++vve+    gv+++pL+ fl+r++ +av+r++++
  gi|320101431|ref|YP_004177023.1|  42 IRPGDIVIGHS-PDLTSKLIP---GYWSHVGMVVWFDSarGDWIVVESLPDGGVQLNPLKSFLSRYDTVAVLRVATT 114
                                       579********.89999****...********9986665578**********************************6 PP

                     Peptidase_C92  77 ltaeqrqkaaeaalrrlgkpYdfgFele...ddrlYCsklVakaykealgikvktvellgklllknpdsklkllele 150
                                         +  r++a+++al++lgkpYd+g   +    +++YCs+lV+++y +a+g   +++ +   +          l++l+
  gi|320101431|ref|YP_004177023.1| 115 --DYIRSRAVAFALSQLGKPYDWGLYTKqvyGSSYYCSELVWASY-KAVG--GPDIDANPGFS---------LKYLY 177
                                       ..99********************666668889************.7766..33333333444.........36789 PP

                     Peptidase_C92 151 tvlpqslaespalelvl 167
                                        v+pq++++++ ++ ++
  gi|320101431|ref|YP_004177023.1| 178 AVAPQEIYDDGDTYIIY 194
                                       9********99988775 PP

>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.005        45      49     103 ..      39     108 ..      18     110 .. 0.77
   2 ?    8.6   0.3    0.0002       1.8       1      36 [.     130     170 ..     130     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.005
                                       GGG--TTEEEEESG........TGGESEEEEEE......ETTEEEEEE.TTEEEEEETTSTTBHSCEEEC CS
                          NLPC_P60  49 kselkrGDLvffkt........kkgisHvgiYl......gngkmlhas.sekvsvsslsekywkkrllgv 103
                                        s +++GD+v+ ++         + +sHvg+ +      g+  +++++ +++v+ ++l++  ++  ++ v
  gi|320101431|ref|YP_004177023.1|  39 PSGIRPGDIVIGHSpdltskliPGYWSHVGMVVwfdsarGDWIVVESLpDGGVQLNPLKSFLSRYDTVAV 108
                                       678899999998888887777778899****999999987777788879999999888876666666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0002
                                       T-BB-TT--BTT....EB-HHHHHHHHHHTT.T----SSHH CS
                          NLPC_P60   1 gkpYrwGGksps....gfDCsglvryafaka.gielprssg 36 
                                       gkpY wG  +++     + Cs lv ++++ + g ++  ++g
  gi|320101431|ref|YP_004177023.1| 130 GKPYDWGLYTKQvygsSYYCSELVWASYKAVgGPDIDANPG 170
                                       89*****87777999999************97777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1444.59
//
Query:       gi|320101432|ref|YP_004177024.1|  [L=117]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-16   59.9   0.0    2.7e-16   59.7   0.0    1.0  1  RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G


Domain annotation for each model (and alignments):
>> 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 !   59.7   0.0   1.5e-20   2.7e-16       2     115 ..       2     112 ..       1     115 [. 0.92

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.5e-20
                      RNA_pol_RpbG   2 vsleckvksieksklkdlkivkikcqne.eielDiiselnif.keedkveviisrekPeyldgkdFcghGylvteke 76 
                                       ++ ec v+++++ + ++++  k +c +   ie++++++++   +   kv++ +s +k e l  +dFc+hGy+v+  e
  gi|320101432|ref|YP_004177024.1|   2 LRDECVVSEVQQLRTPKVYRLKTTCSDGlAIEVELHEDVIAQpRISSKVRINVSGSKEECLG-NDFCAHGYVVSGTE 77 
                                       6789************************9*********887625689***********9999.************** PP

                      RNA_pol_RpbG  77 eenkiitliSlfGllvkisskkdllnelglkvmdkvYlc 115
                                        +     +iSl Gllv+ +s     ++l++k mdkvY+ 
  gi|320101432|ref|YP_004177024.1|  78 IGGLHRVVISLGGLLVILKSP----RPLEFKPMDKVYVG 112
                                       ***99************8887....577*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 839.76
//
Query:       gi|320101433|ref|YP_004177025.1|  [L=149]
Description: Sm ribonucleoprotein-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-27   94.9   0.7    8.9e-27   92.7   0.4    2.1  2  Lsm_C     Lsm C-terminal
    7.2e-08   32.0   0.1    1.2e-07   31.3   0.1    1.4  1  LSM       LSM domain
    6.6e-05   23.0   0.0    0.00012   22.2   0.0    1.4  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> Lsm_C  Lsm C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.14   8.1e+02       2      23 ..      12      33 ..      11      37 .. 0.76
   2 !   92.7   0.4   1.5e-30   8.9e-27       1      63 []      82     144 ..      82     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHS...TTTEEEET CS
                             Lsm_C  2 reFaelvekelnlrpglVkvie 23
                                       e+a+++ k++++  ++ ++++
  gi|320101433|ref|YP_004177025.1| 12 SELASMIDKKIRVVLSDGRYYD 33
                                      5889999999988777777765 PP

  == domain 2  score: 92.7 bits;  conditional E-value: 1.5e-30
                                       HHHHHHHHHHHS...TTTEEEETTTTEEEETTTEEEETTEEE--SHHHHHHHHHHHHHHH-.. CS
                             Lsm_C   1 areFaelvekelnlrpglVkvieeanvvvvldrikVsekGVeGsGplAervyelyeeYiekkk 63 
                                       ++eF+e+v +e++++ ++Vkvi+ea+vv+v++r++V e+GV GsGp+Ae+++++y++Y+e ++
  gi|320101433|ref|YP_004177025.1|  82 PEEFKEWVLREMKIPDHMVKVIPEARVVEVQGRYRVGEDGVIGSGPIAETLHSIYKKYMEYRR 144
                                       69**********************************************************986 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1     2e-11   1.2e-07       2      63 ..      13      70 ..      12      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2e-11
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEE.TTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfD.qfmNlvLedveetlkdkkekrklglvliRGnniv 63
                                       l+++i+kk++v l +gr + G+L+gfD + +N++L+ ++  +      +++ +v+i+G+ i 
  gi|320101433|ref|YP_004177025.1| 13 ELASMIDKKIRVVLSDGRYYDGVLVGFDhPGLNIMLRSAVDEK-----GNRVPRVMIKGERIS 70
                                      6999************************557********9655.....467999999999986 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     2e-08   0.00012       2      66 ..       8      70 ..       7      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2e-08
                                      XX-HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS...........-EEE CS
                            SM-ATX  2 drllflltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkanskssspssgeipd 66
                                       rl+  l+s++ k+++v +++G  y G++ +++   +++++L+ a   k  n  +    +ge + 
  gi|320101433|ref|YP_004177025.1|  8 RRLVSELASMIDKKIRVVLSDGRYYDGVLVGFDH-PGLNIMLRSAVDEKG-NRVPRVMIKGERIS 70
                                      599999****************************.6*********98887.44444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1098.86
//
Query:       gi|320101434|ref|YP_004177026.1|  [L=520]
Description: archaeosine tRNA-ribosyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-62  209.4   0.0    1.1e-61  209.0   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
    4.3e-07   29.9   0.1    9.7e-07   28.8   0.1    1.5  1  DUF5591   Domain of unknown function (DUF5591)


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 !  209.0   0.0   1.2e-65   1.1e-61       3     349 ..      12     333 ..       9     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: 209.0 bits;  conditional E-value: 1.2e-65
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EE CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpil 79 
                                       +Rl++l+++hg+ietP ++pv   +  ++++ d+l  elg + i++n+y +++r++  +    + +h  l+wdk i+
  gi|320101434|ref|YP_004177026.1|  12 GRLARLTTRHGVIETPYLFPV-VDPLKQEVSLDKL-LELGFNGIITNAYLFYKRNKGVV----KPIHGELKWDKTIM 82 
                                       8********************.8889999******.599**********9996544433....79************ PP

                                       EE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHH CS
                               TGT  80 tdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwld 156
                                       tdsgg+qv+               + G+ v++++++++++q+++g Di ++ld+++ ++as+ ++ +sv +T r++ 
  gi|320101434|ref|YP_004177026.1|  83 TDSGGYQVLV--------------Y-GD-VEVDNRTIVAYQRDIGVDIGVILDKPTGNNASYREAVESVYETYRRAV 143
                                       *******874..............4.**.**********************************************99 PP

                                       HHHHHH....SEEEEEE--TT-HHHHHHHHHHHHHH--.SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EE CS
                               TGT 157 rcleah....qalfgivqGglyedlreesaeelakrdf.dgyaigG.lsvge..ekeellevveavtellpedkpry 225
                                       ++        q +  ++qG  y+dl  +s   + ++ + ++ya+g+   + e  ++++++e+   ++ +lp  kp++
  gi|320101434|ref|YP_004177026.1| 144 EASPLIsgsdQLWTLPIQGLPYRDLVLRSSILAWRLPVySVYAVGSpTVLLErySYSKIVELTLLARITLPPGKPIH 220
                                       999655788788*************9999988888765379*****655777788899999999************* PP

                                       ETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHH CS
                               TGT 226 lmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhll 302
                                       ++Gvg+P+ l  +va+G D+fd++ ++++ar+ r+++++g+ ++++ +y     p    C+C++C++yt  +l +l 
  gi|320101434|ref|YP_004177026.1| 221 VFGVGHPMILPFLVAAGGDLFDSASYILYARDERYMVETGTRSIRDLHYL----P----CNCPVCSRYTVRELLELP 289
                                       *********************************************99999....9....******99********** PP

                                       HTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 303 ktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                       + ++    +Ll++HNl+++ +++++iR+aI eg+++e+ e++ r ++
  gi|320101434|ref|YP_004177026.1| 290 RRER---VRLLALHNLYMLAKELRSIRQAIMEGRLWEMLEHRSRGHP 333
                                       9999...**********************************998876 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   1.1e-10   9.7e-07      14      79 ..     389     452 ..     376     461 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.1e-10
                                       -S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT--------- CS
                           DUF5591  14 ppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdi 79 
                                       +p  +  lv++P   +kPy++ +++  ++e+ k +  +v  v+l   lGvvP el ++YP+ q++ 
  gi|320101434|ref|YP_004177026.1| 389 QPGGRGYLVVIPA-YRKPYTSQEEYAVVSEKYKGN-GSVRIVFLHPFLGVVPPELASTYPFYQHES 452
                                       5556677999996.68**************99998.79*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 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:                        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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3654.20
//
Query:       gi|320101435|ref|YP_004177027.1|  [L=244]
Description: ATP-grasp superfamily protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-33  115.9   0.0    3.2e-33  115.6   0.0    1.1  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 !  115.6   0.0   1.8e-37   3.2e-33       1     207 [.      20     220 ..      20     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 1.8e-37
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT.EEE-SEEEEEE.TTT.SEEEEEEEE CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg.relepprlyak.dsgsrdllvlqgr 75 
                                       L++G+ g G+Vg+l++++++++l+++k g+i ++y +p       +l++++ + + p+++ya    gs+ ++vl++ 
  gi|320101435|ref|YP_004177027.1|  20 LVTGYQGFGMVGYLTTRHIVRELKLQKAGFIKTRY-MP-----EFTLYSRDrGLVYPFEVYAGrAGGSNIVVVLHNA 90 
                                       799********************************.**.....9******************965556666666776 PP

                                       -HSCHHH.HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT..-CEEEEHHHHH CS
                              PAC2  76 epilqye.efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees..eyggivgitgl 149
                                       +p  + +  +a+ l+++a++lgvkev+++ggld   r    ++++ek+ ++   +  + +l+++  e+ +++g+ +l
  gi|320101435|ref|YP_004177027.1|  91 TPAERERtMYAEYLASLARDLGVKEVILVGGLDPSIR----EDEKEKYRWIPIGDTGI-RLDAKllEDRHVIGPLAL 162
                                       6666666457777********************5555....67888886666333333.332223477899****** PP

                                       HHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHH CS
                              PAC2 150 LlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeelee 207
                                        +  + ++g+++v +l +++ y pdPka+a+++e++ ++lg+++dt++L e+a  +e+
  gi|320101435|ref|YP_004177027.1| 163 TMVFMNAYGLKGVTILSYTELYRPDPKASAVAVEVVGDILGVKIDTSSLLEEASIIEA 220
                                       *****************************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1862.40
//
Query:       gi|320101436|ref|YP_004177028.1|  [L=162]
Description: PUA domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-17   62.0   0.0      8e-17   61.1   0.0    1.4  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
      8e-16   57.8   0.2    1.4e-15   57.0   0.2    1.4  1  PUA       PUA domain
     0.0042   17.3   0.0     0.0068   16.6   0.0    1.4  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   1.3e-20     8e-17       3      71 .]      16      83 ..      15      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.3e-20
                            TGT_C2  3 lraiadYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                      lr ia  qF  g+gd+++ped+++ +s +t +ir vl+++ r++t+ra d+r+ L+++++r l+ +lp+P
  gi|320101436|ref|YP_004177028.1| 16 LRGIARLQF--GVGDEFIPEDIEVAVSpNTFKIRMVLLNDSRYLTIRAGDYRFNLHVASGRVLNTMLPHP 83
                                      899******..89*******************************************************98 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.2   2.3e-19   1.4e-15       2      72 ..      86     156 ..      85     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.3e-19
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                       rv v++  v ++++g +L+++ v+ ++ d+ ++d+V +v++ gel+avG+a + + e+   k+g +v++++
  gi|320101436|ref|YP_004177028.1|  86 RVYVKEDYVGFVAKGGNLFCKHVLMADPDIAPNDEVLVVSPRGELIAVGRAIVPGREMVYYKRGEAVRVRE 156
                                       799*****************************************************************997 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-06    0.0068      14      53 ..      99     138 ..      86     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-06
                           UPF0113  14 YGrdvlkesilkitesvkenqvvvVlnengeplGiGkirk 53 
                                        G +++ +++l  ++++  n+ v+V++ +ge++++G+++ 
  gi|320101436|ref|YP_004177028.1|  99 KGGNLFCKHVLMADPDIAPNDEVLVVSPRGELIAVGRAIV 138
                                       5999********************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 1320.04
//
Query:       gi|320101437|ref|YP_004177029.1|  [L=418]
Description: adenosylhomocysteinase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-72  241.6   0.0    7.2e-42  143.6   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    3.3e-53  180.1   0.0    4.9e-53  179.5   0.0    1.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    4.6e-09   35.9   0.3    9.1e-09   34.9   0.3    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    6.7e-07   29.0   0.1    1.3e-06   28.1   0.1    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0044   17.3   0.4      0.015   15.5   0.2    2.1  2  TrkA_N         TrkA-N domain
  ------ inclusion threshold ------
      0.068   12.5   3.3       0.26   10.6   3.3    1.8  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.091   12.7   0.2       0.18   11.8   0.2    1.4  1  zf-RNPHF       RNPHF zinc finger


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 !  143.6   0.0   2.8e-45   7.2e-42       1     138 [.       2     134 ..       2     141 .. 0.97
   2 !   98.2   0.0   1.8e-31   4.7e-28     171     286 ..     134     412 ..     133     418 .] 0.98

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 2.8e-45
                                       --B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   1 dykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnif 77 
                                       dy+vkd+sla+ G  +i+ ae++mp lm lr++y+e+kp+kg+r+   lh+t +tavL+++ ++ Gaev  a  n  
  gi|320101437|ref|YP_004177029.1|   2 DYRVKDLSLASQGAAKISWAEQNMPVLMLLRRKYSEAKPFKGVRVGAVLHVTKETAVLMKAFIDAGAEVALAGSNPL 78 
                                       8**************************************************************************** PP

                                       T--HHHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  78 stqdeaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                       stqd++aaa++e gv v+aw+g++ eey wc+e++++w     +p+++lDdG Dl +l+h+
  gi|320101437|ref|YP_004177029.1|  79 STQDDVAAALVEYGVHVYAWRGQSGEEYYWCLEKIVEW-----RPQIVLDDGADLHALIHE 134
                                       ************************************99.....79***************9 PP

  == domain 2  score: 98.2 bits;  conditional E-value: 1.8e-31
                                       THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                         AdoHcyase 171 kkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD........................... 220
                                       +k+ +l+++i G +eetttGv rL  l+++g L+ p i vn++ tk  fD                           
  gi|320101437|ref|YP_004177029.1| 134 EKHVQLASSIVGGTEETTTGVIRLRALEREGLLKYPVIAVNNAYTKHMFDnrygtgqstfdgilratnmliagkvvv 210
                                       5788999********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|320101437|ref|YP_004177029.1| 211 vagygwvgkgiaararglgarrvivvevnpiraleavydgfevmpmseaaevgdifitatgnkavvrrehfekmkng 287
                                       ***************************************************************************** PP

                                       ...........................................................S-HHHHHHHHHHHHHHHH CS
                                       ...........................................................xxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 ...........................................................hpsfvmsasftnqvlaqi 238
                                                                                                  hps vm++sf+nq la +
  gi|320101437|ref|YP_004177029.1| 288 avlanaghfnvevwipdlealsrskrqilpyvteyelsdgrriyllaegrlvnlvaaegHPSEVMDMSFANQFLASL 364
                                       ***************************************************************************** PP

                                       HHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 239 elfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyig 286
                                        + +++ + + kv+  p +lDe varl+le++g++++++t+eq ey++
  gi|320101437|ref|YP_004177029.1| 365 YMLENKGSLPLKVMNPPVELDEMVARLKLESMGIRIDSMTREQEEYVK 412
                                       **********************************************97 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.5   0.0   1.9e-56   4.9e-53       1     161 [.     184     345 ..     184     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 1.9e-56
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-E.EEEE-S-HHHHHHHHCTT-EE--HHHCT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGar.vivtevdPicalqaameGfevvtleevv 76 
                                       n yg+ +s  dgi rat++l+aGkv+vvaGyG vGkG aa  +glGar viv ev+Pi al a+ +Gfev+ + e++
  gi|320101437|ref|YP_004177029.1| 184 NRYGTGQSTFDGILRATNMLIAGKVVVVAGYGWVGKGIAARARGLGARrVIVVEVNPIRALEAVYDGFEVMPMSEAA 260
                                       78********************************************9549*************************** PP

                                       TT-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGS CS
                     AdoHcyase_NAD  77 kkadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGr 153
                                       + +di++t+tGnk ++++eh++kmk+ a+++n Ghf+ e+ +  lea + +k ++ p v +++l+dg++i llaeGr
  gi|320101437|ref|YP_004177029.1| 261 EVGDIFITATGNKAVVRREHFEKMKNGAVLANAGHFNVEVWIPDLEALSRSKRQILPYVTEYELSDGRRIYLLAEGR 337
                                       ***************************************************************************** PP

                                       BCHHHTS- CS
                     AdoHcyase_NAD 154 llnlgcat 161
                                       l+nl +a 
  gi|320101437|ref|YP_004177029.1| 338 LVNLVAAE 345
                                       ****9886 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 !   34.9   0.3   3.5e-12   9.1e-09      32     127 ..     202     294 ..     174     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.5e-12
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTT CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrh 107
                                         ++gk v + G+G +G+ +a r++++g+ +vi++++++ +  e+   g+e++ + e+ +  Di + ++     ++ 
  gi|320101437|ref|YP_004177029.1| 202 MLIAGKVVVVAGYGWVGKGIAARARGLGArRVIVVEVNPIRALEAVYDGFEVMPMSEAAEVGDIFITATG----NKA 274
                                       5689*************************99*****99998888899999*************9987765....999 PP

                                       SBSHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C 108 linaeelakmkkgailiNta 127
                                       ++ +e+++kmk+ga+l N++
  gi|320101437|ref|YP_004177029.1| 275 VVRREHFEKMKNGAVLANAG 294
                                       ******************98 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 !   28.1   0.1   5.2e-10   1.3e-06       2     100 ..     204     299 ..     203     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.2e-10
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       + gk ++v GyG  G+  a   r  g   v+ ++ +   + +A  +gfev+ ++ea++  d+ ++ +    +k+v++
  gi|320101437|ref|YP_004177029.1| 204 IAGKVVVVAGYGWVGKGIAARARGLGARRVIVVEVNPIRALEAVYDGFEVMPMSEAAEVGDIFITAT---GNKAVVR 277
                                       7899***********************98888888888999********************887765...5678999 PP

                                       HHTGGG--TT-EEEESSSHHHH CS
                              IlvN  79 eeiepnlkegkalafahGfnih 100
                                       +e  +++k+g++la a  fn+ 
  gi|320101437|ref|YP_004177029.1| 278 REHFEKMKNGAVLANAGHFNVE 299
                                       9999****************96 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.2   3.1e+03      44      94 ..     120     172 ..     111     185 .. 0.61
   2 !   15.5   0.2   5.9e-06     0.015       1      45 [.     209     254 ..     209     298 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.2
                                       EEES-TTSHHHHHHT.TGGGESEEEE-SSSHHHHHHHHHHH.HHHTSSSEEEE CS
                            TrkA_N  44 vvvgdatdeevLeea.giekadaviaatgddeanilavlla.kelnpkkkiia 94 
                                       +v  d++d ++L +  +++ a++++  t++ ++ ++ + ++ +e   k+++ia
  gi|320101437|ref|YP_004177029.1| 120 IVLDDGADLHALIHEkHVQLASSIVGGTEETTTGVIRLRALeREGLLKYPVIA 172
                                       66667777666654447888888888887777777766666333333344444 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 5.9e-06
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevv 45 
                                       ++++G+G vG+ +a + +  g ++v+v++ ++ r+ e+  +g+ev+
  gi|320101437|ref|YP_004177029.1| 209 VVVAGYGWVGKGIAARARGlGARRVIVVEVNPIRALEAVYDGFEVM 254
                                       79*****************99899********99999999998875 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 ?   10.6   3.3    0.0001      0.26      28     124 ..     205     290 ..     184     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                                       --E.EEEESTSHHHHHHHHHHHHTT-E.EEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BT CS
                       AlaDh_PNT_C  28 pak.vlviGgGvaGlqAiatakglgak.VtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlip 102
                                       ++k v+v G G +G   +a a+glga+ V v++v+p   + le++    +ev+      ++ea++  d+ i++   +
  gi|320101437|ref|YP_004177029.1| 205 AGKvVVVAGYGWVGKGIAARARGLGARrVIVVEVNPI--RALEAVYDG-FEVM-----PMSEAAEVGDIFITA---T 270
                                       4451566799***************964888888875..556665555.3443.....45667778899**99...8 PP

                                       TSS---SC-HHHHHTS-TTEEE CS
                       AlaDh_PNT_C 103 GkkaPkLvteemvksMkpgsVi 124
                                       G+ka  +v++e+ ++Mk+g+V+
  gi|320101437|ref|YP_004177029.1| 271 GNKA--VVRREHFEKMKNGAVL 290
                                       9987..89***********997 PP

>> zf-RNPHF  RNPHF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   6.9e-05      0.18      15      29 ..     179     193 ..     174     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                          zf-RNPHF  15 sgmsDhRYGDgtsTf 29 
                                         m D RYG g+sTf
  gi|320101437|ref|YP_004177029.1| 179 KHMFDNRYGTGQSTF 193
                                       579***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3189.20
//
Query:       gi|320101438|ref|YP_004177030.1|  [L=549]
Description: thermosome subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-180  598.4  13.8   1.1e-179  598.2  13.8    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 !  598.2  13.8    6e-184  1.1e-179       1     490 [.      36     527 ..      36     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 598.2 bits;  conditional E-value: 6e-184
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +++++ktt+GPkGmdKmlv++ g+v++TnDGatil + ei+hPaak+lv++a+sqd+evGDGT  +viLageLl+ a
  gi|320101438|ref|YP_004177030.1|  36 ISEMIKTTYGPKGMDKMLVDALGDVTITNDGATILDKAEIQHPAAKMLVQVAKSQDSEVGDGTKRAVILAGELLKYA 112
                                       799************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e+l+++++hpt+ii+gy++a+e+al++L+++a+ i+   +++e L+kvartsl+sk +++ +e++++++v+Av +++
  gi|320101438|ref|YP_004177030.1| 113 EELLDKNIHPTVIISGYRMAMEEALKILDQMAEPID--LNNEELLRKVARTSLTSKAVHDAREFFADIAVKAVkQVV 187
                                       *******************************66665..5699*******************************9999 PP

                                       CCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 154 eene..keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e++   + +dl++i+++k+ gg l ds lv G+vldk+v++p mp+++enak++lld +Leiek+e++++++++d+e
  gi|320101438|ref|YP_004177030.1| 188 EKRGdkNYVDLDNIQIIKKYGGALLDSMLVYGIVLDKEVVHPGMPRRVENAKIVLLDAPLEIEKPEIDAEIRINDPE 264
                                       888899*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       +lek++++ee++l ++++ki++ g+nvvvcqkgid++a+hflak+gila+rrvk++dle+l +atG+++vs++edlt
  gi|320101438|ref|YP_004177030.1| 265 QLEKFLQQEEEILMKMVDKIASVGANVVVCQKGIDEVAQHFLAKKGILAVRRVKRSDLEKLERATGGRIVSNIEDLT 341
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       pe+lG+a  vee+k+g++k+++ie++k++++++i++rg  +  +de+er+i+dAl++v+ a++d+kv+pGGGa+e+e
  gi|320101438|ref|YP_004177030.1| 342 PEDLGYAALVEERKVGEDKMVFIEGCKNPRSVSIVIRGGLERLVDEAERSIRDALSAVADALRDGKVIPGGGAAEIE 418
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTX.TTEEEETTTTCEEECCCCT CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkge.kelgidvesgeiidlveag 458
                                       lak++++ a++v g+eqlaieafakALe ++ tL eNaGldpi+++ klraah++++ k l id+++g+ +++ e+g
  gi|320101438|ref|YP_004177030.1| 419 LAKHIRRLATRVGGKEQLAIEAFAKALEGLAVTLVENAGLDPIDMVMKLRAAHEREDgKYLSIDLATGDLVNMREKG 495
                                       *****************************************************66554699**************** PP

                                       XEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 459 vvDplkvkrqalksAteaastiLrideiikak 490
                                       v++p+++  +a+k+ teaa+ i+rid++i a 
  gi|320101438|ref|YP_004177030.1| 496 VIEPVSILANAIKAGTEAATIIMRIDDVIAAS 527
                                       *****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4193.13
//
Query:       gi|320101439|ref|YP_004177031.1|  [L=84]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 640.02
//
Query:       gi|320101440|ref|YP_004177032.1|  [L=187]
Description: transcription factor IIE (TFIIE) subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-08   34.7   0.0    2.7e-08   33.6   0.0    1.6  1  TFIIE_alpha    TFIIE alpha subunit
    0.00051   20.1   0.0    0.00075   19.5   0.0    1.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
  ------ inclusion threshold ------
      0.012   15.2   2.0      0.016   14.7   0.7    1.9  2  TF_Zn_Ribbon   TFIIB zinc-binding
      0.014   15.3   0.2      0.031   14.2   0.2    1.5  1  zinc_ribbon_4  zinc-ribbon domain
      0.053   13.2   0.1      0.094   12.5   0.1    1.4  1  zf-CSL         CSL zinc finger


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 !   33.6   0.0   7.4e-12   2.7e-08       2     103 ..      23     122 ..      22     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 7.4e-12
                                       HHHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEEC CS
                       TFIIE_alpha   2 llkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywriny 78 
                                       +l+ +vr++yge   + l  +le+g v+ee l ++++i+ ne r++L ++ e+ +v   + r  + ++    wr+n+
  gi|320101440|ref|YP_004177032.1|  23 VLEDLVRGVYGEPGLKLLRFMLEHGYVAEELLTRDTGIKSNEGRRILQKMSEENIVVPGKLRTGD-GVL-HIWRLNK 97 
                                       68899**************************************************9999999744.343.57***** PP

                                       CCHCCCHHHHHHHHHHHHHHHHCCC CS
                       TFIIE_alpha  79 eklvdvvkrkleevvkkLeekleke 103
                                       + l  +v  +l++ + kL   l++e
  gi|320101440|ref|YP_004177032.1|  98 PGLRSAVLMRLRKAREKLAARLSFE 122
                                       ******************9999998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.1e-07   0.00075      57     108 ..     115     168 ..      93     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.1e-07
                                       TTT-EEEEEEE--EEEETTTS-EEECHH.H..HHS-TTTSSS-EEEEESSSEEEE CS
                              HypA  57 legaeLeieevpvkvrCreCgkefelee.k..alrCpkCgsadveivsGeellvk 108
                                       l+ a+L++e  +++++C +Cgk+++l+e +  ++ Cp+ g+  ve  +Ge ++v 
  gi|320101440|ref|YP_004177032.1| 115 LA-ARLSFEAGNIVYECPRCGKRYTLDEaYvnDFICPSDGEVLVESNKGEAVRVL 168
                                       44.89********************988535688****************99985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1     4e+03      29      38 ..      73      82 ..      72      83 .. 0.81
   2 ?   14.7   0.7   4.4e-06     0.016       1      29 [.     128     156 ..     128     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                      EEECCCCCCC CS
                      TF_Zn_Ribbon 29 lednsidegp 38
                                       e+n++++g+
  gi|320101440|ref|YP_004177032.1| 73 SEENIVVPGK 82
                                      6999999986 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.4e-06
                                       EEETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtdCGlVl 29 
                                       y CP Cg ++++ ++  ++++C++ G+Vl
  gi|320101440|ref|YP_004177032.1| 128 YECPRCGKRYTLDEAYVNDFICPSDGEVL 156
                                       68********9999999******988776 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   8.6e-06     0.031       4      17 ..     129     142 ..     128     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.6e-06
                     zinc_ribbon_4   4 tCpsCkakyeidde 17 
                                       +Cp+C+++y++d++
  gi|320101440|ref|YP_004177032.1| 129 ECPRCGKRYTLDEA 142
                                       7***********97 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.6e-05     0.094      17      36 ..     126     146 ..     116     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                       EEEEE.TTSSEEEEEHHHHHT CS
                            zf-CSL  17 yyypC.RCgdeFelteedlee 36 
                                        +y+C RCg+++ l e+ + +
  gi|320101440|ref|YP_004177032.1| 126 IVYECpRCGKRYTLDEAYVND 146
                                       589*************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1352.35
//
Query:       gi|320101441|ref|YP_004177033.1|  [L=323]
Description: DNA-cytosine methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-49  166.7   0.0    1.9e-33  116.2   0.0    2.0  2  DNA_methylase    C-5 cytosine-specific DNA methylase
     0.0013   18.3   0.0      0.002   17.8   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   2.2e-37   1.9e-33       1     164 [.       5     181 ..       5     208 .. 0.89
   2 !   48.7   0.0   7.3e-17   6.5e-13     263     333 ..     239     314 ..     210     316 .. 0.76

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 2.2e-37
                                       -EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-....GS--..-SEEEE-- CS
                     DNA_methylase   1 lkfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk..kvsigDitkidkk....klpe.diDlLvgGf 69 
                                       +k id f+G+GGf+lg++  g f+  +a++  k aa+tY+anf+   v+++D+++++ +     ++  ++D+++g++
  gi|320101441|ref|YP_004177033.1|   5 YKYIDVFSGAGGFSLGFHLSGrFKSLLAVDSFKPAAETYKANFPhtLVVNEDVKDLTGEiltgLVKPdEVDVVIGSP 81 
                                       689*****************************************9989999******999996444446******** PP

                                       -GGGTECTSE.......E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTE.EEE CS
                     DNA_methylase  70 PCqpfSvaGk.......qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGY.evs 138
                                       PC pf  a          +   d+ g+L+  +irii +++P vf++ENV+ +++       + +l +++ +GY ev+
  gi|320101441|ref|YP_004177033.1|  82 PCEPFTGANPrreknplDRLYSDPMGQLTLHFIRIIGHYRPRVFVMENVPAITED---GLRDALLREFRRVGYgEVY 155
                                       ******99884444444455679999**************************999...5578899********6699 PP

                                       EEEEEGGGTT-SB--EEEEEEEEEGG CS
                     DNA_methylase 139 ykllnasdyGvpQnReRvfivgirkd 164
                                       +++l a+dyG+p  R+Rvfi  ir +
  gi|320101441|ref|YP_004177033.1| 156 FNILLAEDYGTPSHRKRVFISNIRIE 181
                                       ********************988765 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 7.3e-17
                                       TS---EEEETTEEE--T........TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHH CS
                     DNA_methylase 263 elaeagklqknkerfkp.......viekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiake 332
                                        l+++ +l+ n+    p       +i++ + R Lt+rE arl+Gf d+f+f + ++++y ++G++Vp p+++aia  
  gi|320101441|ref|YP_004177033.1| 239 TLPNMVRLNPNSIA--PtvlgssrFIHPFEDRLLTVREQARLMGFTDTFIFIGGREEQYNMVGEAVPAPLAKAIAGH 313
                                       34444444444332..255666679*************************************************987 PP

                                       H CS
                     DNA_methylase 333 i 333
                                       +
  gi|320101441|ref|YP_004177033.1| 314 L 314
                                       6 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.2e-07     0.002       4      81 ..       7      83 ..       4      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-07
                   Methyltransf_15  4 ilDlfsGaGGnviqfalv..fekviaieinleklacaqhNa.evYgvsdkitlvlgdvfellaklklekikvdlvflSp 79
                                       +D+fsGaGG +  f l+  f++  a+++ +   +  + N  +   v++ ++  +g++++ l k   +++  d+v+ Sp
  gi|320101441|ref|YP_004177033.1|  7 YIDVFSGAGGFSLGFHLSgrFKSLLAVDSFKPAAETYKANFpHTLVVNEDVKDLTGEILTGLVK--PDEV--DVVIGSP 81
                                      69**************9999*********99999999999724566799999999999876644..5566..9****** PP

                   Methyltransf_15 80 Pw 81
                                      P+
  gi|320101441|ref|YP_004177033.1| 82 PC 83
                                      95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2474.01
//
Query:       gi|320101442|ref|YP_004177034.1|  [L=148]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   93.1   0.0    1.6e-26   92.7   0.0    1.1  1  DUF2122   RecB-family nuclease (DUF2122)
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.058   13.3   0.0    1.4  1  YppF      YppF-like protein


Domain annotation for each model (and alignments):
>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.0   1.8e-30   1.6e-26       1     106 []      36     140 ..      36     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.8e-30
                           DUF2122   1 GaAAqsGipevlklalklgksllvlpdlkDalellkpekvlllskeegeelleeeeleekgrvllvfsgadegfskk 77 
                                       GaAAq+G+pe++k+a+k+gk+l+vlp+++D   +l +e+v++++++ g e    e +++ grv+++++++d+++s++
  gi|320101442|ref|YP_004177034.1|  36 GAAAQIGVPEAHKVAIKQGKPLIVLPEVSDLRSVLGCERVFYIDES-GVEAQLPEIVNTGGRVAILLGSGDQEPSRR 111
                                       89*******************************************9.9999999999******************** PP

                           DUF2122  78 elelgetvkvegveadvgelaelavvlye 106
                                       e+e +e+v++++v + ++ +a+++v++ye
  gi|320101442|ref|YP_004177034.1| 112 EVEGLEAVWPSNVPRGLPVTALTGVLVYE 140
                                       ***************************96 PP

>> YppF  YppF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.4e-06     0.058      16      33 ..       6      23 ..       2      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-06
                              YppF 16 YepesaneLLDFarklYl 33
                                      Y+p s+ +L+DF + +Y+
  gi|320101442|ref|YP_004177034.1|  6 YSPSSIQKLMDFVKTVYV 23
                                      9****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1111.06
//
Query:       gi|320101443|ref|YP_004177035.1|  [L=405]
Description: proteasome-activating nucleotidase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  148.8   0.0    2.8e-43  147.5   0.0    1.7  1  AAA              ATPase family associated with various cellul
      3e-16   58.9   0.0      7e-16   57.8   0.0    1.6  1  AAA_lid_3        AAA+ lid domain
    8.6e-12   44.8   0.6    2.6e-11   43.3   0.6    1.8  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    3.9e-07   30.3   0.0    1.1e-06   28.8   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    2.6e-06   27.9   0.3    0.00034   21.0   0.0    2.6  2  AAA_16           AAA ATPase domain
    4.2e-06   26.6   0.0    1.1e-05   25.3   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.6e-06   26.4   0.1    1.9e-05   24.6   0.1    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00021   20.9   2.5    0.00029   20.4   1.0    2.0  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    0.00073   19.8   0.2      0.021   15.1   0.0    2.5  2  AAA_22           AAA domain
     0.0012   18.0   0.0     0.0027   16.9   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
     0.0018   18.3   0.0     0.0038   17.2   0.0    1.5  1  AAA_14           AAA domain
     0.0025   17.1   0.2      0.044   13.1   0.0    2.8  3  Zeta_toxin       Zeta toxin
     0.0038   17.0   0.0       0.09   12.5   0.0    2.3  2  AAA_24           AAA domain
     0.0046   16.2   0.0     0.0076   15.5   0.0    1.3  1  TIP49            TIP49 P-loop domain
     0.0061   16.0   0.0      0.013   14.9   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0068   16.7   0.2      0.021   15.1   0.0    1.9  2  AAA_28           AAA domain
      0.007   16.3   0.3      0.045   13.7   0.0    2.3  2  ATPase_2         ATPase domain predominantly from Archaea
       0.01   16.4   0.2      0.049   14.2   0.0    2.3  2  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.026   14.3   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.013   15.8   0.0       0.03   14.7   0.0    1.6  1  RNA_helicase     RNA helicase
      0.014   15.5   0.0      0.043   14.0   0.0    1.9  1  AAA_33           AAA domain
      0.029   13.7   0.1       0.12   11.7   0.1    2.0  1  ATPase           KaiC
       0.04   14.3   0.0       0.11   12.9   0.0    1.9  1  AAA_17           AAA domain
       0.05   13.5   0.1       0.27   11.1   0.0    2.1  2  NACHT            NACHT domain
      0.057   13.9   0.0       0.15   12.6   0.0    1.8  1  ABC_tran         ABC transporter
       0.06   13.0   1.1        6.1    6.5   0.1    2.5  2  AAA_30           AAA domain
      0.071   12.8   0.1       0.29   10.8   0.0    2.0  2  Sigma54_activat  Sigma-54 interaction domain
      0.072   11.3   0.1       0.11   10.8   0.1    1.1  1  Fusion_gly       Fusion glycoprotein F0
       0.14   11.7   0.0       0.25   10.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.14   11.7   0.8       0.34   10.4   0.0    2.0  2  AAA_25           AAA domain
       0.17   11.0   0.0       0.34   10.0   0.0    1.4  1  NB-ARC           NB-ARC domain
       0.19   11.8   0.0       0.37   10.8   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.33   11.1   4.3      0.094   12.8   0.7    2.0  1  bZIP_1           bZIP transcription factor


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 !  147.5   0.0   5.2e-46   2.8e-43       1     132 []     175     308 ..     175     308 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 5.2e-46
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyGppG+GKTllakava e++++f+ i gsel++k++ge+++ +relf+ a++ka psi+fiDEida+a +r   
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAESNATFIAIVGSELVQKFIGEGARIVRELFELARRKA-PSIVFIDEIDAIAAKRidi 250
                                       79******************************************************9.*****************99 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                        +s ++e +r++ qLl+e+dg+k   ++v +i+atnr+d ldpa+lr gRfdr+ie++l
  gi|320101443|ref|YP_004177035.1| 251 GTSGEREVQRTLMQLLAEIDGFKPL-DRVKIIAATNRIDILDPAILRpGRFDRIIEVPL 308
                                       888999999***************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 !   57.8   0.0   1.3e-18     7e-16       1      44 [.     330     373 ..     330     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.3e-18
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       dvd+ eLA++T+G++GA+++a++ eA+ +A+r+++ +++m+df 
  gi|320101443|ref|YP_004177035.1| 330 DVDFMELARLTNGFTGAEIKAVVTEAGYNAIRENRRQVSMRDFL 373
                                       9*****************************************96 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.6   4.7e-14   2.6e-11       4      57 .]      65     117 ..      63     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 4.7e-14
                                       EEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                    Prot_ATP_ID_OB   4 VsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                       V  vl d +ra+Vk+s++ + vv la+ ++r+ ++pg +Va++++  +i+E+LP
  gi|320101443|ref|YP_004177035.1|  65 VEYVLSD-GRAVVKSSTGPNLVVALADNIDRSLIKPGVRVALNQRGSVIVEVLP 117
                                       5557888.*********************************************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 !   28.8   0.0   2.1e-09   1.1e-06       6     103 ..     175     266 ..     171     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.1e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a   ++    ++i +  sel +    + + +   + ++    a  +   iv++DEid i
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAESNA----TFIAIVGSELVQ----KFIGEGARIVRELFELARRKApsIVFIDEIDAI 243
                                       6889******************96....999999999999....55555555555555444444455********** PP

                                       ------------H.HHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSre.gVqrdLLqil 103
                                       ++ +++    S+e +Vqr L+q+l
  gi|320101443|ref|YP_004177035.1| 244 AA-KRIDIGTSGErEVQRTLMQLL 266
                                       **.777777777659*******98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.3e-07   0.00034      24      51 ..     163     199 ..     142     213 .. 0.68
   2 ?    4.2   0.0     0.095        52     122     149 ..     219     245 ..     214     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.3e-07
                            AAA_16  24 p.........elvllsGesGvGKsslvrellralekd 51 
                                                   vll+G++G+GK+ l+++++ + +++
  gi|320101443|ref|YP_004177035.1| 163 LfeeigieppKGVLLYGPPGCGKTLLAKAVAAESNAT 199
                                       245555555699******************9765554 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.095
                            AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                        +++l++l++r + p ++++D+++ + +
  gi|320101443|ref|YP_004177035.1| 219 IVRELFELARR-KAPSIVFIDEIDAIAA 245
                                       56788899999.778*********6554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0     2e-08   1.1e-05      34      97 ..     173     244 ..     166     254 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2e-08
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl......eekdvlfideihrls 97 
                                         vllyGpPG Gkt lak +a+e ++++ +  g  l ++  g+ a ++ +l      ++  ++fidei  ++
  gi|320101443|ref|YP_004177035.1| 173 KGVLLYGPPGCGKTLLAKAVAAESNATFIAIVGSELVQKfiGEGARIVRELfelarrKAPSIVFIDEIDAIA 244
                                       569**********************9987776665443323565656554422222234579******8776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   3.6e-08   1.9e-05       1     124 [.     174     288 ..     174     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.6e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppG+gK+ la+ +aa  n+++  + +++      l+++      + ++   +l + ar   ++i+++DE++
  gi|320101443|ref|YP_004177035.1| 174 GVLLYGPPGCGKTLLAKAVAAESNATFIAIVGSE------LVQKFIG---EGARIVRELFELARrkAPSIVFIDEID 241
                                       59****************************9987......7777763...3333335555555545999******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                        +  + +++  s   e ++ l+++  +++  +   l r+ +ia++n+ d
  gi|320101443|ref|YP_004177035.1| 242 AIAAKRIDIGTSGEREVQRTLMQLLAEIDGFK--PLDRVKIIAATNRID 288
                                       99999998887777777777777666665544..356699999999887 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 !   20.4   1.0   5.3e-07   0.00029       4      56 ..      64     117 ..      61     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.3e-07
                     Prot_ATP_OB_N   4 tflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnE.alvvVealg 56 
                                       ++  v s+++ +  ++ g  ++Va++ ++d + ++pG +V Ln+ ++v+Ve+l+
  gi|320101443|ref|YP_004177035.1|  64 VVEYVLSDGRAVVKSSTGPNLVVALADNIDRSLIKPGVRVALNQrGSVIVEVLP 117
                                       45555557777778999**************************94588999886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.8e-05     0.021       8      29 ..     175     196 ..     170     220 .. 0.86
   2 ?    2.2   0.0      0.38   2.1e+02      81     104 ..     222     244 ..     204     281 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++++G++G+GKT+l++ ++ + 
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAES 196
                                       689**************99886 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.38
                            AAA_22  81 aleqalraravielliiDEaqhlr 104
                                        l + +r++a  +++ iDE++ + 
  gi|320101443|ref|YP_004177035.1| 222 ELFELARRKAP-SIVFIDEIDAIA 244
                                       45555666666.9********985 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     5e-06    0.0027      51     115 ..     170     239 ..     118     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDD 115
                                       +p + vLL+G  G+GK  l ka+ +e +++ ++++  e+ ++ + e  ++v++l    +r+   i+f+D 
  gi|320101443|ref|YP_004177035.1| 170 EPPKGVLLYGPPGCGKTLLAKAVAAESNATFIAIVgsELVQKFIGEGARIVRELFelaRRKAPSIVFIDE 239
                                       57789*****************************977889999999999999876121556668999997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.1e-06    0.0038       5      76 ..     175     243 ..     172     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.1e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k ++ e+      ++ i   +  +k + + +++ ++++e+++++  +++f+DEi  +
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAESN---ATFIAIVGSELVQKFIGEGARIVRELFELARRKAPSIVFIDEIDAI 243
                                       7899***************9888...555555555544444444447888888886667899*******887 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.8   2.1e+03      90     123 ..     103     136 ..      93     155 .. 0.74
   2 !   13.1   0.0   8.1e-05     0.044      14      50 ..     170     204 ..     160     222 .. 0.84
   3 ?    0.5   0.1      0.57   3.1e+02     154     188 ..     360     394 ..     335     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                        Zeta_toxin  90 eaiengyniivegtlrspdvvkklaealkkaGYe 123
                                        a++++ ++ive   ++ d+  + +e ++k G +
  gi|320101443|ref|YP_004177035.1| 103 VALNQRGSVIVEVLPSHVDTYVQSMEVVEKPGVR 136
                                       5677777888887777777777777777766644 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.1e-05
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       e Pk +ll G pG+GK+ la+++++e   +  ++ + 
  gi|320101443|ref|YP_004177035.1| 170 EPPKGVLLYGPPGCGKTLLAKAVAAES--NATFIAIV 204
                                       6799*********************98..56666554 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.57
                        Zeta_toxin 154 vpkeehdeafeglresvealeeekqldrvkikdrd 188
                                       + +++ + +++ + ++ve+l e+k+l  v+ +dr 
  gi|320101443|ref|YP_004177035.1| 360 IRENRRQVSMRDFLKAVEKLREKKRLRGVEEYDRR 394
                                       55566677788888888888888888888855544 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   0.00017      0.09       5      29 ..     175     201 ..     172     250 .. 0.80
   2 ?    2.0   0.0      0.26   1.4e+02      31      70 ..     353     403 ..     343     405 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfi 29 
                                       +l+yGp+g GKT lak    + ++ fi
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVaaESNATFI 201
                                       89**************98776666666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.26
                            AAA_24  31 tekGlksldadkfpdieswedfldevvel.............aaeladyktlv 70 
                                       te+G++++  ++ +   s+ dfl++v++l             ++e ++ +tlv
  gi|320101443|ref|YP_004177035.1| 353 TEAGYNAIRENRRQ--VSMRDFLKAVEKLrekkrlrgveeydRRERDGTQTLV 403
                                       89999999999944..59***********887887777777777777777777 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05    0.0076      51      90 ..     173     210 ..     163     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       ++vLl Gp+g Gkt la a++ e +    f+a++gse+ +
  gi|320101443|ref|YP_004177035.1| 173 KGVLLYGPPGCGKTLLAKAVAAESN--ATFIAIVGSELVQ 210
                                       89*******************9965..88********865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-05     0.013      25      43 ..     175     193 ..     165     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVA 193
                                       89*************9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.9e-05     0.021       2      37 ..     175     211 ..     174     259 .. 0.73
   2 ?   -1.7   0.1       5.7   3.1e+03      26      42 ..     351     367 ..     338     404 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareilee 37 
                                       + + G++++GKT l++a aa+ + + ++ ++ e++++
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAEsNATFIAIVGSELVQK 211
                                       6799***************876444444444444433 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.7
                            AAA_28  26 vvpEaareileeklakg 42 
                                       vv+Ea+   ++e+ ++ 
  gi|320101443|ref|YP_004177035.1| 351 VVTEAGYNAIRENRRQV 367
                                       34555555554444221 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.9   4.8e+03     105     107 ..      37      39 ..       7      90 .. 0.52
   2 !   13.7   0.0   8.2e-05     0.045      18      49 ..     170     200 ..     162     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.9
                          ATPase_2 105 aie 107
                                         e
  gi|320101443|ref|YP_004177035.1|  37 ERE 39 
                                       111 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.2e-05
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdk 49 
                                       ep + +++YGp g+GKt L k ++ +++   +
  gi|320101443|ref|YP_004177035.1| 170 EPPKGVLLYGPPGCGKTLLAKAVAAESN-ATF 200
                                       56667899***********999988773.344 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   9.1e-05     0.049       1      25 [.     175     207 ..     175     271 .. 0.76
   2 ?   -1.4   0.0       6.1   3.3e+03      18      56 ..     336     379 ..     334     402 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.1e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........g 25 
                                       +ll G+pG+GKt lak+++ + +          
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAESNAtfiaivgsE 207
                                       799***************877432456556441 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.1
                            AAA_18  18 Lskrl.gf.gvnlrdvakenglllevdpe...aldeskrldedk 56 
                                       L++++ gf g +++ v++e g+   +++      +++++++e+ 
  gi|320101443|ref|YP_004177035.1| 336 LARLTnGFtGAEIKAVVTEAGYNAIRENRrqvSMRDFLKAVEKL 379
                                       66666566777777777777776666666444333333333322 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 ?   14.3   0.0   4.8e-05     0.026      47      71 ..     172     196 ..     159     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                        ++++l Gp+G GK+ la a++ e 
  gi|320101443|ref|YP_004177035.1| 172 PKGVLLYGPPGCGKTLLAKAVAAES 196
                                       5789****************99875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.5e-05      0.03       1      23 [.     175     197 ..     175     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                       ++lyGp+g+GK++lak +a++  
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAESN 197
                                       689*************9887765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.9e-05     0.043       2      28 ..     175     201 ..     175     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavll 28 
                                       vll G+pG+GK+ la+ ++++  a+++
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAESNATFI 201
                                       7899**************999885544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00022      0.12      14      43 ..     167     196 ..     147     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                            ATPase  14 gGipegrvvlitGepGtGKtifalqFlikg 43 
                                        Gi   + vl++G pG+GKt++a+  + ++
  gi|320101443|ref|YP_004177035.1| 167 IGIEPPKGVLLYGPPGCGKTLLAKAVAAES 196
                                       58888889**************98766554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0002      0.11       1      39 [.     178     217 ..     178     265 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0002
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrggl 39 
                                       +G+PG+GK+ +++ ++ + + t++   G+ l +    +g+
  gi|320101443|ref|YP_004177035.1| 178 YGPPGCGKTLLAKAVAAESNATFIAIvGSELVQKFIGEGA 217
                                       7******************999986557777766655554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0005      0.27       3      22 ..     175     194 ..     173     199 .. 0.89
   2 ?   -0.5   0.0       1.8   9.9e+02      85     114 ..     235     267 ..     207     284 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       v+l G++G+GKT L++ +a 
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAA 194
                                       799*************9986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                                       EEEE-STT-SS-TCH............HHHHHC CS
                             NACHT  85 lilDglDelvtdlgq...kekqpvrtlLselir 114
                                         +D +D ++++      +++++v++ L +l+ 
  gi|320101443|ref|YP_004177035.1| 235 VFIDEIDAIAAKRIDigtSGEREVQRTLMQLLA 267
                                       445666666664444555666666666666654 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   0.00028      0.15       8      37 ..     169     198 ..     166     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00028
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp 37 
                                       +++ + v + G+ G+GK+ L+k++a +++ 
  gi|320101443|ref|YP_004177035.1| 169 IEPPKGVLLYGPPGCGKTLLAKAVAAESNA 198
                                       66777899****************999875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.011       6.1      21      43 ..     175     197 ..     162     249 .. 0.82
   2 ?    4.9   0.1     0.035        19     144     186 ..     353     396 ..     317     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                            AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                       ++l Gp+G GKt + ka+++  +
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAESN 197
                                       6899*********9999976554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.035
                            AAA_30 144 agigtaeLtevvRqke.seeraaalalregdaeealealadrgr 186
                                       +++g   ++e++Rq +  ++ +a+++lre +  + +e +++r+r
  gi|320101443|ref|YP_004177035.1| 353 TEAGYNAIRENRRQVSmRDFLKAVEKLREKKRLRGVEEYDRRER 396
                                       467888999*****7779***********9999999*9999875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00053      0.29      23      54 ..     173     201 ..     158     215 .. 0.81
   2 ?   -3.1   0.0       9.9   5.4e+03      95     106 ..     233     244 ..     223     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfv 54 
                                         vl+ G  G+GK+lla+a+ ++s+   + f+
  gi|320101443|ref|YP_004177035.1| 173 KGVLLYGPPGCGKTLLAKAVAAESN---ATFI 201
                                       679****************998876...4444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.9
                                       SEEEEETGGGS- CS
                   Sigma54_activat  95 GtlfLDeigelp 106
                                       +++f+Dei  + 
  gi|320101443|ref|YP_004177035.1| 233 SIVFIDEIDAIA 244
                                       689*****9876 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00019      0.11     212     297 ..      33     123 ..      27     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                       CCTT-HHHHHHHCT--S-SHHHHHCCTT-EEEEEEEETTTTEEEEEEEEEEEEE.....EEEEEEEEEEE--EEETT CS
                        Fusion_gly 212 llggeleallsklgitssdlkdllesesikgqvilvdleeyvivlevqlPilge.....iddtkvkelskislnrdd 283
                                       ll++e e+ll+k+ +  s+l+++++   i+g v +v  ++  +v + + P l++     id  ++k +  ++ln+ +
  gi|320101443|ref|YP_004177035.1|  33 LLEAEREKLLTKINYYRSELEKMISPPLIEGVVEYVLSDGRAVVKSSTGPNLVValadnIDRSLIKPGVRVALNQRG 109
                                       7899**********************************************99862222266999************* PP

                                       EEEEEES-SEEEEE CS
                        Fusion_gly 284 qewytqvPkvvlnr 297
                                       +     +P++v + 
  gi|320101443|ref|YP_004177035.1| 110 SVIVEVLPSHVDTY 123
                                       *9999999999664 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 ?   10.8   0.0   0.00046      0.25      34      58 ..     173     197 ..     163     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       k vll+Gp G+GKt+++k +  + +
  gi|320101443|ref|YP_004177035.1| 173 KGVLLYGPPGCGKTLLAKAVAAESN 197
                                       789**************99887766 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   0.00063      0.34      36      55 ..     175     194 ..     169     198 .. 0.89
   2 ?   -3.2   0.0       9.6   5.2e+03     131     156 ..     221     245 ..     217     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00063
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +ll+G+pg+GKt la  +a+
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAA 194
                                       69************988876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.6
                            AAA_25 131 daleaaieevegvrlvviDplsralg 156
                                       ++l + +++ + +  v iD ++++ +
  gi|320101443|ref|YP_004177035.1| 221 RELFELARR-KAPSIVFIDEIDAIAA 245
                                       556666666.6788999998887654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00063      0.34      23      44 ..     175     196 ..     163     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00063
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G+GKt lak +  +s
  gi|320101443|ref|YP_004177035.1| 175 VLLYGPPGCGKTLLAKAVAAES 196
                                       779*************998875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00069      0.37      21      45 ..     169     198 ..     138     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00069
                                       E.....EEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE  21 v.....ilLeGdLGaGKTtlvrglakalgv 45 
                                       +     +lL+G+ G+GKT l++++a++ + 
  gi|320101443|ref|YP_004177035.1| 169 IeppkgVLLYGPPGCGKTLLAKAVAAESNA 198
                                       0344449*****************988765 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   0.00017     0.094      26      59 ..      22      55 ..      20      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 26 aeieeLerrvkaLekeNksLkseleelkkevekL 59
                                       +i  Le++v  Le+e ++L  +++ ++ e ek+
  gi|320101443|ref|YP_004177035.1| 22 DYIRYLESKVRLLEAEREKLLTKINYYRSELEKM 55
                                      69999**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 2639.98
//
Query:       gi|320101444|ref|YP_004177036.1|  [L=335]
Description: thioredoxin reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  155.3   0.8    2.3e-45  155.1   0.8    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.6e-23   81.9   0.5    1.9e-18   66.8   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.8e-15   57.2   2.7    6.6e-12   45.8   0.1    2.9  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.4e-11   44.1   5.4    1.5e-06   27.6   1.9    3.4  3  FAD_binding_2   FAD binding domain
      2e-09   37.3   4.9    1.3e-07   31.3   0.0    3.2  4  FAD_oxidored    FAD dependent oxidoreductase
    1.4e-08   34.3   5.1    1.6e-05   24.2   0.9    3.5  4  GIDA            Glucose inhibited division protein A
    5.5e-08   31.9   0.5    0.00098   17.9   0.2    3.2  3  HI0933_like     HI0933-like protein
    1.2e-07   31.2   0.5    9.9e-05   21.7   0.2    2.6  2  Thi4            Thi4 family
    6.3e-06   25.7   6.9    3.4e-05   23.3   0.8    2.5  3  FAD_binding_3   FAD binding domain
    1.8e-05   24.9   1.8     0.0048   17.1   0.2    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00033   21.1   0.4       0.29   11.6   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
    0.00043   20.0   9.4      0.024   14.2   3.3    2.6  3  DAO             FAD dependent oxidoreductase
     0.0012   17.8   3.6       0.24   10.2   0.9    2.3  2  Trp_halogenase  Tryptophan halogenase
     0.0017   18.3   1.9       0.73    9.8   0.0    3.2  3  NAD_binding_9   FAD-NAD(P)-binding
     0.0044   16.1   0.8       0.05   12.7   0.3    2.1  2  Lycopene_cycl   Lycopene cyclase protein
     0.0046   16.4   1.3       0.32   10.4   0.4    2.2  2  PALP            Pyridoxal-phosphate dependent enzyme
     0.0083   15.4   1.1        1.3    8.2   0.4    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.015   14.4   0.5         11    5.1   0.0    3.0  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.075   13.5   0.0         19    5.8   0.0    2.3  2  XdhC_C          XdhC Rossmann domain
      0.092   12.4   0.1        0.4   10.4   0.0    1.9  2  VanW            VanW like 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 !  155.1   0.8   2.5e-48   2.3e-45       1     294 []      21     314 ..      21     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 2.5e-48
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgiel 69 
                                       +dv+v+GgGpAGl+aal+ a++g+k+++v   + +++g +  ++ +  +++ +ei          ++v+k+n  +  
  gi|320101444|ref|YP_004177036.1|  21 YDVIVVGGGPAGLTAALYSARYGFKTIVV---TKLVGGAVTEAPLVDDYPGIPEIPGndlvdkfvKHVRKYNVPVV- 93 
                                       69***************************...66777777778888888888887778445556666666664422. PP

                                       CHCCTCEEEE..ESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSE CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  70 llgeevvkid..pgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkr 144
                                         + evv++   p+  k  + +++  ++  +   ++++A Gs+ r+lg+pG++e vg++v++++++++   k +   
  gi|320101444|ref|YP_004177036.1|  94 -VD-EVVNVSrrPEDNKWCV-ELR--SGGMLCSYAVIIAVGSEKRKLGVPGEKELVGRGVSYCATCDGPLFKDKV-- 163
                                       .22.4555543333334444.223..45579999***********************************999998.. PP

                                       EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..EEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.. RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge..kle.. 217
                                       ++vvGgG+ +   A +lakl+++v+++++rd++      +++ ++ +a+ + ++++ ++t+vke+ g ++   ++  
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLASHVYIIHRRDEFR-----AFKIYVDAARSNPKITLLTNTVVKELLGSEHleAVKiy 235
                                       *********************************6.....6777777777777*****************98855564 PP

                                       .EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC..TECCSS--HHHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                       Pyr_redox_2 218 .vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva..ggkggpelaqaAv 291
                                        ++++ +e++++d +++ +G++p  e++ +k+gl++de+g+ vv+    tn pgi+++GD a    k+++e++ +A 
  gi|320101444|ref|YP_004177036.1| 236 nTQTQREEVLKVDGLFIEIGLQPPVEFF-KKIGLNVDETGRAVVNLDRSTNLPGIFVAGDAAggPYKYRFEQVITAA 311
                                       677777777******************9.*********************************877788999999998 PP

                                       HHH CS
                                       xxx RF
                       Pyr_redox_2 292 qqG 294
                                       + G
  gi|320101444|ref|YP_004177036.1| 312 ADG 314
                                       776 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   0.7   4.7e-05     0.042       1      27 [.      24      49 ..      24      60 .. 0.86
   2 !   66.8   0.0   2.1e-21   1.9e-18      81     305 .]      75     293 ..      66     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                                      i++G+GPaGl+aa+   + g++++ ++
  gi|320101444|ref|YP_004177036.1| 24 IVVGGGPAGLTAALYSARYGFKTI-VV 49
                                      89*******************755.54 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 2.1e-21
                       Pyr_redox_3  81 kealeYlrevaksfelpiklfeeVesvkk.edegfevetske.tyeAkkviiAtGefdkPnklnipGeek...lvkh 152
                                       +++++ + + ++++++p+  +e V+   + ed++  ve +++  + +  viiA G     +kl++pGe++     + 
  gi|320101444|ref|YP_004177036.1|  75 NDLVDKFVKHVRKYNVPVVVDEVVNVSRRpEDNKWCVELRSGgMLCSYAVIIAVGS--EKRKLGVPGEKElvgRGVS 149
                                       556666667789999**99998776555578999****99984677778******9..8999*******84333455 PP

                       Pyr_redox_3 153 yskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslk.pdienrleelvkeekik 228
                                       y    +   ++++ v+V+Gg+n a+  Al l++  ++V +++r++e ++ +    + +  ++ ++++  l ++   +
  gi|320101444|ref|YP_004177036.1| 150 YCATCDGPLFKDKVVAVVGGGNAAFTSALYLAKLASHVYIIHRRDEFRAFK----IYVDaARSNPKITLLTNTVVKE 222
                                       5555677678899999*****************************988875....4333033444444333332235 PP

                       Pyr_redox_3 229 vlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +l  ++++++k     y+ +t++++   + d  ++ +G +p ++f+kk +++ de+gr v++  + +tn+pg+f+aG
  gi|320101444|ref|YP_004177036.1| 223 LLGSEHLEAVK----IYNTQTQREEV-LKVDGLFIEIGLQPPVEFFKKIGLNVDETGRAVVN-LDRSTNLPGIFVAG 293
                                       66666676666....57778888554.444666777**********************9998.578**********9 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.4    0.0011      0.97       2      29 ..      23      50 ..      22      53 .. 0.92
   2 ?   -1.2   0.0       3.5   3.1e+03      41      66 ..      76     101 ..      70     115 .. 0.77
   3 !   45.8   0.1   7.4e-15   6.6e-12       2      78 ..     164     234 ..     163     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvve 29
                                      v+vvGgG  gl +A + a++g k+ vv 
  gi|320101444|ref|YP_004177036.1| 23 VIVVGGGPAGLTAALYSARYGFKTIVVT 50
                                      89*******************9999986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHTTEEEECSEEEEEE CS
                         Pyr_redox  41 easkilqeklekngievllntkveei 66 
                                       ++ + + ++++k ++ v+ +++v+  
  gi|320101444|ref|YP_004177036.1|  76 DLVDKFVKHVRKYNVPVVVDEVVNVS 101
                                       56677889999999999999988755 PP

  == domain 3  score: 45.8 bits;  conditional E-value: 7.4e-15
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvk 77 
                                       v+vvGgG+ +   A +la+l+++V++++r+d+++      a ki  +  + n +i++l+nt+v+e+ gse  +e+vk
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLASHVYIIHRRDEFR------AFKIYVDAARSNpKITLLTNTVVKELLGSEH-LEAVK 233
                                       79********************************......***************************9998.88898 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       +
  gi|320101444|ref|YP_004177036.1| 234 I 234
                                       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 !   27.6   1.9   1.7e-09   1.5e-06       1      31 [.      22      52 ..      22      58 .. 0.95
   2 !    7.5   0.0    0.0021       1.9       2      35 ..     164     197 ..     163     222 .. 0.91
   3 !    8.6   0.0   0.00096      0.86     358     406 ..     249     300 ..     214     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.7e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                                      DviV+G+G AGL+AAl  a+ G k++vv+k 
  gi|320101444|ref|YP_004177036.1| 22 DVIVVGGGPAGLTAALYSARYGFKTIVVTKL 52
                                      9****************************95 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0021
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                       v V+G+G A  ++Al +a+    v ++   +ef+
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLASHVYIIHRRDEFR 197
                                       78******************999*9999888876 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00096
                                       .......EEEEE.EEES-EEEBETTSBE..STTEEESSBTEEE-STCEESSS CS
                     FAD_binding_2 358 gpfyavkvvpaq.hytmgGvetdengrv..ldadgqpipGLYAaGevaaggv 406
                                       g f+++ + p++ ++   G+++de+gr+    +  +++pG + aG +a+g +
  gi|320101444|ref|YP_004177036.1| 249 GLFIEIGLQPPVeFFKKIGLNVDETGRAvvNLDRSTNLPGIFVAGDAAGGPY 300
                                       667777788887688899*********988788899************8766 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.5e-10   1.3e-07       1      47 [.      22      66 ..      22     112 .. 0.80
   2 !    5.9   0.1    0.0078         7       2      32 ..     164     194 ..     164     196 .. 0.94
   3 ?    0.7   0.0      0.29   2.6e+02      90     132 ..     200     242 ..     195     246 .. 0.77
   4 ?   -3.2   0.1       4.3   3.8e+03     128     156 ..     294     324 ..     274     332 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.5e-10
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdi 47
                                      Dv+VvGGgpaG++AA+ +ar G k+++v   + +GG +t + +  d 
  gi|320101444|ref|YP_004177036.1| 22 DVIVVGGGPAGLTAALYSARYGFKTIVVT--KLVGGAVTEAPLVDDY 66
                                      9***************************5..68******98765554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0078
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                       v VvGGg a ++ A+  a+    v ++++r+
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLASHVYIIHRRD 194
                                       89*************************9986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.29
                      FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveske.grk 132
                                       k  +++  +++++t+l+nt+++e   ++  +e+v++ + + +r+
  gi|320101444|ref|YP_004177036.1| 200 KIYVDAARSNPKITLLTNTVVKELLGSE-HLEAVKIYNTQtQRE 242
                                       44555555889**************996.899999998885555 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 4.3
                      FAD_oxidored 128 ke.g.rktirAkvfiDATgdGdlaalaGvpy 156
                                       ++ g  +++r + +i A  dG +aa a ++y
  gi|320101444|ref|YP_004177036.1| 294 DAaGgPYKYRFEQVITAAADGAIAADAACKY 324
                                       4444577788888888999999998887776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.9   1.8e-08   1.6e-05       1      31 [.      22      52 ..      22      62 .. 0.91
   2 ?    0.3   0.0      0.31   2.8e+02     108     153 ..      87     132 ..      75     153 .. 0.74
   3 !    8.9   0.0   0.00081      0.73       2      35 ..     164     196 ..     163     242 .. 0.83
   4 ?   -1.2   0.1      0.93   8.3e+02     354     382 ..     285     319 ..     278     326 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.8e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                      dviV+GgG AG+ AAl +ar G+k++ +t+ 
  gi|320101444|ref|YP_004177036.1| 22 DVIVVGGGPAGLTAALYSARYGFKTIVVTKL 52
                                      8*************************99765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.31
                                       STTEEEEES-EEEEEECT.TEEEEEEETTS-EEEECEEEE--TT-BT CS
                              GIDA 108 epnleiieeeveelivee.kkvkgvvtedgetikakavviatGtflk 153
                                       + n+ ++ +ev +++ +  ++   v +++g ++ + av+ia G+  k
  gi|320101444|ref|YP_004177036.1|  87 KYNVPVVVDEVVNVSRRPeDNKWCVELRSGGMLCSYAVIIAVGS-EK 132
                                       4789999999999987664555669999***************9.33 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00081
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldti 35 
                                       v V+GgG A +  Al +a+l  +v +i h+ d++
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLASHVYII-HRRDEF 196
                                       89**********************999.555554 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.93
                                       SSBTEEE-CGGGTB-S.H.....HHHHHHHHHHHH CS
                              GIDA 354 kvkgLflAGqinGteG.Y.....eEaaaqGllAGi 382
                                       + +g+f+AG+  G    Y     + aaa G +A+ 
  gi|320101444|ref|YP_004177036.1| 285 NLPGIFVAGDAAGGPYkYrfeqvITAAADGAIAAD 319
                                       57999****99997411222222356677777765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.1e-06   0.00098       1      30 [.      21      50 ..      21      54 .. 0.92
   2 !    5.5   0.0    0.0065       5.8     109     164 ..      75     130 ..      71     138 .. 0.93
   3 !    4.9   0.0    0.0097       8.7       3      34 ..     164     195 ..     162     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllle 30
                                      +dviv+GgG+AGl aA+  a+ g +++++ 
  gi|320101444|ref|YP_004177036.1| 21 YDVIVVGGGPAGLTAALYSARYGFKTIVVT 50
                                      59*********************9999875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0065
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +d+vd ++k++++ +v + +++ v+  ++ ed+k  v+++s++ l + ++++A+G+
  gi|320101444|ref|YP_004177036.1|  75 NDLVDKFVKHVRKYNVPVVVDEVVNVSRRPEDNKWCVELRSGGMLCSYAVIIAVGS 130
                                       5899*********************999***********999999999*****997 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0097
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                       v+v+GgG A +  A+ +ak  ++V ++ + ++
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLASHVYIIHRRDE 195
                                       89************************988765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   1.1e-07   9.9e-05      18      51 ..      21      53 ..      14      61 .. 0.89
   2 !    6.9   0.0    0.0035       3.1      19      49 ..     163     192 ..     155     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.1e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersv 51
                                       Dv++vG+G++GLtaa y a+  ++k++++ + v
  gi|320101444|ref|YP_004177036.1| 21 YDVIVVGGGPAGLTAALYSARY-GFKTIVVTKLV 53
                                      6********************9.****9997655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0035
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailer 49 
                                        v++vG+G +  t+a ylak    +v i+ r
  gi|320101444|ref|YP_004177036.1| 163 VVAVVGGGNAAFTSALYLAKL-ASHVYIIHR 192
                                       589*****************8.777777766 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.8   3.8e-08   3.4e-05       2      33 ..      21      52 ..      20      59 .. 0.92
   2 !    5.8   0.0    0.0076       6.8       4      35 ..     164     195 ..     161     200 .. 0.88
   3 ?   -4.1   0.7       7.6   6.9e+03     286     293 ..     289     296 ..     288     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.8e-08
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +dV++VG+GpaGl++al  +++G ++++v+k 
  gi|320101444|ref|YP_004177036.1| 21 YDVIVVGGGPAGLTAALYSARYGFKTIVVTKL 52
                                      79***************************996 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0076
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       V++VG+G a +++al L++    v ++ +r++
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLASHVYIIHRRDE 195
                                       88******************888999998876 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 7.6
                                       EEE-GGGT CS
                     FAD_binding_3 286 vflaGDAa 293
                                       +f+aGDAa
  gi|320101444|ref|YP_004177036.1| 289 IFVAGDAA 296
                                       8******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 !   17.1   0.2   5.4e-06    0.0048       1      25 [.      25      49 ..      25      70 .. 0.85
   2 !    6.7   0.1    0.0095       8.5       1      29 [.     166     194 ..     166     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.4e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlll 25
                                      +vG+G +Gl+aA + a++gf+  ++
  gi|320101444|ref|YP_004177036.1| 25 VVGGGPAGLTAALYSARYGFKTIVV 49
                                      8*******************86665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0095
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                       +vG+G ++ + A +Lak   +v ++ +rd
  gi|320101444|ref|YP_004177036.1| 166 VVGGGNAAFTSALYLAKLASHVYIIHRRD 194
                                       8****************988898887776 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0055         5       9      40 ..      22      53 ..      18     131 .. 0.80
   2 !   11.6   0.0   0.00033      0.29       5      42 ..     159     195 ..     158     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0055
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev 40
                                       v+vvGgG+ +++ +   +++g k +vv++ v
  gi|320101444|ref|YP_004177036.1| 22 DVIVVGGGPAGLTAALYSARYGFKTIVVTKLV 53
                                      699************************99876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00033
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevke 42 
                                       +k+k v vvGgG+ A + +  l++   +v ++  +  e
  gi|320101444|ref|YP_004177036.1| 159 FKDKVVAVVGGGNAAFTSALYLAKLASHVYIIHRRD-E 195
                                       68999**************************98883.3 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   3.3   2.7e-05     0.024       1      26 [.      22      49 ..      22      57 .. 0.87
   2 ?   -2.5   0.0       3.3     3e+03     151     202 ..      80     130 ..      75     145 .. 0.59
   3 !    8.8   0.1    0.0012       1.1       2      32 ..     164     196 ..     163     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtll 26
                                      dv+++GGG +Gl++A++ ar g  ++++
  gi|320101444|ref|YP_004177036.1| 22 DVIVVGGGPAGLTAALYSARYGfkTIVV 49
                                      9******************999985555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.3
                                       HHHHHHHHTT-EEEESECEEEE.EEEETCEEEEE.EECT.EEEEEEEEEEE--GG CS
                               DAO 151 alaraaealGveilegtevtgl.eeedgkvwgve.rttp.gendaadavVnaaGa 202
                                        + + +++  v ++   ev+++ +++++  w ve r  + g   +  av++a G 
  gi|320101444|ref|YP_004177036.1|  80 KFVKHVRKYNVPVVVD-EVVNVsRRPEDNKWCVElR--SgGML-CSYAVIIAVGS 130
                                       5556666666666666.7777634444555888432..32433.33458888875 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0012
                                       EEEECTSHHHHHHHHHHHHT.T.EEEEESSSST CS
                               DAO   2 vviiGGGiiGlstAyeLarr.g.Vtllekgdia 32 
                                       v+++GGG +  + A++La+    V ++ ++d++
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLaShVYIIHRRDEF 196
                                       89***************976348*****99875 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.9   0.00027      0.24       1      29 [.      22      50 ..      22      60 .. 0.83
   2 !    7.9   0.1    0.0014       1.2       2      23 ..     164     185 ..     163     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevt 29
                                      ++++vGGG+aG +aA + a+++ +++ vt
  gi|320101444|ref|YP_004177036.1| 22 DVIVVGGGPAGLTAALYSARYGFKTIVVT 50
                                      699****************9996655555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0014
                                       EEEE--SHHHHHHHHHHHHHTT CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalk 23 
                                       + +vGGG a++++A +lak  +
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLAS 185
                                       78****************9873 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   0.6      0.12   1.1e+02       2      13 ..      25      36 ..      24      43 .. 0.88
   2 !    9.8   0.0   0.00081      0.73     102     155 ..      76     130 ..      75     131 .. 0.83
   3 ?    3.3   0.0     0.084        75       1      58 [.     165     222 ..     165     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                     NAD_binding_9  2 ivGaGprGlavl 13
                                      +vG+Gp+Gl+++
  gi|320101444|ref|YP_004177036.1| 25 VVGGGPAGLTAA 36
                                      8********987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00081
                     NAD_binding_9 102 dlfeellarlpegvtvevhraevvdleeradg..qavlladgaslaadaVvLAlGh 155
                                       dl++++++ ++ + +v v+ +evv++++r++   + v l++g  l   aV++A+G 
  gi|320101444|ref|YP_004177036.1|  76 DLVDKFVKHVR-KYNVPVVVDEVVNVSRRPEDnkWCVELRSGGMLCSYAVIIAVGS 130
                                       56777887775.679************999663257899***************95 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.084
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp.sep.gagrvwrtdqseelllNvpase 58 
                                       a+vG+G ++ + +  L++ a  ++   i+  d+ + +     ++r++ + +ll+N++++e
  gi|320101444|ref|YP_004177036.1| 165 AVVGGGNAAFTSALYLAKLA--SHVYIIHRRDEfRAFkIYVDAARSNPKITLLTNTVVKE 222
                                       89*****************8..88888888888555565577777777888888888765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3   5.6e-05      0.05       1      30 [.      22      49 ..      22      55 .. 0.88
   2 ?    1.6   0.0      0.13   1.1e+02       2      31 ..     164     191 ..     163     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                      Dv+v+G+GpAgl  A  +  a++g k +++
  gi|320101444|ref|YP_004177036.1| 22 DVIVVGGGPAGLTAALYS--ARYGFKTIVV 49
                                      9**************999..8888877666 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlie 31 
                                       v+v+G+G A    A  l  ak + +v +i 
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYL--AKLASHVYIIH 191
                                       79***************..99999999985 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.4   0.00036      0.32      37      85 ..       3      50 ..       1      60 [. 0.86
   2 ?    4.9   0.0     0.017        15      53      88 ..     159     194 ..     143     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                                      TTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEE CS
                              PALP 37 fKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivv 85
                                      fK R      a+ + g +++ v++ ++G +g+ +A+++a++G+k ++v 
  gi|320101444|ref|YP_004177036.1|  3 FKFRITGLSGAAYRSG-ETYDVIVVGGGPAGLTAALYSARYGFKTIVVT 50
                                      7777777666667788.999*************************9985 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                                       TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETT CS
                              PALP  53 tgaktvveassGNhgralAaaaallGlkvtivvpad 88 
                                        + k+v++ ++GN++   A++ a+l   v+i   +d
  gi|320101444|ref|YP_004177036.1| 159 FKDKVVAVVGGGNAAFTSALYLAKLASHVYIIHRRD 194
                                       67789999999****999999998877887775555 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 !    8.2   0.4    0.0015       1.3      30      56 ..      22      48 ..       7      52 .. 0.87
   2 !    5.7   0.0    0.0087       7.8      30      62 ..     163     195 ..     146     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                                      EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtv 56
                                       v+v+GgG aGl A+  +++ g k+ v
  gi|320101444|ref|YP_004177036.1| 22 DVIVVGGGPAGLTAALYSARYGFKTIV 48
                                      69**************99999987765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0087
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                        v v+GgG a   ++   ++l  +V+++  r +
  gi|320101444|ref|YP_004177036.1| 163 VVAVVGGGNAAFTSALYLAKLASHVYIIHRRDE 195
                                       589************************998876 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 ?    2.9   0.0     0.054        48       1      23 [.      19      41 ..      19      51 .. 0.80
   2 ?    3.4   0.0     0.037        34     189     229 ..     159     197 ..      93     201 .. 0.67
   3 ?    5.1   0.0     0.012        11     284     336 ..     201     252 ..     196     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.054
                       K_oxygenase  1 eilDligiGiGpsnLsLaillee 23
                                      e++D+i +G Gp+ L+ a+ ++ 
  gi|320101444|ref|YP_004177036.1| 19 ETYDVIVVGGGPAGLTAALYSAR 41
                                      579**********9998876654 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.037
                       K_oxygenase 189 lakkriaVvGsGqSaaeifedllrrqkkvelklvtrseale 229
                                        + k +aVvG+G  a   +  l++ ++  ++ ++ r+++++
  gi|320101444|ref|YP_004177036.1| 159 FKDKVVAVVGGGNAAFTSALYLAKLAS--HVYIIHRRDEFR 197
                                       567889******998766666555544..677777777776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.012
                       K_oxygenase 284 lyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvl 336
                                       +y +  +++++++ll+n+ v+++  +++    +++ n+++++ee+l+vd +++
  gi|320101444|ref|YP_004177036.1| 201 IYVDAARSNPKITLLTNTVVKELLGSEH-LEAVKIYNTQTQREEVLKVDGLFI 252
                                       68888889999************99985.7789999*************9986 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.021        19       1      80 [.      23     133 ..      23     143 .. 0.66
   2 ?    5.6   0.0     0.023        21       1      43 [.     164     206 ..     164     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.............................-EEE CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.............................tavv 48 
                                       ++++G+g+ +   a + a+ gf+++vv +     +++++p +d+                             + vv
  gi|320101444|ref|YP_004177036.1|  23 VIVVGGGPAGLTAALYSARYGFKTIVVTKLVGG-AVTEAPLVDDypgipeipgndlvdkfvkhvrkynvpvvvDEVV 98 
                                       689************************988753.3444444444455555666666666666666777777777777 PP

                                       E--S-HHHHHHHHHHHSSS-....-SEEEESS-HHH CS
                            XdhC_C  49 vlthdhklDaealeaalrkk....aayigllGSrkk 80 
                                        +++ ++   +++ ++ ++      a i ++GS+k+
  gi|320101444|ref|YP_004177036.1|  99 NVSRRPEDN-KWCVELRSGGmlcsYAVIIAVGSEKR 133
                                       777765544.44444433223433346667777665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.023
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-S CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpead 43 
                                       ++++G+g+ a   a ++a+l  +v+++  r+ef++ + + +a+
  gi|320101444|ref|YP_004177036.1| 164 VAVVGGGNAAFTSALYLAKLASHVYIIHRRDEFRAFKIYVDAA 206
                                       579****************************998544444443 PP

>> VanW  VanW like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.7   1.5e+03      44      70 ..      14      42 ..      10      51 .. 0.70
   2 ?   10.4   0.0   0.00045       0.4      47      84 ..     160     197 ..     153     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                              VanW 44 vivngklvkgv..GGGvcqvsttlynaal 70
                                      ++ +g++ + +  GGG   ++ +ly a +
  gi|320101444|ref|YP_004177036.1| 14 AYRSGETYDVIvvGGGPAGLTAALYSARY 42
                                      56666665544449999999999999876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00045
                              VanW  47 ngklvkgvGGGvcqvsttlynaallagleiverhpHsl 84 
                                       ++k+v  vGGG   ++++ly a l + + i+ r+   +
  gi|320101444|ref|YP_004177036.1| 160 KDKVVAVVGGGNAAFTSALYLAKLASHVYIIHRRDEFR 197
                                       568999*************************9987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2209.70
//
Query:       gi|320101445|ref|YP_004177037.1|  [L=316]
Description: aldo/keto reductase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-74  248.7   0.0    7.6e-74  248.5   0.0    1.0  1  Aldo_ket_red     Aldo/keto reductase family
  ------ inclusion threshold ------
       0.17   11.8   0.4        1.8    8.5   0.0    2.6  3  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.5   0.0   8.5e-78   7.6e-74       1     292 [.      15     305 ..      15     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: 248.5 bits;  conditional E-value: 8.5e-78
                                       .EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSST CS
                      Aldo_ket_red   1 elglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdae 76 
                                       ++glGtwq++   + ++ e a +++ +a+e G+nf+DtA vYg+g see+lG+ l + ++kr+ev+iatK+      
  gi|320101445|ref|YP_004177037.1|  15 RIGLGTWQYSETwGLTEYEAAKKVIAKAVEVGMNFIDTAMVYGRGMSEEFLGRSLRELGVKRDEVFIATKI------ 85 
                                       59********999999999999*************************************************...... PP

                                       TSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.H.HHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HH CS
                      Aldo_ket_red  77 iksglskeniresleeslkrLgtdyvDllllHrpdpslpsi.eevldaleelvkeGkiraiGvSnfsveqleka.kk 151
                                       + + l+++++ +s+e+slkrLg+++vDll+lH+p +++ +  +  ++ale l+  Gk+r+iGvSn++++ +e++ ++
  gi|320101445|ref|YP_004177037.1|  86 PGDFLNPDDVFKSVERSLKRLGVNTVDLLQLHWPPCWHNYPtASYARALERLILHGKVRYIGVSNYPIALIEELrEA 162
                                       999*********************************99944145569***************************999 PP

                                       TTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------..TS-HHHH CS
                      Aldo_ket_red 152 kkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd..ertsknl 226
                                        + ++iv+ q ++nl ++ +ee+l++++++++  +i++spl++G+ltgky+ e+  + k+ r++   +  ++++k  
  gi|320101445|ref|YP_004177037.1| 163 FSFTDIVSMQYRFNLAERWAEEELIPYAEANDFTFIPWSPLAKGALTGKYTLENIGGFKDLRSNEPVFhpSNFEKLT 239
                                       ***************************************************9999887777766655599******* PP

                                       HHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 227 daaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                        ++++l+e+a ++g +++q+al+++++ ++v+++ipga+++eq+ +n++a+ ++ls e++ +l e+
  gi|320101445|ref|YP_004177037.1| 240 PLINTLKEVASKYGRTPSQVALNWLIKYSPVVVPIPGAKTPEQVVENAGAVGWELSFEDWMRLYEV 305
                                       **********************************************************99988765 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.22     2e+03      13      27 ..      30      44 ..      23      46 .. 0.85
   2 ?   -0.8   0.0      0.16   1.4e+03       3      19 ..     177     193 ..     177     195 .. 0.87
   3 ?    8.5   0.0    0.0002       1.8      36      67 ..     209     240 ..     207     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.22
                   HU-CCDC81_bac_2 13 isyeeAlqkiekeve 27
                                      + ye A + i+k+ve
  gi|320101445|ref|YP_004177037.1| 30 TEYEAAKKVIAKAVE 44
                                      579999999999986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.16
                   HU-CCDC81_bac_2   3 LansiaeaegisyeeAl 19 
                                       La+  ae+e i+y eA+
  gi|320101445|ref|YP_004177037.1| 177 LAERWAEEELIPYAEAN 193
                                       788889*********97 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0002
                   HU-CCDC81_bac_2  36 egrveleniGeLslneegkleFepseagnllp 67 
                                       +g+++leniG ++    +  +F+ps+ + l+p
  gi|320101445|ref|YP_004177037.1| 209 TGKYTLENIGGFKDLRSNEPVFHPSNFEKLTP 240
                                       589*********************99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2415.38
//
Query:       gi|320101446|ref|YP_004177038.1|  [L=161]
Description: XRE family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-11   44.1   1.3    2.5e-11   43.5   1.3    1.3  1  HTH_3           Helix-turn-helix
    9.5e-09   35.5   0.4    1.5e-08   34.8   0.4    1.3  1  HTH_31          Helix-turn-helix domain
    2.6e-08   33.8   0.3    4.5e-08   33.0   0.3    1.4  1  HTH_19          Helix-turn-helix domain
     0.0001   22.1   1.6    0.00011   22.0   0.5    1.6  2  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   14.8   0.1      0.031   14.2   0.1    1.3  1  HTH_37          Helix-turn-helix domain
      0.067   13.1   0.2       0.14   12.1   0.2    1.5  1  DUF4428         Domain of unknown function (DUF4428)
      0.096   12.6   0.1         19    5.3   0.0    2.2  2  HTH_1           Bacterial regulatory helix-turn-helix protein
       0.25   11.9   3.6       0.66   10.5   3.6    1.7  1  BMFP            Membrane fusogenic activity
       0.32   11.2   6.6       0.31   11.3   4.5    1.9  2  DUF2703         Domain of unknown function (DUF2703)
       0.62    9.7   3.4          2    8.1   1.1    2.2  2  Sgf11           Sgf11 (transcriptional regulation protein)
       0.69   10.0   4.7       0.67   10.1   0.7    2.3  2  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
        1.5    8.8   6.8        1.5    8.9   5.3    1.7  2  zf-DNL          DNL zinc finger


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   1.3   1.6e-14   2.5e-11       1      53 [.      80     132 ..      80     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.6e-14
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53 
                                       ++e+R+ lg++q+ LA+k+  s + i riE G+ +P l+ + +l+k+Lgv+l 
  gi|320101446|ref|YP_004177038.1|  80 IREARERLGWTQQVLAQKVRESENIIKRIEAGKLKPGLDLARRLEKVLGVKLL 132
                                       8*************************************************986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.4     1e-11   1.5e-08       3      57 ..      77     130 ..      75     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1e-11
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57 
                                       + + r++Rer G++q+ +A+ ++ se  + r+E G+   p ++  ++l  +lg+ 
  gi|320101446|ref|YP_004177038.1|  77 AKRIREARERLGWTQQVLAQKVRESENIIKRIEAGKL-KPGLDLARRLEKVLGVK 130
                                       6799*********************************.6**************85 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.3     3e-11   4.5e-08       2      55 ..      78     130 ..      77     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 3e-11
                            HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                       +r++eaRe lg+tq+ la++++ s + i  iE gk  +p+ +l +++ + lg+ 
  gi|320101446|ref|YP_004177038.1|  78 KRIREARERLGWTQQVLAQKVRESENIIKRIEAGKL-KPGLDLARRLEKVLGVK 130
                                       8*********************************99.99999998888888876 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.1   1.2e+04      51      56 ..      34      39 ..      33      40 .. 0.86
   2 !   22.0   0.5   7.5e-08   0.00011       1      35 [.      79     113 ..      79     116 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.1
                                      HHHHTT CS
                            HTH_25 51 YArlLg 56
                                      YArl+g
  gi|320101446|ref|YP_004177038.1| 34 YARLVG 39
                                      999998 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 7.5e-08
                                       HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                            HTH_25   1 rLraaRearglsleevaketkIrkdylealEeddf 35 
                                       r r+aRe++g++ + +a++ + ++++++++E++++
  gi|320101446|ref|YP_004177038.1|  79 RIREARERLGWTQQVLAQKVRESENIIKRIEAGKL 113
                                       579*****************************987 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.1e-05     0.031      17      56 ..      74     113 ..      62     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                            HTH_37  17 aqlalaiaeliekrelsqseaaqllgiaqPkvsrllrgkl 56 
                                        ++a++i+e +e+++++q+ +aq+   ++  + r++ gkl
  gi|320101446|ref|YP_004177038.1|  74 EDYAKRIREARERLGWTQQVLAQKVRESENIIKRIEAGKL 113
                                       578999*****************************99997 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   0.2   9.2e-05      0.14       2      31 ..       5      38 ..       4      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.2e-05
                           DUF4428  2 CaiCgkKigllkr..lkleDg..yvCkdClkKls 31
                                      C +Cg ++g+ +   + +e    +vC+ C+ +l+
  gi|320101446|ref|YP_004177038.1|  5 CEVCGREVGKNECrkVVVEGSvlTVCPQCYARLV 38
                                      **********75432556666555******9984 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 ?    5.3   0.0     0.013        19      15      41 ..      79     105 ..      70     107 .. 0.84
   2 ?    5.2   0.0     0.014        21      35      48 ..     121     134 ..     119     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                                       SHHHHHHHHTS-HHHHHHHHHHHHHHH CS
                             HTH_1  15 sftrAAeeLglsqpavsrqikrLEeel 41 
                                        +++A e+Lg +q  + + +++ E+ +
  gi|320101446|ref|YP_004177038.1|  79 RIREARERLGWTQQVLAQKVRESENII 105
                                       6888999**************999875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                                       HHHHHHHTS-SEEE CS
                             HTH_1  35 krLEeelgvpLfeR 48 
                                       +rLE+ lgv+L+e 
  gi|320101446|ref|YP_004177038.1| 121 RRLEKVLGVKLLEP 134
                                       79**********95 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.6   0.00044      0.66      48      68 ..      67      87 ..      66     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                              BMFP 48 REEFdvqrevlartrekleaL 68
                                      REEF+v+ + + r re+ e+L
  gi|320101446|ref|YP_004177038.1| 67 REEFEVVEDYAKRIREARERL 87
                                      9***************99976 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.5    0.0002      0.31      82     113 ..       2      32 ..       1      37 [. 0.91
   2 ?   -0.7   0.0       1.1   1.6e+03      13      32 ..      82     101 ..      64     114 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                           DUF2703  82 eelCescgelsGedveCRtlevegkeyealpk 113
                                       +++Ce+cg+  G+  eCR ++veg   ++ p+
  gi|320101446|ref|YP_004177038.1|   2 SCYCEVCGREVGK-NECRKVVVEGSVLTVCPQ 32 
                                       579*******999.9*********99998886 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                           DUF2703  13 etCercgeTgktleeavkel 32 
                                       e+ er g T++ l++ v+e 
  gi|320101446|ref|YP_004177038.1|  82 EARERLGWTQQVLAQKVRES 101
                                       23334444444444444443 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.1    0.0013         2       5      17 ..       3      15 ..       1      15 [. 0.86
   2 ?    1.5   0.0      0.15   2.2e+02       2      10 ..      25      33 ..      24      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                                      EE-TTTSSEEEGG CS
                             Sgf11  5 vtCpnCgRqiaas 17
                                      + C+ CgR++  +
  gi|320101446|ref|YP_004177038.1|  3 CYCEVCGREVGKN 15
                                      89*******9866 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                                      C-EEE-TTT CS
                             Sgf11  2 seyvtCpnC 10
                                      s++++Cp C
  gi|320101446|ref|YP_004177038.1| 25 SVLTVCPQC 33
                                      6789***** 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 ?    1.4   0.7      0.21   3.2e+02      36      55 ..       4      23 ..       1      29 [. 0.80
   2 ?   10.1   0.7   0.00045      0.67      61     117 ..      67     123 ..      13     131 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.21
                    MqsA_antitoxin 36 fCarCGegvldeeeedrlse 55
                                      +C+ CG  v ++e  + ++e
  gi|320101446|ref|YP_004177038.1|  4 YCEVCGREVGKNECRKVVVE 23
                                      9******9999887777766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00045
                    MqsA_antitoxin  61 rkkvnaelvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvkll 117
                                       r++ + +   ++ i++ r++l+ +q+ +a+      n   r e+Gk +p l l + l
  gi|320101446|ref|YP_004177038.1|  67 REEFEVVEDYAKRIREARERLGWTQQVLAQKVRESENIIKRIEAGKLKPGLDLARRL 123
                                       33334444457889999***********999999***************99887654 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.3   0.00098       1.5       3      37 ..       2      36 ..       1      40 [. 0.92
   2 ?   -2.2   0.0       2.8   4.2e+03      43      57 ..      86     104 ..      84     109 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00098
                            zf-DNL  3 tftCkaCetrsskeiskkaYekGvVivqCpgCknr 37
                                      ++ C++C+    k+  +k   +G V+  Cp+C +r
  gi|320101446|ref|YP_004177038.1|  2 SCYCEVCGREVGKNECRKVVVEGSVLTVCPQCYAR 36
                                      678*****************************865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                            zf-DNL  43 nLgwfed....kkktiedi 57 
                                       +Lgw+++    k ++ e+i
  gi|320101446|ref|YP_004177038.1|  86 RLGWTQQvlaqKVRESENI 104
                                       6888877666544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      742  (0.0413855); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1146.31
//
Query:       gi|320101447|ref|YP_004177039.1|  [L=351]
Description: GTP-binding proten HflX [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-18   64.9   0.0    1.2e-17   64.0   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    7.2e-15   55.4   5.3    1.3e-14   54.6   5.3    1.4  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    2.9e-12   47.1   0.0    7.1e-12   45.9   0.0    1.7  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    2.6e-09   36.8   0.0    4.8e-09   35.9   0.0    1.5  1  FeoB_N        Ferrous iron transport protein B
    0.00097   18.7   0.1     0.0047   16.5   0.0    2.0  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0013   18.8   0.0     0.0028   17.7   0.0    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0025   17.3   0.0     0.0061   16.0   0.0    1.7  1  Arf           ADP-ribosylation factor family
     0.0048   17.1   0.0      0.011   16.0   0.0    1.6  1  AAA_28        AAA domain
     0.0053   17.3   0.0     0.0099   16.4   0.0    1.4  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.085   12.9   0.0       0.22   11.5   0.0    1.6  2  Dynamin_N     Dynamin family
       0.12   12.0   1.7         11    5.6   0.2    2.7  3  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.12   12.9   0.1       0.24   11.9   0.1    1.4  1  ABC_tran      ABC transporter
       0.49   10.5   0.0       0.49   10.5   0.0    2.0  2  SUIM_assoc    Unstructured region C-term to UIM in Ataxin3


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 !   64.0   0.0   8.8e-21   1.2e-17       1     114 []     180     300 ..     180     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 8.8e-21
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.. CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.. 75 
                                       +vai G++ +GK++L+naltg    v+ +p+tT+ ++  rv++++  ++l+Dt+G+i   +   ++ +af a  e  
  gi|320101447|ref|YP_004177039.1| 180 HVAITGYTCAGKTSLFNALTGLGKPVGPEPFTTLAPKSSRVAYRDVCFILTDTVGFIR--DLPPEIIEAFYATLEei 254
                                       59****************************************999**********886..22224555555433224 PP

                                       ..TSEEEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEES CS
                          MMR_HSR1  76 ..adlillvvdaseeklkpldeeleellee......akkplilvlnk 114
                                         ad+++ vvdas + l++++ ele ++        ++kp+i++lnk
  gi|320101447|ref|YP_004177039.1| 255 ssADVLVNVVDAS-KPLERIRVELETTRGVfskigvHGKPVIVALNK 300
                                       449********99.77889988888886447779999********98 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   5.3   9.2e-18   1.3e-14       1      79 []      96     173 ..      96     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 9.2e-18
                                       H--SHHHHHHHHHHHHHHHHHHHC..XXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                         GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLe..glgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelq 75 
                                       +A +keak+Q+elA+lky +p ++   +++++ ++    g+ G+G + +e +  ++++++a++++eLe++++ r ++
  gi|320101447|ref|YP_004177039.1|  96 HAGSKEAKMQIELARLKYYIPLVReaVRYAKMGEL---HGFLGAGRYGYEKYYLMLKRKEARVRRELEELRRIRGVR 169
                                       9**********************424334444444...459************************************ PP

                                       ...T CS
                         GTP-bdg_M  76 rkkR 79 
                                       rk+R
  gi|320101447|ref|YP_004177039.1| 170 RKQR 173
                                       ***9 PP

>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   5.1e-15   7.1e-12       6      89 .]      17      94 ..      14      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 5.1e-15
                         GTP-bdg_N  6 EleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRtqLI 84
                                      E   L+kt+  ++  ++v+k+ kp+p ty+ + +++e+ e   e     +++ d+L+p+q+ nL +el+  V+DR +LI
  gi|320101447|ref|YP_004177039.1| 17 EELGLVKTIYSDI--QCVVKVGKPSPGTYLSSERLRELGECGFE----KLVVMDRLKPVQVVNLARELKRDVVDRVMLI 89
                                      5556677766665..5788999****************987655....5788889************************ PP

                         GTP-bdg_N 85 LdIFA 89
                                      L+IFA
  gi|320101447|ref|YP_004177039.1| 90 LEIFA 94
                                      ****8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   3.5e-12   4.8e-09       2     125 ..     180     311 ..     179     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.5e-12
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----S.SSSSSSHHHHHHHHHHHCT CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiY.slsayseeekvardfllee 77 
                                       +va+ G   +Gkt+lfnaltg  + vg  p +t   k+ ++ +++  + ++D  G   +l +  +e   a ++   +
  gi|320101447|ref|YP_004177039.1| 180 HVAITGYTCAGKTSLFNALTGLGKPVGPEPFTTLAPKSSRVAYRDVCFILTDTVGFIrDLPPEIIEAFYA-TLEEIS 255
                                       6899***************************************************751565555555444.344457 PP

                                       SSSEEEEEEEGGG.HHH...HHHHH....HHHHHTTSSEEEEEETHHHHHHTTEEE CS
                            FeoB_N  78 epdvvvnvvdatn.ler...nLyLt....lqllelgvpvvlalnmideaekkgiei 125
                                       ++dv+vnvvda++ ler   +L  t     ++   g+pv++aln++d + +   ++
  gi|320101447|ref|YP_004177039.1| 256 SADVLVNVVDASKpLERirvELETTrgvfSKIGVHGKPVIVALNKVDLLGDYTAKV 311
                                       89*********87345432234433111144555789**********987766655 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 ?   -0.7   0.0      0.63   8.7e+02       6      24 ..     181     199 ..     178     207 .. 0.84
   2 !   16.5   0.0   3.4e-06    0.0047      91     189 ..     254     343 ..     220     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.63
                                       EEEEESTTSSHHHHHHHHH CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLl 24 
                                       ++i g + +GKt+L  +L+
  gi|320101447|ref|YP_004177039.1| 181 VAITGYTCAGKTSLFNALT 199
                                       788888999*****99997 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.4e-06
                                       HHT-SEEEEEEETTTB......STHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  91 lrvlDgavlvvdaveG......vepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekyg 161
                                       ++ +D+ v vvda++         + t+ v+  +  +g p+iv++NK+D l++   + v++v+  l           
  gi|320101447|ref|YP_004177039.1| 254 ISSADVLVNVVDASKPlerirvELETTRGVFSKIGVHGKPVIVALNKVDLLGDYTAK-VRDVEGLL----------- 318
                                       6789**********88777663345677888888889999**********9765544.44555455........... PP

                                       HTTTTTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 162 ekgekevpvvfgSalkgegvktllealv 189
                                       + +    +++++S+   ++++ l+eal+
  gi|320101447|ref|YP_004177039.1| 319 AGN---EELIPVSSTMRFNLELLMEALY 343
                                       122...2466666666666666666665 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     2e-06    0.0028      56     104 ..     292     346 ..     281     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
                      MMR_HSR1_Xtn  56 ipclyvlNKiDl.....isleeldelare....pnsvviSaekelnldeLkekiweeL 104
                                       +p++++lNK+Dl     ++  +++         ++ +++S+ +++nl+ L+e++++ L
  gi|320101447|ref|YP_004177039.1| 292 KPVIVALNKVDLlgdytAKVRDVEG---LlagnEELIPVSSTMRFNLELLMEALYRVL 346
                                       589*********5544444444444...144448*********************977 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.4e-06    0.0061      16     134 ..     180     310 ..     167     345 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-06
                                       EEEEEESTTSSHHHHHHHHHH.SSCEECSS..SSSEEEEEEEETTEEEEEEEE-S.SGGGGG.GGGGGC......TT CS
                               Arf  16 rilllGLDnaGKtTilkklkl.eelvttvP..TigfnveeleiknlkftvwDvGG.qeklRp.lWknYf......ek 81 
                                       ++ + G  +aGKt + + l+  ++ v   P  T+ +++ +++++++ f + D  G  + l p + + ++      ++
  gi|320101447|ref|YP_004177039.1| 180 HVAITGYTCAGKTSLFNALTGlGKPVGPEPftTLAPKSSRVAYRDVCFILTDTVGfIRDLPPeIIEAFYatleeiSS 256
                                       56788999*********99842566665555599******************6552455544244555512211145 PP

                                       ESEEEEEEETT-.CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HH CS
                               Arf  82 tdavifvvDsad.reRleeakeeLkalleeeelkevallvlaNKqDlpealsee 134
                                        d+++ vvD+++  eR++   e  + ++++  ++  +++v  NK Dl ++ +++
  gi|320101447|ref|YP_004177039.1| 257 ADVLVNVVDASKpLERIRVELETTRGVFSKIGVHGKPVIVALNKVDLLGDYTAK 310
                                       7899*****9873589999999999**********************9887654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.8e-06     0.011       2      38 ..     181     217 ..     180     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.8e-06
                            AAA_28   2 ivitGgestGKTtlleaLaargypvvpEaareileek 38 
                                       ++itG  ++GKT+l +aL+  g pv pE+++++  + 
  gi|320101447|ref|YP_004177039.1| 181 VAITGYTCAGKTSLFNALTGLGKPVGPEPFTTLAPKS 217
                                       89***************************99987665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.1e-06    0.0099       5      40 ..     163     199 ..     158     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.1e-06
                            AAA_23   5 enfrsf.rdqeidFskgltlItGpNGaGKTTildAik 40 
                                       + +r   r+q i+ + + ++ItG + aGKT++++A++
  gi|320101447|ref|YP_004177039.1| 163 RRIRGVrRKQRIESGLPHVAITGYTCAGKTSLFNALT 199
                                       55666656678************************97 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.22       1      33 [.     181     212 ..     181     216 .. 0.92
   2 ?   -2.4   0.0       3.2   4.4e+03     122     143 ..     250     271 ..     231     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33 
                                       +a+ G + +GK+S+ naL+g    p+gp+p T 
  gi|320101447|ref|YP_004177039.1| 181 VAITGYTCAGKTSLFNALTGLG-KPVGPEPFTT 212
                                       7999****************99.99***99985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.2
                                       HHHHHSTTEEEEEEEETTS-CC CS
                         Dynamin_N 122 vkeyikkadiilavtsanhdls 143
                                       + e i +ad+++ v++a++ l 
  gi|320101447|ref|YP_004177039.1| 250 TLEEISSADVLVNVVDASKPLE 271
                                       5567889999999999998876 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 ?   -3.0   0.0       3.4   4.7e+03       5      12 ..     130     137 ..     129     138 .. 0.86
   2 ?    5.6   0.2     0.008        11       2      21 ..     180     199 ..     179     206 .. 0.87
   3 ?    4.9   0.0     0.013        17     102     163 ..     246     315 ..     212     327 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.4
                                       EEESTTCC CS
                              cobW   5 ltGflGsG 12 
                                       l GflG+G
  gi|320101447|ref|YP_004177039.1| 130 LHGFLGAG 137
                                       68*****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.008
                                       EEEEEESTTCCHHHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll 21 
                                        + +tG+  +GKT+L n+l+
  gi|320101447|ref|YP_004177039.1| 180 HVAITGYTCAGKTSLFNALT 199
                                       5789************9986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.013
                                       T.SHHHHHCCCECEEEEEEETTTH.....CCHCCHHHHHHH.HHH.TSSEEEEE-HHHHCHC...HHHHH CS
                              cobW 102 t.eeelksdltldavvavvDaknl....eaeeekieekaed.qla.aadllvlnKtDlldee.allekle 163
                                           +l++   +d++v vvDa++       e e+++  + + ++  +  ++ lnK+Dll +  a+++ +e
  gi|320101447|ref|YP_004177039.1| 246 AfYATLEEISSADVLVNVVDASKPleriRVELETTRGVFSKiGVHgKPVIVALNKVDLLGDYtAKVRDVE 315
                                       246778888899999999999887777633333333333331222023345589***9998856666555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00017      0.24      13      37 ..     180     204 ..     174     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                       EEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkp 37 
                                        vai+G + aGK++L+++l+gl kp
  gi|320101447|ref|YP_004177039.1| 180 HVAITGYTCAGKTSLFNALTGLGKP 204
                                       589******************9877 PP

>> SUIM_assoc  Unstructured region C-term to UIM in Ataxin3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035      0.49       9      30 ..      39      66 ..      37     120 .. 0.76
   2 ?   -3.7   3.6       9.6   1.3e+04      16      23 ..     159     166 ..     149     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                        SUIM_assoc  9 tsgtqltsEeLrkrreaYFEK......q 30
                                      ++gt l+sE Lr   e+ FEK       
  gi|320101447|ref|YP_004177039.1| 39 SPGTYLSSERLRELGECGFEKlvvmdrL 66
                                      579******************5555550 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.6
                        SUIM_assoc  16 sEeLrkrr 23 
                                        EeLr++r
  gi|320101447|ref|YP_004177039.1| 159 LEELRRIR 166
                                       59***999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2665.98
//
Query:       gi|320101448|ref|YP_004177040.1|  [L=180]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for 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  167.4   0.0    1.3e-49  167.0   0.0    1.1  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 !  167.0   0.0   7.4e-54   1.3e-49       1     118 [.      55     172 ..      55     173 .. 0.99

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 7.4e-54
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnq 77 
                                       wGg++++e+ ++ +k+++e+k++gg vvhltmyG+++++vi+e+++  +d+lvvvG+ kvp  +ye+adynv++g+q
  gi|320101448|ref|YP_004177040.1|  55 WGGRIHFEMGVDSQKYCREWKRNGGLVVHLTMYGLHVDSVIDEVRRLGRDILVVVGSRKVPGFFYEVADYNVAIGHQ 131
                                       ***************************************************************************** PP

                                       ---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EE CS
                             Trm56  78 PhsevaalaifldrllegkelekefedaklkviPsergkkv 118
                                       Phsevaala+fldrl++g+el+ +f dak++++Ps rgkkv
  gi|320101448|ref|YP_004177040.1| 132 PHSEVAALAVFLDRLFTGRELYLRFPDAKVEIVPSPRGKKV 172
                                       ****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1317.67
//
Query:       gi|320101449|ref|YP_004177041.1|  [L=316]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2411.15
//
Query:       gi|320101450|ref|YP_004177042.1|  [L=904]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-08   34.3  16.5     0.0028   18.1   2.2    3.9  4  NPV_P10         Nucleopolyhedrovirus P10 protein
    3.2e-07   30.4   6.3    6.2e-05   23.0   1.4    2.5  2  DUF1664         Protein of unknown function (DUF1664)
    1.6e-06   28.2  20.6    4.8e-05   23.4  10.4    2.7  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
      6e-05   23.3   0.4        7.1    6.9   0.1    3.1  3  DUF5082         Domain of unknown function (DUF5082)
     0.0004   18.5   3.1    0.00053   18.1   3.1    1.1  1  Prominin        Prominin
     0.0005   20.4  19.3          1    9.8   0.1    4.9  4  LPP             Lipoprotein leucine-zipper
    0.00057   20.2   8.9        1.1    9.7   0.9    4.2  4  FlaC_arch       Flagella accessory protein C (FlaC)
    0.00065   18.8   0.3       0.14   11.1   0.0    2.0  1  IFT57           Intra-flagellar transport protein 57
    0.00065   18.0   0.3     0.0009   17.6   0.3    1.0  1  FPP             Filament-like plant protein, long coiled-coil
    0.00069   19.8  19.9      0.032   14.5   3.3    4.0  3  DUF948          Bacterial protein of unknown function (DUF948
     0.0011   18.9  15.9        0.2   11.4   2.7    2.3  2  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
     0.0021   18.1   0.0     0.0049   16.9   0.0    1.4  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
     0.0021   18.1   5.7        1.8    8.7   1.3    3.2  4  COG2            COG (conserved oligomeric Golgi) complex comp
     0.0024   17.9   3.7     0.0038   17.3   3.7    1.2  1  Serine_rich     Serine rich protein interaction domain
     0.0026   16.5   0.8     0.0037   16.0   0.8    1.1  1  AAA_13          AAA domain
     0.0055   16.3   0.0     0.0096   15.5   0.0    1.3  1  DUF4795         Domain of unknown function (DUF4795)
     0.0061   15.5   0.0     0.0093   14.9   0.0    1.2  1  Spc7            Spc7 kinetochore protein
     0.0062   15.7   2.9        1.6    7.8   0.1    3.0  3  RmuC            RmuC family
     0.0069   16.3   1.5        1.9    8.3   0.3    2.6  2  Sec34           Sec34-like family
     0.0086   16.4   1.6       0.19   12.0   1.0    2.6  3  BLOC1_2         Biogenesis of lysosome-related organelles com
  ------ inclusion threshold ------
      0.013   15.5  15.8       0.32   11.0   9.6    2.4  2  Laminin_II      Laminin Domain II
      0.013   15.0   0.0       0.02   14.4   0.0    1.2  1  MscS_porin      Mechanosensitive ion channel porin domain
      0.014   15.6   0.2       0.41   10.9   0.2    2.4  3  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
       0.02   13.2   1.1      0.026   12.8   1.1    1.1  1  Cast            RIM-binding protein of the cytomatrix active 
      0.022   15.1   4.6       0.59   10.5   0.0    3.7  3  Alanine_zipper  Alanine-zipper, major outer membrane lipoprot
      0.033   13.7   6.0      0.046   13.2   2.9    2.0  2  Allexi_40kDa    Allexivirus 40kDa protein
      0.035   14.2   0.4       0.99    9.5   0.2    2.8  3  DUF2730         Protein of unknown function (DUF2730)
      0.046   13.9   1.6        6.3    7.0   0.5    2.2  2  SesA            N-terminal domain on NACHT_NTPase and P-loop 
      0.049   13.8   3.4       0.22   11.6   3.5    2.0  1  DUF148          Domain of unknown function DUF148
      0.049   12.7   3.5      0.071   12.2   3.5    1.1  1  AIP3            Actin interacting protein 3
      0.051   14.0  14.2        2.7    8.5   2.6    3.9  3  T7SS_ESX_EspC   Excreted virulence factor EspC, type VII ESX 
      0.056   13.3   0.0      0.098   12.5   0.0    1.3  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
      0.064   13.8   0.7        3.6    8.1   0.4    2.5  2  DUF16           Protein of unknown function DUF16
      0.065   13.7   0.8       0.28   11.6   0.0    2.3  2  RCDG1           Renal cancer differentiation gene 1 protein
      0.066   13.6   0.0        3.6    8.0   0.0    3.0  3  CLZ             C-terminal leucine zipper domain of cyclic nu
      0.068   11.4   3.4        5.9    5.0   0.2    2.7  3  COG6            Conserved oligomeric complex COG6
      0.072   13.3   0.2         27    5.1   0.1    3.6  2  XhlA            Haemolysin XhlA
      0.075   11.7   1.9       0.11   11.2   1.9    1.2  1  WEMBL           Weak chloroplast movement under blue light
       0.09   12.6   0.6        8.1    6.2   0.0    2.6  3  Phage_GP20      Phage minor structural protein GP20
       0.09   12.5   1.2       0.13   11.9   1.2    1.1  1  Joubert         Joubert syndrome-associated
       0.11   12.7   4.3        7.8    6.7   0.9    2.8  3  COG5            Golgi transport complex subunit 5
       0.11   10.6   0.0        1.6    6.8   0.0    1.7  2  EzrA            Septation ring formation regulator, EzrA
       0.12   12.6   0.4        7.7    6.8   0.2    3.0  3  WXG100          Proteins of 100 residues with WXG
       0.13   11.6   0.2        0.2   10.9   0.2    1.2  1  ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
       0.14   12.2   3.5       0.22   11.5   0.8    2.2  2  Phasin          Poly(hydroxyalcanoate) granule associated pro
       0.15   11.5   0.3        1.9    7.9   0.1    2.6  3  DegS            Sensor protein DegS
       0.19   11.4   4.0       0.67    9.6   3.7    1.8  2  LXG             LXG domain of WXG superfamily
       0.19   12.2   3.9       0.44   11.0   3.9    1.6  1  Med11           Mediator complex protein
       0.22   11.2   1.5       0.42   10.3   0.4    1.6  1  Laminin_I       Laminin Domain I
       0.23   11.3   0.1       0.36   10.6   0.1    1.2  1  DUF724          Protein of unknown function (DUF724)
       0.27   11.6   1.5         18    5.8   0.1    2.8  2  UPF0184         Uncharacterised protein family (UPF0184)
       0.28   10.9   2.8        1.3    8.8   0.6    2.1  2  DUF745          Protein of unknown function (DUF745)
       0.29    9.3   0.5       0.39    8.9   0.5    1.0  1  Nop14           Nop14-like family
        0.3   10.4   3.2        5.1    6.4   2.0    2.2  2  SF-assemblin    SF-assemblin/beta giardin
       0.31   10.7   0.9        1.6    8.4   0.5    1.9  2  Syntaxin        Syntaxin
       0.32   10.3   0.0         16    4.8   0.1    2.0  2  Tropomyosin     Tropomyosin
       0.37   10.9   2.7        1.3    9.1   2.7    1.9  1  Herpes_UL49_5   Herpesvirus UL49.5 envelope/tegument protein
        0.4   10.8   3.2          1    9.5   1.5    2.0  2  Fib_alpha       Fibrinogen alpha/beta chain family
       0.73   10.2  11.4       0.47   10.9   0.9    3.2  3  Flagellin_C     Bacterial flagellin C-terminal helical region
        1.1    9.7   6.4        2.2    8.7   2.0    2.4  2  Syntaxin_2      Syntaxin-like protein
        1.2    8.9   4.9        2.6    7.8   1.9    2.2  2  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
        1.3    9.2  19.2        1.1    9.5   2.2    3.1  2  BORCS6          BLOC-1-related complex sub-unit 6
        1.3    8.7   4.5        1.6    8.5   3.2    1.7  1  Baculo_p24      Baculovirus P24 capsid protein
        2.5    7.9   4.6         14    5.4   0.1    2.3  2  Sec5            Exocyst complex component Sec5
        3.7    7.4   6.0         21    5.0   0.3    3.2  3  DASH_Duo1       DASH complex subunit Duo1
        5.5    7.4   6.7        7.9    6.9   1.9    3.1  4  DUF4854         Domain of unknown function (DUF4854)
        5.5    7.4  17.3         10    6.5   0.5    5.4  4  Fer4_24         Ferredoxin I 4Fe-4S cluster domain


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.035       9.4      33      66 ..     698     731 ..     689     733 .. 0.79
   2 !   17.8   6.4   1.3e-05    0.0035       5      67 ..     729     787 ..     725     791 .. 0.86
   3 !   18.1   2.2     1e-05    0.0028      11      59 ..     755     800 ..     752     803 .. 0.89
   4 !   15.3   0.8   7.6e-05      0.02       6      66 ..     792     849 ..     789     860 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.035
                           NPV_P10  33 nlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                        + +v+e+ +k+d+ + +L+ l ++v++++ + n
  gi|320101450|ref|YP_004177042.1| 698 TIDNVKEVGSKVDQVAGTLNGLVNTVSSVSAVVN 731
                                       4678888889999999999999999888888877 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.3e-05
                           NPV_P10   5 iLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnp 67 
                                       +   I++++  v++k+dal++ v++ ++   dv+++ +k+da+s+++ ++ +k++++++ Ln+
  gi|320101450|ref|YP_004177042.1| 729 VVNNIKSAVDTVNSKLDALSSTVAS-KT---DVNNVASKVDALSTSVSSVVSKLDSVTSQLNS 787
                                       6678****************99986.44...455578************************94 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1e-05
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                       +d+++v +kVdal+++v +v ++l  vt   ++L++  ++L+++++ ++
  gi|320101450|ref|YP_004177042.1| 755 TDVNNVASKVDALSTSVSSVVSKLDSVT---SQLNSAVQSLNTISSDIS 800
                                       79*********************99965...999999999999987765 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 7.6e-05
                           NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       L  I +di+ +++ V+ ++++v  v++++ +   + + L   s  +  l+t+v + q++Ln
  gi|320101450|ref|YP_004177042.1| 792 LNTISSDISGLKTGVNDVKTAVSGVASKVDN---VASTLSTVSSDVSGLKTSVGSLQNTLN 849
                                       678999*******************999888...569999999999999999999999999 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   0.4    0.0042       1.1      67     117 ..     701     751 ..     689     764 .. 0.67
   2 !   23.0   1.4   2.3e-07   6.2e-05      38     123 ..     766     854 ..     755     855 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0042
                           DUF1664  67 ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       ++++v++k+d+++ + + + + v++v+  +++i++ v++v++    l s++
  gi|320101450|ref|YP_004177042.1| 701 NVKEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTV 751
                                       556666666666666666666666666666666666666666666665554 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 2.3e-07
                           DUF1664  38 slsdavesvskqleqvseslaatkrhL...ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                        ls  v+sv ++l++v ++l+++ + L   ss+i  + + ++++k + + ++++v++v + ls++++dv+ +k+ v 
  gi|320101450|ref|YP_004177042.1| 766 ALSTSVSSVVSKLDSVTSQLNSAVQSLntiSSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVG 842
                                       589999**************9998876333799******************************************** PP

                           DUF1664 112 glesklerieek 123
                                       +l+++l+++++k
  gi|320101450|ref|YP_004177042.1| 843 SLQNTLNTVSGK 854
                                       ******999875 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 !   11.0   6.4    0.0012      0.32      34     102 ..     703     772 ..     687     775 .. 0.68
   2 !   23.4  10.4   1.8e-07   4.8e-05      16     114 ..     755     854 ..     752     872 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0012
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtl..rneLtnlnsiltnLlssvt 102
                                        ++ + +d+++++Ln l + ++s ++++ +++++++++++++l al+ t+  +++ +n+ s++  L +sv 
  gi|320101450|ref|YP_004177042.1| 703 KEVGSKVDQVAGTLNGLVNTVSS-VSAVVNNIKSAVDTVNSKLDALSSTVasKTDVNNVASKVDALSTSVS 772
                                       56677788888888888888887.45577778888888888888888666224567788888877777775 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.8e-07
                      Baculo_PEP_C  16 ldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtn 89 
                                        d++nv + + ++++++ + + + ld++ +qLn+  ++l+  +++++  l+t ++ +++a+  ++   d++ + L +
  gi|320101450|ref|YP_004177042.1| 755 TDVNNVASKVDALSTSV-SSVVSKLDSVTSQLNSAVQSLNTISSDIS-GLKTGVNDVKTAVSGVAskvDNVASTLST 829
                                       46677777777777777.66666677777777777777777666664.57777777777777777777777777777 PP

                      Baculo_PEP_C  90 lnsiltnLlssvtNinstLnnllqa 114
                                       + s+++ L +sv+ +++tLn +   
  gi|320101450|ref|YP_004177042.1| 830 VSSDVSGLKTSVGSLQNTLNTVSGK 854
                                       7777777777777777777765444 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.031       8.3      66     107 ..     710     754 ..     693     757 .. 0.76
   2 ?    6.9   0.1     0.026       7.1      66     102 ..     758     794 ..     752     804 .. 0.61
   3 ?    6.8   0.0     0.029       7.7      73     117 ..     807     854 ..     793     858 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.031
                           DUF5082  66 nnydgirs...nlessyqtyvdkldelidaieeEIerLenqisea 107
                                       +++ g +    n+ ss++++v ++++++d ++++   L +++ ++
  gi|320101450|ref|YP_004177042.1| 710 DQVAGTLNglvNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASK 754
                                       455555556668889999999999999999999988888887766 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.026
                           DUF5082  66 nnydgirsnlessyqtyvdkldelidaieeEIerLen 102
                                       nn+ +++  l +s++ +v+kld++ +++++ ++ L +
  gi|320101450|ref|YP_004177042.1| 758 NNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNT 794
                                       5555555567777777777777777777776666643 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.029
                           DUF5082  73 snlessyqtyvdkldelidai...eeEIerLenqiseaqgvldtlqsq 117
                                        +++++++ + +k+d++ + +   +++++ L++++ ++q+ l+t + +
  gi|320101450|ref|YP_004177042.1| 807 NDVKTAVSGVASKVDNVASTLstvSSDVSGLKTSVGSLQNTLNTVSGK 854
                                       378999999999999987655111679999999999999999887665 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   3.1     2e-06   0.00053     233     435 ..     697     892 ..     687     897 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                          Prominin 233 nvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekld 309
                                       +   +++++++++ ++ ++   L+ + ++ +++    +++++++  v  +l+ + s + ++++ +++ s++++ +  
  gi|320101450|ref|YP_004177042.1| 697 A---TIDNVKEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNVASKVDALSTS 770
                                       3...78999999**************************************9998888888899999*9999997777 PP

                          Prominin 310 tskcldqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprea 386
                                       +s+ +++l++v+++l++  + l+t  ss +    + +n++++ v   +a+ v ++ ++l++ ++ ++ l++++    
  gi|320101450|ref|YP_004177042.1| 771 VSSVVSKLDSVTSQLNSAVQSLNTI-SSDISGLKTGVNDVKTAVS-GVASKVDNVASTLSTVSSDVSGLKTSV--GS 843
                                       7777799999998888877776654.4445566667888887775.566677888888888888888888888..66 PP

                          Prominin 387 ldavisdle.nterssktfddvvekyekyrwliglivcsllllivvilil 435
                                       l++++++++ ++ + ++++d     + +   +igl++ ++ ll  v+ +l
  gi|320101450|ref|YP_004177042.1| 844 LQNTLNTVSgKVDTAISKADAAGASATNAF-YIGLVAVIFALLATVFALL 892
                                       777777777667777766666655555544.4455555544444444444 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   2.2      0.24        65       2      14 ..     730     742 ..     700     762 .. 0.57
   2 ?    3.3   5.4      0.41   1.1e+02       1      26 [.     763     788 ..     743     794 .. 0.73
   3 !    9.1   0.1    0.0063       1.7       2      33 ..     792     823 ..     791     825 .. 0.91
   4 !    9.8   0.1    0.0038         1       3      37 ..     828     862 ..     826     868 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.24
                               LPP   2 ldeLssqVsqLks 14 
                                       ++++ s V + +s
  gi|320101450|ref|YP_004177042.1| 730 VNNIKSAVDTVNS 742
                                       2333333333333 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.41
                               LPP   1 kldeLssqVsqLkskvdqlssdvnsa 26 
                                       k+d Ls+ Vs+  sk d+++s++nsa
  gi|320101450|ref|YP_004177042.1| 763 KVDALSTSVSSVVSKLDSVTSQLNSA 788
                                       56777777777666666666666655 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0063
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaa 33 
                                       l+ +ss++s Lk+ v+ ++  v+ +++ ++++
  gi|320101450|ref|YP_004177042.1| 792 LNTISSDISGLKTGVNDVKTAVSGVASKVDNV 823
                                       689*********************99999876 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0038
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaaqaakeEA 37 
                                       + +ss+Vs Lk+ v +l++ +n ++  +++a   A
  gi|320101450|ref|YP_004177042.1| 828 STVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKA 862
                                       678*******************9999888874444 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   0.1     0.076        20       2      39 ..     702     739 ..     701     741 .. 0.92
   2 !    9.7   0.9    0.0041       1.1       2      52 ..     737     786 ..     736     789 .. 0.94
   3 ?    6.2   1.5     0.053        14       8      26 ..     791     809 ..     763     834 .. 0.51
   4 ?    7.3   0.2     0.023       6.2       7      37 ..     818     848 ..     806     857 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.076
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkd 39 
                                       ++e+ +k++++  +l+ + ++ +++s  v+++k  V  
  gi|320101450|ref|YP_004177042.1| 702 VKEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDT 739
                                       789999***************************99976 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0041
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvN 52 
                                       +d++ +kl+ ls+++++ k++ +++ ++v+ l  +V  ++s  + V+ q N
  gi|320101450|ref|YP_004177042.1| 737 VDTVNSKLDALSSTVAS-KTDVNNVASKVDALSTSVSSVVSKLDSVTSQLN 786
                                       79999**********98.888999************************999 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.053
                         FlaC_arch   8 klsklsteletvkkeneel 26 
                                        l+ +s+ ++ +k+  +++
  gi|320101450|ref|YP_004177042.1| 791 SLNTISSDISGLKTGVNDV 809
                                       2333333333333333333 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.023
                         FlaC_arch   7 nklsklsteletvkkeneelsksveelkenV 37 
                                       +k++++ ++l+tv ++ + l++sv  l+ + 
  gi|320101450|ref|YP_004177042.1| 818 SKVDNVASTLSTVSSDVSGLKTSVGSLQNTL 848
                                       5667777777777777777777777766665 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00052      0.14     226     331 ..     764     872 ..     762     875 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                             IFT57 226 leqmkkhkksieeslpetksqlkklhedisktlekiesrEkyln...sqleellqeyreaqeelsevkekykqlseg 299
                                       ++++++  +s+ ++l +++sql+   + ++   + i+   + +n   + ++   ++  ++  +ls+v+ +++ l+++
  gi|320101450|ref|YP_004177042.1| 764 VDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNdvkTAVSGVASKVDNVASTLSTVSSDVSGLKTS 840
                                       56666667788888888888888888888888888877777665222678888899999999999999999999999 PP

                             IFT57 300 vseltrelaeiseelekvkqemeergssmtDg 331
                                       v +l+++l+++s +++++ ++ +  g+s+t++
  gi|320101450|ref|YP_004177042.1| 841 VGSLQNTLNTVSGKVDTAISKADAAGASATNA 872
                                       99999999999999999999999999999985 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   3.4e-06    0.0009     633     790 ..     692     850 ..     668     869 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-06
                               FPP 633 eikksddidkvalsenkvaqkges.snecaeisklssekeipselplvsgsnesk.keenkllkeeleelksekenl 707
                                       +i++   id+v    +kv q+  + ++ + ++s+ s   ++  ++++++  ++ +  +++  +k +++++ s+ + l
  gi|320101450|ref|YP_004177042.1| 692 NISRAATIDNVKEVGSKVDQVAGTlNGLVNTVSSVSAVVNN-IKSAVDTVNSKLDaLSSTVASKTDVNNVASKVDAL 767
                                       55566666666666666655533323333333333333322.22222222222222456667777888888888888 PP

                               FPP 708 evelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaL 784
                                        ++++s  ++l+s+ +ql+   q+l+ + s+++ lk   + + t +   +    ++ + ++ + ++++ lk+ + +L
  gi|320101450|ref|YP_004177042.1| 768 STSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVGSL 844
                                       88888888888888888888888888888888888888888888888888888888888888888888888888887 PP

                               FPP 785 eveLee 790
                                       ++ L++
  gi|320101450|ref|YP_004177042.1| 845 QNTLNT 850
                                       777765 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.2     0.018       4.7      22      76 ..     703     753 ..     686     763 .. 0.47
   2 !   14.5   3.3   0.00012     0.032      23      88 ..     759     824 ..     752     825 .. 0.92
   3 ?    8.3   1.2      0.01       2.7      25      81 ..     817     866 ..     809     872 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.018
                            DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                       +++++ +d++a t+++l +    ++  v +++++++  ++ vn+kl+++ + +++
  gi|320101450|ref|YP_004177042.1| 703 KEVGSKVDQVAGTLNGLVN----TVSSVSAVVNNIKSAVDTVNSKLDALSSTVAS 753
                                       2222223333333332222....22233333444444444455555555555554 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.00012
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       ++++ +d++++++ ++ +++d+++ +++ +++  n++ +d+++    v+ + +av  ++ +v ++ 
  gi|320101450|ref|YP_004177042.1| 759 NVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVA 824
                                       678889*************************************9999******9999999998875 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.01
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                                       ++ +d++a+t+ ++ ++v ++ + v  l ++ n++   v   + k d+       +g
  gi|320101450|ref|YP_004177042.1| 817 ASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKADA-------AG 866
                                       456777788888888888888888888888888855555555555444.......44 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 !   11.4   2.7   0.00076       0.2     112     170 ..     698     756 ..     687     758 .. 0.86
   2 !   11.3   7.9   0.00086      0.23      95     170 ..     757     832 ..     748     835 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00076
                                       HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 112 trqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                       t  +v+e  ++v++ + +l+ +v++v++v+++v++i++a++   + ++  +++v+  ++
  gi|320101450|ref|YP_004177042.1| 698 TIDNVKEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTD 756
                                       6677888889999999**************************99999999999887665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00086
                                       H..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  95 iieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                       + ++  +++   +s+++++++ ++ +++ +++ ++l++i++ ++ +++ v+++++a++  ++ +++v+++++ v++
  gi|320101450|ref|YP_004177042.1| 757 VNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVSS 832
                                       556778888889999999************************************************9999988865 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 !   16.9   0.0   1.8e-05    0.0049      14     111 ..     752     849 ..     740     853 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-05
                    CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelq 90 
                                       +s+ + +++  kv++L   +  + +++++v+ +  ++ + ++t+ + i  l++  ++ ++ ++ + s  ++++  l 
  gi|320101450|ref|YP_004177042.1| 752 ASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLS 828
                                       67888899********************************************************************* PP

                    CENP-F_leu_zip  91 kkqervseLeslnsslenlle 111
                                       +  + vs L+++  sl+n+l+
  gi|320101450|ref|YP_004177042.1| 829 TVSSDVSGLKTSVGSLQNTLN 849
                                       ******************997 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 !    8.7   1.3    0.0067       1.8      60     129 ..     712     778 ..     709     781 .. 0.59
   2 ?    5.3   0.3     0.072        19      71     108 ..     757     794 ..     754     804 .. 0.63
   3 ?    6.1   0.1      0.04        11      51      96 ..     786     831 ..     780     837 .. 0.48
   4 ?    5.1   0.1     0.085        23      65     108 ..     821     864 ..     807     880 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0067
                              COG2  60 lSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllkldevvekl 129
                                       + g L gl + ++ v+  ++++++ v+ v++kl++ +++v sk    +++++   ++  l  +++ vv+kl
  gi|320101450|ref|YP_004177042.1| 712 VAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASK----TDVNNVAsKVDALSTSVSSVVSKL 778
                                       5667777777777777777777777777777777766666655....444444323444444555555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.072
                              COG2  71 leevesplaaarkkvesvreklsereeeveskleeake 108
                                       +++v s++ a+ + v+sv++kl+   ++++s ++  + 
  gi|320101450|ref|YP_004177042.1| 757 VNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNT 794
                                       56666666666666666666666666666666665544 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.04
                              COG2  51 nedyadFvslSghLvglqeeleevesplaaarkkvesvreklsere 96 
                                       n+ ++    +S+   gl++ ++ v++ ++ + +kv++v + ls  +
  gi|320101450|ref|YP_004177042.1| 786 NSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVS 831
                                       3333333345555555555555555555555555555555555555 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.085
                              COG2  65 vglqeeleevesplaaarkkvesvreklsereeeveskleeake 108
                                         + + l++v+s+++ +++ v s+++ l+  + +v+  +++a +
  gi|320101450|ref|YP_004177042.1| 821 DNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKADA 864
                                       44556777788888888888888888888888888777777665 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.7   1.4e-05    0.0038      13     148 ..     705     843 ..     694     849 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-05
                       Serine_rich  13 lqqevesavskLlsfvsskWRskenleanlqeirlavdrlrtslrefl.eFargalanaaklsdknlqtkLrkqlqk 88 
                                       + ++v++    L ++      + ++++a +++i++avd +++ l  +   +a ++ +n ++++   l+t  +  ++k
  gi|320101450|ref|YP_004177042.1| 705 VGSKVDQVAGTLNGL----VNTVSSVSAVVNNIKSAVDTVNSKLDALSsTVASKTDVNNVASKVDALSTSVSSVVSK 777
                                       334444444444444....44889999*******************973699************************* PP

                       Serine_rich  89 ledsdqilqetsqeLdsceWslealasdkkqek......pddlDrlvmvartvpdDvkqlasfiqg 148
                                       l+   + l ++ q+L++ + +++ l +  ++ k        ++D + ++ +tv+ Dv+ l + + +
  gi|320101450|ref|YP_004177042.1| 778 LDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKtavsgvASKVDNVASTLSTVSSDVSGLKTSVGS 843
                                       ***************************9999999999*99*****************999888866 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.8   1.4e-05    0.0037     296     438 ..     706     854 ..     693     868 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                            AAA_13 296 eskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrk..epfksvel..esvkakiesik 368
                                        sk ++++  l+ ++++    s     ++++k++ ++++++L++l++ +  K +  +++++v+   +sv++ ++++ 
  gi|320101450|ref|YP_004177042.1| 706 GSKVDQVAGTLNGLVNTV---SSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDvnNVASKVDAlsTSVSSVVSKLD 779
                                       444444555554444433...34567788999999999999999999999997432677777742456666668888 PP

                            AAA_13 369 klvaeineliakhNekvanl...eeekeeakkkle..lhlveeleseldeykkkykklekaieklekelkeeeae 438
                                       +  +++n  +++ N +++++   ++ ++++k+++   ++ v ++ s l++  +++++l++++ +l++ l+  + +
  gi|320101450|ref|YP_004177042.1| 780 SVTSQLNSAVQSLNTISSDIsglKTGVNDVKTAVSgvASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGK 854
                                       889999999999998887752225666777777762234467777777777788888888888887777766655 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.6e-05    0.0096       9     164 ..     702     866 ..     681     871 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-05
                           DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq 85 
                                       +k++ +++ ++   l+ l ++v++++   ++ ++ ++++ +++++l ++ a k++v+   ++++  +aL t vs   
  gi|320101450|ref|YP_004177042.1| 702 VKEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVN---NVASKVDALSTSVSSVV 775
                                       444446666666666666666666666666666666666666666666666666665...34555555555555544 PP

                           DUF4795  86 ..fDeakkeLekmleellekle...eqeealkkaldtLq...eelkekld.........rlelepLkeqle...erl 142
                                         +D+++++L+  +++l   ++   +    lk  +++++   + + +k+d           +++ Lk+ +    ++l
  gi|320101450|ref|YP_004177042.1| 776 skLDSVTSQLNSAVQSLNTISSdisG----LKTGVNDVKtavSGVASKVDnvastlstvSSDVSGLKTSVGslqNTL 848
                                       56888888888887766555442222....33333333344446666666664444455555555555443454777 PP

                           DUF4795 143 kelqkelqeamekedkedeaag 164
                                       + ++ +++ a++k d    aag
  gi|320101450|ref|YP_004177042.1| 849 NTVSGKVDTAISKAD----AAG 866
                                       777777776666654....443 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.5e-05    0.0093     156     283 ..     717     849 ..     701     863 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqle 230
                                       + L +  + ++++++++++  ++++++l+ l + +++ ++++    ++ +l  +++++ +++++   +l++  + l+
  gi|320101450|ref|YP_004177042.1| 717 NGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNnvASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLN 793
                                       44555556666666677777777777777777666666665545667777777777777777777777777777777 PP

                              Spc7 231 eleekieelkeqkseleeeiaeaerv...leeckgwsesevsrlkeevkaleeltg 283
                                       +++++i+ lk+  ++++++++   +    +  + +  +s+vs lk++v +l+++++
  gi|320101450|ref|YP_004177042.1| 794 TISSDISGLKTGVNDVKTAVSGVASKvdnVASTLSTVSSDVSGLKTSVGSLQNTLN 849
                                       7777777777776666666654333300033344566899**********999876 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.095        25     224     270 ..     705     751 ..     687     764 .. 0.51
   2 !    7.8   0.1     0.006       1.6     221     269 ..     750     798 ..     744     813 .. 0.82
   3 ?    4.6   0.1     0.058        15     225     270 ..     817     862 ..     806     872 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.095
                              RmuC 224 qeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkl 270
                                       +  +++++a +l+ l + ++++ + +++++++++++++++d + ++ 
  gi|320101450|ref|YP_004177042.1| 705 VGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTV 751
                                       23344445555555555555555555555555555555554444433 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.006
                              RmuC 221 qeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkk 269
                                       + a +  ++++a+++ +l + +++++ +l+++ ++l++a++s++++ + 
  gi|320101450|ref|YP_004177042.1| 750 TVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSD 798
                                       5667788999*********************************995544 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.058
                              RmuC 225 eknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkl 270
                                       + +++++a++l+++ ++++++++++ +l++ l++++ ++d+a++k 
  gi|320101450|ref|YP_004177042.1| 817 ASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKA 862
                                       4567778888888888888888888888888888888888877765 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.066        18       9      59 ..     699     749 ..     696     753 .. 0.80
   2 !    8.3   0.3    0.0072       1.9       9      68 ..     768     827 ..     750     835 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.066
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrlee 59 
                                        ++++e+ +++d++  +L+ l + ++svs+  +++++a +++ ++ + l++
  gi|320101450|ref|YP_004177042.1| 699 IDNVKEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSS 749
                                       567788889999999999999999999999999999999888887777665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0072
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                       + ++ ++++++d++ +qL++  ++ +++s++ s l++  +++ +  + + + ++++ + L
  gi|320101450|ref|YP_004177042.1| 768 STSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTL 827
                                       455566777777777777777777777777777777777766666666666666666655 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 ?    2.9   0.1      0.52   1.4e+02      35      79 ..     708     749 ..     693     755 .. 0.41
   2 !   12.0   1.0   0.00072      0.19       5      89 ..     734     814 ..     731     832 .. 0.83
   3 ?    1.7   0.0       1.2   3.2e+02      23      65 ..     807     849 ..     791     861 .. 0.49

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.52
                           BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       k   +++va  l+  ++ +++ ++ +++ ++ +d ++ +++ L +
  gi|320101450|ref|YP_004177042.1| 708 K---VDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSS 749
                                       2...22222222222222222233333333444444444444444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00072
                           BLOC1_2   5 ekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                       +++ + ++++l+a ++ +   + +N++a +k+++l+++++s+ +kl+ + +   +l++ +q+++ i  +++ L++ v
  gi|320101450|ref|YP_004177042.1| 734 KSAVDTVNSKLDALSSTVASKTDVNNVA-SKVDALSTSVSSVVSKLDSVTS---QLNSAVQSLNTISSDISGLKTGV 806
                                       6677888999999999999989998765.6899999999999988888888...9999999*****99999999998 PP

                           BLOC1_2  82 seLDeysk 89 
                                       + + + ++
  gi|320101450|ref|YP_004177042.1| 807 NDVKTAVS 814
                                       87766655 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.2
                           BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekyeelqpylq 65 
                                       + +++    +++k++++++ ++ ++++++ l+    +lq+ l+
  gi|320101450|ref|YP_004177042.1| 807 NDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLN 849
                                       3333334444444444444444444444444444444444443 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   9.6    0.0012      0.32       6      99 ..     703     806 ..     698     814 .. 0.66
   2 ?    7.7   0.6     0.013       3.4       4      59 ..     812     867 ..     809     872 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvk......dankairdArrsvkkLeklapqLldklk 76 
                                       +e+ +++ +v   l++l + ++ +++ +++i++ v+ +n k++      ++++ ++ + ++v  L   +  +++kl 
  gi|320101450|ref|YP_004177042.1| 703 KEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDalsstvASKTDVNNVASKVDALSTSVSSVVSKLD 779
                                       56666666666666666666666666666666666666666663333333344556677888888888888889988 PP

                                       HHH.HHHHH......HHHHHHHHHHHH CS
                        Laminin_II  77 elk.qleeasss...lsdniseikelI 99 
                                       ++  ql++a +s   +s +is +k  +
  gi|320101450|ref|YP_004177042.1| 780 SVTsQLNSAVQSlntISSDISGLKTGV 806
                                       886255666666778999999998765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArr 59 
                                        ++ + +++ +v + l  +s +++ +k ++ +++++++ +  kv+ a    + A+ 
  gi|320101450|ref|YP_004177042.1| 812 AVSGVASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKADAAGA 867
                                       55556667777777777777777777777777777777777777666666665555 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 ?   14.4   0.0   7.6e-05      0.02      41     139 ..     732     830 ..     718     871 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.6e-05
                        MscS_porin  41 elqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrper 117
                                       + + a+d+   +l++l+   ++ ++ ++ ask +  ++s +   ++l+++ sql ++ + l+++ s++  l t  + 
  gi|320101450|ref|YP_004177042.1| 732 NIKSAVDTVNSKLDALSSTVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVND 808
                                       55788999999999999999999999999************************************************ PP

                        MscS_porin 118 aqqqltearqrlqeirnrLnst 139
                                       + ++ +    + + + + L+  
  gi|320101450|ref|YP_004177042.1| 809 VKTAVSGVASKVDNVASTLSTV 830
                                       **99999999999999988554 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 ?   10.9   0.2    0.0015      0.41      25     101 ..     717     796 ..     697     803 .. 0.75
   2 ?    6.3   0.0     0.042        11      12     100 ..     745     830 ..     742     844 .. 0.73
   3 ?    2.2   0.0      0.76     2e+02      30      69 ..     826     864 ..     798     872 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0015
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  25 kadvdelleldekrrelqveleelqaerNelskeIgkakkkk...edaeeliaevkelkeelkaleaelkeleaele 98 
                                       + +v ++ ++ +   +++++++ ++++  +ls +++++ + +    + ++l  +v+++  +l+ ++ +l+ + + l+
  gi|320101450|ref|YP_004177042.1| 717 NGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNnvaSKVDALSTSVSSVVSKLDSVTSQLNSAVQSLN 793
                                       6678888899999999**********************998866666666666666666677766667766666666 PP

                                       HHH CS
                      Seryl_tRNA_N  99 kll 101
                                       ++ 
  gi|320101450|ref|YP_004177042.1| 794 TIS 796
                                       665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.042
                                       HHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHH CS
                      Seryl_tRNA_N  12 eavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkalea 88 
                                       +a+   ++++ + ++   ++ +l +   ++ ++l+++ ++ N++ ++   ++    d++ l+  v+++k+ ++ +  
  gi|320101450|ref|YP_004177042.1| 745 DALSSTVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISS---DISGLKTGVNDVKTAVSGVAS 818
                                       55556666666666666777778888888888888888888877777777774...688888888888888888888 PP

                                       HHHHHHHHHHHH CS
                      Seryl_tRNA_N  89 elkeleaelekl 100
                                       +++++ + l ++
  gi|320101450|ref|YP_004177042.1| 819 KVDNVASTLSTV 830
                                       888877777665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-T CS
                      Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkkeda 69 
                                       +l  + +    l++ + +lq+  N++s ++  a+ k  da
  gi|320101450|ref|YP_004177042.1| 826 TLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKA-DA 864
                                       4555666677789999999999999999999998765.44 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   9.8e-05     0.026     331     439 ..     749     860 ..     707     868 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.8e-05
                              Cast 331 esltAkeqRAaiLqtevdalrlrleekeqlLnkktkqlqdlteekstlageirdlkdmldvkeRkvnvlqkkienLq 407
                                         ++ k    + + + vdal + +    + L+  t ql++  +   t++++i+ lk  ++  +  v  + +k++n+ 
  gi|320101450|ref|YP_004177042.1| 749 STVASKTDV-NNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVA 824
                                       445555444.445789****************************************8764444578889******** PP

                              Cast 408 eqlrdkdkqlaelkervkslqtD....ssntDtALa 439
                                         l      +++lk  v slq+     s + DtA++
  gi|320101450|ref|YP_004177042.1| 825 STLSTVSSDVSGLKTSVGSLQNTlntvSGKVDTAIS 860
                                       *****************9998541111556677765 PP

>> Alanine_zipper  Alanine-zipper, major outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       3.2   8.7e+02      10      24 ..     730     744 ..     716     753 .. 0.48
   2 ?    3.0   0.1      0.49   1.3e+02       2      36 ..     756     790 ..     755     794 .. 0.87
   3 ?   10.5   0.0    0.0022      0.59       3      41 ..     834     872 ..     832     876 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 3.2
                    Alanine_zipper  10 adqaeqdaaaaksaa 24 
                                       +++++++++ ++s+ 
  gi|320101450|ref|YP_004177042.1| 730 VNNIKSAVDTVNSKL 744
                                       333333333333333 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.49
                    Alanine_zipper   2 qveelqakadqaeqdaaaaksaadeAkskAdeAaa 36 
                                       +v ++ +k+d++++ ++++ s+ d+  s+ ++A +
  gi|320101450|ref|YP_004177042.1| 756 DVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQ 790
                                       688999***************99999988888865 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0022
                    Alanine_zipper   3 veelqakadqaeqdaaaaksaadeAkskAdeAaarAenA 41 
                                       v+ l++ + +++ + + ++ + d+A skAd+A a A nA
  gi|320101450|ref|YP_004177042.1| 834 VSGLKTSVGSLQNTLNTVSGKVDTAISKADAAGASATNA 872
                                       666777788888888888888888888888888888777 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.9   0.00017     0.046      56     154 ..     704     798 ..     695     808 .. 0.67
   2 ?    6.5   1.0     0.019       5.1      56     144 ..     780     858 ..     768     872 .. 0.43

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                      Allexi_40kDa  56 hishdvdsiinklnpv.sll.sqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleel 130
                                        +++ vd++  +ln + +++ s +++++++++a+ t++++ld l+s+  ++++       ++++ k++++ ts+ ++
  gi|320101450|ref|YP_004177042.1| 704 EVGSKVDQVAGTLNGLvNTVsSVSAVVNNIKSAVDTVNSKLDALSSTVASKTD------VNNVASKVDALSTSVSSV 774
                                       67888999999998751333135666777777777777777777666544333......344566788999999999 PP

                      Allexi_40kDa 131 hakldelsssetsesegPsssptk 154
                                         kld ++s+ +s+ ++ ++ +++
  gi|320101450|ref|YP_004177042.1| 775 VSKLDSVTSQLNSAVQSLNTISSD 798
                                       999999999888877765555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.019
                      Allexi_40kDa  56 hishdvdsiinklnpvsllsqttlLselrdalrtltklldklksvekklelsaetasd..skllkklesietsleel 130
                                        ++++++s              ++L+ + +++  l++ ++++k+  + +  + ++  +  s +  +++ ++ts+ +l
  gi|320101450|ref|YP_004177042.1| 780 SVTSQLNSA------------VQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVAStlSTVSSDVSGLKTSVGSL 844
                                       233334444............44455555555555555555555444444444333321123334444455555555 PP

                      Allexi_40kDa 131 hakldelsssetse 144
                                       ++ l+++s +++ +
  gi|320101450|ref|YP_004177042.1| 845 QNTLNTVSGKVDTA 858
                                       44444444333333 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.9     5e+02      40      91 ..     700     749 ..     695     752 .. 0.63
   2 ?    9.5   0.2    0.0037      0.99      24      93 ..     746     820 ..     716     830 .. 0.63
   3 ?    4.7   0.0      0.12        32      33      94 ..     797     856 ..     794     863 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.9
                           DUF2730  40 ekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlsh 91 
                                       ++v+e  ++++++  +++ L ++  +++++  +++++  +++++ ++++ls 
  gi|320101450|ref|YP_004177042.1| 700 DNVKEVGSKVDQVAGTLNGLVNT--VSSVSAVVNNIKSAVDTVNSKLDALSS 749
                                       55666666666666666666543..566667777777777777777777665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0037
                           DUF2730  24 lldskYakredleklaekveendkrlteletkvenLPta.....kdlekLkllladlrgelkaleaevrqlshqv 93 
                                        l+s+ a + d++++a kv+   + ++++ +k++++ ++     + l++++ ++++l+  +++++  v+ ++ +v
  gi|320101450|ref|YP_004177042.1| 746 ALSSTVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQlnsavQSLNTISSDISGLKTGVNDVKTAVSGVASKV 820
                                       467788888888888777777776666666666655443222223355555555555555555555555554444 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.12
                           DUF2730  33 edleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvd 94 
                                       +d++ l+  v++ ++ ++ + +kv+n+  a+ l++++ ++++l+  +  l+++++++s +vd
  gi|320101450|ref|YP_004177042.1| 797 SDISGLKTGVNDVKTAVSGVASKVDNV--ASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVD 856
                                       578888888888999999999999987..456788888888888888888888887777766 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5     0.024       6.3      15      84 ..     710     779 ..     696     791 .. 0.80
   2 ?    6.4   0.1     0.036       9.6       9      72 ..     786     854 ..     778     863 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.024
                              SesA  15 ydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekva 84 
                                        + + +++gl ++ + v++ +  ++ + ++++s+l++ ++  ++++ +++v+ ++++  t+++++  k+ 
  gi|320101450|ref|YP_004177042.1| 710 DQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNVASKVDALSTSVSSVVSKLD 779
                                       33344599***********************************999999999999999999999999983 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.036
                              SesA   9 eaaiklydaikd........ikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckek 72 
                                       ++a +  ++i++        +++ + a + v++++  v  tL+++ s +++ k +  +   ++++l+ ++ k
  gi|320101450|ref|YP_004177042.1| 786 NSAVQSLNTISSdisglktgVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVGS---LQNTLNTVSGK 854
                                       4455555555444444555899999999999999999999999999999998888875...55555555554 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.5   0.00084      0.22       5      77 ..     725     800 ..     721     835 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00084
                            DUF148   5 effaIlknenltiaeieeqleawaekygvtdeykefeakvkaqkeevkknv...tavisnLssvqekleaIldnks 77 
                                       ++ a+++n +   + ++++l+a+ ++   ++++++  +kv a  ++v+  v   ++v s+L s+ ++l++I ++ s
  gi|320101450|ref|YP_004177042.1| 725 SVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNVASKVDALSTSVSSVVsklDSVTSQLNSAVQSLNTISSDIS 800
                                       678999****************************999999988887776551115789999999999999998865 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.5   0.00026     0.071      71     203 ..     723     855 ..     685     863 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX..................... CS
                              AIP3  71 iepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekasesla...............kkelka 132
                                       ++ ++ v ++i++ + ++ ++l  l+s++ s++  ++ +s +  +          a               +++l++
  gi|320101450|ref|YP_004177042.1| 723 VSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNVAS-K-VD----------AlstsvssvvskldsvTSQLNS 787
                                       3455555556666666666666666666654444333311.1.22..........1222222333356666789999 PP

                                       ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHH CS
                              AIP3 133 qlkevqslrrdLavlrqlysefkseikeslselrekakkvkeaslastkkssnrayiekgkkkLseesdkl 203
                                        +++++++  d++ l+   ++ k+ ++   s++ + a+++   ++ s+++s+ ++ + + +++L++ s k+
  gi|320101450|ref|YP_004177042.1| 788 AVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLS--TV-SSDVSGLKTSVGSLQNTLNTVSGKV 855
                                       99999999999999998887777777777777777666666..44.6677777777777777777777655 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8     0.011       2.9       8      47 ..     698     736 ..     696     770 .. 0.71
   2 ?    2.4   1.1      0.83   2.2e+02      19      58 ..     771     792 ..     735     812 .. 0.52
   3 ?    8.5   2.6    0.0099       2.7      11      68 ..     812     872 ..     806     878 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.011
                     T7SS_ESX_EspC   8 dpdhlrelaakhdevaaeiasavaaaagasaavldshGpi 47 
                                       + d ++e+++k+d+va++++ +v+++   ++av+++  + 
  gi|320101450|ref|YP_004177042.1| 698 TIDNVKEVGSKVDQVAGTLNGLVNTV-SSVSAVVNNIKSA 736
                                       6799*********************9.6666666554333 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.83
                     T7SS_ESX_EspC  19 hdevaaeiasavaaaagasaavldshGpicaatndavaaa 58 
                                       +                  ++v++   ++++++n+av+++
  gi|320101450|ref|YP_004177042.1| 771 V------------------SSVVSKLDSVTSQLNSAVQSL 792
                                       2..................333333333333333333332 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0099
                     T7SS_ESX_EspC  11 hlrelaakhdevaaeiasavaaaagasaav...ldshGpicaatndavaaaeaarraagea 68 
                                       ++  +a+k+d+va++++++ + ++g +++v   +++  +++ ++++a+++a aa ++a +a
  gi|320101450|ref|YP_004177042.1| 812 AVSGVASKVDNVASTLSTVSSDVSGLKTSVgslQNTLNTVSGKVDTAISKADAAGASATNA 872
                                       57789******************9999877333689999***************9999876 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00037     0.098      12     149 ..     722     856 ..     700     872 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00037
                                       HHCCHHHCHHCHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHH CS
                    Apolipoprotein  12 yaeeleeqlaplaqelrdrlskeleelrarl..raeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerl 86 
                                       +++ +++ ++ + ++++d+++ +l++l+  +  ++++++v +++ +    v   + ++l+ + ++l+++++ l + +
  gi|320101450|ref|YP_004177042.1| 722 TVSSVSAVVNNI-KSAVDTVNSKLDALSSTVasKTDVNNVASKVDALSTSVS-SVVSKLDSVTSQLNSAVQSL-NTI 795
                                       333333333333.234555555555555555444444444444444444432.23344555555555555555.334 PP

                                       HHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..--- CS
                    Apolipoprotein  87 aadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeve 149
                                       + d+  l+  +    + + ++++++v+++ ++l+  + ++   l+ ++  l+++l++ + +v 
  gi|320101450|ref|YP_004177042.1| 796 SSDISGLKTGVND-VKTAVSGVASKVDNVASTLSTVSSDVSG-LKTSVGSLQNTLNTVSGKVD 856
                                       5555555555544.3335566667777777777766666654.66666666666666555554 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4     0.013       3.6      42     102 ..     722     781 ..     690     804 .. 0.66
   2 ?    3.6   0.0      0.35        94      31     100 ..     787     856 ..     781     859 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.013
                                       HHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
                             DUF16  42 kvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                                       +v++    +n+++ +v++ + k++ l+ ++  + + +n+v + ++ +  ++ ++  +lDs+
  gi|320101450|ref|YP_004177042.1| 722 TVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTD-VNNVASKVDALSTSVSSVVSKLDSV 781
                                       45555555666666666666666666666544443.6666666666666666666666655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.35
                                       .BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHH CS
                             DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlD 100
                                       s  q L+ i   ++ l+  +n ++ +v+    k+++   +  + + ++  ++ ++ ++ +tL++++ ++D
  gi|320101450|ref|YP_004177042.1| 787 SAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVD 856
                                       5568899999999999999999999999999999999999999999999999999999999998888777 PP

>> RCDG1  Renal cancer differentiation gene 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0011      0.28      37      79 ..     690     732 ..     674     735 .. 0.89
   2 ?   -1.1   0.4       9.7   2.6e+03      38      67 ..     767     796 ..     743     812 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0011
                             RCDG1  37 vpsrsqaptvdPleevelqigdaafsliklleatsavsaqvee 79 
                                       v+  s+a t+d + ev  +++  a +l  l+++ s+vsa v++
  gi|320101450|ref|YP_004177042.1| 690 VNNISRAATIDNVKEVGSKVDQVAGTLNGLVNTVSSVSAVVNN 732
                                       5677999********************************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 9.7
                             RCDG1  38 psrsqaptvdPleevelqigdaafslikll 67 
                                        s s +  v  l+ v  q++ a  sl  + 
  gi|320101450|ref|YP_004177042.1| 767 LSTSVSSVVSKLDSVTSQLNSAVQSLNTIS 796
                                       456666889999999999999999887665 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 ?    0.0   0.0       4.2   1.1e+03      29      55 ..     726     752 ..     717     757 .. 0.69
   2 ?    8.0   0.0     0.013       3.6      29      68 ..     753     792 ..     737     794 .. 0.84
   3 ?    0.8   0.0       2.4   6.5e+02      34      61 ..     828     855 ..     803     864 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 4.2
                               CLZ  29 leekverLessLeaLqtrlarLlaeye 55 
                                       +   v++++s++++ + +l  L + + 
  gi|320101450|ref|YP_004177042.1| 726 VSAVVNNIKSAVDTVNSKLDALSSTVA 752
                                       555677777777777777777765554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.013
                               CLZ  29 leekverLessLeaLqtrlarLlaeyessqrkLkqRitkL 68 
                                        ++ v+++ s+++aL t +  ++++++s+ ++L++ ++ L
  gi|320101450|ref|YP_004177042.1| 753 SKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSL 792
                                       4677999999999999999999999999999999999887 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 2.4
                               CLZ  34 erLessLeaLqtrlarLlaeyessqrkL 61 
                                       + + s +  L+t +  L + ++++  k 
  gi|320101450|ref|YP_004177042.1| 828 STVSSDVSGLKTSVGSLQNTLNTVSGKV 855
                                       3333444444444444444444444444 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.12        33      38      87 ..     708     750 ..     694     773 .. 0.45
   2 ?    5.0   0.2     0.022       5.9      38      92 ..     756     810 ..     745     816 .. 0.81
   3 ?    3.6   0.0     0.057        15      38      83 ..     819     864 ..     814     871 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                              COG6  38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkee 87 
                                       + ++va +L+ + ++v++ +++++++k+++++       ++++ ++L+++
  gi|320101450|ref|YP_004177042.1| 708 KVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDT-------VNSKLDALSST 750
                                       33333333333333333333333333333333.......33333333332 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.022
                              COG6  38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkle 92 
                                       + ++va ++++++++v++  +  d+++++l+sa ++ +++ ++++ Lk+  ++++
  gi|320101450|ref|YP_004177042.1| 756 DVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVK 810
                                       5677888889999999999999999999999999999999998888888777666 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.057
                              COG6  38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaee 83 
                                       + ++va +L++++sdv+ l++++ ++++ l++ + + ++ +++a++
  gi|320101450|ref|YP_004177042.1| 819 KVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKADA 864
                                       677899****************************999999999876 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1       0.1        27      10      39 ..     754     783 ..     732     788 .. 0.45
   2 ?    3.4   0.0      0.34        92       4      44 ..     790     830 ..     787     841 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.1
                              XhlA  10 etkldnleervdkleekaaeaeekiknlee 39 
                                       +t+++n  ++vd l    + + +k+++++ 
  gi|320101450|ref|YP_004177042.1| 754 KTDVNNVASKVDALSTSVSSVVSKLDSVTS 783
                                       344444444444444444444444444444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.34
                              XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                       + l++i +++  l++ v++++   + + +k++n+  +l+  
  gi|320101450|ref|YP_004177042.1| 790 QSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTV 830
                                       789*******************************9999865 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.9    0.0004      0.11     245     374 ..     730     864 ..     696     872 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                             WEMBL 245 akdlkskletasallldLkaeLaayve.sklkeeaeeeeee....kksetsikealasarkELeevkaniekakdev 316
                                        +++ks ++t +++l  L + +a  ++ +++ ++ +  +++     ++  s++++l+sa + L+ + ++i+  k+ v
  gi|320101450|ref|YP_004177042.1| 730 VNNIKSAVDTVNSKLDALSSTVASKTDvNNVASKVDALSTSvssvVSKLDSVTSQLNSAVQSLNTISSDISGLKTGV 806
                                       34455555555555555555555544433333333322222444456666777778888888888888888888888 PP

                             WEMBL 317 klLkvaaasLrseLekekaeLaslrqregmasiavssLeaelsrtkselelvqakeke 374
                                       + +k a++ + s++++  ++L+++    +   ++v sL++ l+ +   + ++ +k+ +
  gi|320101450|ref|YP_004177042.1| 807 NDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKADA 864
                                       8888888888888888888888888877777788888888888888777777766665 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.53   1.4e+02      19      55 ..     722     758 ..     699     774 .. 0.64
   2 ?    4.8   0.1     0.081        22       4      53 ..     762     811 ..     756     822 .. 0.78
   3 ?    6.2   0.0      0.03       8.1      14      77 ..     798     860 ..     788     872 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.53
                        Phage_GP20  19 kldeveeerdtlkeqlkdrdkqLedLkkkakdneeLq 55 
                                        +++v + ++++k+ +++ +++L+ L   +   ++++
  gi|320101450|ref|YP_004177042.1| 722 TVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVN 758
                                       4556777778888888888888888876655444333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.081
                        Phage_GP20   4 kkvmkaengkdit.kakldeveeerdtlkeqlkdrdkqLedLkkkakdnee 53 
                                        kv+ a+++++ +  +kld+v+++ ++  ++l++  +++++Lk+ ++d+++
  gi|320101450|ref|YP_004177042.1| 762 SKVD-ALSTSVSSvVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKT 811
                                       5555.5553333367899999999999999999999999999999999876 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.03
                        Phage_GP20  14 dit..kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakia 77 
                                       di+  k+ +++v++++  + +++++  ++L++    + d+  L++ + +lq+++++ + + ++ i+
  gi|320101450|ref|YP_004177042.1| 798 DISglKTGVNDVKTAVSGVASKVDNVASTLSTV---SSDVSGLKTSVGSLQNTLNTVSGKVDTAIS 860
                                       555667777777777777777777777777766...346777777777777777766655555554 PP

>> Joubert  Joubert syndrome-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.2   0.00049      0.13     270     328 ..     721     779 ..     690     782 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00049
                           Joubert 270 rdvvspwtlpseirriLhesrssllqdlspaeeeke.sslsvngldslSeStgSiLSkLD 328
                                       ++v s +++ ++i++   ++ +s l+ ls + ++k   +   +++d+lS S++S+ SkLD
  gi|320101450|ref|YP_004177042.1| 721 NTVSSVSAVVNNIKSAV-DTVNSKLDALSSTVASKTdVNNVASKVDALSTSVSSVVSKLD 779
                                       56778888889999998.7777778878877777765888899****************9 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.058        15      60     110 ..     716     768 ..     699     774 .. 0.75
   2 ?    6.7   0.9     0.029       7.8      42     113 ..     757     831 ..     753     835 .. 0.67
   3 ?    2.2   0.0       0.7   1.9e+02      65     104 ..     825     864 ..     817     872 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.058
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHH..HHHHHHHHHHHH CS
                              COG5  60 LlehlskskslssvlselksslesLsasyerlkskvlep..yeeaeklqsalk 110
                                       L   +++ +s s+v++++ks ++ +++ ++ l+s v  +   +++ +++ al+
  gi|320101450|ref|YP_004177042.1| 716 LNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKtdVNNVASKVDALS 768
                                       5556788999999*********************9987622456666666655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.029
                                       XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHH CS
                              COG5  42 iqeldkrlrqlits...nhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlh 113
                                       ++++ ++++ l ts     ++L + +s+ +s+ ++l+++ s ++ L+  ++ +k+ v+    +++++ s+l+++ 
  gi|320101450|ref|YP_004177042.1| 757 VNNVASKVDALSTSvssVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVS 831
                                       555555555544430003344444455555555699999999999999999999999999999999999888875 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.7
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHH CS
                              COG5  65 skskslssvlselksslesLsasyerlkskvlepyeeaek 104
                                       s+ ++ ss +s lk+s+ sL++ ++ ++ kv + + +a+ 
  gi|320101450|ref|YP_004177042.1| 825 STLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKADA 864
                                       4444555566777777777777777777777766666665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.3        80     443     495 ..     699     751 ..     693     757 .. 0.81
   2 ?    6.8   0.0     0.006       1.6     259     402 ..     769     841 ..     736     859 .. 0.43

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.3
                                       HHHSTTTSTTTHHHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHHHHHHHHHH CS
                              EzrA 443 leelkeasdeieelakeLekkpinikevnkrldeardlveklyektneliktA 495
                                       ++++ke+  +++++a  L+    ++  v++ +++++++v+++++k + l  t+
  gi|320101450|ref|YP_004177042.1| 699 IDNVKEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTV 751
                                       56788888888888889988888899999999999999999888888776665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHTT-..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS CS
                              EzrA 259 kkieeilerlkel..eledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlk 333
                                       +++++++++l+++  +l+++ +                                                       
  gi|320101450|ref|YP_004177042.1| 769 TSVSSVVSKLDSVtsQLNSAVQS------------------------------------------------------ 791
                                       33333333333222223333333...................................................... PP

                                       -GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 334 qsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeilesl 402
                                                          l+++++d+  l++ +++ k+a S ++++++++ ++l+++++++  +++s+
  gi|320101450|ref|YP_004177042.1| 792 -------------------LNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSV 841
                                       ...................33333333333333333333333333333333333333333333333333 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 ?    6.8   0.2     0.029       7.7      13      81 ..     723     792 ..     697     797 .. 0.78
   2 ?    5.9   0.1     0.054        14       9      81 ..     757     827 ..     752     832 .. 0.77
   3 ?    1.2   0.0       1.6   4.4e+02       6      40 ..     813     847 ..     808     859 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHHCGCGCT.HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  13 aarfqkqaeeledelqrlkaevdalqsgWs.GaaadafqaefeewkqaaqklvdaLeeisealkqaanaf 81 
                                        +++++  ++++++++++++++dal+s+    +  +  ++  + +  ++  +v +L++++++l++a +++
  gi|320101450|ref|YP_004177042.1| 723 VSSVSAVVNNIKSAVDTVNSKLDALSSTVAsKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSL 792
                                       5667777788888888888888888666662455566777778888888888888888888888888776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   9 lrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanaf 81 
                                       +  +a+++++ ++++++++++l++  ++l+s+   ++ ++  + +  +k +++++++a ++++++++++a+++
  gi|320101450|ref|YP_004177042.1| 757 VNNVASKVDALSTSVSSVVSKLDSVTSQLNSAV--QSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTL 827
                                       667899999999999999999999999997764..56677777777777777777777777777777777766 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCG CS
                            WXG100   6 peelrqaaarfqkqaeeledelqrlkaevdalqsg 40 
                                        + ++++  +++++ +++++ ++ lk +v +lq++
  gi|320101450|ref|YP_004177042.1| 813 VSGVASKVDNVASTLSTVSSDVSGLKTSVGSLQNT 847
                                       55666667777777777777777777777777664 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00075       0.2      78     221 ..     706     851 ..     693     873 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00075
                    ALIX_LYPXL_bnd  78 raelqkyreileeAsesDkivrqklqenkedlelLsgpeeeleaalpssssaaa.sesveeqirklrsllekldelk 153
                                        +++++  ++l+  +++ + v++ ++++k++++  ++  ++l + + s++  ++  ++v++   +++s ++kld++ 
  gi|320101450|ref|YP_004177042.1| 706 GSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNvASKVDALSTSVSSVVSKLDSVT 782
                                       56788888889999999999999999999999999888999999999777764444555555567777777777777 PP

                    ALIX_LYPXL_bnd 154 aereqllkdlkekaendDitpkl...ltekkr......diaanefealfeeelekydplqeqleqslakqeellkei 221
                                       ++ ++ +++l+    + Di+  l   +    +       +  +++ +  ++ l++ +++++ l++s+ + ++ l+++
  gi|320101450|ref|YP_004177042.1| 783 SQLNSAVQSLN--TISSDISG-LktgV----NdvktavSGV-ASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTV 851
                                       77777777776..44444544.11111....1122222222.33355666666666666666666666666655555 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 ?   11.5   0.8   0.00084      0.22      53     124 ..     703     774 ..     693     776 .. 0.81
   2 ?    0.5   0.1       2.2   5.8e+02      88     122 ..     816     849 ..     776     864 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00084
                            Phasin  53 kvaeekleevresvkskveevkekaeeqwdklekafdervakaLsrlg..vpsredveaLsarvdeLtkelekl 124
                                       k++ +k+++v  +++  v++v+  +++ ++++ +a+d +v++ L  l   v+s++dv++++++vd+L+++++++
  gi|320101450|ref|YP_004177042.1| 703 KEVGSKVDQVAGTLNGLVNTVS-SVSAVVNNIKSAVD-TVNSKLDALSstVASKTDVNNVASKVDALSTSVSSV 774
                                       5677788888888877777775.57788899999997.5999999885449*****************999875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.2
                            Phasin  88 fdervakaLsrlgvpsredveaLsarvdeLtkele 122
                                       + ++v ++ s+l   s +dv+ L+  v +L+++l+
  gi|320101450|ref|YP_004177042.1| 816 VASKVDNVASTLSTVS-SDVSGLKTSVGSLQNTLN 849
                                       2233333333333322.355555555555555444 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.94   2.5e+02     106     149 ..     708     751 ..     700     754 .. 0.76
   2 ?    7.9   0.1    0.0073       1.9      10      72 ..     739     800 ..     728     816 .. 0.83
   3 ?   -1.0   0.0         4   1.1e+03      28      52 ..     840     864 ..     820     871 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.94
                              DegS 106 rRdelerrLkklketierAeklvsqvgvvlnyLsgdlkqvsekl 149
                                       + d++  +L+ l +t+     +v++++++++ ++++l+ +s+++
  gi|320101450|ref|YP_004177042.1| 708 KVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTV 751
                                       55677777888888888888888888888888888888887765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0073
                              DegS  10 tiekskeeifeIaEsarkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFk 72 
                                       t+ +sk +  + + +++++v+++ ++++ l + vs+v+++ d+++++  +a + L ++s+d +
  gi|320101450|ref|YP_004177042.1| 739 TV-NSKLDALSSTVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDIS 800
                                       44.355555556668999****************************************99875 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4
                              DegS  28 everlkkeleelkeevsevikevdk 52 
                                        v +l++ l+++  +v + i+++d+
  gi|320101450|ref|YP_004177042.1| 840 SVGSLQNTLNTVSGKVDTAISKADA 864
                                       5667899999999999999999886 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.7    0.0039         1     119     193 ..     723     796 ..     697     805 .. 0.77
   2 ?    9.6   3.7    0.0025      0.67      62     198 ..     729     864 ..     724     868 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0039
                               LXG 119 kdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemt 193
                                        +++ +++++++  v++++ +++++ +    +k  v+++  k++++ ++ +s +++l+s  ++l++ v++L++  
  gi|320101450|ref|YP_004177042.1| 723 VSSVSAVVNNIKSAVDTVNSKLDALSS-TVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTIS 796
                                       344555668888888888888888555.55678888***********************************9865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0025
                               LXG  62 lltslqdlieqyeefLkkikeales.vepssngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpe 137
                                       +++ +++++++++++L   ++ + s  +++ n   + d+L  +++  ++k+ +vt++l +++++ l+++s  +s  +
  gi|320101450|ref|YP_004177042.1| 729 VVNNIKSAVDTVNSKLDALSSTVASkTDVN-NVASKVDALSTSVSSVVSKLDSVTSQLNSAVQS-LNTISSDISGLK 803
                                       567788888888888888888888856666.777889999999999999999999999999999.999998889999 PP

                               LXG 138 lddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemtskgki 198
                                          ++vk+ ++ + +kv+++   l +   + + + +++ s  ++l+t   ++ +++sk + 
  gi|320101450|ref|YP_004177042.1| 804 TGVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKADA 864
                                       9999999999999999999999999999999999999999999999999999999988775 PP

>> Med11  Mediator complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.9    0.0017      0.44       9      79 ..     728     796 ..     722     869 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0017
                             Med11   9 eIDkdIvslLesasealkaLskppeqepaseseeaqkeafkaatstffstLssvdvrLrrqIyaLeeagii 79 
                                       ++ ++I s  +++ + l+aLs++  ++++ ++  ++ +a  ++ s+ +s L+sv ++L+  +++L+   i+
  gi|320101450|ref|YP_004177042.1| 728 AVVNNIKSAVDTVNSKLDALSSTVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNT--IS 796
                                       56689999999***********99*****************************************98..33 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4    0.0016      0.42       4     110 ..     747     853 ..     744     871 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0016
                         Laminin_I   4 lnsltgale.apykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaeser 79 
                                       l+ +t a++  ++++ ++++ l +  ++ +sk ++  s+++ + + l+++ +++  L + ++ v    + v  ++++
  gi|320101450|ref|YP_004177042.1| 747 LS-STVASKtDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDN 822
                                       55.55555415888888999999999999999999999999999999999999999999999999888888888888 PP

                         Laminin_I  80 tlnnakeLaekikkladnikeilekvatlne 110
                                         +  ++    +  l+ ++  + +   t+++
  gi|320101450|ref|YP_004177042.1| 823 VASTLSTVSSDVSGLKTSVGSLQNTLNTVSG 853
                                       8888888888888888888877777777666 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0013      0.36      48     186 ..     683     825 ..     676     826 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                            DUF724  48 mvsfagllekvkklsiddsrseles....lkeslaeLekhGFdVkalqsrlnkLlslkdeqtklleerkklekkiee 120
                                       m  f+ +++++++    d+++e  s       +l+ L +   +V a+ + ++  +   +++  +l+ + + + ++ +
  gi|320101450|ref|YP_004177042.1| 683 MPGFVYVVNNISRAATIDNVKEVGSkvdqVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNN 759
                                       66788888888887777766555540000555677888888888888888888888888888888888888888999 PP

                            DUF724 121 eesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeavas 186
                                        +s+   l+++++ + +k   +  ql ++ +  ++ +++i+ lk+ +++++++++ v +++++vas
  gi|320101450|ref|YP_004177042.1| 760 VASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVAS 825
                                       999999999999999999999999999999999999999999999999999999999999998886 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.28        74      29      46 ..     731     748 ..     717     753 .. 0.66
   2 ?    5.8   0.1     0.066        18      26      62 ..     755     791 ..     751     800 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.28
                           UPF0184  29 eainsmLDqinsaLDalE 46 
                                       ++i s +D +ns LDal 
  gi|320101450|ref|YP_004177042.1| 731 NNIKSAVDTVNSKLDALS 748
                                       455566666666666653 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.066
                           UPF0184  26 eEyeainsmLDqinsaLDalEernDdlnskLrELles 62 
                                        +++++ s +D++++ +  +  + D++ s+L+  ++s
  gi|320101450|ref|YP_004177042.1| 755 TDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQS 791
                                       567789999**********************987776 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.2     0.097        26      72     161 ..     703     791 ..     691     797 .. 0.56
   2 ?    8.8   0.6    0.0047       1.3      69     178 ..     762     871 ..     750     873 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.097
                            DUF745  72 reaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRv 148
                                       +e  + v+++   l+   +++++++++++++++ ++++++ l+a ++++++ ++v++ a+ ++++ ++ + +  +++
  gi|320101450|ref|YP_004177042.1| 703 KEVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNVAS-KVDALSTSVSSVVSKL 778
                                       555555555555555555555666666666666666666666666666665555554443.3444444455555555 PP

                            DUF745 149 eeLkkqlkearkd 161
                                       +++++ql++a + 
  gi|320101450|ref|YP_004177042.1| 779 DSVTSQLNSAVQS 791
                                       5555555555554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0047
                            DUF745  69 qelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAk 145
                                       +++   ++ v+++ ++l s  +++++a ++ +++ + ++ lk+ ++ +k++++ + +  +++++ l+  ++ +   k
  gi|320101450|ref|YP_004177042.1| 762 SKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLK 838
                                       45555556666666777777777777777777777777777777777777777777777777777777777777777 PP

                            DUF745 146 kRveeLkkqlkearkdlektkkaAykAacAAqe 178
                                       + v +L++ l+++    +   ++A  A ++A +
  gi|320101450|ref|YP_004177042.1| 839 TSVGSLQNTLNTVSGKVDTAISKADAAGASATN 871
                                       777777777776666666655556555555555 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.5    0.0015      0.39     615     772 ..     665     831 ..     661     839 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                             Nop14 615 glflctlvlqyqslSkRyvPEvinfllnlllllapkkskk......kvpgvfpvkevk.psellelkeleekskkek 684
                                       g + ++lv+++ +   + +P ++ ++ n+  +++ ++ k+      +v g+     ++  s + +++++++  +  +
  gi|320101450|ref|YP_004177042.1| 665 GKYAVSLVYSVNNTFMKSMPGFVYVVNNISRAATIDNVKEvgskvdQVAGTLNGLVNTvSSVSAVVNNIKS--AVDT 739
                                       67899999999999999999999999999999988888888887774444444333332344446665653..3334 PP

                             Nop14 685 kqrklslsdllkeesskeeseqlklsllstals.llekfaelyseksafveifepilkllkklk...lkkkklpeel 757
                                        ++kl++ +   +++++ ++   k+++lst +s +++k+  + s++++ v+ +++i++ ++ lk   ++ k+  + +
  gi|320101450|ref|YP_004177042.1| 740 VNSKLDALSSTVASKTDVNNVASKVDALSTSVSsVVSKLDSVTSQLNSAVQSLNTISSDISGLKtgvNDVKTAVSGV 816
                                       457887655555588999999********99874778899999**************99999998888888999999 PP

                             Nop14 758 qekleellaklerll 772
                                       ++k+++++++l++ +
  gi|320101450|ref|YP_004177042.1| 817 ASKVDNVASTLSTVS 831
                                       999999999998765 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.0     0.019       5.1      81     135 ..     724     780 ..     694     797 .. 0.65
   2 ?    2.5   0.0      0.29        79      67     114 ..     815     861 ..     790     873 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.019
                      SF-assemblin  81 eevddlalelkkaveelnekinnveanvenekakrr..daieklakelvkelnelea 135
                                         v  ++ ++k+av+ +n k+  +++ v  +    +  +++++l +++   + +l++
  gi|320101450|ref|YP_004177042.1| 724 SSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNvaSKVDALSTSVSSVVSKLDS 780
                                       45778899******************9976543332114455555554444444433 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.29
                      SF-assemblin  67 efkkeikklqekikeevddlalelkkaveelnekinnveanvenekak 114
                                        + ++++++  +    v   +  lk +v +l +++n v+ +v   + k
  gi|320101450|ref|YP_004177042.1| 815 GVASKVDNVASTLS-TVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISK 861
                                       34556666665554.556667889999999999999999998766654 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0059       1.6      43     110 ..     722     788 ..     690     796 .. 0.73
   2 ?    0.9   0.0       1.1     3e+02       4      75 ..     788     858 ..     779     873 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0059
                          Syntaxin  43 lkkrmesdikeikkraesvkarLeaLdksnkenekksgegsavdRirksqtaaLrkklkevmteynel 110
                                       + + +++ +++ik   ++v+++L+aL+ +++++   ++ +s vd  ++s+ +++ +kl +v ++ n++
  gi|320101450|ref|YP_004177042.1| 722 TVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNVASKVDALSTSVSSVV-SKLDSVTSQLNSA 788
                                       445678899999999999999999999999999999999999998888776554.4666666666655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                          Syntaxin   4 ffkeveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnken 75 
                                         +  ++i+++i+ l++ v+++k + + + +++++ ++ + + ++sd++  k++  s+++ L++ + +++ +
  gi|320101450|ref|YP_004177042.1| 788 AVQSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVAS-TLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTA 858
                                       55666777888888888888888888888777777777.777777888888877777777777776666555 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.06        16       4      69 ..     731     795 ..     728     800 .. 0.84
   2 ?    3.5   0.0      0.14        38       6      73 ..     802     869 ..     797     872 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.06
                       Tropomyosin   4 kqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeea 69 
                                       ++++  +d+++ +l+++ + ++++++   +  + v al  +++ + ++l+++ ++l++a + L+  
  gi|320101450|ref|YP_004177042.1| 731 NNIKSAVDTVNSKLDALSSTVASKTDVN-NVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTI 795
                                       5688889999999999999998877665.56678999********************999999876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                       Tropomyosin   6 veeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaa 73 
                                       +++ +++++ +   + +k+++   +     ++v+ l+ ++  l + l+ ++ ++++a +k + a  +a
  gi|320101450|ref|YP_004177042.1| 802 LKTGVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTAISKADAAGASA 869
                                       67888999999***********************************************9988876655 PP

>> Herpes_UL49_5  Herpesvirus UL49.5 envelope/tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.7     0.005       1.3      59      84 ..     866     891 ..     862     903 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.005
                     Herpes_UL49_5  59 ssaasvlFYisLlavlvallavayna 84 
                                       ++ a+  FYi+L+av+ alla+ +  
  gi|320101450|ref|YP_004177042.1| 866 GASATNAFYIGLVAVIFALLATVFAL 891
                                       6678889*************987755 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 ?    9.5   1.5    0.0038         1      32     127 ..     704     801 ..     697     806 .. 0.64
   2 ?    0.5   0.0       2.3   6.3e+02      31      53 ..     828     850 ..     800     872 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0038
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn......dnvikksskeleeeilrlketidaqes 102
                                       +v  +++++  +l+ + n+ ++++ +v++ik+ +   +++ +        ++ +++    + +++  l  ++++ +s
  gi|320101450|ref|YP_004177042.1| 704 EVGSKVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALsstvasKTDVNN----VASKVDALSTSVSSVVS 776
                                       56666777777777777777777777777776665555444433210000334444....44455588888888888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 103 nirvLqnvlesneqkiqkLeqdidq 127
                                       ++   ++ l+s +q+++ + +di+ 
  gi|320101450|ref|YP_004177042.1| 777 KLDSVTSQLNSAVQSLNTISSDISG 801
                                       8888888888888888888888875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.3
                                       CCCCHHHCCCCCCCCCCCCHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstke 53 
                                       ++v+ d++ l+ ++ +++n+ ++
  gi|320101450|ref|YP_004177042.1| 828 STVSSDVSGLKTSVGSLQNTLNT 850
                                       22222333333333333332222 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4      0.39     1e+02       3      43 ..     711     751 ..     704     760 .. 0.79
   2 ?   10.9   0.9    0.0017      0.47       2      52 ..     762     812 ..     761     819 .. 0.90
   3 ?    1.8   0.3       1.2   3.1e+02       4      48 ..     827     861 ..     811     871 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH CS
                       Flagellin_C   3 ivdeaitdldkvrselGavqnRlesaitnlkaqsenlkaae 43 
                                        v   +++l ++ s++ av n ++sa++ ++   + l++ +
  gi|320101450|ref|YP_004177042.1| 711 QVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLDALSSTV 751
                                       45566889999999999999999999999999888887765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCCHHHH CS
                       Flagellin_C   2 divdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrledvDpa 52 
                                       ++vd  +t++++v s+l +v ++l+sa+++l++ s+ ++  ++  +dv +a
  gi|320101450|ref|YP_004177042.1| 762 SKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTGVNDVKTA 812
                                       579999******************************999999888888665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCC CS
                       Flagellin_C   4 vdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrled 48 
                                       +++ ++d++  ++++G+ qn l+  + +++++          + +
  gi|320101450|ref|YP_004177042.1| 827 LSTVSSDVSGLKTSVGSLQNTLNTVSGKVDTA----------ISK 861
                                       33444555555555555555555444444444..........444 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.0    0.0083       2.2      11      63 ..     740     792 ..     726     795 .. 0.78
   2 ?    6.2   1.2      0.05        13       2      64 ..     772     835 ..     771     864 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0083
                        Syntaxin_2  11 nvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnss 63 
                                        +s+l+ l +++ +k+d  ++ +k++ l ++++ +++k  +  ++l++  +s+
  gi|320101450|ref|YP_004177042.1| 740 VNSKLDALSSTVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSL 792
                                       35666666677777799*******************99999999999988776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.05
                        Syntaxin_2   2 ssnlqkinsnvstleklvkqLgtkk.dteelreklhelieeinelikktnellkklsqldnsss 64 
                                       ss ++k+ s +s+l++ v++L+t   d   l+  ++++ + ++ +++k+ +  + ls+++   s
  gi|320101450|ref|YP_004177042.1| 772 SSVVSKLDSVTSQLNSAVQSLNTISsDISGLKTGVNDVKTAVSGVASKVDNVASTLSTVSSDVS 835
                                       6778888999999999999999985488889988888888888888888888877777665544 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.7     0.054        14      92     175 ..     730     814 ..     697     816 .. 0.77
   2 ?    7.8   1.9    0.0097       2.6      84     162 ..     778     857 ..     752     862 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.054
                      Bacillus_HBL  92 veavdkkdkaellellekLqeeiqqnq..kevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqne 166
                                       v+++ k + +++ ++l +L++++ ++   ++v +++ +L+   +++ ++  + +++++ + + l++ s +is l+  
  gi|320101450|ref|YP_004177042.1| 730 VNNI-KSAVDTVNSKLDALSSTVASKTdvNNVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSDISGLKTG 805
                                       3344.566688899999999998776533677777777777777777778888888888888888889999999999 PP

                      Bacillus_HBL 167 iedlqgkik 175
                                       ++d++ +++
  gi|320101450|ref|YP_004177042.1| 806 VNDVKTAVS 814
                                       999988876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0097
                      Bacillus_HBL  84 FqsyyktlveavdkkdkaellellekLqeeiqqnqkevkqlikeLkklklkl...akdsknFktdvdeltsilagds 157
                                        +s  ++l++av  +  ++++++++ L+++++  + +v  ++ ++ + ++ l    +d++ +kt v  l+++l++ s
  gi|320101450|ref|YP_004177042.1| 778 LDSVTSQLNSAV--QSLNTISSDISGLKTGVNDVKTAVSGVASKVDNVASTLstvSSDVSGLKTSVGSLQNTLNTVS 852
                                       556667788888..677889999999999999999998888777777766552226899999999999999999999 PP

                      Bacillus_HBL 158 gvisq 162
                                       g++++
  gi|320101450|ref|YP_004177042.1| 853 GKVDT 857
                                       99875 PP

>> BORCS6  BLOC-1-related complex sub-unit 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2     0.004       1.1      65     111 ..     702     750 ..     687     755 .. 0.80
   2 ?    1.5   9.2       1.2   3.1e+02      30     110 ..     780     857 ..     758     862 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.004
                            BORCS6  65 aqkvaasvdnllenlssklhsisalt..vgnietykdavdklgdavDss 111
                                        ++v ++vd++  +l++ ++++s+++  v+ni+   d+v++  da+ s 
  gi|320101450|ref|YP_004177042.1| 702 VKEVGSKVDQVAGTLNGLVNTVSSVSavVNNIKSAVDTVNSKLDALSST 750
                                       5799********************9955688888888888877777665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.2
                            BORCS6  30 slsesstpsaslskqllaaqipeidpnvlsdlereaqkvaasvdnllenlssklhsisal..tvgnietykdavdkl 104
                                       s +++ +++ + s  + +++i  + +  ++d++++ + va++vdn+ ++ls++  ++s l  +vg++++  ++v   
  gi|320101450|ref|YP_004177042.1| 780 SVTSQLNSAVQ-SLNTISSDISGLKT-GVNDVKTAVSGVASKVDNVASTLSTVSSDVSGLktSVGSLQNTLNTV--- 851
                                       11111111111.12244555666654.469999999999******99999999999999844566666555544... PP

                            BORCS6 105 gdavDs 110
                                       +  vD+
  gi|320101450|ref|YP_004177042.1| 852 SGKVDT 857
                                       444444 PP

>> Baculo_p24  Baculovirus P24 capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.2    0.0059       1.6     102     176 ..     722     800 ..     715     806 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0059
                        Baculo_p24 102 aqseavdplkdiktqlctlqecleesnvlvnsttesss.n...enieslreilrseeasllsnlnsllesikslqad 174
                                       + s +   +++ik+ + t++++l+  +++v+s+t+ ++ +   + +++    + s+ +s++s+lns+++s+ ++ +d
  gi|320101450|ref|YP_004177042.1| 722 TVSSVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNvAskvDALSTSVSSVVSKLDSVTSQLNSAVQSLNTISSD 798
                                       5566677799**************99999887777766543455666666778889999***************999 PP

                        Baculo_p24 175 lt 176
                                       ++
  gi|320101450|ref|YP_004177042.1| 799 IS 800
                                       86 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.5      0.21        56       6      66 ..     727     788 ..     716     803 .. 0.64
   2 ?    5.4   0.1     0.054        14      19      80 ..     789     851 ..     778     854 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.21
                              Sec5   6 slvksnftkfvk.vkdtldqiykefseskteaqedslveeLeeslneairkttllfkpvlen 66 
                                       s v +n+++ v+ v ++ld++ + + +++  ++  s v+ L++s++++ +k +++  ++ + 
  gi|320101450|ref|YP_004177042.1| 727 SAVVNNIKSAVDtVNSKLDALSSTVASKTDVNNVASKVDALSTSVSSVVSKLDSVTSQLNSA 788
                                       44555666666513345666666665555556666888888888888888888777776654 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.054
                              Sec5  19 kdtldqiykefseskte.aqedslveeLeeslneairkttllfkpvlenkekadklraalevi 80 
                                        ++l++i +++s  kt  ++ +  v+ + +++++++++ +++  +v   k+ + +l+++l+ +
  gi|320101450|ref|YP_004177042.1| 789 VQSLNTISSDISGLKTGvNDVKTAVSGVASKVDNVASTLSTVSSDVSGLKTSVGSLQNTLNTV 851
                                       3456666677776666667888999**********************************9876 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.079        21       8      45 ..     708     745 ..     703     760 .. 0.76
   2 ?    2.4   0.2       0.5   1.3e+02       8      34 ..     770     796 ..     752     804 .. 0.60
   3 ?    0.9   0.1       1.5     4e+02      14      40 ..     818     844 ..     803     857 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.079
                         DASH_Duo1   8 qLrkinevienviesLkkaksniervketvestntLLd 45 
                                       +++++  ++++++++  +++  ++++k++v+++n+ Ld
  gi|320101450|ref|YP_004177042.1| 708 KVDQVAGTLNGLVNTVSSVSAVVNNIKSAVDTVNSKLD 745
                                       67888888888888888888888888888888887555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.5
                         DASH_Duo1   8 qLrkinevienviesLkkaksniervk 34 
                                       ++ ++ + +++v+++L++a + +++++
  gi|320101450|ref|YP_004177042.1| 770 SVSSVVSKLDSVTSQLNSAVQSLNTIS 796
                                       344444445555555555555555554 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.5
                         DASH_Duo1  14 evienviesLkkaksniervketvest 40 
                                       + ++nv ++L +++s+++ +k++v s 
  gi|320101450|ref|YP_004177042.1| 818 SKVDNVASTLSTVSSDVSGLKTSVGSL 844
                                       344455555555555555554444444 PP

>> DUF4854  Domain of unknown function (DUF4854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.51   1.4e+02      41      95 ..     688     742 ..     686     749 .. 0.76
   2 ?    6.9   1.9      0.03       7.9      51      95 ..     725     769 ..     721     777 .. 0.88
   3 ?    2.7   0.5       0.6   1.6e+02      51      86 ..     759     794 ..     753     800 .. 0.73
   4 ?   -0.7   0.0       6.9   1.8e+03      57      78 ..     814     835 ..     803     855 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.51
                           DUF4854  41 ytlskslddaaldalkealaesldsqastfeslakqlkkevkv.enpivvvrvlts 95 
                                       y  ++ +  a++d++ke + +++d+ a t++ l++++ +   v +n++  v  ++s
  gi|320101450|ref|YP_004177042.1| 688 YVVNNISRAATIDNVKE-VGSKVDQVAGTLNGLVNTVSSVSAVvNNIKSAVDTVNS 742
                                       55555566677788776.56889999999999999999988777999888877775 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.03
                           DUF4854  51 aldalkealaesldsqastfeslakqlkkevkvenpivvvrvlts 95 
                                       +++a+ + +++++d  +s +  l ++++++++v+n++  v +l  
  gi|320101450|ref|YP_004177042.1| 725 SVSAVVNNIKSAVDTVNSKLDALSSTVASKTDVNNVASKVDALST 769
                                       67888999******************************9998876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.6
                           DUF4854  51 aldalkealaesldsqastfeslakqlkkevkvenp 86 
                                       ++++  +al++s+ s  s + s+ +ql+++v+  n+
  gi|320101450|ref|YP_004177042.1| 759 NVASKVDALSTSVSSVVSKLDSVTSQLNSAVQSLNT 794
                                       456666788888888888888888888888877554 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 6.9
                           DUF4854  57 ealaesldsqastfeslakqlk 78 
                                       + +a+++d+ ast++ + +++ 
  gi|320101450|ref|YP_004177042.1| 814 SGVASKVDNVASTLSTVSSDVS 835
                                       5578889999999999988774 PP

>> Fer4_24  Ferredoxin I 4Fe-4S cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.07        19      19      35 .]     729     745 ..     727     745 .. 0.90
   2 ?    6.5   0.5     0.037        10      16      34 ..     767     785 ..     761     786 .. 0.88
   3 ?    2.3   0.1       0.8   2.1e+02      19      34 ..     812     827 ..     810     828 .. 0.85
   4 ?    1.4   0.0       1.5   3.9e+02      18      33 ..     846     861 ..     841     863 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.07
                           Fer4_24  19 SiegvmskIdavesKLe 35 
                                       + + + s +d+v sKL+
  gi|320101450|ref|YP_004177042.1| 729 VVNNIKSAVDTVNSKLD 745
                                       678899**********7 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.037
                           Fer4_24  16 LErSiegvmskIdavesKL 34 
                                       L +S ++v sk d+v s L
  gi|320101450|ref|YP_004177042.1| 767 LSTSVSSVVSKLDSVTSQL 785
                                       779*************988 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.8
                           Fer4_24  19 SiegvmskIdavesKL 34 
                                         +gv sk+d v s L
  gi|320101450|ref|YP_004177042.1| 812 AVSGVASKVDNVASTL 827
                                       579********99866 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 1.5
                           Fer4_24  18 rSiegvmskIdavesK 33 
                                         +++v  k+d+  sK
  gi|320101450|ref|YP_004177042.1| 846 NTLNTVSGKVDTAISK 861
                                       579*********9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (904 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1157  (0.0645323); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                       154  (0.00858944); expected 17.9 (0.001)
Passed Fwd filter:                        73  (0.00407162); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              67  [number of targets reported over threshold]
# CPU time: 1.20u 0.35s 00:00:01.54 Elapsed: 00:00:00.46
# Mc/sec: 5912.06
//
Query:       gi|320101451|ref|YP_004177043.1|  [L=1291]
Description: peptidase S8 and S53 subtilisin kexin sedolisin [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-35  120.6   0.0      2e-34  119.3   0.0    1.6  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.0   1.1e-38     2e-34       1     298 []     177     652 ..     177     657 .. 0.78

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 1.1e-38
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag..................................... 40 
                                       g+gv+vav+DtGvd++hp l++++        + +    +                                     
  gi|320101451|ref|YP_004177043.1| 177 GSGVTVAVVDTGVDYGHPNLQNKLIY---W--TGE--YMDaygnlvniteplvldadesqvilfqgytadssgyini 246
                                       79*******************55333...2..111..1113446777889999888888888888777777777777 PP

                                       .........................................................................GGEE CS
                                       .........................................................................xxxx RF
                      Peptidase_S8  41 .........................................................................fnga 44 
                                                                                                                fn++
  gi|320101451|ref|YP_004177043.1| 247 paetvfqvitpsmvnltlttsrslyvgnipsasgvykvgltylslpgvsgavvrfvlladpdtpgvytklyidFNRN 323
                                       77777777777777777777777777777777777777777777777777777777777777777666666664444 PP

                                       TT-SS-TT-SC-S......................................................SS....HHHH CS
                                       xxxxxxxxxxxxx......................................................xxxxxxxxxx RF
                      Peptidase_S8  45 dsettstnwardd......................................................ngnsieHGth 67 
                                       +  t s++ +++                                                       ng    HGt 
  gi|320101451|ref|YP_004177043.1| 324 NVFTDSVDMSASYngsrllvspsqanpsysfgiaggfffdlgwwfgsgrflpgwdlqgnymsifydfNG----HGTA 396
                                       444444443333378888999999999999999999999999999999999999886665555554455....**** PP

                                       HHHHHH-B...SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHH.........HHHHHHCT-SEEEE-EE.... CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxx.... RF
                      Peptidase_S8  68 vAGiaaan.apeegekngvapgakilsvkvldtsggsmetgtelira.........ieeaaedkvdvinmslg.... 130
                                       +A+ +a+    + g  +g+apgak+++vk l   +  +++   l++a         +++    k+dvi++s+g    
  gi|320101451|ref|YP_004177043.1| 397 CASAVAGEdVLYGGLLEGIAPGAKVIGVKSL---WMGNTELGMLWAAgfdvdpnglLYYTGSRKADVISNSWGissf 470
                                       ********8899999***********99988...44443334555557788888888888888999*******7776 PP

                                       ....SCETTCHHCHHHHHH.........HHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES CS
                                       ....xxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 131 ....estslpktgrsieal.........ainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt 194
                                            ++  + t+     +         +++ a    g+++v +aGN g          +v +p+++ +vitvga t
  gi|320101451|ref|YP_004177043.1| 471 iydiSGFGYDFTS-----IlenglvtpgFLDPAF--PGIVIVQAAGNGG------GGYGTVTAPGSAAGVITVGAST 534
                                       6554333333333.....1444577776666666..6************......7899****************** PP

                                       ..............TTSSB-TT--B-TT.......-EEEE-S-....CCCCCCCCCHHHTTTHHEEEE-SHHHCHHH CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 195 ..............tegkiapfSsrGpssdgklkpdivapGgn....ivstwsrqsnnsaglssyqsmsGTSmAsPn 253
                                                     t ++i ++S rGp+ +g lkpd+v  G+     +v  w+r +        y+ + GTS A+P+
  gi|320101451|ref|YP_004177043.1| 535 swwpyyylygyadiTYDQIISWSARGPTPAGYLKPDVVNVGAFgftaSVIGWNRPK--------YTVFGGTSYATPL 603
                                       *****************************************988866777777777........************* PP

                                       HHHHHHHHHHHHTT........--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 254 aagaaAlllsalpk........ltpetvraallntAqdlgkadniesfaqGaG 298
                                        ag++Alll al +         +p tv+++l+ntA+ l    n+ +  qGaG
  gi|320101451|ref|YP_004177043.1| 604 TAGSIALLLGALMEklgdagryTSPFTVKQILMNTADFL----NYPPLDQGAG 652
                                       **********88777999999889999*********766....5667777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.40
# Mc/sec: 9713.73
//
Query:       gi|320101452|ref|YP_004177044.1|  [L=195]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   12.7   0.1       0.43   10.6   0.0    2.1  2  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.4e-05      0.43      20      41 ..      23      44 ..       5      45 .. 0.83
   2 ?   -1.4   0.0      0.13   2.4e+03      10      22 ..      86      99 ..      80     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.4e-05
                             RHH_3 20 LSekTrIprSklldeAiellLe 41
                                      +Se+ + p S l+++A+  lL+
  gi|320101452|ref|YP_004177044.1| 23 VSERYGMPYSVLIEKALGGLLR 44
                                      79***************99997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.13
                             RHH_3 10 dpela.ekLkaLSe 22
                                      d+el+ + L+++S+
  gi|320101452|ref|YP_004177044.1| 86 DEELFtQLLDEVSR 99
                                      66665256788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1443.65
//
Query:       gi|320101453|ref|YP_004177045.1|  [L=167]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-05   22.9   0.8    0.00026   20.8   0.1    2.2  2  RHH_1           Ribbon-helix-helix protein, copG family
     0.0067   16.9   0.0      0.015   15.8   0.0    1.6  2  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys
  ------ inclusion threshold ------
      0.017   15.1   0.3      0.031   14.2   0.3    1.4  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 !   20.8   0.1   4.4e-08   0.00026       3      35 ..       7      39 ..       7      42 .. 0.93
   2 ?   -0.1   0.0      0.17     1e+03      10      26 ..     136     152 ..     132     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-08
                                      EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                             RHH_1  3 sirldeellerLdelarrrgrSrSelIReAlre 35
                                      +i +d+e++e+L e a+rrg S S  +R+++ e
  gi|320101453|ref|YP_004177045.1|  7 TIGVDAEYVEALKEVAKRRGTSISSYMRQLIDE 39
                                      6779**************************987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHTSSHH CS
                             RHH_1  10 llerLdelarrrgrSrS 26 
                                       +l++++ +a+  g S S
  gi|320101453|ref|YP_004177045.1| 136 MLHLIRGMAKGAGLSIS 152
                                       78899999*****9988 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.6e-06     0.015      39      78 ..       2      39 ..       1      40 [. 0.90
   2 ?   -3.0   0.0       1.9   1.1e+04      50      69 ..     133     152 ..     132     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                    CopG_antitoxin 39 kkktksislrlpedlLealkekAnkrdvpyqslikellee 78
                                      +k+ k+i   ++++ +ealke A++r+ +++s++++l+ e
  gi|320101453|ref|YP_004177045.1|  2 RKSRKTI--GVDAEYVEALKEVAKRRGTSISSYMRQLIDE 39
                                      6777888..89************************99875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                    CopG_antitoxin  50 pedlLealkekAnkrdvpyq 69 
                                        + +L  ++  A+  +++++
  gi|320101453|ref|YP_004177045.1| 133 KSRMLHLIRGMAKGAGLSIS 152
                                       67899999999998888776 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   5.2e-06     0.031       2      41 ..       3      42 ..       2      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-06
                             RHH_3  2 ktrttvsidpelaekLkaLSekTrIprSklldeAiellLe 41
                                      k r t+ +d e++e Lk++ ++ +  +S + ++ i+++L+
  gi|320101453|ref|YP_004177045.1|  3 KSRKTIGVDAEYVEALKEVAKRRGTSISSYMRQLIDEVLR 42
                                      7788999******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1291.12
//
Query:       gi|320101454|ref|YP_004177046.1|  [L=209]
Description: proteasome endopeptidase complex subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for 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  175.5   0.0    9.9e-52  175.2   0.0    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.2   0.0   5.5e-56   9.9e-52       5     190 .]       8     186 ..       6     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 5.5e-56
                                       -EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                        Proteasome   5 ttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                       +t++G+k+++gvvlaa+kr+++   +ls++ ++Ki+ ++dh+gv+faGl +D+  lv+ +r ea++y+l++gr+i+ 
  gi|320101454|ref|YP_004177046.1|   8 GTAIGLKTSEGVVLAAEKRLSYDGFVLSRN-ARKIHMVTDHVGVGFAGLMGDVGFLVKVLRLEAKNYELQHGREIRA 83 
                                       69************************9999.7********************************************* PP

                                       HHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTB CS
                        Proteasome  82 erlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedl 158
                                       +    ++a++l+  +++++  p + +++++g+d+eg p+Ly +dp Gs+ieek +va+Gsg++ a +++e +y++ +
  gi|320101454|ref|YP_004177046.1|  84 R----SMAKLLSLILYNYKLAPMLTEVVVGGFDDEG-PSLYILDPVGSLIEEK-YVAVGSGAQLALGYIEPRYSPSI 154
                                       *....999999999999999*************888.***************8.*********************** PP

                                       SHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 159 tleeavelavkalkealerdklsgknievavi 190
                                       tl ea+elav+a++ ++erd+lsg++i++a+i
  gi|320101454|ref|YP_004177046.1| 155 TLAEAEELAVNAIRTVVERDVLSGDGIDLATI 186
                                       *****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 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:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1651.99
//
Query:       gi|320101455|ref|YP_004177047.1|  [L=265]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   0.1       0.51   10.9   0.0    2.0  2  SKICH     SKICH domain


Domain annotation for each model (and alignments):
>> SKICH  SKICH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.9e-05      0.51      13      39 ..      57      83 ..      49      90 .. 0.84
   2 ?   -1.9   0.0      0.28   5.1e+03      93     102 ..     246     255 ..     230     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.9e-05
                             SKICH 13 dedvvvsYtltkdfkpsskDwiGlfkv 39
                                      + d+ ++ ++  d+  +++DwiG+fkv
  gi|320101455|ref|YP_004177047.1| 57 GGDLYMRLKVYGDVDLRDTDWIGVFKV 83
                                      557778889999999***********9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.28
                             SKICH  93 svlGvsepFq 102
                                       s++G+s+ F+
  gi|320101455|ref|YP_004177047.1| 246 SIVGASQRFT 255
                                       7999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1985.43
//
Query:       gi|320101456|ref|YP_004177048.1|  [L=338]
Description: small GTP-binding protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-21   76.3   0.0    2.8e-21   75.7   0.0    1.3  1  MMR_HSR1      50S ribosome-binding GTPase
    1.4e-17   63.2   0.0    2.7e-17   62.3   0.0    1.5  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
    6.9e-13   48.4   0.0    9.7e-13   47.9   0.0    1.2  1  FeoB_N        Ferrous iron transport protein B
    2.2e-05   24.1   0.1     0.0018   17.9   0.1    2.6  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    5.5e-05   23.3   0.2       0.04   14.0   0.0    2.2  2  Dynamin_N     Dynamin family
     0.0011   18.9   1.0        1.5    8.7   0.0    2.8  2  RsgA_GTPase   RsgA GTPase
     0.0044   17.0   0.0     0.0073   16.3   0.0    1.3  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0046   16.4   0.0     0.0065   15.9   0.0    1.3  1  SRPRB         Signal recognition particle receptor beta subun
  ------ inclusion threshold ------
      0.012   15.2   0.1       0.61    9.6   0.1    2.1  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.012   15.2   0.0      0.042   13.5   0.0    1.8  1  Ras           Ras family
      0.059   12.7   0.0       0.08   12.3   0.0    1.2  1  Gtr1_RagA     Gtr1/RagA G protein conserved region
      0.059   13.9   0.0       0.13   12.8   0.0    1.7  1  AAA_18        AAA domain
      0.071   13.0   0.4       0.33   10.8   0.0    2.1  2  NTPase_1      NTPase
      0.086   12.3   0.0        1.4    8.3   0.0    2.2  2  Arf           ADP-ribosylation factor family
      0.089   12.8   0.0       0.26   11.3   0.0    1.8  2  AAA_14        AAA domain
      0.099   12.8   0.1       0.24   11.6   0.1    1.6  1  KN17_SH3      KN17 SH3-like C-terminal domain
        0.1   11.5   0.0       0.21   10.6   0.0    1.4  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.11   12.2   0.0        0.2   11.4   0.0    1.4  1  AAA_24        AAA domain
       0.23   11.7   0.0        4.8    7.4   0.0    2.2  2  Roc           Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   2.9e-24   2.8e-21       1     114 []     163     284 ..     163     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 2.9e-24
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSS..HHHHHHHHHHHHHHHH CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.keielvDtpGlie..gaseekglgkaflale 74 
                                       +v+i+G p vGKStL+++lt+++  ++++p+tTr+i+ g++++++  +i+l+D pG+++   ++++  +++a+lal+
  gi|320101456|ref|YP_004177048.1| 163 RVVIAGVPQVGKSTLLSKLTRARPVIGSYPFTTRNIIVGHIDVDEaGRIVLIDSPGILDtpLEEKNIVEKRAVLALK 239
                                       699***************************************888899********876323344448899999988 PP

                                       C.TSEEEEEEETT....TTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
                          MMR_HSR1  75 e.adlillvvdas....eeklkpldeeleellee..akkplilvlnk 114
                                         ad++l+v+da+      +l+++ + + e+ ++  ++kp++lv+nk
  gi|320101456|ref|YP_004177048.1| 240 HlADHLLFVIDANpsfyY-SLEEQLR-VLETARRlvEGKPVTLVVNK 284
                                       889********9954431.2333322.2333333789*********8 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 !   62.3   0.0   2.8e-20   2.7e-17       2      58 .]     230     286 ..     229     286 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.8e-20
                              NOG1   2 IEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       +Ek+A++ALkhlad  lF++D+ ++ +ysleeQl++le+ + l++ kpv  v+nK+D
  gi|320101456|ref|YP_004177048.1| 230 VEKRAVLALKHLADHLLFVIDANPSFYYSLEEQLRVLETARRLVEGKPVTLVVNKVD 286
                                       7*******************************************************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 !   47.9   0.0     1e-15   9.7e-13       2     154 ..     163     324 ..     162     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1e-15
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT.EEEEEEE----SSSSSSSHHHHHHHHHHH.. CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg.keveivDlPGiYslsayseeekvardfll.. 75 
                                       +v+++G p vGk+tl+ +lt a+  +g +p +t +   g++++++  ++ ++D PGi +  +  e + v ++ +l  
  gi|320101456|ref|YP_004177048.1| 163 RVVIAGVPQVGKSTLLSKLTRARPVIGSYPFTTRNIIVGHIDVDEaGRIVLIDSPGILDT-PLEEKNIVEKRAVLal 238
                                       689***************************************998789*********874.4444444554444434 PP

                                       CTSSSEEEEEEEGG.....GHHHHHHH..HHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTT CS
                            FeoB_N  76 eeepdvvvnvvdat.....nlernLyL..tlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakk 145
                                       ++ +d ++ v+da+     +le +L +  t++ l  g+pv l++n++d + k+ +e  ++++++k g++ +++sa  
  gi|320101456|ref|YP_004177048.1| 239 KHLADHLLFVIDANpsfyySLEEQLRVleTARRLVEGKPVTLVVNKVDSLPKELVEEVVESVESKTGLKPIPVSALL 315
                                       6779*********7444446888887622333344489*************************************98 PP

                                       TBTHHHHHH CS
                            FeoB_N 146 kegieellk 154
                                       + +++ l++
  gi|320101456|ref|YP_004177048.1| 316 GVNLDFLRE 324
                                       888877765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.9e-06    0.0018      91     187 ..     239     325 ..     162     332 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                                       HHT-SEEEEEEETTTBSTHHHHHHHHHHHH.....TTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  91 lrvlDgavlvvdaveGvepqteevlrlalk.....egvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekyg 161
                                          +D  ++v+da+       ee lr++ +     eg p+ +++NK+D l k+ ++e+ve v++k            
  gi|320101456|ref|YP_004177048.1| 239 KHLADHLLFVIDANPSFYYSLEEQLRVLETarrlvEGKPVTLVVNKVDSLpKELVEEVVESVESKT----------- 304
                                       46799*********99888888877777662222245669**********5555667777777665........... PP

                                       HTTTTTEEEEEEBTTTTBTHHHHHHH CS
                          GTP_EFTU 162 ekgekevpvvfgSalkgegvktllea 187
                                              + +++Sal g +++ l e 
  gi|320101456|ref|YP_004177048.1| 305 -----GLKPIPVSALLGVNLDFLREE 325
                                       .....234466666666666555555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1     0.004       3.7       1      38 [.     164     200 ..     164     209 .. 0.77
   2 !   14.0   0.0   4.2e-05      0.04     102     151 ..     210     264 ..     203     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEE CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplel 38 
                                       +++ G    GKS++l +L++++  ++g+ p T r +++
  gi|320101456|ref|YP_004177048.1| 164 VVIAGVPQVGKSTLLSKLTRAR-PVIGSYPFTTRNIIV 200
                                       677888899*************.667777655555444 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.2e-05
                                       SEEEEE---B-SSSGTTSHHHHH....HH.STTEEEEEEEETTS-CCC-CHHHHH CS
                         Dynamin_N 102 gltlvDlPGldsvnkrdqelvke....yi.kkadiilavtsanhdlsnsealfla 151
                                       +++l+D+PG+ +++ +++++v++    ++ + ad +l+v +an ++  s  ++l+
  gi|320101456|ref|YP_004177048.1| 210 RIVLIDSPGILDTPLEEKNIVEKravlALkHLADHLLFVIDANPSFYYSLEEQLR 264
                                       799***************777764443466889***********99877555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.2    0.0032         3      99     122 ..     161     184 ..     134     225 .. 0.72
   2 !    8.7   0.0    0.0016       1.5      37      98 ..     264     327 ..     229     332 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                                       TSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpe 122
                                       d  +v++G   vGKStL+ +l+  
  gi|320101456|ref|YP_004177048.1| 161 DYRVVIAGVPQVGKSTLLSKLTRA 184
                                       4668999************99875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                                       HHHHHHHH..TT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  37 rfLvlaee..kgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellk 98 
                                       r+L +a +  +g ++++v+nK+D l +e   e +++  +++g++++ vsa  + +l+ l+e+l 
  gi|320101456|ref|YP_004177048.1| 264 RVLETARRlvEGKPVTLVVNKVDSLPKELVEEVVESVESKTGLKPIPVSALLGVNLDFLREELV 327
                                       4444443221456899************9444455556789********999999999998875 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 !   16.3   0.0   7.8e-06    0.0073      56     101 ..     276     327 ..     257     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.8e-06
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare......pnsvviSaekelnldeLkekiw 101
                                       +p+ +v+NK+D++ +e ++e+ +        + +++Sa  ++nld L e++ 
  gi|320101456|ref|YP_004177048.1| 276 KPVTLVVNKVDSLPKELVEEVVESvesktgLKPIPVSALLGVNLDFLREELV 327
                                       57889*******999999988885556555599**************99875 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.9e-06    0.0065       5      85 ..     163     251 ..     159     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.9e-06
                                       EEEEE-STTSSHHHHHHHHHHS.S---B---S.S-EEETTG...GGTT-SEEEETT..-GCCSHH.HHHH..HHHHG CS
                             SRPRB   5 avllvGlsdsGKTslftrLttd.svkktvtSq.essaalkvksekgskltliDfPG..heklrqk.llek..lkaks 74 
                                       +v+++G+ + GK +l+ +Lt    v  ++     + ++ +++ ++  ++ liD PG  +  l  k ++ek  ++a +
  gi|320101456|ref|YP_004177048.1| 163 RVVIAGVPQVGKSTLLSKLTRArPVIGSYPFTtRNIIVGHIDVDEAGRIVLIDSPGilDTPLEEKnIVEKraVLALK 239
                                       79******************995344444433489999999999999*********333344433244431122223 PP

                                       G.EEEEEEEEET CS
                             SRPRB  75 s.lkglvfvvDS 85 
                                       + +  l+fv+D+
  gi|320101456|ref|YP_004177048.1| 240 HlADHLLFVIDA 251
                                       335667888885 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 ?    3.5   0.0      0.05        47       3      23 ..     164     184 ..     162     188 .. 0.88
   2 ?    9.6   0.1   0.00065      0.61      83     167 ..     209     301 ..     193     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.05
                                       EEEEESTTCCHHHHHHHHHCT CS
                              cobW   3 tvltGflGsGKTtLlnhllen 23 
                                       +v++G +  GK+tLl++l++ 
  gi|320101456|ref|YP_004177048.1| 164 VVIAGVPQVGKSTLLSKLTRA 184
                                       6899*************9875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00065
                                       -SEEEEEECT.TTTHHHH..HTT.SHHHHHCCCECEEEEEEETTTH.....CCHCCHHHHHHHHHH.TSSEEEEE-H CS
                              cobW  83 ldviliEttG.laePapv..aft.eeelksdltldavvavvDaknl....eaeeekieekaedqla.aadllvlnKt 150
                                         ++li + G l +P +   +++    l+ +  +d++++v+Da+       +e+ +  e+a++ ++ +  +lv+nK+
  gi|320101456|ref|YP_004177048.1| 209 GRIVLIDSPGiLDTPLEEknIVEkRAVLALKHLADHLLFVIDANPSfyysLEEQLRVLETARRLVEgKPVTLVVNKV 285
                                       6788999999666777767655535556669999*********77689875555566666666665245679***** PP

                                       HHHCHC..HHHHHHHHH CS
                              cobW 151 Dlldeeallekleerlr 167
                                       D l++e l+e++ e ++
  gi|320101456|ref|YP_004177048.1| 286 DSLPKE-LVEEVVESVE 301
                                       *****9.5455555544 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.4e-05     0.042       1     159 [.     163     329 ..     163     332 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                                       EEEEEESTTSSHHHHHHHHHHSSCSS.SCTTTSSEEEEEEEEEET..TEEEEEE...EEEETTSGGGHHHHHHHHT. CS
                               Ras   1 KlvlvGdsavGKtslllrfvkdkFke.eyesTigvdfytkeievd..gkevkle...iwDTAGqeefkslrelyyr. 70 
                                       ++v+ G  +vGK++ll + ++ +    +y  T   +  + +i+vd  g+ v ++   i+DT   e+    +++++  
  gi|320101456|ref|YP_004177048.1| 163 RVVIAGVPQVGKSTLLSKLTRARPVIgSYPFTT-RNIIVGHIDVDeaGRIVLIDspgILDTPLEEKNIVEKRAVLAl 238
                                       589999**************9986651555565.9999999999965555655445599999888765555444441 PP

                                       TESEEEEEEETTBHHHHH.THHHHHHHHHHHST..TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTT CS
                               Ras  71 daegillvyditsresfe.nvkkwveeikrvae..envpivLvGnKvDleekravsteegeelakelglkfletSAk 144
                                       +  +  l++ i+ + sf  ++++ ++ +++  +  e  p+ Lv nKvD   k+ v +e +e++ +++glk + +SA 
  gi|320101456|ref|YP_004177048.1| 239 KHLADHLLFVIDANPSFYySLEEQLRVLETARRlvEGKPVTLVVNKVDSLPKELV-EEVVESVESKTGLKPIPVSAL 314
                                       44455788999999998624555555444444466789**********9986666.577899999999********* PP

                                       TTCTHHHHHHHHHHH CS
                               Ras 145 tnenveeafeellre 159
                                          n++ + eel+++
  gi|320101456|ref|YP_004177048.1| 315 LGVNLDFLREELVKA 329
                                       *99998877777765 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.5e-05      0.08      77     139 ..     242     303 ..     166     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.5e-05
                         Gtr1_RagA  77 vgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereeifeerkee 139
                                        + l++V+D++  ++  +le+  ++le++r+  +   v   ++K+D + ++  ee++e+ +++
  gi|320101456|ref|YP_004177048.1| 242 ADHLLFVIDAN-PSFYYSLEEQLRVLETARRLVEGKPVTLVVNKVDSLPKELVEEVVESVESK 303
                                       4589*******.778899999999******************************999988765 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   0.00014      0.13       1      22 [.     164     185 ..     164     282 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       ++++G+p vGK+tl   L +  
  gi|320101456|ref|YP_004177048.1| 164 VVIAGVPQVGKSTLLSKLTRAR 185
                                       79****************7763 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00035      0.33       1      21 [.     163     183 ..     163     191 .. 0.91
   2 ?   -0.2   0.1      0.89   8.4e+02     117     147 ..     268     299 ..     225     305 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                                       EEEEE--TTSSHHHHHHHHHH CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvle 21 
                                       +v+i G p+vGK+Tl++k+++
  gi|320101456|ref|YP_004177048.1| 163 RVVIAGVPQVGKSTLLSKLTR 183
                                       689***************976 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.89
                                       HHHHHHTTTSEEEEE--SS-.-SHHHHHHHT- CS
                          NTPase_1 117 aveevLksekpvlavihrrk.dlalveeirer 147
                                       + +++++ +++ l+v ++ + +++lvee+ e+
  gi|320101456|ref|YP_004177048.1| 268 TARRLVEGKPVTLVVNKVDSlPKELVEEVVES 299
                                       33455555555555555555777888887765 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0015       1.4      12      38 ..     159     185 ..     149     206 .. 0.82
   2 ?    1.6   0.0      0.17   1.6e+02      83     140 ..     243     300 ..     239     328 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                                       TTEEEEEEEESTTSSHHHHHHHHHHSS CS
                               Arf  12 kkelrilllGLDnaGKtTilkklklee 38 
                                       + ++r+++ G  + GK+T+l kl+  +
  gi|320101456|ref|YP_004177048.1| 159 SGDYRVVIAGVPQVGKSTLLSKLTRAR 185
                                       5689*******************8765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                                       SEEEEEEETT-CTTHHHHHHHHHHHCTSGCCT.TSEEEEEEE-TTSTTSS-HHHHHHHT CS
                               Arf  83 davifvvDsadreRleeakeeLkalleeeelk.evallvlaNKqDlpealseeelrell 140
                                       d ++fv+D++ +    + +e+L+ l + ++l    ++ ++ NK D       ee+ e++
  gi|320101456|ref|YP_004177048.1| 243 DHLLFVIDANPSF-YYSLEEQLRVLETARRLVeGKPVTLVVNKVDSLPKELVEEVVESV 300
                                       6789999987654.455667777776666654267888889**9965444444444433 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.26       5      27 ..     164     186 ..     161     230 .. 0.85
   2 ?   -2.0   0.0       3.7   3.5e+03      19      42 ..     238     263 ..     234     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                            AAA_14   5 lvitGaRrvGKTtllkqlikell 27 
                                       +vi G+ +vGK+tll +l + + 
  gi|320101456|ref|YP_004177048.1| 164 VVIAGVPQVGKSTLLSKLTRARP 186
                                       79**************9987665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                            AAA_14  19 lkqlikell..vkkesilyinldder 42 
                                       lk+l+++ll  ++++  +y++l+++ 
  gi|320101456|ref|YP_004177048.1| 238 LKHLADHLLfvIDANPSFYYSLEEQL 263
                                       67777777788888889999988754 PP

>> KN17_SH3  KN17 SH3-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00025      0.24      24      43 ..     134     153 ..     127     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                          KN17_SH3  24 yykkKgvvekvedeyvAevk 43 
                                       +yk+K++v+ +  +yvAev 
  gi|320101456|ref|YP_004177048.1| 134 LYKRKARVIGLVKKYVAEVS 153
                                       8*****************96 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00022      0.21      30      51 ..     162     183 ..     144     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                                       EEEEEEE-TTSSHHHHHHHHHH CS
                              MeaB  30 qvvGltGvPGaGkstlvealgl 51 
                                        +v + GvP +Gkstl+++l+ 
  gi|320101456|ref|YP_004177048.1| 162 YRVVIAGVPQVGKSTLLSKLTR 183
                                       5788***************985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021       0.2       3      26 ..     162     186 ..     160     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                            AAA_24   3 lkiliyGpsgiGKTtlakel.gpkp 26 
                                       ++++i G + +GK+tl+++l   +p
  gi|320101456|ref|YP_004177048.1| 162 YRVVIAGVPQVGKSTLLSKLtRARP 186
                                       89*****************965555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0051       4.8       1      21 [.     163     183 ..     163     198 .. 0.91
   2 ?    2.0   0.0      0.25   2.4e+02      98     119 ..     265     286 ..     239     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0051
                                       EEEEESSTTSSHHHHHHCHCT CS
                               Roc   1 KvvlvGdsgvGKtsllkrfve 21 
                                       +vv+ G  +vGK++ll+++++
  gi|320101456|ref|YP_004177048.1| 163 RVVIAGVPQVGKSTLLSKLTR 183
                                       6899*************9986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.25
                                       HHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  98 WlkelkkvagkspvilvgnkiD 119
                                        l+  ++ ++ +pv lv+nk+D
  gi|320101456|ref|YP_004177048.1| 265 VLETARRLVEGKPVTLVVNKVD 286
                                       455566678899*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2310.18
//
Query:       gi|320101457|ref|YP_004177049.1|  [L=357]
Description: RNA 3'-phosphate cyclase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-80  268.8   0.0    3.1e-80  268.5   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    2.1e-21   76.4   0.0    3.2e-21   75.8   0.0    1.3  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 !  268.5   0.0   3.5e-84   3.1e-80       1     216 [.      10     331 ..      10     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 268.5 bits;  conditional E-value: 3.5e-84
                                       STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikage 77 
                                       +gegGgqiLR alaLs lt +pvrI+nIRa+R++PGLr+qhltav++l+k+t+aeve ae+gste+ FkP+e ++g 
  gi|320101457|ref|YP_004177049.1|  10 IGEGGGQILRYALALSSLTLRPVRIYNIRAKRDNPGLRPQHLTAVEALRKVTGAEVEKAEVGSTEIVFKPTERRSGA 86 
                                       58*********************************************************************9***** PP

                                       EEEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  78 yevdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkG 154
                                       +e+digtAGsi+l+lq+llp+l+f +++s+++lkGgTnv+++p++dy+ +v+l  ++++g +e+++++ +rG+ypkG
  gi|320101457|ref|YP_004177049.1|  87 MEIDIGTAGSISLVLQALLPVLVFGERDSRIRLKGGTNVPWSPPIDYISHVFLYNVRHMG-VEAKVSVARRGHYPKG 162
                                       ************************************************************.7*************** PP

                                       -EEEEEEEE-.-S.---EB.......................................................... CS
                                       xxxxxxxxxxxxx.xxxxx.......................................................... RF
                               RTC 155 gGevelevepskk.lkpie.......................................................... 172
                                       gG v +ev+  k+ lkp+                                                           
  gi|320101457|ref|YP_004177049.1| 163 GGVVDVEVRHLKEpLKPVMivkrgritgftihsycvklphhvavrqlesarstlarvfgekidgsietyppdrdphl 239
                                       ********988877****9********************************************************** PP

                                       ................................................BSS-HHHHHHHHHHHHHHT.-EEEEESS- CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 ................................................acvDehlqdqlilfmaLakgksrirvael 201
                                                                                       +++D+h+ d+li++m La+g sri v+++
  gi|320101457|ref|YP_004177049.1| 240 gpgsgvlvyaeaepgvrlgsdslgekgkpaekvgeeaalrlieeletgMAFDRHMGDMLIPYMFLARGVSRIGVSRI 316
                                       ***************************************************************************** PP

                                       -HHHHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxx RF
                               RTC 202 tlhtetairvieqfl 216
                                       tlh+ tai+v + f+
  gi|320101457|ref|YP_004177049.1| 317 TLHLLTAIEVGKLFF 331
                                       **********99987 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 !   75.8   0.0   3.6e-25   3.2e-21       1     103 []     183     285 ..     183     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 3.6e-25
                                       -S----SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSS.EEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEE CS
                        RTC_insert   1 vdrGrvkrirGvafaarvspsvanrmveaargvLnkllp.dvyiytdvvkegkesgkspGfgisLvaetttegvllg 76 
                                       v+rGr+   ++ +++++++ +va r++e+ar+ L + +  +++  ++++   ++ + +pG+g+++ ae +  gv+lg
  gi|320101457|ref|YP_004177049.1| 183 VKRGRITGFTIHSYCVKLPHHVAVRQLESARSTLARVFGeKIDGSIETYPPDRDPHLGPGSGVLVYAEAE-PGVRLG 258
                                       589*******************************99865599999999999999***************9.6***** PP

                                       EEEEE-TT--HHHHHHHHHHHHHHHHH CS
                        RTC_insert  77 aealgekgvppedvGeeaaeeLleeie 103
                                       +++lgekg+p+e+vGeeaa +L+ee+e
  gi|320101457|ref|YP_004177049.1| 259 SDSLGEKGKPAEKVGEEAALRLIEELE 285
                                       ************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2369.35
//
Query:       gi|320101458|ref|YP_004177050.1|  [L=177]
Description: cytidyltransferase-like domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for 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   51.7   0.0    5.7e-13   49.3   0.0    2.0  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.014   14.7   0.0       0.88    8.7   0.0    2.0  2  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   6.4e-17   5.7e-13       1      65 [.       5      67 ..       5     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 6.4e-17
                                      EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEE CS
                   CTP_transf_like  1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevi 65
                                      l++G+F+p+H GHl+++e+++++++e ++v + s+++     +++++a eR+eml ++ +++ v+
  gi|320101458|ref|YP_004177050.1|  5 LFPGRFQPFHRGHLAVVERLLEEFDE-IVVVIGSAQEGFTC-RNPFTAGERIEMLTRLFRDEHVF 67
                                      799***********************.9999********88.**************996666644 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   9.9e-05      0.88      10      36 ..      10      35 ..       9      45 .. 0.79
   2 ?    4.1   0.0    0.0025        23     204     236 ..     127     157 ..     118     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 9.9e-05
                       HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvviav 36
                                      + PfH+GHl  +e   e++++ +v+++
  gi|320101458|ref|YP_004177050.1| 10 FQPFHRGHLAVVERLLEEFDE-IVVVI 35
                                      67**************99654.44444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0025
                       HIGH_NTase1 204 aSAtaiRkalkeekkleelkklvPestleilke 236
                                        S t iR+++ e   +ee ++lvP +++e+++e
  gi|320101458|ref|YP_004177050.1| 127 YSGTRIRQLIVEG--SEEWRSLVPYTVAEYMEE 157
                                       699*******776..689*********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1297.53
//
Query:       gi|320101459|ref|YP_004177051.1|  [L=647]
Description: KH-domain/beta-lactamase-domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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   83.6   0.0    2.9e-23   82.2   0.0    1.8  1  Beta-Casp      Beta-Casp domain
    3.8e-19   68.4   4.0      1e-18   67.0   2.3    2.3  2  KH_7           KH domain
    4.6e-17   62.1   0.0    4.3e-15   55.7   0.0    2.2  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    2.2e-15   56.3   0.0    7.4e-15   54.6   0.0    1.9  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.9e-10   41.1   3.3    5.4e-09   36.4   3.3    2.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    5.5e-10   39.1   0.2      2e-09   37.2   0.2    1.8  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.04   13.8   0.0       0.12   12.3   0.0    1.8  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0   1.1e-26   2.9e-23       2     110 .]     429     551 ..     428     551 .. 0.82

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 1.1e-26
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG................E-SHH....HHHH..HH.. CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae................veakslewmeskkeeln.. 60 
                                       qe++++L+e++k ++  +++++iy+ + l++++t+++++y+e                  +   ew++      +  
  gi|320101459|ref|YP_004177051.1| 429 QEIILILNEAMKTGR--IPRMNIYVEG-LVNEVTAIHTQYPEylnrslreaiyngdnpF-T--SEWLKPI----Esg 495
                                       9**********9955..7889******.************9988888888877765531.2..2444444....033 PP

                                       ......HS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  61 ......sskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                              +++p+vi+a+sgml+gG+++++l+ l++d+rn++++vgyqaegTlgrk+
  gi|320101459|ref|YP_004177051.1| 496 varpdiVEDRPSVIIATSGMLTGGPAVDYLRLLAGDERNSLVFVGYQAEGTLGRKI 551
                                       3344455589********************************************97 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   2.3   4.1e-22     1e-18       3      66 ..      11      74 ..       9      76 .. 0.94
   2 ?    0.1   0.0      0.32   8.1e+02       6      21 ..      81      96 ..      80      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 4.1e-22
                              KH_7  3 vleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDps 66
                                      ++ el ++i+e++P+e++++++eFEGP +ViY++n +++ +  dl +++Ak++rkR+viR  p+
  gi|320101459|ref|YP_004177051.1| 11 NKLELLKNIMEEIPAELELSNIEFEGPFIVIYVRNREAIEKYLDLAQNIAKKVRKRVVIRVAPE 74
                                      567899******************************************************9887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.32
                              KH_7  6 elkekieeklPkevki 21
                                      e keki+e +Pk++ +
  gi|320101459|ref|YP_004177051.1| 81 EAKEKIKELAPKDAGV 96
                                      689*********9876 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   1.7e-18   4.3e-15       2     176 ..     206     376 ..     205     387 .. 0.86
   2 ?    4.0   0.0     0.011        29      21      57 ..     586     622 ..     577     630 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.7e-18
                     Lactamase_B_6   2 LeldnvkiLlDvGwdeskvslesalkelekv....iptvdliLLshatlehlGayallyakfksklllnipvyatlp 74 
                                       +e  + k+LlD G +   +++  +  +l +v    ++++d ++++ha l+h+G  ++ly     k++ + pvy t+p
  gi|320101459|ref|YP_004177051.1| 206 VETRESKVLLDLGINTGAIDDPGKAYPLLEVdslrLDELDGVIVTHAHLDHVGLVPVLY-----KYGYRGPVYVTKP 277
                                       6777899********998888777777666444448*****************655555.....46889******** PP

                     Lactamase_B_6  75 vvkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkisk 151
                                       + +L  v+l dl+  ++ +g +    ++ +di+++  + +t+ Y   +++     ++ +t ynaGh lG +i +++ 
  gi|320101459|ref|YP_004177051.1| 278 TRELMIVMLKDLVDVTRRSGRY--IPFSEKDISTMLLHTITVDYDEVTDVAP---DIKLTMYNAGHILGSAIVHLHV 349
                                       *************999998877..478999****************999985...89****************9987 PP

                     Lactamase_B_6 152 ese..kivYavdwnhakeshLngaall 176
                                       ++   +ivY  d+  +  ++Ln+a+++
  gi|320101459|ref|YP_004177051.1| 350 GMGlhNIVYTGDFKYSDSRLLNKANTV 376
                                       65444*****************99864 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.011
                     Lactamase_B_6  21 slesalkelekviptvdliLLshatlehlGayallya 57 
                                       + ++ l++ +++ p+   iLL h +++ l+a++ l++
  gi|320101459|ref|YP_004177051.1| 586 DQRELLEYARDISPRPRRILLNHGEPSALSALSTLLK 622
                                       45679999999*********************98876 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 ?   -3.2   0.0       3.3   8.5e+03      20      37 ..     402     420 ..     401     420 .. 0.86
   2 !   54.6   0.0   2.9e-18   7.4e-15       2      54 ..     569     624 ..     568     633 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.3
                             RMMBL  20 nellelirklkprn.vilv 37 
                                       ++l ++++++  r+ ++l+
  gi|320101459|ref|YP_004177051.1| 402 QGLVDIVKRTAERKgIVLI 420
                                       6899999999999999886 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 2.9e-18
                             RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkee 54 
                                       i++k++++ i+ fSgH+d++elle+ r ++pr+  + l+HGe+ a+sal  llk +
  gi|320101459|ref|YP_004177051.1| 569 IHIKLEVYSIEgFSGHSDQRELLEYARDISPRPrrILLNHGEPSALSALSTLLKGD 624
                                       789**********************************************9999744 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   3.3   2.1e-12   5.4e-09       4     162 ..     199     373 ..     197     404 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.1e-12
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH....HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCE CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal....elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgava 76 
                                       ++ +s+l+e+ ++ +L D G+ t a +       +l    l ++++d vi+TH+HlDH+G ++ l +     +++v 
  gi|320101459|ref|YP_004177051.1| 199 VGRSSILVETRESKVLLDLGINTGAIDDPGkaypLLEVDSLRLDELDGVIVTHAHLDHVGLVPVLYKYGYRGPVYVT 275
                                       56799**********************99999***********************************9999999999 PP

                                       HHHHCCHCHHHHHHHHHCCHH............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEET CS
                       Lactamase_B  77 eeapalfmeeaddaasrkgll............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveyg 141
                                       + +++l   +++d                        + + +d de  +   +     + + ++ g+  +h++v++g
  gi|320101459|ref|YP_004177051.1| 276 KPTRELMIVMLKDLVDVTRRSgryipfsekdisTMLLHTITVDYDEVTDVAPDIKLTMYNAGHILGSAIVHLHVGMG 352
                                       9999988888866555444448899***9955433333333444444444444444444556999999********* PP

                                       TCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 142 ggkvlftGDallagetgridl 162
                                         ++++tGD+ ++ ++++   
  gi|320101459|ref|YP_004177051.1| 353 LHNIVYTGDFKYSDSRLLNKA 373
                                       **********99998887766 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 !   37.2   0.2     8e-13     2e-09      27     165 ..     240     388 ..     213     407 .. 0.80
   2 ?   -1.3   0.0      0.52   1.3e+03     176     200 ..     582     608 ..     565     608 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 8e-13
                                       -..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH...........HCCTTCGHHHCHTT....TTEEEE CS
                     Lactamase_B_2  27 elppidaVllthaHyDHlaglltlrelrpkklplyapkgvla...........vleanfvylaleee....pavnvh 88 
                                       +l+++d+V++thaH DH+  ++ l + ++ + p+y++k +++           v ++++ y+ + e+      +++ 
  gi|320101459|ref|YP_004177051.1| 240 RLDELDGVIVTHAHLDHVGLVPVLYK-YGYRGPVYVTKPTRElmivmlkdlvdVTRRSGRYIPFSEKdistMLLHTI 315
                                       4569**************55566666.44457999999999999998888888889999999888889988888888 PP

                                       EE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH....HHHCT-SEEE CS
                     Lactamase_B_2  89 eldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig....erlggadlll 161
                                       ++d +e ++++ +++++t+  a h  g         ++ l ++ g ++++y+gD +y + ++     + +  ++ l+
  gi|320101459|ref|YP_004177051.1| 316 TVDYDEVTDVA-PDIKLTMYNAGHILGS-------AIVHLHVGMGLHNIVYTGDFKYSDSRLLnkanTVFPRVETLI 384
                                       8899******9.6999999999999999.......899999999999**********99664411114555566777 PP

                                       EE-S CS
                     Lactamase_B_2 162 ldit 165
                                       +++t
  gi|320101459|ref|YP_004177051.1| 385 MEGT 388
                                       6666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
                                       HT---STSHHHHCTTSS..SSEEEEES CS
                     Lactamase_B_2 176 mgHltpeeaveaaadlg..akrlvliH 200
                                        gH++++e +e a+d++  ++r +l H
  gi|320101459|ref|YP_004177051.1| 582 SGHSDQRELLEYARDISprPRRILLNH 608
                                       59**************95556776666 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 ?   12.3   0.0   4.6e-05      0.12       5      51 ..     199     258 ..     197     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-05
                     Lactamase_B_3   5 lghnsflletagarilvDPfkanlgyeppa..............eeaDlvlisqaledHah 51 
                                       +g +s+l+et++ ++l+D +  n+g   ++              +e D v++++a+ dH  
  gi|320101459|ref|YP_004177051.1| 199 VGRSSILVETRESKVLLDLGI-NTGAIDDPgkaypllevdslrlDELDGVIVTHAHLDHVG 258
                                       589***************874.3333333346688888999999***************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4620.39
//
Query:       gi|320101460|ref|YP_004177052.1|  [L=208]
Description: proteasome endopeptidase complex subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-50  169.8   1.0    5.4e-50  169.5   1.0    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.5   1.0     3e-54   5.4e-50       5     190 .]       8     187 ..       5     187 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.5 bits;  conditional E-value: 3e-54
                                       -EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                        Proteasome   5 ttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                       tt+vG+   d+vvlaadkratag +++ k  v+Ki++i+d+ +++++Gl+aDa+++v++ar  a+ y+ ++g+pi+v
  gi|320101460|ref|YP_004177052.1|   8 TTTVGLVVGDYVVLAADKRATAGPMVYHKA-VKKISRITDYAALTISGLVADAQYIVEYARFLARDYEAETGKPISV 83 
                                       8*************************7777.9********************************************* PP

                                       HHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTB CS
                        Proteasome  82 erlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedl 158
                                         l++r++  l++y+ +    pf+v+ll++g d +g  +Ly++d  Gs+++ek ++a+Gsgs +a ++le+ y++dl
  gi|320101460|ref|YP_004177052.1|  84 GALASRISLVLSVYLRYV---PFIVQLLLGGRDHTG-ASLYYMDLYGSVTREK-YMATGSGSPVAFGVLEQGYRSDL 155
                                       ********9999999999...************999.7**************8.*********************** PP

                                       SHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 159 tleeavelavkalkealerdklsgknievavi 190
                                       +leea+ la ka+++a+ rd ++g++++v+vi
  gi|320101460|ref|YP_004177052.1| 156 SLEEAKALAFKAVSSAIMRDGFTGEGVDVVVI 187
                                       ******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1723.33
//
Query:       gi|320101461|ref|YP_004177053.1|  [L=352]
Description: 3-dehydroquinate synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-72  243.0   0.2    4.5e-72  242.7   0.2    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    4.9e-21   75.0   1.3    8.4e-20   70.9   1.3    2.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    3.9e-06   26.2   0.2     0.0031   16.7   0.0    2.9  2  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.7   0.2   7.6e-76   4.5e-72       2     250 .]      15     272 ..      14     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 242.7 bits;  conditional E-value: 7.6e-76
                          Fe-ADH_2   2 igegaleklgellkelelk..kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreket 76 
                                       +g+ga  +++++++       ++ lv++ent++a g+ vee l++ g +v+++  v ++a ++++e++++++ e+++
  gi|320101461|ref|YP_004177053.1|  15 VGPGAAARVRDIVEAVPRGsgRIGLVTGENTYRAGGRLVEEVLSKVG-EVKTW--VIGDAAVSTAERVASEAGEHGV 88 
                                       789**********99964325**********************9997.99877..589******************* PP

                          Fe-ADH_2  77 dlvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrl 153
                                        lvv+vGgG++iD+aky+ +++n+++vsvp a+S+DG+asp+asl+   + ++v  +++P+a+iaD+d++++APrrl
  gi|320101461|ref|YP_004177053.1|  89 SLVVGVGGGRVIDVAKYIGFRNNIHVVSVPLAPSHDGIASPFASLKGASRPTSV-YTRTPYAIIADTDLISRAPRRL 164
                                       *************************************************9**99.799******************* PP

                          Fe-ADH_2 154 lasGvGDllgkytaladwklan........evseplaklsaamvqeaaeklvedkke..tealeellea.lalsgig 219
                                       ++sGvGDllgk++a++dw+la+        e++++la+lsa++v   +e + +  +e  + ++e+l+++ +a++++g
  gi|320101461|ref|YP_004177053.1| 165 ILSGVGDLLGKLVAVKDWRLAHrlkgeyygEYAAQLALLSAKHVLRYHELIGSGSQEgiRILVEALISSgVAMCIAG 241
                                       **********************999999999999**********9999999873332223333444443269***** PP

                          Fe-ADH_2 220 isrpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       +srpaSGsEHl+SHald +a+ +alHGeqV+
  gi|320101461|ref|YP_004177053.1| 242 SSRPASGSEHLFSHALDLIAPGRALHGEQVA 272
                                       *****************************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 !   70.9   1.3   1.4e-23   8.4e-20       1     337 [.      10     311 ..      10     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.4e-23
                                       -SEEEEETTGGGGHHHHHTTT..-..EEEEEEEHHHH.HH..THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHH CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkkl..gakralivtdkgslkks.glldkvlesleeagievtvfdgvepnptleeveeaa 74 
                                       P++++ g+ga++++ + +++   g  r+ +vt+++++++  +l+++vl+++     ev+  + v ++  +++ e++a
  gi|320101461|ref|YP_004177053.1|  10 PSKVIVGPGAAARVRDIVEAVprGSGRIGLVTGENTYRAGgRLVEEVLSKV----GEVK--TWVIGDAAVSTAERVA 80 
                                       89****************99977767*********9954414555555555....3333..568999********** PP

                                       TTS-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTS CS
                            Fe-ADH  75 alareegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeeg 151
                                       + a e+g+ +v++vGGG viD+AK+i +  +                  + ++ +P  ++ +  ++p+a +   ++ 
  gi|320101461|ref|YP_004177053.1|  81 SEAGEHGVSLVVGVGGGRVIDVAKYIGFRNN------------------IHVVSVPLAPSHDGIASPFASLK-GAS- 137
                                       *******************************..................9**********************.333. PP

                                       EEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSS.B--HHHHHHHHHHHHHHHHH CS
                            Fe-ADH 152 eklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsda.laleairliaknleravadg 227
                                       + +s++  + +P+++i D++l+  +P+r++ ++++D l + +     + a+ l    + ++a++l++ + + +++  
  gi|320101461|ref|YP_004177053.1| 138 RPTSVY--TRTPYAIIADTDLISRAPRRLILSGVGDLLGKLVAVKDWRLAHRLKGEyYGEYAAQLALLSAKHVLRYH 212
                                       455555..89*******************************998666766666655455566666666666655554 PP

                                       H.....HHHHHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HH CS
                            Fe-ADH 228 e.....dleareqmllastlaglafsnaglg.....avHalahalgalfgiphglanaillpavlrfnaeaaperla 294
                                       e     + e  + +++a + +g+a+  ag +       H ++hal     +p  +++++ ++ ++          + 
  gi|320101461|ref|YP_004177053.1| 213 EligsgSQEGIRILVEALISSGVAMCIAGSSrpasgSEHLFSHALDL--IAPGRALHGEQVALGT----------I- 276
                                       32222455777778888888888877777766556677777777776..3556666666666666..........1. PP

                                       HHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT- CS
                            Fe-ADH 295 qlaralggesdeeaaeeliealrellkelglptsLselgvdee 337
                                        +   +         +   + ++e ++++glpts ++lg++ e
  gi|320101461|ref|YP_004177053.1| 277 -MMLYI-------HGDPRWRLVKEAMERIGLPTSARQLGFKPE 311
                                       .22221.......234445566666666666666666665554 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.3    0.0015       9.1      25      50 ..      82     107 ..      63     120 .. 0.73
   2 !   16.7   0.0   5.1e-07    0.0031      94     256 ..     146     318 ..     143     323 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0015
                                       HTT--TT-EEEEEESHHHHHHHHHHH CS
                      DHQ_synthase  25 eakleRksllialGGGvvgDlaGfvA 50 
                                       ea+ +  sl++ +GGG v D+a ++ 
  gi|320101461|ref|YP_004177053.1|  82 EAGEHGVSLVVGVGGGRVIDVAKYIG 107
                                       444455689************99974 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.1e-07
                                       --SEEEEEGGGGGGS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC...........TTTHHHHHHHHHHH CS
                      DHQ_synthase  94 qPkavlidlevLktLperelraGlaEvi.Kyalikdeelfelleenaeallk...........eeeeealeeliars 158
                                       +P a+++d+++++  p+r + +G+++++ K  ++kd +l ++l+ +     +                  +eli + 
  gi|320101461|ref|YP_004177053.1| 146 TPYAIIADTDLISRAPRRLILSGVGDLLgKLVAVKDWRLAHRLKGEYYGEYAaqlallsakhvL----RYHELIGSG 218
                                       5888888888888888888888888876688888888888888877655555566676643330....344455444 PP

                                       HHHHHHHHHHCCTTTTGGGG........GGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHH CS
                      DHQ_synthase 159 ievkaevveeDekekglral........LnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeve 227
                                        +   +++ e    +g+ ++            H ++Ha++ ++   + lHGe Va+G ++ +++          + +
  gi|320101461|ref|YP_004177053.1| 219 SQEGIRILVEALISSGVAMCiagssrpaSGSEHLFSHALDLIAPG-RALHGEQVALGTIMMLYIHGD------PRWR 288
                                       44444444444444444333111111115667********99877.**************9999844......4566 PP

                                       HHHHHHHHTT---STTTT..-HHHHHHHHT CS
                      DHQ_synthase 228 rllkllkklglpvslkel.leveellealk 256
                                        +++ ++++glp+s ++l +++ee+++al+
  gi|320101461|ref|YP_004177053.1| 289 LVKEAMERIGLPTSARQLgFKPEEVVKALT 318
                                       789999999999999998788888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2593.56
//
Query:       gi|320101462|ref|YP_004177054.1|  [L=231]
Description: FKBP-type peptidylprolyl isomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-08   33.3   0.1    2.6e-07   30.9   0.1    2.1  2  FKBP_C     FKBP-type peptidyl-prolyl cis-trans isomerase
    9.2e-05   22.5   0.0    0.00042   20.4   0.0    2.0  2  FKBP26_C   FKBP26_C-terminal
  ------ inclusion threshold ------
       0.12   12.3   1.1         15    5.6   0.0    3.5  4  GreA_GreB  Transcription elongation factor, GreA/GreB, C-term


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 !   30.9   0.1   4.3e-11   2.6e-07       6      93 ..       4     148 ..       2     149 .. 0.82
   2 ?   -0.4   0.0      0.25   1.5e+03      48      68 ..     172     192 ..     152     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 4.3e-11
                                       -TTCEEEEEEEEEET.TSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGG CS
                            FKBP_C   6 kegdtVtvhykgkle.dgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippe 68 
                                        +gd++ v+y+ +++  ++++d++          ++    + p  + +G+g + +  ee l +  vG + ++++ppe
  gi|320101462|ref|YP_004177054.1|   4 SKGDFILVEYNVRVKeTNTLLDTTdaelakkeniYEegkVYGPTLIILGRGWLNESVEEELLKHDVGSEVEVEVPPE 80 
                                       689***********9789999999999999999844444888999******************************** PP

                                       GTTTT....................................TTBCTTTB.TT............SEEEEEEEE CS
                            FKBP_C  69 laYge....................................kglaggvippn............atLvFeveL 93 
                                        a+ge                                    k+     i+++            +tLvF+v++
  gi|320101462|ref|YP_004177054.1|  81 KAFGErspdkvktfslrefqrrglsvsvgdvvevegrqgvvKN-----ISGGrvtidfnhplagKTLVFKVKI 148
                                       *****99999999999999999999998888888555444311.....2222555555566666*******98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.25
                                       HHHHHTTSBTT-EEEEEEEGG CS
                            FKBP_C  48 feealegmkvGekrtltippe 68 
                                        e  ++ ++ + k t+tip +
  gi|320101462|ref|YP_004177054.1| 172 SEIEVSLLSDEKKLTVTIPGK 192
                                       455566666667777777754 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.5     3e+03      27      40 ..      70      83 ..      64      89 .. 0.85
   2 !   20.4   0.0     7e-08   0.00042       2      61 ..     156     216 ..     155     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.5
                                      TTEEEEE--TTGGG CS
                          FKBP26_C 27 dktvtIelpeeakF 40
                                      +++v++e+p e +F
  gi|320101462|ref|YP_004177054.1| 70 GSEVEVEVPPEKAF 83
                                      67999***999888 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 7e-08
                                       HHHHHHHHHHH..-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TT CS
                          FKBP26_C   2 kekikelIkry..iPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkriee 61 
                                       +ek+k+l +ry  iP  ++ ++ +  ++k++t+++p +++   ++ ++kl++A+d+++ +++
  gi|320101462|ref|YP_004177054.1| 156 VEKLKALASRYlkIPSSEI-EVSLLSDEKKLTVTIPGKYLSKRDLGYSKLALAADVFDTFKD 216
                                       79********955566663.3555567******************************99976 PP

>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0024        15      49      65 ..      63      79 ..      61      83 .. 0.88
   2 ?    2.5   0.1     0.023   1.4e+02      54      68 ..     107     121 ..     104     125 .. 0.79
   3 ?   -1.7   0.0      0.47   2.8e+03      23      37 ..     144     158 ..     139     161 .. 0.78
   4 ?   -0.6   0.0      0.22   1.3e+03      11      30 ..     173     192 ..     170     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0024
                                      HHTT--TT-EE---BTT CS
                         GreA_GreB 49 aLlgkkvGdevevkaps 65
                                      +Ll++ vG evev++p 
  gi|320101462|ref|YP_004177054.1| 63 ELLKHDVGSEVEVEVPP 79
                                      69*************96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.023
                                       -TT-EE---BTTB-- CS
                         GreA_GreB  54 kvGdevevkapsgki 68 
                                       +vGd+vev+  +g +
  gi|320101462|ref|YP_004177054.1| 107 SVGDVVEVEGRQGVV 121
                                       79******9999854 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.47
                                       EEE----TTT-BS-S CS
                         GreA_GreB  23 etytiVgpdeadpsk 37 
                                       ++++iVg+ e  ++k
  gi|320101462|ref|YP_004177054.1| 144 FKVKIVGKLEDTVEK 158
                                       578999998887765 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.22
                                       EEEEE-.SS--EEEE----T CS
                         GreA_GreB  11 tVtledldtgeeetytiVgp 30 
                                        +++  l+++++ t+ti g+
  gi|320101462|ref|YP_004177054.1| 173 EIEVSLLSDEKKLTVTIPGK 192
                                       56677778999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1820.91
//
Query:       gi|320101463|ref|YP_004177055.1|  [L=157]
Description: PUA domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for 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   67.1   1.6    1.4e-18   66.7   1.6    1.2  1  PUA       PUA domain
    3.9e-08   33.5   0.0    5.5e-08   33.0   0.0    1.2  1  DUF1947   Domain of unknown function (DUF1947)
    0.00091   19.4   0.4     0.0038   17.5   0.1    1.9  2  UPF0113   UPF0113 PUA domain
  ------ inclusion threshold ------
       0.12   12.2   0.7       0.27   11.1   0.2    2.0  2  PUA_3     PUA-like domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   1.6     3e-22   1.4e-18       2      73 ..      75     148 ..      74     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 3e-22
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHC.TSEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakik.ggksveierv 73 
                                        + vd+gAv+a+l ga+L++pG+ve++g f++g+ Va+vd + g+++a+G a+ +se l+    +gk+v++ + 
  gi|320101463|ref|YP_004177055.1|  75 SLLVDKGAVQAVLGGADLMVPGIVEARGGFKAGQLVAVVDAEgGRVIALGTALIDSEALKNGVrKGKAVKVLHR 148
                                       679**************************************889****************9877******9885 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.2e-11   5.5e-08       1      64 [.       2      65 ..       2      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.2e-11
                                      --EE--HHHHHHHHHHHHTTT---TT--...-EEEE-SS-EEEEETTEEEEEE.SSSEEE-HHHHH CS
                           DUF1947  1 kRHfLSkKeakeileklkekyisislesdk.iEieeekkeklYlingvpilfe.eekliPtLklLl 64
                                      kR+ LSkK+++ i  +l++++  ++++ d+ +E        ++l+n+ p+l++ ++ +iP L ++ 
  gi|320101463|ref|YP_004177055.1|  2 KRYPLSKKDRRLITGELQKYG--VQVSDDDvLEYYSDGVNEYILVNKAPALMKhGDLWIPCLNYVS 65
                                      79*****************99..6677776699999999***********************9986 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.25   1.1e+03      14      38 ..      21      44 ..      19      50 .. 0.77
   2 !   17.5   0.1   8.4e-07    0.0038       4      56 ..      78     134 ..      75     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.25
                           UPF0113 14 YGrdvlkesilkit.esvkenqvvvV 38
                                      YG +v  + +l+++ ++v+  ++++V
  gi|320101463|ref|YP_004177055.1| 21 YGVQVSDDDVLEYYsDGVN--EYILV 44
                                      9999999999999955555..55554 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 8.4e-07
                           UPF0113   4 vkekaeklFLYGrdvlkesilkitesvkenqvvvV.lnengeplGiGkirkdt...k 56 
                                       v++ a + +L G d++  +i++ ++++k +q v+V + e g+++++G + +d+   k
  gi|320101463|ref|YP_004177055.1|  78 VDKGAVQAVLGGADLMVPGIVEARGGFKAGQLVAVvDAEGGRVIALGTALIDSealK 134
                                       77788999********************7776665166778********99996542 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.4   6.3e+03       5      18 ..      45      58 ..      42      58 .. 0.70
   2 ?   11.1   0.2     6e-05      0.27      23      50 ..      97     125 ..      76     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                             PUA_3  5 kkaekrlrqGhPwv 18
                                      +ka + +++G +w+
  gi|320101463|ref|YP_004177055.1| 45 NKAPALMKHGDLWI 58
                                      56666788888887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6e-05
                             PUA_3  23 iasvegeledGdvVdvfsek.gkflGtGy 50 
                                       i + +g +++G++V v++++ g+ ++ G 
  gi|320101463|ref|YP_004177055.1|  97 IVEARGGFKAGQLVAVVDAEgGRVIALGT 125
                                       45555689**********65388888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1338.02
//
Query:       gi|320101464|ref|YP_004177056.1|  [L=409]
Description: DNA primase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.4e-08   32.4   0.2    3.4e-07   30.6   0.1    2.0  2  Toprim_4   Toprim domain
    4.2e-06   27.1   0.0    1.1e-05   25.8   0.0    1.7  1  Toprim_2   Toprim-like
    0.00088   19.5   0.1     0.0027   17.9   0.0    1.9  2  Toprim     Toprim domain
  ------ inclusion threshold ------
      0.027   14.1   0.3      0.059   13.0   0.3    1.5  1  Rota_NSP4  Rotavirus non structural protein
       0.11   12.5   2.1       0.14   12.2   0.2    2.0  2  NOG1_N     NOG1 N-terminal helical 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 ?   -2.4   0.0         2   7.1e+03      25      47 ..      78      99 ..      77     114 .. 0.68
   2 !   30.6   0.1   9.5e-11   3.4e-07       2      77 ..     167     230 ..     166     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
                          Toprim_4 25 avlggalspldgirpeklktenl 47
                                      a l   ++++d+++p +  + ++
  gi|320101464|ref|YP_004177056.1| 78 ALLAALIETVDKVGPYDSSI-SV 99
                                      56777889999999988777.44 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 9.5e-11
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlael 77 
                                       e+i+VEg+aDv++l ++g++n++a lgga + ++ i+  +l +          k+ +l++dgD+ G+   +++++ 
  gi|320101464|ref|YP_004177056.1| 167 ELILVEGRADVINLLRYGYTNTIA-LGGARRVPETIK--RLAE---------HKKTTLFVDGDHGGDLIIKEVLRN 230
                                       79**********************.888888999999..8888.........6999**********9999988883 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0     3e-09   1.1e-05       1      80 [.     169     240 ..     169     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3e-09
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvreki 77 
                                       +++Eg  D++ l+++g +   n +algG    ++ +k l+++  kk  l +D D  G+  +k++ + ++   v+ ++
  gi|320101464|ref|YP_004177056.1| 169 ILVEGRADVINLLRYGYT---NTIALGGARRVPETIKRLAEH--KKTTLFVDGDHGGDLIIKEVLRNVK---VDYIA 237
                                       69***************7...*********************..99**************998887774...44455 PP

                          Toprim_2  78 rel 80 
                                       r +
  gi|320101464|ref|YP_004177056.1| 238 RAP 240
                                       554 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.9   6.7e+03      39      58 ..     110     141 ..      77     146 .. 0.58
   2 !   17.9   0.0   7.5e-07    0.0027       1      93 [.     167     238 ..     167     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                                       TEEEEE............ECTTTHHHHHHHHH CS
                            Toprim  39 fkpvye............eiedkkkvlkalke 58 
                                       +k+++e            + +d ++ +k+++e
  gi|320101464|ref|YP_004177056.1| 110 IKKIMErtieilrkwgkeKTPDVRELIKSIQE 141
                                       33333344444444445555556666666555 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 7.5e-07
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHH CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGe 77 
                                       el++vEg +d++++ ++   g+++++a+ G  +  et                  +k+la + ++  l  D+D  G 
  gi|320101464|ref|YP_004177056.1| 167 ELILVEGRADVINLLRY---GYTNTIALGGARRVPET------------------IKRLA-EHKKTTLFVDGDHGGD 221
                                       69***************...9************9999..................99999.999************* PP

                                       HHHHHHHHHHT.HHHTT CS
                            Toprim  78 aiawellevlk.ellen 93 
                                        i +e+l ++k +++ +
  gi|320101464|ref|YP_004177056.1| 222 LIIKEVLRNVKvDYIAR 238
                                       ******98887665555 PP

>> Rota_NSP4  Rotavirus non structural protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.7e-05     0.059      73     132 ..      81     141 ..      71     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                         Rota_NSP4  73 vtifntllklagykeqittkdeiekqmdrvvkemrrqlemidklttreieqv.ellkriyd 132
                                        ++++t+ k+  y   i+  d ++ +m+r+ k m r +e++ k    +  +v el+k i +
  gi|320101464|ref|YP_004177056.1|  81 AALIETVDKVGPYDSSISVVDIVDLRMERIKKIMERTIEILRKWGKEKTPDVrELIKSIQE 141
                                       56789999***********************************988777666478888876 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 ?   -1.3   0.1      0.51   1.8e+03      16      31 ..     105     120 ..      94     145 .. 0.47
   2 ?   12.2   0.2   3.8e-05      0.14     115     157 ..     250     292 ..     224     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.51
                            NOG1_N  16 kalrrakraakttkkk 31 
                                         ++r k++ ++t + 
  gi|320101464|ref|YP_004177056.1| 105 LRMERIKKIMERTIEI 120
                                       4444444444443332 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.8e-05
                            NOG1_N 115 addkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLp 157
                                       +++++ea   +++ f+ +++ +k+++k+ +fL +v++kL kLp
  gi|320101464|ref|YP_004177056.1| 250 SREVEEALSRKTDVFQYLEEQVKQGNKDAQFLLQVQRKLHKLP 292
                                       788899999999******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2958.82
//
Query:       gi|320101465|ref|YP_004177057.1|  [L=62]
Description: 50S ribosomal protein L37E [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-24   85.6  11.9    2.1e-24   85.4  11.9    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
        4.2    7.3   9.7         43    4.1   9.7    2.1  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !   85.4  11.9   2.3e-28   2.1e-24       2      53 ..       3      55 ..       2      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.3e-28
                    Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                      kGt+s+Gk+ ++ktHi+CrrCg++s++v k +Ca+cG+ +s+++r+y+W++K+
  gi|320101465|ref|YP_004177057.1|  3 KGTTSMGKHGRSKTHIRCRRCGRHSFNVAKGYCAACGFgRSKRIRRYSWANKK 55
                                      9**************************************************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 ?    4.1   9.7    0.0048        43      13      32 ..      19      39 ..      18      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0048
                           DUF35_N 13 rCpdCGtvqfPPr.avCphCg 32
                                      rC+ CG++ f     +C  Cg
  gi|320101465|ref|YP_004177057.1| 19 RCRRCGRHSFNVAkGYCAACG 39
                                      9*********99999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 477.13
//
Query:       gi|320101466|ref|YP_004177058.1|  [L=75]
Description: LSM family small nuclear ribonucleoprotein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   79.0   0.5    1.7e-22   78.9   0.5    1.0  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.012   15.8   0.1      0.015   15.5   0.1    1.2  1  SM-ATX    Ataxin 2 SM domain
       0.07   13.3   0.0       0.11   12.6   0.0    1.3  1  DUF150_C  RimP C-terminal SH3 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 !   78.9   0.5   2.9e-26   1.7e-22       2      67 .]       8      72 ..       7      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 2.9e-26
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                       l+++i++ v++++k+   lrG+L++fDq++N+vL+d+ee++ d+ ++rklg+v+iRG+++vlis+
  gi|320101466|ref|YP_004177058.1|  8 ILEDSIGRLVLIKTKDSVSLRGKLRSFDQHLNIVLDDTEEIRGDG-SVRKLGTVVIRGDTVVLISP 72
                                      58999****************************************.******************96 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   2.4e-06     0.015       8      52 ..       9      51 ..       3      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                                      HHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS. CS
                            SM-ATX  8 ltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkka 52
                                      l  ++G+ v +++k+    +G +++++    +++vL+ + +++ +
  gi|320101466|ref|YP_004177058.1|  9 LEDSIGRLVLIKTKDSVSLRGKLRSFDQ--HLNIVLDDTEEIRGD 51
                                      6789************************..***********9992 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05      0.11       8      48 ..      10      47 ..       8      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                          DUF150_C  8 arflGelVkvklklpvegrkkftGkivevdeet.itlevdgk 48
                                      + ++G+lV +k+k    ++  ++Gk+ ++d+   i+l+ +++
  gi|320101466|ref|YP_004177058.1| 10 EDSIGRLVLIKTK----DSVSLRGKLRSFDQHLnIVLDDTEE 47
                                      578**********....999**********654477765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 560.27
//
Query:       gi|320101467|ref|YP_004177059.1|  [L=799]
Description: replicative DNA polymerase I [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-70  237.3   0.0    4.2e-70  236.7   0.0    1.1  1  DNA_pol_B       DNA polymerase family B
    2.1e-36  125.7   0.0    6.3e-35  120.9   0.0    2.2  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    5.1e-07   29.8   0.0    1.2e-06   28.6   0.0    1.7  1  RNase_H_2       RNase_H superfamily
     0.0016   18.2   0.0     0.0032   17.2   0.0    1.5  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
  ------ inclusion threshold ------
      0.078   11.8   0.0       0.13   11.1   0.0    1.2  1  DNA_pol_B_2     DNA polymerase type B, organellar and viral
        2.5    8.1   4.3        1.3    9.1   0.1    2.3  2  DUF1664         Protein of unknown function (DUF1664)


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 !  236.7   0.0   1.4e-73   4.2e-70      14     456 ..     386     768 ..     374     770 .. 0.90

  Alignments for each domain:
  == domain 1  score: 236.7 bits;  conditional E-value: 1.4e-73
                                       HHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCH CS
                         DNA_pol_B  14 rveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseee 90 
                                       r e +L+++a ++g  +p+r ek + e   Y+Ga Vl+P  g+++ +++vlDF S+YP+i++++N+ + t+++  e 
  gi|320101467|ref|YP_004177059.1| 386 RLEWFLMKEATRRGELIPNRVEK-EAEP--YKGAVVLQPLPGIHE-NIAVLDFTSMYPNIMIKYNIGPDTILRGGEC 458
                                       77889*************66666.5555..*************97.69************************99988 PP

                                       CCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHH.CS--HHHHHHHHHHHHHHHHHHHHH CS
                         DNA_pol_B  91 akeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelk.eekdefekalldkqQlalKvtaNsv 166
                                       ++e        e +v+p+    ++ ++ +g +  +L+ lla R+++++e+k +  d+ e +lld++Q a+K++aN+ 
  gi|320101467|ref|YP_004177059.1| 459 SSE--------EHNVAPEV-GHCFLREPQGFFKGVLQALLALRRQLRAEMKkHPVDSPEYRLLDERQRAVKILANAA 526
                                       663........23456653.334678899**********************65566679****************** PP

                                       HHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSHH CS
                         DNA_pol_B 167 YGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdve 243
                                       YG++G    r +c + A+ vT+ GR+++ ++ e+ +++                 +lkviYGDTDS+f+e   ++v 
  gi|320101467|ref|YP_004177059.1| 527 YGYMGWVGARWYCRECAEAVTAWGRRTISTVIEHAKSM-----------------GLKVIYGDTDSLFVENIPEKV- 585
                                       *********************************99999.................9************98554444. PP

                                       HHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEE.ETTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHH CS
                         DNA_pol_B 244 ellkigkelaeevseklfkkplklefekvykkllLi.sKKkYaglkvektskanklliKGvdlvRrdncklvkevik 319
                                             kela  v++++    ++++++kvy ++ ++ +KK+Yagl  +     ++++i G + vR d+++++kev +
  gi|320101467|ref|YP_004177059.1| 586 ------KELADFVEKEMG---FEIKVDKVYRRVFFTeAKKRYAGLLED-----GRVDIVGFEAVRGDWAEIAKEVQE 648
                                       ......566667777444...5699*********9846*********9.....99********************** PP

                                       HHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS CS
                         DNA_pol_B 320 kvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlkkrnee 396
                                       kv e ll++    +++e+++++++si+    +el+++++plek+v+ k+l+k+ ++y++++ ph+++ak+l++  + 
  gi|320101467|ref|YP_004177059.1| 649 KVTEILLSE----KNIEKAIDYVRSIV----SELNQGRIPLEKLVIWKTLTKQVDEYEAEA-PHVNAAKKLRRM-GI 715
                                       *********....**************....***************************999.*******99876.89 PP

                                       ---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHHH CS
                         DNA_pol_B 397 apevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkevarll 456
                                        +evgd++ Y++v+          ++serae   +v++ +l +d+ yY++ q+++++ r+l
  gi|320101467|ref|YP_004177059.1| 716 MVEVGDKVGYIVVKGP-------GKISERAEPYMFVKDPRL-VDASYYIDhQIIPAALRIL 768
                                       9**************6.......59*****98888888776.9**************9997 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 !  120.9   0.0   2.1e-38   6.3e-35       2     325 ..      27     297 ..      26     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 2.1e-38
                                       ECTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESS CS
                    DNA_pol_B_exo1   2 teegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsn 78 
                                       t+ g++v+ +   f+pyfY+ a+d+ + e+++  ++ l++ +s  v+    v++v  k+++g   k    l+v++  
  gi|320101467|ref|YP_004177059.1|  27 TRSGERVVLRDRRFRPYFYVVASDKASVEALARKIRALSDPESPIVD----VRPVD-KRFFGKPVK---ALRVTTVI 95 
                                       7899*********************9999999999999988887666....66443.566666666...9******* PP

                                       TCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE..TEEEEGCC--C-.SEEEEEETTTSCEETT CS
                    DNA_pol_B_exo1  79 pnelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvk..kylvraegkisncdveidcdvddliakpk 153
                                       p+ ++k r++ + l+e+ +v e+d+ + +r+ +dn+++++gw   +  +++v+   +++        dv   i+ + 
  gi|320101467|ref|YP_004177059.1|  96 PESVRKYREKARGLSEVAEVLEADIRFSMRYALDNGLEPCGWHVAEvaETPVPSRYRVAR-----AFDVTGFIKPTG 167
                                       ******************************************666655566666666555.....344445555555 PP

                                       TCC..S-EEEEEEEEEETEETTSEETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS----EE--SSTCS CS
                    DNA_pol_B_exo1 154 ese..pplrvlsFDIeckskkgkfpdaensedpiiqIscvl.dglgekepearklftlrecaseeeedfeltpkpey 227
                                       +     +lrvl+FDIe+  + g  p +e+  dp+i I +    g++         ft +  +               
  gi|320101467|ref|YP_004177059.1| 168 DTRppSDLRVLAFDIEVLTESG-SPHPER--DPVIIIGVKTsSGET-------RQFTAEDLD--------------- 219
                                       5557678**********99999.******..**********55555.......778888888............... PP

                                       TTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEE CS
                    DNA_pol_B_exo1 228 pgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskq 304
                                                 +k+++ +f efi +ydPd+++gYN + FD+pY+l+R k l         +l + gr  + e++ s  
  gi|320101467|ref|YP_004177059.1| 220 ----------DKKVIAGFTEFILDYDPDIVVGYNSNHFDWPYLLERSKILGL-------KL-DVGRRSGGEPSTS-- 276
                                       ..........6788**********************************4443.......23.899999999*999.. PP

                                       EECEEEETTSEEEEHHHHHHH CS
                    DNA_pol_B_exo1 305 arekvkisgrihlDlyrvvkr 325
                                       ++++v+i+gr+++Dl++++ +
  gi|320101467|ref|YP_004177059.1| 277 TYGHVSIPGRLNVDLLNYAEE 297
                                       *****************9976 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   4.1e-10   1.2e-06      11     161 ..     192     356 ..     178     360 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.1e-10
                         RNase_H_2  11 spkknliyliGvldvdekeiekltqllaeepeeekailelflellekk..kalvtfngksFDvpflkrlf......k 79 
                                        p+++ ++ iGv   ++ e   ++q+ ae+ +++k i   f+e++ ++  + +v +n ++FD+p+l ++        
  gi|320101467|ref|YP_004177059.1| 192 HPERDPVIIIGVKT-SSGE---TRQFTAEDLDDKKVIAG-FTEFILDYdpDIVVGYNSNHFDWPYLLERSkilglkL 263
                                       46677789999985.3333...568889******99999.668888885455999************9996655431 PP

                         RNase_H_2  80 kyklde..................eefrhiDLlkelrk.kklesysLksvekelgierreedlsGsqavklyqeylr 137
                                           d                   + +  +DLl+ +++  +++  sL  v+ +lg+  r+e +   + v + + +  
  gi|320101467|ref|YP_004177059.1| 264 ----DVgrrsggepststyghvsiPGRLNVDLLNYAEEiPEVKLKSLDVVADYLGVMKRSERVL-VDYVDFPKYW-- 333
                                       ....33556677778878877777777899***9987643444446************954422.2222222333.. PP

                         RNase_H_2 138 tgdeellekilaYNedDvralatl 161
                                        +d+e+ + +l+YN dDv ++  l
  gi|320101467|ref|YP_004177059.1| 334 -RDPEKRRVLLRYNLDDVESTMGL 356
                                       .59999*************99876 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 !   17.2   0.0   1.1e-06    0.0032      27      83 ..     210     267 ..     191     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                    DNA_pol_B_exo2  27 vkslgeeessekelikkffegvekkkpql.VsfngrgfDlpvleyralkhgvsapkyf 83 
                                        +++++e+ ++k++i+ f e++  + p + V++n++ fD p l  r+ + g++     
  gi|320101467|ref|YP_004177059.1| 210 TRQFTAEDLDDKKVIAGFTEFILDYDPDIvVGYNSNHFDWPYLLERSKILGLKLDVGR 267
                                       45678889999****************97369**************988888766555 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 ?   11.1   0.0   4.3e-05      0.13     213     247 ..     413     446 ..     410     453 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                       DNA_pol_B_2 213 yrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthyp 247
                                       y G  + +p   g + eni v D+ S+YP++m +y 
  gi|320101467|ref|YP_004177059.1| 413 YKGAVVlQPL-PG-IHENIAVLDFTSMYPNIMIKYN 446
                                       5666665555.44.459***************9975 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.2      0.68     2e+03      10      26 ..     519     535 ..     515     538 .. 0.81
   2 ?    9.1   0.1   0.00043       1.3      78     115 ..     639     676 ..     626     683 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.68
                           DUF1664  10 aavvgavgYgyvwwkGw 26 
                                       + +++ + Ygy+ w G 
  gi|320101467|ref|YP_004177059.1| 519 VKILANAAYGYMGWVGA 535
                                       66788899******986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00043
                           DUF1664  78 qkeiskeikeevtevredlseigedvesvkeavegles 115
                                        +ei+ke++e+vte+    ++i++ ++ v+++v++l++
  gi|320101467|ref|YP_004177059.1| 639 WAEIAKEVQEKVTEILLSEKNIEKAIDYVRSIVSELNQ 676
                                       5799*******************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (799 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.43
# Mc/sec: 5560.58
//
Query:       gi|320101468|ref|YP_004177060.1|  [L=352]
Description: cell division protein pelota [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-26   91.5   0.0    7.6e-26   90.6   0.0    1.5  1  eRF1_1          eRF1 domain 1
    8.5e-20   71.3   0.3      2e-19   70.1   0.1    1.8  2  eRF1_3          eRF1 domain 3
    2.5e-09   37.6   0.1    5.9e-09   36.3   0.1    1.7  1  eRF1_2          eRF1 domain 2
     0.0045   17.2   3.0     0.0054   17.0   1.0    2.4  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.012   15.0   0.4      0.037   13.4   0.0    1.9  3  DUF2226         Uncharacterized protein conserved in archaea 
       0.11   12.5   0.6        3.5    7.8   0.0    2.7  3  UvrA_inter      UvrA interaction domain
       0.12   12.3   0.1       0.33   10.8   0.1    1.7  2  PRMT5           PRMT5 arginine-N-methyltransferase


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 !   90.6   0.0   2.9e-29   7.6e-26       1     128 [.       1     123 [.       1     124 [. 0.94

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 2.9e-29
                                       HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT CS
                            eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd 77 
                                       mk+l++dl+   +g+v++++ed +dlw l+ ++++gd v a t+r+v+     +  +s+r+ ++L ++ve v+f++ 
  gi|320101468|ref|YP_004177060.1|   1 MKVLEEDLR---NGYVRILVEDRDDLWVLFMVLRKGDVVYARTTREVKP---GEGGSSRRIPMTLGVRVEAVEFQEF 71 
                                       99*****99...9**********************************77...4455589****************** PP

                                       SSEEEEEEEEEEGGGG.--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  78 agvlrisGkvieeneh.vklgafhtldlelkrpftiikeewdsfalerLkea 128
                                       +++lri+G v+e+ e+   +g++ht+++ +++++ti ++ w+++ l+ Lk++
  gi|320101468|ref|YP_004177060.1|  72 TERLRIRGVVVEGPEEyGVKGHYHTINVSPGDQLTIVRDSWSRHSLDLLKKS 123
                                       ************98765889*****************************986 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.2   5.6e+03      64      64 ..     162     162 ..      88     196 .. 0.61
   2 !   70.1   0.1   7.8e-23     2e-19       2     113 .]     251     349 ..     250     349 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.2
                                       H CS
                            eRF1_3  64 e 64 
                                       +
  gi|320101468|ref|YP_004177060.1| 162 K 162
                                       0 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 7.8e-23
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHH CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenv 78 
                                       ++  ++leef + + kd+++++YGv++v +a+ +g+v++L+v+ e+ ++ d+++++             + e++e++
  gi|320101468|ref|YP_004177060.1| 251 VKAGEILEEFKRLIVKDPELVAYGVDDVYEAASYGSVSKLVVVHEMLHEADDERRS------------RVYEVLEKA 315
                                       567799******************************************99986666............4999***** PP

                                       HHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  79 eesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       +e+g++v+i++ +s+ G+++ ++fgG++a+LRy++
  gi|320101468|ref|YP_004177060.1| 316 HETGGEVVIVPGRSDVGAEI-QGFGGVIAVLRYRL 349
                                       ********************.************85 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1   2.3e-12   5.9e-09       3     127 ..     130     241 ..     128     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.3e-12
                                       EEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESE CS
                            eRF1_2   3 glivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkg 79 
                                        l+vld + A i++l+++ +++++++ +++P+K  r    ++      e+++e +l +v++a  ++   v+++ +++
  gi|320101468|ref|YP_004177060.1| 130 LLVVLDYEDACIAVLTEQGVKYVNEVHSELPGKMYR---VNH------EKAVEDYLSEVVSASINT---VQQEGVDA 194
                                       58********************************85...333......799*********999999...89****** PP

                                       EEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC..C CS
                            eRF1_2  80 iilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek..a 127
                                       +i agpg+ k+   + +     l+ + + +  +s+gg +g+ e+l+   +
  gi|320101468|ref|YP_004177060.1| 195 VIAAGPGDLKNRVAEALKTA--LR-RHVYVDSTSTGGCQGVAELLRRdvV 241
                                       ***********998765333..32.3344556889999999999987544 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 !   17.0   1.0   2.1e-06    0.0054      62     132 ..     165     236 ..      60     248 .. 0.89
   2 ?   -2.6   0.0       2.4   6.1e+03     126     137 ..     302     317 ..     285     320 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                    baeRF_family10  62 qrreeeqaerhlkevAellaklleergverlvlgGdeeetaalldrlpkalrarvvgt.lplpvdasaaaVl 132
                                       +  +e+ +e +l ev+ +  + ++++gv++++ +G+ + ++ ++++l+ alr+ v  + ++ ++ +  a++l
  gi|320101468|ref|YP_004177060.1| 165 RVNHEKAVEDYLSEVVSASINTVQQEGVDAVIAAGPGDLKNRVAEALKTALRRHVYVDsTSTGGCQGVAELL 236
                                       55689999*********************************************9998866655533444444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                    baeRF_family10 126 a....saaaVlekaee 137
                                       +       +Vleka+e
  gi|320101468|ref|YP_004177060.1| 302 DerrsRVYEVLEKAHE 317
                                       2223334466666665 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 ?   13.4   0.0   1.4e-05     0.037      30      62 ..      10      42 ..       2      57 .. 0.87
   2 ?   -3.1   0.0       1.5     4e+03     194     212 ..     169     187 ..     148     217 .. 0.64
   3 ?   -2.2   0.1      0.81   2.1e+03      48      64 ..     263     279 ..     236     315 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                           DUF2226 30 lGyvritvkegeklldafilvedGkiVgayled 62
                                       Gyvri+v + ++l   f+++  G +V+a  ++
  gi|320101468|ref|YP_004177060.1| 10 NGYVRILVEDRDDLWVLFMVLRKGDVVYARTTR 42
                                      3****************************9876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                           DUF2226 194 eesietiledvfepsdeel 212
                                       e+ +e  l +v+ +s + +
  gi|320101468|ref|YP_004177060.1| 169 EKAVEDYLSEVVSASINTV 187
                                       4444444444444444444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.81
                           DUF2226  48 ilvedGkiVgayledvr 64 
                                       ++v+d  +V+ +++dv 
  gi|320101468|ref|YP_004177060.1| 263 LIVKDPELVAYGVDDVY 279
                                       34444444444444433 PP

>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.1   5.3e+03      36      51 ..       3      18 ..       2      20 .. 0.77
   2 ?    1.9   0.0     0.091   2.3e+02      52      97 ..     161     216 ..     154     218 .. 0.72
   3 ?    7.8   0.0    0.0014       3.5      72     105 ..     290     325 ..     257     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                        UvrA_inter 36 llenlkkkGfvrvriD 51
                                      +le+  ++G+vr+ ++
  gi|320101468|ref|YP_004177060.1|  3 VLEEDLRNGYVRILVE 18
                                      56777789****9987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.091
                        UvrA_inter  52 geiydldedieldknkkhsievvvDrlvvkke..........ersrlaesvetAlk 97 
                                       g++y+++++  ++ + +  ++  +++++ +             ++r+ae+++tAl+
  gi|320101468|ref|YP_004177060.1| 161 GKMYRVNHEKAVEDYLSEVVSASINTVQQEGVdaviaagpgdLKNRVAEALKTALR 216
                                       78888888888888888888888888885544333333344466999999999996 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0014
                        UvrA_inter  72 evvvDrlv..vkkeersrlaesvetAlklgeglviv 105
                                        vvv ++    ++e rsr+ e +e+A + g ++viv
  gi|320101468|ref|YP_004177060.1| 290 LVVVHEMLheADDERRSRVYEVLEKAHETGGEVVIV 325
                                       4666666522456677******************98 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00013      0.33      43      91 ..     168     216 ..     152     223 .. 0.89
   2 ?   -2.3   0.0       1.4   3.6e+03      18      36 ..     297     315 ..     290     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHCTCCGTCC.-EEEEEEES-TTSHHHHHHHHHHHHHCC CS
                             PRMT5  43 YeeAiekalsdlkkekkkksekklvilvvGaGRGplvdralkaleetkv 91 
                                        e+A+e++ls++++++ ++ +++ v +v+ aG G l +r+ +al+++  
  gi|320101468|ref|YP_004177060.1| 168 HEKAVEDYLSEVVSASINTVQQEGVDAVIAAGPGDLKNRVAEALKTALR 216
                                       699*****************9*********************9998764 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                                       --TTTS---HHHHHHHCC- CS
                             PRMT5  18 LqPlsdnLesatYevFEkd 36 
                                       L+   d+  s +Yev Ek 
  gi|320101468|ref|YP_004177060.1| 297 LHEADDERRSRVYEVLEKA 315
                                       6666788899999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2521.22
//
Query:       gi|320101469|ref|YP_004177061.1|  [L=239]
Description: DNA polymerase beta domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-05   25.3   0.0    2.3e-05   24.6   0.0    1.5  1  NTP_transf_2  Nucleotidyltransferase domain
    0.00011   22.3   0.0    0.00019   21.4   0.0    1.4  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.5e-09   2.3e-05       5      44 ..      29      73 ..      25     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.5e-09
                                      HHHHHHHTT.....TSEEEEEHHHHCTTSCTTSSEEEEEEESTTC CS
                      NTP_transf_2  5 leelkelep.....vakvvlfGSyarGtalkgSDiDllvvlpeev 44
                                      +++  el +     ++ ++++GS+arG+  +gSDiD+++  + ++
  gi|320101469|ref|YP_004177061.1| 29 RRRAAELLGllvegGVNAYIHGSVARGDVWRGSDIDVFIPDNIPS 73
                                      55555555555667999*********************9766665 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.2e-08   0.00019      16      37 ..      46      67 ..      42      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.2e-08
                                      TTEEEEEE-S------EEEEEE CS
                           Polbeta 16 aylFGSrakgkareeSDiDlav 37
                                      ay++GS+a+g+ ++ SDiD+++
  gi|320101469|ref|YP_004177061.1| 46 AYIHGSVARGDVWRGSDIDVFI 67
                                      8*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1675.26
//
Query:       gi|320101470|ref|YP_004177062.1|  [L=353]
Description: peptidase M50 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-12   46.0   7.3    3.4e-11   42.9   7.3    2.1  1  Peptidase_M50  Peptidase family M50
    7.4e-09   35.3   0.3    1.5e-08   34.4   0.3    1.6  1  PDZ_6          PDZ domain
    6.5e-07   29.6   0.0    1.1e-06   28.9   0.0    1.4  1  PDZ            PDZ domain
    1.2e-06   28.7   0.0    2.3e-06   27.8   0.0    1.4  1  PDZ_2          PDZ domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   7.3   7.6e-15   3.4e-11       1     231 [.     110     339 ..     110     350 .. 0.67

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 7.6e-15
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   1 afilllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeak 77 
                                       +f++ ++i   +HE+ H+++A ++gv v+++++ +               + +lpL +yV++++e            
  gi|320101470|ref|YP_004177062.1| 110 FFLASVSIAASLHEYLHAVFALRNGVPVKSYGVML---------------LLILPL-AYVEVDEEA----------- 159
                                       58899999***************************...............999998.*******99........... PP

                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................-EEECECTTTSCEE-SEEEC-...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxx...... RF
                     Peptidase_M50  78 aflkkspwqrllivlAGplanfilailvfvv...................pkkskeseeekrgviGvspkp...... 129
                                        f+k+    r+ ++ AG ++n+ la++ +++                   p           +  Gv+ +       
  gi|320101470|ref|YP_004177062.1| 160 -FRKAGRGGRIGVLSAGVAVNLALAFASMLLlsamsspigvlvtgveegsP----------AYEHGVQVYDvivsvn 225
                                       .****************************9966666665555555544442..........2222222222333333 PP

                                       ............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.............. CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                     Peptidase_M50 130 ............vkkegllealkegvektlkvvvltvkalgklitgklslktlggpisiaqla.............. 180
                                                   v+k      l+ +v +  +                  + +l +pi++++                
  gi|320101470|ref|YP_004177062.1| 226 gtpvrgigdipvVRKLAKPTVLEVAVWRSGSG-----------------IVNLTIPIGVGDERigvylspapstwli 285
                                       33333322222212222222222222222222.................2222222222222233333333333444 PP

                                       ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 181 ...seaaeaglssflqllalisvnLgilNLlPipvLDGghllfalleairrkpl 231
                                          + +a+  +  f  ++ +++++L++lN+ P++v DGg+++ +l  +  ++ +
  gi|320101470|ref|YP_004177062.1| 286 sslGASAALAAYRFTMWMWIVNFSLALLNAAPLFVTDGGRVIGELAGEKWGRVI 339
                                       444778889999*****************************9888777666655 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.3   3.3e-12   1.5e-08       2      50 ..     201     245 ..     200     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.3e-12
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesv 50 
                                       Vt V++gsPA++ G++v D+i+svNG+pv+g     v++ l+    +++
  gi|320101470|ref|YP_004177062.1| 201 VTGVEEGSPAYEHGVQVYDVIVSVNGTPVRGIGDIPVVRKLA----KPT 245
                                       99***************************6655555555554....444 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.5e-10   1.1e-06      24      76 ..     195     246 ..     160     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.5e-10
                                       SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSE CS
                               PDZ  24 gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgk 76 
                                          g+ v+ v++g++a   g++v D+I+svNg++v+++ +  +v ++ +++ +
  gi|320101470|ref|YP_004177062.1| 195 SPIGVLVTGVEEGSPAYEHGVQVYDVIVSVNGTPVRGIGDIPVVRKLAKPT-V 246
                                       4469************************************99999999886.4 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   5.2e-10   2.3e-06      15      47 ..     198     230 ..     187     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.2e-10
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB--S CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkvk 47 
                                       gvlv+ V+eg+Pa ++g++ +Dvi++v+g++v 
  gi|320101470|ref|YP_004177062.1| 198 GVLVTGVEEGSPAYEHGVQVYDVIVSVNGTPVR 230
                                       89****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2637.66
//
Query:       gi|320101471|ref|YP_004177063.1|  [L=353]
Description: L-threonine synthase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-67  226.9   0.1      4e-67  226.7   0.1    1.0  1  PALP            Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.019   14.8   2.4       0.71    9.7   0.2    3.1  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
      0.073   12.5   2.2       0.24   10.9   0.0    2.1  2  Mu-like_Com     Mu-like prophage protein Com
      0.073   13.0   0.6       0.18   11.7   0.6    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.29   11.3   0.5       0.62   10.2   0.5    1.5  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.36   10.3   6.4        3.2    7.3   0.3    2.3  2  zf-ribbon_3     zinc-ribbon domain
       0.36   10.6   7.7        1.7    8.5   0.7    2.2  2  zinc_ribbon_2   zinc-ribbon domain
       0.59   10.2   5.0        5.8    7.0   0.3    2.5  2  Rubredoxin      Rubredoxin
       0.78    9.5   3.9        9.9    6.0   0.2    2.3  2  zf-MIZ          MIZ/SP-RING zinc finger
        0.9    9.5   2.6        6.8    6.7   2.6    2.0  1  Cys_rich_CPXG   Cysteine-rich CPXCG
        1.3    8.9   4.1        9.4    6.2   2.4    2.6  3  HalOD2          Halobacterial output domain 2
        2.1    7.7   4.6         13    5.2   0.4    2.2  2  zf-RanBP        Zn-finger in Ran binding protein and others
        2.4    8.0  11.8         21    4.9  11.7    2.3  1  Rubredoxin_2    Rubredoxin metal binding domain
        2.7    8.1   4.9        7.6    6.7   0.5    2.2  2  UPF0547         Uncharacterised protein family UPF0547


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 !  226.7   0.1   3.1e-70     4e-67       2     294 .]      60     345 ..      59     345 .. 0.91

  Alignments for each domain:
  == domain 1  score: 226.7 bits;  conditional E-value: 3.1e-70
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallG 78 
                                       t g+g+TPlv  +      gv +++KlE+lnp+gSfKdRg + +++++ ++ g + vve +sGN+g+++A++++l+G
  gi|320101471|ref|YP_004177063.1|  60 TRGEGNTPLVSEKM----DGVTVLFKLEYLNPGGSFKDRGSSLAVYYAYKT-GFRSVVEDTSGNTGISVALYSRLYG 131
                                       6799*****65433....4788*************************9999.************************* PP

                                       -EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHH.HHT CS
                              PALP  79 lkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEil.eql 154
                                       l ++i++p++a+++k+++ r+lGa+vve ++   ea+++   l + g+ga++v ++ +++ i+g +ti++E+l e++
  gi|320101471|ref|YP_004177063.1| 132 LNARIYMPRTAPEGKKKAVRMLGAQVVEAPS-RGEAAEM--VLRETGGGAFYVAHTWSYLYILGASTIAWEVLeEDT 205
                                       *****************************55.6666666..78888**************************94444 PP

                                       TTTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.. CS
                              PALP 155 ggkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrrvtvpvsdtiadglavg.. 223
                                          pd+v++pvG+Ggl+ G+++g+ +    ++ +  +r+i+v+     ++++++ +g +++ + ++t+adg+ v+  
  gi|320101471|ref|YP_004177063.1| 206 ---PDYVIAPVGSGGLFLGLVKGFEKaleaGWITkmPRFIAVQGYSTQPVHKAF-KGVEQPGE-ESTLADGIMVPnp 277
                                       ...8**********************7776444499******************.55444444.4**********77 PP

                                       CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 224 spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                          e+ +e+l+r+ ++i  v + e+ +a r+l+ + g +vep+saaa+aal  r+++++ +  +++v+ltg
  gi|320101471|ref|YP_004177063.1| 278 PRLEEIVEALRRYQGDILLVGNTEVEKAWRELW-ELGFLVEPTSAAAYAAL-SRSKNQFTGR-KTLVVLTG 345
                                       7777899**************************.*****************.**********.99999998 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 ?    0.9   0.2      0.32     4e+02       3       8 ..       4       9 ..       3      13 .. 0.86
   2 ?    9.7   0.2   0.00055      0.71       3      16 ..      21      34 ..      20      41 .. 0.86
   3 ?    1.7   0.0      0.18   2.3e+02       9      22 ..     167     180 ..     165     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.32
                                     E-SSS- CS
                    zf-C4_Topoisom 3 kCPkCg 8
                                     kCP Cg
  gi|320101471|ref|YP_004177063.1| 4 KCPYCG 9
                                     8****9 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00055
                                      E-SSS--EEEEEE- CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkrg 16
                                      kCP Cg++Lvl ++
  gi|320101471|ref|YP_004177063.1| 21 KCPRCGKPLVLSYT 34
                                      8*********9665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.18
                                       -EEEEEE-SSSEEE CS
                    zf-C4_Topoisom   9 gdLvlkrgkkGkFv 22 
                                       +++vl+++  G F+
  gi|320101471|ref|YP_004177063.1| 167 AEMVLRETGGGAFY 180
                                       79*********886 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 ?    0.8   0.5      0.25   3.3e+02      25      31 ..       3       9 ..       1      10 [. 0.85
   2 ?   10.9   0.0   0.00019      0.24      17      31 ..      12      26 ..      10      29 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.25
                       Mu-like_Com 25 iKCPRCG 31
                                       KCP CG
  gi|320101471|ref|YP_004177063.1|  3 WKCPYCG 9 
                                      59****9 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                       Mu-like_Com 17 aeAlDeltiKCPRCG 31
                                      a+Al e   KCPRCG
  gi|320101471|ref|YP_004177063.1| 12 ADALKEYYWKCPRCG 26
                                      899***********9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   0.00014      0.18      30      54 ..       4      27 ..       3      29 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgf 54
                                      +C+ Cg + +  l++  +kCp+Cg 
  gi|320101471|ref|YP_004177063.1|  4 KCPYCGFEADA-LKEYYWKCPRCGK 27
                                      6**********.***********95 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 ?   10.2   0.5   0.00049      0.62       1      29 [.       4      32 ..       3      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00049
                          zf-Mss51  1 lCPvpkhkqtapkhvdfeCpdCGiptycs 29
                                      +CP +  + +a k+   +Cp+CG p   s
  gi|320101471|ref|YP_004177063.1|  4 KCPYCGFEADALKEYYWKCPRCGKPLVLS 32
                                      6****99999*************998665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.2    0.0094        12      18      24 ..       4      10 ..       4      11 .. 0.75
   2 ?    7.3   0.3    0.0025       3.2       4      11 ..      21      28 ..      20      31 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0094
                       zf-ribbon_3 18 vCpyCGt 24
                                      +CpyCG 
  gi|320101471|ref|YP_004177063.1|  4 KCPYCGF 10
                                      5999985 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0025
                       zf-ribbon_3  4 rCPnCGap 11
                                      +CP+CG+p
  gi|320101471|ref|YP_004177063.1| 21 KCPRCGKP 28
                                      59999986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.4     0.013        17      16      22 ..       5      11 ..       4      12 .. 0.79
   2 ?    8.5   0.7    0.0013       1.7       1       9 [.      21      29 ..      21      32 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                     zinc_ribbon_2 16 CpyCGtp 22
                                      CpyCG++
  gi|320101471|ref|YP_004177063.1|  5 CPYCGFE 11
                                      8999875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +Cp+CG++l
  gi|320101471|ref|YP_004177063.1| 21 KCPRCGKPL 29
                                      799999987 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0045       5.8      34      44 ..       2      12 ..       1      15 [. 0.82
   2 ?    4.6   0.7     0.027        34      35      41 ..      20      26 ..      17      29 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0045
                                      T-BBTTTB-BG CS
                        Rubredoxin 34 dWvCPdCgvek 44
                                      +W+CP Cg e 
  gi|320101471|ref|YP_004177063.1|  2 HWKCPYCGFEA 12
                                      7******9765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.027
                                      -BBTTTB CS
                        Rubredoxin 35 WvCPdCg 41
                                      W+CP Cg
  gi|320101471|ref|YP_004177063.1| 20 WKCPRCG 26
                                      ******8 PP

>> zf-MIZ  MIZ/SP-RING zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.021        27      41      48 ..       2       9 ..       1      11 [. 0.85
   2 ?    6.0   0.2    0.0077       9.9      38      49 ..      16      27 ..      12      28 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.021
                                      --B-TTT- CS
                            zf-MIZ 41 tWnCPvCs 48
                                      +W+CP C 
  gi|320101471|ref|YP_004177063.1|  2 HWKCPYCG 9 
                                      7******5 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0077
                                      HS---B-TTT-- CS
                            zf-MIZ 38 rtetWnCPvCsk 49
                                      ++ +W+CP C k
  gi|320101471|ref|YP_004177063.1| 16 KEYYWKCPRCGK 27
                                      5568******87 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.6    0.0053       6.8       2      37 ..       4      32 ..       3      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0053
                     Cys_rich_CPXG  2 qCPyCgeeievlvDlsagdqeYieDCqvCCrPivlq 37
                                      +CPyCg e ++l       +eY+  C+ C +P vl 
  gi|320101471|ref|YP_004177063.1|  4 KCPYCGFEADAL-------KEYYWKCPRCGKPLVLS 32
                                      69***9887654.......89999999999999886 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.23   2.9e+02      32      38 ..       3       9 ..       1      14 [. 0.82
   2 ?    6.2   2.4    0.0074       9.4      26      39 ..      14      27 ..       4      32 .. 0.84
   3 ?   -3.7   0.0       9.6   1.2e+04      22      31 ..     148     157 ..     144     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.23
                            HalOD2 32 WkCtrCG 38
                                      WkC  CG
  gi|320101471|ref|YP_004177063.1|  3 WKCPYCG 9 
                                      9999999 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0074
                            HalOD2 26 qLGayvWkCtrCGe 39
                                       L  y WkC rCG+
  gi|320101471|ref|YP_004177063.1| 14 ALKEYYWKCPRCGK 27
                                      567799*******7 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9.6
                            HalOD2  22 eGyrqLGayv 31 
                                       + +r LGa v
  gi|320101471|ref|YP_004177063.1| 148 KAVRMLGAQV 157
                                       5789999987 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.022        28       4      11 ..       2       9 ..       2      11 .. 0.87
   2 ?    5.2   0.4    0.0099        13       4      11 ..      19      26 ..      16      27 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.022
                                      SEE-SSS- CS
                          zf-RanBP  4 dWdCskCl 11
                                      +W+C+ C+
  gi|320101471|ref|YP_004177063.1|  2 HWKCPYCG 9 
                                      6******8 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0099
                                      SEE-SSS- CS
                          zf-RanBP  4 dWdCskCl 11
                                      +W+C+ C+
  gi|320101471|ref|YP_004177063.1| 19 YWKCPRCG 26
                                      8******7 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  11.7     0.017        21       1      21 [.       3      26 ..       3      27 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                      Rubredoxin_2  1 YvCsqCGfes...akwfGrCpsCg 21
                                      + C  CGfe+     ++++Cp Cg
  gi|320101471|ref|YP_004177063.1|  3 WKCPYCGFEAdalKEYYWKCPRCG 26
                                      68999***99444469*******9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5    0.0059       7.6      16      23 ..       4      11 ..       3      12 .. 0.91
   2 ?    3.0   0.3     0.084   1.1e+02       2       8 ..      21      27 ..      21      31 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0059
                           UPF0547 16 fCphCGyv 23
                                      +Cp+CG++
  gi|320101471|ref|YP_004177063.1|  4 KCPYCGFE 11
                                      7*****96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.084
                           UPF0547  2 vCPeCea 8 
                                      +CP+C  
  gi|320101471|ref|YP_004177063.1| 21 KCPRCGK 27
                                      6888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2551.51
//
Query:       gi|320101472|ref|YP_004177064.1|  [L=95]
Description: 30S ribosomal protein S26E [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-24   84.6   3.2    6.4e-24   84.5   3.2    1.1  1  Ribosomal_S26e   Ribosomal protein S26e
     0.0038   17.4   1.1       0.12   12.6   0.6    2.5  2  zf-RING_7        C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.3   0.3      0.011   15.3   0.3    2.0  2  Sgf11            Sgf11 (transcriptional regulation protein)
      0.022   14.8   1.1       0.16   12.0   0.1    2.1  2  DZR              Double zinc ribbon
       0.03   14.2   0.2       0.11   12.5   0.0    2.0  2  zf-C2HC_2        zinc-finger of a C2HC-type
      0.075   13.3   1.0       0.36   11.1   1.3    1.8  2  Yippee-Mis18     Yippee zinc-binding/DNA-binding /Mis18, cent
       0.16   11.9   0.3       0.16   11.9   0.3    2.0  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.28   11.6   3.6        1.1    9.6   0.3    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   3.2   2.9e-27   6.4e-24       1      97 [.       1      93 [.       1      95 [] 0.93

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 2.9e-27
                                      X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHH CS
                    Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscai 79
                                      m+kKR ++gr k ++g+v++v+C+nc+r+vp dKai  + +++ v  + +++l+++      ++ ++ ++++ycvsca+
  gi|320101472|ref|YP_004177064.1|  1 MPKKRESRGRRKGDKGKVEYVQCDNCGRRVPADKAICVTRMYSPVPPQLAEELEKK----GAIIQRYPVTKCYCVSCAV 75
                                      9****************************************************998....4556666678899****** PP

                                      HTTSS----TTTTS--S- CS
                    Ribosomal_S26e 80 hskvvrvRsredrknrep 97
                                      h  +v+vR +e+rk++  
  gi|320101472|ref|YP_004177064.1| 76 HLGIVKVRPEEERKEKPA 93
                                      **************9865 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 !   12.6   0.6   5.4e-05      0.12      21      31 ..      16      28 ..       4      28 .. 0.69
   2 ?    2.7   0.0     0.065   1.4e+02       9      24 ..      45      60 ..      45      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                      TB-..EE-TTT-- CS
                         zf-RING_7 21 dev..vtCpeCGR 31
                                      ++v  v+C++CGR
  gi|320101472|ref|YP_004177064.1| 16 GKVeyVQCDNCGR 28
                                      44555*******9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.065
                                      --CCHHHHHCCSTB-E CS
                         zf-RING_7  9 lppqvlselragdevv 24
                                      +ppq+  el +++ ++
  gi|320101472|ref|YP_004177064.1| 45 VPPQLAEELEKKGAII 60
                                      79*******9998765 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   4.9e-06     0.011       2      14 ..      18      30 ..      17      32 .. 0.87
   2 ?   -3.0   2.2       2.5   5.5e+03       4      10 ..      67      73 ..      65      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
                                      C-EEE-TTTSSEE CS
                             Sgf11  2 seyvtCpnCgRqi 14
                                       eyv+C+nCgR +
  gi|320101472|ref|YP_004177064.1| 18 VEYVQCDNCGRRV 30
                                      69*********98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                                      EEE-TTT CS
                             Sgf11  4 yvtCpnC 10
                                       + C  C
  gi|320101472|ref|YP_004177064.1| 67 KCYCVSC 73
                                      5889998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     7e-05      0.16      28      45 ..      20      37 ..       4      39 .. 0.83
   2 ?    1.8   0.1      0.11   2.5e+02      11      20 ..      66      75 ..      50      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                               DZR 28 edrCpsCgekvdpearfC 45
                                        +C++Cg+ v++++++C
  gi|320101472|ref|YP_004177064.1| 20 YVQCDNCGRRVPADKAIC 37
                                      568999999999999999 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                               DZR 11 darfCseCgt 20
                                       + +C  C  
  gi|320101472|ref|YP_004177064.1| 66 TKCYCVSCAV 75
                                      4556777755 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 ?   12.5   0.0   4.7e-05      0.11       1      12 [.      19      30 ..      19      35 .. 0.82
   2 ?   -2.0   0.0       1.7   3.8e+03      16      21 ..      72      77 ..      71      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                         zf-C2HC_2  1 elvpCpkCgRsF 12
                                      e v+C +CgR+ 
  gi|320101472|ref|YP_004177064.1| 19 EYVQCDNCGRRV 30
                                      579*******86 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                         zf-C2HC_2 16 rlekHe 21
                                      ++++H 
  gi|320101472|ref|YP_004177064.1| 72 SCAVHL 77
                                      699995 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.067   1.5e+02      51      64 ..      16      29 ..       3      33 .. 0.69
   2 ?   11.1   1.3   0.00016      0.36       3      76 ..      21      88 ..      19      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.067
                                      EEEEEEEETTT--E CS
                      Yippee-Mis18 51 ctystlsCkgCnsv 64
                                       +++ ++C +C+  
  gi|320101472|ref|YP_004177064.1| 16 GKVEYVQCDNCGRR 29
                                      67788899999875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                                      EEETTTS-EEEECCCEEEEECCCEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEECSCCC CS
                      Yippee-Mis18  3 fqCkkCktilgdslqlvsegralnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvlGwkYksteeel 76
                                      +qC +C + +    +++       + ++++v  ++  + e++    +++ +++ +C +C+ +lG + ++ eee 
  gi|320101472|ref|YP_004177064.1| 21 VQCDNCGRRVPADKAICV------TRMYSPVPPQLAEELEKKGAIIQRYPVTKCYCVSCAVHLGIVKVRPEEER 88
                                      688888888888888887......677899999999888888886678****************9877777764 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3     7e-05      0.16       4      28 ..      13      37 ..      10      44 .. 0.85
   2 ?   -1.2   0.8      0.86   1.9e+03      12      17 ..      68      73 ..      61      76 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-05
                           DUF35_N  4 aaegrLvgqrCpdCGtvqfPPr.avC 28
                                      ++ g++ + +C++CG+  +P+  a+C
  gi|320101472|ref|YP_004177064.1| 13 GDKGKVEYVQCDNCGRR-VPADkAIC 37
                                      667899999********.79999999 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.86
                           DUF35_N 12 qrCpdC 17
                                      ++C +C
  gi|320101472|ref|YP_004177064.1| 68 CYCVSC 73
                                      567777 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   0.00051       1.1      22      36 ..      14      28 ..       2      52 .. 0.69
   2 ?    3.4   0.3     0.044        99      28      51 ..      67      90 ..      46      94 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00051
                   Lar_restr_allev 22 vaeigq....cvyCadCga 36
                                      +    +    +v+C++Cg 
  gi|320101472|ref|YP_004177064.1| 14 D----KgkveYVQCDNCGR 28
                                      2....13355*******97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.044
                   Lar_restr_allev 28 cvyCadCgastpwfkiaedeaeae 51
                                        yC  C ++   +k +++e+++e
  gi|320101472|ref|YP_004177064.1| 67 KCYCVSCAVHLGIVKVRPEEERKE 90
                                      457777888444444455554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 693.53
//
Query:       gi|320101473|ref|YP_004177065.1|  [L=110]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       385  (0.0214736); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 874.14
//
Query:       gi|320101474|ref|YP_004177066.1|  [L=160]
Description: type 11 methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-10   38.5   0.0    1.4e-09   38.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    4.6e-09   36.9   0.0    6.5e-09   36.4   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    1.4e-07   31.1   0.0    1.5e-07   31.0   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    1.2e-05   25.9   0.0    2.3e-05   24.9   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
      2e-05   24.2   0.0    2.2e-05   24.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.3e-05   24.3   0.0    3.4e-05   23.8   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
    7.8e-05   22.3   0.0    0.00037   20.1   0.0    1.9  1  DOT1             Histone methylation protein DOT1
    0.00054   19.6   0.0    0.00065   19.4   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
    0.00086   18.9   0.0     0.0012   18.5   0.0    1.1  1  MTS              Methyltransferase small domain
      0.001   18.6   0.0     0.0014   18.2   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
     0.0028   17.5   0.0     0.0031   17.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
     0.0031   17.3   0.1     0.0038   17.0   0.1    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0031   18.2   0.0     0.0059   17.3   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.012   14.9   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
      0.019   14.6   0.3       0.36   10.5   0.3    2.1  1  UPF0020          Putative RNA methylase family UPF0020
      0.022   13.9   0.1      0.027   13.6   0.1    1.1  1  Methyltransf_20  Putative methyltransferase
      0.054   12.8   0.0      0.071   12.4   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
      0.061   13.0   0.0       0.11   12.2   0.0    1.3  1  N6_N4_Mtase      DNA methylase
      0.087   12.3   0.0       0.27   10.7   0.0    1.7  2  TrmK             tRNA (adenine(22)-N(1))-methyltransferase
       0.11   12.1   0.0       0.12   11.9   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.12   11.7   0.0       0.16   11.4   0.0    1.2  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.6e-12   1.4e-09       4     127 ..      27     146 ..      24     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.6e-12
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                       g +v+DlGCG G++++++ +e +   + vG++++ e i+ Ar + ++ g++ ++ + qgd++e +  +++    +++
  gi|320101474|ref|YP_004177066.1|  27 GDVVYDLGCGDGRILIVAVKEFN-VRKAVGVERDSERIKEARRRISEEGIEdRAIVVQGDFFEVD--ISE--ATIVT 98 
                                       678****************7655.5678***********************99**********88..443..22222 PP

                   Methyltransf_31  80 snevlnaladpdkile.eiervlkpggilliedpr...llaelpakveeesk 127
                                           l +l++ ++ l+ ++er l++g ++++ ++r   +  e  a+v++e++
  gi|320101474|ref|YP_004177066.1|  99 ----LFLLTSVNEMLRpKLERELRNGARVVSHEFRipgWKHEKTAEVKDENN 146
                                       ....234555666666677777777777777777755433444455555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   7.6e-12   6.5e-09       1      93 [.      30     124 ..      30     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7.6e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       v dlGcG Gr+++ + k+++  k +gv+ ++e +++ar+r++eeg+  ++ +vqgd+ +++  ++++   ++  +++
  gi|320101474|ref|YP_004177066.1|  30 VYDLGCGDGRILIVAVKEFNVRKAVGVERDSERIKEARRRISEEGIedRAIVVQGDFFEVDISEATIVTLFLLTSVN 106
                                       78*****************99**************************9*************9998888888866666 PP

                                       GSSHHHHHHHHHHHHHHE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvL 93 
                                        + +++le+ l++ arv+
  gi|320101474|ref|YP_004177066.1| 107 EMLRPKLERELRNGARVV 124
                                       666688888888888886 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.7e-10   1.5e-07      55     140 ..      19     105 ..      13     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                                       HTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SE CS
                              CMAS  55 leklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdr 130
                                       l+ ++  +G+ + d+GcG G +++ av++++v k vg+   +e+ k a++r+ e+++e+++ v   d+ ++d     
  gi|320101474|ref|YP_004177066.1|  19 LRLAGAGEGDVVYDLGCGDGRILIVAVKEFNVrKAVGVERDSERIKEARRRISEEGIEDRAIVVQGDFFEVDISEAT 95 
                                       55556679************************4589*********************************99998888 PP

                                       EEEES-GGGT CS
                              CMAS 131 vvsvgafehv 140
                                       +v++ ++  v
  gi|320101474|ref|YP_004177066.1|  96 IVTLFLLTSV 105
                                       9888776665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.7e-08   2.3e-05       2      89 ..      32     125 ..      31     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.7e-08
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       d+GcG Gr++    k +  ++ vgv+ + e +k a++++seeg+  +  +v++d+ ++ + ++++   ++  +++ +
  gi|320101474|ref|YP_004177066.1|  32 DLGCGDGRILIVAVKEFnvRKAVGVERDSERIKEARRRISEEGIedRAIVVQGDFFEVDISEATIVTLFLLTSVNEM 108
                                       9*********999988889*************************998788********9999876655555555554 PP

                                       ..CCHHHHHHHHHHHEE CS
                   Methyltransf_11  75 ..edpekalkeiaRvLk 89 
                                         +++e+ l++ aRv+ 
  gi|320101474|ref|YP_004177066.1| 109 lrPKLERELRNGARVVS 125
                                       49999999999999985 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.6e-08   2.2e-05     161     257 ..      26     124 ..      17     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.6e-08
                              PrmA 161 egeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadvivaNI 234
                                       eg+ v D+G+G G iL +a++ ++ +k+v+v  D+  +k a++ ++  ++e++  v ++++ ++   ++a ++    
  gi|320101474|ref|YP_004177066.1|  26 EGDVVYDLGCGDGrILIVAVKEFNVRKAVGVERDSERIKEARRRISEEGIEDRAIV-VQGDFFEvdISEATIVTLFL 101
                                       466899******999*************************************8855.77888865344566666666 PP

                              PrmA 235 Laevlielaedikklvkegglli 257
                                       L +v   l +++ + +++g++++
  gi|320101474|ref|YP_004177066.1| 102 LTSVNEMLRPKLERELRNGARVV 124
                                       66666667788888887777665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0     4e-08   3.4e-05      14      77 ..      26      89 ..      18     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4e-08
                   Methyltransf_18 14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlek 77
                                      +g++v D G+  g + i +vke +++k++ ++  ++ +++a++ i+++g+ed+  v+ +d +e+
  gi|320101474|ref|YP_004177066.1| 26 EGDVVYDLGCGDGRILIVAVKEFNVRKAVGVERDSERIKEARRRISEEGIEDRAIVVQGDFFEV 89
                                      6889****************************************************99998775 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.4e-07   0.00037      28     118 ..      12      94 ..       6     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.4e-07
                                       HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EE CS
                              DOT1  28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakie 104
                                       ++++ e+l     ++ dv +DLG G G++ + a  e++++++vGvE   +         +e ++r++  G++  +i 
  gi|320101474|ref|YP_004177066.1|  12 YPVVREMLRLAGAGEGDVVYDLGCGDGRILIVAVKEFNVRKAVGVERDSER-------IKEARRRISEEGIEDRAI- 80 
                                       667888999999999*******************************76543.......344455555556665554. PP

                                       EESS-STT-HHHHH CS
                              DOT1 105 firksFvenekvee 118
                                        ++++F e ++ e 
  gi|320101474|ref|YP_004177066.1|  81 VVQGDFFEVDISEA 94 
                                       34566666555444 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.6e-07   0.00065      14      55 ..      27      69 ..      11     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.6e-07
                              MetW 14 gsrvldlGcGdGellellkeekqv.dgrGleldeegvaecvak 55
                                      g  v dlGcGdG +l +  +e +v ++ G+e d+e ++e+  +
  gi|320101474|ref|YP_004177066.1| 27 GDVVYDLGCGDGRILIVAVKEFNVrKAVGVERDSERIKEARRR 69
                                      56799********999988888883589*********998665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-06    0.0012      33      91 ..      28      88 ..      17      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                                      SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT CS
                               MTS 33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle 91
                                      + v DlGcG G + +++ ke +  + + v+ d + ++ a++ ++++++e  + vv+ d +e
  gi|320101474|ref|YP_004177066.1| 28 DVVYDLGCGDGRILIVAVKEFNVRKAVGVERDSERIKEARRRISEEGIEdrAIVVQGDFFE 88
                                      5589********************************************9887777777654 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-06    0.0014       4      56 ..      29      81 ..      26     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEE CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlril 56
                                      vv ++GcG G++l+   k++   + +G+E  +++++++ ++i +++++  +i+
  gi|320101474|ref|YP_004177066.1| 29 VVYDLGCGDGRILIVAVKEFNVRKAVGVERDSERIKEARRRISEEGIEDRAIV 81
                                      789*****************************************998776554 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.6e-06    0.0031      11      62 ..      16     100 ..       8     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
                   Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevl.rengf.svtgvDlspeaveiae........................ 61 
                                       ++ +rl++   +g  v d+GcG+G+ l v+ +e+ + + +gv+ ++e +++a+                        
  gi|320101474|ref|YP_004177066.1|  16 REMLRLAG-AGEGDVVYDLGCGDGRILIVAvKEFNVrKAVGVERDSERIKEARrriseegiedraivvqgdffevdi 91 
                                       55667776.67788999*******8888885666668**********999998888888887766655555555555 PP

                   Methyltransf_23  62 ........k 62 
                                                
  gi|320101474|ref|YP_004177066.1|  92 seativtlF 100
                                       555555550 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.4e-06    0.0038      65     132 ..      18      85 ..       7     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.4e-06
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES- CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgD 132
                                       +l l    +g+ v ++G+G G    v  + ++ + ++v++er  e ++ea+r++ ++++e + ivv gD
  gi|320101474|ref|YP_004177066.1|  18 MLRLAGAGEGDVVYDLGCGDGRILIVAVKEFNVR-KAVGVERDSERIKEARRRISEEGIEdRAIVVQGD 85 
                                       444444668999*********8877777666554.58*********************99778888888 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.9e-06    0.0059       2      47 ..      32      77 ..      31     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.9e-06
                   Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennn 47
                                      ++GcG+G++l +  +++   + +gv+ +++ i+ a++++++++ ++
  gi|320101474|ref|YP_004177066.1| 32 DLGCGDGRILIVAVKEFNVRKAVGVERDSERIKEARRRISEEGIED 77
                                      89************************************99987655 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.4e-05     0.012      65     133 ..      29      99 ..      14     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                       EEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS.-----TTEEEEES-TTTS-----SEEEE CS
                    Methyltransf_2  65 slvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehl.sageeervefvgGdffkdslPeaDaill 133
                                       +++D+G G G ++  +v+ +   k++  +  +e +++A++++ + g e+r  +v+Gdff+  + ea ++ l
  gi|320101474|ref|YP_004177066.1|  29 VVYDLGCGDGRILIVAVKEFNVRKAVGVERdSERIKEARRRIsEEGIEDRAIVVQGDFFEVDISEATIVTL 99 
                                       689*****************999987665426889*******88999****************99988876 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00042      0.36      20     113 ..      18      87 ..      14      99 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                                       HHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHH CS
                           UPF0020  20 lvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNa 96 
                                       ++rlag+ +g++ +D  CG G ilI a    + +                          +g++ d++ ++ ar+  
  gi|320101474|ref|YP_004177066.1|  18 MLRLAGAGEGDVVYDLGCGDGRILIVAVKEFNVRK------------------------AVGVERDSERIKEARRRI 70 
                                       99999999999999999999999997765554443........................345555555555555555 PP

                                       HHTT-GGGEEEEE--GG CS
                           UPF0020  97 ekagvgdliefsqadaa 113
                                       ++ g++d+  ++q d+ 
  gi|320101474|ref|YP_004177066.1|  71 SEEGIEDRAIVVQGDFF 87 
                                       55555555555555544 PP

>> Methyltransf_20  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.1e-05     0.027     127     199 ..      20      90 ..      14     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                   Methyltransf_20 127 rlkaegrpvrildiaaGhGryvldalekaeervesillrdyselnveqGraliaekglediarfekgdafdee 199
                                       rl  +g+   + d+ +G Gr ++ a+++ + r+   + rd     +++ r+ i+e+g+ed a + +gd f+ +
  gi|320101474|ref|YP_004177066.1|  20 RLAGAGEGDVVYDLGCGDGRILIVAVKEFNVRKAVGVERDSE--RIKEARRRISEEGIEDRAIVVQGDFFEVD 90 
                                       566666666789*******************99999999954..57899*********************865 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.3e-05     0.071      30      69 ..      10      49 ..       7      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                          N6_Mtase 30 TPrevsklivellepksgesvyDpacGsggllvqaekvlk 69
                                      TP  v++ + +l+   +g +vyD  cG g +l+ a k ++
  gi|320101474|ref|YP_004177066.1| 10 TPYPVVREMLRLAGAGEGDVVYDLGCGDGRILIVAVKEFN 49
                                      9********************************9998765 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.11     177     229 ..      11      66 ..       7      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                       -HHHHHHHH.HHHS-TT-EEEETT-TTTHHHHHHHHT.T.-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 177 PvallerlI.klstkkgdivlDpFaGSGtTavaakel.g.rkfiGieieeeyvela 229
                                       P   +++++ ++   +gd+v D  +G G ++++a ++ + rk++G+e + e+++ a
  gi|320101474|ref|YP_004177066.1|  11 PYPVVREMLrLAGAGEGDVVYDLGCGDGRILIVAVKEfNvRKAVGVERDSERIKEA 66 
                                       6666777774567789*************9987766524499*********99876 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.27       1      60 [.      30      89 ..      30     101 .. 0.92
   2 ?    0.1   0.0      0.59   5.1e+02     150     183 ..      93     126 ..      88     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                              TrmK  1 laDiGsDHAyLpiylvknnkvsvaiagevnegplesAkknvkkskleekievrlgdGlav 60
                                      ++D+G+  +++ i +vk+ +v+ a+ +e  +   ++A++ +++++ e++  v +gd ++v
  gi|320101474|ref|YP_004177066.1| 30 VYDLGCGDGRILIVAVKEFNVRKAVGVERDSERIKEARRRISEEGIEDRAIVVQGDFFEV 89
                                      58******************************************************9987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.59
                              TrmK 150 kdlrlgplLlkeksalfkkkwkkeleklkkilsk 183
                                       ++ ++  +Ll + +++++ k+++el++ ++++s+
  gi|320101474|ref|YP_004177066.1|  93 EATIVTLFLLTSVNEMLRPKLERELRNGARVVSH 126
                                       5566777899999999999999999988877664 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.12       3      61 ..      29     104 ..      27     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvf..ekviaieinleklacaqhNaevYgvsdkitlvlgdvfe...............l 61 
                                       v+ Dl +G G   i   ++f  +k +++e + e+++ a +     g++d+  +v+gd+fe                
  gi|320101474|ref|YP_004177066.1|  29 VVYDLGCGDGRILIVAVKEFnvRKAVGVERDSERIKEARRRISEEGIEDRAIVVQGDFFEvdiseativtlflltS 104
                                       567888888888777777762257899********************************97666666555554441 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.16      34      81 ..      30      79 ..      15     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      EEEES-TTSHHHHHHHHTT-EEE...EEES-HHHHHHHHHHHHHTT-TTEE CS
                              TehB 34 vldlgcgqgrnslylsllgydvt...awdknensiafleeikekenlknis 81
                                      v dlgcg+gr  l ++++ ++v     ++++++ i+  ++ ++ e +++  
  gi|320101474|ref|YP_004177066.1| 30 VYDLGCGDGRI-LIVAVKEFNVRkavGVERDSERIKEARRRISEEGIEDRA 79
                                      68*******95.889******963223677777788888888888777432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1092.85
//
Query:       gi|320101475|ref|YP_004177067.1|  [L=149]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1156.54
//
Query:       gi|320101476|ref|YP_004177068.1|  [L=937]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0038   16.9   0.1      0.034   13.8   0.0    2.1  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0052   16.5   0.0        0.3   10.8   0.0    2.5  2  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
       0.25   10.6   0.2       0.76    9.0   0.1    1.8  2  Beta_elim_lyase  Beta-eliminating lyase
        3.1    8.3   4.4       0.81   10.2   0.1    2.3  3  ZapA             Cell division protein ZapA


Domain annotation for each model (and alignments):
>> 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 !   13.8   0.0   7.6e-06     0.034      18      81 ..     125     187 ..     118     215 .. 0.79
   2 ?   -0.0   0.4      0.13   5.7e+02     175     199 ..     536     554 ..     521     560 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.6e-06
                                       ...--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH.TCTTGG CS
                   MethyltransfD12  18 kd.kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykaliknnveelikelekllekee 81 
                                       kd ++ t+v+p aGgg++ +e ++ g + ++ D+n+ ++ + +a+i+  + ++  +l kl e+ e
  gi|320101476|ref|YP_004177068.1| 125 KDpREITVVDPMAGGGSIPLESLRLGFRTIAGDLNPVSYLILRATIEF-PAKYGRKLLKLVEE-E 187
                                       55566799**************************************96.66666666655433.3 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.13
                                       -TTE.EEEE--S-T.S...TS--GG CS
                   MethyltransfD12 175 kieddivYlDPPYnprqytanytly 199
                                       +++ d+v +DPPY        +++y
  gi|320101476|ref|YP_004177068.1| 536 EKSVDVVDVDPPYYD------QHDY 554
                                       678999*******85......4444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   6.6e-05       0.3      30      64 ..     130     164 ..     117     198 .. 0.77
   2 ?    2.8   0.0     0.018        83     108     132 ..     523     549 ..     514     561 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.6e-05
                                       S-EEETT-TTSHHHHHHHHHHTT--TTTT----SS CS
                           UPF0020  30 epllDPmCGsGtilIEaallganiapgllrefvle 64 
                                        + +DPm G+G+i++E   lg + ++g l +  + 
  gi|320101476|ref|YP_004177068.1| 130 ITVVDPMAGGGSIPLESLRLGFRTIAGDLNPVSYL 164
                                       5789************9999888887777666555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.018
                                       EE--GGG--..STTS---EEEE----- CS
                           UPF0020 108 sqadaakLr..lkegevdvivtnpPYG 132
                                       + +da+++   l+e++vdv+  +pPY 
  gi|320101476|ref|YP_004177068.1| 523 YLWDAREIDkhLPEKSVDVVDVDPPYY 549
                                       568999998888999***********6 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00017      0.76     150     192 ..     311     353 ..     304     354 .. 0.89
   2 ?   -2.3   0.0      0.47   2.1e+03     216     252 ..     866     901 ..     808     910 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEE CS
                   Beta_elim_lyase 150 lrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsv 192
                                       +++v++  ++y  p  lD+AR+++aak+l+  ++e +s  Ds+
  gi|320101476|ref|YP_004177068.1| 311 IAAVQKARERYSPPSELDAARLVDAAKELARCAREEMSRGDSI 353
                                       7788888889999999*********************999985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.47
                                       ..HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHS CS
                   Beta_elim_lyase 216 edylaerveqrkylggglrqagvlaaleagiraleeg 252
                                       e  + e +++++++ + +r+ gv aa e  +  +++ 
  gi|320101476|ref|YP_004177068.1| 866 ETVIGESITLVEQVRKTMRELGVRAA-EDIVLKSDRS 901
                                       56788889999999999999999999.6666666555 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.6   1.2e+04      21      40 ..     176     195 ..     174     200 .. 0.79
   2 ?   -3.2   0.2       2.7   1.2e+04      28      51 ..     309     332 ..     296     349 .. 0.55
   3 ?   10.2   0.1   0.00018      0.81      13      52 ..     384     422 ..     380     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.6
                              ZapA  21 ylreaaklvdekikeireag 40 
                                       y r++ klv+e++++++e +
  gi|320101476|ref|YP_004177068.1| 176 YGRKLLKLVEEEFRMLKEYT 195
                                       55899999999999998865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                              ZapA  28 lvdekikeireaggnlseerllvm 51 
                                       +v + +++ re+++  se +++ +
  gi|320101476|ref|YP_004177068.1| 309 YVIAAVQKARERYSPPSELDAARL 332
                                       555555555555554444444444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00018
                              ZapA  13 aceegeeeylreaaklvdekikeireaggnlseerllvma 52 
                                        +++ e  +l ++ k+v e+++++ e++g+l++  +l ma
  gi|320101476|ref|YP_004177068.1| 384 FTPR-ELLALYKLTKYVRERARQLHEQYGELGDAVALYMA 422
                                       5555.4668999**********************888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (937 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.75u 0.25s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 6173.82
//
Query:       gi|320101477|ref|YP_004177069.1|  [L=916]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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        2.3    8.2   0.0    3.4  3  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.052   13.3   0.0       0.18   11.5   0.0    1.9  1  MIF4G_like  MIF4G like
        0.1   12.4   0.0       0.27   11.1   0.0    1.8  1  rve_3       Integrase core domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00039       2.3       6      49 ..      61     104 ..      56     113 .. 0.83
   2 !    4.1   0.0     0.007        42     122     157 ..     183     220 ..     156     229 .. 0.72
   3 ?   -0.6   0.0      0.19   1.2e+03      44      76 ..     591     621 ..     584     663 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierll 49 
                                       e  +e+i+n++++l+s++   +++ +  G+GKT +++ l   ++
  gi|320101477|ref|YP_004177069.1|  61 EGFAEIIKNIVNTLSSRGVDGIFLDLDMGSGKTHLLTLLLHLFA 104
                                       555799*********99999999***********9988776655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.007
                                       .....HHHTTT-SEEEEETGGGTTS...TTTHHHHHT- CS
                            ResIII 122 eeeseellrdrfdviiiDEaHrlgak..kswreilekf 157
                                        +  ++   +++ +i+iDE H ++     s rei++ f
  gi|320101477|ref|YP_004177069.1| 183 VKLAQSIPLKNHILILIDELHYSAILgtRSSREIVKEF 220
                                       5566677778889*********9885433666665544 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.19
                                       HHHHH-S.....-EEEEESSHHHHHHHHHHGGG CS
                            ResIII  44 lierllkkgkeekflflvprkslleqtleefkk 76 
                                        ++++l+ +   +++f+ pr+   e +++++++
  gi|320101477|ref|YP_004177069.1| 591 EAREYLRRKAMHNVVFVLPRI--KESLIRDMAD 621
                                       456666666777*******97..2333333333 PP

>> MIF4G_like  MIF4G like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.1e-05      0.18      94     121 ..      12      39 ..       2      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.1e-05
                        MIF4G_like  94 sllteicklaPkavaPslGrairllyaa 121
                                         l ei++l+P+ +aPs+G +ir l ++
  gi|320101477|ref|YP_004177069.1|  12 PYLEEIIRLSPDDLAPSFGTVIRALVDQ 39 
                                       5689*******************99876 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.5e-05      0.27       7      49 ..     303     345 ..     297     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.5e-05
                             rve_3   7 yiapgkPqqNglvEsfngtlrdellneelfrslaearekleaw 49 
                                       + + gkP    ++Esfng + + +   + f + ++ r++++a+
  gi|320101477|ref|YP_004177069.1| 303 RLKLGKPFNEVFHESFNGFIERVIKADSDFPDAHHMRSLIKAF 345
                                       56779**********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (916 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); 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: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 6145.42
//
Query:       gi|320101478|ref|YP_004177070.1|  [L=228]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       419  (0.02337); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1721.39
//
Query:       gi|320101479|ref|YP_004177071.1|  [L=282]
Description: D-aminopeptidase DppA [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-81  273.6   0.0    1.8e-81  273.4   0.0    1.0  1  Peptidase_M55  D-aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M55  D-aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.4   0.0     1e-85   1.8e-81       1     263 [.       1     265 [.       1     266 [. 0.98

  Alignments for each domain:
  == domain 1  score: 273.4 bits;  conditional E-value: 1e-85
                     Peptidase_M55   1 MkvyISaDiEGvagvvsweqvepgeaeyerarrlmteevnaaiegalaagatevlVnDsHgsmrNllpeeLdervrl 77 
                                       M++++S+D+EG+  ++s e++  ++a +++arr+ t+   + +e++++ g++ev+++DsHg+m Nl++e+L+e v+l
  gi|320101479|ref|YP_004177071.1|   1 MRLFMSIDMEGMPFIASGEHLYIKGALFSEARRIATRITLWTAEAFHQRGFNEVVIADSHGPMVNLDVESLPEYVTL 77 
                                       9**************************************************************************** PP

                     Peptidase_M55  78 isGkpkplsmmegldesfdavlfvGyHaragtekgvlaHTysgsaieevrlngkevgEfglnaalagelgVPvvlvs 154
                                       i+G p+plsm++g+ e+ dav+f+GyH++agt+k++++HTys++ i ++++ng++++Ef ln+++ag+++ Pv++v+
  gi|320101479|ref|YP_004177071.1|  78 IRGFPRPLSMVTGV-EKADAVVFLGYHSKAGTPKSTFDHTYSSAIIDSLEINGTPASEFLLNTYTAGHFNKPVIMVA 153
                                       *************9.78************************************************************ PP

                     Peptidase_M55 155 GDdalce.eakellpevetvavkeglgrfaakslspeeaeeaireavkeavekake..akplkleepvelevefkst 228
                                       GD+al+e ++++++p+++ v++ke+++rfa+ s s e++++++++av eave++++  akpl++  pve++v+f  t
  gi|320101479|ref|YP_004177071.1| 154 GDKALIEeDVARYTPWATRVTLKESYSRFASSSPSLEKIRKELEKAVVEAVERLNKgeAKPLRARYPVEVKVRFLGT 230
                                       ****976258*******************************************99999******************* PP

                     Peptidase_M55 229 alAdaaslvpgveridartvefeaedveellrale 263
                                       ++Ad+a+l+p +erid++tv++ a+d++e++r++e
  gi|320101479|ref|YP_004177071.1| 231 EMADVAELLPLIERIDGKTVKYVARDIVEAYRIFE 265
                                       ********************************997 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:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2006.61
//
Query:       gi|320101480|ref|YP_004177072.1|  [L=477]
Description: amino acid permease [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-40  139.2  49.8      2e-40  138.9  49.8    1.1  1  AA_permease_2  Amino acid permease
    1.4e-30  106.3  46.7    2.1e-30  105.7  46.7    1.2  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.9  49.8   2.3e-44     2e-40       3     424 ..       9     435 ..       7     442 .. 0.84

  Alignments for each domain:
  == domain 1  score: 138.9 bits;  conditional E-value: 2.3e-44
                     AA_permease_2   3 llsafalvigsvigsgifvkn....laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       +   +al +  ++g+  +  n    +++ +g +++ +++ +v++    ++l+y E++sa++r+gG++ +++ a g  
  gi|320101480|ref|YP_004177072.1|   9 WYHILALGVAGIVGTSWVYLNttfyDLYGPGGVILGYIVATVMAS--LMALAYSEMGSAINREGGEVAFVYPALGAA 83 
                                       666666666666774444444577788889997777666666665..6********999*****************9 PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgn..........twltyliaiaililvalinirgikesak 142
                                         f++aw+++++ ++++ s  ++++++ll++++p+l++             ++++++ +  ++v+++n++g k +++
  gi|320101480|ref|YP_004177072.1|  84 GSFFVAWMFLLGMLAAALSFYVIGIAFLLSWVFPQLNTMplyyvagypvYLPWIIVGYISALIVFALNYFGAKLTGN 160
                                       99**********99998888888***********8865588999999885566777777778899************ PP

                     AA_permease_2 143 iqnilgilkillpliiliilglitvdgggfsslstetdtffpngwpgv..llgllivlwsfdGfesaanvseevkk. 216
                                       +q+ l+il i l  +il++++ i+++ + f         f p++ p v  ++  l  + +++Gfe+   ++ee k  
  gi|320101480|ref|YP_004177072.1| 161 VQTALFILLI-LCGAILVAVAAIYGSLNNFM------PPFKPGTDPAVsaFRFALLGIGYLSGFETLPMIAEESKVs 230
                                       **********.69999999999999777774......567777777644466667778899************7744 PP

                     AA_permease_2 217 .kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavg.gkvvaiivvilialsllgainta 291
                                        +++ +   +++++++++y+l+++a + ++p+ + +++++     +l  e++  ++++ ++++++ +l+l+ + + a
  gi|320101480|ref|YP_004177072.1| 231 pRKFGYLVALSAVLAGMFYTLMMFAGALIIPWQGSSTVAPR----GLIDEMSMiHPALGWVAWLASFLGLVTSWIPA 303
                                       69********************************9998874....466666655689999999999*********** PP

                     AA_permease_2 292 vigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisylllii 367
                                       ++++sr+++alar g +P+ f   + k+g p+ra+++++ +slil+l   l  ++ + + l+vs + l +++l ++i
  gi|320101480|ref|YP_004177072.1| 304 LMTVSRMIYALARGGLFPKQFEYLHpKYGVPTRAMVFVLAISLILGL---L-GRKGLVWFLDVSGVTLGVCWLTTVI 376
                                       ******************************************88762...2.389********************** PP

                     AA_permease_2 368 galilrkkrphlkr....pgkilvaiigalfllfllvalffppkgpatqssliytiiltva 424
                                       ++li rk+ p+l+r    p+++lv+ +++++ l+++v++ +p+   +++  + y ++l++a
  gi|320101480|ref|YP_004177072.1| 377 TMLICRKRYPQLERpfrvPAAWLVGPLALIIGLIVVVTPLIPG--TDVSLVWPYEYVLLIA 435
                                       ************9966666669999999999999999999995..4555456666555554 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7  46.7   2.4e-34   2.1e-30       1     476 [.      11     454 ..      11     456 .. 0.86

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 2.4e-34
                       AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfv 77 
                                       h+l   ++g++Gt     +       Gp+g++l+y++a+v+  l++l+ +e+ +++++ gg  +++   lg + +f+
  gi|320101480|ref|YP_004177072.1|  11 HILALGVAGIVGTSWVYLNTTFYDLYGPGGVILGYIVATVMASLMALAYSEMGSAINREGGEVAFVYPALGAAGSFF 87 
                                       7888899999999999999999999**************************************************** PP

                       AA_permease  78 iGlnylfswitvlaleltaasi..liqfwelvtdlpkawvt..............gavflvvlliinlvgvkvygea 138
                                       ++++ ++++ +++al + +++i  l++++  +++l+++  +              g +  ++++++n++g+k+ g +
  gi|320101480|ref|YP_004177072.1|  88 VAWM-FLLGMLAAALSFYVIGIafLLSWV--FPQLNTMPLYyvagypvylpwiivGYISALIVFALNYFGAKLTGNV 161
                                       ****.666666666666555541166666..999997777799********************************** PP

                       AA_permease 139 efilalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfa...f 212
                                       ++ l++++i++ ++++ v +i+ +  +  +                 + pg        +   +s+f +++++   +
  gi|320101480|ref|YP_004177072.1| 162 QTALFILLILCGAILVAVAAIYGSLNNFMPP----------------FKPG--------TDPAVSAFRFALLGigyL 214
                                       *******************777766665555................7777........566666666666651115 PP

                       AA_permease 213 tGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgv.svl 288
                                       +G+e +++ia+E+k + ++    +    ++ ++fY+l++++  l++p++  + ++       p  ++ ++s++ ++l
  gi|320101480|ref|YP_004177072.1| 215 SGFETLPMIAEESKVSPRKFGYLVALSAVLAGMFYTLMMFAGALIIPWQGSSTVA-------PRGLIDEMSMIhPAL 284
                                       7*************************************************77777.......566777777764789 PP

                       AA_permease 289 aplinaviltaalssansslysasRvlyslakdglaPkvlkk.vskrgvPlraillsmiisllalllaslnlaapiv 364
                                       + +  +++++ ++ s + +l++ sR++y+la+ gl+Pk +++ + k+gvP ra++++++isl++ ll    l     
  gi|320101480|ref|YP_004177072.1| 285 GWVAWLASFLGLVTSWIPALMTVSRMIYALARGGLFPKQFEYlHPKYGVPTRAMVFVLAISLILGLLGRKGLV---- 357
                                       999999*******************************88888358***********************99999.... PP

                       AA_permease 365 fnfllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgp 441
                                         ++l +s++   ++wl + ++ l  Rk +   +r         ++ +  ++lv  + +ii li+ ++++++    +
  gi|320101480|ref|YP_004177072.1| 358 --WFLDVSGVTLGVCWLTTVITMLICRKRYPQLER---------PFRVPAAWLVGPLALIIGLIVVVTPLIP----G 419
                                       ..**************************9655555.........6666677777777777777777776666....4 PP

                       AA_permease 442 kdwgaasfaaaylivllfliilvgvklhvknkrpq 476
                                        d++ +   +  l + ++l+ +++++ +v++++++
  gi|320101480|ref|YP_004177072.1| 420 TDVSLVWPYEYVLLIAWVLLGIFVYFAYVRKRIRE 454
                                       44555555777888999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3262.26
//
Query:       gi|320101481|ref|YP_004177073.1|  [L=340]
Description: membrane dipeptidase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-82  277.2   0.0    1.8e-82  277.1   0.0    1.0  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
  ------ inclusion threshold ------
      0.021   14.6   0.0       0.07   12.9   0.0    2.0  1  Amidohydro_2   Amidohydrolase


Domain annotation for each model (and alignments):
>> Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.1   0.0     2e-86   1.8e-82       7     318 ..       3     336 ..       1     337 [. 0.95

  Alignments for each domain:
  == domain 1  score: 277.1 bits;  conditional E-value: 2e-86
                                       .EEEEEE-HHHHHHHCTTTTT...-TTTHCTSSS-HHHHHHHTEEEEEEEEE--C....................CC CS
                     Peptidase_M19   7 iviDghndlplklrqekkesl...llekdselqtdlerlraggvsavlfaifvpe....................da 60 
                                       +viD h d+++++  ++  +    l  +    + d++++ +g v++v++aif+                      + 
  gi|320101481|ref|YP_004177073.1|   3 PVIDMHEDVSAYFLYHGGGEPlgdLRSDIPGRDADIPKYFRGNVKLVFAAIFPGIetfrpeeskkleklygkwlpAI 79 
                                       89**********9999988888966666677889******************44477*****************999 PP

                                       CCCCHHHHHHHHHHHHHHHHHHGTTTEEE-SSHHHHHHHHH.TT-EEEEEEEESCGGGTT-HHHHHHHHHTTEEEEE CS
                     Peptidase_M19  61 syeeavkatleqidlirrlvrknpeqlklvrtaddierakk.egkiavllgiegaealgddlallrafyalGvrvlg 136
                                        y+   +++le +++++rl +++pe ++lv++a d+er    +gki++l+++egaea+ dd   l  ++++G+r+lg
  gi|320101481|ref|YP_004177073.1|  80 GYRAPQTDVLEHFAIYYRLAEAYPE-ITLVESAGDAERVLSeDGKIGLLIHMEGAEAI-DDPYDLVLLKKMGLRSLG 154
                                       9999********************9.************887589**************.8899999*********** PP

                                       S-SSS-BSSB-BCCGTT.SSSSB-HHHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH-SSE.EECCEEBTTTS--TT CS
                     Peptidase_M19 137 ltynrnnkfAdgaleekdedgGLsefGkelVrelNrlgiliDlShlsektfldvlelSkaPvvaSHSnaralcdhpR 213
                                       lt+n+nnk+++g++++  +d GL++ G+elVr +N+lgi+iDl+h+++kt+l+++++Sk+Pv++SH+n+r+++d pR
  gi|320101481|ref|YP_004177073.1| 155 LTWNYNNKYGSGCTSK--KDYGLTPEGEELVRMANKLGIIIDLAHAGKKTALETMAVSKKPVIISHANVRKFVDTPR 229
                                       ***************9..*********************************************************** PP

                                       SB-HHHHHHHHHTT-EEEE-SSHHHCTTTS--BHHHHHHHHHHHHHHT-GGGEEE---T...TTTSS-BBTBSSGGG CS
                     Peptidase_M19 214 NltDeqlkaiaesgGvvgvtfvpaflkekaeatledvvdhidyivelaGidhVGlGsDf...dgggelpegledvsk 287
                                       N++De+l+a+ ++gGvvg+ +++  + +k+++t+ed+v+h  yi e++G+d  ++G+Df    g +  pegle+v+k
  gi|320101481|ref|YP_004177073.1| 230 NIDDEVLEALHKNGGVVGLSVIGPLIASKPKPTMEDLVQHFLYIHERYGADLLAIGTDFhglLGLP-APEGLESVDK 305
                                       ***********************************************************5533444.49******** PP

                                       HHHHHHHHHHTTS-HHHHHHHHTHHHHHHHH CS
                     Peptidase_M19 288 lpnltaeLlrrgyseadiekilggNflrvle 318
                                       ++ l+++L ++g  ++d++ki+++N+lrv++
  gi|320101481|ref|YP_004177073.1| 306 IQSLLQRLGEKGLGDNDLRKIAYENALRVIK 336
                                       *****************************97 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.8e-06      0.07     212     288 ..     247     334 ..     113     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.8e-06
                                       EECCGHHH..SSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH.........SSHHHH CS
                      Amidohydro_2 212 klsglyte..llyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlval.........lsdeer 277
                                        ls +++   +++  + ++  +++  + e +g+d +  G+D+    +   pe l  +d+++          l d+++
  gi|320101481|ref|YP_004177073.1| 247 GLSVIGPLiaSKPKPTMEDLVQHFLYIHERYGADLLAIGTDFHGLLGLPAPEGLESVDKIQSllqrlgekgLGDNDL 323
                                       55555555666666666777777777788889999999****9999999999999999999999************* PP

                                       HHHHTHHHHHH CS
                      Amidohydro_2 278 ekilggNAarl 288
                                       +ki+++NA r+
  gi|320101481|ref|YP_004177073.1| 324 RKIAYENALRV 334
                                       **********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2558.63
//
Query:       gi|320101482|ref|YP_004177074.1|  [L=218]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-26   91.1  11.8    9.5e-26   90.7  11.8    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 !   90.7  11.8   5.3e-30   9.5e-26       1     184 [.      31     216 ..      31     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 5.3e-30
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g+l+G++a+ ++++ +d++l+++++++l lP++ ++il+          g+     vi+++++++++++rl+r+++ 
  gi|320101482|ref|YP_004177074.1|  31 GTLVGLIAG-YYGGLVDDILSTITDIMLLLPVLPFMILMA------AFMGQDYQNiVIAIAAFTWPGVARLVRAQVA 100
                                       789******.************************999999......78898888879******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       +   + ++eaa+a+Ga+  +i+r ++lP++ p ++++++l+ gg++ + + l+flg    lg+++  + +g ++ ++
  gi|320101482|ref|YP_004177074.1| 101 SLKGSLYIEAAKAYGAGSGRIMRVHILPQLYPLLVAFVVLRTGGAIIAEASLSFLG----LGDPTQKS-WGGMIYWA 172
                                       ********************************************************....99776655.55555555 PP

                      BPD_transp_1 154 s.............nggvlalviavlllnlvadilqrlldprvr 184
                                       +             +++ l++++ v +  l+ +++ ++++pr+r
  gi|320101482|ref|YP_004177074.1| 173 MnsgaissgkwwwiVAPGLMITLTVEATALIGYAIEEYVNPRLR 216
                                       5588889999********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1855.72
//
Query:       gi|320101483|ref|YP_004177075.1|  [L=260]
Description: tRNA (adenine-N(1)-)-methyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  118.3   0.0    4.8e-31  108.3   0.0    2.0  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    2.7e-09   37.0   0.0    4.2e-09   36.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.1e-07   31.0   0.0    8.8e-07   29.6   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
    2.8e-06   27.3   0.0    4.1e-06   26.7   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    9.4e-06   26.2   0.0    3.6e-05   24.3   0.0    2.0  1  Methyltransf_11  Methyltransferase domain
    0.00012   22.7   0.0    0.00029   21.5   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    0.00019   20.8   0.0    0.00038   19.9   0.0    1.6  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00033   20.5   0.4    0.00074   19.3   0.4    1.7  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
     0.0022   17.7   0.1      0.035   13.8   0.1    2.3  1  UPF0020          Putative RNA methylase family UPF0020
     0.0037   18.2   0.0      0.012   16.6   0.0    1.8  2  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.7   0.0       0.25   11.3   0.0    2.6  3  rRNA_methylase   Putative rRNA methylase
      0.028   13.8   0.0      0.041   13.3   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.053   13.0   0.0       0.25   10.8   0.0    1.9  1  Methyltransf_4   Putative methyltransferase
      0.065   13.1   0.0       0.28   11.0   0.0    1.9  1  Methyltransf_23  Methyltransferase domain
       0.17   11.8   0.0       0.33   10.9   0.0    1.4  1  Methyltransf_18  Methyltransferase domain


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 !  108.3   0.0     4e-34   4.8e-31       5     183 ..      62     237 ..      60     239 .. 0.95
   2 !    9.6   0.0   0.00056      0.67     227     247 .]     236     256 ..     234     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 4e-34
                             GCD14   5 vlaptPeLWtlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraeka 81 
                                       v++p P  ++l  +  tqi+y +D  l+i    +kpGs++ e+G Gsg+l+ a+a  ++ tG l+ f+  e+  e+ 
  gi|320101483|ref|YP_004177075.1|  62 VFKPLPHDYALLASRVTQIIYPKDAGLMIYLSGVKPGSRIGEAGVGSGALTIALASIIGETGILYGFDISEKSLENT 138
                                       6788899999999999************************************************************* PP

                             GCD14  82 reefrehelsqlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtcea 158
                                       r ++++++l + v ++++Dv +     ++ +  +a fLD+P Pw+a++ +a+ l + gg l ++ P ++qv +t+ +
  gi|320101483|ref|YP_004177075.1| 139 RINLEKTGLLNRVRLQKHDVREP---VKLPHALNAFFLDIPDPWNAVNTIAELL-EPGGTLLAYIPTVNQVEKTVIT 211
                                       ********************874...48999********************999.99999***************** PP

                             GCD14 159 Lrel.gfteietlevllrtyevrksk 183
                                       Lre+ gf +i+t e llr+y+v k+ 
  gi|320101483|ref|YP_004177075.1| 212 LREHgGFADIHTYETLLREYKVEKNA 237
                                       **9946***************99865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00056
                             GCD14 227 vllkPvselkghtgyLtfatk 247
                                        +++P++ + ghtgy++fa+k
  gi|320101483|ref|YP_004177075.1| 236 NAVRPFTRMIGHTGYIVFARK 256
                                       6789***************85 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   3.5e-12   4.2e-09       6     109 ..     100     197 ..      96     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.5e-12
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlils 80 
                                       r+ ++G G+G+lt++la+ +g+ + ++G+Dise+++e  r n++k gl  +v++++ d+ e  +  l          
  gi|320101483|ref|YP_004177075.1| 100 RIGEAGVGSGALTIALASIIGETGILYGFDISEKSLENTRINLEKTGLLnRVRLQKHDVREpVK--LP-H-----AL 168
                                       6678999****************************************9879**********666..44.2.....34 PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilli 109
                                       n+++ +++dp ++ + i ++l+pgg ll+
  gi|320101483|ref|YP_004177075.1| 169 NAFFLDIPDPWNAVNTIAELLEPGGTLLA 197
                                       566789********************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   7.3e-10   8.8e-07       3      97 .]     103     193 ..     101     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 7.3e-10
                                       EET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaed.lpfedgsfDlvvssgalh 75 
                                       ++G G+G lt+ala  +g  + ++g+Dise+ le++r ++e+ gl  +v+++++d+++ +++++   ++ +      
  gi|320101483|ref|YP_004177075.1| 103 EAGVGSGALTIALASIIGeTGILYGFDISEKSLENTRINLEKTGLlnRVRLQKHDVREpVKLPH-ALNAFF------ 172
                                       78************999769999*********************9***********88344443.333333...... PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                        l+ +d  +a++ ia++L+pgG
  gi|320101483|ref|YP_004177075.1| 173 -LDIPDPWNAVNTIAELLEPGG 193
                                       .355677889999999999998 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   3.5e-09   4.1e-06      62     179 ..      86     204 ..      62     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.5e-09
                                       HHHHHHHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGT CS
                              PCMT  62 valalelle.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkG 136
                                        +l + +l+ +k+g+r+ e G GsG lt  la ++ge+g + + + +++  e+++ nl+k +l  +v ++  D r+ 
  gi|320101483|ref|YP_004177075.1|  86 AGL-MIYLSgVKPGSRIGEAGVGSGALTIALASIIGETGILYGFDISEKSLENTRINLEKTGLLnRVRLQKHDVREP 161
                                       444.456666***************************************************9865899999999999 PP

                                       TGGG-SEEEEEESSBBS.S--HHHHHTEEEEEEEEEEESBSSSE CS
                              PCMT 137 yeekaPYdaihvgaaap.eiPealidQLkeGGrlvvPvgeeeeQ 179
                                       ++     +a ++ +  p +  +++ + L++GG l++ +  + +Q
  gi|320101483|ref|YP_004177075.1| 162 VKLPHALNAFFLDIPDPwNAVNTIAELLEPGGTLLAYIP-TVNQ 204
                                       998888899998887764556777788889999887666.4444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     3e-08   3.6e-05       2      95 ..     103     196 ..     102     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3e-08
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC.TSS-TT-EEEEEEES-CC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaek.lpfednsfDlvvssevlh 72 
                                       ++G+G+G+l+ ala+     + ++g+D+s++ l+  + + ++ gl  +v++++ d+++ ++++        ++ ++ 
  gi|320101483|ref|YP_004177075.1| 103 EAGVGSGALTIALASIIgetGILYGFDISEKSLENTRINLEKTGLlnRVRLQKHDVREpVKLPH------ALNAFFL 173
                                       58************5445667***********************9**9*********9557888......7888889 PP

                                       C-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  73 hvedpekalkeiaRvLkpgGllv 95 
                                        ++dp  a++ ia +L+pgG+l+
  gi|320101483|ref|YP_004177075.1| 174 DIPDPWNAVNTIAELLEPGGTLL 196
                                       99******************986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.5e-07   0.00029       2      99 .]     103     195 ..     103     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-07
                   Methyltransf_12   2 eiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       e G G+G+l+ al+  + ++  ++g Dis++++e+++  l k +    n+v+l++ d+ +     +    + +++l 
  gi|320101483|ref|YP_004177075.1| 103 EAGVGSGALTIALASIIgETGILYGFDISEKSLENTRINLEKTGL--LNRVRLQKHDVREP---VKLPHALNAFFLD 174
                                       789**********99995555666*********777777777666..66999998887643...3666666666666 PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                         +d+  +++ i++lL pgG l
  gi|320101483|ref|YP_004177075.1| 175 I-PDPWNAVNTIAELLEPGGTL 195
                                       5.9*****************86 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.2e-07   0.00038      38     106 ..      88     157 ..      59     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.2e-07
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE-- CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqan 106
                                        ++ l++vk+g+++ +   G+g l+++l++ +ge+g + + Di+e+ L+ ++  l+++g   ++++ + +
  gi|320101483|ref|YP_004177075.1|  88 LMIYLSGVKPGSRIGEAGVGSGALTIALASIIGETGILYGFDISEKSLENTRINLEKTGLLnRVRLQKHD 157
                                       56678999***************************************************98556654443 PP

>> GCD14_N  tRNA methyltransferase complex GCD14 subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.4   6.2e-07   0.00074       4      51 .]       5      52 ..       2      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.2e-07
                           GCD14_N  4 fraGdrVqL.tDaKgrkhtitLepGgefhthrGaieHDdlIGrpeGsVV 51
                                      +r+Gd V    D K r++    ++Gg   t++G+++ Dd++G+p Gs V
  gi|320101483|ref|YP_004177075.1|  5 IREGDDVLVvIDDK-RRFVAKARRGGVLGTDKGVVRLDDVVGKPYGSTV 52
                                      78999997615666.55667889***********************987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   2.9e-05     0.035      20     113 ..      89     159 ..      81     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                                       HHHHTT--TTS-EEETT-TTSHHHHHHH.HHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHH CS
                           UPF0020  20 lvrlagwkpgepllDPmCGsGtilIEaa.llganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareN 95 
                                       +++l+g+kpg+++ +   GsG++ I  a ++g++ +                        lyg+D+ ++ ++ +r N
  gi|320101483|ref|YP_004177075.1|  89 MIYLSGVKPGSRIGEAGVGSGALTIALAsIIGETGI------------------------LYGFDISEKSLENTRIN 141
                                       666666666666666666666666653303334444........................9**************** PP

                                       HHHTT-GGGEEEEE--GG CS
                           UPF0020  96 aekagvgdliefsqadaa 113
                                       +ek+g+ +++ +++ d++
  gi|320101483|ref|YP_004177075.1| 142 LEKTGLLNRVRLQKHDVR 159
                                       **************9997 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       9.7   1.2e+04      96      96 ..      26      26 ..       4      44 .. 0.53
   2 !   16.6   0.0     1e-05     0.012       2     102 ..     103     196 ..     103     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.7
                   Methyltransf_24 96 a 96
                                      +
  gi|320101483|ref|YP_004177075.1| 26 R 26
                                      2 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1e-05
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDg 77 
                                       E Gv sG  t++l++ + ++g   l+ +d  ++  e+++ +++++gl +rvrl k d +e + +l       +f+D 
  gi|320101483|ref|YP_004177075.1| 103 EAGVGSGALTIALASIIGETGI--LYGFDISEKsLENTRINLEKTGLLNRVRLQKHDVREPV-KLP-HALNAFFLDI 175
                                       78999***************97..******99866778899999**************9976.455.5788999999 PP

                   Methyltransf_24  78 ghaaeavledleallprlapggvvl 102
                                       +    +  ++++++ ++l pgg++l
  gi|320101483|ref|YP_004177075.1| 176 P----DPWNAVNTIAELLEPGGTLL 196
                                       8....67777778888888888876 PP

>> rRNA_methylase  Putative rRNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.25       1      31 [.     125     155 ..     125     173 .. 0.90
   2 ?   -0.5   0.0      0.94   1.1e+03      71      88 ..     180     197 ..     175     204 .. 0.87
   3 ?    0.8   0.0      0.37   4.4e+02      70     123 ..     202     257 ..     198     260 .] 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                       EEEEES-HHHHHHHHHHHHHTT-GGSEEEEE CS
                    rRNA_methylase   1 vyafDiQeeAleatkerleeekleervelil 31 
                                       +y+fDi e++le+t+ +le+++l +rv+l +
  gi|320101483|ref|YP_004177075.1| 125 LYGFDISEKSLENTRINLEKTGLLNRVRLQK 155
                                       59**********************9999865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.94
                                       HHHHHHHHHEEEEEEEEE CS
                    rRNA_methylase  71 kAlekalelLkkgGliti 88 
                                       +A++++ elL++gG ++ 
  gi|320101483|ref|YP_004177075.1| 180 NAVNTIAELLEPGGTLLA 197
                                       7999**********8865 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHEE.EEEEEEEEE--ST.CHHHHHHHHHHHHHHTS-TTTEEEEEEEE CS
                    rRNA_methylase  70 lkAlekalelLk.kgGlitivvYpGh.eeGkeEkeavleflssLdqkkyevlkyef 123
                                       ++ +ek++  L+ +gG+  i++Y    +e k Ek+av+ f++ + ++ y v+  + 
  gi|320101483|ref|YP_004177075.1| 202 VNQVEKTVITLReHGGFADIHTYETLlREYKVEKNAVRPFTRMIGHTGYIVFARKL 257
                                       55566665555415677789999765256788999999999999988888876655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-05     0.041     159     215 ..      95     153 ..      86     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                              PrmA 159 vkegeevlDvGtGSGiLaia.aakLgakkv.vavDiDevAvkvakeNaelNkveaklev 215
                                       vk+g+++   G GSG L+ia a+ +g   + ++ Di e +++ ++ N+e+ ++ +++++
  gi|320101483|ref|YP_004177075.1|  95 VKPGSRIGEAGVGSGALTIAlASIIGETGIlYGFDISEKSLENTRINLEKTGLLNRVRL 153
                                       7888888999*********9445567665538****************98877776654 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.25       7      85 ..     103     180 ..      99     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                                       EET-TTSHHHHHHHHHSTTSEEE.EEES-HHHHHHHHHHHHHCTTSS.EEEEES-CCCHHHHCS-TTSEEEEEEES- CS
                    Methyltransf_4   7 eiGcGkGeflvalAkknPdknfl.GiEirvkvvakvlkkiealelkN.lrilrgdalkvllelledgslekifilFP 81 
                                       e G+G+G +++alA    ++ +l G +i++k++++   + e+ +l N +r+ ++d  + +     ++ l+  f+  P
  gi|320101483|ref|YP_004177075.1| 103 EAGVGSGALTIALASIIGETGILyGFDISEKSLENTRINLEKTGLLNrVRLQKHDVREPV---KLPHALNAFFLDIP 176
                                       789****************99888******************988775888888876655...34789********* PP

                                       ---- CS
                    Methyltransf_4  82 DPwf 85 
                                       DPw+
  gi|320101483|ref|YP_004177075.1| 177 DPWN 180
                                       ***7 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.28      88     124 ..     168     204 ..      91     239 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                   Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllseplasl 124
                                       l+ ++  +pdp  ++++ia+ll+pgG ll   p++++
  gi|320101483|ref|YP_004177075.1| 168 LNAFFLDIPDPWNAVNTIAELLEPGGTLLAYIPTVNQ 204
                                       45566679********************988887664 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.33      10      79 ..      93     163 ..      87     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                   Methyltransf_18  10 slvekgsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievrlsdGleklk 79 
                                       s v++gsr+   G   g l+i+l++  g +   +  Di+e++le+ + n+ek+gl +++++   d  e++k
  gi|320101483|ref|YP_004177075.1|  93 SGVKPGSRIGEAGVGSGALTIALASIiGETGILYGFDISEKSLENTRINLEKTGLLNRVRLQKHDVREPVK 163
                                       567888888889999999999999752677778999***********************999888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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):              15  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1879.34
//
Query:       gi|320101484|ref|YP_004177076.1|  [L=152]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   12.3   0.0       0.21   11.7   0.0    1.3  1  DUF3850   Domain of unknown function (DUF3850)


Domain annotation for each model (and alignments):
>> DUF3850  Domain of unknown function (DUF3850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.1e-05      0.21       6      42 ..       8      45 ..       4      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                           DUF3850  6 ilpeyfeaVvsGkKtfeirk.nDrdyqvGDlLvLkeid 42
                                      i+p y   V +G+K+fe+r+    +++ GD ++L  + 
  gi|320101484|ref|YP_004177076.1|  8 IKPVYAYRVFTGSKKFELRRfLGLSVERGDRVILYVTG 45
                                      8999**************99667788888888876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1117.64
//
Query:       gi|320101485|ref|YP_004177077.1|  [L=59]
Description: CopG/Arc/MetJ family transcriptional regulator [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   38.5   0.3    8.4e-10   38.2   0.3    1.1  1  RHH_1           Ribbon-helix-helix protein, copG family
      2e-05   24.8   0.0    2.1e-05   24.7   0.0    1.0  1  RHH_8           Ribbon-Helix-Helix transcriptional regulator 
    3.9e-05   24.0   0.0    4.1e-05   23.9   0.0    1.1  1  ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin t
     0.0015   18.4   0.1      0.002   18.0   0.1    1.3  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


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 !   38.2   0.3   1.9e-13   8.4e-10       2      39 .]      11      49 ..      10      49 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.9e-13
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyler 39
                                      ++++++e ++e +del+r ++ +SrSe+IR A+r++l++
  gi|320101485|ref|YP_004177077.1| 11 ITVKMPELYVEGIDELVRIGRySSRSEVIRVAIRDLLKK 49
                                      8***********************************975 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   4.6e-09   2.1e-05       6      45 ..      11      50 ..       6      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.6e-09
                             RHH_8  6 vtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakh 45
                                      +t+ +  + +  iD Lv+ G Ys+R+++ir air+ L+k+
  gi|320101485|ref|YP_004177077.1| 11 ITVKMPELYVEGIDELVRIGRYSSRSEVIRVAIRDLLKKE 50
                                      789999999999***********************99875 PP

>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   9.2e-09   4.1e-05       9      48 ..      15      54 ..       9      59 .] 0.84

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9.2e-09
                                      --HHHHHHHHHHHCTTS-SSHHHHHHHHHHHHHHHHHHHH CS
                    ParD_antitoxin  9 LgehfsafidsqvaaGrYgsaseviraaLrLLeeretklk 48
                                      + e +   id  v  GrY s sevir a+r L ++e  +k
  gi|320101485|ref|YP_004177077.1| 15 MPELYVEGIDELVRIGRYSSRSEVIRVAIRDLLKKELWVK 54
                                      566777889*********************9988886665 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   4.5e-07     0.002      12      41 ..      23      53 ..      21      59 .] 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.5e-07
                                      XXXXXXXXXXXXXXXXXXXXXXX------.- CS
                    VapB_antitoxin 12 laeAirltglktKrEaVnlALreLiqrrk.r 41
                                      ++e +r+++++ ++E+++ A+r+L++++   
  gi|320101485|ref|YP_004177077.1| 23 IDELVRIGRYSSRSEVIRVAIRDLLKKELwV 53
                                      78889*********************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 439.96
//
Query:       gi|320101486|ref|YP_004177078.1|  [L=470]
Description: glycosyl transferase family protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-11   43.0  14.0    5.4e-11   43.0  14.0    2.9  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
    0.00063   19.4  26.2     0.0044   16.6  18.6    3.9  3  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3      0.51   4.6e+03     121     152 ..      12      21 ..       4      28 .. 0.39
   2 !   43.0  14.0     6e-15   5.4e-11       2     149 ..     152     293 ..     151     307 .. 0.75
   3 ?   -2.0   0.3      0.41   3.7e+03      23      58 ..     426     457 ..     411     468 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.51
                             PMT_2 121 lliaallyllisarrilkekkpylalllalll 152
                                       ll                      ++++al++
  gi|320101486|ref|YP_004177078.1|  12 LL----------------------VAAVALAV 21 
                                       11......................11222211 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 6e-15
                             PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsalftpdap 77 
                                       hPPl  +++a+ + ++g+  +  r++ +++g+ t++llyl +rrl+g + aal+a+ll ++ pl+ +l  +  +d +
  gi|320101486|ref|YP_004177078.1| 152 HPPLGKYIIAFTMYVLGDRPFYWRIPLIVLGASTTILLYLSLRRLTGsTIAALAASLLFTADPLVRTLFSIALLDGF 228
                                       9**********************************************666777777888889988877777776666 PP

                             PMT_2  78 lvllwalalylllraleknklkywllagvlfGlgflsKytaallliaall.yllis.arrilkekkpylallla 149
                                         +    ++++++ a+e++    +++a+ l+  g l+K+t ++ li++l+ yl    +rr    + +y   l a
  gi|320101486|ref|YP_004177078.1| 229 VAF---TSTLAFYLAVERRH--GLAVAASLV--GGLFKFTGLFTLIPLLVlYLRQGlRRRPSPYMLVYT--LTA 293
                                       555...55667788999998..455555554..4589*********98886665553333333333333..222 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.41
                             PMT_2  23 airlvsalagvltilllyllarrlfgkraallaall 58 
                                       ++ l++++ g l++ + y+l r+    + a+la + 
  gi|320101486|ref|YP_004177078.1| 426 SVQLAPFVYGGLVYTAAYALRRE----NLAYLAGFY 457
                                       55555555555555555555444....555555554 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0015        13      40      64 ..     147     171 ..     143     177 .. 0.80
   2 !   16.6  18.6   4.9e-07    0.0044      86     201 ..     175     278 ..     171     319 .. 0.77
   3 ?   -2.4   0.2      0.32   2.9e+03     167     173 ..     400     406 ..     358     421 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0015
                               PMT  40 ffmdvhpplgkmllalggyLagkdg 64 
                                       +   +hpplgk+ +a+ +y+ g  +
  gi|320101486|ref|YP_004177078.1| 147 YLNQEHPPLGKYIIAFTMYVLGDRP 171
                                       556799*************887655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.9e-07
                               PMT  86 RlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkferkapfsr 162
                                       R+  ++lg+ +++l+yl l++l+ s ++al a+ll++ ++++ tl  ++lld + +f  +l++y+ v+   +     
  gi|320101486|ref|YP_004177078.1| 175 RIPLIVLGASTTILLYLSLRRLTGSTIAALAASLLFTADPLVRTLFSIALLDGFVAFTSTLAFYLAVERR-H----- 245
                                       5556889*********************************************************999874.2..... PP

                               PMT 163 swwlwllltgvalglavsvKwvglftvllvgllliwelw 201
                                             l+   +  ++ + K+ glft++++++l + + +
  gi|320101486|ref|YP_004177078.1| 246 -----GLAVAAS-LVGGLFKFTGLFTLIPLLVLYLRQGL 278
                                       .....2333333.35677888888888888888776655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.32
                               PMT 167 wllltgv 173
                                       w++ltgv
  gi|320101486|ref|YP_004177078.1| 400 WVFLTGV 406
                                       3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3161.63
//
Query:       gi|320101487|ref|YP_004177079.1|  [L=255]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score 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   12.0   0.0       0.31   11.0   0.0    1.5  2  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family


Domain annotation for each model (and alignments):
>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.7e-05      0.31      57     120 ..      85     160 ..      38     178 .. 0.75
   2 ?   -2.8   0.0       0.3   5.3e+03      43      68 ..     218     243 ..     205     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.7e-05
                   Glyco_tran_WecB  57 lekaaerlrekypglriagthdg............ykeeeeeaiieainaskpdlllvglGapkqEkwiarlkeel 120
                                       + ++a+r++  +   ++ag+ +             y+e  e+a++e++++ kpd + + lG  ++  ++a+  +++
  gi|320101487|ref|YP_004177079.1|  85 VVTVADRICCSIVAAQVAGYMHRhgygngvfkvffYEEGGEDALAEEVASMKPDAVSIVLGGEQKMSFVASATQRV 160
                                       44555666666668888888877665555555443338999**********************9999999888754 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.3
                   Glyco_tran_WecB  43 eglrvfllGgkpevlekaaerlreky 68 
                                       +  ++ +  gkp+ ++ a+++l+e++
  gi|320101487|ref|YP_004177079.1| 218 NYSKILFTEGKPSLVKYAESNLTEEH 243
                                       45678888888999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1838.05
//
Query:       gi|320101488|ref|YP_004177080.1|  [L=431]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.6    9.1   0.0        1.6    9.1   0.0    3.5  4  DUF4199   Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   7.6     0.082   1.5e+03       3      87 ..     108     180 ..     106     190 .. 0.67
   2 ?   -2.2   0.1      0.27   4.8e+03       6      23 ..     202     218 ..     197     224 .. 0.65
   3 ?    9.1   0.0   9.2e-05       1.6      78     107 ..     233     262 ..     232     266 .. 0.90
   4 ?   -0.9   0.2      0.11   1.9e+03       8      24 ..     290     305 ..     281     343 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.082
                           DUF4199   3 GlilglvwilifllilyllglhqilstgpllgllallllllvpflvylalkkyrkknlgGfisfgqafgfgflislv 79 
                                       G+il+ ++ l++l    + g +      ++l++++ll+++l+ + +++++   r +   G   f   + +++l++ v
  gi|320101488|ref|YP_004177080.1| 108 GFILASMTSLSML---SPGGPE------VFLSVFYLLQSILSTAAALYSVY--RLTT-RGGVYFYPLYAATLLVYGV 172
                                       3333333333333...344443......99*****9999999888888888..8888.5558899999999999988 PP

                           DUF4199  80 agllsavf 87 
                                        g+ + ++
  gi|320101488|ref|YP_004177080.1| 173 YGFDVFAL 180
                                       88755555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.27
                           DUF4199   6 lglvwilifllilyllgl 23 
                                       ++l++ ++f+ +l++lgl
  gi|320101488|ref|YP_004177080.1| 202 TALALSVSFY-MLIPLGL 218
                                       5677777777.7777766 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 9.2e-05
                           DUF4199  78 lvagllsavfqyiyfnfidpdfienyiaei 107
                                       +vaglls+v  +i +  +dp++++n+i  +
  gi|320101488|ref|YP_004177080.1| 233 VVAGLLSGVPLFIAVVAMDPGYFNNVIGDV 262
                                       79*************999*******98766 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.11
                           DUF4199   8 lvwilifllilyllglh 24 
                                        vwil +l ily ++  
  gi|320101488|ref|YP_004177080.1| 290 GVWILGML-ILYSMSPP 305
                                       68888888.78888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3064.65
//
Query:       gi|320101489|ref|YP_004177081.1|  [L=865]
Description: replicative DNA polymerase I [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-43  149.6   0.0    3.2e-43  148.1   0.0    1.7  1  DNA_pol_B       DNA polymerase family B
    1.8e-31  109.5   0.1    6.5e-31  107.7   0.0    1.9  2  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    1.7e-05   24.9   0.0    9.5e-05   22.4   0.0    2.2  2  RNase_H_2       RNase_H superfamily
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.026   14.2   0.0    1.5  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
      0.025   13.4   0.0      0.071   12.0   0.0    1.6  2  DNA_pol_B_2     DNA polymerase type B, organellar and viral
      0.096   12.7   0.0       0.26   11.3   0.0    1.7  1  ACT_6           ACT domain


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 !  148.1   0.0   1.1e-46   3.2e-43      22     419 ..     446     814 ..     427     835 .. 0.77

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 1.1e-46
                                       HHHHTTBE-B-----.--SS............-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-H CS
                         DNA_pol_B  22 lakeegfilpdrtekkgkeee...........gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvas 87 
                                       ++++ ++ +p++++   k+             +Y+Ga+V+eP kg++  +v+vlD aSLYPsii ++Nl+y+t++  
  gi|320101489|ref|YP_004177081.1| 446 EHRRLEYLIPNSEDI-VKYAGragtraiidgkKYAGALVIEPPKGVFF-NVMVLDIASLYPSIIKKYNLSYETVDMP 520
                                       556666666753333.33322344455555546*************96.69***********************999 PP

                                       CCHCC.T--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHH.HHHHH.CS--HHHHHHHHHHHHHHHH CS
                         DNA_pol_B  88 eeeak.eleaedeyleveveprlvefvkksvregllpklLkdllakRkai.kkelk.eekdefekalldkqQlalKv 161
                                         ++  ++++e        + +l+++    ++ gl +++   l + R  i kk+ k ++  + + a +d  Q a+Kv
  gi|320101489|ref|YP_004177081.1| 521 WCKSTiDITDET-------GRKLHRV--CTDKPGLTAQITGILRDFRVGIyKKRAKdKSLPKDTLAWYDVVQRAIKV 588
                                       877664444333.......3333333..334556666665555566765426666633344456789********** PP

                                       HHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S CS
                         DNA_pol_B 162 taNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielk 238
                                       + N+ YG+ G +   l++ a+A+svT++GR+  +++     +                  ++k  YGDTDS+f+   
  gi|320101489|ref|YP_004177081.1| 589 FINASYGVFGDSRFSLFSPAVAESVTAMGRKSFMTIVLKAAEL-----------------GVKPLYGDTDSIFVWNP 648
                                       ******************************9988764433332.................9999**********876 PP

                                       -SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEE.TTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHH CS
                         DNA_pol_B 239 vkdveellkigkelaeevseklfkkplklefekvykkllLis.KKkYaglkvektskanklliKGvdlvRrdncklv 314
                                        +   e+      l++ + e+l    l++e++k ++ ++++  KK Y g + +     + ++iKG+   +r+  ++ 
  gi|320101489|ref|YP_004177081.1| 649 NRGQLEV------LQKWILENLG---LEIELDKEFTYVVFTGlKKNYLGRTGD-----GGIEIKGLVAKKRNTPEFL 711
                                       6554444......5677888444...56888888888899865999***9999.....789**************** PP

                                       HHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHH CS
                         DNA_pol_B 315 kevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlk 391
                                       ke+ +++l +l    ++ ++  +  + l+++lk+ +  l+ ++vpl+ + +  +l+k+p++y++++ ph+ +a +l+
  gi|320101489|ref|YP_004177081.1| 712 KELFQEILGKLKDV-ETPEDFVSFANWLEDRLKEYYVGLKRREVPLDRLAIRVALTKPPSSYTKTKPPHVRAAMQLA 787
                                       *********98766.777888889999*********************************************99998 PP

                                       HHCSS---TTCEEEEEEBETSS.....S CS
                         DNA_pol_B 392 krneeapevgdrisYvivekkkevkkkn 419
                                       +  +  ++ gd+i+Yv v+  +  k  +
  gi|320101489|ref|YP_004177081.1| 788 NY-GISVQEGDVITYVKVKGREGYKAIQ 814
                                       77.7999************988654333 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 !  107.7   0.0   2.2e-34   6.5e-31       6     327 ..      51     348 ..      45     365 .. 0.82
   2 ?   -3.3   0.0       1.2   3.7e+03      33      79 ..     708     766 ..     702     798 .. 0.57

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 2.2e-34
                                       SEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHH CS
                    DNA_pol_B_exo1   6 ksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnel 82 
                                       ++ +v+ +g+kpyf+++ +   ++   ++++kel+++++      ++ e v+k + +  e+   +++k+++++p ++
  gi|320101489|ref|YP_004177081.1|  51 VVKVVDPTGHKPYFLTDLS--LDE---AKSIKELSGDKDV-----DRLEEVVKVNPLTMERV--RVTKIVTKDPLAV 115
                                       45567779***********..333...6899999999964.....45577777777777777..4************ PP

                                       HHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTT..... CS
                    DNA_pol_B_exo1  83 kkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpke..... 154
                                       kk+r+++    ++ +v+e++++y+ ++++dn++ ++  y ++  +  ++ +i++ ++ei  +  + +++ +      
  gi|320101489|ref|YP_004177081.1| 116 KKLRDKV---PKGASVWEAKIKYHSNYIYDNQLIPGMRYVIE--NDGQQPRITLVKPEIPLSLVQSVRELFRkeppe 187
                                       ******8...679*******************9999999999..999999***********9999999888866777 PP

                                       ............CC..S-EEEEEEEEEETE.ETTSEETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS- CS
                    DNA_pol_B_exo1 155 ............se..pplrvlsFDIecks.kkgkfpdaensedpiiqIscvl.dglgekepearklftlrecasee 215
                                                   +e  p+ +  + DIe++  +kg++p++ + e p+i I++ +  g         k++ l+  + ++
  gi|320101489|ref|YP_004177081.1| 188 tvklaedylilfEEapPRAVRVAMDIEVYTpFKGRIPNPRQGEYPVISIAFSSnNGFR-------KVLLLGRPF-KQ 256
                                       777776666666445666677******98636888******************66666.......999999999.67 PP

                                       ---EE--SSTCSTTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTC CS
                    DNA_pol_B_exo1 216 eedfeltpkpeypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkgg 292
                                       ++d  +++ p+  +v+v  fdsEk++L + l+++ +y   v+++YN+dnFDl Yi +Ra               + g
  gi|320101489|ref|YP_004177081.1| 257 RFDYMIEEYPV--DVEVEVFDSEKAMLLEALKTVSKY--PVLLTYNGDNFDLVYIYTRAV--------------RLG 315
                                       77777777776..889999******************..*********************..............444 PP

                                       EECCCCESEEEEEECEEEETTSEEEEHHHHHHHHS CS
                    DNA_pol_B_exo1 293 rskvseigfskqarekvkisgrihlDlyrvvkrkl 327
                                       +     +      ++ v++   +hlDly++++++ 
  gi|320101489|ref|YP_004177081.1| 316 VPRYLVPLSI--GEDMVRLETGVHLDLYKFFSNRA 348
                                       4444444443..35668888888888888888775 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                                       HHHHHHHCCTTCCCEE..........EEEEEECCCCEECCTSSCCHHC..EEEEEESST CS
                    DNA_pol_B_exo1  33 keelkelyeelskkvt..........kivkvelvlkkslygyekkpvp..ylkvsvsnp 79 
                                       +e lkel++e+  k++               e  lk++++g+++++vp   l + v+  
  gi|320101489|ref|YP_004177081.1| 708 PEFLKELFQEILGKLKdvetpedfvsFANWLEDRLKEYYVGLKRREVPldRLAIRVALT 766
                                       55555555555555553333443332112234466788888888888877444444433 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   3.3e+03      16      42 ..      24      49 ..      19      60 .. 0.79
   2 !   22.4   0.0   3.2e-08   9.5e-05      42     105 ..     275     352 ..     261     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                         RNase_H_2 16 liyliGvldvdekeiekltqllaeepe 42
                                        yl+Gv++ d+k  + + ++l ee +
  gi|320101489|ref|YP_004177081.1| 24 PHYLLGVYY-DGKLGRAVLEFLSEEGD 49
                                      579*****5.99999999998888765 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.2e-08
                         RNase_H_2  42 eeekailelflellekkkalvtfngksFDvpflkrlfkkyklde..............eefrhiDLlkelrkkkles 104
                                       + eka+l ++l++++k++ l+t+ng +FD+ ++ +++ +  ++               e   h+DL+k +++  +++
  gi|320101489|ref|YP_004177081.1| 275 DSEKAMLLEALKTVSKYPVLLTYNGDNFDLVYIYTRAVRLGVPRylvplsigedmvrlETGVHLDLYKFFSNRAVKN 351
                                       56777777789**************************777777777777999988887777*******997766655 PP

                         RNase_H_2 105 y 105
                                       y
  gi|320101489|ref|YP_004177081.1| 352 Y 352
                                       4 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 ?   14.2   0.0   8.6e-06     0.026      35      78 ..     275     317 ..     263     353 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.6e-06
                    DNA_pol_B_exo2  35 ssekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvs 78 
                                       +sek+++ + +++v+k+ p l ++ng +fDl  ++ ra++ gv 
  gi|320101489|ref|YP_004177081.1| 275 DSEKAMLLEALKTVSKY-PVLLTYNGDNFDLVYIYTRAVRLGVP 317
                                       67999999999999987.8********************98885 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05     0.071     213     253 ..     478     517 ..     476     538 .. 0.76
   2 ?   -2.6   0.0      0.62   1.9e+03     372     386 ..     584     598 ..     579     600 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                       DNA_pol_B_2 213 yrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthypmPygkp 253
                                       y G  + +p  +g++  n++v D+ SlYPs+ ++y ++y++ 
  gi|320101489|ref|YP_004177081.1| 478 YAGALViEPP-KGVF-FNVMVLDIASLYPSIIKKYNLSYETV 517
                                       5666664333.5666.79*******************99876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.62
                       DNA_pol_B_2 372 siaKlllNsLYGrFa 386
                                         +K   N+ YG F+
  gi|320101489|ref|YP_004177081.1| 584 RAIKVFINASYGVFG 598
                                       5679**********8 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.7e-05      0.26      10      30 ..     541     561 ..     539     565 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                             ACT_6  10 pdrpGltasLtsvlaefgvni 30 
                                       +d+pGlta++t++l +f+v i
  gi|320101489|ref|YP_004177081.1| 541 TDKPGLTAQITGILRDFRVGI 561
                                       7****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (865 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 5829.00
//
Query:       gi|320101490|ref|YP_004177082.1|  [L=120]
Description: Nascent polypeptide associated complex NAC [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   47.5   0.2    1.3e-12   47.5   0.2    1.8  2  NAC       NAC domain
  ------ inclusion threshold ------
       0.03   14.1   0.0        0.3   11.0   0.0    2.1  2  UBA_4     UBA-like domain
       0.09   12.4   0.0        3.6    7.3   0.0    2.2  2  HTH_33    Winged helix-turn helix


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 !   47.5   0.2   2.1e-16   1.3e-12       1      56 [.       6      64 ..       6      65 .. 0.97
   2 ?   -1.9   0.2      0.57   3.4e+03      16      28 ..      72      84 ..      69      91 .. 0.67

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2.1e-16
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                      +++l++ lk++g+  +e++g+++V i ++d   +v+ +P+V   k+ g+  y+v+G++e+
  gi|320101490|ref|YP_004177082.1|  6 PRELKRLLKRMGVevEELNGVKRVEIVFED-RKIVVRDPQVLafKAGGQVFYQVTGTPET 64
                                      689***************************.***********99**************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.57
                               NAC 16 ipgieeVtirksd 28
                                      ++ +eeV    +d
  gi|320101490|ref|YP_004177082.1| 72 VKPVEEVKVSEED 84
                                      6678888766666 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.068   4.1e+02       7      19 ..      55      67 ..      53      71 .. 0.83
   2 ?   11.0   0.0   4.9e-05       0.3       9      33 ..      90     114 ..      83     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.068
                             UBA_4  7 FqaiTGadeekAr 19
                                      F ++TG+ e +A+
  gi|320101490|ref|YP_004177082.1| 55 FYQVTGTPETVAQ 67
                                      6689***998886 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.9e-05
                             UBA_4   9 aiTGadeekArqlLeannWdLerAi 33 
                                       + TGa+ ekAr+ L  + +d+ +Ai
  gi|320101490|ref|YP_004177082.1|  90 EQTGASYEKAREALVKAKGDILQAI 114
                                       55*******************9998 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.014        81      25      35 ..       7      17 ..       5      20 .. 0.82
   2 ?    7.3   0.0    0.0006       3.6       8      49 ..      66     107 ..      63     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.014
                            HTH_33 25 sgvyrlLkrlG 35
                                      + + rlLkr+G
  gi|320101490|ref|YP_004177082.1|  7 RELKRLLKRMG 17
                                      6678******9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0006
                            HTH_33   8 arlaqlieerfgvsysvsgvyrlLkrlGfsyqkPrprapkqd 49 
                                       a+ ++ ++    v++s+  v+ ++   G sy k+r   +k+ 
  gi|320101490|ref|YP_004177082.1|  66 AQAEEAVKPVEEVKVSEEDVRFIMEQTGASYEKAREALVKAK 107
                                       55666666666799*********************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 872.82
//
Query:       gi|320101491|ref|YP_004177083.1|  [L=424]
Description: RNA-metabolising metallo-beta-lactamase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   68.2   0.0    1.2e-18   67.4   0.0    1.4  1  Beta-Casp      Beta-Casp domain
    2.3e-12   46.8   0.0    3.8e-12   46.1   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    2.7e-11   43.2   0.0    7.1e-11   41.9   0.0    1.7  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.5e-09   38.2   0.5    2.8e-09   37.3   0.5    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.6e-06   27.8   0.0    2.6e-06   27.1   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.033   14.1   0.0    1.8  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0     4e-22   1.2e-18      20     110 .]     241     339 ..     229     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 4e-22
                                       -S-EEEEE-HHHHHHHHHGGGGGG...........E-SHH.....HHHH..HHHS-SSEEEEES-TTSSSSHHHHHH CS
                         Beta-Casp  20 lklpiyldsplaskatevYkeyae...........veaks.lewmeskkeelnsskgpkvilassgmlegGrsrell 84 
                                       + +++yld+ +++++t++Y +y++            e+ + ++ + ++k ++   ++p+vi+as gml+gG+s+++l
  gi|320101491|ref|YP_004177083.1| 241 PYIEVYLDG-MIKDITDIYLRYRKylrdpalfnkvFETVNfVTGTRDRK-KI--INKPCVIIASAGMLKGGPSVYYL 313
                                       4489*****.************99********98855555444444443.24..458******************** PP

                                       HHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  85 kklledprntvilvgyqaegTlgrkl 110
                                       kkl ++prn++i+v+yqa+++ g+kl
  gi|320101491|ref|YP_004177083.1| 314 KKLHQNPRNSIIMVSYQAPNSNGHKL 339
                                       ***********************987 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   1.3e-15   3.8e-12       3     179 ..      20     180 ..      18     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.3e-15
                     Lactamase_B_6   3 eldnvkiLlDvGwdeskvslesalkelekvip..tvdliLLshatlehlGayallyakfksklllnipvyatlpvvk 77 
                                       e  + ++LlD G++      e+++  l +++   +v+  ++sha l+h+Ga ++ly++       + ++++t+p+ +
  gi|320101491|ref|YP_004177083.1|  20 EDGSQRFLLDYGVNFD----ERDMPRLPQHVRpvDVSGLIVSHAHLDHVGAAPYLYITG------RPKAFSTKPTLE 86 
                                       5557899******964....4678999999972255669**************999864......7899******** PP

                     Lactamase_B_6  78 LGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskese 154
                                        +r++++d  + + ++ ++d     + ++++ +d+   l Y  +     + dg  ++  naGh +G +i  ++++s 
  gi|320101491|ref|YP_004177083.1|  87 VARLLTMDFLKLNAAVIEYD-----MREFENLYDNTVFLDYGETY----EEDGFKLVFANAGHIIGSSITYLETGSG 154
                                       *********99998887776.....5688*************995....4578999999*************99887 PP

                     Lactamase_B_6 155 .kivYavdwnhakeshLngaalldss 179
                                        +++Y  d+n +    L ga++l++ 
  gi|320101491|ref|YP_004177083.1| 155 rRLMYTGDINDRETWTLPGAETLETG 180
                                       69*****************9998743 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 !   41.9   0.0   2.4e-14   7.1e-11       3      62 .]     352     415 ..     351     415 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2.4e-14
                             RMMBL   3 pvkarieeidfSgHadknellelirklkprn..vilvHGeeeatsalarllkeeeg..idvfiP 62 
                                       +v+ar+e++dfS Ha++ +l +++++ k     +i+vHG ee++ +l++++ ee g  +++++P
  gi|320101491|ref|YP_004177083.1| 352 RVNARVEWLDFSSHAGQKGLVDILSRYKSTVrdIIIVHGGEEEAFSLREAILEELGsdVRIHVP 415
                                       69**************************99999******************9999966666665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.5   9.5e-13   2.8e-09       5      98 ..      13     107 ..       9     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 9.5e-13
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       +  +yl+e++   +L D G+  ++ ++ +    +++ p dv+ +i++H+HlDH+G++++l  +   + +  + ++++
  gi|320101491|ref|YP_004177083.1|  13 GRAAYLVEDGSQRFLLDYGVNFDERDMPR--LPQHVRPVDVSGLIVSHAHLDHVGAAPYLYITGRPKAFSTKPTLEV 87 
                                       5679**********************997..99***************************98888888777777766 PP

                                       CHCHHHHHHHHHCCHH...T CS
                       Lactamase_B  82 lfmeeaddaasrkgll...l 98 
                                        +   +d+       +    
  gi|320101491|ref|YP_004177083.1|  88 ARLLTMDFLKLNAAVIeydM 107
                                       66666665555554445552 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   8.8e-10   2.6e-06       2     165 ..      25     189 ..      24     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 8.8e-10
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvyl 77 
                                       r+L+D g ++ +  +++l P++ r    ++ +++++haH DH+  ++ l   +rpk +    +++v++ l+  f  l
  gi|320101491|ref|YP_004177083.1|  25 RFLLDYGVNFDERDMPRL-PQHVRPV--DVSGLIVSHAHLDHVGAAPYLYItGRPKAFSTKPTLEVARLLTMDFLKL 98 
                                       8999*****999988888.6665555..899************9999999999998888878888888888887777 PP

                                       HCHTTTTEEEEEE-..TTSEEEE......CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S-- CS
                     Lactamase_B_2  78 aleeepavnvheld..wgesfel......gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyi 146
                                       +  +  + +++e++   ++++ l      ++ g  ++++ a+ ++        g  + ++ +g+g+r++y+gD +  
  gi|320101491|ref|YP_004177083.1|  99 NAAVI-EYDMREFEnlYDNTVFLdygetyEEDG--FKLVFANAGHII------GSSITYLETGSGRRLMYTGDINDR 166
                                       76666.777777775433333336666653336..455545555555......458888888***********9965 PP

                                       -....HHHHHHHCT-SEEEEE-S CS
                     Lactamase_B_2 147 p....eeigerlggadlllldit 165
                                       +    + ++++  g++ ++++ t
  gi|320101491|ref|YP_004177083.1| 167 EtwtlPGAETLETGVETVIVEST 189
                                       53223333444455666666655 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 ?   14.1   0.0   1.1e-05     0.033       6     113 ..      13     162 ..      11     172 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                     Lactamase_B_3   6 ghnsflletagarilvDPf......kanlgyeppa........eeaDlvlisqaledHahletlkql.......... 58 
                                       g +++l+e++ +r l+D++      +        +        +++  +++s+a+ dH  +++   +          
  gi|320101491|ref|YP_004177083.1|  13 GRAAYLVEDGSQRFLLDYGvnfderD------M-PrlpqhvrpVDVSGLIVSHAHLDHVGAAPYLYItgrpkafstk 82 
                                       8899**************94443321......2.22445665488888**********9999888774444444333 PP

                     Lactamase_B_3  59 ...............................aenvkvleegeslevggleiravatshdavggsergenngflleqd 104
                                                                      ++n+ +l+ ge++e +g+++        a  g+  g  + +l + +
  gi|320101491|ref|YP_004177083.1|  83 ptlevarlltmdflklnaavieydmrefenlYDNTVFLDYGETYEEDGFKLV------FANAGHIIGSSITYLETGS 153
                                       3333333333333333333333333333333333333333333333333322......2223444555566666666 PP

                     Lactamase_B_3 105 gltiyhlGh 113
                                       g ++++ G+
  gi|320101491|ref|YP_004177083.1| 154 GRRLMYTGD 162
                                       666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 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:                        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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3119.34
//
Query:       gi|320101492|ref|YP_004177084.1|  [L=736]
Description: translation elongation factor 2 (EF-2/EF-G) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  204.5   0.2    2.1e-60  203.6   0.1    1.5  2  GTP_EFTU         Elongation factor Tu GTP binding domain
    1.4e-30  105.6   0.2    7.6e-30  103.2   0.0    2.4  3  EFG_IV           Elongation factor G, domain IV
    3.3e-21   75.1   0.0    9.5e-21   73.6   0.0    1.9  1  EFG_C            Elongation factor G C-terminus
    1.4e-20   73.1   0.0    3.2e-20   72.0   0.0    1.7  1  EFG_II           Elongation Factor G, domain II
    2.7e-13   50.1   0.0    7.3e-13   48.7   0.0    1.8  1  GTP_EFTU_D2      Elongation factor Tu domain 2
    5.5e-05   23.2   0.0    0.00013   22.0   0.0    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.03   14.3   0.1      0.078   13.0   0.1    1.6  1  HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
      0.036   13.5   0.0      0.076   12.4   0.0    1.5  1  SRPRB            Signal recognition particle receptor beta su
      0.062   13.1   0.1        0.2   11.5   0.0    1.9  2  RF3_C            Class II release factor RF3, C-terminal doma
       0.07   12.7   0.0       0.18   11.4   0.0    1.6  1  Ras              Ras family
       0.11   11.7   0.0        0.2   10.9   0.0    1.3  1  Septin           Septin
       0.12   12.3   1.1       0.35   10.8   0.3    2.1  2  RsgA_GTPase      RsgA GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.6   0.1   1.4e-63   2.1e-60       2     193 ..      19     258 ..      18     259 .. 0.92
   2 ?   -3.5   0.0       4.3   6.4e+03      46      76 ..     383     413 ..     359     414 .. 0.73

  Alignments for each domain:
  == domain 1  score: 203.6 bits;  conditional E-value: 1.4e-63
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.T.TCSSEEEEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.k.etkkylinliD 76 
                                       +irnigi +hvDhGKtTL+d+Ll ++g  s+  + a+++ +lD l+ E++r++T+k+a++sl+ + ++k ylinliD
  gi|320101492|ref|YP_004177084.1|  19 QIRNIGITAHVDHGKTTLSDSLLSAAGLLSE--KIAGQALALDYLDVEQKRQMTVKAANASLYhEyKGKPYLINLID 93 
                                       79*****************************..77888999**********************6269********** PP

                                       ESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  77 tPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                       tPGHvdF++++ir+lrv+Dga++vvdaveGv++qte  lr+al+e+v++++fiNK+Drl++el+ +++e++q+l + 
  gi|320101492|ref|YP_004177084.1|  94 TPGHVDFQSKTIRALRVIDGAIVVVDAVEGVMTQTEMYLRVALEERVRPVLFINKIDRLIKELRLSPNEIQQRLVQI 170
                                       **************************************************************************777 PP

                                       ............HHHHHHHHHTTTTTEEEEEEBTTTTBTHH.................................... CS
                          GTP_EFTU 154 ............eeklekygekgekevpvvfgSalkgegvk.................................... 182
                                                   +++ +k++  +  + +v+fgSa + +g++                                    
  gi|320101492|ref|YP_004177084.1| 171 vkdvntliatyaDKEFQKAWLLDPMKGQVAFGSARDRWGLTiplvqqkgikfsdivdvytkgkeavaelqkaaplhe 247
                                       77777776666655555554433389************9999999999999*************************9 PP

                                       HHHHHHHHHSH CS
                          GTP_EFTU 183 tllealvellp 193
                                       ++l+++v+++p
  gi|320101492|ref|YP_004177084.1| 248 AILDMVVKYVP 258
                                       9*******998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.3
                                       SHHHHHHTSCSSCEEEEEETTCSSEEEEEEE CS
                          GTP_EFTU  46 lkeErergiTiksaaisleketkkylinliD 76 
                                       ++ E+ r iT ++ ++ +e +  ++l +l+D
  gi|320101492|ref|YP_004177084.1| 383 TPFEKLRMITESVVTVAIEPKNPQQLTKLVD 413
                                       4668889999999988888777777777777 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.8   4.2e+03      16      65 ..     235     284 ..     228     310 .. 0.62
   2 ?   -2.4   0.0       2.6   3.8e+03       2      19 ..     467     484 ..     466     490 .. 0.79
   3 !  103.2   0.0   5.1e-33   7.6e-30      11     121 .]     516     624 ..     511     624 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                                       CCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHH CS
                            EFG_IV  16 reeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieav 65 
                                       ++ +l+k ++ +    + +++  P++++++   + ++  g +++e +++ 
  gi|320101492|ref|YP_004177084.1| 235 AVAELQKAAPLHEAILDMVVKYVPNPRDAQRYRIPKIWHGDLNHEAVKYM 284
                                       66667777777777777777777777776666666666666666655544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                                       CCESCEE.SS-CCHCCCC CS
                            EFG_IV   2 qVayrEtirkpvkereek 19 
                                        + yrEt+r+ ++ +e+k
  gi|320101492|ref|YP_004177084.1| 467 VIVYRETVRESSQVFEGK 484
                                       578******999877765 PP

  == domain 3  score: 103.2 bits;  conditional E-value: 5.1e-33
                                       S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEE CS
                            EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvk 87 
                                       +++ er+++l +q+g+d ++a+ i++i+++     n++vd+t+g+q+++e++++v +Gf+ a+keGpla epv++vk
  gi|320101492|ref|YP_004177084.1| 516 MDARERAKILREQAGWDADEARRIMAIDEN----LNMLVDMTTGVQYLREIKDTVIQGFRLAMKEGPLAMEPVRGVK 588
                                       677889***********************7....8****************************************** PP

                                       EEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC- CS
                            EFG_IV  88 vtLldgslhe..vdsseaafkpaarralkeallkAs 121
                                       v+L+d+++he   ++++a++ pa+r+a+ +++l+A+
  gi|320101492|ref|YP_004177084.1| 589 VVLHDAVVHEdpAHRGPAQIFPAVRNAIFAGFLTAK 624
                                       *********************************996 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   6.4e-24   9.5e-21       2      86 ..     627     710 ..     626     713 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 6.4e-24
                                       EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEE CS
                             EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgY 78 
                                       +lEPi k++i++p ey+g++ + ++++rG++++++q  ++ +++ aeiP++e+++ a+ Lr++T+G++++  efs++
  gi|320101492|ref|YP_004177084.1| 627 ILEPILKLDIRTPMEYIGNISTVITKKRGKLIEVQQM-ETSARVIAEIPVSESFDIADMLRNVTAGKAIWGQEFSRW 702
                                       89***********************************.*************************************** PP

                                       EE--HHHH CS
                             EFG_C  79 eevpgdkl 86 
                                       ++vp+++l
  gi|320101492|ref|YP_004177084.1| 703 APVPESML 710
                                       ****9876 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 !   72.0   0.0   2.1e-23   3.2e-20       2      73 ..     392     463 ..     391     465 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2.1e-23
                            EFG_II   2 PePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevel 73 
                                        e+v+++aiepk+ ++ +kl +aL +l+ EDp+l v+ +eeT+e++lsG+G+lH+ei+++ lk  y++ev  
  gi|320101492|ref|YP_004177084.1| 392 TESVVTVAIEPKNPQQLTKLVDALYKLHLEDPSLIVKINEETGEYLLSGVGTLHIEIALTLLKDLYGLEVVA 463
                                       589******************************************************************975 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 !   48.7   0.0   4.9e-16   7.3e-13       1      73 [.     307     373 ..     307     374 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 4.9e-16
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G va+gr+ysGtl+ G+ev+++  +        r+ ++   +++++e+ ++  aG+i+a+ gle+a + G+t+
  gi|320101492|ref|YP_004177084.1| 307 GLVATGRIYSGTLRAGEEVWLVNAR-----VPQRVLQVSLYMGPYRELADEITAGNIAAALGLEKA-RSGETV 373
                                       679******************5543.....3488*******************************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 !   22.0   0.0   8.9e-08   0.00013       2     110 ..      23     144 ..      22     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.9e-08
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE....................EEEEECGGCS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke....................ielvDtpGli 57 
                                       ++i  +   GK+tL  +l+ +     ++++g  +   +  v+ k+ +                    i+l+DtpG +
  gi|320101492|ref|YP_004177084.1|  23 IGITAHVDHGKTTLSDSLLSAaGLLSEKIAGQALALDYLDVEQKR-QmtvkaanaslyheykgkpylINLIDTPGHV 98 
                                       566667789**********98446889999999999999998443.356777778888888888888********66 PP

                                       SHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEE CS
                          MMR_HSR1  58 egaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplil 110
                                       +        +k+++al+  d +++vvda e+ +++ +  l   lee+ +p +l
  gi|320101492|ref|YP_004177084.1|  99 D------FQSKTIRALRVIDGAIVVVDAVEGVMTQTEMYLRVALEERVRP-VL 144
                                       6......345566665568********99554555544444444444445.34 PP

>> HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.2e-05     0.078      95     174 ..     499     576 ..     484     590 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                   HIGH_NTase1_ass  95 lPeetievlkeelendnpledirdeekiletvneldldelldlnlldeklankliekrpyesieeikeaiprgfskh 171
                                       l eet+++++e +  ++   d r+  kil++   +d de   +  +de+l   +  +   + ++eik+++ +gf   
  gi|320101492|ref|YP_004177084.1| 499 LNEETLRLMSEGIIVED--MDARERAKILREQAGWDADEARRIMAIDENLNMLVDMTTGVQYLREIKDTVIQGFRLA 573
                                       67899999999886666..467****************************************************887 PP

                   HIGH_NTase1_ass 172 yke 174
                                       +ke
  gi|320101492|ref|YP_004177084.1| 574 MKE 576
                                       776 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.1e-05     0.076      25      85 ..      63     120 ..      21     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                       HS.S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEET CS
                             SRPRB  25 td.svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDS 85 
                                        + + + tv + ++s+ +++ + k   ++liD PGh+ +++k +      + + g + vvD+
  gi|320101492|ref|YP_004177084.1|  63 VEqKRQMTVKAANASLYHEY-KGKPYLINLIDTPGHVDFQSKTIRA---LRVIDGAIVVVDA 120
                                       33233344444455555555.55667799***********998777...7778888888885 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       3.1   4.7e+03      15      60 ..       2      48 ..       1      74 [. 0.74
   2 ?   11.5   0.0   0.00013       0.2      14      89 ..     399     474 ..     393     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.1
                                      EEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TS.S-EEEEESSTHH CS
                             RF3_C 15 vrlkdplkrkqlrkgleqLaeEGavqvfkeeeag.eelilgaVGqLQ 60
                                      vr k++++  ++ + +eq+ + G++    + +++ ++ +l+a G L 
  gi|320101492|ref|YP_004177084.1|  2 VRFKQTSEVLKIMRNIEQIRNIGITAHVDHGKTTlSDSLLSAAGLLS 48
                                      66777777778888999999999888887666666888888888775 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                                       EEEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE-S--EEEEE CS
                             RF3_C  14 rvrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrleslpyslarwv 89 
                                        ++ k+p +  +l  +l +L+ E    + k +e++ e++l+ VG+L  e+  + lk+ Yg+ev  ++  + +   v
  gi|320101492|ref|YP_004177084.1| 399 AIEPKNPQQLTKLVDALYKLHLEDPSLIVKINEETGEYLLSGVGTLHIEIALTLLKDLYGLEVVASPPVIVYRETV 474
                                       57899999******************9**999999***************************98877555555444 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.18      25      82 ..      64     121 ..      55     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                       SSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETT CS
                               Ras  25 keeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydit 82 
                                       +++ ++T+ +++ +   e++gk + +++ DT G  +f+s +   +r  +g+++v d  
  gi|320101492|ref|YP_004177084.1|  64 EQKRQMTVKAANASLYHEYKGKPYLINLIDTPGHVDFQSKTIRALRVIDGAIVVVDAV 121
                                       577899***********************************************98754 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013       0.2      12     131 ..      28     157 ..      21     181 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                       BTTSSCCCCCCTTSSSS----.........--------------S-E..EEEEEEEETTCEEEEEEEE---BSSSSS CS
                            Septin  12 esglGkttlintlfetdliee.........ekleeasekkkktveik..kkkvvieedgvklnltviDtpgfGdavd 77 
                                       +   Gkttl ++l++     +           + +   ++k+++++k  +++   e +g    +++iDtpg+ d+  
  gi|320101492|ref|YP_004177084.1|  28 HVDHGKTTLSDSLLSAAGLLSekiagqalaLDYLDV--EQKRQMTVKaaNASLYHEYKGKPYLINLIDTPGHVDFQS 102
                                       5668********998764444256665543223333..5555555552055555566799999**********9876 PP

                                       H.HCCCHHHHH..HHHHHHHHHHHHCTSS--SS-----EEEEEEEE-TTSSSS-HHH CS
                            Septin  78 n.skswepive..yideqfeeylreesklkRkkivDkRvHaclyfisPtghglkpld 131
                                          ++ ++i     + +  e ++++ +   R    ++Rv  +l fi+   + +k+l 
  gi|320101492|ref|YP_004177084.1| 103 KtIRALRVIDGaiVVVDAVEGVMTQTEMYLRVA-LEERVRPVL-FINKIDRLIKELR 157
                                       624566666432145677888888777776654.567888887.5676776666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.96   1.4e+03     154     160 ..      90      96 ..       5     103 .. 0.53
   2 ?   10.8   0.3   0.00023      0.35      16      77 ..     111     172 ..     102     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.96
                                       EEESS-S CS
                       RsgA_GTPase 154 lliDtPG 160
                                        liDtPG
  gi|320101492|ref|YP_004177084.1|  90 NLIDTPG 96 
                                       3567777 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH..HHHHHHHHHHHTTS CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee..eleelkeelealgy 77 
                                       +d +++vv ++  e  + + + +L +a e++++pv+ +nKiD l +e   + +e++++l ++  
  gi|320101492|ref|YP_004177084.1| 111 IDGAIVVVDAV--EGVMTQTEMYLRVALEERVRPVLFINKIDRLIKELrlSPNEIQQRLVQIVK 172
                                       67778887777..445567799********************8777764655566666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.26s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 5108.09
//
Query:       gi|320101493|ref|YP_004177085.1|  [L=103]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.8   0.1     0.0034   17.7   0.1    1.2  1  DUF3194   Protein of unknown function (DUF3194)


Domain annotation for each model (and alignments):
>> DUF3194  Protein of unknown function (DUF3194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.9e-07    0.0034       2      54 ..      16      69 ..      15     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-07
                                      ---SHHHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEEEEEE.EESSSEEEEEEE CS
                           DUF3194  2 kkLteedldeiseflaeviekkifkkvskkevldlditvev.keneeLdvdvev 54
                                       +Lt++ l++ ++ +++ +++++++k+++k v +  +  ev     +L +d+e+
  gi|320101493|ref|YP_004177085.1| 16 EELTSDVLEDLASEIERKVSEYLSSKLPRKSVFNTTVSLEVeGDHVNLLLDLEA 69
                                      59***************************************6444567677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 776.76
//
Query:       gi|320101494|ref|YP_004177086.1|  [L=121]
Description: prefoldin subunit beta [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   60.2   8.5    1.7e-16   60.1   8.5    1.0  1  Prefoldin_2      Prefoldin subunit
     0.0028   17.6   7.3       0.14   12.0   0.4    2.1  2  Prefoldin        Prefoldin subunit
     0.0053   16.2   0.0     0.0069   15.8   0.0    1.2  1  U79_P34          HSV U79 / HCMV P34
  ------ inclusion threshold ------
      0.048   14.0   0.0       0.06   13.7   0.0    1.2  1  HOASN            Haem-oxygenase-associated N-terminal helices
       0.12   12.6   2.2       0.15   12.3   2.2    1.2  1  DUF29            Domain of unknown function DUF29
        1.1   10.0   5.5        2.6    8.8   0.7    2.1  2  Vir_act_alpha_C  Virulence activator alpha C-term
        1.7    8.8   8.9       0.46   10.6   2.8    2.2  2  bZIP_1           bZIP transcription factor
          2    9.0   8.2        4.6    7.8   7.6    1.7  2  APG6_N           Apg6 coiled-coil region


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 !   60.1   8.5   7.6e-20   1.7e-16       1     104 [.      11     114 ..      11     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 7.6e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       q++i  +q + +   +++++++ +e++l+++e +le+l++l +d++ yk  G vlvk++k++v +eLeerke l+ +
  gi|320101494|ref|YP_004177086.1|  11 QNMIIHYQSILENKAKMEAELRIIEAELSDIENILETLKNLGDDAELYKALGHVLVKKSKADVVKELEERKELLTVK 87 
                                       899999*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklq 104
                                        +++ kql+ l ke  +l+  ++++l 
  gi|320101494|ref|YP_004177086.1|  88 RDKYRKQLDFLTKEAGNLEGRIKEALS 114
                                       ********************9999876 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.4   6.4e-05      0.14       4      37 ..      23      56 ..      20      65 .. 0.83
   2 !    9.6   1.3   0.00035      0.79      69     113 ..      64     108 ..      62     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-T CS
                         Prefoldin  4 eleslqaelaqlkeaieelektletlktlkkede 37
                                      + ++++ael+ ++++++++e++letlk+l +  e
  gi|320101494|ref|YP_004177086.1| 23 NKAKMEAELRIIEAELSDIENILETLKNLGDDAE 56
                                      56889***********************988444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00035
                                       EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  69 yyveksleeAiellkkkleelekqlekleeeleklkdqittlean 113
                                       + v+ks+ + ++ l++++e l+  ++k+ ++l++l++++ +le  
  gi|320101494|ref|YP_004177086.1|  64 VLVKKSKADVVKELEERKELLTVKRDKYRKQLDFLTKEAGNLEGR 108
                                       568888999999999999999999999999999999988777755 PP

>> U79_P34  HSV U79 / HCMV P34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-06    0.0069      76     122 ..      54     100 ..      46     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                           U79_P34  76 kqktlfvrGlllfsksvtsvsqstegrerlltvssengklqvtfvtl 122
                                         + +++ G +l++ks + v+++ e r+ lltv ++  + q+ f+t 
  gi|320101494|ref|YP_004177086.1|  54 DAELYKALGHVLVKKSKADVVKELEERKELLTVKRDKYRKQLDFLTK 100
                                       56789999**********************************99965 PP

>> HOASN  Haem-oxygenase-associated N-terminal helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.7e-05      0.06       9      75 ..       8      76 ..       1      89 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                                      HHHHT--SHHHHHHHHHTSTT--HHHHHHHHHHHHHH..HHHHHTT-HHHHHHHHHHHHHHHH---GGG CS
                             HOASN  9 Palqnlpieeaalladalkvgasldqidlalekllal..aekGlkGdasayaayqalllvlslsddvat 75
                                      P+ qn+ i+   +l +  k++a l+ i+  l+ +  +  + k l+ da+ y a   +l++ s +d v+ 
  gi|320101494|ref|YP_004177086.1|  8 PEVQNMIIHYQSILENKAKMEAELRIIEAELSDIENIleTLKNLGDDAELYKALGHVLVKKSKADVVKE 76
                                      899*******************************998335589*********99999988877766655 PP

>> DUF29  Domain of unknown function DUF29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   6.8e-05      0.15      16     101 ..      30     115 ..      16     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                                       HHHHSS-TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTT..TTHHHHHHHHHHHHHHHHHH-..-GG CS
                             DUF29  16 lLrerkfeelDlenLieEiedlgrsekrelesrlavllehlLkwqyqpe..krsrswrseireqrkeieklledsps 90 
                                        Lr  + e  D+en++e +++lg  +  el + l  +l +  k +  +e  +r++    + ++ rk++  l ++  +
  gi|320101494|ref|YP_004177086.1|  30 ELRIIEAELSDIENILETLKNLG--DDAELYKALGHVLVKKSKADVVKEleERKELLTVKRDKYRKQLDFLTKEAGN 104
                                       5666777888*************..5689999999999999996665551155555555556899************ PP

                                       GG--H....HH CS
                             DUF29  91 Lksyleeelee 101
                                       L+ +++e+l++
  gi|320101494|ref|YP_004177086.1| 105 LEGRIKEALSK 115
                                       ***99999875 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 ?    4.1   0.4     0.033        74      13      50 ..      16      58 ..      10      67 .. 0.75
   2 ?    8.8   0.7    0.0012       2.6      15      45 ..      68      98 ..      63     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.033
                   Vir_act_alpha_C 13 avldpealieeLerrreeheekLaeyeeieerl.....eearg 50
                                      ++ +  + ++++e+ ++  e++L+++e i e l     +++++
  gi|320101494|ref|YP_004177086.1| 16 HYQSILENKAKMEAELRIIEAELSDIENILETLknlgdDAELY 58
                                      5666677889999999999999999999999987777633443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                   Vir_act_alpha_C 15 ldpealieeLerrreeheekLaeyeeieerl 45
                                       +++++++eLe+r+e+ + k ++y++  + l
  gi|320101494|ref|YP_004177086.1| 68 KSKADVVKELEERKELLTVKRDKYRKQLDFL 98
                                      57899*************9999999665544 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.12   2.8e+02      31      60 ..      21      49 ..      16      54 .. 0.54
   2 ?   10.6   2.8    0.0002      0.46      24      60 ..      70     106 ..      67     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 31 LerrvkaLekeNksLkseleelkkevekLk 60
                                      Le+++k +e+e      el+ +++  e+Lk
  gi|320101494|ref|YP_004177086.1| 21 LENKAK-MEAELRIIEAELSDIENILETLK 49
                                      555543.45555555555555555555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  24 KqaeieeLerrvkaLekeNksLkseleelkkevekLk 60 
                                       K   ++eLe+r + L+ +  +++++l+ l+ke  +L+
  gi|320101494|ref|YP_004177086.1|  70 KADVVKELEERKELLTVKRDKYRKQLDFLTKEAGNLE 106
                                       556689**************************98886 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.9    0.0053        12      58      87 ..      19      48 ..       4      57 .. 0.51
   2 ?    7.8   7.6    0.0021       4.6      13      87 ..      26     112 ..      24     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0053
                            APG6_N 58 klekeeeelleeLkelekereeleaelaal 87
                                       + + ++++++eL+ +e+e +++e+ l++l
  gi|320101494|ref|YP_004177086.1| 19 SILENKAKMEAELRIIEAELSDIENILETL 48
                                      333344444444444444444444444333 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0021
                            APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeek............qdeeleeleeeleklekeeeelleeLkeleker 77 
                                       +++ +l+  e+e  + e+ l++lk+  +++e             + + ++elee+ e l  ++++  ++L+ l ke 
  gi|320101494|ref|YP_004177086.1|  26 KMEAELRIIEAELSDIENILETLKNLGDDAELykalghvlvkksKADVVKELEERKELLTVKRDKYRKQLDFLTKEA 102
                                       7999********************99888777999**9*9999888899999999999******************9 PP

                            APG6_N  78 eeleaelaal 87 
                                        +le  ++++
  gi|320101494|ref|YP_004177086.1| 103 GNLEGRIKEA 112
                                       9999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1475  (0.0822689); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 897.84
//
Query:       gi|320101495|ref|YP_004177087.1|  [L=71]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0025   17.9   0.0      0.003   17.7   0.0    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-07     0.003      14      73 ..       7      66 ..       2      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-07
                                      HHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1 14 AsialrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvletm 73
                                      A  +  +L++D e  p+  +    l+g+vL+++ +  ++ +L++  n+ +++l   l++ 
  gi|320101495|ref|YP_004177087.1|  7 AAPVASALKPDLEDMPEGCRGGAVLNGSVLVLRLSCRDAGSLKALNNSSINMLLMLLDVV 66
                                      666789**********99999***********************9999999888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); 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: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 599.84
//
Query:       gi|320101496|ref|YP_004177088.1|  [L=177]
Description: Brix domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   18.4   0.0     0.0024   18.0   0.0    1.2  1  Brix      Brix domain


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    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       2      89 ..       8     101 ..       7     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-07
                                       TT--HHHHHHHHHHHHHCTTSEEEEEEECT-TTTHHHHHHH...-HHHHHHHH..HCTCSEEEEEE..S..STTE.E CS
                              Brix   2 rktssrlrqllkdlrslmkphtasflkrnsnklkdlvelag...vthlellse..kndcslfvfelskk..rPng.p 70 
                                        ++s+r+r++ kdl s++ p+++  ++ +++ ++dlv+ a    v+ ++++ e   n+  l + ++++    P+   
  gi|320101496|ref|YP_004177088.1|   8 HRPSQRTRSFTKDLSSVF-PNSVRVTR-GKKTIDDLVTEAYrsrVSFILVVGEkrGNPSLLNIYRVDSAvlPPRAvE 82 
                                       5789**************.66777555.4447***987777899999999999766666778889988897666569 PP

                                       EEEEEEECECTGGGSTTTS CS
                              Brix  71 tlefkvenyslmkdlkkak 89 
                                       ++   ++ + l+++++ ++
  gi|320101496|ref|YP_004177088.1|  83 MAVILLKGVRLSREIPDSQ 101
                                       9999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1296.18
//
Query:       gi|320101497|ref|YP_004177089.1|  [L=86]
Description: 50S ribosomal protein L37AE [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-33  113.0   2.2    5.5e-33  112.9   2.2    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    2.4e-06   27.4   1.8    3.4e-06   26.9   1.8    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    8.6e-05   22.4   0.4    0.00012   22.0   0.4    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0056   17.0   1.0      0.091   13.2   0.3    2.2  2  zf-H2C2_2        Zinc-finger double domain
     0.0082   16.5   0.4      0.014   15.7   0.4    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0086   15.6   0.2      0.013   14.9   0.2    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.017   15.8   2.4          1   10.1   0.2    2.4  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
      0.034   14.2   1.2       0.47   10.5   0.0    2.0  2  CpXC             CpXC protein
      0.058   13.6   0.1        1.9    8.7   0.0    2.2  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.15   12.0   0.8       0.41   10.6   0.1    1.9  2  zf_CopZ          Zinc binding domain
       0.35   10.3   4.9        4.5    6.8   1.4    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.47   10.8   3.8        1.6    9.2   1.1    2.1  2  DUF4379          Probable Zinc-ribbon domain
        1.2    9.0   7.5        8.4    6.3   0.4    2.3  2  zinc_ribbon_2    zinc-ribbon domain
        3.1    8.2   9.1         16    5.9   9.1    1.9  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase


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 !  112.9   2.2   4.3e-36   5.5e-33       1      82 [.       3      85 ..       3      86 .] 0.97

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 4.3e-36
                                      XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSS.EEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH CS
                   Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgkt.kvkRkavgiwkCkkcgktvaGgAytpettsaktvks 78
                                      rtk+vgiaG+yg+rYG++lrk+v++i ++++a +tCpfcg + +v R ++giw+C+kcg+++ GgAytp+t+ ak +  
  gi|320101497|ref|YP_004177089.1|  3 RTKVVGIAGRYGARYGSTLRKKVRDILEKRYAPHTCPFCGYKgRVVRLSTGIWTCRKCGAKWVGGAYTPKTEVAKLFPD 81
                                      79**************************************999*********************************999 PP

                                      -XXX CS
                   Ribosomal_L37ae 79 airr 82
                                       i r
  gi|320101497|ref|YP_004177089.1| 82 IIVR 85
                                      8765 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 !   26.9   1.8   2.6e-09   3.4e-06      19      45 ..      36      62 ..      24      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.6e-09
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayriktrglfqCkeCrk 45
                                      ++CP+Cg++ ++ r++t g + C++C++
  gi|320101497|ref|YP_004177089.1| 36 HTCPFCGYKgRVVRLST-GIWTCRKCGA 62
                                      67***************.********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 !   22.0   0.4   9.1e-08   0.00012      24      56 ..      31      64 ..      17      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9.1e-08
                    OrfB_Zn_ribbon 24 payTSktCseCgsknke.alsgrtfkCpnCgfea 56
                                      ++y   tC+ Cg+k++  +ls+  ++C++Cg+++
  gi|320101497|ref|YP_004177089.1| 31 KRYAPHTCPFCGYKGRVvRLSTGIWTCRKCGAKW 64
                                      567889*************************986 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.3   7.1e-05     0.091      14      23 ..      35      44 ..      28      46 .. 0.84
   2 ?    2.3   0.0       0.2   2.6e+02      14      21 ..      54      61 ..      50      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                         zf-H2C2_2 14 pyeCplCdka 23
                                      p++Cp+C+++
  gi|320101497|ref|YP_004177089.1| 35 PHTCPFCGYK 44
                                      89******97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                         zf-H2C2_2 14 pyeCplCd 21
                                      +++C +C+
  gi|320101497|ref|YP_004177089.1| 54 IWTCRKCG 61
                                      589****8 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   0.4   1.1e-05     0.014       5      41 ..      37      65 ..      35      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgastpwf 41
                                       CPfCg ++ ++r   + +      +C +Cga  +w+
  gi|320101497|ref|YP_004177089.1| 37 TCPFCGYKGRVVRLSTGIW------TCRKCGA--KWV 65
                                      6********9999877765......8******..333 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.1e-05     0.013       2      28 ..      37      63 ..      36      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                      EETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlV 28
                                      +CP Cg +  v+  ++g  +C +CG+ 
  gi|320101497|ref|YP_004177089.1| 37 TCPFCGYKGRVVRLSTGIWTCRKCGAK 63
                                      8*****877****************86 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 ?   10.1   0.2    0.0008         1       1      15 [.      34      48 ..      34      52 .. 0.80
   2 ?    5.6   0.1      0.02        25       3      11 ..      55      63 ..      53      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0008
                           zf-ISL3  1 aphrCPnCgsktvvk 15
                                      aph+CP Cg k +v+
  gi|320101497|ref|YP_004177089.1| 34 APHTCPFCGYKGRVV 48
                                      69*******995554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
                           zf-ISL3  3 hrCPnCgsk 11
                                      ++C++Cg+k
  gi|320101497|ref|YP_004177089.1| 55 WTCRKCGAK 63
                                      79****987 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00037      0.47      27      49 ..      25      47 ..      19      52 .. 0.87
   2 ?    2.9   0.3     0.084   1.1e+02      38      46 ..      55      63 ..      47      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00037
                              CpXC 27 keklldgslfeatCpkCgatakl 49
                                      + ++l++++  +tCp Cg+++++
  gi|320101497|ref|YP_004177089.1| 25 VRDILEKRYAPHTCPFCGYKGRV 47
                                      57899**************9986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.084
                              CpXC 38 atCpkCgat 46
                                      +tC kCga+
  gi|320101497|ref|YP_004177089.1| 55 WTCRKCGAK 63
                                      899999986 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 ?    8.7   0.0    0.0015       1.9      19      44 ..      18      44 ..      15      46 .. 0.83
   2 ?    3.0   0.1     0.092   1.2e+02       1       8 [.      56      63 ..      56      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                    zinc_ribbon_13 19 Gsgl.skifdvqnkkfitvsCknCgYt 44
                                      Gs+l  k+ d+ +k++   +C  CgY 
  gi|320101497|ref|YP_004177089.1| 18 GSTLrKKVRDILEKRYAPHTCPFCGYK 44
                                      544425799*****************5 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.092
                    zinc_ribbon_13  1 kCpKCgnt 8 
                                      +C+KCg +
  gi|320101497|ref|YP_004177089.1| 56 TCRKCGAK 63
                                      59999876 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00032      0.41       2      18 ..      36      52 ..      35      52 .. 0.90
   2 ?   -0.9   0.1       1.3   1.7e+03       3      10 ..      56      63 ..      55      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                                      -B-TTT--B-EEE-HHH CS
                           zf_CopZ  2 kkCPvCgkkGkkVkliT 18
                                      ++CP Cg kG+ V+l T
  gi|320101497|ref|YP_004177089.1| 36 HTCPFCGYKGRVVRLST 52
                                      68***********9876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                                      B-TTT--B CS
                           zf_CopZ  3 kCPvCgkk 10
                                      +C +Cg+k
  gi|320101497|ref|YP_004177089.1| 56 TCRKCGAK 63
                                      6999*976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.4    0.0035       4.5      18      25 ..      37      44 ..      36      44 .. 0.82
   2 ?    4.9   0.1     0.014        18      18      25 ..      56      63 ..      50      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0035
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +Cp CG+k
  gi|320101497|ref|YP_004177089.1| 37 TCPFCGYK 44
                                      69999986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +C +CG+k
  gi|320101497|ref|YP_004177089.1| 56 TCRKCGAK 63
                                      69999986 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.19   2.4e+02      45      56 .]      27      41 ..      15      41 .. 0.60
   2 ?    9.2   1.1    0.0012       1.6      29      39 ..      54      64 ..      51      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.19
                           DUF4379 45 nrtkgssk...CpkC 56
                                      +  +++     Cp C
  gi|320101497|ref|YP_004177089.1| 27 DILEKRYAphtCPFC 41
                                      44433222455***9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                           DUF4379 29 wWkCakCgheW 39
                                       W+C+kCg +W
  gi|320101497|ref|YP_004177089.1| 54 IWTCRKCGAKW 64
                                      5********** PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.6    0.0077       9.9      16      22 ..      38      44 ..      34      45 .. 0.80
   2 ?    6.3   0.4    0.0065       8.4       2       8 ..      57      63 ..      56      64 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0077
                     zinc_ribbon_2 16 CpyCGtp 22
                                      Cp CG++
  gi|320101497|ref|YP_004177089.1| 38 CPFCGYK 44
                                      9999986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0065
                     zinc_ribbon_2  2 CpnCGae 8 
                                      C +CGa+
  gi|320101497|ref|YP_004177089.1| 57 CRKCGAK 63
                                      6666665 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 ?    5.9   9.1     0.012        16       5      33 ..      37      61 ..      34      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                                      --TTTT-TTTEE.ETT....S-EEETTTTB CS
                    Prim_Zn_Ribbon  5 pCPvCGGrDrFr.fddkdgrGtwfCrqCgg 33
                                       CP CG ++r    +    +G w Cr+C g
  gi|320101497|ref|YP_004177089.1| 37 TCPFCGYKGRVVrLS----TGIWTCRKC-G 61
                                      5********975455....5********.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 638.78
//
Query:       gi|320101498|ref|YP_004177090.1|  [L=286]
Description: ribosomal RNA-processing protein RRP42 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-25   88.8   0.0    1.8e-24   86.7   0.0    1.8  2  RNase_PH    3' exoribonuclease family, domain 1
    5.7e-14   51.9   0.1    1.1e-13   51.0   0.1    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   2.1e-28   1.8e-24       2     132 .]      37     171 ..      36     171 .. 0.95
   2 ?   -0.5   0.0      0.18   1.6e+03      28      87 ..     200     260 ..     194     268 .. 0.55

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 2.1e-28
                                       EEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHH CS
                          RNase_PH   2 lRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeiel 78 
                                       +R+l++  + +++a+GS++++lG t+v+a+v+++  e p+++  ++eg+l+v+ e+ p+as++++  g p++ +ie+
  gi|320101498|ref|YP_004177090.1|  37 YRPLEVVLNPIQKASGSSLVRLGGTQVIAGVKLELGE-PFPD-RPNEGVLQVHAEFVPLASPSFEP-GPPDENSIEI 110
                                       8**********************************99.8888.455799***************77.9********* PP

                                       HHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  79 srlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       +r+++r+lr+   +        ++k  + +  di+++++ g ++ da+++a++lALa+a+ip
  gi|320101498|ref|YP_004177090.1| 111 ARIIDRSLREPKAVkldtlvvePGKVVWVVFDDIYLVDHQG-NITDASMMASMLALATARIP 171
                                       **********99978888899999*9***************.*******************9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
                                       EEEEEEEEEEE.E-TCCG--CC..EEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHC CS
                          RNase_PH  28 vlasvtgpiee.rpseerddae..galdveveyapfasgerrregrpsdeeielsrlleralr 87 
                                       v  +++g++ + +ps e ++a     l++ v+ a  + g  +r g ++ +  +l++++++al+
  gi|320101498|ref|YP_004177090.1| 200 VTMGIYGDTIVvDPSLE-EEAVldSFLTIAVDEAGRICGVQKR-GMKGFSRNTLENAVNTALS 260
                                       44555555544444444.2222324466666666433333333.6677777777777777776 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 !   51.0   0.1   1.2e-17   1.1e-13       2      66 ..     196     260 ..     195     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.2e-17
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                       +v+ vt+g+ +d++v+Dp++eEe++ ++ lt+av++ ++++ ++k g +++++ tl++a+ +A++
  gi|320101498|ref|YP_004177090.1| 196 LVVTVTMGIYGDTIVVDPSLEEEAVLDSFLTIAVDEAGRICGVQKRGMKGFSRNTLENAVNTALS 260
                                       89**********************************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2111.03
//
Query:       gi|320101499|ref|YP_004177091.1|  [L=243]
Description: ribosomal RNA-processing protein RRP41/SKI6 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-37  127.2   0.0      7e-37  126.9   0.0    1.1  1  RNase_PH    3' exoribonuclease family, domain 1
    3.2e-16   59.1   0.2    5.9e-16   58.2   0.2    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 !  126.9   0.0   7.8e-41     7e-37       1     132 []      22     151 ..      22     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 7.8e-41
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG..--CCEEEECCCCECCCCEC-C...S...HHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer..ddaegaldveveyapfasgerrregrpsdee 75 
                                       elR+++i++gvl++anGSa++e+G+tk la+v+gp+e+ p+ ++  d+a  +l v++ +apf++ er++   ps++e
  gi|320101499|ref|YP_004177091.1|  22 ELRPVRIAIGVLKNANGSALVEYGNTKALAAVYGPREAMPKHISlpDRA--VLRVRYHMAPFSTSERKS-PAPSRRE 95 
                                       79************************************77766663544..5***************66.78***** PP

                                       HHHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  76 ielsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       iels+++ +al++++ + ++p+  id++i++l++dg ++  a  +aaslALadagip
  gi|320101499|ref|YP_004177091.1|  96 IELSKVIREALESVVFTTQYPRASIDVFIEILQADG-GTRTAGLTAASLALADAGIP 151
                                       ************************************.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.2   6.6e-20   5.9e-16       1      67 []     154     219 ..     154     219 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 6.6e-20
                                       S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                        RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                       ++vi+v+vgkv++ +vlD +  E++++e+dl++ +a + ++++l++++g  l++e++++a+e+A kg
  gi|320101499|ref|YP_004177091.1| 154 DLVIGVAVGKVGGVLVLDINELEDEYGEADLPVGIAPNTNEIVLLQLNGV-LTPEEFKQAMEMAFKG 219
                                       68************************************************.*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1819.16
//
Query:       gi|320101500|ref|YP_004177092.1|  [L=238]
Description: ribosomal RNA-processing protein RRP4 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-08   33.6   0.0      7e-08   32.7   0.0    1.5  1  KH_6      KH domain
    0.00041   20.1   0.0    0.00081   19.2   0.0    1.6  1  KH_1      KH domain
    0.00053   19.8   0.1     0.0016   18.3   0.1    1.8  2  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.2e-11     7e-08       1      45 [.     153     200 ..     153     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.2e-11
                              KH_6   1 GmlfeVslslvrRllnhvLeeLgka...gpfeiavGlNGriWvksesp 45 
                                       G+++eV++s+v Rl    +++ +      +++i++ +NG++W+k+ ++
  gi|320101500|ref|YP_004177092.1| 153 GVVVEVKPSKVARLVGRKGSMYNILtstSGCDITIAQNGYVWLKCRDE 200
                                       9**************777777753233444***************876 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.4e-07   0.00081       3      36 ..     155     188 ..     153     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-07
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEE CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvp 36 
                                       +++v+ s+v r++G++Gs+ + + + +g+ I++ 
  gi|320101500|ref|YP_004177092.1| 155 VVEVKPSKVARLVGRKGSMYNILTSTSGCDITIA 188
                                       6899*********************77*****76 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   2.6e-07    0.0016      11      70 ..     141     197 ..     137     206 .. 0.87
   2 ?   -1.6   0.0      0.42   2.5e+03      12      36 ..     199     219 ..     195     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.6e-07
                                       ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEE CS
                              KH_2  11 kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklni 70 
                                       +++g++  +I    ++v++ ++ s+ ++++G++Gs+ + ++++ + di + +++ V+l+ 
  gi|320101500|ref|YP_004177092.1| 141 TMKGKGLGKI---VDGVVVEVKPSKVARLVGRKGSMYNILTSTSGCDITIAQNGYVWLKC 197
                                       5566666666...489********************************999999999985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.42
                                       CETEEEEEEECCSCEEEEEEEESCH CS
                              KH_2  12 kagvskveIertanrviiviresqp 36 
                                       ++ + kv I    +++++++ ++++
  gi|320101500|ref|YP_004177092.1| 199 DEHTTKVLI----QAIRLIESKAHM 219
                                       556778999....999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1714.27
//
Query:       gi|320101501|ref|YP_004177093.1|  [L=231]
Description: Ribosome maturation protein SBDS [Desulfurococcus mucosus DSM 2162]
Scores for 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   73.5   0.0    1.7e-20   72.9   0.0    1.3  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    6.1e-19   68.1   0.3    8.4e-19   67.7   0.3    1.2  1  SBDS_C    SBDS protein C-terminal domain
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.35   10.9   0.0    1.6  1  EFG_C     Elongation factor G C-terminus


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   2.9e-24   1.7e-20       3      88 .]       6      91 ..       4      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 2.9e-24
                                      EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE CS
                              SBDS  3 sivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiq 81
                                      +i+ry+ +++rFe++v+++ +l+ +egk ++++e ++ + ++++a+kG +as +++ ++fgt++   ++ eI+k+Ge+q
  gi|320101501|ref|YP_004177093.1|  6 VIARYEAKGHRFEVLVDPDLALKIKEGKPVSIDEAIAGDFVYKDARKGLKASPESMREVFGTDDPRTVALEIVKRGELQ 84
                                      799**************************************************************************** PP

                                      --HHHHH CS
                              SBDS 82 vsaeerk 88
                                      +++e+r+
  gi|320101501|ref|YP_004177093.1| 85 LTTEQRR 91
                                      ****996 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 !   67.7   0.3   1.4e-22   8.4e-19       2     115 ..      98     215 ..      97     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.4e-22
                                       HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CC CS
                            SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikd 78 
                                       + +i++++a+++v+p+tk p++ ++ e a++++++ +++ k+a++Q+ +++ +L + ipi+ a+  +++ +p++ + 
  gi|320101501|ref|YP_004177093.1|  98 KAQILNLIARNAVDPKTKLPIPLKRLELAMEQARVTIDPYKPAEQQMEHIVSQLAKVIPIKVAKAYVAVRIPSEHAG 174
                                       679*********************************************************************88888 PP

                                       CHHHHHHHH.HH.......S.EEEEEE.EEGGGHHHHHHHH CS
                            SBDS_C  79 kilklieqv.esqk..vaekewevvvl.iePgaykeleefv 115
                                       k+lk +++   s+k  + e+    + l i++g+++el + v
  gi|320101501|ref|YP_004177093.1| 175 KALKPLQSFgVSKKvqWREDGSLYMELeIPAGLQQELIDRV 215
                                       88888888755544323333344777789999999998876 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 ?   10.9   0.0   5.8e-05      0.35       9      71 ..     164     225 ..     162     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.8e-05
                                       EEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EE CS
                             EFG_C   9 veievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsf 71 
                                       v +++p+e+ gk+++ l+s  G  ++++ +++g   +e eiP+   +++ +++++lTkG g++
  gi|320101501|ref|YP_004177093.1| 164 VAVRIPSEHAGKALKPLQSF-GVSKKVQWREDGSLYMELEIPAGLQQELIDRVNALTKGSGEV 225
                                       67999*********888875.77777777779*****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1781.48
//
Query:       gi|320101502|ref|YP_004177094.1|  [L=246]
Description: proteasome endopeptidase complex subunit alpha [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  184.2   0.1    2.1e-54  183.9   0.1    1.2  1  Proteasome      Proteasome subunit
    1.1e-14   53.8   0.4    1.1e-14   53.8   0.4    2.0  2  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.1   2.4e-58   2.1e-54       1     179 [.      32     206 ..      32     216 .. 0.96

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 2.4e-58
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       v++G+t++Gi++k   ++aa+kr      l++++ ++Kifkiddh+g+++aG+a+D+r+l+++a ++a l+r+ y++
  gi|320101502|ref|YP_004177094.1|  32 VRRGWTTIGIRTKSASIVAAEKRKI--TPLVDEKAIQKIFKIDDHVGASYAGMAGDGRILINYAISQALLHRFYYDE 106
                                       679*******************999..8888********************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       p pve+l++ v++ +qaytq++g+rpfgv+++iagvde+g  +L++++psG y+++ +a+aiG++s+ ++++lek+y
  gi|320101502|ref|YP_004177094.1| 107 PAPVEYLAKLVCDVKQAYTQHAGVRPFGVAMIIAGVDEKG-TQLFMTEPSGRYLSY-YATAIGEKSNNVIEFLEKNY 181
                                       *************************************999.7**************.8*****99************ PP

                                       STTBSHHHHHHHHHHHHHHHHHHBT CS
                        Proteasome 155 kedltleeavelavkalkealerdk 179
                                       k dl+++e ++l v +l  ++e+  
  gi|320101502|ref|YP_004177094.1| 182 KYDLDVDESLKLTVLTLAGIVEGKP 206
                                       ****************998888664 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 !   53.8   0.4   1.2e-18   1.1e-14       1      23 []       9      31 ..       9      31 .. 0.99
   2 ?   -3.1   0.1      0.74   6.6e+03      11      15 ..      85      89 ..      85      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.2e-18
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr++t+FSPdGR++QVEYA++A
  gi|320101502|ref|YP_004177094.1|  9 YDRAITIFSPDGRIYQVEYAFEA 31
                                      **********************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.74
                    Proteasome_A_N 11 dGRLf 15
                                      dGR++
  gi|320101502|ref|YP_004177094.1| 85 DGRIL 89
                                      9**96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1798.15
//
Query:       gi|320101503|ref|YP_004177095.1|  [L=156]
Description: Ribonuclease P-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-10   39.0   0.0    1.3e-09   38.2   0.0    1.4  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 !   38.2   0.0   7.2e-14   1.3e-09       1     101 [.      56     151 ..      56     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 7.2e-14
                                       EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT-- CS
                     RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlit 77 
                                       RY++++++++++   +++  l +a  +  +e+fG+  l k++   +++ f ++++ +++R+s+ + +  +a+L  ++
  gi|320101503|ref|YP_004177095.1|  56 RYIAFSLVCDKP---VDKGVLEDAFTRLYTEYFGKSTLQKASP--QLILFLEDKQAGVLRTSHLYRDHTVAVLGALK 127
                                       9**********4...569*************************..89****************************** PP

                                       EETTEEEEEEEEEEESSHHHHHHH CS
                     RNase_P_Rpp14  78 kiegrpvvfrvvrvsGTikkaeee 101
                                       ++++ ++v+ ++++ G+++k++e+
  gi|320101503|ref|YP_004177095.1| 128 HVGDSKCVVIPLKTCGSLRKCREA 151
                                       *********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1202.57
//
Query:       gi|320101504|ref|YP_004177096.1|  [L=203]
Description: ribonuclease P subunit P30 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   22.0   0.0    0.00015   21.3   0.0    1.4  1  RNase_P_p30  RNase P subunit p30
  ------ inclusion threshold ------
      0.022   14.4   0.3       0.11   12.3   0.0    2.0  2  HeH          HeH/LEM domain


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.7e-08   0.00015      57     199 ..      32     170 ..       3     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-08
                                       HHHHHHH..HHSSEEEEEEES-H.HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHH CS
                       RNase_P_p30  57 lkkelsglkllsRvtlvvsdpsklqrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktir 133
                                       ++  ++g+ +++Rv   + d ++l+++  +      +av P + ++ r+ + + ++D i +   +   f +++k+ +
  gi|320101504|ref|YP_004177096.1|  32 EQAGFNGVAVVRRVDAATGDVAELRSILAEHGGSAYIAVTPLSLRVARWSAHDERIDTIVMTGGN-IEF-FDKKQFS 106
                                       5566888999************99999999999999*********************99998865.555.9****** PP

                                       HHHHHT-EEEEESHHHHHS-HHHHHHHHHHHHHHHHHHHH--EEEE--BSSGGG---HHHHHHHHH CS
                       RNase_P_p30 134 aAvergvafEinyspllrdsglaRrnfisnarkllrltrgkgvviSSgAesplelRnpydiinLlk 199
                                       a    g  +E++ ++ lr +  +  +f ++++  lr   g ++v  SgA+ ++el +py i+++l 
  gi|320101504|ref|YP_004177096.1| 107 AMKTYGKPLEVSVGDFLRLDDVKGGQFYRRVNLALR--MGIRLVTGSGARWWWELYHPYVIVSMLS 170
                                       *********************999999999986666..5899********************9986 PP

>> HeH  HeH/LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.2e-05      0.11       6      17 ..      52      63 ..      52      63 .. 0.97
   2 ?   -0.7   0.0      0.13   1.2e+03       1       8 [.      72      79 ..      72      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                               HeH  6 VaqLRriLvehg 17
                                      Va+LR+iL+ehg
  gi|320101504|ref|YP_004177096.1| 52 VAELRSILAEHG 63
                                      9**********8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                               HeH  1 pksLtVaq 8 
                                      p sL+Va+
  gi|320101504|ref|YP_004177096.1| 72 PLSLRVAR 79
                                      77****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1600.63
//
Query:       gi|320101505|ref|YP_004177097.1|  [L=158]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  107.5   0.0    5.8e-31  107.2   0.0    1.1  1  RNA_binding  RNA binding
  ------ inclusion threshold ------
      0.046   13.5   0.1      0.086   12.6   0.1    1.5  1  Rtt106_N     Histone chaperone Rtt106 N-terminal domain


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 !  107.2   0.0   6.5e-35   5.8e-31       2     119 .]      17     137 ..      16     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 6.5e-35
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTS...E---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHH CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpee...eveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeike 75 
                                       +e++ f+haTEd+++V+++l nllp+e   +v + ee +eG+ygn+i+++++++ + + +k+l++l + ++++e+++
  gi|320101505|ref|YP_004177097.1|  17 VELSSFCHATEDCSRVRSSLLNLLPPElrsRVVLVEEALEGYYGNRIVVVKTQILE-ECEKILEYLSSIMSSSEKSI 92 
                                       899*************************9987889********************9.55****************** PP

                                       HHHCCHCCB-.TTSEEEEEEEHHHHHTT---BESSSSEEEEEEEE CS
                       RNA_binding  76 Llkeleervd.ekgklylrldKQaaylgklslvegddvIkvkikv 119
                                       L+ +l+ r+d ++g+l+lr++KQ+a++g+ +l ++ddv+kv++++
  gi|320101505|ref|YP_004177097.1|  93 LKATLPLRLDqRTGRLILRFSKQDAFRGEARLLDSDDVVKVVLHF 137
                                       **********999****************************9875 PP

>> Rtt106_N  Histone chaperone Rtt106 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   9.6e-06     0.086       3      21 ..      34      52 ..      32      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.6e-06
                          Rtt106_N  3 eSFldkLPaeLrskvskIt 21
                                       S l+ LP eLrs+v+ + 
  gi|320101505|ref|YP_004177097.1| 34 SSLLNLLPPELRSRVVLVE 52
                                      599************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1151.66
//
Query:       gi|320101506|ref|YP_004177098.1|  [L=220]
Description: 50S ribosomal protein L15 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-81  271.6   0.9    3.4e-81  271.6   0.9    1.6  2  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
      0.018   14.6   0.1       0.04   13.5   0.1    1.5  1  Rpn9_C          Rpn9 C-terminal helix


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 !  271.6   0.9   3.8e-85   3.4e-81       1     182 [.       4     183 ..       4     192 .. 0.95
   2 ?   -0.8   0.3      0.12     1e+03     152     171 ..     188     207 ..     180     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 271.6 bits;  conditional E-value: 3.8e-85
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++y+y++e+wk+   d+l+ l+++rl+e+r+ep+vvrv+ ptrldrAr+LGYkak G+++vrvrvr+Gg++k  ++ 
  gi|320101506|ref|YP_004177098.1|   4 SMYHYIAETWKEG-GDELESLMKQRLIEWRREPSVVRVDAPTRLDRARALGYKAKVGFIIVRVRVRKGGQRK--PRP 77 
                                       79*********76.789*******************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                        +gr+pkr+gv+ + paksl+ iaeer++rk+p+l+vLnSY+v+eDg+yk++Evi+vDp+h++i +d++inwic+++
  gi|320101506|ref|YP_004177098.1|  78 DSGRRPKRMGVYGYAPAKSLRLIAEERAARKFPGLEVLNSYYVAEDGRYKWFEVIMVDPHHPSICSDPEINWICEPQ 154
                                       ***************************************************************************** PP

                                       GTTGGGGT-SHHHHHHTT-S-SS..TT-T CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkg.lkgae 182
                                       +++R++rGltsagkk+RGlrk++ l+g+ 
  gi|320101506|ref|YP_004177098.1| 155 NRGRVFRGLTSAGKKMRGLRKSRgLRGTV 183
                                       *******************9865266555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.12
                                       SGGGTTGGGGT-SHHHHHHT CS
                    Ribosomal_L15e 152 kkvhkhRelrGltsagkksR 171
                                       k ++k+Relr    a++ +R
  gi|320101506|ref|YP_004177098.1| 188 KRKQKERELRKRHEASRGAR 207
                                       66788888888777776666 PP

>> Rpn9_C  Rpn9 C-terminal helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.4e-06      0.04      10      20 ..      24      34 ..      22      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-06
                                      HHHHHHHHHHH CS
                            Rpn9_C 10 MKdrLVeWdeq 20
                                      MK+rL+eW+ +
  gi|320101506|ref|YP_004177098.1| 24 MKQRLIEWRRE 34
                                      ********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1630.43
//
Query:       gi|320101507|ref|YP_004177099.1|  [L=411]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-35  120.9   0.0    1.2e-34  119.3   0.0    1.8  2  MMR_HSR1_C    GTPase of unknown function C-terminal
    6.4e-22   77.8   0.0    1.8e-21   76.4   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
      1e-12   47.9   0.0    2.5e-12   46.6   0.0    1.6  1  TGS           TGS domain
    1.4e-08   34.4   0.3    3.4e-06   26.7   0.1    3.0  3  FeoB_N        Ferrous iron transport protein B
     0.0058   16.2   0.1        4.3    6.8   0.0    3.0  3  GTP_EFTU      Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.29   11.1   0.0    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.22   11.2   0.0       0.87    9.2   0.0    1.8  1  Peripla_BP_6  Periplasmic binding protein


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 ?   -1.7   0.0       1.7   4.2e+03      65      91 ..     134     158 ..     107     166 .. 0.72
   2 !  119.3   0.0   4.6e-38   1.2e-34       1     112 []     229     337 ..     229     337 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                        MMR_HSR1_C  65 eldekqkkaLekirdlvlkrygsTGVq 91 
                                       +  e+ +k L++i++++  + + T ++
  gi|320101507|ref|YP_004177099.1| 134 DPVEEAEKILNEINEWF--KATVTRIW 158
                                       45677788899999944..66677666 PP

  == domain 2  score: 119.3 bits;  conditional E-value: 4.6e-38
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       a+NK+D+p a++++++lk+++ +++ v+pvsA  E++Lrkaa++gli+Y+pgd++f++ke   ++l+ +q kaL+ i
  gi|320101507|ref|YP_004177099.1| 229 AANKIDVPIAADYVKELKKRFGDEN-VIPVSALGEYILRKAAQNGLIEYIPGDSSFRVKEA--SRLTGEQLKALKLI 302
                                       89********************888.*********************************99..56************ PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       +++vlk+ygsTGVqe+ln+avf+ l+livVYPVed
  gi|320101507|ref|YP_004177099.1| 303 EENVLKHYGSTGVQELLNTAVFKKLGLIVVYPVED 337
                                       *********************************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 !   76.4   0.0   6.9e-25   1.8e-21       2      98 ..       8     147 ..       7     167 .. 0.76
   2 ?   -3.1   0.0       3.3   8.3e+03     101     114 .]     219     232 ..     189     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 6.9e-25
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE..........................EEEEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke..........................ielvD 52 
                                       +++vG++NvGKStL++a+t + a+++++p+tT+++n g  +++  +                          ++++D
  gi|320101507|ref|YP_004177099.1|   8 IGVVGKTNVGKSTLFSAMTLAPAKIANHPFTTIEPNIGVGHVRV-KcahvelglpgcnprsglcisgqrfipVKVID 83 
                                       89***********************************9765331.123344555566666666666667777***** PP

                                       CGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.................TTCSHHHHHHHH CS
                          MMR_HSR1  53 tpGliegaseekglgkaflalee.adlillvvdas.................eeklkpldeele 98 
                                       ++Gli gas+++glg++f +  + ad++++vvdas                  e+ +++ +e++
  gi|320101507|ref|YP_004177099.1|  84 VAGLIPGASTGRGLGNKFMDDLRqADVLIHVVDASgstdlegnpvppgtqdpVEEAEKILNEIN 147
                                       *******************977769********9988887777776665333112233333333 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                                       HHHTTSEEEEEEES CS
                          MMR_HSR1 101 leeakkplilvlnk 114
                                       l+e  kp+i+++nk
  gi|320101507|ref|YP_004177099.1| 219 LREISKPVIIAANK 232
                                       34467888888887 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   9.8e-16   2.5e-12       5      59 ..     349     403 ..     345     404 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 9.8e-16
                                       ETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS   5 tPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       +Pd+ +  +p ++t++++Ay +h++l+++f+yA      +r g dh Le+gdvv+Iv
  gi|320101507|ref|YP_004177099.1| 349 LPDAYL--VPGNTTARELAYMVHTELGESFLYAVDARrkRRIGEDHILENGDVVKIV 403
                                       455555..899999***********************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 !   26.7   0.1   1.3e-09   3.4e-06       3      51 ..       8      56 ..       6      65 .. 0.80
   2 ?   -1.0   0.0      0.45   1.2e+03      77      89 ..     106     118 ..      80     122 .. 0.86
   3 ?    4.1   0.0     0.012        30      97     143 ..     215     259 ..     207     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.3e-09
                                      EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEE CS
                            FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkevei 51
                                      + +vG+ nvGk+tlf a+t a  k++N+p +t+e + g  +++ k +++
  gi|320101507|ref|YP_004177099.1|  8 IGVVGKTNVGKSTLFSAMTLAPAKIANHPFTTIEPNIGVGHVRVKCAHV 56
                                      679*******************************998876655444443 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.45
                                       TSSSEEEEEEEGG CS
                            FeoB_N  77 eepdvvvnvvdat 89 
                                       +++dv+++vvda+
  gi|320101507|ref|YP_004177099.1| 106 RQADVLIHVVDAS 118
                                       5789*******96 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.012
                                       HHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT.S-EEEEBT CS
                            FeoB_N  97 LtlqllelgvpvvlalnmideaekkgieidlkkLsekLg.vpvvktsa 143
                                       + + l e+++pv++a n+id+  ++ +   +k+L++++g  +v+++sa
  gi|320101507|ref|YP_004177099.1| 215 FAVTLREISKPVIIAANKIDVPIAADY---VKELKKRFGdENVIPVSA 259
                                       678899**************8766655...466666665334666665 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0017       4.3       6      32 ..       8      34 ..       5      41 .. 0.88
   2 ?    0.6   0.0      0.14   3.6e+02      91     105 ..     105     119 ..      98     148 .. 0.81
   3 !    4.8   0.0    0.0072        18     119     180 ..     220     295 ..     214     335 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0017
                                      EEEEESTTSSHHHHHHHHHHHTTSSCH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaisk 32
                                      ig++g ++ GK+TL  +++ +  +i++
  gi|320101507|ref|YP_004177099.1|  8 IGVVGKTNVGKSTLFSAMTLAPAKIAN 34
                                      89***************9988777765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.14
                                       HHT-SEEEEEEETTT CS
                          GTP_EFTU  91 lrvlDgavlvvdave 105
                                       lr++D+ + vvda+ 
  gi|320101507|ref|YP_004177099.1| 105 LRQADVLIHVVDASG 119
                                       799999999999974 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0072
                                       HHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH.................HHHHHHHHHTTT.......TTEEEE CS
                          GTP_EFTU 119 lkegvpiivfiNKmDrlkaelkeiveevkqklsrk.................eeklekygekge.......kevpvv 171
                                       ++   p+i++ NK+D ++a     v+e+k+++ ++                 +        +g        + + v 
  gi|320101507|ref|YP_004177099.1| 220 REISKPVIIAANKIDVPIA--ADYVKELKKRFGDEnvipvsalgeyilrkaaQ--------NGLieyipgdSSFRVK 286
                                       5556789********9954..34556666666554555666666444444431........2213333333456666 PP

                                       EEBTTTTBT CS
                          GTP_EFTU 172 fgSalkgeg 180
                                        +S l+ge+
  gi|320101507|ref|YP_004177099.1| 287 EASRLTGEQ 295
                                       666666553 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   0.0   0.00011      0.29      56      90 ..     224     262 ..     208     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                      MMR_HSR1_Xtn  56 ipclyvlNKiDl.isleeldelare...pnsvviSaeke 90 
                                       +p++++ NKiD  i  ++++el+++   +n++++Sa  e
  gi|320101507|ref|YP_004177099.1| 224 KPVIIAANKIDVpIAADYVKELKKRfgdENVIPVSALGE 262
                                       689*********9***********77768******9765 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00034      0.87     204     303 ..     188     295 ..     105     314 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHTT-SSSCEEEECCC-CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHH CS
                      Peripla_BP_6 204 aallkaaaeaGldakrillvswsgseedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaa 280
                                        +++ a+++aGl +k++    w++ +  l a+  +   + +++++  +  d p++ ++v+++++++g++++   +a+
  gi|320101507|ref|YP_004177099.1| 188 HHVIEAVRRAGLEGKPF--KNWTLEDVGLFAVTLREISKPVIIAA--NKIDVPIAADYVKELKKRFGDENVIPVSAL 260
                                       568999*******9955..56***********9999999999966..46889*****************99999999 PP

                                       HHHHHHHHHHHHH............HCCTHCCHHH CS
                      Peripla_BP_6 281 ggyiaadllleal............kaagsltrea 303
                                       g yi   +  ++l            k+a  lt+e+
  gi|320101507|ref|YP_004177099.1| 261 GEYILRKAAQNGLieyipgdssfrvKEASRLTGEQ 295
                                       99987777766665555555555555554555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3129.51
//
Query:       gi|320101508|ref|YP_004177100.1|  [L=119]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-19   67.8   0.1    1.5e-17   63.8   0.1    2.0  1  DUF2095       Uncharacterized protein conserved in archaea (D
  ------ inclusion threshold ------
      0.077   13.1   0.0       0.11   12.6   0.0    1.2  1  ORF6C         ORF6C domain
       0.12   11.8   0.0       0.15   11.4   0.0    1.4  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !   63.8   0.1   2.5e-21   1.5e-17      15     127 ..       5     108 ..       2     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.5e-21
                           DUF2095  15 ydleefkrrfpalareleeer.gleidairldeeevleeeeeegkidfsgynptiidflrrcetdeealeiinwmee 90 
                                       y +++f++++p lare+ + + g +i+   +      +   +     +sgy pt+id++rrc++  eale+i+++ +
  gi|320101508|ref|YP_004177100.1|   5 YRIDDFRKKYPHLAREILDGEgGQSIELT-V------D---MGYSDPWSGYVPTVIDYIRRCKSVSEALEVIDYLVK 71 
                                       99**************7655404444322.1......1...2223469***************************** PP

                           DUF2095  91 rgeithemakelrvvlvkkgvrafgpkkewgwyerhg 127
                                       + e++   a elr  l +kg+  fg +k+  +y +  
  gi|320101508|ref|YP_004177100.1|  72 HEELSTRDAEELRTLLREKGLEFFGGRKQDDYYYKEA 108
                                       ****************************999998765 PP

>> ORF6C  ORF6C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05      0.11      17      68 ..      60     109 ..      53     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                             ORF6C  17 eeidervkkLeenmpldesekeeiqkkvkkkvvellggkkspaykdkslrkk 68 
                                       +e  e +++L +   l+++++ee++++ ++k  e+ gg k   y  k+  ++
  gi|320101508|ref|YP_004177100.1|  60 SEALEVIDYLVKHEELSTRDAEELRTLLREKGLEFFGGRKQDDYYYKE--AR 109
                                       55667789999*****************************99998777..33 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 ?   11.4   0.0   2.6e-05      0.15      21      75 ..      71     115 ..      20     119 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                                       HHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHH CS
                      AP_endonuc_2  21 pvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkra 75 
                                       +  els  +++elr +l+e gl+ ++ + + +++y +      +    ++++++a
  gi|320101508|ref|YP_004177100.1|  71 KHEELSTRDAEELRTLLREKGLEFFGGRKQDDYYYKE------A----RRYWEKA 115
                                       334448899**************99999999999933......3....3444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 944.99
//
Query:       gi|320101509|ref|YP_004177101.1|  [L=436]
Description: nucleotidyltransferase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  103.8   0.0    1.5e-29  103.3   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    3.4e-15   55.1  14.9    4.3e-07   29.4   0.2    5.4  4  Hexapep          Bacterial transferase hexapeptide (six repea
    1.2e-13   51.7   0.0    1.7e-13   51.2   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00015   21.6   0.0    0.00023   21.0   0.0    1.2  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.016   14.9  10.2       0.92    9.3   0.1    4.3  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
      0.058   11.5   0.2      0.098   10.8   0.2    1.3  1  DUF4954          Domain of unknown function (DUF4954)


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0     5e-33   1.5e-29       1     245 [.      13     240 ..      13     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 5e-33
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kavILa G+G RL+P+t t++k+l+p+l k ++++  l+rla   ++e+++v+  +   ++ + + eg k+  ++ +
  gi|320101509|ref|YP_004177101.1|  13 KAVILAAGNGVRLRPITETRPKPLIPILCK-PMLEWHLERLAG-VVDEVVLVVG-YMG-EAVRRFVEGMKLPFKTRF 85 
                                       79****************************.***********5.8888555555.444.555566667789****** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       + + e++gt dAv++++  l+ +++   vlv+ +D+++     +++ + + ++     ++++++ve++++yGv+  +
  gi|320101509|ref|YP_004177101.1|  86 VEQGEPRGTGDAVVKGVSGLDSDEE---VLVIYSDVFTPV---NIIPEIAGAEG---NILVASEVENPRDYGVVI-E 152
                                       ********************98885...********9984...44444444444...578899*********996.5 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       e+g  +r  EKP+e   s l++ GiY     v ++la+ d+++++rge e+tdil+ + ++g +   +   ++  W 
  gi|320101509|ref|YP_004177101.1| 153 ENGYFKRVLEKPAESY-SRLINGGIYKLR--VGDILANsDIAPSPRGELEFTDILNNMSRRGVEIRVHRLPGS-SWI 225
                                       5699**********99.*******66555..555555569********************9977777777776.6** PP

                                       EXSSHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanekl 245
                                       D+G++  llean+  
  gi|320101509|ref|YP_004177101.1| 226 DIGKPWQLLEANKMA 240
                                       ***********9865 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2   1.4e-10   4.3e-07       1      35 [.     261     295 ..     261     296 .. 0.96
   2 !   19.2   0.1   2.3e-07   0.00069       3      34 ..     281     312 ..     279     313 .. 0.79
   3 !    5.2   0.3    0.0063        19       3      33 ..     316     345 ..     314     348 .. 0.86
   4 !   22.9   1.2   1.6e-08   4.7e-05       1      34 [.     373     406 ..     373     408 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.4e-10
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++IG+++++ pf+vi g+V I  +v Ig++++i+
  gi|320101509|ref|YP_004177101.1| 261 DVFIGEGSIVKPFTVIEGPVYIDQGVEIGPNARIR 295
                                       68*******************************97 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.3e-07
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                        I ++v Igp+a i++  +I +++kIg  v +
  gi|320101509|ref|YP_004177101.1| 281 YIDQGVEIGPNARIRPWSVICKGSKIGFSVEV 312
                                       67788889999999999999999999887766 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0063
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                       +I +nv+  + a+i g+ +I + v +gag+ 
  gi|320101509|ref|YP_004177101.1| 316 IILENVHASHLAYI-GDSIICEEVNLGAGTI 345
                                       67789999999***.9999*********985 PP

  == domain 4  score: 22.9 bits;  conditional E-value: 1.6e-08
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       ++vIG +v+ g ++ ++++Vk+G+n+ I +g+v+
  gi|320101509|ref|YP_004177101.1| 373 GAVIGAGVKTGVNVSLMPGVKVGSNTWIMPGSVV 406
                                       689*****************************98 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 !   51.2   0.0   5.8e-17   1.7e-13       1     107 [.      14     128 ..      14     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 5.8e-17
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-E....EE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrv....vede 66 
                                       aviLA+G++ R+      ++K+l+p+  kp+le++l++l+ + vdevv+v+g+  e+v++ +++ ++++    ve+ 
  gi|320101509|ref|YP_004177101.1|  14 AVILAAGNGVRLRpitetRPKPLIPILCKPMLEWHLERLAGV-VDEVVLVVGYmgEAVRRFVEGMKLPFktrfVEQ- 88 
                                       79**********6554435***********************.**********98999999988865544441555. PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHH CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverl 107
                                        + +g++ ++  +++ + +++ vlv+  D+ + + +++ ++
  gi|320101509|ref|YP_004177101.1|  89 GEPRGTGDAVVKGVSGLDSDEEVLVIYSDV-FTPVNIIPEI 128
                                       5679*************9***********8.5566666555 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 !   21.0   0.0   7.8e-08   0.00023       3      97 ..      14     113 ..      12     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.8e-08
                                       EEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE CS
                              IspD   3 vvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlva 72 
                                       +vi AAG+G R++   + +pK ++ +  +++le+ ++ l++  +vd++v+vv     e+++ +        +   v+
  gi|320101509|ref|YP_004177101.1|  14 AVILAAGNGVRLRpitETRPKPLIPILCKPMLEWHLERLAG--VVDEVVLVVGYMG-EAVRRFVEGmklpFKTRFVE 87 
                                       89*********85333899********************99..9***999997654.33333333323336789*** PP

                                       --SSHH..HHHHHHHHTTSSTTSEEEE CS
                              IspD  73 GGdeRa..esVlnglkalegeakfVLv 97 
                                        G+ R   ++V++g+  l+ ++++ Lv
  gi|320101509|ref|YP_004177101.1|  88 QGEPRGtgDAVVKGVSGLDSDEEV-LV 113
                                       ***9954489*******9988554.43 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.5    0.0007       2.1       1      29 [.     255     291 ..     255     300 .. 0.70
   2 ?   -1.0   0.2       0.5   1.5e+03      14      30 ..     327     344 ..     320     345 .. 0.71
   3 ?    9.3   0.1   0.00031      0.92       3      34 .]     375     408 ..     373     408 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0007
                                       .EEE-TT-EE-TT-EE........SEEE-TT-EE-TT CS
                         Hexapep_2   1 pviIGdnCliGanagi........GvslGdncvvgaG 29 
                                       pv+I+ +++iG  +++        +v +  ++ +g++
  gi|320101509|ref|YP_004177101.1| 255 PVHIEGDVFIGEGSIVkpftviegPVYIDQGVEIGPN 291
                                       8*************96654556753555555555544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.5
                                       -EES.EEE-TT-EE-TT- CS
                         Hexapep_2  14 agiG.vslGdncvvgaGv 30 
                                       a+iG  ++++++ +gaG 
  gi|320101509|ref|YP_004177101.1| 327 AYIGdSIICEEVNLGAGT 344
                                       666546788888888885 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00031
                                       EE-TT-EE-TT-E.E.SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   3 iIGdnCliGanag.i.GvslGdncvvgaGvvita 34 
                                        IG+ +  G+n   + Gv++G n  + +G+v+++
  gi|320101509|ref|YP_004177101.1| 375 VIGAGVKTGVNVSlMpGVKVGSNTWIMPGSVVYR 408
                                       5888888899966379****************95 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   3.3e-05     0.098     216     280 ..     284     349 ..     243     357 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.3e-05
                           DUF4954 216 apveiGegViled.fiissGskikdgavisrcfvGqavklkkqfsaedsllfaNcqgengEavaif 280
                                       + veiG +  ++  ++i++Gski  ++ ++++++ ++v+ ++ + + ds++ +  ++  g + a++
  gi|320101509|ref|YP_004177101.1| 284 QGVEIGPNARIRPwSVICKGSKIGFSVEVKESIILENVHASHLAYIGDSIICEEVNLGAGTITANL 349
                                       3455555555543379***********************************999999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3516.41
//
Query:       gi|320101510|ref|YP_004177102.1|  [L=215]
Description: 30S ribosomal protein S3AE [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  229.7   1.7    2.9e-68  229.5   1.7    1.0  1  Ribosomal_S3Ae   Ribosomal S3Ae family
  ------ inclusion threshold ------
      0.042   13.4   0.0      0.089   12.4   0.0    1.5  1  Abhydro_lipase   Partial alpha/beta-hydrolase lipase region
       0.11   13.0   0.0       0.26   11.8   0.0    1.7  1  S-l_SbsC_C       S-layer protein SbsC C-terminal domain
       0.87    9.5   3.7        7.5    6.5   0.0    2.7  3  Post_transc_reg  Post-transcriptional regulator


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.5   1.7   6.4e-72   2.9e-68       6     202 .]       9     194 ..       4     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 229.5 bits;  conditional E-value: 6.4e-72
                                       -S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEESSE CS
                    Ribosomal_S3Ae   6 vvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqgkn 82 
                                       v+Dk+k K+W++v aP+ +g +++G+t++       + +ekl+grv+e++l+D+t+d   q+++kl+l++ +v+g++
  gi|320101510|ref|YP_004177102.1|   9 VKDKWKIKKWFEVVAPASLGGVSLGTTPA-------DMPEKLIGRVIETTLYDITGDI-TQVHVKLYLQVVSVEGNK 77 
                                       89***************************.......*********************9.668*************** PP

                                       EEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  83 altnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteease 159
                                       a+t+Fkg+el+rD++rsl+r++ss+I+ i+dv+tkDgy+lr+++va+T++r   +k+sqk+aIr++m++++ ++a e
  gi|320101510|ref|YP_004177102.1|  78 AVTRFKGHELARDYMRSLIRRKSSKIQGIFDVTTKDGYILRLTIVALTSYR---CKTSQKRAIRRVMRDYIYKKAGE 151
                                       ***************************************************...*********************** PP

                                       S-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                    Ribosomal_S3Ae 160 ldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                       l+l+el++++++ ++++ei + a+kIyp+r+ve++K+k+l  P
  gi|320101510|ref|YP_004177102.1| 152 LTLDELIQEIMSYKVSNEISELARKIYPIRRVEVYKSKLLMVP 194
                                       ************66*************************9765 PP

>> Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05     0.089      15      28 ..     107     120 ..     103     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                    Abhydro_lipase  15 heVqTeDGYiLtlh 28 
                                       + V+T+DGYiL l 
  gi|320101510|ref|YP_004177102.1| 107 FDVTTKDGYILRLT 120
                                       68*********986 PP

>> S-l_SbsC_C  S-layer protein SbsC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.8e-05      0.26      37      83 ..      45      87 ..      32      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.8e-05
                        S-l_SbsC_C 37 gsklsgaaaaytsgtditditatagqyillyeVDasgkivayasiqv 83
                                      g  + ++   y    dit  ++ ++ y++++ V +++ +  ++  ++
  gi|320101510|ref|YP_004177102.1| 45 GRVIETT--LYDITGDIT--QVHVKLYLQVVSVEGNKAVTRFKGHEL 87
                                      5555554..577888999..9******************99986665 PP

>> Post_transc_reg  Post-transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.5       2.1   9.3e+03      36      45 ..       8      17 ..       6      21 .. 0.70
   2 ?    3.6   0.0     0.014        62      47      74 ..      50      77 ..      46      85 .. 0.85
   3 ?    6.5   0.0    0.0017       7.5      30      62 ..     135     167 ..     124     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.1
                   Post_transc_reg 36 lvekkwKkke 45
                                      +v+ kwK k+
  gi|320101510|ref|YP_004177102.1|  8 VVKDKWKIKK 17
                                      5788999443 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                   Post_transc_reg 47 lrlhelvqdilslkineymsyltveayk 74
                                      + l+++  di ++ ++ y++ ++ve  k
  gi|320101510|ref|YP_004177102.1| 50 TTLYDITGDITQVHVKLYLQVVSVEGNK 77
                                      679***************9999988766 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0017
                   Post_transc_reg  30 ediwnylvekkwKkkeelrlhelvqdilslkin 62 
                                       + i++ + ++  Kk  el l el+q+i+s k++
  gi|320101510|ref|YP_004177102.1| 135 RAIRRVMRDYIYKKAGELTLDELIQEIMSYKVS 167
                                       5677778888899****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1543.34
//
Query:       gi|320101511|ref|YP_004177103.1|  [L=86]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 641.96
//
Query:       gi|320101512|ref|YP_004177104.1|  [L=380]
Description: phosphoesterase RecJ domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.019   15.6   0.0      0.035   14.7   0.0    1.4  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
      0.082   12.6   0.3       0.65    9.7   0.1    2.1  2  DUF3334          Protein of unknown function (DUF3334)


Domain annotation for each model (and alignments):
>> 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 ?   14.7   0.0   3.9e-06     0.035      23      69 ..     195     240 ..     178     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-06
                                       GGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT CS
                   Arg_tRNA_synt_N  23 eiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei 69 
                                         +i++ +n+k  D+ +n  m+lak+l+ + +e+ ++i   +  +++
  gi|320101512|ref|YP_004177104.1| 195 LRNIDA-SNEKELDLLLNFLMELAKALNLSINELSNKILGDFVIPPD 240
                                       345665.9******************************988766655 PP

>> DUF3334  Protein of unknown function (DUF3334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   7.2e-05      0.65     132     183 ..       9      60 ..       5      97 .. 0.90
   2 ?    0.6   0.0     0.043   3.8e+02     102     115 ..     224     237 ..     214     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7.2e-05
                           DUF3334 132 mltlnkevtlsvdtnldrpearrvsfkteknnifylelamdktefikledfe 183
                                       ++t nk + +  dt ld+  a  + +kt +++ f + +++d    i  +df 
  gi|320101512|ref|YP_004177104.1|   9 LITKNKSIRILTDTSLDSLLAAGILMKTLREHNFTVRVTLDAKTVIDERDFP 60 
                                       6788******************************************999996 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.043
                           DUF3334 102 lGelmnqivGdftg 115
                                       + el n+i+Gdf+ 
  gi|320101512|ref|YP_004177104.1| 224 INELSNKILGDFVI 237
                                       679*********84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2852.37
//
Query:       gi|320101513|ref|YP_004177105.1|  [L=160]
Description: 30S ribosomal protein S15 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-24   83.5   0.0    1.8e-23   82.4   0.0    1.6  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    1.7e-17   63.4   0.2    2.5e-17   62.8   0.2    1.3  1  Ribosomal_S15    Ribosomal protein S15


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.0     2e-27   1.8e-23       5      60 .]       3      60 ..       1      60 [. 0.94

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 2e-27
                                      SSSSS--------S-SS--TTS-..--HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N  5 hsrgkGkSgSarPyrreapsWlk..lskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      ++r++G+S+S+rP+r  +p+Wlk  +s+++ve l+v+lakkG+tpS+IGviLRDqyG+
  gi|320101513|ref|YP_004177105.1|  3 KKRDRGSSHSTRPARAGPPRWLKldMSPNDVELLVVELAKKGYTPSMIGVILRDQYGI 60
                                      4899******************95569******************************9 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.2   2.8e-21   2.5e-17       3      80 ..      73     148 ..      71     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.8e-21
                                       HHHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHH CS
                     Ribosomal_S15   3 elikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkkliek 77 
                                       e++++++ +      ++++++ l+++++nl++hl+e++kD hs+rgL++++sk+++l+kY+kr  +  +++k+  ek
  gi|320101513|ref|YP_004177105.1|  73 EILEKHGVKI----TIPEDLMSLIQKAVNLRRHLEEHPKDTHSQRGLIEVESKIHRLVKYYKRIGRlpPDWKYDPEK 145
                                       5677777777....899***********************************************9999*******99 PP

                                       CTS CS
                     Ribosomal_S15  78 lgl 80 
                                       + l
  gi|320101513|ref|YP_004177105.1| 146 ARL 148
                                       876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1170.69
//
Query:       gi|320101514|ref|YP_004177106.1|  [L=192]
Description: dITPase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-41  140.1   0.0    8.7e-41  139.9   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 !  139.9   0.0   4.8e-45   8.7e-41       1     186 [.       4     180 ..       4     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 4.8e-45
                                       EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTT CS
                        Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLng 75 
                                       +++ +gNk+K++e++e+ ++ +++v  l   e ++ +E+q +++  +al  a   +   g+pvl++D gL+++aLng
  gi|320101514|ref|YP_004177106.1|   4 LLLLSGNKHKYAEIAEVAGRYGVKVTPL---EGFK-VEIQdDDLSRIALTAALIGYSiLGKPVLVEDAGLFIKALNG 76 
                                       5789*************98888888776...3334.4999999********99877745999*************** PP

                                       TBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGG CS
                        Ham1p_like  76 lPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDp 152
                                       +PG+ys+++ ++ +    ++ kl+e+++  e  r A f++v + +    ++++   Gev G i+ ep+g++gfG+Dp
  gi|320101514|ref|YP_004177106.1|  77 FPGPYSSYVFKTLGV--HGILKLMEGVA--E--RDACFKSVAVAVVD--GNVVKGYGEVCGYITVEPKGSRGFGFDP 145
                                       *********753322..25555555553..5..9******9766653..4445688********************* PP

                                       GEEETT-SS.BTTTS.CHHHHHHSHHHHHHHHHHH CS
                        Ham1p_like 153 iFvpeegek.tfaelskeeknaiShRgkAleklle 186
                                       iF p+++ + tfae++ +ekn++ShR+kA++++ e
  gi|320101514|ref|YP_004177106.1| 146 IFTPRDQPGrTFAEMDVAEKNKYSHRAKAVAAVFE 180
                                       ****955555********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1408.62
//
Query:       gi|320101515|ref|YP_004177107.1|  [L=226]
Description: Mn2+dependent serine/threonine protein kinase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-12   47.9   0.0    1.6e-12   47.4   0.0    1.2  1  RIO1         RIO1 family
    1.7e-11   44.5   0.1    8.4e-05   22.6   0.0    2.2  2  APH          Phosphotransferase enzyme family
    2.6e-09   36.8   0.0      3e-09   36.6   0.0    1.1  1  Pkinase      Protein kinase domain
      8e-07   28.6   0.0    1.8e-06   27.5   0.0    1.6  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
    8.3e-06   25.3   0.0      1e-05   25.0   0.0    1.1  1  Pkinase_Tyr  Protein tyrosine kinase
  ------ inclusion threshold ------
       0.17   11.6   0.0       0.29   10.8   0.0    1.4  1  DUF3990      Protein of unknown function (DUF3990)
        0.2   10.5   0.0       0.29    9.9   0.0    1.1  1  YukC         WXG100 protein secretion system (Wss), protein Y


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 !   47.4   0.0   6.3e-16   1.6e-12      49     150 ..      45     145 ..      22     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 6.3e-16
                                       HHHHHHHHHHHHHHHHHHHTT--S--EE..EEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHH CS
                              RIO1  49 klvklwaekEfrnLkrleeagvpvPkpi..elkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklyk 123
                                         ++  ++ E ++L +l++ag++vP pi  ++++ vlvme+++  g ++ +   + + e   +++++v + + +l++
  gi|320101515|ref|YP_004177107.1|  45 LFIQSRTRTEAKILVELYTAGINVPAPIivDIENGVLVMEYVE--GERMSEALGAMSIEAVVDAARDVGR-QTALMH 118
                                       567788999******************744779**********..6666655444434466667777777.678888 PP

                                       TSTEEESS-STTSEEEETTEEEE--GT CS
                              RIO1 124 eaglvHaDLSeyNvlvdedkvviIDvs 150
                                       ++g+ H+DL   N++ ++ +v+iID++
  gi|320101515|ref|YP_004177107.1| 119 NMGVYHGDLTLANMIRSRRGVYIIDFG 145
                                       *************************96 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.1e-07   0.00028      36     108 ..      50     120 ..      12     123 .. 0.91
   2 !   22.6   0.0   3.3e-08   8.4e-05     168     228 ..     122     182 ..     119     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS...HHHHHHHHHHHHHHHHHHCCHHCH CS
                               APH  36 eirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr...klsaaqlpellealgeflaalhqv 108
                                       ++r e+++l  L  ag+ vP+++       +i+  ++++eyv+g+ +++   ++s +   ++++++g+  a +h++
  gi|320101515|ref|YP_004177107.1|  50 RTRTEAKILVELYTAGINVPAPII-----VDIENGVLVMEYVEGERMSEalgAMSIEAVVDAARDVGRQTALMHNM 120
                                       578899***********9999999.....667777***************************************98 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.3e-08
                                       EE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH...HHCSCHCCCHCHHHHHHHH CS
                               APH 168 llHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll...rswtseldpeflaallray 228
                                       + HgDl + N++       v ++iDf++ag++  + + a+ +   r  +s+l+p +l+ + +a 
  gi|320101515|ref|YP_004177107.1| 122 VYHGDLTLANMIRS--RRGV-YIIDFGLAGYSTDIEEYAIDIhllRKSVSTLHPPLLQPFMDAF 182
                                       67************..5555.7**********88888865333335566667666666655554 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.2e-12     3e-09      42     148 ..      43     150 ..      12     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.2e-12
                                       H.....HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHH CS
                           Pkinase  42 e.....kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegley 113
                                       +     +++++E kil +l    i     ++ + ++ +lv+eyveg+ + ++l    ++s e + + a+ + +  + 
  gi|320101515|ref|YP_004177107.1|  43 DslfiqSRTRTEAKILVELYTAGINVPAPIIVDIENGVLVMEYVEGERMSEALG---AMSIEAVVDAARDVGRQTAL 116
                                       244555788999999999999999999999999**************9999995...7******************* PP

                                       HHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEES CS
                           Pkinase 114 lHskgiiHrDlKpeNiLidekgelKitDFGlakel 148
                                       +H++g+ H Dl  +N++ + ++ + i+DFGla   
  gi|320101515|ref|YP_004177107.1| 117 MHNMGVYHGDLTLANMIRS-RRGVYIIDFGLAGYS 150
                                       ***************8887.8889*******9765 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   7.1e-10   1.8e-06      53     169 ..      46     147 ..      22     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 7.1e-10
                               Kdo  53 lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgr 129
                                       + + r + E ++l +L+ ag++vp p+   ++        +l++e +eg +  e+l a    ++ e      ++vgr
  gi|320101515|ref|YP_004177107.1|  46 FIQSRTRTEAKILVELYTAGINVPAPIIVDIEN------GVLVMEYVEGERMSEALGA----MSIEAVVDAARDVGR 112
                                       6778999*********************99985......589*******886666666....47777778899**** PP

                               Kdo 130 liaklhragvnHadlyaknillqqeeeeeaeiwliDldka 169
                                         a +h++gv+H+dl   n+    ++     +++iD+  a
  gi|320101515|ref|YP_004177107.1| 113 QTALMHNMGVYHGDLTLANMIRSRRG-----VYIIDFGLA 147
                                       *******************9888887.....999999655 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     4e-09     1e-05      48     159 ..      51     156 ..      14     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4e-09
                                       HHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTE CS
                       Pkinase_Tyr  48 lleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskkl 124
                                         +eaki+ +l    i     ++++ e+ ++v+eyv+g  +++ L +      +++ +++ a +v +  + ++++ +
  gi|320101515|ref|YP_004177107.1|  51 TRTEAKILVELYTAGINVPAPIIVDIENGVLVMEYVEGERMSEALGAM-----SIEAVVDAARDVGRQTALMHNMGV 122
                                       56789999999888888888888888999*************999886.....9*********************** PP

                                       EEST-SGGGEEEEETTEEEE-STTTHEETTTSSEE CS
                       Pkinase_Tyr 125 vHrdlaarNvLlsenkvvkisDfGLardiekddey 159
                                        H dl+  N+ +++++ v i DfGLa   ++ +ey
  gi|320101515|ref|YP_004177107.1| 123 YHGDLTLANM-IRSRRGVYIIDFGLAGYSTDIEEY 156
                                       *********5.67799999******9887666655 PP

>> DUF3990  Protein of unknown function (DUF3990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.29       1      42 [.     120     161 ..     120     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                           DUF3990   1 miLYHGskeevekpdlsksrkkkDFGkGFYlteskeqAkewa 42 
                                       m +YHG  +  + ++ +++    DFG   Y t+++e A ++ 
  gi|320101515|ref|YP_004177107.1| 120 MGVYHGDLTLANMIRSRRGVYIIDFGLAGYSTDIEEYAIDIH 161
                                       779*********************************998765 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 ?    9.9   0.0   0.00011      0.29     218     248 ..     175     205 ..     170     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YukC 218 kqPkqealieaneaylkkdYsevidtLekvd 248
                                       +qP+ +a++ea++ y k +Y+e +++L +v+
  gi|320101515|ref|YP_004177107.1| 175 LQPFMDAFMEAYKGYYKGNYEELLQRLREVS 205
                                       69*************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1678.18
//
Query:       gi|320101516|ref|YP_004177108.1|  [L=355]
Description: metalloendopeptidase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (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  238.4   0.0    1.4e-70  238.1   0.0    1.0  1  Peptidase_M22  Glycoprotease family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.1   0.0   7.7e-75   1.4e-70       2     271 .]      45     322 ..      44     322 .. 0.93

  Alignments for each domain:
  == domain 1  score: 238.1 bits;  conditional E-value: 7.7e-75
                                       CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHH CS
                     Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglal 78 
                                       vlanv +++k   +++GG +P++as +H+++ ++l++eal +ag+s+++l+aIav+ gPG +++LrvGv+ A+ l+ 
  gi|320101516|ref|YP_004177108.1|  45 VLANVNSQYK---PEKGGLHPREASLHHVKAAPQLLREALGKAGVSVRELNAIAVSIGPGIGPCLRVGVTLARFLSK 118
                                       7777777776...99************************************************************** PP

                                       HCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..S... CS
                     Peptidase_M22  79 alnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpy... 152
                                        +++P+v+Vnh  ah++ ++l+++ ++Pv+++vsGg+t+v++ k++r++++getld+ +g+ +d +ar +g+     
  gi|320101516|ref|YP_004177108.1| 119 YYGIPFVPVNHAVAHIEIGKLYSGFNDPVIVYVSGGNTMVVVQKDKRFRVMGETLDIPLGNLFDTFAREIGIAPpyv 195
                                       **********************76799****************99***************************99445 PP

                                       .SCCHHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHHST.T.....HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Peptidase_M22 153 .pggpkieklakeg.kkiefprplkgldfsfsGlktavlkelek.e.....vedlaasfqeavvdhlvekteralkl 221
                                        +g  +++ +a  + +   +p+++kg d+sfsGl ta+l+++++ +        ++ s+ e+++++l+e++er+l+l
  gi|320101516|ref|YP_004177108.1| 196 tEGRHAVDICADWNpDFQPLPYTVKGSDLSFSGLLTAALRLAREaRgdkgiLGRICNSLRETAFNMLIEVSERVLAL 272
                                       3345588877776656667***********************55435789*9************************* PP

                                       CTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                     Peptidase_M22 222 pkakelvilGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                       +++k+l+++GGva+n+ Lr ++e++ + +g+k++ +p++   dn+amia+
  gi|320101516|ref|YP_004177108.1| 273 TGKKQLLLVGGVASNRVLRGKMETLTSMYGVKYYGTPPDVAGDNGAMIAY 322
                                       ***********************99888********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2731.12
//
Query:       gi|320101517|ref|YP_004177109.1|  [L=53]
Description: 30S ribosomal protein S27AE [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-16   58.5   4.0    5.9e-16   58.4   4.0    1.0  1  Ribosomal_S27    Ribosomal protein S27a
     0.0055   16.8   1.6     0.0059   16.7   1.6    1.1  1  Ribosomal_L37ae  Ribosomal L37ae protein family
     0.0087   15.9   1.2      0.019   14.9   1.2    1.6  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
  ------ inclusion threshold ------
       0.01   15.8   3.2      0.013   15.5   3.2    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.012   15.7   0.4      0.014   15.6   0.4    1.1  1  zf-piccolo       Piccolo Zn-finger
      0.016   15.1   0.8      0.017   15.0   0.8    1.1  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.023   14.4   3.0       0.42   10.4   0.1    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.054   13.5   1.2      0.056   13.5   1.2    1.0  1  DUF1451          Zinc-ribbon containing domain
      0.068   12.6   3.9      0.073   12.5   0.1    2.1  2  zf-ribbon_3      zinc-ribbon domain
      0.075   13.2   1.8        0.1   12.7   1.8    1.2  1  DUF2387          Probable metal-binding protein (DUF2387)
      0.082   12.5   0.8      0.079   12.6   0.8    1.1  1  DpnI             Dam-replacing family
       0.11   12.4   5.5        0.7    9.9   5.5    2.0  1  Nudix_N_2        Nudix N-terminal
       0.21   11.1   3.6        4.4    6.9   0.5    2.2  2  zf_C2H2_10       C2H2 type zinc-finger


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   4.0   4.3e-19   5.9e-16       1      45 []       4      49 ..       4      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 4.3e-19
                                      SSSSCCESS.SSSEEESS-B-SS-S-TTSBEEECTT...EEEESSTTTE CS
                     Ribosomal_S27  1 vlkyYkvdd.sgkverlrkeCpreCGaGvfMAehkd...RkyCGkCglT 45
                                      ++k+Y+vd+ +g+v+r++k Cp+ C  G fMA hk+   R++CGkC +T
  gi|320101517|ref|YP_004177109.1|  4 IHKLYEVDYkTGTVKRKNKMCPK-C--GSFMAFHKEpvaRWHCGKCNYT 49
                                      69*********************.*..********************99 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.6   4.3e-06    0.0059      30      60 ..      18      49 ..       5      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-06
                                      HHS-BEESSSSSS.EEEEEETTEEEETTTTEE CS
                   Ribosomal_L37ae 30 qhakytCpfcgkt.kvkRkavgiwkCkkcgkt 60
                                      ++++  Cp+cg+  + +++ v  w+C+kc++t
  gi|320101517|ref|YP_004177109.1| 18 KRKNKMCPKCGSFmAFHKEPVARWHCGKCNYT 49
                                      566679*****9879**************987 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 !   14.9   1.2   1.3e-05     0.019       4      31 ..      24      50 ..      22      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                      ESTTTSBEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYee 31
                                      CpkCg+ +   +     +  C +C Y e
  gi|320101517|ref|YP_004177109.1| 24 CPKCGSFMAFHKEPVA-RWHCGKCNYTE 50
                                      ********97654433.256******75 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   3.2   9.3e-06     0.013      20      46 .]      23      49 ..      12      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.3e-06
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCrkq 46
                                       CP+Cgs  a+  +   +++C +C+++
  gi|320101517|ref|YP_004177109.1| 23 MCPKCGSFMAFHKEPVARWHCGKCNYT 49
                                      5*****7766666669********985 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.4   9.9e-06     0.014      19      54 ..      11      47 ..       4      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.9e-06
                        zf-piccolo 19 nyntCt.eCkkqvCnlCGFnptphltekkeWlclnCQ 54
                                      +y+t t + k+++C +CG  +  h + +  W c +C 
  gi|320101517|ref|YP_004177109.1| 11 DYKTGTvKRKNKMCPKCGSFMAFHKEPVARWHCGKCN 47
                                      566665356899******888888888*********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 ?   15.0   0.8   1.2e-05     0.017      13      55 ..       6      49 ..       1      51 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                    OrfB_Zn_ribbon 13 keyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfe 55
                                      k y + +++       k C++Cgs +   +    +++C +C+++
  gi|320101517|ref|YP_004177109.1|  6 KLYEVDYKTGTVKRKNKMCPKCGSFMAFhKEPVARWHCGKCNYT 49
                                      555666666666666699******9988889**********986 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 ?   10.4   0.1    0.0003      0.42       2      15 ..      20      33 ..      19      36 .. 0.84
   2 ?    4.7   0.4     0.018        25       4      10 ..      41      47 ..      39      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                     A2L_zn_ribbon  2 nlkvCsvCggngil 15
                                      ++k+C +Cg+++ +
  gi|320101517|ref|YP_004177109.1| 20 KNKMCPKCGSFMAF 33
                                      789*******9977 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
                     A2L_zn_ribbon  4 kvCsvCg 10
                                      ++C +C+
  gi|320101517|ref|YP_004177109.1| 41 WHCGKCN 47
                                      8999997 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.2   4.1e-05     0.056     103     144 ..      11      52 ..       5      53 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                           DUF1451 103 vyqsGevvglGtlvCekCgkelalkkte.eippCpkCgateFr 144
                                        y++G v    + +C kCg  +a++k      +C kC+ te+ 
  gi|320101517|ref|YP_004177109.1|  11 DYKTGTVKRK-NKMCPKCGSFMAFHKEPvARWHCGKCNYTEYV 52 
                                       6888877665.567**********875505569*******996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.3e-05     0.073      13      25 ..      18      30 ..      15      31 .. 0.75
   2 ?    1.2   0.6      0.19   2.6e+02       7      10 ..      42      45 ..      41      49 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                       zf-ribbon_3 13 ssddnvCpyCGtk 25
                                      +   ++Cp+CG++
  gi|320101517|ref|YP_004177109.1| 18 KRKNKMCPKCGSF 30
                                      6677899999987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                       zf-ribbon_3  7 nCGa 10
                                      +CG+
  gi|320101517|ref|YP_004177109.1| 42 HCGK 45
                                      4554 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.8   7.5e-05       0.1      10      41 ..      23      51 ..      21      53 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-05
                           DUF2387 10 vCPrCsemDkirmweedeveyrECvsCgftde 41
                                      +CP+C +    +++++++v    C +C++t+ 
  gi|320101517|ref|YP_004177109.1| 23 MCPKCGS---FMAFHKEPVARWHCGKCNYTEY 51
                                      6999986...79******************96 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   5.7e-05     0.079      29      60 ..      19      47 ..       7      53 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                                      HHH---TTT--SS-EE--------EEE-TTT- CS
                              DpnI 29 aknlyCpkCgskklsefennkpvaDfyCesck 60
                                      +kn  CpkCgs    +f+  +pva ++C +c+
  gi|320101517|ref|YP_004177109.1| 19 RKNKMCPKCGSF--MAFH-KEPVARWHCGKCN 47
                                      6899******98..4454.57**********8 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.5   0.00051       0.7       3      33 ..      24      51 ..      22      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00051
                                      -TTT--B-EEE--TT-SS-EEEETTTTEEE- CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgtihY 33
                                      C++CG+ ++ +    +   R  C +C+++ Y
  gi|320101517|ref|YP_004177109.1| 24 CPKCGSFMAFHK---EPVARWHCGKCNYTEY 51
                                      ******998665...6799***********9 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0032       4.4       5       9 ..      24      28 ..      21      31 .. 0.84
   2 ?    5.3   0.2      0.01        14       4      11 ..      42      49 ..      40      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0032
                        zf_C2H2_10  5 CPKCq 9 
                                      CPKC+
  gi|320101517|ref|YP_004177109.1| 24 CPKCG 28
                                      ****7 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                        zf_C2H2_10  4 sCPKCqek 11
                                       C KC++ 
  gi|320101517|ref|YP_004177109.1| 42 HCGKCNYT 49
                                      5*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 461.37
//
Query:       gi|320101518|ref|YP_004177110.1|  [L=114]
Description: 30S ribosomal protein S24 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-20   73.4   0.1    1.4e-20   73.0   0.1    1.1  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.1   7.8e-25   1.4e-20       2      73 ..      30     101 ..      29     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 7.8e-25
                                       EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTS CS
                    Ribosomal_S24e   2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRngl 73 
                                       + v Hp+++tpsk  +r +lak+y    +lv++++++t++G g + ++a++Yds+e+ k fEp+++++Rn+ 
  gi|320101518|ref|YP_004177110.1|  30 IRVGHPNEGTPSKGLLRLELAKIYGKGVNLVYIRNVKTEYGLGVSLVEAHVYDSEERVKLFEPEYIIKRNEE 101
                                       7899******************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 965.81
//
Query:       gi|320101519|ref|YP_004177111.1|  [L=163]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-14   51.5   0.0    1.4e-13   50.6   0.0    1.5  1  DUF359    Protein of unknown function (DUF359)


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   7.6e-18   1.4e-13       6     113 ..      47     139 ..      44     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 7.6e-18
                            DUF359   6 lkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEEDLa 82 
                                       ++++++  l + D ktkR+ +     +   ++  ++  +++ Np+G i+ ++++a  +    ++   i V GEEDL+
  gi|320101519|ref|YP_004177111.1|  47 VSRNHTVALRVTDAKTKRSMT-----V---DTGLSRCDTTIVNPPGSISMQAFTA--SL--MKQAKGICVIGEEDLL 111
                                       5667888999*********22.....1...2344566799*********888765..33..4778899********* PP

                            DUF359  83 vlpaillapegsvvvYGqpdeGvvlvkvtee 113
                                       v+p++l      +v+YGqpd+Gvv     e+
  gi|320101519|ref|YP_004177111.1| 112 VIPFTLTW---GSVIYGQPDTGVVKTASRER 139
                                       ****9975...56**********97665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 1218.21
//
Query:       gi|320101520|ref|YP_004177112.1|  [L=68]
Description: DNA-directed RNA polymerase subunit E'' [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-15   54.8   0.2      9e-15   54.5   0.2    1.1  1  Spt4            Spt4/RpoE2 zinc finger
    0.00052   19.6   1.3    0.00075   19.1   1.3    1.3  1  zinc_ribbon_2   zinc-ribbon domain
     0.0015   18.5   2.1      0.002   18.1   2.1    1.2  1  DZR             Double zinc ribbon
      0.002   18.0   2.2     0.0029   17.5   2.2    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0077   17.0   1.5       0.01   16.6   1.5    1.2  1  zinc_ribbon_15  zinc-ribbon family
     0.0079   16.2   0.4       0.01   15.9   0.4    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0084   16.4   1.9     0.0098   16.2   1.9    1.1  1  zf-C4H2         Zinc finger-containing protein
  ------ inclusion threshold ------
      0.012   15.3   1.2      0.015   15.0   1.2    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.013   15.5   4.6       0.02   15.0   4.6    1.3  1  UPF0547         Uncharacterised protein family UPF0547
      0.029   14.0   1.5      0.053   13.2   0.1    1.9  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.09   12.3   0.9       0.13   11.8   0.0    1.8  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.11   11.3   0.2      0.098   11.4   0.2    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.28   11.3   4.4        3.5    7.8   3.8    2.1  2  Zn-ribbon_8     Zinc ribbon domain
        0.3   10.6   3.4       0.55    9.7   3.4    1.5  1  zf-ribbon_3     zinc-ribbon domain
        1.3    9.3   4.4       0.67   10.3   0.4    2.0  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
        2.6    8.1   6.1         19    5.4   5.1    2.3  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.2     8e-18     9e-15       2      76 ..       9      67 ..       8      68 .] 0.97

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 8e-18
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkv 76
                                      +AC++C+ ++++++   + Cp+C           +s++++ e++G+v+++dpe+S +Ak   l+ k+pg+Y +k+
  gi|320101520|ref|YP_004177112.1|  9 KACRKCRSLVPKNA---TVCPVC-----------GSQDFTMEWSGVVIVIDPENSRIAKT--LEIKTPGKYVVKI 67
                                      9************9...******...........**************************..***********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 !   19.1   1.3   6.7e-07   0.00075       2      21 ..      11      30 ..      10      31 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.7e-07
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      C +C   +++na+ Cp CG+
  gi|320101520|ref|YP_004177112.1| 11 CRKCRSLVPKNATVCPVCGS 30
                                      *******************7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.1   1.8e-06     0.002      28      49 .]       8      29 ..       2      31 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                       ++C +C + v+++a++Cp CG
  gi|320101520|ref|YP_004177112.1|  8 FKACRKCRSLVPKNATVCPVCG 29
                                      5789999999999999999998 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 !   17.5   2.2   2.6e-06    0.0029      14      36 ..      11      33 ..       8      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                           DUF35_N 14 CpdCGtvqfPPr.avCphCgsddl 36
                                      C++C ++ +P+   vCp Cgs d+
  gi|320101520|ref|YP_004177112.1| 11 CRKCRSL-VPKNaTVCPVCGSQDF 33
                                      *******.7************998 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.5   9.1e-06      0.01      62      86 .]       5      29 ..       1      29 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.1e-06
                    zinc_ribbon_15 62 ssekkeCknCgkeveeefkyCpkCg 86
                                      s+  k C++C++ v ++ + Cp Cg
  gi|320101520|ref|YP_004177112.1|  5 SKAFKACRKCRSLVPKNATVCPVCG 29
                                      455899******************9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   8.9e-06      0.01      70     100 ..       8      36 ..       2      45 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.9e-06
                                       EEEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgsadveiv 100
                                          Cr+C++ + ++  a+ Cp Cgs+d+++ 
  gi|320101520|ref|YP_004177112.1|   8 FKACRKCRSLVPKN--ATVCPVCGSQDFTME 36 
                                       567*****999876..468*******99875 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.9   8.7e-06    0.0098     177     199 ..       7      29 ..       1      32 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.7e-06
                           zf-C4H2 177 PMKsClsChqqIHRNAPiCPlCK 199
                                         K+C  C   + +NA +CP+C 
  gi|320101520|ref|YP_004177112.1|   7 AFKACRKCRSLVPKNATVCPVCG 29 
                                       67********************5 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.2   1.3e-05     0.015      71     100 ..       6      35 ..       2      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                           TackOD1  71 drirlCpsCksghlnvrevCpkCkSidiee 100
                                       + +++C++C+s   +   vCp C+S d++ 
  gi|320101520|ref|YP_004177112.1|   6 KAFKACRKCRSLVPKNATVCPVCGSQDFTM 35 
                                       56789*********************9876 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   4.6   1.8e-05      0.02       1      21 [.       9      29 ..       9      31 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                           UPF0547  1 KvCPeCeakvPvaaqfCphCG 21
                                      K C  C++ vP +a +Cp CG
  gi|320101520|ref|YP_004177112.1|  9 KACRKCRSLVPKNATVCPVCG 29
                                      88******************9 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.95   1.1e+03       6      12 ..      10      16 ..       9      18 .. 0.68
   2 ?   13.2   0.1   4.7e-05     0.053       6      16 ..      24      34 ..      22      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.95
                           zf-RRN7  6 pCgvCgc 12
                                      +C  C++
  gi|320101520|ref|YP_004177112.1| 10 ACRKCRS 16
                                      6777765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.7e-05
                           zf-RRN7  6 pCgvCgcrsft 16
                                      +C+vCg+ +ft
  gi|320101520|ref|YP_004177112.1| 24 VCPVCGSQDFT 34
                                      8*********8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       2.2   2.5e+03       3       7 ..      11      15 ..      10      19 .. 0.65
   2 ?   11.8   0.0   0.00012      0.13       2      16 ..      24      47 ..      23      51 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.2
                                      ETTTT CS
                      TF_Zn_Ribbon  3 CPnCg 7 
                                      C +C 
  gi|320101520|ref|YP_004177112.1| 11 CRKCR 15
                                      66665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                                      EETTTTCEEC.........HEETS CS
                      TF_Zn_Ribbon  2 kCPnCgstnl.........veDpe 16
                                      +CP+Cgs ++         v Dpe
  gi|320101520|ref|YP_004177112.1| 24 VCPVCGSQDFtmewsgvviVIDPE 47
                                      8******88646666666666665 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   8.7e-05     0.098     505     534 ..       6      37 ..       2      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.7e-05
                                       --EEEETT.--..EESSSB-TTT--BE.EEEE CS
                              NRDD 505 pkidvCnecgy..kgeiekCpkCgseeevevi 534
                                       + ++ C++c     +  + Cp+Cgs++ +  +
  gi|320101520|ref|YP_004177112.1|   6 KAFKACRKCRSlvPKNATVCPVCGSQDFTMEW 37 
                                       67899******98666688*****88755555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.051        57      23      37 ..       5      19 ..       1      21 [. 0.69
   2 ?    7.8   3.8    0.0031       3.5      19      35 ..      18      32 ..       8      34 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.051
                       Zn-ribbon_8 23 dapltaCPeCgsevr 37
                                       ++ +aC +C s v 
  gi|320101520|ref|YP_004177112.1|  5 SKAFKACRKCRSLVP 19
                                      456788****98665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0031
                       Zn-ribbon_8 19 qsisdapltaCPeCgs.e 35
                                      ++ +    t+CP Cgs +
  gi|320101520|ref|YP_004177112.1| 18 VPKN---ATVCPVCGSqD 32
                                      4323...677*****955 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.4   0.00049      0.55       3      24 ..       9      30 ..       7      31 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00049
                       zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGt 24
                                      + C +C +++ + ++vCp CG+
  gi|320101520|ref|YP_004177112.1|  9 KACRKCRSLVPKNATVCPVCGS 30
                                      67889999889**********7 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2      0.53   5.9e+02      28      32 ..      11      15 ..       8      24 .. 0.79
   2 ?   10.3   0.4    0.0006      0.67       5      13 ..      24      32 ..      20      34 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.53
                                      ETTTT CS
                    Prim_Zn_Ribbon 28 CrqCg 32
                                      Cr+C 
  gi|320101520|ref|YP_004177112.1| 11 CRKCR 15
                                      ****3 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0006
                                      --TTTT-TT CS
                    Prim_Zn_Ribbon  5 pCPvCGGrD 13
                                       CPvCG++D
  gi|320101520|ref|YP_004177112.1| 24 VCPVCGSQD 32
                                      5******98 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 ?    0.9   0.8       0.4   4.4e+02      21      25 ..      11      15 ..       4      20 .. 0.67
   2 ?    5.4   5.1     0.017        19      16      28 ..      20      32 ..      10      39 .. 0.83
   3 ?   -2.5   0.0       4.8   5.3e+03      28      38 ..      53      63 ..      49      63 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.4
                     Zn_Tnp_IS1595 21 CPhCg 25
                                      C +C 
  gi|320101520|ref|YP_004177112.1| 11 CRKCR 15
                                      66665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                     Zn_Tnp_IS1595 16 pngfvCPhCgsrk 28
                                      +n  vCP Cgs+ 
  gi|320101520|ref|YP_004177112.1| 20 KNATVCPVCGSQD 32
                                      57789*****985 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.8
                     Zn_Tnp_IS1595 28 kayriktrglf 38
                                      k  +ikt+g++
  gi|320101520|ref|YP_004177112.1| 53 KTLEIKTPGKY 63
                                      66788888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 535.92
//
Query:       gi|320101521|ref|YP_004177113.1|  [L=189]
Description: DNA-directed RNA polymerase subunit E' [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-14   54.0   0.1    6.8e-14   52.0   0.0    1.9  2  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    2.2e-09   37.5   1.4    2.2e-09   37.5   1.4    1.9  2  S1             S1 RNA binding domain
     0.0015   18.8   0.0     0.0023   18.2   0.0    1.4  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 !   52.0   0.0   1.1e-17   6.8e-14       1      70 []       8      85 ..       8      85 .. 0.96
   2 ?   -0.8   0.0      0.33     2e+03      35      55 ..     109     129 ..      92     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.1e-17
                                      EEEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETT........TEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  1 edtvrlePsylgstledallerllekyegkvvps........lGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      +d+vr++Ps +g+++++ +le+l+++yeg +           lG++v + d + +++g++l+g+G++y++V+  alvF
  gi|320101521|ref|YP_004177113.1|  8 RDVVRIPPSKFGRPVKNVALEELRSRYEGAITSIetprgeskLGIVVTIVDANVDENGRILPGDGATYHDVEMYALVF 85
                                      69****************************9988889899889**********************************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                                       TEEEEEEEEEEEECCEEE-TT CS
                       SHS2_Rpb7-N  35 lGvivavldiaeysegkvlgg 55 
                                       lGv+     i+++se kv+ +
  gi|320101521|ref|YP_004177113.1| 109 LGVLDGFIHINQVSEEKVVFD 129
                                       566667778999999999866 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.69   4.1e+03       8      16 ..      34      42 ..      32      62 .. 0.69
   2 !   37.5   1.4   3.7e-13   2.2e-09       2      70 ..      87     154 ..      86     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.69
                                      EEEEEEEEE CS
                                S1  8 veGeVtsvt 16
                                      +eG +ts++
  gi|320101521|ref|YP_004177113.1| 34 YEGAITSIE 42
                                      677777775 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 3.7e-13
                                       STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEE CS
                                S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrri 70 
                                       p++ evveGe + vtk G++V+lg   +gf++++++s ++ v+dp ++  v +e + +++k d+ r++i
  gi|320101521|ref|YP_004177113.1|  87 PFIKEVVEGEAVTVTKSGIYVNLG-VLDGFIHINQVSEEKVVFDPARTALVLEESRRVIEKGDVLRAKI 154
                                       8999********************.**************888888888888888888888888766654 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 !   18.2   0.0   3.8e-07    0.0023       1      72 [.      87     155 ..      87     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.8e-07
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEE CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrve 72 
                                       Pf+ ev++g     t+ gi v+lg++d ++  ++   e+  fd+++ a v+e    ++  +++g+ +r ++ 
  gi|320101521|ref|YP_004177113.1|  87 PFIKEVVEGEAVTVTKSGIYVNLGVLDGFIHINQVSEEKVVFDPARTALVLEE---SRRVIEKGDVLRAKIY 155
                                       9**************************9655566778999********99875...8888999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1628.03
//
Query:       gi|320101522|ref|YP_004177114.1|  [L=140]
Description: 30S processome protein Utp24 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-25   88.0   0.2    6.1e-25   87.8   0.2    1.0  1  PIN_9     PIN like domain
    6.4e-05   23.3   0.0    8.8e-05   22.8   0.0    1.2  1  Fcf1      Fcf1
     0.0018   18.8   0.1      0.004   17.7   0.1    1.5  1  PIN       PIN domain
     0.0033   17.2   0.0     0.0053   16.5   0.0    1.4  1  DUF5615   Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
      0.025   14.1   0.0      0.055   13.1   0.0    1.5  1  LEM       LEM domain
      0.045   14.0   0.0       0.21   11.9   0.0    2.0  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.2     2e-28   6.1e-25       1     115 [.       9     126 ..       9     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 2e-28
                             PIN_9   1 vilDtnaLmipvqfgvdifeele.rllgsvelvvpkavleELerlakagkgkertaakvalsLaer.ceiveae... 72 
                                       v+lDtn+L++ ++ g+ +++++e +ll + +++v ++vl+EL++la++gk++ ++ a++al++ +r ce+ve +   
  gi|320101522|ref|YP_004177114.1|   9 VLLDTNMLLLMAE-GIPLMDQIEeKLLAKPRYIVITPVLNELAKLASTGKPSVSRRARLALEIISRfCEVVEYQlkp 84 
                                       89******99765.9*****9962688************************************9999*******999 PP

                             PIN_9  73 eekaDdailelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                       +ek+Ddai+++a e +a +++T+DreL++rl+e+g+p i+LR+
  gi|320101522|ref|YP_004177114.1|  85 GEKVDDAIVRYALENEA-IVATSDRELRRRLREHGLPEIYLRE 126
                                       999***********995.555*********************7 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.9e-08   8.8e-05       3      96 ..      33     130 ..      31     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                                       CTS-EEEEEEHHHHHHHHHCT..........-HHHHHHHTT.SEEE----SS---HHHHHHHHH-BTB-TT-EEEE- CS
                              Fcf1   3 LqakvkpliTqCviaeleklgkk........lkealkiakt.ferlkCnhkkptsaddClvsvvkkkknkkryivAt 70 
                                       L ak   ++ + v++el kl ++         + al+i+ + +e+++ + k + + dd +v+       +++ ivAt
  gi|320101522|ref|YP_004177114.1|  33 LLAKPRYIVITPVLNELAKLASTgkpsvsrrARLALEIISRfCEVVEYQLKPGEKVDDAIVRYAL----ENEAIVAT 105
                                       55666677777799999999955555544446777777776567777777667788888888888....5789**** PP

                                       S-HHHHHHHHTSTT--EEEEE--EEE CS
                              Fcf1  71 qDkdlrrrlrkipgvPilyikrsvmv 96 
                                        D++lrrrlr+  g+P +y++++   
  gi|320101522|ref|YP_004177114.1| 106 SDRELRRRLRE-HGLPEIYLREESWR 130
                                       **********8.69999999887665 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.3e-06     0.004       1      91 [.       9      97 ..       9     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                                      EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                               PIN  1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiae 79
                                      ++lDT+ l+ + +g +  +++++ l +  + ++   vl El+  ++   + +  ++++++l+++ + +++++   +  e
  gi|320101522|ref|YP_004177114.1|  9 VLLDTNMLLLMAEGIPLMDQIEEKLLAKPRYIVITPVLNELAKLAST-GKPSVSRRARLALEIISRFCEVVEYQLKPGE 86
                                      68*******999*********9999999*******************.7788888888888888********9998888 PP

                                      HHHHHHHHHHSB CS
                               PIN 80 eaaeialkygll 91
                                      ++ + + +y  l
  gi|320101522|ref|YP_004177114.1| 87 KVDDAIVRYA-L 97
                                      8888888884.3 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-06    0.0053      19      66 ..      72     118 ..      60     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                           DUF5615  19 eaghdvlhvrelglegasDeeileyAkeedriivTkDkDFgellllgg 66 
                                       +++ +v+   +l+  +  D++i++yA e+++i+ T D+  +++l+ +g
  gi|320101522|ref|YP_004177114.1|  72 SRFCEVVEY-QLKPGEKVDDAIVRYALENEAIVATSDRELRRRLREHG 118
                                       555555555.44444589*******************99888777766 PP

>> LEM  LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05     0.055       6      20 ..     106     120 ..     103     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                               LEM   6 sDeeLreeLkkyGvs 20 
                                       sD eLr++L+++G++
  gi|320101522|ref|YP_004177114.1| 106 SDRELRRRLREHGLP 120
                                       9************85 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.9e-05      0.21       2      64 ..      10      78 ..       9     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                             PIN_4  2 VlDTnvlLhdpealksf.......keehdvviPitVleELdklKkgsserelarlarqanrlldelleke 64
                                       lDTn+lL + e +  +         + + ++   Vl+EL kl ++ +  +++r+ar a++++    e  
  gi|320101522|ref|YP_004177114.1| 10 LLDTNMLLLMAEGIPLMdqieeklLAKPRYIVITPVLNELAKLASTGK-PSVSRRARLALEIISRFCEVV 78
                                      59******999876655666888866677777789********99998.99*********9997765543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1178.40
//
Query:       gi|320101523|ref|YP_004177115.1|  [L=418]
Description: translation initiation factor 2 subunit gamma (aeIF-2g) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-32  112.9   0.7      8e-32  110.3   0.7    2.0  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    6.4e-28   96.8   0.4    6.4e-28   96.8   0.4    1.9  2  eIF2_C        Initiation factor eIF2 gamma, C terminal
    4.2e-05   23.3   0.9      0.095   12.4   0.1    2.3  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
    7.6e-05   22.7   0.6     0.0013   18.7   0.1    2.4  2  RsgA_GTPase   RsgA GTPase
    8.7e-05   22.8   1.9    0.00021   21.6   1.2    2.1  2  GTP_EFTU_D2   Elongation factor Tu domain 2
    0.00013   22.0   0.0    0.00027   21.0   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.016   15.2   0.1      0.031   14.3   0.1    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.017   14.7   1.5        3.8    7.0   0.0    2.4  2  FeoB_N        Ferrous iron transport protein B
       0.03   13.3   1.0       0.19   10.7   0.1    2.1  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.15   11.7   0.2        6.9    6.2   0.0    2.2  2  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.7   4.5e-35     8e-32       4     193 ..      10     200 ..       8     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 4.5e-35
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig++ghvDhGKtTL+ +L+    a                ++ E erg+Tik   +  +                
  gi|320101523|ref|YP_004177115.1|  10 VNIGVVGHVDHGKTTLVQALTGVWTAK---------------HSMELERGMTIKLGYADGNiaycdgmptpdayttk 71 
                                       79******************9555444...............45677777777777777667777777777777778 PP

                                       .......TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESC CS
                          GTP_EFTU  65 .......ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKm 132
                                              ++   ++++ +D+PGH++++ ++  g+ ++Dga+lv++a+e  ++pqt e+l  ++ +g++ i+++ NK+
  gi|320101523|ref|YP_004177115.1|  72 eqcpdgsESRLIRRVSYVDAPGHESYMTTMLSGAMIMDGAILVIAANEPcPQPQTVEHLMALNILGIRnIVIVQNKI 148
                                       888877567888999********************************9879*****************999999*** PP

                                       GST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 133 Drl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       D + k++  e  +e+  kl      ++  +++   + pv+++Sal++ ++++ll+a+ e +p
  gi|320101523|ref|YP_004177115.1| 149 DVVdKKRALENYNEIL-KL------VKGTVAE---NAPVIPVSALHNVNIDALLQAIEETIP 200
                                       ***6666666666666.44......4444433...57********************99998 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.5   6.3e+03      26      47 ..     159     180 ..     134     188 .. 0.64
   2 !   96.8   0.4   3.6e-31   6.4e-28       2      86 .]     329     413 ..     328     413 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.5
                                       -TTEEEEEEETTEEEEEEEEEE CS
                            eIF2_C  26 kkkEvLmlniGsastggvvtsv 47 
                                       + +E+L l  G+ +  + v+ v
  gi|320101523|ref|YP_004177115.1| 159 NYNEILKLVKGTVAENAPVIPV 180
                                       4578888888888777777655 PP

  == domain 2  score: 96.8 bits;  conditional E-value: 3.6e-31
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSE CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrW 78 
                                       +le++y+l+er+vg++e  k  +l+ +E++ + iG+as ++vv+sv+kd+++++L++Pv+++ g++ia+sRrv +rW
  gi|320101523|ref|YP_004177115.1| 329 TLEVRYQLFERIVGARELVKLPPLQANEKIAVAIGAASRVAVVKSVRKDVMTIELTDPVATWSGSRIAISRRVLARW 405
                                       69*************************************************************************** PP

                                       EEEEEEEE CS
                            eIF2_C  79 rLiGwGei 86 
                                       rL GwG+i
  gi|320101523|ref|YP_004177115.1| 406 RLAGWGII 413
                                       ******97 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00048      0.87       4      23 ..      12      31 ..      10      49 .. 0.86
   2 !   12.4   0.1   5.3e-05     0.095      41     142 ..      89     196 ..      83     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00048
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      i ++G+v+ GKttL qal+g
  gi|320101523|ref|YP_004177115.1| 12 IGVVGHVDHGKTTLVQALTG 31
                                      5589**************87 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.3e-05
                         PduV-EutP  41 iDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi......itkidlaedeenieav 111
                                       +D+PG    ++++++++ + ++  d   lv +a+e  +  p+++ ++++ +++Gi        kid+++++ ++e+ 
  gi|320101523|ref|YP_004177115.1|  89 VDAPG----HESYMTTMLSGAMIMDGAILVIAANE-PCPQPQTVEHLMALNILGIrnivivQNKIDVVDKKRALENY 160
                                       56666....45677777777777776666665554.466778888888777777533321147************** PP

                         PduV-EutP 112 eelLks.....aGaekifevsavekegieellkyle 142
                                       +e Lk      a  + ++ vsa+++++i+ ll+ +e
  gi|320101523|ref|YP_004177115.1| 161 NEILKLvkgtvAENAPVIPVSALHNVNIDALLQAIE 196
                                       ***986222113345689*************99987 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 ..      14      44 ..       9      46 .. 0.75
   2 !   18.7   0.1     7e-07    0.0013      16      99 ..     108     197 ..      80     201 .. 0.79

  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++ s +l+rG
  gi|320101523|ref|YP_004177115.1|  14 VVGHVDHGKTTLVQALTGV---WTAKHSMELERG 44 
                                       5788889*********986...555555555555 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 7e-07
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllvsak 85 
                                       +d +++v++++ep  ++++++ +++l +  gi ++viv nKiD++++++      e+ +l + + a + +v+ vsa 
  gi|320101523|ref|YP_004177115.1| 108 MDGAILVIAANEPCPQPQTVEHLMAL-NILGIrNIVIVQNKIDVVDKKRalenynEILKLVKGTVAENAPVIPVSAL 183
                                       6999****************986655.556665999************96664444444455555678899999999 PP

                                       THTTHHHHHHHCTT CS
                       RsgA_GTPase  86 tkegleelkellkd 99 
                                       ++ ++++l +++++
  gi|320101523|ref|YP_004177115.1| 184 HNVNIDALLQAIEE 197
                                       99999999888876 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.8   6.8e+03      13      21 ..      41      49 ..      40      54 .. 0.79
   2 !   21.6   1.2   1.2e-07   0.00021       1      65 [.     232     307 ..     232     318 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.8
                                      EETTEEEEE CS
                       GTP_EFTU_D2 13 lkkGdevri 21
                                      l++G+++++
  gi|320101523|ref|YP_004177115.1| 41 LERGMTIKL 49
                                      889999998 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.2e-07
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE..........EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke..........ivtrissletfhededeavaganaGvivaikgled 65 
                                       G+v++g++ +G++++Gdev il+ ++++  +           +t i  +   +  ++ea +g+ + + +++++  +
  gi|320101523|ref|YP_004177115.1| 232 GGVIGGTLLQGKFRVGDEVTILPgMRVQVGGaksqtfkyepVTTSIEEIRYGNLVVEEAKPGGLVALQTKLDPSLT 307
                                       89***********************986555888888888888888888888888888888888888888776655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.5e-07   0.00027       1      99 [.      11     129 ..      11     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.5e-07
                                       EEEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEE...ETTEE........................ CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvk...lkgke........................ 47 
                                       ++++vG+   GK+tL++altg    k  ++ + g T++  ++  +       +                        
  gi|320101523|ref|YP_004177115.1|  11 NIGVVGHVDHGKTTLVQALTGVwtaKHSMELERGMTIKLGYADGNiayC---Dgmptpdayttkeqcpdgsesrlir 84 
                                       599******************6622455666678888887777663331...1233555556666667777777777 PP

                                       .EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHH CS
                          MMR_HSR1  48 .ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeelee 99 
                                        +  vD pG  e      +   ++l+    +d ++lv+ a+ e   p+ +++e 
  gi|320101523|ref|YP_004177115.1|  85 rVSYVDAPG-HE------SYMTTMLSGAMiMDGAILVIAAN-E-PCPQPQTVEH 129
                                       7********.44......55566665444479999999866.3.2233333333 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.7e-05     0.031      58     100 ..     141     195 ..     111     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                      MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                        ++v NKiD ++++   e ++e              ++++Sa +++n+d+L+++i
  gi|320101523|ref|YP_004177115.1| 141 IVIVQNKIDVVDKKRALENYNEilklvkgtvaenAPVIPVSALHNVNIDALLQAI 195
                                       57899*****87765444333335668888887668999*************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 ?    7.0   0.0    0.0021       3.8       2      23 ..      11      32 ..      10      37 .. 0.90
   2 ?    6.4   0.3    0.0033       5.9     106     156 .]     139     195 ..     109     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0021
                                      EEEEEESTTSSHHHHHHHHHTT CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                      ++ +vG  + Gkttl+ altg+
  gi|320101523|ref|YP_004177115.1| 11 NIGVVGHVDHGKTTLVQALTGV 32
                                      6889****************96 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0033
                                       SSEEEEEETHHHHHHTTEEE-HHHHHHHH......TS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekL......gvpvvktsakkkegieellkai 156
                                        ++v++ n+id+++kk+   + +++ + +      + pv+++sa ++ +i++ll+ai
  gi|320101523|ref|YP_004177115.1| 139 RNIVIVQNKIDVVDKKRALENYNEILKLVkgtvaeNAPVIPVSALHNVNIDALLQAI 195
                                       4688999********99988888877766322333589***************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 ?    0.8   0.1      0.11   1.9e+02      31      51 ..      11      31 ..       9      38 .. 0.87
   2 ?   10.7   0.1   0.00011      0.19     165     228 ..     135     198 ..     124     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.11
                                      EEEEEE-TTSSHHHHHHHHHH CS
                              MeaB 31 vvGltGvPGaGkstlvealgl 51
                                       +G+ G    Gk tlv+al+ 
  gi|320101523|ref|YP_004177115.1| 11 NIGVVGHVDHGKTTLVQALTG 31
                                      59****************985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                                       CHHH-SEEEE.E---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHH CS
                              MeaB 165 ileiaDiivv.nkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieeh 228
                                       il i +i++v nk D  + ++a ++++ +l+l + + +e +++v+ +sa+++  id l++aiee 
  gi|320101523|ref|YP_004177115.1| 135 ILGIRNIVIVqNKIDVVDKKRALENYNEILKLVKGTVAE-NAPVIPVSALHNVNIDALLQAIEET 198
                                       666777765559*******************99887665.889*******************985 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 ?    3.2   0.0     0.032        58       3      22 ..      12      34 ..      10      42 .. 0.77
   2 ?    6.2   0.0    0.0039       6.9     109     170 ..     105     168 ..      92     173 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.032
                                      EEEEESTTCCHHHHHHHHH...C CS
                              cobW  3 tvltGflGsGKTtLlnhll...e 22
                                      ++++G +  GKTtL+++l+   +
  gi|320101523|ref|YP_004177115.1| 12 IGVVGHVDHGKTTLVQALTgvwT 34
                                      578999999******99975553 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0039
                                       CCCECEEEEEEETTTH.CCHCCHHHHHH.HHHHTSS.EEEEE-HHHHCHC..HHHHHHHHHHHH CS
                              cobW 109 dltldavvavvDaknleaeeekieekae.dqlaaad.llvlnKtDlldeeallekleerlrqln 170
                                       ++ +d+ + v+ a++   + ++ e+++  + l   + ++v nK+D++d+++ le+ +e+l+ ++
  gi|320101523|ref|YP_004177115.1| 105 AMIMDGAILVIAANEPCPQPQTVEHLMAlNILGIRNiVIVQNKIDVVDKKRALENYNEILKLVK 168
                                       55667777777775553333333333330333333415677*********88899999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3043.81
//
Query:       gi|320101524|ref|YP_004177116.1|  [L=218]
Description: 30S ribosomal protein S6 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-32  112.3   0.1    3.8e-32  110.9   0.0    1.8  2  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 ?   -2.8   0.0      0.33   5.8e+03       1      18 [.       4      22 ..       4      35 .. 0.58
   2 !  110.9   0.0   2.1e-36   3.8e-32      13     114 ..     117     215 ..     111     218 .] 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.33
                                      -EEEEEETTT.TEEEEEE- CS
                     Ribosomal_S6e  1 mklnisdpat.gkqkliev 18
                                      +k+++ dp+  +k+kl++v
  gi|320101524|ref|YP_004177116.1|  4 FKIVVNDPEApKKEKLVKV 22
                                      5777888765134444444 PP

  == domain 2  score: 110.9 bits;  conditional E-value: 2.1e-36
                                       EEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSSSS-SSSSS CS
                     Ribosomal_S6e  13 qklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggvgyrprrkG 89 
                                       + +i v+++++++l+g rig+ +dg+++G  lkg+ l itggsd +Gfpm+++v++p ++++Lls+  +g++p+++G
  gi|320101524|ref|YP_004177116.1| 117 AWQIRVNDERTQSLLGLRIGDSIDGSIVG--LKGVRLTITGGSDISGFPMRPDVSGPVKKKVLLSG-PPGFHPEEDG 190
                                       6689999**********************..***********************************.********** PP

                                       -EEEEEEE-SB--SSEEEEEEEEEE CS
                     Ribosomal_S6e  90 erkrksvrGcivsadisqlnlvivk 114
                                       er+rk+vrG++++ di+q+n++i+ 
  gi|320101524|ref|YP_004177116.1| 191 ERRRKMVRGNTIAPDIVQVNTKITY 215
                                       **********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1634.10
//
Query:       gi|320101525|ref|YP_004177117.1|  [L=604]
Description: translation initiation factor eaIF-5B [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  126.6   3.0    6.4e-37  125.3   3.0    1.8  1  GTP_EFTU_D4  Elongation factor Tu domain 4
    1.5e-31  109.4   0.0    2.3e-30  105.6   0.0    2.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.7e-20   73.1   0.1    4.4e-20   71.8   0.1    1.7  1  IF-2         Translation-initiation factor 2
      4e-12   46.3   1.8    5.2e-11   42.8   0.0    2.9  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    6.8e-07   29.4   0.1    2.5e-06   27.6   0.0    2.0  2  MMR_HSR1     50S ribosome-binding GTPase
     0.0061   16.8   0.0       0.03   14.6   0.0    2.2  1  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0091   16.1   0.0       0.12   12.4   0.0    2.6  3  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.013   15.0   0.0        5.4    6.4   0.0    3.0  3  Arf          ADP-ribosylation factor family
      0.015   14.9   0.0       0.13   11.8   0.0    2.3  2  Ras          Ras family
       0.02   14.7   0.0      0.079   12.7   0.0    2.0  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.066   13.5   0.0       0.14   12.4   0.0    1.5  1  AAA_22       AAA domain
      0.069   13.1   0.4        4.6    7.1   0.0    3.0  4  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3   3.0   4.3e-40   6.4e-37       1      86 []     471     557 ..     471     557 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 4.3e-40
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-.TT CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegki.vG 76 
                                       rPgki+++pg vfrrs+paivGvevlgG+ikp+++l+++dGr++G+++qi+d+++ l+ea  Gq+vaisi+gk+ vG
  gi|320101525|ref|YP_004177117.1| 471 RPGKIRVIPGAVFRRSEPAIVGVEVLGGRIKPNYPLMTSDGRSIGTVMQIRDRDNVLKEAIVGQQVAISIKGKVmVG 547
                                       7**************************************************************************** PP

                                       TS--TT-EEE CS
                       GTP_EFTU_D4  77 rqikegdily 86 
                                       r+i+egdily
  gi|320101525|ref|YP_004177117.1| 548 RHIDEGDILY 557
                                       *********9 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 !  105.6   0.0   1.5e-33   2.3e-30       5     189 ..      13     220 ..      10     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 1.5e-33
                                       EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSG CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHv 81 
                                        i+++ghvDhGKtTL+d++  ++ a ++ ge ++ +      ++   + +         +   +   + +iDtPGH+
  gi|320101525|ref|YP_004177117.1|  13 IIVVLGHVDHGKTTLLDKIRGTAVARKEPGEITQ-HVGASVVPASVLKKLAEPLRKYFPKLVIEIPGLLFIDTPGHE 88 
                                       689*****************99999998888775.5566777777777666555544333368999*********** PP

                                       GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST........HHHHHHHHHHHHHHH CS
                          GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl........kaelkeiveevkqkl 150
                                        Fs+   rg +v+D+a+lvvd+ eG +pqt e ++++++++vp++v+ NK+Dr+           l+ i ++  ++l
  gi|320101525|ref|YP_004177117.1|  89 LFSNLRKRGGSVADMAILVVDIIEGFQPQTVEAINILKEKKVPFVVAANKIDRIegwkphadTPFLESIRDQSPRTL 165
                                       *******************************************************9999886333444444444444 PP

                                       HHH.......HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 151 srk.......eeklekygekge.........kevpvvfgSalkgegvktllealv 189
                                       s          +kl + g+++e         ++v +v++Sa++geg+ +ll  + 
  gi|320101525|ref|YP_004177117.1| 166 SLLeekiyglVGKLYEHGFEAErfdrvrdfrRTVAIVPISAKTGEGIPELLALIA 220
                                       222444555544555555554478888888899*****************99876 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.1   2.9e-23   4.4e-20       6     104 ..     351     450 ..     346     451 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 2.9e-23
                                       HCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH...ST...EEEEEESSSC CS
                              IF-2   6 eeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa...sn...aiiigFnvkv 76 
                                       ++i  + ++ +v++kaD+ G+leAl ea+++      +++v  ++vG++t++Dv  as+   s+   ++i+ Fnvkv
  gi|320101525|ref|YP_004177117.1| 351 SQIRFRAESDGVVLKADTLGTLEALIEAMRRE-----NIPVKLADVGHVTRNDVIEASVvkkSKpeyGVILSFNVKV 422
                                       55554556778********************7.....59******************9965433788********** PP

                                       THHHHHCCCCCTSEEEEESSHHHHHHHH CS
                              IF-2  77 skkakklaekegvkirlynvIYkliddv 104
                                        ++a++l++keg+ ++++nvIY+l++++
  gi|320101525|ref|YP_004177117.1| 423 LPEAEELIAKEGIPVFKHNVIYQLLEEY 450
                                       *************************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 !   42.8   0.0   3.5e-14   5.2e-11       1      73 [.     252     330 ..     252     331 .. 0.93
   2 ?    1.6   0.5      0.24   3.6e+02       4      61 ..     491     543 ..     489     557 .. 0.67

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.5e-14
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea...........vaganaGvivaikgled 65 
                                       Gt++++++y+G+l+++d  ++ g n+    +ivtr++sl+++++ ++ +            + a+ Gv+va++gled
  gi|320101525|ref|YP_004177117.1| 252 GTTIDVIIYDGVLRRNDVFVVAGrNG----PIVTRVRSLLMPRP-LQDMrmhegrfinvdLVTAATGVKVAAPGLED 323
                                       9********************99887....9***********66.666669************************** PP

                                       GSSTTCEE CS
                       GTP_EFTU_D2  66 aiivGdtl 73 
                                       a ++G+++
  gi|320101525|ref|YP_004177117.1| 324 A-LAGSPF 330
                                       8.***986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.24
                                       EEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEES CS
                       GTP_EFTU_D2   4 algrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaik 61 
                                       +++ v  G +k++  ++   +d +++  ++++ ++    + ++ea++g+++ + +++k
  gi|320101525|ref|YP_004177117.1| 491 VGVEVLGGRIKPNYPLMT--SD-GRS--IGTVMQIRDRDNVLKEAIVGQQVAISIKGK 543
                                       566666666666666666..43.344..777778888888888888888888888876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.7e-09   2.5e-06       2     114 .]      14     138 ..      13     138 .. 0.71
   2 ?   -2.4   0.0       3.3   4.9e+03      48      58 ..     363     373 ..     327     410 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.7e-09
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE...ETTEE...................EEEEECGGC CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk...lkgke...................ielvDtpGl 56 
                                       ++++G+   GK+tL+ ++ g+++  ++    T+++    v    l   +                   + ++DtpG 
  gi|320101525|ref|YP_004177117.1|  14 IVVLGHVDHGKTTLLDKIRGTAVARKEPGEITQHVGASVVPasvL---KklaeplrkyfpklvieipgLLFIDTPG- 86 
                                       799***************996444444445566665555543331...1344456667777777777799******. PP

                                       SSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  57 iegaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                        e       +++  ++  + ad+++lvvd+  e+++p+  e  ++l+e+k p+++++nk
  gi|320101525|ref|YP_004177117.1|  87 HE-----L-FSNLRKRGGSvADMAILVVDII-EGFQPQTVEAINILKEKKVPFVVAANK 138
                                       44.....2.222222222348********99.78**********************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.3
                                       EEEEECGGCSS CS
                          MMR_HSR1  48 ielvDtpGlie 58 
                                       +  +Dt G +e
  gi|320101525|ref|YP_004177117.1| 363 VLKADTLGTLE 373
                                       33344444332 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 !   14.6   0.0     2e-05      0.03       2     119 ..      14     140 ..      13     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                       EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGGSGGCTTB..TTTTC.....EEEEEEEE-SGG CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtkikgvend..kkvkk.....vklniWDtaGqe 67 
                                       +v++G    GKt+ll+++    + +ke    ++ +g++++  +v   k++ +   k   k       l + Dt G+e
  gi|320101525|ref|YP_004177117.1|  14 IVVLGHVDHGKTTLLDKIRGTAVARKEpgeiTQHVGASVVPASVL--KKLAEPlrKYFPKlvieiPGLLFIDTPGHE 88 
                                       799***************998887765332367889999887663..333222102222211111346789****** PP

                                       CTTTT-HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                               Roc  68 rfrslhplylreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiD 119
                                        f++l++   + a++ailv+d  +  +  + ++ ++   + k p+++ +nkiD
  gi|320101525|ref|YP_004177117.1|  89 LFSNLRKRGGSVADMAILVVDIIEGFQ-PQTVEAINILKEkKVPFVVAANKID 140
                                       *********************544332.234566666555155888999***9 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   8.3e-05      0.12       1      33 [.      14      46 ..      14      49 .. 0.94
   2 ?   -1.3   0.0       1.3     2e+03     101     111 ..      77      87 ..      71     111 .. 0.83
   3 ?   -0.9   0.0      0.97   1.5e+03     121     154 ..     555     588 ..     542     602 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33
                                      i+v+G++ +GK+++l+++ g ++  ++p+ +T+
  gi|320101525|ref|YP_004177117.1| 14 IVVLGHVDHGKTTLLDKIRGTAVARKEPGEITQ 46
                                      89************************9999997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                                       -SEEEEE---B CS
                         Dynamin_N 101 kgltlvDlPGl 111
                                       +gl ++D+PG 
  gi|320101525|ref|YP_004177117.1|  77 PGLLFIDTPGH 87 
                                       78999*****6 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.97
                                       HHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHH CS
                         Dynamin_N 121 lvkeyikkadiilavtsanhdlsnsealflarev 154
                                       ++ + i + ++ l++t +n++ls+ e+l l++ +
  gi|320101525|ref|YP_004177117.1| 555 ILYTDIPRDHVRLWLTTFNSELSDDEKLVLKEII 588
                                       5566677788899***********9999998866 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0036       5.4      12      44 ..       9      41 ..       2      52 .. 0.83
   2 ?    4.5   0.0     0.014        22     108     133 ..     122     147 ..      86     173 .. 0.80
   3 ?   -0.9   0.0      0.66   9.8e+02     148     170 ..     196     218 ..     177     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0036
                                      TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSS CS
                               Arf 12 kkelrilllGLDnaGKtTilkklkleelvttvP 44
                                       ++  i++lG    GKtT+l k++   +++  P
  gi|320101525|ref|YP_004177117.1|  9 MRQPIIVVLGHVDHGKTTLLDKIRGTAVARKEP 41
                                      5666799****9***********9999888877 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                                       CTSGCCTTSEEEEEEE-TTSTTSS-H CS
                               Arf 108 leeeelkevallvlaNKqDlpealse 133
                                       ++  + k+v+++v aNK+D  e  + 
  gi|320101525|ref|YP_004177117.1| 122 INILKEKKVPFVVAANKIDRIEGWKP 147
                                       44455679***********9876655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.66
                                       SSSEEEEEEBTTTTBTHHHHHHH CS
                               Arf 148 krkleiqkcsavkgeglkeglew 170
                                       +r++ i+  sa +geg+ e l  
  gi|320101525|ref|YP_004177117.1| 196 RRTVAIVPISAKTGEGIPELLAL 218
                                       58999************998865 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.41   6.1e+02       2      16 ..      14      28 ..      13      41 .. 0.90
   2 ?   11.8   0.0   8.8e-05      0.13      52     117 ..      81     142 ..      74     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.41
                                      EEEEESTTSSHHHHH CS
                               Ras  2 lvlvGdsavGKtsll 16
                                      +v++G    GKt+ll
  gi|320101525|ref|YP_004177117.1| 14 IVVLGHVDHGKTTLL 28
                                      79***********98 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.8e-05
                                       EEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGG CS
                               Ras  52 iwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDle 117
                                         DT G e f++lr+   + a++++lv di +   f+   + ve i+  +e++vp+v+ +nK+D  
  gi|320101525|ref|YP_004177117.1|  81 FIDTPGHELFSNLRKRGGSVADMAILVVDIIEG--FQ--PQTVEAINILKEKKVPFVVAANKIDRI 142
                                       57****************************975..54..36677888888888**********965 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   1.9e+03       1      24 [.      16      39 ..      16      44 .. 0.80
   2 ?   12.7   0.0   5.3e-05     0.079     140     237 ..     113     221 ..      56     225 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrg 24
                                      v+G++  GKtt+  ++  ++ +r+
  gi|320101525|ref|YP_004177117.1| 16 VLGHVDHGKTTLLDKIRGTAVARK 39
                                      7899999*****999877766665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.3e-05
                        ATP_bind_1 140 kfisgllsalsamlrlelPhvvvlnkfDllkek....lekeleffed..vealslllekee......ekykk.laea 203
                                        f  +++ a++++ + ++P+vv+ nk+D ++      ++  le + d  + +lsll+e  +      + y++  +++
  gi|320101525|ref|YP_004177117.1| 113 GFQPQTVEAINILKEKKVPFVVAANKIDRIEGWkphaDTPFLESIRDqsPRTLSLLEE--KiyglvgKLYEHgFEAE 187
                                       455566778899999*************988555333333333333311223333333..25799984444414556 PP

                        ATP_bind_1 204 iaelleefalvlrflplssekeesiedllslide 237
                                         + + +f ++  ++p+s++++e+i +ll+li  
  gi|320101525|ref|YP_004177117.1| 188 RFDRVRDFRRTVAIVPISAKTGEGIPELLALIAG 221
                                       678899*****9*****************99975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.7e-05      0.14       4     128 ..      10     135 ..       6     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.7e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelka...erlss 75 
                                       ++ i+vv G++  GKTtll +++ ++++++++ e  ++++   v +++++++++ lr+ + +l  e  +        
  gi|320101525|ref|YP_004177117.1|  10 RQPIIVVLGHVDHGKTTLLDKIRGTAVARKEPGEitQHVGASVVPASVLKKLAEPLRKYFPKLVIEIPGllfIDTPG 86 
                                       5789***********************99999999977777777777777777777777777777777766657777 PP

                            AAA_22  76 eellealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                       +el++ l++   + a+ ++l++D ++ + +++ +e + ++l+  +k+v+++++
  gi|320101525|ref|YP_004177117.1|  87 HELFSNLRKRGGSVADMAILVVDIIEGF-QPQTVEAI-NILK--EKKVPFVVA 135
                                       8888777777777666799999999999.88888887.5555..788888765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0031       4.6      95     126 ..       7      38 ..       3      57 .. 0.80
   2 ?   -1.7   0.0       1.5   2.3e+03     147     162 ..      74      88 ..      71      94 .. 0.77
   3 ?    2.3   0.1     0.095   1.4e+02      13      60 ..      98     143 ..      87     160 .. 0.82
   4 ?   -3.3   0.0       4.9   7.3e+03      77      99 ..     199     221 ..     191     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0031
                                       HHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallpelelk 126
                                       +++++ ++v++G+   GK+tL++++++++ ++
  gi|320101525|ref|YP_004177117.1|   7 TWMRQPIIVVLGHVDHGKTTLLDKIRGTAVAR 38 
                                       6889999*******************986443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                       EEETTTEEEESS-SSS CS
                       RsgA_GTPase 147 lelaegglliDtPGfr 162
                                       +e++ g l iDtPG +
  gi|320101525|ref|YP_004177117.1|  74 IEIP-GLLFIDTPGHE 88 
                                       5666.7889*****65 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.095
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG-- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlle 60 
                                        +  d +++vv +  + +++++++ ++ +++ek+++ v++ nKiD +e
  gi|320101525|ref|YP_004177117.1|  98 GSVADMAILVVDII-EGFQPQTVE-AINILKEKKVPFVVAANKIDRIE 143
                                       55678889999998.899999998.57888999************887 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 4.9
                                       SEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd 99 
                                       ++++ +sakt+eg+ el +l+++
  gi|320101525|ref|YP_004177117.1| 199 VAIVPISAKTGEGIPELLALIAG 221
                                       67888999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4040.52
//
Query:       gi|320101526|ref|YP_004177118.1|  [L=61]
Description: 50S ribosomal protein L24 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-23   82.4   1.2    2.2e-23   82.3   1.2    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    3.3e-06   26.9   1.0    3.3e-06   26.9   1.0    1.4  2  zf-FCS          MYM-type Zinc finger with FCS sequence motif
     0.0011   19.0   0.0     0.0016   18.5   0.0    1.2  1  YHS             YHS domain
     0.0092   15.9   2.4       0.47   10.5   0.2    2.1  2  DUF2116         Uncharacterized protein containing a Zn-ribbo
  ------ inclusion threshold ------
      0.015   15.1   4.2       0.25   11.3   4.2    2.0  1  VATC            Vms1-associating treble clef domain
      0.016   15.6   0.1      0.016   15.5   0.1    1.1  1  NosL            NosL
      0.027   13.9   0.3      0.045   13.2   0.3    1.4  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
      0.031   14.9   0.3      0.037   14.6   0.3    1.1  1  SOBP            Sine oculis-binding protein
      0.055   13.5   0.1      0.065   13.2   0.1    1.1  1  Baculo_RING     Baculovirus U-box/Ring-like 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 !   82.3   1.2   1.1e-26   2.2e-23       2      59 ..       3      60 ..       2      61 .] 0.94

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.1e-26
                                      XX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXX CS
                    Ribosomal_L24e  2 ktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrah 59
                                      +  kC F+g++i+PG+G+++v nDg+++ F+ssKc k++++kr Prk kWT +y +++
  gi|320101526|ref|YP_004177118.1|  3 RQAKCVFCGSEIEPGTGVMYVMNDGTILWFCSSKCLKNYRMKRDPRKYKWTLKYGQQA 60
                                      5679************************************************997765 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 !   26.9   1.0   1.6e-09   3.3e-06       3      41 .]       4      41 ..       3      41 .. 0.94
   2 ?   -2.8   0.0       3.2   6.3e+03      11      18 ..      49      56 ..      48      59 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.6e-09
                            zf-FCS  3 kkrCwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41
                                      +++C fC+ +i+ ++  + ++ ndg +  FCS+ Cl+ Y
  gi|320101526|ref|YP_004177118.1|  4 QAKCVFCGSEIEPGT-GVMYVMNDGTILWFCSSKCLKNY 41
                                      689************.699*****************988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                            zf-FCS 11 kyikgkpe 18
                                      ky+++ ++
  gi|320101526|ref|YP_004177118.1| 49 KYKWTLKY 56
                                      78888776 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     8e-07    0.0016       6      44 ..      10      50 ..       8      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8e-07
                               YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkdkF..edePekY 44
                                      cg+ +++++   ++  +G+   FcS +C+     +++P kY
  gi|320101526|ref|YP_004177118.1| 10 CGSEIEPGTGVMYVMNDGTILWFCSSKCLKNYrmKRDPRKY 50
                                      *****************************987334788888 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 !    5.8   0.1     0.007        14       6      16 ..       7      17 ..       4      21 .. 0.87
   2 !   10.5   0.2   0.00024      0.47      19      34 ..      32      47 ..      29      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.007
                           DUF2116  6 CivCGkaIpld 16
                                      C+ CG  I+++
  gi|320101526|ref|YP_004177118.1|  7 CVFCGSEIEPG 17
                                      ********986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00024
                           DUF2116 19 fCsekCqeeyekkrkk 34
                                      fCs kC ++y+ kr  
  gi|320101526|ref|YP_004177118.1| 32 FCSSKCLKNYRMKRDP 47
                                      9**********99864 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.2   0.00012      0.25       4      38 ..       5      44 ..       2      48 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                              VATC  4 lrCsiCgesleg..kvyFekfdfr...YCstkClraHRra 38
                                       +C +Cg+++e+   v +   d +   +Cs kCl++ R +
  gi|320101526|ref|YP_004177118.1|  5 AKCVFCGSEIEPgtGVMYVMNDGTilwFCSSKCLKNYRMK 44
                                      689999999998453455555543344********98865 PP

>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   8.2e-06     0.016       6      55 ..       3      49 ..       1      60 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.2e-06
                              NosL  6 aeaecdvCgMliaehpgpkgqifyededepakFcstrdlfafllepeerk 55
                                      ++a+c +Cg  i+  pg     +++d ++ ++Fcs+++l ++ ++++ rk
  gi|320101526|ref|YP_004177118.1|  3 RQAKCVFCGSEIE--PGTGVMYVMND-GTILWFCSSKCLKNYRMKRDPRK 49
                                      5789999998887..55544445555.9***************9998776 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   2.3e-05     0.045      15      51 ..       6      46 ..       4      49 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                            zf-FLZ 15 aCflCkkkLgegkDiymYrGdka....FCSeeC.Rqqqield 51
                                      +C +C  ++++g  + mY  + +    FCS+ C  + +++ d
  gi|320101526|ref|YP_004177118.1|  6 KCVFCGSEIEPGTGV-MYVMNDGtilwFCSSKClKNYRMKRD 46
                                      7************88.44444433567******334466666 PP

>> SOBP  Sine oculis-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   1.9e-05     0.037      23      38 ..      29      44 ..      20      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                              SOBP 23 qLQFCSdKClNQYKMq 38
                                       L FCS+KCl  Y+M+
  gi|320101526|ref|YP_004177118.1| 29 ILWFCSSKCLKNYRMK 44
                                      589************6 PP

>> Baculo_RING  Baculovirus U-box/Ring-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.2e-05     0.065      27      80 ..       5      56 ..       2      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                       Baculo_RING 27 tecaiclediddnrGvvaitdtGlldlekvlhkecikrfrreekrdp..ykrviky 80
                                       +c  c  +i+   Gv+++ + G +        +c k +r   krdp  yk  +ky
  gi|320101526|ref|YP_004177118.1|  5 AKCVFCGSEIEPGTGVMYVMNDGTIL--WFCSSKCLKNYRM--KRDPrkYKWTLKY 56
                                      57****************99999764..466789*****65..5666336666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 452.22
//
Query:       gi|320101527|ref|YP_004177119.1|  [L=90]
Description: 30S ribosomal protein S28E [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-30  104.2   5.1    3.7e-30  103.7   5.1    1.2  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 !  103.7   5.1     2e-34   3.7e-30       4      64 .]      26      86 ..      23      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 2e-34
                                      EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  4 klAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                       +AeVi++lgrtG++Ge++qVrv++leg+d+grii+RnVkGPvr+GDi++L+EterEAr+L
  gi|320101527|ref|YP_004177119.1| 26 FPAEVIQILGRTGVTGEIIQVRVRVLEGRDRGRIITRNVKGPVRVGDIVILRETEREARKL 86
                                      58**********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:01.12
# Mc/sec: 243.03
//
Query:       gi|320101528|ref|YP_004177120.1|  [L=127]
Description: 50S ribosomal protein L7AE [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-32  109.2   1.5    8.3e-32  108.8   1.5    1.2  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    4.4e-05   23.3   0.2    8.3e-05   22.4   0.2    1.6  1  PELOTA_1        PELOTA RNA binding domain
     0.0044   17.1   0.0      0.005   16.9   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 !  108.8   1.5   1.4e-35   8.3e-32       2      94 ..      18     111 ..      17     112 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 1.4e-35
                                       HHHHHHHHHHHHTE.EEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSS CS
                    Ribosomal_L7Ae   2 aieevlkkakkagk.lvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkk 77 
                                       ++++++ k++++g+ +++G++e+tka+erg+aklv++Aedvep+e++++l+ lc+ek++pyv+v+sk++LG+++g +
  gi|320101528|ref|YP_004177120.1|  18 KVYQAVAKVRETGGkVKKGTNETTKAVERGQAKLVVIAEDVEPPEIVAHLPLLCEEKKIPYVYVPSKQKLGQAAGIE 94 
                                       799999999999988************************************************************** PP

                                       SECSEEEEEESTTTHHH CS
                    Ribosomal_L7Ae  78 rpvsalaikdegdskdl 94 
                                       + ++++ai+d+g +kd+
  gi|320101528|ref|YP_004177120.1|  95 VSAASVAIVDVGGAKDI 111
                                       *************9987 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   1.4e-08   8.3e-05      21      71 ..      32      84 ..      12      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-08
                          PELOTA_1 21 liKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                       +K g  E+T+++ R + + v+++++ e  + +ahl lL++ek++p++ vp++
  gi|320101528|ref|YP_004177120.1| 32 KVKKGTNETTKAVERGQAKLVVIAEDVEppEIVAHLPLLCEEKKIPYVYVPSK 84
                                      79*********************9988865679**************999876 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 !   16.9   0.0   8.4e-07     0.005      34     130 ..      15     103 ..       6     125 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.4e-07
                      RNase_P_pop3  34 lqekvlkklvrlleskeneeseltvglneivelLecsesddvvllvcnkD.tPsvLlsqlpllvavanltvklvqlp 109
                                       l ekv + + +++e    +  ++  g ne  +  e    +++ l+v+ +D +P  ++ +lpll++ ++  ++ v +p
  gi|320101528|ref|YP_004177120.1|  15 LAEKVYQAVAKVRE----TGGKVKKGTNETTKAVE---RGQAKLVVIAEDvEPPEIVAHLPLLCEEKK--IPYVYVP 82 
                                       45566666666666....566899999**999999...55556667777766999***********99..7777777 PP

                      RNase_P_pop3 110 ksaqakldeklGlskagmllv 130
                                        + +   +  + +s a + +v
  gi|320101528|ref|YP_004177120.1|  83 SKQKLGQAAGIEVSAASVAIV 103
                                       654433333333444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 872.50
//
Query:       gi|320101529|ref|YP_004177121.1|  [L=589]
Description: glutamyl-tRNA synthetase [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-75  254.0   0.0    2.4e-75  253.3   0.0    1.3  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    1.1e-19   70.9   0.0    2.4e-19   69.8   0.0    1.6  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
  ------ inclusion threshold ------
       0.13   11.1   0.2       0.19   10.5   0.2    1.1  1  API5            Apoptosis inhibitory protein 5 (API5)
       0.26   12.1   0.6        4.3    8.2   0.1    2.9  3  KMP11           Kinetoplastid membrane protein 11


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 !  253.3   0.0   5.4e-79   2.4e-75       1     299 [.     106     401 ..     106     414 .. 0.95

  Alignments for each domain:
  == domain 1  score: 253.3 bits;  conditional E-value: 5.4e-79
                                       S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC-..-HHHHHHHHHHHHHTT---SSEEEEGG CS
                      tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpere..keeaeesiledlkwlgikwdekptyqs 75 
                                       kV+tRfaP+P    H+G+a+ all+y +A  +nG++ilR+eDTdp  +   +ea ++i+++l wlg+kw  + + qs
  gi|320101529|ref|YP_004177121.1| 106 KVVTRFAPNPDYTIHLGNARPALLSYWYAELYNGRMILRFEDTDPRIKspYPEAYTKIKDALRWLGVKW-SEEYVQS 181
                                       79******************************************97551258*****************.779**** PP

                                       GGHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBT CS
                      tRNA-synt_1c  76 drfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkide 152
                                        r+++++++a eLik+G AYv++c+  e +++r++   +++++rd ++e+nl+ f ++m +g++ +++av+R+k d 
  gi|320101529|ref|YP_004177121.1| 182 LRMEIFYEVARELIKRGGAYVDNCRDKEFRSYRNA--GKACPHRDTPVEDNLEKF-DKMLEGHYGEGEAVLRVKTDL 255
                                       *********************************99..9999**************.89******************* PP

                                       TSS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.- CS
                      tRNA-synt_1c 153 ess.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevp 228
                                       +++   +rD v+ r+  +++  h+++++++ + PtY+fa  +dD+l+++thvlr++e+ +nt k+  l++ +g++ p
  gi|320101529|ref|YP_004177121.1| 256 AHPdPSVRDWVAFRVIDTSKTPHPVTGERYVVWPTYNFAAGVDDHLMGVTHVLRAKEHVSNTVKQKYLYDHMGWKYP 332
                                       *******************99******************************************************88 PP

                                       EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEE CS
                      tRNA-synt_1c 229 pfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnr 299
                                       + ih + rl le+  lSK k+  lv+e+ +   dd+r+ ++n+l r+G+  e + +++++ ++  ++  ++
  gi|320101529|ref|YP_004177121.1| 333 ETIH-FGRLSLEGVILSKSKMRRLVKEQGISPYDDPRLGTINGLKRRGILRETIWKIVKEVGIKPID-AKI 401
                                       8887.79****************************************************99998776.444 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 !   69.8   0.0   5.5e-23   2.4e-19       1     174 []     418     575 ..     418     575 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 5.5e-23
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrl..kpgeevrLkelynikve 75 
                                       A+RymaV +p+ +++++l+   e ++++p+hp+++e  + +++ ++ iyi+  D++ +  ++ + +r ++l n++++
  gi|320101529|ref|YP_004177121.1| 418 ANRYMAVDEPIPLVLKGLEG--ELKAQIPVHPSRREHYEYTLTDDSVIYISSRDLRLIlnSEHRVFRAMGLANFTIS 492
                                       89**************9884..79******************************66551144578999********8 PP

                    tRNA-synt_1c_C  76 evekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvl.eegla 150
                                       e +   +g+   l +++++ s ++ar+ ++ ii+Wvs++e+++                 +ll p       ++ l+
  gi|320101529|ref|YP_004177121.1| 493 EHVFI-DGK-PALVARLHSVSQDDARRMNApIIQWVSDKEKATL----------------SLLVPSDVDLKeTRYLV 551
                                       87633.444.456889999999999************9998888................666665554434899** PP

                    tRNA-synt_1c_C 151 epalanlkkgdivQfeRiGyfrvd 174
                                       e+ + + k+++ivQ+ R G++r+d
  gi|320101529|ref|YP_004177121.1| 552 EKRILSEKPDSIVQLYRVGFARID 575
                                       **********************98 PP

>> API5  Apoptosis inhibitory protein 5 (API5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   4.1e-05      0.19     111     166 ..      12      66 ..       8      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.1e-05
                              API5 111 veldavhkallsllkldakasltalfkqieteeetvRekvlkfireklftlkeell 166
                                       v   a ++al++ +k+d ka l+a+++++  e  ++R +v +fi+  + ++ ee+ 
  gi|320101529|ref|YP_004177121.1|  12 VREAAFKHALVNAVKHDGKADLKAVMSKVIGETPEIRSRVKEFIEV-IRSIVEEVN 66 
                                       55678899***********************************974.666666666 PP

>> KMP11  Kinetoplastid membrane protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00095       4.3      41      87 ..      44      91 ..      31      93 .. 0.89
   2 ?    0.1   0.0      0.32   1.4e+03      45      59 ..     228     242 ..     221     253 .. 0.82
   3 ?   -2.1   0.0       1.5   6.8e+03      10      41 ..     505     535 ..     502     561 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00095
                             KMP11 41 spemkehyekfekmikehtekfnkk.mrehsehfkakfaelleqqkaa 87
                                      +pe++   + f  +i+   e  nk  ++e+ +  k+++ elle++k+a
  gi|320101529|ref|YP_004177121.1| 44 TPEIRSRVKEFIEVIRSIVEEVNKMsLEEQLKLVKTNWPELLEERKEA 91
                                      6999*******************96267788899************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.32
                             KMP11  45 kehyekfekmikeht 59 
                                        +  ekf+km++ h 
  gi|320101529|ref|YP_004177121.1| 228 EDNLEKFDKMLEGHY 242
                                       567899999999885 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.5
                             KMP11  10 akldrldeefakkmeeqnkkffadkpdeatls 41 
                                       a+l  + ++ a++m+    ++ +dk  +atls
  gi|320101529|ref|YP_004177121.1| 505 ARLHSVSQDDARRMNAPIIQWVSDKE-KATLS 535
                                       77788888889999998888888884.56665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4132.83
//
Query:       gi|320101530|ref|YP_004177122.1|  [L=161]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   55.3   0.2    8.1e-15   55.1   0.2    1.0  1  DUF2118   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.093   12.4   0.0        0.1   12.3   0.0    1.1  1  DTW       DTW domain


Domain annotation for each model (and alignments):
>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.2     9e-19   8.1e-15       2     148 ..       5     149 ..       4     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 9e-19
                           DUF2118   2 klPrlYvEgkeseeevevileeeee...vekfadkveekklkgkvvYeelldeivdvleekvtrdviivlpderkli 75 
                                        +P+++vE  es+   +vi ++  +   +e+ a + e  k +g  +Yee + ++vd+ +   +r++ii  ++++   
  gi|320101530|ref|YP_004177122.1|   5 IFPEIFVEDVESN---RVICVKDSKfilLENTATREECSKHYGSIPYEE-VLNYVDLEKPALKRSIIILDKKRNGVA 77 
                                       69***********...88877777622245667777788899*******.889************999988888888 PP

                           DUF2118  76 llkkGdk.lklipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfikeepagkrpnyiyyi 148
                                       ll +G+  l l +v g   + +v   +rv++gd +a+vttrk evr   +  eg  + +   + +k+++ i+++
  gi|320101530|ref|YP_004177122.1|  78 LLFPGETpLCLQEVRGRA-VFYVGNPERVRKGDLIAYVTTRKNEVRNEYSLCEGFLLAVIDLTWEKPER-IVVV 149
                                       999997626666777755.5678889*****************************99999988855555.4444 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05       0.1      71     129 ..      67     147 ..      11     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                               DTW  71 allkdpkrksvllFPsknaksledllase......................aakase...kkeefeekrlillDGTW 122
                                        +l+++++ ++llFP+++   l+++  +                       +   +e   + +  e   l ++D TW
  gi|320101530|ref|YP_004177122.1|  67 IILDKKRNGVALLFPGETPLCLQEVRGRAvfyvgnpervrkgdliayvttrK---NEvrnEYSLCEGFLLAVIDLTW 140
                                       4667777778*************999998***********999999986541...3344456677888999****** PP

                               DTW 123 sqAkkil 129
                                       ++ ++i+
  gi|320101530|ref|YP_004177122.1| 141 EKPERIV 147
                                       **99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1255.31
//
Query:       gi|320101531|ref|YP_004177123.1|  [L=372]
Description: isopentenyl-diphosphate delta-isomerase [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-17   61.4   0.0    1.7e-15   56.9   0.0    2.3  1  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.057   12.5   0.0      0.094   11.8   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 !   56.9   0.0   1.9e-19   1.7e-15       5     343 ..       4     341 ..       1     345 [. 0.84

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.9e-19
                                       S-HHHHHHHH--STTSHHHHHHHHG.GGGEEE---SSSS-S..S-B--EEETTEEESSSEEE--BSTGGGTSTTHHH CS
                            FMN_dh   5 lpkkafayvaggagdevtlrenraa.ferirlrprvlrdvs..kvdlsttllGqklslPvliaPvglaklahpdgel 78 
                                       +++++ ++++ + +  v +++n ++ +++i+l++r++ + +  +vd s ++lG++l++P++i  +          ++
  gi|320101531|ref|YP_004177123.1|   4 VQSRKLHHIEVALDPRVDFEDNCSDlYREIQLVHRAFPGFElgDVDSSLEFLGYRLEAPLMITGMTGGHPSLTGINR 80 
                                       56677788888888888899998764899********9876226799****************997777777789** PP

                                       HHHHHHHHHTS-EEEETT-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHH CS
                            FMN_dh  79 alaraaakagipfvlstvastsleevaaaaegplwfqlyvpkdrelteellkraeaagykalvltvDtpvlgkRerd 155
                                       ala+ a+k  + ++++++         +    +++ +  v++d +    ++ ++    ++   ++ Dt v      +
  gi|320101531|ref|YP_004177123.1|  81 ALAELAEKKRVAIGVGSQRAIVTSGFRE----DVVASYRVVRDVARDVPVIGNIGLNTLND--VEYDTIVKLVEVLE 151
                                       ******************8877777766....8999999****999999998886665554..68888887766555 PP

                                       HHC.T--BSTT-T.G.TTGGGSTSGSCCTTH..THHHHHHCCCHB-TC--HHHHHHHHHHHSSEEEEEEE...-SHH CS
                            FMN_dh 156 lrn.gfslppklklrnllqelakpewaaealkkasaaaefvgkqldpsltwddikwlreqtklplvvKGv...ltae 228
                                        ++  ++l+p+       qe+ +pe+ ++++          ++        +++++l +++  p++vK+v   l+ e
  gi|320101531|ref|YP_004177123.1| 152 ADAlAIHLNPA-------QEVIQPEGDTRFN----------HR------LLEKVRELVKTLGKPVIVKEVgngLSME 205
                                       55424667776.......8899999999998..........33......3589************************ PP

                                       HHHHHHHTTESEEEE--GGG.......................TSSTT---HHHCHHHHHHHH..SS-EEEESS--S CS
                            FMN_dh 229 dakraveaGvdgivvSNHGG.......................RqldgapatidvLpeiveavggrievlvDgGirr 282
                                       ++k   +aGv +  v+   G                           g p++++v+ +   a   +  ++++gG++ 
  gi|320101531|ref|YP_004177123.1| 206 TVKVFHDAGVRIYDVAGACGtnwalvealrnqpgtpryecgimLAKWGIPTPLSVIETRFTAT--DSFIIASGGVWD 280
                                       ********************9999998887777777777776655556777777776665555..589********* PP

                                       HHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHC CS
                            FMN_dh 283 GsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvaeldr 343
                                       G  ++  + lGAd+ +l++p+l  l  +G + +e +l++   el+++m l G+++++el++
  gi|320101531|ref|YP_004177123.1| 281 GFKAAVNIVLGADMAGLAKPLLKKLLKEGLKQAETYLDTYVFELKTAMFLSGARTLRELRE 341
                                       **********************************************************987 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 ?   11.8   0.0   1.1e-05     0.094     185     305 ..     173     300 ..     154     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                                       SSHHHHHHHHHHHHHH-TTSEEEEE.EE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---.HHHHH CS
                      Glu_synthase 185 ysiedlaqliedLkevnkeakvsvK.lvaeagvetiaagvakanadiilidGleGGTGAspkssikhaGlP.lelal 259
                                       +  + l +++++L +    ++v vK ++ +  +et+++   +a++ i  + G  G   A  + ++++ G+P  e ++
  gi|320101531|ref|YP_004177123.1| 173 RFNHRLLEKVRELVKTL-GKPVIVKeVGNGLSMETVKV-FHDAGVRIYDVAGACGTNWALVEALRNQPGTPrYECGI 247
                                       55566788888887755.799999945578899****9.899*****************************645665 PP

                                       HHHH.......HHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHH CS
                      Glu_synthase 260 aevd.......qtlkeeglrdrvsliadGglktgadvvkalalGAdavgigta 305
                                         ++        ++ +        +ia+Gg+  g + ++ ++lGAd  g+++ 
  gi|320101531|ref|YP_004177123.1| 248 MLAKwgiptplSVIETRFTATDSFIIASGGVWDGFKAAVNIVLGADMAGLAKP 300
                                       5554222211033444444456679*********************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2814.06
//
Query:       gi|320101532|ref|YP_004177124.1|  [L=283]
Description: hypothetical protein [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-76  255.5   0.0    5.3e-76  255.3   0.0    1.0  1  Memo            Memo-like protein
    1.2e-05   24.6   0.1    2.1e-05   23.7   0.1    1.4  1  LigB            Catalytic LigB subunit of aromatic ring-openi
  ------ inclusion threshold ------
      0.027   13.9   0.0      0.037   13.5   0.0    1.1  1  ABC_transp_aux  ABC-type uncharacterized transport system


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.3   0.0   8.8e-80   5.3e-76       2     270 ..       6     279 ..       5     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 255.3 bits;  conditional E-value: 8.8e-80
                              Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei.......arviis.......PHagyvysgevaakayaeles.skv 63 
                                       a vAG fYp++ eel k +e+++++ +g++++            s       PHagy+ysg+vaa+ay+ ++   ++
  gi|320101532|ref|YP_004177124.1|   6 AVVAGYFYPDKREELVKVIEWSFKHGVGPGSTpsvseapV----SniigyvvPHAGYIYSGPVAAHAYYDMAVnGRP 78 
                                       679***************************9988865543....34455889********************9999* PP

                              Memo  64 ervvilGpsHtilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekk 140
                                       +++vilG +Ht++g+ vsv++ + +eTP+Gdl vD e++e +vk++++a++de+a+l+EHS+Evqlpf+++l +  +
  gi|320101532|ref|YP_004177124.1|  79 DTIVILGTNHTGMGRIVSVYPGGLWETPIGDLTVDGEVAEGIVKHSSVAEFDEYAHLEEHSVEVQLPFIAYLYNG-R 154
                                       ***************************************************************************.6 PP

                              Memo 141 fkivPilvsaqseetakevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelk 215
                                       ++ivP+++ ++++++a++++ea+ +v + +   +++++SsD++Hy+     p++++ ++ D  +i+++ +l++++++
  gi|320101532|ref|YP_004177124.1| 155 VRIVPVVIRVHTPDIARDLAEAIRRVTESSGkkIIILASSDFNHYE-----PHDETVRK-DMAAINEILKLDSDGFY 225
                                       ****************************9988788899********.....******99.***************** PP

                              Memo 216 eylektnnticGekpiavilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                       +++ + +++icG + i+ ++++ + lg  ka llk+a+s+d+++d++ vV+yas+
  gi|320101532|ref|YP_004177124.1| 226 NTMLRDDISICGPGGIMTLIEYTRMLG-GKALLLKHATSGDTSGDRSHVVGYASI 279
                                       ***************************.9************************96 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 !   23.7   0.1   3.6e-09   2.1e-05      39     202 ..      74     216 ..      45     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.6e-09
                              LigB  39 aeksPdtiivvsphhltdvnpvfvlgvaeefeaiddfgkflprleyelkgnpeLaekiaealkksgidlavesnsmk 115
                                        + +Pdti++  + h+       +++v +  + +++       + ++l ++ e+ae i+++   +++d  +      
  gi|320101532|ref|YP_004177124.1|  74 VNGRPDTIVILGTNHTGMGR---IVSVYP-GGLWET-------PIGDLTVDGEVAEGIVKHSSVAEFDEYA----HL 135
                                       44589999999888888333...344444.233333.......5677889999**************9544....44 PP

                              LigB 116 lDHGtlvPLelmlp.deakvpvikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaak 191
                                        +H + v L ++    +  v+ ++v++ +     +++   ++L eA+r+ +e++ k++ il+s ++ H+ + de+  
  gi|320101532|ref|YP_004177124.1| 136 EEHSVEVQLPFIAYlYNGRVRIVPVVIRV-----HTPDIARDLAEAIRRVTESSGKKIIILASSDFNHYEPHDETVR 207
                                       46666666666655433589999999998.....9*********************************999988887 PP

                              LigB 192 adaqtlllnee 202
                                       +d+    +ne+
  gi|320101532|ref|YP_004177124.1| 208 KDM--AAINEI 216
                                       777..345554 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.2e-06     0.037     101     161 ..     139     203 ..     126     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-06
                    ABC_transp_aux 101 ktkrvymglvieygdkeetipllkntsesnlEyeltsairkltdkkkpkvgflt....ghgelsl 161
                                       ++++  + ++  y+++++++p++    +  +  +l+ air++t+++ +k+ +l+    +h e+ +
  gi|320101532|ref|YP_004177124.1| 139 SVEVQLPFIAYLYNGRVRIVPVVIRVHTPDIARDLAEAIRRVTESSGKKIIILAssdfNHYEPHD 203
                                       447777889999*****************************************844444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2104.20
//
Query:       gi|320101533|ref|YP_004177125.1|  [L=219]
Description: 30S ribosomal protein S2P [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-24   86.7   0.0    3.3e-15   55.9   0.0    2.0  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
      0.053   13.1   0.3       0.16   11.5   0.3    1.6  2  Peripla_BP_4  Periplasmic binding protein domain
       0.17   12.0   0.0       0.25   11.4   0.0    1.3  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 !   29.1   0.0   8.5e-11   5.1e-07       2      95 ..      33     123 ..      32     130 .. 0.92
   2 !   55.9   0.0   5.5e-19   3.3e-15     148     213 ..     131     196 ..     126     198 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 8.5e-11
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L+agvh+G  t+  ++ m+p++y +r+ g +i+d++k+ + lr a k++++   + +ki  v+ ++  ++  +++++
  gi|320101533|ref|YP_004177125.1|  33 LSAGVHIG--THICTKFMEPFVYRVRSdGLYILDVRKIDERLRIAGKFLSRY--QPEKIAVVSVRQYGRKPAQKMCQ 105
                                       79******..667799*******999549********************986..6678999999************* PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTN 95 
                                        ++    + r+++Gt+TN
  gi|320101533|ref|YP_004177125.1| 106 YVGCKPFTGRFMPGTFTN 123
                                       ****************** PP

  == domain 2  score: 55.9 bits;  conditional E-value: 5.5e-19
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                        Pd+vvv+d++++  a+kEa++ gip++a+ Dt+   d vd +Ip+N++  +s+ l++ +l+++i 
  gi|320101533|ref|YP_004177125.1| 131 EPDVVVVTDTRSDAQALKEAAETGIPIVAFADTDNRVDYVDLIIPGNNKGRKSLALLYWILTRQIL 196
                                       6************************************************************99886 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 ?   -1.4   0.0      0.24   1.4e+03      73     104 ..      79     111 ..      74     114 .. 0.77
   2 ?   11.5   0.3   2.7e-05      0.16      57      99 ..     133     169 ..     130     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.24
                                       HHHHHHTT-EEEEESTT.GCTTT-CEEEEEC-H CS
                      Peripla_BP_4  73 lkkakaaGIpVvafdsd.dapsgerlayvgfdn 104
                                       l + + ++I Vv++ +   +p+ + + yvg   
  gi|320101533|ref|YP_004177125.1|  79 LSRYQPEKIAVVSVRQYgRKPAQKMCQYVGCKP 111
                                       566677889999988888889999999999866 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.7e-05
                                       SEEEE--SSHHHHHHHHHHHHHTT-EEEEESTTGCTTT-CEEE CS
                      Peripla_BP_4  57 dgiivapvdstalapalkkakaaGIpVvafdsddapsgerlay 99 
                                       d+++v+  d+   a+alk+a++ GIp+vaf       ++r+ y
  gi|320101533|ref|YP_004177125.1| 133 DVVVVT--DTRSDAQALKEAAETGIPIVAFADT----DNRVDY 169
                                       555555..44445589*************9766....344444 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 ?   11.4   0.0   4.3e-05      0.25      43      74 ..     128     159 ..      81     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
                            BRCT_3  43 islgkldvvvtdsscpeevlkkaeqlkipvvS 74 
                                       i ++   vvvtd++  +++lk+a++ +ip+v+
  gi|320101533|ref|YP_004177125.1| 128 IYFEPDVVVVTDTRSDAQALKEAAETGIPIVA 159
                                       566665688*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1608.05
//
Query:       gi|320101534|ref|YP_004177126.1|  [L=66]
Description: DNA-directed RNA polymerase subunit N [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  104.0   0.2    4.2e-30  103.8   0.2    1.0  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
    0.00074   19.7   0.0    0.00099   19.3   0.0    1.2  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 
  ------ inclusion threshold ------
      0.026   14.4   1.4       0.04   13.8   1.4    1.4  1  FYRN            F/Y-rich N-terminus


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.2     7e-34   4.2e-30       1      58 [.       1      58 [.       1      59 [. 0.97

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 7e-34
                                      ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHH CS
                         RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliek 58
                                      M++PVrCFtCG++ig++w+ey +++e+geep+++Ld+Lg+kryCCrrm+l+ vd+  +
  gi|320101534|ref|YP_004177126.1|  1 MLFPVRCFTCGRPIGHLWDEYIKRVEQGEEPGKVLDDLGVKRYCCRRMFLSYVDVSRE 58
                                      9*****************************************************9876 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.7e-07   0.00099       1      52 [.       1      57 [.       1      65 [. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-07
                    Chordopox_RPO7  1 mvfplvCstCGrDlse..eryrLlvkk.kkLkdvlat..vkrkCCrlkLstqiepqr 52
                                      m fp+ C tCGr + +    y   v++ ++  +vl+   vkr CCr      ++  r
  gi|320101534|ref|YP_004177126.1|  1 MLFPVRCFTCGRPIGHlwDEYIKRVEQgEEPGKVLDDlgVKRYCCRRMFLSYVDVSR 57
                                      99***********99843345555555267789**863479****966555566555 PP

>> FYRN  F/Y-rich N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.4   6.7e-06      0.04      29      51 .]      43      65 ..      41      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-06
                              FYRN 29 YkstRlYwstkdprkrclYtceI 51
                                      Y+++R++ s++d ++ +lY  +I
  gi|320101534|ref|YP_004177126.1| 43 YCCRRMFLSYVDVSREILYFPKI 65
                                      *******************8666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 480.05
//
Query:       gi|320101535|ref|YP_004177127.1|  [L=140]
Description: 30S ribosomal protein S9 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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  119.0   0.0    1.9e-34  118.8   0.0    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.0     1e-38   1.9e-34       1     121 []      16     140 .]      16     140 .] 0.96

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1e-38
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiar 76 
                                       G+rK+s+Ar+ ik+g g++ +n+++le  ++ e ar+k+lepl l+g l k +dv+v+v+gGG ++qaeA+r +iar
  gi|320101535|ref|YP_004177127.1|  16 GKRKTSIARAVIKPGAGRVWINNTPLEI-IPFELARMKILEPLLLIGDLAKtIDVKVNVNGGGYMSQAEAARIAIAR 91 
                                       8***************************.999***************99988************************* PP

                                       HHHHHHH.HH.HHHHC..TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  77 aLvalek.ee.kkeLk..kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       +Lv++ + ++ k++Lk  ++ +l  DpR++E+kK g+  AR+++q+s+R
  gi|320101535|ref|YP_004177127.1|  92 GLVEFFEsDHvKTILKeyDRYMLSGDPRQTEPKKWGRYSARRRWQKSYR 140
                                       ****9875456999*9999****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1028.29
//
Query:       gi|320101536|ref|YP_004177128.1|  [L=150]
Description: 50S ribosomal protein L13 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-10   41.5   1.5    3.1e-08   33.9   1.5    2.4  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 !   33.9   1.5   1.7e-12   3.1e-08       4     115 ..       8     109 ..       5     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.7e-12
                                       EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE.-SSTTSEEEEEHHHH CS
                     Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrh.tgypgglkevtakel 79 
                                        +DA++qvlgr+as +ak L              G  v+v+naek +++g+k +    y+   +   + +  +    
  gi|320101536|ref|YP_004177128.1|   8 YVDASNQVLGRVASIVAKKLL------------EGYRVIVVNAEKAVVSGEKNRVIAGYKLlLNVKTHYNPEKTGIR 72 
                                       69**************98775............4677**************98875544440444455555555556 PP

                                       HCCSHHHHHHHHHHCCS-S.SHHHHHHGCTEEEESSS CS
                     Ribosomal_L13  80 lekkpeeilekaVkgmLpk.nklgrrrlkrLkvyage 115
                                       + + p +i++++V+gmLp  +  gr+ ++rL+vy g 
  gi|320101536|ref|YP_004177128.1|  73 RPRTPVNIFKRTVRGMLPVdQPKGREAYRRLRVYVGV 109
                                       68899*************7255899999******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1162.94
//
Query:       gi|320101537|ref|YP_004177129.1|  [L=120]
Description: 50S ribosomal protein L18 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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   36.8   0.1    2.8e-09   36.6   0.1    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
      3e-07   31.2   0.0    4.8e-07   30.5   0.0    1.5  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   3.1e-13   2.8e-09      21     137 ..       8     118 ..       2     120 .] 0.86

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.1e-13
                     Ribosomal_L18  21 nvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPkl 97 
                                       n+ l+  ++  r  a R+++     v   L +  + r+++ +sr+ +++      + i+vv g+v+    l + P +
  gi|320101537|ref|YP_004177129.1|   8 NIVLRKTIEELRRQASRSNAPIWGAVAEELSKPTRRRRAVNVSRINRHTA----PGDIVVVPGKVLGAGDLDH-P-V 78 
                                       55555555555556779999999**********************99988....469*********9888754.5.8 PP

                     Ribosomal_L18  98 svaALrftetararilkaGGeiltlDqLalraPtGkntvL 137
                                       +vaA+ f++ta ++i+++GG +l + +L  ++P G+n+ +
  gi|320101537|ref|YP_004177129.1|  79 TVAAFSFSKTAIEKIVRSGGRVLHIMDLLRENPSGSNVKI 118
                                       9************************************865 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   5.4e-11   4.8e-07      72     126 ..      44     100 ..      10     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.4e-11
                                       --EEEGGGTTTTSSS......SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  72 aeeidleelaeaglikk..kdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                                       +  ++++++ ++           Kvlg g+l ++++v a +fSk+A+ekI + GG+v
  gi|320101537|ref|YP_004177129.1|  44 RRAVNVSRINRHTAPGDivVVPGKVLGAGDLDHPVTVAAFSFSKTAIEKIVRSGGRV 100
                                       45555555522222222433334********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 865.23
//
Query:       gi|320101538|ref|YP_004177130.1|  [L=280]
Description: DNA-directed RNA polymerase subunit D [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-29  101.0   0.0      1e-28   99.9   0.0    1.5  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    2.4e-14   52.5   0.0    3.2e-14   52.1   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    3.1e-06   27.2   8.0    7.5e-06   26.0   8.0    1.7  1  Fer4_9         4Fe-4S dicluster domain
    6.8e-06   26.6  13.0    0.00018   22.0  11.3    2.4  2  Fer4_7         4Fe-4S dicluster domain
    2.2e-05   24.1  12.2     0.0018   18.0   2.4    3.2  2  Fer4           4Fe-4S binding domain
    6.2e-05   22.9  13.1    0.00092   19.2   1.8    2.4  2  Fer4_6         4Fe-4S binding domain
    0.00013   22.0  10.9    0.00013   22.0  10.9    1.6  1  Fer4_10        4Fe-4S dicluster domain
    0.00015   22.2   3.6       0.11   13.0   0.6    2.5  2  Fer4_17        4Fe-4S dicluster domain
     0.0015   18.7  10.7     0.0058   16.7  10.7    2.0  2  Fer4_21        4Fe-4S dicluster domain
     0.0052   17.7  11.5       0.57   11.2   1.9    2.5  2  Fer4_16        4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.034   14.6  12.8        0.6   10.6   2.5    2.4  3  Fer4_8         4Fe-4S dicluster domain
       0.15   13.1  16.7        0.4   11.7   4.1    2.4  2  Fer4_3         4Fe-4S binding domain
       0.18   12.4  12.1       0.84   10.3   1.6    2.4  2  Fer4_4         4Fe-4S binding domain
       0.18   12.0  13.3       0.48   10.6   3.4    2.4  2  Fer4_2         4Fe-4S binding domain
       0.83    9.9   7.3        5.2    7.3   0.7    2.2  2  Fer4_18        4Fe-4S dicluster domain
        1.3    8.9   6.4       0.42   10.5   0.9    2.4  2  RLI            Possible Fer4-like domain in RNase L inhibitor
        5.1    7.7  11.9          2    9.0   1.4    2.4  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 !   99.9   0.0   9.7e-32     1e-28       1     112 []      44     161 ..      44     161 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 9.7e-32
                                       EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-E..TSSSSTTCSEEEEEEEEESSEC....EEGGGCBE CS
                     RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelve..eeeegeeeksvelkLnvkgpge....vtagdlkl 71 
                                       V i en+sv++DE++aHrlglipl+s+++l++++  +e++e  e+  +++++  +l+L++kgp++    +++++l++
  gi|320101538|ref|YP_004177130.1|  44 VAITENSSVFYDEYIAHRLGLIPLKSDEALHKYKPPEECAEagEKGVFSQDCFATLRLEAKGPEDgvltIYSEMLES 120
                                       789************************************94468999****************************** PP

                                       SSSSCEESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  72 edadveivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       +d+dv++v+ +++++ L+ +q+++lea+++ G+Gkehak+s
  gi|320101538|ref|YP_004177130.1| 121 SDPDVTPVYGKVPVVRLTRNQSIRLEAYARLGRGKEHAKWS 161
                                       ****************************************8 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 !   52.1   0.0   3.1e-17   3.2e-14       3      69 .]      16     266 ..      14     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.1e-17
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                         RNA_pol_L   3 llrgvdhtlgNaLRrillsevpgvaiea................................................. 30 
                                        l+g+ + + N+LRr+++sevp++a++                                                  
  gi|320101538|ref|YP_004177130.1|  16 HLKGIPLHVVNSLRRTIISEVPTMAVDYvaitenssvfydeyiahrlgliplksdealhkykppeecaeagekgvfs 92 
                                       689999**************************************************************999999999 PP

                                       .....................................................................xx...... RF
                         RNA_pol_L  31 .....................................................................pv...... 32 
                                                                                                            pv      
  gi|320101538|ref|YP_004177130.1|  93 qdcfatlrleakgpedgvltiysemlessdpdvtpvygkvpvvrltrnqsirleayarlgrgkehakwsPVsvathk 169
                                       99999999999999999999999999999999998888887777777777777777777777777666611555555 PP

                                       ............................................................xxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  33 ............................................................vkvntdkdklilevetd 49 
                                                                                                   vkv+  ++++il+ e +
  gi|320101538|ref|YP_004177130.1| 170 yipvitvnaekcqgtkcsrcantcpkgvfeasgdairvkedrvlectfcrlcentcpagaVKVSWRDNEYILSLELT 246
                                       5555777777777777777777777788888888888888888888888888888888889**************** PP

                                       xxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  50 gslkPeealkeAlkiLkekl 69 
                                       g+l+++++l+eA++iL +kl
  gi|320101538|ref|YP_004177130.1| 247 GALSARNVLLEAVNILSRKL 266
                                       ****************9997 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   8.0   7.1e-09   7.5e-06       3      50 ..     184     229 ..     169     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.1e-09
                            Fer4_9   3 tgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       t+C +C + Cp+gv++ +  +  ++ ++    +C++C+ C++ Cp ga
  gi|320101538|ref|YP_004177130.1| 184 TKCSRCANTCPKGVFEASGDAIRVKEDRVL--ECTFCRLCENTCPAGA 229
                                       56*************999999998877765..5************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 !   15.6   3.3   1.7e-05     0.018      24      52 .]     167     197 ..     155     197 .. 0.78
   2 !   22.0  11.3   1.7e-07   0.00018       3      52 .]     184     229 ..     184     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                            Fer4_7  24 nekgtekveidpekClg..CgaCvavCPtga 52 
                                        +k ++ +++++ekC+g  C +C+++CP+g+
  gi|320101538|ref|YP_004177130.1| 167 THKYIPVITVNAEKCQGtkCSRCANTCPKGV 197
                                       44566889*******7544999******996 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.7e-07
                            Fer4_7   3 igCgaCvaaCpvkaieldeeenekgtekveid.pekClgCgaCvavCPtga 52 
                                       ++C +C+++Cp +++e   +       +v+ d   +C++C+ C+++CP+ga
  gi|320101538|ref|YP_004177130.1| 184 TKCSRCANTCPKGVFEASGD----A-IRVKEDrVLECTFCRLCENTCPAGA 229
                                       58**************9876....2.2333332568*************97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   2.4     0.001       1.1       3      23 ..     176     198 ..     174     199 .. 0.73
   2 !   18.0   2.4   1.7e-06    0.0018       7      23 ..     214     230 ..     213     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                                       EETTTS..SS-THHHHHSTTTEE CS
                              Fer4   3 ideekC..igCGaCvevCPvgAI 23 
                                       ++ ekC  ++C +C++ CP g+ 
  gi|320101538|ref|YP_004177130.1| 176 VNAEKCqgTKCSRCANTCPKGVF 198
                                       5666663356*********9975 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.7e-06
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                        C++C +C++ CP gA 
  gi|320101538|ref|YP_004177130.1| 214 ECTFCRLCENTCPAGAV 230
                                       5***************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 !   19.2   1.8   8.7e-07   0.00092       1      23 [.     173     197 ..     173     200 .. 0.89
   2 !    8.7   3.9    0.0018       1.9       9      23 ..     215     229 ..     215     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.7e-07
                            Fer4_6   1 vveidpdkCig..CgdCvrvCPega 23 
                                       v++++++kC g  C +C++ CP g+
  gi|320101538|ref|YP_004177130.1| 173 VITVNAEKCQGtkCSRCANTCPKGV 197
                                       79********666*********886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                            Fer4_6   9 CigCgdCvrvCPega 23 
                                       C+ C+ C++ CP+ga
  gi|320101538|ref|YP_004177130.1| 215 CTFCRLCENTCPAGA 229
                                       555**********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 !   22.0  10.9   1.3e-07   0.00013       3      56 .]     175     226 ..     173     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                           Fer4_10   3 vidddtC..irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +++++C  ++C +C + CP      + ++  + + ++++ v +Ct+c  C   CP
  gi|320101538|ref|YP_004177130.1| 175 TVNAEKCqgTKCSRCANTCPK----GVFEASGDAIRVKEDRVLECTFCRLCENTCP 226
                                       578999*888***********....888888899999999***************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 !    9.7   0.1    0.0012       1.3      42      60 ..     177     197 ..     135     198 .. 0.77
   2 !   13.0   0.6   0.00011      0.11      41      59 ..     210     228 ..     200     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                           Fer4_17  42 kaslC..ieCgeCerkCPqgl 60 
                                       +a++C  ++C +C+  CP+g+
  gi|320101538|ref|YP_004177130.1| 177 NAEKCqgTKCSRCANTCPKGV 197
                                       567775578*********986 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                           Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                       +++ +C+ C++Ce  CP+g
  gi|320101538|ref|YP_004177130.1| 210 DRVLECTFCRLCENTCPAG 228
                                       57789************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 !    8.9   2.5    0.0016       1.7      33      52 ..     173     194 ..     161     200 .. 0.72
   2 !   16.7  10.7   5.5e-06    0.0058       3      58 ..     176     231 ..     174     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                           Fer4_21  33 vlkvvedeCvG..CnlCssvCP 52 
                                       v++v +++C G  C  C++ CP
  gi|320101538|ref|YP_004177130.1| 173 VITVNAEKCQGtkCSRCANTCP 194
                                       3466689998877999*****9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.5e-06
                           Fer4_21   3 idedkC..igCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       ++ +kC   +C +C+ +C+++  +a ++da +v + +  eC+ C lC + CP  ++++
  gi|320101538|ref|YP_004177130.1| 176 VNAEKCqgTKCSRCANTCPKGVFEA-SGDAIRVKEDRVLECTFCRLCENTCPA-GAVK 231
                                       6677784458*********755544.34444444444569************5.7775 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 !   11.2   1.9   0.00054      0.57       3      20 ..     184     201 ..     180     214 .. 0.81
   2 !   11.0   2.4   0.00062      0.65       2      19 ..     215     232 ..     214     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00054
                           Fer4_16   3 gtCgkCaevCPtnaikek 20 
                                       ++C +Ca++CP +++++ 
  gi|320101538|ref|YP_004177130.1| 184 TKCSRCANTCPKGVFEAS 201
                                       68**********999876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00062
                           Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                       C+ C+ C ++CP++a+k 
  gi|320101538|ref|YP_004177130.1| 215 CTFCRLCENTCPAGAVKV 232
                                       999999999999999875 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.4     0.005       5.3      47      65 .]     177     197 ..     133     197 .. 0.69
   2 ?    6.3  14.7     0.013        13       6      64 ..     184     228 ..     178     232 .. 0.80
   3 ?   10.6   2.5   0.00057       0.6       4      63 ..     214     227 ..     209     247 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.005
                            Fer4_8  47 alwsC..ttcgaCtevCpvgi 65 
                                       ++++C  t c +C++ Cp+g+
  gi|320101538|ref|YP_004177130.1| 177 NAEKCqgTKCSRCANTCPKGV 197
                                       566776678888999999986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                            Fer4_8   6 ieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ++C++C ++Cp      k  ++a g+a+  v  e++      + +Ct c+ C++ Cp g
  gi|320101538|ref|YP_004177130.1| 184 TKCSRCANTCP------KGVFEASGDAIR-VK-EDR------VLECTFCRLCENTCPAG 228
                                       58********9......667788888777.44.455......69*************86 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00057
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       +C+ C +C+++Cp                                               
  gi|320101538|ref|YP_004177130.1| 214 ECTFCRLCENTCP----------------------------------------------A 227
                                       4666666666665..............................................3 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.7     0.013        14       1      14 [.     181     196 ..     181     197 .. 0.81
   2 ?   11.7   4.1   0.00037       0.4       1      15 []     215     229 ..     215     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                            Fer4_3   1 Ctg..CgaCvevCPvg 14 
                                       C+g  C++C + CP+g
  gi|320101538|ref|YP_004177130.1| 181 CQGtkCSRCANTCPKG 196
                                       55444*********98 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00037
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct C++C++ CP gA
  gi|320101538|ref|YP_004177130.1| 215 CTFCRLCENTCPAGA 229
                                       ************998 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.2      0.01        11       2      16 ..     179     195 ..     178     200 .. 0.82
   2 ?   10.3   1.6    0.0008      0.84       4      17 .]     215     228 ..     209     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.01
                            Fer4_4   2 erC..igCgsCvaaCPq 16 
                                       e+C  + C +C ++CP 
  gi|320101538|ref|YP_004177130.1| 179 EKCqgTKCSRCANTCPK 195
                                       8995558889******6 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0008
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C+ C+ C+++CP g
  gi|320101538|ref|YP_004177130.1| 215 CTFCRLCENTCPAG 228
                                       999*********65 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.4   0.00045      0.48       2      21 ..     173     194 ..     172     195 .. 0.92
   2 ?    6.5   2.3    0.0092       9.7      10      22 .]     215     227 ..     207     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00045
                            Fer4_2   2 pvvvdtdrCig..CgaCvsaCP 21 
                                       ++ v++++C g  C+ C + CP
  gi|320101538|ref|YP_004177130.1| 173 VITVNAEKCQGtkCSRCANTCP 194
                                       6899*****9999********9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0092
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       C+ C+ C + CPa
  gi|320101538|ref|YP_004177130.1| 215 CTFCRLCENTCPA 227
                                       777*********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 ?    4.6   8.1     0.033        35      55      95 ..     177     225 ..     126     227 .. 0.66
   2 ?    7.3   0.7    0.0049       5.2      54      74 ..     208     228 ..     199     260 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.033
                           Fer4_18  55 ekgagdcidcescvkvcPtgi........dirkGlqleciscllcidac 95 
                                       ++++ + ++c+ c + cP g+         +++   lec  c lc ++c
  gi|320101538|ref|YP_004177130.1| 177 NAEKCQGTKCSRCANTCPKGVfeasgdaiRVKEDRVLECTFCRLCENTC 225
                                       445566699*********98644333211466778899*******9999 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0049
                           Fer4_18  54 kekgagdcidcescvkvcPtg 74 
                                       ke+ + +c+ c+ c + cP g
  gi|320101538|ref|YP_004177130.1| 208 KEDRVLECTFCRLCENTCPAG 228
                                       4566789************87 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 ?   10.5   0.9    0.0004      0.42       6      26 ..     176     194 ..     171     195 .. 0.89
   2 ?    0.6   0.5      0.49   5.2e+02      17      32 ..     219     232 ..     218     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                                       ES---------TTHHHHHTTS CS
                               RLI   6 vdadqCdPKKCtgkkcarfcp 26 
                                       v+a++C+  KC+   ca  cp
  gi|320101538|ref|YP_004177130.1| 176 VNAEKCQGTKCSR--CANTCP 194
                                       89**********9..*****9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.49
                                       TTHHHHHTTSEEEESS CS
                               RLI  17 tgkkcarfcpvrlvrt 32 
                                       +   c+  cp+ +v++
  gi|320101538|ref|YP_004177130.1| 219 R--LCENTCPAGAVKV 232
                                       4..4*******88875 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.4    0.0019         2       1      33 [.     176     209 ..     176     214 .. 0.76
   2 ?    3.7   3.4     0.085        90       5      18 ..     214     227 ..     210     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                           Fer4_13   1 VDrdtC..iacgaCvelaPd.vFeeddeggasvvae 33 
                                       V+ ++C  + c  C++++P+ vFe   +  a +v+e
  gi|320101538|ref|YP_004177130.1| 176 VNAEKCqgTKCSRCANTCPKgVFEASGD--AIRVKE 209
                                       6777883357*********879999987..666666 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.085
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                       +C+ c +C +++P 
  gi|320101538|ref|YP_004177130.1| 214 ECTFCRLCENTCPA 227
                                       7************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2010.90
//
Query:       gi|320101539|ref|YP_004177131.1|  [L=133]
Description: 30S ribosomal protein S11 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-48  163.3   2.0    2.7e-48  162.9   2.0    1.1  1  Ribosomal_S11  Ribosomal protein S11


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 !  162.9   2.0   1.5e-52   2.7e-48       1     110 []      11     129 ..      11     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 1.5e-52
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       G+ahi++s nntii+itd++Gae++++ +Gg++vka+r k+sPyaa++aa++aa++++dkGi+a+++kv++      
  gi|320101539|ref|YP_004177131.1|  11 GIAHIYSSPNNTIIHITDVTGAETVSRWSGGMVVKADReKPSPYAAMMAASRAANEAMDKGITALHIKVRApgghgp 87 
                                       9**************************************************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG++aa+ralar+G++igriedvtPiPhd++rrp++rr
  gi|320101539|ref|YP_004177131.1|  88 ktPGPGAQAAIRALARSGFIIGRIEDVTPIPHDTTRRPGGRR 129
                                       ****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 985.39
//
Query:       gi|320101540|ref|YP_004177132.1|  [L=170]
Description: 30S ribosomal protein S4 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-14   52.9   0.3    5.2e-14   51.7   0.3    1.6  1  S4        S4 domain
  ------ inclusion threshold ------
      0.081   12.7   0.0       0.11   12.3   0.0    1.2  1  TyrRSs_C  Tyrosyl-tRNA synthetase C-terminal domain
       0.14   12.5   0.0       0.85   10.0   0.0    2.0  2  YlaH      YlaH-like protein


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 !   51.7   0.3   8.7e-18   5.2e-14       1      46 [.     103     148 ..     103     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 8.7e-18
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                       rRL+++++++gla++  eArqlI hG++ + G+++++p+ +V++ +
  gi|320101540|ref|YP_004177132.1| 103 RRLQTLVYKKGLAKTLHEARQLIVHGHIAIGGRRIRSPGRIVSVDE 148
                                       8*****************************************9876 PP

>> TyrRSs_C  Tyrosyl-tRNA synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.9e-05      0.11      20      55 ..     102     137 ..      97     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                                       S-SHHHHHHHTTS-STHHHHHHHHHHT-EEEEE--S CS
                          TyrRSs_C  20 nksiariLyaaGLasskseghrliakkgayvgsrpg 55 
                                       ++ ++ ++y+ GLa++  e+++li++  + +g+r+ 
  gi|320101540|ref|YP_004177132.1| 102 ERRLQTLVYKKGLAKTLHEARQLIVHGHIAIGGRRI 137
                                       5677889*************************9875 PP

>> YlaH  YlaH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   1.5e+03      31      48 ..      17      34 ..      14      37 .. 0.83
   2 ?   10.0   0.0   0.00014      0.85      17      45 ..     105     133 ..     100     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                              YlaH 31 pilkevivYilLalGslv 48
                                      p+ + v++Y + ++G+  
  gi|320101540|ref|YP_004177132.1| 17 PWRRDVLMYEMRLIGTYG 34
                                      88999****999999865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00014
                              YlaH  17 LsiivfklgFakkLpilkevivYilLalG 45 
                                       L ++v+k+g ak L  ++++iv   +a+G
  gi|320101540|ref|YP_004177132.1| 105 LQTLVYKKGLAKTLHEARQLIVHGHIAIG 133
                                       889*******************9988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1305.10
//
Query:       gi|320101541|ref|YP_004177133.1|  [L=162]
Description: 30S ribosomal protein S13 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-40  135.9   0.0    1.2e-39  135.6   0.0    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6   0.0   6.6e-44   1.2e-39       1     128 []      12     140 ..      12     140 .. 1.00

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 6.6e-44
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdi 76 
                                       Ril+td+dg+  +++ l ++kG+G+  + ++++ +++d ++r+g l+++ ++ iee+v n+ +y ip+wi nr+kd+
  gi|320101541|ref|YP_004177133.1|  12 RILETDVDGELPLVYGLSEVKGLGYAFSLAVCRVLGLDPRQRTGFLSDDTVKSIEEVVRNPGKYGIPAWIyNRRKDY 88 
                                       99*************************************************************************** PP

                     Ribosomal_S13  77 kdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                        +G+d h+++ +l  +++edieR+k+i+s+rG+RH  GlkvRGQrT+ttgRt
  gi|320101541|ref|YP_004177133.1|  89 ATGQDLHLTSANLIYYVKEDIEREKRIKSWRGIRHALGLKVRGQRTRTTGRT 140
                                       ***************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1179.89
//
Query:       gi|320101542|ref|YP_004177134.1|  [L=103]
Description: 30S ribosomal protein S10P [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-24   85.6   0.2    2.3e-24   85.5   0.2    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.028   15.2   0.1      0.069   14.0   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 !   85.5   0.2   2.5e-28   2.3e-24       1      97 [.       8     101 ..       8     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 2.5e-28
                                       EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HH CS
                     Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatke 76 
                                       +i++ S++ k+L+++v ki++++k++g+++ gp+plPtkr ++ ++k ph++ kk  e++e+r+hkRl+ i   +++
  gi|320101542|ref|YP_004177134.1|   8 KIKIWSTNVKVLDDFVGKITDIVKKTGVRMDGPIPLPTKRMKIRTMKLPHGEgKKKYEKWEMRIHKRLLYIA-EDER 83 
                                       699********************************************************************4.7888 PP

                                       HHHHHS-...S---SS-EEEE CS
                     Ribosomal_S10  77 tidtllkllqlnlpegVsvev 97 
                                       ++++l++   +++p+ + +e+
  gi|320101542|ref|YP_004177134.1|  84 VMKQLIR---VRIPPEIWMEI 101
                                       9999999...*********98 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.7e-06     0.069       3      52 ..       4      49 ..       4      53 .. 0.93
   2 ?   -1.8   0.1      0.65   5.8e+03      55      73 ..      71      89 ..      61      94 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-06
                            PriA_C  3 srlalirvsgkdeekveeaaeelaellkealkleeveilgpapapiakik 52
                                      +r+++i++ +++ + + +++ ++ +++k+    ++v++ gp+p p +++k
  gi|320101542|ref|YP_004177134.1|  4 TRMVKIKIWSTNVKVLDDFVGKITDIVKK----TGVRMDGPIPLPTKRMK 49
                                      69**************************9....6799**********998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.65
                            PriA_C 55 yryqillksksrkalqkll 73
                                       + ++l  +++++ +++l+
  gi|320101542|ref|YP_004177134.1| 71 IHKRLLYIAEDERVMKQLI 89
                                      4455555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 770.38
//
Query:       gi|320101543|ref|YP_004177135.1|  [L=438]
Description: translation elongation factor 1A (EF-1A/EF-Tu) [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-54  184.4   0.0    2.6e-54  183.7   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.2e-37  126.1   0.4    3.2e-36  124.0   0.1    2.3  3  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    2.4e-15   56.7   2.9    5.2e-15   55.6   2.9    1.6  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    5.1e-05   23.3   0.0    0.00045   20.3   0.0    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0043   16.9   2.7     0.0043   16.9   2.7    2.5  3  GTP_EFTU_D4  Elongation factor Tu domain 4
  ------ inclusion threshold ------
      0.054   13.5   0.0        9.5    6.2   0.0    2.5  2  Dynamin_N    Dynamin family
      0.093   12.5   0.1        5.6    6.7   0.0    2.7  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.11   12.0   0.1       0.41   10.1   0.0    1.9  2  SRPRB        Signal recognition particle receptor beta subuni


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 !  183.7   0.0   1.2e-57   2.6e-54       1     190 [.       6     223 ..       6     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 183.7 bits;  conditional E-value: 1.2e-57
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST............HCHSHHHHHHTSCSSCEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv............lDtlkeErergiTiksaais 62 
                                       k+++ni+iighvDhGK+T+t+++ly++g  ++k+ k    e  +             lD++keErerg+Ti+ + ++
  gi|320101543|ref|YP_004177135.1|   6 KPHLNIVIIGHVDHGKSTMTGHILYRLGYFDEKTVKMieeE--SKkmgkesfkfawlLDRMKEERERGVTISLSYMK 80 
                                       579*****************************887777532..224689999************************* PP

                                       EETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEES CS
                          GTP_EFTU  63 leketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNK 131
                                       +e  tkky +++iD+PGH+dF+k++i+g++++D a+lvv+a++G        e qt+e++ la+++g++ +iv+iNK
  gi|320101543|ref|YP_004177135.1|  81 FE--TKKYFFTIIDAPGHRDFVKNMITGASQADAAILVVSARKGefeagmsAEGQTREHAILARTMGINqLIVAINK 155
                                       **..************************************************************************* PP

                                       CGST.....HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHHH CS
                          GTP_EFTU 132 mDrl.....kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealve 190
                                       mD +     +++++ei+e +  k+      l+  g++ + ++p++++Sa++ge++             tl+eal++
  gi|320101543|ref|YP_004177135.1| 156 MDATeppysEKRYNEIKEILG-KF------LKGLGYDVS-KIPFIPISAWTGENLIerspnmpwyngpTLVEALDT 223
                                       ****88886666666665555.66......899999995.*************87656666666666677777665 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 ?   -1.5   0.0       1.4   3.1e+03       4      30 ..     106     131 ..     103     161 .. 0.72
   2 ?   -2.6   0.0       2.9   6.5e+03      55      75 ..     282     302 ..     273     306 .. 0.71
   3 !  124.0   0.1   1.4e-39   3.2e-36       3     111 ..     323     429 ..     321     430 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                                       EECCEEEEEEESSS..SS-BSTT-EEE CS
                       GTP_EFTU_D3   4 phtkfeAqvyilekerhtpitagYrpv 30 
                                        +++ +A +++++  r++++ ag ++ 
  gi|320101543|ref|YP_004177135.1| 106 GASQADAAILVVSA-RKGEFEAGMSAE 131
                                       56677889999999.999999887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                                       B-BSS-SSCCSTT-CEEEEEE CS
                       GTP_EFTU_D3  55 kvsekkpefvkpGdnviveve 75 
                                       +++++k e + pGdn+ ++v+
  gi|320101543|ref|YP_004177135.1| 282 ETHHTKIEKAEPGDNIGFNVK 302
                                       344567788899999988876 PP

  == domain 3  score: 124.0 bits;  conditional E-value: 1.4e-39
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCE CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikp 79 
                                       + +++f+A+++++ +  +t+i  gY+pv++++ta+v+++++e+++k+d++t+k+ ek+p+f+k+Gd +iv+ ++ikp
  gi|320101543|ref|YP_004177135.1| 323 TVADEFTARIMVMWH--PTAIAVGYTPVIHVHTASVACRITEIIAKIDPRTGKEIEKNPQFLKQGDIAIVKFKPIKP 397
                                       67899**********..************************************************************ PP

                                       EEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  80 ialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       +++ek+s++p lGrFa+R++g+T+++G+v ei
  gi|320101543|ref|YP_004177135.1| 398 LVVEKYSDFPGLGRFAMRDMGKTIGIGQVLEI 429
                                       ******************************99 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   2.9   2.3e-18   5.2e-15       1      72 [.     249     314 ..     249     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.3e-18
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                       G+v  grv++G+lk+Gd+v++++      + v +++s+et+h + + a++g+n+G++v++++ +d i++Gd+
  gi|320101543|ref|YP_004177135.1| 249 GVVPVGRVETGVLKVGDKVVFMPA-----GLVAEVKSIETHHTKIEKAEPGDNIGFNVKGVEKKD-IKRGDV 314
                                       8899*****************664.....789*********************************.*****9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     2e-07   0.00045       1      92 [.      10     126 ..      10     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2e-07
                                       EEEEEESTTSSHHHHHHHHH................T...............STEEESSSTTSSSSEEEEEEEETTE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinalt................g...............ekaivsdkpgtTrdinegrvklkgk 46 
                                       +++i+G+   GKSt+   ++                +               ++ + +++ g+T+   + ++++k+ 
  gi|320101543|ref|YP_004177135.1|  10 NIVIIGHVDHGKSTMTGHILyrlgyfdektvkmieeEskkmgkesfkfawllDRMKEERERGVTISLSYMKFETKKY 86 
                                       589****************966666666665555550555666667676665699999999**********999999 PP

                                       EEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHH CS
                          MMR_HSR1  47 eielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkp 92 
                                        ++++D pG  +    +  +++ +    +ad+++lvv+a+++++++
  gi|320101543|ref|YP_004177135.1|  87 FFTIIDAPG--H----RDFVKNMITGASQADAAILVVSARKGEFEA 126
                                       9********..3....23466666667779*******988443322 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3   7.3e+03      68      86 .]      11      30 ..       8      30 .. 0.77
   2 !   16.9   2.7   1.9e-06    0.0043      21      84 ..     253     314 ..     239     315 .. 0.90
   3 ?   -1.9   0.1       1.5   3.3e+03      40      57 ..     417     436 ..     412     438 .] 0.62

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                                      EEEESS-.TTTS--TT-EEE CS
                       GTP_EFTU_D4 68 isiegki.vGrqikegdily 86
                                      i i g++  G++   g ily
  gi|320101543|ref|YP_004177135.1| 11 IVIIGHVdHGKSTMTGHILY 30
                                      77888888888888888887 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.9e-06
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                       vG +v +Gv+k+g k++      v e+++i++++ k+e+a+ G++++  ++g    ++ik gd+
  gi|320101543|ref|YP_004177135.1| 253 VG-RVETGVLKVGDKVVFMPAGLVAEVKSIETHHTKIEKAEPGDNIGFNVKGVE-KKDIKRGDV 314
                                       78.9***********99877779****************************966.788999986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                                       TE.E..EEEEEEEEETTEEE CS
                       GTP_EFTU_D4  40 dGre..vGeilqiqdkgkkl 57 
                                        G++  +G++l+i+  + ++
  gi|320101543|ref|YP_004177135.1| 417 MGKTigIGQVLEIKPAQVNI 436
                                       56551156888888777666 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.011        26       1      18 [.      11      28 ..      11      32 .. 0.86
   2 ?    6.2   0.0    0.0042       9.5      53     144 ..      45     126 ..      30     150 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
                                      EEEEEBTTTTHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaL 18
                                      i+++G++ +GKS++  ++
  gi|320101543|ref|YP_004177135.1| 11 IVIIGHVDHGKSTMTGHI 28
                                      89***********97666 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0042
                                       SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTT CS
                         Dynamin_N  53 eelkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikka 129
                                       ee k+  k+  +f  + + +++e+e+         ++ +++ +++ ++   t++D PG  +  k   ++++ + +  
  gi|320101543|ref|YP_004177135.1|  45 EESKKMGKESFKFAWLLDRMKEERERGV-------TISLSYMKFETKKYFFTIIDAPGHRDFVK---NMITGASQAD 111
                                       3444446666667777777766666666.......3467777788888889*******988433...5788888888 PP

                                       EEEEEEEETTS-CCC CS
                         Dynamin_N 130 diilavtsanhdlsn 144
                                       ++il+v++ + ++  
  gi|320101543|ref|YP_004177135.1| 112 AAILVVSARKGEFEA 126
                                       888888776666665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.046     1e+02       3      21 ..      10      28 ..       8      47 .. 0.80
   2 ?    6.7   0.0    0.0025       5.6      25      75 ..      75     121 ..      66     136 .. 0.90
   3 ?   -3.1   0.0       2.6   5.7e+03      92     117 ..     360     384 ..     350     390 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.046
                         PduV-EutP  3 killiGkvgsGKttLtqal 21
                                      +i++iG+v+ GK t+t ++
  gi|320101543|ref|YP_004177135.1| 10 NIVIIGHVDHGKSTMTGHI 28
                                      699***********99776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0025
                         PduV-EutP  25 elkYkktqaiefsdeviDtPGeylenrklysalivtsaeadvialvqdate 75 
                                       +l+Y k  + ++  ++iD+PG    +r + + +i+ + +ad   lv++a +
  gi|320101543|ref|YP_004177135.1|  75 SLSYMKFETKKYFFTIIDAPG----HRDFVKNMITGASQADAAILVVSARK 121
                                       68999999999999*******....79***************999999876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.6
                         PduV-EutP  92 viGiitkidlaedeenieaveelLks 117
                                       +  ii kid   + ++ie+  ++Lk+
  gi|320101543|ref|YP_004177135.1| 360 ITEIIAKIDPR-TGKEIEKNPQFLKQ 384
                                       55689999987.77888887777776 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.36   8.1e+02       5      25 ..      10      30 ..       7      63 .. 0.68
   2 ?   10.1   0.0   0.00018      0.41      41      97 ..      79     131 ..      47     182 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.36
                                      EEEEE-STTSSHHHHHHHHHH CS
                             SRPRB  5 avllvGlsdsGKTslftrLtt 25
                                      +++++G  d GK ++  +++ 
  gi|320101543|ref|YP_004177135.1| 10 NIVIIGHVDHGKSTMTGHILY 30
                                      58999******9988665554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                                       TTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS-HHHHHHHHH CS
                             SRPRB  41 lkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDStidpkevkevAE 97 
                                        k+ ++k+  +t+iD PGh  + +++++     s++ + + vv +   + e+   AE
  gi|320101543|ref|YP_004177135.1|  79 MKF-ETKKYFFTIIDAPGHRDFVKNMITG---ASQADAAILVVSARKGEFEAGMSAE 131
                                       334.678889************9999998...5666666777765555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3094.33
//
Query:       gi|320101544|ref|YP_004177136.1|  [L=198]
Description: 30S ribosomal protein S7 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-43  147.0   0.3    3.8e-43  146.7   0.3    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   0.3   2.1e-47   3.8e-43      17     149 .]      57     198 .]      48     198 .] 0.93

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 2.1e-47
                                       STTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEE CS
                      Ribosomal_S7  17 kynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpv 89 
                                       k + ++ve+link+m+     Gkk+lA++iv++a+dii+ kt+++p++vl++A+en++Pr+e++++++GG+ty+v+v
  gi|320101544|ref|YP_004177136.1|  57 KTHVPIVERLINKVMRpgrnMGKKHLAYNIVKKAFDIIHIKTGENPIQVLVRAIENAAPREETTRIMYGGITYHVSV 133
                                       47899**************99******************************************************** PP

                                       EE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  90 evrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       +v+p Rr +lAlr+++e+a   ++ +  +++e+LaeE++ Aa ++  ++a++k+ee++r+A ++r
  gi|320101544|ref|YP_004177136.1| 134 DVAPLRRIDLALRHLTEGArmkAFHSPIPIEEALAEEIVLAASNDpkSYAIQKKEEIERIALSSR 198
                                       *******************54445555678**************999**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1528.97
//
Query:       gi|320101545|ref|YP_004177137.1|  [L=148]
Description: 30S ribosomal protein S12 [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-45  152.6   0.2    3.5e-45  152.3   0.2    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 !  152.3   0.2     2e-49   3.5e-45       8     113 ..      40     146 ..      32     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 2e-49
                                       -S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--...... CS
                   Ribosom_S12_S23   8 tksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk.gka 83 
                                       +  d+legap++rG+vlekv++e++kPnsA+Rk+vrv+L kngk vtaf+p +g +n++dEhdev+++Gi+++ g +
  gi|320101545|ref|YP_004177137.1|  40 KLRDPLEGAPMARGIVLEKVGIESRKPNSAVRKCVRVQLVKNGKVVTAFVPWDGGVNYIDEHDEVIIEGIGGPlGGS 116
                                       3359************************************************************************* PP

                                       BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  84 vkDlpGvrykvvkvagvslkalskykkekp 113
                                        +D+pGvrykvv v+gvslkal+ +kk+kp
  gi|320101545|ref|YP_004177137.1| 117 LGDIPGVRYKVVMVNGVSLKALWLGKKQKP 146
                                       ***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 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:                        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 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1250.90
//
Query:       gi|320101546|ref|YP_004177138.1|  [L=148]
Description: NusA family KH domain-containing protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-14   53.3   1.8    1.9e-08   34.0   0.2    2.2  2  KH_2      KH domain
    2.3e-13   50.0   1.1    1.1e-11   44.6   0.2    2.2  2  KH_5      NusA-like KH domain
      1e-08   34.9   0.1     0.0012   18.7   0.0    2.2  2  KH_4      KH domain
    0.00084   19.1   0.3       0.28   11.1   0.0    2.8  3  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 !   34.0   0.2   4.3e-12   1.9e-08       6      65 ..      20      79 ..      18     104 .. 0.87
   2 !   19.1   0.3   1.9e-07   0.00083      29      58 ..     111     140 ..      81     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.3e-12
                                      HHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC CS
                              KH_2  6 laveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk 65
                                      l +e+++a v+++++e+++nrvi+ +  +  g++IG +G  +++++k l+k+ie++ ++ 
  gi|320101546|ref|YP_004177138.1| 20 LLNELTGAVVRDCIVEEENNRVIFLVNPEDVGRAIGPKGFFVQRLKKILNKNIEIVGYSS 79
                                      55789999**********************************************988775 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.9e-07
                                       EEEEESCHHHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2  29 iviresqpgivIGkgGsnikkigkelrkdi 58 
                                       + +  + +gi+IGk+G+n+++ +  l++ +
  gi|320101546|ref|YP_004177138.1| 111 VAVDPADKGIAIGKNGRNVQRARLILKRHF 140
                                       4577899***************99888766 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.2   2.4e-15   1.1e-11       2      68 ..      38      98 ..      37      99 .. 0.97
   2 ?    4.2   0.1      0.01        47       7      32 ..     111     131 ..     106     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.4e-15
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68
                                      ++r+++ V  ++     vG ++g kG  ++ +++ L +++i++v +s++l+e ++ al+Pa+++++k
  gi|320101546|ref|YP_004177138.1| 38 NNRVIFLVNPED-----VGRAIGPKGFFVQRLKKIL-NKNIEIVGYSSNLEEQVKYALAPARIKEIK 98
                                      699*********.....*******************.****************************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.01
                              KH_5   7 vaVkshnpnvdpvGaivgkkGsrika 32 
                                       vaV   +      G ++gk+G++++ 
  gi|320101546|ref|YP_004177138.1| 111 VAVDPAD-----KGIAIGKNGRNVQR 131
                                       6666677.....899********985 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   6.2e-06     0.028      18      59 ..      28      69 ..      17      74 .. 0.82
   2 !   18.7   0.0   2.7e-07    0.0012      20      52 ..      97     130 ..      80     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.2e-06
                              KH_4 18 vevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvs 59
                                      v  ++  eee++++   v++ed+Gr IG +G  ++ l+ +++
  gi|320101546|ref|YP_004177138.1| 28 VVRDCIVEEENNRVIFLVNPEDVGRAIGPKGFFVQRLKKILN 69
                                      55577789999*******************988877777665 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.7e-07
                              KH_4  20 vtee.eeeeeveielnvegedlGrvIGkrGrtld 52 
                                       ++++ + + ++++ ++v++ d+G+ IGk+Gr+++
  gi|320101546|ref|YP_004177138.1|  97 IKLStKPDGSKVLYVAVDPADKGIAIGKNGRNVQ 130
                                       44443457899********************987 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.9   8.7e+03      28      36 ..       5      12 ..       3      15 .. 0.68
   2 !   11.1   0.0   6.2e-05      0.28       3      39 ..      42      79 ..      39      88 .. 0.82
   3 !    5.5   0.0    0.0034        15       8      24 ..     115     131 ..     108     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                                      HHT-EEEEE CS
                              KH_1 28 etgakIkvp 36
                                      ++++kI+ p
  gi|320101546|ref|YP_004177138.1|  5 KSQVKIT-P 12
                                      5788888.6 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.2e-05
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.ST CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.se 39
                                       +lv+ + vgr IG++G  ++++++  + +I +++ s+
  gi|320101546|ref|YP_004177138.1| 42 IFLVNPEDVGRAIGPKGFFVQRLKKILNKNIEIVGySS 79
                                      46999999***************998888888885554 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0034
                                       GGHHHHHHTGGGHHHHH CS
                              KH_1   8 sslvgriIGkgGsnIke 24 
                                           g  IGk+G+n+++
  gi|320101546|ref|YP_004177138.1| 115 PADKGIAIGKNGRNVQR 131
                                       5557888*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1252.91
//
Query:       gi|320101547|ref|YP_004177139.1|  [L=106]
Description: 50S ribosomal protein L30 [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-19   67.7   0.0    6.6e-19   67.4   0.0    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
       0.14   12.6   0.0       0.23   11.9   0.0    1.3  1  DUF2274         Protein of unknown function (DUF2274)


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 !   67.4   0.0   7.3e-23   6.6e-19       4      94 ..       8      98 ..       6      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 7.3e-23
                                      HHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEES.CHHHHHHHTTSSSECS CS
                    Ribosomal_L7Ae  4 eevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvk.skkeLGelvgkkrpvs 81
                                       +++++a+++g++v+G++ev +++ +g+ak vi+A +++pe k++ l++++k  ++p++k +  + eLG+l+g+++  s
  gi|320101547|ref|YP_004177139.1|  8 LKAIRVAAETGHVVYGAREVRRLVLHGKAKAVIIAVNAPPEVKRD-LTYYAKLSGIPVIKFPgTNMELGTLLGRPHSIS 85
                                      6899*****************************************.************99995458************* PP

                                      EEEEEESTTTHHH CS
                    Ribosomal_L7Ae 82 alaikdegdskdl 94
                                      ++a++d+g+s++l
  gi|320101547|ref|YP_004177139.1| 86 SIAVVDPGQSNIL 98
                                      **********997 PP

>> DUF2274  Protein of unknown function (DUF2274)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.6e-05      0.23      12      35 ..      36      59 ..      29      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                           DUF2274 12 dkpvkltvelpaalhrdLaaYael 35
                                       k+v ++v+ p++++rdL+ Ya+l
  gi|320101547|ref|YP_004177139.1| 36 AKAVIIAVNAPPEVKRDLTYYAKL 59
                                      689999****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); 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: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 898.14
//
Query:       gi|320101548|ref|YP_004177140.1|  [L=407]
Description: DNA-directed RNA polymerase subunit A' [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-55  187.0   0.3    5.5e-55  186.7   0.3    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.087   12.7   0.2        1.9    8.4   0.1    3.0  3  IF2_N           Translation initiation factor IF-2, N-termina
       0.89    9.4   3.8         43    4.0   0.0    3.5  3  DUF348          G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.7   0.3   9.1e-59   5.5e-55      66     264 ..      56     338 ..       9     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: 186.7 bits;  conditional E-value: 9.1e-59
                                       S.....B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSC CS
                                       x.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  66 g.....lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeake 137
                                       +     l+epGeavG+iaaQS+GeP+TQ+tl+ FH+aGv + nvtlG+prl ei+++ k+ +++  +++lvde++ +
  gi|320101548|ref|YP_004177140.1|  56 EryhssLIEPGEAVGTIAAQSLGEPSTQMTLRVFHYAGVREYNVTLGLPRLIEIVDARKKPETPITEIYLVDEYKGS 132
                                       0333339********************************************************************** PP

                                       HHHCHHHHHHHSE................................................................ CS
                                       xxxxxxxxxxxxx................................................................ RF
                    RNA_pol_Rpb1_5 138 lekakkvkkaiek................................................................ 150
                                        eka++++++ie                                                                 
  gi|320101548|ref|YP_004177140.1| 133 EEKAREIARRIEAtyvenivkeldidlfegkatlrldpemledkgvsvgeviekleelgvgdvsegdnpyevvislk 209
                                       ********999999*************************************************************** PP

                                       ......................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHH CS
                                       ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ......................gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaei 205
                                                             gik+i++++++  ++g    +e+v+  eg nl+ev+ ve+ vd +++++n+i+ei
  gi|320101548|ref|YP_004177140.1| 210 eeyldygkleklrskilsthlkGIKEIRKVIIQ--KRG----DEYVIVAEGSNLEEVMRVEG-VDWRRVYTNNIQEI 279
                                       ********9999999999988888888888887..223....46799***************.************** PP

                                       HHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 206 leilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkael 264
                                        e+lgieaar+a+++ei+e+++ qg++v+ rH++l++d+mt +g++ +v+r+G+  ++ 
  gi|320101548|ref|YP_004177140.1| 280 EEVLGIEAARQAIIREIREILEDQGLDVDIRHIMLLADMMTWTGHVRQVGRMGVAGEKP 338
                                       *****************************************************987665 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 ?    0.0   0.0      0.13   7.6e+02      36      50 ..       1      15 [.       1      18 [. 0.89
   2 ?   -3.2   0.0       1.3   8.1e+03      10      31 ..      74      95 ..      74      99 .. 0.73
   3 ?    8.4   0.1   0.00032       1.9      14      33 ..     177     195 ..     174     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.13
                             IF2_N 36 sssLDeetaeliaee 50
                                      +++L++e+++ i +e
  gi|320101548|ref|YP_004177140.1|  1 MHGLSAEEIQRIIDE 15
                                      799*******99987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                             IF2_N 10 AkeLgvkskevikkLfkelGie 31
                                      A+ Lg +s++   + f+++G+ 
  gi|320101548|ref|YP_004177140.1| 74 AQSLGEPSTQMTLRVFHYAGVR 95
                                      6778888888777777777776 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00032
                             IF2_N  14 gvkskevikkLfkelGievk 33 
                                       gv++ evi+kL +elG+ ++
  gi|320101548|ref|YP_004177140.1| 177 GVSVGEVIEKL-EELGVGDV 195
                                       799********.77**9655 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1    0.0075        45      21      32 ..     171     182 ..     171     194 .. 0.91
   2 ?   -0.5   0.1      0.17     1e+03      20      30 ..     297     307 ..     296     308 .. 0.84
   3 ?    4.0   0.0    0.0072        43      14      35 ..     345     364 ..     335     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0075
                                       HHHHHTT----T CS
                            DUF348  21 dlLeeagitlge 32 
                                       ++Le++g+++ge
  gi|320101548|ref|YP_004177140.1| 171 EMLEDKGVSVGE 182
                                       7999***99998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                                       HHHHHHTT--- CS
                            DUF348  20 gdlLeeagitl 30 
                                        ++Le++g+++
  gi|320101548|ref|YP_004177140.1| 297 REILEDQGLDV 307
                                       589*****987 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0072
                                       ---SSHHHHHHHTT----TT-E CS
                            DUF348  14 TaadTVgdlLeeagitlgeqDk 35 
                                       T++ TV+ lLe+a    ge+Dk
  gi|320101548|ref|YP_004177140.1| 345 TFEMTVQKLLESA--ATGEEDK 364
                                       9999*******88..4457666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 3244.92
//
Query:       gi|320101549|ref|YP_004177141.1|  [L=885]
Description: DNA-directed RNA polymerase subunit A' [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-98  330.4   0.0    1.5e-98  330.0   0.0    1.1  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    1.3e-73  246.7   0.0    2.1e-73  246.0   0.0    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    4.1e-38  130.8   0.0    7.9e-38  129.9   0.0    1.5  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    1.2e-26   92.8   0.0    2.4e-26   91.8   0.0    1.5  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    6.7e-26   91.3   0.0    1.2e-25   90.5   0.0    1.3  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
       0.33   10.4   6.4        1.8    8.1   0.1    3.3  3  zf-ribbon_3     zinc-ribbon domain
       0.47   10.6   2.4         13    6.0   0.0    3.1  3  Zn-ribbon_8     Zinc ribbon domain
        1.4    8.8   5.8         16    5.4   0.2    3.4  3  zf-FPG_IleRS    Zinc finger found in FPG and IleRS


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 !  330.0   0.0  6.8e-102   1.5e-98       2     312 .]       7     317 ..       6     317 .. 0.91

  Alignments for each domain:
  == domain 1  score: 330.0 bits;  conditional E-value: 6.8e-102
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       ++i +++fgi+sp+eirk+Sv+++ +ae+++++  +P +gG++D rlg+i+    C +Cg+++ +C+ghfGhieLak
  gi|320101549|ref|YP_004177141.1|   7 NRITRVKFGILSPDEIRKMSVTQIFSAEVYDNDG-SPIDGGVMDRRLGAIEPGEACPICGNTRDSCPGHFGHIELAK 82 
                                       689****************************995.****************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC.........CCHHHHHHHHCCS-BE-SSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldeekkkllsklkkrekleelk.........krlkaieelckkinlcekCg 146
                                       Pv+h+gf+k il  l+ +c++c++l + ee+++ + +l       +l+         + ++ i+++ +  ++c +Cg
  gi|320101549|ref|YP_004177141.1|  83 PVIHVGFVKHILMYLRATCRNCGRLKIPEEERNEYLRLL-----SDLHelgapylikRFHEYIRRKASAAEVCPHCG 154
                                       ****************************99885444433.....222222244455478899*************** PP

                                       SB-EEEEEETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 147 avqpkleeegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvq 223
                                       ++q k+  + ek ++ + ++ e+   kl++++v+  l++i+d+dv++lg +++ +rPew++ltvlPVpP ++RPsv 
  gi|320101549|ref|YP_004177141.1| 155 VKQYKV--KLEKPHT-FYEQTEKGLVKLTPSEVRGRLEKIPDDDVKLLGGDPRDARPEWMVLTVLPVPPRSVRPSVL 228
                                       888555..4555544.4444554789*************************************************** PP

                                       SSSSSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 224 ldggrrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqr 300
                                       l++g rsedDlt+kl+dii++NnrL+++ e gap++iie+e+elLQ+hv+t+fdne +g++ a+++s++ lk++ qr
  gi|320101549|ref|YP_004177141.1| 229 LETGIRSEDDLTHKLVDIIRTNNRLREHVEGGAPSAIIEDEWELLQYHVTTYFDNEAPGIPVAKHRSGKTLKGIAQR 305
                                       ***************************************************************************** PP

                                       HTSSSSCCCCCT CS
                                       xxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 301 LkGKeGrfRgnL 312
                                       LkGKeGrfR+nL
  gi|320101549|ref|YP_004177141.1| 306 LKGKEGRFRNNL 317
                                       ***********9 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.0   0.0   9.2e-77   2.1e-73       1     166 []     319     485 ..     319     485 .. 0.99

  Alignments for each domain:
  == domain 1  score: 246.0 bits;  conditional E-value: 9.2e-77
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrvd+saR+v+spdp+l+++evgvP  va++ltvpe+vt++ni+++r+lv ngpe++Pga+yv r dg++ +lk  
  gi|320101549|ref|YP_004177141.1| 319 GKRVDFSARTVVSPDPSLSINEVGVPEDVARILTVPERVTPWNIEEMRRLVLNGPEKWPGANYVVRPDGRKISLKFV 395
                                       9**************************************************************************** PP

                                       -S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SS CS
                    RNA_pol_Rpb1_2  78 kr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqs 153
                                       +r ++a++le g iverh++dgdvvl+NRqPsLh++s+mah v+vl++kt+rlnl+v+ +yNaDFDGDemnlh+pqs
  gi|320101549|ref|YP_004177141.1| 396 DRkAAAEALEPGFIVERHLMDGDVVLFNRQPSLHRISVMAHIVRVLPYKTFRLNLLVCPPYNADFDGDEMNLHVPQS 472
                                       9966999********************************************************************** PP

                                       HHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 154 eearaEaeelllv 166
                                       eear+Ea+ l+lv
  gi|320101549|ref|YP_004177141.1| 473 EEARTEARLLMLV 485
                                       **********986 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 !  129.9   0.0   3.5e-41   7.9e-38       1     154 [.     488     652 ..     488     655 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 3.5e-41
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHC CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpn 77 
                                       +il+p+ g P+ig  QD ++G+y+lT + ++++++++  ll     +    + ++pailkp+elwtgkq++s++lp+
  gi|320101549|ref|YP_004177141.1| 488 HILTPRYGGPIIGGLQDYISGAYILTSKTTLLSKDDVVDLLAVTGYK---GEIPEPAILKPRELWTGKQLVSLFLPK 561
                                       79****************************************99766...689************************ PP

                                       CCCEEEE.SSSS...............STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_3  78 einyerk.neek...............dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslq 138
                                       ++ny+r  +                  d+ v++kng+l++Gv+dk+ +g+++ +sl+h l+keyg +  + f+d++ 
  gi|320101549|ref|YP_004177141.1| 562 DFNYKRNsK--IgsaaalrcidedcphDSMVIVKNGVLLEGVLDKASIGREEPESLVHWLIKEYGEDYGRMFMDRVY 636
                                       ******542..25688999999******************************************************* PP

                                       HHHHHHHHHHCEB-TG CS
                    RNA_pol_Rpb1_3 139 rlgfkyllqsgftigi 154
                                       +++++++ ++gft+++
  gi|320101549|ref|YP_004177141.1| 637 KMFIRMSEKHGFTMSY 652
                                       **************96 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 !   91.8   0.0   1.1e-29   2.4e-26       2     108 .]     681     787 ..     680     787 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.1e-29
                                       HHHCTHTCCHHHTTHCHHHHHH.HHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEE CS
                    RNA_pol_Rpb1_4   2 eeaerygkledlpgksleelfe.akinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqn 77 
                                       ++++r g+l+  pgk+ ee++e ++i+++++k  d++ +++  +    N++++M+++Ga+G+++n++q+a++lGqq+
  gi|320101549|ref|YP_004177141.1| 681 SKYRR-GELQARPGKTPEETLEdEIIDTLSKKLLDSVAEVITPYFTLVNPVVVMARTGARGNPVNLTQMAALLGQQT 756
                                       67788.9***************9999******************9966***************************** PP

                                       BTTBSS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  78 vegkripkgfsgrtlphfkkidespesrGFv 108
                                       v+gkr  +g+ gr+lphfk+ d +pe+rGF+
  gi|320101549|ref|YP_004177141.1| 757 VRGKRLTRGYLGRALPHFKPEDLGPEARGFI 787
                                       ******************************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 !   90.5   0.0   5.2e-29   1.2e-25       1      66 [.     794     859 ..     794     878 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 5.2e-29
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL++ e ffh+ +gReGLiDtAv+T++sGY+qRrl++al+d+ v+yd++vr ++geivq+lygedg
  gi|320101549|ref|YP_004177141.1| 794 GLNPVEMFFHAAAGREGLIDTAVRTSQSGYMQRRLINALQDLRVEYDGSVRLTTGEIVQLLYGEDG 859
                                       9****************************************************************8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3     0.028        63       5      10 ..      61      66 ..      58      70 .. 0.72
   2 ?    0.5   0.1       0.2   4.4e+02      18      23 ..     100     105 ..      99     109 .. 0.85
   3 ?    8.1   0.1   0.00082       1.8      16      25 ..     147     156 ..     144     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.028
                       zf-ribbon_3  5 CPnCGa 10
                                      CP CG+
  gi|320101549|ref|YP_004177141.1| 61 CPICGN 66
                                      777775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                       zf-ribbon_3  18 vCpyCG 23 
                                       +C +CG
  gi|320101549|ref|YP_004177141.1| 100 TCRNCG 105
                                       699998 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00082
                       zf-ribbon_3  16 dnvCpyCGtk 25 
                                       + vCp+CG k
  gi|320101549|ref|YP_004177141.1| 147 AEVCPHCGVK 156
                                       689*****76 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.066   1.5e+02      24      34 ..      56      66 ..      45      69 .. 0.77
   2 ?   -1.0   0.1       0.9     2e+03       8      12 ..     101     105 ..      97     109 .. 0.63
   3 ?    6.0   0.0    0.0056        13      21      34 ..     142     155 ..     134     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.066
                       Zn-ribbon_8 24 apltaCPeCgs 34
                                      +p +aCP Cg 
  gi|320101549|ref|YP_004177141.1| 56 EPGEACPICGN 66
                                      56788****96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.9
                       Zn-ribbon_8   8 CeeCg 12 
                                       C++Cg
  gi|320101549|ref|YP_004177141.1| 101 CRNCG 105
                                       66665 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0056
                       Zn-ribbon_8  21 isdapltaCPeCgs 34 
                                        + ++ ++CP+Cg 
  gi|320101549|ref|YP_004177141.1| 142 RKASAAEVCPHCGV 155
                                       33345667****96 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0072        16       1      11 [.      58      68 ..      58      70 .. 0.89
   2 ?    1.4   0.1      0.14     3e+02       4      17 ..     101     115 ..      99     118 .. 0.75
   3 ?    2.9   0.1     0.044        99      22      27 ..     148     153 ..     139     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0072
                                      TSB-TTT--BB CS
                      zf-FPG_IleRS  1 GepCpRCwryi 11
                                      Ge Cp C+++ 
  gi|320101549|ref|YP_004177141.1| 58 GEACPICGNTR 68
                                      89*******85 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                                       -TTT--B.BEEEECT CS
                      zf-FPG_IleRS   4 CpRCwry.iervgqa 17 
                                       C+ C+r  i++++ +
  gi|320101549|ref|YP_004177141.1| 101 CRNCGRLkIPEEERN 115
                                       ******977776655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.044
                                       EE-TTT CS
                      zf-FPG_IleRS  22 yfCprC 27 
                                       ++Cp+C
  gi|320101549|ref|YP_004177141.1| 148 EVCPHC 153
                                       455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (885 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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):               8  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 5923.59
//
Query:       gi|320101550|ref|YP_004177142.1|  [L=1165]
Description: DNA-directed RNA polymerase subunit B' ;DNA-directed RNA polymerase subunit B' [Desulfurococcus mucosus DSM 2162]
Scores for complete 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-134  446.3   0.2   1.8e-133  445.4   0.0    1.5  2  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    3.4e-46  157.3   0.1    4.7e-46  156.9   0.1    1.2  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
      1e-27   96.3   0.1    1.9e-27   95.5   0.1    1.5  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    1.8e-26   92.1   0.0    4.8e-26   90.7   0.0    1.8  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    2.3e-25   89.3   0.1    1.5e-24   86.7   0.1    2.2  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    6.9e-22   77.5   1.3    2.1e-21   76.0   1.3    1.9  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    4.7e-08   33.5   0.1    1.5e-07   31.9   0.1    1.9  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5


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 ?   -3.1   0.0       1.2     3e+03     179     213 ..     574     608 ..     565     632 .. 0.80
   2 !  445.4   0.0    7e-137  1.8e-133       2     390 .]     692    1063 ..     691    1063 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.2
                                       .-----------..-B---EE--TT-EEEEEEEEE CS
                    RNA_pol_Rpb2_6 179 ekllraifgekarevkdtslrvksgeegvVdkvkv 213
                                       e+l rai + +++ +  + ++v + ++g+Vd+v v
  gi|320101550|ref|YP_004177142.1| 574 EELARAIRELRRKGKISSEVNVAHINSGYVDEVVV 608
                                       67788888887777888899999999999999998 PP

  == domain 2  score: 445.4 bits;  conditional E-value: 7e-137
                                        HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS- CS
                    RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgela 76  
                                        a+++p++eh+qspr+++q+am+kq+lg+y++n  +r++++ ++l+++qkPlv+t+ +++ ++        ++e +
  gi|320101550|ref|YP_004177142.1|  692 ASIIPYPEHNQSPRNMYQSAMAKQSLGLYAANFQRRMDTRGHFLHYPQKPLVQTR-AMDVIG--------YNERP 757 
                                        899****************************************************.******........***** PP

                                        SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS-.--.-S--..-....-SS-GGGS CS
                    RNA_pol_Rpb2_6   77 lGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklge.eeitrdipnv....seealkkL 146 
                                        +Gqn+vVAv++y+GYn+EDa+iln+++vdr++++s++++ y++   ++++g  +eit   +n     +++a++kL
  gi|320101550|ref|YP_004177142.1|  758 AGQNMVVAVLTYTGYNMEDALILNKSSVDRGLARSTFFRLYTTVEYKYPGGIqDEITIPSTNIrgyrGQKAYEKL 832 
                                        ****************************************9999999998887999988877799999******* PP

                                        -TTSB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......E CS
                    RNA_pol_Rpb2_6  147 dedGivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgde 221 
                                        +edGiv +++ v+ gd+l+gk+  ++ ++       ++ +  ++ + +dts+ ++++e+gvVd+v +       +
  gi|320101550|ref|YP_004177142.1|  833 EEDGIVAPETPVTGGDVLIGKI--SPPRFL----SAQEYEVGSTLTRQDTSVVMRHEEKGVVDTVLI-------T 894 
                                        *********************9..666665....23344444445589*******************.......8 PP

                                        E-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHH CS
                    RNA_pol_Rpb2_6  222 lkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtl 296 
                                         ++++nkl+kv+v++ R +++GDKfasrhGqKGvv+l++pq DmPf+e+G+v+D+++NP+++PSRmt++ql+E++
  gi|320101550|ref|YP_004177142.1|  895 MDSEGNKLIKVRVRDLRIPELGDKFASRHGQKGVVGLLVPQYDMPFTEEGVVPDLIINPHAFPSRMTVAQLMESI 969 
                                        9999*********************************************************************** PP

                                        HHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS--- CS
                    RNA_pol_Rpb2_6  297 lgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKiha 371 
                                        +gkaaaleg+ +dat+F ++  ee++  ++++g++ +G+e +ydGrtGe l+a++f+Gv+Yy+kL+h+v+dK+ha
  gi|320101550|ref|YP_004177142.1|  970 AGKAAALEGRTFDATPFYKTPIEELQVIIKRHGYSPTGEEAMYDGRTGELLDAPVFIGVVYYQKLHHMVSDKMHA 1044
                                        ******************7777***************************************************** PP

                                        -SS--B-TTT--B-SCGGG CS
                    RNA_pol_Rpb2_6  372 RstGpyslltqQPlgGkaq 390 
                                        R++Gp++ lt+QP++G+++
  gi|320101550|ref|YP_004177142.1| 1045 RARGPVQILTRQPTEGRSR 1063
                                        *****************86 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.9   0.1   1.8e-49   4.7e-46       1     202 [.      25     417 ..      25     418 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.9 bits;  conditional E-value: 1.8e-49
                                       CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltY 77 
                                       gLv+q+ldS++ f+++ l  i +e  +i+++e+         +  +++r+++P+ +++++ e++  P+e+rlrnltY
  gi|320101550|ref|YP_004177142.1|  25 GLVRQHLDSYERFLKELLPSILEEFREIRIAEKT-------RIVIEKYRVDEPKWTSIEGIEESKSPMECRLRNLTY 94 
                                       69******************************95.......7999******************************** PP

                                       EEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  78 saplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqe 154
                                         p+yv ++       +    +e+e+++ +lP+Ml+s+ + ls++++eelv+++E+p d+GGyFiinG+ekvivaqe
  gi|320101550|ref|YP_004177142.1|  95 ATPVYVTVRIED----ESGYTREQELKLMDLPVMLKSSIDPLSKLTPEELVAMGEDPRDPGGYFIINGSEKVIVAQE 167
                                       ********9988....89999******************************************************** PP

                                       E............................................................................ CS
                                       x............................................................................ RF
                    RNA_pol_Rpb2_1 155 k............................................................................ 155
                                       +                                                                            
  gi|320101550|ref|YP_004177142.1| 168 Dlasnniivdampegssvthvakvtsvargrrsqlvierrkdgvfyasfqghkfpavmlmvalglaseaeilyatsl 244
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|320101550|ref|YP_004177142.1| 245 kpevhnhllpsiiqiqevlpkleipegaseeeverlkeeyrrrvveealdfiaskfiigkpreerilraqrllderl 321
                                       ***************************************************************************** PP

                                       .................................................XHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                       .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 .................................................laGeLlaslfrvllkklerdvkerlqks 183
                                                                                        laG++la l+r ++  + r++ke ++k+
  gi|320101550|ref|YP_004177142.1| 322 lphigtdpspetrlrkavfigqmisriielylgyrspddkdhyrnkrlkLAGDMLATLLRAAIMGFSREIKEGVEKQ 398
                                       ***************************************************************************** PP

                                       HCTSSSSSHHHHSCSHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 184 leklddlmlqllvnakpit 202
                                       l k +++ l+++ + + it
  gi|320101550|ref|YP_004177142.1| 399 LAKTRKVDLKMVFKPSIIT 417
                                       **********999998887 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 !   95.5   0.1   7.5e-31   1.9e-27       1      85 [.    1065    1155 ..    1065    1157 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 7.5e-31
                                        BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHH CS
                    RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafk 69  
                                        GGlr GEME+d+l+++G+a+lLke +t++SD++ ++vc+ c+ + +++      +C+++k++  +++ve+++afk
  gi|320101550|ref|YP_004177142.1| 1065 GGLRWGEMEVDCLVGHGSAMLLKEAMTDRSDSTIIYVCELCGSMGWYDrnkgkyMCPVHKERGVLKPVEVSYAFK 1139
                                        9**********************************************9*************************** PP

                                        HHHHHHHHTTBEEEEE CS
                    RNA_pol_Rpb2_7   70 lLlqeLqslgialkll 85  
                                        lLlqeL+slgi+++l+
  gi|320101550|ref|YP_004177142.1| 1140 LLLQELMSLGIRPRLI 1155
                                        *************987 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 !   90.7   0.0   1.9e-29   4.8e-26       1      68 []     438     502 ..     438     502 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 1.9e-29
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                       q+ldr+n+ls+lshlrrv s+   l + + ++e+R+lh ++wGr+Cp+eTPEG+n+Glvk+Lal+++v
  gi|320101550|ref|YP_004177142.1| 438 QLLDRTNMLSTLSHLRRVVSP---LARGQPHFEARELHGTQWGRMCPFETPEGANIGLVKNLALMTNV 502
                                       89*******************...*****************************************987 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 !   86.7   0.1   5.9e-28   1.5e-24       1     190 []     170     370 ..     170     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 5.9e-28
                                       -TSCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTS CS
                    RNA_pol_Rpb2_2   1 rsngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericy 75 
                                       +sn i+v ++++ +++  +a+vts+   +r++++ +++++++++++     +k p+v+++ Algl s+ eIl++ + 
  gi|320101550|ref|YP_004177142.1| 170 ASNNIIVDAMPEGSSVthVAKVTSVARGRRSQLVIERRKDGVFYASF--QGHKFPAVMLMVALGLASEAEILYATSL 244
                                       689************99999999999999999999999999999998..7889***********************6 PP

                                       .....................SSTTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHH CS
                    RNA_pol_Rpb2_2  76 .....................dsedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkry 131
                                                             +      ee  e+l+e+      eeald+i +++ +++++e+r+ +a+++l+   
  gi|320101550|ref|YP_004177142.1| 245 kpevhnhllpsiiqiqevlpkLEIPEGASEEEVERLKEEYRRRVVEEALDFIASKFIIGKPREERILRAQRLLD--- 318
                                       78899***********999985555555566666777777777789**************************94... PP

                                       HHHHHTTTTSSTTTTTSSSTCHH...HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 132 dlgeigreklnkhlglseslenkr.lkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                              e+l++h+g++ s e +r  ka +i+ mi r+++l lg r++DD+Dh++nkR++
  gi|320101550|ref|YP_004177142.1| 319 -------ERLLPHIGTDPSPE-TRlRKAVFIGQMISRIIELYLGYRSPDDKDHYRNKRLK 370
                                       .......56666*******55.565*********************************96 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 !   76.0   1.3   8.1e-25   2.1e-21       1      62 []     560     623 ..     560     623 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 8.1e-25
                                       EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT..T--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnek..qkevkiatDgGRvcRPliiVe 62 
                                       Vf+NG+l+G++r++++l++++RelRRkgkis+ev++++ ++   +ev ++tD GR++RPli+Ve
  gi|320101550|ref|YP_004177142.1| 560 VFLNGKLVGYHRNGEELARAIRELRRKGKISSEVNVAHINSgyVDEVVVNTDPGRIRRPLIVVE 623
                                       9************************************99998899******************7 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   5.8e-11   1.5e-07       1      33 [.     644     676 ..     644     689 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.8e-11
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleks 33 
                                       ++dL+++g++EylD  EEe+a+Ia+ p  + ++
  gi|320101550|ref|YP_004177142.1| 644 FEDLVKQGIIEYLDPDEEENAYIALEPGSVGAE 676
                                       89************************9877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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:                         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: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.43
# Mc/sec: 8105.76
//
Query:       gi|320101551|ref|YP_004177143.1|  [L=83]
Description: DNA-directed RNA polymerase subunit H [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-33  114.1   0.0    2.2e-33  113.9   0.0    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.15   12.0   0.0    1.4  1  GreA_GreB       Transcription elongation factor, GreA/GreB, C


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 !  113.9   0.0   2.5e-37   2.2e-33       1      73 []       5      77 ..       5      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 2.5e-37
                                      ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      +n+++HelvPkhe+l +ee+ ++lkkl+++++qLP+is +Dpva+++g+k+Gd+vk++rks+tage++tYR+V
  gi|320101551|ref|YP_004177143.1|  5 INVLEHELVPKHEILPPEEAYQVLKKLGVEPWQLPWISINDPVAKAIGAKPGDIVKVIRKSPTAGEFITYRYV 77
                                      69*********************************************************************98 PP

>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05      0.15      25      64 ..      25      64 ..      16      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                                      E----TTT-BS.-SSB--TTSHHHHHHTT--TT-EE---BT CS
                         GreA_GreB 25 ytiVgpdeadp.skgkiSveSPlGkaLlgkkvGdevevkap 64
                                      y+++ +  ++p +  +iS++ P++ka +g+k Gd v+v  +
  gi|320101551|ref|YP_004177143.1| 25 YQVLKKLGVEPwQLPWISINDPVAKA-IGAKPGDIVKVIRK 64
                                      5555555566634459**********.5*********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 583.27
//
Query:       gi|320101552|ref|YP_004177144.1|  [L=243]
Description: ABC transporter-like protein [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-28   99.6   0.0    3.1e-28   99.0   0.0    1.3  1  ABC_tran        ABC transporter
    4.5e-08   33.3   0.6     0.0025   17.7   0.2    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0006   19.3   0.1      0.097   12.1   0.0    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
    0.00083   19.8   0.0      0.001   19.5   0.0    1.2  1  AAA_16          AAA ATPase domain
     0.0011   19.4   0.1     0.0063   16.9   0.1    2.0  1  AAA             ATPase family associated with various cellula
     0.0016   18.4   0.0     0.0027   17.6   0.0    1.3  1  RsgA_GTPase     RsgA GTPase
     0.0021   18.0   0.0     0.0039   17.1   0.0    1.4  1  Rad17           Rad17 P-loop domain
     0.0028   18.2   0.2     0.0046   17.5   0.2    1.2  1  AAA_23          AAA domain
     0.0075   16.0   0.2      0.015   15.0   0.2    1.4  1  AAA_29          P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   14.9   0.1      0.024   13.8   0.1    1.5  1  NB-ARC          NB-ARC domain
      0.017   15.4   0.1      0.029   14.6   0.1    1.7  1  AAA_22          AAA domain
      0.032   13.9   0.1      0.039   13.7   0.1    1.2  1  AAA_15          AAA ATPase domain
      0.046   14.0   0.1      0.097   12.9   0.1    1.5  1  AAA_28          AAA domain
      0.049   13.5   0.0      0.078   12.9   0.0    1.3  1  ATPase_2        ATPase domain predominantly from Archaea
      0.056   13.4   0.0      0.091   12.7   0.0    1.3  1  NACHT           NACHT domain
      0.084   11.7   0.3        1.3    7.7   0.0    2.2  2  ABC_ATPase      Predicted ATPase of the ABC class
      0.095   13.2   0.1       0.18   12.3   0.1    1.5  1  AAA_18          AAA domain
       0.13   12.7   0.1       0.24   11.8   0.1    1.5  1  RNA_helicase    RNA helicase
       0.13   12.3   0.0       0.22   11.6   0.0    1.5  1  MMR_HSR1        50S ribosome-binding GTPase
       0.14   11.9   0.7       0.26   11.0   0.4    1.6  2  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 !   99.0   0.0   3.5e-31   3.1e-28      11     136 ..      33     156 ..      24     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 3.5e-31
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren........ 79 
                                       +e +ai+G++G+GKStLlk++ag +kp++G+i           + + +   g+++q p+l p ltv +n        
  gi|320101552|ref|YP_004177144.1|  33 SEFIAILGPSGCGKSTLLKIIAGIEKPDSGSI-----------EARGNITYGFVFQSPTLLPWLTVLDNaalpliak 98 
                                       5899****************************...........567788889************************* PP

                                       .....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                            e+++++ ++ls +gl++++d       ++LSgG+kqrv +aral+ +p++ll+DEp+
  gi|320101552|ref|YP_004177144.1|  99 giskkEARDKARRYLSLVGLQGFEDFYP----NELSGGMKQRVNIARALAVEPSILLMDEPF 156
                                       **98888888************999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   2.8e-06    0.0025       1      23 [.      35      57 ..      35      84 .. 0.69
   2 !   14.3   0.0   3.1e-05     0.027     228     298 ..     120     191 ..      79     194 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + ++ Gp g+GKS+LL+++ ++ 
  gi|320101552|ref|YP_004177144.1| 35 FIAILGPSGCGKSTLLKIIAGIE 57
                                      6799***************8872 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.1e-05
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ell.......kelsrngaQviltT 296
                                       +  ++ ++elS G+k+   ++ al+  +   s+ll DEp + L+P   + l  e++                vi++T
  gi|320101552|ref|YP_004177144.1| 120 GFEDFYPNELSGGMKQRVNIARALAVEP---SILLMDEPFSQLDPLTAEALRaEVVdlwlsgvTTV----EGVIMVT 189
                                       45568889*********9*******999...**************666666544443334432222....3466666 PP

                            AAA_21 297 HS 298
                                       H+
  gi|320101552|ref|YP_004177144.1| 190 HN 191
                                       65 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   0.0   0.00011     0.097      17      44 ..      26      53 ..      22      56 .. 0.88
   2 ?    5.2   0.0     0.014        12     130     179 ..     122     167 ..      95     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                      EEEEETTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 17 tvilpfsksftaivGpNGSGKsnlldAi 44
                                      +++l++ ++f ai+Gp G+GKs ll  i
  gi|320101552|ref|YP_004177144.1| 26 SITLDIGSEFIAILGPSGCGKSTLLKII 53
                                      57889999**************998755 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                                       TT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 130 agiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                       +++++++LSgG k+ v +a  +A++     ++ l+De  ++LD    +++
  gi|320101552|ref|YP_004177144.1| 122 EDFYPNELSGGMKQRVNIARALAVEP----SILLMDEPFSQLDPLTAEAL 167
                                       567899*************9999753....57788888888887665554 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   1.2e-06     0.001      13      95 ..      21     106 ..      16     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
                            AAA_16  13 lsalervrsgrp.elvllsGesGvGKsslvrellralekd.......ggiflrgkcdqlesaipysalaqalareel 81 
                                       l++l+++  + + e + + G+sG+GKs+l++ ++  +ek        +g  ++g   q+    ++++++++l++   
  gi|320101552|ref|YP_004177144.1|  21 LRVLDSITLDIGsEFIAILGPSGCGKSTLLKIIA-GIEKPdsgsieaRGNITYGFVFQS---PTLLPWLTVLDN-AA 92 
                                       555553333333489***************9999.566663444433222233333333...344567777755.66 PP

                            AAA_16  82 lrqlldeaesaele 95 
                                       l  ++   +++e++
  gi|320101552|ref|YP_004177144.1|  93 LPLIAKGISKKEAR 106
                                       66666664443333 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   0.1     7e-06    0.0063       3      66 ..      38     154 ..      36     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7e-06
                                       EESSTTSSHHHHHHHHHHH.......HTHE...............................EEEEETTTCSSS.... CS
                               AAA   3 lyGppGtGKTllakavake.......lgve...............................fleisgsellsk.... 37 
                                       + Gp G+GK++l k +a         +  e                                          k    
  gi|320101552|ref|YP_004177144.1|  38 ILGPSGCGKSTLLKIIAGIekpdsgsI--EargnitygfvfqsptllpwltvldnaalpliA----------Kgisk 102
                                       78****************944444431..133445555555555666666655555555542..........13333 PP

                                       ......................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 ......................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                             y  e +  +++ ++ a++ a +psil++DE
  gi|320101552|ref|YP_004177144.1| 103 keardkarrylslvglqgfedfYPNELSGGMKQRVNIARALAvEPSILLMDE 154
                                       3334447777777777777777999999*******9999999999******9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     3e-06    0.0027      91     130 ..      25      64 ..      18      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                                       HHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  91 eelkellkdktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++++  + +++++++G+SG GKStL++ +++ ++   g++
  gi|320101552|ref|YP_004177144.1|  25 DSITLDIGSEFIAILGPSGCGKSTLLKIIAGIEKPDSGSI 64 
                                       566677788999***************9998766666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.4e-06    0.0039      47      68 ..      35      56 ..      19      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.4e-06
                             Rad17 47 iLLisGPsGCgkstvvkvLske 68
                                       + i GPsGCgkst +k+++ +
  gi|320101552|ref|YP_004177144.1| 35 FIAILGPSGCGKSTLLKIIAGI 56
                                      56799*************9866 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   5.1e-06    0.0046      12      39 ..      26      53 ..      19      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.1e-06
                            AAA_23 12 dqeidFskgltlItGpNGaGKTTildAi 39
                                        ++d ++ + +I Gp G+GK+T+l  i
  gi|320101552|ref|YP_004177144.1| 26 SITLDIGSEFIAILGPSGCGKSTLLKII 53
                                      55788999*****************887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.7e-05     0.015      19      39 ..      29      50 ..      23      56 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                            AAA_29 19 idlkg.atlltGpsGsGKSTll 39
                                      +d  + ++ + GpsG GKSTll
  gi|320101552|ref|YP_004177144.1| 29 LDIGSeFIAILGPSGCGKSTLL 50
                                      444445899************8 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   0.1   2.7e-05     0.024      15      40 ..      28      53 ..      17      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                                      TTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakqi 40
                                        +++s ++a+ G  G+GK+tl+k i
  gi|320101552|ref|YP_004177144.1| 28 TLDIGSEFIAILGPSGCGKSTLLKII 53
                                      5688999***************9866 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.3e-05     0.029       6      26 ..      34      54 ..      31     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                       ++++ G+sG+GK+tll+ ++
  gi|320101552|ref|YP_004177144.1| 34 EFIAILGPSGCGKSTLLKIIA 54
                                      589*************99665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.3e-05     0.039      12      43 ..      22      53 ..      21     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                            AAA_15 12 RslkdveidlseeltvliGkNnsGKSsileal 43
                                      R l+++++d+ +e+  + G+ ++GKS++l+++
  gi|320101552|ref|YP_004177144.1| 22 RVLDSITLDIGSEFIAILGPSGCGKSTLLKII 53
                                      6688899***********************99 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00011     0.097       2      20 ..      36      54 ..      35      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      i+i+G++++GK+tll+ +a
  gi|320101552|ref|YP_004177144.1| 36 IAILGPSGCGKSTLLKIIA 54
                                      89*************9887 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 ?   12.9   0.0   8.7e-05     0.078      20      41 ..      33      54 ..      19      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeii 41
                                      +e++ i Gp g+GK++Llk i+
  gi|320101552|ref|YP_004177144.1| 33 SEFIAILGPSGCGKSTLLKIIA 54
                                      67899*************9775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001     0.091       3      21 ..      36      54 ..      34      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      +++ G++G+GK+tLl+ +a
  gi|320101552|ref|YP_004177144.1| 36 IAILGPSGCGKSTLLKIIA 54
                                      799************9776 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.096        86     247     264 ..      36      53 ..      28      57 .. 0.83
   2 ?    7.7   0.0    0.0015       1.3     317     366 ..     123     172 ..     117     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.096
                                       EEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 247 tlIvGggfhGKsTLLeAl 264
                                       ++I G+   GKsTLL+ +
  gi|320101552|ref|YP_004177144.1|  36 IAILGPSGCGKSTLLKII 53 
                                       68999999*******976 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0015
                                       TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS CS
                        ABC_ATPase 317 kfstedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelv 366
                                       +f  ++ SG + q +ni++al ++ ++lL+DE  s    +   ++ +e+v
  gi|320101552|ref|YP_004177144.1| 123 DFYPNELSGGMKQRVNIARALAVEPSILLMDEPFSQLDPLTAEALRAEVV 172
                                       5667788*************************887666666555555555 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    0.0002      0.18       1      19 [.      36      54 ..      36      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                            AAA_18  1 IlltGtpGvGKttlakeLs 19
                                      I++ G++G+GK+tl k ++
  gi|320101552|ref|YP_004177144.1| 36 IAILGPSGCGKSTLLKIIA 54
                                      89************99874 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00027      0.24       1      19 [.      36      54 ..      36      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                      RNA_helicase  1 iwlyGpsgeGKStlakeLa 19
                                      i + Gpsg+GKStl k +a
  gi|320101552|ref|YP_004177144.1| 36 IAILGPSGCGKSTLLKIIA 54
                                      5689**********99854 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.22       2      21 ..      36      55 ..      35     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      +ai+G +  GKStL++ + g
  gi|320101552|ref|YP_004177144.1| 36 IAILGPSGCGKSTLLKIIAG 55
                                      89*************99987 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00029      0.26       1      19 [.      36      54 ..      36      63 .. 0.93
   2 ?   -3.8   0.0        10     9e+03     165     182 ..      98     115 ..      94     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                      EEEE-STTSSHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvarala 19
                                      iai GP+g GKs++ +++a
  gi|320101552|ref|YP_004177144.1| 36 IAILGPSGCGKSTLLKIIA 54
                                      89**************998 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 10
                                       HHHHHHHHHHHCTSSS-S CS
                    Cytidylate_kin 165 aeikeRDklDkerevgpL 182
                                       + i ++ ++Dk+r++  L
  gi|320101552|ref|YP_004177144.1|  98 KGISKKEARDKARRYLSL 115
                                       567888889998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1682.26
//
Query:       gi|320101553|ref|YP_004177145.1|  [L=497]
Description: binding-protein-dependent transport system inner membrane protein [Desulfurococcus mucosus DSM 2162]
Scores for 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-23   81.5  47.7    8.8e-14   51.7  18.1    3.1  3  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
        0.3   10.5   0.0       0.46    9.9   0.0    1.1  1  Glyco_tran_WbsX  Glycosyltransferase WbsX


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 !   51.7  18.1   9.8e-18   8.8e-14       2     176 ..      30     204 ..      27     210 .. 0.90
   2 ?   -0.8   1.1      0.12   1.1e+03      58     171 ..     286     310 ..     229     323 .. 0.58
   3 !   39.5  15.7   5.2e-14   4.6e-10      20     167 ..     328     476 ..     308     491 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 9.8e-18
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalr 77 
                                       i +G+ +a  r++ + ++l+pl ++l+s+P++ ++++++ ++ +l + + +  + +++ll++++++ +++ +++a++
  gi|320101553|ref|YP_004177145.1|  30 ISIGVAMA--RRRLVEEVLLPLLDILQSIPVLGFFPVVFTLLLMLPARQVALEAaAVFLLTTGLLWNMIFGVYSAVK 104
                                       66788888..***************************9999988888886666669********************* PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydysei 153
                                       sl+ d    a ++G++ + ++ ++ +P+a   +++  i++++g +   + +e ++s+p    +l l ++++y y+e+
  gi|320101553|ref|YP_004177145.1| 105 SLDPDILLMADVYGLKAFSRLAYIYVPSARAALAANSIISWAGGWFFLTSVEVIASGPQeYRLLGLGSLIMYLYNEG 181
                                       *******************************************************9999766666777888999999 PP

                      BPD_transp_1 154 snggvlalviavlllnlvadilq 176
                                         +g+++++++++l+++++++l+
  gi|320101553|ref|YP_004177145.1| 182 DTWGFYTAILLLFLMIVSSYLLV 204
                                       97888888888888888777764 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.12
                      BPD_transp_1  58 illllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw 134
                                       +++ + + +                                                                    
  gi|320101553|ref|YP_004177145.1| 286 FISSFLSNF-------------------------------------------------------------------- 294
                                       222222222.................................................................... PP

                      BPD_transp_1 135 pGlgtllleailgydyseisnggvlalviavlllnlv 171
                                                             ++la v a+ ll+lv
  gi|320101553|ref|YP_004177145.1| 295 ---------------------LISLARVSAITLLSLV 310
                                       .....................2333333333333333 PP

  == domain 3  score: 39.5 bits;  conditional E-value: 5.2e-14
                      BPD_transp_1  20 lrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwq 96 
                                       + ++ +vl s+P +++++ll     + s l +l+  v++l   ++  ++  i+  ++ ++ ++l+e+ar++G++ + 
  gi|320101553|ref|YP_004177145.1| 328 IAFIGEVLGSIPAIIWWPLLS---PLASPLPWLVSLVVFLQGSFWYEFFN-IMLFGVPEVREELMELARVYGVKGFN 400
                                       567778999**********99...67788888888888888888887765.5567899******************* PP

                      BPD_transp_1  97 ifrkvvlPnalppiitglilafggllggavlleflgswpG........lgtllleailgydyseisnggvlalviav 165
                                        fr+++lP++lp+i++g++ a+gg+++ ++++e++ s  G        +g++l +   + ++ ++s  ++l  ++++
  gi|320101553|ref|YP_004177145.1| 401 YFRYILLPSLLPSIASGALSAWGGAWNSTIVAEYFSS--GiltvdlggVGSTLARYVYSGNLEAAS-LTILLWAVMI 474
                                       **********************************995..444666666888888888888888777.3333333333 PP

                      BPD_transp_1 166 ll 167
                                       ++
  gi|320101553|ref|YP_004177145.1| 475 VV 476
                                       33 PP

>> Glyco_tran_WbsX  Glycosyltransferase WbsX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   5.1e-05      0.46      55      79 ..     380     404 ..     371     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5.1e-05
                   Glyco_tran_WbsX  55 ekevleeqaelakeygiegfcyyhY 79 
                                        +ev+ee +ela+ yg++gf y+ Y
  gi|320101553|ref|YP_004177145.1| 380 VPEVREELMELARVYGVKGFNYFRY 404
                                       5899*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 3504.91
//
Query:       gi|320101554|ref|YP_004177146.1|  [L=170]
Description: nitrate/sulfonate/bicarbonate family ABC transporter ATPase subunit [Desulfurococcus mucosus DSM 2162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-16   58.9   0.0    8.4e-16   58.6   0.0    1.1  1  AAA_assoc_C  C-terminal AAA-associated domain


Domain annotation for each model (and alignments):
>> 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 !   58.6   0.0   4.7e-20   8.4e-16       2     117 ..      39     152 ..      38     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 4.7e-20
                       AAA_assoc_C   2 eLaeelelevddLlpiveaaelLglveveegdielTelGrkfveadikerKeifreql..lklvplaaairrvLder 76 
                                       ++++ ++ ++  L +++++ae Lglv++e+g ++l e Grk++ead k+ ++++re +  +k++pl+++ + +    
  gi|320101554|ref|YP_004177146.1|  39 HIGDLTGESIALLPKVIDVAETLGLVKYENGYLTLEEPGRKVAEADPKRLRKLLRELVieKKVEPLHEIYEML---V 112
                                       677778888999*********************************************9334679999999987...6 PP

                       AAA_assoc_C  77 enkrlpeerfldeLeeklseeeaertletaieWgrYaelfe 117
                                       ++k++p+ ++ +++e++++    e   + ++ Wg+Y ++f+
  gi|320101554|ref|YP_004177146.1| 113 KRKSIPRGELTRVIEKHYK-RMDEGVARNILVWGAYLGMFK 152
                                       899****************.66788999999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1300.51
//
[ok]
